#include /*I "petscdmplex.h" I*/ #include #include #include #include static PetscErrorCode DMPlexConvertPlex(DM dm, DM *plex, PetscBool copy) { PetscBool isPlex; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); if (isPlex) { *plex = dm; ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); } else { ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); if (!*plex) { ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); if (copy) { const char *comps[3] = {"A", "dmAux"}; PetscObject obj; PetscInt i; { /* Run the subdomain hook (this will copy the DMSNES/DMTS) */ DMSubDomainHookLink link; for (link = dm->subdomainhook; link; link = link->next) { if (link->ddhook) {ierr = (*link->ddhook)(dm, *plex, link->ctx);CHKERRQ(ierr);} } } for (i = 0; i < 3; i++) { ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); } } } else { ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); } } PetscFunctionReturn(0); } static PetscErrorCode PetscContainerUserDestroy_PetscFEGeom (void *ctx) { PetscFEGeom *geom = (PetscFEGeom *) ctx; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscFEGeomDestroy(&geom);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) { char composeStr[33] = {0}; PetscObjectId id; PetscContainer container; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetId((PetscObject)quad,&id);CHKERRQ(ierr); ierr = PetscSNPrintf(composeStr, 32, "DMPlexGetFEGeom_%x\n", id);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);CHKERRQ(ierr); if (container) { ierr = PetscContainerGetPointer(container, (void **) geom);CHKERRQ(ierr); } else { ierr = DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);CHKERRQ(ierr); ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); ierr = PetscContainerSetPointer(container, (void *) *geom);CHKERRQ(ierr); ierr = PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);CHKERRQ(ierr); ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); } PetscFunctionReturn(0); } static PetscErrorCode DMPlexRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) { PetscFunctionBegin; *geom = NULL; PetscFunctionReturn(0); } /*@ DMPlexGetScale - Get the scale for the specified fundamental unit Not collective Input Arguments: + dm - the DM - unit - The SI unit Output Argument: . scale - The value used to scale all quantities with this unit Level: advanced .seealso: DMPlexSetScale(), PetscUnit @*/ PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) { DM_Plex *mesh = (DM_Plex*) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(scale, 3); *scale = mesh->scale[unit]; PetscFunctionReturn(0); } /*@ DMPlexSetScale - Set the scale for the specified fundamental unit Not collective Input Arguments: + dm - the DM . unit - The SI unit - scale - The value used to scale all quantities with this unit Level: advanced .seealso: DMPlexGetScale(), PetscUnit @*/ PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) { DM_Plex *mesh = (DM_Plex*) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); mesh->scale[unit] = scale; PetscFunctionReturn(0); } static PetscErrorCode DMPlexProjectRigidBody_Private(PetscInt dim, PetscReal t, const PetscReal X[], PetscInt Nc, PetscScalar *mode, void *ctx) { 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}}}; PetscInt *ctxInt = (PetscInt *) ctx; PetscInt dim2 = ctxInt[0]; PetscInt d = ctxInt[1]; PetscInt i, j, k = dim > 2 ? d - dim : d; PetscFunctionBegin; if (dim != dim2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input dimension %D does not match context dimension %D", dim, dim2); for (i = 0; i < dim; i++) mode[i] = 0.; if (d < dim) { mode[d] = 1.; /* Translation along axis d */ } else { for (i = 0; i < dim; i++) { for (j = 0; j < dim; j++) { mode[j] += eps[i][j][k]*X[i]; /* Rotation about axis d */ } } } PetscFunctionReturn(0); } /*@ DMPlexCreateRigidBody - For the default global section, create rigid body modes by function space interpolation Collective on dm Input Arguments: . dm - the DM Output Argument: . sp - the null space Note: This is necessary to provide a suitable coarse space for algebraic multigrid Level: advanced .seealso: MatNullSpaceCreate(), PCGAMG @*/ PetscErrorCode DMPlexCreateRigidBody(DM dm, MatNullSpace *sp) { MPI_Comm comm; Vec mode[6]; PetscSection section, globalSection; PetscInt dim, dimEmbed, n, m, mmin, d, i, j; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); if (dim == 1) { ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); m = (dim*(dim+1))/2; ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetUp(mode[0]);CHKERRQ(ierr); ierr = VecGetSize(mode[0], &n);CHKERRQ(ierr); mmin = PetscMin(m, n); for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} for (d = 0; d < m; d++) { PetscInt ctx[2]; PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private; void *voidctx = (void *) (&ctx[0]); ctx[0] = dimEmbed; ctx[1] = d; ierr = DMProjectFunction(dm, 0.0, &func, &voidctx, INSERT_VALUES, mode[d]);CHKERRQ(ierr); } /* Orthonormalize system */ for (i = 0; i < mmin; ++i) { PetscScalar dots[6]; ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); ierr = VecMDot(mode[i], mmin-i-1, mode+i+1, dots+i+1);CHKERRQ(ierr); for (j = i+1; j < mmin; ++j) { dots[j] *= -1.0; ierr = VecAXPY(mode[j], dots[j], mode[i]);CHKERRQ(ierr); } } ierr = MatNullSpaceCreate(comm, PETSC_FALSE, mmin, mode, sp);CHKERRQ(ierr); for (i = 0; i < m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} PetscFunctionReturn(0); } /*@ DMPlexCreateRigidBodies - For the default global section, create rigid body modes by function space interpolation Collective on dm Input Arguments: + dm - the DM . nb - The number of bodies . label - The DMLabel marking each domain . nids - The number of ids per body - ids - An array of the label ids in sequence for each domain Output Argument: . sp - the null space Note: This is necessary to provide a suitable coarse space for algebraic multigrid Level: advanced .seealso: MatNullSpaceCreate() @*/ PetscErrorCode DMPlexCreateRigidBodies(DM dm, PetscInt nb, DMLabel label, const PetscInt nids[], const PetscInt ids[], MatNullSpace *sp) { MPI_Comm comm; PetscSection section, globalSection; Vec *mode; PetscScalar *dots; PetscInt dim, dimEmbed, n, m, b, d, i, j, off; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr); ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); m = nb * (dim*(dim+1))/2; ierr = PetscMalloc2(m, &mode, m, &dots);CHKERRQ(ierr); ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetUp(mode[0]);CHKERRQ(ierr); for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} for (b = 0, off = 0; b < nb; ++b) { for (d = 0; d < m/nb; ++d) { PetscInt ctx[2]; PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private; void *voidctx = (void *) (&ctx[0]); ctx[0] = dimEmbed; ctx[1] = d; ierr = DMProjectFunctionLabel(dm, 0.0, label, nids[b], &ids[off], 0, NULL, &func, &voidctx, INSERT_VALUES, mode[d]);CHKERRQ(ierr); off += nids[b]; } } /* Orthonormalize system */ for (i = 0; i < m; ++i) { PetscScalar dots[6]; ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); ierr = VecMDot(mode[i], m-i-1, mode+i+1, dots+i+1);CHKERRQ(ierr); for (j = i+1; j < m; ++j) { dots[j] *= -1.0; ierr = VecAXPY(mode[j], dots[j], mode[i]);CHKERRQ(ierr); } } ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} ierr = PetscFree2(mode, dots);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexSetMaxProjectionHeight - In DMPlexProjectXXXLocal() functions, the projected values of a basis function's dofs are computed by associating the basis function with one of the mesh points in its transitively-closed support, and evaluating the dual space basis of that point. A basis function is associated with the point in its transitively-closed support whose mesh height is highest (w.r.t. DAG height), but not greater than the maximum projection height, which is set with this function. By default, the maximum projection height is zero, which means that only mesh cells are used to project basis functions. A height of one, for example, evaluates a cell-interior basis functions using its cells dual space basis, but all other basis functions with the dual space basis of a face. Input Parameters: + dm - the DMPlex object - height - the maximum projection height >= 0 Level: advanced .seealso: DMPlexGetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal() @*/ PetscErrorCode DMPlexSetMaxProjectionHeight(DM dm, PetscInt height) { DM_Plex *plex = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); plex->maxProjectionHeight = height; PetscFunctionReturn(0); } /*@ DMPlexGetMaxProjectionHeight - Get the maximum height (w.r.t. DAG) of mesh points used to evaluate dual bases in DMPlexProjectXXXLocal() functions. Input Parameters: . dm - the DMPlex object Output Parameters: . height - the maximum projection height Level: intermediate .seealso: DMPlexSetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal() @*/ PetscErrorCode DMPlexGetMaxProjectionHeight(DM dm, PetscInt *height) { DM_Plex *plex = (DM_Plex *) dm->data; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); *height = plex->maxProjectionHeight; PetscFunctionReturn(0); } typedef struct { PetscReal alpha; /* The first Euler angle, and in 2D the only one */ PetscReal beta; /* The second Euler angle */ PetscReal gamma; /* The third Euler angle */ PetscInt dim; /* The dimension of R */ PetscScalar *R; /* The rotation matrix, transforming a vector in the local basis to the global basis */ PetscScalar *RT; /* The transposed rotation matrix, transforming a vector in the global basis to the local basis */ } RotCtx; /* Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that 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: $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis. $ 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. $ The XYZ system rotates a third time about the z axis by gamma. */ static PetscErrorCode DMPlexBasisTransformSetUp_Rotation_Internal(DM dm, void *ctx) { RotCtx *rc = (RotCtx *) ctx; PetscInt dim = rc->dim; PetscReal c1, s1, c2, s2, c3, s3; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscMalloc2(PetscSqr(dim), &rc->R, PetscSqr(dim), &rc->RT);CHKERRQ(ierr); switch (dim) { case 2: c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha); rc->R[0] = c1;rc->R[1] = s1; rc->R[2] = -s1;rc->R[3] = c1; ierr = PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));CHKERRQ(ierr); DMPlex_Transpose2D_Internal(rc->RT);break; break; case 3: c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha); c2 = PetscCosReal(rc->beta); s2 = PetscSinReal(rc->beta); c3 = PetscCosReal(rc->gamma);s3 = PetscSinReal(rc->gamma); rc->R[0] = c1*c3 - c2*s1*s3;rc->R[1] = c3*s1 + c1*c2*s3;rc->R[2] = s2*s3; rc->R[3] = -c1*s3 - c2*c3*s1;rc->R[4] = c1*c2*c3 - s1*s3; rc->R[5] = c3*s2; rc->R[6] = s1*s2; rc->R[7] = -c1*s2; rc->R[8] = c2; ierr = PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));CHKERRQ(ierr); DMPlex_Transpose3D_Internal(rc->RT);break; break; default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim); } PetscFunctionReturn(0); } static PetscErrorCode DMPlexBasisTransformDestroy_Rotation_Internal(DM dm, void *ctx) { RotCtx *rc = (RotCtx *) ctx; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscFree2(rc->R, rc->RT);CHKERRQ(ierr); ierr = PetscFree(rc);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexBasisTransformGetMatrix_Rotation_Internal(DM dm, const PetscReal x[], PetscBool l2g, const PetscScalar **A, void *ctx) { RotCtx *rc = (RotCtx *) ctx; PetscFunctionBeginHot; PetscValidPointer(ctx, 5); if (l2g) {*A = rc->R;} else {*A = rc->RT;} PetscFunctionReturn(0); } PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscReal *y, PetscReal *z, void *ctx) { PetscErrorCode ierr; PetscFunctionBegin; #if defined(PETSC_USE_COMPLEX) switch (dim) { case 2: { PetscScalar yt[2], zt[2]; yt[0] = y[0]; yt[1] = y[1]; ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);CHKERRQ(ierr); z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); } break; case 3: { PetscScalar yt[3], zt[3]; yt[0] = y[0]; yt[1] = y[1]; yt[2] = y[2]; ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);CHKERRQ(ierr); z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); z[2] = PetscRealPart(zt[2]); } break; } #else ierr = DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, y, z, ctx);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } PetscErrorCode DMPlexBasisTransformApply_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscScalar *y, PetscScalar *z, void *ctx) { const PetscScalar *A; PetscErrorCode ierr; PetscFunctionBeginHot; ierr = (*dm->transformGetMatrix)(dm, x, l2g, &A, ctx);CHKERRQ(ierr); switch (dim) { case 2: DMPlex_Mult2D_Internal(A, 1, y, z);break; case 3: DMPlex_Mult3D_Internal(A, 1, y, z);break; } PetscFunctionReturn(0); } static PetscErrorCode DMPlexBasisTransformField_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscInt f, PetscBool l2g, PetscScalar *a) { PetscSection ts; const PetscScalar *ta, *tva; PetscInt dof; PetscErrorCode ierr; PetscFunctionBeginHot; ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(ts, p, f, &dof);CHKERRQ(ierr); ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRead(tdm, p, f, ta, (void *) &tva);CHKERRQ(ierr); if (l2g) { switch (dof) { case 4: DMPlex_Mult2D_Internal(tva, 1, a, a);break; case 9: DMPlex_Mult3D_Internal(tva, 1, a, a);break; } } else { switch (dof) { case 4: DMPlex_MultTranspose2D_Internal(tva, 1, a, a);break; case 9: DMPlex_MultTranspose3D_Internal(tva, 1, a, a);break; } } ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexBasisTransformFieldTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt pf, PetscInt f, PetscInt pg, PetscInt g, PetscBool l2g, PetscInt lda, PetscScalar *a) { PetscSection s, ts; const PetscScalar *ta, *tvaf, *tvag; PetscInt fdof, gdof, fpdof, gpdof; PetscErrorCode ierr; PetscFunctionBeginHot; ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(s, pf, f, &fpdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(s, pg, g, &gpdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(ts, pf, f, &fdof);CHKERRQ(ierr); ierr = PetscSectionGetFieldDof(ts, pg, g, &gdof);CHKERRQ(ierr); ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRead(tdm, pf, f, ta, (void *) &tvaf);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRead(tdm, pg, g, ta, (void *) &tvag);CHKERRQ(ierr); if (l2g) { switch (fdof) { case 4: DMPlex_MatMult2D_Internal(tvaf, gpdof, lda, a, a);break; case 9: DMPlex_MatMult3D_Internal(tvaf, gpdof, lda, a, a);break; } switch (gdof) { case 4: DMPlex_MatMultTransposeLeft2D_Internal(tvag, fpdof, lda, a, a);break; case 9: DMPlex_MatMultTransposeLeft3D_Internal(tvag, fpdof, lda, a, a);break; } } else { switch (fdof) { case 4: DMPlex_MatMultTranspose2D_Internal(tvaf, gpdof, lda, a, a);break; case 9: DMPlex_MatMultTranspose3D_Internal(tvaf, gpdof, lda, a, a);break; } switch (gdof) { case 4: DMPlex_MatMultLeft2D_Internal(tvag, fpdof, lda, a, a);break; case 9: DMPlex_MatMultLeft3D_Internal(tvag, fpdof, lda, a, a);break; } } ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode DMPlexBasisTransformPoint_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool fieldActive[], PetscBool l2g, PetscScalar *a) { PetscSection s; PetscSection clSection; IS clPoints; const PetscInt *clp; PetscInt *points = NULL; PetscInt Nf, f, Np, cp, dof, d = 0; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); ierr = DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { for (cp = 0; cp < Np*2; cp += 2) { ierr = PetscSectionGetFieldDof(s, points[cp], f, &dof);CHKERRQ(ierr); if (!dof) continue; if (fieldActive[f]) {ierr = DMPlexBasisTransformField_Internal(dm, tdm, tv, points[cp], f, l2g, &a[d]);CHKERRQ(ierr);} d += dof; } } ierr = DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool l2g, PetscInt lda, PetscScalar *a) { PetscSection s; PetscSection clSection; IS clPoints; const PetscInt *clp; PetscInt *points = NULL; PetscInt Nf, f, g, Np, cpf, cpg, fdof, gdof, r, c = 0; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); ierr = DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); for (f = 0, r = 0; f < Nf; ++f) { for (cpf = 0; cpf < Np*2; cpf += 2) { ierr = PetscSectionGetFieldDof(s, points[cpf], f, &fdof);CHKERRQ(ierr); for (g = 0, c = 0; g < Nf; ++g) { for (cpg = 0; cpg < Np*2; cpg += 2) { ierr = PetscSectionGetFieldDof(s, points[cpg], g, &gdof);CHKERRQ(ierr); ierr = DMPlexBasisTransformFieldTensor_Internal(dm, tdm, tv, points[cpf], f, points[cpg], g, l2g, lda, &a[r*lda+c]);CHKERRQ(ierr); c += gdof; } } if (c != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of columns %D should be %D", c, lda); r += fdof; } } if (r != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of rows %D should be %D", c, lda); ierr = DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexBasisTransform_Internal(DM dm, Vec lv, PetscBool l2g) { DM tdm; Vec tv; PetscSection ts, s; const PetscScalar *ta; PetscScalar *a, *va; PetscInt pStart, pEnd, p, Nf, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); ierr = DMGetLocalSection(tdm, &ts);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); ierr = VecGetArray(lv, &a);CHKERRQ(ierr); ierr = VecGetArrayRead(tv, &ta);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { for (f = 0; f < Nf; ++f) { ierr = DMPlexPointLocalFieldRef(dm, p, f, a, (void *) &va);CHKERRQ(ierr); ierr = DMPlexBasisTransformField_Internal(dm, tdm, tv, p, f, l2g, va);CHKERRQ(ierr); } } ierr = VecRestoreArray(lv, &a);CHKERRQ(ierr); ierr = VecRestoreArrayRead(tv, &ta);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexGlobalToLocalBasis - Transform the values in the given local vector from the global basis to the local basis Input Parameters: + dm - The DM - lv - A local vector with values in the global basis Output Parameters: . lv - A local vector with values in the local basis 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. Level: developer .seealso: DMPlexLocalToGlobalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation() @*/ PetscErrorCode DMPlexGlobalToLocalBasis(DM dm, Vec lv) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(lv, VEC_CLASSID, 2); ierr = DMPlexBasisTransform_Internal(dm, lv, PETSC_FALSE);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexLocalToGlobalBasis - Transform the values in the given local vector from the local basis to the global basis Input Parameters: + dm - The DM - lv - A local vector with values in the local basis Output Parameters: . lv - A local vector with values in the global basis 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. Level: developer .seealso: DMPlexGlobalToLocalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation() @*/ PetscErrorCode DMPlexLocalToGlobalBasis(DM dm, Vec lv) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(lv, VEC_CLASSID, 2); ierr = DMPlexBasisTransform_Internal(dm, lv, PETSC_TRUE);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexCreateBasisRotation - Create an internal transformation from the global basis, used to specify boundary conditions and global solutions, to a local basis, appropriate for discretization integrals and assembly. Input Parameters: + dm - The DM . alpha - The first Euler angle, and in 2D the only one . beta - The second Euler angle - gamma - The third Euler angle Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that 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: $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis. $ 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. $ The XYZ system rotates a third time about the z axis by gamma. Level: developer .seealso: DMPlexGlobalToLocalBasis(), DMPlexLocalToGlobalBasis() @*/ PetscErrorCode DMPlexCreateBasisRotation(DM dm, PetscReal alpha, PetscReal beta, PetscReal gamma) { RotCtx *rc; PetscInt cdim; PetscErrorCode ierr; ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); ierr = PetscMalloc1(1, &rc);CHKERRQ(ierr); dm->transformCtx = rc; dm->transformSetUp = DMPlexBasisTransformSetUp_Rotation_Internal; dm->transformDestroy = DMPlexBasisTransformDestroy_Rotation_Internal; dm->transformGetMatrix = DMPlexBasisTransformGetMatrix_Rotation_Internal; rc->dim = cdim; rc->alpha = alpha; rc->beta = beta; rc->gamma = gamma; ierr = (*dm->transformSetUp)(dm, dm->transformCtx);CHKERRQ(ierr); ierr = DMConstructBasisTransform_Internal(dm);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexInsertBoundaryValuesEssential - Insert boundary values into a local vector using a function of the coordinates Input Parameters: + dm - The DM, with a PetscDS that matches the problem being constrained . time - The time . field - The field to constrain . Nc - The number of constrained field components, or 0 for all components . comps - An array of constrained component numbers, or NULL for all components . label - The DMLabel defining constrained points . numids - The number of DMLabel ids for constrained points . ids - An array of ids for constrained points . func - A pointwise function giving boundary values - ctx - An optional user context for bcFunc Output Parameter: . locX - A local vector to receives the boundary values Level: developer .seealso: DMPlexInsertBoundaryValuesEssentialField(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary() @*/ 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) { PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx); void **ctxs; PetscInt numFields; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); funcs[field] = func; ctxs[field] = ctx; ierr = DMProjectFunctionLabelLocal(dm, time, label, numids, ids, Nc, comps, funcs, ctxs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexInsertBoundaryValuesEssentialField - Insert boundary values into a local vector using a function of the coordinates and field data Input Parameters: + dm - The DM, with a PetscDS that matches the problem being constrained . time - The time . locU - A local vector with the input solution values . field - The field to constrain . Nc - The number of constrained field components, or 0 for all components . comps - An array of constrained component numbers, or NULL for all components . label - The DMLabel defining constrained points . numids - The number of DMLabel ids for constrained points . ids - An array of ids for constrained points . func - A pointwise function giving boundary values - ctx - An optional user context for bcFunc Output Parameter: . locX - A local vector to receives the boundary values Level: developer .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary() @*/ PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], void (*func)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), void *ctx, Vec locX) { void (**funcs)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); void **ctxs; PetscInt numFields; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); funcs[field] = func; ctxs[field] = ctx; ierr = DMProjectFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexInsertBoundaryValuesEssentialBdField - Insert boundary values into a local vector using a function of the coodinates and boundary field data Collective on dm Input Parameters: + dm - The DM, with a PetscDS that matches the problem being constrained . time - The time . locU - A local vector with the input solution values . field - The field to constrain . Nc - The number of constrained field components, or 0 for all components . comps - An array of constrained component numbers, or NULL for all components . label - The DMLabel defining constrained points . numids - The number of DMLabel ids for constrained points . ids - An array of ids for constrained points . func - A pointwise function giving boundary values, the calling sequence is given in DMProjectBdFieldLabelLocal() - ctx - An optional user context for bcFunc Output Parameter: . locX - A local vector to receive the boundary values Level: developer .seealso: DMProjectBdFieldLabelLocal(), DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary() @*/ PetscErrorCode DMPlexInsertBoundaryValuesEssentialBdField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], void (*func)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), void *ctx, Vec locX) { void (**funcs)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); void **ctxs; PetscInt numFields; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); ierr = PetscCalloc2(numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); funcs[field] = func; ctxs[field] = ctx; ierr = DMProjectBdFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);CHKERRQ(ierr); ierr = PetscFree2(funcs,ctxs);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexInsertBoundaryValuesRiemann - Insert boundary values into a local vector Input Parameters: + dm - The DM, with a PetscDS that matches the problem being constrained . time - The time . faceGeometry - A vector with the FVM face geometry information . cellGeometry - A vector with the FVM cell geometry information . Grad - A vector with the FVM cell gradient information . field - The field to constrain . Nc - The number of constrained field components, or 0 for all components . comps - An array of constrained component numbers, or NULL for all components . label - The DMLabel defining constrained points . numids - The number of DMLabel ids for constrained points . ids - An array of ids for constrained points . func - A pointwise function giving boundary values - ctx - An optional user context for bcFunc Output Parameter: . locX - A local vector to receives the boundary values Note: This implementation currently ignores the numcomps/comps argument from DMAddBoundary() Level: developer .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary() @*/ 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[], PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *ctx, Vec locX) { PetscDS prob; PetscSF sf; DM dmFace, dmCell, dmGrad; const PetscScalar *facegeom, *cellgeom = NULL, *grad; const PetscInt *leaves; PetscScalar *x, *fx; PetscInt dim, nleaves, loc, fStart, fEnd, pdim, i; PetscErrorCode ierr, ierru = 0; PetscFunctionBegin; ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);CHKERRQ(ierr); nleaves = PetscMax(0, nleaves); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); if (cellGeometry) { ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); } if (Grad) { PetscFV fv; ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fv);CHKERRQ(ierr); ierr = VecGetDM(Grad, &dmGrad);CHKERRQ(ierr); ierr = VecGetArrayRead(Grad, &grad);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, pdim, MPIU_SCALAR, &fx);CHKERRQ(ierr); } ierr = VecGetArray(locX, &x);CHKERRQ(ierr); for (i = 0; i < numids; ++i) { IS faceIS; const PetscInt *faces; PetscInt numFaces, f; ierr = DMLabelGetStratumIS(label, ids[i], &faceIS);CHKERRQ(ierr); if (!faceIS) continue; /* No points with that id on this process */ ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f) { const PetscInt face = faces[f], *cells; PetscFVFaceGeom *fg; if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */ ierr = PetscFindInt(face, nleaves, (PetscInt *) leaves, &loc);CHKERRQ(ierr); if (loc >= 0) continue; ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); if (Grad) { PetscFVCellGeom *cg; PetscScalar *cx, *cgrad; PetscScalar *xG; PetscReal dx[3]; PetscInt d; ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dm, cells[0], x, &cx);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);CHKERRQ(ierr); DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, fg->centroid, dx); for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DMPlex_DotD_Internal(dim, &cgrad[d*dim], dx); ierru = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx); if (ierru) { ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); goto cleanup; } } else { PetscScalar *xI; PetscScalar *xG; ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);CHKERRQ(ierr); ierru = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx); if (ierru) { ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); goto cleanup; } } } ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); } cleanup: ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr); if (Grad) { ierr = DMRestoreWorkArray(dm, pdim, MPIU_SCALAR, &fx);CHKERRQ(ierr); ierr = VecRestoreArrayRead(Grad, &grad);CHKERRQ(ierr); } if (cellGeometry) {ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);} ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); CHKERRQ(ierru); PetscFunctionReturn(0); } PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) { PetscDS prob; PetscInt numBd, b; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); for (b = 0; b < numBd; ++b) { DMBoundaryConditionType type; const char *name, *labelname; DMLabel label; PetscInt field, Nc; const PetscInt *comps; PetscObject obj; PetscClassId id; void (*func)(void); PetscInt numids; const PetscInt *ids; void *ctx; ierr = DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, &func, &numids, &ids, &ctx);CHKERRQ(ierr); if (insertEssential != (type & DM_BC_ESSENTIAL)) continue; ierr = DMGetLabel(dm, labelname, &label);CHKERRQ(ierr); if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name); ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { switch (type) { /* for FEM, there is no insertion to be done for non-essential boundary conditions */ case DM_BC_ESSENTIAL: ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func, ctx, locX);CHKERRQ(ierr); ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); break; case DM_BC_ESSENTIAL_FIELD: ierr = DMPlexLabelAddCells(dm,label);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids, (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func, ctx, locX);CHKERRQ(ierr); ierr = DMPlexLabelClearCells(dm,label);CHKERRQ(ierr); break; default: break; } } else if (id == PETSCFV_CLASSID) { if (!faceGeomFVM) continue; ierr = DMPlexInsertBoundaryValuesRiemann(dm, time, faceGeomFVM, cellGeomFVM, gradFVM, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*)) func, ctx, locX);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); } PetscFunctionReturn(0); } /*@ DMPlexInsertBoundaryValues - Puts coefficients which represent boundary values into the local solution vector Input Parameters: + dm - The DM . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions . time - The time . faceGeomFVM - Face geometry data for FV discretizations . cellGeomFVM - Cell geometry data for FV discretizations - gradFVM - Gradient reconstruction data for FV discretizations Output Parameters: . locX - Solution updated with boundary values Level: developer .seealso: DMProjectFunctionLabelLocal() @*/ PetscErrorCode DMPlexInsertBoundaryValues(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(locX, VEC_CLASSID, 2); if (faceGeomFVM) {PetscValidHeaderSpecific(faceGeomFVM, VEC_CLASSID, 4);} if (cellGeomFVM) {PetscValidHeaderSpecific(cellGeomFVM, VEC_CLASSID, 5);} if (gradFVM) {PetscValidHeaderSpecific(gradFVM, VEC_CLASSID, 6);} ierr = PetscTryMethod(dm,"DMPlexInsertBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX,time,faceGeomFVM,cellGeomFVM,gradFVM));CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode DMComputeL2Diff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) { Vec localX; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, localX, time, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMPlexComputeL2DiffLocal(dm, time, funcs, ctxs, localX, diff);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMComputeL2DiffLocal - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. Collective on dm Input Parameters: + dm - The DM . time - The time . funcs - The functions to evaluate for each field component . ctxs - Optional array of contexts to pass to each function, or NULL. - localX - The coefficient vector u_h, a local vector Output Parameter: . diff - The diff ||u - u_h||_2 Level: developer .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff() @*/ PetscErrorCode DMPlexComputeL2DiffLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec localX, PetscReal *diff) { const PetscInt debug = ((DM_Plex*)dm->data)->printL2; DM tdm; Vec tv; PetscSection section; PetscQuadrature quad; PetscFEGeom fegeom; PetscScalar *funcVal, *interpolant; PetscReal *coords, *gcoords; PetscReal localDiff = 0.0; const PetscReal *quadWeights; PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cellHeight, cStart, cEnd, c, field, fieldOffset; PetscBool transform; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); fegeom.dimEmbed = coordDim; ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; PetscInt Nc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); numComponents += Nc; } ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);CHKERRQ(ierr); if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); ierr = PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { PetscScalar *x = NULL; PetscReal elemDiff = 0.0; PetscInt qc = 0; ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); for (field = 0, fieldOffset = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; void * const ctx = ctxs ? ctxs[field] : NULL; PetscInt Nb, Nc, q, fc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); if (debug) { char title[1024]; ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", field);CHKERRQ(ierr); ierr = DMPrintCellVector(c, title, Nb, &x[fieldOffset]);CHKERRQ(ierr); } for (q = 0; q < Nq; ++q) { PetscFEGeom qgeom; qgeom.dimEmbed = fegeom.dimEmbed; qgeom.J = &fegeom.J[q*coordDim*coordDim]; qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; qgeom.detJ = &fegeom.detJ[q]; 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); if (transform) { gcoords = &coords[coordDim*Nq]; ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);CHKERRQ(ierr); } else { gcoords = &coords[coordDim*q]; } ierr = (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx); if (ierr) { PetscErrorCode ierr2; ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); CHKERRQ(ierr); } if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);CHKERRQ(ierr);} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); for (fc = 0; fc < Nc; ++fc) { const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; if (debug) {ierr = 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]));CHKERRQ(ierr);} elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; } } fieldOffset += Nb; qc += Nc; } ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D diff %g\n", c, (double)elemDiff);CHKERRQ(ierr);} localDiff += elemDiff; } ierr = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); ierr = MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); *diff = PetscSqrtReal(*diff); PetscFunctionReturn(0); } 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) { const PetscInt debug = ((DM_Plex*)dm->data)->printL2; DM tdm; PetscSection section; PetscQuadrature quad; Vec localX, tv; PetscScalar *funcVal, *interpolant; const PetscReal *quadWeights; PetscFEGeom fegeom; PetscReal *coords, *gcoords; PetscReal localDiff = 0.0; PetscInt dim, coordDim, qNc = 0, Nq = 0, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset; PetscBool transform; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); fegeom.dimEmbed = coordDim; ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { PetscFE fe; PetscInt Nc; ierr = DMGetField(dm, field, NULL, (PetscObject *) &fe);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); numComponents += Nc; } ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);CHKERRQ(ierr); if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); /* ierr = DMProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */ ierr = PetscMalloc6(numComponents,&funcVal,coordDim*Nq,&coords,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ,numComponents*coordDim,&interpolant,Nq,&fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { PetscScalar *x = NULL; PetscReal elemDiff = 0.0; PetscInt qc = 0; ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); for (field = 0, fieldOffset = 0; field < numFields; ++field) { PetscFE fe; void * const ctx = ctxs ? ctxs[field] : NULL; PetscInt Nb, Nc, q, fc; ierr = DMGetField(dm, field, NULL, (PetscObject *) &fe);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); if (debug) { char title[1024]; ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", field);CHKERRQ(ierr); ierr = DMPrintCellVector(c, title, Nb, &x[fieldOffset]);CHKERRQ(ierr); } for (q = 0; q < Nq; ++q) { PetscFEGeom qgeom; qgeom.dimEmbed = fegeom.dimEmbed; qgeom.J = &fegeom.J[q*coordDim*coordDim]; qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; qgeom.detJ = &fegeom.detJ[q]; 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); if (transform) { gcoords = &coords[coordDim*Nq]; ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);CHKERRQ(ierr); } else { gcoords = &coords[coordDim*q]; } ierr = (*funcs[field])(coordDim, time, gcoords, n, Nc, funcVal, ctx); if (ierr) { PetscErrorCode ierr2; ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); ierr2 = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr2); CHKERRQ(ierr); } if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} ierr = PetscFEInterpolateGradient_Static(fe, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr); /* Overwrite with the dot product if the normal is given */ if (n) { for (fc = 0; fc < Nc; ++fc) { PetscScalar sum = 0.0; PetscInt d; for (d = 0; d < dim; ++d) sum += interpolant[fc*dim+d]*n[d]; interpolant[fc] = sum; } } for (fc = 0; fc < Nc; ++fc) { const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; if (debug) {ierr = 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]));CHKERRQ(ierr);} elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; } } fieldOffset += Nb; qc += Nc; } ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D diff %g\n", c, (double)elemDiff);CHKERRQ(ierr);} localDiff += elemDiff; } ierr = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); ierr = MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); *diff = PetscSqrtReal(*diff); PetscFunctionReturn(0); } PetscErrorCode DMComputeL2FieldDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) { const PetscInt debug = ((DM_Plex*)dm->data)->printL2; DM tdm; PetscSection section; PetscQuadrature quad; Vec localX, tv; PetscFEGeom fegeom; PetscScalar *funcVal, *interpolant; PetscReal *coords, *gcoords; PetscReal *localDiff; const PetscReal *quadPoints, *quadWeights; PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset; PetscBool transform; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = VecSet(localX, 0.0);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); ierr = DMGetBasisTransformDM_Internal(dm, &tdm);CHKERRQ(ierr); ierr = DMGetBasisTransformVec_Internal(dm, &tv);CHKERRQ(ierr); ierr = DMHasBasisTransform(dm, &transform);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; PetscInt Nc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); numComponents += Nc; } ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); ierr = PetscCalloc7(numFields,&localDiff,numComponents,&funcVal,numComponents,&interpolant,coordDim*(Nq+1),&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { PetscScalar *x = NULL; PetscInt qc = 0; ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); for (field = 0, fieldOffset = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; void * const ctx = ctxs ? ctxs[field] : NULL; PetscInt Nb, Nc, q, fc; PetscReal elemDiff = 0.0; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); if (debug) { char title[1024]; ierr = PetscSNPrintf(title, 1023, "Solution for Field %D", field);CHKERRQ(ierr); ierr = DMPrintCellVector(c, title, Nb, &x[fieldOffset]);CHKERRQ(ierr); } for (q = 0; q < Nq; ++q) { PetscFEGeom qgeom; qgeom.dimEmbed = fegeom.dimEmbed; qgeom.J = &fegeom.J[q*coordDim*coordDim]; qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; qgeom.detJ = &fegeom.detJ[q]; if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature point %D", (double)fegeom.detJ[q], c, q); if (transform) { gcoords = &coords[coordDim*Nq]; ierr = DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);CHKERRQ(ierr); } else { gcoords = &coords[coordDim*q]; } ierr = (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx); if (ierr) { PetscErrorCode ierr2; ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); ierr2 = PetscFree7(localDiff,funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); CHKERRQ(ierr); } if (transform) {ierr = DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);CHKERRQ(ierr);} if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);CHKERRQ(ierr);} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); for (fc = 0; fc < Nc; ++fc) { const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; if (debug) {ierr = 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]));CHKERRQ(ierr);} elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; } } fieldOffset += Nb; qc += Nc; localDiff[field] += elemDiff; if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %D field %D cum diff %g\n", c, field, (double)localDiff[field]);CHKERRQ(ierr);} } ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); } ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); ierr = MPIU_Allreduce(localDiff, diff, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); for (field = 0; field < numFields; ++field) diff[field] = PetscSqrtReal(diff[field]); ierr = PetscFree7(localDiff,funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C 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. Collective on dm Input Parameters: + dm - The DM . time - The time . funcs - The functions to evaluate for each field component: NULL means that component does not contribute to error calculation . ctxs - Optional array of contexts to pass to each function, or NULL. - X - The coefficient vector u_h Output Parameter: . D - A Vec which holds the difference ||u - u_h||_2 for each cell Level: developer .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff() @*/ PetscErrorCode DMPlexComputeL2DiffVec(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, Vec D) { PetscSection section; PetscQuadrature quad; Vec localX; PetscFEGeom fegeom; PetscScalar *funcVal, *interpolant; PetscReal *coords; const PetscReal *quadPoints, *quadWeights; PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset; PetscErrorCode ierr; PetscFunctionBegin; ierr = VecSet(D, 0.0);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; PetscInt Nc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); numComponents += Nc; } ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); ierr = PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { PetscScalar *x = NULL; PetscScalar elemDiff = 0.0; PetscInt qc = 0; ierr = DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); for (field = 0, fieldOffset = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; void * const ctx = ctxs ? ctxs[field] : NULL; PetscInt Nb, Nc, q, fc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); if (funcs[field]) { for (q = 0; q < Nq; ++q) { PetscFEGeom qgeom; qgeom.dimEmbed = fegeom.dimEmbed; qgeom.J = &fegeom.J[q*coordDim*coordDim]; qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; qgeom.detJ = &fegeom.detJ[q]; 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); ierr = (*funcs[field])(coordDim, time, &coords[q*coordDim], Nc, funcVal, ctx); if (ierr) { PetscErrorCode ierr2; ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2); ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2); CHKERRQ(ierr); } if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);CHKERRQ(ierr);} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); for (fc = 0; fc < Nc; ++fc) { const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)]; elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]; } } } fieldOffset += Nb; qc += Nc; } ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); ierr = VecSetValue(D, c - cStart, elemDiff, INSERT_VALUES);CHKERRQ(ierr); } ierr = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); ierr = VecSqrtAbs(D);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexComputeGradientClementInterpolant - This function computes the L2 projection of the cellwise gradient of a function u onto P1, and stores it in a Vec. Collective on dm Input Parameters: + dm - The DM - LocX - The coefficient vector u_h Output Parameter: . locC - A Vec which holds the Clement interpolant of the gradient Notes: Add citation to (Clement, 1975) and definition of the interpolant \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 Level: developer .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff() @*/ PetscErrorCode DMPlexComputeGradientClementInterpolant(DM dm, Vec locX, Vec locC) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscInt debug = mesh->printFEM; DM dmC; PetscSection section; PetscQuadrature quad; PetscScalar *interpolant, *gradsum; PetscFEGeom fegeom; PetscReal *coords; const PetscReal *quadPoints, *quadWeights; PetscInt dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, vStart, vEnd, v, field, fieldOffset; PetscErrorCode ierr; PetscFunctionBegin; ierr = VecGetDM(locC, &dmC);CHKERRQ(ierr); ierr = VecSet(locC, 0.0);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &coordDim);CHKERRQ(ierr); fegeom.dimEmbed = coordDim; ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); for (field = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; PetscInt Nc; ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetQuadrature(fv, &quad);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); numComponents += Nc; } ierr = PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);CHKERRQ(ierr); if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents); ierr = PetscMalloc6(coordDim*numComponents*2,&gradsum,coordDim*numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscScalar volsum = 0.0; PetscInt *star = NULL; PetscInt starSize, st, d, fc; ierr = PetscArrayzero(gradsum, coordDim*numComponents);CHKERRQ(ierr); ierr = DMPlexGetTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); for (st = 0; st < starSize*2; st += 2) { const PetscInt cell = star[st]; PetscScalar *grad = &gradsum[coordDim*numComponents]; PetscScalar *x = NULL; PetscReal vol = 0.0; if ((cell < cStart) || (cell >= cEnd)) continue; ierr = DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr); for (field = 0, fieldOffset = 0; field < numFields; ++field) { PetscObject obj; PetscClassId id; PetscInt Nb, Nc, q, qc = 0; ierr = PetscArrayzero(grad, coordDim*numComponents);CHKERRQ(ierr); ierr = DMGetField(dm, field, NULL, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {ierr = PetscFEGetNumComponents((PetscFE) obj, &Nc);CHKERRQ(ierr);ierr = PetscFEGetDimension((PetscFE) obj, &Nb);CHKERRQ(ierr);} else if (id == PETSCFV_CLASSID) {ierr = PetscFVGetNumComponents((PetscFV) obj, &Nc);CHKERRQ(ierr);Nb = 1;} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); for (q = 0; q < Nq; ++q) { PetscFEGeom qgeom; qgeom.dimEmbed = fegeom.dimEmbed; qgeom.J = &fegeom.J[q*coordDim*coordDim]; qgeom.invJ = &fegeom.invJ[q*coordDim*coordDim]; qgeom.detJ = &fegeom.detJ[q]; 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); if (ierr) { PetscErrorCode ierr2; ierr2 = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr2); ierr2 = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr2); ierr2 = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2); CHKERRQ(ierr); } if (id == PETSCFE_CLASSID) {ierr = PetscFEInterpolateGradient_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);CHKERRQ(ierr);} else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field); for (fc = 0; fc < Nc; ++fc) { const PetscReal wt = quadWeights[q*qNc+qc+fc]; for (d = 0; d < coordDim; ++d) grad[fc*coordDim+d] += interpolant[fc*dim+d]*wt*fegeom.detJ[q]; } vol += quadWeights[q*qNc]*fegeom.detJ[q]; } fieldOffset += Nb; qc += Nc; } ierr = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr); for (fc = 0; fc < numComponents; ++fc) { for (d = 0; d < coordDim; ++d) { gradsum[fc*coordDim+d] += grad[fc*coordDim+d]; } } volsum += vol; if (debug) { ierr = PetscPrintf(PETSC_COMM_SELF, "Cell %D gradient: [", cell);CHKERRQ(ierr); for (fc = 0; fc < numComponents; ++fc) { for (d = 0; d < coordDim; ++d) { if (fc || d > 0) {ierr = PetscPrintf(PETSC_COMM_SELF, ", ");CHKERRQ(ierr);} ierr = PetscPrintf(PETSC_COMM_SELF, "%g", (double)PetscRealPart(grad[fc*coordDim+d]));CHKERRQ(ierr); } } ierr = PetscPrintf(PETSC_COMM_SELF, "]\n");CHKERRQ(ierr); } } for (fc = 0; fc < numComponents; ++fc) { for (d = 0; d < coordDim; ++d) gradsum[fc*coordDim+d] /= volsum; } ierr = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); ierr = DMPlexVecSetClosure(dmC, NULL, locC, v, gradsum, INSERT_VALUES);CHKERRQ(ierr); } ierr = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexComputeIntegral_Internal(DM dm, Vec X, PetscInt cStart, PetscInt cEnd, PetscScalar *cintegral, void *user) { DM dmAux = NULL; PetscDS prob, probAux = NULL; PetscSection section, sectionAux; Vec locX, locA; PetscInt dim, numCells = cEnd - cStart, c, f; PetscBool useFVM = PETSC_FALSE; /* DS */ PetscInt Nf, totDim, *uOff, *uOff_x, numConstants; PetscInt NfAux, totDimAux, *aOff; PetscScalar *u, *a; const PetscScalar *constants; /* Geometry */ PetscFEGeom *cgeomFEM; DM dmGrad; PetscQuadrature affineQuad = NULL; Vec cellGeometryFVM = NULL, faceGeometryFVM = NULL, locGrad = NULL; PetscFVCellGeom *cgeomFVM; const PetscScalar *lgrad; PetscInt maxDegree; DMField coordField; IS cellIS; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); /* Determine which discretizations we have */ for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFV_CLASSID) useFVM = PETSC_TRUE; } /* Get local solution with boundary values */ ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); /* Read DS information */ ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); ierr = PetscDSGetComponentOffsets(prob, &uOff);CHKERRQ(ierr); ierr = PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);CHKERRQ(ierr); ierr = ISCreateStride(PETSC_COMM_SELF,numCells,cStart,1,&cellIS);CHKERRQ(ierr); ierr = PetscDSGetConstants(prob, &numConstants, &constants);CHKERRQ(ierr); /* Read Auxiliary DS information */ ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); if (dmAux) { ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); ierr = PetscDSGetNumFields(probAux, &NfAux);CHKERRQ(ierr); ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); ierr = PetscDSGetComponentOffsets(probAux, &aOff);CHKERRQ(ierr); } /* Allocate data arrays */ ierr = PetscCalloc1(numCells*totDim, &u);CHKERRQ(ierr); if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} /* Read out geometry */ ierr = DMGetCoordinateField(dm,&coordField);CHKERRQ(ierr); ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); if (maxDegree <= 1) { ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); if (affineQuad) { ierr = DMFieldCreateFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); } } if (useFVM) { PetscFV fv = NULL; Vec grad; PetscInt fStart, fEnd; PetscBool compGrad; for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFV_CLASSID) {fv = (PetscFV) obj; break;} } ierr = PetscFVGetComputeGradients(fv, &compGrad);CHKERRQ(ierr); ierr = PetscFVSetComputeGradients(fv, PETSC_TRUE);CHKERRQ(ierr); ierr = DMPlexComputeGeometryFVM(dm, &cellGeometryFVM, &faceGeometryFVM);CHKERRQ(ierr); ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometryFVM, cellGeometryFVM, &dmGrad);CHKERRQ(ierr); ierr = PetscFVSetComputeGradients(fv, compGrad);CHKERRQ(ierr); ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); /* Reconstruct and limit cell gradients */ ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); ierr = DMPlexReconstructGradients_Internal(dm, fv, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); /* Communicate gradient values */ ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); /* Handle non-essential (e.g. outflow) boundary values */ ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, 0.0, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); } /* Read out data from inputs */ for (c = cStart; c < cEnd; ++c) { PetscScalar *x = NULL; PetscInt i; ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); if (dmAux) { ierr = DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); } } /* Do integration for each field */ for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; PetscQuadrature q; PetscFEGeom *chunkGeom = NULL; PetscInt Nq, Nb; ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); ierr = PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); blockSize = Nb*Nq; batchSize = numBlocks * blockSize; ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); numChunks = numCells / (numBatches*batchSize); Ne = numChunks*numBatches*batchSize; Nr = numCells % (numBatches*batchSize); offset = numCells - Nr; if (!affineQuad) { ierr = DMFieldCreateFEGeom(coordField,cellIS,q,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); } ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrate(prob, f, Ne, chunkGeom, u, probAux, a, cintegral);CHKERRQ(ierr); ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrate(prob, f, Nr, chunkGeom, &u[offset*totDim], probAux, &a[offset*totDimAux], &cintegral[offset*Nf]);CHKERRQ(ierr); ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); if (!affineQuad) { ierr = PetscFEGeomDestroy(&cgeomFEM);CHKERRQ(ierr); } } else if (id == PETSCFV_CLASSID) { PetscInt foff; PetscPointFunc obj_func; PetscScalar lint; ierr = PetscDSGetObjective(prob, f, &obj_func);CHKERRQ(ierr); ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); if (obj_func) { for (c = 0; c < numCells; ++c) { PetscScalar *u_x; ierr = DMPlexPointLocalRead(dmGrad, c, lgrad, &u_x);CHKERRQ(ierr); 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); cintegral[c*Nf+f] += PetscRealPart(lint)*cgeomFVM[c].volume; } } } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); } /* Cleanup data arrays */ if (useFVM) { ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); ierr = VecRestoreArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); ierr = VecDestroy(&faceGeometryFVM);CHKERRQ(ierr); ierr = VecDestroy(&cellGeometryFVM);CHKERRQ(ierr); ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); } if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} ierr = PetscFree(u);CHKERRQ(ierr); /* Cleanup */ if (affineQuad) { ierr = PetscFEGeomDestroy(&cgeomFEM);CHKERRQ(ierr); } ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); ierr = ISDestroy(&cellIS);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexComputeIntegralFEM - Form the integral over the domain from the global input X using pointwise functions specified by the user Input Parameters: + dm - The mesh . X - Global input vector - user - The user context Output Parameter: . integral - Integral for each field Level: developer .seealso: DMPlexComputeResidualFEM() @*/ PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscScalar *integral, void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; PetscScalar *cintegral, *lintegral; PetscInt Nf, f, cellHeight, cStart, cEnd, cell; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(X, VEC_CLASSID, 2); PetscValidPointer(integral, 3); ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); /* TODO Introduce a loop over large chunks (right now this is a single chunk) */ ierr = PetscCalloc2(Nf, &lintegral, (cEnd-cStart)*Nf, &cintegral);CHKERRQ(ierr); ierr = DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);CHKERRQ(ierr); /* Sum up values */ for (cell = cStart; cell < cEnd; ++cell) { const PetscInt c = cell - cStart; if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);CHKERRQ(ierr);} for (f = 0; f < Nf; ++f) lintegral[f] += cintegral[c*Nf+f]; } ierr = MPIU_Allreduce(lintegral, integral, Nf, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); if (mesh->printFEM) { ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Integral:");CHKERRQ(ierr); for (f = 0; f < Nf; ++f) {ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", (double) PetscRealPart(integral[f]));CHKERRQ(ierr);} ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");CHKERRQ(ierr); } ierr = PetscFree2(lintegral, cintegral);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexComputeCellwiseIntegralFEM - Form the vector of cellwise integrals F from the global input X using pointwise functions specified by the user Input Parameters: + dm - The mesh . X - Global input vector - user - The user context Output Parameter: . integral - Cellwise integrals for each field Level: developer .seealso: DMPlexComputeResidualFEM() @*/ PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM dm, Vec X, Vec F, void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; DM dmF; PetscSection sectionF; PetscScalar *cintegral, *af; PetscInt Nf, f, cellHeight, cStart, cEnd, cell; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(X, VEC_CLASSID, 2); PetscValidHeaderSpecific(F, VEC_CLASSID, 3); ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); /* TODO Introduce a loop over large chunks (right now this is a single chunk) */ ierr = PetscCalloc1((cEnd-cStart)*Nf, &cintegral);CHKERRQ(ierr); ierr = DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);CHKERRQ(ierr); /* Put values in F*/ ierr = VecGetDM(F, &dmF);CHKERRQ(ierr); ierr = DMGetLocalSection(dmF, §ionF);CHKERRQ(ierr); ierr = VecGetArray(F, &af);CHKERRQ(ierr); for (cell = cStart; cell < cEnd; ++cell) { const PetscInt c = cell - cStart; PetscInt dof, off; if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);CHKERRQ(ierr);} ierr = PetscSectionGetDof(sectionF, cell, &dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(sectionF, cell, &off);CHKERRQ(ierr); if (dof != Nf) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of cell dofs %D != %D", dof, Nf); for (f = 0; f < Nf; ++f) af[off+f] = cintegral[c*Nf+f]; } ierr = VecRestoreArray(F, &af);CHKERRQ(ierr); ierr = PetscFree(cintegral);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode DMPlexComputeBdIntegral_Internal(DM dm, Vec locX, IS pointIS, void (*func)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), PetscScalar *fintegral, void *user) { DM plex = NULL, plexA = NULL; DMEnclosureType encAux; PetscDS prob, probAux = NULL; PetscSection section, sectionAux = NULL; Vec locA = NULL; DMField coordField; PetscInt Nf, totDim, *uOff, *uOff_x; PetscInt NfAux = 0, totDimAux = 0, *aOff = NULL; PetscScalar *u, *a = NULL; const PetscScalar *constants; PetscInt numConstants, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); /* Determine which discretizations we have */ for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFV_CLASSID) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Not supported for FVM (field %D)", f); } /* Read DS information */ ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); ierr = PetscDSGetComponentOffsets(prob, &uOff);CHKERRQ(ierr); ierr = PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);CHKERRQ(ierr); ierr = PetscDSGetConstants(prob, &numConstants, &constants);CHKERRQ(ierr); /* Read Auxiliary DS information */ ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); if (locA) { DM dmAux; ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); ierr = PetscDSGetNumFields(probAux, &NfAux);CHKERRQ(ierr); ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); ierr = PetscDSGetComponentOffsets(probAux, &aOff);CHKERRQ(ierr); } /* Integrate over points */ { PetscFEGeom *fgeom, *chunkGeom = NULL; PetscInt maxDegree; PetscQuadrature qGeom = NULL; const PetscInt *points; PetscInt numFaces, face, Nq, field; PetscInt numChunks, chunkSize, chunk, Nr, offset; ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); ierr = PetscCalloc2(numFaces*totDim, &u, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); ierr = DMFieldGetDegree(coordField, pointIS, NULL, &maxDegree);CHKERRQ(ierr); for (field = 0; field < Nf; ++field) { PetscFE fe; ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField, pointIS, &qGeom);CHKERRQ(ierr);} if (!qGeom) { ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) qGeom);CHKERRQ(ierr); } ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexGetFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);CHKERRQ(ierr); for (face = 0; face < numFaces; ++face) { const PetscInt point = points[face], *support, *cone; PetscScalar *x = NULL; PetscInt i, coneSize, faceLoc; ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", face, support[0]); fgeom->face[face][0] = faceLoc; ierr = DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); if (locA) { PetscInt subp; ierr = DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDimAux; ++i) a[f*totDimAux+i] = x[i]; ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); } } /* Get blocking */ { PetscQuadrature q; PetscInt numBatches, batchSize, numBlocks, blockSize; PetscInt Nq, Nb; ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); ierr = PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); blockSize = Nb*Nq; batchSize = numBlocks * blockSize; chunkSize = numBatches*batchSize; ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); numChunks = numFaces / chunkSize; Nr = numFaces % chunkSize; offset = numFaces - Nr; } /* Do integration for each field */ for (chunk = 0; chunk < numChunks; ++chunk) { ierr = PetscFEGeomGetChunk(fgeom, chunk*chunkSize, (chunk+1)*chunkSize, &chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrateBd(prob, field, func, chunkSize, chunkGeom, u, probAux, a, fintegral);CHKERRQ(ierr); ierr = PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);CHKERRQ(ierr); } ierr = PetscFEGeomGetChunk(fgeom, offset, numFaces, &chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrateBd(prob, field, func, Nr, chunkGeom, &u[offset*totDim], probAux, a ? &a[offset*totDimAux] : NULL, &fintegral[offset*Nf]);CHKERRQ(ierr); ierr = PetscFEGeomRestoreChunk(fgeom, offset, numFaces, &chunkGeom);CHKERRQ(ierr); /* Cleanup data arrays */ ierr = DMPlexRestoreFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);CHKERRQ(ierr); ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); ierr = PetscFree2(u, a);CHKERRQ(ierr); ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); } } if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} PetscFunctionReturn(0); } /*@ DMPlexComputeBdIntegral - Form the integral over the specified boundary from the global input X using pointwise functions specified by the user Input Parameters: + dm - The mesh . X - Global input vector . label - The boundary DMLabel . numVals - The number of label values to use, or PETSC_DETERMINE for all values . vals - The label values to use, or PETSC_NULL for all values . func = The function to integrate along the boundary - user - The user context Output Parameter: . integral - Integral for each field Level: developer .seealso: DMPlexComputeIntegralFEM(), DMPlexComputeBdResidualFEM() @*/ PetscErrorCode DMPlexComputeBdIntegral(DM dm, Vec X, DMLabel label, PetscInt numVals, const PetscInt vals[], void (*func)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]), PetscScalar *integral, void *user) { Vec locX; PetscSection section; DMLabel depthLabel; IS facetIS; PetscInt dim, Nf, f, v; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(X, VEC_CLASSID, 2); PetscValidPointer(label, 3); if (vals) PetscValidPointer(vals, 5); PetscValidPointer(integral, 6); ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); /* Get local solution with boundary values */ ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr); /* Loop over label values */ ierr = PetscArrayzero(integral, Nf);CHKERRQ(ierr); for (v = 0; v < numVals; ++v) { IS pointIS; PetscInt numFaces, face; PetscScalar *fintegral; ierr = DMLabelGetStratumIS(label, vals[v], &pointIS);CHKERRQ(ierr); if (!pointIS) continue; /* No points with that id on this process */ { IS isectIS; /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ ierr = ISIntersect_Caching_Internal(facetIS, pointIS, &isectIS);CHKERRQ(ierr); ierr = ISDestroy(&pointIS);CHKERRQ(ierr); pointIS = isectIS; } ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); ierr = PetscCalloc1(numFaces*Nf, &fintegral);CHKERRQ(ierr); ierr = DMPlexComputeBdIntegral_Internal(dm, locX, pointIS, func, fintegral, user);CHKERRQ(ierr); /* Sum point contributions into integral */ for (f = 0; f < Nf; ++f) for (face = 0; face < numFaces; ++face) integral[f] += fintegral[face*Nf+f]; ierr = PetscFree(fintegral);CHKERRQ(ierr); ierr = ISDestroy(&pointIS);CHKERRQ(ierr); } ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr); ierr = ISDestroy(&facetIS);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexComputeInterpolatorNested - Form the local portion of the interpolation matrix I from the coarse DM to a uniformly refined DM. Input Parameters: + dmc - The coarse mesh . dmf - The fine mesh . isRefined - Flag indicating regular refinement, rather than the same topology - user - The user context Output Parameter: . In - The interpolation matrix Level: developer .seealso: DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM() @*/ PetscErrorCode DMPlexComputeInterpolatorNested(DM dmc, DM dmf, PetscBool isRefined, Mat In, void *user) { DM_Plex *mesh = (DM_Plex *) dmc->data; const char *name = "Interpolator"; PetscDS cds, rds; PetscFE *feRef; PetscFV *fvRef; PetscSection fsection, fglobalSection; PetscSection csection, cglobalSection; PetscScalar *elemMat; PetscInt dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c; PetscInt cTotDim, rTotDim = 0; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); ierr = DMGetDimension(dmf, &dim);CHKERRQ(ierr); ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMGetDS(dmc, &cds);CHKERRQ(ierr); ierr = DMGetDS(dmf, &rds);CHKERRQ(ierr); ierr = PetscCalloc2(Nf, &feRef, Nf, &fvRef);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscInt rNb = 0, Nc = 0; ierr = PetscDSGetDiscretization(rds, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; if (isRefined) { ierr = PetscFERefine(fe, &feRef[f]);CHKERRQ(ierr); } else { ierr = PetscObjectReference((PetscObject) fe);CHKERRQ(ierr); feRef[f] = fe; } ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; PetscDualSpace Q; if (isRefined) { ierr = PetscFVRefine(fv, &fvRef[f]);CHKERRQ(ierr); } else { ierr = PetscObjectReference((PetscObject) fv);CHKERRQ(ierr); fvRef[f] = fv; } ierr = PetscFVGetDualSpace(fvRef[f], &Q);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(Q, &rNb);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); } rTotDim += rNb; } ierr = PetscDSGetTotalDimension(cds, &cTotDim);CHKERRQ(ierr); ierr = PetscMalloc1(rTotDim*cTotDim,&elemMat);CHKERRQ(ierr); ierr = PetscArrayzero(elemMat, rTotDim*cTotDim);CHKERRQ(ierr); for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) { PetscDualSpace Qref; PetscQuadrature f; const PetscReal *qpoints, *qweights; PetscReal *points; PetscInt npoints = 0, Nc, Np, fpdim, i, k, p, d; /* Compose points from all dual basis functionals */ if (feRef[fieldI]) { ierr = PetscFEGetDualSpace(feRef[fieldI], &Qref);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(feRef[fieldI], &Nc);CHKERRQ(ierr); } else { ierr = PetscFVGetDualSpace(fvRef[fieldI], &Qref);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fvRef[fieldI], &Nc);CHKERRQ(ierr); } ierr = PetscDualSpaceGetDimension(Qref, &fpdim);CHKERRQ(ierr); for (i = 0; i < fpdim; ++i) { ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, NULL, NULL);CHKERRQ(ierr); npoints += Np; } ierr = PetscMalloc1(npoints*dim,&points);CHKERRQ(ierr); for (i = 0, k = 0; i < fpdim; ++i) { ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d]; } for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) { PetscObject obj; PetscClassId id; PetscInt NcJ = 0, cpdim = 0, j, qNc; ierr = PetscDSGetDiscretization(cds, fieldJ, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; PetscTabulation T = NULL; /* Evaluate basis at points */ ierr = PetscFEGetNumComponents(fe, &NcJ);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); /* For now, fields only interpolate themselves */ if (fieldI == fieldJ) { 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); ierr = PetscFECreateTabulation(fe, 1, npoints, points, 0, &T);CHKERRQ(ierr); for (i = 0, k = 0; i < fpdim; ++i) { ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);CHKERRQ(ierr); 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); for (p = 0; p < Np; ++p, ++k) { for (j = 0; j < cpdim; ++j) { /* cTotDim: Total columns in element interpolation matrix, sum of number of dual basis functionals in each field offsetI, offsetJ: Offsets into the larger element interpolation matrix for different fields fpdim, i, cpdim, j: Dofs for fine and coarse grids, correspond to dual space basis functionals qNC, Nc, Ncj, c: Number of components in this field Np, p: Number of quad points in the fine grid functional i k: i*Np + p, overall point number for the interpolation */ 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]; } } } ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);CHKERRQ(ierr); } } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; /* Evaluate constant function at points */ ierr = PetscFVGetNumComponents(fv, &NcJ);CHKERRQ(ierr); cpdim = 1; /* For now, fields only interpolate themselves */ if (fieldI == fieldJ) { 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); for (i = 0, k = 0; i < fpdim; ++i) { ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);CHKERRQ(ierr); 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); for (p = 0; p < Np; ++p, ++k) { for (j = 0; j < cpdim; ++j) { for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += 1.0*qweights[p*qNc+c]; } } } } } offsetJ += cpdim; } offsetI += fpdim; ierr = PetscFree(points);CHKERRQ(ierr); } if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);CHKERRQ(ierr);} /* Preallocate matrix */ { Mat preallocator; PetscScalar *vals; PetscInt *cellCIndices, *cellFIndices; PetscInt locRows, locCols, cell; ierr = MatGetLocalSize(In, &locRows, &locCols);CHKERRQ(ierr); ierr = MatCreate(PetscObjectComm((PetscObject) In), &preallocator);CHKERRQ(ierr); ierr = MatSetType(preallocator, MATPREALLOCATOR);CHKERRQ(ierr); ierr = MatSetSizes(preallocator, locRows, locCols, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetUp(preallocator);CHKERRQ(ierr); ierr = PetscCalloc3(rTotDim*cTotDim, &vals,cTotDim,&cellCIndices,rTotDim,&cellFIndices);CHKERRQ(ierr); for (cell = cStart; cell < cEnd; ++cell) { if (isRefined) { ierr = DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, cell, cellCIndices, cellFIndices);CHKERRQ(ierr); ierr = MatSetValues(preallocator, rTotDim, cellFIndices, cTotDim, cellCIndices, vals, INSERT_VALUES);CHKERRQ(ierr); } else { ierr = DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, preallocator, cell, vals, INSERT_VALUES);CHKERRQ(ierr); } } ierr = PetscFree3(vals,cellCIndices,cellFIndices);CHKERRQ(ierr); ierr = MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatPreallocatorPreallocate(preallocator, PETSC_TRUE, In);CHKERRQ(ierr); ierr = MatDestroy(&preallocator);CHKERRQ(ierr); } /* Fill matrix */ ierr = MatZeroEntries(In);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { if (isRefined) { ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); } else { ierr = DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); } } for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);} ierr = PetscFree2(feRef,fvRef);CHKERRQ(ierr); ierr = PetscFree(elemMat);CHKERRQ(ierr); ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); if (mesh->printFEM) { ierr = PetscPrintf(PetscObjectComm((PetscObject)In), "%s:\n", name);CHKERRQ(ierr); ierr = MatChop(In, 1.0e-10);CHKERRQ(ierr); ierr = MatView(In, NULL);CHKERRQ(ierr); } ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode DMPlexComputeMassMatrixNested(DM dmc, DM dmf, Mat mass, void *user) { SETERRQ(PetscObjectComm((PetscObject) dmc), PETSC_ERR_SUP, "Laziness"); } /*@ DMPlexComputeInterpolatorGeneral - Form the local portion of the interpolation matrix I from the coarse DM to a non-nested fine DM. Input Parameters: + dmf - The fine mesh . dmc - The coarse mesh - user - The user context Output Parameter: . In - The interpolation matrix Level: developer .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM() @*/ PetscErrorCode DMPlexComputeInterpolatorGeneral(DM dmc, DM dmf, Mat In, void *user) { DM_Plex *mesh = (DM_Plex *) dmf->data; const char *name = "Interpolator"; PetscDS prob; PetscSection fsection, csection, globalFSection, globalCSection; PetscHSetIJ ht; PetscLayout rLayout; PetscInt *dnz, *onz; PetscInt locRows, rStart, rEnd; PetscReal *x, *v0, *J, *invJ, detJ; PetscReal *v0c, *Jc, *invJc, detJc; PetscScalar *elemMat; PetscInt dim, Nf, field, totDim, cStart, cEnd, cell, ccell; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dmc, &dim);CHKERRQ(ierr); ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); ierr = PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);CHKERRQ(ierr); ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); ierr = PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); ierr = PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);CHKERRQ(ierr); ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr); ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); ierr = PetscMalloc1(totDim, &elemMat);CHKERRQ(ierr); ierr = MatGetLocalSize(In, &locRows, NULL);CHKERRQ(ierr); ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) In), &rLayout);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr); ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr); ierr = PetscCalloc2(locRows,&dnz,locRows,&onz);CHKERRQ(ierr); ierr = PetscHSetIJCreate(&ht);CHKERRQ(ierr); for (field = 0; field < Nf; ++field) { PetscObject obj; PetscClassId id; PetscDualSpace Q = NULL; PetscQuadrature f; const PetscReal *qpoints; PetscInt Nc, Np, fpdim, i, d; ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetDualSpace(fe, &Q);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); Nc = 1; } ierr = PetscDualSpaceGetDimension(Q, &fpdim);CHKERRQ(ierr); /* For each fine grid cell */ for (cell = cStart; cell < cEnd; ++cell) { PetscInt *findices, *cindices; PetscInt numFIndices, numCIndices; ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim); for (i = 0; i < fpdim; ++i) { Vec pointVec; PetscScalar *pV; PetscSF coarseCellSF = NULL; const PetscSFNode *coarseCells; PetscInt numCoarseCells, q, c; /* Get points from the dual basis functional quadrature */ ierr = PetscDualSpaceGetFunctional(Q, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); ierr = VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);CHKERRQ(ierr); ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (q = 0; q < Np; ++q) { const PetscReal xi0[3] = {-1., -1., -1.}; /* Transform point to real space */ CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ /* OPT: Pack all quad points from fine cell */ ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); ierr = PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");CHKERRQ(ierr); /* Update preallocation info */ ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); { PetscHashIJKey key; PetscBool missing; key.i = findices[i]; if (key.i >= 0) { /* Get indices for coarse elements */ for (ccell = 0; ccell < numCoarseCells; ++ccell) { ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); for (c = 0; c < numCIndices; ++c) { key.j = cindices[c]; if (key.j < 0) continue; ierr = PetscHSetIJQueryAdd(ht, key, &missing);CHKERRQ(ierr); if (missing) { if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart]; else ++onz[key.i-rStart]; } } ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); } } } ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); ierr = VecDestroy(&pointVec);CHKERRQ(ierr); } ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); } } ierr = PetscHSetIJDestroy(&ht);CHKERRQ(ierr); ierr = MatXAIJSetPreallocation(In, 1, dnz, onz, NULL, NULL);CHKERRQ(ierr); ierr = MatSetOption(In, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); for (field = 0; field < Nf; ++field) { PetscObject obj; PetscClassId id; PetscDualSpace Q = NULL; PetscTabulation T = NULL; PetscQuadrature f; const PetscReal *qpoints, *qweights; PetscInt Nc, qNc, Np, fpdim, i, d; ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetDualSpace(fe, &Q);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); ierr = PetscFECreateTabulation(fe, 1, 1, x, 0, &T);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; ierr = PetscFVGetDualSpace(fv, &Q);CHKERRQ(ierr); Nc = 1; } else SETERRQ1(PetscObjectComm((PetscObject)dmc),PETSC_ERR_ARG_WRONG,"Unknown discretization type for field %D",field); ierr = PetscDualSpaceGetDimension(Q, &fpdim);CHKERRQ(ierr); /* For each fine grid cell */ for (cell = cStart; cell < cEnd; ++cell) { PetscInt *findices, *cindices; PetscInt numFIndices, numCIndices; ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim); for (i = 0; i < fpdim; ++i) { Vec pointVec; PetscScalar *pV; PetscSF coarseCellSF = NULL; const PetscSFNode *coarseCells; PetscInt numCoarseCells, cpdim, q, c, j; /* Get points from the dual basis functional quadrature */ ierr = PetscDualSpaceGetFunctional(Q, i, &f);CHKERRQ(ierr); ierr = PetscQuadratureGetData(f, NULL, &qNc, &Np, &qpoints, &qweights);CHKERRQ(ierr); 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); ierr = VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);CHKERRQ(ierr); ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (q = 0; q < Np; ++q) { const PetscReal xi0[3] = {-1., -1., -1.}; /* Transform point to real space */ CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ /* OPT: Read this out from preallocation information */ ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); /* Update preallocation info */ ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (ccell = 0; ccell < numCoarseCells; ++ccell) { PetscReal pVReal[3]; const PetscReal xi0[3] = {-1., -1., -1.}; ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); /* Transform points from real space to coarse reference space */ ierr = DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);CHKERRQ(ierr); for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]); CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; /* Evaluate coarse basis on contained point */ ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); ierr = PetscFEComputeTabulation(fe, 1, x, 0, T);CHKERRQ(ierr); ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); /* Get elemMat entries by multiplying by weight */ for (j = 0; j < cpdim; ++j) { for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*qweights[ccell*qNc + c]; } } else { cpdim = 1; for (j = 0; j < cpdim; ++j) { for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*qweights[ccell*qNc + c]; } } /* Update interpolator */ if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); ierr = MatSetValues(In, 1, &findices[i], numCIndices, cindices, elemMat, INSERT_VALUES);CHKERRQ(ierr); ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); ierr = VecDestroy(&pointVec);CHKERRQ(ierr); } ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); } if (id == PETSCFE_CLASSID) {ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);} } ierr = PetscFree3(v0,J,invJ);CHKERRQ(ierr); ierr = PetscFree3(v0c,Jc,invJc);CHKERRQ(ierr); ierr = PetscFree(elemMat);CHKERRQ(ierr); ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexComputeMassMatrixGeneral - Form the local portion of the mass matrix M from the coarse DM to a non-nested fine DM. Input Parameters: + dmf - The fine mesh . dmc - The coarse mesh - user - The user context Output Parameter: . mass - The mass matrix Level: developer .seealso: DMPlexComputeMassMatrixNested(), DMPlexComputeInterpolatorNested(), DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM() @*/ PetscErrorCode DMPlexComputeMassMatrixGeneral(DM dmc, DM dmf, Mat mass, void *user) { DM_Plex *mesh = (DM_Plex *) dmf->data; const char *name = "Mass Matrix"; PetscDS prob; PetscSection fsection, csection, globalFSection, globalCSection; PetscHSetIJ ht; PetscLayout rLayout; PetscInt *dnz, *onz; PetscInt locRows, rStart, rEnd; PetscReal *x, *v0, *J, *invJ, detJ; PetscReal *v0c, *Jc, *invJc, detJc; PetscScalar *elemMat; PetscInt dim, Nf, field, totDim, cStart, cEnd, cell, ccell; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinateDim(dmc, &dim);CHKERRQ(ierr); ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); ierr = PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);CHKERRQ(ierr); ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); ierr = PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); ierr = PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);CHKERRQ(ierr); ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr); ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); ierr = PetscMalloc1(totDim, &elemMat);CHKERRQ(ierr); ierr = MatGetLocalSize(mass, &locRows, NULL);CHKERRQ(ierr); ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) mass), &rLayout);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr); ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr); ierr = PetscCalloc2(locRows,&dnz,locRows,&onz);CHKERRQ(ierr); ierr = PetscHSetIJCreate(&ht);CHKERRQ(ierr); for (field = 0; field < Nf; ++field) { PetscObject obj; PetscClassId id; PetscQuadrature quad; const PetscReal *qpoints; PetscInt Nq, Nc, i, d; ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {ierr = PetscFEGetQuadrature((PetscFE) obj, &quad);CHKERRQ(ierr);} else {ierr = PetscFVGetQuadrature((PetscFV) obj, &quad);CHKERRQ(ierr);} ierr = PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, NULL);CHKERRQ(ierr); /* For each fine grid cell */ for (cell = cStart; cell < cEnd; ++cell) { Vec pointVec; PetscScalar *pV; PetscSF coarseCellSF = NULL; const PetscSFNode *coarseCells; PetscInt numCoarseCells, q, c; PetscInt *findices, *cindices; PetscInt numFIndices, numCIndices; ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); /* Get points from the quadrature */ ierr = VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);CHKERRQ(ierr); ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (q = 0; q < Nq; ++q) { const PetscReal xi0[3] = {-1., -1., -1.}; /* Transform point to real space */ CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); ierr = PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");CHKERRQ(ierr); /* Update preallocation info */ ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); { PetscHashIJKey key; PetscBool missing; for (i = 0; i < numFIndices; ++i) { key.i = findices[i]; if (key.i >= 0) { /* Get indices for coarse elements */ for (ccell = 0; ccell < numCoarseCells; ++ccell) { ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); for (c = 0; c < numCIndices; ++c) { key.j = cindices[c]; if (key.j < 0) continue; ierr = PetscHSetIJQueryAdd(ht, key, &missing);CHKERRQ(ierr); if (missing) { if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart]; else ++onz[key.i-rStart]; } } ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); } } } } ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); ierr = VecDestroy(&pointVec);CHKERRQ(ierr); ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); } } ierr = PetscHSetIJDestroy(&ht);CHKERRQ(ierr); ierr = MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);CHKERRQ(ierr); ierr = MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); for (field = 0; field < Nf; ++field) { PetscObject obj; PetscClassId id; PetscTabulation T, Tfine; PetscQuadrature quad; const PetscReal *qpoints, *qweights; PetscInt Nq, Nc, i, d; ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { ierr = PetscFEGetQuadrature((PetscFE) obj, &quad);CHKERRQ(ierr); ierr = PetscFEGetCellTabulation((PetscFE) obj, &Tfine);CHKERRQ(ierr); ierr = PetscFECreateTabulation((PetscFE) obj, 1, 1, x, 0, &T);CHKERRQ(ierr); } else { ierr = PetscFVGetQuadrature((PetscFV) obj, &quad);CHKERRQ(ierr); } ierr = PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, &qweights);CHKERRQ(ierr); /* For each fine grid cell */ for (cell = cStart; cell < cEnd; ++cell) { Vec pointVec; PetscScalar *pV; PetscSF coarseCellSF = NULL; const PetscSFNode *coarseCells; PetscInt numCoarseCells, cpdim, q, c, j; PetscInt *findices, *cindices; PetscInt numFIndices, numCIndices; ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); /* Get points from the quadrature */ ierr = VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);CHKERRQ(ierr); ierr = VecSetBlockSize(pointVec, dim);CHKERRQ(ierr); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (q = 0; q < Nq; ++q) { const PetscReal xi0[3] = {-1., -1., -1.}; /* Transform point to real space */ CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x); for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d]; } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */ ierr = DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);CHKERRQ(ierr); /* Update matrix */ ierr = PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);CHKERRQ(ierr); if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located"); ierr = VecGetArray(pointVec, &pV);CHKERRQ(ierr); for (ccell = 0; ccell < numCoarseCells; ++ccell) { PetscReal pVReal[3]; const PetscReal xi0[3] = {-1., -1., -1.}; ierr = DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); /* Transform points from real space to coarse reference space */ ierr = DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);CHKERRQ(ierr); for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]); CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; /* Evaluate coarse basis on contained point */ ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); ierr = PetscFEComputeTabulation(fe, 1, x, 0, T);CHKERRQ(ierr); /* Get elemMat entries by multiplying by weight */ for (i = 0; i < numFIndices; ++i) { ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); for (j = 0; j < cpdim; ++j) { 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; } /* Update interpolator */ if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); ierr = MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);CHKERRQ(ierr); } } else { cpdim = 1; for (i = 0; i < numFIndices; ++i) { ierr = PetscArrayzero(elemMat, cpdim);CHKERRQ(ierr); for (j = 0; j < cpdim; ++j) { for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*1.0*qweights[ccell*Nc + c]*detJ; } /* Update interpolator */ if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);CHKERRQ(ierr);} ierr = PetscPrintf(PETSC_COMM_SELF, "Nq: %D %D Nf: %D %D Nc: %D %D\n", ccell, Nq, i, numFIndices, j, numCIndices);CHKERRQ(ierr); if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim); ierr = MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);CHKERRQ(ierr); } } ierr = DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);CHKERRQ(ierr); } ierr = VecRestoreArray(pointVec, &pV);CHKERRQ(ierr); ierr = PetscSFDestroy(&coarseCellSF);CHKERRQ(ierr); ierr = VecDestroy(&pointVec);CHKERRQ(ierr); ierr = DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);CHKERRQ(ierr); } if (id == PETSCFE_CLASSID) {ierr = PetscTabulationDestroy(&T);CHKERRQ(ierr);} } ierr = PetscFree3(v0,J,invJ);CHKERRQ(ierr); ierr = PetscFree3(v0c,Jc,invJc);CHKERRQ(ierr); ierr = PetscFree(elemMat);CHKERRQ(ierr); ierr = MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ DMPlexComputeInjectorFEM - Compute a mapping from coarse unknowns to fine unknowns Input Parameters: + dmc - The coarse mesh - dmf - The fine mesh - user - The user context Output Parameter: . sc - The mapping Level: developer .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM() @*/ PetscErrorCode DMPlexComputeInjectorFEM(DM dmc, DM dmf, VecScatter *sc, void *user) { PetscDS prob; PetscFE *feRef; PetscFV *fvRef; Vec fv, cv; IS fis, cis; PetscSection fsection, fglobalSection, csection, cglobalSection; PetscInt *cmap, *cellCIndices, *cellFIndices, *cindices, *findices; PetscInt cTotDim, fTotDim = 0, Nf, f, field, cStart, cEnd, c, dim, d, startC, endC, offsetC, offsetF, m; PetscBool *needAvg; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(DMPLEX_InjectorFEM,dmc,dmf,0,0);CHKERRQ(ierr); ierr = DMGetDimension(dmf, &dim);CHKERRQ(ierr); ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr); ierr = DMGetGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMGetDS(dmc, &prob);CHKERRQ(ierr); ierr = PetscCalloc3(Nf,&feRef,Nf,&fvRef,Nf,&needAvg);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscInt fNb = 0, Nc = 0; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; PetscSpace sp; PetscInt maxDegree; ierr = PetscFERefine(fe, &feRef[f]);CHKERRQ(ierr); ierr = PetscFEGetDimension(feRef[f], &fNb);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); ierr = PetscFEGetBasisSpace(fe, &sp);CHKERRQ(ierr); ierr = PetscSpaceGetDegree(sp, NULL, &maxDegree);CHKERRQ(ierr); if (!maxDegree) needAvg[f] = PETSC_TRUE; } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; PetscDualSpace Q; ierr = PetscFVRefine(fv, &fvRef[f]);CHKERRQ(ierr); ierr = PetscFVGetDualSpace(fvRef[f], &Q);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(Q, &fNb);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); needAvg[f] = PETSC_TRUE; } fTotDim += fNb; } ierr = PetscDSGetTotalDimension(prob, &cTotDim);CHKERRQ(ierr); ierr = PetscMalloc1(cTotDim,&cmap);CHKERRQ(ierr); for (field = 0, offsetC = 0, offsetF = 0; field < Nf; ++field) { PetscFE feC; PetscFV fvC; PetscDualSpace QF, QC; PetscInt order = -1, NcF, NcC, fpdim, cpdim; if (feRef[field]) { ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &feC);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(feC, &NcC);CHKERRQ(ierr); ierr = PetscFEGetNumComponents(feRef[field], &NcF);CHKERRQ(ierr); ierr = PetscFEGetDualSpace(feRef[field], &QF);CHKERRQ(ierr); ierr = PetscDualSpaceGetOrder(QF, &order);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(QF, &fpdim);CHKERRQ(ierr); ierr = PetscFEGetDualSpace(feC, &QC);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(QC, &cpdim);CHKERRQ(ierr); } else { ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fvC);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fvC, &NcC);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fvRef[field], &NcF);CHKERRQ(ierr); ierr = PetscFVGetDualSpace(fvRef[field], &QF);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(QF, &fpdim);CHKERRQ(ierr); ierr = PetscFVGetDualSpace(fvC, &QC);CHKERRQ(ierr); ierr = PetscDualSpaceGetDimension(QC, &cpdim);CHKERRQ(ierr); } 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); for (c = 0; c < cpdim; ++c) { PetscQuadrature cfunc; const PetscReal *cqpoints, *cqweights; PetscInt NqcC, NpC; PetscBool found = PETSC_FALSE; ierr = PetscDualSpaceGetFunctional(QC, c, &cfunc);CHKERRQ(ierr); ierr = PetscQuadratureGetData(cfunc, NULL, &NqcC, &NpC, &cqpoints, &cqweights);CHKERRQ(ierr); 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); if (NpC != 1 && feRef[field]) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Do not know how to do injection for moments"); for (f = 0; f < fpdim; ++f) { PetscQuadrature ffunc; const PetscReal *fqpoints, *fqweights; PetscReal sum = 0.0; PetscInt NqcF, NpF; ierr = PetscDualSpaceGetFunctional(QF, f, &ffunc);CHKERRQ(ierr); ierr = PetscQuadratureGetData(ffunc, NULL, &NqcF, &NpF, &fqpoints, &fqweights);CHKERRQ(ierr); 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); if (NpC != NpF) continue; for (d = 0; d < dim; ++d) sum += PetscAbsReal(cqpoints[d] - fqpoints[d]); if (sum > 1.0e-9) continue; for (d = 0; d < NcC; ++d) sum += PetscAbsReal(cqweights[d]*fqweights[d]); if (sum < 1.0e-9) continue; cmap[offsetC+c] = offsetF+f; found = PETSC_TRUE; break; } if (!found) { /* TODO We really want the average here, but some asshole put VecScatter in the interface */ if (fvRef[field] || (feRef[field] && order == 0)) { cmap[offsetC+c] = offsetF+0; } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate matching functional for injection"); } } offsetC += cpdim; offsetF += fpdim; } for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);ierr = PetscFVDestroy(&fvRef[f]);CHKERRQ(ierr);} ierr = PetscFree3(feRef,fvRef,needAvg);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmf, &fv);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmc, &cv);CHKERRQ(ierr); ierr = VecGetOwnershipRange(cv, &startC, &endC);CHKERRQ(ierr); ierr = PetscSectionGetConstrainedStorageSize(cglobalSection, &m);CHKERRQ(ierr); ierr = PetscMalloc2(cTotDim,&cellCIndices,fTotDim,&cellFIndices);CHKERRQ(ierr); ierr = PetscMalloc1(m,&cindices);CHKERRQ(ierr); ierr = PetscMalloc1(m,&findices);CHKERRQ(ierr); for (d = 0; d < m; ++d) cindices[d] = findices[d] = -1; for (c = cStart; c < cEnd; ++c) { ierr = DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, c, cellCIndices, cellFIndices);CHKERRQ(ierr); for (d = 0; d < cTotDim; ++d) { if ((cellCIndices[d] < startC) || (cellCIndices[d] >= endC)) continue; 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]]); cindices[cellCIndices[d]-startC] = cellCIndices[d]; findices[cellCIndices[d]-startC] = cellFIndices[cmap[d]]; } } ierr = PetscFree(cmap);CHKERRQ(ierr); ierr = PetscFree2(cellCIndices,cellFIndices);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF, m, cindices, PETSC_OWN_POINTER, &cis);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF, m, findices, PETSC_OWN_POINTER, &fis);CHKERRQ(ierr); ierr = VecScatterCreate(cv, cis, fv, fis, sc);CHKERRQ(ierr); ierr = ISDestroy(&cis);CHKERRQ(ierr); ierr = ISDestroy(&fis);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmf, &fv);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmc, &cv);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_InjectorFEM,dmc,dmf,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexGetCellFields - Retrieve the field values values for a chunk of cells Input Parameters: + dm - The DM . cellIS - The cells to include . locX - A local vector with the solution fields . locX_t - A local vector with solution field time derivatives, or NULL - locA - A local vector with auxiliary fields, or NULL Output Parameters: + u - The field coefficients . u_t - The fields derivative coefficients - a - The auxiliary field coefficients Level: developer .seealso: DMPlexGetFaceFields() @*/ PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) { DM plex, plexA = NULL; DMEnclosureType encAux; PetscSection section, sectionAux; PetscDS prob; const PetscInt *cells; PetscInt cStart, cEnd, numCells, totDim, totDimAux, c; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} PetscValidPointer(u, 7); PetscValidPointer(u_t, 8); PetscValidPointer(a, 9); ierr = DMPlexConvertPlex(dm, &plex, PETSC_FALSE);CHKERRQ(ierr); ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = DMGetCellDS(dm, cStart, &prob);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); if (locA) { DM dmAux; PetscDS probAux; ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); ierr = DMGetEnclosureRelation(dmAux, dm, &encAux);CHKERRQ(ierr); ierr = DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);CHKERRQ(ierr); ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); } numCells = cEnd - cStart; ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);CHKERRQ(ierr); if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} for (c = cStart; c < cEnd; ++c) { const PetscInt cell = cells ? cells[c] : c; const PetscInt cind = c - cStart; PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; PetscInt i; ierr = DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i]; ierr = DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); if (locX_t) { ierr = DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i]; ierr = DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); } if (locA) { PetscInt subcell; ierr = DMGetEnclosurePoint(plexA, dm, encAux, cell, &subcell);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subcell, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i]; ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subcell, NULL, &x);CHKERRQ(ierr); } } ierr = DMDestroy(&plex);CHKERRQ(ierr); if (locA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexRestoreCellFields - Restore the field values values for a chunk of cells Input Parameters: + dm - The DM . cellIS - The cells to include . locX - A local vector with the solution fields . locX_t - A local vector with solution field time derivatives, or NULL - locA - A local vector with auxiliary fields, or NULL Output Parameters: + u - The field coefficients . u_t - The fields derivative coefficients - a - The auxiliary field coefficients Level: developer .seealso: DMPlexGetFaceFields() @*/ PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);CHKERRQ(ierr); if (locX_t) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);CHKERRQ(ierr);} if (locA) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);CHKERRQ(ierr);} PetscFunctionReturn(0); } /*@C DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces Input Parameters: + dm - The DM . fStart - The first face to include . fEnd - The first face to exclude . locX - A local vector with the solution fields . locX_t - A local vector with solution field time derivatives, or NULL . faceGeometry - A local vector with face geometry . cellGeometry - A local vector with cell geometry - locaGrad - A local vector with field gradients, or NULL Output Parameters: + Nface - The number of faces with field values . uL - The field values at the left side of the face - uR - The field values at the right side of the face Level: developer .seealso: DMPlexGetCellFields() @*/ 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) { DM dmFace, dmCell, dmGrad = NULL; PetscSection section; PetscDS prob; DMLabel ghostLabel; const PetscScalar *facegeom, *cellgeom, *x, *lgrad; PetscBool *isFE; PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} PetscValidPointer(uL, 9); PetscValidPointer(uR, 10); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} else {isFE[f] = PETSC_FALSE;} } ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); if (locGrad) { ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); } ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);CHKERRQ(ierr); /* Right now just eat the extra work for FE (could make a cell loop) */ for (face = fStart, iface = 0; face < fEnd; ++face) { const PetscInt *cells; PetscFVFaceGeom *fg; PetscFVCellGeom *cgL, *cgR; PetscScalar *xL, *xR, *gL, *gR; PetscScalar *uLl = *uL, *uRl = *uR; PetscInt ghost, nsupp, nchild; ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscInt off; ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); if (isFE[f]) { const PetscInt *cone; PetscInt comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d; xL = xR = NULL; ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cells[0], &coneSizeL);CHKERRQ(ierr); for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break; ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cells[1], &coneSizeR);CHKERRQ(ierr); for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break; 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]); /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ /* TODO: this is a hack that might not be right for nonconforming */ if (faceLocL < coneSizeL) { ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); if (rdof == ldof && faceLocR < coneSizeR) {ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} else {for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} } else { ierr = PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr); ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); for(d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d]; } ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); } else { PetscFV fv; PetscInt numComp, c; ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); if (dmGrad) { PetscReal dxL[3], dxR[3]; ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); for (c = 0; c < numComp; ++c) { uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); } } else { for (c = 0; c < numComp; ++c) { uLl[iface*Nc+off+c] = xL[c]; uRl[iface*Nc+off+c] = xR[c]; } } } } ++iface; } *Nface = iface; ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); if (locGrad) { ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); } ierr = PetscFree(isFE);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces Input Parameters: + dm - The DM . fStart - The first face to include . fEnd - The first face to exclude . locX - A local vector with the solution fields . locX_t - A local vector with solution field time derivatives, or NULL . faceGeometry - A local vector with face geometry . cellGeometry - A local vector with cell geometry - locaGrad - A local vector with field gradients, or NULL Output Parameters: + Nface - The number of faces with field values . uL - The field values at the left side of the face - uR - The field values at the right side of the face Level: developer .seealso: DMPlexGetFaceFields() @*/ 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) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces Input Parameters: + dm - The DM . fStart - The first face to include . fEnd - The first face to exclude . faceGeometry - A local vector with face geometry - cellGeometry - A local vector with cell geometry Output Parameters: + Nface - The number of faces with field values . fgeom - The extract the face centroid and normal - vol - The cell volume Level: developer .seealso: DMPlexGetCellFields() @*/ PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) { DM dmFace, dmCell; DMLabel ghostLabel; const PetscScalar *facegeom, *cellgeom; PetscInt dim, numFaces = fEnd - fStart, iface, face; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); PetscValidPointer(fgeom, 6); PetscValidPointer(vol, 7); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);CHKERRQ(ierr); for (face = fStart, iface = 0; face < fEnd; ++face) { const PetscInt *cells; PetscFVFaceGeom *fg; PetscFVCellGeom *cgL, *cgR; PetscFVFaceGeom *fgeoml = *fgeom; PetscReal *voll = *vol; PetscInt ghost, d, nchild, nsupp; ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); for (d = 0; d < dim; ++d) { fgeoml[iface].centroid[d] = fg->centroid[d]; fgeoml[iface].normal[d] = fg->normal[d]; } voll[iface*2+0] = cgL->volume; voll[iface*2+1] = cgR->volume; ++iface; } *Nface = iface; ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces Input Parameters: + dm - The DM . fStart - The first face to include . fEnd - The first face to exclude . faceGeometry - A local vector with face geometry - cellGeometry - A local vector with cell geometry Output Parameters: + Nface - The number of faces with field values . fgeom - The extract the face centroid and normal - vol - The cell volume Level: developer .seealso: DMPlexGetFaceFields() @*/ PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) { PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscFree(*fgeom);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) { char composeStr[33] = {0}; PetscObjectId id; PetscContainer container; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetId((PetscObject)quad,&id);CHKERRQ(ierr); ierr = PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);CHKERRQ(ierr); if (container) { ierr = PetscContainerGetPointer(container, (void **) geom);CHKERRQ(ierr); } else { ierr = DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);CHKERRQ(ierr); ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); ierr = PetscContainerSetPointer(container, (void *) *geom);CHKERRQ(ierr); ierr = PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);CHKERRQ(ierr); ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); } PetscFunctionReturn(0); } PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) { PetscFunctionBegin; *geom = NULL; PetscFunctionReturn(0); } PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM dm, PetscSection section, IS cellIS, PetscReal t, Vec locX, Vec locX_t, Vec locF, void *user) { DM_Plex *mesh = (DM_Plex *) dm->data; const char *name = "Residual"; DM dmAux = NULL; DMLabel ghostLabel = NULL; PetscDS prob = NULL; PetscDS probAux = NULL; PetscBool useFEM = PETSC_FALSE; PetscBool isImplicit = (locX_t || t == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; DMField coordField = NULL; Vec locA; PetscScalar *u = NULL, *u_t, *a, *uL = NULL, *uR = NULL; IS chunkIS; const PetscInt *cells; PetscInt cStart, cEnd, numCells; PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk, fStart, fEnd; PetscInt maxDegree = PETSC_MAX_INT; PetscQuadrature affineQuad = NULL, *quads = NULL; PetscFEGeom *affineGeom = NULL, **geoms = NULL; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); /* FEM+FVM */ /* 1: Get sizes from dm and dmAux */ ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); if (locA) { ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); } /* 2: Get geometric data */ for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscBool fimp; ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); if (isImplicit != fimp) continue; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} if (id == PETSCFV_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Use of FVM with PCPATCH not yet implemented"); } if (useFEM) { ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); ierr = DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);CHKERRQ(ierr); if (maxDegree <= 1) { ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); if (affineQuad) { ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); } } else { ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscBool fimp; ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); if (isImplicit != fimp) continue; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); } } } } /* Loop over chunks */ ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} numCells = cEnd - cStart; numChunks = 1; cellChunkSize = numCells/numChunks; numChunks = PetscMin(1,numCells); for (chunk = 0; chunk < numChunks; ++chunk) { PetscScalar *elemVec, *fluxL = NULL, *fluxR = NULL; PetscReal *vol = NULL; PetscFVFaceGeom *fgeom = NULL; PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; PetscInt numFaces = 0; /* Extract field coefficients */ if (useFEM) { ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); ierr = PetscArrayzero(elemVec, numCells*totDim);CHKERRQ(ierr); } /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ /* Loop over fields */ for (f = 0; f < Nf; ++f) { PetscObject obj; PetscClassId id; PetscBool fimp; PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); if (isImplicit != fimp) continue; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) { PetscFE fe = (PetscFE) obj; PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; PetscFEGeom *chunkGeom = NULL; PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; PetscInt Nq, Nb; ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); blockSize = Nb; batchSize = numBlocks * blockSize; ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); numChunks = numCells / (numBatches*batchSize); Ne = numChunks*numBatches*batchSize; Nr = numCells % (numBatches*batchSize); offset = numCells - Nr; /* Integrate FE residual to get elemVec (need fields at quadrature points) */ /* 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) */ ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); ierr = PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); } else if (id == PETSCFV_CLASSID) { PetscFV fv = (PetscFV) obj; Ne = numFaces; /* Riemann solve over faces (need fields at face centroids) */ /* We need to evaluate FE fields at those coordinates */ ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); } /* Loop over domain */ if (useFEM) { /* Add elemVec to locX */ for (c = cS; c < cE; ++c) { const PetscInt cell = cells ? cells[c] : c; const PetscInt cind = c - cStart; if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} if (ghostLabel) { PetscInt ghostVal; ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); if (ghostVal > 0) continue; } ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); } } /* Handle time derivative */ if (locX_t) { PetscScalar *x_t, *fa; ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) { PetscFV fv; PetscObject obj; PetscClassId id; PetscInt pdim, d; ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); if (id != PETSCFV_CLASSID) continue; fv = (PetscFV) obj; ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); for (c = cS; c < cE; ++c) { const PetscInt cell = cells ? cells[c] : c; PetscScalar *u_t, *r; if (ghostLabel) { PetscInt ghostVal; ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); if (ghostVal > 0) continue; } ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); for (d = 0; d < pdim; ++d) r[d] += u_t[d]; } } ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); } if (useFEM) { ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); } } if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); /* TODO Could include boundary residual here (see DMPlexComputeResidual_Internal) */ if (useFEM) { if (maxDegree <= 1) { ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); } else { for (f = 0; f < Nf; ++f) { ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); } ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); } } ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /* 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 X - The local solution vector X_t - The local solution time derviative vector, or NULL */ PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx) { DM_Plex *mesh = (DM_Plex *) dm->data; const char *name = "Jacobian", *nameP = "JacobianPre"; DM dmAux = NULL; PetscDS prob, probAux = NULL; PetscSection sectionAux = NULL; Vec A; DMField coordField; PetscFEGeom *cgeomFEM; PetscQuadrature qGeom = NULL; Mat J = Jac, JP = JacP; PetscScalar *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL; PetscBool hasJac, hasPrec, hasDyn, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE; const PetscInt *cells; PetscInt Nf, fieldI, fieldJ, maxDegree, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0; PetscErrorCode ierr; PetscFunctionBegin; CHKMEMQ; ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); if (dmAux) { ierr = DMGetLocalSection(dmAux, §ionAux);CHKERRQ(ierr); ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); } /* Get flags */ ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); ierr = DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); for (fieldI = 0; fieldI < Nf; ++fieldI) { PetscObject disc; PetscClassId id; ierr = PetscDSGetDiscretization(prob, fieldI, &disc);CHKERRQ(ierr); ierr = PetscObjectGetClassId(disc, &id);CHKERRQ(ierr); if (id == PETSCFE_CLASSID) {isFE[fieldI] = PETSC_TRUE;} else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;} } ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE; hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; ierr = PetscObjectTypeCompare((PetscObject) Jac, MATIS, &isMatIS);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); /* Setup input data and temp arrays (should be DMGetWorkArray) */ if (isMatISP || isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &globalSection);CHKERRQ(ierr);} if (isMatIS) {ierr = MatISGetLocalMat(Jac, &J);CHKERRQ(ierr);} if (isMatISP) {ierr = MatISGetLocalMat(JacP, &JP);CHKERRQ(ierr);} if (hasFV) {ierr = MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr);} /* No allocated space for FV stuff, so ignore the zero entries */ ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); if (probAux) {ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr);} CHKMEMQ; /* Compute batch sizes */ if (isFE[0]) { PetscFE fe; PetscQuadrature q; PetscInt numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb; ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); ierr = PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); blockSize = Nb*numQuadPoints; batchSize = numBlocks * blockSize; chunkSize = numBatches * batchSize; numChunks = numCells / chunkSize + numCells % chunkSize; ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); } else { chunkSize = numCells; numChunks = 1; } /* Get work space */ wsz = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize; ierr = DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);CHKERRQ(ierr); ierr = PetscArrayzero(work, wsz);CHKERRQ(ierr); off = 0; u = X ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; u_t = X_t ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; a = dmAux ? (sz = chunkSize*totDimAux, off += sz, work+off-sz) : NULL; elemMat = hasJac ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; elemMatD = hasDyn ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz); /* Setup geometry */ ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); ierr = DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);CHKERRQ(ierr); if (maxDegree <= 1) {ierr = DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);CHKERRQ(ierr);} if (!qGeom) { PetscFE fe; ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) qGeom);CHKERRQ(ierr); } ierr = DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); /* Compute volume integrals */ if (assembleJac) {ierr = MatZeroEntries(J);CHKERRQ(ierr);} ierr = MatZeroEntries(JP);CHKERRQ(ierr); for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) { const PetscInt Ncell = PetscMin(chunkSize, numCells - offCell); PetscInt c; /* Extract values */ for (c = 0; c < Ncell; ++c) { const PetscInt cell = cells ? cells[c+offCell] : c+offCell; PetscScalar *x = NULL, *x_t = NULL; PetscInt i; if (X) { ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); } if (X_t) { ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); } if (dmAux) { ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); } } CHKMEMQ; for (fieldI = 0; fieldI < Nf; ++fieldI) { PetscFE fe; ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { if (hasJac) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr);} if (hasPrec) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr);} if (hasDyn) {ierr = PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr);} } /* For finite volume, add the identity */ if (!isFE[fieldI]) { PetscFV fv; PetscInt eOffset = 0, Nc, fc, foff; ierr = PetscDSGetFieldOffset(prob, fieldI, &foff);CHKERRQ(ierr); ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) { for (fc = 0; fc < Nc; ++fc) { const PetscInt i = foff + fc; if (hasJac) {elemMat [eOffset+i*totDim+i] = 1.0;} if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;} } } } } CHKMEMQ; /* Add contribution from X_t */ if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} /* Insert values into matrix */ for (c = 0; c < Ncell; ++c) { const PetscInt cell = cells ? cells[c+offCell] : c+offCell; if (mesh->printFEM > 1) { if (hasJac) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} if (hasPrec) {ierr = DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} } if (assembleJac) {ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr);} ierr = DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); } CHKMEMQ; } /* Cleanup */ ierr = DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} ierr = DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); ierr = 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);CHKERRQ(ierr); /* Compute boundary integrals */ /* ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx);CHKERRQ(ierr); */ /* Assemble matrix */ if (assembleJac) {ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);} ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); CHKMEMQ; PetscFunctionReturn(0); }