Actual source code: ts.c

petsc-3.7.2 2016-06-05
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  2: #include <petsc/private/tsimpl.h>        /*I "petscts.h"  I*/
  3: #include <petscdmshell.h>
  4: #include <petscdmda.h>
  5: #include <petscviewer.h>
  6: #include <petscdraw.h>

  8: /* Logging support */
  9: PetscClassId  TS_CLASSID, DMTS_CLASSID;
 10: PetscLogEvent TS_AdjointStep, TS_Step, TS_PseudoComputeTimeStep, TS_FunctionEval, TS_JacobianEval;

 12: const char *const TSExactFinalTimeOptions[] = {"UNSPECIFIED","STEPOVER","INTERPOLATE","MATCHSTEP","TSExactFinalTimeOption","TS_EXACTFINALTIME_",0};

 14: struct _n_TSMonitorDrawCtx {
 15:   PetscViewer   viewer;
 16:   Vec           initialsolution;
 17:   PetscBool     showinitial;
 18:   PetscInt      howoften;  /* when > 0 uses step % howoften, when negative only final solution plotted */
 19:   PetscBool     showtimestepandtime;
 20: };

 24: /*@C
 25:    TSMonitorSetFromOptions - Sets a monitor function and viewer appropriate for the type indicated by the user

 27:    Collective on TS

 29:    Input Parameters:
 30: +  ts - TS object you wish to monitor
 31: .  name - the monitor type one is seeking
 32: .  help - message indicating what monitoring is done
 33: .  manual - manual page for the monitor
 34: .  monitor - the monitor function
 35: -  monitorsetup - a function that is called once ONLY if the user selected this monitor that may set additional features of the TS or PetscViewer objects

 37:    Level: developer

 39: .seealso: PetscOptionsGetViewer(), PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
 40:           PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
 41:           PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
 42:           PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
 43:           PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
 44:           PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
 45:           PetscOptionsFList(), PetscOptionsEList()
 46: @*/
 47: PetscErrorCode  TSMonitorSetFromOptions(TS ts,const char name[],const char help[], const char manual[],PetscErrorCode (*monitor)(TS,PetscInt,PetscReal,Vec,PetscViewerAndFormat*),PetscErrorCode (*monitorsetup)(TS,PetscViewerAndFormat*))
 48: {
 49:   PetscErrorCode    ierr;
 50:   PetscViewer       viewer;
 51:   PetscViewerFormat format;
 52:   PetscBool         flg;

 55:   PetscOptionsGetViewer(PetscObjectComm((PetscObject)ts),((PetscObject)ts)->prefix,name,&viewer,&format,&flg);
 56:   if (flg) {
 57:     PetscViewerAndFormat *vf;
 58:     PetscViewerAndFormatCreate(viewer,format,&vf);
 59:     PetscObjectDereference((PetscObject)viewer);
 60:     if (monitorsetup) {
 61:       (*monitorsetup)(ts,vf);
 62:     }
 63:     TSMonitorSet(ts,(PetscErrorCode (*)(TS,PetscInt,PetscReal,Vec,void*))monitor,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);
 64:   }
 65:   return(0);
 66: }

 70: /*@C
 71:    TSAdjointMonitorSetFromOptions - Sets a monitor function and viewer appropriate for the type indicated by the user

 73:    Collective on TS

 75:    Input Parameters:
 76: +  ts - TS object you wish to monitor
 77: .  name - the monitor type one is seeking
 78: .  help - message indicating what monitoring is done
 79: .  manual - manual page for the monitor
 80: .  monitor - the monitor function
 81: -  monitorsetup - a function that is called once ONLY if the user selected this monitor that may set additional features of the TS or PetscViewer objects

 83:    Level: developer

 85: .seealso: PetscOptionsGetViewer(), PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
 86:           PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
 87:           PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
 88:           PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
 89:           PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
 90:           PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
 91:           PetscOptionsFList(), PetscOptionsEList()
 92: @*/
 93: PetscErrorCode  TSAdjointMonitorSetFromOptions(TS ts,const char name[],const char help[], const char manual[],PetscErrorCode (*monitor)(TS,PetscInt,PetscReal,Vec,PetscInt,Vec*,Vec*,PetscViewerAndFormat*),PetscErrorCode (*monitorsetup)(TS,PetscViewerAndFormat*))
 94: {
 95:   PetscErrorCode    ierr;
 96:   PetscViewer       viewer;
 97:   PetscViewerFormat format;
 98:   PetscBool         flg;

101:   PetscOptionsGetViewer(PetscObjectComm((PetscObject)ts),((PetscObject)ts)->prefix,name,&viewer,&format,&flg);
102:   if (flg) {
103:     PetscViewerAndFormat *vf;
104:     PetscViewerAndFormatCreate(viewer,format,&vf);
105:     PetscObjectDereference((PetscObject)viewer);
106:     if (monitorsetup) {
107:       (*monitorsetup)(ts,vf);
108:     }
109:     TSAdjointMonitorSet(ts,(PetscErrorCode (*)(TS,PetscInt,PetscReal,Vec,PetscInt,Vec*,Vec*,void*))monitor,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);
110:   }
111:   return(0);
112: }

116: /*@
117:    TSSetFromOptions - Sets various TS parameters from user options.

119:    Collective on TS

121:    Input Parameter:
122: .  ts - the TS context obtained from TSCreate()

124:    Options Database Keys:
125: +  -ts_type <type> - TSEULER, TSBEULER, TSSUNDIALS, TSPSEUDO, TSCN, TSRK, TSTHETA, TSALPHA, TSGL, TSSSP
126: .  -ts_save_trajectory - checkpoint the solution at each time-step
127: .  -ts_max_steps <maxsteps> - maximum number of time-steps to take
128: .  -ts_final_time <time> - maximum time to compute to
129: .  -ts_dt <dt> - initial time step
130: .  -ts_exact_final_time <stepover,interpolate,matchstep> whether to stop at the exact given final time and how to compute the solution at that ti,e
131: .  -ts_max_snes_failures <maxfailures> - Maximum number of nonlinear solve failures allowed
132: .  -ts_max_reject <maxrejects> - Maximum number of step rejections before step fails
133: .  -ts_error_if_step_fails <true,false> - Error if no step succeeds
134: .  -ts_rtol <rtol> - relative tolerance for local truncation error
135: .  -ts_atol <atol> Absolute tolerance for local truncation error
136: .  -ts_adjoint_solve <yes,no> After solving the ODE/DAE solve the adjoint problem (requires -ts_save_trajectory)
137: .  -ts_fd_color - Use finite differences with coloring to compute IJacobian
138: .  -ts_monitor - print information at each timestep
139: .  -ts_monitor_lg_solution - Monitor solution graphically
140: .  -ts_monitor_lg_error - Monitor error graphically
141: .  -ts_monitor_lg_timestep - Monitor timestep size graphically
142: .  -ts_monitor_lg_snes_iterations - Monitor number nonlinear iterations for each timestep graphically
143: .  -ts_monitor_lg_ksp_iterations - Monitor number nonlinear iterations for each timestep graphically
144: .  -ts_monitor_sp_eig - Monitor eigenvalues of linearized operator graphically
145: .  -ts_monitor_draw_solution - Monitor solution graphically
146: .  -ts_monitor_draw_solution_phase  <xleft,yleft,xright,yright> - Monitor solution graphically with phase diagram, requires problem with exactly 2 degrees of freedom
147: .  -ts_monitor_draw_error - Monitor error graphically, requires use to have provided TSSetSolutionFunction()
148: .  -ts_monitor_solution [ascii binary draw][:filename][:viewerformat] - monitors the solution at each timestep
149: .  -ts_monitor_solution_vtk <filename.vts> - Save each time step to a binary file, use filename-%%03D.vts
150: .  -ts_monitor_envelope - determine maximum and minimum value of each component of the solution over the solution time
151: .  -ts_adjoint_monitor - print information at each adjoint time step
152: -  -ts_adjoint_monitor_draw_sensi - monitor the sensitivity of the first cost function wrt initial conditions (lambda[0]) graphically

154:    Developer Note: We should unify all the -ts_monitor options in the way that -xxx_view has been unified

156:    Level: beginner

158: .keywords: TS, timestep, set, options, database

160: .seealso: TSGetType()
161: @*/
162: PetscErrorCode  TSSetFromOptions(TS ts)
163: {
164:   PetscBool              opt,flg,tflg;
165:   PetscErrorCode         ierr;
166:   char                   monfilename[PETSC_MAX_PATH_LEN];
167:   PetscReal              time_step;
168:   TSExactFinalTimeOption eftopt;
169:   char                   dir[16];
170:   TSIFunction            ifun;
171:   const char             *defaultType;
172:   char                   typeName[256];


177:   TSRegisterAll();
178:   TSGetIFunction(ts,NULL,&ifun,NULL);

180:   PetscObjectOptionsBegin((PetscObject)ts);
181:   if (((PetscObject)ts)->type_name)
182:     defaultType = ((PetscObject)ts)->type_name;
183:   else
184:     defaultType = ifun ? TSBEULER : TSEULER;
185:   PetscOptionsFList("-ts_type","TS method","TSSetType",TSList,defaultType,typeName,256,&opt);
186:   if (opt) {
187:     TSSetType(ts,typeName);
188:   } else {
189:     TSSetType(ts,defaultType);
190:   }

192:   /* Handle generic TS options */
193:   PetscOptionsInt("-ts_max_steps","Maximum number of time steps","TSSetDuration",ts->max_steps,&ts->max_steps,NULL);
194:   PetscOptionsReal("-ts_final_time","Time to run to","TSSetDuration",ts->max_time,&ts->max_time,NULL);
195:   PetscOptionsReal("-ts_init_time","Initial time","TSSetTime",ts->ptime,&ts->ptime,NULL);
196:   PetscOptionsReal("-ts_dt","Initial time step","TSSetTimeStep",ts->time_step,&time_step,&flg);
197:   if (flg) {TSSetTimeStep(ts,time_step);}
198:   PetscOptionsEnum("-ts_exact_final_time","Option for handling of final time step","TSSetExactFinalTime",TSExactFinalTimeOptions,(PetscEnum)ts->exact_final_time,(PetscEnum*)&eftopt,&flg);
199:   if (flg) {TSSetExactFinalTime(ts,eftopt);}
200:   PetscOptionsInt("-ts_max_snes_failures","Maximum number of nonlinear solve failures","TSSetMaxSNESFailures",ts->max_snes_failures,&ts->max_snes_failures,NULL);
201:   PetscOptionsInt("-ts_max_reject","Maximum number of step rejections before step fails","TSSetMaxStepRejections",ts->max_reject,&ts->max_reject,NULL);
202:   PetscOptionsBool("-ts_error_if_step_fails","Error if no step succeeds","TSSetErrorIfStepFails",ts->errorifstepfailed,&ts->errorifstepfailed,NULL);
203:   PetscOptionsReal("-ts_rtol","Relative tolerance for local truncation error","TSSetTolerances",ts->rtol,&ts->rtol,NULL);
204:   PetscOptionsReal("-ts_atol","Absolute tolerance for local truncation error","TSSetTolerances",ts->atol,&ts->atol,NULL);

206: #if defined(PETSC_HAVE_SAWS)
207:   {
208:   PetscBool set;
209:   flg  = PETSC_FALSE;
210:   PetscOptionsBool("-ts_saws_block","Block for SAWs memory snooper at end of TSSolve","PetscObjectSAWsBlock",((PetscObject)ts)->amspublishblock,&flg,&set);
211:   if (set) {
212:     PetscObjectSAWsSetBlock((PetscObject)ts,flg);
213:   }
214:   }
215: #endif

217:   /* Monitor options */
218:   TSMonitorSetFromOptions(ts,"-ts_monitor","Monitor time and timestep size","TSMonitorDefault",TSMonitorDefault,NULL);
219:   TSMonitorSetFromOptions(ts,"-ts_monitor_solution","View the solution at each timestep","TSMonitorSolution",TSMonitorSolution,NULL);
220:   TSAdjointMonitorSetFromOptions(ts,"-ts_adjoint_monitor","Monitor adjoint timestep size","TSAdjointMonitorDefault",TSAdjointMonitorDefault,NULL);

222:   PetscOptionsString("-ts_monitor_python","Use Python function","TSMonitorSet",0,monfilename,PETSC_MAX_PATH_LEN,&flg);
223:   if (flg) {PetscPythonMonitorSet((PetscObject)ts,monfilename);}

225:   PetscOptionsName("-ts_monitor_lg_solution","Monitor solution graphically","TSMonitorLGSolution",&opt);
226:   if (opt) {
227:     TSMonitorLGCtx ctx;
228:     PetscInt       howoften = 1;

230:     PetscOptionsInt("-ts_monitor_lg_solution","Monitor solution graphically","TSMonitorLGSolution",howoften,&howoften,NULL);
231:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,400,300,howoften,&ctx);
232:     TSMonitorSet(ts,TSMonitorLGSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
233:   }

235:   PetscOptionsName("-ts_monitor_lg_error","Monitor error graphically","TSMonitorLGError",&opt);
236:   if (opt) {
237:     TSMonitorLGCtx ctx;
238:     PetscInt       howoften = 1;

240:     PetscOptionsInt("-ts_monitor_lg_error","Monitor error graphically","TSMonitorLGError",howoften,&howoften,NULL);
241:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,400,300,howoften,&ctx);
242:     TSMonitorSet(ts,TSMonitorLGError,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
243:   }

245:   PetscOptionsName("-ts_monitor_lg_timestep","Monitor timestep size graphically","TSMonitorLGTimeStep",&opt);
246:   if (opt) {
247:     TSMonitorLGCtx ctx;
248:     PetscInt       howoften = 1;

250:     PetscOptionsInt("-ts_monitor_lg_timestep","Monitor timestep size graphically","TSMonitorLGTimeStep",howoften,&howoften,NULL);
251:     TSMonitorLGCtxCreate(PetscObjectComm((PetscObject)ts),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,howoften,&ctx);
252:     TSMonitorSet(ts,TSMonitorLGTimeStep,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
253:   }
254:   PetscOptionsName("-ts_monitor_lg_snes_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGSNESIterations",&opt);
255:   if (opt) {
256:     TSMonitorLGCtx ctx;
257:     PetscInt       howoften = 1;

259:     PetscOptionsInt("-ts_monitor_lg_snes_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGSNESIterations",howoften,&howoften,NULL);
260:     TSMonitorLGCtxCreate(PetscObjectComm((PetscObject)ts),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,howoften,&ctx);
261:     TSMonitorSet(ts,TSMonitorLGSNESIterations,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
262:   }
263:   PetscOptionsName("-ts_monitor_lg_ksp_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGKSPIterations",&opt);
264:   if (opt) {
265:     TSMonitorLGCtx ctx;
266:     PetscInt       howoften = 1;

268:     PetscOptionsInt("-ts_monitor_lg_ksp_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGKSPIterations",howoften,&howoften,NULL);
269:     TSMonitorLGCtxCreate(PetscObjectComm((PetscObject)ts),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,howoften,&ctx);
270:     TSMonitorSet(ts,TSMonitorLGKSPIterations,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
271:   }
272:   PetscOptionsName("-ts_monitor_sp_eig","Monitor eigenvalues of linearized operator graphically","TSMonitorSPEig",&opt);
273:   if (opt) {
274:     TSMonitorSPEigCtx ctx;
275:     PetscInt          howoften = 1;

277:     PetscOptionsInt("-ts_monitor_sp_eig","Monitor eigenvalues of linearized operator graphically","TSMonitorSPEig",howoften,&howoften,NULL);
278:     TSMonitorSPEigCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
279:     TSMonitorSet(ts,TSMonitorSPEig,ctx,(PetscErrorCode (*)(void**))TSMonitorSPEigCtxDestroy);
280:   }
281:   opt  = PETSC_FALSE;
282:   PetscOptionsName("-ts_monitor_draw_solution","Monitor solution graphically","TSMonitorDrawSolution",&opt);
283:   if (opt) {
284:     TSMonitorDrawCtx ctx;
285:     PetscInt         howoften = 1;

287:     PetscOptionsInt("-ts_monitor_draw_solution","Monitor solution graphically","TSMonitorDrawSolution",howoften,&howoften,NULL);
288:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
289:     TSMonitorSet(ts,TSMonitorDrawSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
290:   }
291:   opt  = PETSC_FALSE;
292:   PetscOptionsName("-ts_adjoint_monitor_draw_sensi","Monitor adjoint sensitivities (lambda only) graphically","TSAdjointMonitorDrawSensi",&opt);
293:   if (opt) {
294:     TSMonitorDrawCtx ctx;
295:     PetscInt         howoften = 1;

297:     PetscOptionsInt("-ts_adjoint_monitor_draw_sensi","Monitor adjoint sensitivities (lambda only) graphically","TSAdjointMonitorDrawSensi",howoften,&howoften,NULL);
298:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
299:     TSAdjointMonitorSet(ts,TSAdjointMonitorDrawSensi,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
300:   }
301:   opt  = PETSC_FALSE;
302:   PetscOptionsName("-ts_monitor_draw_solution_phase","Monitor solution graphically","TSMonitorDrawSolutionPhase",&opt);
303:   if (opt) {
304:     TSMonitorDrawCtx ctx;
305:     PetscReal        bounds[4];
306:     PetscInt         n = 4;
307:     PetscDraw        draw;
308:     PetscDrawAxis    axis;

310:     PetscOptionsRealArray("-ts_monitor_draw_solution_phase","Monitor solution graphically","TSMonitorDrawSolutionPhase",bounds,&n,NULL);
311:     if (n != 4) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Must provide bounding box of phase field");
312:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,1,&ctx);
313:     PetscViewerDrawGetDraw(ctx->viewer,0,&draw);
314:     PetscViewerDrawGetDrawAxis(ctx->viewer,0,&axis);
315:     PetscDrawAxisSetLimits(axis,bounds[0],bounds[2],bounds[1],bounds[3]);
316:     PetscDrawAxisSetLabels(axis,"Phase Diagram","Variable 1","Variable 2");
317:     TSMonitorSet(ts,TSMonitorDrawSolutionPhase,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
318:   }
319:   opt  = PETSC_FALSE;
320:   PetscOptionsName("-ts_monitor_draw_error","Monitor error graphically","TSMonitorDrawError",&opt);
321:   if (opt) {
322:     TSMonitorDrawCtx ctx;
323:     PetscInt         howoften = 1;

325:     PetscOptionsInt("-ts_monitor_draw_error","Monitor error graphically","TSMonitorDrawError",howoften,&howoften,NULL);
326:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
327:     TSMonitorSet(ts,TSMonitorDrawError,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
328:   }

330:   opt  = PETSC_FALSE;
331:   PetscOptionsString("-ts_monitor_solution_vtk","Save each time step to a binary file, use filename-%%03D.vts","TSMonitorSolutionVTK",0,monfilename,PETSC_MAX_PATH_LEN,&flg);
332:   if (flg) {
333:     const char *ptr,*ptr2;
334:     char       *filetemplate;
335:     if (!monfilename[0]) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"-ts_monitor_solution_vtk requires a file template, e.g. filename-%%03D.vts");
336:     /* Do some cursory validation of the input. */
337:     PetscStrstr(monfilename,"%",(char**)&ptr);
338:     if (!ptr) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"-ts_monitor_solution_vtk requires a file template, e.g. filename-%%03D.vts");
339:     for (ptr++; ptr && *ptr; ptr++) {
340:       PetscStrchr("DdiouxX",*ptr,(char**)&ptr2);
341:       if (!ptr2 && (*ptr < '0' || '9' < *ptr)) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"Invalid file template argument to -ts_monitor_solution_vtk, should look like filename-%%03D.vts");
342:       if (ptr2) break;
343:     }
344:     PetscStrallocpy(monfilename,&filetemplate);
345:     TSMonitorSet(ts,TSMonitorSolutionVTK,filetemplate,(PetscErrorCode (*)(void**))TSMonitorSolutionVTKDestroy);
346:   }

348:   PetscOptionsString("-ts_monitor_dmda_ray","Display a ray of the solution","None","y=0",dir,16,&flg);
349:   if (flg) {
350:     TSMonitorDMDARayCtx *rayctx;
351:     int                  ray = 0;
352:     DMDADirection        ddir;
353:     DM                   da;
354:     PetscMPIInt          rank;

356:     if (dir[1] != '=') SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Unknown ray %s",dir);
357:     if (dir[0] == 'x') ddir = DMDA_X;
358:     else if (dir[0] == 'y') ddir = DMDA_Y;
359:     else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Unknown ray %s",dir);
360:     sscanf(dir+2,"%d",&ray);

362:     PetscInfo2(((PetscObject)ts),"Displaying DMDA ray %c = %D\n",dir[0],ray);
363:     PetscNew(&rayctx);
364:     TSGetDM(ts,&da);
365:     DMDAGetRay(da,ddir,ray,&rayctx->ray,&rayctx->scatter);
366:     MPI_Comm_rank(PetscObjectComm((PetscObject)ts),&rank);
367:     if (!rank) {
368:       PetscViewerDrawOpen(PETSC_COMM_SELF,0,0,0,0,600,300,&rayctx->viewer);
369:     }
370:     rayctx->lgctx = NULL;
371:     TSMonitorSet(ts,TSMonitorDMDARay,rayctx,TSMonitorDMDARayDestroy);
372:   }
373:   PetscOptionsString("-ts_monitor_lg_dmda_ray","Display a ray of the solution","None","x=0",dir,16,&flg);
374:   if (flg) {
375:     TSMonitorDMDARayCtx *rayctx;
376:     int                 ray = 0;
377:     DMDADirection       ddir;
378:     DM                  da;
379:     PetscInt            howoften = 1;

381:     if (dir[1] != '=') SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_ARG_WRONG, "Malformed ray %s", dir);
382:     if      (dir[0] == 'x') ddir = DMDA_X;
383:     else if (dir[0] == 'y') ddir = DMDA_Y;
384:     else SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_ARG_WRONG, "Unknown ray direction %s", dir);
385:     sscanf(dir+2, "%d", &ray);

387:     PetscInfo2(((PetscObject) ts),"Displaying LG DMDA ray %c = %D\n", dir[0], ray);
388:     PetscNew(&rayctx);
389:     TSGetDM(ts, &da);
390:     DMDAGetRay(da, ddir, ray, &rayctx->ray, &rayctx->scatter);
391:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&rayctx->lgctx);
392:     TSMonitorSet(ts, TSMonitorLGDMDARay, rayctx, TSMonitorDMDARayDestroy);
393:   }

395:   PetscOptionsName("-ts_monitor_envelope","Monitor maximum and minimum value of each component of the solution","TSMonitorEnvelope",&opt);
396:   if (opt) {
397:     TSMonitorEnvelopeCtx ctx;

399:     TSMonitorEnvelopeCtxCreate(ts,&ctx);
400:     TSMonitorSet(ts,TSMonitorEnvelope,ctx,(PetscErrorCode (*)(void**))TSMonitorEnvelopeCtxDestroy);
401:   }

403:   flg  = PETSC_FALSE;
404:   PetscOptionsBool("-ts_fd_color", "Use finite differences with coloring to compute IJacobian", "TSComputeJacobianDefaultColor", flg, &flg, NULL);
405:   if (flg) {
406:     DM   dm;
407:     DMTS tdm;

409:     TSGetDM(ts, &dm);
410:     DMGetDMTS(dm, &tdm);
411:     tdm->ijacobianctx = NULL;
412:     TSSetIJacobian(ts, NULL, NULL, TSComputeIJacobianDefaultColor, 0);
413:     PetscInfo(ts, "Setting default finite difference coloring Jacobian matrix\n");
414:   }

416:   if (ts->adapt) {
417:     TSAdaptSetFromOptions(PetscOptionsObject,ts->adapt);
418:   }

420:   /* Handle specific TS options */
421:   if (ts->ops->setfromoptions) {
422:     (*ts->ops->setfromoptions)(PetscOptionsObject,ts);
423:   }

425:   /* TS trajectory must be set after TS, since it may use some TS options above */
426:   tflg = ts->trajectory ? PETSC_TRUE : PETSC_FALSE;
427:   PetscOptionsBool("-ts_save_trajectory","Save the solution at each timestep","TSSetSaveTrajectory",tflg,&tflg,NULL);
428:   if (tflg) {
429:     TSSetSaveTrajectory(ts);
430:   }
431:   tflg = ts->adjoint_solve ? PETSC_TRUE : PETSC_FALSE;
432:   PetscOptionsBool("-ts_adjoint_solve","Solve the adjoint problem immediately after solving the forward problem","",tflg,&tflg,&flg);
433:   if (flg) {
434:     TSSetSaveTrajectory(ts);
435:     ts->adjoint_solve = tflg;
436:   }

438:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
439:   PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject)ts);
440:   PetscOptionsEnd();

442:   if (ts->trajectory) {
443:     TSTrajectorySetFromOptions(ts->trajectory,ts);
444:   }

446:   TSGetSNES(ts,&ts->snes);
447:   if (ts->problem_type == TS_LINEAR) {SNESSetType(ts->snes,SNESKSPONLY);}
448:   SNESSetFromOptions(ts->snes);
449:   return(0);
450: }

454: /*@
455:    TSSetSaveTrajectory - Causes the TS to save its solutions as it iterates forward in time in a TSTrajectory object

457:    Collective on TS

459:    Input Parameters:
460: .  ts - the TS context obtained from TSCreate()

462: Note: This routine should be called after all TS options have been set

464:    Level: intermediate

466: .seealso: TSGetTrajectory(), TSAdjointSolve()

468: .keywords: TS, set, checkpoint,
469: @*/
470: PetscErrorCode  TSSetSaveTrajectory(TS ts)
471: {

476:   if (!ts->trajectory) {
477:     TSTrajectoryCreate(PetscObjectComm((PetscObject)ts),&ts->trajectory);
478:     TSTrajectorySetFromOptions(ts->trajectory,ts);
479:   }
480:   return(0);
481: }

485: /*@
486:    TSComputeRHSJacobian - Computes the Jacobian matrix that has been
487:       set with TSSetRHSJacobian().

489:    Collective on TS and Vec

491:    Input Parameters:
492: +  ts - the TS context
493: .  t - current timestep
494: -  U - input vector

496:    Output Parameters:
497: +  A - Jacobian matrix
498: .  B - optional preconditioning matrix
499: -  flag - flag indicating matrix structure

501:    Notes:
502:    Most users should not need to explicitly call this routine, as it
503:    is used internally within the nonlinear solvers.

505:    See KSPSetOperators() for important information about setting the
506:    flag parameter.

508:    Level: developer

510: .keywords: SNES, compute, Jacobian, matrix

512: .seealso:  TSSetRHSJacobian(), KSPSetOperators()
513: @*/
514: PetscErrorCode  TSComputeRHSJacobian(TS ts,PetscReal t,Vec U,Mat A,Mat B)
515: {
517:   PetscObjectState Ustate;
518:   DM             dm;
519:   DMTS           tsdm;
520:   TSRHSJacobian  rhsjacobianfunc;
521:   void           *ctx;
522:   TSIJacobian    ijacobianfunc;
523:   TSRHSFunction  rhsfunction;

529:   TSGetDM(ts,&dm);
530:   DMGetDMTS(dm,&tsdm);
531:   DMTSGetRHSJacobian(dm,&rhsjacobianfunc,&ctx);
532:   DMTSGetIJacobian(dm,&ijacobianfunc,NULL);
533:   DMTSGetRHSFunction(dm,&rhsfunction,&ctx);
534:   PetscObjectStateGet((PetscObject)U,&Ustate);
535:   if (ts->rhsjacobian.time == t && (ts->problem_type == TS_LINEAR || (ts->rhsjacobian.X == U && ts->rhsjacobian.Xstate == Ustate)) && (rhsfunction != TSComputeRHSFunctionLinear)) {
536:     return(0);
537:   }

539:   if (!rhsjacobianfunc && !ijacobianfunc) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"Must call TSSetRHSJacobian() and / or TSSetIJacobian()");

541:   if (ts->rhsjacobian.reuse) {
542:     MatShift(A,-ts->rhsjacobian.shift);
543:     MatScale(A,1./ts->rhsjacobian.scale);
544:     if (A != B) {
545:       MatShift(B,-ts->rhsjacobian.shift);
546:       MatScale(B,1./ts->rhsjacobian.scale);
547:     }
548:     ts->rhsjacobian.shift = 0;
549:     ts->rhsjacobian.scale = 1.;
550:   }

552:   if (rhsjacobianfunc) {
553:     PetscBool missing;
554:     PetscLogEventBegin(TS_JacobianEval,ts,U,A,B);
555:     PetscStackPush("TS user Jacobian function");
556:     (*rhsjacobianfunc)(ts,t,U,A,B,ctx);
557:     PetscStackPop;
558:     PetscLogEventEnd(TS_JacobianEval,ts,U,A,B);
559:     if (A) {
560:       MatMissingDiagonal(A,&missing,NULL);
561:       if (missing) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Amat passed to TSSetRHSJacobian() must have all diagonal entries set, if they are zero you must still set them with a zero value");
562:     }
563:     if (B && B != A) {
564:       MatMissingDiagonal(B,&missing,NULL);
565:       if (missing) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Bmat passed to TSSetRHSJacobian() must have all diagonal entries set, if they are zero you must still set them with a zero value");
566:     }
567:   } else {
568:     MatZeroEntries(A);
569:     if (A != B) {MatZeroEntries(B);}
570:   }
571:   ts->rhsjacobian.time       = t;
572:   ts->rhsjacobian.X          = U;
573:   PetscObjectStateGet((PetscObject)U,&ts->rhsjacobian.Xstate);
574:   return(0);
575: }

579: /*@
580:    TSComputeRHSFunction - Evaluates the right-hand-side function.

582:    Collective on TS and Vec

584:    Input Parameters:
585: +  ts - the TS context
586: .  t - current time
587: -  U - state vector

589:    Output Parameter:
590: .  y - right hand side

592:    Note:
593:    Most users should not need to explicitly call this routine, as it
594:    is used internally within the nonlinear solvers.

596:    Level: developer

598: .keywords: TS, compute

600: .seealso: TSSetRHSFunction(), TSComputeIFunction()
601: @*/
602: PetscErrorCode TSComputeRHSFunction(TS ts,PetscReal t,Vec U,Vec y)
603: {
605:   TSRHSFunction  rhsfunction;
606:   TSIFunction    ifunction;
607:   void           *ctx;
608:   DM             dm;

614:   TSGetDM(ts,&dm);
615:   DMTSGetRHSFunction(dm,&rhsfunction,&ctx);
616:   DMTSGetIFunction(dm,&ifunction,NULL);

618:   if (!rhsfunction && !ifunction) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"Must call TSSetRHSFunction() and / or TSSetIFunction()");

620:   PetscLogEventBegin(TS_FunctionEval,ts,U,y,0);
621:   if (rhsfunction) {
622:     PetscStackPush("TS user right-hand-side function");
623:     (*rhsfunction)(ts,t,U,y,ctx);
624:     PetscStackPop;
625:   } else {
626:     VecZeroEntries(y);
627:   }

629:   PetscLogEventEnd(TS_FunctionEval,ts,U,y,0);
630:   return(0);
631: }

635: /*@
636:    TSComputeSolutionFunction - Evaluates the solution function.

638:    Collective on TS and Vec

640:    Input Parameters:
641: +  ts - the TS context
642: -  t - current time

644:    Output Parameter:
645: .  U - the solution

647:    Note:
648:    Most users should not need to explicitly call this routine, as it
649:    is used internally within the nonlinear solvers.

651:    Level: developer

653: .keywords: TS, compute

655: .seealso: TSSetSolutionFunction(), TSSetRHSFunction(), TSComputeIFunction()
656: @*/
657: PetscErrorCode TSComputeSolutionFunction(TS ts,PetscReal t,Vec U)
658: {
659:   PetscErrorCode     ierr;
660:   TSSolutionFunction solutionfunction;
661:   void               *ctx;
662:   DM                 dm;

667:   TSGetDM(ts,&dm);
668:   DMTSGetSolutionFunction(dm,&solutionfunction,&ctx);

670:   if (solutionfunction) {
671:     PetscStackPush("TS user solution function");
672:     (*solutionfunction)(ts,t,U,ctx);
673:     PetscStackPop;
674:   }
675:   return(0);
676: }
679: /*@
680:    TSComputeForcingFunction - Evaluates the forcing function.

682:    Collective on TS and Vec

684:    Input Parameters:
685: +  ts - the TS context
686: -  t - current time

688:    Output Parameter:
689: .  U - the function value

691:    Note:
692:    Most users should not need to explicitly call this routine, as it
693:    is used internally within the nonlinear solvers.

695:    Level: developer

697: .keywords: TS, compute

699: .seealso: TSSetSolutionFunction(), TSSetRHSFunction(), TSComputeIFunction()
700: @*/
701: PetscErrorCode TSComputeForcingFunction(TS ts,PetscReal t,Vec U)
702: {
703:   PetscErrorCode     ierr, (*forcing)(TS,PetscReal,Vec,void*);
704:   void               *ctx;
705:   DM                 dm;

710:   TSGetDM(ts,&dm);
711:   DMTSGetForcingFunction(dm,&forcing,&ctx);

713:   if (forcing) {
714:     PetscStackPush("TS user forcing function");
715:     (*forcing)(ts,t,U,ctx);
716:     PetscStackPop;
717:   }
718:   return(0);
719: }

723: static PetscErrorCode TSGetRHSVec_Private(TS ts,Vec *Frhs)
724: {
725:   Vec            F;

729:   *Frhs = NULL;
730:   TSGetIFunction(ts,&F,NULL,NULL);
731:   if (!ts->Frhs) {
732:     VecDuplicate(F,&ts->Frhs);
733:   }
734:   *Frhs = ts->Frhs;
735:   return(0);
736: }

740: static PetscErrorCode TSGetRHSMats_Private(TS ts,Mat *Arhs,Mat *Brhs)
741: {
742:   Mat            A,B;

746:   if (Arhs) *Arhs = NULL;
747:   if (Brhs) *Brhs = NULL;
748:   TSGetIJacobian(ts,&A,&B,NULL,NULL);
749:   if (Arhs) {
750:     if (!ts->Arhs) {
751:       MatDuplicate(A,MAT_DO_NOT_COPY_VALUES,&ts->Arhs);
752:     }
753:     *Arhs = ts->Arhs;
754:   }
755:   if (Brhs) {
756:     if (!ts->Brhs) {
757:       if (A != B) {
758:         MatDuplicate(B,MAT_DO_NOT_COPY_VALUES,&ts->Brhs);
759:       } else {
760:         PetscObjectReference((PetscObject)ts->Arhs);
761:         ts->Brhs = ts->Arhs;
762:       }
763:     }
764:     *Brhs = ts->Brhs;
765:   }
766:   return(0);
767: }

771: /*@
772:    TSComputeIFunction - Evaluates the DAE residual written in implicit form F(t,U,Udot)=0

774:    Collective on TS and Vec

776:    Input Parameters:
777: +  ts - the TS context
778: .  t - current time
779: .  U - state vector
780: .  Udot - time derivative of state vector
781: -  imex - flag indicates if the method is IMEX so that the RHSFunction should be kept separate

783:    Output Parameter:
784: .  Y - right hand side

786:    Note:
787:    Most users should not need to explicitly call this routine, as it
788:    is used internally within the nonlinear solvers.

790:    If the user did did not write their equations in implicit form, this
791:    function recasts them in implicit form.

793:    Level: developer

795: .keywords: TS, compute

797: .seealso: TSSetIFunction(), TSComputeRHSFunction()
798: @*/
799: PetscErrorCode TSComputeIFunction(TS ts,PetscReal t,Vec U,Vec Udot,Vec Y,PetscBool imex)
800: {
802:   TSIFunction    ifunction;
803:   TSRHSFunction  rhsfunction;
804:   void           *ctx;
805:   DM             dm;


813:   TSGetDM(ts,&dm);
814:   DMTSGetIFunction(dm,&ifunction,&ctx);
815:   DMTSGetRHSFunction(dm,&rhsfunction,NULL);

817:   if (!rhsfunction && !ifunction) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"Must call TSSetRHSFunction() and / or TSSetIFunction()");

819:   PetscLogEventBegin(TS_FunctionEval,ts,U,Udot,Y);
820:   if (ifunction) {
821:     PetscStackPush("TS user implicit function");
822:     (*ifunction)(ts,t,U,Udot,Y,ctx);
823:     PetscStackPop;
824:   }
825:   if (imex) {
826:     if (!ifunction) {
827:       VecCopy(Udot,Y);
828:     }
829:   } else if (rhsfunction) {
830:     if (ifunction) {
831:       Vec Frhs;
832:       TSGetRHSVec_Private(ts,&Frhs);
833:       TSComputeRHSFunction(ts,t,U,Frhs);
834:       VecAXPY(Y,-1,Frhs);
835:     } else {
836:       TSComputeRHSFunction(ts,t,U,Y);
837:       VecAYPX(Y,-1,Udot);
838:     }
839:   }
840:   PetscLogEventEnd(TS_FunctionEval,ts,U,Udot,Y);
841:   return(0);
842: }

846: /*@
847:    TSComputeIJacobian - Evaluates the Jacobian of the DAE

849:    Collective on TS and Vec

851:    Input
852:       Input Parameters:
853: +  ts - the TS context
854: .  t - current timestep
855: .  U - state vector
856: .  Udot - time derivative of state vector
857: .  shift - shift to apply, see note below
858: -  imex - flag indicates if the method is IMEX so that the RHSJacobian should be kept separate

860:    Output Parameters:
861: +  A - Jacobian matrix
862: .  B - optional preconditioning matrix
863: -  flag - flag indicating matrix structure

865:    Notes:
866:    If F(t,U,Udot)=0 is the DAE, the required Jacobian is

868:    dF/dU + shift*dF/dUdot

870:    Most users should not need to explicitly call this routine, as it
871:    is used internally within the nonlinear solvers.

873:    Level: developer

875: .keywords: TS, compute, Jacobian, matrix

877: .seealso:  TSSetIJacobian()
878: @*/
879: PetscErrorCode TSComputeIJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat A,Mat B,PetscBool imex)
880: {
882:   TSIJacobian    ijacobian;
883:   TSRHSJacobian  rhsjacobian;
884:   DM             dm;
885:   void           *ctx;


896:   TSGetDM(ts,&dm);
897:   DMTSGetIJacobian(dm,&ijacobian,&ctx);
898:   DMTSGetRHSJacobian(dm,&rhsjacobian,NULL);

900:   if (!rhsjacobian && !ijacobian) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"Must call TSSetRHSJacobian() and / or TSSetIJacobian()");

902:   PetscLogEventBegin(TS_JacobianEval,ts,U,A,B);
903:   if (ijacobian) {
904:     PetscBool missing;
905:     PetscStackPush("TS user implicit Jacobian");
906:     (*ijacobian)(ts,t,U,Udot,shift,A,B,ctx);
907:     PetscStackPop;
908:     if (A) {
909:       MatMissingDiagonal(A,&missing,NULL);
910:       if (missing) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Amat passed to TSSetIJacobian() must have all diagonal entries set, if they are zero you must still set them with a zero value");
911:     }
912:     if (B && B != A) {
913:       MatMissingDiagonal(B,&missing,NULL);
914:       if (missing) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Bmat passed to TSSetIJacobian() must have all diagonal entries set, if they are zero you must still set them with a zero value");
915:     }
916:   }
917:   if (imex) {
918:     if (!ijacobian) {  /* system was written as Udot = G(t,U) */
919:       MatZeroEntries(A);
920:       MatShift(A,shift);
921:       if (A != B) {
922:         MatZeroEntries(B);
923:         MatShift(B,shift);
924:       }
925:     }
926:   } else {
927:     Mat Arhs = NULL,Brhs = NULL;
928:     if (rhsjacobian) {
929:       if (ijacobian) {
930:         TSGetRHSMats_Private(ts,&Arhs,&Brhs);
931:       } else {
932:         TSGetIJacobian(ts,&Arhs,&Brhs,NULL,NULL);
933:       }
934:       TSComputeRHSJacobian(ts,t,U,Arhs,Brhs);
935:     }
936:     if (Arhs == A) {           /* No IJacobian, so we only have the RHS matrix */
937:       ts->rhsjacobian.scale = -1;
938:       ts->rhsjacobian.shift = shift;
939:       MatScale(A,-1);
940:       MatShift(A,shift);
941:       if (A != B) {
942:         MatScale(B,-1);
943:         MatShift(B,shift);
944:       }
945:     } else if (Arhs) {          /* Both IJacobian and RHSJacobian */
946:       MatStructure axpy = DIFFERENT_NONZERO_PATTERN;
947:       if (!ijacobian) {         /* No IJacobian provided, but we have a separate RHS matrix */
948:         MatZeroEntries(A);
949:         MatShift(A,shift);
950:         if (A != B) {
951:           MatZeroEntries(B);
952:           MatShift(B,shift);
953:         }
954:       }
955:       MatAXPY(A,-1,Arhs,axpy);
956:       if (A != B) {
957:         MatAXPY(B,-1,Brhs,axpy);
958:       }
959:     }
960:   }
961:   PetscLogEventEnd(TS_JacobianEval,ts,U,A,B);
962:   return(0);
963: }

967: /*@C
968:     TSSetRHSFunction - Sets the routine for evaluating the function,
969:     where U_t = G(t,u).

971:     Logically Collective on TS

973:     Input Parameters:
974: +   ts - the TS context obtained from TSCreate()
975: .   r - vector to put the computed right hand side (or NULL to have it created)
976: .   f - routine for evaluating the right-hand-side function
977: -   ctx - [optional] user-defined context for private data for the
978:           function evaluation routine (may be NULL)

980:     Calling sequence of func:
981: $     func (TS ts,PetscReal t,Vec u,Vec F,void *ctx);

983: +   t - current timestep
984: .   u - input vector
985: .   F - function vector
986: -   ctx - [optional] user-defined function context

988:     Level: beginner

990:     Notes: You must call this function or TSSetIFunction() to define your ODE. You cannot use this function when solving a DAE.

992: .keywords: TS, timestep, set, right-hand-side, function

994: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSSetIFunction()
995: @*/
996: PetscErrorCode  TSSetRHSFunction(TS ts,Vec r,PetscErrorCode (*f)(TS,PetscReal,Vec,Vec,void*),void *ctx)
997: {
999:   SNES           snes;
1000:   Vec            ralloc = NULL;
1001:   DM             dm;


1007:   TSGetDM(ts,&dm);
1008:   DMTSSetRHSFunction(dm,f,ctx);
1009:   TSGetSNES(ts,&snes);
1010:   if (!r && !ts->dm && ts->vec_sol) {
1011:     VecDuplicate(ts->vec_sol,&ralloc);
1012:     r = ralloc;
1013:   }
1014:   SNESSetFunction(snes,r,SNESTSFormFunction,ts);
1015:   VecDestroy(&ralloc);
1016:   return(0);
1017: }

1021: /*@C
1022:     TSSetSolutionFunction - Provide a function that computes the solution of the ODE or DAE

1024:     Logically Collective on TS

1026:     Input Parameters:
1027: +   ts - the TS context obtained from TSCreate()
1028: .   f - routine for evaluating the solution
1029: -   ctx - [optional] user-defined context for private data for the
1030:           function evaluation routine (may be NULL)

1032:     Calling sequence of func:
1033: $     func (TS ts,PetscReal t,Vec u,void *ctx);

1035: +   t - current timestep
1036: .   u - output vector
1037: -   ctx - [optional] user-defined function context

1039:     Notes:
1040:     This routine is used for testing accuracy of time integration schemes when you already know the solution.
1041:     If analytic solutions are not known for your system, consider using the Method of Manufactured Solutions to
1042:     create closed-form solutions with non-physical forcing terms.

1044:     For low-dimensional problems solved in serial, such as small discrete systems, TSMonitorLGError() can be used to monitor the error history.

1046:     Level: beginner

1048: .keywords: TS, timestep, set, right-hand-side, function

1050: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSComputeSolutionFunction(), TSSetForcingFunction()
1051: @*/
1052: PetscErrorCode  TSSetSolutionFunction(TS ts,PetscErrorCode (*f)(TS,PetscReal,Vec,void*),void *ctx)
1053: {
1055:   DM             dm;

1059:   TSGetDM(ts,&dm);
1060:   DMTSSetSolutionFunction(dm,f,ctx);
1061:   return(0);
1062: }

1066: /*@C
1067:     TSSetForcingFunction - Provide a function that computes a forcing term for a ODE or PDE

1069:     Logically Collective on TS

1071:     Input Parameters:
1072: +   ts - the TS context obtained from TSCreate()
1073: .   f - routine for evaluating the forcing function
1074: -   ctx - [optional] user-defined context for private data for the
1075:           function evaluation routine (may be NULL)

1077:     Calling sequence of func:
1078: $     func (TS ts,PetscReal t,Vec u,void *ctx);

1080: +   t - current timestep
1081: .   u - output vector
1082: -   ctx - [optional] user-defined function context

1084:     Notes:
1085:     This routine is useful for testing accuracy of time integration schemes when using the Method of Manufactured Solutions to
1086:     create closed-form solutions with a non-physical forcing term.

1088:     For low-dimensional problems solved in serial, such as small discrete systems, TSMonitorLGError() can be used to monitor the error history.

1090:     Level: beginner

1092: .keywords: TS, timestep, set, right-hand-side, function

1094: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSComputeSolutionFunction(), TSSetSolutionFunction()
1095: @*/
1096: PetscErrorCode  TSSetForcingFunction(TS ts,TSForcingFunction f,void *ctx)
1097: {
1099:   DM             dm;

1103:   TSGetDM(ts,&dm);
1104:   DMTSSetForcingFunction(dm,f,ctx);
1105:   return(0);
1106: }

1110: /*@C
1111:    TSSetRHSJacobian - Sets the function to compute the Jacobian of G,
1112:    where U_t = G(U,t), as well as the location to store the matrix.

1114:    Logically Collective on TS

1116:    Input Parameters:
1117: +  ts  - the TS context obtained from TSCreate()
1118: .  Amat - (approximate) Jacobian matrix
1119: .  Pmat - matrix from which preconditioner is to be constructed (usually the same as Amat)
1120: .  f   - the Jacobian evaluation routine
1121: -  ctx - [optional] user-defined context for private data for the
1122:          Jacobian evaluation routine (may be NULL)

1124:    Calling sequence of f:
1125: $     func (TS ts,PetscReal t,Vec u,Mat A,Mat B,void *ctx);

1127: +  t - current timestep
1128: .  u - input vector
1129: .  Amat - (approximate) Jacobian matrix
1130: .  Pmat - matrix from which preconditioner is to be constructed (usually the same as Amat)
1131: -  ctx - [optional] user-defined context for matrix evaluation routine

1133:    Notes:
1134:    You must set all the diagonal entries of the matrices, if they are zero you must still set them with a zero value

1136:    The TS solver may modify the nonzero structure and the entries of the matrices Amat and Pmat between the calls to f()
1137:    You should not assume the values are the same in the next call to f() as you set them in the previous call.

1139:    Level: beginner

1141: .keywords: TS, timestep, set, right-hand-side, Jacobian

1143: .seealso: SNESComputeJacobianDefaultColor(), TSSetRHSFunction(), TSRHSJacobianSetReuse(), TSSetIJacobian()

1145: @*/
1146: PetscErrorCode  TSSetRHSJacobian(TS ts,Mat Amat,Mat Pmat,TSRHSJacobian f,void *ctx)
1147: {
1149:   SNES           snes;
1150:   DM             dm;
1151:   TSIJacobian    ijacobian;


1160:   TSGetDM(ts,&dm);
1161:   DMTSSetRHSJacobian(dm,f,ctx);
1162:   if (f == TSComputeRHSJacobianConstant) {
1163:     /* Handle this case automatically for the user; otherwise user should call themselves. */
1164:     TSRHSJacobianSetReuse(ts,PETSC_TRUE);
1165:   }
1166:   DMTSGetIJacobian(dm,&ijacobian,NULL);
1167:   TSGetSNES(ts,&snes);
1168:   if (!ijacobian) {
1169:     SNESSetJacobian(snes,Amat,Pmat,SNESTSFormJacobian,ts);
1170:   }
1171:   if (Amat) {
1172:     PetscObjectReference((PetscObject)Amat);
1173:     MatDestroy(&ts->Arhs);
1174:     ts->Arhs = Amat;
1175:   }
1176:   if (Pmat) {
1177:     PetscObjectReference((PetscObject)Pmat);
1178:     MatDestroy(&ts->Brhs);
1179:     ts->Brhs = Pmat;
1180:   }
1181:   return(0);
1182: }


1187: /*@C
1188:    TSSetIFunction - Set the function to compute F(t,U,U_t) where F() = 0 is the DAE to be solved.

1190:    Logically Collective on TS

1192:    Input Parameters:
1193: +  ts  - the TS context obtained from TSCreate()
1194: .  r   - vector to hold the residual (or NULL to have it created internally)
1195: .  f   - the function evaluation routine
1196: -  ctx - user-defined context for private data for the function evaluation routine (may be NULL)

1198:    Calling sequence of f:
1199: $  f(TS ts,PetscReal t,Vec u,Vec u_t,Vec F,ctx);

1201: +  t   - time at step/stage being solved
1202: .  u   - state vector
1203: .  u_t - time derivative of state vector
1204: .  F   - function vector
1205: -  ctx - [optional] user-defined context for matrix evaluation routine

1207:    Important:
1208:    The user MUST call either this routine or TSSetRHSFunction() to define the ODE.  When solving DAEs you must use this function.

1210:    Level: beginner

1212: .keywords: TS, timestep, set, DAE, Jacobian

1214: .seealso: TSSetRHSJacobian(), TSSetRHSFunction(), TSSetIJacobian()
1215: @*/
1216: PetscErrorCode  TSSetIFunction(TS ts,Vec r,TSIFunction f,void *ctx)
1217: {
1219:   SNES           snes;
1220:   Vec            ralloc = NULL;
1221:   DM             dm;


1227:   TSGetDM(ts,&dm);
1228:   DMTSSetIFunction(dm,f,ctx);

1230:   TSGetSNES(ts,&snes);
1231:   if (!r && !ts->dm && ts->vec_sol) {
1232:     VecDuplicate(ts->vec_sol,&ralloc);
1233:     r  = ralloc;
1234:   }
1235:   SNESSetFunction(snes,r,SNESTSFormFunction,ts);
1236:   VecDestroy(&ralloc);
1237:   return(0);
1238: }

1242: /*@C
1243:    TSGetIFunction - Returns the vector where the implicit residual is stored and the function/contex to compute it.

1245:    Not Collective

1247:    Input Parameter:
1248: .  ts - the TS context

1250:    Output Parameter:
1251: +  r - vector to hold residual (or NULL)
1252: .  func - the function to compute residual (or NULL)
1253: -  ctx - the function context (or NULL)

1255:    Level: advanced

1257: .keywords: TS, nonlinear, get, function

1259: .seealso: TSSetIFunction(), SNESGetFunction()
1260: @*/
1261: PetscErrorCode TSGetIFunction(TS ts,Vec *r,TSIFunction *func,void **ctx)
1262: {
1264:   SNES           snes;
1265:   DM             dm;

1269:   TSGetSNES(ts,&snes);
1270:   SNESGetFunction(snes,r,NULL,NULL);
1271:   TSGetDM(ts,&dm);
1272:   DMTSGetIFunction(dm,func,ctx);
1273:   return(0);
1274: }

1278: /*@C
1279:    TSGetRHSFunction - Returns the vector where the right hand side is stored and the function/context to compute it.

1281:    Not Collective

1283:    Input Parameter:
1284: .  ts - the TS context

1286:    Output Parameter:
1287: +  r - vector to hold computed right hand side (or NULL)
1288: .  func - the function to compute right hand side (or NULL)
1289: -  ctx - the function context (or NULL)

1291:    Level: advanced

1293: .keywords: TS, nonlinear, get, function

1295: .seealso: TSSetRHSFunction(), SNESGetFunction()
1296: @*/
1297: PetscErrorCode TSGetRHSFunction(TS ts,Vec *r,TSRHSFunction *func,void **ctx)
1298: {
1300:   SNES           snes;
1301:   DM             dm;

1305:   TSGetSNES(ts,&snes);
1306:   SNESGetFunction(snes,r,NULL,NULL);
1307:   TSGetDM(ts,&dm);
1308:   DMTSGetRHSFunction(dm,func,ctx);
1309:   return(0);
1310: }

1314: /*@C
1315:    TSSetIJacobian - Set the function to compute the matrix dF/dU + a*dF/dU_t where F(t,U,U_t) is the function
1316:         provided with TSSetIFunction().

1318:    Logically Collective on TS

1320:    Input Parameters:
1321: +  ts  - the TS context obtained from TSCreate()
1322: .  Amat - (approximate) Jacobian matrix
1323: .  Pmat - matrix used to compute preconditioner (usually the same as Amat)
1324: .  f   - the Jacobian evaluation routine
1325: -  ctx - user-defined context for private data for the Jacobian evaluation routine (may be NULL)

1327:    Calling sequence of f:
1328: $  f(TS ts,PetscReal t,Vec U,Vec U_t,PetscReal a,Mat Amat,Mat Pmat,void *ctx);

1330: +  t    - time at step/stage being solved
1331: .  U    - state vector
1332: .  U_t  - time derivative of state vector
1333: .  a    - shift
1334: .  Amat - (approximate) Jacobian of F(t,U,W+a*U), equivalent to dF/dU + a*dF/dU_t
1335: .  Pmat - matrix used for constructing preconditioner, usually the same as Amat
1336: -  ctx  - [optional] user-defined context for matrix evaluation routine

1338:    Notes:
1339:    The matrices Amat and Pmat are exactly the matrices that are used by SNES for the nonlinear solve.

1341:    If you know the operator Amat has a null space you can use MatSetNullSpace() and MatSetTransposeNullSpace() to supply the null
1342:    space to Amat and the KSP solvers will automatically use that null space as needed during the solution process.

1344:    The matrix dF/dU + a*dF/dU_t you provide turns out to be
1345:    the Jacobian of F(t,U,W+a*U) where F(t,U,U_t) = 0 is the DAE to be solved.
1346:    The time integrator internally approximates U_t by W+a*U where the positive "shift"
1347:    a and vector W depend on the integration method, step size, and past states. For example with
1348:    the backward Euler method a = 1/dt and W = -a*U(previous timestep) so
1349:    W + a*U = a*(U - U(previous timestep)) = (U - U(previous timestep))/dt

1351:    You must set all the diagonal entries of the matrices, if they are zero you must still set them with a zero value

1353:    The TS solver may modify the nonzero structure and the entries of the matrices Amat and Pmat between the calls to f()
1354:    You should not assume the values are the same in the next call to f() as you set them in the previous call.

1356:    Level: beginner

1358: .keywords: TS, timestep, DAE, Jacobian

1360: .seealso: TSSetIFunction(), TSSetRHSJacobian(), SNESComputeJacobianDefaultColor(), SNESComputeJacobianDefault(), TSSetRHSFunction()

1362: @*/
1363: PetscErrorCode  TSSetIJacobian(TS ts,Mat Amat,Mat Pmat,TSIJacobian f,void *ctx)
1364: {
1366:   SNES           snes;
1367:   DM             dm;


1376:   TSGetDM(ts,&dm);
1377:   DMTSSetIJacobian(dm,f,ctx);

1379:   TSGetSNES(ts,&snes);
1380:   SNESSetJacobian(snes,Amat,Pmat,SNESTSFormJacobian,ts);
1381:   return(0);
1382: }

1386: /*@
1387:    TSRHSJacobianSetReuse - restore RHS Jacobian before re-evaluating.  Without this flag, TS will change the sign and
1388:    shift the RHS Jacobian for a finite-time-step implicit solve, in which case the user function will need to recompute
1389:    the entire Jacobian.  The reuse flag must be set if the evaluation function will assume that the matrix entries have
1390:    not been changed by the TS.

1392:    Logically Collective

1394:    Input Arguments:
1395: +  ts - TS context obtained from TSCreate()
1396: -  reuse - PETSC_TRUE if the RHS Jacobian

1398:    Level: intermediate

1400: .seealso: TSSetRHSJacobian(), TSComputeRHSJacobianConstant()
1401: @*/
1402: PetscErrorCode TSRHSJacobianSetReuse(TS ts,PetscBool reuse)
1403: {
1405:   ts->rhsjacobian.reuse = reuse;
1406:   return(0);
1407: }

1411: /*@C
1412:    TSSetI2Function - Set the function to compute F(t,U,U_t,U_tt) where F = 0 is the DAE to be solved.

1414:    Logically Collective on TS

1416:    Input Parameters:
1417: +  ts  - the TS context obtained from TSCreate()
1418: .  F   - vector to hold the residual (or NULL to have it created internally)
1419: .  fun - the function evaluation routine
1420: -  ctx - user-defined context for private data for the function evaluation routine (may be NULL)

1422:    Calling sequence of fun:
1423: $  fun(TS ts,PetscReal t,Vec U,Vec U_t,Vec U_tt,Vec F,ctx);

1425: +  t    - time at step/stage being solved
1426: .  U    - state vector
1427: .  U_t  - time derivative of state vector
1428: .  U_tt - second time derivative of state vector
1429: .  F    - function vector
1430: -  ctx  - [optional] user-defined context for matrix evaluation routine (may be NULL)

1432:    Level: beginner

1434: .keywords: TS, timestep, set, ODE, DAE, Function

1436: .seealso: TSSetI2Jacobian()
1437: @*/
1438: PetscErrorCode TSSetI2Function(TS ts,Vec F,TSI2Function fun,void *ctx)
1439: {
1440:   DM             dm;

1446:   TSSetIFunction(ts,F,NULL,NULL);
1447:   TSGetDM(ts,&dm);
1448:   DMTSSetI2Function(dm,fun,ctx);
1449:   return(0);
1450: }

1454: /*@C
1455:   TSGetI2Function - Returns the vector where the implicit residual is stored and the function/contex to compute it.

1457:   Not Collective

1459:   Input Parameter:
1460: . ts - the TS context

1462:   Output Parameter:
1463: + r - vector to hold residual (or NULL)
1464: . fun - the function to compute residual (or NULL)
1465: - ctx - the function context (or NULL)

1467:   Level: advanced

1469: .keywords: TS, nonlinear, get, function

1471: .seealso: TSSetI2Function(), SNESGetFunction()
1472: @*/
1473: PetscErrorCode TSGetI2Function(TS ts,Vec *r,TSI2Function *fun,void **ctx)
1474: {
1476:   SNES           snes;
1477:   DM             dm;

1481:   TSGetSNES(ts,&snes);
1482:   SNESGetFunction(snes,r,NULL,NULL);
1483:   TSGetDM(ts,&dm);
1484:   DMTSGetI2Function(dm,fun,ctx);
1485:   return(0);
1486: }

1490: /*@C
1491:    TSSetI2Jacobian - Set the function to compute the matrix dF/dU + v*dF/dU_t  + a*dF/dU_tt
1492:         where F(t,U,U_t,U_tt) is the function you provided with TSSetI2Function().

1494:    Logically Collective on TS

1496:    Input Parameters:
1497: +  ts  - the TS context obtained from TSCreate()
1498: .  J   - Jacobian matrix
1499: .  P   - preconditioning matrix for J (may be same as J)
1500: .  jac - the Jacobian evaluation routine
1501: -  ctx - user-defined context for private data for the Jacobian evaluation routine (may be NULL)

1503:    Calling sequence of jac:
1504: $  jac(TS ts,PetscReal t,Vec U,Vec U_t,Vec U_tt,PetscReal v,PetscReal a,Mat J,Mat P,void *ctx);

1506: +  t    - time at step/stage being solved
1507: .  U    - state vector
1508: .  U_t  - time derivative of state vector
1509: .  U_tt - second time derivative of state vector
1510: .  v    - shift for U_t
1511: .  a    - shift for U_tt
1512: .  J    - Jacobian of G(U) = F(t,U,W+v*U,W'+a*U), equivalent to dF/dU + v*dF/dU_t  + a*dF/dU_tt
1513: .  P    - preconditioning matrix for J, may be same as J
1514: -  ctx  - [optional] user-defined context for matrix evaluation routine

1516:    Notes:
1517:    The matrices J and P are exactly the matrices that are used by SNES for the nonlinear solve.

1519:    The matrix dF/dU + v*dF/dU_t + a*dF/dU_tt you provide turns out to be
1520:    the Jacobian of G(U) = F(t,U,W+v*U,W'+a*U) where F(t,U,U_t,U_tt) = 0 is the DAE to be solved.
1521:    The time integrator internally approximates U_t by W+v*U and U_tt by W'+a*U  where the positive "shift"
1522:    parameters 'v' and 'a' and vectors W, W' depend on the integration method, step size, and past states.

1524:    Level: beginner

1526: .keywords: TS, timestep, set, ODE, DAE, Jacobian

1528: .seealso: TSSetI2Function()
1529: @*/
1530: PetscErrorCode TSSetI2Jacobian(TS ts,Mat J,Mat P,TSI2Jacobian jac,void *ctx)
1531: {
1532:   DM             dm;

1539:   TSSetIJacobian(ts,J,P,NULL,NULL);
1540:   TSGetDM(ts,&dm);
1541:   DMTSSetI2Jacobian(dm,jac,ctx);
1542:   return(0);
1543: }

1547: /*@C
1548:   TSGetI2Jacobian - Returns the implicit Jacobian at the present timestep.

1550:   Not Collective, but parallel objects are returned if TS is parallel

1552:   Input Parameter:
1553: . ts  - The TS context obtained from TSCreate()

1555:   Output Parameters:
1556: + J  - The (approximate) Jacobian of F(t,U,U_t,U_tt)
1557: . P - The matrix from which the preconditioner is constructed, often the same as J
1558: . jac - The function to compute the Jacobian matrices
1559: - ctx - User-defined context for Jacobian evaluation routine

1561:   Notes: You can pass in NULL for any return argument you do not need.

1563:   Level: advanced

1565: .seealso: TSGetTimeStep(), TSGetMatrices(), TSGetTime(), TSGetTimeStepNumber()

1567: .keywords: TS, timestep, get, matrix, Jacobian
1568: @*/
1569: PetscErrorCode  TSGetI2Jacobian(TS ts,Mat *J,Mat *P,TSI2Jacobian *jac,void **ctx)
1570: {
1572:   SNES           snes;
1573:   DM             dm;

1576:   TSGetSNES(ts,&snes);
1577:   SNESSetUpMatrices(snes);
1578:   SNESGetJacobian(snes,J,P,NULL,NULL);
1579:   TSGetDM(ts,&dm);
1580:   DMTSGetI2Jacobian(dm,jac,ctx);
1581:   return(0);
1582: }

1586: /*@
1587:   TSComputeI2Function - Evaluates the DAE residual written in implicit form F(t,U,U_t,U_tt) = 0

1589:   Collective on TS and Vec

1591:   Input Parameters:
1592: + ts - the TS context
1593: . t - current time
1594: . U - state vector
1595: . V - time derivative of state vector (U_t)
1596: - A - second time derivative of state vector (U_tt)

1598:   Output Parameter:
1599: . F - the residual vector

1601:   Note:
1602:   Most users should not need to explicitly call this routine, as it
1603:   is used internally within the nonlinear solvers.

1605:   Level: developer

1607: .keywords: TS, compute, function, vector

1609: .seealso: TSSetI2Function()
1610: @*/
1611: PetscErrorCode TSComputeI2Function(TS ts,PetscReal t,Vec U,Vec V,Vec A,Vec F)
1612: {
1613:   DM             dm;
1614:   TSI2Function   I2Function;
1615:   void           *ctx;
1616:   TSRHSFunction  rhsfunction;


1626:   TSGetDM(ts,&dm);
1627:   DMTSGetI2Function(dm,&I2Function,&ctx);
1628:   DMTSGetRHSFunction(dm,&rhsfunction,NULL);

1630:   if (!I2Function) {
1631:     TSComputeIFunction(ts,t,U,A,F,PETSC_FALSE);
1632:     return(0);
1633:   }

1635:   PetscLogEventBegin(TS_FunctionEval,ts,U,V,F);

1637:   PetscStackPush("TS user implicit function");
1638:   I2Function(ts,t,U,V,A,F,ctx);
1639:   PetscStackPop;

1641:   if (rhsfunction) {
1642:     Vec Frhs;
1643:     TSGetRHSVec_Private(ts,&Frhs);
1644:     TSComputeRHSFunction(ts,t,U,Frhs);
1645:     VecAXPY(F,-1,Frhs);
1646:   }

1648:   PetscLogEventEnd(TS_FunctionEval,ts,U,V,F);
1649:   return(0);
1650: }

1654: /*@
1655:   TSComputeI2Jacobian - Evaluates the Jacobian of the DAE

1657:   Collective on TS and Vec

1659:   Input Parameters:
1660: + ts - the TS context
1661: . t - current timestep
1662: . U - state vector
1663: . V - time derivative of state vector
1664: . A - second time derivative of state vector
1665: . shiftV - shift to apply, see note below
1666: - shiftA - shift to apply, see note below

1668:   Output Parameters:
1669: + J - Jacobian matrix
1670: - P - optional preconditioning matrix

1672:   Notes:
1673:   If F(t,U,V,A)=0 is the DAE, the required Jacobian is

1675:   dF/dU + shiftV*dF/dV + shiftA*dF/dA

1677:   Most users should not need to explicitly call this routine, as it
1678:   is used internally within the nonlinear solvers.

1680:   Level: developer

1682: .keywords: TS, compute, Jacobian, matrix

1684: .seealso:  TSSetI2Jacobian()
1685: @*/
1686: PetscErrorCode TSComputeI2Jacobian(TS ts,PetscReal t,Vec U,Vec V,Vec A,PetscReal shiftV,PetscReal shiftA,Mat J,Mat P)
1687: {
1688:   DM             dm;
1689:   TSI2Jacobian   I2Jacobian;
1690:   void           *ctx;
1691:   TSRHSJacobian  rhsjacobian;


1702:   TSGetDM(ts,&dm);
1703:   DMTSGetI2Jacobian(dm,&I2Jacobian,&ctx);
1704:   DMTSGetRHSJacobian(dm,&rhsjacobian,NULL);

1706:   if (!I2Jacobian) {
1707:     TSComputeIJacobian(ts,t,U,A,shiftA,J,P,PETSC_FALSE);
1708:     return(0);
1709:   }

1711:   PetscLogEventBegin(TS_JacobianEval,ts,U,J,P);

1713:   PetscStackPush("TS user implicit Jacobian");
1714:   I2Jacobian(ts,t,U,V,A,shiftV,shiftA,J,P,ctx);
1715:   PetscStackPop;

1717:   if (rhsjacobian) {
1718:     Mat Jrhs,Prhs; MatStructure axpy = DIFFERENT_NONZERO_PATTERN;
1719:     TSGetRHSMats_Private(ts,&Jrhs,&Prhs);
1720:     TSComputeRHSJacobian(ts,t,U,Jrhs,Prhs);
1721:     MatAXPY(J,-1,Jrhs,axpy);
1722:     if (P != J) {MatAXPY(P,-1,Prhs,axpy);}
1723:   }

1725:   PetscLogEventEnd(TS_JacobianEval,ts,U,J,P);
1726:   return(0);
1727: }

1731: /*@
1732:    TS2SetSolution - Sets the initial solution and time derivative vectors
1733:    for use by the TS routines handling second order equations.

1735:    Logically Collective on TS and Vec

1737:    Input Parameters:
1738: +  ts - the TS context obtained from TSCreate()
1739: .  u - the solution vector
1740: -  v - the time derivative vector

1742:    Level: beginner

1744: .keywords: TS, timestep, set, solution, initial conditions
1745: @*/
1746: PetscErrorCode  TS2SetSolution(TS ts,Vec u,Vec v)
1747: {

1754:   TSSetSolution(ts,u);
1755:   PetscObjectReference((PetscObject)v);
1756:   VecDestroy(&ts->vec_dot);
1757:   ts->vec_dot = v;
1758:   return(0);
1759: }

1763: /*@
1764:    TS2GetSolution - Returns the solution and time derivative at the present timestep
1765:    for second order equations. It is valid to call this routine inside the function
1766:    that you are evaluating in order to move to the new timestep. This vector not
1767:    changed until the solution at the next timestep has been calculated.

1769:    Not Collective, but Vec returned is parallel if TS is parallel

1771:    Input Parameter:
1772: .  ts - the TS context obtained from TSCreate()

1774:    Output Parameter:
1775: +  u - the vector containing the solution
1776: -  v - the vector containing the time derivative

1778:    Level: intermediate

1780: .seealso: TS2SetSolution(), TSGetTimeStep(), TSGetTime()

1782: .keywords: TS, timestep, get, solution
1783: @*/
1784: PetscErrorCode  TS2GetSolution(TS ts,Vec *u,Vec *v)
1785: {
1790:   if (u) *u = ts->vec_sol;
1791:   if (v) *v = ts->vec_dot;
1792:   return(0);
1793: }

1797: /*@C
1798:   TSLoad - Loads a KSP that has been stored in binary  with KSPView().

1800:   Collective on PetscViewer

1802:   Input Parameters:
1803: + newdm - the newly loaded TS, this needs to have been created with TSCreate() or
1804:            some related function before a call to TSLoad().
1805: - viewer - binary file viewer, obtained from PetscViewerBinaryOpen()

1807:    Level: intermediate

1809:   Notes:
1810:    The type is determined by the data in the file, any type set into the TS before this call is ignored.

1812:   Notes for advanced users:
1813:   Most users should not need to know the details of the binary storage
1814:   format, since TSLoad() and TSView() completely hide these details.
1815:   But for anyone who's interested, the standard binary matrix storage
1816:   format is
1817: .vb
1818:      has not yet been determined
1819: .ve

1821: .seealso: PetscViewerBinaryOpen(), TSView(), MatLoad(), VecLoad()
1822: @*/
1823: PetscErrorCode  TSLoad(TS ts, PetscViewer viewer)
1824: {
1826:   PetscBool      isbinary;
1827:   PetscInt       classid;
1828:   char           type[256];
1829:   DMTS           sdm;
1830:   DM             dm;

1835:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
1836:   if (!isbinary) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid viewer; open viewer with PetscViewerBinaryOpen()");

1838:   PetscViewerBinaryRead(viewer,&classid,1,NULL,PETSC_INT);
1839:   if (classid != TS_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Not TS next in file");
1840:   PetscViewerBinaryRead(viewer,type,256,NULL,PETSC_CHAR);
1841:   TSSetType(ts, type);
1842:   if (ts->ops->load) {
1843:     (*ts->ops->load)(ts,viewer);
1844:   }
1845:   DMCreate(PetscObjectComm((PetscObject)ts),&dm);
1846:   DMLoad(dm,viewer);
1847:   TSSetDM(ts,dm);
1848:   DMCreateGlobalVector(ts->dm,&ts->vec_sol);
1849:   VecLoad(ts->vec_sol,viewer);
1850:   DMGetDMTS(ts->dm,&sdm);
1851:   DMTSLoad(sdm,viewer);
1852:   return(0);
1853: }

1855: #include <petscdraw.h>
1856: #if defined(PETSC_HAVE_SAWS)
1857: #include <petscviewersaws.h>
1858: #endif
1861: /*@C
1862:     TSView - Prints the TS data structure.

1864:     Collective on TS

1866:     Input Parameters:
1867: +   ts - the TS context obtained from TSCreate()
1868: -   viewer - visualization context

1870:     Options Database Key:
1871: .   -ts_view - calls TSView() at end of TSStep()

1873:     Notes:
1874:     The available visualization contexts include
1875: +     PETSC_VIEWER_STDOUT_SELF - standard output (default)
1876: -     PETSC_VIEWER_STDOUT_WORLD - synchronized standard
1877:          output where only the first processor opens
1878:          the file.  All other processors send their
1879:          data to the first processor to print.

1881:     The user can open an alternative visualization context with
1882:     PetscViewerASCIIOpen() - output to a specified file.

1884:     Level: beginner

1886: .keywords: TS, timestep, view

1888: .seealso: PetscViewerASCIIOpen()
1889: @*/
1890: PetscErrorCode  TSView(TS ts,PetscViewer viewer)
1891: {
1893:   TSType         type;
1894:   PetscBool      iascii,isstring,isundials,isbinary,isdraw;
1895:   DMTS           sdm;
1896: #if defined(PETSC_HAVE_SAWS)
1897:   PetscBool      issaws;
1898: #endif

1902:   if (!viewer) {
1903:     PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)ts),&viewer);
1904:   }

1908:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
1909:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);
1910:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
1911:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
1912: #if defined(PETSC_HAVE_SAWS)
1913:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);
1914: #endif
1915:   if (iascii) {
1916:     PetscObjectPrintClassNamePrefixType((PetscObject)ts,viewer);
1917:     PetscViewerASCIIPrintf(viewer,"  maximum steps=%D\n",ts->max_steps);
1918:     PetscViewerASCIIPrintf(viewer,"  maximum time=%g\n",(double)ts->max_time);
1919:     if (ts->problem_type == TS_NONLINEAR) {
1920:       PetscViewerASCIIPrintf(viewer,"  total number of nonlinear solver iterations=%D\n",ts->snes_its);
1921:       PetscViewerASCIIPrintf(viewer,"  total number of nonlinear solve failures=%D\n",ts->num_snes_failures);
1922:     }
1923:     PetscViewerASCIIPrintf(viewer,"  total number of linear solver iterations=%D\n",ts->ksp_its);
1924:     PetscViewerASCIIPrintf(viewer,"  total number of rejected steps=%D\n",ts->reject);
1925:     DMGetDMTS(ts->dm,&sdm);
1926:     DMTSView(sdm,viewer);
1927:     if (ts->ops->view) {
1928:       PetscViewerASCIIPushTab(viewer);
1929:       (*ts->ops->view)(ts,viewer);
1930:       PetscViewerASCIIPopTab(viewer);
1931:     }
1932:   } else if (isstring) {
1933:     TSGetType(ts,&type);
1934:     PetscViewerStringSPrintf(viewer," %-7.7s",type);
1935:   } else if (isbinary) {
1936:     PetscInt    classid = TS_FILE_CLASSID;
1937:     MPI_Comm    comm;
1938:     PetscMPIInt rank;
1939:     char        type[256];

1941:     PetscObjectGetComm((PetscObject)ts,&comm);
1942:     MPI_Comm_rank(comm,&rank);
1943:     if (!rank) {
1944:       PetscViewerBinaryWrite(viewer,&classid,1,PETSC_INT,PETSC_FALSE);
1945:       PetscStrncpy(type,((PetscObject)ts)->type_name,256);
1946:       PetscViewerBinaryWrite(viewer,type,256,PETSC_CHAR,PETSC_FALSE);
1947:     }
1948:     if (ts->ops->view) {
1949:       (*ts->ops->view)(ts,viewer);
1950:     }
1951:     DMView(ts->dm,viewer);
1952:     VecView(ts->vec_sol,viewer);
1953:     DMGetDMTS(ts->dm,&sdm);
1954:     DMTSView(sdm,viewer);
1955:   } else if (isdraw) {
1956:     PetscDraw draw;
1957:     char      str[36];
1958:     PetscReal x,y,bottom,h;

1960:     PetscViewerDrawGetDraw(viewer,0,&draw);
1961:     PetscDrawGetCurrentPoint(draw,&x,&y);
1962:     PetscStrcpy(str,"TS: ");
1963:     PetscStrcat(str,((PetscObject)ts)->type_name);
1964:     PetscDrawStringBoxed(draw,x,y,PETSC_DRAW_BLACK,PETSC_DRAW_BLACK,str,NULL,&h);
1965:     bottom = y - h;
1966:     PetscDrawPushCurrentPoint(draw,x,bottom);
1967:     if (ts->ops->view) {
1968:       (*ts->ops->view)(ts,viewer);
1969:     }
1970:     PetscDrawPopCurrentPoint(draw);
1971: #if defined(PETSC_HAVE_SAWS)
1972:   } else if (issaws) {
1973:     PetscMPIInt rank;
1974:     const char  *name;

1976:     PetscObjectGetName((PetscObject)ts,&name);
1977:     MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
1978:     if (!((PetscObject)ts)->amsmem && !rank) {
1979:       char       dir[1024];

1981:       PetscObjectViewSAWs((PetscObject)ts,viewer);
1982:       PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/time_step",name);
1983:       PetscStackCallSAWs(SAWs_Register,(dir,&ts->steps,1,SAWs_READ,SAWs_INT));
1984:       PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/time",name);
1985:       PetscStackCallSAWs(SAWs_Register,(dir,&ts->ptime,1,SAWs_READ,SAWs_DOUBLE));
1986:     }
1987:     if (ts->ops->view) {
1988:       (*ts->ops->view)(ts,viewer);
1989:     }
1990: #endif
1991:   }

1993:   PetscViewerASCIIPushTab(viewer);
1994:   PetscObjectTypeCompare((PetscObject)ts,TSSUNDIALS,&isundials);
1995:   PetscViewerASCIIPopTab(viewer);
1996:   return(0);
1997: }


2002: /*@
2003:    TSSetApplicationContext - Sets an optional user-defined context for
2004:    the timesteppers.

2006:    Logically Collective on TS

2008:    Input Parameters:
2009: +  ts - the TS context obtained from TSCreate()
2010: -  usrP - optional user context

2012:    Fortran Notes: To use this from Fortran you must write a Fortran interface definition for this
2013:     function that tells Fortran the Fortran derived data type that you are passing in as the ctx argument.

2015:    Level: intermediate

2017: .keywords: TS, timestep, set, application, context

2019: .seealso: TSGetApplicationContext()
2020: @*/
2021: PetscErrorCode  TSSetApplicationContext(TS ts,void *usrP)
2022: {
2025:   ts->user = usrP;
2026:   return(0);
2027: }

2031: /*@
2032:     TSGetApplicationContext - Gets the user-defined context for the
2033:     timestepper.

2035:     Not Collective

2037:     Input Parameter:
2038: .   ts - the TS context obtained from TSCreate()

2040:     Output Parameter:
2041: .   usrP - user context

2043:    Fortran Notes: To use this from Fortran you must write a Fortran interface definition for this
2044:     function that tells Fortran the Fortran derived data type that you are passing in as the ctx argument.

2046:     Level: intermediate

2048: .keywords: TS, timestep, get, application, context

2050: .seealso: TSSetApplicationContext()
2051: @*/
2052: PetscErrorCode  TSGetApplicationContext(TS ts,void *usrP)
2053: {
2056:   *(void**)usrP = ts->user;
2057:   return(0);
2058: }

2062: /*@
2063:    TSGetTimeStepNumber - Gets the number of time steps completed.

2065:    Not Collective

2067:    Input Parameter:
2068: .  ts - the TS context obtained from TSCreate()

2070:    Output Parameter:
2071: .  iter - number of steps completed so far

2073:    Level: intermediate

2075: .keywords: TS, timestep, get, iteration, number
2076: .seealso: TSGetTime(), TSGetTimeStep(), TSSetPreStep(), TSSetPreStage(), TSSetPostStage(), TSSetPostStep()
2077: @*/
2078: PetscErrorCode  TSGetTimeStepNumber(TS ts,PetscInt *iter)
2079: {
2083:   *iter = ts->steps;
2084:   return(0);
2085: }

2089: /*@
2090:    TSSetInitialTimeStep - Sets the initial timestep to be used,
2091:    as well as the initial time.

2093:    Logically Collective on TS

2095:    Input Parameters:
2096: +  ts - the TS context obtained from TSCreate()
2097: .  initial_time - the initial time
2098: -  time_step - the size of the timestep

2100:    Level: intermediate

2102: .seealso: TSSetTimeStep(), TSGetTimeStep()

2104: .keywords: TS, set, initial, timestep
2105: @*/
2106: PetscErrorCode  TSSetInitialTimeStep(TS ts,PetscReal initial_time,PetscReal time_step)
2107: {

2112:   TSSetTimeStep(ts,time_step);
2113:   TSSetTime(ts,initial_time);
2114:   return(0);
2115: }

2119: /*@
2120:    TSSetTimeStep - Allows one to reset the timestep at any time,
2121:    useful for simple pseudo-timestepping codes.

2123:    Logically Collective on TS

2125:    Input Parameters:
2126: +  ts - the TS context obtained from TSCreate()
2127: -  time_step - the size of the timestep

2129:    Level: intermediate

2131: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

2133: .keywords: TS, set, timestep
2134: @*/
2135: PetscErrorCode  TSSetTimeStep(TS ts,PetscReal time_step)
2136: {
2140:   ts->time_step = time_step;
2141:   return(0);
2142: }

2146: /*@
2147:    TSSetExactFinalTime - Determines whether to adapt the final time step to
2148:      match the exact final time, interpolate solution to the exact final time,
2149:      or just return at the final time TS computed.

2151:   Logically Collective on TS

2153:    Input Parameter:
2154: +   ts - the time-step context
2155: -   eftopt - exact final time option

2157: $  TS_EXACTFINALTIME_STEPOVER    - Don't do anything if final time is exceeded
2158: $  TS_EXACTFINALTIME_INTERPOLATE - Interpolate back to final time
2159: $  TS_EXACTFINALTIME_MATCHSTEP - Adapt final time step to match the final time

2161:    Options Database:
2162: .   -ts_exact_final_time <stepover,interpolate,matchstep> - select the final step at runtime

2164:    Warning: If you use the option TS_EXACTFINALTIME_STEPOVER the solution may be at a very different time
2165:     then the final time you selected.

2167:    Level: beginner

2169: .seealso: TSExactFinalTimeOption
2170: @*/
2171: PetscErrorCode  TSSetExactFinalTime(TS ts,TSExactFinalTimeOption eftopt)
2172: {
2176:   ts->exact_final_time = eftopt;
2177:   return(0);
2178: }

2182: /*@
2183:    TSGetTimeStep - Gets the current timestep size.

2185:    Not Collective

2187:    Input Parameter:
2188: .  ts - the TS context obtained from TSCreate()

2190:    Output Parameter:
2191: .  dt - the current timestep size

2193:    Level: intermediate

2195: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

2197: .keywords: TS, get, timestep
2198: @*/
2199: PetscErrorCode  TSGetTimeStep(TS ts,PetscReal *dt)
2200: {
2204:   *dt = ts->time_step;
2205:   return(0);
2206: }

2210: /*@
2211:    TSGetSolution - Returns the solution at the present timestep. It
2212:    is valid to call this routine inside the function that you are evaluating
2213:    in order to move to the new timestep. This vector not changed until
2214:    the solution at the next timestep has been calculated.

2216:    Not Collective, but Vec returned is parallel if TS is parallel

2218:    Input Parameter:
2219: .  ts - the TS context obtained from TSCreate()

2221:    Output Parameter:
2222: .  v - the vector containing the solution

2224:    Note: If you used TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP); this does not return the solution at the requested
2225:    final time. It returns the solution at the next timestep.

2227:    Level: intermediate

2229: .seealso: TSGetTimeStep(), TSGetTime(), TSGetSolveTime()

2231: .keywords: TS, timestep, get, solution
2232: @*/
2233: PetscErrorCode  TSGetSolution(TS ts,Vec *v)
2234: {
2238:   *v = ts->vec_sol;
2239:   return(0);
2240: }

2244: /*@
2245:    TSGetCostGradients - Returns the gradients from the TSAdjointSolve()

2247:    Not Collective, but Vec returned is parallel if TS is parallel

2249:    Input Parameter:
2250: .  ts - the TS context obtained from TSCreate()

2252:    Output Parameter:
2253: +  lambda - vectors containing the gradients of the cost functions with respect to the ODE/DAE solution variables
2254: -  mu - vectors containing the gradients of the cost functions with respect to the problem parameters

2256:    Level: intermediate

2258: .seealso: TSGetTimeStep()

2260: .keywords: TS, timestep, get, sensitivity
2261: @*/
2262: PetscErrorCode  TSGetCostGradients(TS ts,PetscInt *numcost,Vec **lambda,Vec **mu)
2263: {
2266:   if (numcost) *numcost = ts->numcost;
2267:   if (lambda)  *lambda  = ts->vecs_sensi;
2268:   if (mu)      *mu      = ts->vecs_sensip;
2269:   return(0);
2270: }

2272: /* ----- Routines to initialize and destroy a timestepper ---- */
2275: /*@
2276:   TSSetProblemType - Sets the type of problem to be solved.

2278:   Not collective

2280:   Input Parameters:
2281: + ts   - The TS
2282: - type - One of TS_LINEAR, TS_NONLINEAR where these types refer to problems of the forms
2283: .vb
2284:          U_t - A U = 0      (linear)
2285:          U_t - A(t) U = 0   (linear)
2286:          F(t,U,U_t) = 0     (nonlinear)
2287: .ve

2289:    Level: beginner

2291: .keywords: TS, problem type
2292: .seealso: TSSetUp(), TSProblemType, TS
2293: @*/
2294: PetscErrorCode  TSSetProblemType(TS ts, TSProblemType type)
2295: {

2300:   ts->problem_type = type;
2301:   if (type == TS_LINEAR) {
2302:     SNES snes;
2303:     TSGetSNES(ts,&snes);
2304:     SNESSetType(snes,SNESKSPONLY);
2305:   }
2306:   return(0);
2307: }

2311: /*@C
2312:   TSGetProblemType - Gets the type of problem to be solved.

2314:   Not collective

2316:   Input Parameter:
2317: . ts   - The TS

2319:   Output Parameter:
2320: . type - One of TS_LINEAR, TS_NONLINEAR where these types refer to problems of the forms
2321: .vb
2322:          M U_t = A U
2323:          M(t) U_t = A(t) U
2324:          F(t,U,U_t)
2325: .ve

2327:    Level: beginner

2329: .keywords: TS, problem type
2330: .seealso: TSSetUp(), TSProblemType, TS
2331: @*/
2332: PetscErrorCode  TSGetProblemType(TS ts, TSProblemType *type)
2333: {
2337:   *type = ts->problem_type;
2338:   return(0);
2339: }

2343: /*@
2344:    TSSetUp - Sets up the internal data structures for the later use
2345:    of a timestepper.

2347:    Collective on TS

2349:    Input Parameter:
2350: .  ts - the TS context obtained from TSCreate()

2352:    Notes:
2353:    For basic use of the TS solvers the user need not explicitly call
2354:    TSSetUp(), since these actions will automatically occur during
2355:    the call to TSStep().  However, if one wishes to control this
2356:    phase separately, TSSetUp() should be called after TSCreate()
2357:    and optional routines of the form TSSetXXX(), but before TSStep().

2359:    Level: advanced

2361: .keywords: TS, timestep, setup

2363: .seealso: TSCreate(), TSStep(), TSDestroy()
2364: @*/
2365: PetscErrorCode  TSSetUp(TS ts)
2366: {
2368:   DM             dm;
2369:   PetscErrorCode (*func)(SNES,Vec,Vec,void*);
2370:   PetscErrorCode (*jac)(SNES,Vec,Mat,Mat,void*);
2371:   TSIFunction    ifun;
2372:   TSIJacobian    ijac;
2373:   TSI2Jacobian   i2jac;
2374:   TSRHSJacobian  rhsjac;

2378:   if (ts->setupcalled) return(0);

2380:   ts->total_steps = 0;
2381:   if (!((PetscObject)ts)->type_name) {
2382:     TSGetIFunction(ts,NULL,&ifun,NULL);
2383:     TSSetType(ts,ifun ? TSBEULER : TSEULER);
2384:   }

2386:   if (!ts->vec_sol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call TSSetSolution() first");

2388:   if (ts->rhsjacobian.reuse) {
2389:     Mat Amat,Pmat;
2390:     SNES snes;
2391:     TSGetSNES(ts,&snes);
2392:     SNESGetJacobian(snes,&Amat,&Pmat,NULL,NULL);
2393:     /* Matching matrices implies that an IJacobian is NOT set, because if it had been set, the IJacobian's matrix would
2394:      * have displaced the RHS matrix */
2395:     if (Amat == ts->Arhs) {
2396:       MatDuplicate(ts->Arhs,MAT_DO_NOT_COPY_VALUES,&Amat);
2397:       SNESSetJacobian(snes,Amat,NULL,NULL,NULL);
2398:       MatDestroy(&Amat);
2399:     }
2400:     if (Pmat == ts->Brhs) {
2401:       MatDuplicate(ts->Brhs,MAT_DO_NOT_COPY_VALUES,&Pmat);
2402:       SNESSetJacobian(snes,NULL,Pmat,NULL,NULL);
2403:       MatDestroy(&Pmat);
2404:     }
2405:   }
2406:   if (ts->ops->setup) {
2407:     (*ts->ops->setup)(ts);
2408:   }

2410:   /* In the case where we've set a DMTSFunction or what have you, we need the default SNESFunction
2411:      to be set right but can't do it elsewhere due to the overreliance on ctx=ts.
2412:    */
2413:   TSGetDM(ts,&dm);
2414:   DMSNESGetFunction(dm,&func,NULL);
2415:   if (!func) {
2416:     DMSNESSetFunction(dm,SNESTSFormFunction,ts);
2417:   }
2418:   /* If the SNES doesn't have a jacobian set and the TS has an ijacobian or rhsjacobian set, set the SNES to use it.
2419:      Otherwise, the SNES will use coloring internally to form the Jacobian.
2420:    */
2421:   DMSNESGetJacobian(dm,&jac,NULL);
2422:   DMTSGetIJacobian(dm,&ijac,NULL);
2423:   DMTSGetI2Jacobian(dm,&i2jac,NULL);
2424:   DMTSGetRHSJacobian(dm,&rhsjac,NULL);
2425:   if (!jac && (ijac || i2jac || rhsjac)) {
2426:     DMSNESSetJacobian(dm,SNESTSFormJacobian,ts);
2427:   }
2428:   ts->setupcalled = PETSC_TRUE;
2429:   return(0);
2430: }

2434: /*@
2435:    TSAdjointSetUp - Sets up the internal data structures for the later use
2436:    of an adjoint solver

2438:    Collective on TS

2440:    Input Parameter:
2441: .  ts - the TS context obtained from TSCreate()

2443:    Level: advanced

2445: .keywords: TS, timestep, setup

2447: .seealso: TSCreate(), TSAdjointStep(), TSSetCostGradients()
2448: @*/
2449: PetscErrorCode  TSAdjointSetUp(TS ts)
2450: {

2455:   if (ts->adjointsetupcalled) return(0);
2456:   if (!ts->vecs_sensi) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call TSSetCostGradients() first");

2458:   if (ts->vec_costintegral) { /* if there is integral in the cost function*/
2459:     VecDuplicateVecs(ts->vecs_sensi[0],ts->numcost,&ts->vecs_drdy);
2460:     if (ts->vecs_sensip){
2461:       VecDuplicateVecs(ts->vecs_sensip[0],ts->numcost,&ts->vecs_drdp);
2462:     }
2463:   }

2465:   if (ts->ops->adjointsetup) {
2466:     (*ts->ops->adjointsetup)(ts);
2467:   }
2468:   ts->adjointsetupcalled = PETSC_TRUE;
2469:   return(0);
2470: }

2474: /*@
2475:    TSReset - Resets a TS context and removes any allocated Vecs and Mats.

2477:    Collective on TS

2479:    Input Parameter:
2480: .  ts - the TS context obtained from TSCreate()

2482:    Level: beginner

2484: .keywords: TS, timestep, reset

2486: .seealso: TSCreate(), TSSetup(), TSDestroy()
2487: @*/
2488: PetscErrorCode  TSReset(TS ts)
2489: {


2495:   if (ts->ops->reset) {
2496:     (*ts->ops->reset)(ts);
2497:   }
2498:   if (ts->snes) {SNESReset(ts->snes);}
2499:   if (ts->adapt) {TSAdaptReset(ts->adapt);}

2501:   MatDestroy(&ts->Arhs);
2502:   MatDestroy(&ts->Brhs);
2503:   VecDestroy(&ts->Frhs);
2504:   VecDestroy(&ts->vec_sol);
2505:   VecDestroy(&ts->vec_dot);
2506:   VecDestroy(&ts->vatol);
2507:   VecDestroy(&ts->vrtol);
2508:   VecDestroyVecs(ts->nwork,&ts->work);

2510:  if (ts->vec_costintegral) {
2511:     VecDestroyVecs(ts->numcost,&ts->vecs_drdy);
2512:     if (ts->vecs_drdp){
2513:       VecDestroyVecs(ts->numcost,&ts->vecs_drdp);
2514:     }
2515:   }
2516:   ts->vecs_sensi  = NULL;
2517:   ts->vecs_sensip = NULL;
2518:   MatDestroy(&ts->Jacp);
2519:   VecDestroy(&ts->vec_costintegral);
2520:   VecDestroy(&ts->vec_costintegrand);
2521:   ts->setupcalled = PETSC_FALSE;
2522:   return(0);
2523: }

2527: /*@
2528:    TSDestroy - Destroys the timestepper context that was created
2529:    with TSCreate().

2531:    Collective on TS

2533:    Input Parameter:
2534: .  ts - the TS context obtained from TSCreate()

2536:    Level: beginner

2538: .keywords: TS, timestepper, destroy

2540: .seealso: TSCreate(), TSSetUp(), TSSolve()
2541: @*/
2542: PetscErrorCode  TSDestroy(TS *ts)
2543: {

2547:   if (!*ts) return(0);
2549:   if (--((PetscObject)(*ts))->refct > 0) {*ts = 0; return(0);}

2551:   TSReset((*ts));

2553:   /* if memory was published with SAWs then destroy it */
2554:   PetscObjectSAWsViewOff((PetscObject)*ts);
2555:   if ((*ts)->ops->destroy) {(*(*ts)->ops->destroy)((*ts));}

2557:   TSTrajectoryDestroy(&(*ts)->trajectory);

2559:   TSAdaptDestroy(&(*ts)->adapt);
2560:   TSEventDestroy(&(*ts)->event);

2562:   SNESDestroy(&(*ts)->snes);
2563:   DMDestroy(&(*ts)->dm);
2564:   TSMonitorCancel((*ts));
2565:   TSAdjointMonitorCancel((*ts));

2567:   PetscHeaderDestroy(ts);
2568:   return(0);
2569: }

2573: /*@
2574:    TSGetSNES - Returns the SNES (nonlinear solver) associated with
2575:    a TS (timestepper) context. Valid only for nonlinear problems.

2577:    Not Collective, but SNES is parallel if TS is parallel

2579:    Input Parameter:
2580: .  ts - the TS context obtained from TSCreate()

2582:    Output Parameter:
2583: .  snes - the nonlinear solver context

2585:    Notes:
2586:    The user can then directly manipulate the SNES context to set various
2587:    options, etc.  Likewise, the user can then extract and manipulate the
2588:    KSP, KSP, and PC contexts as well.

2590:    TSGetSNES() does not work for integrators that do not use SNES; in
2591:    this case TSGetSNES() returns NULL in snes.

2593:    Level: beginner

2595: .keywords: timestep, get, SNES
2596: @*/
2597: PetscErrorCode  TSGetSNES(TS ts,SNES *snes)
2598: {

2604:   if (!ts->snes) {
2605:     SNESCreate(PetscObjectComm((PetscObject)ts),&ts->snes);
2606:     SNESSetFunction(ts->snes,NULL,SNESTSFormFunction,ts);
2607:     PetscLogObjectParent((PetscObject)ts,(PetscObject)ts->snes);
2608:     PetscObjectIncrementTabLevel((PetscObject)ts->snes,(PetscObject)ts,1);
2609:     if (ts->dm) {SNESSetDM(ts->snes,ts->dm);}
2610:     if (ts->problem_type == TS_LINEAR) {
2611:       SNESSetType(ts->snes,SNESKSPONLY);
2612:     }
2613:   }
2614:   *snes = ts->snes;
2615:   return(0);
2616: }

2620: /*@
2621:    TSSetSNES - Set the SNES (nonlinear solver) to be used by the timestepping context

2623:    Collective

2625:    Input Parameter:
2626: +  ts - the TS context obtained from TSCreate()
2627: -  snes - the nonlinear solver context

2629:    Notes:
2630:    Most users should have the TS created by calling TSGetSNES()

2632:    Level: developer

2634: .keywords: timestep, set, SNES
2635: @*/
2636: PetscErrorCode TSSetSNES(TS ts,SNES snes)
2637: {
2639:   PetscErrorCode (*func)(SNES,Vec,Mat,Mat,void*);

2644:   PetscObjectReference((PetscObject)snes);
2645:   SNESDestroy(&ts->snes);

2647:   ts->snes = snes;

2649:   SNESSetFunction(ts->snes,NULL,SNESTSFormFunction,ts);
2650:   SNESGetJacobian(ts->snes,NULL,NULL,&func,NULL);
2651:   if (func == SNESTSFormJacobian) {
2652:     SNESSetJacobian(ts->snes,NULL,NULL,SNESTSFormJacobian,ts);
2653:   }
2654:   return(0);
2655: }

2659: /*@
2660:    TSGetKSP - Returns the KSP (linear solver) associated with
2661:    a TS (timestepper) context.

2663:    Not Collective, but KSP is parallel if TS is parallel

2665:    Input Parameter:
2666: .  ts - the TS context obtained from TSCreate()

2668:    Output Parameter:
2669: .  ksp - the nonlinear solver context

2671:    Notes:
2672:    The user can then directly manipulate the KSP context to set various
2673:    options, etc.  Likewise, the user can then extract and manipulate the
2674:    KSP and PC contexts as well.

2676:    TSGetKSP() does not work for integrators that do not use KSP;
2677:    in this case TSGetKSP() returns NULL in ksp.

2679:    Level: beginner

2681: .keywords: timestep, get, KSP
2682: @*/
2683: PetscErrorCode  TSGetKSP(TS ts,KSP *ksp)
2684: {
2686:   SNES           snes;

2691:   if (!((PetscObject)ts)->type_name) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"KSP is not created yet. Call TSSetType() first");
2692:   if (ts->problem_type != TS_LINEAR) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Linear only; use TSGetSNES()");
2693:   TSGetSNES(ts,&snes);
2694:   SNESGetKSP(snes,ksp);
2695:   return(0);
2696: }

2698: /* ----------- Routines to set solver parameters ---------- */

2702: /*@
2703:    TSGetDuration - Gets the maximum number of timesteps to use and
2704:    maximum time for iteration.

2706:    Not Collective

2708:    Input Parameters:
2709: +  ts       - the TS context obtained from TSCreate()
2710: .  maxsteps - maximum number of iterations to use, or NULL
2711: -  maxtime  - final time to iterate to, or NULL

2713:    Level: intermediate

2715: .keywords: TS, timestep, get, maximum, iterations, time
2716: @*/
2717: PetscErrorCode  TSGetDuration(TS ts, PetscInt *maxsteps, PetscReal *maxtime)
2718: {
2721:   if (maxsteps) {
2723:     *maxsteps = ts->max_steps;
2724:   }
2725:   if (maxtime) {
2727:     *maxtime = ts->max_time;
2728:   }
2729:   return(0);
2730: }

2734: /*@
2735:    TSSetDuration - Sets the maximum number of timesteps to use and
2736:    maximum time for iteration.

2738:    Logically Collective on TS

2740:    Input Parameters:
2741: +  ts - the TS context obtained from TSCreate()
2742: .  maxsteps - maximum number of iterations to use
2743: -  maxtime - final time to iterate to

2745:    Options Database Keys:
2746: .  -ts_max_steps <maxsteps> - Sets maxsteps
2747: .  -ts_final_time <maxtime> - Sets maxtime

2749:    Notes:
2750:    The default maximum number of iterations is 5000. Default time is 5.0

2752:    Level: intermediate

2754: .keywords: TS, timestep, set, maximum, iterations

2756: .seealso: TSSetExactFinalTime()
2757: @*/
2758: PetscErrorCode  TSSetDuration(TS ts,PetscInt maxsteps,PetscReal maxtime)
2759: {
2764:   if (maxsteps >= 0) ts->max_steps = maxsteps;
2765:   if (maxtime != PETSC_DEFAULT) ts->max_time = maxtime;
2766:   return(0);
2767: }

2771: /*@
2772:    TSSetSolution - Sets the initial solution vector
2773:    for use by the TS routines.

2775:    Logically Collective on TS and Vec

2777:    Input Parameters:
2778: +  ts - the TS context obtained from TSCreate()
2779: -  u - the solution vector

2781:    Level: beginner

2783: .keywords: TS, timestep, set, solution, initial conditions
2784: @*/
2785: PetscErrorCode  TSSetSolution(TS ts,Vec u)
2786: {
2788:   DM             dm;

2793:   PetscObjectReference((PetscObject)u);
2794:   VecDestroy(&ts->vec_sol);
2795:   ts->vec_sol = u;

2797:   TSGetDM(ts,&dm);
2798:   DMShellSetGlobalVector(dm,u);
2799:   return(0);
2800: }

2804: /*@
2805:    TSAdjointSetSteps - Sets the number of steps the adjoint solver should take backward in time

2807:    Logically Collective on TS

2809:    Input Parameters:
2810: +  ts - the TS context obtained from TSCreate()
2811: .  steps - number of steps to use

2813:    Level: intermediate

2815:    Notes: Normally one does not call this and TSAdjointSolve() integrates back to the original timestep. One can call this
2816:           so as to integrate back to less than the original timestep

2818: .keywords: TS, timestep, set, maximum, iterations

2820: .seealso: TSSetExactFinalTime()
2821: @*/
2822: PetscErrorCode  TSAdjointSetSteps(TS ts,PetscInt steps)
2823: {
2827:   if (steps < 0) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_OUTOFRANGE,"Cannot step back a negative number of steps");
2828:   if (steps > ts->total_steps) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_OUTOFRANGE,"Cannot step back more than the total number of forward steps");
2829:   ts->adjoint_max_steps = steps;
2830:   return(0);
2831: }

2835: /*@
2836:    TSSetCostGradients - Sets the initial value of the gradients of the cost function w.r.t. initial conditions and w.r.t. the problem parameters 
2837:       for use by the TSAdjoint routines.

2839:    Logically Collective on TS and Vec

2841:    Input Parameters:
2842: +  ts - the TS context obtained from TSCreate()
2843: .  lambda - gradients with respect to the initial condition variables, the dimension and parallel layout of these vectors is the same as the ODE solution vector
2844: -  mu - gradients with respect to the parameters, the number of entries in these vectors is the same as the number of parameters

2846:    Level: beginner

2848:    Notes: the entries in these vectors must be correctly initialized with the values lamda_i = df/dy|finaltime  mu_i = df/dp|finaltime

2850: .keywords: TS, timestep, set, sensitivity, initial conditions
2851: @*/
2852: PetscErrorCode  TSSetCostGradients(TS ts,PetscInt numcost,Vec *lambda,Vec *mu)
2853: {
2857:   ts->vecs_sensi  = lambda;
2858:   ts->vecs_sensip = mu;
2859:   if (ts->numcost && ts->numcost!=numcost) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"The number of cost functions (2rd parameter of TSSetCostIntegrand()) is inconsistent with the one set by TSSetCostIntegrand");
2860:   ts->numcost  = numcost;
2861:   return(0);
2862: }

2866: /*@C
2867:   TSAdjointSetRHSJacobian - Sets the function that computes the Jacobian of G w.r.t. the parameters p where y_t = G(y,p,t), as well as the location to store the matrix.

2869:   Logically Collective on TS

2871:   Input Parameters:
2872: + ts   - The TS context obtained from TSCreate()
2873: - func - The function

2875:   Calling sequence of func:
2876: $ func (TS ts,PetscReal t,Vec y,Mat A,void *ctx);
2877: +   t - current timestep
2878: .   y - input vector (current ODE solution)
2879: .   A - output matrix
2880: -   ctx - [optional] user-defined function context

2882:   Level: intermediate

2884:   Notes: Amat has the same number of rows and the same row parallel layout as u, Amat has the same number of columns and parallel layout as p

2886: .keywords: TS, sensitivity
2887: .seealso:
2888: @*/
2889: PetscErrorCode  TSAdjointSetRHSJacobian(TS ts,Mat Amat,PetscErrorCode (*func)(TS,PetscReal,Vec,Mat,void*),void *ctx)
2890: {


2897:   ts->rhsjacobianp    = func;
2898:   ts->rhsjacobianpctx = ctx;
2899:   if(Amat) {
2900:     PetscObjectReference((PetscObject)Amat);
2901:     MatDestroy(&ts->Jacp);
2902:     ts->Jacp = Amat;
2903:   }
2904:   return(0);
2905: }

2909: /*@C
2910:   TSAdjointComputeRHSJacobian - Runs the user-defined Jacobian function.

2912:   Collective on TS

2914:   Input Parameters:
2915: . ts   - The TS context obtained from TSCreate()

2917:   Level: developer

2919: .keywords: TS, sensitivity
2920: .seealso: TSAdjointSetRHSJacobian()
2921: @*/
2922: PetscErrorCode  TSAdjointComputeRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat)
2923: {


2931:   PetscStackPush("TS user JacobianP function for sensitivity analysis");
2932:   (*ts->rhsjacobianp)(ts,t,X,Amat,ts->rhsjacobianpctx);
2933:   PetscStackPop;
2934:   return(0);
2935: }

2939: /*@C
2940:     TSSetCostIntegrand - Sets the routine for evaluating the integral term in one or more cost functions

2942:     Logically Collective on TS

2944:     Input Parameters:
2945: +   ts - the TS context obtained from TSCreate()
2946: .   numcost - number of gradients to be computed, this is the number of cost functions
2947: .   rf - routine for evaluating the integrand function
2948: .   drdyf - function that computes the gradients of the r's with respect to y,NULL if not a function y
2949: .   drdpf - function that computes the gradients of the r's with respect to p, NULL if not a function of p
2950: .   fwd ï¼ flag indicating whether to evaluate cost integral in the forward run or the adjoint run
2951: -   ctx - [optional] user-defined context for private data for the function evaluation routine (may be NULL)

2953:     Calling sequence of rf:
2954: $     rf(TS ts,PetscReal t,Vec y,Vec f[],void *ctx);

2956: +   t - current timestep
2957: .   y - input vector
2958: .   f - function result; one vector entry for each cost function
2959: -   ctx - [optional] user-defined function context

2961:    Calling sequence of drdyf:
2962: $    PetscErroCode drdyf(TS ts,PetscReal t,Vec y,Vec *drdy,void *ctx);

2964:    Calling sequence of drdpf:
2965: $    PetscErroCode drdpf(TS ts,PetscReal t,Vec y,Vec *drdp,void *ctx);

2967:     Level: intermediate

2969:     Notes: For optimization there is generally a single cost function, numcost = 1. For sensitivities there may be multiple cost functions

2971: .keywords: TS, sensitivity analysis, timestep, set, quadrature, function

2973: .seealso: TSAdjointSetRHSJacobian(),TSGetCostGradients(), TSSetCostGradients()
2974: @*/
2975: PetscErrorCode  TSSetCostIntegrand(TS ts,PetscInt numcost,PetscErrorCode (*rf)(TS,PetscReal,Vec,Vec,void*),
2976:                                                           PetscErrorCode (*drdyf)(TS,PetscReal,Vec,Vec*,void*),
2977:                                                           PetscErrorCode (*drdpf)(TS,PetscReal,Vec,Vec*,void*),
2978:                                                           PetscBool fwd,void *ctx)
2979: {

2984:   if (ts->numcost && ts->numcost!=numcost) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"The number of cost functions (2rd parameter of TSSetCostIntegrand()) is inconsistent with the one set by TSSetCostGradients()");
2985:   if (!ts->numcost) ts->numcost=numcost;

2987:   ts->costintegralfwd  = fwd; /* Evaluate the cost integral in forward run if fwd is true */
2988:   VecCreateSeq(PETSC_COMM_SELF,numcost,&ts->vec_costintegral);
2989:   VecDuplicate(ts->vec_costintegral,&ts->vec_costintegrand);
2990:   ts->costintegrand    = rf;
2991:   ts->costintegrandctx = ctx;
2992:   ts->drdyfunction     = drdyf;
2993:   ts->drdpfunction     = drdpf;
2994:   return(0);
2995: }

2999: /*@
3000:    TSGetCostIntegral - Returns the values of the integral term in the cost functions.
3001:    It is valid to call the routine after a backward run.

3003:    Not Collective

3005:    Input Parameter:
3006: .  ts - the TS context obtained from TSCreate()

3008:    Output Parameter:
3009: .  v - the vector containing the integrals for each cost function

3011:    Level: intermediate

3013: .seealso: TSSetCostIntegrand()

3015: .keywords: TS, sensitivity analysis
3016: @*/
3017: PetscErrorCode  TSGetCostIntegral(TS ts,Vec *v)
3018: {
3022:   *v = ts->vec_costintegral;
3023:   return(0);
3024: }

3028: /*@
3029:    TSAdjointComputeCostIntegrand - Evaluates the integral function in the cost functions.

3031:    Input Parameters:
3032: +  ts - the TS context
3033: .  t - current time
3034: -  y - state vector, i.e. current solution

3036:    Output Parameter:
3037: .  q - vector of size numcost to hold the outputs

3039:    Note:
3040:    Most users should not need to explicitly call this routine, as it
3041:    is used internally within the sensitivity analysis context.

3043:    Level: developer

3045: .keywords: TS, compute

3047: .seealso: TSSetCostIntegrand()
3048: @*/
3049: PetscErrorCode TSAdjointComputeCostIntegrand(TS ts,PetscReal t,Vec y,Vec q)
3050: {


3058:   PetscLogEventBegin(TS_FunctionEval,ts,y,q,0);
3059:   if (ts->costintegrand) {
3060:     PetscStackPush("TS user integrand in the cost function");
3061:     (*ts->costintegrand)(ts,t,y,q,ts->costintegrandctx);
3062:     PetscStackPop;
3063:   } else {
3064:     VecZeroEntries(q);
3065:   }

3067:   PetscLogEventEnd(TS_FunctionEval,ts,y,q,0);
3068:   return(0);
3069: }

3073: /*@
3074:   TSAdjointComputeDRDYFunction - Runs the user-defined DRDY function.

3076:   Collective on TS

3078:   Input Parameters:
3079: . ts   - The TS context obtained from TSCreate()

3081:   Notes:
3082:   TSAdjointComputeDRDYFunction() is typically used for sensitivity implementation,
3083:   so most users would not generally call this routine themselves.

3085:   Level: developer

3087: .keywords: TS, sensitivity
3088: .seealso: TSAdjointComputeDRDYFunction()
3089: @*/
3090: PetscErrorCode  TSAdjointComputeDRDYFunction(TS ts,PetscReal t,Vec y,Vec *drdy)
3091: {


3098:   PetscStackPush("TS user DRDY function for sensitivity analysis");
3099:   (*ts->drdyfunction)(ts,t,y,drdy,ts->costintegrandctx);
3100:   PetscStackPop;
3101:   return(0);
3102: }

3106: /*@
3107:   TSAdjointComputeDRDPFunction - Runs the user-defined DRDP function.

3109:   Collective on TS

3111:   Input Parameters:
3112: . ts   - The TS context obtained from TSCreate()

3114:   Notes:
3115:   TSDRDPFunction() is typically used for sensitivity implementation,
3116:   so most users would not generally call this routine themselves.

3118:   Level: developer

3120: .keywords: TS, sensitivity
3121: .seealso: TSAdjointSetDRDPFunction()
3122: @*/
3123: PetscErrorCode  TSAdjointComputeDRDPFunction(TS ts,PetscReal t,Vec y,Vec *drdp)
3124: {


3131:   PetscStackPush("TS user DRDP function for sensitivity analysis");
3132:   (*ts->drdpfunction)(ts,t,y,drdp,ts->costintegrandctx);
3133:   PetscStackPop;
3134:   return(0);
3135: }

3139: /*@C
3140:   TSSetPreStep - Sets the general-purpose function
3141:   called once at the beginning of each time step.

3143:   Logically Collective on TS

3145:   Input Parameters:
3146: + ts   - The TS context obtained from TSCreate()
3147: - func - The function

3149:   Calling sequence of func:
3150: . func (TS ts);

3152:   Level: intermediate

3154:   Note:
3155:   If a step is rejected, TSStep() will call this routine again before each attempt.
3156:   The last completed time step number can be queried using TSGetTimeStepNumber(), the
3157:   size of the step being attempted can be obtained using TSGetTimeStep().

3159: .keywords: TS, timestep
3160: .seealso: TSSetPreStage(), TSSetPostStage(), TSSetPostStep(), TSStep()
3161: @*/
3162: PetscErrorCode  TSSetPreStep(TS ts, PetscErrorCode (*func)(TS))
3163: {
3166:   ts->prestep = func;
3167:   return(0);
3168: }

3172: /*@
3173:   TSPreStep - Runs the user-defined pre-step function.

3175:   Collective on TS

3177:   Input Parameters:
3178: . ts   - The TS context obtained from TSCreate()

3180:   Notes:
3181:   TSPreStep() is typically used within time stepping implementations,
3182:   so most users would not generally call this routine themselves.

3184:   Level: developer

3186: .keywords: TS, timestep
3187: .seealso: TSSetPreStep(), TSPreStage(), TSPostStage(), TSPostStep()
3188: @*/
3189: PetscErrorCode  TSPreStep(TS ts)
3190: {

3195:   if (ts->prestep) {
3196:     PetscStackCallStandard((*ts->prestep),(ts));
3197:   }
3198:   return(0);
3199: }

3203: /*@C
3204:   TSSetPreStage - Sets the general-purpose function
3205:   called once at the beginning of each stage.

3207:   Logically Collective on TS

3209:   Input Parameters:
3210: + ts   - The TS context obtained from TSCreate()
3211: - func - The function

3213:   Calling sequence of func:
3214: . PetscErrorCode func(TS ts, PetscReal stagetime);

3216:   Level: intermediate

3218:   Note:
3219:   There may be several stages per time step. If the solve for a given stage fails, the step may be rejected and retried.
3220:   The time step number being computed can be queried using TSGetTimeStepNumber() and the total size of the step being
3221:   attempted can be obtained using TSGetTimeStep(). The time at the start of the step is available via TSGetTime().

3223: .keywords: TS, timestep
3224: .seealso: TSSetPostStage(), TSSetPreStep(), TSSetPostStep(), TSGetApplicationContext()
3225: @*/
3226: PetscErrorCode  TSSetPreStage(TS ts, PetscErrorCode (*func)(TS,PetscReal))
3227: {
3230:   ts->prestage = func;
3231:   return(0);
3232: }

3236: /*@C
3237:   TSSetPostStage - Sets the general-purpose function
3238:   called once at the end of each stage.

3240:   Logically Collective on TS

3242:   Input Parameters:
3243: + ts   - The TS context obtained from TSCreate()
3244: - func - The function

3246:   Calling sequence of func:
3247: . PetscErrorCode func(TS ts, PetscReal stagetime, PetscInt stageindex, Vec* Y);

3249:   Level: intermediate

3251:   Note:
3252:   There may be several stages per time step. If the solve for a given stage fails, the step may be rejected and retried.
3253:   The time step number being computed can be queried using TSGetTimeStepNumber() and the total size of the step being
3254:   attempted can be obtained using TSGetTimeStep(). The time at the start of the step is available via TSGetTime().

3256: .keywords: TS, timestep
3257: .seealso: TSSetPreStage(), TSSetPreStep(), TSSetPostStep(), TSGetApplicationContext()
3258: @*/
3259: PetscErrorCode  TSSetPostStage(TS ts, PetscErrorCode (*func)(TS,PetscReal,PetscInt,Vec*))
3260: {
3263:   ts->poststage = func;
3264:   return(0);
3265: }

3269: /*@
3270:   TSPreStage - Runs the user-defined pre-stage function set using TSSetPreStage()

3272:   Collective on TS

3274:   Input Parameters:
3275: . ts          - The TS context obtained from TSCreate()
3276:   stagetime   - The absolute time of the current stage

3278:   Notes:
3279:   TSPreStage() is typically used within time stepping implementations,
3280:   most users would not generally call this routine themselves.

3282:   Level: developer

3284: .keywords: TS, timestep
3285: .seealso: TSPostStage(), TSSetPreStep(), TSPreStep(), TSPostStep()
3286: @*/
3287: PetscErrorCode  TSPreStage(TS ts, PetscReal stagetime)
3288: {

3293:   if (ts->prestage) {
3294:     PetscStackCallStandard((*ts->prestage),(ts,stagetime));
3295:   }
3296:   return(0);
3297: }

3301: /*@
3302:   TSPostStage - Runs the user-defined post-stage function set using TSSetPostStage()

3304:   Collective on TS

3306:   Input Parameters:
3307: . ts          - The TS context obtained from TSCreate()
3308:   stagetime   - The absolute time of the current stage
3309:   stageindex  - Stage number
3310:   Y           - Array of vectors (of size = total number
3311:                 of stages) with the stage solutions

3313:   Notes:
3314:   TSPostStage() is typically used within time stepping implementations,
3315:   most users would not generally call this routine themselves.

3317:   Level: developer

3319: .keywords: TS, timestep
3320: .seealso: TSPreStage(), TSSetPreStep(), TSPreStep(), TSPostStep()
3321: @*/
3322: PetscErrorCode  TSPostStage(TS ts, PetscReal stagetime, PetscInt stageindex, Vec *Y)
3323: {

3328:   if (ts->poststage) {
3329:     PetscStackCallStandard((*ts->poststage),(ts,stagetime,stageindex,Y));
3330:   }
3331:   return(0);
3332: }

3336: /*@C
3337:   TSSetPostStep - Sets the general-purpose function
3338:   called once at the end of each time step.

3340:   Logically Collective on TS

3342:   Input Parameters:
3343: + ts   - The TS context obtained from TSCreate()
3344: - func - The function

3346:   Calling sequence of func:
3347: $ func (TS ts);

3349:   Level: intermediate

3351: .keywords: TS, timestep
3352: .seealso: TSSetPreStep(), TSSetPreStage(), TSGetTimeStep(), TSGetTimeStepNumber(), TSGetTime()
3353: @*/
3354: PetscErrorCode  TSSetPostStep(TS ts, PetscErrorCode (*func)(TS))
3355: {
3358:   ts->poststep = func;
3359:   return(0);
3360: }

3364: /*@
3365:   TSPostStep - Runs the user-defined post-step function.

3367:   Collective on TS

3369:   Input Parameters:
3370: . ts   - The TS context obtained from TSCreate()

3372:   Notes:
3373:   TSPostStep() is typically used within time stepping implementations,
3374:   so most users would not generally call this routine themselves.

3376:   Level: developer

3378: .keywords: TS, timestep
3379: @*/
3380: PetscErrorCode  TSPostStep(TS ts)
3381: {

3386:   if (ts->poststep) {
3387:     PetscStackCallStandard((*ts->poststep),(ts));
3388:   }
3389:   return(0);
3390: }

3392: /* ------------ Routines to set performance monitoring options ----------- */

3396: /*@C
3397:    TSMonitorSet - Sets an ADDITIONAL function that is to be used at every
3398:    timestep to display the iteration's  progress.

3400:    Logically Collective on TS

3402:    Input Parameters:
3403: +  ts - the TS context obtained from TSCreate()
3404: .  monitor - monitoring routine
3405: .  mctx - [optional] user-defined context for private data for the
3406:              monitor routine (use NULL if no context is desired)
3407: -  monitordestroy - [optional] routine that frees monitor context
3408:           (may be NULL)

3410:    Calling sequence of monitor:
3411: $    int monitor(TS ts,PetscInt steps,PetscReal time,Vec u,void *mctx)

3413: +    ts - the TS context
3414: .    steps - iteration number (after the final time step the monitor routine may be called with a step of -1, this indicates the solution has been interpolated to this time)
3415: .    time - current time
3416: .    u - current iterate
3417: -    mctx - [optional] monitoring context

3419:    Notes:
3420:    This routine adds an additional monitor to the list of monitors that
3421:    already has been loaded.

3423:    Fortran notes: Only a single monitor function can be set for each TS object

3425:    Level: intermediate

3427: .keywords: TS, timestep, set, monitor

3429: .seealso: TSMonitorDefault(), TSMonitorCancel()
3430: @*/
3431: PetscErrorCode  TSMonitorSet(TS ts,PetscErrorCode (*monitor)(TS,PetscInt,PetscReal,Vec,void*),void *mctx,PetscErrorCode (*mdestroy)(void**))
3432: {
3435:   if (ts->numbermonitors >= MAXTSMONITORS) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many monitors set");
3436:   ts->monitor[ts->numbermonitors]          = monitor;
3437:   ts->monitordestroy[ts->numbermonitors]   = mdestroy;
3438:   ts->monitorcontext[ts->numbermonitors++] = (void*)mctx;
3439:   return(0);
3440: }

3444: /*@C
3445:    TSMonitorCancel - Clears all the monitors that have been set on a time-step object.

3447:    Logically Collective on TS

3449:    Input Parameters:
3450: .  ts - the TS context obtained from TSCreate()

3452:    Notes:
3453:    There is no way to remove a single, specific monitor.

3455:    Level: intermediate

3457: .keywords: TS, timestep, set, monitor

3459: .seealso: TSMonitorDefault(), TSMonitorSet()
3460: @*/
3461: PetscErrorCode  TSMonitorCancel(TS ts)
3462: {
3464:   PetscInt       i;

3468:   for (i=0; i<ts->numbermonitors; i++) {
3469:     if (ts->monitordestroy[i]) {
3470:       (*ts->monitordestroy[i])(&ts->monitorcontext[i]);
3471:     }
3472:   }
3473:   ts->numbermonitors = 0;
3474:   return(0);
3475: }

3479: /*@C
3480:    TSMonitorDefault - The Default monitor, prints the timestep and time for each step

3482:    Level: intermediate

3484: .keywords: TS, set, monitor

3486: .seealso:  TSMonitorSet()
3487: @*/
3488: PetscErrorCode TSMonitorDefault(TS ts,PetscInt step,PetscReal ptime,Vec v,PetscViewerAndFormat *vf)
3489: {
3491:   PetscViewer    viewer =  vf->viewer;
3492:   PetscBool      iascii,ibinary;

3496:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
3497:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&ibinary);
3498:   PetscViewerPushFormat(viewer,vf->format);
3499:   if (iascii) {
3500:     PetscViewerASCIIAddTab(viewer,((PetscObject)ts)->tablevel);
3501:     if (step == -1){ /* this indicates it is an interpolated solution */
3502:       PetscViewerASCIIPrintf(viewer,"Interpolated solution at time %g between steps %D and %D\n",(double)ptime,ts->steps-1,ts->steps);
3503:     } else {
3504:       PetscViewerASCIIPrintf(viewer,"%D TS dt %g time %g%s",step,(double)ts->time_step,(double)ptime,ts->steprollback ? " (r)\n" : "\n");
3505:     }
3506:     PetscViewerASCIISubtractTab(viewer,((PetscObject)ts)->tablevel);
3507:   } else if (ibinary) {
3508:     PetscMPIInt rank;
3509:     MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&rank);
3510:     if (!rank) {
3511:       PetscRealView(1,&ptime,viewer);
3512:     } else {
3513:       PetscRealView(0,&ptime,viewer);
3514:     }
3515:   }
3516:   PetscViewerPopFormat(viewer);
3517:   return(0);
3518: }

3522: /*@C
3523:    TSAdjointMonitorSet - Sets an ADDITIONAL function that is to be used at every
3524:    timestep to display the iteration's  progress.

3526:    Logically Collective on TS

3528:    Input Parameters:
3529: +  ts - the TS context obtained from TSCreate()
3530: .  adjointmonitor - monitoring routine
3531: .  adjointmctx - [optional] user-defined context for private data for the
3532:              monitor routine (use NULL if no context is desired)
3533: -  adjointmonitordestroy - [optional] routine that frees monitor context
3534:           (may be NULL)

3536:    Calling sequence of monitor:
3537: $    int adjointmonitor(TS ts,PetscInt steps,PetscReal time,Vec u,PetscInt numcost,Vec *lambda, Vec *mu,void *adjointmctx)

3539: +    ts - the TS context
3540: .    steps - iteration number (after the final time step the monitor routine is called with a step of -1, this is at the final time which may have
3541:                                been interpolated to)
3542: .    time - current time
3543: .    u - current iterate
3544: .    numcost - number of cost functionos
3545: .    lambda - sensitivities to initial conditions
3546: .    mu - sensitivities to parameters
3547: -    adjointmctx - [optional] adjoint monitoring context

3549:    Notes:
3550:    This routine adds an additional monitor to the list of monitors that
3551:    already has been loaded.

3553:    Fortran notes: Only a single monitor function can be set for each TS object

3555:    Level: intermediate

3557: .keywords: TS, timestep, set, adjoint, monitor

3559: .seealso: TSAdjointMonitorCancel()
3560: @*/
3561: PetscErrorCode  TSAdjointMonitorSet(TS ts,PetscErrorCode (*adjointmonitor)(TS,PetscInt,PetscReal,Vec,PetscInt,Vec*,Vec*,void*),void *adjointmctx,PetscErrorCode (*adjointmdestroy)(void**))
3562: {
3565:   if (ts->numberadjointmonitors >= MAXTSMONITORS) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many adjoint monitors set");
3566:   ts->adjointmonitor[ts->numberadjointmonitors]          = adjointmonitor;
3567:   ts->adjointmonitordestroy[ts->numberadjointmonitors]   = adjointmdestroy;
3568:   ts->adjointmonitorcontext[ts->numberadjointmonitors++] = (void*)adjointmctx;
3569:   return(0);
3570: }

3574: /*@C
3575:    TSAdjointMonitorCancel - Clears all the adjoint monitors that have been set on a time-step object.

3577:    Logically Collective on TS

3579:    Input Parameters:
3580: .  ts - the TS context obtained from TSCreate()

3582:    Notes:
3583:    There is no way to remove a single, specific monitor.

3585:    Level: intermediate

3587: .keywords: TS, timestep, set, adjoint, monitor

3589: .seealso: TSAdjointMonitorSet()
3590: @*/
3591: PetscErrorCode  TSAdjointMonitorCancel(TS ts)
3592: {
3594:   PetscInt       i;

3598:   for (i=0; i<ts->numberadjointmonitors; i++) {
3599:     if (ts->adjointmonitordestroy[i]) {
3600:       (*ts->adjointmonitordestroy[i])(&ts->adjointmonitorcontext[i]);
3601:     }
3602:   }
3603:   ts->numberadjointmonitors = 0;
3604:   return(0);
3605: }

3609: /*@C
3610:    TSAdjointMonitorDefault - the default monitor of adjoint computations

3612:    Level: intermediate

3614: .keywords: TS, set, monitor

3616: .seealso: TSAdjointMonitorSet()
3617: @*/
3618: PetscErrorCode TSAdjointMonitorDefault(TS ts,PetscInt step,PetscReal ptime,Vec v,PetscInt numcost,Vec *lambda,Vec *mu,PetscViewerAndFormat *vf)
3619: {
3621:   PetscViewer    viewer = vf->viewer;

3625:   PetscViewerPushFormat(viewer,vf->format);
3626:   PetscViewerASCIIAddTab(viewer,((PetscObject)ts)->tablevel);
3627:   PetscViewerASCIIPrintf(viewer,"%D TS dt %g time %g%s",step,(double)ts->time_step,(double)ptime,ts->steprollback ? " (r)\n" : "\n");
3628:   PetscViewerASCIISubtractTab(viewer,((PetscObject)ts)->tablevel);
3629:   PetscViewerPopFormat(viewer);
3630:   return(0);
3631: }

3635: /*@
3636:    TSInterpolate - Interpolate the solution computed during the previous step to an arbitrary location in the interval

3638:    Collective on TS

3640:    Input Argument:
3641: +  ts - time stepping context
3642: -  t - time to interpolate to

3644:    Output Argument:
3645: .  U - state at given time

3647:    Level: intermediate

3649:    Developer Notes:
3650:    TSInterpolate() and the storing of previous steps/stages should be generalized to support delay differential equations and continuous adjoints.

3652: .keywords: TS, set

3654: .seealso: TSSetExactFinalTime(), TSSolve()
3655: @*/
3656: PetscErrorCode TSInterpolate(TS ts,PetscReal t,Vec U)
3657: {

3663:   if (t < ts->ptime_prev || t > ts->ptime) SETERRQ3(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_OUTOFRANGE,"Requested time %g not in last time steps [%g,%g]",t,(double)ts->ptime_prev,(double)ts->ptime);
3664:   if (!ts->ops->interpolate) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"%s does not provide interpolation",((PetscObject)ts)->type_name);
3665:   (*ts->ops->interpolate)(ts,t,U);
3666:   return(0);
3667: }

3671: /*@
3672:    TSStep - Steps one time step

3674:    Collective on TS

3676:    Input Parameter:
3677: .  ts - the TS context obtained from TSCreate()

3679:    Level: developer

3681:    Notes:
3682:    The public interface for the ODE/DAE solvers is TSSolve(), you should almost for sure be using that routine and not this routine.

3684:    The hook set using TSSetPreStep() is called before each attempt to take the step. In general, the time step size may
3685:    be changed due to adaptive error controller or solve failures. Note that steps may contain multiple stages.

3687:    This may over-step the final time provided in TSSetDuration() depending on the time-step used. TSSolve() interpolates to exactly the
3688:    time provided in TSSetDuration(). One can use TSInterpolate() to determine an interpolated solution within the final timestep.

3690: .keywords: TS, timestep, solve

3692: .seealso: TSCreate(), TSSetUp(), TSDestroy(), TSSolve(), TSSetPreStep(), TSSetPreStage(), TSSetPostStage(), TSInterpolate()
3693: @*/
3694: PetscErrorCode  TSStep(TS ts)
3695: {
3696:   PetscErrorCode   ierr;
3697:   static PetscBool cite = PETSC_FALSE;
3698:   PetscReal        ptime;

3702:   PetscCitationsRegister("@techreport{tspaper,\n"
3703:                                 "  title       = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library},\n"
3704:                                 "  author      = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and Barry F. Smith},\n"
3705:                                 "  type        = {Preprint},\n"
3706:                                 "  number      = {ANL/MCS-P5061-0114},\n"
3707:                                 "  institution = {Argonne National Laboratory},\n"
3708:                                 "  year        = {2014}\n}\n",&cite);

3710:   TSSetUp(ts);
3711:   TSTrajectorySetUp(ts->trajectory,ts);

3713:   if (ts->exact_final_time == TS_EXACTFINALTIME_UNSPECIFIED) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONGSTATE,"You must call TSSetExactFinalTime() or use -ts_exact_final_time <stepover,interpolate,matchstep> before calling TSStep()");
3714:   if (ts->exact_final_time == TS_EXACTFINALTIME_MATCHSTEP && !ts->adapt) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Since TS is not adaptive you cannot use TS_EXACTFINALTIME_MATCHSTEP, suggest TS_EXACTFINALTIME_INTERPOLATE");

3716:   if (!ts->steps) ts->ptime_prev = ts->ptime;
3717:   ts->reason = TS_CONVERGED_ITERATING;
3718:   ptime = ts->ptime; ts->ptime_prev_rollback = ts->ptime_prev;
3719:   if (!ts->ops->step) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSStep not implemented for type '%s'",((PetscObject)ts)->type_name);
3720:   PetscLogEventBegin(TS_Step,ts,0,0,0);
3721:   (*ts->ops->step)(ts);
3722:   PetscLogEventEnd(TS_Step,ts,0,0,0);
3723:   ts->ptime_prev = ptime;
3724:   ts->steps++; ts->total_steps++;
3725:   ts->steprollback = PETSC_FALSE;
3726:   ts->steprestart  = PETSC_FALSE;

3728:   if (ts->reason < 0) {
3729:     if (ts->errorifstepfailed) {
3730:       if (ts->reason == TS_DIVERGED_NONLINEAR_SOLVE) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s, increase -ts_max_snes_failures or make negative to attempt recovery",TSConvergedReasons[ts->reason]);
3731:       else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s",TSConvergedReasons[ts->reason]);
3732:     }
3733:   } else if (!ts->reason) {
3734:     if (ts->steps >= ts->max_steps)     ts->reason = TS_CONVERGED_ITS;
3735:     else if (ts->ptime >= ts->max_time) ts->reason = TS_CONVERGED_TIME;
3736:   }
3737:   return(0);
3738: }

3742: /*@
3743:    TSAdjointStep - Steps one time step backward in the adjoint run

3745:    Collective on TS

3747:    Input Parameter:
3748: .  ts - the TS context obtained from TSCreate()

3750:    Level: intermediate

3752: .keywords: TS, adjoint, step

3754: .seealso: TSAdjointSetUp(), TSAdjointSolve()
3755: @*/
3756: PetscErrorCode  TSAdjointStep(TS ts)
3757: {
3758:   DM               dm;
3759:   PetscErrorCode   ierr;

3763:   TSGetDM(ts,&dm);
3764:   TSAdjointSetUp(ts);

3766:   VecViewFromOptions(ts->vec_sol,(PetscObject)ts,"-ts_view_solution");

3768:   ts->reason = TS_CONVERGED_ITERATING;
3769:   ts->ptime_prev = ts->ptime;
3770:   if (!ts->ops->adjointstep) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed because the adjoint of  %s has not been implemented, try other time stepping methods for adjoint sensitivity analysis",((PetscObject)ts)->type_name);
3771:   PetscLogEventBegin(TS_AdjointStep,ts,0,0,0);
3772:   (*ts->ops->adjointstep)(ts);
3773:   PetscLogEventEnd(TS_AdjointStep,ts,0,0,0);
3774:   ts->steps++; ts->total_steps--;

3776:   if (ts->reason < 0) {
3777:     if (ts->errorifstepfailed) {
3778:       if (ts->reason == TS_DIVERGED_NONLINEAR_SOLVE) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s, increase -ts_max_snes_failures or make negative to attempt recovery",TSConvergedReasons[ts->reason]);
3779:       else if (ts->reason == TS_DIVERGED_STEP_REJECTED) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s, increase -ts_max_reject or make negative to attempt recovery",TSConvergedReasons[ts->reason]);
3780:       else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s",TSConvergedReasons[ts->reason]);
3781:     }
3782:   } else if (!ts->reason) {
3783:     if (ts->steps >= ts->adjoint_max_steps) ts->reason = TS_CONVERGED_ITS;
3784:   }
3785:   return(0);
3786: }

3790: /*@
3791:    TSEvaluateWLTE - Evaluate the weighted local truncation error norm
3792:    at the end of a time step with a given order of accuracy.

3794:    Collective on TS

3796:    Input Arguments:
3797: +  ts - time stepping context
3798: .  wnormtype - norm type, either NORM_2 or NORM_INFINITY
3799: -  order - optional, desired order for the error evaluation or PETSC_DECIDE

3801:    Output Arguments:
3802: +  order - optional, the actual order of the error evaluation
3803: -  wlte - the weighted local truncation error norm

3805:    Level: advanced

3807:    Notes:
3808:    If the timestepper cannot evaluate the error in a particular step
3809:    (eg. in the first step or restart steps after event handling),
3810:    this routine returns wlte=-1.0 .

3812: .seealso: TSStep(), TSAdapt, TSErrorWeightedNorm()
3813: @*/
3814: PetscErrorCode TSEvaluateWLTE(TS ts,NormType wnormtype,PetscInt *order,PetscReal *wlte)
3815: {

3825:   if (wnormtype != NORM_2 && wnormtype != NORM_INFINITY) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"No support for norm type %s",NormTypes[wnormtype]);
3826:   if (!ts->ops->evaluatewlte) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSEvaluateWLTE not implemented for type '%s'",((PetscObject)ts)->type_name);
3827:   (*ts->ops->evaluatewlte)(ts,wnormtype,order,wlte);
3828:   return(0);
3829: }

3833: /*@
3834:    TSEvaluateStep - Evaluate the solution at the end of a time step with a given order of accuracy.

3836:    Collective on TS

3838:    Input Arguments:
3839: +  ts - time stepping context
3840: .  order - desired order of accuracy
3841: -  done - whether the step was evaluated at this order (pass NULL to generate an error if not available)

3843:    Output Arguments:
3844: .  U - state at the end of the current step

3846:    Level: advanced

3848:    Notes:
3849:    This function cannot be called until all stages have been evaluated.
3850:    It is normally called by adaptive controllers before a step has been accepted and may also be called by the user after TSStep() has returned.

3852: .seealso: TSStep(), TSAdapt
3853: @*/
3854: PetscErrorCode TSEvaluateStep(TS ts,PetscInt order,Vec U,PetscBool *done)
3855: {

3862:   if (!ts->ops->evaluatestep) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSEvaluateStep not implemented for type '%s'",((PetscObject)ts)->type_name);
3863:   (*ts->ops->evaluatestep)(ts,order,U,done);
3864:   return(0);
3865: }

3869: /*@
3870:  TSForwardCostIntegral - Evaluate the cost integral in the forward run.
3871:  
3872:  Collective on TS
3873:  
3874:  Input Arguments:
3875:  .  ts - time stepping context
3876:  
3877:  Level: advanced
3878:  
3879:  Notes:
3880:  This function cannot be called until TSStep() has been completed.
3881:  
3882:  .seealso: TSSolve(), TSAdjointCostIntegral()
3883:  @*/
3884: PetscErrorCode TSForwardCostIntegral(TS ts)
3885: {
3888:     if (!ts->ops->forwardintegral) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"%s does not provide integral evaluation in the forward run",((PetscObject)ts)->type_name);
3889:     (*ts->ops->forwardintegral)(ts);
3890:     return(0);
3891: }

3895: /*@
3896:    TSSolve - Steps the requested number of timesteps.

3898:    Collective on TS

3900:    Input Parameter:
3901: +  ts - the TS context obtained from TSCreate()
3902: -  u - the solution vector  (can be null if TSSetSolution() was used and TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP) was not used,
3903:                              otherwise must contain the initial conditions and will contain the solution at the final requested time

3905:    Level: beginner

3907:    Notes:
3908:    The final time returned by this function may be different from the time of the internally
3909:    held state accessible by TSGetSolution() and TSGetTime() because the method may have
3910:    stepped over the final time.

3912: .keywords: TS, timestep, solve

3914: .seealso: TSCreate(), TSSetSolution(), TSStep(), TSGetTime(), TSGetSolveTime()
3915: @*/
3916: PetscErrorCode TSSolve(TS ts,Vec u)
3917: {
3918:   Vec               solution;
3919:   PetscErrorCode    ierr;


3925:   if (ts->exact_final_time == TS_EXACTFINALTIME_INTERPOLATE) {   /* Need ts->vec_sol to be distinct so it is not overwritten when we interpolate at the end */
3927:     if (!ts->vec_sol || u == ts->vec_sol) {
3928:       VecDuplicate(u,&solution);
3929:       TSSetSolution(ts,solution);
3930:       VecDestroy(&solution); /* grant ownership */
3931:     }
3932:     VecCopy(u,ts->vec_sol);
3933:   } else if (u) {
3934:     TSSetSolution(ts,u);
3935:   }
3936:   TSSetUp(ts);
3937:   TSTrajectorySetUp(ts->trajectory,ts);

3939:   if (ts->exact_final_time == TS_EXACTFINALTIME_UNSPECIFIED) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONGSTATE,"You must call TSSetExactFinalTime() or use -ts_exact_final_time <stepover,interpolate,matchstep> before calling TSSolve()");
3940:   if (ts->exact_final_time == TS_EXACTFINALTIME_MATCHSTEP && !ts->adapt) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Since TS is not adaptive you cannot use TS_EXACTFINALTIME_MATCHSTEP, suggest TS_EXACTFINALTIME_INTERPOLATE");

3942:   /* reset time step and iteration counters */
3943:   ts->steps             = 0;
3944:   ts->ksp_its           = 0;
3945:   ts->snes_its          = 0;
3946:   ts->num_snes_failures = 0;
3947:   ts->reject            = 0;
3948:   ts->reason            = TS_CONVERGED_ITERATING;

3950:   TSViewFromOptions(ts,NULL,"-ts_view_pre");

3952:   if (ts->ops->solve) { /* This private interface is transitional and should be removed when all implementations are updated. */
3953:     (*ts->ops->solve)(ts);
3954:     if (u) {VecCopy(ts->vec_sol,u);}
3955:     ts->solvetime = ts->ptime;
3956:     solution = ts->vec_sol;
3957:   } else { /* Step the requested number of timesteps. */
3958:     if (ts->steps >= ts->max_steps)     ts->reason = TS_CONVERGED_ITS;
3959:     else if (ts->ptime >= ts->max_time) ts->reason = TS_CONVERGED_TIME;
3960:     TSTrajectorySet(ts->trajectory,ts,ts->steps,ts->ptime,ts->vec_sol);
3961:     TSEventInitialize(ts->event,ts,ts->ptime,ts->vec_sol);
3962:     ts->steprollback = PETSC_FALSE;
3963:     ts->steprestart  = PETSC_TRUE;

3965:     while (!ts->reason) {
3966:       TSMonitor(ts,ts->steps,ts->ptime,ts->vec_sol);
3967:       if (!ts->steprollback) {
3968:         TSPreStep(ts);
3969:       }
3970:       TSStep(ts);
3971:       TSEventHandler(ts);
3972:       if (!ts->steprollback) {
3973:         if (ts->vec_costintegral && ts->costintegralfwd) {
3974:           TSForwardCostIntegral(ts);
3975:         }
3976:         TSTrajectorySet(ts->trajectory,ts,ts->steps,ts->ptime,ts->vec_sol);
3977:         TSPostStep(ts);
3978:       }
3979:     }
3980:     TSMonitor(ts,ts->steps,ts->ptime,ts->vec_sol);

3982:     if (ts->exact_final_time == TS_EXACTFINALTIME_INTERPOLATE && ts->ptime > ts->max_time) {
3983:       TSInterpolate(ts,ts->max_time,u);
3984:       ts->solvetime = ts->max_time;
3985:       solution = u;
3986:       TSMonitor(ts,-1,ts->solvetime,solution);
3987:     } else {
3988:       if (u) {VecCopy(ts->vec_sol,u);}
3989:       ts->solvetime = ts->ptime;
3990:       solution = ts->vec_sol;
3991:     }
3992:   }

3994:   TSViewFromOptions(ts,NULL,"-ts_view");
3995:   VecViewFromOptions(solution,NULL,"-ts_view_solution");
3996:   PetscObjectSAWsBlock((PetscObject)ts);
3997:   if (ts->adjoint_solve) {
3998:     TSAdjointSolve(ts);
3999:   }
4000:   return(0);
4001: }

4005: /*@
4006:  TSAdjointCostIntegral - Evaluate the cost integral in the adjoint run.
4007:  
4008:  Collective on TS
4009:  
4010:  Input Arguments:
4011:  .  ts - time stepping context
4012:  
4013:  Level: advanced
4014:  
4015:  Notes:
4016:  This function cannot be called until TSAdjointStep() has been completed.
4017:  
4018:  .seealso: TSAdjointSolve(), TSAdjointStep
4019:  @*/
4020: PetscErrorCode TSAdjointCostIntegral(TS ts)
4021: {
4024:     if (!ts->ops->adjointintegral) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"%s does not provide integral evaluation in the adjoint run",((PetscObject)ts)->type_name);
4025:     (*ts->ops->adjointintegral)(ts);
4026:     return(0);
4027: }

4031: /*@
4032:    TSAdjointSolve - Solves the discrete ajoint problem for an ODE/DAE

4034:    Collective on TS

4036:    Input Parameter:
4037: .  ts - the TS context obtained from TSCreate()

4039:    Options Database:
4040: . -ts_adjoint_view_solution <viewerinfo> - views the first gradient with respect to the initial conditions

4042:    Level: intermediate

4044:    Notes:
4045:    This must be called after a call to TSSolve() that solves the forward problem

4047:    By default this will integrate back to the initial time, one can use TSAdjointSetSteps() to step back to a later time

4049: .keywords: TS, timestep, solve

4051: .seealso: TSCreate(), TSSetCostGradients(), TSSetSolution(), TSAdjointStep()
4052: @*/
4053: PetscErrorCode TSAdjointSolve(TS ts)
4054: {
4055:   PetscErrorCode    ierr;

4059:   TSAdjointSetUp(ts);

4061:   /* reset time step and iteration counters */
4062:   ts->steps             = 0;
4063:   ts->ksp_its           = 0;
4064:   ts->snes_its          = 0;
4065:   ts->num_snes_failures = 0;
4066:   ts->reject            = 0;
4067:   ts->reason            = TS_CONVERGED_ITERATING;

4069:   if (!ts->adjoint_max_steps) ts->adjoint_max_steps = ts->total_steps;

4071:   if (ts->steps >= ts->adjoint_max_steps)     ts->reason = TS_CONVERGED_ITS;
4072:   while (!ts->reason) {
4073:     TSTrajectoryGet(ts->trajectory,ts,ts->total_steps,&ts->ptime);
4074:     TSAdjointMonitor(ts,ts->total_steps,ts->ptime,ts->vec_sol,ts->numcost,ts->vecs_sensi,ts->vecs_sensip);
4075:     TSAdjointEventHandler(ts);
4076:     TSAdjointStep(ts);
4077:     if (ts->vec_costintegral && !ts->costintegralfwd) {
4078:       TSAdjointCostIntegral(ts);
4079:     }
4080:   }
4081:   TSTrajectoryGet(ts->trajectory,ts,ts->total_steps,&ts->ptime);
4082:   TSAdjointMonitor(ts,ts->total_steps,ts->ptime,ts->vec_sol,ts->numcost,ts->vecs_sensi,ts->vecs_sensip);
4083:   ts->solvetime = ts->ptime;
4084:   TSTrajectoryViewFromOptions(ts->trajectory,NULL,"-ts_trajectory_view");
4085:   VecViewFromOptions(ts->vecs_sensi[0],(PetscObject) ts, "-ts_adjoint_view_solution");
4086:   return(0);
4087: }

4091: /*@C
4092:    TSMonitor - Runs all user-provided monitor routines set using TSMonitorSet()

4094:    Collective on TS

4096:    Input Parameters:
4097: +  ts - time stepping context obtained from TSCreate()
4098: .  step - step number that has just completed
4099: .  ptime - model time of the state
4100: -  u - state at the current model time

4102:    Notes:
4103:    TSMonitor() is typically used automatically within the time stepping implementations.
4104:    Users would almost never call this routine directly.

4106:    A step of -1 indicates that the monitor is being called on a solution obtained by interpolating from computed solutions

4108:    Level: developer

4110: .keywords: TS, timestep
4111: @*/
4112: PetscErrorCode TSMonitor(TS ts,PetscInt step,PetscReal ptime,Vec u)
4113: {
4114:   DM             dm;
4115:   PetscInt       i,n = ts->numbermonitors;


4122:   TSGetDM(ts,&dm);
4123:   DMSetOutputSequenceNumber(dm,step,ptime);

4125:   VecLockPush(u);
4126:   for (i=0; i<n; i++) {
4127:     (*ts->monitor[i])(ts,step,ptime,u,ts->monitorcontext[i]);
4128:   }
4129:   VecLockPop(u);
4130:   return(0);
4131: }

4135: /*@C
4136:    TSAdjointMonitor - Runs all user-provided adjoint monitor routines set using TSAdjointMonitorSet()

4138:    Collective on TS

4140:    Input Parameters:
4141: +  ts - time stepping context obtained from TSCreate()
4142: .  step - step number that has just completed
4143: .  ptime - model time of the state
4144: .  u - state at the current model time
4145: .  numcost - number of cost functions (dimension of lambda  or mu)
4146: .  lambda - vectors containing the gradients of the cost functions with respect to the ODE/DAE solution variables
4147: -  mu - vectors containing the gradients of the cost functions with respect to the problem parameters

4149:    Notes:
4150:    TSAdjointMonitor() is typically used automatically within the time stepping implementations.
4151:    Users would almost never call this routine directly.

4153:    Level: developer

4155: .keywords: TS, timestep
4156: @*/
4157: PetscErrorCode TSAdjointMonitor(TS ts,PetscInt step,PetscReal ptime,Vec u,PetscInt numcost,Vec *lambda, Vec *mu)
4158: {
4160:   PetscInt       i,n = ts->numberadjointmonitors;

4165:   VecLockPush(u);
4166:   for (i=0; i<n; i++) {
4167:     (*ts->adjointmonitor[i])(ts,step,ptime,u,numcost,lambda,mu,ts->adjointmonitorcontext[i]);
4168:   }
4169:   VecLockPop(u);
4170:   return(0);
4171: }

4173: /* ------------------------------------------------------------------------*/
4176: /*@C
4177:    TSMonitorLGCtxCreate - Creates a TSMonitorLGCtx context for use with
4178:    TS to monitor the solution process graphically in various ways

4180:    Collective on TS

4182:    Input Parameters:
4183: +  host - the X display to open, or null for the local machine
4184: .  label - the title to put in the title bar
4185: .  x, y - the screen coordinates of the upper left coordinate of the window
4186: .  m, n - the screen width and height in pixels
4187: -  howoften - if positive then determines the frequency of the plotting, if -1 then only at the final time

4189:    Output Parameter:
4190: .  ctx - the context

4192:    Options Database Key:
4193: +  -ts_monitor_lg_timestep - automatically sets line graph monitor
4194: .  -ts_monitor_lg_solution - monitor the solution (or certain values of the solution by calling TSMonitorLGSetDisplayVariables() or TSMonitorLGCtxSetDisplayVariables())
4195: .  -ts_monitor_lg_error -  monitor the error
4196: .  -ts_monitor_lg_ksp_iterations - monitor the number of KSP iterations needed for each timestep
4197: .  -ts_monitor_lg_snes_iterations - monitor the number of SNES iterations needed for each timestep
4198: -  -lg_use_markers <true,false> - mark the data points (at each time step) on the plot; default is true

4200:    Notes:
4201:    Use TSMonitorLGCtxDestroy() to destroy.

4203:    One can provide a function that transforms the solution before plotting it with TSMonitorLGCtxSetTransform() or TSMonitorLGSetTransform()

4205:    Many of the functions that control the monitoring have two forms: TSMonitorLGSet/GetXXXX() and TSMonitorLGCtxSet/GetXXXX() the first take a TS object as the
4206:    first argument (if that TS object does not have a TSMonitorLGCtx associated with it the function call is ignored) and the second takes a TSMonitorLGCtx object
4207:    as the first argument.

4209:    One can control the names displayed for each solution or error variable with TSMonitorLGCtxSetVariableNames() or TSMonitorLGSetVariableNames()


4212:    Level: intermediate

4214: .keywords: TS, monitor, line graph, residual

4216: .seealso: TSMonitorLGTimeStep(), TSMonitorSet(), TSMonitorLGSolution(), TSMonitorLGError(), TSMonitorDefault(), VecView(), 
4217:            TSMonitorLGCtxCreate(), TSMonitorLGCtxSetVariableNames(), TSMonitorLGCtxGetVariableNames(),
4218:            TSMonitorLGSetVariableNames(), TSMonitorLGGetVariableNames(), TSMonitorLGSetDisplayVariables(), TSMonitorLGCtxSetDisplayVariables(),
4219:            TSMonitorLGCtxSetTransform(), TSMonitorLGSetTransform(), TSMonitorLGError(), TSMonitorLGSNESIterations(), TSMonitorLGKSPIterations(),
4220:            TSMonitorEnvelopeCtxCreate(), TSMonitorEnvelopeGetBounds(), TSMonitorEnvelopeCtxDestroy(), TSMonitorEnvelop()

4222: @*/
4223: PetscErrorCode  TSMonitorLGCtxCreate(MPI_Comm comm,const char host[],const char label[],int x,int y,int m,int n,PetscInt howoften,TSMonitorLGCtx *ctx)
4224: {
4225:   PetscDraw      draw;

4229:   PetscNew(ctx);
4230:   PetscDrawCreate(comm,host,label,x,y,m,n,&draw);
4231:   PetscDrawSetFromOptions(draw);
4232:   PetscDrawLGCreate(draw,1,&(*ctx)->lg);
4233:   PetscDrawLGSetFromOptions((*ctx)->lg);
4234:   PetscDrawDestroy(&draw);
4235:   (*ctx)->howoften = howoften;
4236:   return(0);
4237: }

4241: PetscErrorCode TSMonitorLGTimeStep(TS ts,PetscInt step,PetscReal ptime,Vec v,void *monctx)
4242: {
4243:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
4244:   PetscReal      x   = ptime,y;

4248:   if (step < 0) return(0); /* -1 indicates an interpolated solution */
4249:   if (!step) {
4250:     PetscDrawAxis axis;
4251:     PetscDrawLGGetAxis(ctx->lg,&axis);
4252:     PetscDrawAxisSetLabels(axis,"Timestep as function of time","Time","Time Step");
4253:     PetscDrawLGReset(ctx->lg);
4254:   }
4255:   TSGetTimeStep(ts,&y);
4256:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
4257:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
4258:     PetscDrawLGDraw(ctx->lg);
4259:     PetscDrawLGSave(ctx->lg);
4260:   }
4261:   return(0);
4262: }

4266: /*@C
4267:    TSMonitorLGCtxDestroy - Destroys a line graph context that was created
4268:    with TSMonitorLGCtxCreate().

4270:    Collective on TSMonitorLGCtx

4272:    Input Parameter:
4273: .  ctx - the monitor context

4275:    Level: intermediate

4277: .keywords: TS, monitor, line graph, destroy

4279: .seealso: TSMonitorLGCtxCreate(),  TSMonitorSet(), TSMonitorLGTimeStep();
4280: @*/
4281: PetscErrorCode  TSMonitorLGCtxDestroy(TSMonitorLGCtx *ctx)
4282: {

4286:   if ((*ctx)->transformdestroy) {
4287:     ((*ctx)->transformdestroy)((*ctx)->transformctx);
4288:   }
4289:   PetscDrawLGDestroy(&(*ctx)->lg);
4290:   PetscStrArrayDestroy(&(*ctx)->names);
4291:   PetscStrArrayDestroy(&(*ctx)->displaynames);
4292:   PetscFree((*ctx)->displayvariables);
4293:   PetscFree((*ctx)->displayvalues);
4294:   PetscFree(*ctx);
4295:   return(0);
4296: }

4300: /*@
4301:    TSGetTime - Gets the time of the most recently completed step.

4303:    Not Collective

4305:    Input Parameter:
4306: .  ts - the TS context obtained from TSCreate()

4308:    Output Parameter:
4309: .  t  - the current time. This time may not corresponds to the final time set with TSSetDuration(), use TSGetSolveTime().

4311:    Level: beginner

4313:    Note:
4314:    When called during time step evaluation (e.g. during residual evaluation or via hooks set using TSSetPreStep(),
4315:    TSSetPreStage(), TSSetPostStage(), or TSSetPostStep()), the time is the time at the start of the step being evaluated.

4317: .seealso: TSSetInitialTimeStep(), TSGetTimeStep(), TSGetSolveTime()

4319: .keywords: TS, get, time
4320: @*/
4321: PetscErrorCode  TSGetTime(TS ts,PetscReal *t)
4322: {
4326:   *t = ts->ptime;
4327:   return(0);
4328: }

4332: /*@
4333:    TSGetPrevTime - Gets the starting time of the previously completed step.

4335:    Not Collective

4337:    Input Parameter:
4338: .  ts - the TS context obtained from TSCreate()

4340:    Output Parameter:
4341: .  t  - the previous time

4343:    Level: beginner

4345: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

4347: .keywords: TS, get, time
4348: @*/
4349: PetscErrorCode  TSGetPrevTime(TS ts,PetscReal *t)
4350: {
4354:   *t = ts->ptime_prev;
4355:   return(0);
4356: }

4360: /*@
4361:    TSSetTime - Allows one to reset the time.

4363:    Logically Collective on TS

4365:    Input Parameters:
4366: +  ts - the TS context obtained from TSCreate()
4367: -  time - the time

4369:    Level: intermediate

4371: .seealso: TSGetTime(), TSSetDuration()

4373: .keywords: TS, set, time
4374: @*/
4375: PetscErrorCode  TSSetTime(TS ts, PetscReal t)
4376: {
4380:   ts->ptime = t;
4381:   return(0);
4382: }

4386: /*@C
4387:    TSSetOptionsPrefix - Sets the prefix used for searching for all
4388:    TS options in the database.

4390:    Logically Collective on TS

4392:    Input Parameter:
4393: +  ts     - The TS context
4394: -  prefix - The prefix to prepend to all option names

4396:    Notes:
4397:    A hyphen (-) must NOT be given at the beginning of the prefix name.
4398:    The first character of all runtime options is AUTOMATICALLY the
4399:    hyphen.

4401:    Level: advanced

4403: .keywords: TS, set, options, prefix, database

4405: .seealso: TSSetFromOptions()

4407: @*/
4408: PetscErrorCode  TSSetOptionsPrefix(TS ts,const char prefix[])
4409: {
4411:   SNES           snes;

4415:   PetscObjectSetOptionsPrefix((PetscObject)ts,prefix);
4416:   TSGetSNES(ts,&snes);
4417:   SNESSetOptionsPrefix(snes,prefix);
4418:   return(0);
4419: }


4424: /*@C
4425:    TSAppendOptionsPrefix - Appends to the prefix used for searching for all
4426:    TS options in the database.

4428:    Logically Collective on TS

4430:    Input Parameter:
4431: +  ts     - The TS context
4432: -  prefix - The prefix to prepend to all option names

4434:    Notes:
4435:    A hyphen (-) must NOT be given at the beginning of the prefix name.
4436:    The first character of all runtime options is AUTOMATICALLY the
4437:    hyphen.

4439:    Level: advanced

4441: .keywords: TS, append, options, prefix, database

4443: .seealso: TSGetOptionsPrefix()

4445: @*/
4446: PetscErrorCode  TSAppendOptionsPrefix(TS ts,const char prefix[])
4447: {
4449:   SNES           snes;

4453:   PetscObjectAppendOptionsPrefix((PetscObject)ts,prefix);
4454:   TSGetSNES(ts,&snes);
4455:   SNESAppendOptionsPrefix(snes,prefix);
4456:   return(0);
4457: }

4461: /*@C
4462:    TSGetOptionsPrefix - Sets the prefix used for searching for all
4463:    TS options in the database.

4465:    Not Collective

4467:    Input Parameter:
4468: .  ts - The TS context

4470:    Output Parameter:
4471: .  prefix - A pointer to the prefix string used

4473:    Notes: On the fortran side, the user should pass in a string 'prifix' of
4474:    sufficient length to hold the prefix.

4476:    Level: intermediate

4478: .keywords: TS, get, options, prefix, database

4480: .seealso: TSAppendOptionsPrefix()
4481: @*/
4482: PetscErrorCode  TSGetOptionsPrefix(TS ts,const char *prefix[])
4483: {

4489:   PetscObjectGetOptionsPrefix((PetscObject)ts,prefix);
4490:   return(0);
4491: }

4495: /*@C
4496:    TSGetRHSJacobian - Returns the Jacobian J at the present timestep.

4498:    Not Collective, but parallel objects are returned if TS is parallel

4500:    Input Parameter:
4501: .  ts  - The TS context obtained from TSCreate()

4503:    Output Parameters:
4504: +  Amat - The (approximate) Jacobian J of G, where U_t = G(U,t)  (or NULL)
4505: .  Pmat - The matrix from which the preconditioner is constructed, usually the same as Amat  (or NULL)
4506: .  func - Function to compute the Jacobian of the RHS  (or NULL)
4507: -  ctx - User-defined context for Jacobian evaluation routine  (or NULL)

4509:    Notes: You can pass in NULL for any return argument you do not need.

4511:    Level: intermediate

4513: .seealso: TSGetTimeStep(), TSGetMatrices(), TSGetTime(), TSGetTimeStepNumber()

4515: .keywords: TS, timestep, get, matrix, Jacobian
4516: @*/
4517: PetscErrorCode  TSGetRHSJacobian(TS ts,Mat *Amat,Mat *Pmat,TSRHSJacobian *func,void **ctx)
4518: {
4520:   SNES           snes;
4521:   DM             dm;

4524:   TSGetSNES(ts,&snes);
4525:   SNESGetJacobian(snes,Amat,Pmat,NULL,NULL);
4526:   TSGetDM(ts,&dm);
4527:   DMTSGetRHSJacobian(dm,func,ctx);
4528:   return(0);
4529: }

4533: /*@C
4534:    TSGetIJacobian - Returns the implicit Jacobian at the present timestep.

4536:    Not Collective, but parallel objects are returned if TS is parallel

4538:    Input Parameter:
4539: .  ts  - The TS context obtained from TSCreate()

4541:    Output Parameters:
4542: +  Amat  - The (approximate) Jacobian of F(t,U,U_t)
4543: .  Pmat - The matrix from which the preconditioner is constructed, often the same as Amat
4544: .  f   - The function to compute the matrices
4545: - ctx - User-defined context for Jacobian evaluation routine

4547:    Notes: You can pass in NULL for any return argument you do not need.

4549:    Level: advanced

4551: .seealso: TSGetTimeStep(), TSGetRHSJacobian(), TSGetMatrices(), TSGetTime(), TSGetTimeStepNumber()

4553: .keywords: TS, timestep, get, matrix, Jacobian
4554: @*/
4555: PetscErrorCode  TSGetIJacobian(TS ts,Mat *Amat,Mat *Pmat,TSIJacobian *f,void **ctx)
4556: {
4558:   SNES           snes;
4559:   DM             dm;

4562:   TSGetSNES(ts,&snes);
4563:   SNESSetUpMatrices(snes);
4564:   SNESGetJacobian(snes,Amat,Pmat,NULL,NULL);
4565:   TSGetDM(ts,&dm);
4566:   DMTSGetIJacobian(dm,f,ctx);
4567:   return(0);
4568: }


4573: /*@C
4574:    TSMonitorDrawSolution - Monitors progress of the TS solvers by calling
4575:    VecView() for the solution at each timestep

4577:    Collective on TS

4579:    Input Parameters:
4580: +  ts - the TS context
4581: .  step - current time-step
4582: .  ptime - current time
4583: -  dummy - either a viewer or NULL

4585:    Options Database:
4586: .   -ts_monitor_draw_solution_initial - show initial solution as well as current solution

4588:    Notes: the initial solution and current solution are not display with a common axis scaling so generally the option -ts_monitor_draw_solution_initial
4589:        will look bad

4591:    Level: intermediate

4593: .keywords: TS,  vector, monitor, view

4595: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
4596: @*/
4597: PetscErrorCode  TSMonitorDrawSolution(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
4598: {
4599:   PetscErrorCode   ierr;
4600:   TSMonitorDrawCtx ictx = (TSMonitorDrawCtx)dummy;
4601:   PetscDraw        draw;

4604:   if (!step && ictx->showinitial) {
4605:     if (!ictx->initialsolution) {
4606:       VecDuplicate(u,&ictx->initialsolution);
4607:     }
4608:     VecCopy(u,ictx->initialsolution);
4609:   }
4610:   if (!(((ictx->howoften > 0) && (!(step % ictx->howoften))) || ((ictx->howoften == -1) && ts->reason))) return(0);

4612:   if (ictx->showinitial) {
4613:     PetscReal pause;
4614:     PetscViewerDrawGetPause(ictx->viewer,&pause);
4615:     PetscViewerDrawSetPause(ictx->viewer,0.0);
4616:     VecView(ictx->initialsolution,ictx->viewer);
4617:     PetscViewerDrawSetPause(ictx->viewer,pause);
4618:     PetscViewerDrawSetHold(ictx->viewer,PETSC_TRUE);
4619:   }
4620:   VecView(u,ictx->viewer);
4621:   if (ictx->showtimestepandtime) {
4622:     PetscReal xl,yl,xr,yr,h;
4623:     char      time[32];

4625:     PetscViewerDrawGetDraw(ictx->viewer,0,&draw);
4626:     PetscSNPrintf(time,32,"Timestep %d Time %g",(int)step,(double)ptime);
4627:     PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
4628:     h    = yl + .95*(yr - yl);
4629:     PetscDrawStringCentered(draw,.5*(xl+xr),h,PETSC_DRAW_BLACK,time);
4630:     PetscDrawFlush(draw);
4631:   }

4633:   if (ictx->showinitial) {
4634:     PetscViewerDrawSetHold(ictx->viewer,PETSC_FALSE);
4635:   }
4636:   return(0);
4637: }

4641: /*@C
4642:    TSAdjointMonitorDrawSensi - Monitors progress of the adjoint TS solvers by calling
4643:    VecView() for the sensitivities to initial states at each timestep

4645:    Collective on TS

4647:    Input Parameters:
4648: +  ts - the TS context
4649: .  step - current time-step
4650: .  ptime - current time
4651: .  u - current state
4652: .  numcost - number of cost functions
4653: .  lambda - sensitivities to initial conditions
4654: .  mu - sensitivities to parameters
4655: -  dummy - either a viewer or NULL

4657:    Level: intermediate

4659: .keywords: TS,  vector, adjoint, monitor, view

4661: .seealso: TSAdjointMonitorSet(), TSAdjointMonitorDefault(), VecView()
4662: @*/
4663: PetscErrorCode  TSAdjointMonitorDrawSensi(TS ts,PetscInt step,PetscReal ptime,Vec u,PetscInt numcost,Vec *lambda,Vec *mu,void *dummy)
4664: {
4665:   PetscErrorCode   ierr;
4666:   TSMonitorDrawCtx ictx = (TSMonitorDrawCtx)dummy;
4667:   PetscDraw        draw;
4668:   PetscReal        xl,yl,xr,yr,h;
4669:   char             time[32];

4672:   if (!(((ictx->howoften > 0) && (!(step % ictx->howoften))) || ((ictx->howoften == -1) && ts->reason))) return(0);

4674:   VecView(lambda[0],ictx->viewer);
4675:   PetscViewerDrawGetDraw(ictx->viewer,0,&draw);
4676:   PetscSNPrintf(time,32,"Timestep %d Time %g",(int)step,(double)ptime);
4677:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
4678:   h    = yl + .95*(yr - yl);
4679:   PetscDrawStringCentered(draw,.5*(xl+xr),h,PETSC_DRAW_BLACK,time);
4680:   PetscDrawFlush(draw);
4681:   return(0);
4682: }

4686: /*@C
4687:    TSMonitorDrawSolutionPhase - Monitors progress of the TS solvers by plotting the solution as a phase diagram

4689:    Collective on TS

4691:    Input Parameters:
4692: +  ts - the TS context
4693: .  step - current time-step
4694: .  ptime - current time
4695: -  dummy - either a viewer or NULL

4697:    Level: intermediate

4699: .keywords: TS,  vector, monitor, view

4701: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
4702: @*/
4703: PetscErrorCode  TSMonitorDrawSolutionPhase(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
4704: {
4705:   PetscErrorCode    ierr;
4706:   TSMonitorDrawCtx  ictx = (TSMonitorDrawCtx)dummy;
4707:   PetscDraw         draw;
4708:   PetscDrawAxis     axis;
4709:   PetscInt          n;
4710:   PetscMPIInt       size;
4711:   PetscReal         U0,U1,xl,yl,xr,yr,h;
4712:   char              time[32];
4713:   const PetscScalar *U;

4716:   MPI_Comm_size(PetscObjectComm((PetscObject)ts),&size);
4717:   if (size != 1) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Only allowed for sequential runs");
4718:   VecGetSize(u,&n);
4719:   if (n != 2) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Only for ODEs with two unknowns");

4721:   PetscViewerDrawGetDraw(ictx->viewer,0,&draw);
4722:   PetscViewerDrawGetDrawAxis(ictx->viewer,0,&axis);
4723:   PetscDrawAxisGetLimits(axis,&xl,&xr,&yl,&yr);
4724:   if (!step) {
4725:     PetscDrawClear(draw);
4726:     PetscDrawAxisDraw(axis);
4727:   }

4729:   VecGetArrayRead(u,&U);
4730:   U0 = PetscRealPart(U[0]);
4731:   U1 = PetscRealPart(U[1]);
4732:   VecRestoreArrayRead(u,&U);
4733:   if ((U0 < xl) || (U1 < yl) || (U0 > xr) || (U1 > yr)) return(0);

4735:   PetscDrawCollectiveBegin(draw);
4736:   PetscDrawPoint(draw,U0,U1,PETSC_DRAW_BLACK);
4737:   if (ictx->showtimestepandtime) {
4738:     PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
4739:     PetscSNPrintf(time,32,"Timestep %d Time %g",(int)step,(double)ptime);
4740:     h    = yl + .95*(yr - yl);
4741:     PetscDrawStringCentered(draw,.5*(xl+xr),h,PETSC_DRAW_BLACK,time);
4742:   }
4743:   PetscDrawCollectiveEnd(draw);
4744:   PetscDrawFlush(draw);
4745:   PetscDrawSave(draw);
4746:   return(0);
4747: }


4752: /*@C
4753:    TSMonitorDrawCtxDestroy - Destroys the monitor context for TSMonitorDrawSolution()

4755:    Collective on TS

4757:    Input Parameters:
4758: .    ctx - the monitor context

4760:    Level: intermediate

4762: .keywords: TS,  vector, monitor, view

4764: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorDrawSolution(), TSMonitorDrawError()
4765: @*/
4766: PetscErrorCode  TSMonitorDrawCtxDestroy(TSMonitorDrawCtx *ictx)
4767: {

4771:   PetscViewerDestroy(&(*ictx)->viewer);
4772:   VecDestroy(&(*ictx)->initialsolution);
4773:   PetscFree(*ictx);
4774:   return(0);
4775: }

4779: /*@C
4780:    TSMonitorDrawCtxCreate - Creates the monitor context for TSMonitorDrawCtx

4782:    Collective on TS

4784:    Input Parameter:
4785: .    ts - time-step context

4787:    Output Patameter:
4788: .    ctx - the monitor context

4790:    Options Database:
4791: .   -ts_monitor_draw_solution_initial - show initial solution as well as current solution

4793:    Level: intermediate

4795: .keywords: TS,  vector, monitor, view

4797: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorDrawCtx()
4798: @*/
4799: PetscErrorCode  TSMonitorDrawCtxCreate(MPI_Comm comm,const char host[],const char label[],int x,int y,int m,int n,PetscInt howoften,TSMonitorDrawCtx *ctx)
4800: {
4801:   PetscErrorCode   ierr;

4804:   PetscNew(ctx);
4805:   PetscViewerDrawOpen(comm,host,label,x,y,m,n,&(*ctx)->viewer);
4806:   PetscViewerSetFromOptions((*ctx)->viewer);

4808:   (*ctx)->howoften    = howoften;
4809:   (*ctx)->showinitial = PETSC_FALSE;
4810:   PetscOptionsGetBool(NULL,NULL,"-ts_monitor_draw_solution_initial",&(*ctx)->showinitial,NULL);

4812:   (*ctx)->showtimestepandtime = PETSC_FALSE;
4813:   PetscOptionsGetBool(NULL,NULL,"-ts_monitor_draw_solution_show_time",&(*ctx)->showtimestepandtime,NULL);
4814:   return(0);
4815: }

4819: /*@C
4820:    TSMonitorDrawError - Monitors progress of the TS solvers by calling
4821:    VecView() for the error at each timestep

4823:    Collective on TS

4825:    Input Parameters:
4826: +  ts - the TS context
4827: .  step - current time-step
4828: .  ptime - current time
4829: -  dummy - either a viewer or NULL

4831:    Level: intermediate

4833: .keywords: TS,  vector, monitor, view

4835: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
4836: @*/
4837: PetscErrorCode  TSMonitorDrawError(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
4838: {
4839:   PetscErrorCode   ierr;
4840:   TSMonitorDrawCtx ctx    = (TSMonitorDrawCtx)dummy;
4841:   PetscViewer      viewer = ctx->viewer;
4842:   Vec              work;

4845:   if (!(((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason))) return(0);
4846:   VecDuplicate(u,&work);
4847:   TSComputeSolutionFunction(ts,ptime,work);
4848:   VecAXPY(work,-1.0,u);
4849:   VecView(work,viewer);
4850:   VecDestroy(&work);
4851:   return(0);
4852: }

4854: #include <petsc/private/dmimpl.h>
4857: /*@
4858:    TSSetDM - Sets the DM that may be used by some preconditioners

4860:    Logically Collective on TS and DM

4862:    Input Parameters:
4863: +  ts - the preconditioner context
4864: -  dm - the dm

4866:    Level: intermediate


4869: .seealso: TSGetDM(), SNESSetDM(), SNESGetDM()
4870: @*/
4871: PetscErrorCode  TSSetDM(TS ts,DM dm)
4872: {
4874:   SNES           snes;
4875:   DMTS           tsdm;

4879:   PetscObjectReference((PetscObject)dm);
4880:   if (ts->dm) {               /* Move the DMTS context over to the new DM unless the new DM already has one */
4881:     if (ts->dm->dmts && !dm->dmts) {
4882:       DMCopyDMTS(ts->dm,dm);
4883:       DMGetDMTS(ts->dm,&tsdm);
4884:       if (tsdm->originaldm == ts->dm) { /* Grant write privileges to the replacement DM */
4885:         tsdm->originaldm = dm;
4886:       }
4887:     }
4888:     DMDestroy(&ts->dm);
4889:   }
4890:   ts->dm = dm;

4892:   TSGetSNES(ts,&snes);
4893:   SNESSetDM(snes,dm);
4894:   return(0);
4895: }

4899: /*@
4900:    TSGetDM - Gets the DM that may be used by some preconditioners

4902:    Not Collective

4904:    Input Parameter:
4905: . ts - the preconditioner context

4907:    Output Parameter:
4908: .  dm - the dm

4910:    Level: intermediate


4913: .seealso: TSSetDM(), SNESSetDM(), SNESGetDM()
4914: @*/
4915: PetscErrorCode  TSGetDM(TS ts,DM *dm)
4916: {

4921:   if (!ts->dm) {
4922:     DMShellCreate(PetscObjectComm((PetscObject)ts),&ts->dm);
4923:     if (ts->snes) {SNESSetDM(ts->snes,ts->dm);}
4924:   }
4925:   *dm = ts->dm;
4926:   return(0);
4927: }

4931: /*@
4932:    SNESTSFormFunction - Function to evaluate nonlinear residual

4934:    Logically Collective on SNES

4936:    Input Parameter:
4937: + snes - nonlinear solver
4938: . U - the current state at which to evaluate the residual
4939: - ctx - user context, must be a TS

4941:    Output Parameter:
4942: . F - the nonlinear residual

4944:    Notes:
4945:    This function is not normally called by users and is automatically registered with the SNES used by TS.
4946:    It is most frequently passed to MatFDColoringSetFunction().

4948:    Level: advanced

4950: .seealso: SNESSetFunction(), MatFDColoringSetFunction()
4951: @*/
4952: PetscErrorCode  SNESTSFormFunction(SNES snes,Vec U,Vec F,void *ctx)
4953: {
4954:   TS             ts = (TS)ctx;

4962:   (ts->ops->snesfunction)(snes,U,F,ts);
4963:   return(0);
4964: }

4968: /*@
4969:    SNESTSFormJacobian - Function to evaluate the Jacobian

4971:    Collective on SNES

4973:    Input Parameter:
4974: + snes - nonlinear solver
4975: . U - the current state at which to evaluate the residual
4976: - ctx - user context, must be a TS

4978:    Output Parameter:
4979: + A - the Jacobian
4980: . B - the preconditioning matrix (may be the same as A)
4981: - flag - indicates any structure change in the matrix

4983:    Notes:
4984:    This function is not normally called by users and is automatically registered with the SNES used by TS.

4986:    Level: developer

4988: .seealso: SNESSetJacobian()
4989: @*/
4990: PetscErrorCode  SNESTSFormJacobian(SNES snes,Vec U,Mat A,Mat B,void *ctx)
4991: {
4992:   TS             ts = (TS)ctx;

5003:   (ts->ops->snesjacobian)(snes,U,A,B,ts);
5004:   return(0);
5005: }

5009: /*@C
5010:    TSComputeRHSFunctionLinear - Evaluate the right hand side via the user-provided Jacobian, for linear problems Udot = A U only

5012:    Collective on TS

5014:    Input Arguments:
5015: +  ts - time stepping context
5016: .  t - time at which to evaluate
5017: .  U - state at which to evaluate
5018: -  ctx - context

5020:    Output Arguments:
5021: .  F - right hand side

5023:    Level: intermediate

5025:    Notes:
5026:    This function is intended to be passed to TSSetRHSFunction() to evaluate the right hand side for linear problems.
5027:    The matrix (and optionally the evaluation context) should be passed to TSSetRHSJacobian().

5029: .seealso: TSSetRHSFunction(), TSSetRHSJacobian(), TSComputeRHSJacobianConstant()
5030: @*/
5031: PetscErrorCode TSComputeRHSFunctionLinear(TS ts,PetscReal t,Vec U,Vec F,void *ctx)
5032: {
5034:   Mat            Arhs,Brhs;

5037:   TSGetRHSMats_Private(ts,&Arhs,&Brhs);
5038:   TSComputeRHSJacobian(ts,t,U,Arhs,Brhs);
5039:   MatMult(Arhs,U,F);
5040:   return(0);
5041: }

5045: /*@C
5046:    TSComputeRHSJacobianConstant - Reuses a Jacobian that is time-independent.

5048:    Collective on TS

5050:    Input Arguments:
5051: +  ts - time stepping context
5052: .  t - time at which to evaluate
5053: .  U - state at which to evaluate
5054: -  ctx - context

5056:    Output Arguments:
5057: +  A - pointer to operator
5058: .  B - pointer to preconditioning matrix
5059: -  flg - matrix structure flag

5061:    Level: intermediate

5063:    Notes:
5064:    This function is intended to be passed to TSSetRHSJacobian() to evaluate the Jacobian for linear time-independent problems.

5066: .seealso: TSSetRHSFunction(), TSSetRHSJacobian(), TSComputeRHSFunctionLinear()
5067: @*/
5068: PetscErrorCode TSComputeRHSJacobianConstant(TS ts,PetscReal t,Vec U,Mat A,Mat B,void *ctx)
5069: {
5071:   return(0);
5072: }

5076: /*@C
5077:    TSComputeIFunctionLinear - Evaluate the left hand side via the user-provided Jacobian, for linear problems only

5079:    Collective on TS

5081:    Input Arguments:
5082: +  ts - time stepping context
5083: .  t - time at which to evaluate
5084: .  U - state at which to evaluate
5085: .  Udot - time derivative of state vector
5086: -  ctx - context

5088:    Output Arguments:
5089: .  F - left hand side

5091:    Level: intermediate

5093:    Notes:
5094:    The assumption here is that the left hand side is of the form A*Udot (and not A*Udot + B*U). For other cases, the
5095:    user is required to write their own TSComputeIFunction.
5096:    This function is intended to be passed to TSSetIFunction() to evaluate the left hand side for linear problems.
5097:    The matrix (and optionally the evaluation context) should be passed to TSSetIJacobian().

5099:    Note that using this function is NOT equivalent to using TSComputeRHSFunctionLinear() since that solves Udot = A U

5101: .seealso: TSSetIFunction(), TSSetIJacobian(), TSComputeIJacobianConstant(), TSComputeRHSFunctionLinear()
5102: @*/
5103: PetscErrorCode TSComputeIFunctionLinear(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,void *ctx)
5104: {
5106:   Mat            A,B;

5109:   TSGetIJacobian(ts,&A,&B,NULL,NULL);
5110:   TSComputeIJacobian(ts,t,U,Udot,1.0,A,B,PETSC_TRUE);
5111:   MatMult(A,Udot,F);
5112:   return(0);
5113: }

5117: /*@C
5118:    TSComputeIJacobianConstant - Reuses a time-independent for a semi-implicit DAE or ODE

5120:    Collective on TS

5122:    Input Arguments:
5123: +  ts - time stepping context
5124: .  t - time at which to evaluate
5125: .  U - state at which to evaluate
5126: .  Udot - time derivative of state vector
5127: .  shift - shift to apply
5128: -  ctx - context

5130:    Output Arguments:
5131: +  A - pointer to operator
5132: .  B - pointer to preconditioning matrix
5133: -  flg - matrix structure flag

5135:    Level: advanced

5137:    Notes:
5138:    This function is intended to be passed to TSSetIJacobian() to evaluate the Jacobian for linear time-independent problems.

5140:    It is only appropriate for problems of the form

5142: $     M Udot = F(U,t)

5144:   where M is constant and F is non-stiff.  The user must pass M to TSSetIJacobian().  The current implementation only
5145:   works with IMEX time integration methods such as TSROSW and TSARKIMEX, since there is no support for de-constructing
5146:   an implicit operator of the form

5148: $    shift*M + J

5150:   where J is the Jacobian of -F(U).  Support may be added in a future version of PETSc, but for now, the user must store
5151:   a copy of M or reassemble it when requested.

5153: .seealso: TSSetIFunction(), TSSetIJacobian(), TSComputeIFunctionLinear()
5154: @*/
5155: PetscErrorCode TSComputeIJacobianConstant(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat A,Mat B,void *ctx)
5156: {

5160:   MatScale(A, shift / ts->ijacobian.shift);
5161:   ts->ijacobian.shift = shift;
5162:   return(0);
5163: }

5167: /*@
5168:    TSGetEquationType - Gets the type of the equation that TS is solving.

5170:    Not Collective

5172:    Input Parameter:
5173: .  ts - the TS context

5175:    Output Parameter:
5176: .  equation_type - see TSEquationType

5178:    Level: beginner

5180: .keywords: TS, equation type

5182: .seealso: TSSetEquationType(), TSEquationType
5183: @*/
5184: PetscErrorCode  TSGetEquationType(TS ts,TSEquationType *equation_type)
5185: {
5189:   *equation_type = ts->equation_type;
5190:   return(0);
5191: }

5195: /*@
5196:    TSSetEquationType - Sets the type of the equation that TS is solving.

5198:    Not Collective

5200:    Input Parameter:
5201: +  ts - the TS context
5202: -  equation_type - see TSEquationType

5204:    Level: advanced

5206: .keywords: TS, equation type

5208: .seealso: TSGetEquationType(), TSEquationType
5209: @*/
5210: PetscErrorCode  TSSetEquationType(TS ts,TSEquationType equation_type)
5211: {
5214:   ts->equation_type = equation_type;
5215:   return(0);
5216: }

5220: /*@
5221:    TSGetConvergedReason - Gets the reason the TS iteration was stopped.

5223:    Not Collective

5225:    Input Parameter:
5226: .  ts - the TS context

5228:    Output Parameter:
5229: .  reason - negative value indicates diverged, positive value converged, see TSConvergedReason or the
5230:             manual pages for the individual convergence tests for complete lists

5232:    Level: beginner

5234:    Notes:
5235:    Can only be called after the call to TSSolve() is complete.

5237: .keywords: TS, nonlinear, set, convergence, test

5239: .seealso: TSSetConvergenceTest(), TSConvergedReason
5240: @*/
5241: PetscErrorCode  TSGetConvergedReason(TS ts,TSConvergedReason *reason)
5242: {
5246:   *reason = ts->reason;
5247:   return(0);
5248: }

5252: /*@
5253:    TSSetConvergedReason - Sets the reason for handling the convergence of TSSolve.

5255:    Not Collective

5257:    Input Parameter:
5258: +  ts - the TS context
5259: .  reason - negative value indicates diverged, positive value converged, see TSConvergedReason or the
5260:             manual pages for the individual convergence tests for complete lists

5262:    Level: advanced

5264:    Notes:
5265:    Can only be called during TSSolve() is active.

5267: .keywords: TS, nonlinear, set, convergence, test

5269: .seealso: TSConvergedReason
5270: @*/
5271: PetscErrorCode  TSSetConvergedReason(TS ts,TSConvergedReason reason)
5272: {
5275:   ts->reason = reason;
5276:   return(0);
5277: }

5281: /*@
5282:    TSGetSolveTime - Gets the time after a call to TSSolve()

5284:    Not Collective

5286:    Input Parameter:
5287: .  ts - the TS context

5289:    Output Parameter:
5290: .  ftime - the final time. This time corresponds to the final time set with TSSetDuration()

5292:    Level: beginner

5294:    Notes:
5295:    Can only be called after the call to TSSolve() is complete.

5297: .keywords: TS, nonlinear, set, convergence, test

5299: .seealso: TSSetConvergenceTest(), TSConvergedReason
5300: @*/
5301: PetscErrorCode  TSGetSolveTime(TS ts,PetscReal *ftime)
5302: {
5306:   *ftime = ts->solvetime;
5307:   return(0);
5308: }

5312: /*@
5313:    TSGetTotalSteps - Gets the total number of steps done since the last call to TSSetUp() or TSCreate()

5315:    Not Collective

5317:    Input Parameter:
5318: .  ts - the TS context

5320:    Output Parameter:
5321: .  steps - the number of steps

5323:    Level: beginner

5325:    Notes:
5326:    Includes the number of steps for all calls to TSSolve() since TSSetUp() was called

5328: .keywords: TS, nonlinear, set, convergence, test

5330: .seealso: TSSetConvergenceTest(), TSConvergedReason
5331: @*/
5332: PetscErrorCode  TSGetTotalSteps(TS ts,PetscInt *steps)
5333: {
5337:   *steps = ts->total_steps;
5338:   return(0);
5339: }

5343: /*@
5344:    TSGetSNESIterations - Gets the total number of nonlinear iterations
5345:    used by the time integrator.

5347:    Not Collective

5349:    Input Parameter:
5350: .  ts - TS context

5352:    Output Parameter:
5353: .  nits - number of nonlinear iterations

5355:    Notes:
5356:    This counter is reset to zero for each successive call to TSSolve().

5358:    Level: intermediate

5360: .keywords: TS, get, number, nonlinear, iterations

5362: .seealso:  TSGetKSPIterations()
5363: @*/
5364: PetscErrorCode TSGetSNESIterations(TS ts,PetscInt *nits)
5365: {
5369:   *nits = ts->snes_its;
5370:   return(0);
5371: }

5375: /*@
5376:    TSGetKSPIterations - Gets the total number of linear iterations
5377:    used by the time integrator.

5379:    Not Collective

5381:    Input Parameter:
5382: .  ts - TS context

5384:    Output Parameter:
5385: .  lits - number of linear iterations

5387:    Notes:
5388:    This counter is reset to zero for each successive call to TSSolve().

5390:    Level: intermediate

5392: .keywords: TS, get, number, linear, iterations

5394: .seealso:  TSGetSNESIterations(), SNESGetKSPIterations()
5395: @*/
5396: PetscErrorCode TSGetKSPIterations(TS ts,PetscInt *lits)
5397: {
5401:   *lits = ts->ksp_its;
5402:   return(0);
5403: }

5407: /*@
5408:    TSGetStepRejections - Gets the total number of rejected steps.

5410:    Not Collective

5412:    Input Parameter:
5413: .  ts - TS context

5415:    Output Parameter:
5416: .  rejects - number of steps rejected

5418:    Notes:
5419:    This counter is reset to zero for each successive call to TSSolve().

5421:    Level: intermediate

5423: .keywords: TS, get, number

5425: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetSNESFailures(), TSSetMaxSNESFailures(), TSSetErrorIfStepFails()
5426: @*/
5427: PetscErrorCode TSGetStepRejections(TS ts,PetscInt *rejects)
5428: {
5432:   *rejects = ts->reject;
5433:   return(0);
5434: }

5438: /*@
5439:    TSGetSNESFailures - Gets the total number of failed SNES solves

5441:    Not Collective

5443:    Input Parameter:
5444: .  ts - TS context

5446:    Output Parameter:
5447: .  fails - number of failed nonlinear solves

5449:    Notes:
5450:    This counter is reset to zero for each successive call to TSSolve().

5452:    Level: intermediate

5454: .keywords: TS, get, number

5456: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSSetMaxSNESFailures()
5457: @*/
5458: PetscErrorCode TSGetSNESFailures(TS ts,PetscInt *fails)
5459: {
5463:   *fails = ts->num_snes_failures;
5464:   return(0);
5465: }

5469: /*@
5470:    TSSetMaxStepRejections - Sets the maximum number of step rejections before a step fails

5472:    Not Collective

5474:    Input Parameter:
5475: +  ts - TS context
5476: -  rejects - maximum number of rejected steps, pass -1 for unlimited

5478:    Notes:
5479:    The counter is reset to zero for each step

5481:    Options Database Key:
5482:  .  -ts_max_reject - Maximum number of step rejections before a step fails

5484:    Level: intermediate

5486: .keywords: TS, set, maximum, number

5488: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxSNESFailures(), TSGetStepRejections(), TSGetSNESFailures(), TSSetErrorIfStepFails(), TSGetConvergedReason()
5489: @*/
5490: PetscErrorCode TSSetMaxStepRejections(TS ts,PetscInt rejects)
5491: {
5494:   ts->max_reject = rejects;
5495:   return(0);
5496: }

5500: /*@
5501:    TSSetMaxSNESFailures - Sets the maximum number of failed SNES solves

5503:    Not Collective

5505:    Input Parameter:
5506: +  ts - TS context
5507: -  fails - maximum number of failed nonlinear solves, pass -1 for unlimited

5509:    Notes:
5510:    The counter is reset to zero for each successive call to TSSolve().

5512:    Options Database Key:
5513:  .  -ts_max_snes_failures - Maximum number of nonlinear solve failures

5515:    Level: intermediate

5517: .keywords: TS, set, maximum, number

5519: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSGetSNESFailures(), SNESGetConvergedReason(), TSGetConvergedReason()
5520: @*/
5521: PetscErrorCode TSSetMaxSNESFailures(TS ts,PetscInt fails)
5522: {
5525:   ts->max_snes_failures = fails;
5526:   return(0);
5527: }

5531: /*@
5532:    TSSetErrorIfStepFails - Error if no step succeeds

5534:    Not Collective

5536:    Input Parameter:
5537: +  ts - TS context
5538: -  err - PETSC_TRUE to error if no step succeeds, PETSC_FALSE to return without failure

5540:    Options Database Key:
5541:  .  -ts_error_if_step_fails - Error if no step succeeds

5543:    Level: intermediate

5545: .keywords: TS, set, error

5547: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSGetSNESFailures(), TSSetErrorIfStepFails(), TSGetConvergedReason()
5548: @*/
5549: PetscErrorCode TSSetErrorIfStepFails(TS ts,PetscBool err)
5550: {
5553:   ts->errorifstepfailed = err;
5554:   return(0);
5555: }

5559: /*@C
5560:    TSMonitorSolution - Monitors progress of the TS solvers by VecView() for the solution at each timestep. Normally the viewer is a binary file or a PetscDraw object

5562:    Collective on TS

5564:    Input Parameters:
5565: +  ts - the TS context
5566: .  step - current time-step
5567: .  ptime - current time
5568: .  u - current state
5569: -  vf - viewer and its format

5571:    Level: intermediate

5573: .keywords: TS,  vector, monitor, view

5575: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
5576: @*/
5577: PetscErrorCode  TSMonitorSolution(TS ts,PetscInt step,PetscReal ptime,Vec u,PetscViewerAndFormat *vf)
5578: {

5582:   PetscViewerPushFormat(vf->viewer,vf->format);
5583:   VecView(u,vf->viewer);
5584:   PetscViewerPopFormat(vf->viewer);
5585:   return(0);
5586: }

5590: /*@C
5591:    TSMonitorSolutionVTK - Monitors progress of the TS solvers by VecView() for the solution at each timestep.

5593:    Collective on TS

5595:    Input Parameters:
5596: +  ts - the TS context
5597: .  step - current time-step
5598: .  ptime - current time
5599: .  u - current state
5600: -  filenametemplate - string containing a format specifier for the integer time step (e.g. %03D)

5602:    Level: intermediate

5604:    Notes:
5605:    The VTK format does not allow writing multiple time steps in the same file, therefore a different file will be written for each time step.
5606:    These are named according to the file name template.

5608:    This function is normally passed as an argument to TSMonitorSet() along with TSMonitorSolutionVTKDestroy().

5610: .keywords: TS,  vector, monitor, view

5612: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
5613: @*/
5614: PetscErrorCode TSMonitorSolutionVTK(TS ts,PetscInt step,PetscReal ptime,Vec u,void *filenametemplate)
5615: {
5617:   char           filename[PETSC_MAX_PATH_LEN];
5618:   PetscViewer    viewer;

5621:   if (step < 0) return(0); /* -1 indicates interpolated solution */
5622:   PetscSNPrintf(filename,sizeof(filename),(const char*)filenametemplate,step);
5623:   PetscViewerVTKOpen(PetscObjectComm((PetscObject)ts),filename,FILE_MODE_WRITE,&viewer);
5624:   VecView(u,viewer);
5625:   PetscViewerDestroy(&viewer);
5626:   return(0);
5627: }

5631: /*@C
5632:    TSMonitorSolutionVTKDestroy - Destroy context for monitoring

5634:    Collective on TS

5636:    Input Parameters:
5637: .  filenametemplate - string containing a format specifier for the integer time step (e.g. %03D)

5639:    Level: intermediate

5641:    Note:
5642:    This function is normally passed to TSMonitorSet() along with TSMonitorSolutionVTK().

5644: .keywords: TS,  vector, monitor, view

5646: .seealso: TSMonitorSet(), TSMonitorSolutionVTK()
5647: @*/
5648: PetscErrorCode TSMonitorSolutionVTKDestroy(void *filenametemplate)
5649: {

5653:   PetscFree(*(char**)filenametemplate);
5654:   return(0);
5655: }

5659: /*@
5660:    TSGetAdapt - Get the adaptive controller context for the current method

5662:    Collective on TS if controller has not been created yet

5664:    Input Arguments:
5665: .  ts - time stepping context

5667:    Output Arguments:
5668: .  adapt - adaptive controller

5670:    Level: intermediate

5672: .seealso: TSAdapt, TSAdaptSetType(), TSAdaptChoose()
5673: @*/
5674: PetscErrorCode TSGetAdapt(TS ts,TSAdapt *adapt)
5675: {

5681:   if (!ts->adapt) {
5682:     TSAdaptCreate(PetscObjectComm((PetscObject)ts),&ts->adapt);
5683:     PetscLogObjectParent((PetscObject)ts,(PetscObject)ts->adapt);
5684:     PetscObjectIncrementTabLevel((PetscObject)ts->adapt,(PetscObject)ts,1);
5685:   }
5686:   *adapt = ts->adapt;
5687:   return(0);
5688: }

5692: /*@
5693:    TSSetTolerances - Set tolerances for local truncation error when using adaptive controller

5695:    Logically Collective

5697:    Input Arguments:
5698: +  ts - time integration context
5699: .  atol - scalar absolute tolerances, PETSC_DECIDE to leave current value
5700: .  vatol - vector of absolute tolerances or NULL, used in preference to atol if present
5701: .  rtol - scalar relative tolerances, PETSC_DECIDE to leave current value
5702: -  vrtol - vector of relative tolerances or NULL, used in preference to atol if present

5704:    Options Database keys:
5705: +  -ts_rtol <rtol> - relative tolerance for local truncation error
5706: -  -ts_atol <atol> Absolute tolerance for local truncation error

5708:    Notes:
5709:    With PETSc's implicit schemes for DAE problems, the calculation of the local truncation error
5710:    (LTE) includes both the differential and the algebraic variables. If one wants the LTE to be
5711:    computed only for the differential or the algebraic part then this can be done using the vector of
5712:    tolerances vatol. For example, by setting the tolerance vector with the desired tolerance for the 
5713:    differential part and infinity for the algebraic part, the LTE calculation will include only the
5714:    differential variables.

5716:    Level: beginner

5718: .seealso: TS, TSAdapt, TSVecNormWRMS(), TSGetTolerances()
5719: @*/
5720: PetscErrorCode TSSetTolerances(TS ts,PetscReal atol,Vec vatol,PetscReal rtol,Vec vrtol)
5721: {

5725:   if (atol != PETSC_DECIDE && atol != PETSC_DEFAULT) ts->atol = atol;
5726:   if (vatol) {
5727:     PetscObjectReference((PetscObject)vatol);
5728:     VecDestroy(&ts->vatol);
5729:     ts->vatol = vatol;
5730:   }
5731:   if (rtol != PETSC_DECIDE && rtol != PETSC_DEFAULT) ts->rtol = rtol;
5732:   if (vrtol) {
5733:     PetscObjectReference((PetscObject)vrtol);
5734:     VecDestroy(&ts->vrtol);
5735:     ts->vrtol = vrtol;
5736:   }
5737:   return(0);
5738: }

5742: /*@
5743:    TSGetTolerances - Get tolerances for local truncation error when using adaptive controller

5745:    Logically Collective

5747:    Input Arguments:
5748: .  ts - time integration context

5750:    Output Arguments:
5751: +  atol - scalar absolute tolerances, NULL to ignore
5752: .  vatol - vector of absolute tolerances, NULL to ignore
5753: .  rtol - scalar relative tolerances, NULL to ignore
5754: -  vrtol - vector of relative tolerances, NULL to ignore

5756:    Level: beginner

5758: .seealso: TS, TSAdapt, TSVecNormWRMS(), TSSetTolerances()
5759: @*/
5760: PetscErrorCode TSGetTolerances(TS ts,PetscReal *atol,Vec *vatol,PetscReal *rtol,Vec *vrtol)
5761: {
5763:   if (atol)  *atol  = ts->atol;
5764:   if (vatol) *vatol = ts->vatol;
5765:   if (rtol)  *rtol  = ts->rtol;
5766:   if (vrtol) *vrtol = ts->vrtol;
5767:   return(0);
5768: }

5772: /*@
5773:    TSErrorWeightedNorm2 - compute a weighted 2-norm of the difference between two state vectors

5775:    Collective on TS

5777:    Input Arguments:
5778: +  ts - time stepping context
5779: .  U - state vector, usually ts->vec_sol
5780: -  Y - state vector to be compared to U

5782:    Output Arguments:
5783: .  norm - weighted norm, a value of 1.0 is considered small

5785:    Level: developer

5787: .seealso: TSErrorWeightedNorm(), TSErrorWeightedNormInfinity()
5788: @*/
5789: PetscErrorCode TSErrorWeightedNorm2(TS ts,Vec U,Vec Y,PetscReal *norm)
5790: {
5791:   PetscErrorCode    ierr;
5792:   PetscInt          i,n,N,rstart;
5793:   const PetscScalar *u,*y;
5794:   PetscReal         sum,gsum;
5795:   PetscReal         tol;

5805:   if (U == Y) SETERRQ(PetscObjectComm((PetscObject)U),PETSC_ERR_ARG_IDN,"U and Y cannot be the same vector");

5807:   VecGetSize(U,&N);
5808:   VecGetLocalSize(U,&n);
5809:   VecGetOwnershipRange(U,&rstart,NULL);
5810:   VecGetArrayRead(U,&u);
5811:   VecGetArrayRead(Y,&y);
5812:   sum  = 0.;
5813:   if (ts->vatol && ts->vrtol) {
5814:     const PetscScalar *atol,*rtol;
5815:     VecGetArrayRead(ts->vatol,&atol);
5816:     VecGetArrayRead(ts->vrtol,&rtol);
5817:     for (i=0; i<n; i++) {
5818:       tol = PetscRealPart(atol[i]) + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5819:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
5820:     }
5821:     VecRestoreArrayRead(ts->vatol,&atol);
5822:     VecRestoreArrayRead(ts->vrtol,&rtol);
5823:   } else if (ts->vatol) {       /* vector atol, scalar rtol */
5824:     const PetscScalar *atol;
5825:     VecGetArrayRead(ts->vatol,&atol);
5826:     for (i=0; i<n; i++) {
5827:       tol = PetscRealPart(atol[i]) + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5828:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
5829:     }
5830:     VecRestoreArrayRead(ts->vatol,&atol);
5831:   } else if (ts->vrtol) {       /* scalar atol, vector rtol */
5832:     const PetscScalar *rtol;
5833:     VecGetArrayRead(ts->vrtol,&rtol);
5834:     for (i=0; i<n; i++) {
5835:       tol = ts->atol + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5836:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
5837:     }
5838:     VecRestoreArrayRead(ts->vrtol,&rtol);
5839:   } else {                      /* scalar atol, scalar rtol */
5840:     for (i=0; i<n; i++) {
5841:       tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5842:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
5843:     }
5844:   }
5845:   VecRestoreArrayRead(U,&u);
5846:   VecRestoreArrayRead(Y,&y);

5848:   MPIU_Allreduce(&sum,&gsum,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));
5849:   *norm = PetscSqrtReal(gsum / N);

5851:   if (PetscIsInfOrNanScalar(*norm)) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_FP,"Infinite or not-a-number generated in norm");
5852:   return(0);
5853: }

5857: /*@
5858:    TSErrorWeightedNormInfinity - compute a weighted infinity-norm of the difference between two state vectors

5860:    Collective on TS

5862:    Input Arguments:
5863: +  ts - time stepping context
5864: .  U - state vector, usually ts->vec_sol
5865: -  Y - state vector to be compared to U

5867:    Output Arguments:
5868: .  norm - weighted norm, a value of 1.0 is considered small

5870:    Level: developer

5872: .seealso: TSErrorWeightedNorm(), TSErrorWeightedNorm2()
5873: @*/
5874: PetscErrorCode TSErrorWeightedNormInfinity(TS ts,Vec U,Vec Y,PetscReal *norm)
5875: {
5876:   PetscErrorCode    ierr;
5877:   PetscInt          i,n,N,rstart,k;
5878:   const PetscScalar *u,*y;
5879:   PetscReal         max,gmax;
5880:   PetscReal         tol;

5890:   if (U == Y) SETERRQ(PetscObjectComm((PetscObject)U),PETSC_ERR_ARG_IDN,"U and Y cannot be the same vector");

5892:   VecGetSize(U,&N);
5893:   VecGetLocalSize(U,&n);
5894:   VecGetOwnershipRange(U,&rstart,NULL);
5895:   VecGetArrayRead(U,&u);
5896:   VecGetArrayRead(Y,&y);
5897:   if (ts->vatol && ts->vrtol) {
5898:     const PetscScalar *atol,*rtol;
5899:     VecGetArrayRead(ts->vatol,&atol);
5900:     VecGetArrayRead(ts->vrtol,&rtol);
5901:     k = 0;
5902:     tol = PetscRealPart(atol[k]) + PetscRealPart(rtol[k]) * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
5903:     max = PetscAbsScalar(y[k] - u[k]) / tol;
5904:     for (i=1; i<n; i++) {
5905:       tol = PetscRealPart(atol[i]) + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5906:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
5907:     }
5908:     VecRestoreArrayRead(ts->vatol,&atol);
5909:     VecRestoreArrayRead(ts->vrtol,&rtol);
5910:   } else if (ts->vatol) {       /* vector atol, scalar rtol */
5911:     const PetscScalar *atol;
5912:     VecGetArrayRead(ts->vatol,&atol);
5913:     k = 0;
5914:     tol = PetscRealPart(atol[k]) + ts->rtol * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
5915:     max = PetscAbsScalar(y[k] - u[k]) / tol;
5916:     for (i=1; i<n; i++) {
5917:       tol = PetscRealPart(atol[i]) + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5918:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
5919:     }
5920:     VecRestoreArrayRead(ts->vatol,&atol);
5921:   } else if (ts->vrtol) {       /* scalar atol, vector rtol */
5922:     const PetscScalar *rtol;
5923:     VecGetArrayRead(ts->vrtol,&rtol);
5924:     k = 0;
5925:     tol = ts->atol + PetscRealPart(rtol[k]) * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
5926:     max = PetscAbsScalar(y[k] - u[k]) / tol;
5927:     for (i=1; i<n; i++) {
5928:       tol = ts->atol + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5929:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
5930:     }
5931:     VecRestoreArrayRead(ts->vrtol,&rtol);
5932:   } else {                      /* scalar atol, scalar rtol */
5933:     k = 0;
5934:     tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
5935:     max = PetscAbsScalar(y[k] - u[k]) / tol;
5936:     for (i=1; i<n; i++) {
5937:       tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
5938:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
5939:     }
5940:   }
5941:   VecRestoreArrayRead(U,&u);
5942:   VecRestoreArrayRead(Y,&y);

5944:   MPIU_Allreduce(&max,&gmax,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));
5945:   *norm = gmax;

5947:   if (PetscIsInfOrNanScalar(*norm)) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_FP,"Infinite or not-a-number generated in norm");
5948:   return(0);
5949: }

5953: /*@
5954:    TSErrorWeightedNorm - compute a weighted norm of the difference between two state vectors

5956:    Collective on TS

5958:    Input Arguments:
5959: +  ts - time stepping context
5960: .  U - state vector, usually ts->vec_sol
5961: .  Y - state vector to be compared to U
5962: -  wnormtype - norm type, either NORM_2 or NORM_INFINITY

5964:    Output Arguments:
5965: .  norm - weighted norm, a value of 1.0 is considered small


5968:    Options Database Keys:
5969: .  -ts_adapt_wnormtype <wnormtype> - 2, INFINITY

5971:    Level: developer

5973: .seealso: TSErrorWeightedNormInfinity(), TSErrorWeightedNorm2()
5974: @*/
5975: PetscErrorCode TSErrorWeightedNorm(TS ts,Vec U,Vec Y,NormType wnormtype,PetscReal *norm)
5976: {

5980:   if (wnormtype == NORM_2) {
5981:     TSErrorWeightedNorm2(ts,U,Y,norm);
5982:   } else if(wnormtype == NORM_INFINITY) {
5983:     TSErrorWeightedNormInfinity(ts,U,Y,norm);
5984:   } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for norm type %s",NormTypes[wnormtype]);
5985:   return(0);
5986: }

5990: /*@
5991:    TSSetCFLTimeLocal - Set the local CFL constraint relative to forward Euler

5993:    Logically Collective on TS

5995:    Input Arguments:
5996: +  ts - time stepping context
5997: -  cfltime - maximum stable time step if using forward Euler (value can be different on each process)

5999:    Note:
6000:    After calling this function, the global CFL time can be obtained by calling TSGetCFLTime()

6002:    Level: intermediate

6004: .seealso: TSGetCFLTime(), TSADAPTCFL
6005: @*/
6006: PetscErrorCode TSSetCFLTimeLocal(TS ts,PetscReal cfltime)
6007: {
6010:   ts->cfltime_local = cfltime;
6011:   ts->cfltime       = -1.;
6012:   return(0);
6013: }

6017: /*@
6018:    TSGetCFLTime - Get the maximum stable time step according to CFL criteria applied to forward Euler

6020:    Collective on TS

6022:    Input Arguments:
6023: .  ts - time stepping context

6025:    Output Arguments:
6026: .  cfltime - maximum stable time step for forward Euler

6028:    Level: advanced

6030: .seealso: TSSetCFLTimeLocal()
6031: @*/
6032: PetscErrorCode TSGetCFLTime(TS ts,PetscReal *cfltime)
6033: {

6037:   if (ts->cfltime < 0) {
6038:     MPIU_Allreduce(&ts->cfltime_local,&ts->cfltime,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));
6039:   }
6040:   *cfltime = ts->cfltime;
6041:   return(0);
6042: }

6046: /*@
6047:    TSVISetVariableBounds - Sets the lower and upper bounds for the solution vector. xl <= x <= xu

6049:    Input Parameters:
6050: .  ts   - the TS context.
6051: .  xl   - lower bound.
6052: .  xu   - upper bound.

6054:    Notes:
6055:    If this routine is not called then the lower and upper bounds are set to
6056:    PETSC_NINFINITY and PETSC_INFINITY respectively during SNESSetUp().

6058:    Level: advanced

6060: @*/
6061: PetscErrorCode TSVISetVariableBounds(TS ts, Vec xl, Vec xu)
6062: {
6064:   SNES           snes;

6067:   TSGetSNES(ts,&snes);
6068:   SNESVISetVariableBounds(snes,xl,xu);
6069:   return(0);
6070: }

6072: #if defined(PETSC_HAVE_MATLAB_ENGINE)
6073: #include <mex.h>

6075: typedef struct {char *funcname; mxArray *ctx;} TSMatlabContext;

6079: /*
6080:    TSComputeFunction_Matlab - Calls the function that has been set with
6081:                          TSSetFunctionMatlab().

6083:    Collective on TS

6085:    Input Parameters:
6086: +  snes - the TS context
6087: -  u - input vector

6089:    Output Parameter:
6090: .  y - function vector, as set by TSSetFunction()

6092:    Notes:
6093:    TSComputeFunction() is typically used within nonlinear solvers
6094:    implementations, so most users would not generally call this routine
6095:    themselves.

6097:    Level: developer

6099: .keywords: TS, nonlinear, compute, function

6101: .seealso: TSSetFunction(), TSGetFunction()
6102: */
6103: PetscErrorCode  TSComputeFunction_Matlab(TS snes,PetscReal time,Vec u,Vec udot,Vec y, void *ctx)
6104: {
6105:   PetscErrorCode  ierr;
6106:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
6107:   int             nlhs  = 1,nrhs = 7;
6108:   mxArray         *plhs[1],*prhs[7];
6109:   long long int   lx = 0,lxdot = 0,ly = 0,ls = 0;


6119:   PetscMemcpy(&ls,&snes,sizeof(snes));
6120:   PetscMemcpy(&lx,&u,sizeof(u));
6121:   PetscMemcpy(&lxdot,&udot,sizeof(udot));
6122:   PetscMemcpy(&ly,&y,sizeof(u));

6124:   prhs[0] =  mxCreateDoubleScalar((double)ls);
6125:   prhs[1] =  mxCreateDoubleScalar(time);
6126:   prhs[2] =  mxCreateDoubleScalar((double)lx);
6127:   prhs[3] =  mxCreateDoubleScalar((double)lxdot);
6128:   prhs[4] =  mxCreateDoubleScalar((double)ly);
6129:   prhs[5] =  mxCreateString(sctx->funcname);
6130:   prhs[6] =  sctx->ctx;
6131:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSComputeFunctionInternal");
6132:    mxGetScalar(plhs[0]);
6133:   mxDestroyArray(prhs[0]);
6134:   mxDestroyArray(prhs[1]);
6135:   mxDestroyArray(prhs[2]);
6136:   mxDestroyArray(prhs[3]);
6137:   mxDestroyArray(prhs[4]);
6138:   mxDestroyArray(prhs[5]);
6139:   mxDestroyArray(plhs[0]);
6140:   return(0);
6141: }


6146: /*
6147:    TSSetFunctionMatlab - Sets the function evaluation routine and function
6148:    vector for use by the TS routines in solving ODEs
6149:    equations from MATLAB. Here the function is a string containing the name of a MATLAB function

6151:    Logically Collective on TS

6153:    Input Parameters:
6154: +  ts - the TS context
6155: -  func - function evaluation routine

6157:    Calling sequence of func:
6158: $    func (TS ts,PetscReal time,Vec u,Vec udot,Vec f,void *ctx);

6160:    Level: beginner

6162: .keywords: TS, nonlinear, set, function

6164: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
6165: */
6166: PetscErrorCode  TSSetFunctionMatlab(TS ts,const char *func,mxArray *ctx)
6167: {
6168:   PetscErrorCode  ierr;
6169:   TSMatlabContext *sctx;

6172:   /* currently sctx is memory bleed */
6173:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
6174:   PetscStrallocpy(func,&sctx->funcname);
6175:   /*
6176:      This should work, but it doesn't
6177:   sctx->ctx = ctx;
6178:   mexMakeArrayPersistent(sctx->ctx);
6179:   */
6180:   sctx->ctx = mxDuplicateArray(ctx);

6182:   TSSetIFunction(ts,NULL,TSComputeFunction_Matlab,sctx);
6183:   return(0);
6184: }

6188: /*
6189:    TSComputeJacobian_Matlab - Calls the function that has been set with
6190:                          TSSetJacobianMatlab().

6192:    Collective on TS

6194:    Input Parameters:
6195: +  ts - the TS context
6196: .  u - input vector
6197: .  A, B - the matrices
6198: -  ctx - user context

6200:    Level: developer

6202: .keywords: TS, nonlinear, compute, function

6204: .seealso: TSSetFunction(), TSGetFunction()
6205: @*/
6206: PetscErrorCode  TSComputeJacobian_Matlab(TS ts,PetscReal time,Vec u,Vec udot,PetscReal shift,Mat A,Mat B,void *ctx)
6207: {
6208:   PetscErrorCode  ierr;
6209:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
6210:   int             nlhs  = 2,nrhs = 9;
6211:   mxArray         *plhs[2],*prhs[9];
6212:   long long int   lx = 0,lxdot = 0,lA = 0,ls = 0, lB = 0;


6218:   /* call Matlab function in ctx with arguments u and y */

6220:   PetscMemcpy(&ls,&ts,sizeof(ts));
6221:   PetscMemcpy(&lx,&u,sizeof(u));
6222:   PetscMemcpy(&lxdot,&udot,sizeof(u));
6223:   PetscMemcpy(&lA,A,sizeof(u));
6224:   PetscMemcpy(&lB,B,sizeof(u));

6226:   prhs[0] =  mxCreateDoubleScalar((double)ls);
6227:   prhs[1] =  mxCreateDoubleScalar((double)time);
6228:   prhs[2] =  mxCreateDoubleScalar((double)lx);
6229:   prhs[3] =  mxCreateDoubleScalar((double)lxdot);
6230:   prhs[4] =  mxCreateDoubleScalar((double)shift);
6231:   prhs[5] =  mxCreateDoubleScalar((double)lA);
6232:   prhs[6] =  mxCreateDoubleScalar((double)lB);
6233:   prhs[7] =  mxCreateString(sctx->funcname);
6234:   prhs[8] =  sctx->ctx;
6235:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSComputeJacobianInternal");
6236:    mxGetScalar(plhs[0]);
6237:   mxDestroyArray(prhs[0]);
6238:   mxDestroyArray(prhs[1]);
6239:   mxDestroyArray(prhs[2]);
6240:   mxDestroyArray(prhs[3]);
6241:   mxDestroyArray(prhs[4]);
6242:   mxDestroyArray(prhs[5]);
6243:   mxDestroyArray(prhs[6]);
6244:   mxDestroyArray(prhs[7]);
6245:   mxDestroyArray(plhs[0]);
6246:   mxDestroyArray(plhs[1]);
6247:   return(0);
6248: }


6253: /*
6254:    TSSetJacobianMatlab - Sets the Jacobian function evaluation routine and two empty Jacobian matrices
6255:    vector for use by the TS routines in solving ODEs from MATLAB. Here the function is a string containing the name of a MATLAB function

6257:    Logically Collective on TS

6259:    Input Parameters:
6260: +  ts - the TS context
6261: .  A,B - Jacobian matrices
6262: .  func - function evaluation routine
6263: -  ctx - user context

6265:    Calling sequence of func:
6266: $    flag = func (TS ts,PetscReal time,Vec u,Vec udot,Mat A,Mat B,void *ctx);


6269:    Level: developer

6271: .keywords: TS, nonlinear, set, function

6273: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
6274: */
6275: PetscErrorCode  TSSetJacobianMatlab(TS ts,Mat A,Mat B,const char *func,mxArray *ctx)
6276: {
6277:   PetscErrorCode  ierr;
6278:   TSMatlabContext *sctx;

6281:   /* currently sctx is memory bleed */
6282:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
6283:   PetscStrallocpy(func,&sctx->funcname);
6284:   /*
6285:      This should work, but it doesn't
6286:   sctx->ctx = ctx;
6287:   mexMakeArrayPersistent(sctx->ctx);
6288:   */
6289:   sctx->ctx = mxDuplicateArray(ctx);

6291:   TSSetIJacobian(ts,A,B,TSComputeJacobian_Matlab,sctx);
6292:   return(0);
6293: }

6297: /*
6298:    TSMonitor_Matlab - Calls the function that has been set with TSMonitorSetMatlab().

6300:    Collective on TS

6302: .seealso: TSSetFunction(), TSGetFunction()
6303: @*/
6304: PetscErrorCode  TSMonitor_Matlab(TS ts,PetscInt it, PetscReal time,Vec u, void *ctx)
6305: {
6306:   PetscErrorCode  ierr;
6307:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
6308:   int             nlhs  = 1,nrhs = 6;
6309:   mxArray         *plhs[1],*prhs[6];
6310:   long long int   lx = 0,ls = 0;


6316:   PetscMemcpy(&ls,&ts,sizeof(ts));
6317:   PetscMemcpy(&lx,&u,sizeof(u));

6319:   prhs[0] =  mxCreateDoubleScalar((double)ls);
6320:   prhs[1] =  mxCreateDoubleScalar((double)it);
6321:   prhs[2] =  mxCreateDoubleScalar((double)time);
6322:   prhs[3] =  mxCreateDoubleScalar((double)lx);
6323:   prhs[4] =  mxCreateString(sctx->funcname);
6324:   prhs[5] =  sctx->ctx;
6325:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSMonitorInternal");
6326:    mxGetScalar(plhs[0]);
6327:   mxDestroyArray(prhs[0]);
6328:   mxDestroyArray(prhs[1]);
6329:   mxDestroyArray(prhs[2]);
6330:   mxDestroyArray(prhs[3]);
6331:   mxDestroyArray(prhs[4]);
6332:   mxDestroyArray(plhs[0]);
6333:   return(0);
6334: }


6339: /*
6340:    TSMonitorSetMatlab - Sets the monitor function from Matlab

6342:    Level: developer

6344: .keywords: TS, nonlinear, set, function

6346: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
6347: */
6348: PetscErrorCode  TSMonitorSetMatlab(TS ts,const char *func,mxArray *ctx)
6349: {
6350:   PetscErrorCode  ierr;
6351:   TSMatlabContext *sctx;

6354:   /* currently sctx is memory bleed */
6355:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
6356:   PetscStrallocpy(func,&sctx->funcname);
6357:   /*
6358:      This should work, but it doesn't
6359:   sctx->ctx = ctx;
6360:   mexMakeArrayPersistent(sctx->ctx);
6361:   */
6362:   sctx->ctx = mxDuplicateArray(ctx);

6364:   TSMonitorSet(ts,TSMonitor_Matlab,sctx,NULL);
6365:   return(0);
6366: }
6367: #endif

6371: /*@C
6372:    TSMonitorLGSolution - Monitors progress of the TS solvers by plotting each component of the solution vector
6373:        in a time based line graph

6375:    Collective on TS

6377:    Input Parameters:
6378: +  ts - the TS context
6379: .  step - current time-step
6380: .  ptime - current time
6381: .  u - current solution
6382: -  dctx - the TSMonitorLGCtx object that contains all the options for the monitoring, this is created with TSMonitorLGCtxCreate()

6384:    Options Database:
6385: .   -ts_monitor_lg_solution_variables

6387:    Level: intermediate

6389:    Notes: Each process in a parallel run displays its component solutions in a separate window

6391: .keywords: TS,  vector, monitor, view

6393: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGCtxCreate(), TSMonitorLGCtxSetVariableNames(), TSMonitorLGCtxGetVariableNames(),
6394:            TSMonitorLGSetVariableNames(), TSMonitorLGGetVariableNames(), TSMonitorLGSetDisplayVariables(), TSMonitorLGCtxSetDisplayVariables(),
6395:            TSMonitorLGCtxSetTransform(), TSMonitorLGSetTransform(), TSMonitorLGError(), TSMonitorLGSNESIterations(), TSMonitorLGKSPIterations(),
6396:            TSMonitorEnvelopeCtxCreate(), TSMonitorEnvelopeGetBounds(), TSMonitorEnvelopeCtxDestroy(), TSMonitorEnvelop()
6397: @*/
6398: PetscErrorCode  TSMonitorLGSolution(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dctx)
6399: {
6400:   PetscErrorCode    ierr;
6401:   TSMonitorLGCtx    ctx = (TSMonitorLGCtx)dctx;
6402:   const PetscScalar *yy;
6403:   Vec               v;

6406:   if (step < 0) return(0); /* -1 indicates interpolated solution */
6407:   if (!step) {
6408:     PetscDrawAxis axis;
6409:     PetscInt      dim;
6410:     PetscDrawLGGetAxis(ctx->lg,&axis);
6411:     PetscDrawAxisSetLabels(axis,"Solution as function of time","Time","Solution");
6412:     if (ctx->names && !ctx->displaynames) {
6413:       char      **displaynames;
6414:       PetscBool flg;
6415:       VecGetLocalSize(u,&dim);
6416:       PetscMalloc((dim+1)*sizeof(char*),&displaynames);
6417:       PetscMemzero(displaynames,(dim+1)*sizeof(char*));
6418:       PetscOptionsGetStringArray(((PetscObject)ts)->options,((PetscObject)ts)->prefix,"-ts_monitor_lg_solution_variables",displaynames,&dim,&flg);
6419:       if (flg) {
6420:         TSMonitorLGCtxSetDisplayVariables(ctx,(const char *const *)displaynames);
6421:       }
6422:       PetscStrArrayDestroy(&displaynames);
6423:     }
6424:     if (ctx->displaynames) {
6425:       PetscDrawLGSetDimension(ctx->lg,ctx->ndisplayvariables);
6426:       PetscDrawLGSetLegend(ctx->lg,(const char *const *)ctx->displaynames);
6427:     } else if (ctx->names) {
6428:       VecGetLocalSize(u,&dim);
6429:       PetscDrawLGSetDimension(ctx->lg,dim);
6430:       PetscDrawLGSetLegend(ctx->lg,(const char *const *)ctx->names);
6431:     } else {
6432:       VecGetLocalSize(u,&dim);
6433:       PetscDrawLGSetDimension(ctx->lg,dim);
6434:     }
6435:     PetscDrawLGReset(ctx->lg);
6436:   }

6438:   if (!ctx->transform) v = u;
6439:   else {(*ctx->transform)(ctx->transformctx,u,&v);}
6440:   VecGetArrayRead(v,&yy);
6441:   if (ctx->displaynames) {
6442:     PetscInt i;
6443:     for (i=0; i<ctx->ndisplayvariables; i++)
6444:       ctx->displayvalues[i] = PetscRealPart(yy[ctx->displayvariables[i]]);
6445:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,ctx->displayvalues);
6446:   } else {
6447: #if defined(PETSC_USE_COMPLEX)
6448:     PetscInt  i,n;
6449:     PetscReal *yreal;
6450:     VecGetLocalSize(v,&n);
6451:     PetscMalloc1(n,&yreal);
6452:     for (i=0; i<n; i++) yreal[i] = PetscRealPart(yy[i]);
6453:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yreal);
6454:     PetscFree(yreal);
6455: #else
6456:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yy);
6457: #endif
6458:   }
6459:   VecRestoreArrayRead(v,&yy);
6460:   if (ctx->transform) {VecDestroy(&v);}

6462:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
6463:     PetscDrawLGDraw(ctx->lg);
6464:     PetscDrawLGSave(ctx->lg);
6465:   }
6466:   return(0);
6467: }


6472: /*@C
6473:    TSMonitorLGSetVariableNames - Sets the name of each component in the solution vector so that it may be displayed in the plot

6475:    Collective on TS

6477:    Input Parameters:
6478: +  ts - the TS context
6479: -  names - the names of the components, final string must be NULL

6481:    Level: intermediate

6483:    Notes: If the TS object does not have a TSMonitorLGCtx associated with it then this function is ignored

6485: .keywords: TS,  vector, monitor, view

6487: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables(), TSMonitorLGCtxSetVariableNames()
6488: @*/
6489: PetscErrorCode  TSMonitorLGSetVariableNames(TS ts,const char * const *names)
6490: {
6491:   PetscErrorCode    ierr;
6492:   PetscInt          i;

6495:   for (i=0; i<ts->numbermonitors; i++) {
6496:     if (ts->monitor[i] == TSMonitorLGSolution) {
6497:       TSMonitorLGCtxSetVariableNames((TSMonitorLGCtx)ts->monitorcontext[i],names);
6498:       break;
6499:     }
6500:   }
6501:   return(0);
6502: }

6506: /*@C
6507:    TSMonitorLGCtxSetVariableNames - Sets the name of each component in the solution vector so that it may be displayed in the plot

6509:    Collective on TS

6511:    Input Parameters:
6512: +  ts - the TS context
6513: -  names - the names of the components, final string must be NULL

6515:    Level: intermediate

6517: .keywords: TS,  vector, monitor, view

6519: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables(), TSMonitorLGSetVariableNames()
6520: @*/
6521: PetscErrorCode  TSMonitorLGCtxSetVariableNames(TSMonitorLGCtx ctx,const char * const *names)
6522: {
6523:   PetscErrorCode    ierr;

6526:   PetscStrArrayDestroy(&ctx->names);
6527:   PetscStrArrayallocpy(names,&ctx->names);
6528:   return(0);
6529: }

6533: /*@C
6534:    TSMonitorLGGetVariableNames - Gets the name of each component in the solution vector so that it may be displayed in the plot

6536:    Collective on TS

6538:    Input Parameter:
6539: .  ts - the TS context

6541:    Output Parameter:
6542: .  names - the names of the components, final string must be NULL

6544:    Level: intermediate

6546:    Notes: If the TS object does not have a TSMonitorLGCtx associated with it then this function is ignored

6548: .keywords: TS,  vector, monitor, view

6550: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables()
6551: @*/
6552: PetscErrorCode  TSMonitorLGGetVariableNames(TS ts,const char *const **names)
6553: {
6554:   PetscInt       i;

6557:   *names = NULL;
6558:   for (i=0; i<ts->numbermonitors; i++) {
6559:     if (ts->monitor[i] == TSMonitorLGSolution) {
6560:       TSMonitorLGCtx  ctx = (TSMonitorLGCtx) ts->monitorcontext[i];
6561:       *names = (const char *const *)ctx->names;
6562:       break;
6563:     }
6564:   }
6565:   return(0);
6566: }

6570: /*@C
6571:    TSMonitorLGCtxSetDisplayVariables - Sets the variables that are to be display in the monitor

6573:    Collective on TS

6575:    Input Parameters:
6576: +  ctx - the TSMonitorLG context
6577: .  displaynames - the names of the components, final string must be NULL

6579:    Level: intermediate

6581: .keywords: TS,  vector, monitor, view

6583: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames()
6584: @*/
6585: PetscErrorCode  TSMonitorLGCtxSetDisplayVariables(TSMonitorLGCtx ctx,const char * const *displaynames)
6586: {
6587:   PetscInt          j = 0,k;
6588:   PetscErrorCode    ierr;

6591:   if (!ctx->names) return(0);
6592:   PetscStrArrayDestroy(&ctx->displaynames);
6593:   PetscStrArrayallocpy(displaynames,&ctx->displaynames);
6594:   while (displaynames[j]) j++;
6595:   ctx->ndisplayvariables = j;
6596:   PetscMalloc1(ctx->ndisplayvariables,&ctx->displayvariables);
6597:   PetscMalloc1(ctx->ndisplayvariables,&ctx->displayvalues);
6598:   j = 0;
6599:   while (displaynames[j]) {
6600:     k = 0;
6601:     while (ctx->names[k]) {
6602:       PetscBool flg;
6603:       PetscStrcmp(displaynames[j],ctx->names[k],&flg);
6604:       if (flg) {
6605:         ctx->displayvariables[j] = k;
6606:         break;
6607:       }
6608:       k++;
6609:     }
6610:     j++;
6611:   }
6612:   return(0);
6613: }


6618: /*@C
6619:    TSMonitorLGSetDisplayVariables - Sets the variables that are to be display in the monitor

6621:    Collective on TS

6623:    Input Parameters:
6624: +  ts - the TS context
6625: .  displaynames - the names of the components, final string must be NULL

6627:    Notes: If the TS object does not have a TSMonitorLGCtx associated with it then this function is ignored

6629:    Level: intermediate

6631: .keywords: TS,  vector, monitor, view

6633: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames()
6634: @*/
6635: PetscErrorCode  TSMonitorLGSetDisplayVariables(TS ts,const char * const *displaynames)
6636: {
6637:   PetscInt          i;
6638:   PetscErrorCode    ierr;

6641:   for (i=0; i<ts->numbermonitors; i++) {
6642:     if (ts->monitor[i] == TSMonitorLGSolution) {
6643:       TSMonitorLGCtxSetDisplayVariables((TSMonitorLGCtx)ts->monitorcontext[i],displaynames);
6644:       break;
6645:     }
6646:   }
6647:   return(0);
6648: }

6652: /*@C
6653:    TSMonitorLGSetTransform - Solution vector will be transformed by provided function before being displayed

6655:    Collective on TS

6657:    Input Parameters:
6658: +  ts - the TS context
6659: .  transform - the transform function
6660: .  destroy - function to destroy the optional context
6661: -  ctx - optional context used by transform function

6663:    Notes: If the TS object does not have a TSMonitorLGCtx associated with it then this function is ignored

6665:    Level: intermediate

6667: .keywords: TS,  vector, monitor, view

6669: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames(), TSMonitorLGCtxSetTransform()
6670: @*/
6671: PetscErrorCode  TSMonitorLGSetTransform(TS ts,PetscErrorCode (*transform)(void*,Vec,Vec*),PetscErrorCode (*destroy)(void*),void *tctx)
6672: {
6673:   PetscInt          i;
6674:   PetscErrorCode    ierr;

6677:   for (i=0; i<ts->numbermonitors; i++) {
6678:     if (ts->monitor[i] == TSMonitorLGSolution) {
6679:       TSMonitorLGCtxSetTransform((TSMonitorLGCtx)ts->monitorcontext[i],transform,destroy,tctx);
6680:     }
6681:   }
6682:   return(0);
6683: }

6687: /*@C
6688:    TSMonitorLGCtxSetTransform - Solution vector will be transformed by provided function before being displayed

6690:    Collective on TSLGCtx

6692:    Input Parameters:
6693: +  ts - the TS context
6694: .  transform - the transform function
6695: .  destroy - function to destroy the optional context
6696: -  ctx - optional context used by transform function

6698:    Level: intermediate

6700: .keywords: TS,  vector, monitor, view

6702: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames(), TSMonitorLGSetTransform()
6703: @*/
6704: PetscErrorCode  TSMonitorLGCtxSetTransform(TSMonitorLGCtx ctx,PetscErrorCode (*transform)(void*,Vec,Vec*),PetscErrorCode (*destroy)(void*),void *tctx)
6705: {
6707:   ctx->transform    = transform;
6708:   ctx->transformdestroy = destroy;
6709:   ctx->transformctx = tctx;
6710:   return(0);
6711: }

6715: /*@C
6716:    TSMonitorLGError - Monitors progress of the TS solvers by plotting each component of the solution vector
6717:        in a time based line graph

6719:    Collective on TS

6721:    Input Parameters:
6722: +  ts - the TS context
6723: .  step - current time-step
6724: .  ptime - current time
6725: .  u - current solution
6726: -  dctx - TSMonitorLGCtx object created with TSMonitorLGCtxCreate()

6728:    Level: intermediate

6730:    Notes: Each process in a parallel run displays its component errors in a separate window

6732:    The user must provide the solution using TSSetSolutionFunction() to use this monitor.

6734:    Options Database Keys:
6735: .  -ts_monitor_lg_error - create a graphical monitor of error history

6737: .keywords: TS,  vector, monitor, view

6739: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSSetSolutionFunction()
6740: @*/
6741: PetscErrorCode  TSMonitorLGError(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
6742: {
6743:   PetscErrorCode    ierr;
6744:   TSMonitorLGCtx    ctx = (TSMonitorLGCtx)dummy;
6745:   const PetscScalar *yy;
6746:   Vec               y;

6749:   if (!step) {
6750:     PetscDrawAxis axis;
6751:     PetscInt      dim;
6752:     PetscDrawLGGetAxis(ctx->lg,&axis);
6753:     PetscDrawAxisSetLabels(axis,"Error in solution as function of time","Time","Solution");
6754:     VecGetLocalSize(u,&dim);
6755:     PetscDrawLGSetDimension(ctx->lg,dim);
6756:     PetscDrawLGReset(ctx->lg);
6757:   }
6758:   VecDuplicate(u,&y);
6759:   TSComputeSolutionFunction(ts,ptime,y);
6760:   VecAXPY(y,-1.0,u);
6761:   VecGetArrayRead(y,&yy);
6762: #if defined(PETSC_USE_COMPLEX)
6763:   {
6764:     PetscReal *yreal;
6765:     PetscInt  i,n;
6766:     VecGetLocalSize(y,&n);
6767:     PetscMalloc1(n,&yreal);
6768:     for (i=0; i<n; i++) yreal[i] = PetscRealPart(yy[i]);
6769:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yreal);
6770:     PetscFree(yreal);
6771:   }
6772: #else
6773:   PetscDrawLGAddCommonPoint(ctx->lg,ptime,yy);
6774: #endif
6775:   VecRestoreArrayRead(y,&yy);
6776:   VecDestroy(&y);
6777:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
6778:     PetscDrawLGDraw(ctx->lg);
6779:     PetscDrawLGSave(ctx->lg);
6780:   }
6781:   return(0);
6782: }

6786: PetscErrorCode TSMonitorLGSNESIterations(TS ts,PetscInt n,PetscReal ptime,Vec v,void *monctx)
6787: {
6788:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
6789:   PetscReal      x   = ptime,y;
6791:   PetscInt       its;

6794:   if (n < 0) return(0); /* -1 indicates interpolated solution */
6795:   if (!n) {
6796:     PetscDrawAxis axis;
6797:     PetscDrawLGGetAxis(ctx->lg,&axis);
6798:     PetscDrawAxisSetLabels(axis,"Nonlinear iterations as function of time","Time","SNES Iterations");
6799:     PetscDrawLGReset(ctx->lg);
6800:     ctx->snes_its = 0;
6801:   }
6802:   TSGetSNESIterations(ts,&its);
6803:   y    = its - ctx->snes_its;
6804:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
6805:   if (((ctx->howoften > 0) && (!(n % ctx->howoften)) && (n > -1)) || ((ctx->howoften == -1) && (n == -1))) {
6806:     PetscDrawLGDraw(ctx->lg);
6807:     PetscDrawLGSave(ctx->lg);
6808:   }
6809:   ctx->snes_its = its;
6810:   return(0);
6811: }

6815: PetscErrorCode TSMonitorLGKSPIterations(TS ts,PetscInt n,PetscReal ptime,Vec v,void *monctx)
6816: {
6817:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
6818:   PetscReal      x   = ptime,y;
6820:   PetscInt       its;

6823:   if (n < 0) return(0); /* -1 indicates interpolated solution */
6824:   if (!n) {
6825:     PetscDrawAxis axis;
6826:     PetscDrawLGGetAxis(ctx->lg,&axis);
6827:     PetscDrawAxisSetLabels(axis,"Linear iterations as function of time","Time","KSP Iterations");
6828:     PetscDrawLGReset(ctx->lg);
6829:     ctx->ksp_its = 0;
6830:   }
6831:   TSGetKSPIterations(ts,&its);
6832:   y    = its - ctx->ksp_its;
6833:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
6834:   if (((ctx->howoften > 0) && (!(n % ctx->howoften)) && (n > -1)) || ((ctx->howoften == -1) && (n == -1))) {
6835:     PetscDrawLGDraw(ctx->lg);
6836:     PetscDrawLGSave(ctx->lg);
6837:   }
6838:   ctx->ksp_its = its;
6839:   return(0);
6840: }

6844: /*@
6845:    TSComputeLinearStability - computes the linear stability function at a point

6847:    Collective on TS and Vec

6849:    Input Parameters:
6850: +  ts - the TS context
6851: -  xr,xi - real and imaginary part of input arguments

6853:    Output Parameters:
6854: .  yr,yi - real and imaginary part of function value

6856:    Level: developer

6858: .keywords: TS, compute

6860: .seealso: TSSetRHSFunction(), TSComputeIFunction()
6861: @*/
6862: PetscErrorCode TSComputeLinearStability(TS ts,PetscReal xr,PetscReal xi,PetscReal *yr,PetscReal *yi)
6863: {

6868:   if (!ts->ops->linearstability) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Linearized stability function not provided for this method");
6869:   (*ts->ops->linearstability)(ts,xr,xi,yr,yi);
6870:   return(0);
6871: }

6873: /* ------------------------------------------------------------------------*/
6876: /*@C
6877:    TSMonitorEnvelopeCtxCreate - Creates a context for use with TSMonitorEnvelope()

6879:    Collective on TS

6881:    Input Parameters:
6882: .  ts  - the ODE solver object

6884:    Output Parameter:
6885: .  ctx - the context

6887:    Level: intermediate

6889: .keywords: TS, monitor, line graph, residual, seealso

6891: .seealso: TSMonitorLGTimeStep(), TSMonitorSet(), TSMonitorLGSolution(), TSMonitorLGError()

6893: @*/
6894: PetscErrorCode  TSMonitorEnvelopeCtxCreate(TS ts,TSMonitorEnvelopeCtx *ctx)
6895: {

6899:   PetscNew(ctx);
6900:   return(0);
6901: }

6905: /*@C
6906:    TSMonitorEnvelope - Monitors the maximum and minimum value of each component of the solution

6908:    Collective on TS

6910:    Input Parameters:
6911: +  ts - the TS context
6912: .  step - current time-step
6913: .  ptime - current time
6914: .  u  - current solution
6915: -  dctx - the envelope context

6917:    Options Database:
6918: .  -ts_monitor_envelope

6920:    Level: intermediate

6922:    Notes: after a solve you can use TSMonitorEnvelopeGetBounds() to access the envelope

6924: .keywords: TS,  vector, monitor, view

6926: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorEnvelopeGetBounds(), TSMonitorEnvelopeCtxCreate()
6927: @*/
6928: PetscErrorCode  TSMonitorEnvelope(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dctx)
6929: {
6930:   PetscErrorCode       ierr;
6931:   TSMonitorEnvelopeCtx ctx = (TSMonitorEnvelopeCtx)dctx;

6934:   if (!ctx->max) {
6935:     VecDuplicate(u,&ctx->max);
6936:     VecDuplicate(u,&ctx->min);
6937:     VecCopy(u,ctx->max);
6938:     VecCopy(u,ctx->min);
6939:   } else {
6940:     VecPointwiseMax(ctx->max,u,ctx->max);
6941:     VecPointwiseMin(ctx->min,u,ctx->min);
6942:   }
6943:   return(0);
6944: }


6949: /*@C
6950:    TSMonitorEnvelopeGetBounds - Gets the bounds for the components of the solution

6952:    Collective on TS

6954:    Input Parameter:
6955: .  ts - the TS context

6957:    Output Parameter:
6958: +  max - the maximum values
6959: -  min - the minimum values

6961:    Notes: If the TS does not have a TSMonitorEnvelopeCtx associated with it then this function is ignored

6963:    Level: intermediate

6965: .keywords: TS,  vector, monitor, view

6967: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables()
6968: @*/
6969: PetscErrorCode  TSMonitorEnvelopeGetBounds(TS ts,Vec *max,Vec *min)
6970: {
6971:   PetscInt i;

6974:   if (max) *max = NULL;
6975:   if (min) *min = NULL;
6976:   for (i=0; i<ts->numbermonitors; i++) {
6977:     if (ts->monitor[i] == TSMonitorEnvelope) {
6978:       TSMonitorEnvelopeCtx  ctx = (TSMonitorEnvelopeCtx) ts->monitorcontext[i];
6979:       if (max) *max = ctx->max;
6980:       if (min) *min = ctx->min;
6981:       break;
6982:     }
6983:   }
6984:   return(0);
6985: }

6989: /*@C
6990:    TSMonitorEnvelopeCtxDestroy - Destroys a context that was created  with TSMonitorEnvelopeCtxCreate().

6992:    Collective on TSMonitorEnvelopeCtx

6994:    Input Parameter:
6995: .  ctx - the monitor context

6997:    Level: intermediate

6999: .keywords: TS, monitor, line graph, destroy

7001: .seealso: TSMonitorLGCtxCreate(),  TSMonitorSet(), TSMonitorLGTimeStep()
7002: @*/
7003: PetscErrorCode  TSMonitorEnvelopeCtxDestroy(TSMonitorEnvelopeCtx *ctx)
7004: {

7008:   VecDestroy(&(*ctx)->min);
7009:   VecDestroy(&(*ctx)->max);
7010:   PetscFree(*ctx);
7011:   return(0);
7012: }

7016: /*@
7017:    TSRollBack - Rolls back one time step

7019:    Collective on TS

7021:    Input Parameter:
7022: .  ts - the TS context obtained from TSCreate()

7024:    Level: advanced

7026: .keywords: TS, timestep, rollback

7028: .seealso: TSCreate(), TSSetUp(), TSDestroy(), TSSolve(), TSSetPreStep(), TSSetPreStage(), TSInterpolate()
7029: @*/
7030: PetscErrorCode  TSRollBack(TS ts)
7031: {

7036:   if (ts->steprollback) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONGSTATE,"TSRollBack already called");
7037:   if (!ts->ops->rollback) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSRollBack not implemented for type '%s'",((PetscObject)ts)->type_name);
7038:   (*ts->ops->rollback)(ts);
7039:   ts->time_step = ts->ptime - ts->ptime_prev;
7040:   ts->ptime = ts->ptime_prev;
7041:   ts->ptime_prev = ts->ptime_prev_rollback;
7042:   ts->steps--; ts->total_steps--;
7043:   ts->steprollback = PETSC_TRUE;
7044:   return(0);
7045: }

7049: /*@
7050:    TSGetStages - Get the number of stages and stage values

7052:    Input Parameter:
7053: .  ts - the TS context obtained from TSCreate()

7055:    Level: advanced

7057: .keywords: TS, getstages

7059: .seealso: TSCreate()
7060: @*/
7061: PetscErrorCode  TSGetStages(TS ts,PetscInt *ns,Vec **Y)
7062: {


7069:   if (!ts->ops->getstages) *ns=0;
7070:   else {
7071:     (*ts->ops->getstages)(ts,ns,Y);
7072:   }
7073:   return(0);
7074: }

7078: /*@C
7079:   TSComputeIJacobianDefaultColor - Computes the Jacobian using finite differences and coloring to exploit matrix sparsity.

7081:   Collective on SNES

7083:   Input Parameters:
7084: + ts - the TS context
7085: . t - current timestep
7086: . U - state vector
7087: . Udot - time derivative of state vector
7088: . shift - shift to apply, see note below
7089: - ctx - an optional user context

7091:   Output Parameters:
7092: + J - Jacobian matrix (not altered in this routine)
7093: - B - newly computed Jacobian matrix to use with preconditioner (generally the same as J)

7095:   Level: intermediate

7097:   Notes:
7098:   If F(t,U,Udot)=0 is the DAE, the required Jacobian is

7100:   dF/dU + shift*dF/dUdot

7102:   Most users should not need to explicitly call this routine, as it
7103:   is used internally within the nonlinear solvers.

7105:   This will first try to get the coloring from the DM.  If the DM type has no coloring
7106:   routine, then it will try to get the coloring from the matrix.  This requires that the
7107:   matrix have nonzero entries precomputed.

7109: .keywords: TS, finite differences, Jacobian, coloring, sparse
7110: .seealso: TSSetIJacobian(), MatFDColoringCreate(), MatFDColoringSetFunction()
7111: @*/
7112: PetscErrorCode TSComputeIJacobianDefaultColor(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat J,Mat B,void *ctx)
7113: {
7114:   SNES           snes;
7115:   MatFDColoring  color;
7116:   PetscBool      hascolor, matcolor = PETSC_FALSE;

7120:   PetscOptionsGetBool(((PetscObject)ts)->options,((PetscObject) ts)->prefix, "-ts_fd_color_use_mat", &matcolor, NULL);
7121:   PetscObjectQuery((PetscObject) B, "TSMatFDColoring", (PetscObject *) &color);
7122:   if (!color) {
7123:     DM         dm;
7124:     ISColoring iscoloring;

7126:     TSGetDM(ts, &dm);
7127:     DMHasColoring(dm, &hascolor);
7128:     if (hascolor && !matcolor) {
7129:       DMCreateColoring(dm, IS_COLORING_GLOBAL, &iscoloring);
7130:       MatFDColoringCreate(B, iscoloring, &color);
7131:       MatFDColoringSetFunction(color, (PetscErrorCode (*)(void)) SNESTSFormFunction, (void *) ts);
7132:       MatFDColoringSetFromOptions(color);
7133:       MatFDColoringSetUp(B, iscoloring, color);
7134:       ISColoringDestroy(&iscoloring);
7135:     } else {
7136:       MatColoring mc;

7138:       MatColoringCreate(B, &mc);
7139:       MatColoringSetDistance(mc, 2);
7140:       MatColoringSetType(mc, MATCOLORINGSL);
7141:       MatColoringSetFromOptions(mc);
7142:       MatColoringApply(mc, &iscoloring);
7143:       MatColoringDestroy(&mc);
7144:       MatFDColoringCreate(B, iscoloring, &color);
7145:       MatFDColoringSetFunction(color, (PetscErrorCode (*)(void)) SNESTSFormFunction, (void *) ts);
7146:       MatFDColoringSetFromOptions(color);
7147:       MatFDColoringSetUp(B, iscoloring, color);
7148:       ISColoringDestroy(&iscoloring);
7149:     }
7150:     PetscObjectCompose((PetscObject) B, "TSMatFDColoring", (PetscObject) color);
7151:     PetscObjectDereference((PetscObject) color);
7152:   }
7153:   TSGetSNES(ts, &snes);
7154:   MatFDColoringApply(B, color, U, snes);
7155:   if (J != B) {
7156:     MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
7157:     MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
7158:   }
7159:   return(0);
7160: }

7164: /*@
7165:     TSSetFunctionDomainError - Set the function testing if the current state vector is valid

7167:     Input Parameters:
7168:     ts - the TS context
7169:     func - function called within TSFunctionDomainError

7171:     Level: intermediate

7173: .keywords: TS, state, domain
7174: .seealso: TSAdaptCheckStage(), TSFunctionDomainError()
7175: @*/

7177: PetscErrorCode TSSetFunctionDomainError(TS ts, PetscErrorCode (*func)(TS,PetscReal,Vec,PetscBool*))
7178: {
7181:   ts->functiondomainerror = func;
7182:   return(0);
7183: }

7187: /*@
7188:     TSFunctionDomainError - Check if the current state is valid

7190:     Input Parameters:
7191:     ts - the TS context
7192:     stagetime - time of the simulation
7193:     Y - state vector to check.

7195:     Output Parameter:
7196:     accept - Set to PETSC_FALSE if the current state vector is valid.

7198:     Note:
7199:     This function should be used to ensure the state is in a valid part of the space.
7200:     For example, one can ensure here all values are positive.

7202:     Level: advanced
7203: @*/
7204: PetscErrorCode TSFunctionDomainError(TS ts,PetscReal stagetime,Vec Y,PetscBool* accept)
7205: {


7211:   *accept = PETSC_TRUE;
7212:   if (ts->functiondomainerror) {
7213:     PetscStackCallStandard((*ts->functiondomainerror),(ts,stagetime,Y,accept));
7214:   }
7215:   return(0);
7216: }

7218: #undef  __FUNCT__
7220: /*@C
7221:   TSClone - This function clones a time step object. 

7223:   Collective on MPI_Comm

7225:   Input Parameter:
7226: . tsin    - The input TS

7228:   Output Parameter:
7229: . tsout   - The output TS (cloned)

7231:   Notes:
7232:   This function is used to create a clone of a TS object. It is used in ARKIMEX for initializing the slope for first stage explicit methods. It will likely be replaced in the future with a mechanism of switching methods on the fly. 

7234:   When using TSDestroy() on a clone the user has to first reset the correct TS reference in the embedded SNES object: e.g.: by running SNES snes_dup=NULL; TSGetSNES(ts,&snes_dup); TSSetSNES(ts,snes_dup);

7236:   Level: developer

7238: .keywords: TS, clone
7239: .seealso: TSCreate(), TSSetType(), TSSetUp(), TSDestroy(), TSSetProblemType()
7240: @*/
7241: PetscErrorCode  TSClone(TS tsin, TS *tsout)
7242: {
7243:   TS             t;
7245:   SNES           snes_start;
7246:   DM             dm;
7247:   TSType         type;

7251:   *tsout = NULL;

7253:   PetscHeaderCreate(t, TS_CLASSID, "TS", "Time stepping", "TS", PetscObjectComm((PetscObject)tsin), TSDestroy, TSView);

7255:   /* General TS description */
7256:   t->numbermonitors    = 0;
7257:   t->setupcalled       = 0;
7258:   t->ksp_its           = 0;
7259:   t->snes_its          = 0;
7260:   t->nwork             = 0;
7261:   t->rhsjacobian.time  = -1e20;
7262:   t->rhsjacobian.scale = 1.;
7263:   t->ijacobian.shift   = 1.;

7265:   TSGetSNES(tsin,&snes_start);
7266:   TSSetSNES(t,snes_start);

7268:   TSGetDM(tsin,&dm);
7269:   TSSetDM(t,dm);

7271:   t->adapt = tsin->adapt;
7272:   PetscObjectReference((PetscObject)t->adapt);

7274:   t->problem_type      = tsin->problem_type;
7275:   t->ptime             = tsin->ptime;
7276:   t->time_step         = tsin->time_step;
7277:   t->max_time          = tsin->max_time;
7278:   t->steps             = tsin->steps;
7279:   t->max_steps         = tsin->max_steps;
7280:   t->equation_type     = tsin->equation_type;
7281:   t->atol              = tsin->atol;
7282:   t->rtol              = tsin->rtol;
7283:   t->max_snes_failures = tsin->max_snes_failures;
7284:   t->max_reject        = tsin->max_reject;
7285:   t->errorifstepfailed = tsin->errorifstepfailed;

7287:   TSGetType(tsin,&type);
7288:   TSSetType(t,type);

7290:   t->vec_sol           = NULL;

7292:   t->cfltime          = tsin->cfltime;
7293:   t->cfltime_local    = tsin->cfltime_local;
7294:   t->exact_final_time = tsin->exact_final_time;

7296:   PetscMemcpy(t->ops,tsin->ops,sizeof(struct _TSOps));

7298:   if (((PetscObject)tsin)->fortran_func_pointers) {
7299:     PetscInt i;
7300:     PetscMalloc((10)*sizeof(void(*)(void)),&((PetscObject)t)->fortran_func_pointers);
7301:     for (i=0; i<10; i++) {
7302:       ((PetscObject)t)->fortran_func_pointers[i] = ((PetscObject)tsin)->fortran_func_pointers[i];
7303:     }
7304:   }
7305:   *tsout = t;
7306:   return(0);
7307: }