Date: 2015-10-02T22:26:30+00:00

Actual source code: ts.c
petsc-3.6.2 2015-10-02
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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_Step, TS_PseudoComputeTimeStep, TS_FunctionEval, TS_JacobianEval;

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

     14: struct _n_TSMonitorDrawCtx {
     15:   PetscViewer   viewer;
     16:   PetscDrawAxis axis;
     17:   Vec           initialsolution;
     18:   PetscBool     showinitial;
     19:   PetscInt      howoften;  /* when > 0 uses step % howoften, when negative only final solution plotted */
     20:   PetscBool     showtimestepandtime;
     21:   int           color;
     22: };

     26: /*@
     27:    TSSetFromOptions - Sets various TS parameters from user options.

     29:    Collective on TS

     31:    Input Parameter:
     32: .  ts - the TS context obtained from TSCreate()

     34:    Options Database Keys:
     35: +  -ts_type <type> - TSEULER, TSBEULER, TSSUNDIALS, TSPSEUDO, TSCN, TSRK, TSTHETA, TSGL, TSSSP
     36: .  -ts_save_trajectory - checkpoint the solution at each time-step
     37: .  -ts_max_steps <maxsteps> - maximum number of time-steps to take
     38: .  -ts_final_time <time> - maximum time to compute to
     39: .  -ts_dt <dt> - initial time step
     40: .  -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
     41: .  -ts_max_snes_failures <maxfailures> - Maximum number of nonlinear solve failures allowed
     42: .  -ts_max_reject <maxrejects> - Maximum number of step rejections before step fails
     43: .  -ts_error_if_step_fails <true,false> - Error if no step succeeds
     44: .  -ts_rtol <rtol> - relative tolerance for local truncation error
     45: .  -ts_atol <atol> Absolute tolerance for local truncation error
     46: .  -ts_adjoint_solve <yes,no> After solving the ODE/DAE solve the adjoint problem (requires -ts_save_trajectory)
     47: .  -ts_fd_color - Use finite differences with coloring to compute IJacobian
     48: .  -ts_monitor - print information at each timestep
     49: .  -ts_monitor_lg_timestep - Monitor timestep size graphically
     50: .  -ts_monitor_lg_solution - Monitor solution graphically
     51: .  -ts_monitor_lg_error - Monitor error graphically
     52: .  -ts_monitor_lg_snes_iterations - Monitor number nonlinear iterations for each timestep graphically
     53: .  -ts_monitor_lg_ksp_iterations - Monitor number nonlinear iterations for each timestep graphically
     54: .  -ts_monitor_sp_eig - Monitor eigenvalues of linearized operator graphically
     55: .  -ts_monitor_draw_solution - Monitor solution graphically
     56: .  -ts_monitor_draw_solution_phase  <xleft,yleft,xright,yright> - Monitor solution graphically with phase diagram, requires problem with exactly 2 degrees of freedom
     57: .  -ts_monitor_draw_error - Monitor error graphically, requires use to have provided TSSetSolutionFunction()
     58: .  -ts_monitor_solution_binary <filename> - Save each solution to a binary file
     59: .  -ts_monitor_solution_vtk <filename.vts> - Save each time step to a binary file, use filename-%%03D.vts
     60: -  -ts_monitor_envelope - determine maximum and minimum value of each component of the solution over the solution time

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

     64:    Level: beginner

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

     68: .seealso: TSGetType()
     69: @*/
     70: PetscErrorCode  TSSetFromOptions(TS ts)
     71: {
     72:   PetscBool              opt,flg,tflg;
     73:   PetscErrorCode         ierr;
     74:   PetscViewer            monviewer;
     75:   char                   monfilename[PETSC_MAX_PATH_LEN];
     76:   SNES                   snes;
     77:   TSAdapt                adapt;
     78:   PetscReal              time_step;
     79:   TSExactFinalTimeOption eftopt;
     80:   char                   dir[16];
     81:   const char             *defaultType;
     82:   char                   typeName[256];

     86:   PetscObjectOptionsBegin((PetscObject)ts);
     87:   if (((PetscObject)ts)->type_name) defaultType = ((PetscObject)ts)->type_name;
     88:   else defaultType = TSEULER;

     90:   TSRegisterAll();
     91:   PetscOptionsFList("-ts_type", "TS method"," TSSetType", TSList, defaultType, typeName, 256, &opt);
     92:   if (opt) {
     93:     TSSetType(ts, typeName);
     94:   } else {
     95:     TSSetType(ts, defaultType);
     96:   }

     98:   /* Handle generic TS options */
     99:   if (ts->trajectory) tflg = PETSC_TRUE;
    100:   else tflg = PETSC_FALSE;
    101:   PetscOptionsBool("-ts_save_trajectory","Save the solution at each timestep","TSSetSaveTrajectory",tflg,&tflg,NULL);
    102:   if (tflg) {TSSetSaveTrajectory(ts);}
    103:   if (ts->adjoint_solve) tflg = PETSC_TRUE;
    104:   else tflg = PETSC_FALSE;
    105:   PetscOptionsBool("-ts_adjoint_solve","Solve the adjoint problem immediately after solving the forward problem","",tflg,&tflg,&flg);
    106:   if (flg) {
    107:     TSSetSaveTrajectory(ts);
    108:     ts->adjoint_solve = tflg;
    109:   }
    110:   PetscOptionsInt("-ts_max_steps","Maximum number of time steps","TSSetDuration",ts->max_steps,&ts->max_steps,NULL);
    111:   PetscOptionsReal("-ts_final_time","Time to run to","TSSetDuration",ts->max_time,&ts->max_time,NULL);
    112:   PetscOptionsReal("-ts_init_time","Initial time","TSSetTime",ts->ptime,&ts->ptime,NULL);
    113:   PetscOptionsReal("-ts_dt","Initial time step","TSSetTimeStep",ts->time_step,&time_step,&flg);
    114:   if (flg) {
    115:     TSSetTimeStep(ts,time_step);
    116:   }
    117:   PetscOptionsEnum("-ts_exact_final_time","Option for handling of final time step","TSSetExactFinalTime",TSExactFinalTimeOptions,(PetscEnum)ts->exact_final_time,(PetscEnum*)&eftopt,&flg);
    118:   if (flg) {TSSetExactFinalTime(ts,eftopt);}
    119:   PetscOptionsInt("-ts_max_snes_failures","Maximum number of nonlinear solve failures","TSSetMaxSNESFailures",ts->max_snes_failures,&ts->max_snes_failures,NULL);
    120:   PetscOptionsInt("-ts_max_reject","Maximum number of step rejections before step fails","TSSetMaxStepRejections",ts->max_reject,&ts->max_reject,NULL);
    121:   PetscOptionsBool("-ts_error_if_step_fails","Error if no step succeeds","TSSetErrorIfStepFails",ts->errorifstepfailed,&ts->errorifstepfailed,NULL);
    122:   PetscOptionsReal("-ts_rtol","Relative tolerance for local truncation error","TSSetTolerances",ts->rtol,&ts->rtol,NULL);
    123:   PetscOptionsReal("-ts_atol","Absolute tolerance for local truncation error","TSSetTolerances",ts->atol,&ts->atol,NULL);

    125: #if defined(PETSC_HAVE_SAWS)
    126:   {
    127:   PetscBool set;
    128:   flg  = PETSC_FALSE;
    129:   PetscOptionsBool("-ts_saws_block","Block for SAWs memory snooper at end of TSSolve","PetscObjectSAWsBlock",((PetscObject)ts)->amspublishblock,&flg,&set);
    130:   if (set) {
    131:     PetscObjectSAWsSetBlock((PetscObject)ts,flg);
    132:   }
    133:   }
    134: #endif

    136:   /* Monitor options */
    137:   PetscOptionsString("-ts_monitor","Monitor timestep size","TSMonitorDefault","stdout",monfilename,PETSC_MAX_PATH_LEN,&flg);
    138:   if (flg) {
    139:     PetscViewerASCIIOpen(PetscObjectComm((PetscObject)ts),monfilename,&monviewer);
    140:     TSMonitorSet(ts,TSMonitorDefault,monviewer,(PetscErrorCode (*)(void**))PetscViewerDestroy);
    141:   }
    142:   PetscOptionsString("-ts_monitor_python","Use Python function","TSMonitorSet",0,monfilename,PETSC_MAX_PATH_LEN,&flg);
    143:   if (flg) {PetscPythonMonitorSet((PetscObject)ts,monfilename);}

    145:   PetscOptionsName("-ts_monitor_lg_timestep","Monitor timestep size graphically","TSMonitorLGTimeStep",&opt);
    146:   if (opt) {
    147:     TSMonitorLGCtx ctx;
    148:     PetscInt       howoften = 1;

    150:     PetscOptionsInt("-ts_monitor_lg_timestep","Monitor timestep size graphically","TSMonitorLGTimeStep",howoften,&howoften,NULL);
    151:     TSMonitorLGCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
    152:     TSMonitorSet(ts,TSMonitorLGTimeStep,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
    153:   }
    154:   PetscOptionsName("-ts_monitor_lg_solution","Monitor solution graphically","TSMonitorLGSolution",&opt);
    155:   if (opt) {
    156:     TSMonitorLGCtx ctx;
    157:     PetscInt       howoften = 1;

    159:     PetscOptionsInt("-ts_monitor_lg_solution","Monitor solution graphically","TSMonitorLGSolution",howoften,&howoften,NULL);
    160:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&ctx);
    161:     TSMonitorSet(ts,TSMonitorLGSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
    162:   }
    163:   PetscOptionsName("-ts_monitor_lg_error","Monitor error graphically","TSMonitorLGError",&opt);
    164:   if (opt) {
    165:     TSMonitorLGCtx ctx;
    166:     PetscInt       howoften = 1;

    168:     PetscOptionsInt("-ts_monitor_lg_error","Monitor error graphically","TSMonitorLGError",howoften,&howoften,NULL);
    169:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&ctx);
    170:     TSMonitorSet(ts,TSMonitorLGError,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
    171:   }
    172:   PetscOptionsName("-ts_monitor_lg_snes_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGSNESIterations",&opt);
    173:   if (opt) {
    174:     TSMonitorLGCtx ctx;
    175:     PetscInt       howoften = 1;

    177:     PetscOptionsInt("-ts_monitor_lg_snes_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGSNESIterations",howoften,&howoften,NULL);
    178:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
    179:     TSMonitorSet(ts,TSMonitorLGSNESIterations,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
    180:   }
    181:   PetscOptionsName("-ts_monitor_lg_ksp_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGKSPIterations",&opt);
    182:   if (opt) {
    183:     TSMonitorLGCtx ctx;
    184:     PetscInt       howoften = 1;

    186:     PetscOptionsInt("-ts_monitor_lg_ksp_iterations","Monitor number nonlinear iterations for each timestep graphically","TSMonitorLGKSPIterations",howoften,&howoften,NULL);
    187:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,300,300,howoften,&ctx);
    188:     TSMonitorSet(ts,TSMonitorLGKSPIterations,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);
    189:   }
    190:   PetscOptionsName("-ts_monitor_sp_eig","Monitor eigenvalues of linearized operator graphically","TSMonitorSPEig",&opt);
    191:   if (opt) {
    192:     TSMonitorSPEigCtx ctx;
    193:     PetscInt          howoften = 1;

    195:     PetscOptionsInt("-ts_monitor_sp_eig","Monitor eigenvalues of linearized operator graphically","TSMonitorSPEig",howoften,&howoften,NULL);
    196:     TSMonitorSPEigCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&ctx);
    197:     TSMonitorSet(ts,TSMonitorSPEig,ctx,(PetscErrorCode (*)(void**))TSMonitorSPEigCtxDestroy);
    198:   }
    199:   opt  = PETSC_FALSE;
    200:   PetscOptionsName("-ts_monitor_draw_solution","Monitor solution graphically","TSMonitorDrawSolution",&opt);
    201:   if (opt) {
    202:     TSMonitorDrawCtx ctx;
    203:     PetscInt         howoften = 1;

    205:     PetscOptionsInt("-ts_monitor_draw_solution","Monitor solution graphically","TSMonitorDrawSolution",howoften,&howoften,NULL);
    206:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&ctx);
    207:     TSMonitorSet(ts,TSMonitorDrawSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
    208:   }
    209:   opt  = PETSC_FALSE;
    210:   PetscOptionsName("-ts_monitor_draw_solution_phase","Monitor solution graphically","TSMonitorDrawSolutionPhase",&opt);
    211:   if (opt) {
    212:     TSMonitorDrawCtx ctx;
    213:     PetscReal        bounds[4];
    214:     PetscInt         n = 4;
    215:     PetscDraw        draw;

    217:     PetscOptionsRealArray("-ts_monitor_draw_solution_phase","Monitor solution graphically","TSMonitorDrawSolutionPhase",bounds,&n,NULL);
    218:     if (n != 4) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Must provide bounding box of phase field");
    219:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,1,&ctx);
    220:     PetscViewerDrawGetDraw(ctx->viewer,0,&draw);
    221:     PetscDrawClear(draw);
    222:     PetscDrawAxisCreate(draw,&ctx->axis);
    223:     PetscDrawAxisSetLimits(ctx->axis,bounds[0],bounds[2],bounds[1],bounds[3]);
    224:     PetscDrawAxisSetLabels(ctx->axis,"Phase Diagram","Variable 1","Variable 2");
    225:     PetscDrawAxisDraw(ctx->axis);
    226:     /* PetscDrawSetCoordinates(draw,bounds[0],bounds[1],bounds[2],bounds[3]); */
    227:     TSMonitorSet(ts,TSMonitorDrawSolutionPhase,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
    228:   }
    229:   opt  = PETSC_FALSE;
    230:   PetscOptionsName("-ts_monitor_draw_error","Monitor error graphically","TSMonitorDrawError",&opt);
    231:   if (opt) {
    232:     TSMonitorDrawCtx ctx;
    233:     PetscInt         howoften = 1;

    235:     PetscOptionsInt("-ts_monitor_draw_error","Monitor error graphically","TSMonitorDrawError",howoften,&howoften,NULL);
    236:     TSMonitorDrawCtxCreate(PetscObjectComm((PetscObject)ts),0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&ctx);
    237:     TSMonitorSet(ts,TSMonitorDrawError,ctx,(PetscErrorCode (*)(void**))TSMonitorDrawCtxDestroy);
    238:   }
    239:   opt  = PETSC_FALSE;
    240:   PetscOptionsString("-ts_monitor_solution_binary","Save each solution to a binary file","TSMonitorSolutionBinary",0,monfilename,PETSC_MAX_PATH_LEN,&flg);
    241:   if (flg) {
    242:     PetscViewer ctx;
    243:     if (monfilename[0]) {
    244:       PetscViewerBinaryOpen(PetscObjectComm((PetscObject)ts),monfilename,FILE_MODE_WRITE,&ctx);
    245:       TSMonitorSet(ts,TSMonitorSolutionBinary,ctx,(PetscErrorCode (*)(void**))PetscViewerDestroy);
    246:     } else {
    247:       ctx = PETSC_VIEWER_BINARY_(PetscObjectComm((PetscObject)ts));
    248:       TSMonitorSet(ts,TSMonitorSolutionBinary,ctx,(PetscErrorCode (*)(void**))NULL);
    249:     }
    250:   }
    251:   opt  = PETSC_FALSE;
    252:   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);
    253:   if (flg) {
    254:     const char *ptr,*ptr2;
    255:     char       *filetemplate;
    256:     if (!monfilename[0]) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"-ts_monitor_solution_vtk requires a file template, e.g. filename-%%03D.vts");
    257:     /* Do some cursory validation of the input. */
    258:     PetscStrstr(monfilename,"%",(char**)&ptr);
    259:     if (!ptr) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_USER,"-ts_monitor_solution_vtk requires a file template, e.g. filename-%%03D.vts");
    260:     for (ptr++; ptr && *ptr; ptr++) {
    261:       PetscStrchr("DdiouxX",*ptr,(char**)&ptr2);
    262:       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");
    263:       if (ptr2) break;
    264:     }
    265:     PetscStrallocpy(monfilename,&filetemplate);
    266:     TSMonitorSet(ts,TSMonitorSolutionVTK,filetemplate,(PetscErrorCode (*)(void**))TSMonitorSolutionVTKDestroy);
    267:   }

    269:   PetscOptionsString("-ts_monitor_dmda_ray","Display a ray of the solution","None","y=0",dir,16,&flg);
    270:   if (flg) {
    271:     TSMonitorDMDARayCtx *rayctx;
    272:     int                  ray = 0;
    273:     DMDADirection        ddir;
    274:     DM                   da;
    275:     PetscMPIInt          rank;

    277:     if (dir[1] != '=') SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Unknown ray %s",dir);
    278:     if (dir[0] == 'x') ddir = DMDA_X;
    279:     else if (dir[0] == 'y') ddir = DMDA_Y;
    280:     else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Unknown ray %s",dir);
    281:     sscanf(dir+2,"%d",&ray);

    283:     PetscInfo2(((PetscObject)ts),"Displaying DMDA ray %c = %D\n",dir[0],ray);
    284:     PetscNew(&rayctx);
    285:     TSGetDM(ts,&da);
    286:     DMDAGetRay(da,ddir,ray,&rayctx->ray,&rayctx->scatter);
    287:     MPI_Comm_rank(PetscObjectComm((PetscObject)ts),&rank);
    288:     if (!rank) {
    289:       PetscViewerDrawOpen(PETSC_COMM_SELF,0,0,0,0,600,300,&rayctx->viewer);
    290:     }
    291:     rayctx->lgctx = NULL;
    292:     TSMonitorSet(ts,TSMonitorDMDARay,rayctx,TSMonitorDMDARayDestroy);
    293:   }
    294:   PetscOptionsString("-ts_monitor_lg_dmda_ray","Display a ray of the solution","None","x=0",dir,16,&flg);
    295:   if (flg) {
    296:     TSMonitorDMDARayCtx *rayctx;
    297:     int                 ray = 0;
    298:     DMDADirection       ddir;
    299:     DM                  da;
    300:     PetscInt            howoften = 1;

    302:     if (dir[1] != '=') SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_ARG_WRONG, "Malformed ray %s", dir);
    303:     if      (dir[0] == 'x') ddir = DMDA_X;
    304:     else if (dir[0] == 'y') ddir = DMDA_Y;
    305:     else SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_ARG_WRONG, "Unknown ray direction %s", dir);
    306:     sscanf(dir+2, "%d", &ray);

    308:     PetscInfo2(((PetscObject) ts),"Displaying LG DMDA ray %c = %D\n", dir[0], ray);
    309:     PetscNew(&rayctx);
    310:     TSGetDM(ts, &da);
    311:     DMDAGetRay(da, ddir, ray, &rayctx->ray, &rayctx->scatter);
    312:     TSMonitorLGCtxCreate(PETSC_COMM_SELF,0,0,PETSC_DECIDE,PETSC_DECIDE,600,400,howoften,&rayctx->lgctx);
    313:     TSMonitorSet(ts, TSMonitorLGDMDARay, rayctx, TSMonitorDMDARayDestroy);
    314:   }

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

    320:     TSMonitorEnvelopeCtxCreate(ts,&ctx);
    321:     TSMonitorSet(ts,TSMonitorEnvelope,ctx,(PetscErrorCode (*)(void**))TSMonitorEnvelopeCtxDestroy);
    322:   }

    324:   flg  = PETSC_FALSE;
    325:   PetscOptionsBool("-ts_fd_color", "Use finite differences with coloring to compute IJacobian", "TSComputeJacobianDefaultColor", flg, &flg, NULL);
    326:   if (flg) {
    327:     DM   dm;
    328:     DMTS tdm;

    330:     TSGetDM(ts, &dm);
    331:     DMGetDMTS(dm, &tdm);
    332:     tdm->ijacobianctx = NULL;
    333:     TSSetIJacobian(ts, NULL, NULL, TSComputeIJacobianDefaultColor, 0);
    334:     PetscInfo(ts, "Setting default finite difference coloring Jacobian matrix\n");
    335:   }

    337:   /*
    338:      This code is all wrong. One is creating objects inside the TSSetFromOptions() so if run with the options gui
    339:      will bleed memory. Also one is using a PetscOptionsBegin() inside a PetscOptionsBegin()
    340:   */
    341:   TSGetAdapt(ts,&adapt);
    342:   TSAdaptSetFromOptions(PetscOptionsObject,adapt);

    344:     /* Handle specific TS options */
    345:   if (ts->ops->setfromoptions) {
    346:     (*ts->ops->setfromoptions)(PetscOptionsObject,ts);
    347:   }
    348:   PetscOptionsEnd();

    350:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
    351:   PetscObjectProcessOptionsHandlers((PetscObject)ts);

    353:   if (ts->trajectory) {
    354:     TSTrajectorySetFromOptions(ts->trajectory);
    355:   }

    357:   TSGetSNES(ts,&snes);
    358:   if (snes) {
    359:     if (ts->problem_type == TS_LINEAR) {SNESSetType(snes,SNESKSPONLY);}
    360:     SNESSetFromOptions(ts->snes);
    361:   }
    362:   return(0);
    363: }

    367: /*@
    368:    TSSetSaveTrajectory - Causes the TS to save its solutions as it iterates forward in time in a TSTrajectory object

    370:    Collective on TS

    372:    Input Parameters:
    373: .  ts - the TS context obtained from TSCreate()

    376:    Level: intermediate

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

    380: .keywords: TS, set, checkpoint,
    381: @*/
    382: PetscErrorCode  TSSetSaveTrajectory(TS ts)
    383: {

    388:   if (!ts->trajectory) {
    389:     TSTrajectoryCreate(PetscObjectComm((PetscObject)ts),&ts->trajectory);
    390:     TSTrajectorySetType(ts->trajectory,TSTRAJECTORYBASIC);
    391:   }
    392:   return(0);
    393: }

    397: /*@
    398:    TSComputeRHSJacobian - Computes the Jacobian matrix that has been
    399:       set with TSSetRHSJacobian().

    401:    Collective on TS and Vec

    403:    Input Parameters:
    404: +  ts - the TS context
    405: .  t - current timestep
    406: -  U - input vector

    408:    Output Parameters:
    409: +  A - Jacobian matrix
    410: .  B - optional preconditioning matrix
    411: -  flag - flag indicating matrix structure

    413:    Notes:
    414:    Most users should not need to explicitly call this routine, as it
    415:    is used internally within the nonlinear solvers.

    417:    See KSPSetOperators() for important information about setting the
    418:    flag parameter.

    420:    Level: developer

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

    424: .seealso:  TSSetRHSJacobian(), KSPSetOperators()
    425: @*/
    426: PetscErrorCode  TSComputeRHSJacobian(TS ts,PetscReal t,Vec U,Mat A,Mat B)
    427: {
    429:   PetscObjectState Ustate;
    430:   DM             dm;
    431:   DMTS           tsdm;
    432:   TSRHSJacobian  rhsjacobianfunc;
    433:   void           *ctx;
    434:   TSIJacobian    ijacobianfunc;
    435:   TSRHSFunction  rhsfunction;

    441:   TSGetDM(ts,&dm);
    442:   DMGetDMTS(dm,&tsdm);
    443:   DMTSGetRHSJacobian(dm,&rhsjacobianfunc,&ctx);
    444:   DMTSGetIJacobian(dm,&ijacobianfunc,NULL);
    445:   DMTSGetRHSFunction(dm,&rhsfunction,&ctx);
    446:   PetscObjectStateGet((PetscObject)U,&Ustate);
    447:   if (ts->rhsjacobian.time == t && (ts->problem_type == TS_LINEAR || (ts->rhsjacobian.X == U && ts->rhsjacobian.Xstate == Ustate)) && (rhsfunction != TSComputeRHSFunctionLinear)) {
    448:     return(0);
    449:   }

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

    453:   if (ts->rhsjacobian.reuse) {
    454:     MatShift(A,-ts->rhsjacobian.shift);
    455:     MatScale(A,1./ts->rhsjacobian.scale);
    456:     if (A != B) {
    457:       MatShift(B,-ts->rhsjacobian.shift);
    458:       MatScale(B,1./ts->rhsjacobian.scale);
    459:     }
    460:     ts->rhsjacobian.shift = 0;
    461:     ts->rhsjacobian.scale = 1.;
    462:   }

    464:   if (rhsjacobianfunc) {
    465:     PetscLogEventBegin(TS_JacobianEval,ts,U,A,B);
    466:     PetscStackPush("TS user Jacobian function");
    467:     (*rhsjacobianfunc)(ts,t,U,A,B,ctx);
    468:     PetscStackPop;
    469:     PetscLogEventEnd(TS_JacobianEval,ts,U,A,B);
    470:     /* make sure user returned a correct Jacobian and preconditioner */
    473:   } else {
    474:     MatZeroEntries(A);
    475:     if (A != B) {MatZeroEntries(B);}
    476:   }
    477:   ts->rhsjacobian.time       = t;
    478:   ts->rhsjacobian.X          = U;
    479:   PetscObjectStateGet((PetscObject)U,&ts->rhsjacobian.Xstate);
    480:   return(0);
    481: }

    485: /*@
    486:    TSComputeRHSFunction - Evaluates the right-hand-side function.

    488:    Collective on TS and Vec

    490:    Input Parameters:
    491: +  ts - the TS context
    492: .  t - current time
    493: -  U - state vector

    495:    Output Parameter:
    496: .  y - right hand side

    498:    Note:
    499:    Most users should not need to explicitly call this routine, as it
    500:    is used internally within the nonlinear solvers.

    502:    Level: developer

    504: .keywords: TS, compute

    506: .seealso: TSSetRHSFunction(), TSComputeIFunction()
    507: @*/
    508: PetscErrorCode TSComputeRHSFunction(TS ts,PetscReal t,Vec U,Vec y)
    509: {
    511:   TSRHSFunction  rhsfunction;
    512:   TSIFunction    ifunction;
    513:   void           *ctx;
    514:   DM             dm;

    520:   TSGetDM(ts,&dm);
    521:   DMTSGetRHSFunction(dm,&rhsfunction,&ctx);
    522:   DMTSGetIFunction(dm,&ifunction,NULL);

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

    526:   PetscLogEventBegin(TS_FunctionEval,ts,U,y,0);
    527:   if (rhsfunction) {
    528:     PetscStackPush("TS user right-hand-side function");
    529:     (*rhsfunction)(ts,t,U,y,ctx);
    530:     PetscStackPop;
    531:   } else {
    532:     VecZeroEntries(y);
    533:   }

    535:   PetscLogEventEnd(TS_FunctionEval,ts,U,y,0);
    536:   return(0);
    537: }

    541: /*@
    542:    TSComputeSolutionFunction - Evaluates the solution function.

    544:    Collective on TS and Vec

    546:    Input Parameters:
    547: +  ts - the TS context
    548: -  t - current time

    550:    Output Parameter:
    551: .  U - the solution

    553:    Note:
    554:    Most users should not need to explicitly call this routine, as it
    555:    is used internally within the nonlinear solvers.

    557:    Level: developer

    559: .keywords: TS, compute

    561: .seealso: TSSetSolutionFunction(), TSSetRHSFunction(), TSComputeIFunction()
    562: @*/
    563: PetscErrorCode TSComputeSolutionFunction(TS ts,PetscReal t,Vec U)
    564: {
    565:   PetscErrorCode     ierr;
    566:   TSSolutionFunction solutionfunction;
    567:   void               *ctx;
    568:   DM                 dm;

    573:   TSGetDM(ts,&dm);
    574:   DMTSGetSolutionFunction(dm,&solutionfunction,&ctx);

    576:   if (solutionfunction) {
    577:     PetscStackPush("TS user solution function");
    578:     (*solutionfunction)(ts,t,U,ctx);
    579:     PetscStackPop;
    580:   }
    581:   return(0);
    582: }
    585: /*@
    586:    TSComputeForcingFunction - Evaluates the forcing function.

    588:    Collective on TS and Vec

    590:    Input Parameters:
    591: +  ts - the TS context
    592: -  t - current time

    594:    Output Parameter:
    595: .  U - the function value

    597:    Note:
    598:    Most users should not need to explicitly call this routine, as it
    599:    is used internally within the nonlinear solvers.

    601:    Level: developer

    603: .keywords: TS, compute

    605: .seealso: TSSetSolutionFunction(), TSSetRHSFunction(), TSComputeIFunction()
    606: @*/
    607: PetscErrorCode TSComputeForcingFunction(TS ts,PetscReal t,Vec U)
    608: {
    609:   PetscErrorCode     ierr, (*forcing)(TS,PetscReal,Vec,void*);
    610:   void               *ctx;
    611:   DM                 dm;

    616:   TSGetDM(ts,&dm);
    617:   DMTSGetForcingFunction(dm,&forcing,&ctx);

    619:   if (forcing) {
    620:     PetscStackPush("TS user forcing function");
    621:     (*forcing)(ts,t,U,ctx);
    622:     PetscStackPop;
    623:   }
    624:   return(0);
    625: }

    629: static PetscErrorCode TSGetRHSVec_Private(TS ts,Vec *Frhs)
    630: {
    631:   Vec            F;

    635:   *Frhs = NULL;
    636:   TSGetIFunction(ts,&F,NULL,NULL);
    637:   if (!ts->Frhs) {
    638:     VecDuplicate(F,&ts->Frhs);
    639:   }
    640:   *Frhs = ts->Frhs;
    641:   return(0);
    642: }

    646: static PetscErrorCode TSGetRHSMats_Private(TS ts,Mat *Arhs,Mat *Brhs)
    647: {
    648:   Mat            A,B;

    652:   if (Arhs) *Arhs = NULL;
    653:   if (Brhs) *Brhs = NULL;
    654:   TSGetIJacobian(ts,&A,&B,NULL,NULL);
    655:   if (Arhs) {
    656:     if (!ts->Arhs) {
    657:       MatDuplicate(A,MAT_DO_NOT_COPY_VALUES,&ts->Arhs);
    658:     }
    659:     *Arhs = ts->Arhs;
    660:   }
    661:   if (Brhs) {
    662:     if (!ts->Brhs) {
    663:       if (A != B) {
    664:         MatDuplicate(B,MAT_DO_NOT_COPY_VALUES,&ts->Brhs);
    665:       } else {
    666:         ts->Brhs = ts->Arhs;
    667:         PetscObjectReference((PetscObject)ts->Arhs);
    668:       }
    669:     }
    670:     *Brhs = ts->Brhs;
    671:   }
    672:   return(0);
    673: }

    677: /*@
    678:    TSComputeIFunction - Evaluates the DAE residual written in implicit form F(t,U,Udot)=0

    680:    Collective on TS and Vec

    682:    Input Parameters:
    683: +  ts - the TS context
    684: .  t - current time
    685: .  U - state vector
    686: .  Udot - time derivative of state vector
    687: -  imex - flag indicates if the method is IMEX so that the RHSFunction should be kept separate

    689:    Output Parameter:
    690: .  Y - right hand side

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

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

    699:    Level: developer

    701: .keywords: TS, compute

    703: .seealso: TSSetIFunction(), TSComputeRHSFunction()
    704: @*/
    705: PetscErrorCode TSComputeIFunction(TS ts,PetscReal t,Vec U,Vec Udot,Vec Y,PetscBool imex)
    706: {
    708:   TSIFunction    ifunction;
    709:   TSRHSFunction  rhsfunction;
    710:   void           *ctx;
    711:   DM             dm;

    719:   TSGetDM(ts,&dm);
    720:   DMTSGetIFunction(dm,&ifunction,&ctx);
    721:   DMTSGetRHSFunction(dm,&rhsfunction,NULL);

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

    725:   PetscLogEventBegin(TS_FunctionEval,ts,U,Udot,Y);
    726:   if (ifunction) {
    727:     PetscStackPush("TS user implicit function");
    728:     (*ifunction)(ts,t,U,Udot,Y,ctx);
    729:     PetscStackPop;
    730:   }
    731:   if (imex) {
    732:     if (!ifunction) {
    733:       VecCopy(Udot,Y);
    734:     }
    735:   } else if (rhsfunction) {
    736:     if (ifunction) {
    737:       Vec Frhs;
    738:       TSGetRHSVec_Private(ts,&Frhs);
    739:       TSComputeRHSFunction(ts,t,U,Frhs);
    740:       VecAXPY(Y,-1,Frhs);
    741:     } else {
    742:       TSComputeRHSFunction(ts,t,U,Y);
    743:       VecAYPX(Y,-1,Udot);
    744:     }
    745:   }
    746:   PetscLogEventEnd(TS_FunctionEval,ts,U,Udot,Y);
    747:   return(0);
    748: }

    752: /*@
    753:    TSComputeIJacobian - Evaluates the Jacobian of the DAE

    755:    Collective on TS and Vec

    757:    Input
    758:       Input Parameters:
    759: +  ts - the TS context
    760: .  t - current timestep
    761: .  U - state vector
    762: .  Udot - time derivative of state vector
    763: .  shift - shift to apply, see note below
    764: -  imex - flag indicates if the method is IMEX so that the RHSJacobian should be kept separate

    766:    Output Parameters:
    767: +  A - Jacobian matrix
    768: .  B - optional preconditioning matrix
    769: -  flag - flag indicating matrix structure

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

    774:    dF/dU + shift*dF/dUdot

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

    779:    Level: developer

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

    783: .seealso:  TSSetIJacobian()
    784: @*/
    785: PetscErrorCode TSComputeIJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat A,Mat B,PetscBool imex)
    786: {
    788:   TSIJacobian    ijacobian;
    789:   TSRHSJacobian  rhsjacobian;
    790:   DM             dm;
    791:   void           *ctx;

    802:   TSGetDM(ts,&dm);
    803:   DMTSGetIJacobian(dm,&ijacobian,&ctx);
    804:   DMTSGetRHSJacobian(dm,&rhsjacobian,NULL);

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

    808:   PetscLogEventBegin(TS_JacobianEval,ts,U,A,B);
    809:   if (ijacobian) {
    810:     PetscStackPush("TS user implicit Jacobian");
    811:     (*ijacobian)(ts,t,U,Udot,shift,A,B,ctx);
    812:     PetscStackPop;
    813:     /* make sure user returned a correct Jacobian and preconditioner */
    816:   }
    817:   if (imex) {
    818:     if (!ijacobian) {  /* system was written as Udot = G(t,U) */
    819:       MatZeroEntries(A);
    820:       MatShift(A,shift);
    821:       if (A != B) {
    822:         MatZeroEntries(B);
    823:         MatShift(B,shift);
    824:       }
    825:     }
    826:   } else {
    827:     Mat Arhs = NULL,Brhs = NULL;
    828:     if (rhsjacobian) {
    829:       if (ijacobian) {
    830:         TSGetRHSMats_Private(ts,&Arhs,&Brhs);
    831:       } else {
    832:         TSGetIJacobian(ts,&Arhs,&Brhs,NULL,NULL);
    833:       }
    834:       TSComputeRHSJacobian(ts,t,U,Arhs,Brhs);
    835:     }
    836:     if (Arhs == A) {           /* No IJacobian, so we only have the RHS matrix */
    837:       ts->rhsjacobian.scale = -1;
    838:       ts->rhsjacobian.shift = shift;
    839:       MatScale(A,-1);
    840:       MatShift(A,shift);
    841:       if (A != B) {
    842:         MatScale(B,-1);
    843:         MatShift(B,shift);
    844:       }
    845:     } else if (Arhs) {          /* Both IJacobian and RHSJacobian */
    846:       MatStructure axpy = DIFFERENT_NONZERO_PATTERN;
    847:       if (!ijacobian) {         /* No IJacobian provided, but we have a separate RHS matrix */
    848:         MatZeroEntries(A);
    849:         MatShift(A,shift);
    850:         if (A != B) {
    851:           MatZeroEntries(B);
    852:           MatShift(B,shift);
    853:         }
    854:       }
    855:       MatAXPY(A,-1,Arhs,axpy);
    856:       if (A != B) {
    857:         MatAXPY(B,-1,Brhs,axpy);
    858:       }
    859:     }
    860:   }
    861:   PetscLogEventEnd(TS_JacobianEval,ts,U,A,B);
    862:   return(0);
    863: }

    867: /*@C
    868:     TSSetRHSFunction - Sets the routine for evaluating the function,
    869:     where U_t = G(t,u).

    871:     Logically Collective on TS

    873:     Input Parameters:
    874: +   ts - the TS context obtained from TSCreate()
    875: .   r - vector to put the computed right hand side (or NULL to have it created)
    876: .   f - routine for evaluating the right-hand-side function
    877: -   ctx - [optional] user-defined context for private data for the
    878:           function evaluation routine (may be NULL)

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

    883: +   t - current timestep
    884: .   u - input vector
    885: .   F - function vector
    886: -   ctx - [optional] user-defined function context

    888:     Level: beginner

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

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

    894: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSSetIFunction()
    895: @*/
    896: PetscErrorCode  TSSetRHSFunction(TS ts,Vec r,PetscErrorCode (*f)(TS,PetscReal,Vec,Vec,void*),void *ctx)
    897: {
    899:   SNES           snes;
    900:   Vec            ralloc = NULL;
    901:   DM             dm;

    907:   TSGetDM(ts,&dm);
    908:   DMTSSetRHSFunction(dm,f,ctx);
    909:   TSGetSNES(ts,&snes);
    910:   if (!r && !ts->dm && ts->vec_sol) {
    911:     VecDuplicate(ts->vec_sol,&ralloc);
    912:     r    = ralloc;
    913:   }
    914:   SNESSetFunction(snes,r,SNESTSFormFunction,ts);
    915:   VecDestroy(&ralloc);
    916:   return(0);
    917: }

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

    924:     Logically Collective on TS

    926:     Input Parameters:
    927: +   ts - the TS context obtained from TSCreate()
    928: .   f - routine for evaluating the solution
    929: -   ctx - [optional] user-defined context for private data for the
    930:           function evaluation routine (may be NULL)

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

    935: +   t - current timestep
    936: .   u - output vector
    937: -   ctx - [optional] user-defined function context

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

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

    946:     Level: beginner

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

    950: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSComputeSolutionFunction(), TSSetForcingFunction()
    951: @*/
    952: PetscErrorCode  TSSetSolutionFunction(TS ts,PetscErrorCode (*f)(TS,PetscReal,Vec,void*),void *ctx)
    953: {
    955:   DM             dm;

    959:   TSGetDM(ts,&dm);
    960:   DMTSSetSolutionFunction(dm,f,ctx);
    961:   return(0);
    962: }

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

    969:     Logically Collective on TS

    971:     Input Parameters:
    972: +   ts - the TS context obtained from TSCreate()
    973: .   f - routine for evaluating the forcing function
    974: -   ctx - [optional] user-defined context for private data for the
    975:           function evaluation routine (may be NULL)

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

    980: +   t - current timestep
    981: .   u - output vector
    982: -   ctx - [optional] user-defined function context

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

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

    990:     Level: beginner

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

    994: .seealso: TSSetRHSJacobian(), TSSetIJacobian(), TSComputeSolutionFunction(), TSSetSolutionFunction()
    995: @*/
    996: PetscErrorCode  TSSetForcingFunction(TS ts,PetscErrorCode (*f)(TS,PetscReal,Vec,void*),void *ctx)
    997: {
    999:   DM             dm;

    1003:   TSGetDM(ts,&dm);
    1004:   DMTSSetForcingFunction(dm,f,ctx);
    1005:   return(0);
    1006: }

    1010: /*@C
    1011:    TSSetRHSJacobian - Sets the function to compute the Jacobian of G,
    1012:    where U_t = G(U,t), as well as the location to store the matrix.

    1014:    Logically Collective on TS

    1016:    Input Parameters:
    1017: +  ts  - the TS context obtained from TSCreate()
    1018: .  Amat - (approximate) Jacobian matrix
    1019: .  Pmat - matrix from which preconditioner is to be constructed (usually the same as Amat)
    1020: .  f   - the Jacobian evaluation routine
    1021: -  ctx - [optional] user-defined context for private data for the
    1022:          Jacobian evaluation routine (may be NULL)

    1024:    Calling sequence of f:
    1025: $     func (TS ts,PetscReal t,Vec u,Mat A,Mat B,void *ctx);

    1027: +  t - current timestep
    1028: .  u - input vector
    1029: .  Amat - (approximate) Jacobian matrix
    1030: .  Pmat - matrix from which preconditioner is to be constructed (usually the same as Amat)
    1031: -  ctx - [optional] user-defined context for matrix evaluation routine

    1034:    Level: beginner

    1036: .keywords: TS, timestep, set, right-hand-side, Jacobian

    1038: .seealso: SNESComputeJacobianDefaultColor(), TSSetRHSFunction(), TSRHSJacobianSetReuse(), TSSetIJacobian()

    1040: @*/
    1041: PetscErrorCode  TSSetRHSJacobian(TS ts,Mat Amat,Mat Pmat,TSRHSJacobian f,void *ctx)
    1042: {
    1044:   SNES           snes;
    1045:   DM             dm;
    1046:   TSIJacobian    ijacobian;

    1055:   TSGetDM(ts,&dm);
    1056:   DMTSSetRHSJacobian(dm,f,ctx);
    1057:   if (f == TSComputeRHSJacobianConstant) {
    1058:     /* Handle this case automatically for the user; otherwise user should call themselves. */
    1059:     TSRHSJacobianSetReuse(ts,PETSC_TRUE);
    1060:   }
    1061:   DMTSGetIJacobian(dm,&ijacobian,NULL);
    1062:   TSGetSNES(ts,&snes);
    1063:   if (!ijacobian) {
    1064:     SNESSetJacobian(snes,Amat,Pmat,SNESTSFormJacobian,ts);
    1065:   }
    1066:   if (Amat) {
    1067:     PetscObjectReference((PetscObject)Amat);
    1068:     MatDestroy(&ts->Arhs);

    1070:     ts->Arhs = Amat;
    1071:   }
    1072:   if (Pmat) {
    1073:     PetscObjectReference((PetscObject)Pmat);
    1074:     MatDestroy(&ts->Brhs);

    1076:     ts->Brhs = Pmat;
    1077:   }
    1078:   return(0);
    1079: }

    1084: /*@C
    1085:    TSSetIFunction - Set the function to compute F(t,U,U_t) where F() = 0 is the DAE to be solved.

    1087:    Logically Collective on TS

    1089:    Input Parameters:
    1090: +  ts  - the TS context obtained from TSCreate()
    1091: .  r   - vector to hold the residual (or NULL to have it created internally)
    1092: .  f   - the function evaluation routine
    1093: -  ctx - user-defined context for private data for the function evaluation routine (may be NULL)

    1095:    Calling sequence of f:
    1096: $  f(TS ts,PetscReal t,Vec u,Vec u_t,Vec F,ctx);

    1098: +  t   - time at step/stage being solved
    1099: .  u   - state vector
    1100: .  u_t - time derivative of state vector
    1101: .  F   - function vector
    1102: -  ctx - [optional] user-defined context for matrix evaluation routine

    1104:    Important:
    1105:    The user MUST call either this routine or TSSetRHSFunction() to define the ODE.  When solving DAEs you must use this function.

    1107:    Level: beginner

    1109: .keywords: TS, timestep, set, DAE, Jacobian

    1111: .seealso: TSSetRHSJacobian(), TSSetRHSFunction(), TSSetIJacobian()
    1112: @*/
    1113: PetscErrorCode  TSSetIFunction(TS ts,Vec res,TSIFunction f,void *ctx)
    1114: {
    1116:   SNES           snes;
    1117:   Vec            resalloc = NULL;
    1118:   DM             dm;

    1124:   TSGetDM(ts,&dm);
    1125:   DMTSSetIFunction(dm,f,ctx);

    1127:   TSGetSNES(ts,&snes);
    1128:   if (!res && !ts->dm && ts->vec_sol) {
    1129:     VecDuplicate(ts->vec_sol,&resalloc);
    1130:     res  = resalloc;
    1131:   }
    1132:   SNESSetFunction(snes,res,SNESTSFormFunction,ts);
    1133:   VecDestroy(&resalloc);
    1134:   return(0);
    1135: }

    1139: /*@C
    1140:    TSGetIFunction - Returns the vector where the implicit residual is stored and the function/contex to compute it.

    1142:    Not Collective

    1144:    Input Parameter:
    1145: .  ts - the TS context

    1147:    Output Parameter:
    1148: +  r - vector to hold residual (or NULL)
    1149: .  func - the function to compute residual (or NULL)
    1150: -  ctx - the function context (or NULL)

    1152:    Level: advanced

    1154: .keywords: TS, nonlinear, get, function

    1156: .seealso: TSSetIFunction(), SNESGetFunction()
    1157: @*/
    1158: PetscErrorCode TSGetIFunction(TS ts,Vec *r,TSIFunction *func,void **ctx)
    1159: {
    1161:   SNES           snes;
    1162:   DM             dm;

    1166:   TSGetSNES(ts,&snes);
    1167:   SNESGetFunction(snes,r,NULL,NULL);
    1168:   TSGetDM(ts,&dm);
    1169:   DMTSGetIFunction(dm,func,ctx);
    1170:   return(0);
    1171: }

    1175: /*@C
    1176:    TSGetRHSFunction - Returns the vector where the right hand side is stored and the function/context to compute it.

    1178:    Not Collective

    1180:    Input Parameter:
    1181: .  ts - the TS context

    1183:    Output Parameter:
    1184: +  r - vector to hold computed right hand side (or NULL)
    1185: .  func - the function to compute right hand side (or NULL)
    1186: -  ctx - the function context (or NULL)

    1188:    Level: advanced

    1190: .keywords: TS, nonlinear, get, function

    1192: .seealso: TSSetRHSFunction(), SNESGetFunction()
    1193: @*/
    1194: PetscErrorCode TSGetRHSFunction(TS ts,Vec *r,TSRHSFunction *func,void **ctx)
    1195: {
    1197:   SNES           snes;
    1198:   DM             dm;

    1202:   TSGetSNES(ts,&snes);
    1203:   SNESGetFunction(snes,r,NULL,NULL);
    1204:   TSGetDM(ts,&dm);
    1205:   DMTSGetRHSFunction(dm,func,ctx);
    1206:   return(0);
    1207: }

    1211: /*@C
    1212:    TSSetIJacobian - Set the function to compute the matrix dF/dU + a*dF/dU_t where F(t,U,U_t) is the function
    1213:         provided with TSSetIFunction().

    1215:    Logically Collective on TS

    1217:    Input Parameters:
    1218: +  ts  - the TS context obtained from TSCreate()
    1219: .  Amat - (approximate) Jacobian matrix
    1220: .  Pmat - matrix used to compute preconditioner (usually the same as Amat)
    1221: .  f   - the Jacobian evaluation routine
    1222: -  ctx - user-defined context for private data for the Jacobian evaluation routine (may be NULL)

    1224:    Calling sequence of f:
    1225: $  f(TS ts,PetscReal t,Vec U,Vec U_t,PetscReal a,Mat Amat,Mat Pmat,void *ctx);

    1227: +  t    - time at step/stage being solved
    1228: .  U    - state vector
    1229: .  U_t  - time derivative of state vector
    1230: .  a    - shift
    1231: .  Amat - (approximate) Jacobian of F(t,U,W+a*U), equivalent to dF/dU + a*dF/dU_t
    1232: .  Pmat - matrix used for constructing preconditioner, usually the same as Amat
    1233: -  ctx  - [optional] user-defined context for matrix evaluation routine

    1235:    Notes:
    1236:    The matrices Amat and Pmat are exactly the matrices that are used by SNES for the nonlinear solve.

    1238:    If you know the operator Amat has a null space you can use MatSetNullSpace() and MatSetTransposeNullSpace() to supply the null
    1239:    space to Amat and the KSP solvers will automatically use that null space as needed during the solution process.

    1241:    The matrix dF/dU + a*dF/dU_t you provide turns out to be
    1242:    the Jacobian of F(t,U,W+a*U) where F(t,U,U_t) = 0 is the DAE to be solved.
    1243:    The time integrator internally approximates U_t by W+a*U where the positive "shift"
    1244:    a and vector W depend on the integration method, step size, and past states. For example with
    1245:    the backward Euler method a = 1/dt and W = -a*U(previous timestep) so
    1246:    W + a*U = a*(U - U(previous timestep)) = (U - U(previous timestep))/dt

    1248:    Level: beginner

    1250: .keywords: TS, timestep, DAE, Jacobian

    1252: .seealso: TSSetIFunction(), TSSetRHSJacobian(), SNESComputeJacobianDefaultColor(), SNESComputeJacobianDefault(), TSSetRHSFunction()

    1254: @*/
    1255: PetscErrorCode  TSSetIJacobian(TS ts,Mat Amat,Mat Pmat,TSIJacobian f,void *ctx)
    1256: {
    1258:   SNES           snes;
    1259:   DM             dm;

    1268:   TSGetDM(ts,&dm);
    1269:   DMTSSetIJacobian(dm,f,ctx);

    1271:   TSGetSNES(ts,&snes);
    1272:   SNESSetJacobian(snes,Amat,Pmat,SNESTSFormJacobian,ts);
    1273:   return(0);
    1274: }

    1278: /*@
    1279:    TSRHSJacobianSetReuse - restore RHS Jacobian before re-evaluating.  Without this flag, TS will change the sign and
    1280:    shift the RHS Jacobian for a finite-time-step implicit solve, in which case the user function will need to recompute
    1281:    the entire Jacobian.  The reuse flag must be set if the evaluation function will assume that the matrix entries have
    1282:    not been changed by the TS.

    1284:    Logically Collective

    1286:    Input Arguments:
    1287: +  ts - TS context obtained from TSCreate()
    1288: -  reuse - PETSC_TRUE if the RHS Jacobian

    1290:    Level: intermediate

    1292: .seealso: TSSetRHSJacobian(), TSComputeRHSJacobianConstant()
    1293: @*/
    1294: PetscErrorCode TSRHSJacobianSetReuse(TS ts,PetscBool reuse)
    1295: {
    1297:   ts->rhsjacobian.reuse = reuse;
    1298:   return(0);
    1299: }

    1303: /*@C
    1304:   TSLoad - Loads a KSP that has been stored in binary  with KSPView().

    1306:   Collective on PetscViewer

    1308:   Input Parameters:
    1309: + newdm - the newly loaded TS, this needs to have been created with TSCreate() or
    1310:            some related function before a call to TSLoad().
    1311: - viewer - binary file viewer, obtained from PetscViewerBinaryOpen()

    1313:    Level: intermediate

    1315:   Notes:
    1316:    The type is determined by the data in the file, any type set into the TS before this call is ignored.

    1318:   Notes for advanced users:
    1319:   Most users should not need to know the details of the binary storage
    1320:   format, since TSLoad() and TSView() completely hide these details.
    1321:   But for anyone who's interested, the standard binary matrix storage
    1322:   format is
    1323: .vb
    1324:      has not yet been determined
    1325: .ve

    1327: .seealso: PetscViewerBinaryOpen(), TSView(), MatLoad(), VecLoad()
    1328: @*/
    1329: PetscErrorCode  TSLoad(TS ts, PetscViewer viewer)
    1330: {
    1332:   PetscBool      isbinary;
    1333:   PetscInt       classid;
    1334:   char           type[256];
    1335:   DMTS           sdm;
    1336:   DM             dm;

    1341:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
    1342:   if (!isbinary) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid viewer; open viewer with PetscViewerBinaryOpen()");

    1344:   PetscViewerBinaryRead(viewer,&classid,1,NULL,PETSC_INT);
    1345:   if (classid != TS_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_WRONG,"Not TS next in file");
    1346:   PetscViewerBinaryRead(viewer,type,256,NULL,PETSC_CHAR);
    1347:   TSSetType(ts, type);
    1348:   if (ts->ops->load) {
    1349:     (*ts->ops->load)(ts,viewer);
    1350:   }
    1351:   DMCreate(PetscObjectComm((PetscObject)ts),&dm);
    1352:   DMLoad(dm,viewer);
    1353:   TSSetDM(ts,dm);
    1354:   DMCreateGlobalVector(ts->dm,&ts->vec_sol);
    1355:   VecLoad(ts->vec_sol,viewer);
    1356:   DMGetDMTS(ts->dm,&sdm);
    1357:   DMTSLoad(sdm,viewer);
    1358:   return(0);
    1359: }

    1361: #include <petscdraw.h>
    1362: #if defined(PETSC_HAVE_SAWS)
    1363: #include <petscviewersaws.h>
    1364: #endif
    1367: /*@C
    1368:     TSView - Prints the TS data structure.

    1370:     Collective on TS

    1372:     Input Parameters:
    1373: +   ts - the TS context obtained from TSCreate()
    1374: -   viewer - visualization context

    1376:     Options Database Key:
    1377: .   -ts_view - calls TSView() at end of TSStep()

    1379:     Notes:
    1380:     The available visualization contexts include
    1381: +     PETSC_VIEWER_STDOUT_SELF - standard output (default)
    1382: -     PETSC_VIEWER_STDOUT_WORLD - synchronized standard
    1383:          output where only the first processor opens
    1384:          the file.  All other processors send their
    1385:          data to the first processor to print.

    1387:     The user can open an alternative visualization context with
    1388:     PetscViewerASCIIOpen() - output to a specified file.

    1390:     Level: beginner

    1392: .keywords: TS, timestep, view

    1394: .seealso: PetscViewerASCIIOpen()
    1395: @*/
    1396: PetscErrorCode  TSView(TS ts,PetscViewer viewer)
    1397: {
    1399:   TSType         type;
    1400:   PetscBool      iascii,isstring,isundials,isbinary,isdraw;
    1401:   DMTS           sdm;
    1402: #if defined(PETSC_HAVE_SAWS)
    1403:   PetscBool      issaws;
    1404: #endif

    1408:   if (!viewer) {
    1409:     PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)ts),&viewer);
    1410:   }

    1414:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
    1415:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);
    1416:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
    1417:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
    1418: #if defined(PETSC_HAVE_SAWS)
    1419:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);
    1420: #endif
    1421:   if (iascii) {
    1422:     PetscObjectPrintClassNamePrefixType((PetscObject)ts,viewer);
    1423:     PetscViewerASCIIPrintf(viewer,"  maximum steps=%D\n",ts->max_steps);
    1424:     PetscViewerASCIIPrintf(viewer,"  maximum time=%g\n",(double)ts->max_time);
    1425:     if (ts->problem_type == TS_NONLINEAR) {
    1426:       PetscViewerASCIIPrintf(viewer,"  total number of nonlinear solver iterations=%D\n",ts->snes_its);
    1427:       PetscViewerASCIIPrintf(viewer,"  total number of nonlinear solve failures=%D\n",ts->num_snes_failures);
    1428:     }
    1429:     PetscViewerASCIIPrintf(viewer,"  total number of linear solver iterations=%D\n",ts->ksp_its);
    1430:     PetscViewerASCIIPrintf(viewer,"  total number of rejected steps=%D\n",ts->reject);
    1431:     DMGetDMTS(ts->dm,&sdm);
    1432:     DMTSView(sdm,viewer);
    1433:     if (ts->ops->view) {
    1434:       PetscViewerASCIIPushTab(viewer);
    1435:       (*ts->ops->view)(ts,viewer);
    1436:       PetscViewerASCIIPopTab(viewer);
    1437:     }
    1438:   } else if (isstring) {
    1439:     TSGetType(ts,&type);
    1440:     PetscViewerStringSPrintf(viewer," %-7.7s",type);
    1441:   } else if (isbinary) {
    1442:     PetscInt    classid = TS_FILE_CLASSID;
    1443:     MPI_Comm    comm;
    1444:     PetscMPIInt rank;
    1445:     char        type[256];

    1447:     PetscObjectGetComm((PetscObject)ts,&comm);
    1448:     MPI_Comm_rank(comm,&rank);
    1449:     if (!rank) {
    1450:       PetscViewerBinaryWrite(viewer,&classid,1,PETSC_INT,PETSC_FALSE);
    1451:       PetscStrncpy(type,((PetscObject)ts)->type_name,256);
    1452:       PetscViewerBinaryWrite(viewer,type,256,PETSC_CHAR,PETSC_FALSE);
    1453:     }
    1454:     if (ts->ops->view) {
    1455:       (*ts->ops->view)(ts,viewer);
    1456:     }
    1457:     DMView(ts->dm,viewer);
    1458:     VecView(ts->vec_sol,viewer);
    1459:     DMGetDMTS(ts->dm,&sdm);
    1460:     DMTSView(sdm,viewer);
    1461:   } else if (isdraw) {
    1462:     PetscDraw draw;
    1463:     char      str[36];
    1464:     PetscReal x,y,bottom,h;

    1466:     PetscViewerDrawGetDraw(viewer,0,&draw);
    1467:     PetscDrawGetCurrentPoint(draw,&x,&y);
    1468:     PetscStrcpy(str,"TS: ");
    1469:     PetscStrcat(str,((PetscObject)ts)->type_name);
    1470:     PetscDrawStringBoxed(draw,x,y,PETSC_DRAW_BLACK,PETSC_DRAW_BLACK,str,NULL,&h);
    1471:     bottom = y - h;
    1472:     PetscDrawPushCurrentPoint(draw,x,bottom);
    1473:     if (ts->ops->view) {
    1474:       (*ts->ops->view)(ts,viewer);
    1475:     }
    1476:     PetscDrawPopCurrentPoint(draw);
    1477: #if defined(PETSC_HAVE_SAWS)
    1478:   } else if (issaws) {
    1479:     PetscMPIInt rank;
    1480:     const char  *name;

    1482:     PetscObjectGetName((PetscObject)ts,&name);
    1483:     MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
    1484:     if (!((PetscObject)ts)->amsmem && !rank) {
    1485:       char       dir[1024];

    1487:       PetscObjectViewSAWs((PetscObject)ts,viewer);
    1488:       PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/time_step",name);
    1489:       PetscStackCallSAWs(SAWs_Register,(dir,&ts->steps,1,SAWs_READ,SAWs_INT));
    1490:       PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/time",name);
    1491:       PetscStackCallSAWs(SAWs_Register,(dir,&ts->ptime,1,SAWs_READ,SAWs_DOUBLE));
    1492:     }
    1493:     if (ts->ops->view) {
    1494:       (*ts->ops->view)(ts,viewer);
    1495:     }
    1496: #endif
    1497:   }

    1499:   PetscViewerASCIIPushTab(viewer);
    1500:   PetscObjectTypeCompare((PetscObject)ts,TSSUNDIALS,&isundials);
    1501:   PetscViewerASCIIPopTab(viewer);
    1502:   return(0);
    1503: }

    1508: /*@
    1509:    TSSetApplicationContext - Sets an optional user-defined context for
    1510:    the timesteppers.

    1512:    Logically Collective on TS

    1514:    Input Parameters:
    1515: +  ts - the TS context obtained from TSCreate()
    1516: -  usrP - optional user context

    1518:    Level: intermediate

    1520: .keywords: TS, timestep, set, application, context

    1522: .seealso: TSGetApplicationContext()
    1523: @*/
    1524: PetscErrorCode  TSSetApplicationContext(TS ts,void *usrP)
    1525: {
    1528:   ts->user = usrP;
    1529:   return(0);
    1530: }

    1534: /*@
    1535:     TSGetApplicationContext - Gets the user-defined context for the
    1536:     timestepper.

    1538:     Not Collective

    1540:     Input Parameter:
    1541: .   ts - the TS context obtained from TSCreate()

    1543:     Output Parameter:
    1544: .   usrP - user context

    1546:     Level: intermediate

    1548: .keywords: TS, timestep, get, application, context

    1550: .seealso: TSSetApplicationContext()
    1551: @*/
    1552: PetscErrorCode  TSGetApplicationContext(TS ts,void *usrP)
    1553: {
    1556:   *(void**)usrP = ts->user;
    1557:   return(0);
    1558: }

    1562: /*@
    1563:    TSGetTimeStepNumber - Gets the number of time steps completed.

    1565:    Not Collective

    1567:    Input Parameter:
    1568: .  ts - the TS context obtained from TSCreate()

    1570:    Output Parameter:
    1571: .  iter - number of steps completed so far

    1573:    Level: intermediate

    1575: .keywords: TS, timestep, get, iteration, number
    1576: .seealso: TSGetTime(), TSGetTimeStep(), TSSetPreStep(), TSSetPreStage(), TSSetPostStage(), TSSetPostStep()
    1577: @*/
    1578: PetscErrorCode  TSGetTimeStepNumber(TS ts,PetscInt *iter)
    1579: {
    1583:   *iter = ts->steps;
    1584:   return(0);
    1585: }

    1589: /*@
    1590:    TSSetInitialTimeStep - Sets the initial timestep to be used,
    1591:    as well as the initial time.

    1593:    Logically Collective on TS

    1595:    Input Parameters:
    1596: +  ts - the TS context obtained from TSCreate()
    1597: .  initial_time - the initial time
    1598: -  time_step - the size of the timestep

    1600:    Level: intermediate

    1602: .seealso: TSSetTimeStep(), TSGetTimeStep()

    1604: .keywords: TS, set, initial, timestep
    1605: @*/
    1606: PetscErrorCode  TSSetInitialTimeStep(TS ts,PetscReal initial_time,PetscReal time_step)
    1607: {

    1612:   TSSetTimeStep(ts,time_step);
    1613:   TSSetTime(ts,initial_time);
    1614:   return(0);
    1615: }

    1619: /*@
    1620:    TSSetTimeStep - Allows one to reset the timestep at any time,
    1621:    useful for simple pseudo-timestepping codes.

    1623:    Logically Collective on TS

    1625:    Input Parameters:
    1626: +  ts - the TS context obtained from TSCreate()
    1627: -  time_step - the size of the timestep

    1629:    Level: intermediate

    1631: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

    1633: .keywords: TS, set, timestep
    1634: @*/
    1635: PetscErrorCode  TSSetTimeStep(TS ts,PetscReal time_step)
    1636: {
    1640:   ts->time_step      = time_step;
    1641:   ts->time_step_orig = time_step;
    1642:   return(0);
    1643: }

    1647: /*@
    1648:    TSSetExactFinalTime - Determines whether to adapt the final time step to
    1649:      match the exact final time, interpolate solution to the exact final time,
    1650:      or just return at the final time TS computed.

    1652:   Logically Collective on TS

    1654:    Input Parameter:
    1655: +   ts - the time-step context
    1656: -   eftopt - exact final time option

    1658:    Level: beginner

    1660: .seealso: TSExactFinalTimeOption
    1661: @*/
    1662: PetscErrorCode  TSSetExactFinalTime(TS ts,TSExactFinalTimeOption eftopt)
    1663: {
    1667:   ts->exact_final_time = eftopt;
    1668:   return(0);
    1669: }

    1673: /*@
    1674:    TSGetTimeStep - Gets the current timestep size.

    1676:    Not Collective

    1678:    Input Parameter:
    1679: .  ts - the TS context obtained from TSCreate()

    1681:    Output Parameter:
    1682: .  dt - the current timestep size

    1684:    Level: intermediate

    1686: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

    1688: .keywords: TS, get, timestep
    1689: @*/
    1690: PetscErrorCode  TSGetTimeStep(TS ts,PetscReal *dt)
    1691: {
    1695:   *dt = ts->time_step;
    1696:   return(0);
    1697: }

    1701: /*@
    1702:    TSGetSolution - Returns the solution at the present timestep. It
    1703:    is valid to call this routine inside the function that you are evaluating
    1704:    in order to move to the new timestep. This vector not changed until
    1705:    the solution at the next timestep has been calculated.

    1707:    Not Collective, but Vec returned is parallel if TS is parallel

    1709:    Input Parameter:
    1710: .  ts - the TS context obtained from TSCreate()

    1712:    Output Parameter:
    1713: .  v - the vector containing the solution

    1715:    Level: intermediate

    1717: .seealso: TSGetTimeStep()

    1719: .keywords: TS, timestep, get, solution
    1720: @*/
    1721: PetscErrorCode  TSGetSolution(TS ts,Vec *v)
    1722: {
    1726:   *v = ts->vec_sol;
    1727:   return(0);
    1728: }

    1732: /*@
    1733:    TSGetCostGradients - Returns the gradients from the TSAdjointSolve()

    1735:    Not Collective, but Vec returned is parallel if TS is parallel

    1737:    Input Parameter:
    1738: .  ts - the TS context obtained from TSCreate()

    1740:    Output Parameter:
    1741: +  lambda - vectors containing the gradients of the cost functions with respect to the ODE/DAE solution variables
    1742: -  mu - vectors containing the gradients of the cost functions with respect to the problem parameters

    1744:    Level: intermediate

    1746: .seealso: TSGetTimeStep()

    1748: .keywords: TS, timestep, get, sensitivity
    1749: @*/
    1750: PetscErrorCode  TSGetCostGradients(TS ts,PetscInt *numcost,Vec **lambda,Vec **mu)
    1751: {
    1754:   if (numcost) *numcost = ts->numcost;
    1755:   if (lambda)  *lambda  = ts->vecs_sensi;
    1756:   if (mu)      *mu      = ts->vecs_sensip;
    1757:   return(0);
    1758: }

    1760: /* ----- Routines to initialize and destroy a timestepper ---- */
    1763: /*@
    1764:   TSSetProblemType - Sets the type of problem to be solved.

    1766:   Not collective

    1768:   Input Parameters:
    1769: + ts   - The TS
    1770: - type - One of TS_LINEAR, TS_NONLINEAR where these types refer to problems of the forms
    1771: .vb
    1772:          U_t - A U = 0      (linear)
    1773:          U_t - A(t) U = 0   (linear)
    1774:          F(t,U,U_t) = 0     (nonlinear)
    1775: .ve

    1777:    Level: beginner

    1779: .keywords: TS, problem type
    1780: .seealso: TSSetUp(), TSProblemType, TS
    1781: @*/
    1782: PetscErrorCode  TSSetProblemType(TS ts, TSProblemType type)
    1783: {

    1788:   ts->problem_type = type;
    1789:   if (type == TS_LINEAR) {
    1790:     SNES snes;
    1791:     TSGetSNES(ts,&snes);
    1792:     SNESSetType(snes,SNESKSPONLY);
    1793:   }
    1794:   return(0);
    1795: }

    1799: /*@C
    1800:   TSGetProblemType - Gets the type of problem to be solved.

    1802:   Not collective

    1804:   Input Parameter:
    1805: . ts   - The TS

    1807:   Output Parameter:
    1808: . type - One of TS_LINEAR, TS_NONLINEAR where these types refer to problems of the forms
    1809: .vb
    1810:          M U_t = A U
    1811:          M(t) U_t = A(t) U
    1812:          F(t,U,U_t)
    1813: .ve

    1815:    Level: beginner

    1817: .keywords: TS, problem type
    1818: .seealso: TSSetUp(), TSProblemType, TS
    1819: @*/
    1820: PetscErrorCode  TSGetProblemType(TS ts, TSProblemType *type)
    1821: {
    1825:   *type = ts->problem_type;
    1826:   return(0);
    1827: }

    1831: /*@
    1832:    TSSetUp - Sets up the internal data structures for the later use
    1833:    of a timestepper.

    1835:    Collective on TS

    1837:    Input Parameter:
    1838: .  ts - the TS context obtained from TSCreate()

    1840:    Notes:
    1841:    For basic use of the TS solvers the user need not explicitly call
    1842:    TSSetUp(), since these actions will automatically occur during
    1843:    the call to TSStep().  However, if one wishes to control this
    1844:    phase separately, TSSetUp() should be called after TSCreate()
    1845:    and optional routines of the form TSSetXXX(), but before TSStep().

    1847:    Level: advanced

    1849: .keywords: TS, timestep, setup

    1851: .seealso: TSCreate(), TSStep(), TSDestroy()
    1852: @*/
    1853: PetscErrorCode  TSSetUp(TS ts)
    1854: {
    1856:   DM             dm;
    1857:   PetscErrorCode (*func)(SNES,Vec,Vec,void*);
    1858:   PetscErrorCode (*jac)(SNES,Vec,Mat,Mat,void*);
    1859:   TSIJacobian    ijac;
    1860:   TSRHSJacobian  rhsjac;

    1864:   if (ts->setupcalled) return(0);

    1866:   ts->total_steps = 0;
    1867:   if (!((PetscObject)ts)->type_name) {
    1868:     TSSetType(ts,TSEULER);
    1869:   }

    1871:   if (!ts->vec_sol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call TSSetSolution() first");

    1874:   TSGetAdapt(ts,&ts->adapt);

    1876:   if (ts->rhsjacobian.reuse) {
    1877:     Mat Amat,Pmat;
    1878:     SNES snes;
    1879:     TSGetSNES(ts,&snes);
    1880:     SNESGetJacobian(snes,&Amat,&Pmat,NULL,NULL);
    1881:     /* Matching matrices implies that an IJacobian is NOT set, because if it had been set, the IJacobian's matrix would
    1882:      * have displaced the RHS matrix */
    1883:     if (Amat == ts->Arhs) {
    1884:       MatDuplicate(ts->Arhs,MAT_DO_NOT_COPY_VALUES,&Amat);
    1885:       SNESSetJacobian(snes,Amat,NULL,NULL,NULL);
    1886:       MatDestroy(&Amat);
    1887:     }
    1888:     if (Pmat == ts->Brhs) {
    1889:       MatDuplicate(ts->Brhs,MAT_DO_NOT_COPY_VALUES,&Pmat);
    1890:       SNESSetJacobian(snes,NULL,Pmat,NULL,NULL);
    1891:       MatDestroy(&Pmat);
    1892:     }
    1893:   }
    1894:   if (ts->ops->setup) {
    1895:     (*ts->ops->setup)(ts);
    1896:   }

    1898:   /* in the case where we've set a DMTSFunction or what have you, we need the default SNESFunction
    1899:    to be set right but can't do it elsewhere due to the overreliance on ctx=ts.
    1900:    */
    1901:   TSGetDM(ts,&dm);
    1902:   DMSNESGetFunction(dm,&func,NULL);
    1903:   if (!func) {
    1904:     ierr =DMSNESSetFunction(dm,SNESTSFormFunction,ts);
    1905:   }
    1906:   /* if the SNES doesn't have a jacobian set and the TS has an ijacobian or rhsjacobian set, set the SNES to use it.
    1907:      Otherwise, the SNES will use coloring internally to form the Jacobian.
    1908:    */
    1909:   DMSNESGetJacobian(dm,&jac,NULL);
    1910:   DMTSGetIJacobian(dm,&ijac,NULL);
    1911:   DMTSGetRHSJacobian(dm,&rhsjac,NULL);
    1912:   if (!jac && (ijac || rhsjac)) {
    1913:     DMSNESSetJacobian(dm,SNESTSFormJacobian,ts);
    1914:   }
    1915:   ts->setupcalled = PETSC_TRUE;
    1916:   return(0);
    1917: }

    1921: /*@
    1922:    TSAdjointSetUp - Sets up the internal data structures for the later use
    1923:    of an adjoint solver

    1925:    Collective on TS

    1927:    Input Parameter:
    1928: .  ts - the TS context obtained from TSCreate()

    1930:    Level: advanced

    1932: .keywords: TS, timestep, setup

    1934: .seealso: TSCreate(), TSAdjointStep(), TSSetCostGradients()
    1935: @*/
    1936: PetscErrorCode  TSAdjointSetUp(TS ts)
    1937: {

    1942:   if (ts->adjointsetupcalled) return(0);
    1943:   if (!ts->vecs_sensi) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call TSSetCostGradients() first");

    1945:   if (ts->vec_costintegral) { /* if there is integral in the cost function*/
    1946:     VecDuplicateVecs(ts->vecs_sensi[0],ts->numcost,&ts->vecs_drdy);
    1947:     if (ts->vecs_sensip){
    1948:       VecDuplicateVecs(ts->vecs_sensip[0],ts->numcost,&ts->vecs_drdp);
    1949:     }
    1950:   }

    1952:   if (ts->ops->adjointsetup) {
    1953:     (*ts->ops->adjointsetup)(ts);
    1954:   }
    1955:   ts->adjointsetupcalled = PETSC_TRUE;
    1956:   return(0);
    1957: }

    1961: /*@
    1962:    TSReset - Resets a TS context and removes any allocated Vecs and Mats.

    1964:    Collective on TS

    1966:    Input Parameter:
    1967: .  ts - the TS context obtained from TSCreate()

    1969:    Level: beginner

    1971: .keywords: TS, timestep, reset

    1973: .seealso: TSCreate(), TSSetup(), TSDestroy()
    1974: @*/
    1975: PetscErrorCode  TSReset(TS ts)
    1976: {

    1982:   if (ts->ops->reset) {
    1983:     (*ts->ops->reset)(ts);
    1984:   }
    1985:   if (ts->snes) {SNESReset(ts->snes);}
    1986:   if (ts->adapt) {TSAdaptReset(ts->adapt);}

    1988:   MatDestroy(&ts->Arhs);
    1989:   MatDestroy(&ts->Brhs);
    1990:   VecDestroy(&ts->Frhs);
    1991:   VecDestroy(&ts->vec_sol);
    1992:   VecDestroy(&ts->vatol);
    1993:   VecDestroy(&ts->vrtol);
    1994:   VecDestroyVecs(ts->nwork,&ts->work);

    1996:  if (ts->vec_costintegral) {
    1997:     VecDestroyVecs(ts->numcost,&ts->vecs_drdy);
    1998:     if (ts->vecs_drdp){
    1999:       VecDestroyVecs(ts->numcost,&ts->vecs_drdp);
    2000:     }
    2001:   }
    2002:   ts->vecs_sensi  = NULL;
    2003:   ts->vecs_sensip = NULL;
    2004:   MatDestroy(&ts->Jacp);
    2005:   VecDestroy(&ts->vec_costintegral);
    2006:   VecDestroy(&ts->vec_costintegrand);
    2007:   ts->setupcalled = PETSC_FALSE;
    2008:   return(0);
    2009: }

    2013: /*@
    2014:    TSDestroy - Destroys the timestepper context that was created
    2015:    with TSCreate().

    2017:    Collective on TS

    2019:    Input Parameter:
    2020: .  ts - the TS context obtained from TSCreate()

    2022:    Level: beginner

    2024: .keywords: TS, timestepper, destroy

    2026: .seealso: TSCreate(), TSSetUp(), TSSolve()
    2027: @*/
    2028: PetscErrorCode  TSDestroy(TS *ts)
    2029: {

    2033:   if (!*ts) return(0);
    2035:   if (--((PetscObject)(*ts))->refct > 0) {*ts = 0; return(0);}

    2037:   TSReset((*ts));

    2039:   /* if memory was published with SAWs then destroy it */
    2040:   PetscObjectSAWsViewOff((PetscObject)*ts);
    2041:   if ((*ts)->ops->destroy) {(*(*ts)->ops->destroy)((*ts));}

    2043:   TSTrajectoryDestroy(&(*ts)->trajectory);

    2045:   TSAdaptDestroy(&(*ts)->adapt);
    2046:   if ((*ts)->event) {
    2047:     TSEventMonitorDestroy(&(*ts)->event);
    2048:   }
    2049:   SNESDestroy(&(*ts)->snes);
    2050:   DMDestroy(&(*ts)->dm);
    2051:   TSMonitorCancel((*ts));

    2053:   PetscHeaderDestroy(ts);
    2054:   return(0);
    2055: }

    2059: /*@
    2060:    TSGetSNES - Returns the SNES (nonlinear solver) associated with
    2061:    a TS (timestepper) context. Valid only for nonlinear problems.

    2063:    Not Collective, but SNES is parallel if TS is parallel

    2065:    Input Parameter:
    2066: .  ts - the TS context obtained from TSCreate()

    2068:    Output Parameter:
    2069: .  snes - the nonlinear solver context

    2071:    Notes:
    2072:    The user can then directly manipulate the SNES context to set various
    2073:    options, etc.  Likewise, the user can then extract and manipulate the
    2074:    KSP, KSP, and PC contexts as well.

    2076:    TSGetSNES() does not work for integrators that do not use SNES; in
    2077:    this case TSGetSNES() returns NULL in snes.

    2079:    Level: beginner

    2081: .keywords: timestep, get, SNES
    2082: @*/
    2083: PetscErrorCode  TSGetSNES(TS ts,SNES *snes)
    2084: {

    2090:   if (!ts->snes) {
    2091:     SNESCreate(PetscObjectComm((PetscObject)ts),&ts->snes);
    2092:     SNESSetFunction(ts->snes,NULL,SNESTSFormFunction,ts);
    2093:     PetscLogObjectParent((PetscObject)ts,(PetscObject)ts->snes);
    2094:     PetscObjectIncrementTabLevel((PetscObject)ts->snes,(PetscObject)ts,1);
    2095:     if (ts->dm) {SNESSetDM(ts->snes,ts->dm);}
    2096:     if (ts->problem_type == TS_LINEAR) {
    2097:       SNESSetType(ts->snes,SNESKSPONLY);
    2098:     }
    2099:   }
    2100:   *snes = ts->snes;
    2101:   return(0);
    2102: }

    2106: /*@
    2107:    TSSetSNES - Set the SNES (nonlinear solver) to be used by the timestepping context

    2109:    Collective

    2111:    Input Parameter:
    2112: +  ts - the TS context obtained from TSCreate()
    2113: -  snes - the nonlinear solver context

    2115:    Notes:
    2116:    Most users should have the TS created by calling TSGetSNES()

    2118:    Level: developer

    2120: .keywords: timestep, set, SNES
    2121: @*/
    2122: PetscErrorCode TSSetSNES(TS ts,SNES snes)
    2123: {
    2125:   PetscErrorCode (*func)(SNES,Vec,Mat,Mat,void*);

    2130:   PetscObjectReference((PetscObject)snes);
    2131:   SNESDestroy(&ts->snes);

    2133:   ts->snes = snes;

    2135:   SNESSetFunction(ts->snes,NULL,SNESTSFormFunction,ts);
    2136:   SNESGetJacobian(ts->snes,NULL,NULL,&func,NULL);
    2137:   if (func == SNESTSFormJacobian) {
    2138:     SNESSetJacobian(ts->snes,NULL,NULL,SNESTSFormJacobian,ts);
    2139:   }
    2140:   return(0);
    2141: }

    2145: /*@
    2146:    TSGetKSP - Returns the KSP (linear solver) associated with
    2147:    a TS (timestepper) context.

    2149:    Not Collective, but KSP is parallel if TS is parallel

    2151:    Input Parameter:
    2152: .  ts - the TS context obtained from TSCreate()

    2154:    Output Parameter:
    2155: .  ksp - the nonlinear solver context

    2157:    Notes:
    2158:    The user can then directly manipulate the KSP context to set various
    2159:    options, etc.  Likewise, the user can then extract and manipulate the
    2160:    KSP and PC contexts as well.

    2162:    TSGetKSP() does not work for integrators that do not use KSP;
    2163:    in this case TSGetKSP() returns NULL in ksp.

    2165:    Level: beginner

    2167: .keywords: timestep, get, KSP
    2168: @*/
    2169: PetscErrorCode  TSGetKSP(TS ts,KSP *ksp)
    2170: {
    2172:   SNES           snes;

    2177:   if (!((PetscObject)ts)->type_name) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"KSP is not created yet. Call TSSetType() first");
    2178:   if (ts->problem_type != TS_LINEAR) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Linear only; use TSGetSNES()");
    2179:   TSGetSNES(ts,&snes);
    2180:   SNESGetKSP(snes,ksp);
    2181:   return(0);
    2182: }

    2184: /* ----------- Routines to set solver parameters ---------- */

    2188: /*@
    2189:    TSGetDuration - Gets the maximum number of timesteps to use and
    2190:    maximum time for iteration.

    2192:    Not Collective

    2194:    Input Parameters:
    2195: +  ts       - the TS context obtained from TSCreate()
    2196: .  maxsteps - maximum number of iterations to use, or NULL
    2197: -  maxtime  - final time to iterate to, or NULL

    2199:    Level: intermediate

    2201: .keywords: TS, timestep, get, maximum, iterations, time
    2202: @*/
    2203: PetscErrorCode  TSGetDuration(TS ts, PetscInt *maxsteps, PetscReal *maxtime)
    2204: {
    2207:   if (maxsteps) {
    2209:     *maxsteps = ts->max_steps;
    2210:   }
    2211:   if (maxtime) {
    2213:     *maxtime = ts->max_time;
    2214:   }
    2215:   return(0);
    2216: }

    2220: /*@
    2221:    TSSetDuration - Sets the maximum number of timesteps to use and
    2222:    maximum time for iteration.

    2224:    Logically Collective on TS

    2226:    Input Parameters:
    2227: +  ts - the TS context obtained from TSCreate()
    2228: .  maxsteps - maximum number of iterations to use
    2229: -  maxtime - final time to iterate to

    2231:    Options Database Keys:
    2232: .  -ts_max_steps <maxsteps> - Sets maxsteps
    2233: .  -ts_final_time <maxtime> - Sets maxtime

    2235:    Notes:
    2236:    The default maximum number of iterations is 5000. Default time is 5.0

    2238:    Level: intermediate

    2240: .keywords: TS, timestep, set, maximum, iterations

    2242: .seealso: TSSetExactFinalTime()
    2243: @*/
    2244: PetscErrorCode  TSSetDuration(TS ts,PetscInt maxsteps,PetscReal maxtime)
    2245: {
    2250:   if (maxsteps >= 0) ts->max_steps = maxsteps;
    2251:   if (maxtime != PETSC_DEFAULT) ts->max_time = maxtime;
    2252:   return(0);
    2253: }

    2257: /*@
    2258:    TSSetSolution - Sets the initial solution vector
    2259:    for use by the TS routines.

    2261:    Logically Collective on TS and Vec

    2263:    Input Parameters:
    2264: +  ts - the TS context obtained from TSCreate()
    2265: -  u - the solution vector

    2267:    Level: beginner

    2269: .keywords: TS, timestep, set, solution, initial conditions
    2270: @*/
    2271: PetscErrorCode  TSSetSolution(TS ts,Vec u)
    2272: {
    2274:   DM             dm;

    2279:   PetscObjectReference((PetscObject)u);
    2280:   VecDestroy(&ts->vec_sol);

    2282:   ts->vec_sol = u;

    2284:   TSGetDM(ts,&dm);
    2285:   DMShellSetGlobalVector(dm,u);
    2286:   return(0);
    2287: }

    2291: /*@
    2292:    TSAdjointSetSteps - Sets the number of steps the adjoint solver should take backward in time

    2294:    Logically Collective on TS

    2296:    Input Parameters:
    2297: +  ts - the TS context obtained from TSCreate()
    2298: .  steps - number of steps to use

    2300:    Level: intermediate

    2302:    Notes: Normally one does not call this and TSAdjointSolve() integrates back to the original timestep. One can call this
    2303:           so as to integrate back to less than the original timestep

    2305: .keywords: TS, timestep, set, maximum, iterations

    2307: .seealso: TSSetExactFinalTime()
    2308: @*/
    2309: PetscErrorCode  TSAdjointSetSteps(TS ts,PetscInt steps)
    2310: {
    2314:   if (steps < 0) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_OUTOFRANGE,"Cannot step back a negative number of steps");
    2315:   if (steps > ts->total_steps) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_OUTOFRANGE,"Cannot step back more than the total number of forward steps");
    2316:   ts->adjoint_max_steps = steps;
    2317:   return(0);
    2318: }

    2322: /*@
    2323:    TSSetCostGradients - Sets the initial value of the gradients of the cost function w.r.t. initial conditions and w.r.t. the problem parameters
    2324:       for use by the TSAdjoint routines.

    2326:    Logically Collective on TS and Vec

    2328:    Input Parameters:
    2329: +  ts - the TS context obtained from TSCreate()
    2330: .  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
    2331: -  mu - gradients with respect to the parameters, the number of entries in these vectors is the same as the number of parameters

    2333:    Level: beginner

    2335:    Notes: the entries in these vectors must be correctly initialized with the values lamda_i = df/dy|finaltime  mu_i = df/dp|finaltime

    2337: .keywords: TS, timestep, set, sensitivity, initial conditions
    2338: @*/
    2339: PetscErrorCode  TSSetCostGradients(TS ts,PetscInt numcost,Vec *lambda,Vec *mu)
    2340: {
    2344:   ts->vecs_sensi  = lambda;
    2345:   ts->vecs_sensip = mu;
    2346:   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");
    2347:   ts->numcost  = numcost;
    2348:   return(0);
    2349: }

    2353: /*@C
    2354:   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.

    2356:   Logically Collective on TS

    2358:   Input Parameters:
    2359: + ts   - The TS context obtained from TSCreate()
    2360: - func - The function

    2362:   Calling sequence of func:
    2363: $ func (TS ts,PetscReal t,Vec y,Mat A,void *ctx);
    2364: +   t - current timestep
    2365: .   y - input vector (current ODE solution)
    2366: .   A - output matrix
    2367: -   ctx - [optional] user-defined function context

    2369:   Level: intermediate

    2371:   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

    2373: .keywords: TS, sensitivity
    2374: .seealso:
    2375: @*/
    2376: PetscErrorCode  TSAdjointSetRHSJacobian(TS ts,Mat Amat,PetscErrorCode (*func)(TS,PetscReal,Vec,Mat,void*),void *ctx)
    2377: {

    2384:   ts->rhsjacobianp    = func;
    2385:   ts->rhsjacobianpctx = ctx;
    2386:   if(Amat) {
    2387:     PetscObjectReference((PetscObject)Amat);
    2388:     MatDestroy(&ts->Jacp);
    2389:     ts->Jacp = Amat;
    2390:   }
    2391:   return(0);
    2392: }

    2396: /*@C
    2397:   TSAdjointComputeRHSJacobian - Runs the user-defined Jacobian function.

    2399:   Collective on TS

    2401:   Input Parameters:
    2402: . ts   - The TS context obtained from TSCreate()

    2404:   Level: developer

    2406: .keywords: TS, sensitivity
    2407: .seealso: TSAdjointSetRHSJacobian()
    2408: @*/
    2409: PetscErrorCode  TSAdjointComputeRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat)
    2410: {

    2418:   PetscStackPush("TS user JacobianP function for sensitivity analysis");
    2419:   (*ts->rhsjacobianp)(ts,t,X,Amat,ts->rhsjacobianpctx);
    2420:   PetscStackPop;
    2421:   return(0);
    2422: }

    2426: /*@C
    2427:     TSSetCostIntegrand - Sets the routine for evaluating the integral term in one or more cost functions

    2429:     Logically Collective on TS

    2431:     Input Parameters:
    2432: +   ts - the TS context obtained from TSCreate()
    2433: .   numcost - number of gradients to be computed, this is the number of cost functions
    2434: .   rf - routine for evaluating the integrand function
    2435: .   drdyf - function that computes the gradients of the r's with respect to y,NULL if not a function y
    2436: .   drdpf - function that computes the gradients of the r's with respect to p, NULL if not a function of p
    2437: -   ctx - [optional] user-defined context for private data for the function evaluation routine (may be NULL)

    2439:     Calling sequence of rf:
    2440: $     rf(TS ts,PetscReal t,Vec y,Vec f[],void *ctx);

    2442: +   t - current timestep
    2443: .   y - input vector
    2444: .   f - function result; one vector entry for each cost function
    2445: -   ctx - [optional] user-defined function context

    2447:    Calling sequence of drdyf:
    2448: $    PetscErroCode drdyf(TS ts,PetscReal t,Vec y,Vec *drdy,void *ctx);

    2450:    Calling sequence of drdpf:
    2451: $    PetscErroCode drdpf(TS ts,PetscReal t,Vec y,Vec *drdp,void *ctx);

    2453:     Level: intermediate

    2455:     Notes: For optimization there is generally a single cost function, numcost = 1. For sensitivities there may be multiple cost functions

    2457: .keywords: TS, sensitivity analysis, timestep, set, quadrature, function

    2459: .seealso: TSAdjointSetRHSJacobian(),TSGetCostGradients(), TSSetCostGradients()
    2460: @*/
    2461: PetscErrorCode  TSSetCostIntegrand(TS ts,PetscInt numcost, PetscErrorCode (*rf)(TS,PetscReal,Vec,Vec,void*),
    2462:                                                                   PetscErrorCode (*drdyf)(TS,PetscReal,Vec,Vec*,void*),
    2463:                                                                   PetscErrorCode (*drdpf)(TS,PetscReal,Vec,Vec*,void*),void *ctx)
    2464: {

    2469:   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()");
    2470:   if (!ts->numcost) ts->numcost=numcost;

    2472:   VecCreateSeq(PETSC_COMM_SELF,numcost,&ts->vec_costintegral);
    2473:   VecDuplicate(ts->vec_costintegral,&ts->vec_costintegrand);
    2474:   ts->costintegrand    = rf;
    2475:   ts->costintegrandctx = ctx;
    2476:   ts->drdyfunction     = drdyf;
    2477:   ts->drdpfunction     = drdpf;
    2478:   return(0);
    2479: }

    2483: /*@
    2484:    TSGetCostIntegral - Returns the values of the integral term in the cost functions.
    2485:    It is valid to call the routine after a backward run.

    2487:    Not Collective

    2489:    Input Parameter:
    2490: .  ts - the TS context obtained from TSCreate()

    2492:    Output Parameter:
    2493: .  v - the vector containing the integrals for each cost function

    2495:    Level: intermediate

    2497: .seealso: TSSetCostIntegrand()

    2499: .keywords: TS, sensitivity analysis
    2500: @*/
    2501: PetscErrorCode  TSGetCostIntegral(TS ts,Vec *v)
    2502: {
    2506:   *v = ts->vec_costintegral;
    2507:   return(0);
    2508: }

    2512: /*@
    2513:    TSAdjointComputeCostIntegrand - Evaluates the integral function in the cost functions.

    2515:    Input Parameters:
    2516: +  ts - the TS context
    2517: .  t - current time
    2518: -  y - state vector, i.e. current solution

    2520:    Output Parameter:
    2521: .  q - vector of size numcost to hold the outputs

    2523:    Note:
    2524:    Most users should not need to explicitly call this routine, as it
    2525:    is used internally within the sensitivity analysis context.

    2527:    Level: developer

    2529: .keywords: TS, compute

    2531: .seealso: TSSetCostIntegrand()
    2532: @*/
    2533: PetscErrorCode TSAdjointComputeCostIntegrand(TS ts,PetscReal t,Vec y,Vec q)
    2534: {

    2542:   PetscLogEventBegin(TS_FunctionEval,ts,y,q,0);
    2543:   if (ts->costintegrand) {
    2544:     PetscStackPush("TS user integrand in the cost function");
    2545:     (*ts->costintegrand)(ts,t,y,q,ts->costintegrandctx);
    2546:     PetscStackPop;
    2547:   } else {
    2548:     VecZeroEntries(q);
    2549:   }

    2551:   PetscLogEventEnd(TS_FunctionEval,ts,y,q,0);
    2552:   return(0);
    2553: }

    2557: /*@
    2558:   TSAdjointComputeDRDYFunction - Runs the user-defined DRDY function.

    2560:   Collective on TS

    2562:   Input Parameters:
    2563: . ts   - The TS context obtained from TSCreate()

    2565:   Notes:
    2566:   TSAdjointComputeDRDYFunction() is typically used for sensitivity implementation,
    2567:   so most users would not generally call this routine themselves.

    2569:   Level: developer

    2571: .keywords: TS, sensitivity
    2572: .seealso: TSAdjointComputeDRDYFunction()
    2573: @*/
    2574: PetscErrorCode  TSAdjointComputeDRDYFunction(TS ts,PetscReal t,Vec y,Vec *drdy)
    2575: {

    2582:   PetscStackPush("TS user DRDY function for sensitivity analysis");
    2583:   (*ts->drdyfunction)(ts,t,y,drdy,ts->costintegrandctx);
    2584:   PetscStackPop;
    2585:   return(0);
    2586: }

    2590: /*@
    2591:   TSAdjointComputeDRDPFunction - Runs the user-defined DRDP function.

    2593:   Collective on TS

    2595:   Input Parameters:
    2596: . ts   - The TS context obtained from TSCreate()

    2598:   Notes:
    2599:   TSDRDPFunction() is typically used for sensitivity implementation,
    2600:   so most users would not generally call this routine themselves.

    2602:   Level: developer

    2604: .keywords: TS, sensitivity
    2605: .seealso: TSAdjointSetDRDPFunction()
    2606: @*/
    2607: PetscErrorCode  TSAdjointComputeDRDPFunction(TS ts,PetscReal t,Vec y,Vec *drdp)
    2608: {

    2615:   PetscStackPush("TS user DRDP function for sensitivity analysis");
    2616:   (*ts->drdpfunction)(ts,t,y,drdp,ts->costintegrandctx);
    2617:   PetscStackPop;
    2618:   return(0);
    2619: }

    2623: /*@C
    2624:   TSSetPreStep - Sets the general-purpose function
    2625:   called once at the beginning of each time step.

    2627:   Logically Collective on TS

    2629:   Input Parameters:
    2630: + ts   - The TS context obtained from TSCreate()
    2631: - func - The function

    2633:   Calling sequence of func:
    2634: . func (TS ts);

    2636:   Level: intermediate

    2638:   Note:
    2639:   If a step is rejected, TSStep() will call this routine again before each attempt.
    2640:   The last completed time step number can be queried using TSGetTimeStepNumber(), the
    2641:   size of the step being attempted can be obtained using TSGetTimeStep().

    2643: .keywords: TS, timestep
    2644: .seealso: TSSetPreStage(), TSSetPostStage(), TSSetPostStep(), TSStep()
    2645: @*/
    2646: PetscErrorCode  TSSetPreStep(TS ts, PetscErrorCode (*func)(TS))
    2647: {
    2650:   ts->prestep = func;
    2651:   return(0);
    2652: }

    2656: /*@
    2657:   TSPreStep - Runs the user-defined pre-step function.

    2659:   Collective on TS

    2661:   Input Parameters:
    2662: . ts   - The TS context obtained from TSCreate()

    2664:   Notes:
    2665:   TSPreStep() is typically used within time stepping implementations,
    2666:   so most users would not generally call this routine themselves.

    2668:   Level: developer

    2670: .keywords: TS, timestep
    2671: .seealso: TSSetPreStep(), TSPreStage(), TSPostStage(), TSPostStep()
    2672: @*/
    2673: PetscErrorCode  TSPreStep(TS ts)
    2674: {

    2679:   if (ts->prestep) {
    2680:     PetscStackCallStandard((*ts->prestep),(ts));
    2681:   }
    2682:   return(0);
    2683: }

    2687: /*@C
    2688:   TSSetPreStage - Sets the general-purpose function
    2689:   called once at the beginning of each stage.

    2691:   Logically Collective on TS

    2693:   Input Parameters:
    2694: + ts   - The TS context obtained from TSCreate()
    2695: - func - The function

    2697:   Calling sequence of func:
    2698: . PetscErrorCode func(TS ts, PetscReal stagetime);

    2700:   Level: intermediate

    2702:   Note:
    2703:   There may be several stages per time step. If the solve for a given stage fails, the step may be rejected and retried.
    2704:   The time step number being computed can be queried using TSGetTimeStepNumber() and the total size of the step being
    2705:   attempted can be obtained using TSGetTimeStep(). The time at the start of the step is available via TSGetTime().

    2707: .keywords: TS, timestep
    2708: .seealso: TSSetPostStage(), TSSetPreStep(), TSSetPostStep(), TSGetApplicationContext()
    2709: @*/
    2710: PetscErrorCode  TSSetPreStage(TS ts, PetscErrorCode (*func)(TS,PetscReal))
    2711: {
    2714:   ts->prestage = func;
    2715:   return(0);
    2716: }

    2720: /*@C
    2721:   TSSetPostStage - Sets the general-purpose function
    2722:   called once at the end of each stage.

    2724:   Logically Collective on TS

    2726:   Input Parameters:
    2727: + ts   - The TS context obtained from TSCreate()
    2728: - func - The function

    2730:   Calling sequence of func:
    2731: . PetscErrorCode func(TS ts, PetscReal stagetime, PetscInt stageindex, Vec* Y);

    2733:   Level: intermediate

    2735:   Note:
    2736:   There may be several stages per time step. If the solve for a given stage fails, the step may be rejected and retried.
    2737:   The time step number being computed can be queried using TSGetTimeStepNumber() and the total size of the step being
    2738:   attempted can be obtained using TSGetTimeStep(). The time at the start of the step is available via TSGetTime().

    2740: .keywords: TS, timestep
    2741: .seealso: TSSetPreStage(), TSSetPreStep(), TSSetPostStep(), TSGetApplicationContext()
    2742: @*/
    2743: PetscErrorCode  TSSetPostStage(TS ts, PetscErrorCode (*func)(TS,PetscReal,PetscInt,Vec*))
    2744: {
    2747:   ts->poststage = func;
    2748:   return(0);
    2749: }

    2753: /*@
    2754:   TSPreStage - Runs the user-defined pre-stage function set using TSSetPreStage()

    2756:   Collective on TS

    2758:   Input Parameters:
    2759: . ts          - The TS context obtained from TSCreate()
    2760:   stagetime   - The absolute time of the current stage

    2762:   Notes:
    2763:   TSPreStage() is typically used within time stepping implementations,
    2764:   most users would not generally call this routine themselves.

    2766:   Level: developer

    2768: .keywords: TS, timestep
    2769: .seealso: TSPostStage(), TSSetPreStep(), TSPreStep(), TSPostStep()
    2770: @*/
    2771: PetscErrorCode  TSPreStage(TS ts, PetscReal stagetime)
    2772: {

    2777:   if (ts->prestage) {
    2778:     PetscStackCallStandard((*ts->prestage),(ts,stagetime));
    2779:   }
    2780:   return(0);
    2781: }

    2785: /*@
    2786:   TSPostStage - Runs the user-defined post-stage function set using TSSetPostStage()

    2788:   Collective on TS

    2790:   Input Parameters:
    2791: . ts          - The TS context obtained from TSCreate()
    2792:   stagetime   - The absolute time of the current stage
    2793:   stageindex  - Stage number
    2794:   Y           - Array of vectors (of size = total number
    2795:                 of stages) with the stage solutions

    2797:   Notes:
    2798:   TSPostStage() is typically used within time stepping implementations,
    2799:   most users would not generally call this routine themselves.

    2801:   Level: developer

    2803: .keywords: TS, timestep
    2804: .seealso: TSPreStage(), TSSetPreStep(), TSPreStep(), TSPostStep()
    2805: @*/
    2806: PetscErrorCode  TSPostStage(TS ts, PetscReal stagetime, PetscInt stageindex, Vec *Y)
    2807: {

    2812:   if (ts->poststage) {
    2813:     PetscStackCallStandard((*ts->poststage),(ts,stagetime,stageindex,Y));
    2814:   }
    2815:   return(0);
    2816: }

    2820: /*@C
    2821:   TSSetPostStep - Sets the general-purpose function
    2822:   called once at the end of each time step.

    2824:   Logically Collective on TS

    2826:   Input Parameters:
    2827: + ts   - The TS context obtained from TSCreate()
    2828: - func - The function

    2830:   Calling sequence of func:
    2831: $ func (TS ts);

    2833:   Level: intermediate

    2835: .keywords: TS, timestep
    2836: .seealso: TSSetPreStep(), TSSetPreStage(), TSGetTimeStep(), TSGetTimeStepNumber(), TSGetTime()
    2837: @*/
    2838: PetscErrorCode  TSSetPostStep(TS ts, PetscErrorCode (*func)(TS))
    2839: {
    2842:   ts->poststep = func;
    2843:   return(0);
    2844: }

    2848: /*@
    2849:   TSPostStep - Runs the user-defined post-step function.

    2851:   Collective on TS

    2853:   Input Parameters:
    2854: . ts   - The TS context obtained from TSCreate()

    2856:   Notes:
    2857:   TSPostStep() is typically used within time stepping implementations,
    2858:   so most users would not generally call this routine themselves.

    2860:   Level: developer

    2862: .keywords: TS, timestep
    2863: @*/
    2864: PetscErrorCode  TSPostStep(TS ts)
    2865: {

    2870:   if (ts->poststep) {
    2871:     PetscStackCallStandard((*ts->poststep),(ts));
    2872:   }
    2873:   return(0);
    2874: }

    2876: /* ------------ Routines to set performance monitoring options ----------- */

    2880: /*@C
    2881:    TSMonitorSet - Sets an ADDITIONAL function that is to be used at every
    2882:    timestep to display the iteration's  progress.

    2884:    Logically Collective on TS

    2886:    Input Parameters:
    2887: +  ts - the TS context obtained from TSCreate()
    2888: .  monitor - monitoring routine
    2889: .  mctx - [optional] user-defined context for private data for the
    2890:              monitor routine (use NULL if no context is desired)
    2891: -  monitordestroy - [optional] routine that frees monitor context
    2892:           (may be NULL)

    2894:    Calling sequence of monitor:
    2895: $    int monitor(TS ts,PetscInt steps,PetscReal time,Vec u,void *mctx)

    2897: +    ts - the TS context
    2898: .    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
    2899:                                been interpolated to)
    2900: .    time - current time
    2901: .    u - current iterate
    2902: -    mctx - [optional] monitoring context

    2904:    Notes:
    2905:    This routine adds an additional monitor to the list of monitors that
    2906:    already has been loaded.

    2908:    Fortran notes: Only a single monitor function can be set for each TS object

    2910:    Level: intermediate

    2912: .keywords: TS, timestep, set, monitor

    2914: .seealso: TSMonitorDefault(), TSMonitorCancel()
    2915: @*/
    2916: PetscErrorCode  TSMonitorSet(TS ts,PetscErrorCode (*monitor)(TS,PetscInt,PetscReal,Vec,void*),void *mctx,PetscErrorCode (*mdestroy)(void**))
    2917: {
    2920:   if (ts->numbermonitors >= MAXTSMONITORS) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many monitors set");
    2921:   ts->monitor[ts->numbermonitors]          = monitor;
    2922:   ts->monitordestroy[ts->numbermonitors]   = mdestroy;
    2923:   ts->monitorcontext[ts->numbermonitors++] = (void*)mctx;
    2924:   return(0);
    2925: }

    2929: /*@C
    2930:    TSMonitorCancel - Clears all the monitors that have been set on a time-step object.

    2932:    Logically Collective on TS

    2934:    Input Parameters:
    2935: .  ts - the TS context obtained from TSCreate()

    2937:    Notes:
    2938:    There is no way to remove a single, specific monitor.

    2940:    Level: intermediate

    2942: .keywords: TS, timestep, set, monitor

    2944: .seealso: TSMonitorDefault(), TSMonitorSet()
    2945: @*/
    2946: PetscErrorCode  TSMonitorCancel(TS ts)
    2947: {
    2949:   PetscInt       i;

    2953:   for (i=0; i<ts->numbermonitors; i++) {
    2954:     if (ts->monitordestroy[i]) {
    2955:       (*ts->monitordestroy[i])(&ts->monitorcontext[i]);
    2956:     }
    2957:   }
    2958:   ts->numbermonitors = 0;
    2959:   return(0);
    2960: }

    2964: /*@
    2965:    TSMonitorDefault - Sets the Default monitor

    2967:    Level: intermediate

    2969: .keywords: TS, set, monitor

    2971: .seealso: TSMonitorDefault(), TSMonitorSet()
    2972: @*/
    2973: PetscErrorCode TSMonitorDefault(TS ts,PetscInt step,PetscReal ptime,Vec v,void *dummy)
    2974: {
    2976:   PetscViewer    viewer = dummy ? (PetscViewer) dummy : PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)ts));

    2979:   PetscViewerASCIIAddTab(viewer,((PetscObject)ts)->tablevel);
    2980:   PetscViewerASCIIPrintf(viewer,"%D TS dt %g time %g%s",step,(double)ts->time_step,(double)ptime,ts->steprollback ? " (r)\n" : "\n");
    2981:   PetscViewerASCIISubtractTab(viewer,((PetscObject)ts)->tablevel);
    2982:   return(0);
    2983: }

    2987: /*@
    2988:    TSSetRetainStages - Request that all stages in the upcoming step be stored so that interpolation will be available.

    2990:    Logically Collective on TS

    2992:    Input Argument:
    2993: .  ts - time stepping context

    2995:    Output Argument:
    2996: .  flg - PETSC_TRUE or PETSC_FALSE

    2998:    Level: intermediate

    3000: .keywords: TS, set

    3002: .seealso: TSInterpolate(), TSSetPostStep()
    3003: @*/
    3004: PetscErrorCode TSSetRetainStages(TS ts,PetscBool flg)
    3005: {
    3008:   ts->retain_stages = flg;
    3009:   return(0);
    3010: }

    3014: /*@
    3015:    TSInterpolate - Interpolate the solution computed during the previous step to an arbitrary location in the interval

    3017:    Collective on TS

    3019:    Input Argument:
    3020: +  ts - time stepping context
    3021: -  t - time to interpolate to

    3023:    Output Argument:
    3024: .  U - state at given time

    3026:    Notes:
    3027:    The user should call TSSetRetainStages() before taking a step in which interpolation will be requested.

    3029:    Level: intermediate

    3031:    Developer Notes:
    3032:    TSInterpolate() and the storing of previous steps/stages should be generalized to support delay differential equations and continuous adjoints.

    3034: .keywords: TS, set

    3036: .seealso: TSSetRetainStages(), TSSetPostStep()
    3037: @*/
    3038: PetscErrorCode TSInterpolate(TS ts,PetscReal t,Vec U)
    3039: {

    3045:   if (t < ts->ptime - ts->time_step_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-ts->time_step_prev),(double)ts->ptime);
    3046:   if (!ts->ops->interpolate) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"%s does not provide interpolation",((PetscObject)ts)->type_name);
    3047:   (*ts->ops->interpolate)(ts,t,U);
    3048:   return(0);
    3049: }

    3053: /*@
    3054:    TSStep - Steps one time step

    3056:    Collective on TS

    3058:    Input Parameter:
    3059: .  ts - the TS context obtained from TSCreate()

    3061:    Level: developer

    3063:    Notes:
    3064:    The public interface for the ODE/DAE solvers is TSSolve(), you should almost for sure be using that routine and not this routine.

    3066:    The hook set using TSSetPreStep() is called before each attempt to take the step. In general, the time step size may
    3067:    be changed due to adaptive error controller or solve failures. Note that steps may contain multiple stages.

    3069:    This may over-step the final time provided in TSSetDuration() depending on the time-step used. TSSolve() interpolates to exactly the
    3070:    time provided in TSSetDuration(). One can use TSInterpolate() to determine an interpolated solution within the final timestep.

    3072: .keywords: TS, timestep, solve

    3074: .seealso: TSCreate(), TSSetUp(), TSDestroy(), TSSolve(), TSSetPreStep(), TSSetPreStage(), TSSetPostStage(), TSInterpolate()
    3075: @*/
    3076: PetscErrorCode  TSStep(TS ts)
    3077: {
    3078:   DM               dm;
    3079:   PetscErrorCode   ierr;
    3080:   static PetscBool cite = PETSC_FALSE;

    3084:   PetscCitationsRegister("@techreport{tspaper,\n"
    3085:                                 "  title       = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library},\n"
    3086:                                 "  author      = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and Barry F. Smith},\n"
    3087:                                 "  type        = {Preprint},\n"
    3088:                                 "  number      = {ANL/MCS-P5061-0114},\n"
    3089:                                 "  institution = {Argonne National Laboratory},\n"
    3090:                                 "  year        = {2014}\n}\n",&cite);

    3092:   TSGetDM(ts, &dm);
    3093:   TSSetUp(ts);

    3095:   ts->reason = TS_CONVERGED_ITERATING;
    3096:   ts->ptime_prev = ts->ptime;
    3097:   DMSetOutputSequenceNumber(dm, ts->steps, ts->ptime);

    3099:   if (!ts->ops->step) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSStep not implemented for type '%s'",((PetscObject)ts)->type_name);
    3100:   PetscLogEventBegin(TS_Step,ts,0,0,0);
    3101:   (*ts->ops->step)(ts);
    3102:   PetscLogEventEnd(TS_Step,ts,0,0,0);

    3104:   ts->time_step_prev = ts->ptime - ts->ptime_prev;
    3105:   DMSetOutputSequenceNumber(dm, ts->steps, ts->ptime);

    3107:   if (ts->reason < 0) {
    3108:     if (ts->errorifstepfailed) {
    3109:       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]);
    3110:       else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s",TSConvergedReasons[ts->reason]);
    3111:     }
    3112:   } else if (!ts->reason) {
    3113:     if (ts->steps >= ts->max_steps)     ts->reason = TS_CONVERGED_ITS;
    3114:     else if (ts->ptime >= ts->max_time) ts->reason = TS_CONVERGED_TIME;
    3115:   }
    3116:   ts->total_steps++;
    3117:   ts->steprollback = PETSC_FALSE;
    3118:   return(0);
    3119: }

    3123: /*@
    3124:    TSAdjointStep - Steps one time step backward in the adjoint run

    3126:    Collective on TS

    3128:    Input Parameter:
    3129: .  ts - the TS context obtained from TSCreate()

    3131:    Level: intermediate

    3133: .keywords: TS, adjoint, step

    3135: .seealso: TSAdjointSetUp(), TSAdjointSolve()
    3136: @*/
    3137: PetscErrorCode  TSAdjointStep(TS ts)
    3138: {
    3139:   DM               dm;
    3140:   PetscErrorCode   ierr;

    3144:   TSGetDM(ts, &dm);
    3145:   TSAdjointSetUp(ts);

    3147:   ts->reason = TS_CONVERGED_ITERATING;
    3148:   ts->ptime_prev = ts->ptime;
    3149:   DMSetOutputSequenceNumber(dm, ts->steps, ts->ptime);
    3150:   VecViewFromOptions(ts->vec_sol,(PetscObject)ts, "-ts_view_solution");

    3152:   PetscLogEventBegin(TS_Step,ts,0,0,0);
    3153:   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);
    3154:   (*ts->ops->adjointstep)(ts);
    3155:   PetscLogEventEnd(TS_Step,ts,0,0,0);

    3157:   ts->time_step_prev = ts->ptime - ts->ptime_prev;
    3158:   DMSetOutputSequenceNumber(dm, ts->steps, ts->ptime);

    3160:   if (ts->reason < 0) {
    3161:     if (ts->errorifstepfailed) {
    3162:       if (ts->reason == TS_DIVERGED_NONLINEAR_SOLVE) {
    3163:         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]);
    3164:       } else if (ts->reason == TS_DIVERGED_STEP_REJECTED) {
    3165:         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]);
    3166:       } else SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_NOT_CONVERGED,"TSStep has failed due to %s",TSConvergedReasons[ts->reason]);
    3167:     }
    3168:   } else if (!ts->reason) {
    3169:     if (ts->steps >= ts->adjoint_max_steps)     ts->reason = TS_CONVERGED_ITS;
    3170:     else if (ts->ptime >= ts->max_time)         ts->reason = TS_CONVERGED_TIME;
    3171:   }
    3172:   ts->total_steps--;
    3173:   return(0);
    3174: }

    3178: /*@
    3179:    TSEvaluateStep - Evaluate the solution at the end of a time step with a given order of accuracy.

    3181:    Collective on TS

    3183:    Input Arguments:
    3184: +  ts - time stepping context
    3185: .  order - desired order of accuracy
    3186: -  done - whether the step was evaluated at this order (pass NULL to generate an error if not available)

    3188:    Output Arguments:
    3189: .  U - state at the end of the current step

    3191:    Level: advanced

    3193:    Notes:
    3194:    This function cannot be called until all stages have been evaluated.
    3195:    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.

    3197: .seealso: TSStep(), TSAdapt
    3198: @*/
    3199: PetscErrorCode TSEvaluateStep(TS ts,PetscInt order,Vec U,PetscBool *done)
    3200: {

    3207:   if (!ts->ops->evaluatestep) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSEvaluateStep not implemented for type '%s'",((PetscObject)ts)->type_name);
    3208:   (*ts->ops->evaluatestep)(ts,order,U,done);
    3209:   return(0);
    3210: }

    3215: /*@
    3216:    TSSolve - Steps the requested number of timesteps.

    3218:    Collective on TS

    3220:    Input Parameter:
    3221: +  ts - the TS context obtained from TSCreate()
    3222: -  u - the solution vector  (can be null if TSSetSolution() was used, otherwise must contain the initial conditions)

    3224:    Level: beginner

    3226:    Notes:
    3227:    The final time returned by this function may be different from the time of the internally
    3228:    held state accessible by TSGetSolution() and TSGetTime() because the method may have
    3229:    stepped over the final time.

    3231: .keywords: TS, timestep, solve

    3233: .seealso: TSCreate(), TSSetSolution(), TSStep()
    3234: @*/
    3235: PetscErrorCode TSSolve(TS ts,Vec u)
    3236: {
    3237:   Vec               solution;
    3238:   PetscErrorCode    ierr;

    3243:   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 */
    3245:     if (!ts->vec_sol || u == ts->vec_sol) {
    3246:       VecDuplicate(u,&solution);
    3247:       TSSetSolution(ts,solution);
    3248:       VecDestroy(&solution); /* grant ownership */
    3249:     }
    3250:     VecCopy(u,ts->vec_sol);
    3251:   } else if (u) {
    3252:     TSSetSolution(ts,u);
    3253:   }
    3254:   TSSetUp(ts);
    3255:   /* reset time step and iteration counters */
    3256:   ts->steps             = 0;
    3257:   ts->ksp_its           = 0;
    3258:   ts->snes_its          = 0;
    3259:   ts->num_snes_failures = 0;
    3260:   ts->reject            = 0;
    3261:   ts->reason            = TS_CONVERGED_ITERATING;

    3263:   TSViewFromOptions(ts,NULL,"-ts_view_pre");
    3264:   {
    3265:     DM dm;
    3266:     TSGetDM(ts, &dm);
    3267:     DMSetOutputSequenceNumber(dm, ts->steps, ts->ptime);
    3268:   }

    3270:   if (ts->ops->solve) {         /* This private interface is transitional and should be removed when all implementations are updated. */
    3271:     (*ts->ops->solve)(ts);
    3272:     VecCopy(ts->vec_sol,u);
    3273:     ts->solvetime = ts->ptime;
    3274:   } else {
    3275:     /* steps the requested number of timesteps. */
    3276:     if (ts->steps >= ts->max_steps)     ts->reason = TS_CONVERGED_ITS;
    3277:     else if (ts->ptime >= ts->max_time) ts->reason = TS_CONVERGED_TIME;
    3278:     TSTrajectorySet(ts->trajectory,ts,ts->steps,ts->ptime,ts->vec_sol);
    3279:     if (ts->vec_costintegral) ts->costintegralfwd=PETSC_TRUE;
    3280:     if(ts->event) {
    3281:       TSEventMonitorInitialize(ts);
    3282:     }
    3283:     while (!ts->reason) {
    3284:       TSMonitor(ts,ts->steps,ts->ptime,ts->vec_sol);
    3285:       TSStep(ts);
    3286:       if (ts->event) {
    3287:         TSEventMonitor(ts);
    3288:       }
    3289:       if(!ts->steprollback) {
    3290:         TSTrajectorySet(ts->trajectory,ts,ts->steps,ts->ptime,ts->vec_sol);
    3291:         TSPostStep(ts);
    3292:       }
    3293:     }
    3294:     if (ts->exact_final_time == TS_EXACTFINALTIME_INTERPOLATE && ts->ptime > ts->max_time) {
    3295:       TSInterpolate(ts,ts->max_time,u);
    3296:       ts->solvetime = ts->max_time;
    3297:       solution = u;
    3298:     } else {
    3299:       if (u) {VecCopy(ts->vec_sol,u);}
    3300:       ts->solvetime = ts->ptime;
    3301:       solution = ts->vec_sol;
    3302:     }
    3303:     TSMonitor(ts,ts->steps,ts->solvetime,solution);
    3304:     VecViewFromOptions(solution,(PetscObject) ts,"-ts_view_solution");
    3305:   }

    3307:   TSViewFromOptions(ts,NULL,"-ts_view");
    3308:   VecViewFromOptions(ts->vec_sol,NULL,"-ts_view_solution");
    3309:   PetscObjectSAWsBlock((PetscObject)ts);
    3310:   if (ts->adjoint_solve) {
    3311:     TSAdjointSolve(ts);
    3312:   }
    3313:   return(0);
    3314: }

    3318: /*@
    3319:    TSAdjointSolve - Solves the discrete ajoint problem for an ODE/DAE

    3321:    Collective on TS

    3323:    Input Parameter:
    3324: .  ts - the TS context obtained from TSCreate()

    3326:    Options Database:
    3327: . -ts_adjoint_view_solution <viewerinfo> - views the first gradient with respect to the initial conditions

    3329:    Level: intermediate

    3331:    Notes:
    3332:    This must be called after a call to TSSolve() that solves the forward problem

    3334:    By default this will integrate back to the initial time, one can use TSAdjointSetSteps() to step back to a later time

    3336: .keywords: TS, timestep, solve

    3338: .seealso: TSCreate(), TSSetCostGradients(), TSSetSolution(), TSAdjointStep()
    3339: @*/
    3340: PetscErrorCode TSAdjointSolve(TS ts)
    3341: {
    3342:   PetscErrorCode    ierr;

    3346:   TSAdjointSetUp(ts);
    3347:   /* reset time step and iteration counters */
    3348:   ts->steps             = 0;
    3349:   ts->ksp_its           = 0;
    3350:   ts->snes_its          = 0;
    3351:   ts->num_snes_failures = 0;
    3352:   ts->reject            = 0;
    3353:   ts->reason            = TS_CONVERGED_ITERATING;

    3355:   if (!ts->adjoint_max_steps) ts->adjoint_max_steps = ts->total_steps;

    3357:   if (ts->steps >= ts->adjoint_max_steps)     ts->reason = TS_CONVERGED_ITS;
    3358:   while (!ts->reason) {
    3359:     TSTrajectoryGet(ts->trajectory,ts,ts->total_steps,&ts->ptime);
    3360:     TSMonitor(ts,ts->total_steps,ts->ptime,ts->vec_sol);
    3361:     if (ts->event) {
    3362:       TSAdjointEventMonitor(ts);
    3363:     }
    3364:     TSAdjointStep(ts);
    3365:   }
    3366:   ts->solvetime = ts->ptime;
    3367:   VecViewFromOptions(ts->vecs_sensi[0],(PetscObject) ts, "-ts_adjoint_view_solution");
    3368:   return(0);
    3369: }

    3373: /*@
    3374:    TSMonitor - Runs all user-provided monitor routines set using TSMonitorSet()

    3376:    Collective on TS

    3378:    Input Parameters:
    3379: +  ts - time stepping context obtained from TSCreate()
    3380: .  step - step number that has just completed
    3381: .  ptime - model time of the state
    3382: -  u - state at the current model time

    3384:    Notes:
    3385:    TSMonitor() is typically used within the time stepping implementations.
    3386:    Users might call this function when using the TSStep() interface instead of TSSolve().

    3388:    Level: advanced

    3390: .keywords: TS, timestep
    3391: @*/
    3392: PetscErrorCode TSMonitor(TS ts,PetscInt step,PetscReal ptime,Vec u)
    3393: {
    3395:   PetscInt       i,n = ts->numbermonitors;

    3400:   VecLockPush(u);
    3401:   for (i=0; i<n; i++) {
    3402:     (*ts->monitor[i])(ts,step,ptime,u,ts->monitorcontext[i]);
    3403:   }
    3404:   VecLockPop(u);
    3405:   return(0);
    3406: }

    3408: /* ------------------------------------------------------------------------*/
    3411: /*@C
    3412:    TSMonitorLGCtxCreate - Creates a line graph context for use with
    3413:    TS to monitor the solution process graphically in various ways

    3415:    Collective on TS

    3417:    Input Parameters:
    3418: +  host - the X display to open, or null for the local machine
    3419: .  label - the title to put in the title bar
    3420: .  x, y - the screen coordinates of the upper left coordinate of the window
    3421: .  m, n - the screen width and height in pixels
    3422: -  howoften - if positive then determines the frequency of the plotting, if -1 then only at the final time

    3424:    Output Parameter:
    3425: .  ctx - the context

    3427:    Options Database Key:
    3428: +  -ts_monitor_lg_timestep - automatically sets line graph monitor
    3429: .  -ts_monitor_lg_solution -
    3430: .  -ts_monitor_lg_error -
    3431: .  -ts_monitor_lg_ksp_iterations -
    3432: .  -ts_monitor_lg_snes_iterations -
    3433: -  -lg_use_markers <true,false> - mark the data points (at each time step) on the plot; default is true

    3435:    Notes:
    3436:    Use TSMonitorLGCtxDestroy() to destroy.

    3438:    Level: intermediate

    3440: .keywords: TS, monitor, line graph, residual, seealso

    3442: .seealso: TSMonitorLGTimeStep(), TSMonitorSet(), TSMonitorLGSolution(), TSMonitorLGError()

    3444: @*/
    3445: PetscErrorCode  TSMonitorLGCtxCreate(MPI_Comm comm,const char host[],const char label[],int x,int y,int m,int n,PetscInt howoften,TSMonitorLGCtx *ctx)
    3446: {
    3447:   PetscDraw      win;

    3451:   PetscNew(ctx);
    3452:   PetscDrawCreate(comm,host,label,x,y,m,n,&win);
    3453:   PetscDrawSetFromOptions(win);
    3454:   PetscDrawLGCreate(win,1,&(*ctx)->lg);
    3455:   PetscLogObjectParent((PetscObject)(*ctx)->lg,(PetscObject)win);
    3456:   PetscDrawLGSetUseMarkers((*ctx)->lg,PETSC_TRUE);
    3457:   PetscDrawLGSetFromOptions((*ctx)->lg);
    3458:   (*ctx)->howoften = howoften;
    3459:   return(0);
    3460: }

    3464: PetscErrorCode TSMonitorLGTimeStep(TS ts,PetscInt step,PetscReal ptime,Vec v,void *monctx)
    3465: {
    3466:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
    3467:   PetscReal      x   = ptime,y;

    3471:   if (!step) {
    3472:     PetscDrawAxis axis;
    3473:     PetscDrawLGGetAxis(ctx->lg,&axis);
    3474:     PetscDrawAxisSetLabels(axis,"Timestep as function of time","Time","Time step");
    3475:     PetscDrawLGReset(ctx->lg);
    3476:   }
    3477:   TSGetTimeStep(ts,&y);
    3478:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
    3479:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
    3480:     PetscDrawLGDraw(ctx->lg);
    3481:   }
    3482:   return(0);
    3483: }

    3487: /*@C
    3488:    TSMonitorLGCtxDestroy - Destroys a line graph context that was created
    3489:    with TSMonitorLGCtxCreate().

    3491:    Collective on TSMonitorLGCtx

    3493:    Input Parameter:
    3494: .  ctx - the monitor context

    3496:    Level: intermediate

    3498: .keywords: TS, monitor, line graph, destroy

    3500: .seealso: TSMonitorLGCtxCreate(),  TSMonitorSet(), TSMonitorLGTimeStep();
    3501: @*/
    3502: PetscErrorCode  TSMonitorLGCtxDestroy(TSMonitorLGCtx *ctx)
    3503: {
    3504:   PetscDraw      draw;

    3508:   if ((*ctx)->transformdestroy) {
    3509:     ((*ctx)->transformdestroy)((*ctx)->transformctx);
    3510:   }
    3511:   PetscDrawLGGetDraw((*ctx)->lg,&draw);
    3512:   PetscDrawDestroy(&draw);
    3513:   PetscDrawLGDestroy(&(*ctx)->lg);
    3514:   PetscStrArrayDestroy(&(*ctx)->names);
    3515:   PetscStrArrayDestroy(&(*ctx)->displaynames);
    3516:   PetscFree((*ctx)->displayvariables);
    3517:   PetscFree((*ctx)->displayvalues);
    3518:   PetscFree(*ctx);
    3519:   return(0);
    3520: }

    3524: /*@
    3525:    TSGetTime - Gets the time of the most recently completed step.

    3527:    Not Collective

    3529:    Input Parameter:
    3530: .  ts - the TS context obtained from TSCreate()

    3532:    Output Parameter:
    3533: .  t  - the current time

    3535:    Level: beginner

    3537:    Note:
    3538:    When called during time step evaluation (e.g. during residual evaluation or via hooks set using TSSetPreStep(),
    3539:    TSSetPreStage(), TSSetPostStage(), or TSSetPostStep()), the time is the time at the start of the step being evaluated.

    3541: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

    3543: .keywords: TS, get, time
    3544: @*/
    3545: PetscErrorCode  TSGetTime(TS ts,PetscReal *t)
    3546: {
    3550:   *t = ts->ptime;
    3551:   return(0);
    3552: }

    3556: /*@
    3557:    TSGetPrevTime - Gets the starting time of the previously completed step.

    3559:    Not Collective

    3561:    Input Parameter:
    3562: .  ts - the TS context obtained from TSCreate()

    3564:    Output Parameter:
    3565: .  t  - the previous time

    3567:    Level: beginner

    3569: .seealso: TSSetInitialTimeStep(), TSGetTimeStep()

    3571: .keywords: TS, get, time
    3572: @*/
    3573: PetscErrorCode  TSGetPrevTime(TS ts,PetscReal *t)
    3574: {
    3578:   *t = ts->ptime_prev;
    3579:   return(0);
    3580: }

    3584: /*@
    3585:    TSSetTime - Allows one to reset the time.

    3587:    Logically Collective on TS

    3589:    Input Parameters:
    3590: +  ts - the TS context obtained from TSCreate()
    3591: -  time - the time

    3593:    Level: intermediate

    3595: .seealso: TSGetTime(), TSSetDuration()

    3597: .keywords: TS, set, time
    3598: @*/
    3599: PetscErrorCode  TSSetTime(TS ts, PetscReal t)
    3600: {
    3604:   ts->ptime = t;
    3605:   return(0);
    3606: }

    3610: /*@C
    3611:    TSSetOptionsPrefix - Sets the prefix used for searching for all
    3612:    TS options in the database.

    3614:    Logically Collective on TS

    3616:    Input Parameter:
    3617: +  ts     - The TS context
    3618: -  prefix - The prefix to prepend to all option names

    3620:    Notes:
    3621:    A hyphen (-) must NOT be given at the beginning of the prefix name.
    3622:    The first character of all runtime options is AUTOMATICALLY the
    3623:    hyphen.

    3625:    Level: advanced

    3627: .keywords: TS, set, options, prefix, database

    3629: .seealso: TSSetFromOptions()

    3631: @*/
    3632: PetscErrorCode  TSSetOptionsPrefix(TS ts,const char prefix[])
    3633: {
    3635:   SNES           snes;

    3639:   PetscObjectSetOptionsPrefix((PetscObject)ts,prefix);
    3640:   TSGetSNES(ts,&snes);
    3641:   SNESSetOptionsPrefix(snes,prefix);
    3642:   return(0);
    3643: }

    3648: /*@C
    3649:    TSAppendOptionsPrefix - Appends to the prefix used for searching for all
    3650:    TS options in the database.

    3652:    Logically Collective on TS

    3654:    Input Parameter:
    3655: +  ts     - The TS context
    3656: -  prefix - The prefix to prepend to all option names

    3658:    Notes:
    3659:    A hyphen (-) must NOT be given at the beginning of the prefix name.
    3660:    The first character of all runtime options is AUTOMATICALLY the
    3661:    hyphen.

    3663:    Level: advanced

    3665: .keywords: TS, append, options, prefix, database

    3667: .seealso: TSGetOptionsPrefix()

    3669: @*/
    3670: PetscErrorCode  TSAppendOptionsPrefix(TS ts,const char prefix[])
    3671: {
    3673:   SNES           snes;

    3677:   PetscObjectAppendOptionsPrefix((PetscObject)ts,prefix);
    3678:   TSGetSNES(ts,&snes);
    3679:   SNESAppendOptionsPrefix(snes,prefix);
    3680:   return(0);
    3681: }

    3685: /*@C
    3686:    TSGetOptionsPrefix - Sets the prefix used for searching for all
    3687:    TS options in the database.

    3689:    Not Collective

    3691:    Input Parameter:
    3692: .  ts - The TS context

    3694:    Output Parameter:
    3695: .  prefix - A pointer to the prefix string used

    3697:    Notes: On the fortran side, the user should pass in a string 'prifix' of
    3698:    sufficient length to hold the prefix.

    3700:    Level: intermediate

    3702: .keywords: TS, get, options, prefix, database

    3704: .seealso: TSAppendOptionsPrefix()
    3705: @*/
    3706: PetscErrorCode  TSGetOptionsPrefix(TS ts,const char *prefix[])
    3707: {

    3713:   PetscObjectGetOptionsPrefix((PetscObject)ts,prefix);
    3714:   return(0);
    3715: }

    3719: /*@C
    3720:    TSGetRHSJacobian - Returns the Jacobian J at the present timestep.

    3722:    Not Collective, but parallel objects are returned if TS is parallel

    3724:    Input Parameter:
    3725: .  ts  - The TS context obtained from TSCreate()

    3727:    Output Parameters:
    3728: +  Amat - The (approximate) Jacobian J of G, where U_t = G(U,t)  (or NULL)
    3729: .  Pmat - The matrix from which the preconditioner is constructed, usually the same as Amat  (or NULL)
    3730: .  func - Function to compute the Jacobian of the RHS  (or NULL)
    3731: -  ctx - User-defined context for Jacobian evaluation routine  (or NULL)

    3733:    Notes: You can pass in NULL for any return argument you do not need.

    3735:    Level: intermediate

    3737: .seealso: TSGetTimeStep(), TSGetMatrices(), TSGetTime(), TSGetTimeStepNumber()

    3739: .keywords: TS, timestep, get, matrix, Jacobian
    3740: @*/
    3741: PetscErrorCode  TSGetRHSJacobian(TS ts,Mat *Amat,Mat *Pmat,TSRHSJacobian *func,void **ctx)
    3742: {
    3744:   SNES           snes;
    3745:   DM             dm;

    3748:   TSGetSNES(ts,&snes);
    3749:   SNESGetJacobian(snes,Amat,Pmat,NULL,NULL);
    3750:   TSGetDM(ts,&dm);
    3751:   DMTSGetRHSJacobian(dm,func,ctx);
    3752:   return(0);
    3753: }

    3757: /*@C
    3758:    TSGetIJacobian - Returns the implicit Jacobian at the present timestep.

    3760:    Not Collective, but parallel objects are returned if TS is parallel

    3762:    Input Parameter:
    3763: .  ts  - The TS context obtained from TSCreate()

    3765:    Output Parameters:
    3766: +  Amat  - The (approximate) Jacobian of F(t,U,U_t)
    3767: .  Pmat - The matrix from which the preconditioner is constructed, often the same as Amat
    3768: .  f   - The function to compute the matrices
    3769: - ctx - User-defined context for Jacobian evaluation routine

    3771:    Notes: You can pass in NULL for any return argument you do not need.

    3773:    Level: advanced

    3775: .seealso: TSGetTimeStep(), TSGetRHSJacobian(), TSGetMatrices(), TSGetTime(), TSGetTimeStepNumber()

    3777: .keywords: TS, timestep, get, matrix, Jacobian
    3778: @*/
    3779: PetscErrorCode  TSGetIJacobian(TS ts,Mat *Amat,Mat *Pmat,TSIJacobian *f,void **ctx)
    3780: {
    3782:   SNES           snes;
    3783:   DM             dm;

    3786:   TSGetSNES(ts,&snes);
    3787:   SNESSetUpMatrices(snes);
    3788:   SNESGetJacobian(snes,Amat,Pmat,NULL,NULL);
    3789:   TSGetDM(ts,&dm);
    3790:   DMTSGetIJacobian(dm,f,ctx);
    3791:   return(0);
    3792: }

    3797: /*@C
    3798:    TSMonitorDrawSolution - Monitors progress of the TS solvers by calling
    3799:    VecView() for the solution at each timestep

    3801:    Collective on TS

    3803:    Input Parameters:
    3804: +  ts - the TS context
    3805: .  step - current time-step
    3806: .  ptime - current time
    3807: -  dummy - either a viewer or NULL

    3809:    Options Database:
    3810: .   -ts_monitor_draw_solution_initial - show initial solution as well as current solution

    3812:    Notes: the initial solution and current solution are not display with a common axis scaling so generally the option -ts_monitor_draw_solution_initial
    3813:        will look bad

    3815:    Level: intermediate

    3817: .keywords: TS,  vector, monitor, view

    3819: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    3820: @*/
    3821: PetscErrorCode  TSMonitorDrawSolution(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    3822: {
    3823:   PetscErrorCode   ierr;
    3824:   TSMonitorDrawCtx ictx = (TSMonitorDrawCtx)dummy;
    3825:   PetscDraw        draw;

    3828:   if (!step && ictx->showinitial) {
    3829:     if (!ictx->initialsolution) {
    3830:       VecDuplicate(u,&ictx->initialsolution);
    3831:     }
    3832:     VecCopy(u,ictx->initialsolution);
    3833:   }
    3834:   if (!(((ictx->howoften > 0) && (!(step % ictx->howoften))) || ((ictx->howoften == -1) && ts->reason))) return(0);

    3836:   if (ictx->showinitial) {
    3837:     PetscReal pause;
    3838:     PetscViewerDrawGetPause(ictx->viewer,&pause);
    3839:     PetscViewerDrawSetPause(ictx->viewer,0.0);
    3840:     VecView(ictx->initialsolution,ictx->viewer);
    3841:     PetscViewerDrawSetPause(ictx->viewer,pause);
    3842:     PetscViewerDrawSetHold(ictx->viewer,PETSC_TRUE);
    3843:   }
    3844:   VecView(u,ictx->viewer);
    3845:   if (ictx->showtimestepandtime) {
    3846:     PetscReal xl,yl,xr,yr,h;
    3847:     char      time[32];

    3849:     PetscViewerDrawGetDraw(ictx->viewer,0,&draw);
    3850:     PetscSNPrintf(time,32,"Timestep %d Time %g",(int)step,(double)ptime);
    3851:     PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
    3852:     h    = yl + .95*(yr - yl);
    3853:     PetscDrawStringCentered(draw,.5*(xl+xr),h,PETSC_DRAW_BLACK,time);
    3854:     PetscDrawFlush(draw);
    3855:   }

    3857:   if (ictx->showinitial) {
    3858:     PetscViewerDrawSetHold(ictx->viewer,PETSC_FALSE);
    3859:   }
    3860:   return(0);
    3861: }

    3865: /*@C
    3866:    TSMonitorDrawSolutionPhase - Monitors progress of the TS solvers by plotting the solution as a phase diagram

    3868:    Collective on TS

    3870:    Input Parameters:
    3871: +  ts - the TS context
    3872: .  step - current time-step
    3873: .  ptime - current time
    3874: -  dummy - either a viewer or NULL

    3876:    Level: intermediate

    3878: .keywords: TS,  vector, monitor, view

    3880: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    3881: @*/
    3882: PetscErrorCode  TSMonitorDrawSolutionPhase(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    3883: {
    3884:   PetscErrorCode    ierr;
    3885:   TSMonitorDrawCtx  ictx = (TSMonitorDrawCtx)dummy;
    3886:   PetscDraw         draw;
    3887:   MPI_Comm          comm;
    3888:   PetscInt          n;
    3889:   PetscMPIInt       size;
    3890:   PetscReal         xl,yl,xr,yr,h;
    3891:   char              time[32];
    3892:   const PetscScalar *U;

    3895:   PetscObjectGetComm((PetscObject)ts,&comm);
    3896:   MPI_Comm_size(comm,&size);
    3897:   if (size != 1) SETERRQ(comm,PETSC_ERR_SUP,"Only allowed for sequential runs");
    3898:   VecGetSize(u,&n);
    3899:   if (n != 2) SETERRQ(comm,PETSC_ERR_SUP,"Only for ODEs with two unknowns");

    3901:   PetscViewerDrawGetDraw(ictx->viewer,0,&draw);

    3903:   VecGetArrayRead(u,&U);
    3904:   PetscDrawAxisGetLimits(ictx->axis,&xl,&xr,&yl,&yr);
    3905:   if ((PetscRealPart(U[0]) < xl) || (PetscRealPart(U[1]) < yl) || (PetscRealPart(U[0]) > xr) || (PetscRealPart(U[1]) > yr)) {
    3906:       VecRestoreArrayRead(u,&U);
    3907:       return(0);
    3908:   }
    3909:   if (!step) ictx->color++;
    3910:   PetscDrawPoint(draw,PetscRealPart(U[0]),PetscRealPart(U[1]),ictx->color);
    3911:   VecRestoreArrayRead(u,&U);

    3913:   if (ictx->showtimestepandtime) {
    3914:     PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
    3915:     PetscSNPrintf(time,32,"Timestep %d Time %g",(int)step,(double)ptime);
    3916:     h    = yl + .95*(yr - yl);
    3917:     PetscDrawStringCentered(draw,.5*(xl+xr),h,PETSC_DRAW_BLACK,time);
    3918:   }
    3919:   PetscDrawFlush(draw);
    3920:   return(0);
    3921: }

    3926: /*@C
    3927:    TSMonitorDrawCtxDestroy - Destroys the monitor context for TSMonitorDrawSolution()

    3929:    Collective on TS

    3931:    Input Parameters:
    3932: .    ctx - the monitor context

    3934:    Level: intermediate

    3936: .keywords: TS,  vector, monitor, view

    3938: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorDrawSolution(), TSMonitorDrawError()
    3939: @*/
    3940: PetscErrorCode  TSMonitorDrawCtxDestroy(TSMonitorDrawCtx *ictx)
    3941: {

    3945:   PetscDrawAxisDestroy(&(*ictx)->axis);
    3946:   PetscViewerDestroy(&(*ictx)->viewer);
    3947:   VecDestroy(&(*ictx)->initialsolution);
    3948:   PetscFree(*ictx);
    3949:   return(0);
    3950: }

    3954: /*@C
    3955:    TSMonitorDrawCtxCreate - Creates the monitor context for TSMonitorDrawCtx

    3957:    Collective on TS

    3959:    Input Parameter:
    3960: .    ts - time-step context

    3962:    Output Patameter:
    3963: .    ctx - the monitor context

    3965:    Options Database:
    3966: .   -ts_monitor_draw_solution_initial - show initial solution as well as current solution

    3968:    Level: intermediate

    3970: .keywords: TS,  vector, monitor, view

    3972: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorDrawCtx()
    3973: @*/
    3974: PetscErrorCode  TSMonitorDrawCtxCreate(MPI_Comm comm,const char host[],const char label[],int x,int y,int m,int n,PetscInt howoften,TSMonitorDrawCtx *ctx)
    3975: {
    3976:   PetscErrorCode   ierr;

    3979:   PetscNew(ctx);
    3980:   PetscViewerDrawOpen(comm,host,label,x,y,m,n,&(*ctx)->viewer);
    3981:   PetscViewerSetFromOptions((*ctx)->viewer);

    3983:   (*ctx)->howoften    = howoften;
    3984:   (*ctx)->showinitial = PETSC_FALSE;
    3985:   PetscOptionsGetBool(NULL,"-ts_monitor_draw_solution_initial",&(*ctx)->showinitial,NULL);

    3987:   (*ctx)->showtimestepandtime = PETSC_FALSE;
    3988:   PetscOptionsGetBool(NULL,"-ts_monitor_draw_solution_show_time",&(*ctx)->showtimestepandtime,NULL);
    3989:   (*ctx)->color = PETSC_DRAW_WHITE;
    3990:   return(0);
    3991: }

    3995: /*@C
    3996:    TSMonitorDrawError - Monitors progress of the TS solvers by calling
    3997:    VecView() for the error at each timestep

    3999:    Collective on TS

    4001:    Input Parameters:
    4002: +  ts - the TS context
    4003: .  step - current time-step
    4004: .  ptime - current time
    4005: -  dummy - either a viewer or NULL

    4007:    Level: intermediate

    4009: .keywords: TS,  vector, monitor, view

    4011: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    4012: @*/
    4013: PetscErrorCode  TSMonitorDrawError(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    4014: {
    4015:   PetscErrorCode   ierr;
    4016:   TSMonitorDrawCtx ctx    = (TSMonitorDrawCtx)dummy;
    4017:   PetscViewer      viewer = ctx->viewer;
    4018:   Vec              work;

    4021:   if (!(((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason))) return(0);
    4022:   VecDuplicate(u,&work);
    4023:   TSComputeSolutionFunction(ts,ptime,work);
    4024:   VecAXPY(work,-1.0,u);
    4025:   VecView(work,viewer);
    4026:   VecDestroy(&work);
    4027:   return(0);
    4028: }

    4030: #include <petsc/private/dmimpl.h>
    4033: /*@
    4034:    TSSetDM - Sets the DM that may be used by some preconditioners

    4036:    Logically Collective on TS and DM

    4038:    Input Parameters:
    4039: +  ts - the preconditioner context
    4040: -  dm - the dm

    4042:    Level: intermediate

    4045: .seealso: TSGetDM(), SNESSetDM(), SNESGetDM()
    4046: @*/
    4047: PetscErrorCode  TSSetDM(TS ts,DM dm)
    4048: {
    4050:   SNES           snes;
    4051:   DMTS           tsdm;

    4055:   PetscObjectReference((PetscObject)dm);
    4056:   if (ts->dm) {               /* Move the DMTS context over to the new DM unless the new DM already has one */
    4057:     if (ts->dm->dmts && !dm->dmts) {
    4058:       DMCopyDMTS(ts->dm,dm);
    4059:       DMGetDMTS(ts->dm,&tsdm);
    4060:       if (tsdm->originaldm == ts->dm) { /* Grant write privileges to the replacement DM */
    4061:         tsdm->originaldm = dm;
    4062:       }
    4063:     }
    4064:     DMDestroy(&ts->dm);
    4065:   }
    4066:   ts->dm = dm;

    4068:   TSGetSNES(ts,&snes);
    4069:   SNESSetDM(snes,dm);
    4070:   return(0);
    4071: }

    4075: /*@
    4076:    TSGetDM - Gets the DM that may be used by some preconditioners

    4078:    Not Collective

    4080:    Input Parameter:
    4081: . ts - the preconditioner context

    4083:    Output Parameter:
    4084: .  dm - the dm

    4086:    Level: intermediate

    4089: .seealso: TSSetDM(), SNESSetDM(), SNESGetDM()
    4090: @*/
    4091: PetscErrorCode  TSGetDM(TS ts,DM *dm)
    4092: {

    4097:   if (!ts->dm) {
    4098:     DMShellCreate(PetscObjectComm((PetscObject)ts),&ts->dm);
    4099:     if (ts->snes) {SNESSetDM(ts->snes,ts->dm);}
    4100:   }
    4101:   *dm = ts->dm;
    4102:   return(0);
    4103: }

    4107: /*@
    4108:    SNESTSFormFunction - Function to evaluate nonlinear residual

    4110:    Logically Collective on SNES

    4112:    Input Parameter:
    4113: + snes - nonlinear solver
    4114: . U - the current state at which to evaluate the residual
    4115: - ctx - user context, must be a TS

    4117:    Output Parameter:
    4118: . F - the nonlinear residual

    4120:    Notes:
    4121:    This function is not normally called by users and is automatically registered with the SNES used by TS.
    4122:    It is most frequently passed to MatFDColoringSetFunction().

    4124:    Level: advanced

    4126: .seealso: SNESSetFunction(), MatFDColoringSetFunction()
    4127: @*/
    4128: PetscErrorCode  SNESTSFormFunction(SNES snes,Vec U,Vec F,void *ctx)
    4129: {
    4130:   TS             ts = (TS)ctx;

    4138:   (ts->ops->snesfunction)(snes,U,F,ts);
    4139:   return(0);
    4140: }

    4144: /*@
    4145:    SNESTSFormJacobian - Function to evaluate the Jacobian

    4147:    Collective on SNES

    4149:    Input Parameter:
    4150: + snes - nonlinear solver
    4151: . U - the current state at which to evaluate the residual
    4152: - ctx - user context, must be a TS

    4154:    Output Parameter:
    4155: + A - the Jacobian
    4156: . B - the preconditioning matrix (may be the same as A)
    4157: - flag - indicates any structure change in the matrix

    4159:    Notes:
    4160:    This function is not normally called by users and is automatically registered with the SNES used by TS.

    4162:    Level: developer

    4164: .seealso: SNESSetJacobian()
    4165: @*/
    4166: PetscErrorCode  SNESTSFormJacobian(SNES snes,Vec U,Mat A,Mat B,void *ctx)
    4167: {
    4168:   TS             ts = (TS)ctx;

    4179:   (ts->ops->snesjacobian)(snes,U,A,B,ts);
    4180:   return(0);
    4181: }

    4185: /*@C
    4186:    TSComputeRHSFunctionLinear - Evaluate the right hand side via the user-provided Jacobian, for linear problems only

    4188:    Collective on TS

    4190:    Input Arguments:
    4191: +  ts - time stepping context
    4192: .  t - time at which to evaluate
    4193: .  U - state at which to evaluate
    4194: -  ctx - context

    4196:    Output Arguments:
    4197: .  F - right hand side

    4199:    Level: intermediate

    4201:    Notes:
    4202:    This function is intended to be passed to TSSetRHSFunction() to evaluate the right hand side for linear problems.
    4203:    The matrix (and optionally the evaluation context) should be passed to TSSetRHSJacobian().

    4205: .seealso: TSSetRHSFunction(), TSSetRHSJacobian(), TSComputeRHSJacobianConstant()
    4206: @*/
    4207: PetscErrorCode TSComputeRHSFunctionLinear(TS ts,PetscReal t,Vec U,Vec F,void *ctx)
    4208: {
    4210:   Mat            Arhs,Brhs;

    4213:   TSGetRHSMats_Private(ts,&Arhs,&Brhs);
    4214:   TSComputeRHSJacobian(ts,t,U,Arhs,Brhs);
    4215:   MatMult(Arhs,U,F);
    4216:   return(0);
    4217: }

    4221: /*@C
    4222:    TSComputeRHSJacobianConstant - Reuses a Jacobian that is time-independent.

    4224:    Collective on TS

    4226:    Input Arguments:
    4227: +  ts - time stepping context
    4228: .  t - time at which to evaluate
    4229: .  U - state at which to evaluate
    4230: -  ctx - context

    4232:    Output Arguments:
    4233: +  A - pointer to operator
    4234: .  B - pointer to preconditioning matrix
    4235: -  flg - matrix structure flag

    4237:    Level: intermediate

    4239:    Notes:
    4240:    This function is intended to be passed to TSSetRHSJacobian() to evaluate the Jacobian for linear time-independent problems.

    4242: .seealso: TSSetRHSFunction(), TSSetRHSJacobian(), TSComputeRHSFunctionLinear()
    4243: @*/
    4244: PetscErrorCode TSComputeRHSJacobianConstant(TS ts,PetscReal t,Vec U,Mat A,Mat B,void *ctx)
    4245: {
    4247:   return(0);
    4248: }

    4252: /*@C
    4253:    TSComputeIFunctionLinear - Evaluate the left hand side via the user-provided Jacobian, for linear problems only

    4255:    Collective on TS

    4257:    Input Arguments:
    4258: +  ts - time stepping context
    4259: .  t - time at which to evaluate
    4260: .  U - state at which to evaluate
    4261: .  Udot - time derivative of state vector
    4262: -  ctx - context

    4264:    Output Arguments:
    4265: .  F - left hand side

    4267:    Level: intermediate

    4269:    Notes:
    4270:    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
    4271:    user is required to write their own TSComputeIFunction.
    4272:    This function is intended to be passed to TSSetIFunction() to evaluate the left hand side for linear problems.
    4273:    The matrix (and optionally the evaluation context) should be passed to TSSetIJacobian().

    4275: .seealso: TSSetIFunction(), TSSetIJacobian(), TSComputeIJacobianConstant()
    4276: @*/
    4277: PetscErrorCode TSComputeIFunctionLinear(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,void *ctx)
    4278: {
    4280:   Mat            A,B;

    4283:   TSGetIJacobian(ts,&A,&B,NULL,NULL);
    4284:   TSComputeIJacobian(ts,t,U,Udot,1.0,A,B,PETSC_TRUE);
    4285:   MatMult(A,Udot,F);
    4286:   return(0);
    4287: }

    4291: /*@C
    4292:    TSComputeIJacobianConstant - Reuses a time-independent for a semi-implicit DAE or ODE

    4294:    Collective on TS

    4296:    Input Arguments:
    4297: +  ts - time stepping context
    4298: .  t - time at which to evaluate
    4299: .  U - state at which to evaluate
    4300: .  Udot - time derivative of state vector
    4301: .  shift - shift to apply
    4302: -  ctx - context

    4304:    Output Arguments:
    4305: +  A - pointer to operator
    4306: .  B - pointer to preconditioning matrix
    4307: -  flg - matrix structure flag

    4309:    Level: advanced

    4311:    Notes:
    4312:    This function is intended to be passed to TSSetIJacobian() to evaluate the Jacobian for linear time-independent problems.

    4314:    It is only appropriate for problems of the form

    4316: $     M Udot = F(U,t)

    4318:   where M is constant and F is non-stiff.  The user must pass M to TSSetIJacobian().  The current implementation only
    4319:   works with IMEX time integration methods such as TSROSW and TSARKIMEX, since there is no support for de-constructing
    4320:   an implicit operator of the form

    4322: $    shift*M + J

    4324:   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
    4325:   a copy of M or reassemble it when requested.

    4327: .seealso: TSSetIFunction(), TSSetIJacobian(), TSComputeIFunctionLinear()
    4328: @*/
    4329: PetscErrorCode TSComputeIJacobianConstant(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat A,Mat B,void *ctx)
    4330: {

    4334:   MatScale(A, shift / ts->ijacobian.shift);
    4335:   ts->ijacobian.shift = shift;
    4336:   return(0);
    4337: }

    4341: /*@
    4342:    TSGetEquationType - Gets the type of the equation that TS is solving.

    4344:    Not Collective

    4346:    Input Parameter:
    4347: .  ts - the TS context

    4349:    Output Parameter:
    4350: .  equation_type - see TSEquationType

    4352:    Level: beginner

    4354: .keywords: TS, equation type

    4356: .seealso: TSSetEquationType(), TSEquationType
    4357: @*/
    4358: PetscErrorCode  TSGetEquationType(TS ts,TSEquationType *equation_type)
    4359: {
    4363:   *equation_type = ts->equation_type;
    4364:   return(0);
    4365: }

    4369: /*@
    4370:    TSSetEquationType - Sets the type of the equation that TS is solving.

    4372:    Not Collective

    4374:    Input Parameter:
    4375: +  ts - the TS context
    4376: -  equation_type - see TSEquationType

    4378:    Level: advanced

    4380: .keywords: TS, equation type

    4382: .seealso: TSGetEquationType(), TSEquationType
    4383: @*/
    4384: PetscErrorCode  TSSetEquationType(TS ts,TSEquationType equation_type)
    4385: {
    4388:   ts->equation_type = equation_type;
    4389:   return(0);
    4390: }

    4394: /*@
    4395:    TSGetConvergedReason - Gets the reason the TS iteration was stopped.

    4397:    Not Collective

    4399:    Input Parameter:
    4400: .  ts - the TS context

    4402:    Output Parameter:
    4403: .  reason - negative value indicates diverged, positive value converged, see TSConvergedReason or the
    4404:             manual pages for the individual convergence tests for complete lists

    4406:    Level: beginner

    4408:    Notes:
    4409:    Can only be called after the call to TSSolve() is complete.

    4411: .keywords: TS, nonlinear, set, convergence, test

    4413: .seealso: TSSetConvergenceTest(), TSConvergedReason
    4414: @*/
    4415: PetscErrorCode  TSGetConvergedReason(TS ts,TSConvergedReason *reason)
    4416: {
    4420:   *reason = ts->reason;
    4421:   return(0);
    4422: }

    4426: /*@
    4427:    TSSetConvergedReason - Sets the reason for handling the convergence of TSSolve.

    4429:    Not Collective

    4431:    Input Parameter:
    4432: +  ts - the TS context
    4433: .  reason - negative value indicates diverged, positive value converged, see TSConvergedReason or the
    4434:             manual pages for the individual convergence tests for complete lists

    4436:    Level: advanced

    4438:    Notes:
    4439:    Can only be called during TSSolve() is active.

    4441: .keywords: TS, nonlinear, set, convergence, test

    4443: .seealso: TSConvergedReason
    4444: @*/
    4445: PetscErrorCode  TSSetConvergedReason(TS ts,TSConvergedReason reason)
    4446: {
    4449:   ts->reason = reason;
    4450:   return(0);
    4451: }

    4455: /*@
    4456:    TSGetSolveTime - Gets the time after a call to TSSolve()

    4458:    Not Collective

    4460:    Input Parameter:
    4461: .  ts - the TS context

    4463:    Output Parameter:
    4464: .  ftime - the final time. This time should correspond to the final time set with TSSetDuration()

    4466:    Level: beginner

    4468:    Notes:
    4469:    Can only be called after the call to TSSolve() is complete.

    4471: .keywords: TS, nonlinear, set, convergence, test

    4473: .seealso: TSSetConvergenceTest(), TSConvergedReason
    4474: @*/
    4475: PetscErrorCode  TSGetSolveTime(TS ts,PetscReal *ftime)
    4476: {
    4480:   *ftime = ts->solvetime;
    4481:   return(0);
    4482: }

    4486: /*@
    4487:    TSGetTotalSteps - Gets the total number of steps done since the last call to TSSetUp() or TSCreate()

    4489:    Not Collective

    4491:    Input Parameter:
    4492: .  ts - the TS context

    4494:    Output Parameter:
    4495: .  steps - the number of steps

    4497:    Level: beginner

    4499:    Notes:
    4500:    Includes the number of steps for all calls to TSSolve() since TSSetUp() was called

    4502: .keywords: TS, nonlinear, set, convergence, test

    4504: .seealso: TSSetConvergenceTest(), TSConvergedReason
    4505: @*/
    4506: PetscErrorCode  TSGetTotalSteps(TS ts,PetscInt *steps)
    4507: {
    4511:   *steps = ts->total_steps;
    4512:   return(0);
    4513: }

    4517: /*@
    4518:    TSGetSNESIterations - Gets the total number of nonlinear iterations
    4519:    used by the time integrator.

    4521:    Not Collective

    4523:    Input Parameter:
    4524: .  ts - TS context

    4526:    Output Parameter:
    4527: .  nits - number of nonlinear iterations

    4529:    Notes:
    4530:    This counter is reset to zero for each successive call to TSSolve().

    4532:    Level: intermediate

    4534: .keywords: TS, get, number, nonlinear, iterations

    4536: .seealso:  TSGetKSPIterations()
    4537: @*/
    4538: PetscErrorCode TSGetSNESIterations(TS ts,PetscInt *nits)
    4539: {
    4543:   *nits = ts->snes_its;
    4544:   return(0);
    4545: }

    4549: /*@
    4550:    TSGetKSPIterations - Gets the total number of linear iterations
    4551:    used by the time integrator.

    4553:    Not Collective

    4555:    Input Parameter:
    4556: .  ts - TS context

    4558:    Output Parameter:
    4559: .  lits - number of linear iterations

    4561:    Notes:
    4562:    This counter is reset to zero for each successive call to TSSolve().

    4564:    Level: intermediate

    4566: .keywords: TS, get, number, linear, iterations

    4568: .seealso:  TSGetSNESIterations(), SNESGetKSPIterations()
    4569: @*/
    4570: PetscErrorCode TSGetKSPIterations(TS ts,PetscInt *lits)
    4571: {
    4575:   *lits = ts->ksp_its;
    4576:   return(0);
    4577: }

    4581: /*@
    4582:    TSGetStepRejections - Gets the total number of rejected steps.

    4584:    Not Collective

    4586:    Input Parameter:
    4587: .  ts - TS context

    4589:    Output Parameter:
    4590: .  rejects - number of steps rejected

    4592:    Notes:
    4593:    This counter is reset to zero for each successive call to TSSolve().

    4595:    Level: intermediate

    4597: .keywords: TS, get, number

    4599: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetSNESFailures(), TSSetMaxSNESFailures(), TSSetErrorIfStepFails()
    4600: @*/
    4601: PetscErrorCode TSGetStepRejections(TS ts,PetscInt *rejects)
    4602: {
    4606:   *rejects = ts->reject;
    4607:   return(0);
    4608: }

    4612: /*@
    4613:    TSGetSNESFailures - Gets the total number of failed SNES solves

    4615:    Not Collective

    4617:    Input Parameter:
    4618: .  ts - TS context

    4620:    Output Parameter:
    4621: .  fails - number of failed nonlinear solves

    4623:    Notes:
    4624:    This counter is reset to zero for each successive call to TSSolve().

    4626:    Level: intermediate

    4628: .keywords: TS, get, number

    4630: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSSetMaxSNESFailures()
    4631: @*/
    4632: PetscErrorCode TSGetSNESFailures(TS ts,PetscInt *fails)
    4633: {
    4637:   *fails = ts->num_snes_failures;
    4638:   return(0);
    4639: }

    4643: /*@
    4644:    TSSetMaxStepRejections - Sets the maximum number of step rejections before a step fails

    4646:    Not Collective

    4648:    Input Parameter:
    4649: +  ts - TS context
    4650: -  rejects - maximum number of rejected steps, pass -1 for unlimited

    4652:    Notes:
    4653:    The counter is reset to zero for each step

    4655:    Options Database Key:
    4656:  .  -ts_max_reject - Maximum number of step rejections before a step fails

    4658:    Level: intermediate

    4660: .keywords: TS, set, maximum, number

    4662: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxSNESFailures(), TSGetStepRejections(), TSGetSNESFailures(), TSSetErrorIfStepFails(), TSGetConvergedReason()
    4663: @*/
    4664: PetscErrorCode TSSetMaxStepRejections(TS ts,PetscInt rejects)
    4665: {
    4668:   ts->max_reject = rejects;
    4669:   return(0);
    4670: }

    4674: /*@
    4675:    TSSetMaxSNESFailures - Sets the maximum number of failed SNES solves

    4677:    Not Collective

    4679:    Input Parameter:
    4680: +  ts - TS context
    4681: -  fails - maximum number of failed nonlinear solves, pass -1 for unlimited

    4683:    Notes:
    4684:    The counter is reset to zero for each successive call to TSSolve().

    4686:    Options Database Key:
    4687:  .  -ts_max_snes_failures - Maximum number of nonlinear solve failures

    4689:    Level: intermediate

    4691: .keywords: TS, set, maximum, number

    4693: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSGetSNESFailures(), SNESGetConvergedReason(), TSGetConvergedReason()
    4694: @*/
    4695: PetscErrorCode TSSetMaxSNESFailures(TS ts,PetscInt fails)
    4696: {
    4699:   ts->max_snes_failures = fails;
    4700:   return(0);
    4701: }

    4705: /*@
    4706:    TSSetErrorIfStepFails - Error if no step succeeds

    4708:    Not Collective

    4710:    Input Parameter:
    4711: +  ts - TS context
    4712: -  err - PETSC_TRUE to error if no step succeeds, PETSC_FALSE to return without failure

    4714:    Options Database Key:
    4715:  .  -ts_error_if_step_fails - Error if no step succeeds

    4717:    Level: intermediate

    4719: .keywords: TS, set, error

    4721: .seealso:  TSGetSNESIterations(), TSGetKSPIterations(), TSSetMaxStepRejections(), TSGetStepRejections(), TSGetSNESFailures(), TSSetErrorIfStepFails(), TSGetConvergedReason()
    4722: @*/
    4723: PetscErrorCode TSSetErrorIfStepFails(TS ts,PetscBool err)
    4724: {
    4727:   ts->errorifstepfailed = err;
    4728:   return(0);
    4729: }

    4733: /*@C
    4734:    TSMonitorSolutionBinary - Monitors progress of the TS solvers by VecView() for the solution at each timestep. Normally the viewer is a binary file

    4736:    Collective on TS

    4738:    Input Parameters:
    4739: +  ts - the TS context
    4740: .  step - current time-step
    4741: .  ptime - current time
    4742: .  u - current state
    4743: -  viewer - binary viewer

    4745:    Level: intermediate

    4747: .keywords: TS,  vector, monitor, view

    4749: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    4750: @*/
    4751: PetscErrorCode  TSMonitorSolutionBinary(TS ts,PetscInt step,PetscReal ptime,Vec u,void *viewer)
    4752: {
    4754:   PetscViewer    v = (PetscViewer)viewer;

    4757:   VecView(u,v);
    4758:   return(0);
    4759: }

    4763: /*@C
    4764:    TSMonitorSolutionVTK - Monitors progress of the TS solvers by VecView() for the solution at each timestep.

    4766:    Collective on TS

    4768:    Input Parameters:
    4769: +  ts - the TS context
    4770: .  step - current time-step
    4771: .  ptime - current time
    4772: .  u - current state
    4773: -  filenametemplate - string containing a format specifier for the integer time step (e.g. %03D)

    4775:    Level: intermediate

    4777:    Notes:
    4778:    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.
    4779:    These are named according to the file name template.

    4781:    This function is normally passed as an argument to TSMonitorSet() along with TSMonitorSolutionVTKDestroy().

    4783: .keywords: TS,  vector, monitor, view

    4785: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    4786: @*/
    4787: PetscErrorCode TSMonitorSolutionVTK(TS ts,PetscInt step,PetscReal ptime,Vec u,void *filenametemplate)
    4788: {
    4790:   char           filename[PETSC_MAX_PATH_LEN];
    4791:   PetscViewer    viewer;

    4794:   PetscSNPrintf(filename,sizeof(filename),(const char*)filenametemplate,step);
    4795:   PetscViewerVTKOpen(PetscObjectComm((PetscObject)ts),filename,FILE_MODE_WRITE,&viewer);
    4796:   VecView(u,viewer);
    4797:   PetscViewerDestroy(&viewer);
    4798:   return(0);
    4799: }

    4803: /*@C
    4804:    TSMonitorSolutionVTKDestroy - Destroy context for monitoring

    4806:    Collective on TS

    4808:    Input Parameters:
    4809: .  filenametemplate - string containing a format specifier for the integer time step (e.g. %03D)

    4811:    Level: intermediate

    4813:    Note:
    4814:    This function is normally passed to TSMonitorSet() along with TSMonitorSolutionVTK().

    4816: .keywords: TS,  vector, monitor, view

    4818: .seealso: TSMonitorSet(), TSMonitorSolutionVTK()
    4819: @*/
    4820: PetscErrorCode TSMonitorSolutionVTKDestroy(void *filenametemplate)
    4821: {

    4825:   PetscFree(*(char**)filenametemplate);
    4826:   return(0);
    4827: }

    4831: /*@
    4832:    TSGetAdapt - Get the adaptive controller context for the current method

    4834:    Collective on TS if controller has not been created yet

    4836:    Input Arguments:
    4837: .  ts - time stepping context

    4839:    Output Arguments:
    4840: .  adapt - adaptive controller

    4842:    Level: intermediate

    4844: .seealso: TSAdapt, TSAdaptSetType(), TSAdaptChoose()
    4845: @*/
    4846: PetscErrorCode TSGetAdapt(TS ts,TSAdapt *adapt)
    4847: {

    4853:   if (!ts->adapt) {
    4854:     TSAdaptCreate(PetscObjectComm((PetscObject)ts),&ts->adapt);
    4855:     PetscLogObjectParent((PetscObject)ts,(PetscObject)ts->adapt);
    4856:     PetscObjectIncrementTabLevel((PetscObject)ts->adapt,(PetscObject)ts,1);
    4857:   }
    4858:   *adapt = ts->adapt;
    4859:   return(0);
    4860: }

    4864: /*@
    4865:    TSSetTolerances - Set tolerances for local truncation error when using adaptive controller

    4867:    Logically Collective

    4869:    Input Arguments:
    4870: +  ts - time integration context
    4871: .  atol - scalar absolute tolerances, PETSC_DECIDE to leave current value
    4872: .  vatol - vector of absolute tolerances or NULL, used in preference to atol if present
    4873: .  rtol - scalar relative tolerances, PETSC_DECIDE to leave current value
    4874: -  vrtol - vector of relative tolerances or NULL, used in preference to atol if present

    4876:    Options Database keys:
    4877: +  -ts_rtol <rtol> - relative tolerance for local truncation error
    4878: -  -ts_atol <atol> Absolute tolerance for local truncation error

    4880:    Notes:
    4881:    With PETSc's implicit schemes for DAE problems, the calculation of the local truncation error
    4882:    (LTE) includes both the differential and the algebraic variables. If one wants the LTE to be
    4883:    computed only for the differential or the algebraic part then this can be done using the vector of
    4884:    tolerances vatol. For example, by setting the tolerance vector with the desired tolerance for the
    4885:    differential part and infinity for the algebraic part, the LTE calculation will include only the
    4886:    differential variables.

    4888:    Level: beginner

    4890: .seealso: TS, TSAdapt, TSVecNormWRMS(), TSGetTolerances()
    4891: @*/
    4892: PetscErrorCode TSSetTolerances(TS ts,PetscReal atol,Vec vatol,PetscReal rtol,Vec vrtol)
    4893: {

    4897:   if (atol != PETSC_DECIDE && atol != PETSC_DEFAULT) ts->atol = atol;
    4898:   if (vatol) {
    4899:     PetscObjectReference((PetscObject)vatol);
    4900:     VecDestroy(&ts->vatol);

    4902:     ts->vatol = vatol;
    4903:   }
    4904:   if (rtol != PETSC_DECIDE && rtol != PETSC_DEFAULT) ts->rtol = rtol;
    4905:   if (vrtol) {
    4906:     PetscObjectReference((PetscObject)vrtol);
    4907:     VecDestroy(&ts->vrtol);

    4909:     ts->vrtol = vrtol;
    4910:   }
    4911:   return(0);
    4912: }

    4916: /*@
    4917:    TSGetTolerances - Get tolerances for local truncation error when using adaptive controller

    4919:    Logically Collective

    4921:    Input Arguments:
    4922: .  ts - time integration context

    4924:    Output Arguments:
    4925: +  atol - scalar absolute tolerances, NULL to ignore
    4926: .  vatol - vector of absolute tolerances, NULL to ignore
    4927: .  rtol - scalar relative tolerances, NULL to ignore
    4928: -  vrtol - vector of relative tolerances, NULL to ignore

    4930:    Level: beginner

    4932: .seealso: TS, TSAdapt, TSVecNormWRMS(), TSSetTolerances()
    4933: @*/
    4934: PetscErrorCode TSGetTolerances(TS ts,PetscReal *atol,Vec *vatol,PetscReal *rtol,Vec *vrtol)
    4935: {
    4937:   if (atol)  *atol  = ts->atol;
    4938:   if (vatol) *vatol = ts->vatol;
    4939:   if (rtol)  *rtol  = ts->rtol;
    4940:   if (vrtol) *vrtol = ts->vrtol;
    4941:   return(0);
    4942: }

    4946: /*@
    4947:    TSErrorWeightedNorm2 - compute a weighted 2-norm of the difference between two state vectors

    4949:    Collective on TS

    4951:    Input Arguments:
    4952: +  ts - time stepping context
    4953: .  U - state vector, usually ts->vec_sol
    4954: -  Y - state vector to be compared to U

    4956:    Output Arguments:
    4957: .  norm - weighted norm, a value of 1.0 is considered small

    4959:    Level: developer

    4961: .seealso: TSErrorWeightedNorm(), TSErrorWeightedNormInfinity()
    4962: @*/
    4963: PetscErrorCode TSErrorWeightedNorm2(TS ts,Vec U,Vec Y,PetscReal *norm)
    4964: {
    4965:   PetscErrorCode    ierr;
    4966:   PetscInt          i,n,N,rstart;
    4967:   const PetscScalar *u,*y;
    4968:   PetscReal         sum,gsum;
    4969:   PetscReal         tol;

    4979:   if (U == Y) SETERRQ(PetscObjectComm((PetscObject)U),PETSC_ERR_ARG_IDN,"U and Y cannot be the same vector");

    4981:   VecGetSize(U,&N);
    4982:   VecGetLocalSize(U,&n);
    4983:   VecGetOwnershipRange(U,&rstart,NULL);
    4984:   VecGetArrayRead(U,&u);
    4985:   VecGetArrayRead(Y,&y);
    4986:   sum  = 0.;
    4987:   if (ts->vatol && ts->vrtol) {
    4988:     const PetscScalar *atol,*rtol;
    4989:     VecGetArrayRead(ts->vatol,&atol);
    4990:     VecGetArrayRead(ts->vrtol,&rtol);
    4991:     for (i=0; i<n; i++) {
    4992:       tol = PetscRealPart(atol[i]) + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    4993:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
    4994:     }
    4995:     VecRestoreArrayRead(ts->vatol,&atol);
    4996:     VecRestoreArrayRead(ts->vrtol,&rtol);
    4997:   } else if (ts->vatol) {       /* vector atol, scalar rtol */
    4998:     const PetscScalar *atol;
    4999:     VecGetArrayRead(ts->vatol,&atol);
    5000:     for (i=0; i<n; i++) {
    5001:       tol = PetscRealPart(atol[i]) + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5002:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
    5003:     }
    5004:     VecRestoreArrayRead(ts->vatol,&atol);
    5005:   } else if (ts->vrtol) {       /* scalar atol, vector rtol */
    5006:     const PetscScalar *rtol;
    5007:     VecGetArrayRead(ts->vrtol,&rtol);
    5008:     for (i=0; i<n; i++) {
    5009:       tol = ts->atol + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5010:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
    5011:     }
    5012:     VecRestoreArrayRead(ts->vrtol,&rtol);
    5013:   } else {                      /* scalar atol, scalar rtol */
    5014:     for (i=0; i<n; i++) {
    5015:       tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5016:       sum += PetscSqr(PetscAbsScalar(y[i] - u[i]) / tol);
    5017:     }
    5018:   }
    5019:   VecRestoreArrayRead(U,&u);
    5020:   VecRestoreArrayRead(Y,&y);

    5022:   MPI_Allreduce(&sum,&gsum,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));
    5023:   *norm = PetscSqrtReal(gsum / N);

    5025:   if (PetscIsInfOrNanScalar(*norm)) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_FP,"Infinite or not-a-number generated in norm");
    5026:   return(0);
    5027: }

    5031: /*@
    5032:    TSErrorWeightedNormInfinity - compute a weighted infinity-norm of the difference between two state vectors

    5034:    Collective on TS

    5036:    Input Arguments:
    5037: +  ts - time stepping context
    5038: .  U - state vector, usually ts->vec_sol
    5039: -  Y - state vector to be compared to U

    5041:    Output Arguments:
    5042: .  norm - weighted norm, a value of 1.0 is considered small

    5044:    Level: developer

    5046: .seealso: TSErrorWeightedNorm(), TSErrorWeightedNorm2()
    5047: @*/
    5048: PetscErrorCode TSErrorWeightedNormInfinity(TS ts,Vec U,Vec Y,PetscReal *norm)
    5049: {
    5050:   PetscErrorCode    ierr;
    5051:   PetscInt          i,n,N,rstart,k;
    5052:   const PetscScalar *u,*y;
    5053:   PetscReal         max,gmax;
    5054:   PetscReal         tol;

    5064:   if (U == Y) SETERRQ(PetscObjectComm((PetscObject)U),PETSC_ERR_ARG_IDN,"U and Y cannot be the same vector");

    5066:   VecGetSize(U,&N);
    5067:   VecGetLocalSize(U,&n);
    5068:   VecGetOwnershipRange(U,&rstart,NULL);
    5069:   VecGetArrayRead(U,&u);
    5070:   VecGetArrayRead(Y,&y);
    5071:   if (ts->vatol && ts->vrtol) {
    5072:     const PetscScalar *atol,*rtol;
    5073:     VecGetArrayRead(ts->vatol,&atol);
    5074:     VecGetArrayRead(ts->vrtol,&rtol);
    5075:     k = 0;
    5076:     tol = PetscRealPart(atol[k]) + PetscRealPart(rtol[k]) * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
    5077:     max = PetscAbsScalar(y[k] - u[k]) / tol;
    5078:     for (i=1; i<n; i++) {
    5079:       tol = PetscRealPart(atol[i]) + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5080:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
    5081:     }
    5082:     VecRestoreArrayRead(ts->vatol,&atol);
    5083:     VecRestoreArrayRead(ts->vrtol,&rtol);
    5084:   } else if (ts->vatol) {       /* vector atol, scalar rtol */
    5085:     const PetscScalar *atol;
    5086:     VecGetArrayRead(ts->vatol,&atol);
    5087:     k = 0;
    5088:     tol = PetscRealPart(atol[k]) + ts->rtol * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
    5089:     max = PetscAbsScalar(y[k] - u[k]) / tol;
    5090:     for (i=1; i<n; i++) {
    5091:       tol = PetscRealPart(atol[i]) + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5092:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
    5093:     }
    5094:     VecRestoreArrayRead(ts->vatol,&atol);
    5095:   } else if (ts->vrtol) {       /* scalar atol, vector rtol */
    5096:     const PetscScalar *rtol;
    5097:     VecGetArrayRead(ts->vrtol,&rtol);
    5098:     k = 0;
    5099:     tol = ts->atol + PetscRealPart(rtol[k]) * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
    5100:     max = PetscAbsScalar(y[k] - u[k]) / tol;
    5101:     for (i=1; i<n; i++) {
    5102:       tol = ts->atol + PetscRealPart(rtol[i]) * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5103:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
    5104:     }
    5105:     VecRestoreArrayRead(ts->vrtol,&rtol);
    5106:   } else {                      /* scalar atol, scalar rtol */
    5107:     k = 0;
    5108:     tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[k]),PetscAbsScalar(y[k]));
    5109:     max = PetscAbsScalar(y[k] - u[k]) / tol;
    5110:     for (i=1; i<n; i++) {
    5111:       tol = ts->atol + ts->rtol * PetscMax(PetscAbsScalar(u[i]),PetscAbsScalar(y[i]));
    5112:       max = PetscMax(max,PetscAbsScalar(y[i] - u[i]) / tol);
    5113:     }
    5114:   }
    5115:   VecRestoreArrayRead(U,&u);
    5116:   VecRestoreArrayRead(Y,&y);

    5118:   MPI_Allreduce(&max,&gmax,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));
    5119:   *norm = gmax;

    5121:   if (PetscIsInfOrNanScalar(*norm)) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_FP,"Infinite or not-a-number generated in norm");
    5122:   return(0);
    5123: }

    5127: /*@
    5128:    TSErrorWeightedNorm - compute a weighted norm of the difference between two state vectors

    5130:    Collective on TS

    5132:    Input Arguments:
    5133: +  ts - time stepping context
    5134: .  U - state vector, usually ts->vec_sol
    5135: .  Y - state vector to be compared to U
    5136: -  wnormtype - norm type, either NORM_2 or NORM_INFINITY

    5138:    Output Arguments:
    5139: .  norm - weighted norm, a value of 1.0 is considered small

    5142:    Options Database Keys:
    5143: .  -ts_adapt_wnormtype <wnormtype> - 2, INFINITY

    5145:    Level: developer

    5147: .seealso: TSErrorWeightedNormInfinity(), TSErrorWeightedNorm2()
    5148: @*/
    5149: PetscErrorCode TSErrorWeightedNorm(TS ts,Vec U,Vec Y,NormType wnormtype,PetscReal *norm)
    5150: {

    5154:   if (wnormtype == NORM_2) {
    5155:     TSErrorWeightedNorm2(ts,U,Y,norm);
    5156:   } else if(wnormtype == NORM_INFINITY) {
    5157:     TSErrorWeightedNormInfinity(ts,U,Y,norm);
    5158:   } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for norm type %s",NormTypes[wnormtype]);
    5159:   return(0);
    5160: }

    5164: /*@
    5165:    TSSetCFLTimeLocal - Set the local CFL constraint relative to forward Euler

    5167:    Logically Collective on TS

    5169:    Input Arguments:
    5170: +  ts - time stepping context
    5171: -  cfltime - maximum stable time step if using forward Euler (value can be different on each process)

    5173:    Note:
    5174:    After calling this function, the global CFL time can be obtained by calling TSGetCFLTime()

    5176:    Level: intermediate

    5178: .seealso: TSGetCFLTime(), TSADAPTCFL
    5179: @*/
    5180: PetscErrorCode TSSetCFLTimeLocal(TS ts,PetscReal cfltime)
    5181: {
    5184:   ts->cfltime_local = cfltime;
    5185:   ts->cfltime       = -1.;
    5186:   return(0);
    5187: }

    5191: /*@
    5192:    TSGetCFLTime - Get the maximum stable time step according to CFL criteria applied to forward Euler

    5194:    Collective on TS

    5196:    Input Arguments:
    5197: .  ts - time stepping context

    5199:    Output Arguments:
    5200: .  cfltime - maximum stable time step for forward Euler

    5202:    Level: advanced

    5204: .seealso: TSSetCFLTimeLocal()
    5205: @*/
    5206: PetscErrorCode TSGetCFLTime(TS ts,PetscReal *cfltime)
    5207: {

    5211:   if (ts->cfltime < 0) {
    5212:     MPI_Allreduce(&ts->cfltime_local,&ts->cfltime,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));
    5213:   }
    5214:   *cfltime = ts->cfltime;
    5215:   return(0);
    5216: }

    5220: /*@
    5221:    TSVISetVariableBounds - Sets the lower and upper bounds for the solution vector. xl <= x <= xu

    5223:    Input Parameters:
    5224: .  ts   - the TS context.
    5225: .  xl   - lower bound.
    5226: .  xu   - upper bound.

    5228:    Notes:
    5229:    If this routine is not called then the lower and upper bounds are set to
    5230:    PETSC_NINFINITY and PETSC_INFINITY respectively during SNESSetUp().

    5232:    Level: advanced

    5234: @*/
    5235: PetscErrorCode TSVISetVariableBounds(TS ts, Vec xl, Vec xu)
    5236: {
    5238:   SNES           snes;

    5241:   TSGetSNES(ts,&snes);
    5242:   SNESVISetVariableBounds(snes,xl,xu);
    5243:   return(0);
    5244: }

    5246: #if defined(PETSC_HAVE_MATLAB_ENGINE)
    5247: #include <mex.h>

    5249: typedef struct {char *funcname; mxArray *ctx;} TSMatlabContext;

    5253: /*
    5254:    TSComputeFunction_Matlab - Calls the function that has been set with
    5255:                          TSSetFunctionMatlab().

    5257:    Collective on TS

    5259:    Input Parameters:
    5260: +  snes - the TS context
    5261: -  u - input vector

    5263:    Output Parameter:
    5264: .  y - function vector, as set by TSSetFunction()

    5266:    Notes:
    5267:    TSComputeFunction() is typically used within nonlinear solvers
    5268:    implementations, so most users would not generally call this routine
    5269:    themselves.

    5271:    Level: developer

    5273: .keywords: TS, nonlinear, compute, function

    5275: .seealso: TSSetFunction(), TSGetFunction()
    5276: */
    5277: PetscErrorCode  TSComputeFunction_Matlab(TS snes,PetscReal time,Vec u,Vec udot,Vec y, void *ctx)
    5278: {
    5279:   PetscErrorCode  ierr;
    5280:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
    5281:   int             nlhs  = 1,nrhs = 7;
    5282:   mxArray         *plhs[1],*prhs[7];
    5283:   long long int   lx = 0,lxdot = 0,ly = 0,ls = 0;

    5293:   PetscMemcpy(&ls,&snes,sizeof(snes));
    5294:   PetscMemcpy(&lx,&u,sizeof(u));
    5295:   PetscMemcpy(&lxdot,&udot,sizeof(udot));
    5296:   PetscMemcpy(&ly,&y,sizeof(u));

    5298:   prhs[0] =  mxCreateDoubleScalar((double)ls);
    5299:   prhs[1] =  mxCreateDoubleScalar(time);
    5300:   prhs[2] =  mxCreateDoubleScalar((double)lx);
    5301:   prhs[3] =  mxCreateDoubleScalar((double)lxdot);
    5302:   prhs[4] =  mxCreateDoubleScalar((double)ly);
    5303:   prhs[5] =  mxCreateString(sctx->funcname);
    5304:   prhs[6] =  sctx->ctx;
    5305:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSComputeFunctionInternal");
    5306:    mxGetScalar(plhs[0]);
    5307:   mxDestroyArray(prhs[0]);
    5308:   mxDestroyArray(prhs[1]);
    5309:   mxDestroyArray(prhs[2]);
    5310:   mxDestroyArray(prhs[3]);
    5311:   mxDestroyArray(prhs[4]);
    5312:   mxDestroyArray(prhs[5]);
    5313:   mxDestroyArray(plhs[0]);
    5314:   return(0);
    5315: }

    5320: /*
    5321:    TSSetFunctionMatlab - Sets the function evaluation routine and function
    5322:    vector for use by the TS routines in solving ODEs
    5323:    equations from MATLAB. Here the function is a string containing the name of a MATLAB function

    5325:    Logically Collective on TS

    5327:    Input Parameters:
    5328: +  ts - the TS context
    5329: -  func - function evaluation routine

    5331:    Calling sequence of func:
    5332: $    func (TS ts,PetscReal time,Vec u,Vec udot,Vec f,void *ctx);

    5334:    Level: beginner

    5336: .keywords: TS, nonlinear, set, function

    5338: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
    5339: */
    5340: PetscErrorCode  TSSetFunctionMatlab(TS ts,const char *func,mxArray *ctx)
    5341: {
    5342:   PetscErrorCode  ierr;
    5343:   TSMatlabContext *sctx;

    5346:   /* currently sctx is memory bleed */
    5347:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
    5348:   PetscStrallocpy(func,&sctx->funcname);
    5349:   /*
    5350:      This should work, but it doesn't
    5351:   sctx->ctx = ctx;
    5352:   mexMakeArrayPersistent(sctx->ctx);
    5353:   */
    5354:   sctx->ctx = mxDuplicateArray(ctx);

    5356:   TSSetIFunction(ts,NULL,TSComputeFunction_Matlab,sctx);
    5357:   return(0);
    5358: }

    5362: /*
    5363:    TSComputeJacobian_Matlab - Calls the function that has been set with
    5364:                          TSSetJacobianMatlab().

    5366:    Collective on TS

    5368:    Input Parameters:
    5369: +  ts - the TS context
    5370: .  u - input vector
    5371: .  A, B - the matrices
    5372: -  ctx - user context

    5374:    Level: developer

    5376: .keywords: TS, nonlinear, compute, function

    5378: .seealso: TSSetFunction(), TSGetFunction()
    5379: @*/
    5380: PetscErrorCode  TSComputeJacobian_Matlab(TS ts,PetscReal time,Vec u,Vec udot,PetscReal shift,Mat A,Mat B,void *ctx)
    5381: {
    5382:   PetscErrorCode  ierr;
    5383:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
    5384:   int             nlhs  = 2,nrhs = 9;
    5385:   mxArray         *plhs[2],*prhs[9];
    5386:   long long int   lx = 0,lxdot = 0,lA = 0,ls = 0, lB = 0;

    5392:   /* call Matlab function in ctx with arguments u and y */

    5394:   PetscMemcpy(&ls,&ts,sizeof(ts));
    5395:   PetscMemcpy(&lx,&u,sizeof(u));
    5396:   PetscMemcpy(&lxdot,&udot,sizeof(u));
    5397:   PetscMemcpy(&lA,A,sizeof(u));
    5398:   PetscMemcpy(&lB,B,sizeof(u));

    5400:   prhs[0] =  mxCreateDoubleScalar((double)ls);
    5401:   prhs[1] =  mxCreateDoubleScalar((double)time);
    5402:   prhs[2] =  mxCreateDoubleScalar((double)lx);
    5403:   prhs[3] =  mxCreateDoubleScalar((double)lxdot);
    5404:   prhs[4] =  mxCreateDoubleScalar((double)shift);
    5405:   prhs[5] =  mxCreateDoubleScalar((double)lA);
    5406:   prhs[6] =  mxCreateDoubleScalar((double)lB);
    5407:   prhs[7] =  mxCreateString(sctx->funcname);
    5408:   prhs[8] =  sctx->ctx;
    5409:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSComputeJacobianInternal");
    5410:    mxGetScalar(plhs[0]);
    5411:   mxDestroyArray(prhs[0]);
    5412:   mxDestroyArray(prhs[1]);
    5413:   mxDestroyArray(prhs[2]);
    5414:   mxDestroyArray(prhs[3]);
    5415:   mxDestroyArray(prhs[4]);
    5416:   mxDestroyArray(prhs[5]);
    5417:   mxDestroyArray(prhs[6]);
    5418:   mxDestroyArray(prhs[7]);
    5419:   mxDestroyArray(plhs[0]);
    5420:   mxDestroyArray(plhs[1]);
    5421:   return(0);
    5422: }

    5427: /*
    5428:    TSSetJacobianMatlab - Sets the Jacobian function evaluation routine and two empty Jacobian matrices
    5429:    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

    5431:    Logically Collective on TS

    5433:    Input Parameters:
    5434: +  ts - the TS context
    5435: .  A,B - Jacobian matrices
    5436: .  func - function evaluation routine
    5437: -  ctx - user context

    5439:    Calling sequence of func:
    5440: $    flag = func (TS ts,PetscReal time,Vec u,Vec udot,Mat A,Mat B,void *ctx);

    5443:    Level: developer

    5445: .keywords: TS, nonlinear, set, function

    5447: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
    5448: */
    5449: PetscErrorCode  TSSetJacobianMatlab(TS ts,Mat A,Mat B,const char *func,mxArray *ctx)
    5450: {
    5451:   PetscErrorCode  ierr;
    5452:   TSMatlabContext *sctx;

    5455:   /* currently sctx is memory bleed */
    5456:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
    5457:   PetscStrallocpy(func,&sctx->funcname);
    5458:   /*
    5459:      This should work, but it doesn't
    5460:   sctx->ctx = ctx;
    5461:   mexMakeArrayPersistent(sctx->ctx);
    5462:   */
    5463:   sctx->ctx = mxDuplicateArray(ctx);

    5465:   TSSetIJacobian(ts,A,B,TSComputeJacobian_Matlab,sctx);
    5466:   return(0);
    5467: }

    5471: /*
    5472:    TSMonitor_Matlab - Calls the function that has been set with TSMonitorSetMatlab().

    5474:    Collective on TS

    5476: .seealso: TSSetFunction(), TSGetFunction()
    5477: @*/
    5478: PetscErrorCode  TSMonitor_Matlab(TS ts,PetscInt it, PetscReal time,Vec u, void *ctx)
    5479: {
    5480:   PetscErrorCode  ierr;
    5481:   TSMatlabContext *sctx = (TSMatlabContext*)ctx;
    5482:   int             nlhs  = 1,nrhs = 6;
    5483:   mxArray         *plhs[1],*prhs[6];
    5484:   long long int   lx = 0,ls = 0;

    5490:   PetscMemcpy(&ls,&ts,sizeof(ts));
    5491:   PetscMemcpy(&lx,&u,sizeof(u));

    5493:   prhs[0] =  mxCreateDoubleScalar((double)ls);
    5494:   prhs[1] =  mxCreateDoubleScalar((double)it);
    5495:   prhs[2] =  mxCreateDoubleScalar((double)time);
    5496:   prhs[3] =  mxCreateDoubleScalar((double)lx);
    5497:   prhs[4] =  mxCreateString(sctx->funcname);
    5498:   prhs[5] =  sctx->ctx;
    5499:    mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscTSMonitorInternal");
    5500:    mxGetScalar(plhs[0]);
    5501:   mxDestroyArray(prhs[0]);
    5502:   mxDestroyArray(prhs[1]);
    5503:   mxDestroyArray(prhs[2]);
    5504:   mxDestroyArray(prhs[3]);
    5505:   mxDestroyArray(prhs[4]);
    5506:   mxDestroyArray(plhs[0]);
    5507:   return(0);
    5508: }

    5513: /*
    5514:    TSMonitorSetMatlab - Sets the monitor function from Matlab

    5516:    Level: developer

    5518: .keywords: TS, nonlinear, set, function

    5520: .seealso: TSGetFunction(), TSComputeFunction(), TSSetJacobian(), TSSetFunction()
    5521: */
    5522: PetscErrorCode  TSMonitorSetMatlab(TS ts,const char *func,mxArray *ctx)
    5523: {
    5524:   PetscErrorCode  ierr;
    5525:   TSMatlabContext *sctx;

    5528:   /* currently sctx is memory bleed */
    5529:   PetscMalloc(sizeof(TSMatlabContext),&sctx);
    5530:   PetscStrallocpy(func,&sctx->funcname);
    5531:   /*
    5532:      This should work, but it doesn't
    5533:   sctx->ctx = ctx;
    5534:   mexMakeArrayPersistent(sctx->ctx);
    5535:   */
    5536:   sctx->ctx = mxDuplicateArray(ctx);

    5538:   TSMonitorSet(ts,TSMonitor_Matlab,sctx,NULL);
    5539:   return(0);
    5540: }
    5541: #endif

    5545: /*@C
    5546:    TSMonitorLGSolution - Monitors progress of the TS solvers by plotting each component of the solution vector
    5547:        in a time based line graph

    5549:    Collective on TS

    5551:    Input Parameters:
    5552: +  ts - the TS context
    5553: .  step - current time-step
    5554: .  ptime - current time
    5555: -  lg - a line graph object

    5557:    Options Database:
    5558: .   -ts_monitor_lg_solution_variables

    5560:    Level: intermediate

    5562:     Notes: each process in a parallel run displays its component solutions in a separate window

    5564: .keywords: TS,  vector, monitor, view

    5566: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView()
    5567: @*/
    5568: PetscErrorCode  TSMonitorLGSolution(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    5569: {
    5570:   PetscErrorCode    ierr;
    5571:   TSMonitorLGCtx    ctx = (TSMonitorLGCtx)dummy;
    5572:   const PetscScalar *yy;
    5573:   PetscInt          dim;
    5574:   Vec               v;

    5577:   if (!step) {
    5578:     PetscDrawAxis axis;
    5579:     PetscDrawLGGetAxis(ctx->lg,&axis);
    5580:     PetscDrawAxisSetLabels(axis,"Solution as function of time","Time","Solution");
    5581:     if (ctx->names && !ctx->displaynames) {
    5582:       char      **displaynames;
    5583:       PetscBool flg;

    5585:       VecGetLocalSize(u,&dim);
    5586:       PetscMalloc((dim+1)*sizeof(char*),&displaynames);
    5587:       PetscMemzero(displaynames,(dim+1)*sizeof(char*));
    5588:       PetscOptionsGetStringArray(((PetscObject)ts)->prefix,"-ts_monitor_lg_solution_variables",displaynames,&dim,&flg);
    5589:       if (flg) {
    5590:         TSMonitorLGCtxSetDisplayVariables(ctx,(const char *const *)displaynames);
    5591:       }
    5592:       PetscStrArrayDestroy(&displaynames);
    5593:     }
    5594:     if (ctx->displaynames) {
    5595:       PetscDrawLGSetDimension(ctx->lg,ctx->ndisplayvariables);
    5596:       PetscDrawLGSetLegend(ctx->lg,(const char *const *)ctx->displaynames);
    5597:     } else if (ctx->names) {
    5598:       VecGetLocalSize(u,&dim);
    5599:       PetscDrawLGSetDimension(ctx->lg,dim);
    5600:       PetscDrawLGSetLegend(ctx->lg,(const char *const *)ctx->names);
    5601:     }
    5602:     PetscDrawLGReset(ctx->lg);
    5603:   }
    5604:   if (ctx->transform) {
    5605:     (*ctx->transform)(ctx->transformctx,u,&v);
    5606:   } else {
    5607:     v = u;
    5608:   }
    5609:   VecGetArrayRead(v,&yy);
    5610: #if defined(PETSC_USE_COMPLEX)
    5611:   {
    5612:     PetscReal *yreal;
    5613:     PetscInt  i,n;
    5614:     VecGetLocalSize(v,&n);
    5615:     PetscMalloc1(n,&yreal);
    5616:     for (i=0; i<n; i++) yreal[i] = PetscRealPart(yy[i]);
    5617:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yreal);
    5618:     PetscFree(yreal);
    5619:   }
    5620: #else
    5621:   if (ctx->displaynames) {
    5622:     PetscInt i;
    5623:     for (i=0; i<ctx->ndisplayvariables; i++) {
    5624:       ctx->displayvalues[i] = yy[ctx->displayvariables[i]];
    5625:     }
    5626:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,ctx->displayvalues);
    5627:   } else {
    5628:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yy);
    5629:   }
    5630: #endif
    5631:   VecRestoreArrayRead(v,&yy);
    5632:   if (ctx->transform) {
    5633:     VecDestroy(&v);
    5634:   }
    5635:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
    5636:     PetscDrawLGDraw(ctx->lg);
    5637:   }
    5638:   return(0);
    5639: }

    5644: /*@C
    5645:    TSMonitorLGSetVariableNames - Sets the name of each component in the solution vector so that it may be displayed in the plot

    5647:    Collective on TS

    5649:    Input Parameters:
    5650: +  ts - the TS context
    5651: -  names - the names of the components, final string must be NULL

    5653:    Level: intermediate

    5655: .keywords: TS,  vector, monitor, view

    5657: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables(), TSMonitorLGCtxSetVariableNames()
    5658: @*/
    5659: PetscErrorCode  TSMonitorLGSetVariableNames(TS ts,const char * const *names)
    5660: {
    5661:   PetscErrorCode    ierr;
    5662:   PetscInt          i;

    5665:   for (i=0; i<ts->numbermonitors; i++) {
    5666:     if (ts->monitor[i] == TSMonitorLGSolution) {
    5667:       TSMonitorLGCtxSetVariableNames((TSMonitorLGCtx)ts->monitorcontext[i],names);
    5668:       break;
    5669:     }
    5670:   }
    5671:   return(0);
    5672: }

    5676: /*@C
    5677:    TSMonitorLGCtxSetVariableNames - Sets the name of each component in the solution vector so that it may be displayed in the plot

    5679:    Collective on TS

    5681:    Input Parameters:
    5682: +  ts - the TS context
    5683: -  names - the names of the components, final string must be NULL

    5685:    Level: intermediate

    5687: .keywords: TS,  vector, monitor, view

    5689: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables(), TSMonitorLGSetVariableNames()
    5690: @*/
    5691: PetscErrorCode  TSMonitorLGCtxSetVariableNames(TSMonitorLGCtx ctx,const char * const *names)
    5692: {
    5693:   PetscErrorCode    ierr;

    5696:   PetscStrArrayDestroy(&ctx->names);
    5697:   PetscStrArrayallocpy(names,&ctx->names);
    5698:   return(0);
    5699: }

    5703: /*@C
    5704:    TSMonitorLGGetVariableNames - Gets the name of each component in the solution vector so that it may be displayed in the plot

    5706:    Collective on TS

    5708:    Input Parameter:
    5709: .  ts - the TS context

    5711:    Output Parameter:
    5712: .  names - the names of the components, final string must be NULL

    5714:    Level: intermediate

    5716: .keywords: TS,  vector, monitor, view

    5718: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables()
    5719: @*/
    5720: PetscErrorCode  TSMonitorLGGetVariableNames(TS ts,const char *const **names)
    5721: {
    5722:   PetscInt       i;

    5725:   *names = NULL;
    5726:   for (i=0; i<ts->numbermonitors; i++) {
    5727:     if (ts->monitor[i] == TSMonitorLGSolution) {
    5728:       TSMonitorLGCtx  ctx = (TSMonitorLGCtx) ts->monitorcontext[i];
    5729:       *names = (const char *const *)ctx->names;
    5730:       break;
    5731:     }
    5732:   }
    5733:   return(0);
    5734: }

    5738: /*@C
    5739:    TSMonitorLGCtxSetDisplayVariables - Sets the variables that are to be display in the monitor

    5741:    Collective on TS

    5743:    Input Parameters:
    5744: +  ctx - the TSMonitorLG context
    5745: .  displaynames - the names of the components, final string must be NULL

    5747:    Level: intermediate

    5749: .keywords: TS,  vector, monitor, view

    5751: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames()
    5752: @*/
    5753: PetscErrorCode  TSMonitorLGCtxSetDisplayVariables(TSMonitorLGCtx ctx,const char * const *displaynames)
    5754: {
    5755:   PetscInt          j = 0,k;
    5756:   PetscErrorCode    ierr;

    5759:   if (!ctx->names) return(0);
    5760:   PetscStrArrayDestroy(&ctx->displaynames);
    5761:   PetscStrArrayallocpy(displaynames,&ctx->displaynames);
    5762:   while (displaynames[j]) j++;
    5763:   ctx->ndisplayvariables = j;
    5764:   PetscMalloc1(ctx->ndisplayvariables,&ctx->displayvariables);
    5765:   PetscMalloc1(ctx->ndisplayvariables,&ctx->displayvalues);
    5766:   j = 0;
    5767:   while (displaynames[j]) {
    5768:     k = 0;
    5769:     while (ctx->names[k]) {
    5770:       PetscBool flg;
    5771:       PetscStrcmp(displaynames[j],ctx->names[k],&flg);
    5772:       if (flg) {
    5773:         ctx->displayvariables[j] = k;
    5774:         break;
    5775:       }
    5776:       k++;
    5777:     }
    5778:     j++;
    5779:   }
    5780:   return(0);
    5781: }

    5786: /*@C
    5787:    TSMonitorLGSetDisplayVariables - Sets the variables that are to be display in the monitor

    5789:    Collective on TS

    5791:    Input Parameters:
    5792: +  ts - the TS context
    5793: .  displaynames - the names of the components, final string must be NULL

    5795:    Level: intermediate

    5797: .keywords: TS,  vector, monitor, view

    5799: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames()
    5800: @*/
    5801: PetscErrorCode  TSMonitorLGSetDisplayVariables(TS ts,const char * const *displaynames)
    5802: {
    5803:   PetscInt          i;
    5804:   PetscErrorCode    ierr;

    5807:   for (i=0; i<ts->numbermonitors; i++) {
    5808:     if (ts->monitor[i] == TSMonitorLGSolution) {
    5809:       TSMonitorLGCtxSetDisplayVariables((TSMonitorLGCtx)ts->monitorcontext[i],displaynames);
    5810:       break;
    5811:     }
    5812:   }
    5813:   return(0);
    5814: }

    5818: /*@C
    5819:    TSMonitorLGSetTransform - Solution vector will be transformed by provided function before being displayed

    5821:    Collective on TS

    5823:    Input Parameters:
    5824: +  ts - the TS context
    5825: .  transform - the transform function
    5826: .  destroy - function to destroy the optional context
    5827: -  ctx - optional context used by transform function

    5829:    Level: intermediate

    5831: .keywords: TS,  vector, monitor, view

    5833: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames(), TSMonitorLGCtxSetTransform()
    5834: @*/
    5835: PetscErrorCode  TSMonitorLGSetTransform(TS ts,PetscErrorCode (*transform)(void*,Vec,Vec*),PetscErrorCode (*destroy)(void*),void *tctx)
    5836: {
    5837:   PetscInt          i;
    5838:   PetscErrorCode    ierr;

    5841:   for (i=0; i<ts->numbermonitors; i++) {
    5842:     if (ts->monitor[i] == TSMonitorLGSolution) {
    5843:       TSMonitorLGCtxSetTransform((TSMonitorLGCtx)ts->monitorcontext[i],transform,destroy,tctx);
    5844:     }
    5845:   }
    5846:   return(0);
    5847: }

    5851: /*@C
    5852:    TSMonitorLGCtxSetTransform - Solution vector will be transformed by provided function before being displayed

    5854:    Collective on TSLGCtx

    5856:    Input Parameters:
    5857: +  ts - the TS context
    5858: .  transform - the transform function
    5859: .  destroy - function to destroy the optional context
    5860: -  ctx - optional context used by transform function

    5862:    Level: intermediate

    5864: .keywords: TS,  vector, monitor, view

    5866: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetVariableNames(), TSMonitorLGSetTransform()
    5867: @*/
    5868: PetscErrorCode  TSMonitorLGCtxSetTransform(TSMonitorLGCtx ctx,PetscErrorCode (*transform)(void*,Vec,Vec*),PetscErrorCode (*destroy)(void*),void *tctx)
    5869: {
    5871:   ctx->transform    = transform;
    5872:   ctx->transformdestroy = destroy;
    5873:   ctx->transformctx = tctx;
    5874:   return(0);
    5875: }

    5879: /*@C
    5880:    TSMonitorLGError - Monitors progress of the TS solvers by plotting each component of the solution vector
    5881:        in a time based line graph

    5883:    Collective on TS

    5885:    Input Parameters:
    5886: +  ts - the TS context
    5887: .  step - current time-step
    5888: .  ptime - current time
    5889: -  lg - a line graph object

    5891:    Level: intermediate

    5893:    Notes:
    5894:    Only for sequential solves.

    5896:    The user must provide the solution using TSSetSolutionFunction() to use this monitor.

    5898:    Options Database Keys:
    5899: .  -ts_monitor_lg_error - create a graphical monitor of error history

    5901: .keywords: TS,  vector, monitor, view

    5903: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSSetSolutionFunction()
    5904: @*/
    5905: PetscErrorCode  TSMonitorLGError(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    5906: {
    5907:   PetscErrorCode    ierr;
    5908:   TSMonitorLGCtx    ctx = (TSMonitorLGCtx)dummy;
    5909:   const PetscScalar *yy;
    5910:   Vec               y;
    5911:   PetscInt          dim;

    5914:   if (!step) {
    5915:     PetscDrawAxis axis;
    5916:     PetscDrawLGGetAxis(ctx->lg,&axis);
    5917:     PetscDrawAxisSetLabels(axis,"Error in solution as function of time","Time","Solution");
    5918:     VecGetLocalSize(u,&dim);
    5919:     PetscDrawLGSetDimension(ctx->lg,dim);
    5920:     PetscDrawLGReset(ctx->lg);
    5921:   }
    5922:   VecDuplicate(u,&y);
    5923:   TSComputeSolutionFunction(ts,ptime,y);
    5924:   VecAXPY(y,-1.0,u);
    5925:   VecGetArrayRead(y,&yy);
    5926: #if defined(PETSC_USE_COMPLEX)
    5927:   {
    5928:     PetscReal *yreal;
    5929:     PetscInt  i,n;
    5930:     VecGetLocalSize(y,&n);
    5931:     PetscMalloc1(n,&yreal);
    5932:     for (i=0; i<n; i++) yreal[i] = PetscRealPart(yy[i]);
    5933:     PetscDrawLGAddCommonPoint(ctx->lg,ptime,yreal);
    5934:     PetscFree(yreal);
    5935:   }
    5936: #else
    5937:   PetscDrawLGAddCommonPoint(ctx->lg,ptime,yy);
    5938: #endif
    5939:   VecRestoreArrayRead(y,&yy);
    5940:   VecDestroy(&y);
    5941:   if (((ctx->howoften > 0) && (!(step % ctx->howoften))) || ((ctx->howoften == -1) && ts->reason)) {
    5942:     PetscDrawLGDraw(ctx->lg);
    5943:   }
    5944:   return(0);
    5945: }

    5949: PetscErrorCode TSMonitorLGSNESIterations(TS ts,PetscInt n,PetscReal ptime,Vec v,void *monctx)
    5950: {
    5951:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
    5952:   PetscReal      x   = ptime,y;
    5954:   PetscInt       its;

    5957:   if (!n) {
    5958:     PetscDrawAxis axis;

    5960:     PetscDrawLGGetAxis(ctx->lg,&axis);
    5961:     PetscDrawAxisSetLabels(axis,"Nonlinear iterations as function of time","Time","SNES Iterations");
    5962:     PetscDrawLGReset(ctx->lg);

    5964:     ctx->snes_its = 0;
    5965:   }
    5966:   TSGetSNESIterations(ts,&its);
    5967:   y    = its - ctx->snes_its;
    5968:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
    5969:   if (((ctx->howoften > 0) && (!(n % ctx->howoften)) && (n > -1)) || ((ctx->howoften == -1) && (n == -1))) {
    5970:     PetscDrawLGDraw(ctx->lg);
    5971:   }
    5972:   ctx->snes_its = its;
    5973:   return(0);
    5974: }

    5978: PetscErrorCode TSMonitorLGKSPIterations(TS ts,PetscInt n,PetscReal ptime,Vec v,void *monctx)
    5979: {
    5980:   TSMonitorLGCtx ctx = (TSMonitorLGCtx) monctx;
    5981:   PetscReal      x   = ptime,y;
    5983:   PetscInt       its;

    5986:   if (!n) {
    5987:     PetscDrawAxis axis;

    5989:     PetscDrawLGGetAxis(ctx->lg,&axis);
    5990:     PetscDrawAxisSetLabels(axis,"Linear iterations as function of time","Time","KSP Iterations");
    5991:     PetscDrawLGReset(ctx->lg);

    5993:     ctx->ksp_its = 0;
    5994:   }
    5995:   TSGetKSPIterations(ts,&its);
    5996:   y    = its - ctx->ksp_its;
    5997:   PetscDrawLGAddPoint(ctx->lg,&x,&y);
    5998:   if (((ctx->howoften > 0) && (!(n % ctx->howoften)) && (n > -1)) || ((ctx->howoften == -1) && (n == -1))) {
    5999:     PetscDrawLGDraw(ctx->lg);
    6000:   }
    6001:   ctx->ksp_its = its;
    6002:   return(0);
    6003: }

    6007: /*@
    6008:    TSComputeLinearStability - computes the linear stability function at a point

    6010:    Collective on TS and Vec

    6012:    Input Parameters:
    6013: +  ts - the TS context
    6014: -  xr,xi - real and imaginary part of input arguments

    6016:    Output Parameters:
    6017: .  yr,yi - real and imaginary part of function value

    6019:    Level: developer

    6021: .keywords: TS, compute

    6023: .seealso: TSSetRHSFunction(), TSComputeIFunction()
    6024: @*/
    6025: PetscErrorCode TSComputeLinearStability(TS ts,PetscReal xr,PetscReal xi,PetscReal *yr,PetscReal *yi)
    6026: {

    6031:   if (!ts->ops->linearstability) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"Linearized stability function not provided for this method");
    6032:   (*ts->ops->linearstability)(ts,xr,xi,yr,yi);
    6033:   return(0);
    6034: }

    6036: /* ------------------------------------------------------------------------*/
    6039: /*@C
    6040:    TSMonitorEnvelopeCtxCreate - Creates a context for use with TSMonitorEnvelope()

    6042:    Collective on TS

    6044:    Input Parameters:
    6045: .  ts  - the ODE solver object

    6047:    Output Parameter:
    6048: .  ctx - the context

    6050:    Level: intermediate

    6052: .keywords: TS, monitor, line graph, residual, seealso

    6054: .seealso: TSMonitorLGTimeStep(), TSMonitorSet(), TSMonitorLGSolution(), TSMonitorLGError()

    6056: @*/
    6057: PetscErrorCode  TSMonitorEnvelopeCtxCreate(TS ts,TSMonitorEnvelopeCtx *ctx)
    6058: {

    6062:   PetscNew(ctx);
    6063:   return(0);
    6064: }

    6068: /*@C
    6069:    TSMonitorEnvelope - Monitors the maximum and minimum value of each component of the solution

    6071:    Collective on TS

    6073:    Input Parameters:
    6074: +  ts - the TS context
    6075: .  step - current time-step
    6076: .  ptime - current time
    6077: -  ctx - the envelope context

    6079:    Options Database:
    6080: .  -ts_monitor_envelope

    6082:    Level: intermediate

    6084:    Notes: after a solve you can use TSMonitorEnvelopeGetBounds() to access the envelope

    6086: .keywords: TS,  vector, monitor, view

    6088: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorEnvelopeGetBounds()
    6089: @*/
    6090: PetscErrorCode  TSMonitorEnvelope(TS ts,PetscInt step,PetscReal ptime,Vec u,void *dummy)
    6091: {
    6092:   PetscErrorCode       ierr;
    6093:   TSMonitorEnvelopeCtx ctx = (TSMonitorEnvelopeCtx)dummy;

    6096:   if (!ctx->max) {
    6097:     VecDuplicate(u,&ctx->max);
    6098:     VecDuplicate(u,&ctx->min);
    6099:     VecCopy(u,ctx->max);
    6100:     VecCopy(u,ctx->min);
    6101:   } else {
    6102:     VecPointwiseMax(ctx->max,u,ctx->max);
    6103:     VecPointwiseMin(ctx->min,u,ctx->min);
    6104:   }
    6105:   return(0);
    6106: }

    6111: /*@C
    6112:    TSMonitorEnvelopeGetBounds - Gets the bounds for the components of the solution

    6114:    Collective on TS

    6116:    Input Parameter:
    6117: .  ts - the TS context

    6119:    Output Parameter:
    6120: +  max - the maximum values
    6121: -  min - the minimum values

    6123:    Level: intermediate

    6125: .keywords: TS,  vector, monitor, view

    6127: .seealso: TSMonitorSet(), TSMonitorDefault(), VecView(), TSMonitorLGSetDisplayVariables()
    6128: @*/
    6129: PetscErrorCode  TSMonitorEnvelopeGetBounds(TS ts,Vec *max,Vec *min)
    6130: {
    6131:   PetscInt i;

    6134:   if (max) *max = NULL;
    6135:   if (min) *min = NULL;
    6136:   for (i=0; i<ts->numbermonitors; i++) {
    6137:     if (ts->monitor[i] == TSMonitorEnvelope) {
    6138:       TSMonitorEnvelopeCtx  ctx = (TSMonitorEnvelopeCtx) ts->monitorcontext[i];
    6139:       if (max) *max = ctx->max;
    6140:       if (min) *min = ctx->min;
    6141:       break;
    6142:     }
    6143:   }
    6144:   return(0);
    6145: }

    6149: /*@C
    6150:    TSMonitorEnvelopeCtxDestroy - Destroys a context that was created  with TSMonitorEnvelopeCtxCreate().

    6152:    Collective on TSMonitorEnvelopeCtx

    6154:    Input Parameter:
    6155: .  ctx - the monitor context

    6157:    Level: intermediate

    6159: .keywords: TS, monitor, line graph, destroy

    6161: .seealso: TSMonitorLGCtxCreate(),  TSMonitorSet(), TSMonitorLGTimeStep();
    6162: @*/
    6163: PetscErrorCode  TSMonitorEnvelopeCtxDestroy(TSMonitorEnvelopeCtx *ctx)
    6164: {

    6168:   VecDestroy(&(*ctx)->min);
    6169:   VecDestroy(&(*ctx)->max);
    6170:   PetscFree(*ctx);
    6171:   return(0);
    6172: }

    6176: /*@
    6177:    TSRollBack - Rolls back one time step

    6179:    Collective on TS

    6181:    Input Parameter:
    6182: .  ts - the TS context obtained from TSCreate()

    6184:    Level: advanced

    6186: .keywords: TS, timestep, rollback

    6188: .seealso: TSCreate(), TSSetUp(), TSDestroy(), TSSolve(), TSSetPreStep(), TSSetPreStage(), TSInterpolate()
    6189: @*/
    6190: PetscErrorCode  TSRollBack(TS ts)
    6191: {

    6197:   if (!ts->ops->rollback) SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_SUP,"TSRollBack not implemented for type '%s'",((PetscObject)ts)->type_name);
    6198:   (*ts->ops->rollback)(ts);
    6199:   ts->time_step = ts->ptime - ts->ptime_prev;
    6200:   ts->ptime = ts->ptime_prev;
    6201:   ts->steprollback = PETSC_TRUE; /* Flag to indicate that the step is rollbacked */
    6202:   return(0);
    6203: }

    6207: /*@
    6208:    TSGetStages - Get the number of stages and stage values

    6210:    Input Parameter:
    6211: .  ts - the TS context obtained from TSCreate()

    6213:    Level: advanced

    6215: .keywords: TS, getstages

    6217: .seealso: TSCreate()
    6218: @*/
    6219: PetscErrorCode  TSGetStages(TS ts,PetscInt *ns, Vec **Y)
    6220: {

    6227:   if (!ts->ops->getstages) *ns=0;
    6228:   else {
    6229:     (*ts->ops->getstages)(ts,ns,Y);
    6230:   }
    6231:   return(0);
    6232: }

    6236: /*@C
    6237:   TSComputeIJacobianDefaultColor - Computes the Jacobian using finite differences and coloring to exploit matrix sparsity.

    6239:   Collective on SNES

    6241:   Input Parameters:
    6242: + ts - the TS context
    6243: . t - current timestep
    6244: . U - state vector
    6245: . Udot - time derivative of state vector
    6246: . shift - shift to apply, see note below
    6247: - ctx - an optional user context

    6249:   Output Parameters:
    6250: + J - Jacobian matrix (not altered in this routine)
    6251: - B - newly computed Jacobian matrix to use with preconditioner (generally the same as J)

    6253:   Level: intermediate

    6255:   Notes:
    6256:   If F(t,U,Udot)=0 is the DAE, the required Jacobian is

    6258:   dF/dU + shift*dF/dUdot

    6260:   Most users should not need to explicitly call this routine, as it
    6261:   is used internally within the nonlinear solvers.

    6263:   This will first try to get the coloring from the DM.  If the DM type has no coloring
    6264:   routine, then it will try to get the coloring from the matrix.  This requires that the
    6265:   matrix have nonzero entries precomputed.

    6267: .keywords: TS, finite differences, Jacobian, coloring, sparse
    6268: .seealso: TSSetIJacobian(), MatFDColoringCreate(), MatFDColoringSetFunction()
    6269: @*/
    6270: PetscErrorCode TSComputeIJacobianDefaultColor(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat J,Mat B,void *ctx)
    6271: {
    6272:   SNES           snes;
    6273:   MatFDColoring  color;
    6274:   PetscBool      hascolor, matcolor = PETSC_FALSE;

    6278:   PetscOptionsGetBool(((PetscObject) ts)->prefix, "-ts_fd_color_use_mat", &matcolor, NULL);
    6279:   PetscObjectQuery((PetscObject) B, "TSMatFDColoring", (PetscObject *) &color);
    6280:   if (!color) {
    6281:     DM         dm;
    6282:     ISColoring iscoloring;

    6284:     TSGetDM(ts, &dm);
    6285:     DMHasColoring(dm, &hascolor);
    6286:     if (hascolor && !matcolor) {
    6287:       DMCreateColoring(dm, IS_COLORING_GLOBAL, &iscoloring);
    6288:       MatFDColoringCreate(B, iscoloring, &color);
    6289:       MatFDColoringSetFunction(color, (PetscErrorCode (*)(void)) SNESTSFormFunction, (void *) ts);
    6290:       MatFDColoringSetFromOptions(color);
    6291:       MatFDColoringSetUp(B, iscoloring, color);
    6292:       ISColoringDestroy(&iscoloring);
    6293:     } else {
    6294:       MatColoring mc;

    6296:       MatColoringCreate(B, &mc);
    6297:       MatColoringSetDistance(mc, 2);
    6298:       MatColoringSetType(mc, MATCOLORINGSL);
    6299:       MatColoringSetFromOptions(mc);
    6300:       MatColoringApply(mc, &iscoloring);
    6301:       MatColoringDestroy(&mc);
    6302:       MatFDColoringCreate(B, iscoloring, &color);
    6303:       MatFDColoringSetFunction(color, (PetscErrorCode (*)(void)) SNESTSFormFunction, (void *) ts);
    6304:       MatFDColoringSetFromOptions(color);
    6305:       MatFDColoringSetUp(B, iscoloring, color);
    6306:       ISColoringDestroy(&iscoloring);
    6307:     }
    6308:     PetscObjectCompose((PetscObject) B, "TSMatFDColoring", (PetscObject) color);
    6309:     PetscObjectDereference((PetscObject) color);
    6310:   }
    6311:   TSGetSNES(ts, &snes);
    6312:   MatFDColoringApply(B, color, U, snes);
    6313:   if (J != B) {
    6314:     MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
    6315:     MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
    6316:   }
    6317:   return(0);
    6318: }

    6320: #undef  __FUNCT__
    6322: /*@C
    6323:   TSClone - This function clones a time step object.

    6325:   Collective on MPI_Comm

    6327:   Input Parameter:
    6328: . tsin    - The input TS

    6330:   Output Parameter:
    6331: . tsout   - The output TS (cloned)

    6333:   Notes:
    6334:   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.

    6336:   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);

    6338:   Level: developer

    6340: .keywords: TS, clone
    6341: .seealso: TSCreate(), TSSetType(), TSSetUp(), TSDestroy(), TSSetProblemType()
    6342: @*/
    6343: PetscErrorCode  TSClone(TS tsin, TS *tsout)
    6344: {
    6345:   TS             t;
    6347:   SNES           snes_start;
    6348:   DM             dm;
    6349:   TSType         type;

    6353:   *tsout = NULL;

    6355:   PetscHeaderCreate(t, TS_CLASSID, "TS", "Time stepping", "TS", PetscObjectComm((PetscObject)tsin), TSDestroy, TSView);

    6357:   /* General TS description */
    6358:   t->numbermonitors    = 0;
    6359:   t->setupcalled       = 0;
    6360:   t->ksp_its           = 0;
    6361:   t->snes_its          = 0;
    6362:   t->nwork             = 0;
    6363:   t->rhsjacobian.time  = -1e20;
    6364:   t->rhsjacobian.scale = 1.;
    6365:   t->ijacobian.shift   = 1.;

    6367:   TSGetSNES(tsin,&snes_start);
    6368:   TSSetSNES(t,snes_start);

    6370:   TSGetDM(tsin,&dm);
    6371:   TSSetDM(t,dm);

    6373:   t->adapt=tsin->adapt;
    6374:   PetscObjectReference((PetscObject)t->adapt);

    6376:   t->problem_type      = tsin->problem_type;
    6377:   t->ptime             = tsin->ptime;
    6378:   t->time_step         = tsin->time_step;
    6379:   t->time_step_orig    = tsin->time_step_orig;
    6380:   t->max_time          = tsin->max_time;
    6381:   t->steps             = tsin->steps;
    6382:   t->max_steps         = tsin->max_steps;
    6383:   t->equation_type     = tsin->equation_type;
    6384:   t->atol              = tsin->atol;
    6385:   t->rtol              = tsin->rtol;
    6386:   t->max_snes_failures = tsin->max_snes_failures;
    6387:   t->max_reject        = tsin->max_reject;
    6388:   t->errorifstepfailed = tsin->errorifstepfailed;

    6390:   TSGetType(tsin,&type);
    6391:   TSSetType(t,type);

    6393:   t->vec_sol           = NULL;

    6395:   t->cfltime          = tsin->cfltime;
    6396:   t->cfltime_local    = tsin->cfltime_local;
    6397:   t->exact_final_time = tsin->exact_final_time;

    6399:   PetscMemcpy(t->ops,tsin->ops,sizeof(struct _TSOps));

    6401:   *tsout = t;
    6402:   return(0);
    6403: }