Actual source code: plexfem.c
petsc-3.15.0 2021-03-30
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      1: #include <petsc/private/dmpleximpl.h>
      2: #include <petscsf.h>

      4: #include <petsc/private/hashsetij.h>
      5: #include <petsc/private/petscfeimpl.h>
      6: #include <petsc/private/petscfvimpl.h>

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

     14:   PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
     15:   if (isPlex) {
     16:     *plex = dm;
     17:     PetscObjectReference((PetscObject) dm);
     18:   } else {
     19:     PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
     20:     if (!*plex) {
     21:       DMConvert(dm,DMPLEX,plex);
     22:       PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
     23:       if (copy) {
     24:         const char *comps[3] = {"A", "dmAux"};
     25:         PetscObject obj;
     26:         PetscInt    i;

     28:         {
     29:           /* Run the subdomain hook (this will copy the DMSNES/DMTS) */
     30:           DMSubDomainHookLink link;
     31:           for (link = dm->subdomainhook; link; link = link->next) {
     32:             if (link->ddhook) {(*link->ddhook)(dm, *plex, link->ctx);}
     33:           }
     34:         }
     35:         for (i = 0; i < 3; i++) {
     36:           PetscObjectQuery((PetscObject) dm, comps[i], &obj);
     37:           PetscObjectCompose((PetscObject) *plex, comps[i], obj);
     38:         }
     39:       }
     40:     } else {
     41:       PetscObjectReference((PetscObject) *plex);
     42:     }
     43:   }
     44:   return(0);
     45: }

     47: static PetscErrorCode PetscContainerUserDestroy_PetscFEGeom (void *ctx)
     48: {
     49:   PetscFEGeom *geom = (PetscFEGeom *) ctx;

     53:   PetscFEGeomDestroy(&geom);
     54:   return(0);
     55: }

     57: static PetscErrorCode DMPlexGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
     58: {
     59:   char            composeStr[33] = {0};
     60:   PetscObjectId   id;
     61:   PetscContainer  container;
     62:   PetscErrorCode  ierr;

     65:   PetscObjectGetId((PetscObject)quad,&id);
     66:   PetscSNPrintf(composeStr, 32, "DMPlexGetFEGeom_%x\n", id);
     67:   PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);
     68:   if (container) {
     69:     PetscContainerGetPointer(container, (void **) geom);
     70:   } else {
     71:     DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);
     72:     PetscContainerCreate(PETSC_COMM_SELF,&container);
     73:     PetscContainerSetPointer(container, (void *) *geom);
     74:     PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);
     75:     PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);
     76:     PetscContainerDestroy(&container);
     77:   }
     78:   return(0);
     79: }

     81: static PetscErrorCode DMPlexRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
     82: {
     84:   *geom = NULL;
     85:   return(0);
     86: }

     88: /*@
     89:   DMPlexGetScale - Get the scale for the specified fundamental unit

     91:   Not collective

     93:   Input Arguments:
     94: + dm   - the DM
     95: - unit - The SI unit

     97:   Output Argument:
     98: . scale - The value used to scale all quantities with this unit

    100:   Level: advanced

    102: .seealso: DMPlexSetScale(), PetscUnit
    103: @*/
    104: PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale)
    105: {
    106:   DM_Plex *mesh = (DM_Plex*) dm->data;

    111:   *scale = mesh->scale[unit];
    112:   return(0);
    113: }

    115: /*@
    116:   DMPlexSetScale - Set the scale for the specified fundamental unit

    118:   Not collective

    120:   Input Arguments:
    121: + dm   - the DM
    122: . unit - The SI unit
    123: - scale - The value used to scale all quantities with this unit

    125:   Level: advanced

    127: .seealso: DMPlexGetScale(), PetscUnit
    128: @*/
    129: PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale)
    130: {
    131:   DM_Plex *mesh = (DM_Plex*) dm->data;

    135:   mesh->scale[unit] = scale;
    136:   return(0);
    137: }

    139: static PetscErrorCode DMPlexProjectRigidBody_Private(PetscInt dim, PetscReal t, const PetscReal X[], PetscInt Nc, PetscScalar *mode, void *ctx)
    140: {
    141:   const PetscInt eps[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}};
    142:   PetscInt *ctxInt  = (PetscInt *) ctx;
    143:   PetscInt  dim2    = ctxInt[0];
    144:   PetscInt  d       = ctxInt[1];
    145:   PetscInt  i, j, k = dim > 2 ? d - dim : d;

    148:   if (dim != dim2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input dimension %D does not match context dimension %D", dim, dim2);
    149:   for (i = 0; i < dim; i++) mode[i] = 0.;
    150:   if (d < dim) {
    151:     mode[d] = 1.; /* Translation along axis d */
    152:   } else {
    153:     for (i = 0; i < dim; i++) {
    154:       for (j = 0; j < dim; j++) {
    155:         mode[j] += eps[i][j][k]*X[i]; /* Rotation about axis d */
    156:       }
    157:     }
    158:   }
    159:   return(0);
    160: }

    162: /*@
    163:   DMPlexCreateRigidBody - For the default global section, create rigid body modes by function space interpolation

    165:   Collective on dm

    167:   Input Arguments:
    168: + dm - the DM
    169: - field - The field number for the rigid body space, or 0 for the default

    171:   Output Argument:
    172: . sp - the null space

    174:   Note: This is necessary to provide a suitable coarse space for algebraic multigrid

    176:   Level: advanced

    178: .seealso: MatNullSpaceCreate(), PCGAMG
    179: @*/
    180: PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscInt field, MatNullSpace *sp)
    181: {
    182:   PetscErrorCode (**func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *);
    183:   MPI_Comm          comm;
    184:   Vec               mode[6];
    185:   PetscSection      section, globalSection;
    186:   PetscInt          dim, dimEmbed, Nf, n, m, mmin, d, i, j;
    187:   PetscErrorCode    ierr;

    190:   PetscObjectGetComm((PetscObject) dm, &comm);
    191:   DMGetDimension(dm, &dim);
    192:   DMGetCoordinateDim(dm, &dimEmbed);
    193:   DMGetNumFields(dm, &Nf);
    194:   if (Nf && (field < 0 || field >= Nf)) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Field %D is not in [0, Nf)", field, Nf);
    195:   if (dim == 1 && Nf < 2) {
    196:     MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);
    197:     return(0);
    198:   }
    199:   DMGetLocalSection(dm, &section);
    200:   DMGetGlobalSection(dm, &globalSection);
    201:   PetscSectionGetConstrainedStorageSize(globalSection, &n);
    202:   PetscCalloc1(Nf, &func);
    203:   m    = (dim*(dim+1))/2;
    204:   VecCreate(comm, &mode[0]);
    205:   VecSetSizes(mode[0], n, PETSC_DETERMINE);
    206:   VecSetUp(mode[0]);
    207:   VecGetSize(mode[0], &n);
    208:   mmin = PetscMin(m, n);
    209:   func[field] = DMPlexProjectRigidBody_Private;
    210:   for (i = 1; i < m; ++i) {VecDuplicate(mode[0], &mode[i]);}
    211:   for (d = 0; d < m; d++) {
    212:     PetscInt ctx[2];
    213:     void    *voidctx = (void *) (&ctx[0]);

    215:     ctx[0] = dimEmbed;
    216:     ctx[1] = d;
    217:     DMProjectFunction(dm, 0.0, func, &voidctx, INSERT_VALUES, mode[d]);
    218:   }
    219:   /* Orthonormalize system */
    220:   for (i = 0; i < mmin; ++i) {
    221:     PetscScalar dots[6];

    223:     VecNormalize(mode[i], NULL);
    224:     VecMDot(mode[i], mmin-i-1, mode+i+1, dots+i+1);
    225:     for (j = i+1; j < mmin; ++j) {
    226:       dots[j] *= -1.0;
    227:       VecAXPY(mode[j], dots[j], mode[i]);
    228:     }
    229:   }
    230:   MatNullSpaceCreate(comm, PETSC_FALSE, mmin, mode, sp);
    231:   for (i = 0; i < m; ++i) {VecDestroy(&mode[i]);}
    232:   PetscFree(func);
    233:   return(0);
    234: }

    236: /*@
    237:   DMPlexCreateRigidBodies - For the default global section, create rigid body modes by function space interpolation

    239:   Collective on dm

    241:   Input Arguments:
    242: + dm    - the DM
    243: . nb    - The number of bodies
    244: . label - The DMLabel marking each domain
    245: . nids  - The number of ids per body
    246: - ids   - An array of the label ids in sequence for each domain

    248:   Output Argument:
    249: . sp - the null space

    251:   Note: This is necessary to provide a suitable coarse space for algebraic multigrid

    253:   Level: advanced

    255: .seealso: MatNullSpaceCreate()
    256: @*/
    257: PetscErrorCode DMPlexCreateRigidBodies(DM dm, PetscInt nb, DMLabel label, const PetscInt nids[], const PetscInt ids[], MatNullSpace *sp)
    258: {
    259:   MPI_Comm       comm;
    260:   PetscSection   section, globalSection;
    261:   Vec           *mode;
    262:   PetscScalar   *dots;
    263:   PetscInt       dim, dimEmbed, n, m, b, d, i, j, off;

    267:   PetscObjectGetComm((PetscObject)dm,&comm);
    268:   DMGetDimension(dm, &dim);
    269:   DMGetCoordinateDim(dm, &dimEmbed);
    270:   DMGetLocalSection(dm, &section);
    271:   DMGetGlobalSection(dm, &globalSection);
    272:   PetscSectionGetConstrainedStorageSize(globalSection, &n);
    273:   m    = nb * (dim*(dim+1))/2;
    274:   PetscMalloc2(m, &mode, m, &dots);
    275:   VecCreate(comm, &mode[0]);
    276:   VecSetSizes(mode[0], n, PETSC_DETERMINE);
    277:   VecSetUp(mode[0]);
    278:   for (i = 1; i < m; ++i) {VecDuplicate(mode[0], &mode[i]);}
    279:   for (b = 0, off = 0; b < nb; ++b) {
    280:     for (d = 0; d < m/nb; ++d) {
    281:       PetscInt         ctx[2];
    282:       PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private;
    283:       void            *voidctx = (void *) (&ctx[0]);

    285:       ctx[0] = dimEmbed;
    286:       ctx[1] = d;
    287:       DMProjectFunctionLabel(dm, 0.0, label, nids[b], &ids[off], 0, NULL, &func, &voidctx, INSERT_VALUES, mode[d]);
    288:       off   += nids[b];
    289:     }
    290:   }
    291:   /* Orthonormalize system */
    292:   for (i = 0; i < m; ++i) {
    293:     PetscScalar dots[6];

    295:     VecNormalize(mode[i], NULL);
    296:     VecMDot(mode[i], m-i-1, mode+i+1, dots+i+1);
    297:     for (j = i+1; j < m; ++j) {
    298:       dots[j] *= -1.0;
    299:       VecAXPY(mode[j], dots[j], mode[i]);
    300:     }
    301:   }
    302:   MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);
    303:   for (i = 0; i< m; ++i) {VecDestroy(&mode[i]);}
    304:   PetscFree2(mode, dots);
    305:   return(0);
    306: }

    308: /*@
    309:   DMPlexSetMaxProjectionHeight - In DMPlexProjectXXXLocal() functions, the projected values of a basis function's dofs
    310:   are computed by associating the basis function with one of the mesh points in its transitively-closed support, and
    311:   evaluating the dual space basis of that point.  A basis function is associated with the point in its
    312:   transitively-closed support whose mesh height is highest (w.r.t. DAG height), but not greater than the maximum
    313:   projection height, which is set with this function.  By default, the maximum projection height is zero, which means
    314:   that only mesh cells are used to project basis functions.  A height of one, for example, evaluates a cell-interior
    315:   basis functions using its cells dual space basis, but all other basis functions with the dual space basis of a face.

    317:   Input Parameters:
    318: + dm - the DMPlex object
    319: - height - the maximum projection height >= 0

    321:   Level: advanced

    323: .seealso: DMPlexGetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
    324: @*/
    325: PetscErrorCode DMPlexSetMaxProjectionHeight(DM dm, PetscInt height)
    326: {
    327:   DM_Plex *plex = (DM_Plex *) dm->data;

    331:   plex->maxProjectionHeight = height;
    332:   return(0);
    333: }

    335: /*@
    336:   DMPlexGetMaxProjectionHeight - Get the maximum height (w.r.t. DAG) of mesh points used to evaluate dual bases in
    337:   DMPlexProjectXXXLocal() functions.

    339:   Input Parameters:
    340: . dm - the DMPlex object

    342:   Output Parameters:
    343: . height - the maximum projection height

    345:   Level: intermediate

    347: .seealso: DMPlexSetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
    348: @*/
    349: PetscErrorCode DMPlexGetMaxProjectionHeight(DM dm, PetscInt *height)
    350: {
    351:   DM_Plex *plex = (DM_Plex *) dm->data;

    355:   *height = plex->maxProjectionHeight;
    356:   return(0);
    357: }

    359: typedef struct {
    360:   PetscReal    alpha; /* The first Euler angle, and in 2D the only one */
    361:   PetscReal    beta;  /* The second Euler angle */
    362:   PetscReal    gamma; /* The third Euler angle */
    363:   PetscInt     dim;   /* The dimension of R */
    364:   PetscScalar *R;     /* The rotation matrix, transforming a vector in the local basis to the global basis */
    365:   PetscScalar *RT;    /* The transposed rotation matrix, transforming a vector in the global basis to the local basis */
    366: } RotCtx;

    368: /*
    369:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
    370:   we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows:
    371:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
    372:   $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis.
    373:   $ The XYZ system rotates a third time about the z axis by gamma.
    374: */
    375: static PetscErrorCode DMPlexBasisTransformSetUp_Rotation_Internal(DM dm, void *ctx)
    376: {
    377:   RotCtx        *rc  = (RotCtx *) ctx;
    378:   PetscInt       dim = rc->dim;
    379:   PetscReal      c1, s1, c2, s2, c3, s3;

    383:   PetscMalloc2(PetscSqr(dim), &rc->R, PetscSqr(dim), &rc->RT);
    384:   switch (dim) {
    385:   case 2:
    386:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
    387:     rc->R[0] =  c1;rc->R[1] = s1;
    388:     rc->R[2] = -s1;rc->R[3] = c1;
    389:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
    390:     DMPlex_Transpose2D_Internal(rc->RT);
    391:     break;
    392:   case 3:
    393:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
    394:     c2 = PetscCosReal(rc->beta); s2 = PetscSinReal(rc->beta);
    395:     c3 = PetscCosReal(rc->gamma);s3 = PetscSinReal(rc->gamma);
    396:     rc->R[0] =  c1*c3 - c2*s1*s3;rc->R[1] =  c3*s1    + c1*c2*s3;rc->R[2] = s2*s3;
    397:     rc->R[3] = -c1*s3 - c2*c3*s1;rc->R[4] =  c1*c2*c3 - s1*s3;   rc->R[5] = c3*s2;
    398:     rc->R[6] =  s1*s2;           rc->R[7] = -c1*s2;              rc->R[8] = c2;
    399:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
    400:     DMPlex_Transpose3D_Internal(rc->RT);
    401:     break;
    402:   default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim);
    403:   }
    404:   return(0);
    405: }

    407: static PetscErrorCode DMPlexBasisTransformDestroy_Rotation_Internal(DM dm, void *ctx)
    408: {
    409:   RotCtx        *rc = (RotCtx *) ctx;

    413:   PetscFree2(rc->R, rc->RT);
    414:   PetscFree(rc);
    415:   return(0);
    416: }

    418: static PetscErrorCode DMPlexBasisTransformGetMatrix_Rotation_Internal(DM dm, const PetscReal x[], PetscBool l2g, const PetscScalar **A, void *ctx)
    419: {
    420:   RotCtx *rc = (RotCtx *) ctx;

    424:   if (l2g) {*A = rc->R;}
    425:   else     {*A = rc->RT;}
    426:   return(0);
    427: }

    429: PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscReal *y, PetscReal *z, void *ctx)
    430: {

    434:   #if defined(PETSC_USE_COMPLEX)
    435:   switch (dim) {
    436:     case 2:
    437:     {
    438:       PetscScalar yt[2], zt[2] = {0.0,0.0};

    440:       yt[0] = y[0]; yt[1] = y[1];
    441:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
    442:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]);
    443:     }
    444:     break;
    445:     case 3:
    446:     {
    447:       PetscScalar yt[3], zt[3] = {0.0,0.0,0.0};

    449:       yt[0] = y[0]; yt[1] = y[1]; yt[2] = y[2];
    450:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
    451:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); z[2] = PetscRealPart(zt[2]);
    452:     }
    453:     break;
    454:   }
    455:   #else
    456:   DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, y, z, ctx);
    457:   #endif
    458:   return(0);
    459: }

    461: PetscErrorCode DMPlexBasisTransformApply_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscScalar *y, PetscScalar *z, void *ctx)
    462: {
    463:   const PetscScalar *A;
    464:   PetscErrorCode     ierr;

    467:   (*dm->transformGetMatrix)(dm, x, l2g, &A, ctx);
    468:   switch (dim) {
    469:   case 2: DMPlex_Mult2D_Internal(A, 1, y, z);break;
    470:   case 3: DMPlex_Mult3D_Internal(A, 1, y, z);break;
    471:   }
    472:   return(0);
    473: }

    475: static PetscErrorCode DMPlexBasisTransformField_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscInt f, PetscBool l2g, PetscScalar *a)
    476: {
    477:   PetscSection       ts;
    478:   const PetscScalar *ta, *tva;
    479:   PetscInt           dof;
    480:   PetscErrorCode     ierr;

    483:   DMGetLocalSection(tdm, &ts);
    484:   PetscSectionGetFieldDof(ts, p, f, &dof);
    485:   VecGetArrayRead(tv, &ta);
    486:   DMPlexPointLocalFieldRead(tdm, p, f, ta, (void *) &tva);
    487:   if (l2g) {
    488:     switch (dof) {
    489:     case 4: DMPlex_Mult2D_Internal(tva, 1, a, a);break;
    490:     case 9: DMPlex_Mult3D_Internal(tva, 1, a, a);break;
    491:     }
    492:   } else {
    493:     switch (dof) {
    494:     case 4: DMPlex_MultTranspose2D_Internal(tva, 1, a, a);break;
    495:     case 9: DMPlex_MultTranspose3D_Internal(tva, 1, a, a);break;
    496:     }
    497:   }
    498:   VecRestoreArrayRead(tv, &ta);
    499:   return(0);
    500: }

    502: static PetscErrorCode DMPlexBasisTransformFieldTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt pf, PetscInt f, PetscInt pg, PetscInt g, PetscBool l2g, PetscInt lda, PetscScalar *a)
    503: {
    504:   PetscSection       s, ts;
    505:   const PetscScalar *ta, *tvaf, *tvag;
    506:   PetscInt           fdof, gdof, fpdof, gpdof;
    507:   PetscErrorCode     ierr;

    510:   DMGetLocalSection(dm, &s);
    511:   DMGetLocalSection(tdm, &ts);
    512:   PetscSectionGetFieldDof(s, pf, f, &fpdof);
    513:   PetscSectionGetFieldDof(s, pg, g, &gpdof);
    514:   PetscSectionGetFieldDof(ts, pf, f, &fdof);
    515:   PetscSectionGetFieldDof(ts, pg, g, &gdof);
    516:   VecGetArrayRead(tv, &ta);
    517:   DMPlexPointLocalFieldRead(tdm, pf, f, ta, (void *) &tvaf);
    518:   DMPlexPointLocalFieldRead(tdm, pg, g, ta, (void *) &tvag);
    519:   if (l2g) {
    520:     switch (fdof) {
    521:     case 4: DMPlex_MatMult2D_Internal(tvaf, gpdof, lda, a, a);break;
    522:     case 9: DMPlex_MatMult3D_Internal(tvaf, gpdof, lda, a, a);break;
    523:     }
    524:     switch (gdof) {
    525:     case 4: DMPlex_MatMultTransposeLeft2D_Internal(tvag, fpdof, lda, a, a);break;
    526:     case 9: DMPlex_MatMultTransposeLeft3D_Internal(tvag, fpdof, lda, a, a);break;
    527:     }
    528:   } else {
    529:     switch (fdof) {
    530:     case 4: DMPlex_MatMultTranspose2D_Internal(tvaf, gpdof, lda, a, a);break;
    531:     case 9: DMPlex_MatMultTranspose3D_Internal(tvaf, gpdof, lda, a, a);break;
    532:     }
    533:     switch (gdof) {
    534:     case 4: DMPlex_MatMultLeft2D_Internal(tvag, fpdof, lda, a, a);break;
    535:     case 9: DMPlex_MatMultLeft3D_Internal(tvag, fpdof, lda, a, a);break;
    536:     }
    537:   }
    538:   VecRestoreArrayRead(tv, &ta);
    539:   return(0);
    540: }

    542: PetscErrorCode DMPlexBasisTransformPoint_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool fieldActive[], PetscBool l2g, PetscScalar *a)
    543: {
    544:   PetscSection    s;
    545:   PetscSection    clSection;
    546:   IS              clPoints;
    547:   const PetscInt *clp;
    548:   PetscInt       *points = NULL;
    549:   PetscInt        Nf, f, Np, cp, dof, d = 0;
    550:   PetscErrorCode  ierr;

    553:   DMGetLocalSection(dm, &s);
    554:   PetscSectionGetNumFields(s, &Nf);
    555:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
    556:   for (f = 0; f < Nf; ++f) {
    557:     for (cp = 0; cp < Np*2; cp += 2) {
    558:       PetscSectionGetFieldDof(s, points[cp], f, &dof);
    559:       if (!dof) continue;
    560:       if (fieldActive[f]) {DMPlexBasisTransformField_Internal(dm, tdm, tv, points[cp], f, l2g, &a[d]);}
    561:       d += dof;
    562:     }
    563:   }
    564:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
    565:   return(0);
    566: }

    568: PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool l2g, PetscInt lda, PetscScalar *a)
    569: {
    570:   PetscSection    s;
    571:   PetscSection    clSection;
    572:   IS              clPoints;
    573:   const PetscInt *clp;
    574:   PetscInt       *points = NULL;
    575:   PetscInt        Nf, f, g, Np, cpf, cpg, fdof, gdof, r, c = 0;
    576:   PetscErrorCode  ierr;

    579:   DMGetLocalSection(dm, &s);
    580:   PetscSectionGetNumFields(s, &Nf);
    581:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
    582:   for (f = 0, r = 0; f < Nf; ++f) {
    583:     for (cpf = 0; cpf < Np*2; cpf += 2) {
    584:       PetscSectionGetFieldDof(s, points[cpf], f, &fdof);
    585:       for (g = 0, c = 0; g < Nf; ++g) {
    586:         for (cpg = 0; cpg < Np*2; cpg += 2) {
    587:           PetscSectionGetFieldDof(s, points[cpg], g, &gdof);
    588:           DMPlexBasisTransformFieldTensor_Internal(dm, tdm, tv, points[cpf], f, points[cpg], g, l2g, lda, &a[r*lda+c]);
    589:           c += gdof;
    590:         }
    591:       }
    592:       if (c != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of columns %D should be %D", c, lda);
    593:       r += fdof;
    594:     }
    595:   }
    596:   if (r != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of rows %D should be %D", c, lda);
    597:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
    598:   return(0);
    599: }

    601: static PetscErrorCode DMPlexBasisTransform_Internal(DM dm, Vec lv, PetscBool l2g)
    602: {
    603:   DM                 tdm;
    604:   Vec                tv;
    605:   PetscSection       ts, s;
    606:   const PetscScalar *ta;
    607:   PetscScalar       *a, *va;
    608:   PetscInt           pStart, pEnd, p, Nf, f;
    609:   PetscErrorCode     ierr;

    612:   DMGetBasisTransformDM_Internal(dm, &tdm);
    613:   DMGetBasisTransformVec_Internal(dm, &tv);
    614:   DMGetLocalSection(tdm, &ts);
    615:   DMGetLocalSection(dm, &s);
    616:   PetscSectionGetChart(s, &pStart, &pEnd);
    617:   PetscSectionGetNumFields(s, &Nf);
    618:   VecGetArray(lv, &a);
    619:   VecGetArrayRead(tv, &ta);
    620:   for (p = pStart; p < pEnd; ++p) {
    621:     for (f = 0; f < Nf; ++f) {
    622:       DMPlexPointLocalFieldRef(dm, p, f, a, (void *) &va);
    623:       DMPlexBasisTransformField_Internal(dm, tdm, tv, p, f, l2g, va);
    624:     }
    625:   }
    626:   VecRestoreArray(lv, &a);
    627:   VecRestoreArrayRead(tv, &ta);
    628:   return(0);
    629: }

    631: /*@
    632:   DMPlexGlobalToLocalBasis - Transform the values in the given local vector from the global basis to the local basis

    634:   Input Parameters:
    635: + dm - The DM
    636: - lv - A local vector with values in the global basis

    638:   Output Parameters:
    639: . lv - A local vector with values in the local basis

    641:   Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user will have a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal.

    643:   Level: developer

    645: .seealso: DMPlexLocalToGlobalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation()
    646: @*/
    647: PetscErrorCode DMPlexGlobalToLocalBasis(DM dm, Vec lv)
    648: {

    654:   DMPlexBasisTransform_Internal(dm, lv, PETSC_FALSE);
    655:   return(0);
    656: }

    658: /*@
    659:   DMPlexLocalToGlobalBasis - Transform the values in the given local vector from the local basis to the global basis

    661:   Input Parameters:
    662: + dm - The DM
    663: - lv - A local vector with values in the local basis

    665:   Output Parameters:
    666: . lv - A local vector with values in the global basis

    668:   Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user would want a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal.

    670:   Level: developer

    672: .seealso: DMPlexGlobalToLocalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation()
    673: @*/
    674: PetscErrorCode DMPlexLocalToGlobalBasis(DM dm, Vec lv)
    675: {

    681:   DMPlexBasisTransform_Internal(dm, lv, PETSC_TRUE);
    682:   return(0);
    683: }

    685: /*@
    686:   DMPlexCreateBasisRotation - Create an internal transformation from the global basis, used to specify boundary conditions
    687:     and global solutions, to a local basis, appropriate for discretization integrals and assembly.

    689:   Input Parameters:
    690: + dm    - The DM
    691: . alpha - The first Euler angle, and in 2D the only one
    692: . beta  - The second Euler angle
    693: - gamma - The third Euler angle

    695:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
    696:   we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows:
    697:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
    698:   $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis.
    699:   $ The XYZ system rotates a third time about the z axis by gamma.

    701:   Level: developer

    703: .seealso: DMPlexGlobalToLocalBasis(), DMPlexLocalToGlobalBasis()
    704: @*/
    705: PetscErrorCode DMPlexCreateBasisRotation(DM dm, PetscReal alpha, PetscReal beta, PetscReal gamma)
    706: {
    707:   RotCtx        *rc;
    708:   PetscInt       cdim;

    711:   DMGetCoordinateDim(dm, &cdim);
    712:   PetscMalloc1(1, &rc);
    713:   dm->transformCtx       = rc;
    714:   dm->transformSetUp     = DMPlexBasisTransformSetUp_Rotation_Internal;
    715:   dm->transformDestroy   = DMPlexBasisTransformDestroy_Rotation_Internal;
    716:   dm->transformGetMatrix = DMPlexBasisTransformGetMatrix_Rotation_Internal;
    717:   rc->dim   = cdim;
    718:   rc->alpha = alpha;
    719:   rc->beta  = beta;
    720:   rc->gamma = gamma;
    721:   (*dm->transformSetUp)(dm, dm->transformCtx);
    722:   DMConstructBasisTransform_Internal(dm);
    723:   return(0);
    724: }

    726: /*@C
    727:   DMPlexInsertBoundaryValuesEssential - Insert boundary values into a local vector using a function of the coordinates

    729:   Input Parameters:
    730: + dm     - The DM, with a PetscDS that matches the problem being constrained
    731: . time   - The time
    732: . field  - The field to constrain
    733: . Nc     - The number of constrained field components, or 0 for all components
    734: . comps  - An array of constrained component numbers, or NULL for all components
    735: . label  - The DMLabel defining constrained points
    736: . numids - The number of DMLabel ids for constrained points
    737: . ids    - An array of ids for constrained points
    738: . func   - A pointwise function giving boundary values
    739: - ctx    - An optional user context for bcFunc

    741:   Output Parameter:
    742: . locX   - A local vector to receives the boundary values

    744:   Level: developer

    746: .seealso: DMPlexInsertBoundaryValuesEssentialField(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary()
    747: @*/
    748: PetscErrorCode DMPlexInsertBoundaryValuesEssential(DM dm, PetscReal time, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *), void *ctx, Vec locX)
    749: {
    750:   PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx);
    751:   void            **ctxs;
    752:   PetscInt          numFields;
    753:   PetscErrorCode    ierr;

    756:   DMGetNumFields(dm, &numFields);
    757:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
    758:   funcs[field] = func;
    759:   ctxs[field]  = ctx;
    760:   DMProjectFunctionLabelLocal(dm, time, label, numids, ids, Nc, comps, funcs, ctxs, INSERT_BC_VALUES, locX);
    761:   PetscFree2(funcs,ctxs);
    762:   return(0);
    763: }

    765: /*@C
    766:   DMPlexInsertBoundaryValuesEssentialField - Insert boundary values into a local vector using a function of the coordinates and field data

    768:   Input Parameters:
    769: + dm     - The DM, with a PetscDS that matches the problem being constrained
    770: . time   - The time
    771: . locU   - A local vector with the input solution values
    772: . field  - The field to constrain
    773: . Nc     - The number of constrained field components, or 0 for all components
    774: . comps  - An array of constrained component numbers, or NULL for all components
    775: . label  - The DMLabel defining constrained points
    776: . numids - The number of DMLabel ids for constrained points
    777: . ids    - An array of ids for constrained points
    778: . func   - A pointwise function giving boundary values
    779: - ctx    - An optional user context for bcFunc

    781:   Output Parameter:
    782: . locX   - A local vector to receives the boundary values

    784:   Level: developer

    786: .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary()
    787: @*/
    788: PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
    789:                                                         void (*func)(PetscInt, PetscInt, PetscInt,
    790:                                                                      const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    791:                                                                      const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    792:                                                                      PetscReal, const PetscReal[], PetscInt, const PetscScalar[],
    793:                                                                      PetscScalar[]),
    794:                                                         void *ctx, Vec locX)
    795: {
    796:   void (**funcs)(PetscInt, PetscInt, PetscInt,
    797:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    798:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    799:                  PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]);
    800:   void            **ctxs;
    801:   PetscInt          numFields;
    802:   PetscErrorCode    ierr;

    805:   DMGetNumFields(dm, &numFields);
    806:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
    807:   funcs[field] = func;
    808:   ctxs[field]  = ctx;
    809:   DMProjectFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);
    810:   PetscFree2(funcs,ctxs);
    811:   return(0);
    812: }

    814: /*@C
    815:   DMPlexInsertBoundaryValuesEssentialBdField - Insert boundary values into a local vector using a function of the coodinates and boundary field data

    817:   Collective on dm

    819:   Input Parameters:
    820: + dm     - The DM, with a PetscDS that matches the problem being constrained
    821: . time   - The time
    822: . locU   - A local vector with the input solution values
    823: . field  - The field to constrain
    824: . Nc     - The number of constrained field components, or 0 for all components
    825: . comps  - An array of constrained component numbers, or NULL for all components
    826: . label  - The DMLabel defining constrained points
    827: . numids - The number of DMLabel ids for constrained points
    828: . ids    - An array of ids for constrained points
    829: . func   - A pointwise function giving boundary values, the calling sequence is given in DMProjectBdFieldLabelLocal()
    830: - ctx    - An optional user context for bcFunc

    832:   Output Parameter:
    833: . locX   - A local vector to receive the boundary values

    835:   Level: developer

    837: .seealso: DMProjectBdFieldLabelLocal(), DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
    838: @*/
    839: PetscErrorCode DMPlexInsertBoundaryValuesEssentialBdField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
    840:                                                           void (*func)(PetscInt, PetscInt, PetscInt,
    841:                                                                        const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    842:                                                                        const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    843:                                                                        PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[],
    844:                                                                        PetscScalar[]),
    845:                                                           void *ctx, Vec locX)
    846: {
    847:   void (**funcs)(PetscInt, PetscInt, PetscInt,
    848:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    849:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    850:                  PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]);
    851:   void            **ctxs;
    852:   PetscInt          numFields;
    853:   PetscErrorCode    ierr;

    856:   DMGetNumFields(dm, &numFields);
    857:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
    858:   funcs[field] = func;
    859:   ctxs[field]  = ctx;
    860:   DMProjectBdFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);
    861:   PetscFree2(funcs,ctxs);
    862:   return(0);
    863: }

    865: /*@C
    866:   DMPlexInsertBoundaryValuesRiemann - Insert boundary values into a local vector

    868:   Input Parameters:
    869: + dm     - The DM, with a PetscDS that matches the problem being constrained
    870: . time   - The time
    871: . faceGeometry - A vector with the FVM face geometry information
    872: . cellGeometry - A vector with the FVM cell geometry information
    873: . Grad         - A vector with the FVM cell gradient information
    874: . field  - The field to constrain
    875: . Nc     - The number of constrained field components, or 0 for all components
    876: . comps  - An array of constrained component numbers, or NULL for all components
    877: . label  - The DMLabel defining constrained points
    878: . numids - The number of DMLabel ids for constrained points
    879: . ids    - An array of ids for constrained points
    880: . func   - A pointwise function giving boundary values
    881: - ctx    - An optional user context for bcFunc

    883:   Output Parameter:
    884: . locX   - A local vector to receives the boundary values

    886:   Note: This implementation currently ignores the numcomps/comps argument from DMAddBoundary()

    888:   Level: developer

    890: .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
    891: @*/
    892: PetscErrorCode DMPlexInsertBoundaryValuesRiemann(DM dm, PetscReal time, Vec faceGeometry, Vec cellGeometry, Vec Grad, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
    893:                                                  PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *ctx, Vec locX)
    894: {
    895:   PetscDS            prob;
    896:   PetscSF            sf;
    897:   DM                 dmFace, dmCell, dmGrad;
    898:   const PetscScalar *facegeom, *cellgeom = NULL, *grad;
    899:   const PetscInt    *leaves;
    900:   PetscScalar       *x, *fx;
    901:   PetscInt           dim, nleaves, loc, fStart, fEnd, pdim, i;
    902:   PetscErrorCode     ierr, ierru = 0;

    905:   DMGetPointSF(dm, &sf);
    906:   PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
    907:   nleaves = PetscMax(0, nleaves);
    908:   DMGetDimension(dm, &dim);
    909:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    910:   DMGetDS(dm, &prob);
    911:   VecGetDM(faceGeometry, &dmFace);
    912:   VecGetArrayRead(faceGeometry, &facegeom);
    913:   if (cellGeometry) {
    914:     VecGetDM(cellGeometry, &dmCell);
    915:     VecGetArrayRead(cellGeometry, &cellgeom);
    916:   }
    917:   if (Grad) {
    918:     PetscFV fv;

    920:     PetscDSGetDiscretization(prob, field, (PetscObject *) &fv);
    921:     VecGetDM(Grad, &dmGrad);
    922:     VecGetArrayRead(Grad, &grad);
    923:     PetscFVGetNumComponents(fv, &pdim);
    924:     DMGetWorkArray(dm, pdim, MPIU_SCALAR, &fx);
    925:   }
    926:   VecGetArray(locX, &x);
    927:   for (i = 0; i < numids; ++i) {
    928:     IS              faceIS;
    929:     const PetscInt *faces;
    930:     PetscInt        numFaces, f;

    932:     DMLabelGetStratumIS(label, ids[i], &faceIS);
    933:     if (!faceIS) continue; /* No points with that id on this process */
    934:     ISGetLocalSize(faceIS, &numFaces);
    935:     ISGetIndices(faceIS, &faces);
    936:     for (f = 0; f < numFaces; ++f) {
    937:       const PetscInt         face = faces[f], *cells;
    938:       PetscFVFaceGeom        *fg;

    940:       if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */
    941:       PetscFindInt(face, nleaves, (PetscInt *) leaves, &loc);
    942:       if (loc >= 0) continue;
    943:       DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
    944:       DMPlexGetSupport(dm, face, &cells);
    945:       if (Grad) {
    946:         PetscFVCellGeom       *cg;
    947:         PetscScalar           *cx, *cgrad;
    948:         PetscScalar           *xG;
    949:         PetscReal              dx[3];
    950:         PetscInt               d;

    952:         DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);
    953:         DMPlexPointLocalRead(dm, cells[0], x, &cx);
    954:         DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad);
    955:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
    956:         DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, fg->centroid, dx);
    957:         for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DMPlex_DotD_Internal(dim, &cgrad[d*dim], dx);
    958:         ierru = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx);
    959:         if (ierru) {
    960:           ISRestoreIndices(faceIS, &faces);
    961:           ISDestroy(&faceIS);
    962:           goto cleanup;
    963:         }
    964:       } else {
    965:         PetscScalar       *xI;
    966:         PetscScalar       *xG;

    968:         DMPlexPointLocalRead(dm, cells[0], x, &xI);
    969:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
    970:         ierru = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx);
    971:         if (ierru) {
    972:           ISRestoreIndices(faceIS, &faces);
    973:           ISDestroy(&faceIS);
    974:           goto cleanup;
    975:         }
    976:       }
    977:     }
    978:     ISRestoreIndices(faceIS, &faces);
    979:     ISDestroy(&faceIS);
    980:   }
    981:   cleanup:
    982:   VecRestoreArray(locX, &x);
    983:   if (Grad) {
    984:     DMRestoreWorkArray(dm, pdim, MPIU_SCALAR, &fx);
    985:     VecRestoreArrayRead(Grad, &grad);
    986:   }
    987:   if (cellGeometry) {VecRestoreArrayRead(cellGeometry, &cellgeom);}
    988:   VecRestoreArrayRead(faceGeometry, &facegeom);
    989:   CHKERRQ(ierru);
    990:   return(0);
    991: }

    993: static PetscErrorCode zero(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx)
    994: {
    995:   PetscInt c;
    996:   for (c = 0; c < Nc; ++c) u[c] = 0.0;
    997:   return 0;
    998: }

    1000: PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
    1001: {
    1002:   PetscObject    isZero;
    1003:   PetscDS        prob;
    1004:   PetscInt       numBd, b;

    1008:   DMGetDS(dm, &prob);
    1009:   PetscDSGetNumBoundary(prob, &numBd);
    1010:   PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);
    1011:   for (b = 0; b < numBd; ++b) {
    1012:     DMBoundaryConditionType type;
    1013:     const char             *name, *labelname;
    1014:     DMLabel                 label;
    1015:     PetscInt                field, Nc;
    1016:     const PetscInt         *comps;
    1017:     PetscObject             obj;
    1018:     PetscClassId            id;
    1019:     void                    (*func)(void);
    1020:     PetscInt                numids;
    1021:     const PetscInt         *ids;
    1022:     void                   *ctx;

    1024:     DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, &func, NULL, &numids, &ids, &ctx);
    1025:     if (insertEssential != (type & DM_BC_ESSENTIAL)) continue;
    1026:     DMGetLabel(dm, labelname, &label);
    1027:     if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name);
    1028:     DMGetField(dm, field, NULL, &obj);
    1029:     PetscObjectGetClassId(obj, &id);
    1030:     if (id == PETSCFE_CLASSID) {
    1031:       switch (type) {
    1032:         /* for FEM, there is no insertion to be done for non-essential boundary conditions */
    1033:       case DM_BC_ESSENTIAL:
    1034:         if (isZero) func = (void (*)(void)) zero;
    1035:         DMPlexLabelAddCells(dm,label);
    1036:         DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func, ctx, locX);
    1037:         DMPlexLabelClearCells(dm,label);
    1038:         break;
    1039:       case DM_BC_ESSENTIAL_FIELD:
    1040:         DMPlexLabelAddCells(dm,label);
    1041:         DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids,
    1042:                                                         (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    1043:                                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    1044:                                                                   PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func, ctx, locX);
    1045:         DMPlexLabelClearCells(dm,label);
    1046:         break;
    1047:       default: break;
    1048:       }
    1049:     } else if (id == PETSCFV_CLASSID) {
    1050:       if (!faceGeomFVM) continue;
    1051:       DMPlexInsertBoundaryValuesRiemann(dm, time, faceGeomFVM, cellGeomFVM, gradFVM, field, Nc, comps, label, numids, ids,
    1052:                                                (PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*)) func, ctx, locX);
    1053:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1054:   }
    1055:   return(0);
    1056: }

    1058: PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
    1059: {
    1060:   PetscObject    isZero;
    1061:   PetscDS        prob;
    1062:   PetscInt       numBd, b;

    1066:   if (!locX) return(0);
    1067:   DMGetDS(dm, &prob);
    1068:   PetscDSGetNumBoundary(prob, &numBd);
    1069:   PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);
    1070:   for (b = 0; b < numBd; ++b) {
    1071:     DMBoundaryConditionType type;
    1072:     const char             *name, *labelname;
    1073:     DMLabel                 label;
    1074:     PetscInt                field, Nc;
    1075:     const PetscInt         *comps;
    1076:     PetscObject             obj;
    1077:     PetscClassId            id;
    1078:     void                    (*func_t)(void);
    1079:     PetscInt                numids;
    1080:     const PetscInt         *ids;
    1081:     void                   *ctx;

    1083:     DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, NULL, &func_t, &numids, &ids, &ctx);
    1084:     if (!func_t) continue;
    1085:     if (insertEssential != (type & DM_BC_ESSENTIAL)) continue;
    1086:     DMGetLabel(dm, labelname, &label);
    1087:     if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name);
    1088:     DMGetField(dm, field, NULL, &obj);
    1089:     PetscObjectGetClassId(obj, &id);
    1090:     if (id == PETSCFE_CLASSID) {
    1091:       switch (type) {
    1092:         /* for FEM, there is no insertion to be done for non-essential boundary conditions */
    1093:       case DM_BC_ESSENTIAL:
    1094:         if (isZero) func_t = (void (*)(void)) zero;
    1095:         DMPlexLabelAddCells(dm,label);
    1096:         DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func_t, ctx, locX);
    1097:         DMPlexLabelClearCells(dm,label);
    1098:         break;
    1099:       case DM_BC_ESSENTIAL_FIELD:
    1100:         DMPlexLabelAddCells(dm,label);
    1101:         DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids,
    1102:                                                         (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    1103:                                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    1104:                                                                   PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func_t, ctx, locX);
    1105:         DMPlexLabelClearCells(dm,label);
    1106:         break;
    1107:       default: break;
    1108:       }
    1109:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1110:   }
    1111:   return(0);
    1112: }

    1114: /*@
    1115:   DMPlexInsertBoundaryValues - Puts coefficients which represent boundary values into the local solution vector

    1117:   Input Parameters:
    1118: + dm - The DM
    1119: . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions
    1120: . time - The time
    1121: . faceGeomFVM - Face geometry data for FV discretizations
    1122: . cellGeomFVM - Cell geometry data for FV discretizations
    1123: - gradFVM - Gradient reconstruction data for FV discretizations

    1125:   Output Parameters:
    1126: . locX - Solution updated with boundary values

    1128:   Level: developer

    1130: .seealso: DMProjectFunctionLabelLocal()
    1131: @*/
    1132: PetscErrorCode DMPlexInsertBoundaryValues(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
    1133: {

    1142:   PetscTryMethod(dm,"DMPlexInsertBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX,time,faceGeomFVM,cellGeomFVM,gradFVM));
    1143:   return(0);
    1144: }

    1146: /*@
    1147:   DMPlexInsertTimeDerivativeBoundaryValues - Puts coefficients which represent boundary values of the time derviative into the local solution vector

    1149:   Input Parameters:
    1150: + dm - The DM
    1151: . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions
    1152: . time - The time
    1153: . faceGeomFVM - Face geometry data for FV discretizations
    1154: . cellGeomFVM - Cell geometry data for FV discretizations
    1155: - gradFVM - Gradient reconstruction data for FV discretizations

    1157:   Output Parameters:
    1158: . locX_t - Solution updated with boundary values

    1160:   Level: developer

    1162: .seealso: DMProjectFunctionLabelLocal()
    1163: @*/
    1164: PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues(DM dm, PetscBool insertEssential, Vec locX_t, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
    1165: {

    1174:   PetscTryMethod(dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX_t,time,faceGeomFVM,cellGeomFVM,gradFVM));
    1175:   return(0);
    1176: }

    1178: PetscErrorCode DMComputeL2Diff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
    1179: {
    1180:   Vec              localX;
    1181:   PetscErrorCode   ierr;

    1184:   DMGetLocalVector(dm, &localX);
    1185:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, localX, time, NULL, NULL, NULL);
    1186:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
    1187:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
    1188:   DMPlexComputeL2DiffLocal(dm, time, funcs, ctxs, localX, diff);
    1189:   DMRestoreLocalVector(dm, &localX);
    1190:   return(0);
    1191: }

    1193: /*@C
    1194:   DMComputeL2DiffLocal - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.

    1196:   Collective on dm

    1198:   Input Parameters:
    1199: + dm     - The DM
    1200: . time   - The time
    1201: . funcs  - The functions to evaluate for each field component
    1202: . ctxs   - Optional array of contexts to pass to each function, or NULL.
    1203: - localX - The coefficient vector u_h, a local vector

    1205:   Output Parameter:
    1206: . diff - The diff ||u - u_h||_2

    1208:   Level: developer

    1210: .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff()
    1211: @*/
    1212: PetscErrorCode DMPlexComputeL2DiffLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec localX, PetscReal *diff)
    1213: {
    1214:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
    1215:   DM               tdm;
    1216:   Vec              tv;
    1217:   PetscSection     section;
    1218:   PetscQuadrature  quad;
    1219:   PetscFEGeom      fegeom;
    1220:   PetscScalar     *funcVal, *interpolant;
    1221:   PetscReal       *coords, *gcoords;
    1222:   PetscReal        localDiff = 0.0;
    1223:   const PetscReal *quadWeights;
    1224:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cellHeight, cStart, cEnd, c, field, fieldOffset;
    1225:   PetscBool        transform;
    1226:   PetscErrorCode   ierr;

    1229:   DMGetDimension(dm, &dim);
    1230:   DMGetCoordinateDim(dm, &coordDim);
    1231:   fegeom.dimEmbed = coordDim;
    1232:   DMGetLocalSection(dm, &section);
    1233:   PetscSectionGetNumFields(section, &numFields);
    1234:   DMGetBasisTransformDM_Internal(dm, &tdm);
    1235:   DMGetBasisTransformVec_Internal(dm, &tv);
    1236:   DMHasBasisTransform(dm, &transform);
    1237:   for (field = 0; field < numFields; ++field) {
    1238:     PetscObject  obj;
    1239:     PetscClassId id;
    1240:     PetscInt     Nc;

    1242:     DMGetField(dm, field, NULL, &obj);
    1243:     PetscObjectGetClassId(obj, &id);
    1244:     if (id == PETSCFE_CLASSID) {
    1245:       PetscFE fe = (PetscFE) obj;

    1247:       PetscFEGetQuadrature(fe, &quad);
    1248:       PetscFEGetNumComponents(fe, &Nc);
    1249:     } else if (id == PETSCFV_CLASSID) {
    1250:       PetscFV fv = (PetscFV) obj;

    1252:       PetscFVGetQuadrature(fv, &quad);
    1253:       PetscFVGetNumComponents(fv, &Nc);
    1254:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1255:     numComponents += Nc;
    1256:   }
    1257:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
    1258:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
    1259:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
    1260:   DMPlexGetVTKCellHeight(dm, &cellHeight);
    1261:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
    1262:   for (c = cStart; c < cEnd; ++c) {
    1263:     PetscScalar *x = NULL;
    1264:     PetscReal    elemDiff = 0.0;
    1265:     PetscInt     qc = 0;

    1267:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1268:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

    1270:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
    1271:       PetscObject  obj;
    1272:       PetscClassId id;
    1273:       void * const ctx = ctxs ? ctxs[field] : NULL;
    1274:       PetscInt     Nb, Nc, q, fc;

    1276:       DMGetField(dm, field, NULL, &obj);
    1277:       PetscObjectGetClassId(obj, &id);
    1278:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
    1279:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
    1280:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1281:       if (debug) {
    1282:         char title[1024];
    1283:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
    1284:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
    1285:       }
    1286:       for (q = 0; q < Nq; ++q) {
    1287:         PetscFEGeom qgeom;

    1289:         qgeom.dimEmbed = fegeom.dimEmbed;
    1290:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
    1291:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
    1292:         qgeom.detJ     = &fegeom.detJ[q];
    1293:         if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, point %D", (double)fegeom.detJ[q], c, q);
    1294:         if (transform) {
    1295:           gcoords = &coords[coordDim*Nq];
    1296:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
    1297:         } else {
    1298:           gcoords = &coords[coordDim*q];
    1299:         }
    1300:         (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx);
    1301:         if (ierr) {
    1302:           PetscErrorCode ierr2;
    1303:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
    1304:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
    1305:           ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
    1306:
    1307:         }
    1308:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
    1309:         if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
    1310:         else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
    1311:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1312:         for (fc = 0; fc < Nc; ++fc) {
    1313:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
    1314:           if (debug) {PetscPrintf(PETSC_COMM_SELF, "    elem %D field %D,%D point %g %g %g diff %g\n", c, field, fc, (double)(coordDim > 0 ? coords[coordDim*q] : 0.), (double)(coordDim > 1 ? coords[coordDim*q+1] : 0.),(double)(coordDim > 2 ? coords[coordDim*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
    1315:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
    1316:         }
    1317:       }
    1318:       fieldOffset += Nb;
    1319:       qc += Nc;
    1320:     }
    1321:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
    1322:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
    1323:     localDiff += elemDiff;
    1324:   }
    1325:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
    1326:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
    1327:   *diff = PetscSqrtReal(*diff);
    1328:   return(0);
    1329: }

    1331: PetscErrorCode DMComputeL2GradientDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff)
    1332: {
    1333:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
    1334:   DM               tdm;
    1335:   PetscSection     section;
    1336:   PetscQuadrature  quad;
    1337:   Vec              localX, tv;
    1338:   PetscScalar     *funcVal, *interpolant;
    1339:   const PetscReal *quadWeights;
    1340:   PetscFEGeom      fegeom;
    1341:   PetscReal       *coords, *gcoords;
    1342:   PetscReal        localDiff = 0.0;
    1343:   PetscInt         dim, coordDim, qNc = 0, Nq = 0, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset;
    1344:   PetscBool        transform;
    1345:   PetscErrorCode   ierr;

    1348:   DMGetDimension(dm, &dim);
    1349:   DMGetCoordinateDim(dm, &coordDim);
    1350:   fegeom.dimEmbed = coordDim;
    1351:   DMGetLocalSection(dm, &section);
    1352:   PetscSectionGetNumFields(section, &numFields);
    1353:   DMGetLocalVector(dm, &localX);
    1354:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
    1355:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
    1356:   DMGetBasisTransformDM_Internal(dm, &tdm);
    1357:   DMGetBasisTransformVec_Internal(dm, &tv);
    1358:   DMHasBasisTransform(dm, &transform);
    1359:   for (field = 0; field < numFields; ++field) {
    1360:     PetscFE  fe;
    1361:     PetscInt Nc;

    1363:     DMGetField(dm, field, NULL, (PetscObject *) &fe);
    1364:     PetscFEGetQuadrature(fe, &quad);
    1365:     PetscFEGetNumComponents(fe, &Nc);
    1366:     numComponents += Nc;
    1367:   }
    1368:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
    1369:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
    1370:   /* DMProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX); */
    1371:   PetscMalloc6(numComponents,&funcVal,coordDim*Nq,&coords,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ,numComponents*coordDim,&interpolant,Nq,&fegeom.detJ);
    1372:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
    1373:   for (c = cStart; c < cEnd; ++c) {
    1374:     PetscScalar *x = NULL;
    1375:     PetscReal    elemDiff = 0.0;
    1376:     PetscInt     qc = 0;

    1378:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1379:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

    1381:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
    1382:       PetscFE          fe;
    1383:       void * const     ctx = ctxs ? ctxs[field] : NULL;
    1384:       PetscInt         Nb, Nc, q, fc;

    1386:       DMGetField(dm, field, NULL, (PetscObject *) &fe);
    1387:       PetscFEGetDimension(fe, &Nb);
    1388:       PetscFEGetNumComponents(fe, &Nc);
    1389:       if (debug) {
    1390:         char title[1024];
    1391:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
    1392:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
    1393:       }
    1394:       for (q = 0; q < Nq; ++q) {
    1395:         PetscFEGeom qgeom;

    1397:         qgeom.dimEmbed = fegeom.dimEmbed;
    1398:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
    1399:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
    1400:         qgeom.detJ     = &fegeom.detJ[q];
    1401:         if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q);
    1402:         if (transform) {
    1403:           gcoords = &coords[coordDim*Nq];
    1404:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
    1405:         } else {
    1406:           gcoords = &coords[coordDim*q];
    1407:         }
    1408:         (*funcs[field])(coordDim, time, gcoords, n, Nc, funcVal, ctx);
    1409:         if (ierr) {
    1410:           PetscErrorCode ierr2;
    1411:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
    1412:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
    1413:           ierr2 = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr2);
    1414:
    1415:         }
    1416:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
    1417:         PetscFEInterpolateGradient_Static(fe, 1, &x[fieldOffset], &qgeom, q, interpolant);
    1418:         /* Overwrite with the dot product if the normal is given */
    1419:         if (n) {
    1420:           for (fc = 0; fc < Nc; ++fc) {
    1421:             PetscScalar sum = 0.0;
    1422:             PetscInt    d;
    1423:             for (d = 0; d < dim; ++d) sum += interpolant[fc*dim+d]*n[d];
    1424:             interpolant[fc] = sum;
    1425:           }
    1426:         }
    1427:         for (fc = 0; fc < Nc; ++fc) {
    1428:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
    1429:           if (debug) {PetscPrintf(PETSC_COMM_SELF, "    elem %D fieldDer %D,%D diff %g\n", c, field, fc, (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
    1430:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
    1431:         }
    1432:       }
    1433:       fieldOffset += Nb;
    1434:       qc          += Nc;
    1435:     }
    1436:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
    1437:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
    1438:     localDiff += elemDiff;
    1439:   }
    1440:   PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);
    1441:   DMRestoreLocalVector(dm, &localX);
    1442:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
    1443:   *diff = PetscSqrtReal(*diff);
    1444:   return(0);
    1445: }

    1447: PetscErrorCode DMComputeL2FieldDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
    1448: {
    1449:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
    1450:   DM               tdm;
    1451:   DMLabel          depthLabel;
    1452:   PetscSection     section;
    1453:   Vec              localX, tv;
    1454:   PetscReal       *localDiff;
    1455:   PetscInt         dim, depth, dE, Nf, f, Nds, s;
    1456:   PetscBool        transform;
    1457:   PetscErrorCode   ierr;

    1460:   DMGetDimension(dm, &dim);
    1461:   DMGetCoordinateDim(dm, &dE);
    1462:   DMGetLocalSection(dm, &section);
    1463:   DMGetLocalVector(dm, &localX);
    1464:   DMGetBasisTransformDM_Internal(dm, &tdm);
    1465:   DMGetBasisTransformVec_Internal(dm, &tv);
    1466:   DMHasBasisTransform(dm, &transform);
    1467:   DMGetNumFields(dm, &Nf);
    1468:   DMPlexGetDepthLabel(dm, &depthLabel);
    1469:   DMLabelGetNumValues(depthLabel, &depth);

    1471:   VecSet(localX, 0.0);
    1472:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
    1473:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
    1474:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
    1475:   DMGetNumDS(dm, &Nds);
    1476:   PetscCalloc1(Nf, &localDiff);
    1477:   for (s = 0; s < Nds; ++s) {
    1478:     PetscDS          ds;
    1479:     DMLabel          label;
    1480:     IS               fieldIS, pointIS;
    1481:     const PetscInt  *fields, *points = NULL;
    1482:     PetscQuadrature  quad;
    1483:     const PetscReal *quadPoints, *quadWeights;
    1484:     PetscFEGeom      fegeom;
    1485:     PetscReal       *coords, *gcoords;
    1486:     PetscScalar     *funcVal, *interpolant;
    1487:     PetscBool        isHybrid;
    1488:     PetscInt         qNc, Nq, totNc, cStart = 0, cEnd, c, dsNf;

    1490:     DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);
    1491:     ISGetIndices(fieldIS, &fields);
    1492:     PetscDSGetHybrid(ds, &isHybrid);
    1493:     PetscDSGetNumFields(ds, &dsNf);
    1494:     PetscDSGetTotalComponents(ds, &totNc);
    1495:     PetscDSGetQuadrature(ds, &quad);
    1496:     PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
    1497:     if ((qNc != 1) && (qNc != totNc)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, totNc);
    1498:     PetscCalloc6(totNc, &funcVal, totNc, &interpolant, dE*(Nq+1), &coords,Nq, &fegeom.detJ, dE*dE*Nq, &fegeom.J, dE*dE*Nq, &fegeom.invJ);
    1499:     if (!label) {
    1500:       DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
    1501:     } else {
    1502:       DMLabelGetStratumIS(label, 1, &pointIS);
    1503:       ISGetLocalSize(pointIS, &cEnd);
    1504:       ISGetIndices(pointIS, &points);
    1505:     }
    1506:     for (c = cStart; c < cEnd; ++c) {
    1507:       const PetscInt cell = points ? points[c] : c;
    1508:       PetscScalar   *x    = NULL;
    1509:       PetscInt       qc   = 0, fOff = 0, dep, fStart = isHybrid ? dsNf-1 : 0;

    1511:       DMLabelGetValue(depthLabel, cell, &dep);
    1512:       if (dep != depth-1) continue;
    1513:       if (isHybrid) {
    1514:         const PetscInt *cone;

    1516:         DMPlexGetCone(dm, cell, &cone);
    1517:         DMPlexComputeCellGeometryFEM(dm, cone[0], quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1518:       } else {
    1519:         DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1520:       }
    1521:       DMPlexVecGetClosure(dm, NULL, localX, cell, NULL, &x);
    1522:       for (f = fStart; f < dsNf; ++f) {
    1523:         PetscObject  obj;
    1524:         PetscClassId id;
    1525:         void * const ctx = ctxs ? ctxs[fields[f]] : NULL;
    1526:         PetscInt     Nb, Nc, q, fc;
    1527:         PetscReal    elemDiff = 0.0;

    1529:         PetscDSGetDiscretization(ds, f, &obj);
    1530:         PetscObjectGetClassId(obj, &id);
    1531:         if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
    1532:         else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
    1533:         else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]);
    1534:         if (debug) {
    1535:           char title[1024];
    1536:           PetscSNPrintf(title, 1023, "Solution for Field %D", fields[f]);
    1537:           DMPrintCellVector(cell, title, Nb, &x[fOff]);
    1538:         }
    1539:         for (q = 0; q < Nq; ++q) {
    1540:           PetscFEGeom qgeom;

    1542:           qgeom.dimEmbed = fegeom.dimEmbed;
    1543:           qgeom.J        = &fegeom.J[q*dE*dE];
    1544:           qgeom.invJ     = &fegeom.invJ[q*dE*dE];
    1545:           qgeom.detJ     = &fegeom.detJ[q];
    1546:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for cell %D, quadrature point %D", (double)fegeom.detJ[q], cell, q);
    1547:           if (transform) {
    1548:             gcoords = &coords[dE*Nq];
    1549:             DMPlexBasisTransformApplyReal_Internal(dm, &coords[dE*q], PETSC_TRUE, dE, &coords[dE*q], gcoords, dm->transformCtx);
    1550:           } else {
    1551:             gcoords = &coords[dE*q];
    1552:           }
    1553:           (*funcs[fields[f]])(dE, time, gcoords, Nc, funcVal, ctx);
    1554:           if (ierr) {
    1555:             PetscErrorCode ierr2;
    1556:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);CHKERRQ(ierr2);
    1557:             ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
    1558:             ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
    1559:
    1560:           }
    1561:           if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[dE*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
    1562:           /* Call once for each face, except for lagrange field */
    1563:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fOff], &qgeom, q, interpolant);}
    1564:           else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fOff], q, interpolant);}
    1565:           else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]);
    1566:           for (fc = 0; fc < Nc; ++fc) {
    1567:             const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
    1568:             if (debug) {PetscPrintf(PETSC_COMM_SELF, "    cell %D field %D,%D point %g %g %g diff %g\n", cell, fields[f], fc, (double)(dE > 0 ? coords[dE*q] : 0.), (double)(dE > 1 ? coords[dE*q+1] : 0.),(double)(dE > 2 ? coords[dE*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
    1569:             elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
    1570:           }
    1571:         }
    1572:         fOff += Nb;
    1573:         qc   += Nc;
    1574:         localDiff[fields[f]] += elemDiff;
    1575:         if (debug) {PetscPrintf(PETSC_COMM_SELF, "  cell %D field %D cum diff %g\n", cell, fields[f], (double)localDiff[fields[f]]);}
    1576:       }
    1577:       DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);
    1578:     }
    1579:     if (label) {
    1580:       ISRestoreIndices(pointIS, &points);
    1581:       ISDestroy(&pointIS);
    1582:     }
    1583:     ISRestoreIndices(fieldIS, &fields);
    1584:     PetscFree6(funcVal, interpolant, coords, fegeom.detJ, fegeom.J, fegeom.invJ);
    1585:   }
    1586:   DMRestoreLocalVector(dm, &localX);
    1587:   MPIU_Allreduce(localDiff, diff, Nf, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
    1588:   PetscFree(localDiff);
    1589:   for (f = 0; f < Nf; ++f) diff[f] = PetscSqrtReal(diff[f]);
    1590:   return(0);
    1591: }

    1593: /*@C
    1594:   DMPlexComputeL2DiffVec - This function computes the cellwise L_2 difference between a function u and an FEM interpolant solution u_h, and stores it in a Vec.

    1596:   Collective on dm

    1598:   Input Parameters:
    1599: + dm    - The DM
    1600: . time  - The time
    1601: . funcs - The functions to evaluate for each field component: NULL means that component does not contribute to error calculation
    1602: . ctxs  - Optional array of contexts to pass to each function, or NULL.
    1603: - X     - The coefficient vector u_h

    1605:   Output Parameter:
    1606: . D - A Vec which holds the difference ||u - u_h||_2 for each cell

    1608:   Level: developer

    1610: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
    1611: @*/
    1612: PetscErrorCode DMPlexComputeL2DiffVec(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, Vec D)
    1613: {
    1614:   PetscSection     section;
    1615:   PetscQuadrature  quad;
    1616:   Vec              localX;
    1617:   PetscFEGeom      fegeom;
    1618:   PetscScalar     *funcVal, *interpolant;
    1619:   PetscReal       *coords;
    1620:   const PetscReal *quadPoints, *quadWeights;
    1621:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset;
    1622:   PetscErrorCode   ierr;

    1625:   VecSet(D, 0.0);
    1626:   DMGetDimension(dm, &dim);
    1627:   DMGetCoordinateDim(dm, &coordDim);
    1628:   DMGetLocalSection(dm, &section);
    1629:   PetscSectionGetNumFields(section, &numFields);
    1630:   DMGetLocalVector(dm, &localX);
    1631:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
    1632:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
    1633:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
    1634:   for (field = 0; field < numFields; ++field) {
    1635:     PetscObject  obj;
    1636:     PetscClassId id;
    1637:     PetscInt     Nc;

    1639:     DMGetField(dm, field, NULL, &obj);
    1640:     PetscObjectGetClassId(obj, &id);
    1641:     if (id == PETSCFE_CLASSID) {
    1642:       PetscFE fe = (PetscFE) obj;

    1644:       PetscFEGetQuadrature(fe, &quad);
    1645:       PetscFEGetNumComponents(fe, &Nc);
    1646:     } else if (id == PETSCFV_CLASSID) {
    1647:       PetscFV fv = (PetscFV) obj;

    1649:       PetscFVGetQuadrature(fv, &quad);
    1650:       PetscFVGetNumComponents(fv, &Nc);
    1651:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1652:     numComponents += Nc;
    1653:   }
    1654:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
    1655:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
    1656:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
    1657:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
    1658:   for (c = cStart; c < cEnd; ++c) {
    1659:     PetscScalar *x = NULL;
    1660:     PetscScalar  elemDiff = 0.0;
    1661:     PetscInt     qc = 0;

    1663:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1664:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

    1666:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
    1667:       PetscObject  obj;
    1668:       PetscClassId id;
    1669:       void * const ctx = ctxs ? ctxs[field] : NULL;
    1670:       PetscInt     Nb, Nc, q, fc;

    1672:       DMGetField(dm, field, NULL, &obj);
    1673:       PetscObjectGetClassId(obj, &id);
    1674:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
    1675:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
    1676:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1677:       if (funcs[field]) {
    1678:         for (q = 0; q < Nq; ++q) {
    1679:           PetscFEGeom qgeom;

    1681:           qgeom.dimEmbed = fegeom.dimEmbed;
    1682:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
    1683:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
    1684:           qgeom.detJ     = &fegeom.detJ[q];
    1685:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q);
    1686:           (*funcs[field])(coordDim, time, &coords[q*coordDim], Nc, funcVal, ctx);
    1687:           if (ierr) {
    1688:             PetscErrorCode ierr2;
    1689:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
    1690:             ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
    1691:             ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
    1692:
    1693:           }
    1694:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
    1695:           else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
    1696:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1697:           for (fc = 0; fc < Nc; ++fc) {
    1698:             const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
    1699:             elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
    1700:           }
    1701:         }
    1702:       }
    1703:       fieldOffset += Nb;
    1704:       qc          += Nc;
    1705:     }
    1706:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
    1707:     VecSetValue(D, c - cStart, elemDiff, INSERT_VALUES);
    1708:   }
    1709:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
    1710:   DMRestoreLocalVector(dm, &localX);
    1711:   VecSqrtAbs(D);
    1712:   return(0);
    1713: }

    1715: /*@C
    1716:   DMPlexComputeGradientClementInterpolant - This function computes the L2 projection of the cellwise gradient of a function u onto P1, and stores it in a Vec.

    1718:   Collective on dm

    1720:   Input Parameters:
    1721: + dm - The DM
    1722: - LocX  - The coefficient vector u_h

    1724:   Output Parameter:
    1725: . locC - A Vec which holds the Clement interpolant of the gradient

    1727:   Notes:
    1728:     Add citation to (Clement, 1975) and definition of the interpolant
    1729:   \nabla u_h(v_i) = \sum_{T_i \in support(v_i)} |T_i| \nabla u_h(T_i) / \sum_{T_i \in support(v_i)} |T_i| where |T_i| is the cell volume

    1731:   Level: developer

    1733: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
    1734: @*/
    1735: PetscErrorCode DMPlexComputeGradientClementInterpolant(DM dm, Vec locX, Vec locC)
    1736: {
    1737:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
    1738:   PetscInt         debug = mesh->printFEM;
    1739:   DM               dmC;
    1740:   PetscSection     section;
    1741:   PetscQuadrature  quad;
    1742:   PetscScalar     *interpolant, *gradsum;
    1743:   PetscFEGeom      fegeom;
    1744:   PetscReal       *coords;
    1745:   const PetscReal *quadPoints, *quadWeights;
    1746:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, vStart, vEnd, v, field, fieldOffset;
    1747:   PetscErrorCode   ierr;

    1750:   VecGetDM(locC, &dmC);
    1751:   VecSet(locC, 0.0);
    1752:   DMGetDimension(dm, &dim);
    1753:   DMGetCoordinateDim(dm, &coordDim);
    1754:   fegeom.dimEmbed = coordDim;
    1755:   DMGetLocalSection(dm, &section);
    1756:   PetscSectionGetNumFields(section, &numFields);
    1757:   for (field = 0; field < numFields; ++field) {
    1758:     PetscObject  obj;
    1759:     PetscClassId id;
    1760:     PetscInt     Nc;

    1762:     DMGetField(dm, field, NULL, &obj);
    1763:     PetscObjectGetClassId(obj, &id);
    1764:     if (id == PETSCFE_CLASSID) {
    1765:       PetscFE fe = (PetscFE) obj;

    1767:       PetscFEGetQuadrature(fe, &quad);
    1768:       PetscFEGetNumComponents(fe, &Nc);
    1769:     } else if (id == PETSCFV_CLASSID) {
    1770:       PetscFV fv = (PetscFV) obj;

    1772:       PetscFVGetQuadrature(fv, &quad);
    1773:       PetscFVGetNumComponents(fv, &Nc);
    1774:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1775:     numComponents += Nc;
    1776:   }
    1777:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
    1778:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
    1779:   PetscMalloc6(coordDim*numComponents*2,&gradsum,coordDim*numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
    1780:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
    1781:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
    1782:   for (v = vStart; v < vEnd; ++v) {
    1783:     PetscScalar volsum = 0.0;
    1784:     PetscInt   *star = NULL;
    1785:     PetscInt    starSize, st, d, fc;

    1787:     PetscArrayzero(gradsum, coordDim*numComponents);
    1788:     DMPlexGetTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
    1789:     for (st = 0; st < starSize*2; st += 2) {
    1790:       const PetscInt cell = star[st];
    1791:       PetscScalar   *grad = &gradsum[coordDim*numComponents];
    1792:       PetscScalar   *x    = NULL;
    1793:       PetscReal      vol  = 0.0;

    1795:       if ((cell < cStart) || (cell >= cEnd)) continue;
    1796:       DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
    1797:       DMPlexVecGetClosure(dm, NULL, locX, cell, NULL, &x);
    1798:       for (field = 0, fieldOffset = 0; field < numFields; ++field) {
    1799:         PetscObject  obj;
    1800:         PetscClassId id;
    1801:         PetscInt     Nb, Nc, q, qc = 0;

    1803:         PetscArrayzero(grad, coordDim*numComponents);
    1804:         DMGetField(dm, field, NULL, &obj);
    1805:         PetscObjectGetClassId(obj, &id);
    1806:         if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
    1807:         else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
    1808:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1809:         for (q = 0; q < Nq; ++q) {
    1810:           PetscFEGeom qgeom;

    1812:           qgeom.dimEmbed = fegeom.dimEmbed;
    1813:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
    1814:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
    1815:           qgeom.detJ     = &fegeom.detJ[q];
    1816:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], cell, q);
    1817:           if (ierr) {
    1818:             PetscErrorCode ierr2;
    1819:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr2);
    1820:             ierr2 = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr2);
    1821:             ierr2 = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
    1822:
    1823:           }
    1824:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolateGradient_Static((PetscFE) obj, 1, &x[fieldOffset], &qgeom, q, interpolant);}
    1825:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
    1826:           for (fc = 0; fc < Nc; ++fc) {
    1827:             const PetscReal wt = quadWeights[q*qNc+qc+fc];

    1829:             for (d = 0; d < coordDim; ++d) grad[fc*coordDim+d] += interpolant[fc*dim+d]*wt*fegeom.detJ[q];
    1830:           }
    1831:           vol += quadWeights[q*qNc]*fegeom.detJ[q];
    1832:         }
    1833:         fieldOffset += Nb;
    1834:         qc          += Nc;
    1835:       }
    1836:       DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);
    1837:       for (fc = 0; fc < numComponents; ++fc) {
    1838:         for (d = 0; d < coordDim; ++d) {
    1839:           gradsum[fc*coordDim+d] += grad[fc*coordDim+d];
    1840:         }
    1841:       }
    1842:       volsum += vol;
    1843:       if (debug) {
    1844:         PetscPrintf(PETSC_COMM_SELF, "Cell %D gradient: [", cell);
    1845:         for (fc = 0; fc < numComponents; ++fc) {
    1846:           for (d = 0; d < coordDim; ++d) {
    1847:             if (fc || d > 0) {PetscPrintf(PETSC_COMM_SELF, ", ");}
    1848:             PetscPrintf(PETSC_COMM_SELF, "%g", (double)PetscRealPart(grad[fc*coordDim+d]));
    1849:           }
    1850:         }
    1851:         PetscPrintf(PETSC_COMM_SELF, "]\n");
    1852:       }
    1853:     }
    1854:     for (fc = 0; fc < numComponents; ++fc) {
    1855:       for (d = 0; d < coordDim; ++d) gradsum[fc*coordDim+d] /= volsum;
    1856:     }
    1857:     DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
    1858:     DMPlexVecSetClosure(dmC, NULL, locC, v, gradsum, INSERT_VALUES);
    1859:   }
    1860:   PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
    1861:   return(0);
    1862: }

    1864: static PetscErrorCode DMPlexComputeIntegral_Internal(DM dm, Vec X, PetscInt cStart, PetscInt cEnd, PetscScalar *cintegral, void *user)
    1865: {
    1866:   DM                 dmAux = NULL;
    1867:   PetscDS            prob,    probAux = NULL;
    1868:   PetscSection       section, sectionAux;
    1869:   Vec                locX,    locA;
    1870:   PetscInt           dim, numCells = cEnd - cStart, c, f;
    1871:   PetscBool          useFVM = PETSC_FALSE;
    1872:   /* DS */
    1873:   PetscInt           Nf,    totDim,    *uOff, *uOff_x, numConstants;
    1874:   PetscInt           NfAux, totDimAux, *aOff;
    1875:   PetscScalar       *u, *a;
    1876:   const PetscScalar *constants;
    1877:   /* Geometry */
    1878:   PetscFEGeom       *cgeomFEM;
    1879:   DM                 dmGrad;
    1880:   PetscQuadrature    affineQuad = NULL;
    1881:   Vec                cellGeometryFVM = NULL, faceGeometryFVM = NULL, locGrad = NULL;
    1882:   PetscFVCellGeom   *cgeomFVM;
    1883:   const PetscScalar *lgrad;
    1884:   PetscInt           maxDegree;
    1885:   DMField            coordField;
    1886:   IS                 cellIS;
    1887:   PetscErrorCode     ierr;

    1890:   DMGetDS(dm, &prob);
    1891:   DMGetDimension(dm, &dim);
    1892:   DMGetLocalSection(dm, &section);
    1893:   PetscSectionGetNumFields(section, &Nf);
    1894:   /* Determine which discretizations we have */
    1895:   for (f = 0; f < Nf; ++f) {
    1896:     PetscObject  obj;
    1897:     PetscClassId id;

    1899:     PetscDSGetDiscretization(prob, f, &obj);
    1900:     PetscObjectGetClassId(obj, &id);
    1901:     if (id == PETSCFV_CLASSID) useFVM = PETSC_TRUE;
    1902:   }
    1903:   /* Get local solution with boundary values */
    1904:   DMGetLocalVector(dm, &locX);
    1905:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
    1906:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
    1907:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
    1908:   /* Read DS information */
    1909:   PetscDSGetTotalDimension(prob, &totDim);
    1910:   PetscDSGetComponentOffsets(prob, &uOff);
    1911:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
    1912:   ISCreateStride(PETSC_COMM_SELF,numCells,cStart,1,&cellIS);
    1913:   PetscDSGetConstants(prob, &numConstants, &constants);
    1914:   /* Read Auxiliary DS information */
    1915:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
    1916:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    1917:   if (dmAux) {
    1918:     DMGetDS(dmAux, &probAux);
    1919:     PetscDSGetNumFields(probAux, &NfAux);
    1920:     DMGetLocalSection(dmAux, &sectionAux);
    1921:     PetscDSGetTotalDimension(probAux, &totDimAux);
    1922:     PetscDSGetComponentOffsets(probAux, &aOff);
    1923:   }
    1924:   /* Allocate data  arrays */
    1925:   PetscCalloc1(numCells*totDim, &u);
    1926:   if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
    1927:   /* Read out geometry */
    1928:   DMGetCoordinateField(dm,&coordField);
    1929:   DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
    1930:   if (maxDegree <= 1) {
    1931:     DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
    1932:     if (affineQuad) {
    1933:       DMFieldCreateFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&cgeomFEM);
    1934:     }
    1935:   }
    1936:   if (useFVM) {
    1937:     PetscFV   fv = NULL;
    1938:     Vec       grad;
    1939:     PetscInt  fStart, fEnd;
    1940:     PetscBool compGrad;

    1942:     for (f = 0; f < Nf; ++f) {
    1943:       PetscObject  obj;
    1944:       PetscClassId id;

    1946:       PetscDSGetDiscretization(prob, f, &obj);
    1947:       PetscObjectGetClassId(obj, &id);
    1948:       if (id == PETSCFV_CLASSID) {fv = (PetscFV) obj; break;}
    1949:     }
    1950:     PetscFVGetComputeGradients(fv, &compGrad);
    1951:     PetscFVSetComputeGradients(fv, PETSC_TRUE);
    1952:     DMPlexComputeGeometryFVM(dm, &cellGeometryFVM, &faceGeometryFVM);
    1953:     DMPlexComputeGradientFVM(dm, fv, faceGeometryFVM, cellGeometryFVM, &dmGrad);
    1954:     PetscFVSetComputeGradients(fv, compGrad);
    1955:     VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
    1956:     /* Reconstruct and limit cell gradients */
    1957:     DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    1958:     DMGetGlobalVector(dmGrad, &grad);
    1959:     DMPlexReconstructGradients_Internal(dm, fv, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
    1960:     /* Communicate gradient values */
    1961:     DMGetLocalVector(dmGrad, &locGrad);
    1962:     DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
    1963:     DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
    1964:     DMRestoreGlobalVector(dmGrad, &grad);
    1965:     /* Handle non-essential (e.g. outflow) boundary values */
    1966:     DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, 0.0, faceGeometryFVM, cellGeometryFVM, locGrad);
    1967:     VecGetArrayRead(locGrad, &lgrad);
    1968:   }
    1969:   /* Read out data from inputs */
    1970:   for (c = cStart; c < cEnd; ++c) {
    1971:     PetscScalar *x = NULL;
    1972:     PetscInt     i;

    1974:     DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);
    1975:     for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
    1976:     DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);
    1977:     if (dmAux) {
    1978:       DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);
    1979:       for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
    1980:       DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);
    1981:     }
    1982:   }
    1983:   /* Do integration for each field */
    1984:   for (f = 0; f < Nf; ++f) {
    1985:     PetscObject  obj;
    1986:     PetscClassId id;
    1987:     PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

    1989:     PetscDSGetDiscretization(prob, f, &obj);
    1990:     PetscObjectGetClassId(obj, &id);
    1991:     if (id == PETSCFE_CLASSID) {
    1992:       PetscFE         fe = (PetscFE) obj;
    1993:       PetscQuadrature q;
    1994:       PetscFEGeom     *chunkGeom = NULL;
    1995:       PetscInt        Nq, Nb;

    1997:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    1998:       PetscFEGetQuadrature(fe, &q);
    1999:       PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
    2000:       PetscFEGetDimension(fe, &Nb);
    2001:       blockSize = Nb*Nq;
    2002:       batchSize = numBlocks * blockSize;
    2003:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    2004:       numChunks = numCells / (numBatches*batchSize);
    2005:       Ne        = numChunks*numBatches*batchSize;
    2006:       Nr        = numCells % (numBatches*batchSize);
    2007:       offset    = numCells - Nr;
    2008:       if (!affineQuad) {
    2009:         DMFieldCreateFEGeom(coordField,cellIS,q,PETSC_FALSE,&cgeomFEM);
    2010:       }
    2011:       PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
    2012:       PetscFEIntegrate(prob, f, Ne, chunkGeom, u, probAux, a, cintegral);
    2013:       PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);
    2014:       PetscFEIntegrate(prob, f, Nr, chunkGeom, &u[offset*totDim], probAux, &a[offset*totDimAux], &cintegral[offset*Nf]);
    2015:       PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);
    2016:       if (!affineQuad) {
    2017:         PetscFEGeomDestroy(&cgeomFEM);
    2018:       }
    2019:     } else if (id == PETSCFV_CLASSID) {
    2020:       PetscInt       foff;
    2021:       PetscPointFunc obj_func;
    2022:       PetscScalar    lint;

    2024:       PetscDSGetObjective(prob, f, &obj_func);
    2025:       PetscDSGetFieldOffset(prob, f, &foff);
    2026:       if (obj_func) {
    2027:         for (c = 0; c < numCells; ++c) {
    2028:           PetscScalar *u_x;

    2030:           DMPlexPointLocalRead(dmGrad, c, lgrad, &u_x);
    2031:           obj_func(dim, Nf, NfAux, uOff, uOff_x, &u[totDim*c+foff], NULL, u_x, aOff, NULL, &a[totDimAux*c], NULL, NULL, 0.0, cgeomFVM[c].centroid, numConstants, constants, &lint);
    2032:           cintegral[c*Nf+f] += PetscRealPart(lint)*cgeomFVM[c].volume;
    2033:         }
    2034:       }
    2035:     } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
    2036:   }
    2037:   /* Cleanup data arrays */
    2038:   if (useFVM) {
    2039:     VecRestoreArrayRead(locGrad, &lgrad);
    2040:     VecRestoreArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
    2041:     DMRestoreLocalVector(dmGrad, &locGrad);
    2042:     VecDestroy(&faceGeometryFVM);
    2043:     VecDestroy(&cellGeometryFVM);
    2044:     DMDestroy(&dmGrad);
    2045:   }
    2046:   if (dmAux) {PetscFree(a);}
    2047:   PetscFree(u);
    2048:   /* Cleanup */
    2049:   if (affineQuad) {
    2050:     PetscFEGeomDestroy(&cgeomFEM);
    2051:   }
    2052:   PetscQuadratureDestroy(&affineQuad);
    2053:   ISDestroy(&cellIS);
    2054:   DMRestoreLocalVector(dm, &locX);
    2055:   return(0);
    2056: }

    2058: /*@
    2059:   DMPlexComputeIntegralFEM - Form the integral over the domain from the global input X using pointwise functions specified by the user

    2061:   Input Parameters:
    2062: + dm - The mesh
    2063: . X  - Global input vector
    2064: - user - The user context

    2066:   Output Parameter:
    2067: . integral - Integral for each field

    2069:   Level: developer

    2071: .seealso: DMPlexComputeResidualFEM()
    2072: @*/
    2073: PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscScalar *integral, void *user)
    2074: {
    2075:   DM_Plex       *mesh = (DM_Plex *) dm->data;
    2076:   PetscScalar   *cintegral, *lintegral;
    2077:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cell;

    2084:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
    2085:   DMGetNumFields(dm, &Nf);
    2086:   DMPlexGetVTKCellHeight(dm, &cellHeight);
    2087:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
    2088:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
    2089:   PetscCalloc2(Nf, &lintegral, (cEnd-cStart)*Nf, &cintegral);
    2090:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
    2091:   /* Sum up values */
    2092:   for (cell = cStart; cell < cEnd; ++cell) {
    2093:     const PetscInt c = cell - cStart;

    2095:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
    2096:     for (f = 0; f < Nf; ++f) lintegral[f] += cintegral[c*Nf+f];
    2097:   }
    2098:   MPIU_Allreduce(lintegral, integral, Nf, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject) dm));
    2099:   if (mesh->printFEM) {
    2100:     PetscPrintf(PetscObjectComm((PetscObject) dm), "Integral:");
    2101:     for (f = 0; f < Nf; ++f) {PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", (double) PetscRealPart(integral[f]));}
    2102:     PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");
    2103:   }
    2104:   PetscFree2(lintegral, cintegral);
    2105:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
    2106:   return(0);
    2107: }

    2109: /*@
    2110:   DMPlexComputeCellwiseIntegralFEM - Form the vector of cellwise integrals F from the global input X using pointwise functions specified by the user

    2112:   Input Parameters:
    2113: + dm - The mesh
    2114: . X  - Global input vector
    2115: - user - The user context

    2117:   Output Parameter:
    2118: . integral - Cellwise integrals for each field

    2120:   Level: developer

    2122: .seealso: DMPlexComputeResidualFEM()
    2123: @*/
    2124: PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM dm, Vec X, Vec F, void *user)
    2125: {
    2126:   DM_Plex       *mesh = (DM_Plex *) dm->data;
    2127:   DM             dmF;
    2128:   PetscSection   sectionF;
    2129:   PetscScalar   *cintegral, *af;
    2130:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cell;

    2137:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
    2138:   DMGetNumFields(dm, &Nf);
    2139:   DMPlexGetVTKCellHeight(dm, &cellHeight);
    2140:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
    2141:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
    2142:   PetscCalloc1((cEnd-cStart)*Nf, &cintegral);
    2143:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
    2144:   /* Put values in F*/
    2145:   VecGetDM(F, &dmF);
    2146:   DMGetLocalSection(dmF, &sectionF);
    2147:   VecGetArray(F, &af);
    2148:   for (cell = cStart; cell < cEnd; ++cell) {
    2149:     const PetscInt c = cell - cStart;
    2150:     PetscInt       dof, off;

    2152:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
    2153:     PetscSectionGetDof(sectionF, cell, &dof);
    2154:     PetscSectionGetOffset(sectionF, cell, &off);
    2155:     if (dof != Nf) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of cell dofs %D != %D", dof, Nf);
    2156:     for (f = 0; f < Nf; ++f) af[off+f] = cintegral[c*Nf+f];
    2157:   }
    2158:   VecRestoreArray(F, &af);
    2159:   PetscFree(cintegral);
    2160:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
    2161:   return(0);
    2162: }

    2164: static PetscErrorCode DMPlexComputeBdIntegral_Internal(DM dm, Vec locX, IS pointIS,
    2165:                                                        void (*func)(PetscInt, PetscInt, PetscInt,
    2166:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    2167:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    2168:                                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
    2169:                                                        PetscScalar *fintegral, void *user)
    2170: {
    2171:   DM                 plex = NULL, plexA = NULL;
    2172:   DMEnclosureType    encAux;
    2173:   PetscDS            prob, probAux = NULL;
    2174:   PetscSection       section, sectionAux = NULL;
    2175:   Vec                locA = NULL;
    2176:   DMField            coordField;
    2177:   PetscInt           Nf,        totDim,        *uOff, *uOff_x;
    2178:   PetscInt           NfAux = 0, totDimAux = 0, *aOff = NULL;
    2179:   PetscScalar       *u, *a = NULL;
    2180:   const PetscScalar *constants;
    2181:   PetscInt           numConstants, f;
    2182:   PetscErrorCode     ierr;

    2185:   DMGetCoordinateField(dm, &coordField);
    2186:   DMConvert(dm, DMPLEX, &plex);
    2187:   DMGetDS(dm, &prob);
    2188:   DMGetLocalSection(dm, &section);
    2189:   PetscSectionGetNumFields(section, &Nf);
    2190:   /* Determine which discretizations we have */
    2191:   for (f = 0; f < Nf; ++f) {
    2192:     PetscObject  obj;
    2193:     PetscClassId id;

    2195:     PetscDSGetDiscretization(prob, f, &obj);
    2196:     PetscObjectGetClassId(obj, &id);
    2197:     if (id == PETSCFV_CLASSID) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Not supported for FVM (field %D)", f);
    2198:   }
    2199:   /* Read DS information */
    2200:   PetscDSGetTotalDimension(prob, &totDim);
    2201:   PetscDSGetComponentOffsets(prob, &uOff);
    2202:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
    2203:   PetscDSGetConstants(prob, &numConstants, &constants);
    2204:   /* Read Auxiliary DS information */
    2205:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    2206:   if (locA) {
    2207:     DM dmAux;

    2209:     VecGetDM(locA, &dmAux);
    2210:     DMGetEnclosureRelation(dmAux, dm, &encAux);
    2211:     DMConvert(dmAux, DMPLEX, &plexA);
    2212:     DMGetDS(dmAux, &probAux);
    2213:     PetscDSGetNumFields(probAux, &NfAux);
    2214:     DMGetLocalSection(dmAux, &sectionAux);
    2215:     PetscDSGetTotalDimension(probAux, &totDimAux);
    2216:     PetscDSGetComponentOffsets(probAux, &aOff);
    2217:   }
    2218:   /* Integrate over points */
    2219:   {
    2220:     PetscFEGeom    *fgeom, *chunkGeom = NULL;
    2221:     PetscInt        maxDegree;
    2222:     PetscQuadrature qGeom = NULL;
    2223:     const PetscInt *points;
    2224:     PetscInt        numFaces, face, Nq, field;
    2225:     PetscInt        numChunks, chunkSize, chunk, Nr, offset;

    2227:     ISGetLocalSize(pointIS, &numFaces);
    2228:     ISGetIndices(pointIS, &points);
    2229:     PetscCalloc2(numFaces*totDim, &u, locA ? numFaces*totDimAux : 0, &a);
    2230:     DMFieldGetDegree(coordField, pointIS, NULL, &maxDegree);
    2231:     for (field = 0; field < Nf; ++field) {
    2232:       PetscFE fe;

    2234:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
    2235:       if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, pointIS, &qGeom);}
    2236:       if (!qGeom) {
    2237:         PetscFEGetFaceQuadrature(fe, &qGeom);
    2238:         PetscObjectReference((PetscObject) qGeom);
    2239:       }
    2240:       PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
    2241:       DMPlexGetFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
    2242:       for (face = 0; face < numFaces; ++face) {
    2243:         const PetscInt point = points[face], *support;
    2244:         PetscScalar    *x    = NULL;
    2245:         PetscInt       i;

    2247:         DMPlexGetSupport(dm, point, &support);
    2248:         DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
    2249:         for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
    2250:         DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
    2251:         if (locA) {
    2252:           PetscInt subp;
    2253:           DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
    2254:           DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
    2255:           for (i = 0; i < totDimAux; ++i) a[f*totDimAux+i] = x[i];
    2256:           DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
    2257:         }
    2258:       }
    2259:       /* Get blocking */
    2260:       {
    2261:         PetscQuadrature q;
    2262:         PetscInt        numBatches, batchSize, numBlocks, blockSize;
    2263:         PetscInt        Nq, Nb;

    2265:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    2266:         PetscFEGetQuadrature(fe, &q);
    2267:         PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
    2268:         PetscFEGetDimension(fe, &Nb);
    2269:         blockSize = Nb*Nq;
    2270:         batchSize = numBlocks * blockSize;
    2271:         chunkSize = numBatches*batchSize;
    2272:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    2273:         numChunks = numFaces / chunkSize;
    2274:         Nr        = numFaces % chunkSize;
    2275:         offset    = numFaces - Nr;
    2276:       }
    2277:       /* Do integration for each field */
    2278:       for (chunk = 0; chunk < numChunks; ++chunk) {
    2279:         PetscFEGeomGetChunk(fgeom, chunk*chunkSize, (chunk+1)*chunkSize, &chunkGeom);
    2280:         PetscFEIntegrateBd(prob, field, func, chunkSize, chunkGeom, u, probAux, a, fintegral);
    2281:         PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
    2282:       }
    2283:       PetscFEGeomGetChunk(fgeom, offset, numFaces, &chunkGeom);
    2284:       PetscFEIntegrateBd(prob, field, func, Nr, chunkGeom, &u[offset*totDim], probAux, a ? &a[offset*totDimAux] : NULL, &fintegral[offset*Nf]);
    2285:       PetscFEGeomRestoreChunk(fgeom, offset, numFaces, &chunkGeom);
    2286:       /* Cleanup data arrays */
    2287:       DMPlexRestoreFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
    2288:       PetscQuadratureDestroy(&qGeom);
    2289:       PetscFree2(u, a);
    2290:       ISRestoreIndices(pointIS, &points);
    2291:     }
    2292:   }
    2293:   if (plex)  {DMDestroy(&plex);}
    2294:   if (plexA) {DMDestroy(&plexA);}
    2295:   return(0);
    2296: }

    2298: /*@
    2299:   DMPlexComputeBdIntegral - Form the integral over the specified boundary from the global input X using pointwise functions specified by the user

    2301:   Input Parameters:
    2302: + dm      - The mesh
    2303: . X       - Global input vector
    2304: . label   - The boundary DMLabel
    2305: . numVals - The number of label values to use, or PETSC_DETERMINE for all values
    2306: . vals    - The label values to use, or PETSC_NULL for all values
    2307: . func    = The function to integrate along the boundary
    2308: - user    - The user context

    2310:   Output Parameter:
    2311: . integral - Integral for each field

    2313:   Level: developer

    2315: .seealso: DMPlexComputeIntegralFEM(), DMPlexComputeBdResidualFEM()
    2316: @*/
    2317: PetscErrorCode DMPlexComputeBdIntegral(DM dm, Vec X, DMLabel label, PetscInt numVals, const PetscInt vals[],
    2318:                                        void (*func)(PetscInt, PetscInt, PetscInt,
    2319:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    2320:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
    2321:                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
    2322:                                        PetscScalar *integral, void *user)
    2323: {
    2324:   Vec            locX;
    2325:   PetscSection   section;
    2326:   DMLabel        depthLabel;
    2327:   IS             facetIS;
    2328:   PetscInt       dim, Nf, f, v;

    2337:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
    2338:   DMPlexGetDepthLabel(dm, &depthLabel);
    2339:   DMGetDimension(dm, &dim);
    2340:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
    2341:   DMGetLocalSection(dm, &section);
    2342:   PetscSectionGetNumFields(section, &Nf);
    2343:   /* Get local solution with boundary values */
    2344:   DMGetLocalVector(dm, &locX);
    2345:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
    2346:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
    2347:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
    2348:   /* Loop over label values */
    2349:   PetscArrayzero(integral, Nf);
    2350:   for (v = 0; v < numVals; ++v) {
    2351:     IS           pointIS;
    2352:     PetscInt     numFaces, face;
    2353:     PetscScalar *fintegral;

    2355:     DMLabelGetStratumIS(label, vals[v], &pointIS);
    2356:     if (!pointIS) continue; /* No points with that id on this process */
    2357:     {
    2358:       IS isectIS;

    2360:       /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
    2361:       ISIntersect_Caching_Internal(facetIS, pointIS, &isectIS);
    2362:       ISDestroy(&pointIS);
    2363:       pointIS = isectIS;
    2364:     }
    2365:     ISGetLocalSize(pointIS, &numFaces);
    2366:     PetscCalloc1(numFaces*Nf, &fintegral);
    2367:     DMPlexComputeBdIntegral_Internal(dm, locX, pointIS, func, fintegral, user);
    2368:     /* Sum point contributions into integral */
    2369:     for (f = 0; f < Nf; ++f) for (face = 0; face < numFaces; ++face) integral[f] += fintegral[face*Nf+f];
    2370:     PetscFree(fintegral);
    2371:     ISDestroy(&pointIS);
    2372:   }
    2373:   DMRestoreLocalVector(dm, &locX);
    2374:   ISDestroy(&facetIS);
    2375:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
    2376:   return(0);
    2377: }

    2379: /*@
    2380:   DMPlexComputeInterpolatorNested - Form the local portion of the interpolation matrix I from the coarse DM to a uniformly refined DM.

    2382:   Input Parameters:
    2383: + dmc  - The coarse mesh
    2384: . dmf  - The fine mesh
    2385: . isRefined - Flag indicating regular refinement, rather than the same topology
    2386: - user - The user context

    2388:   Output Parameter:
    2389: . In  - The interpolation matrix

    2391:   Level: developer

    2393: .seealso: DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
    2394: @*/
    2395: PetscErrorCode DMPlexComputeInterpolatorNested(DM dmc, DM dmf, PetscBool isRefined, Mat In, void *user)
    2396: {
    2397:   DM_Plex          *mesh  = (DM_Plex *) dmc->data;
    2398:   const char       *name  = "Interpolator";
    2399:   PetscFE          *feRef;
    2400:   PetscFV          *fvRef;
    2401:   PetscSection      fsection, fglobalSection;
    2402:   PetscSection      csection, cglobalSection;
    2403:   PetscScalar      *elemMat;
    2404:   PetscInt          dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c;
    2405:   PetscInt          cTotDim=0, rTotDim = 0;
    2406:   PetscErrorCode    ierr;

    2409:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
    2410:   DMGetDimension(dmf, &dim);
    2411:   DMGetLocalSection(dmf, &fsection);
    2412:   DMGetGlobalSection(dmf, &fglobalSection);
    2413:   DMGetLocalSection(dmc, &csection);
    2414:   DMGetGlobalSection(dmc, &cglobalSection);
    2415:   PetscSectionGetNumFields(fsection, &Nf);
    2416:   DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);
    2417:   PetscCalloc2(Nf, &feRef, Nf, &fvRef);
    2418:   for (f = 0; f < Nf; ++f) {
    2419:     PetscObject  obj, objc;
    2420:     PetscClassId id, idc;
    2421:     PetscInt     rNb = 0, Nc = 0, cNb = 0;

    2423:     DMGetField(dmf, f, NULL, &obj);
    2424:     PetscObjectGetClassId(obj, &id);
    2425:     if (id == PETSCFE_CLASSID) {
    2426:       PetscFE fe = (PetscFE) obj;

    2428:       if (isRefined) {
    2429:         PetscFERefine(fe, &feRef[f]);
    2430:       } else {
    2431:         PetscObjectReference((PetscObject) fe);
    2432:         feRef[f] = fe;
    2433:       }
    2434:       PetscFEGetDimension(feRef[f], &rNb);
    2435:       PetscFEGetNumComponents(fe, &Nc);
    2436:     } else if (id == PETSCFV_CLASSID) {
    2437:       PetscFV        fv = (PetscFV) obj;
    2438:       PetscDualSpace Q;

    2440:       if (isRefined) {
    2441:         PetscFVRefine(fv, &fvRef[f]);
    2442:       } else {
    2443:         PetscObjectReference((PetscObject) fv);
    2444:         fvRef[f] = fv;
    2445:       }
    2446:       PetscFVGetDualSpace(fvRef[f], &Q);
    2447:       PetscDualSpaceGetDimension(Q, &rNb);
    2448:       PetscFVGetDualSpace(fv, &Q);
    2449:       PetscFVGetNumComponents(fv, &Nc);
    2450:     }
    2451:     DMGetField(dmc, f, NULL, &objc);
    2452:     PetscObjectGetClassId(objc, &idc);
    2453:     if (idc == PETSCFE_CLASSID) {
    2454:       PetscFE fe = (PetscFE) objc;

    2456:       PetscFEGetDimension(fe, &cNb);
    2457:     } else if (id == PETSCFV_CLASSID) {
    2458:       PetscFV        fv = (PetscFV) obj;
    2459:       PetscDualSpace Q;

    2461:       PetscFVGetDualSpace(fv, &Q);
    2462:       PetscDualSpaceGetDimension(Q, &cNb);
    2463:     }
    2464:     rTotDim += rNb;
    2465:     cTotDim += cNb;
    2466:   }
    2467:   PetscMalloc1(rTotDim*cTotDim,&elemMat);
    2468:   PetscArrayzero(elemMat, rTotDim*cTotDim);
    2469:   for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) {
    2470:     PetscDualSpace   Qref;
    2471:     PetscQuadrature  f;
    2472:     const PetscReal *qpoints, *qweights;
    2473:     PetscReal       *points;
    2474:     PetscInt         npoints = 0, Nc, Np, fpdim, i, k, p, d;

    2476:     /* Compose points from all dual basis functionals */
    2477:     if (feRef[fieldI]) {
    2478:       PetscFEGetDualSpace(feRef[fieldI], &Qref);
    2479:       PetscFEGetNumComponents(feRef[fieldI], &Nc);
    2480:     } else {
    2481:       PetscFVGetDualSpace(fvRef[fieldI], &Qref);
    2482:       PetscFVGetNumComponents(fvRef[fieldI], &Nc);
    2483:     }
    2484:     PetscDualSpaceGetDimension(Qref, &fpdim);
    2485:     for (i = 0; i < fpdim; ++i) {
    2486:       PetscDualSpaceGetFunctional(Qref, i, &f);
    2487:       PetscQuadratureGetData(f, NULL, NULL, &Np, NULL, NULL);
    2488:       npoints += Np;
    2489:     }
    2490:     PetscMalloc1(npoints*dim,&points);
    2491:     for (i = 0, k = 0; i < fpdim; ++i) {
    2492:       PetscDualSpaceGetFunctional(Qref, i, &f);
    2493:       PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
    2494:       for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d];
    2495:     }

    2497:     for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) {
    2498:       PetscObject  obj;
    2499:       PetscClassId id;
    2500:       PetscInt     NcJ = 0, cpdim = 0, j, qNc;

    2502:       DMGetField(dmc, fieldJ, NULL, &obj);
    2503:       PetscObjectGetClassId(obj, &id);
    2504:       if (id == PETSCFE_CLASSID) {
    2505:         PetscFE           fe = (PetscFE) obj;
    2506:         PetscTabulation T  = NULL;

    2508:         /* Evaluate basis at points */
    2509:         PetscFEGetNumComponents(fe, &NcJ);
    2510:         PetscFEGetDimension(fe, &cpdim);
    2511:         /* For now, fields only interpolate themselves */
    2512:         if (fieldI == fieldJ) {
    2513:           if (Nc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %D does not match coarse field %D", Nc, NcJ);
    2514:           PetscFECreateTabulation(fe, 1, npoints, points, 0, &T);
    2515:           for (i = 0, k = 0; i < fpdim; ++i) {
    2516:             PetscDualSpaceGetFunctional(Qref, i, &f);
    2517:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
    2518:             if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ);
    2519:             for (p = 0; p < Np; ++p, ++k) {
    2520:               for (j = 0; j < cpdim; ++j) {
    2521:                 /*
    2522:                    cTotDim:            Total columns in element interpolation matrix, sum of number of dual basis functionals in each field
    2523:                    offsetI, offsetJ:   Offsets into the larger element interpolation matrix for different fields
    2524:                    fpdim, i, cpdim, j: Dofs for fine and coarse grids, correspond to dual space basis functionals
    2525:                    qNC, Nc, Ncj, c:    Number of components in this field
    2526:                    Np, p:              Number of quad points in the fine grid functional i
    2527:                    k:                  i*Np + p, overall point number for the interpolation
    2528:                 */
    2529:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += T->T[0][k*cpdim*NcJ+j*Nc+c]*qweights[p*qNc+c];
    2530:               }
    2531:             }
    2532:           }
    2533:           PetscTabulationDestroy(&T);
    2534:         }
    2535:       } else if (id == PETSCFV_CLASSID) {
    2536:         PetscFV        fv = (PetscFV) obj;

    2538:         /* Evaluate constant function at points */
    2539:         PetscFVGetNumComponents(fv, &NcJ);
    2540:         cpdim = 1;
    2541:         /* For now, fields only interpolate themselves */
    2542:         if (fieldI == fieldJ) {
    2543:           if (Nc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %D does not match coarse field %D", Nc, NcJ);
    2544:           for (i = 0, k = 0; i < fpdim; ++i) {
    2545:             PetscDualSpaceGetFunctional(Qref, i, &f);
    2546:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
    2547:             if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ);
    2548:             for (p = 0; p < Np; ++p, ++k) {
    2549:               for (j = 0; j < cpdim; ++j) {
    2550:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += 1.0*qweights[p*qNc+c];
    2551:               }
    2552:             }
    2553:           }
    2554:         }
    2555:       }
    2556:       offsetJ += cpdim;
    2557:     }
    2558:     offsetI += fpdim;
    2559:     PetscFree(points);
    2560:   }
    2561:   if (mesh->printFEM > 1) {DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);}
    2562:   /* Preallocate matrix */
    2563:   {
    2564:     Mat          preallocator;
    2565:     PetscScalar *vals;
    2566:     PetscInt    *cellCIndices, *cellFIndices;
    2567:     PetscInt     locRows, locCols, cell;

    2569:     MatGetLocalSize(In, &locRows, &locCols);
    2570:     MatCreate(PetscObjectComm((PetscObject) In), &preallocator);
    2571:     MatSetType(preallocator, MATPREALLOCATOR);
    2572:     MatSetSizes(preallocator, locRows, locCols, PETSC_DETERMINE, PETSC_DETERMINE);
    2573:     MatSetUp(preallocator);
    2574:     PetscCalloc3(rTotDim*cTotDim, &vals,cTotDim,&cellCIndices,rTotDim,&cellFIndices);
    2575:     for (cell = cStart; cell < cEnd; ++cell) {
    2576:       if (isRefined) {
    2577:         DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, cell, cellCIndices, cellFIndices);
    2578:         MatSetValues(preallocator, rTotDim, cellFIndices, cTotDim, cellCIndices, vals, INSERT_VALUES);
    2579:       } else {
    2580:         DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, preallocator, cell, vals, INSERT_VALUES);
    2581:       }
    2582:     }
    2583:     PetscFree3(vals,cellCIndices,cellFIndices);
    2584:     MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);
    2585:     MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);
    2586:     MatPreallocatorPreallocate(preallocator, PETSC_TRUE, In);
    2587:     MatDestroy(&preallocator);
    2588:   }
    2589:   /* Fill matrix */
    2590:   MatZeroEntries(In);
    2591:   for (c = cStart; c < cEnd; ++c) {
    2592:     if (isRefined) {
    2593:       DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);
    2594:     } else {
    2595:       DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);
    2596:     }
    2597:   }
    2598:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);}
    2599:   PetscFree2(feRef,fvRef);
    2600:   PetscFree(elemMat);
    2601:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
    2602:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
    2603:   if (mesh->printFEM) {
    2604:     PetscPrintf(PetscObjectComm((PetscObject)In), "%s:\n", name);
    2605:     MatChop(In, 1.0e-10);
    2606:     MatView(In, NULL);
    2607:   }
    2608:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
    2609:   return(0);
    2610: }

    2612: PetscErrorCode DMPlexComputeMassMatrixNested(DM dmc, DM dmf, Mat mass, void *user)
    2613: {
    2614:   SETERRQ(PetscObjectComm((PetscObject) dmc), PETSC_ERR_SUP, "Laziness");
    2615: }

    2617: /*@
    2618:   DMPlexComputeInterpolatorGeneral - Form the local portion of the interpolation matrix I from the coarse DM to a non-nested fine DM.

    2620:   Input Parameters:
    2621: + dmf  - The fine mesh
    2622: . dmc  - The coarse mesh
    2623: - user - The user context

    2625:   Output Parameter:
    2626: . In  - The interpolation matrix

    2628:   Level: developer

    2630: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
    2631: @*/
    2632: PetscErrorCode DMPlexComputeInterpolatorGeneral(DM dmc, DM dmf, Mat In, void *user)
    2633: {
    2634:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
    2635:   const char    *name = "Interpolator";
    2636:   PetscDS        prob;
    2637:   PetscSection   fsection, csection, globalFSection, globalCSection;
    2638:   PetscHSetIJ    ht;
    2639:   PetscLayout    rLayout;
    2640:   PetscInt      *dnz, *onz;
    2641:   PetscInt       locRows, rStart, rEnd;
    2642:   PetscReal     *x, *v0, *J, *invJ, detJ;
    2643:   PetscReal     *v0c, *Jc, *invJc, detJc;
    2644:   PetscScalar   *elemMat;
    2645:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

    2649:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
    2650:   DMGetCoordinateDim(dmc, &dim);
    2651:   DMGetDS(dmc, &prob);
    2652:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
    2653:   PetscDSGetNumFields(prob, &Nf);
    2654:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
    2655:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
    2656:   DMGetLocalSection(dmf, &fsection);
    2657:   DMGetGlobalSection(dmf, &globalFSection);
    2658:   DMGetLocalSection(dmc, &csection);
    2659:   DMGetGlobalSection(dmc, &globalCSection);
    2660:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
    2661:   PetscDSGetTotalDimension(prob, &totDim);
    2662:   PetscMalloc1(totDim, &elemMat);

    2664:   MatGetLocalSize(In, &locRows, NULL);
    2665:   PetscLayoutCreate(PetscObjectComm((PetscObject) In), &rLayout);
    2666:   PetscLayoutSetLocalSize(rLayout, locRows);
    2667:   PetscLayoutSetBlockSize(rLayout, 1);
    2668:   PetscLayoutSetUp(rLayout);
    2669:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
    2670:   PetscLayoutDestroy(&rLayout);
    2671:   PetscCalloc2(locRows,&dnz,locRows,&onz);
    2672:   PetscHSetIJCreate(&ht);
    2673:   for (field = 0; field < Nf; ++field) {
    2674:     PetscObject      obj;
    2675:     PetscClassId     id;
    2676:     PetscDualSpace   Q = NULL;
    2677:     PetscQuadrature  f;
    2678:     const PetscReal *qpoints;
    2679:     PetscInt         Nc, Np, fpdim, i, d;

    2681:     PetscDSGetDiscretization(prob, field, &obj);
    2682:     PetscObjectGetClassId(obj, &id);
    2683:     if (id == PETSCFE_CLASSID) {
    2684:       PetscFE fe = (PetscFE) obj;

    2686:       PetscFEGetDualSpace(fe, &Q);
    2687:       PetscFEGetNumComponents(fe, &Nc);
    2688:     } else if (id == PETSCFV_CLASSID) {
    2689:       PetscFV fv = (PetscFV) obj;

    2691:       PetscFVGetDualSpace(fv, &Q);
    2692:       Nc   = 1;
    2693:     }
    2694:     PetscDualSpaceGetDimension(Q, &fpdim);
    2695:     /* For each fine grid cell */
    2696:     for (cell = cStart; cell < cEnd; ++cell) {
    2697:       PetscInt *findices,   *cindices;
    2698:       PetscInt  numFIndices, numCIndices;

    2700:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2701:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
    2702:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
    2703:       for (i = 0; i < fpdim; ++i) {
    2704:         Vec             pointVec;
    2705:         PetscScalar    *pV;
    2706:         PetscSF         coarseCellSF = NULL;
    2707:         const PetscSFNode *coarseCells;
    2708:         PetscInt        numCoarseCells, q, c;

    2710:         /* Get points from the dual basis functional quadrature */
    2711:         PetscDualSpaceGetFunctional(Q, i, &f);
    2712:         PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
    2713:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
    2714:         VecSetBlockSize(pointVec, dim);
    2715:         VecGetArray(pointVec, &pV);
    2716:         for (q = 0; q < Np; ++q) {
    2717:           const PetscReal xi0[3] = {-1., -1., -1.};

    2719:           /* Transform point to real space */
    2720:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
    2721:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
    2722:         }
    2723:         VecRestoreArray(pointVec, &pV);
    2724:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
    2725:         /* OPT: Pack all quad points from fine cell */
    2726:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
    2727:         PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
    2728:         /* Update preallocation info */
    2729:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
    2730:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
    2731:         {
    2732:           PetscHashIJKey key;
    2733:           PetscBool      missing;

    2735:           key.i = findices[i];
    2736:           if (key.i >= 0) {
    2737:             /* Get indices for coarse elements */
    2738:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
    2739:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2740:               for (c = 0; c < numCIndices; ++c) {
    2741:                 key.j = cindices[c];
    2742:                 if (key.j < 0) continue;
    2743:                 PetscHSetIJQueryAdd(ht, key, &missing);
    2744:                 if (missing) {
    2745:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
    2746:                   else                                     ++onz[key.i-rStart];
    2747:                 }
    2748:               }
    2749:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2750:             }
    2751:           }
    2752:         }
    2753:         PetscSFDestroy(&coarseCellSF);
    2754:         VecDestroy(&pointVec);
    2755:       }
    2756:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2757:     }
    2758:   }
    2759:   PetscHSetIJDestroy(&ht);
    2760:   MatXAIJSetPreallocation(In, 1, dnz, onz, NULL, NULL);
    2761:   MatSetOption(In, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
    2762:   PetscFree2(dnz,onz);
    2763:   for (field = 0; field < Nf; ++field) {
    2764:     PetscObject       obj;
    2765:     PetscClassId      id;
    2766:     PetscDualSpace    Q = NULL;
    2767:     PetscTabulation T = NULL;
    2768:     PetscQuadrature   f;
    2769:     const PetscReal  *qpoints, *qweights;
    2770:     PetscInt          Nc, qNc, Np, fpdim, i, d;

    2772:     PetscDSGetDiscretization(prob, field, &obj);
    2773:     PetscObjectGetClassId(obj, &id);
    2774:     if (id == PETSCFE_CLASSID) {
    2775:       PetscFE fe = (PetscFE) obj;

    2777:       PetscFEGetDualSpace(fe, &Q);
    2778:       PetscFEGetNumComponents(fe, &Nc);
    2779:       PetscFECreateTabulation(fe, 1, 1, x, 0, &T);
    2780:     } else if (id == PETSCFV_CLASSID) {
    2781:       PetscFV fv = (PetscFV) obj;

    2783:       PetscFVGetDualSpace(fv, &Q);
    2784:       Nc   = 1;
    2785:     } else SETERRQ1(PetscObjectComm((PetscObject)dmc),PETSC_ERR_ARG_WRONG,"Unknown discretization type for field %D",field);
    2786:     PetscDualSpaceGetDimension(Q, &fpdim);
    2787:     /* For each fine grid cell */
    2788:     for (cell = cStart; cell < cEnd; ++cell) {
    2789:       PetscInt *findices,   *cindices;
    2790:       PetscInt  numFIndices, numCIndices;

    2792:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2793:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
    2794:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
    2795:       for (i = 0; i < fpdim; ++i) {
    2796:         Vec             pointVec;
    2797:         PetscScalar    *pV;
    2798:         PetscSF         coarseCellSF = NULL;
    2799:         const PetscSFNode *coarseCells;
    2800:         PetscInt        numCoarseCells, cpdim, q, c, j;

    2802:         /* Get points from the dual basis functional quadrature */
    2803:         PetscDualSpaceGetFunctional(Q, i, &f);
    2804:         PetscQuadratureGetData(f, NULL, &qNc, &Np, &qpoints, &qweights);
    2805:         if (qNc != Nc) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, Nc);
    2806:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
    2807:         VecSetBlockSize(pointVec, dim);
    2808:         VecGetArray(pointVec, &pV);
    2809:         for (q = 0; q < Np; ++q) {
    2810:           const PetscReal xi0[3] = {-1., -1., -1.};

    2812:           /* Transform point to real space */
    2813:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
    2814:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
    2815:         }
    2816:         VecRestoreArray(pointVec, &pV);
    2817:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
    2818:         /* OPT: Read this out from preallocation information */
    2819:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
    2820:         /* Update preallocation info */
    2821:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
    2822:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
    2823:         VecGetArray(pointVec, &pV);
    2824:         for (ccell = 0; ccell < numCoarseCells; ++ccell) {
    2825:           PetscReal pVReal[3];
    2826:           const PetscReal xi0[3] = {-1., -1., -1.};

    2828:           DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2829:           /* Transform points from real space to coarse reference space */
    2830:           DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
    2831:           for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
    2832:           CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

    2834:           if (id == PETSCFE_CLASSID) {
    2835:             PetscFE fe = (PetscFE) obj;

    2837:             /* Evaluate coarse basis on contained point */
    2838:             PetscFEGetDimension(fe, &cpdim);
    2839:             PetscFEComputeTabulation(fe, 1, x, 0, T);
    2840:             PetscArrayzero(elemMat, cpdim);
    2841:             /* Get elemMat entries by multiplying by weight */
    2842:             for (j = 0; j < cpdim; ++j) {
    2843:               for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*qweights[ccell*qNc + c];
    2844:             }
    2845:           } else {
    2846:             cpdim = 1;
    2847:             for (j = 0; j < cpdim; ++j) {
    2848:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*qweights[ccell*qNc + c];
    2849:             }
    2850:           }
    2851:           /* Update interpolator */
    2852:           if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
    2853:           if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
    2854:           MatSetValues(In, 1, &findices[i], numCIndices, cindices, elemMat, INSERT_VALUES);
    2855:           DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2856:         }
    2857:         VecRestoreArray(pointVec, &pV);
    2858:         PetscSFDestroy(&coarseCellSF);
    2859:         VecDestroy(&pointVec);
    2860:       }
    2861:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2862:     }
    2863:     if (id == PETSCFE_CLASSID) {PetscTabulationDestroy(&T);}
    2864:   }
    2865:   PetscFree3(v0,J,invJ);
    2866:   PetscFree3(v0c,Jc,invJc);
    2867:   PetscFree(elemMat);
    2868:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
    2869:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
    2870:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
    2871:   return(0);
    2872: }

    2874: /*@
    2875:   DMPlexComputeMassMatrixGeneral - Form the local portion of the mass matrix M from the coarse DM to a non-nested fine DM.

    2877:   Input Parameters:
    2878: + dmf  - The fine mesh
    2879: . dmc  - The coarse mesh
    2880: - user - The user context

    2882:   Output Parameter:
    2883: . mass  - The mass matrix

    2885:   Level: developer

    2887: .seealso: DMPlexComputeMassMatrixNested(), DMPlexComputeInterpolatorNested(), DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
    2888: @*/
    2889: PetscErrorCode DMPlexComputeMassMatrixGeneral(DM dmc, DM dmf, Mat mass, void *user)
    2890: {
    2891:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
    2892:   const char    *name = "Mass Matrix";
    2893:   PetscDS        prob;
    2894:   PetscSection   fsection, csection, globalFSection, globalCSection;
    2895:   PetscHSetIJ    ht;
    2896:   PetscLayout    rLayout;
    2897:   PetscInt      *dnz, *onz;
    2898:   PetscInt       locRows, rStart, rEnd;
    2899:   PetscReal     *x, *v0, *J, *invJ, detJ;
    2900:   PetscReal     *v0c, *Jc, *invJc, detJc;
    2901:   PetscScalar   *elemMat;
    2902:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

    2906:   DMGetCoordinateDim(dmc, &dim);
    2907:   DMGetDS(dmc, &prob);
    2908:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
    2909:   PetscDSGetNumFields(prob, &Nf);
    2910:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
    2911:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
    2912:   DMGetLocalSection(dmf, &fsection);
    2913:   DMGetGlobalSection(dmf, &globalFSection);
    2914:   DMGetLocalSection(dmc, &csection);
    2915:   DMGetGlobalSection(dmc, &globalCSection);
    2916:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
    2917:   PetscDSGetTotalDimension(prob, &totDim);
    2918:   PetscMalloc1(totDim, &elemMat);

    2920:   MatGetLocalSize(mass, &locRows, NULL);
    2921:   PetscLayoutCreate(PetscObjectComm((PetscObject) mass), &rLayout);
    2922:   PetscLayoutSetLocalSize(rLayout, locRows);
    2923:   PetscLayoutSetBlockSize(rLayout, 1);
    2924:   PetscLayoutSetUp(rLayout);
    2925:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
    2926:   PetscLayoutDestroy(&rLayout);
    2927:   PetscCalloc2(locRows,&dnz,locRows,&onz);
    2928:   PetscHSetIJCreate(&ht);
    2929:   for (field = 0; field < Nf; ++field) {
    2930:     PetscObject      obj;
    2931:     PetscClassId     id;
    2932:     PetscQuadrature  quad;
    2933:     const PetscReal *qpoints;
    2934:     PetscInt         Nq, Nc, i, d;

    2936:     PetscDSGetDiscretization(prob, field, &obj);
    2937:     PetscObjectGetClassId(obj, &id);
    2938:     if (id == PETSCFE_CLASSID) {PetscFEGetQuadrature((PetscFE) obj, &quad);}
    2939:     else                       {PetscFVGetQuadrature((PetscFV) obj, &quad);}
    2940:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, NULL);
    2941:     /* For each fine grid cell */
    2942:     for (cell = cStart; cell < cEnd; ++cell) {
    2943:       Vec                pointVec;
    2944:       PetscScalar       *pV;
    2945:       PetscSF            coarseCellSF = NULL;
    2946:       const PetscSFNode *coarseCells;
    2947:       PetscInt           numCoarseCells, q, c;
    2948:       PetscInt          *findices,   *cindices;
    2949:       PetscInt           numFIndices, numCIndices;

    2951:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2952:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
    2953:       /* Get points from the quadrature */
    2954:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
    2955:       VecSetBlockSize(pointVec, dim);
    2956:       VecGetArray(pointVec, &pV);
    2957:       for (q = 0; q < Nq; ++q) {
    2958:         const PetscReal xi0[3] = {-1., -1., -1.};

    2960:         /* Transform point to real space */
    2961:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
    2962:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
    2963:       }
    2964:       VecRestoreArray(pointVec, &pV);
    2965:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
    2966:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
    2967:       PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
    2968:       /* Update preallocation info */
    2969:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
    2970:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
    2971:       {
    2972:         PetscHashIJKey key;
    2973:         PetscBool      missing;

    2975:         for (i = 0; i < numFIndices; ++i) {
    2976:           key.i = findices[i];
    2977:           if (key.i >= 0) {
    2978:             /* Get indices for coarse elements */
    2979:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
    2980:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2981:               for (c = 0; c < numCIndices; ++c) {
    2982:                 key.j = cindices[c];
    2983:                 if (key.j < 0) continue;
    2984:                 PetscHSetIJQueryAdd(ht, key, &missing);
    2985:                 if (missing) {
    2986:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
    2987:                   else                                     ++onz[key.i-rStart];
    2988:                 }
    2989:               }
    2990:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    2991:             }
    2992:           }
    2993:         }
    2994:       }
    2995:       PetscSFDestroy(&coarseCellSF);
    2996:       VecDestroy(&pointVec);
    2997:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    2998:     }
    2999:   }
    3000:   PetscHSetIJDestroy(&ht);
    3001:   MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);
    3002:   MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
    3003:   PetscFree2(dnz,onz);
    3004:   for (field = 0; field < Nf; ++field) {
    3005:     PetscObject       obj;
    3006:     PetscClassId      id;
    3007:     PetscTabulation T, Tfine;
    3008:     PetscQuadrature   quad;
    3009:     const PetscReal  *qpoints, *qweights;
    3010:     PetscInt          Nq, Nc, i, d;

    3012:     PetscDSGetDiscretization(prob, field, &obj);
    3013:     PetscObjectGetClassId(obj, &id);
    3014:     if (id == PETSCFE_CLASSID) {
    3015:       PetscFEGetQuadrature((PetscFE) obj, &quad);
    3016:       PetscFEGetCellTabulation((PetscFE) obj, 1, &Tfine);
    3017:       PetscFECreateTabulation((PetscFE) obj, 1, 1, x, 0, &T);
    3018:     } else {
    3019:       PetscFVGetQuadrature((PetscFV) obj, &quad);
    3020:     }
    3021:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, &qweights);
    3022:     /* For each fine grid cell */
    3023:     for (cell = cStart; cell < cEnd; ++cell) {
    3024:       Vec                pointVec;
    3025:       PetscScalar       *pV;
    3026:       PetscSF            coarseCellSF = NULL;
    3027:       const PetscSFNode *coarseCells;
    3028:       PetscInt           numCoarseCells, cpdim, q, c, j;
    3029:       PetscInt          *findices,   *cindices;
    3030:       PetscInt           numFIndices, numCIndices;

    3032:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    3033:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
    3034:       /* Get points from the quadrature */
    3035:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
    3036:       VecSetBlockSize(pointVec, dim);
    3037:       VecGetArray(pointVec, &pV);
    3038:       for (q = 0; q < Nq; ++q) {
    3039:         const PetscReal xi0[3] = {-1., -1., -1.};

    3041:         /* Transform point to real space */
    3042:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
    3043:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
    3044:       }
    3045:       VecRestoreArray(pointVec, &pV);
    3046:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
    3047:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
    3048:       /* Update matrix */
    3049:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
    3050:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
    3051:       VecGetArray(pointVec, &pV);
    3052:       for (ccell = 0; ccell < numCoarseCells; ++ccell) {
    3053:         PetscReal pVReal[3];
    3054:         const PetscReal xi0[3] = {-1., -1., -1.};

    3057:         DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    3058:         /* Transform points from real space to coarse reference space */
    3059:         DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
    3060:         for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
    3061:         CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

    3063:         if (id == PETSCFE_CLASSID) {
    3064:           PetscFE fe = (PetscFE) obj;

    3066:           /* Evaluate coarse basis on contained point */
    3067:           PetscFEGetDimension(fe, &cpdim);
    3068:           PetscFEComputeTabulation(fe, 1, x, 0, T);
    3069:           /* Get elemMat entries by multiplying by weight */
    3070:           for (i = 0; i < numFIndices; ++i) {
    3071:             PetscArrayzero(elemMat, cpdim);
    3072:             for (j = 0; j < cpdim; ++j) {
    3073:               for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*Tfine->T[0][(ccell*numFIndices + i)*Nc + c]*qweights[ccell*Nc + c]*detJ;
    3074:             }
    3075:             /* Update interpolator */
    3076:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
    3077:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
    3078:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
    3079:           }
    3080:         } else {
    3081:           cpdim = 1;
    3082:           for (i = 0; i < numFIndices; ++i) {
    3083:             PetscArrayzero(elemMat, cpdim);
    3084:             for (j = 0; j < cpdim; ++j) {
    3085:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*1.0*qweights[ccell*Nc + c]*detJ;
    3086:             }
    3087:             /* Update interpolator */
    3088:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
    3089:             PetscPrintf(PETSC_COMM_SELF, "Nq: %D %D Nf: %D %D Nc: %D %D\n", ccell, Nq, i, numFIndices, j, numCIndices);
    3090:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
    3091:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
    3092:           }
    3093:         }
    3094:         DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
    3095:       }
    3096:       VecRestoreArray(pointVec, &pV);
    3097:       PetscSFDestroy(&coarseCellSF);
    3098:       VecDestroy(&pointVec);
    3099:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
    3100:     }
    3101:     if (id == PETSCFE_CLASSID) {PetscTabulationDestroy(&T);}
    3102:   }
    3103:   PetscFree3(v0,J,invJ);
    3104:   PetscFree3(v0c,Jc,invJc);
    3105:   PetscFree(elemMat);
    3106:   MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);
    3107:   MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);
    3108:   return(0);
    3109: }

    3111: /*@
    3112:   DMPlexComputeInjectorFEM - Compute a mapping from coarse unknowns to fine unknowns

    3114:   Input Parameters:
    3115: + dmc  - The coarse mesh
    3116: - dmf  - The fine mesh
    3117: - user - The user context

    3119:   Output Parameter:
    3120: . sc   - The mapping

    3122:   Level: developer

    3124: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
    3125: @*/
    3126: PetscErrorCode DMPlexComputeInjectorFEM(DM dmc, DM dmf, VecScatter *sc, void *user)
    3127: {
    3128:   PetscDS        prob;
    3129:   PetscFE       *feRef;
    3130:   PetscFV       *fvRef;
    3131:   Vec            fv, cv;
    3132:   IS             fis, cis;
    3133:   PetscSection   fsection, fglobalSection, csection, cglobalSection;
    3134:   PetscInt      *cmap, *cellCIndices, *cellFIndices, *cindices, *findices;
    3135:   PetscInt       cTotDim, fTotDim = 0, Nf, f, field, cStart, cEnd, c, dim, d, startC, endC, offsetC, offsetF, m;
    3136:   PetscBool     *needAvg;

    3140:   PetscLogEventBegin(DMPLEX_InjectorFEM,dmc,dmf,0,0);
    3141:   DMGetDimension(dmf, &dim);
    3142:   DMGetLocalSection(dmf, &fsection);
    3143:   DMGetGlobalSection(dmf, &fglobalSection);
    3144:   DMGetLocalSection(dmc, &csection);
    3145:   DMGetGlobalSection(dmc, &cglobalSection);
    3146:   PetscSectionGetNumFields(fsection, &Nf);
    3147:   DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);
    3148:   DMGetDS(dmc, &prob);
    3149:   PetscCalloc3(Nf,&feRef,Nf,&fvRef,Nf,&needAvg);
    3150:   for (f = 0; f < Nf; ++f) {
    3151:     PetscObject  obj;
    3152:     PetscClassId id;
    3153:     PetscInt     fNb = 0, Nc = 0;

    3155:     PetscDSGetDiscretization(prob, f, &obj);
    3156:     PetscObjectGetClassId(obj, &id);
    3157:     if (id == PETSCFE_CLASSID) {
    3158:       PetscFE    fe = (PetscFE) obj;
    3159:       PetscSpace sp;
    3160:       PetscInt   maxDegree;

    3162:       PetscFERefine(fe, &feRef[f]);
    3163:       PetscFEGetDimension(feRef[f], &fNb);
    3164:       PetscFEGetNumComponents(fe, &Nc);
    3165:       PetscFEGetBasisSpace(fe, &sp);
    3166:       PetscSpaceGetDegree(sp, NULL, &maxDegree);
    3167:       if (!maxDegree) needAvg[f] = PETSC_TRUE;
    3168:     } else if (id == PETSCFV_CLASSID) {
    3169:       PetscFV        fv = (PetscFV) obj;
    3170:       PetscDualSpace Q;

    3172:       PetscFVRefine(fv, &fvRef[f]);
    3173:       PetscFVGetDualSpace(fvRef[f], &Q);
    3174:       PetscDualSpaceGetDimension(Q, &fNb);
    3175:       PetscFVGetNumComponents(fv, &Nc);
    3176:       needAvg[f] = PETSC_TRUE;
    3177:     }
    3178:     fTotDim += fNb;
    3179:   }
    3180:   PetscDSGetTotalDimension(prob, &cTotDim);
    3181:   PetscMalloc1(cTotDim,&cmap);
    3182:   for (field = 0, offsetC = 0, offsetF = 0; field < Nf; ++field) {
    3183:     PetscFE        feC;
    3184:     PetscFV        fvC;
    3185:     PetscDualSpace QF, QC;
    3186:     PetscInt       order = -1, NcF, NcC, fpdim, cpdim;

    3188:     if (feRef[field]) {
    3189:       PetscDSGetDiscretization(prob, field, (PetscObject *) &feC);
    3190:       PetscFEGetNumComponents(feC, &NcC);
    3191:       PetscFEGetNumComponents(feRef[field], &NcF);
    3192:       PetscFEGetDualSpace(feRef[field], &QF);
    3193:       PetscDualSpaceGetOrder(QF, &order);
    3194:       PetscDualSpaceGetDimension(QF, &fpdim);
    3195:       PetscFEGetDualSpace(feC, &QC);
    3196:       PetscDualSpaceGetDimension(QC, &cpdim);
    3197:     } else {
    3198:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fvC);
    3199:       PetscFVGetNumComponents(fvC, &NcC);
    3200:       PetscFVGetNumComponents(fvRef[field], &NcF);
    3201:       PetscFVGetDualSpace(fvRef[field], &QF);
    3202:       PetscDualSpaceGetDimension(QF, &fpdim);
    3203:       PetscFVGetDualSpace(fvC, &QC);
    3204:       PetscDualSpaceGetDimension(QC, &cpdim);
    3205:     }
    3206:     if (NcF != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %D does not match coarse field %D", NcF, NcC);
    3207:     for (c = 0; c < cpdim; ++c) {
    3208:       PetscQuadrature  cfunc;
    3209:       const PetscReal *cqpoints, *cqweights;
    3210:       PetscInt         NqcC, NpC;
    3211:       PetscBool        found = PETSC_FALSE;

    3213:       PetscDualSpaceGetFunctional(QC, c, &cfunc);
    3214:       PetscQuadratureGetData(cfunc, NULL, &NqcC, &NpC, &cqpoints, &cqweights);
    3215:       if (NqcC != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcC, NcC);
    3216:       if (NpC != 1 && feRef[field]) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Do not know how to do injection for moments");
    3217:       for (f = 0; f < fpdim; ++f) {
    3218:         PetscQuadrature  ffunc;
    3219:         const PetscReal *fqpoints, *fqweights;
    3220:         PetscReal        sum = 0.0;
    3221:         PetscInt         NqcF, NpF;

    3223:         PetscDualSpaceGetFunctional(QF, f, &ffunc);
    3224:         PetscQuadratureGetData(ffunc, NULL, &NqcF, &NpF, &fqpoints, &fqweights);
    3225:         if (NqcF != NcF) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcF, NcF);
    3226:         if (NpC != NpF) continue;
    3227:         for (d = 0; d < dim; ++d) sum += PetscAbsReal(cqpoints[d] - fqpoints[d]);
    3228:         if (sum > 1.0e-9) continue;
    3229:         for (d = 0; d < NcC; ++d) sum += PetscAbsReal(cqweights[d]*fqweights[d]);
    3230:         if (sum < 1.0e-9) continue;
    3231:         cmap[offsetC+c] = offsetF+f;
    3232:         found = PETSC_TRUE;
    3233:         break;
    3234:       }
    3235:       if (!found) {
    3236:         /* TODO We really want the average here, but some asshole put VecScatter in the interface */
    3237:         if (fvRef[field] || (feRef[field] && order == 0)) {
    3238:           cmap[offsetC+c] = offsetF+0;
    3239:         } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate matching functional for injection");
    3240:       }
    3241:     }
    3242:     offsetC += cpdim;
    3243:     offsetF += fpdim;
    3244:   }
    3245:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);PetscFVDestroy(&fvRef[f]);}
    3246:   PetscFree3(feRef,fvRef,needAvg);

    3248:   DMGetGlobalVector(dmf, &fv);
    3249:   DMGetGlobalVector(dmc, &cv);
    3250:   VecGetOwnershipRange(cv, &startC, &endC);
    3251:   PetscSectionGetConstrainedStorageSize(cglobalSection, &m);
    3252:   PetscMalloc2(cTotDim,&cellCIndices,fTotDim,&cellFIndices);
    3253:   PetscMalloc1(m,&cindices);
    3254:   PetscMalloc1(m,&findices);
    3255:   for (d = 0; d < m; ++d) cindices[d] = findices[d] = -1;
    3256:   for (c = cStart; c < cEnd; ++c) {
    3257:     DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, c, cellCIndices, cellFIndices);
    3258:     for (d = 0; d < cTotDim; ++d) {
    3259:       if ((cellCIndices[d] < startC) || (cellCIndices[d] >= endC)) continue;
    3260:       if ((findices[cellCIndices[d]-startC] >= 0) && (findices[cellCIndices[d]-startC] != cellFIndices[cmap[d]])) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Coarse dof %D maps to both %D and %D", cindices[cellCIndices[d]-startC], findices[cellCIndices[d]-startC], cellFIndices[cmap[d]]);
    3261:       cindices[cellCIndices[d]-startC] = cellCIndices[d];
    3262:       findices[cellCIndices[d]-startC] = cellFIndices[cmap[d]];
    3263:     }
    3264:   }
    3265:   PetscFree(cmap);
    3266:   PetscFree2(cellCIndices,cellFIndices);

    3268:   ISCreateGeneral(PETSC_COMM_SELF, m, cindices, PETSC_OWN_POINTER, &cis);
    3269:   ISCreateGeneral(PETSC_COMM_SELF, m, findices, PETSC_OWN_POINTER, &fis);
    3270:   VecScatterCreate(cv, cis, fv, fis, sc);
    3271:   ISDestroy(&cis);
    3272:   ISDestroy(&fis);
    3273:   DMRestoreGlobalVector(dmf, &fv);
    3274:   DMRestoreGlobalVector(dmc, &cv);
    3275:   PetscLogEventEnd(DMPLEX_InjectorFEM,dmc,dmf,0,0);
    3276:   return(0);
    3277: }

    3279: /*@C
    3280:   DMPlexGetCellFields - Retrieve the field values values for a chunk of cells

    3282:   Input Parameters:
    3283: + dm     - The DM
    3284: . cellIS - The cells to include
    3285: . locX   - A local vector with the solution fields
    3286: . locX_t - A local vector with solution field time derivatives, or NULL
    3287: - locA   - A local vector with auxiliary fields, or NULL

    3289:   Output Parameters:
    3290: + u   - The field coefficients
    3291: . u_t - The fields derivative coefficients
    3292: - a   - The auxiliary field coefficients

    3294:   Level: developer

    3296: .seealso: DMPlexGetFaceFields()
    3297: @*/
    3298: PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
    3299: {
    3300:   DM              plex, plexA = NULL;
    3301:   DMEnclosureType encAux;
    3302:   PetscSection    section, sectionAux;
    3303:   PetscDS         prob;
    3304:   const PetscInt *cells;
    3305:   PetscInt        cStart, cEnd, numCells, totDim, totDimAux, c;
    3306:   PetscErrorCode  ierr;

    3316:   DMPlexConvertPlex(dm, &plex, PETSC_FALSE);
    3317:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    3318:   DMGetLocalSection(dm, &section);
    3319:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);
    3320:   PetscDSGetTotalDimension(prob, &totDim);
    3321:   if (locA) {
    3322:     DM      dmAux;
    3323:     PetscDS probAux;

    3325:     VecGetDM(locA, &dmAux);
    3326:     DMGetEnclosureRelation(dmAux, dm, &encAux);
    3327:     DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);
    3328:     DMGetLocalSection(dmAux, &sectionAux);
    3329:     DMGetDS(dmAux, &probAux);
    3330:     PetscDSGetTotalDimension(probAux, &totDimAux);
    3331:   }
    3332:   numCells = cEnd - cStart;
    3333:   DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);
    3334:   if (locX_t) {DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);} else {*u_t = NULL;}
    3335:   if (locA)   {DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);} else {*a = NULL;}
    3336:   for (c = cStart; c < cEnd; ++c) {
    3337:     const PetscInt cell = cells ? cells[c] : c;
    3338:     const PetscInt cind = c - cStart;
    3339:     PetscScalar   *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a;
    3340:     PetscInt       i;

    3342:     DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);
    3343:     for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i];
    3344:     DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);
    3345:     if (locX_t) {
    3346:       DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);
    3347:       for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i];
    3348:       DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);
    3349:     }
    3350:     if (locA) {
    3351:       PetscInt subcell;
    3352:       DMGetEnclosurePoint(plexA, dm, encAux, cell, &subcell);
    3353:       DMPlexVecGetClosure(plexA, sectionAux, locA, subcell, NULL, &x);
    3354:       for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i];
    3355:       DMPlexVecRestoreClosure(plexA, sectionAux, locA, subcell, NULL, &x);
    3356:     }
    3357:   }
    3358:   DMDestroy(&plex);
    3359:   if (locA) {DMDestroy(&plexA);}
    3360:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    3361:   return(0);
    3362: }

    3364: /*@C
    3365:   DMPlexRestoreCellFields - Restore the field values values for a chunk of cells

    3367:   Input Parameters:
    3368: + dm     - The DM
    3369: . cellIS - The cells to include
    3370: . locX   - A local vector with the solution fields
    3371: . locX_t - A local vector with solution field time derivatives, or NULL
    3372: - locA   - A local vector with auxiliary fields, or NULL

    3374:   Output Parameters:
    3375: + u   - The field coefficients
    3376: . u_t - The fields derivative coefficients
    3377: - a   - The auxiliary field coefficients

    3379:   Level: developer

    3381: .seealso: DMPlexGetFaceFields()
    3382: @*/
    3383: PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
    3384: {

    3388:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);
    3389:   if (locX_t) {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);}
    3390:   if (locA)   {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);}
    3391:   return(0);
    3392: }

    3394: static PetscErrorCode DMPlexGetHybridAuxFields(DM dmAux, PetscDS dsAux[], IS cellIS, Vec locA, PetscScalar *a[])
    3395: {
    3396:   DM              plexA;
    3397:   PetscSection    sectionAux;
    3398:   const PetscInt *cells;
    3399:   PetscInt        cStart, cEnd, numCells, c, totDimAux[2];
    3400:   PetscErrorCode  ierr;

    3403:   if (!locA) return(0);
    3408:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    3409:   DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);
    3410:   DMGetLocalSection(dmAux, &sectionAux);
    3411:   numCells = cEnd - cStart;
    3412:   PetscDSGetTotalDimension(dsAux[0], &totDimAux[0]);
    3413:   DMGetWorkArray(dmAux, numCells*totDimAux[0], MPIU_SCALAR, &a[0]);
    3414:   PetscDSGetTotalDimension(dsAux[1], &totDimAux[1]);
    3415:   DMGetWorkArray(dmAux, numCells*totDimAux[1], MPIU_SCALAR, &a[1]);
    3416:   for (c = cStart; c < cEnd; ++c) {
    3417:     const PetscInt  cell = cells ? cells[c] : c;
    3418:     const PetscInt  cind = c - cStart;
    3419:     const PetscInt *cone, *ornt;
    3420:     PetscInt        c;

    3422:     DMPlexGetCone(dmAux, cell, &cone);
    3423:     DMPlexGetConeOrientation(dmAux, cell, &ornt);
    3424:     for (c = 0; c < 2; ++c) {
    3425:       PetscScalar   *x = NULL, *al = a[c];
    3426:       const PetscInt tdA = totDimAux[c];
    3427:       PetscInt       Na, i;

    3429:       if (ornt[c]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_SUP, "Face %D in hybrid cell %D has orientation %D != 0", cone[c], cell, ornt[c]);
    3430:       DMPlexVecGetClosure(plexA, sectionAux, locA, cone[c], &Na, &x);
    3431:       for (i = 0; i < Na; ++i) al[cind*tdA+i] = x[i];
    3432:       DMPlexVecRestoreClosure(plexA, sectionAux, locA, cone[c], &Na, &x);
    3433:     }
    3434:   }
    3435:   DMDestroy(&plexA);
    3436:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    3437:   return(0);
    3438: }

    3440: static PetscErrorCode DMPlexRestoreHybridAuxFields(DM dmAux, PetscDS dsAux[], IS cellIS, Vec locA, PetscScalar *a[])
    3441: {

    3445:   if (!locA) return(0);
    3446:   DMRestoreWorkArray(dmAux, 0, MPIU_SCALAR, &a[0]);
    3447:   DMRestoreWorkArray(dmAux, 0, MPIU_SCALAR, &a[1]);
    3448:   return(0);
    3449: }

    3451: /*@C
    3452:   DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces

    3454:   Input Parameters:
    3455: + dm     - The DM
    3456: . fStart - The first face to include
    3457: . fEnd   - The first face to exclude
    3458: . locX   - A local vector with the solution fields
    3459: . locX_t - A local vector with solution field time derivatives, or NULL
    3460: . faceGeometry - A local vector with face geometry
    3461: . cellGeometry - A local vector with cell geometry
    3462: - locaGrad - A local vector with field gradients, or NULL

    3464:   Output Parameters:
    3465: + Nface - The number of faces with field values
    3466: . uL - The field values at the left side of the face
    3467: - uR - The field values at the right side of the face

    3469:   Level: developer

    3471: .seealso: DMPlexGetCellFields()
    3472: @*/
    3473: PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR)
    3474: {
    3475:   DM                 dmFace, dmCell, dmGrad = NULL;
    3476:   PetscSection       section;
    3477:   PetscDS            prob;
    3478:   DMLabel            ghostLabel;
    3479:   const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
    3480:   PetscBool         *isFE;
    3481:   PetscInt           dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face;
    3482:   PetscErrorCode     ierr;

    3493:   DMGetDimension(dm, &dim);
    3494:   DMGetDS(dm, &prob);
    3495:   DMGetLocalSection(dm, &section);
    3496:   PetscDSGetNumFields(prob, &Nf);
    3497:   PetscDSGetTotalComponents(prob, &Nc);
    3498:   PetscMalloc1(Nf, &isFE);
    3499:   for (f = 0; f < Nf; ++f) {
    3500:     PetscObject  obj;
    3501:     PetscClassId id;

    3503:     PetscDSGetDiscretization(prob, f, &obj);
    3504:     PetscObjectGetClassId(obj, &id);
    3505:     if (id == PETSCFE_CLASSID)      {isFE[f] = PETSC_TRUE;}
    3506:     else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;}
    3507:     else                            {isFE[f] = PETSC_FALSE;}
    3508:   }
    3509:   DMGetLabel(dm, "ghost", &ghostLabel);
    3510:   VecGetArrayRead(locX, &x);
    3511:   VecGetDM(faceGeometry, &dmFace);
    3512:   VecGetArrayRead(faceGeometry, &facegeom);
    3513:   VecGetDM(cellGeometry, &dmCell);
    3514:   VecGetArrayRead(cellGeometry, &cellgeom);
    3515:   if (locGrad) {
    3516:     VecGetDM(locGrad, &dmGrad);
    3517:     VecGetArrayRead(locGrad, &lgrad);
    3518:   }
    3519:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);
    3520:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);
    3521:   /* Right now just eat the extra work for FE (could make a cell loop) */
    3522:   for (face = fStart, iface = 0; face < fEnd; ++face) {
    3523:     const PetscInt        *cells;
    3524:     PetscFVFaceGeom       *fg;
    3525:     PetscFVCellGeom       *cgL, *cgR;
    3526:     PetscScalar           *xL, *xR, *gL, *gR;
    3527:     PetscScalar           *uLl = *uL, *uRl = *uR;
    3528:     PetscInt               ghost, nsupp, nchild;

    3530:     DMLabelGetValue(ghostLabel, face, &ghost);
    3531:     DMPlexGetSupportSize(dm, face, &nsupp);
    3532:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
    3533:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
    3534:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
    3535:     DMPlexGetSupport(dm, face, &cells);
    3536:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
    3537:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
    3538:     for (f = 0; f < Nf; ++f) {
    3539:       PetscInt off;

    3541:       PetscDSGetComponentOffset(prob, f, &off);
    3542:       if (isFE[f]) {
    3543:         const PetscInt *cone;
    3544:         PetscInt        comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d;

    3546:         xL = xR = NULL;
    3547:         PetscSectionGetFieldComponents(section, f, &comp);
    3548:         DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
    3549:         DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
    3550:         DMPlexGetCone(dm, cells[0], &cone);
    3551:         DMPlexGetConeSize(dm, cells[0], &coneSizeL);
    3552:         for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break;
    3553:         DMPlexGetCone(dm, cells[1], &cone);
    3554:         DMPlexGetConeSize(dm, cells[1], &coneSizeR);
    3555:         for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break;
    3556:         if (faceLocL == coneSizeL && faceLocR == coneSizeR) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of cell %D or cell %D", face, cells[0], cells[1]);
    3557:         /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */
    3558:         /* TODO: this is a hack that might not be right for nonconforming */
    3559:         if (faceLocL < coneSizeL) {
    3560:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);
    3561:           if (rdof == ldof && faceLocR < coneSizeR) {PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);}
    3562:           else              {for (d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];}
    3563:         }
    3564:         else {
    3565:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);
    3566:           PetscSectionGetFieldComponents(section, f, &comp);
    3567:           for (d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d];
    3568:         }
    3569:         DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
    3570:         DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
    3571:       } else {
    3572:         PetscFV  fv;
    3573:         PetscInt numComp, c;

    3575:         PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);
    3576:         PetscFVGetNumComponents(fv, &numComp);
    3577:         DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);
    3578:         DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);
    3579:         if (dmGrad) {
    3580:           PetscReal dxL[3], dxR[3];

    3582:           DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);
    3583:           DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);
    3584:           DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL);
    3585:           DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR);
    3586:           for (c = 0; c < numComp; ++c) {
    3587:             uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL);
    3588:             uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR);
    3589:           }
    3590:         } else {
    3591:           for (c = 0; c < numComp; ++c) {
    3592:             uLl[iface*Nc+off+c] = xL[c];
    3593:             uRl[iface*Nc+off+c] = xR[c];
    3594:           }
    3595:         }
    3596:       }
    3597:     }
    3598:     ++iface;
    3599:   }
    3600:   *Nface = iface;
    3601:   VecRestoreArrayRead(locX, &x);
    3602:   VecRestoreArrayRead(faceGeometry, &facegeom);
    3603:   VecRestoreArrayRead(cellGeometry, &cellgeom);
    3604:   if (locGrad) {
    3605:     VecRestoreArrayRead(locGrad, &lgrad);
    3606:   }
    3607:   PetscFree(isFE);
    3608:   return(0);
    3609: }

    3611: /*@C
    3612:   DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces

    3614:   Input Parameters:
    3615: + dm     - The DM
    3616: . fStart - The first face to include
    3617: . fEnd   - The first face to exclude
    3618: . locX   - A local vector with the solution fields
    3619: . locX_t - A local vector with solution field time derivatives, or NULL
    3620: . faceGeometry - A local vector with face geometry
    3621: . cellGeometry - A local vector with cell geometry
    3622: - locaGrad - A local vector with field gradients, or NULL

    3624:   Output Parameters:
    3625: + Nface - The number of faces with field values
    3626: . uL - The field values at the left side of the face
    3627: - uR - The field values at the right side of the face

    3629:   Level: developer

    3631: .seealso: DMPlexGetFaceFields()
    3632: @*/
    3633: PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR)
    3634: {

    3638:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);
    3639:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);
    3640:   return(0);
    3641: }

    3643: /*@C
    3644:   DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces

    3646:   Input Parameters:
    3647: + dm     - The DM
    3648: . fStart - The first face to include
    3649: . fEnd   - The first face to exclude
    3650: . faceGeometry - A local vector with face geometry
    3651: - cellGeometry - A local vector with cell geometry

    3653:   Output Parameters:
    3654: + Nface - The number of faces with field values
    3655: . fgeom - The extract the face centroid and normal
    3656: - vol   - The cell volume

    3658:   Level: developer

    3660: .seealso: DMPlexGetCellFields()
    3661: @*/
    3662: PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
    3663: {
    3664:   DM                 dmFace, dmCell;
    3665:   DMLabel            ghostLabel;
    3666:   const PetscScalar *facegeom, *cellgeom;
    3667:   PetscInt           dim, numFaces = fEnd - fStart, iface, face;
    3668:   PetscErrorCode     ierr;

    3676:   DMGetDimension(dm, &dim);
    3677:   DMGetLabel(dm, "ghost", &ghostLabel);
    3678:   VecGetDM(faceGeometry, &dmFace);
    3679:   VecGetArrayRead(faceGeometry, &facegeom);
    3680:   VecGetDM(cellGeometry, &dmCell);
    3681:   VecGetArrayRead(cellGeometry, &cellgeom);
    3682:   PetscMalloc1(numFaces, fgeom);
    3683:   DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);
    3684:   for (face = fStart, iface = 0; face < fEnd; ++face) {
    3685:     const PetscInt        *cells;
    3686:     PetscFVFaceGeom       *fg;
    3687:     PetscFVCellGeom       *cgL, *cgR;
    3688:     PetscFVFaceGeom       *fgeoml = *fgeom;
    3689:     PetscReal             *voll   = *vol;
    3690:     PetscInt               ghost, d, nchild, nsupp;

    3692:     DMLabelGetValue(ghostLabel, face, &ghost);
    3693:     DMPlexGetSupportSize(dm, face, &nsupp);
    3694:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
    3695:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
    3696:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
    3697:     DMPlexGetSupport(dm, face, &cells);
    3698:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
    3699:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
    3700:     for (d = 0; d < dim; ++d) {
    3701:       fgeoml[iface].centroid[d] = fg->centroid[d];
    3702:       fgeoml[iface].normal[d]   = fg->normal[d];
    3703:     }
    3704:     voll[iface*2+0] = cgL->volume;
    3705:     voll[iface*2+1] = cgR->volume;
    3706:     ++iface;
    3707:   }
    3708:   *Nface = iface;
    3709:   VecRestoreArrayRead(faceGeometry, &facegeom);
    3710:   VecRestoreArrayRead(cellGeometry, &cellgeom);
    3711:   return(0);
    3712: }

    3714: /*@C
    3715:   DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces

    3717:   Input Parameters:
    3718: + dm     - The DM
    3719: . fStart - The first face to include
    3720: . fEnd   - The first face to exclude
    3721: . faceGeometry - A local vector with face geometry
    3722: - cellGeometry - A local vector with cell geometry

    3724:   Output Parameters:
    3725: + Nface - The number of faces with field values
    3726: . fgeom - The extract the face centroid and normal
    3727: - vol   - The cell volume

    3729:   Level: developer

    3731: .seealso: DMPlexGetFaceFields()
    3732: @*/
    3733: PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
    3734: {

    3738:   PetscFree(*fgeom);
    3739:   DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);
    3740:   return(0);
    3741: }

    3743: PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
    3744: {
    3745:   char            composeStr[33] = {0};
    3746:   PetscObjectId   id;
    3747:   PetscContainer  container;
    3748:   PetscErrorCode  ierr;

    3751:   PetscObjectGetId((PetscObject)quad,&id);
    3752:   PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);
    3753:   PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);
    3754:   if (container) {
    3755:     PetscContainerGetPointer(container, (void **) geom);
    3756:   } else {
    3757:     DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);
    3758:     PetscContainerCreate(PETSC_COMM_SELF,&container);
    3759:     PetscContainerSetPointer(container, (void *) *geom);
    3760:     PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);
    3761:     PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);
    3762:     PetscContainerDestroy(&container);
    3763:   }
    3764:   return(0);
    3765: }

    3767: PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
    3768: {
    3770:   *geom = NULL;
    3771:   return(0);
    3772: }

    3774: PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM dm, PetscSection section, IS cellIS, PetscReal t, Vec locX, Vec locX_t, Vec locF, void *user)
    3775: {
    3776:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
    3777:   const char      *name       = "Residual";
    3778:   DM               dmAux      = NULL;
    3779:   DMLabel          ghostLabel = NULL;
    3780:   PetscDS          prob       = NULL;
    3781:   PetscDS          probAux    = NULL;
    3782:   PetscBool        useFEM     = PETSC_FALSE;
    3783:   PetscBool        isImplicit = (locX_t || t == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
    3784:   DMField          coordField = NULL;
    3785:   Vec              locA;
    3786:   PetscScalar     *u = NULL, *u_t, *a, *uL = NULL, *uR = NULL;
    3787:   IS               chunkIS;
    3788:   const PetscInt  *cells;
    3789:   PetscInt         cStart, cEnd, numCells;
    3790:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk, fStart, fEnd;
    3791:   PetscInt         maxDegree = PETSC_MAX_INT;
    3792:   PetscHashFormKey key;
    3793:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
    3794:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
    3795:   PetscErrorCode   ierr;

    3798:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
    3799:   /* FEM+FVM */
    3800:   /* 1: Get sizes from dm and dmAux */
    3801:   DMGetLabel(dm, "ghost", &ghostLabel);
    3802:   DMGetDS(dm, &prob);
    3803:   PetscDSGetNumFields(prob, &Nf);
    3804:   PetscDSGetTotalDimension(prob, &totDim);
    3805:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    3806:   if (locA) {
    3807:     VecGetDM(locA, &dmAux);
    3808:     DMGetDS(dmAux, &probAux);
    3809:     PetscDSGetTotalDimension(probAux, &totDimAux);
    3810:   }
    3811:   /* 2: Get geometric data */
    3812:   for (f = 0; f < Nf; ++f) {
    3813:     PetscObject  obj;
    3814:     PetscClassId id;
    3815:     PetscBool    fimp;

    3817:     PetscDSGetImplicit(prob, f, &fimp);
    3818:     if (isImplicit != fimp) continue;
    3819:     PetscDSGetDiscretization(prob, f, &obj);
    3820:     PetscObjectGetClassId(obj, &id);
    3821:     if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
    3822:     if (id == PETSCFV_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Use of FVM with PCPATCH not yet implemented");
    3823:   }
    3824:   if (useFEM) {
    3825:     DMGetCoordinateField(dm, &coordField);
    3826:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
    3827:     if (maxDegree <= 1) {
    3828:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
    3829:       if (affineQuad) {
    3830:         DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    3831:       }
    3832:     } else {
    3833:       PetscCalloc2(Nf,&quads,Nf,&geoms);
    3834:       for (f = 0; f < Nf; ++f) {
    3835:         PetscObject  obj;
    3836:         PetscClassId id;
    3837:         PetscBool    fimp;

    3839:         PetscDSGetImplicit(prob, f, &fimp);
    3840:         if (isImplicit != fimp) continue;
    3841:         PetscDSGetDiscretization(prob, f, &obj);
    3842:         PetscObjectGetClassId(obj, &id);
    3843:         if (id == PETSCFE_CLASSID) {
    3844:           PetscFE fe = (PetscFE) obj;

    3846:           PetscFEGetQuadrature(fe, &quads[f]);
    3847:           PetscObjectReference((PetscObject)quads[f]);
    3848:           DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
    3849:         }
    3850:       }
    3851:     }
    3852:   }
    3853:   /* Loop over chunks */
    3854:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    3855:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    3856:   if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
    3857:   numCells      = cEnd - cStart;
    3858:   numChunks     = 1;
    3859:   cellChunkSize = numCells/numChunks;
    3860:   numChunks     = PetscMin(1,numCells);
    3861:   key.label     = NULL;
    3862:   key.value     = 0;
    3863:   for (chunk = 0; chunk < numChunks; ++chunk) {
    3864:     PetscScalar     *elemVec, *fluxL = NULL, *fluxR = NULL;
    3865:     PetscReal       *vol = NULL;
    3866:     PetscFVFaceGeom *fgeom = NULL;
    3867:     PetscInt         cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
    3868:     PetscInt         numFaces = 0;

    3870:     /* Extract field coefficients */
    3871:     if (useFEM) {
    3872:       ISGetPointSubrange(chunkIS, cS, cE, cells);
    3873:       DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
    3874:       DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
    3875:       PetscArrayzero(elemVec, numCells*totDim);
    3876:     }
    3877:     /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
    3878:     /* Loop over fields */
    3879:     for (f = 0; f < Nf; ++f) {
    3880:       PetscObject  obj;
    3881:       PetscClassId id;
    3882:       PetscBool    fimp;
    3883:       PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

    3885:       key.field = f;
    3886:       PetscDSGetImplicit(prob, f, &fimp);
    3887:       if (isImplicit != fimp) continue;
    3888:       PetscDSGetDiscretization(prob, f, &obj);
    3889:       PetscObjectGetClassId(obj, &id);
    3890:       if (id == PETSCFE_CLASSID) {
    3891:         PetscFE         fe = (PetscFE) obj;
    3892:         PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
    3893:         PetscFEGeom    *chunkGeom = NULL;
    3894:         PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
    3895:         PetscInt        Nq, Nb;

    3897:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    3898:         PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
    3899:         PetscFEGetDimension(fe, &Nb);
    3900:         blockSize = Nb;
    3901:         batchSize = numBlocks * blockSize;
    3902:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    3903:         numChunks = numCells / (numBatches*batchSize);
    3904:         Ne        = numChunks*numBatches*batchSize;
    3905:         Nr        = numCells % (numBatches*batchSize);
    3906:         offset    = numCells - Nr;
    3907:         /* Integrate FE residual to get elemVec (need fields at quadrature points) */
    3908:         /*   For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */
    3909:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
    3910:         PetscFEIntegrateResidual(prob, key, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
    3911:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
    3912:         PetscFEIntegrateResidual(prob, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
    3913:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
    3914:       } else if (id == PETSCFV_CLASSID) {
    3915:         PetscFV fv = (PetscFV) obj;

    3917:         Ne = numFaces;
    3918:         /* Riemann solve over faces (need fields at face centroids) */
    3919:         /*   We need to evaluate FE fields at those coordinates */
    3920:         PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
    3921:       } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
    3922:     }
    3923:     /* Loop over domain */
    3924:     if (useFEM) {
    3925:       /* Add elemVec to locX */
    3926:       for (c = cS; c < cE; ++c) {
    3927:         const PetscInt cell = cells ? cells[c] : c;
    3928:         const PetscInt cind = c - cStart;

    3930:         if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
    3931:         if (ghostLabel) {
    3932:           PetscInt ghostVal;

    3934:           DMLabelGetValue(ghostLabel,cell,&ghostVal);
    3935:           if (ghostVal > 0) continue;
    3936:         }
    3937:         DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
    3938:       }
    3939:     }
    3940:     /* Handle time derivative */
    3941:     if (locX_t) {
    3942:       PetscScalar *x_t, *fa;

    3944:       VecGetArray(locF, &fa);
    3945:       VecGetArray(locX_t, &x_t);
    3946:       for (f = 0; f < Nf; ++f) {
    3947:         PetscFV      fv;
    3948:         PetscObject  obj;
    3949:         PetscClassId id;
    3950:         PetscInt     pdim, d;

    3952:         PetscDSGetDiscretization(prob, f, &obj);
    3953:         PetscObjectGetClassId(obj, &id);
    3954:         if (id != PETSCFV_CLASSID) continue;
    3955:         fv   = (PetscFV) obj;
    3956:         PetscFVGetNumComponents(fv, &pdim);
    3957:         for (c = cS; c < cE; ++c) {
    3958:           const PetscInt cell = cells ? cells[c] : c;
    3959:           PetscScalar   *u_t, *r;

    3961:           if (ghostLabel) {
    3962:             PetscInt ghostVal;

    3964:             DMLabelGetValue(ghostLabel, cell, &ghostVal);
    3965:             if (ghostVal > 0) continue;
    3966:           }
    3967:           DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
    3968:           DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
    3969:           for (d = 0; d < pdim; ++d) r[d] += u_t[d];
    3970:         }
    3971:       }
    3972:       VecRestoreArray(locX_t, &x_t);
    3973:       VecRestoreArray(locF, &fa);
    3974:     }
    3975:     if (useFEM) {
    3976:       DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
    3977:       DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
    3978:     }
    3979:   }
    3980:   if (useFEM) {ISDestroy(&chunkIS);}
    3981:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    3982:   /* TODO Could include boundary residual here (see DMPlexComputeResidual_Internal) */
    3983:   if (useFEM) {
    3984:     if (maxDegree <= 1) {
    3985:       DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    3986:       PetscQuadratureDestroy(&affineQuad);
    3987:     } else {
    3988:       for (f = 0; f < Nf; ++f) {
    3989:         DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
    3990:         PetscQuadratureDestroy(&quads[f]);
    3991:       }
    3992:       PetscFree2(quads,geoms);
    3993:     }
    3994:   }
    3995:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
    3996:   return(0);
    3997: }

    3999: /*
    4000:   We always assemble JacP, and if the matrix is different from Jac and two different sets of point functions are provided, we also assemble Jac

    4002:   X   - The local solution vector
    4003:   X_t - The local solution time derviative vector, or NULL
    4004: */
    4005: PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS,
    4006:                                                     PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx)
    4007: {
    4008:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
    4009:   const char      *name = "Jacobian", *nameP = "JacobianPre";
    4010:   DM               dmAux = NULL;
    4011:   PetscDS          prob,   probAux = NULL;
    4012:   PetscSection     sectionAux = NULL;
    4013:   Vec              A;
    4014:   DMField          coordField;
    4015:   PetscFEGeom     *cgeomFEM;
    4016:   PetscQuadrature  qGeom = NULL;
    4017:   Mat              J = Jac, JP = JacP;
    4018:   PetscScalar     *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL;
    4019:   PetscBool        hasJac, hasPrec, hasDyn, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE;
    4020:   const PetscInt  *cells;
    4021:   PetscHashFormKey key;
    4022:   PetscInt         Nf, fieldI, fieldJ, maxDegree, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0;
    4023:   PetscErrorCode   ierr;

    4026:   CHKMEMQ;
    4027:   ISGetLocalSize(cellIS, &numCells);
    4028:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    4029:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
    4030:   DMGetDS(dm, &prob);
    4031:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
    4032:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
    4033:   if (dmAux) {
    4034:     DMGetLocalSection(dmAux, &sectionAux);
    4035:     DMGetDS(dmAux, &probAux);
    4036:   }
    4037:   /* Get flags */
    4038:   PetscDSGetNumFields(prob, &Nf);
    4039:   DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);
    4040:   for (fieldI = 0; fieldI < Nf; ++fieldI) {
    4041:     PetscObject  disc;
    4042:     PetscClassId id;
    4043:     PetscDSGetDiscretization(prob, fieldI, &disc);
    4044:     PetscObjectGetClassId(disc, &id);
    4045:     if (id == PETSCFE_CLASSID)      {isFE[fieldI] = PETSC_TRUE;}
    4046:     else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;}
    4047:   }
    4048:   PetscDSHasJacobian(prob, &hasJac);
    4049:   PetscDSHasJacobianPreconditioner(prob, &hasPrec);
    4050:   PetscDSHasDynamicJacobian(prob, &hasDyn);
    4051:   assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE;
    4052:   hasDyn      = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
    4053:   PetscObjectTypeCompare((PetscObject) Jac,  MATIS, &isMatIS);
    4054:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
    4055:   /* Setup input data and temp arrays (should be DMGetWorkArray) */
    4056:   if (isMatISP || isMatISP) {DMPlexGetSubdomainSection(dm, &globalSection);}
    4057:   if (isMatIS)  {MatISGetLocalMat(Jac,  &J);}
    4058:   if (isMatISP) {MatISGetLocalMat(JacP, &JP);}
    4059:   if (hasFV)    {MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);} /* No allocated space for FV stuff, so ignore the zero entries */
    4060:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
    4061:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
    4062:   PetscDSGetTotalDimension(prob, &totDim);
    4063:   if (probAux) {PetscDSGetTotalDimension(probAux, &totDimAux);}
    4064:   CHKMEMQ;
    4065:   /* Compute batch sizes */
    4066:   if (isFE[0]) {
    4067:     PetscFE         fe;
    4068:     PetscQuadrature q;
    4069:     PetscInt        numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb;

    4071:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
    4072:     PetscFEGetQuadrature(fe, &q);
    4073:     PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);
    4074:     PetscFEGetDimension(fe, &Nb);
    4075:     PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    4076:     blockSize = Nb*numQuadPoints;
    4077:     batchSize = numBlocks  * blockSize;
    4078:     chunkSize = numBatches * batchSize;
    4079:     numChunks = numCells / chunkSize + numCells % chunkSize;
    4080:     PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    4081:   } else {
    4082:     chunkSize = numCells;
    4083:     numChunks = 1;
    4084:   }
    4085:   /* Get work space */
    4086:   wsz  = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize;
    4087:   DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);
    4088:   PetscArrayzero(work, wsz);
    4089:   off      = 0;
    4090:   u        = X       ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
    4091:   u_t      = X_t     ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
    4092:   a        = dmAux   ? (sz = chunkSize*totDimAux,     off += sz, work+off-sz) : NULL;
    4093:   elemMat  = hasJac  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
    4094:   elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
    4095:   elemMatD = hasDyn  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
    4096:   if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz);
    4097:   /* Setup geometry */
    4098:   DMGetCoordinateField(dm, &coordField);
    4099:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
    4100:   if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);}
    4101:   if (!qGeom) {
    4102:     PetscFE fe;

    4104:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
    4105:     PetscFEGetQuadrature(fe, &qGeom);
    4106:     PetscObjectReference((PetscObject) qGeom);
    4107:   }
    4108:   DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
    4109:   /* Compute volume integrals */
    4110:   if (assembleJac) {MatZeroEntries(J);}
    4111:   MatZeroEntries(JP);
    4112:   key.label = NULL;
    4113:   key.value = 0;
    4114:   for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) {
    4115:     const PetscInt   Ncell = PetscMin(chunkSize, numCells - offCell);
    4116:     PetscInt         c;

    4118:     /* Extract values */
    4119:     for (c = 0; c < Ncell; ++c) {
    4120:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
    4121:       PetscScalar   *x = NULL,  *x_t = NULL;
    4122:       PetscInt       i;

    4124:       if (X) {
    4125:         DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
    4126:         for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
    4127:         DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
    4128:       }
    4129:       if (X_t) {
    4130:         DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
    4131:         for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i];
    4132:         DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
    4133:       }
    4134:       if (dmAux) {
    4135:         DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);
    4136:         for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
    4137:         DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);
    4138:       }
    4139:     }
    4140:     CHKMEMQ;
    4141:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
    4142:       PetscFE fe;
    4143:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
    4144:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
    4145:         key.field = fieldI*Nf + fieldJ;
    4146:         if (hasJac)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN,     key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);}
    4147:         if (hasPrec) {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);}
    4148:         if (hasDyn)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);}
    4149:       }
    4150:       /* For finite volume, add the identity */
    4151:       if (!isFE[fieldI]) {
    4152:         PetscFV  fv;
    4153:         PetscInt eOffset = 0, Nc, fc, foff;

    4155:         PetscDSGetFieldOffset(prob, fieldI, &foff);
    4156:         PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
    4157:         PetscFVGetNumComponents(fv, &Nc);
    4158:         for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) {
    4159:           for (fc = 0; fc < Nc; ++fc) {
    4160:             const PetscInt i = foff + fc;
    4161:             if (hasJac)  {elemMat [eOffset+i*totDim+i] = 1.0;}
    4162:             if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;}
    4163:           }
    4164:         }
    4165:       }
    4166:     }
    4167:     CHKMEMQ;
    4168:     /*   Add contribution from X_t */
    4169:     if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
    4170:     /* Insert values into matrix */
    4171:     for (c = 0; c < Ncell; ++c) {
    4172:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
    4173:       if (mesh->printFEM > 1) {
    4174:         if (hasJac)  {DMPrintCellMatrix(cell, name,  totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);}
    4175:         if (hasPrec) {DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);}
    4176:       }
    4177:       if (assembleJac) {DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);}
    4178:       DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);
    4179:     }
    4180:     CHKMEMQ;
    4181:   }
    4182:   /* Cleanup */
    4183:   DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
    4184:   PetscQuadratureDestroy(&qGeom);
    4185:   if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
    4186:   DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);
    4187:   DMRestoreWorkArray(dm, ((1 + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize, MPIU_SCALAR, &work);
    4188:   /* Compute boundary integrals */
    4189:   /* DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx); */
    4190:   /* Assemble matrix */
    4191:   if (assembleJac) {MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);}
    4192:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
    4193:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
    4194:   CHKMEMQ;
    4195:   return(0);
    4196: }

    4198: /******** FEM Assembly Function ********/

    4200: static PetscErrorCode DMConvertPlex_Internal(DM dm, DM *plex, PetscBool copy)
    4201: {
    4202:   PetscBool      isPlex;

    4206:   PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
    4207:   if (isPlex) {
    4208:     *plex = dm;
    4209:     PetscObjectReference((PetscObject) dm);
    4210:   } else {
    4211:     PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
    4212:     if (!*plex) {
    4213:       DMConvert(dm,DMPLEX,plex);
    4214:       PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
    4215:       if (copy) {
    4216:         const char *comps[] = {"A", "dmAux"};
    4217:         PetscObject obj;
    4218:         PetscInt    i;

    4220:         for (i = 0; i < 2; ++i) {
    4221:           PetscObjectQuery((PetscObject) dm, comps[i], &obj);
    4222:           PetscObjectCompose((PetscObject) *plex, comps[i], obj);
    4223:         }
    4224:       }
    4225:     } else {
    4226:       PetscObjectReference((PetscObject) *plex);
    4227:     }
    4228:   }
    4229:   return(0);
    4230: }

    4232: /*@
    4233:   DMPlexGetGeometryFVM - Return precomputed geometric data

    4235:   Collective on DM

    4237:   Input Parameter:
    4238: . dm - The DM

    4240:   Output Parameters:
    4241: + facegeom - The values precomputed from face geometry
    4242: . cellgeom - The values precomputed from cell geometry
    4243: - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell

    4245:   Level: developer

    4247: .seealso: DMPlexTSSetRHSFunctionLocal()
    4248: @*/
    4249: PetscErrorCode DMPlexGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius)
    4250: {
    4251:   DM             plex;

    4256:   DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);
    4257:   DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);
    4258:   if (minRadius) {DMPlexGetMinRadius(plex, minRadius);}
    4259:   DMDestroy(&plex);
    4260:   return(0);
    4261: }

    4263: /*@
    4264:   DMPlexGetGradientDM - Return gradient data layout

    4266:   Collective on DM

    4268:   Input Parameters:
    4269: + dm - The DM
    4270: - fv - The PetscFV

    4272:   Output Parameter:
    4273: . dmGrad - The layout for gradient values

    4275:   Level: developer

    4277: .seealso: DMPlexSNESGetGeometryFVM()
    4278: @*/
    4279: PetscErrorCode DMPlexGetGradientDM(DM dm, PetscFV fv, DM *dmGrad)
    4280: {
    4281:   DM             plex;
    4282:   PetscBool      computeGradients;

    4289:   PetscFVGetComputeGradients(fv, &computeGradients);
    4290:   if (!computeGradients) {*dmGrad = NULL; return(0);}
    4291:   DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);
    4292:   DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);
    4293:   DMDestroy(&plex);
    4294:   return(0);
    4295: }

    4297: static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS)
    4298: {
    4299:   DM_Plex         *mesh = (DM_Plex *) dm->data;
    4300:   DM               plex = NULL, plexA = NULL;
    4301:   DMEnclosureType  encAux;
    4302:   PetscDS          prob, probAux = NULL;
    4303:   PetscSection     section, sectionAux = NULL;
    4304:   Vec              locA = NULL;
    4305:   PetscScalar     *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL;
    4306:   PetscInt         v;
    4307:   PetscInt         totDim, totDimAux = 0;
    4308:   PetscErrorCode   ierr;

    4311:   DMConvert(dm, DMPLEX, &plex);
    4312:   DMGetLocalSection(dm, &section);
    4313:   DMGetDS(dm, &prob);
    4314:   PetscDSGetTotalDimension(prob, &totDim);
    4315:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    4316:   if (locA) {
    4317:     DM dmAux;

    4319:     VecGetDM(locA, &dmAux);
    4320:     DMGetEnclosureRelation(dmAux, dm, &encAux);
    4321:     DMConvert(dmAux, DMPLEX, &plexA);
    4322:     DMGetDS(plexA, &probAux);
    4323:     PetscDSGetTotalDimension(probAux, &totDimAux);
    4324:     DMGetLocalSection(plexA, &sectionAux);
    4325:   }
    4326:   for (v = 0; v < numValues; ++v) {
    4327:     PetscFEGeom    *fgeom;
    4328:     PetscInt        maxDegree;
    4329:     PetscQuadrature qGeom = NULL;
    4330:     IS              pointIS;
    4331:     const PetscInt *points;
    4332:     PetscInt        numFaces, face, Nq;

    4334:     DMLabelGetStratumIS(label, values[v], &pointIS);
    4335:     if (!pointIS) continue; /* No points with that id on this process */
    4336:     {
    4337:       IS isectIS;

    4339:       /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
    4340:       ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
    4341:       ISDestroy(&pointIS);
    4342:       pointIS = isectIS;
    4343:     }
    4344:     ISGetLocalSize(pointIS,&numFaces);
    4345:     ISGetIndices(pointIS,&points);
    4346:     PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);
    4347:     DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
    4348:     if (maxDegree <= 1) {
    4349:       DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
    4350:     }
    4351:     if (!qGeom) {
    4352:       PetscFE fe;

    4354:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
    4355:       PetscFEGetFaceQuadrature(fe, &qGeom);
    4356:       PetscObjectReference((PetscObject)qGeom);
    4357:     }
    4358:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
    4359:     DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
    4360:     for (face = 0; face < numFaces; ++face) {
    4361:       const PetscInt point = points[face], *support;
    4362:       PetscScalar   *x     = NULL;
    4363:       PetscInt       i;

    4365:       DMPlexGetSupport(dm, point, &support);
    4366:       DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
    4367:       for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
    4368:       DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
    4369:       if (locX_t) {
    4370:         DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
    4371:         for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
    4372:         DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
    4373:       }
    4374:       if (locA) {
    4375:         PetscInt subp;

    4377:         DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
    4378:         DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
    4379:         for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
    4380:         DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
    4381:       }
    4382:     }
    4383:     PetscArrayzero(elemVec, numFaces*totDim);
    4384:     {
    4385:       PetscFE         fe;
    4386:       PetscInt        Nb;
    4387:       PetscFEGeom     *chunkGeom = NULL;
    4388:       /* Conforming batches */
    4389:       PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
    4390:       /* Remainder */
    4391:       PetscInt        Nr, offset;

    4393:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
    4394:       PetscFEGetDimension(fe, &Nb);
    4395:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    4396:       /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */
    4397:       blockSize = Nb;
    4398:       batchSize = numBlocks * blockSize;
    4399:        PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    4400:       numChunks = numFaces / (numBatches*batchSize);
    4401:       Ne        = numChunks*numBatches*batchSize;
    4402:       Nr        = numFaces % (numBatches*batchSize);
    4403:       offset    = numFaces - Nr;
    4404:       PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
    4405:       PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
    4406:       PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
    4407:       PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
    4408:       PetscFEIntegrateBdResidual(prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);
    4409:       PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
    4410:     }
    4411:     for (face = 0; face < numFaces; ++face) {
    4412:       const PetscInt point = points[face], *support;

    4414:       if (mesh->printFEM > 1) {DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);}
    4415:       DMPlexGetSupport(plex, point, &support);
    4416:       DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);
    4417:     }
    4418:     DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
    4419:     PetscQuadratureDestroy(&qGeom);
    4420:     ISRestoreIndices(pointIS, &points);
    4421:     ISDestroy(&pointIS);
    4422:     PetscFree4(u, u_t, elemVec, a);
    4423:   }
    4424:   DMDestroy(&plex);
    4425:   DMDestroy(&plexA);
    4426:   return(0);
    4427: }

    4429: PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF)
    4430: {
    4431:   DMField        coordField;
    4432:   DMLabel        depthLabel;
    4433:   IS             facetIS;
    4434:   PetscInt       dim;

    4438:   DMGetDimension(dm, &dim);
    4439:   DMPlexGetDepthLabel(dm, &depthLabel);
    4440:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
    4441:   DMGetCoordinateField(dm, &coordField);
    4442:   DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
    4443:   ISDestroy(&facetIS);
    4444:   return(0);
    4445: }

    4447: PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
    4448: {
    4449:   PetscDS        prob;
    4450:   PetscInt       numBd, bd;
    4451:   DMField        coordField = NULL;
    4452:   IS             facetIS    = NULL;
    4453:   DMLabel        depthLabel;
    4454:   PetscInt       dim;

    4458:   DMGetDS(dm, &prob);
    4459:   DMPlexGetDepthLabel(dm, &depthLabel);
    4460:   DMGetDimension(dm, &dim);
    4461:   DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);
    4462:   PetscDSGetNumBoundary(prob, &numBd);
    4463:   for (bd = 0; bd < numBd; ++bd) {
    4464:     DMBoundaryConditionType type;
    4465:     const char             *bdLabel;
    4466:     DMLabel                 label;
    4467:     const PetscInt         *values;
    4468:     PetscInt                field, numValues;
    4469:     PetscObject             obj;
    4470:     PetscClassId            id;

    4472:     PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, NULL, &numValues, &values, NULL);
    4473:     PetscDSGetDiscretization(prob, field, &obj);
    4474:     PetscObjectGetClassId(obj, &id);
    4475:     if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
    4476:     if (!facetIS) {
    4477:       DMLabel  depthLabel;
    4478:       PetscInt dim;

    4480:       DMPlexGetDepthLabel(dm, &depthLabel);
    4481:       DMGetDimension(dm, &dim);
    4482:       DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);
    4483:     }
    4484:     DMGetCoordinateField(dm, &coordField);
    4485:     DMGetLabel(dm, bdLabel, &label);
    4486:     DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
    4487:   }
    4488:   ISDestroy(&facetIS);
    4489:   return(0);
    4490: }

    4492: PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscHashFormKey key, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
    4493: {
    4494:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
    4495:   const char      *name       = "Residual";
    4496:   DM               dmAux      = NULL;
    4497:   DM               dmGrad     = NULL;
    4498:   DMLabel          ghostLabel = NULL;
    4499:   PetscDS          ds         = NULL;
    4500:   PetscDS          dsAux      = NULL;
    4501:   PetscSection     section    = NULL;
    4502:   PetscBool        useFEM     = PETSC_FALSE;
    4503:   PetscBool        useFVM     = PETSC_FALSE;
    4504:   PetscBool        isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
    4505:   PetscFV          fvm        = NULL;
    4506:   PetscFVCellGeom *cgeomFVM   = NULL;
    4507:   PetscFVFaceGeom *fgeomFVM   = NULL;
    4508:   DMField          coordField = NULL;
    4509:   Vec              locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL;
    4510:   PetscScalar     *u = NULL, *u_t, *a, *uL, *uR;
    4511:   IS               chunkIS;
    4512:   const PetscInt  *cells;
    4513:   PetscInt         cStart, cEnd, numCells;
    4514:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd;
    4515:   PetscInt         maxDegree = PETSC_MAX_INT;
    4516:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
    4517:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
    4518:   PetscErrorCode   ierr;

    4521:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
    4522:   /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */
    4523:   /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */
    4524:   /* FEM+FVM */
    4525:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    4526:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    4527:   /* 1: Get sizes from dm and dmAux */
    4528:   DMGetLocalSection(dm, &section);
    4529:   DMGetLabel(dm, "ghost", &ghostLabel);
    4530:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &ds);
    4531:   PetscDSGetNumFields(ds, &Nf);
    4532:   PetscDSGetTotalDimension(ds, &totDim);
    4533:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    4534:   if (locA) {
    4535:     PetscInt subcell;
    4536:     VecGetDM(locA, &dmAux);
    4537:     DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);
    4538:     DMGetCellDS(dmAux, subcell, &dsAux);
    4539:     PetscDSGetTotalDimension(dsAux, &totDimAux);
    4540:   }
    4541:   /* 2: Get geometric data */
    4542:   for (f = 0; f < Nf; ++f) {
    4543:     PetscObject  obj;
    4544:     PetscClassId id;
    4545:     PetscBool    fimp;

    4547:     PetscDSGetImplicit(ds, f, &fimp);
    4548:     if (isImplicit != fimp) continue;
    4549:     PetscDSGetDiscretization(ds, f, &obj);
    4550:     PetscObjectGetClassId(obj, &id);
    4551:     if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
    4552:     if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;}
    4553:   }
    4554:   if (useFEM) {
    4555:     DMGetCoordinateField(dm, &coordField);
    4556:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
    4557:     if (maxDegree <= 1) {
    4558:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
    4559:       if (affineQuad) {
    4560:         DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    4561:       }
    4562:     } else {
    4563:       PetscCalloc2(Nf,&quads,Nf,&geoms);
    4564:       for (f = 0; f < Nf; ++f) {
    4565:         PetscObject  obj;
    4566:         PetscClassId id;
    4567:         PetscBool    fimp;

    4569:         PetscDSGetImplicit(ds, f, &fimp);
    4570:         if (isImplicit != fimp) continue;
    4571:         PetscDSGetDiscretization(ds, f, &obj);
    4572:         PetscObjectGetClassId(obj, &id);
    4573:         if (id == PETSCFE_CLASSID) {
    4574:           PetscFE fe = (PetscFE) obj;

    4576:           PetscFEGetQuadrature(fe, &quads[f]);
    4577:           PetscObjectReference((PetscObject)quads[f]);
    4578:           DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
    4579:         }
    4580:       }
    4581:     }
    4582:   }
    4583:   if (useFVM) {
    4584:     DMPlexGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);
    4585:     VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);
    4586:     VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
    4587:     /* Reconstruct and limit cell gradients */
    4588:     DMPlexGetGradientDM(dm, fvm, &dmGrad);
    4589:     if (dmGrad) {
    4590:       DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
    4591:       DMGetGlobalVector(dmGrad, &grad);
    4592:       DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
    4593:       /* Communicate gradient values */
    4594:       DMGetLocalVector(dmGrad, &locGrad);
    4595:       DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
    4596:       DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
    4597:       DMRestoreGlobalVector(dmGrad, &grad);
    4598:     }
    4599:     /* Handle non-essential (e.g. outflow) boundary values */
    4600:     DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);
    4601:   }
    4602:   /* Loop over chunks */
    4603:   if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
    4604:   numCells      = cEnd - cStart;
    4605:   numChunks     = 1;
    4606:   cellChunkSize = numCells/numChunks;
    4607:   faceChunkSize = (fEnd - fStart)/numChunks;
    4608:   numChunks     = PetscMin(1,numCells);
    4609:   for (chunk = 0; chunk < numChunks; ++chunk) {
    4610:     PetscScalar     *elemVec, *fluxL, *fluxR;
    4611:     PetscReal       *vol;
    4612:     PetscFVFaceGeom *fgeom;
    4613:     PetscInt         cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
    4614:     PetscInt         fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face;

    4616:     /* Extract field coefficients */
    4617:     if (useFEM) {
    4618:       ISGetPointSubrange(chunkIS, cS, cE, cells);
    4619:       DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
    4620:       DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
    4621:       PetscArrayzero(elemVec, numCells*totDim);
    4622:     }
    4623:     if (useFVM) {
    4624:       DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
    4625:       DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
    4626:       DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
    4627:       DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
    4628:       PetscArrayzero(fluxL, numFaces*totDim);
    4629:       PetscArrayzero(fluxR, numFaces*totDim);
    4630:     }
    4631:     /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
    4632:     /* Loop over fields */
    4633:     for (f = 0; f < Nf; ++f) {
    4634:       PetscObject  obj;
    4635:       PetscClassId id;
    4636:       PetscBool    fimp;
    4637:       PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

    4639:       key.field = f;
    4640:       PetscDSGetImplicit(ds, f, &fimp);
    4641:       if (isImplicit != fimp) continue;
    4642:       PetscDSGetDiscretization(ds, f, &obj);
    4643:       PetscObjectGetClassId(obj, &id);
    4644:       if (id == PETSCFE_CLASSID) {
    4645:         PetscFE         fe = (PetscFE) obj;
    4646:         PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
    4647:         PetscFEGeom    *chunkGeom = NULL;
    4648:         PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
    4649:         PetscInt        Nq, Nb;

    4651:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    4652:         PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
    4653:         PetscFEGetDimension(fe, &Nb);
    4654:         blockSize = Nb;
    4655:         batchSize = numBlocks * blockSize;
    4656:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    4657:         numChunks = numCells / (numBatches*batchSize);
    4658:         Ne        = numChunks*numBatches*batchSize;
    4659:         Nr        = numCells % (numBatches*batchSize);
    4660:         offset    = numCells - Nr;
    4661:         /* Integrate FE residual to get elemVec (need fields at quadrature points) */
    4662:         /*   For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */
    4663:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
    4664:         PetscFEIntegrateResidual(ds, key, Ne, chunkGeom, u, u_t, dsAux, a, t, elemVec);
    4665:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
    4666:         PetscFEIntegrateResidual(ds, key, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
    4667:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
    4668:       } else if (id == PETSCFV_CLASSID) {
    4669:         PetscFV fv = (PetscFV) obj;

    4671:         Ne = numFaces;
    4672:         /* Riemann solve over faces (need fields at face centroids) */
    4673:         /*   We need to evaluate FE fields at those coordinates */
    4674:         PetscFVIntegrateRHSFunction(fv, ds, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
    4675:       } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
    4676:     }
    4677:     /* Loop over domain */
    4678:     if (useFEM) {
    4679:       /* Add elemVec to locX */
    4680:       for (c = cS; c < cE; ++c) {
    4681:         const PetscInt cell = cells ? cells[c] : c;
    4682:         const PetscInt cind = c - cStart;

    4684:         if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
    4685:         if (ghostLabel) {
    4686:           PetscInt ghostVal;

    4688:           DMLabelGetValue(ghostLabel,cell,&ghostVal);
    4689:           if (ghostVal > 0) continue;
    4690:         }
    4691:         DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
    4692:       }
    4693:     }
    4694:     if (useFVM) {
    4695:       PetscScalar *fa;
    4696:       PetscInt     iface;

    4698:       VecGetArray(locF, &fa);
    4699:       for (f = 0; f < Nf; ++f) {
    4700:         PetscFV      fv;
    4701:         PetscObject  obj;
    4702:         PetscClassId id;
    4703:         PetscInt     foff, pdim;

    4705:         PetscDSGetDiscretization(ds, f, &obj);
    4706:         PetscDSGetFieldOffset(ds, f, &foff);
    4707:         PetscObjectGetClassId(obj, &id);
    4708:         if (id != PETSCFV_CLASSID) continue;
    4709:         fv   = (PetscFV) obj;
    4710:         PetscFVGetNumComponents(fv, &pdim);
    4711:         /* Accumulate fluxes to cells */
    4712:         for (face = fS, iface = 0; face < fE; ++face) {
    4713:           const PetscInt *scells;
    4714:           PetscScalar    *fL = NULL, *fR = NULL;
    4715:           PetscInt        ghost, d, nsupp, nchild;

    4717:           DMLabelGetValue(ghostLabel, face, &ghost);
    4718:           DMPlexGetSupportSize(dm, face, &nsupp);
    4719:           DMPlexGetTreeChildren(dm, face, &nchild, NULL);
    4720:           if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
    4721:           DMPlexGetSupport(dm, face, &scells);
    4722:           DMLabelGetValue(ghostLabel,scells[0],&ghost);
    4723:           if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);}
    4724:           DMLabelGetValue(ghostLabel,scells[1],&ghost);
    4725:           if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);}
    4726:           for (d = 0; d < pdim; ++d) {
    4727:             if (fL) fL[d] -= fluxL[iface*totDim+foff+d];
    4728:             if (fR) fR[d] += fluxR[iface*totDim+foff+d];
    4729:           }
    4730:           ++iface;
    4731:         }
    4732:       }
    4733:       VecRestoreArray(locF, &fa);
    4734:     }
    4735:     /* Handle time derivative */
    4736:     if (locX_t) {
    4737:       PetscScalar *x_t, *fa;

    4739:       VecGetArray(locF, &fa);
    4740:       VecGetArray(locX_t, &x_t);
    4741:       for (f = 0; f < Nf; ++f) {
    4742:         PetscFV      fv;
    4743:         PetscObject  obj;
    4744:         PetscClassId id;
    4745:         PetscInt     pdim, d;

    4747:         PetscDSGetDiscretization(ds, f, &obj);
    4748:         PetscObjectGetClassId(obj, &id);
    4749:         if (id != PETSCFV_CLASSID) continue;
    4750:         fv   = (PetscFV) obj;
    4751:         PetscFVGetNumComponents(fv, &pdim);
    4752:         for (c = cS; c < cE; ++c) {
    4753:           const PetscInt cell = cells ? cells[c] : c;
    4754:           PetscScalar   *u_t, *r;

    4756:           if (ghostLabel) {
    4757:             PetscInt ghostVal;

    4759:             DMLabelGetValue(ghostLabel, cell, &ghostVal);
    4760:             if (ghostVal > 0) continue;
    4761:           }
    4762:           DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
    4763:           DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
    4764:           for (d = 0; d < pdim; ++d) r[d] += u_t[d];
    4765:         }
    4766:       }
    4767:       VecRestoreArray(locX_t, &x_t);
    4768:       VecRestoreArray(locF, &fa);
    4769:     }
    4770:     if (useFEM) {
    4771:       DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
    4772:       DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
    4773:     }
    4774:     if (useFVM) {
    4775:       DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
    4776:       DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
    4777:       DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
    4778:       DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
    4779:       if (dmGrad) {DMRestoreLocalVector(dmGrad, &locGrad);}
    4780:     }
    4781:   }
    4782:   if (useFEM) {ISDestroy(&chunkIS);}
    4783:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);

    4785:   if (useFEM) {
    4786:     DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);

    4788:     if (maxDegree <= 1) {
    4789:       DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    4790:       PetscQuadratureDestroy(&affineQuad);
    4791:     } else {
    4792:       for (f = 0; f < Nf; ++f) {
    4793:         DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
    4794:         PetscQuadratureDestroy(&quads[f]);
    4795:       }
    4796:       PetscFree2(quads,geoms);
    4797:     }
    4798:   }

    4800:   /* FEM */
    4801:   /* 1: Get sizes from dm and dmAux */
    4802:   /* 2: Get geometric data */
    4803:   /* 3: Handle boundary values */
    4804:   /* 4: Loop over domain */
    4805:   /*   Extract coefficients */
    4806:   /* Loop over fields */
    4807:   /*   Set tiling for FE*/
    4808:   /*   Integrate FE residual to get elemVec */
    4809:   /*     Loop over subdomain */
    4810:   /*       Loop over quad points */
    4811:   /*         Transform coords to real space */
    4812:   /*         Evaluate field and aux fields at point */
    4813:   /*         Evaluate residual at point */
    4814:   /*         Transform residual to real space */
    4815:   /*       Add residual to elemVec */
    4816:   /* Loop over domain */
    4817:   /*   Add elemVec to locX */

    4819:   /* FVM */
    4820:   /* Get geometric data */
    4821:   /* If using gradients */
    4822:   /*   Compute gradient data */
    4823:   /*   Loop over domain faces */
    4824:   /*     Count computational faces */
    4825:   /*     Reconstruct cell gradient */
    4826:   /*   Loop over domain cells */
    4827:   /*     Limit cell gradients */
    4828:   /* Handle boundary values */
    4829:   /* Loop over domain faces */
    4830:   /*   Read out field, centroid, normal, volume for each side of face */
    4831:   /* Riemann solve over faces */
    4832:   /* Loop over domain faces */
    4833:   /*   Accumulate fluxes to cells */
    4834:   /* TODO Change printFEM to printDisc here */
    4835:   if (mesh->printFEM) {
    4836:     Vec         locFbc;
    4837:     PetscInt    pStart, pEnd, p, maxDof;
    4838:     PetscScalar *zeroes;

    4840:     VecDuplicate(locF,&locFbc);
    4841:     VecCopy(locF,locFbc);
    4842:     PetscSectionGetChart(section,&pStart,&pEnd);
    4843:     PetscSectionGetMaxDof(section,&maxDof);
    4844:     PetscCalloc1(maxDof,&zeroes);
    4845:     for (p = pStart; p < pEnd; p++) {
    4846:       VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);
    4847:     }
    4848:     PetscFree(zeroes);
    4849:     DMPrintLocalVec(dm, name, mesh->printTol, locFbc);
    4850:     VecDestroy(&locFbc);
    4851:   }
    4852:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
    4853:   return(0);
    4854: }

    4856: /*
    4857:   1) Allow multiple kernels for BdResidual for hybrid DS

    4859:   DONE 2) Get out dsAux for either side at the same time as cohesive cell dsAux

    4861:   DONE 3) Change DMGetCellFields() to get different aux data a[] for each side
    4862:      - I think I just need to replace a[] with the closure from each face

    4864:   4) Run both kernels for each non-hybrid field with correct dsAux, and then hybrid field as before
    4865: */
    4866: PetscErrorCode DMPlexComputeResidual_Hybrid_Internal(DM dm, PetscHashFormKey key[], IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
    4867: {
    4868:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
    4869:   const char      *name       = "Hybrid Residual";
    4870:   DM               dmAux      = NULL;
    4871:   DMLabel          ghostLabel = NULL;
    4872:   PetscDS          ds         = NULL;
    4873:   PetscDS          dsAux[3]   = {NULL, NULL, NULL};
    4874:   PetscSection     section    = NULL;
    4875:   DMField          coordField = NULL;
    4876:   Vec              locA;
    4877:   PetscScalar     *u = NULL, *u_t, *a[3];
    4878:   PetscScalar     *elemVec;
    4879:   IS               chunkIS;
    4880:   const PetscInt  *cells;
    4881:   PetscInt        *faces;
    4882:   PetscInt         cStart, cEnd, numCells;
    4883:   PetscInt         Nf, f, totDim, totDimAux[3], numChunks, cellChunkSize, chunk;
    4884:   PetscInt         maxDegree = PETSC_MAX_INT;
    4885:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
    4886:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
    4887:   PetscErrorCode   ierr;

    4890:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
    4891:   /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */
    4892:   /* FEM */
    4893:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    4894:   /* 1: Get sizes from dm and dmAux */
    4895:   DMGetSection(dm, &section);
    4896:   DMGetLabel(dm, "ghost", &ghostLabel);
    4897:   DMGetCellDS(dm, cStart, &ds);
    4898:   PetscDSGetNumFields(ds, &Nf);
    4899:   PetscDSGetTotalDimension(ds, &totDim);
    4900:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    4901:   if (locA) {
    4902:     VecGetDM(locA, &dmAux);
    4903:     DMGetCellDS(dmAux, cStart, &dsAux[2]);
    4904:     PetscDSGetTotalDimension(dsAux[2], &totDimAux[2]);
    4905:     {
    4906:       const PetscInt *cone;
    4907:       PetscInt        c;

    4909:       DMPlexGetCone(dm, cStart, &cone);
    4910:       for (c = 0; c < 2; ++c) {
    4911:         const PetscInt *support;
    4912:         PetscInt ssize, s;

    4914:         DMPlexGetSupport(dm, cone[c], &support);
    4915:         DMPlexGetSupportSize(dm, cone[c], &ssize);
    4916:         if (ssize != 2) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D from cell %D has support size %D != 2", cone[c], cStart, ssize);
    4917:         if      (support[0] == cStart) s = 1;
    4918:         else if (support[1] == cStart) s = 0;
    4919:         else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D does not have cell %D in its support", cone[c], cStart);
    4920:         DMGetCellDS(dmAux, support[s], &dsAux[c]);
    4921:         PetscDSGetTotalDimension(dsAux[c], &totDimAux[c]);
    4922:       }
    4923:     }
    4924:   }
    4925:   /* 2: Setup geometric data */
    4926:   DMGetCoordinateField(dm, &coordField);
    4927:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
    4928:   if (maxDegree > 1) {
    4929:     PetscCalloc2(Nf, &quads, Nf, &geoms);
    4930:     for (f = 0; f < Nf; ++f) {
    4931:       PetscFE fe;

    4933:       PetscDSGetDiscretization(ds, f, (PetscObject *) &fe);
    4934:       if (fe) {
    4935:         PetscFEGetQuadrature(fe, &quads[f]);
    4936:         PetscObjectReference((PetscObject) quads[f]);
    4937:       }
    4938:     }
    4939:   }
    4940:   /* Loop over chunks */
    4941:   numCells      = cEnd - cStart;
    4942:   cellChunkSize = numCells;
    4943:   numChunks     = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize);
    4944:   PetscCalloc1(2*cellChunkSize, &faces);
    4945:   ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);
    4946:   /* Extract field coefficients */
    4947:   /* NOTE This needs the end cap faces to have identical orientations */
    4948:   DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a[2]);
    4949:   DMPlexGetHybridAuxFields(dm, dsAux, cellIS, locA, a);
    4950:   DMGetWorkArray(dm, cellChunkSize*totDim, MPIU_SCALAR, &elemVec);
    4951:   for (chunk = 0; chunk < numChunks; ++chunk) {
    4952:     PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;

    4954:     PetscMemzero(elemVec, cellChunkSize*totDim * sizeof(PetscScalar));
    4955:     /* Get faces */
    4956:     for (c = cS; c < cE; ++c) {
    4957:       const PetscInt  cell = cells ? cells[c] : c;
    4958:       const PetscInt *cone;
    4959:       DMPlexGetCone(dm, cell, &cone);
    4960:       faces[(c-cS)*2+0] = cone[0];
    4961:       faces[(c-cS)*2+1] = cone[1];
    4962:     }
    4963:     ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);
    4964:     /* Get geometric data */
    4965:     if (maxDegree <= 1) {
    4966:       if (!affineQuad) {DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);}
    4967:       if (affineQuad)  {DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);}
    4968:     } else {
    4969:       for (f = 0; f < Nf; ++f) {
    4970:         if (quads[f]) {DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);}
    4971:       }
    4972:     }
    4973:     /* Loop over fields */
    4974:     for (f = 0; f < Nf; ++f) {
    4975:       PetscFE         fe;
    4976:       PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
    4977:       PetscFEGeom    *chunkGeom = NULL;
    4978:       PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
    4979:       PetscInt        numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb;

    4981:       PetscDSGetDiscretization(ds, f, (PetscObject *) &fe);
    4982:       if (!fe) continue;
    4983:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    4984:       PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
    4985:       PetscFEGetDimension(fe, &Nb);
    4986:       blockSize = Nb;
    4987:       batchSize = numBlocks * blockSize;
    4988:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    4989:       numChunks = numCells / (numBatches*batchSize);
    4990:       Ne        = numChunks*numBatches*batchSize;
    4991:       Nr        = numCells % (numBatches*batchSize);
    4992:       offset    = numCells - Nr;
    4993:       if (f == Nf-1) {
    4994:         key[2].field = f;
    4995:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
    4996:         PetscFEIntegrateHybridResidual(ds, key[2], Ne, chunkGeom, u, u_t, dsAux[2], a[2], t, elemVec);
    4997:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
    4998:         PetscFEIntegrateHybridResidual(ds, key[2], Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[2], &a[2][offset*totDimAux[2]], t, &elemVec[offset*totDim]);
    4999:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
    5000:       } else {
    5001:         key[0].field = f;
    5002:         key[1].field = f;
    5003:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
    5004:         PetscFEIntegrateHybridResidual(ds, key[0], Ne, chunkGeom, u, u_t, dsAux[0], a[0], t, elemVec);
    5005:         PetscFEIntegrateHybridResidual(ds, key[1], Ne, chunkGeom, u, u_t, dsAux[1], a[1], t, elemVec);
    5006:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
    5007:         PetscFEIntegrateHybridResidual(ds, key[0], Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[0], &a[0][offset*totDimAux[0]], t, &elemVec[offset*totDim]);
    5008:         PetscFEIntegrateHybridResidual(ds, key[1], Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, dsAux[1], &a[1][offset*totDimAux[1]], t, &elemVec[offset*totDim]);
    5009:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
    5010:       }
    5011:     }
    5012:     /* Add elemVec to locX */
    5013:     for (c = cS; c < cE; ++c) {
    5014:       const PetscInt cell = cells ? cells[c] : c;
    5015:       const PetscInt cind = c - cStart;

    5017:       if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
    5018:       if (ghostLabel) {
    5019:         PetscInt ghostVal;

    5021:         DMLabelGetValue(ghostLabel,cell,&ghostVal);
    5022:         if (ghostVal > 0) continue;
    5023:       }
    5024:       DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
    5025:     }
    5026:   }
    5027:   DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a[2]);
    5028:   DMPlexRestoreHybridAuxFields(dm, dsAux, cellIS, locA, a);
    5029:   DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
    5030:   PetscFree(faces);
    5031:   ISDestroy(&chunkIS);
    5032:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    5033:   if (maxDegree <= 1) {
    5034:     DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    5035:     PetscQuadratureDestroy(&affineQuad);
    5036:   } else {
    5037:     for (f = 0; f < Nf; ++f) {
    5038:       if (geoms) {DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);}
    5039:       if (quads) {PetscQuadratureDestroy(&quads[f]);}
    5040:     }
    5041:     PetscFree2(quads,geoms);
    5042:   }
    5043:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
    5044:   return(0);
    5045: }

    5047: PetscErrorCode DMPlexComputeBdJacobian_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt fieldI, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, DMField coordField, IS facetIS)
    5048: {
    5049:   DM_Plex        *mesh = (DM_Plex *) dm->data;
    5050:   DM              plex = NULL, plexA = NULL, tdm;
    5051:   DMEnclosureType encAux;
    5052:   PetscDS         prob, probAux = NULL;
    5053:   PetscSection    section, sectionAux = NULL;
    5054:   PetscSection    globalSection, subSection = NULL;
    5055:   Vec             locA = NULL, tv;
    5056:   PetscScalar    *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL;
    5057:   PetscInt        v;
    5058:   PetscInt        Nf, totDim, totDimAux = 0;
    5059:   PetscBool       isMatISP, transform;
    5060:   PetscErrorCode  ierr;

    5063:   DMConvert(dm, DMPLEX, &plex);
    5064:   DMHasBasisTransform(dm, &transform);
    5065:   DMGetBasisTransformDM_Internal(dm, &tdm);
    5066:   DMGetBasisTransformVec_Internal(dm, &tv);
    5067:   DMGetLocalSection(dm, &section);
    5068:   DMGetDS(dm, &prob);
    5069:   PetscDSGetNumFields(prob, &Nf);
    5070:   PetscDSGetTotalDimension(prob, &totDim);
    5071:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    5072:   if (locA) {
    5073:     DM dmAux;

    5075:     VecGetDM(locA, &dmAux);
    5076:     DMGetEnclosureRelation(dmAux, dm, &encAux);
    5077:     DMConvert(dmAux, DMPLEX, &plexA);
    5078:     DMGetDS(plexA, &probAux);
    5079:     PetscDSGetTotalDimension(probAux, &totDimAux);
    5080:     DMGetLocalSection(plexA, &sectionAux);
    5081:   }

    5083:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
    5084:   DMGetGlobalSection(dm, &globalSection);
    5085:   if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
    5086:   for (v = 0; v < numValues; ++v) {
    5087:     PetscFEGeom    *fgeom;
    5088:     PetscInt        maxDegree;
    5089:     PetscQuadrature qGeom = NULL;
    5090:     IS              pointIS;
    5091:     const PetscInt *points;
    5092:     PetscInt        numFaces, face, Nq;

    5094:     DMLabelGetStratumIS(label, values[v], &pointIS);
    5095:     if (!pointIS) continue; /* No points with that id on this process */
    5096:     {
    5097:       IS isectIS;

    5099:       /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */
    5100:       ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
    5101:       ISDestroy(&pointIS);
    5102:       pointIS = isectIS;
    5103:     }
    5104:     ISGetLocalSize(pointIS, &numFaces);
    5105:     ISGetIndices(pointIS, &points);
    5106:     PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);
    5107:     DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
    5108:     if (maxDegree <= 1) {
    5109:       DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
    5110:     }
    5111:     if (!qGeom) {
    5112:       PetscFE fe;

    5114:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
    5115:       PetscFEGetFaceQuadrature(fe, &qGeom);
    5116:       PetscObjectReference((PetscObject)qGeom);
    5117:     }
    5118:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
    5119:     DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
    5120:     for (face = 0; face < numFaces; ++face) {
    5121:       const PetscInt point = points[face], *support;
    5122:       PetscScalar   *x     = NULL;
    5123:       PetscInt       i;

    5125:       DMPlexGetSupport(dm, point, &support);
    5126:       DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
    5127:       for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
    5128:       DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
    5129:       if (locX_t) {
    5130:         DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
    5131:         for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
    5132:         DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
    5133:       }
    5134:       if (locA) {
    5135:         PetscInt subp;
    5136:         DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
    5137:         DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
    5138:         for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
    5139:         DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
    5140:       }
    5141:     }
    5142:     PetscArrayzero(elemMat, numFaces*totDim*totDim);
    5143:     {
    5144:       PetscFE         fe;
    5145:       PetscInt        Nb;
    5146:       /* Conforming batches */
    5147:       PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
    5148:       /* Remainder */
    5149:       PetscFEGeom    *chunkGeom = NULL;
    5150:       PetscInt        fieldJ, Nr, offset;

    5152:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
    5153:       PetscFEGetDimension(fe, &Nb);
    5154:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    5155:       blockSize = Nb;
    5156:       batchSize = numBlocks * blockSize;
    5157:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    5158:       numChunks = numFaces / (numBatches*batchSize);
    5159:       Ne        = numChunks*numBatches*batchSize;
    5160:       Nr        = numFaces % (numBatches*batchSize);
    5161:       offset    = numFaces - Nr;
    5162:       PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
    5163:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
    5164:         PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
    5165:       }
    5166:       PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
    5167:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
    5168:         PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, X_tShift, &elemMat[offset*totDim*totDim]);
    5169:       }
    5170:       PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
    5171:     }
    5172:     for (face = 0; face < numFaces; ++face) {
    5173:       const PetscInt point = points[face], *support;

    5175:       /* Transform to global basis before insertion in Jacobian */
    5176:       DMPlexGetSupport(plex, point, &support);
    5177:       if (transform) {DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);}
    5178:       if (mesh->printFEM > 1) {DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);}
    5179:       if (!isMatISP) {
    5180:         DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
    5181:       } else {
    5182:         Mat lJ;

    5184:         MatISGetLocalMat(JacP, &lJ);
    5185:         DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
    5186:       }
    5187:     }
    5188:     DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
    5189:     PetscQuadratureDestroy(&qGeom);
    5190:     ISRestoreIndices(pointIS, &points);
    5191:     ISDestroy(&pointIS);
    5192:     PetscFree4(u, u_t, elemMat, a);
    5193:   }
    5194:   if (plex)  {DMDestroy(&plex);}
    5195:   if (plexA) {DMDestroy(&plexA);}
    5196:   return(0);
    5197: }

    5199: PetscErrorCode DMPlexComputeBdJacobianSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP)
    5200: {
    5201:   DMField        coordField;
    5202:   DMLabel        depthLabel;
    5203:   IS             facetIS;
    5204:   PetscInt       dim;

    5208:   DMGetDimension(dm, &dim);
    5209:   DMPlexGetDepthLabel(dm, &depthLabel);
    5210:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
    5211:   DMGetCoordinateField(dm, &coordField);
    5212:   DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
    5213:   ISDestroy(&facetIS);
    5214:   return(0);
    5215: }

    5217: PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
    5218: {
    5219:   PetscDS          prob;
    5220:   PetscInt         dim, numBd, bd;
    5221:   DMLabel          depthLabel;
    5222:   DMField          coordField = NULL;
    5223:   IS               facetIS;
    5224:   PetscErrorCode   ierr;

    5227:   DMGetDS(dm, &prob);
    5228:   DMPlexGetDepthLabel(dm, &depthLabel);
    5229:   DMGetDimension(dm, &dim);
    5230:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
    5231:   PetscDSGetNumBoundary(prob, &numBd);
    5232:   DMGetCoordinateField(dm, &coordField);
    5233:   for (bd = 0; bd < numBd; ++bd) {
    5234:     DMBoundaryConditionType type;
    5235:     const char             *bdLabel;
    5236:     DMLabel                 label;
    5237:     const PetscInt         *values;
    5238:     PetscInt                fieldI, numValues;
    5239:     PetscObject             obj;
    5240:     PetscClassId            id;

    5242:     PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, NULL, &numValues, &values, NULL);
    5243:     PetscDSGetDiscretization(prob, fieldI, &obj);
    5244:     PetscObjectGetClassId(obj, &id);
    5245:     if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
    5246:     DMGetLabel(dm, bdLabel, &label);
    5247:     DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
    5248:   }
    5249:   ISDestroy(&facetIS);
    5250:   return(0);
    5251: }

    5253: PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, PetscHashFormKey key, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user)
    5254: {
    5255:   DM_Plex        *mesh  = (DM_Plex *) dm->data;
    5256:   const char     *name  = "Jacobian";
    5257:   DM              dmAux, plex, tdm;
    5258:   DMEnclosureType encAux;
    5259:   Vec             A, tv;
    5260:   DMField         coordField;
    5261:   PetscDS         prob, probAux = NULL;
    5262:   PetscSection    section, globalSection, subSection, sectionAux;
    5263:   PetscScalar    *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL;
    5264:   const PetscInt *cells;
    5265:   PetscInt        Nf, fieldI, fieldJ;
    5266:   PetscInt        totDim, totDimAux, cStart, cEnd, numCells, c;
    5267:   PetscBool       isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform;
    5268:   PetscErrorCode  ierr;

    5271:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
    5272:   ISGetLocalSize(cellIS, &numCells);
    5273:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    5274:   DMHasBasisTransform(dm, &transform);
    5275:   DMGetBasisTransformDM_Internal(dm, &tdm);
    5276:   DMGetBasisTransformVec_Internal(dm, &tv);
    5277:   DMGetLocalSection(dm, &section);
    5278:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
    5279:   DMGetGlobalSection(dm, &globalSection);
    5280:   if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
    5281:   ISGetLocalSize(cellIS, &numCells);
    5282:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    5283:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);
    5284:   PetscDSGetNumFields(prob, &Nf);
    5285:   PetscDSGetTotalDimension(prob, &totDim);
    5286:   PetscDSHasJacobian(prob, &hasJac);
    5287:   PetscDSHasJacobianPreconditioner(prob, &hasPrec);
    5288:   /* user passed in the same matrix, avoid double contributions and
    5289:      only assemble the Jacobian */
    5290:   if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE;
    5291:   PetscDSHasDynamicJacobian(prob, &hasDyn);
    5292:   hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
    5293:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
    5294:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
    5295:   if (dmAux) {
    5296:     DMGetEnclosureRelation(dmAux, dm, &encAux);
    5297:     DMConvert(dmAux, DMPLEX, &plex);
    5298:     DMGetLocalSection(plex, &sectionAux);
    5299:     DMGetDS(dmAux, &probAux);
    5300:     PetscDSGetTotalDimension(probAux, &totDimAux);
    5301:   }
    5302:   PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,hasJac ? numCells*totDim*totDim : 0,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);
    5303:   if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
    5304:   DMGetCoordinateField(dm, &coordField);
    5305:   for (c = cStart; c < cEnd; ++c) {
    5306:     const PetscInt cell = cells ? cells[c] : c;
    5307:     const PetscInt cind = c - cStart;
    5308:     PetscScalar   *x = NULL,  *x_t = NULL;
    5309:     PetscInt       i;

    5311:     DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
    5312:     for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i];
    5313:     DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
    5314:     if (X_t) {
    5315:       DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
    5316:       for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i];
    5317:       DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
    5318:     }
    5319:     if (dmAux) {
    5320:       PetscInt subcell;
    5321:       DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);
    5322:       DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);
    5323:       for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i];
    5324:       DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);
    5325:     }
    5326:   }
    5327:   if (hasJac)  {PetscArrayzero(elemMat,  numCells*totDim*totDim);}
    5328:   if (hasPrec) {PetscArrayzero(elemMatP, numCells*totDim*totDim);}
    5329:   if (hasDyn)  {PetscArrayzero(elemMatD, numCells*totDim*totDim);}
    5330:   for (fieldI = 0; fieldI < Nf; ++fieldI) {
    5331:     PetscClassId    id;
    5332:     PetscFE         fe;
    5333:     PetscQuadrature qGeom = NULL;
    5334:     PetscInt        Nb;
    5335:     /* Conforming batches */
    5336:     PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
    5337:     /* Remainder */
    5338:     PetscInt        Nr, offset, Nq;
    5339:     PetscInt        maxDegree;
    5340:     PetscFEGeom     *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL;

    5342:     PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
    5343:     PetscObjectGetClassId((PetscObject) fe, &id);
    5344:     if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;}
    5345:     PetscFEGetDimension(fe, &Nb);
    5346:     PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
    5347:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
    5348:     if (maxDegree <= 1) {
    5349:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);
    5350:     }
    5351:     if (!qGeom) {
    5352:       PetscFEGetQuadrature(fe,&qGeom);
    5353:       PetscObjectReference((PetscObject)qGeom);
    5354:     }
    5355:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
    5356:     DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
    5357:     blockSize = Nb;
    5358:     batchSize = numBlocks * blockSize;
    5359:     PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
    5360:     numChunks = numCells / (numBatches*batchSize);
    5361:     Ne        = numChunks*numBatches*batchSize;
    5362:     Nr        = numCells % (numBatches*batchSize);
    5363:     offset    = numCells - Nr;
    5364:     PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
    5365:     PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);
    5366:     for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
    5367:       key.field = fieldI*Nf+fieldJ;
    5368:       if (hasJac) {
    5369:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
    5370:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
    5371:       }
    5372:       if (hasPrec) {
    5373:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);
    5374:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);
    5375:       }
    5376:       if (hasDyn) {
    5377:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);
    5378:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, key, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);
    5379:       }
    5380:     }
    5381:     PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);
    5382:     PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);
    5383:     DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
    5384:     PetscQuadratureDestroy(&qGeom);
    5385:   }
    5386:   /*   Add contribution from X_t */
    5387:   if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
    5388:   if (hasFV) {
    5389:     PetscClassId id;
    5390:     PetscFV      fv;
    5391:     PetscInt     offsetI, NcI, NbI = 1, fc, f;

    5393:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
    5394:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
    5395:       PetscDSGetFieldOffset(prob, fieldI, &offsetI);
    5396:       PetscObjectGetClassId((PetscObject) fv, &id);
    5397:       if (id != PETSCFV_CLASSID) continue;
    5398:       /* Put in the identity */
    5399:       PetscFVGetNumComponents(fv, &NcI);
    5400:       for (c = cStart; c < cEnd; ++c) {
    5401:         const PetscInt cind    = c - cStart;
    5402:         const PetscInt eOffset = cind*totDim*totDim;
    5403:         for (fc = 0; fc < NcI; ++fc) {
    5404:           for (f = 0; f < NbI; ++f) {
    5405:             const PetscInt i = offsetI + f*NcI+fc;
    5406:             if (hasPrec) {
    5407:               if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;}
    5408:               elemMatP[eOffset+i*totDim+i] = 1.0;
    5409:             } else {elemMat[eOffset+i*totDim+i] = 1.0;}
    5410:           }
    5411:         }
    5412:       }
    5413:     }
    5414:     /* No allocated space for FV stuff, so ignore the zero entries */
    5415:     MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);
    5416:   }
    5417:   /* Insert values into matrix */
    5418:   isMatIS = PETSC_FALSE;
    5419:   if (hasPrec && hasJac) {
    5420:     PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);
    5421:   }
    5422:   if (isMatIS && !subSection) {
    5423:     DMPlexGetSubdomainSection(dm, &subSection);
    5424:   }
    5425:   for (c = cStart; c < cEnd; ++c) {
    5426:     const PetscInt cell = cells ? cells[c] : c;
    5427:     const PetscInt cind = c - cStart;

    5429:     /* Transform to global basis before insertion in Jacobian */
    5430:     if (transform) {DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);}
    5431:     if (hasPrec) {
    5432:       if (hasJac) {
    5433:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
    5434:         if (!isMatIS) {
    5435:           DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5436:         } else {
    5437:           Mat lJ;

    5439:           MatISGetLocalMat(Jac,&lJ);
    5440:           DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5441:         }
    5442:       }
    5443:       if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);}
    5444:       if (!isMatISP) {
    5445:         DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
    5446:       } else {
    5447:         Mat lJ;

    5449:         MatISGetLocalMat(JacP,&lJ);
    5450:         DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
    5451:       }
    5452:     } else {
    5453:       if (hasJac) {
    5454:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
    5455:         if (!isMatISP) {
    5456:           DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5457:         } else {
    5458:           Mat lJ;

    5460:           MatISGetLocalMat(JacP,&lJ);
    5461:           DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5462:         }
    5463:       }
    5464:     }
    5465:   }
    5466:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    5467:   if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
    5468:   PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);
    5469:   if (dmAux) {
    5470:     PetscFree(a);
    5471:     DMDestroy(&plex);
    5472:   }
    5473:   /* Compute boundary integrals */
    5474:   DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);
    5475:   /* Assemble matrix */
    5476:   if (hasJac && hasPrec) {
    5477:     MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);
    5478:     MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);
    5479:   }
    5480:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);
    5481:   MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
    5482:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
    5483:   return(0);
    5484: }

    5486: PetscErrorCode DMPlexComputeJacobian_Hybrid_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec locX, Vec locX_t, Mat Jac, Mat JacP, void *user)
    5487: {
    5488:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
    5489:   const char      *name       = "Hybrid Jacobian";
    5490:   DM               dmAux      = NULL;
    5491:   DM               plex       = NULL;
    5492:   DM               plexA      = NULL;
    5493:   DMLabel          ghostLabel = NULL;
    5494:   PetscDS          prob       = NULL;
    5495:   PetscDS          probAux    = NULL;
    5496:   PetscSection     section    = NULL;
    5497:   DMField          coordField = NULL;
    5498:   Vec              locA;
    5499:   PetscScalar     *u = NULL, *u_t, *a = NULL;
    5500:   PetscScalar     *elemMat, *elemMatP;
    5501:   PetscSection     globalSection, subSection, sectionAux;
    5502:   IS               chunkIS;
    5503:   const PetscInt  *cells;
    5504:   PetscInt        *faces;
    5505:   PetscInt         cStart, cEnd, numCells;
    5506:   PetscInt         Nf, fieldI, fieldJ, totDim, totDimAux, numChunks, cellChunkSize, chunk;
    5507:   PetscInt         maxDegree = PETSC_MAX_INT;
    5508:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
    5509:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
    5510:   PetscBool        isMatIS = PETSC_FALSE, isMatISP = PETSC_FALSE, hasBdJac, hasBdPrec;
    5511:   PetscErrorCode   ierr;

    5514:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
    5515:   ISGetLocalSize(cellIS, &numCells);
    5516:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
    5517:   DMConvert(dm, DMPLEX, &plex);
    5518:   DMGetSection(dm, &section);
    5519:   DMGetGlobalSection(dm, &globalSection);
    5520:   DMGetLabel(dm, "ghost", &ghostLabel);
    5521:   DMGetCellDS(dm, cStart, &prob);
    5522:   PetscDSGetNumFields(prob, &Nf);
    5523:   PetscDSGetTotalDimension(prob, &totDim);
    5524:   PetscDSHasBdJacobian(prob, &hasBdJac);
    5525:   PetscDSHasBdJacobianPreconditioner(prob, &hasBdPrec);
    5526:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
    5527:   if (isMatISP) {DMPlexGetSubdomainSection(plex, &subSection);}
    5528:   if (hasBdPrec && hasBdJac) {PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);}
    5529:   if (isMatIS && !subSection) {DMPlexGetSubdomainSection(plex, &subSection);}
    5530:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
    5531:   if (locA) {
    5532:     VecGetDM(locA, &dmAux);
    5533:     DMConvert(dmAux, DMPLEX, &plexA);
    5534:     DMGetSection(dmAux, &sectionAux);
    5535:     DMGetCellDS(dmAux, cStart, &probAux);
    5536:     PetscDSGetTotalDimension(probAux, &totDimAux);
    5537:   }
    5538:   DMGetCoordinateField(dm, &coordField);
    5539:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
    5540:   if (maxDegree > 1) {
    5541:     PetscInt f;
    5542:     PetscCalloc2(Nf,&quads,Nf,&geoms);
    5543:     for (f = 0; f < Nf; ++f) {
    5544:       PetscFE fe;

    5546:       PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);
    5547:       if (fe) {
    5548:         PetscFEGetQuadrature(fe, &quads[f]);
    5549:         PetscObjectReference((PetscObject) quads[f]);
    5550:       }
    5551:     }
    5552:   }
    5553:   cellChunkSize = numCells;
    5554:   numChunks     = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize);
    5555:   PetscCalloc1(2*cellChunkSize, &faces);
    5556:   ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);
    5557:   DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
    5558:   DMGetWorkArray(dm, hasBdJac  ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);
    5559:   DMGetWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);
    5560:   for (chunk = 0; chunk < numChunks; ++chunk) {
    5561:     PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;

    5563:     if (hasBdJac)  {PetscMemzero(elemMat,  numCells*totDim*totDim * sizeof(PetscScalar));}
    5564:     if (hasBdPrec) {PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));}
    5565:     /* Get faces */
    5566:     for (c = cS; c < cE; ++c) {
    5567:       const PetscInt  cell = cells ? cells[c] : c;
    5568:       const PetscInt *cone;
    5569:       DMPlexGetCone(plex, cell, &cone);
    5570:       faces[(c-cS)*2+0] = cone[0];
    5571:       faces[(c-cS)*2+1] = cone[1];
    5572:     }
    5573:     ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);
    5574:     if (maxDegree <= 1) {
    5575:       if (!affineQuad) {DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);}
    5576:       if (affineQuad)  {DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);}
    5577:     } else {
    5578:       PetscInt f;
    5579:       for (f = 0; f < Nf; ++f) {
    5580:         if (quads[f]) {DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);}
    5581:       }
    5582:     }

    5584:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
    5585:       PetscFE         feI;
    5586:       PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[fieldI];
    5587:       PetscFEGeom    *chunkGeom = NULL, *remGeom = NULL;
    5588:       PetscQuadrature quad = affineQuad ? affineQuad : quads[fieldI];
    5589:       PetscInt        numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb;

    5591:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &feI);
    5592:       if (!feI) continue;
    5593:       PetscFEGetTileSizes(feI, NULL, &numBlocks, NULL, &numBatches);
    5594:       PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
    5595:       PetscFEGetDimension(feI, &Nb);
    5596:       blockSize = Nb;
    5597:       batchSize = numBlocks * blockSize;
    5598:       PetscFESetTileSizes(feI, blockSize, numBlocks, batchSize, numBatches);
    5599:       numChunks = numCells / (numBatches*batchSize);
    5600:       Ne        = numChunks*numBatches*batchSize;
    5601:       Nr        = numCells % (numBatches*batchSize);
    5602:       offset    = numCells - Nr;
    5603:       PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
    5604:       PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);
    5605:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
    5606:         PetscFE feJ;

    5608:         PetscDSGetDiscretization(prob, fieldJ, (PetscObject *) &feJ);
    5609:         if (!feJ) continue;
    5610:         if (hasBdJac) {
    5611:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
    5612:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
    5613:         }
    5614:         if (hasBdPrec) {
    5615:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);
    5616:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);
    5617:         }
    5618:       }
    5619:       PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);
    5620:       PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);
    5621:     }
    5622:     /* Insert values into matrix */
    5623:     for (c = cS; c < cE; ++c) {
    5624:       const PetscInt cell = cells ? cells[c] : c;
    5625:       const PetscInt cind = c - cS;

    5627:       if (hasBdPrec) {
    5628:         if (hasBdJac) {
    5629:           if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
    5630:           if (!isMatIS) {
    5631:             DMPlexMatSetClosure(plex, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5632:           } else {
    5633:             Mat lJ;

    5635:             MatISGetLocalMat(Jac,&lJ);
    5636:             DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5637:           }
    5638:         }
    5639:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);}
    5640:         if (!isMatISP) {
    5641:           DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
    5642:         } else {
    5643:           Mat lJ;

    5645:           MatISGetLocalMat(JacP,&lJ);
    5646:           DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
    5647:         }
    5648:       } else if (hasBdJac) {
    5649:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
    5650:         if (!isMatISP) {
    5651:           DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5652:         } else {
    5653:           Mat lJ;

    5655:           MatISGetLocalMat(JacP,&lJ);
    5656:           DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
    5657:         }
    5658:       }
    5659:     }
    5660:   }
    5661:   DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
    5662:   DMRestoreWorkArray(dm, hasBdJac  ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);
    5663:   DMRestoreWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);
    5664:   PetscFree(faces);
    5665:   ISDestroy(&chunkIS);
    5666:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
    5667:   if (maxDegree <= 1) {
    5668:     DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
    5669:     PetscQuadratureDestroy(&affineQuad);
    5670:   } else {
    5671:     PetscInt f;
    5672:     for (f = 0; f < Nf; ++f) {
    5673:       if (geoms) {DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE, &geoms[f]);}
    5674:       if (quads) {PetscQuadratureDestroy(&quads[f]);}
    5675:     }
    5676:     PetscFree2(quads,geoms);
    5677:   }
    5678:   if (dmAux) {DMDestroy(&plexA);}
    5679:   DMDestroy(&plex);
    5680:   /* Assemble matrix */
    5681:   if (hasBdJac && hasBdPrec) {
    5682:     MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);
    5683:     MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);
    5684:   }
    5685:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);
    5686:   MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
    5687:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
    5688:   return(0);
    5689: }