Date: 2015-10-02T22:29:38+00:00

Actual source code: characteristic.c
petsc-3.6.2 2015-10-02
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      2: #include <petsc/private/characteristicimpl.h> /*I "petsccharacteristic.h" I*/
      3: #include <petscdmda.h>
      4: #include <petscviewer.h>

      6: PetscClassId  CHARACTERISTIC_CLASSID;
      7: PetscLogEvent CHARACTERISTIC_SetUp, CHARACTERISTIC_Solve, CHARACTERISTIC_QueueSetup, CHARACTERISTIC_DAUpdate;
      8: PetscLogEvent CHARACTERISTIC_HalfTimeLocal, CHARACTERISTIC_HalfTimeRemote, CHARACTERISTIC_HalfTimeExchange;
      9: PetscLogEvent CHARACTERISTIC_FullTimeLocal, CHARACTERISTIC_FullTimeRemote, CHARACTERISTIC_FullTimeExchange;
     10: /*
     11:    Contains the list of registered characteristic routines
     12: */
     13: PetscFunctionList CharacteristicList              = NULL;
     14: PetscBool         CharacteristicRegisterAllCalled = PETSC_FALSE;

     16: PetscErrorCode DMDAGetNeighborsRank(DM, PetscMPIInt []);
     17: PetscInt       DMDAGetNeighborRelative(DM, PassiveReal, PassiveReal);
     18: PetscErrorCode DMDAMapToPeriodicDomain(DM, PetscScalar []);

     20: PetscErrorCode CharacteristicHeapSort(Characteristic, Queue, PetscInt);
     21: PetscErrorCode CharacteristicSiftDown(Characteristic, Queue, PetscInt, PetscInt);

     25: PetscErrorCode CharacteristicView(Characteristic c, PetscViewer viewer)
     26: {
     27:   PetscBool      iascii;

     32:   if (!viewer) {
     33:     PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)c),&viewer);
     34:   }

     38:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
     39:   if (!iascii) {
     40:     if (c->ops->view) {
     41:       (*c->ops->view)(c, viewer);
     42:     }
     43:   }
     44:   return(0);
     45: }

     49: PetscErrorCode CharacteristicDestroy(Characteristic *c)
     50: {

     54:   if (!*c) return(0);
     56:   if (--((PetscObject)(*c))->refct > 0) return(0);

     58:   if ((*c)->ops->destroy) {
     59:     (*(*c)->ops->destroy)((*c));
     60:   }
     61:   MPI_Type_free(&(*c)->itemType);
     62:   PetscFree((*c)->queue);
     63:   PetscFree((*c)->queueLocal);
     64:   PetscFree((*c)->queueRemote);
     65:   PetscFree((*c)->neighbors);
     66:   PetscFree((*c)->needCount);
     67:   PetscFree((*c)->localOffsets);
     68:   PetscFree((*c)->fillCount);
     69:   PetscFree((*c)->remoteOffsets);
     70:   PetscFree((*c)->request);
     71:   PetscFree((*c)->status);
     72:   PetscHeaderDestroy(c);
     73:   return(0);
     74: }

     78: PetscErrorCode CharacteristicCreate(MPI_Comm comm, Characteristic *c)
     79: {
     80:   Characteristic newC;

     85:   *c = NULL;
     86:   CharacteristicInitializePackage();

     88:   PetscHeaderCreate(newC, CHARACTERISTIC_CLASSID, "Characteristic", "Characteristic", "SemiLagrange", comm, CharacteristicDestroy, CharacteristicView);
     89:   *c   = newC;

     91:   newC->structured          = PETSC_TRUE;
     92:   newC->numIds              = 0;
     93:   newC->velocityDA          = NULL;
     94:   newC->velocity            = NULL;
     95:   newC->velocityOld         = NULL;
     96:   newC->numVelocityComp     = 0;
     97:   newC->velocityComp        = NULL;
     98:   newC->velocityInterp      = NULL;
     99:   newC->velocityInterpLocal = NULL;
    100:   newC->velocityCtx         = NULL;
    101:   newC->fieldDA             = NULL;
    102:   newC->field               = NULL;
    103:   newC->numFieldComp        = 0;
    104:   newC->fieldComp           = NULL;
    105:   newC->fieldInterp         = NULL;
    106:   newC->fieldInterpLocal    = NULL;
    107:   newC->fieldCtx            = NULL;
    108:   newC->itemType            = 0;
    109:   newC->queue               = NULL;
    110:   newC->queueSize           = 0;
    111:   newC->queueMax            = 0;
    112:   newC->queueLocal          = NULL;
    113:   newC->queueLocalSize      = 0;
    114:   newC->queueLocalMax       = 0;
    115:   newC->queueRemote         = NULL;
    116:   newC->queueRemoteSize     = 0;
    117:   newC->queueRemoteMax      = 0;
    118:   newC->numNeighbors        = 0;
    119:   newC->neighbors           = NULL;
    120:   newC->needCount           = NULL;
    121:   newC->localOffsets        = NULL;
    122:   newC->fillCount           = NULL;
    123:   newC->remoteOffsets       = NULL;
    124:   newC->request             = NULL;
    125:   newC->status              = NULL;
    126:   return(0);
    127: }

    131: /*@C
    132:    CharacteristicSetType - Builds Characteristic for a particular solver.

    134:    Logically Collective on Characteristic

    136:    Input Parameters:
    137: +  c    - the method of characteristics context
    138: -  type - a known method

    140:    Options Database Key:
    141: .  -characteristic_type <method> - Sets the method; use -help for a list
    142:     of available methods

    144:    Notes:
    145:    See "include/petsccharacteristic.h" for available methods

    147:   Normally, it is best to use the CharacteristicSetFromOptions() command and
    148:   then set the Characteristic type from the options database rather than by using
    149:   this routine.  Using the options database provides the user with
    150:   maximum flexibility in evaluating the many different Krylov methods.
    151:   The CharacteristicSetType() routine is provided for those situations where it
    152:   is necessary to set the iterative solver independently of the command
    153:   line or options database.  This might be the case, for example, when
    154:   the choice of iterative solver changes during the execution of the
    155:   program, and the user's application is taking responsibility for
    156:   choosing the appropriate method.  In other words, this routine is
    157:   not for beginners.

    159:   Level: intermediate

    161: .keywords: Characteristic, set, method

    163: .seealso: CharacteristicType

    165: @*/
    166: PetscErrorCode CharacteristicSetType(Characteristic c, CharacteristicType type)
    167: {
    168:   PetscErrorCode ierr, (*r)(Characteristic);
    169:   PetscBool      match;

    175:   PetscObjectTypeCompare((PetscObject) c, type, &match);
    176:   if (match) return(0);

    178:   if (c->data) {
    179:     /* destroy the old private Characteristic context */
    180:     (*c->ops->destroy)(c);
    181:     c->ops->destroy = NULL;
    182:     c->data         = 0;
    183:   }

    185:    PetscFunctionListFind(CharacteristicList,type,&r);
    186:   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown Characteristic type given: %s", type);
    187:   c->setupcalled = 0;
    188:   (*r)(c);
    189:   PetscObjectChangeTypeName((PetscObject) c, type);
    190:   return(0);
    191: }

    195: /*@
    196:    CharacteristicSetUp - Sets up the internal data structures for the
    197:    later use of an iterative solver.

    199:    Collective on Characteristic

    201:    Input Parameter:
    202: .  ksp   - iterative context obtained from CharacteristicCreate()

    204:    Level: developer

    206: .keywords: Characteristic, setup

    208: .seealso: CharacteristicCreate(), CharacteristicSolve(), CharacteristicDestroy()
    209: @*/
    210: PetscErrorCode CharacteristicSetUp(Characteristic c)
    211: {

    217:   if (!((PetscObject)c)->type_name) {
    218:     CharacteristicSetType(c, CHARACTERISTICDA);
    219:   }

    221:   if (c->setupcalled == 2) return(0);

    223:   PetscLogEventBegin(CHARACTERISTIC_SetUp,c,0,0,0);
    224:   if (!c->setupcalled) {
    225:     (*c->ops->setup)(c);
    226:   }
    227:   PetscLogEventEnd(CHARACTERISTIC_SetUp,c,0,0,0);
    228:   c->setupcalled = 2;
    229:   return(0);
    230: }

    234: /*@C
    235:   CharacteristicRegister -  Adds a solver to the method of characteristics package.

    237:    Not Collective

    239:    Input Parameters:
    240: +  name_solver - name of a new user-defined solver
    241: -  routine_create - routine to create method context

    243:   Sample usage:
    244: .vb
    245:     CharacteristicRegister("my_char", MyCharCreate);
    246: .ve

    248:   Then, your Characteristic type can be chosen with the procedural interface via
    249: .vb
    250:     CharacteristicCreate(MPI_Comm, Characteristic* &char);
    251:     CharacteristicSetType(char,"my_char");
    252: .ve
    253:    or at runtime via the option
    254: .vb
    255:     -characteristic_type my_char
    256: .ve

    258:    Notes:
    259:    CharacteristicRegister() may be called multiple times to add several user-defined solvers.

    261: .keywords: Characteristic, register

    263: .seealso: CharacteristicRegisterAll(), CharacteristicRegisterDestroy()

    265:   Level: advanced
    266: @*/
    267: PetscErrorCode CharacteristicRegister(const char sname[],PetscErrorCode (*function)(Characteristic))
    268: {

    272:   PetscFunctionListAdd(&CharacteristicList,sname,function);
    273:   return(0);
    274: }

    278: PetscErrorCode CharacteristicSetVelocityInterpolation(Characteristic c, DM da, Vec v, Vec vOld, PetscInt numComponents, PetscInt components[], PetscErrorCode (*interp)(Vec, PetscReal[], PetscInt, PetscInt[], PetscScalar[], void*), void *ctx)
    279: {
    281:   c->velocityDA      = da;
    282:   c->velocity        = v;
    283:   c->velocityOld     = vOld;
    284:   c->numVelocityComp = numComponents;
    285:   c->velocityComp    = components;
    286:   c->velocityInterp  = interp;
    287:   c->velocityCtx     = ctx;
    288:   return(0);
    289: }

    293: PetscErrorCode CharacteristicSetVelocityInterpolationLocal(Characteristic c, DM da, Vec v, Vec vOld, PetscInt numComponents, PetscInt components[], PetscErrorCode (*interp)(void*, PetscReal [], PetscInt, PetscInt[], PetscScalar[], void*), void *ctx)
    294: {
    296:   c->velocityDA          = da;
    297:   c->velocity            = v;
    298:   c->velocityOld         = vOld;
    299:   c->numVelocityComp     = numComponents;
    300:   c->velocityComp        = components;
    301:   c->velocityInterpLocal = interp;
    302:   c->velocityCtx         = ctx;
    303:   return(0);
    304: }

    308: PetscErrorCode CharacteristicSetFieldInterpolation(Characteristic c, DM da, Vec v, PetscInt numComponents, PetscInt components[], PetscErrorCode (*interp)(Vec, PetscReal[], PetscInt, PetscInt[], PetscScalar[], void*), void *ctx)
    309: {
    311: #if 0
    312:   if (numComponents > 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP, "Fields with more than 2 components are not supported. Send mail to petsc-maint@mcs.anl.gov.");
    313: #endif
    314:   c->fieldDA      = da;
    315:   c->field        = v;
    316:   c->numFieldComp = numComponents;
    317:   c->fieldComp    = components;
    318:   c->fieldInterp  = interp;
    319:   c->fieldCtx     = ctx;
    320:   return(0);
    321: }

    325: PetscErrorCode CharacteristicSetFieldInterpolationLocal(Characteristic c, DM da, Vec v, PetscInt numComponents, PetscInt components[], PetscErrorCode (*interp)(void*, PetscReal[], PetscInt, PetscInt[], PetscScalar [], void*), void *ctx)
    326: {
    328: #if 0
    329:   if (numComponents > 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP, "Fields with more than 2 components are not supported. Send mail to petsc-maint@mcs.anl.gov.");
    330: #endif
    331:   c->fieldDA          = da;
    332:   c->field            = v;
    333:   c->numFieldComp     = numComponents;
    334:   c->fieldComp        = components;
    335:   c->fieldInterpLocal = interp;
    336:   c->fieldCtx         = ctx;
    337:   return(0);
    338: }

    342: PetscErrorCode CharacteristicSolve(Characteristic c, PetscReal dt, Vec solution)
    343: {
    344:   CharacteristicPointDA2D Qi;
    345:   DM                      da = c->velocityDA;
    346:   Vec                     velocityLocal, velocityLocalOld;
    347:   Vec                     fieldLocal;
    348:   DMDALocalInfo           info;
    349:   PetscScalar             **solArray;
    350:   void                    *velocityArray;
    351:   void                    *velocityArrayOld;
    352:   void                    *fieldArray;
    353:   PassiveScalar           *interpIndices;
    354:   PassiveScalar           *velocityValues, *velocityValuesOld;
    355:   PassiveScalar           *fieldValues;
    356:   PetscMPIInt             rank;
    357:   PetscInt                dim;
    358:   PetscMPIInt             neighbors[9];
    359:   PetscInt                dof;
    360:   PetscInt                gx, gy;
    361:   PetscInt                n, is, ie, js, je, comp;
    362:   PetscErrorCode          ierr;

    365:   c->queueSize = 0;
    366:   MPI_Comm_rank(PetscObjectComm((PetscObject)c), &rank);
    367:   DMDAGetNeighborsRank(da, neighbors);
    368:   CharacteristicSetNeighbors(c, 9, neighbors);
    369:   CharacteristicSetUp(c);
    370:   /* global and local grid info */
    371:   DMDAGetInfo(da, &dim, &gx, &gy, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
    372:   DMDAGetLocalInfo(da, &info);
    373:   is   = info.xs;          ie   = info.xs+info.xm;
    374:   js   = info.ys;          je   = info.ys+info.ym;
    375:   /* Allocation */
    376:   PetscMalloc1(dim,                &interpIndices);
    377:   PetscMalloc1(c->numVelocityComp, &velocityValues);
    378:   PetscMalloc1(c->numVelocityComp, &velocityValuesOld);
    379:   PetscMalloc1(c->numFieldComp,    &fieldValues);
    380:   PetscLogEventBegin(CHARACTERISTIC_Solve,0,0,0,0);

    382:   /* -----------------------------------------------------------------------
    383:      PART 1, AT t-dt/2
    384:      -----------------------------------------------------------------------*/
    385:   PetscLogEventBegin(CHARACTERISTIC_QueueSetup,0,0,0,0);
    386:   /* GET POSITION AT HALF TIME IN THE PAST */
    387:   if (c->velocityInterpLocal) {
    388:     DMGetLocalVector(c->velocityDA, &velocityLocal);
    389:     DMGetLocalVector(c->velocityDA, &velocityLocalOld);
    390:     DMGlobalToLocalBegin(c->velocityDA, c->velocity, INSERT_VALUES, velocityLocal);
    391:     DMGlobalToLocalEnd(c->velocityDA, c->velocity, INSERT_VALUES, velocityLocal);
    392:     DMGlobalToLocalBegin(c->velocityDA, c->velocityOld, INSERT_VALUES, velocityLocalOld);
    393:     DMGlobalToLocalEnd(c->velocityDA, c->velocityOld, INSERT_VALUES, velocityLocalOld);
    394:     DMDAVecGetArray(c->velocityDA, velocityLocal,    &velocityArray);
    395:     DMDAVecGetArray(c->velocityDA, velocityLocalOld, &velocityArrayOld);
    396:   }
    397:   PetscInfo(NULL, "Calculating position at t_{n - 1/2}\n");
    398:   for (Qi.j = js; Qi.j < je; Qi.j++) {
    399:     for (Qi.i = is; Qi.i < ie; Qi.i++) {
    400:       interpIndices[0] = Qi.i;
    401:       interpIndices[1] = Qi.j;
    402:       if (c->velocityInterpLocal) c->velocityInterpLocal(velocityArray, interpIndices, c->numVelocityComp, c->velocityComp, velocityValues, c->velocityCtx);
    403:       else c->velocityInterp(c->velocity, interpIndices, c->numVelocityComp, c->velocityComp, velocityValues, c->velocityCtx);
    404:       Qi.x = Qi.i - velocityValues[0]*dt/2.0;
    405:       Qi.y = Qi.j - velocityValues[1]*dt/2.0;

    407:       /* Determine whether the position at t - dt/2 is local */
    408:       Qi.proc = DMDAGetNeighborRelative(da, Qi.x, Qi.y);

    410:       /* Check for Periodic boundaries and move all periodic points back onto the domain */
    411:       DMDAMapCoordsToPeriodicDomain(da,&(Qi.x),&(Qi.y));
    412:       CharacteristicAddPoint(c, &Qi);
    413:     }
    414:   }
    415:   PetscLogEventEnd(CHARACTERISTIC_QueueSetup,0,0,0,0);

    417:   PetscLogEventBegin(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);
    418:   CharacteristicSendCoordinatesBegin(c);
    419:   PetscLogEventEnd(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);

    421:   PetscLogEventBegin(CHARACTERISTIC_HalfTimeLocal,0,0,0,0);
    422:   /* Calculate velocity at t_n+1/2 (local values) */
    423:   PetscInfo(NULL, "Calculating local velocities at t_{n - 1/2}\n");
    424:   for (n = 0; n < c->queueSize; n++) {
    425:     Qi = c->queue[n];
    426:     if (c->neighbors[Qi.proc] == rank) {
    427:       interpIndices[0] = Qi.x;
    428:       interpIndices[1] = Qi.y;
    429:       if (c->velocityInterpLocal) {
    430:         c->velocityInterpLocal(velocityArray,    interpIndices, c->numVelocityComp, c->velocityComp, velocityValues,    c->velocityCtx);
    431:         c->velocityInterpLocal(velocityArrayOld, interpIndices, c->numVelocityComp, c->velocityComp, velocityValuesOld, c->velocityCtx);
    432:       } else {
    433:         c->velocityInterp(c->velocity,    interpIndices, c->numVelocityComp, c->velocityComp, velocityValues,    c->velocityCtx);
    434:         c->velocityInterp(c->velocityOld, interpIndices, c->numVelocityComp, c->velocityComp, velocityValuesOld, c->velocityCtx);
    435:       }
    436:       Qi.x = 0.5*(velocityValues[0] + velocityValuesOld[0]);
    437:       Qi.y = 0.5*(velocityValues[1] + velocityValuesOld[1]);
    438:     }
    439:     c->queue[n] = Qi;
    440:   }
    441:   PetscLogEventEnd(CHARACTERISTIC_HalfTimeLocal,0,0,0,0);

    443:   PetscLogEventBegin(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);
    444:   CharacteristicSendCoordinatesEnd(c);
    445:   PetscLogEventEnd(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);

    448:   /* Calculate velocity at t_n+1/2 (fill remote requests) */
    449:   PetscLogEventBegin(CHARACTERISTIC_HalfTimeRemote,0,0,0,0);
    450:   PetscInfo1(NULL, "Calculating %d remote velocities at t_{n - 1/2}\n", c->queueRemoteSize);
    451:   for (n = 0; n < c->queueRemoteSize; n++) {
    452:     Qi = c->queueRemote[n];
    453:     interpIndices[0] = Qi.x;
    454:     interpIndices[1] = Qi.y;
    455:     if (c->velocityInterpLocal) {
    456:       c->velocityInterpLocal(velocityArray,    interpIndices, c->numVelocityComp, c->velocityComp, velocityValues,    c->velocityCtx);
    457:       c->velocityInterpLocal(velocityArrayOld, interpIndices, c->numVelocityComp, c->velocityComp, velocityValuesOld, c->velocityCtx);
    458:     } else {
    459:       c->velocityInterp(c->velocity,    interpIndices, c->numVelocityComp, c->velocityComp, velocityValues,    c->velocityCtx);
    460:       c->velocityInterp(c->velocityOld, interpIndices, c->numVelocityComp, c->velocityComp, velocityValuesOld, c->velocityCtx);
    461:     }
    462:     Qi.x = 0.5*(velocityValues[0] + velocityValuesOld[0]);
    463:     Qi.y = 0.5*(velocityValues[1] + velocityValuesOld[1]);
    464:     c->queueRemote[n] = Qi;
    465:   }
    466:   PetscLogEventEnd(CHARACTERISTIC_HalfTimeRemote,0,0,0,0);
    467:   PetscLogEventBegin(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);
    468:   CharacteristicGetValuesBegin(c);
    469:   CharacteristicGetValuesEnd(c);
    470:   if (c->velocityInterpLocal) {
    471:     DMDAVecRestoreArray(c->velocityDA, velocityLocal,    &velocityArray);
    472:     DMDAVecRestoreArray(c->velocityDA, velocityLocalOld, &velocityArrayOld);
    473:     DMRestoreLocalVector(c->velocityDA, &velocityLocal);
    474:     DMRestoreLocalVector(c->velocityDA, &velocityLocalOld);
    475:   }
    476:   PetscLogEventEnd(CHARACTERISTIC_HalfTimeExchange,0,0,0,0);

    478:   /* -----------------------------------------------------------------------
    479:      PART 2, AT t-dt
    480:      -----------------------------------------------------------------------*/

    482:   /* GET POSITION AT t_n (local values) */
    483:   PetscLogEventBegin(CHARACTERISTIC_FullTimeLocal,0,0,0,0);
    484:   PetscInfo(NULL, "Calculating position at t_{n}\n");
    485:   for (n = 0; n < c->queueSize; n++) {
    486:     Qi   = c->queue[n];
    487:     Qi.x = Qi.i - Qi.x*dt;
    488:     Qi.y = Qi.j - Qi.y*dt;

    490:     /* Determine whether the position at t-dt is local */
    491:     Qi.proc = DMDAGetNeighborRelative(da, Qi.x, Qi.y);

    493:     /* Check for Periodic boundaries and move all periodic points back onto the domain */
    494:     DMDAMapCoordsToPeriodicDomain(da,&(Qi.x),&(Qi.y));

    496:     c->queue[n] = Qi;
    497:   }
    498:   PetscLogEventEnd(CHARACTERISTIC_FullTimeLocal,0,0,0,0);

    500:   PetscLogEventBegin(CHARACTERISTIC_FullTimeExchange,0,0,0,0);
    501:   CharacteristicSendCoordinatesBegin(c);
    502:   PetscLogEventEnd(CHARACTERISTIC_FullTimeExchange,0,0,0,0);

    504:   /* GET VALUE AT FULL TIME IN THE PAST (LOCAL REQUESTS) */
    505:   PetscLogEventBegin(CHARACTERISTIC_FullTimeLocal,0,0,0,0);
    506:   if (c->fieldInterpLocal) {
    507:     DMGetLocalVector(c->fieldDA, &fieldLocal);
    508:     DMGlobalToLocalBegin(c->fieldDA, c->field, INSERT_VALUES, fieldLocal);
    509:     DMGlobalToLocalEnd(c->fieldDA, c->field, INSERT_VALUES, fieldLocal);
    510:     DMDAVecGetArray(c->fieldDA, fieldLocal, &fieldArray);
    511:   }
    512:   PetscInfo(NULL, "Calculating local field at t_{n}\n");
    513:   for (n = 0; n < c->queueSize; n++) {
    514:     if (c->neighbors[c->queue[n].proc] == rank) {
    515:       interpIndices[0] = c->queue[n].x;
    516:       interpIndices[1] = c->queue[n].y;
    517:       if (c->fieldInterpLocal) c->fieldInterpLocal(fieldArray, interpIndices, c->numFieldComp, c->fieldComp, fieldValues, c->fieldCtx);
    518:       else c->fieldInterp(c->field, interpIndices, c->numFieldComp, c->fieldComp, fieldValues, c->fieldCtx);
    519:       for (comp = 0; comp < c->numFieldComp; comp++) c->queue[n].field[comp] = fieldValues[comp];
    520:     }
    521:   }
    522:   PetscLogEventEnd(CHARACTERISTIC_FullTimeLocal,0,0,0,0);

    524:   PetscLogEventBegin(CHARACTERISTIC_FullTimeExchange,0,0,0,0);
    525:   CharacteristicSendCoordinatesEnd(c);
    526:   PetscLogEventEnd(CHARACTERISTIC_FullTimeExchange,0,0,0,0);

    528:   /* GET VALUE AT FULL TIME IN THE PAST (REMOTE REQUESTS) */
    529:   PetscLogEventBegin(CHARACTERISTIC_FullTimeRemote,0,0,0,0);
    530:   PetscInfo1(NULL, "Calculating %d remote field points at t_{n}\n", c->queueRemoteSize);
    531:   for (n = 0; n < c->queueRemoteSize; n++) {
    532:     interpIndices[0] = c->queueRemote[n].x;
    533:     interpIndices[1] = c->queueRemote[n].y;

    535:     /* for debugging purposes */
    536:     if (1) { /* hacked bounds test...let's do better */
    537:       PetscScalar im = interpIndices[0]; PetscScalar jm = interpIndices[1];

    539:       if ((im < (PetscScalar) is - 1.) || (im > (PetscScalar) ie) || (jm < (PetscScalar)  js - 1.) || (jm > (PetscScalar) je)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB, "Nonlocal point: (%g,%g)", im, jm);
    540:     }

    542:     if (c->fieldInterpLocal) c->fieldInterpLocal(fieldArray, interpIndices, c->numFieldComp, c->fieldComp, fieldValues, c->fieldCtx);
    543:     else c->fieldInterp(c->field, interpIndices, c->numFieldComp, c->fieldComp, fieldValues, c->fieldCtx);
    544:     for (comp = 0; comp < c->numFieldComp; comp++) c->queueRemote[n].field[comp] = fieldValues[comp];
    545:   }
    546:   PetscLogEventEnd(CHARACTERISTIC_FullTimeRemote,0,0,0,0);

    548:   PetscLogEventBegin(CHARACTERISTIC_FullTimeExchange,0,0,0,0);
    549:   CharacteristicGetValuesBegin(c);
    550:   CharacteristicGetValuesEnd(c);
    551:   if (c->fieldInterpLocal) {
    552:     DMDAVecRestoreArray(c->fieldDA, fieldLocal, &fieldArray);
    553:     DMRestoreLocalVector(c->fieldDA, &fieldLocal);
    554:   }
    555:   PetscLogEventEnd(CHARACTERISTIC_FullTimeExchange,0,0,0,0);

    557:   /* Return field of characteristics at t_n-1 */
    558:   PetscLogEventBegin(CHARACTERISTIC_DAUpdate,0,0,0,0);
    559:   DMDAGetInfo(c->fieldDA,0,0,0,0,0,0,0,&dof,0,0,0,0,0);
    560:   DMDAVecGetArray(c->fieldDA, solution, &solArray);
    561:   for (n = 0; n < c->queueSize; n++) {
    562:     Qi = c->queue[n];
    563:     for (comp = 0; comp < c->numFieldComp; comp++) solArray[Qi.j][Qi.i*dof+c->fieldComp[comp]] = Qi.field[comp];
    564:   }
    565:   DMDAVecRestoreArray(c->fieldDA, solution, &solArray);
    566:   PetscLogEventEnd(CHARACTERISTIC_DAUpdate,0,0,0,0);
    567:   PetscLogEventEnd(CHARACTERISTIC_Solve,0,0,0,0);

    569:   /* Cleanup */
    570:   PetscFree(interpIndices);
    571:   PetscFree(velocityValues);
    572:   PetscFree(velocityValuesOld);
    573:   PetscFree(fieldValues);
    574:   return(0);
    575: }

    579: PetscErrorCode CharacteristicSetNeighbors(Characteristic c, PetscInt numNeighbors, PetscMPIInt neighbors[])
    580: {

    584:   c->numNeighbors = numNeighbors;
    585:   PetscFree(c->neighbors);
    586:   PetscMalloc1(numNeighbors, &c->neighbors);
    587:   PetscMemcpy(c->neighbors, neighbors, numNeighbors * sizeof(PetscMPIInt));
    588:   return(0);
    589: }

    593: PetscErrorCode CharacteristicAddPoint(Characteristic c, CharacteristicPointDA2D *point)
    594: {
    596:   if (c->queueSize >= c->queueMax) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Exceeeded maximum queue size %d", c->queueMax);
    597:   c->queue[c->queueSize++] = *point;
    598:   return(0);
    599: }

    603: int CharacteristicSendCoordinatesBegin(Characteristic c)
    604: {
    605:   PetscMPIInt    rank, tag = 121;
    606:   PetscInt       i, n;

    610:   MPI_Comm_rank(PetscObjectComm((PetscObject)c), &rank);
    611:   CharacteristicHeapSort(c, c->queue, c->queueSize);
    612:   PetscMemzero(c->needCount, c->numNeighbors * sizeof(PetscInt));
    613:   for (i = 0;  i < c->queueSize; i++) c->needCount[c->queue[i].proc]++;
    614:   c->fillCount[0] = 0;
    615:   for (n = 1; n < c->numNeighbors; n++) {
    616:     MPI_Irecv(&(c->fillCount[n]), 1, MPIU_INT, c->neighbors[n], tag, PetscObjectComm((PetscObject)c), &(c->request[n-1]));
    617:   }
    618:   for (n = 1; n < c->numNeighbors; n++) {
    619:     MPI_Send(&(c->needCount[n]), 1, MPIU_INT, c->neighbors[n], tag, PetscObjectComm((PetscObject)c));
    620:   }
    621:   MPI_Waitall(c->numNeighbors-1, c->request, c->status);
    622:   /* Initialize the remote queue */
    623:   c->queueLocalMax  = c->localOffsets[0]  = 0;
    624:   c->queueRemoteMax = c->remoteOffsets[0] = 0;
    625:   for (n = 1; n < c->numNeighbors; n++) {
    626:     c->remoteOffsets[n] = c->queueRemoteMax;
    627:     c->queueRemoteMax  += c->fillCount[n];
    628:     c->localOffsets[n]  = c->queueLocalMax;
    629:     c->queueLocalMax   += c->needCount[n];
    630:   }
    631:   /* HACK BEGIN */
    632:   for (n = 1; n < c->numNeighbors; n++) c->localOffsets[n] += c->needCount[0];
    633:   c->needCount[0] = 0;
    634:   /* HACK END */
    635:   if (c->queueRemoteMax) {
    636:     PetscMalloc(sizeof(CharacteristicPointDA2D) * c->queueRemoteMax, &c->queueRemote);
    637:   } else c->queueRemote = NULL;
    638:   c->queueRemoteSize = c->queueRemoteMax;

    640:   /* Send and Receive requests for values at t_n+1/2, giving the coordinates for interpolation */
    641:   for (n = 1; n < c->numNeighbors; n++) {
    642:     PetscInfo2(NULL, "Receiving %d requests for values from proc %d\n", c->fillCount[n], c->neighbors[n]);
    643:     MPI_Irecv(&(c->queueRemote[c->remoteOffsets[n]]), c->fillCount[n], c->itemType, c->neighbors[n], tag, PetscObjectComm((PetscObject)c), &(c->request[n-1]));
    644:   }
    645:   for (n = 1; n < c->numNeighbors; n++) {
    646:     PetscInfo2(NULL, "Sending %d requests for values from proc %d\n", c->needCount[n], c->neighbors[n]);
    647:     MPI_Send(&(c->queue[c->localOffsets[n]]), c->needCount[n], c->itemType, c->neighbors[n], tag, PetscObjectComm((PetscObject)c));
    648:   }
    649:   return(0);
    650: }

    654: PetscErrorCode CharacteristicSendCoordinatesEnd(Characteristic c)
    655: {
    656: #if 0
    657:   PetscMPIInt rank;
    658:   PetscInt    n;
    659: #endif

    663:   MPI_Waitall(c->numNeighbors-1, c->request, c->status);
    664: #if 0
    665:   MPI_Comm_rank(PetscObjectComm((PetscObject)c), &rank);
    666:   for (n = 0; n < c->queueRemoteSize; n++) {
    667:     if (c->neighbors[c->queueRemote[n].proc] == rank) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "This is messed up, n = %d proc = %d", n, c->queueRemote[n].proc);
    668:   }
    669: #endif
    670:   return(0);
    671: }

    675: PetscErrorCode CharacteristicGetValuesBegin(Characteristic c)
    676: {
    677:   PetscMPIInt    tag = 121;
    678:   PetscInt       n;

    682:   /* SEND AND RECIEVE FILLED REQUESTS for velocities at t_n+1/2 */
    683:   for (n = 1; n < c->numNeighbors; n++) {
    684:     MPI_Irecv(&(c->queue[c->localOffsets[n]]), c->needCount[n], c->itemType, c->neighbors[n], tag, PetscObjectComm((PetscObject)c), &(c->request[n-1]));
    685:   }
    686:   for (n = 1; n < c->numNeighbors; n++) {
    687:     MPI_Send(&(c->queueRemote[c->remoteOffsets[n]]), c->fillCount[n], c->itemType, c->neighbors[n], tag, PetscObjectComm((PetscObject)c));
    688:   }
    689:   return(0);
    690: }

    694: PetscErrorCode CharacteristicGetValuesEnd(Characteristic c)
    695: {

    699:   MPI_Waitall(c->numNeighbors-1, c->request, c->status);
    700:   /* Free queue of requests from other procs */
    701:   PetscFree(c->queueRemote);
    702:   return(0);
    703: }

    705: /*---------------------------------------------------------------------*/
    708: /*
    709:   Based on code from http://linux.wku.edu/~lamonml/algor/sort/heap.html
    710: */
    711: PetscErrorCode CharacteristicHeapSort(Characteristic c, Queue queue, PetscInt size)
    712: /*---------------------------------------------------------------------*/
    713: {
    714:   PetscErrorCode          ierr;
    715:   CharacteristicPointDA2D temp;
    716:   PetscInt                n;

    719:   if (0) { /* Check the order of the queue before sorting */
    720:     PetscInfo(NULL, "Before Heap sort\n");
    721:     for (n=0; n<size; n++) {
    722:       PetscInfo2(NULL,"%d %d\n",n,queue[n].proc);
    723:     }
    724:   }

    726:   /* SORTING PHASE */
    727:   for (n = (size / 2)-1; n >= 0; n--) {
    728:     CharacteristicSiftDown(c, queue, n, size-1); /* Rich had size-1 here, Matt had size*/
    729:   }
    730:   for (n = size-1; n >= 1; n--) {
    731:     temp     = queue[0];
    732:     queue[0] = queue[n];
    733:     queue[n] = temp;
    734:     CharacteristicSiftDown(c, queue, 0, n-1);
    735:   }
    736:   if (0) { /* Check the order of the queue after sorting */
    737:     PetscInfo(NULL, "Avter  Heap sort\n");
    738:     for (n=0; n<size; n++) {
    739:       PetscInfo2(NULL,"%d %d\n",n,queue[n].proc);
    740:     }
    741:   }
    742:   return(0);
    743: }

    745: /*---------------------------------------------------------------------*/
    748: /*
    749:   Based on code from http://linux.wku.edu/~lamonml/algor/sort/heap.html
    750: */
    751: PetscErrorCode CharacteristicSiftDown(Characteristic c, Queue queue, PetscInt root, PetscInt bottom)
    752: /*---------------------------------------------------------------------*/
    753: {
    754:   PetscBool               done = PETSC_FALSE;
    755:   PetscInt                maxChild;
    756:   CharacteristicPointDA2D temp;

    759:   while ((root*2 <= bottom) && (!done)) {
    760:     if (root*2 == bottom) maxChild = root * 2;
    761:     else if (queue[root*2].proc > queue[root*2+1].proc) maxChild = root * 2;
    762:     else maxChild = root * 2 + 1;

    764:     if (queue[root].proc < queue[maxChild].proc) {
    765:       temp            = queue[root];
    766:       queue[root]     = queue[maxChild];
    767:       queue[maxChild] = temp;
    768:       root            = maxChild;
    769:     } else done = PETSC_TRUE;
    770:   }
    771:   return(0);
    772: }

    776: /* [center, left, top-left, top, top-right, right, bottom-right, bottom, bottom-left] */
    777: PetscErrorCode DMDAGetNeighborsRank(DM da, PetscMPIInt neighbors[])
    778: {
    779:   DMBoundaryType   bx, by;
    780:   PetscBool        IPeriodic = PETSC_FALSE, JPeriodic = PETSC_FALSE;
    781:   MPI_Comm         comm;
    782:   PetscMPIInt      rank;
    783:   PetscInt         **procs,pi,pj,pim,pip,pjm,pjp,PI,PJ;
    784:   PetscErrorCode   ierr;

    787:   PetscObjectGetComm((PetscObject) da, &comm);
    788:   MPI_Comm_rank(comm, &rank);
    789:   DMDAGetInfo(da, 0, 0, 0, 0, &PI,&PJ, 0, 0, 0, &bx, &by,0, 0);

    791:   if (bx == DM_BOUNDARY_PERIODIC) IPeriodic = PETSC_TRUE;
    792:   if (by == DM_BOUNDARY_PERIODIC) JPeriodic = PETSC_TRUE;

    794:   neighbors[0] = rank;
    795:   rank = 0;
    796:   PetscMalloc1(PJ,&procs);
    797:   for (pj=0; pj<PJ; pj++) {
    798:     PetscMalloc1(PI,&(procs[pj]));
    799:     for (pi=0; pi<PI; pi++) {
    800:       procs[pj][pi] = rank;
    801:       rank++;
    802:     }
    803:   }

    805:   pi  = neighbors[0] % PI;
    806:   pj  = neighbors[0] / PI;
    807:   pim = pi-1;  if (pim<0) pim=PI-1;
    808:   pip = (pi+1)%PI;
    809:   pjm = pj-1;  if (pjm<0) pjm=PJ-1;
    810:   pjp = (pj+1)%PJ;

    812:   neighbors[1] = procs[pj] [pim];
    813:   neighbors[2] = procs[pjp][pim];
    814:   neighbors[3] = procs[pjp][pi];
    815:   neighbors[4] = procs[pjp][pip];
    816:   neighbors[5] = procs[pj] [pip];
    817:   neighbors[6] = procs[pjm][pip];
    818:   neighbors[7] = procs[pjm][pi];
    819:   neighbors[8] = procs[pjm][pim];

    821:   if (!IPeriodic) {
    822:     if (pi==0)    neighbors[1]=neighbors[2]=neighbors[8]=neighbors[0];
    823:     if (pi==PI-1) neighbors[4]=neighbors[5]=neighbors[6]=neighbors[0];
    824:   }

    826:   if (!JPeriodic) {
    827:     if (pj==0)    neighbors[6]=neighbors[7]=neighbors[8]=neighbors[0];
    828:     if (pj==PJ-1) neighbors[2]=neighbors[3]=neighbors[4]=neighbors[0];
    829:   }

    831:   for (pj = 0; pj < PJ; pj++) {
    832:     PetscFree(procs[pj]);
    833:   }
    834:   PetscFree(procs);
    835:   return(0);
    836: }

    840: /*
    841:   SUBDOMAIN NEIGHBORHOOD PROCESS MAP:
    842:     2 | 3 | 4
    843:     __|___|__
    844:     1 | 0 | 5
    845:     __|___|__
    846:     8 | 7 | 6
    847:       |   |
    848: */
    849: PetscInt DMDAGetNeighborRelative(DM da, PassiveReal ir, PassiveReal jr)
    850: {
    851:   DMDALocalInfo  info;
    852:   PassiveReal    is,ie,js,je;

    855:   DMDAGetLocalInfo(da, &info);
    856:   is   = (PassiveReal) info.xs - 0.5; ie = (PassiveReal) info.xs + info.xm - 0.5;
    857:   js   = (PassiveReal) info.ys - 0.5; je = (PassiveReal) info.ys + info.ym - 0.5;

    859:   if (ir >= is && ir <= ie) { /* center column */
    860:     if (jr >= js && jr <= je) return 0;
    861:     else if (jr < js)         return 7;
    862:     else                      return 3;
    863:   } else if (ir < is) {     /* left column */
    864:     if (jr >= js && jr <= je) return 1;
    865:     else if (jr < js)         return 8;
    866:     else                      return 2;
    867:   } else {                  /* right column */
    868:     if (jr >= js && jr <= je) return 5;
    869:     else if (jr < js)         return 6;
    870:     else                      return 4;
    871:   }
    872: }