Actual source code: dmplexts.c

      1: #include <petsc/private/dmpleximpl.h>
      2: #include <petsc/private/tsimpl.h>
      3: #include <petsc/private/snesimpl.h>
      4: #include <petscds.h>
      5: #include <petscfv.h>

      7: static PetscErrorCode DMTSConvertPlex(DM dm, DM *plex, PetscBool copy)
      8: {
      9:   PetscBool      isPlex;

     11:   PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
     12:   if (isPlex) {
     13:     *plex = dm;
     14:     PetscObjectReference((PetscObject) dm);
     15:   } else {
     16:     PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
     17:     if (!*plex) {
     18:       DMConvert(dm,DMPLEX,plex);
     19:       PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
     20:       if (copy) {
     21:         DMCopyDMTS(dm, *plex);
     22:         DMCopyDMSNES(dm, *plex);
     23:         DMCopyAuxiliaryVec(dm, *plex);
     24:       }
     25:     } else {
     26:       PetscObjectReference((PetscObject) *plex);
     27:     }
     28:   }
     29:   return 0;
     30: }

     32: /*@
     33:   DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user

     35:   Input Parameters:
     36: + dm - The mesh
     37: . t - The time
     38: . locX  - Local solution
     39: - user - The user context

     41:   Output Parameter:
     42: . F  - Global output vector

     44:   Level: developer

     46: .seealso: DMPlexComputeJacobianActionFEM()
     47: @*/
     48: PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
     49: {
     50:   Vec          locF;
     51:   IS           cellIS;
     52:   DM           plex;
     53:   PetscInt     depth;
     54:   PetscFormKey key = {NULL, 0, 0, 0};

     56:   DMTSConvertPlex(dm,&plex,PETSC_TRUE);
     57:   DMPlexGetDepth(plex, &depth);
     58:   DMGetStratumIS(plex, "dim", depth, &cellIS);
     59:   if (!cellIS) DMGetStratumIS(plex, "depth", depth, &cellIS);
     60:   DMGetLocalVector(plex, &locF);
     61:   VecZeroEntries(locF);
     62:   DMPlexComputeResidual_Internal(plex, key, cellIS, time, locX, NULL, time, locF, user);
     63:   DMLocalToGlobalBegin(plex, locF, ADD_VALUES, F);
     64:   DMLocalToGlobalEnd(plex, locF, ADD_VALUES, F);
     65:   DMRestoreLocalVector(plex, &locF);
     66:   ISDestroy(&cellIS);
     67:   DMDestroy(&plex);
     68:   return 0;
     69: }

     71: /*@
     72:   DMPlexTSComputeBoundary - Insert the essential boundary values for the local input X and/or its time derivative X_t using pointwise functions specified by the user

     74:   Input Parameters:
     75: + dm - The mesh
     76: . t - The time
     77: . locX  - Local solution
     78: . locX_t - Local solution time derivative, or NULL
     79: - user - The user context

     81:   Level: developer

     83: .seealso: DMPlexComputeJacobianActionFEM()
     84: @*/
     85: PetscErrorCode DMPlexTSComputeBoundary(DM dm, PetscReal time, Vec locX, Vec locX_t, void *user)
     86: {
     87:   DM             plex;
     88:   Vec            faceGeometryFVM = NULL;
     89:   PetscInt       Nf, f;

     91:   DMTSConvertPlex(dm, &plex, PETSC_TRUE);
     92:   DMGetNumFields(plex, &Nf);
     93:   if (!locX_t) {
     94:     /* This is the RHS part */
     95:     for (f = 0; f < Nf; f++) {
     96:       PetscObject  obj;
     97:       PetscClassId id;

     99:       DMGetField(plex, f, NULL, &obj);
    100:       PetscObjectGetClassId(obj, &id);
    101:       if (id == PETSCFV_CLASSID) {
    102:         DMPlexGetGeometryFVM(plex, &faceGeometryFVM, NULL, NULL);
    103:         break;
    104:       }
    105:     }
    106:   }
    107:   DMPlexInsertBoundaryValues(plex, PETSC_TRUE, locX, time, faceGeometryFVM, NULL, NULL);
    108:   DMPlexInsertTimeDerivativeBoundaryValues(plex, PETSC_TRUE, locX_t, time, faceGeometryFVM, NULL, NULL);
    109:   DMDestroy(&plex);
    110:   return 0;
    111: }

    113: /*@
    114:   DMPlexTSComputeIFunctionFEM - Form the local residual F from the local input X using pointwise functions specified by the user

    116:   Input Parameters:
    117: + dm - The mesh
    118: . t - The time
    119: . locX  - Local solution
    120: . locX_t - Local solution time derivative, or NULL
    121: - user - The user context

    123:   Output Parameter:
    124: . locF  - Local output vector

    126:   Level: developer

    128: .seealso: DMPlexTSComputeIFunctionFEM(), DMPlexTSComputeRHSFunctionFEM()
    129: @*/
    130: PetscErrorCode DMPlexTSComputeIFunctionFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user)
    131: {
    132:   DM             plex;
    133:   IS             allcellIS;
    134:   PetscInt       Nds, s;

    136:   DMTSConvertPlex(dm, &plex, PETSC_TRUE);
    137:   DMPlexGetAllCells_Internal(plex, &allcellIS);
    138:   DMGetNumDS(dm, &Nds);
    139:   for (s = 0; s < Nds; ++s) {
    140:     PetscDS          ds;
    141:     IS               cellIS;
    142:     PetscFormKey key;

    144:     DMGetRegionNumDS(dm, s, &key.label, NULL, &ds);
    145:     key.value = 0;
    146:     key.field = 0;
    147:     key.part  = 0;
    148:     if (!key.label) {
    149:       PetscObjectReference((PetscObject) allcellIS);
    150:       cellIS = allcellIS;
    151:     } else {
    152:       IS pointIS;

    154:       key.value = 1;
    155:       DMLabelGetStratumIS(key.label, key.value, &pointIS);
    156:       ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);
    157:       ISDestroy(&pointIS);
    158:     }
    159:     DMPlexComputeResidual_Internal(plex, key, cellIS, time, locX, locX_t, time, locF, user);
    160:     ISDestroy(&cellIS);
    161:   }
    162:   ISDestroy(&allcellIS);
    163:   DMDestroy(&plex);
    164:   return 0;
    165: }

    167: /*@
    168:   DMPlexTSComputeIJacobianFEM - Form the local Jacobian J from the local input X using pointwise functions specified by the user

    170:   Input Parameters:
    171: + dm - The mesh
    172: . t - The time
    173: . locX  - Local solution
    174: . locX_t - Local solution time derivative, or NULL
    175: . X_tshift - The multiplicative parameter for dF/du_t
    176: - user - The user context

    178:   Output Parameter:
    179: . locF  - Local output vector

    181:   Level: developer

    183: .seealso: DMPlexTSComputeIFunctionFEM(), DMPlexTSComputeRHSFunctionFEM()
    184: @*/
    185: PetscErrorCode DMPlexTSComputeIJacobianFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
    186: {
    187:   DM             plex;
    188:   IS             allcellIS;
    189:   PetscBool      hasJac, hasPrec;
    190:   PetscInt       Nds, s;

    192:   DMTSConvertPlex(dm, &plex, PETSC_TRUE);
    193:   DMPlexGetAllCells_Internal(plex, &allcellIS);
    194:   DMGetNumDS(dm, &Nds);
    195:   for (s = 0; s < Nds; ++s) {
    196:     PetscDS          ds;
    197:     IS               cellIS;
    198:     PetscFormKey key;

    200:     DMGetRegionNumDS(dm, s, &key.label, NULL, &ds);
    201:     key.value = 0;
    202:     key.field = 0;
    203:     key.part  = 0;
    204:     if (!key.label) {
    205:       PetscObjectReference((PetscObject) allcellIS);
    206:       cellIS = allcellIS;
    207:     } else {
    208:       IS pointIS;

    210:       key.value = 1;
    211:       DMLabelGetStratumIS(key.label, key.value, &pointIS);
    212:       ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);
    213:       ISDestroy(&pointIS);
    214:     }
    215:     if (!s) {
    216:       PetscDSHasJacobian(ds, &hasJac);
    217:       PetscDSHasJacobianPreconditioner(ds, &hasPrec);
    218:       if (hasJac && hasPrec) MatZeroEntries(Jac);
    219:       MatZeroEntries(JacP);
    220:     }
    221:     DMPlexComputeJacobian_Internal(plex, key, cellIS, time, X_tShift, locX, locX_t, Jac, JacP, user);
    222:     ISDestroy(&cellIS);
    223:   }
    224:   ISDestroy(&allcellIS);
    225:   DMDestroy(&plex);
    226:   return 0;
    227: }

    229: /*@
    230:   DMPlexTSComputeRHSFunctionFEM - Form the local residual G from the local input X using pointwise functions specified by the user

    232:   Input Parameters:
    233: + dm - The mesh
    234: . t - The time
    235: . locX  - Local solution
    236: - user - The user context

    238:   Output Parameter:
    239: . locG  - Local output vector

    241:   Level: developer

    243: .seealso: DMPlexTSComputeIFunctionFEM(), DMPlexTSComputeIJacobianFEM()
    244: @*/
    245: PetscErrorCode DMPlexTSComputeRHSFunctionFEM(DM dm, PetscReal time, Vec locX, Vec locG, void *user)
    246: {
    247:   DM             plex;
    248:   IS             allcellIS;
    249:   PetscInt       Nds, s;

    251:   DMTSConvertPlex(dm, &plex, PETSC_TRUE);
    252:   DMPlexGetAllCells_Internal(plex, &allcellIS);
    253:   DMGetNumDS(dm, &Nds);
    254:   for (s = 0; s < Nds; ++s) {
    255:     PetscDS          ds;
    256:     IS               cellIS;
    257:     PetscFormKey key;

    259:     DMGetRegionNumDS(dm, s, &key.label, NULL, &ds);
    260:     key.value = 0;
    261:     key.field = 0;
    262:     key.part  = 100;
    263:     if (!key.label) {
    264:       PetscObjectReference((PetscObject) allcellIS);
    265:       cellIS = allcellIS;
    266:     } else {
    267:       IS pointIS;

    269:       key.value = 1;
    270:       DMLabelGetStratumIS(key.label, key.value, &pointIS);
    271:       ISIntersect_Caching_Internal(allcellIS, pointIS, &cellIS);
    272:       ISDestroy(&pointIS);
    273:     }
    274:     DMPlexComputeResidual_Internal(plex, key, cellIS, time, locX, NULL, time, locG, user);
    275:     ISDestroy(&cellIS);
    276:   }
    277:   ISDestroy(&allcellIS);
    278:   DMDestroy(&plex);
    279:   return 0;
    280: }

    282: /*@C
    283:   DMTSCheckResidual - Check the residual of the exact solution

    285:   Input Parameters:
    286: + ts  - the TS object
    287: . dm  - the DM
    288: . t   - the time
    289: . u   - a DM vector
    290: . u_t - a DM vector
    291: - tol - A tolerance for the check, or -1 to print the results instead

    293:   Output Parameters:
    294: . residual - The residual norm of the exact solution, or NULL

    296:   Level: developer

    298: .seealso: DNTSCheckFromOptions(), DMTSCheckJacobian(), DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckJacobian()
    299: @*/
    300: PetscErrorCode DMTSCheckResidual(TS ts, DM dm, PetscReal t, Vec u, Vec u_t, PetscReal tol, PetscReal *residual)
    301: {
    302:   MPI_Comm       comm;
    303:   Vec            r;
    304:   PetscReal      res;

    310:   PetscObjectGetComm((PetscObject) ts, &comm);
    311:   DMComputeExactSolution(dm, t, u, u_t);
    312:   VecDuplicate(u, &r);
    313:   TSComputeIFunction(ts, t, u, u_t, r, PETSC_FALSE);
    314:   VecNorm(r, NORM_2, &res);
    315:   if (tol >= 0.0) {
    317:   } else if (residual) {
    318:     *residual = res;
    319:   } else {
    320:     PetscPrintf(comm, "L_2 Residual: %g\n", (double)res);
    321:     VecChop(r, 1.0e-10);
    322:     PetscObjectCompose((PetscObject) r, "__Vec_bc_zero__", (PetscObject) dm);
    323:     PetscObjectSetName((PetscObject) r, "Initial Residual");
    324:     PetscObjectSetOptionsPrefix((PetscObject)r,"res_");
    325:     VecViewFromOptions(r, NULL, "-vec_view");
    326:     PetscObjectCompose((PetscObject) r, "__Vec_bc_zero__", NULL);
    327:   }
    328:   VecDestroy(&r);
    329:   return 0;
    330: }

    332: /*@C
    333:   DMTSCheckJacobian - Check the Jacobian of the exact solution against the residual using the Taylor Test

    335:   Input Parameters:
    336: + ts  - the TS object
    337: . dm  - the DM
    338: . t   - the time
    339: . u   - a DM vector
    340: . u_t - a DM vector
    341: - tol - A tolerance for the check, or -1 to print the results instead

    343:   Output Parameters:
    344: + isLinear - Flag indicaing that the function looks linear, or NULL
    345: - convRate - The rate of convergence of the linear model, or NULL

    347:   Level: developer

    349: .seealso: DNTSCheckFromOptions(), DMTSCheckResidual(), DNSNESCheckFromOptions(), DMSNESCheckDiscretization(), DMSNESCheckResidual()
    350: @*/
    351: PetscErrorCode DMTSCheckJacobian(TS ts, DM dm, PetscReal t, Vec u, Vec u_t, PetscReal tol, PetscBool *isLinear, PetscReal *convRate)
    352: {
    353:   MPI_Comm       comm;
    354:   PetscDS        ds;
    355:   Mat            J, M;
    356:   MatNullSpace   nullspace;
    357:   PetscReal      dt, shift, slope, intercept;
    358:   PetscBool      hasJac, hasPrec, isLin = PETSC_FALSE;

    365:   PetscObjectGetComm((PetscObject) ts, &comm);
    366:   DMComputeExactSolution(dm, t, u, u_t);
    367:   /* Create and view matrices */
    368:   TSGetTimeStep(ts, &dt);
    369:   shift = 1.0/dt;
    370:   DMCreateMatrix(dm, &J);
    371:   DMGetDS(dm, &ds);
    372:   PetscDSHasJacobian(ds, &hasJac);
    373:   PetscDSHasJacobianPreconditioner(ds, &hasPrec);
    374:   if (hasJac && hasPrec) {
    375:     DMCreateMatrix(dm, &M);
    376:     TSComputeIJacobian(ts, t, u, u_t, shift, J, M, PETSC_FALSE);
    377:     PetscObjectSetName((PetscObject) M, "Preconditioning Matrix");
    378:     PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");
    379:     MatViewFromOptions(M, NULL, "-mat_view");
    380:     MatDestroy(&M);
    381:   } else {
    382:     TSComputeIJacobian(ts, t, u, u_t, shift, J, J, PETSC_FALSE);
    383:   }
    384:   PetscObjectSetName((PetscObject) J, "Jacobian");
    385:   PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");
    386:   MatViewFromOptions(J, NULL, "-mat_view");
    387:   /* Check nullspace */
    388:   MatGetNullSpace(J, &nullspace);
    389:   if (nullspace) {
    390:     PetscBool isNull;
    391:     MatNullSpaceTest(nullspace, J, &isNull);
    393:   }
    394:   /* Taylor test */
    395:   {
    396:     PetscRandom rand;
    397:     Vec         du, uhat, uhat_t, r, rhat, df;
    398:     PetscReal   h;
    399:     PetscReal  *es, *hs, *errors;
    400:     PetscReal   hMax = 1.0, hMin = 1e-6, hMult = 0.1;
    401:     PetscInt    Nv, v;

    403:     /* Choose a perturbation direction */
    404:     PetscRandomCreate(comm, &rand);
    405:     VecDuplicate(u, &du);
    406:     VecSetRandom(du, rand);
    407:     PetscRandomDestroy(&rand);
    408:     VecDuplicate(u, &df);
    409:     MatMult(J, du, df);
    410:     /* Evaluate residual at u, F(u), save in vector r */
    411:     VecDuplicate(u, &r);
    412:     TSComputeIFunction(ts, t, u, u_t, r, PETSC_FALSE);
    413:     /* Look at the convergence of our Taylor approximation as we approach u */
    414:     for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv);
    415:     PetscCalloc3(Nv, &es, Nv, &hs, Nv, &errors);
    416:     VecDuplicate(u, &uhat);
    417:     VecDuplicate(u, &uhat_t);
    418:     VecDuplicate(u, &rhat);
    419:     for (h = hMax, Nv = 0; h >= hMin; h *= hMult, ++Nv) {
    420:       VecWAXPY(uhat, h, du, u);
    421:       VecWAXPY(uhat_t, h*shift, du, u_t);
    422:       /* F(\hat u, \hat u_t) \approx F(u, u_t) + J(u, u_t) (uhat - u) + J_t(u, u_t) (uhat_t - u_t) = F(u) + h * J(u) du + h * shift * J_t(u) du = F(u) + h F' du */
    423:       TSComputeIFunction(ts, t, uhat, uhat_t, rhat, PETSC_FALSE);
    424:       VecAXPBYPCZ(rhat, -1.0, -h, 1.0, r, df);
    425:       VecNorm(rhat, NORM_2, &errors[Nv]);

    427:       es[Nv] = PetscLog10Real(errors[Nv]);
    428:       hs[Nv] = PetscLog10Real(h);
    429:     }
    430:     VecDestroy(&uhat);
    431:     VecDestroy(&uhat_t);
    432:     VecDestroy(&rhat);
    433:     VecDestroy(&df);
    434:     VecDestroy(&r);
    435:     VecDestroy(&du);
    436:     for (v = 0; v < Nv; ++v) {
    437:       if ((tol >= 0) && (errors[v] > tol)) break;
    438:       else if (errors[v] > PETSC_SMALL)    break;
    439:     }
    440:     if (v == Nv) isLin = PETSC_TRUE;
    441:     PetscLinearRegression(Nv, hs, es, &slope, &intercept);
    442:     PetscFree3(es, hs, errors);
    443:     /* Slope should be about 2 */
    444:     if (tol >= 0) {
    446:     } else if (isLinear || convRate) {
    447:       if (isLinear) *isLinear = isLin;
    448:       if (convRate) *convRate = slope;
    449:     } else {
    450:       if (!isLin) PetscPrintf(comm, "Taylor approximation converging at order %3.2f\n", (double) slope);
    451:       else        PetscPrintf(comm, "Function appears to be linear\n");
    452:     }
    453:   }
    454:   MatDestroy(&J);
    455:   return 0;
    456: }

    458: /*@C
    459:   DMTSCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information

    461:   Input Parameters:
    462: + ts - the TS object
    463: - u  - representative TS vector

    465:   Note: The user must call PetscDSSetExactSolution() beforehand

    467:   Level: developer
    468: @*/
    469: PetscErrorCode DMTSCheckFromOptions(TS ts, Vec u)
    470: {
    471:   DM             dm;
    472:   SNES           snes;
    473:   Vec            sol, u_t;
    474:   PetscReal      t;
    475:   PetscBool      check;

    477:   PetscOptionsHasName(((PetscObject)ts)->options,((PetscObject)ts)->prefix, "-dmts_check", &check);
    478:   if (!check) return 0;
    479:   VecDuplicate(u, &sol);
    480:   VecCopy(u, sol);
    481:   TSSetSolution(ts, u);
    482:   TSGetDM(ts, &dm);
    483:   TSSetUp(ts);
    484:   TSGetSNES(ts, &snes);
    485:   SNESSetSolution(snes, u);

    487:   TSGetTime(ts, &t);
    488:   DMSNESCheckDiscretization(snes, dm, t, sol, -1.0, NULL);
    489:   DMGetGlobalVector(dm, &u_t);
    490:   DMTSCheckResidual(ts, dm, t, sol, u_t, -1.0, NULL);
    491:   DMTSCheckJacobian(ts, dm, t, sol, u_t, -1.0, NULL, NULL);
    492:   DMRestoreGlobalVector(dm, &u_t);

    494:   VecDestroy(&sol);
    495:   return 0;
    496: }