#define PETSC_DESIRE_FEATURE_TEST_MACROS /* for fileno() */ #define PETSCDM_DLL #include /*I "petscdmplex.h" I*/ /* Utility struct to store the contents of a Fluent file in memory */ typedef struct { int index; /* Type of section */ unsigned int zoneID; unsigned int first; unsigned int last; int type; int nd; /* Either ND or element-type */ void *data; } FluentSection; /*@ DMPlexCreateFluentFromFile - Create a `DMPLEX` mesh from a Fluent mesh file Collective Input Parameters: + comm - The MPI communicator . filename - Name of the Fluent mesh file - interpolate - Create faces and edges in the mesh Output Parameter: . dm - The `DM` object representing the mesh Level: beginner .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMPlexCreateFromFile()`, `DMPlexCreateFluent()`, `DMPlexCreate()` @*/ PetscErrorCode DMPlexCreateFluentFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) { PetscViewer viewer; PetscFunctionBegin; /* Create file viewer and build plex */ PetscCall(PetscViewerCreate(comm, &viewer)); PetscCall(PetscViewerSetType(viewer, PETSCVIEWERASCII)); PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ)); PetscCall(PetscViewerFileSetName(viewer, filename)); PetscCall(DMPlexCreateFluent(comm, viewer, interpolate, dm)); PetscCall(PetscViewerDestroy(&viewer)); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode DMPlexCreateFluent_ReadString(PetscViewer viewer, char *buffer, char delim) { PetscInt ret, i = 0; PetscFunctionBegin; do PetscCall(PetscViewerRead(viewer, &buffer[i++], 1, &ret, PETSC_CHAR)); while (ret > 0 && buffer[i - 1] != '\0' && buffer[i - 1] != delim && i < PETSC_MAX_PATH_LEN - 1); if (!ret) buffer[i - 1] = '\0'; else buffer[i] = '\0'; PetscCheck(i < PETSC_MAX_PATH_LEN - 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Buffer overflow! This is not a valid Fluent file."); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode DMPlexCreateFluent_ReadValues(PetscViewer viewer, void *data, PetscInt count, PetscDataType dtype, PetscBool binary, PetscInt *numClosingParens) { int fdes = 0; FILE *file; PetscInt i; PetscFunctionBegin; *numClosingParens = 0; if (binary) { /* Extract raw file descriptor to read binary block */ PetscCall(PetscViewerASCIIGetPointer(viewer, &file)); PetscCall(PetscFFlush(file)); fdes = fileno(file); } if (!binary && dtype == PETSC_INT) { char cbuf[256]; unsigned int ibuf; int snum; /* Parse hexadecimal ascii integers */ for (i = 0; i < count; i++) { size_t len; PetscCall(PetscViewerRead(viewer, cbuf, 1, NULL, PETSC_STRING)); snum = sscanf(cbuf, "%x", &ibuf); PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); ((PetscInt *)data)[i] = (PetscInt)ibuf; // Check for trailing parentheses PetscCall(PetscStrlen(cbuf, &len)); while (cbuf[len - 1] == ')' && len > 0) { ++(*numClosingParens); --len; } } } else if (binary && dtype == PETSC_INT) { /* Always read 32-bit ints and cast to PetscInt */ int *ibuf; PetscCall(PetscMalloc1(count, &ibuf)); PetscCall(PetscBinaryRead(fdes, ibuf, count, NULL, PETSC_ENUM)); PetscCall(PetscByteSwap(ibuf, PETSC_ENUM, count)); for (i = 0; i < count; i++) ((PetscInt *)data)[i] = ibuf[i]; PetscCall(PetscFree(ibuf)); } else if (binary && dtype == PETSC_SCALAR) { float *fbuf; /* Always read 32-bit floats and cast to PetscScalar */ PetscCall(PetscMalloc1(count, &fbuf)); PetscCall(PetscBinaryRead(fdes, fbuf, count, NULL, PETSC_FLOAT)); PetscCall(PetscByteSwap(fbuf, PETSC_FLOAT, count)); for (i = 0; i < count; i++) ((PetscScalar *)data)[i] = fbuf[i]; PetscCall(PetscFree(fbuf)); } else { PetscCall(PetscViewerASCIIRead(viewer, data, count, NULL, dtype)); } PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode DMPlexCreateFluent_ReadSection(PetscViewer viewer, FluentSection *s) { char buffer[PETSC_MAX_PATH_LEN]; int snum; PetscFunctionBegin; /* Fast-forward to next section and derive its index */ PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '(')); PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ' ')); snum = sscanf(buffer, "%d", &s->index); /* If we can't match an index return -1 to signal end-of-file */ if (snum < 1) { s->index = -1; PetscFunctionReturn(PETSC_SUCCESS); } if (s->index == 0) { /* Comment */ PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); } else if (s->index == 2) { /* Dimension */ PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); snum = sscanf(buffer, "%d", &s->nd); PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else if (s->index == 10 || s->index == 2010) { /* Vertices */ PetscInt numClosingParens = 0; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); snum = sscanf(buffer, "(%x %x %x %d %d)", &s->zoneID, &s->first, &s->last, &s->type, &s->nd); PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); if (s->zoneID > 0) { PetscInt numCoords = s->last - s->first + 1; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '(')); PetscCall(PetscMalloc1(s->nd * numCoords, (PetscScalar **)&s->data)); PetscCall(DMPlexCreateFluent_ReadValues(viewer, s->data, s->nd * numCoords, PETSC_SCALAR, s->index == 2010 ? PETSC_TRUE : PETSC_FALSE, &numClosingParens)); if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; } if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; PetscCheck(!numClosingParens, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else if (s->index == 12 || s->index == 2012) { /* Cells */ PetscInt numClosingParens = 0; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); snum = sscanf(buffer, "(%x", &s->zoneID); PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); if (s->zoneID == 0) { /* Header section */ snum = sscanf(buffer, "(%x %x %x %d)", &s->zoneID, &s->first, &s->last, &s->nd); PetscCheck(snum == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else { /* Data section */ snum = sscanf(buffer, "(%x %x %x %d %d)", &s->zoneID, &s->first, &s->last, &s->type, &s->nd); PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); if (s->nd == 0) { /* Read cell type definitions for mixed cells */ PetscInt numCells = s->last - s->first + 1; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '(')); PetscCall(PetscMalloc1(numCells, (PetscInt **)&s->data)); PetscCall(DMPlexCreateFluent_ReadValues(viewer, s->data, numCells, PETSC_INT, s->index == 2012 ? PETSC_TRUE : PETSC_FALSE, &numClosingParens)); if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; } } if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; PetscCheck(!numClosingParens, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else if (s->index == 13 || s->index == 2013) { /* Faces */ PetscInt numClosingParens = 0; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); snum = sscanf(buffer, "(%x", &s->zoneID); PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); if (s->zoneID == 0) { /* Header section */ snum = sscanf(buffer, "(%x %x %x %d)", &s->zoneID, &s->first, &s->last, &s->nd); PetscCheck(snum == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else { /* Data section */ PetscInt numEntries, numFaces, maxsize = 0, offset = 0; snum = sscanf(buffer, "(%x %x %x %d %d)", &s->zoneID, &s->first, &s->last, &s->type, &s->nd); PetscCheck(snum == 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '(')); switch (s->nd) { case 0: numEntries = PETSC_DETERMINE; break; case 2: numEntries = 2 + 2; break; /* linear */ case 3: numEntries = 2 + 3; break; /* triangular */ case 4: numEntries = 2 + 4; break; /* quadrilateral */ default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown face type in Fluent file"); } numFaces = s->last - s->first + 1; if (numEntries != PETSC_DETERMINE) { /* Allocate space only if we already know the size of the block */ PetscCall(PetscMalloc1(numEntries * numFaces, (PetscInt **)&s->data)); } for (PetscInt f = 0; f < numFaces; f++) { if (s->nd == 0) { /* Determine the size of the block for "mixed" facets */ PetscInt numFaceVert = 0; PetscCall(DMPlexCreateFluent_ReadValues(viewer, &numFaceVert, 1, PETSC_INT, s->index == 2013 ? PETSC_TRUE : PETSC_FALSE, &numClosingParens)); if (!f) { maxsize = (numFaceVert + 3) * numFaces; PetscCall(PetscMalloc1(maxsize, (PetscInt **)&s->data)); } else { if (offset + numFaceVert + 3 >= maxsize) { PetscInt *tmp; PetscCall(PetscMalloc1(maxsize * 2, &tmp)); PetscCall(PetscArraycpy(tmp, (PetscInt *)s->data, maxsize)); PetscCall(PetscFree(s->data)); maxsize *= 2; s->data = tmp; } } ((PetscInt *)s->data)[offset] = numFaceVert; ++offset; numEntries = numFaceVert + 2; } PetscCall(DMPlexCreateFluent_ReadValues(viewer, &(((PetscInt *)s->data)[offset]), numEntries, PETSC_INT, s->index == 2013 ? PETSC_TRUE : PETSC_FALSE, &numClosingParens)); offset += numEntries; } if (s->nd != 0) PetscCall(PetscMPIIntCast(numEntries - 2, &s->nd)); if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; } if (!numClosingParens) PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); else --numClosingParens; PetscCheck(!numClosingParens, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file"); } else if (s->index == 39) { /* Label information */ char labelName[PETSC_MAX_PATH_LEN]; char caseName[PETSC_MAX_PATH_LEN]; PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, ')')); snum = sscanf(buffer, "(%u %s %s %d)", &s->zoneID, caseName, labelName, &s->nd); PetscCheck(snum == 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file: %d", snum); PetscInt depth = 1; do { /* Match parentheses when parsing unknown sections */ do PetscCall(PetscViewerRead(viewer, &buffer[0], 1, NULL, PETSC_CHAR)); while (buffer[0] != '(' && buffer[0] != ')'); if (buffer[0] == '(') depth++; if (buffer[0] == ')') depth--; } while (depth > 0); PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '\n')); PetscCall(PetscStrallocpy(labelName, (char **)&s->data)); PetscCall(PetscInfo((PetscObject)viewer, "CASE: Zone ID %u is label %s\n", s->zoneID, labelName)); } else { /* Unknown section type */ PetscInt depth = 1; do { /* Match parentheses when parsing unknown sections */ do PetscCall(PetscViewerRead(viewer, &buffer[0], 1, NULL, PETSC_CHAR)); while (buffer[0] != '(' && buffer[0] != ')'); if (buffer[0] == '(') depth++; if (buffer[0] == ')') depth--; } while (depth > 0); PetscCall(DMPlexCreateFluent_ReadString(viewer, buffer, '\n')); } PetscFunctionReturn(PETSC_SUCCESS); } // Inserts point `face` with orientation `ornt` into the cone of point `cell` at position `c`, which is the first empty slot static PetscErrorCode InsertFace(DM dm, PetscInt cell, PetscInt face, PetscInt ornt) { const PetscInt *cone; PetscInt coneSize, c; PetscFunctionBegin; PetscCall(DMPlexGetCone(dm, cell, &cone)); PetscCall(DMPlexGetConeSize(dm, cell, &coneSize)); for (c = 0; c < coneSize; ++c) if (cone[c] < 0) break; PetscCheck(c < coneSize, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %" PetscInt_FMT " could not be inserted in cone of cell %" PetscInt_FMT " with size %" PetscInt_FMT, face, cell, coneSize); PetscCall(DMPlexInsertCone(dm, cell, c, face)); PetscCall(DMPlexInsertConeOrientation(dm, cell, c, ornt)); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode ReorderPolygon(DM dm, PetscInt cell) { const PetscInt *cone, *ornt; PetscInt coneSize, newCone[16], newOrnt[16]; PetscFunctionBegin; PetscCall(DMPlexGetOrientedCone(dm, cell, &cone, &ornt)); PetscCall(DMPlexGetConeSize(dm, cell, &coneSize)); newCone[0] = cone[0]; newOrnt[0] = ornt[0]; for (PetscInt c = 1; c < coneSize; ++c) { const PetscInt *fcone; PetscInt firstVertex, lastVertex, c2; PetscCall(DMPlexGetCone(dm, newCone[c - 1], &fcone)); lastVertex = newOrnt[c - 1] ? fcone[0] : fcone[1]; for (c2 = 0; c2 < coneSize; ++c2) { const PetscInt *fcone2; PetscCall(DMPlexGetCone(dm, cone[c2], &fcone2)); firstVertex = ornt[c2] ? fcone2[1] : fcone2[0]; if (lastVertex == firstVertex) { // Point `cell` matched point `lastVertex` on face `cone[c2]` with orientation `ornt[c2]` break; } } PetscCheck(c2 < coneSize, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find a face match as position %" PetscInt_FMT, cell, c); newCone[c] = cone[c2]; newOrnt[c] = ornt[c2]; } { const PetscInt *fcone, *fcone2; PetscInt vertex, vertex2; PetscCall(DMPlexGetCone(dm, newCone[coneSize - 1], &fcone)); PetscCall(DMPlexGetCone(dm, newCone[0], &fcone2)); vertex = newOrnt[coneSize - 1] ? fcone[0] : fcone[1]; vertex2 = newOrnt[0] ? fcone2[1] : fcone2[0]; PetscCheck(vertex == vertex2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " did not match at the endpoint", cell); } PetscCall(DMPlexSetCone(dm, cell, newCone)); PetscCall(DMPlexSetConeOrientation(dm, cell, newOrnt)); PetscCall(DMPlexRestoreOrientedCone(dm, cell, &cone, &ornt)); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode ReorderTetrahedron(PetscViewer viewer, DM dm, PetscInt cell) { const PetscInt *cone, *ornt, *fcone, *fornt, *farr, faces[4] = {0, 1, 3, 2}; PetscInt newCone[16], newOrnt[16]; PetscFunctionBegin; PetscCall(DMPlexGetOrientedCone(dm, cell, &cone, &ornt)); newCone[0] = cone[0]; newOrnt[0] = ornt[0]; PetscCall(DMPlexGetOrientedCone(dm, newCone[0], &fcone, &fornt)); farr = DMPolytopeTypeGetArrangement(DM_POLYTOPE_TRIANGLE, newOrnt[0]); // Loop over each edge in the initial triangle for (PetscInt e = 0; e < 3; ++e) { const PetscInt edge = fcone[farr[e * 2 + 0]], eornt = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr[e * 2 + 1], fornt[farr[e * 2 + 0]]); PetscInt c; // Loop over each remaining face in the tetrahedron // On face `newCone[0]`, trying to match edge `edge` with final orientation `eornt` to an edge on another face for (c = 1; c < 4; ++c) { const PetscInt *fcone2, *fornt2, *farr2; PetscInt c2; PetscBool flip = PETSC_FALSE; // Checking face `cone[c]` with orientation `ornt[c]` PetscCall(DMPlexGetOrientedCone(dm, cone[c], &fcone2, &fornt2)); farr2 = DMPolytopeTypeGetArrangement(DM_POLYTOPE_TRIANGLE, ornt[c]); // Check for edge for (c2 = 0; c2 < 3; ++c2) { const PetscInt edge2 = fcone2[farr2[c2 * 2 + 0]], eornt2 = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr2[c2 * 2 + 1], fornt2[farr2[c2 * 2 + 0]]); // Trying to match edge `edge2` with final orientation `eornt2` if (edge == edge2) { //PetscCheck(eornt == -(eornt2 + 1), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell % " PetscInt_FMT " edge %" PetscInt_FMT " (%" PetscInt_FMT ") found twice with the same orientation in face %" PetscInt_FMT " edge %" PetscInt_FMT, cell, edge, e, c, c2); // Matched face `newCone[0]` with orientation `newOrnt[0]` to face `cone[c]` with orientation `ornt[c]` along edge `edge` PetscCall(PetscInfo((PetscObject)viewer, "CASE: Matched cell %" PetscInt_FMT " edge %" PetscInt_FMT "/%" PetscInt_FMT " (%" PetscInt_FMT ") to face %" PetscInt_FMT "/%" PetscInt_FMT " edge %" PetscInt_FMT " (%" PetscInt_FMT ")\n", cell, edge, e, eornt, cone[c], c, c2, eornt2)); flip = eornt != -(eornt2 + 1) ? PETSC_TRUE : PETSC_FALSE; break; } } if (c2 < 3) { newCone[faces[e + 1]] = cone[c]; // Compute new orientation of face based on which edge was matched (only the first edge matches a side different from 0) // Face 1 should match its edge 2 // Face 2 should match its edge 0 // Face 3 should match its edge 0 if (flip) { newOrnt[faces[e + 1]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_TRIANGLE, -((c2 + (!e ? 1 : 2)) % 3 + 1), ornt[c]); } else { newOrnt[faces[e + 1]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_TRIANGLE, !e ? (c2 + 1) % 3 : c2, ornt[c]); } break; } } PetscCheck(c < 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find a face match for edge %" PetscInt_FMT, cell, e); } PetscCall(DMPlexRestoreOrientedCone(dm, newCone[0], &fcone, &fornt)); PetscCall(DMPlexSetCone(dm, cell, newCone)); PetscCall(DMPlexSetConeOrientation(dm, cell, newOrnt)); PetscCall(DMPlexRestoreOrientedCone(dm, cell, &cone, &ornt)); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode ReorderHexahedron(DM dm, PetscInt cell) { const PetscInt *cone, *ornt, *fcone, *fornt, *farr; const PetscInt faces[6] = {0, 5, 3, 4, 2, 1}; PetscInt used[6] = {1, 0, 0, 0, 0, 0}; PetscInt newCone[16], newOrnt[16]; PetscFunctionBegin; PetscCall(DMPlexGetOrientedCone(dm, cell, &cone, &ornt)); newCone[0] = cone[0]; newOrnt[0] = ornt[0]; PetscCall(DMPlexGetOrientedCone(dm, newCone[0], &fcone, &fornt)); farr = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, newOrnt[0]); // Loop over each edge in the initial quadrilateral for (PetscInt e = 0; e < 4; ++e) { const PetscInt edge = fcone[farr[e * 2 + 0]], eornt = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr[e * 2 + 1], fornt[farr[e * 2 + 0]]); PetscInt c; // Loop over each remaining face in the hexahedron // On face `newCone[0]`, trying to match edge `edge` with final orientation `eornt` to an edge on another face for (c = 1; c < 6; ++c) { const PetscInt *fcone2, *fornt2, *farr2; PetscInt c2; // Checking face `cone[c]` with orientation `ornt[c]` PetscCall(DMPlexGetOrientedCone(dm, cone[c], &fcone2, &fornt2)); farr2 = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, ornt[c]); // Check for edge for (c2 = 0; c2 < 4; ++c2) { const PetscInt edge2 = fcone2[farr2[c2 * 2 + 0]], eornt2 = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr2[c2 * 2 + 1], fornt2[farr2[c2 * 2 + 0]]); // Trying to match edge `edge2` with final orientation `eornt2` if (edge == edge2) { PetscCheck(eornt == -(eornt2 + 1), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " found twice with the same orientation", edge); // Matched face `newCone[0]` with orientation `newOrnt[0]` to face `cone[c]` with orientation `ornt[c]` along edge `edge` break; } } if (c2 < 4) { used[c] = 1; newCone[faces[e + 1]] = cone[c]; // Compute new orientation of face based on which edge was matched (only the first edge matches a side different from 0) newOrnt[faces[e + 1]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_QUADRILATERAL, !e ? (c2 + 1) % 4 : c2, ornt[c]); break; } } PetscCheck(c < 6, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find a face match for edge %" PetscInt_FMT, cell, e); } PetscCall(DMPlexRestoreOrientedCone(dm, newCone[0], &fcone, &fornt)); // Add last face { PetscInt c, c2; for (c = 1; c < 6; ++c) if (!used[c]) break; PetscCheck(c < 6, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find an available face", cell); // Match first edge to 3rd edge in newCone[2] { const PetscInt *fcone2, *fornt2, *farr2; PetscCall(DMPlexGetOrientedCone(dm, newCone[2], &fcone, &fornt)); farr = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, newOrnt[2]); PetscCall(DMPlexGetOrientedCone(dm, cone[c], &fcone2, &fornt2)); farr2 = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, ornt[c]); const PetscInt e = 2; const PetscInt edge = fcone[farr[e * 2 + 0]], eornt = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr[e * 2 + 1], fornt[farr[e * 2 + 0]]); // Trying to match edge `edge` with final orientation `eornt` of face `newCone[2]` to some edge of face `cone[c]` with orientation `ornt[c]` for (c2 = 0; c2 < 4; ++c2) { const PetscInt edge2 = fcone2[farr2[c2 * 2 + 0]], eornt2 = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr2[c2 * 2 + 1], fornt2[farr2[c2 * 2 + 0]]); // Trying to match edge `edge2` with final orientation `eornt2` if (edge == edge2) { PetscCheck(eornt == -(eornt2 + 1), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " found twice with the same orientation", edge); // Matched face `newCone[2]` with orientation `newOrnt[2]` to face `cone[c]` with orientation `ornt[c]` along edge `edge` break; } } PetscCheck(c2 < 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not fit last face in"); } newCone[faces[5]] = cone[c]; // Compute new orientation of face based on which edge was matched newOrnt[faces[5]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_QUADRILATERAL, c2, ornt[c]); PetscCall(DMPlexRestoreOrientedCone(dm, newCone[0], &fcone, &fornt)); } PetscCall(DMPlexSetCone(dm, cell, newCone)); PetscCall(DMPlexSetConeOrientation(dm, cell, newOrnt)); PetscCall(DMPlexRestoreOrientedCone(dm, cell, &cone, &ornt)); PetscFunctionReturn(PETSC_SUCCESS); } // {0, 1, 2}, {3, 4, 5}, {0, 2, 4, 3}, {2, 1, 5, 4}, {1, 0, 3, 5} static PetscErrorCode ReorderWedge(DM dm, PetscInt cell) { const PetscInt *cone, *ornt, *fcone, *fornt, *farr; const PetscInt faces[5] = {0, 4, 3, 2, 1}; PetscInt used[5] = {0, 0, 0, 0, 0}; PetscInt newCone[16], newOrnt[16], cS, bottom = 0; PetscFunctionBegin; PetscCall(DMPlexGetConeSize(dm, cell, &cS)); PetscCall(DMPlexGetOrientedCone(dm, cell, &cone, &ornt)); for (PetscInt c = 0; c < cS; ++c) { DMPolytopeType ct; PetscCall(DMPlexGetCellType(dm, cone[c], &ct)); if (ct == DM_POLYTOPE_TRIANGLE) { bottom = c; break; } } used[bottom] = 1; newCone[0] = cone[bottom]; newOrnt[0] = ornt[bottom]; PetscCall(DMPlexGetOrientedCone(dm, newCone[0], &fcone, &fornt)); farr = DMPolytopeTypeGetArrangement(DM_POLYTOPE_TRIANGLE, newOrnt[0]); // Loop over each edge in the initial triangle for (PetscInt e = 0; e < 3; ++e) { const PetscInt edge = fcone[farr[e * 2 + 0]], eornt = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr[e * 2 + 1], fornt[farr[e * 2 + 0]]); PetscInt c; // Loop over each remaining face in the prism // On face `newCone[0]`, trying to match edge `edge` with final orientation `eornt` to an edge on another face for (c = 0; c < 5; ++c) { const PetscInt *fcone2, *fornt2, *farr2; DMPolytopeType ct; PetscInt c2; if (c == bottom) continue; PetscCall(DMPlexGetCellType(dm, cone[c], &ct)); if (ct != DM_POLYTOPE_QUADRILATERAL) continue; // Checking face `cone[c]` with orientation `ornt[c]` PetscCall(DMPlexGetOrientedCone(dm, cone[c], &fcone2, &fornt2)); farr2 = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, ornt[c]); // Check for edge for (c2 = 0; c2 < 4; ++c2) { const PetscInt edge2 = fcone2[farr2[c2 * 2 + 0]], eornt2 = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr2[c2 * 2 + 1], fornt2[farr2[c2 * 2 + 0]]); // Trying to match edge `edge2` with final orientation `eornt2` if (edge == edge2) { PetscCheck(eornt == -(eornt2 + 1), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " found twice with the same orientation", edge); // Matched face `newCone[0]` with orientation `newOrnt[0]` to face `cone[c]` with orientation `ornt[c]` along edge `edge` break; } } if (c2 < 4) { used[c] = 1; newCone[faces[e + 1]] = cone[c]; // Compute new orientation of face based on which edge was matched, edge 0 should always match the bottom newOrnt[faces[e + 1]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_QUADRILATERAL, c2, ornt[c]); break; } } PetscCheck(c < 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find a face match for edge %" PetscInt_FMT, cell, e); } PetscCall(DMPlexRestoreOrientedCone(dm, newCone[0], &fcone, &fornt)); // Add last face { PetscInt c, c2; for (c = 0; c < 5; ++c) if (!used[c]) break; PetscCheck(c < 5, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %" PetscInt_FMT " could not find an available face", cell); // Match first edge to 3rd edge in newCone[2] { const PetscInt *fcone2, *fornt2, *farr2; PetscCall(DMPlexGetOrientedCone(dm, newCone[2], &fcone, &fornt)); farr = DMPolytopeTypeGetArrangement(DM_POLYTOPE_QUADRILATERAL, newOrnt[2]); PetscCall(DMPlexGetOrientedCone(dm, cone[c], &fcone2, &fornt2)); farr2 = DMPolytopeTypeGetArrangement(DM_POLYTOPE_TRIANGLE, ornt[c]); const PetscInt e = 2; const PetscInt edge = fcone[farr[e * 2 + 0]], eornt = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr[e * 2 + 1], fornt[farr[e * 2 + 0]]); // Trying to match edge `edge` with final orientation `eornt` of face `newCone[2]` to some edge of face `cone[c]` with orientation `ornt[c]` for (c2 = 0; c2 < 3; ++c2) { const PetscInt edge2 = fcone2[farr2[c2 * 2 + 0]], eornt2 = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_SEGMENT, farr2[c2 * 2 + 1], fornt2[farr2[c2 * 2 + 0]]); // Trying to match edge `edge2` with final orientation `eornt2` if (edge == edge2) { PetscCheck(eornt == -(eornt2 + 1), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Edge %" PetscInt_FMT " found twice with the same orientation", edge); // Matched face `newCone[2]` with orientation `newOrnt[2]` to face `cone[c]` with orientation `ornt[c]` along edge `edge` break; } } PetscCheck(c2 < 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not fit last face in"); } newCone[faces[4]] = cone[c]; // Compute new orientation of face based on which edge was matched newOrnt[faces[4]] = DMPolytopeTypeComposeOrientation(DM_POLYTOPE_TRIANGLE, c2, ornt[c]); PetscCall(DMPlexRestoreOrientedCone(dm, newCone[0], &fcone, &fornt)); } PetscCall(DMPlexSetCone(dm, cell, newCone)); PetscCall(DMPlexSetConeOrientation(dm, cell, newOrnt)); PetscCall(DMPlexRestoreOrientedCone(dm, cell, &cone, &ornt)); PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode ReorderCell(PetscViewer viewer, DM dm, PetscInt cell, DMPolytopeType ct) { PetscFunctionBegin; switch (ct) { case DM_POLYTOPE_TRIANGLE: case DM_POLYTOPE_QUADRILATERAL: PetscCall(ReorderPolygon(dm, cell)); break; case DM_POLYTOPE_TETRAHEDRON: PetscCall(ReorderTetrahedron(viewer, dm, cell)); break; case DM_POLYTOPE_HEXAHEDRON: PetscCall(ReorderHexahedron(dm, cell)); break; case DM_POLYTOPE_TRI_PRISM: PetscCall(ReorderWedge(dm, cell)); break; default: PetscCheck(0, PETSC_COMM_SELF, PETSC_ERR_SUP, "Celltype %s is unsupported", DMPolytopeTypes[ct]); break; } PetscFunctionReturn(PETSC_SUCCESS); } static PetscErrorCode GetNumCellFaces(int nd, PetscInt *numCellFaces, DMPolytopeType *ct) { PetscFunctionBegin; *ct = DM_POLYTOPE_POINT; switch (nd) { case 0: *numCellFaces = PETSC_DETERMINE; break; case 1: *numCellFaces = 3; *ct = DM_POLYTOPE_TRIANGLE; break; case 2: *numCellFaces = 4; *ct = DM_POLYTOPE_TETRAHEDRON; break; case 3: *numCellFaces = 4; *ct = DM_POLYTOPE_QUADRILATERAL; break; case 4: *numCellFaces = 6; *ct = DM_POLYTOPE_HEXAHEDRON; break; case 5: *numCellFaces = 5; *ct = DM_POLYTOPE_PYRAMID; break; case 6: *numCellFaces = 5; *ct = DM_POLYTOPE_TRI_PRISM; break; default: *numCellFaces = PETSC_DETERMINE; } PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMPlexCreateFluent - Create a `DMPLEX` mesh from a Fluent mesh file . Collective Input Parameters: + comm - The MPI communicator . viewer - The `PetscViewer` associated with a Fluent mesh file - interpolate - Create faces and edges in the mesh Output Parameter: . dm - The `DM` object representing the mesh Level: beginner .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreate()` @*/ PetscErrorCode DMPlexCreateFluent(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm) { PetscInt dim = PETSC_DETERMINE; PetscInt numCells = 0; PetscInt numVertices = 0; PetscInt *cellSizes = NULL; DMPolytopeType *cellTypes = NULL; PetscInt numFaces = 0; PetscInt *faces = NULL; PetscInt *faceSizes = NULL; PetscInt *faceAdjCell = NULL; PetscInt *cellVertices = NULL; unsigned int *faceZoneIDs = NULL; DMLabel faceSets = NULL; DMLabel *zoneLabels = NULL; const char **zoneNames = NULL; unsigned int maxZoneID = 0; PetscScalar *coordsIn = NULL; PetscScalar *coords; PetscSection coordSection; Vec coordinates; PetscInt coordSize, maxFaceSize = 0, totFaceVert = 0, f; PetscMPIInt rank; PetscFunctionBegin; PetscCallMPI(MPI_Comm_rank(comm, &rank)); if (rank == 0) { FluentSection s; s.data = NULL; numFaces = PETSC_DETERMINE; do { PetscCall(DMPlexCreateFluent_ReadSection(viewer, &s)); if (s.index == 2) { /* Dimension */ dim = s.nd; PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found dimension: %" PetscInt_FMT "\n", dim)); } else if (s.index == 10 || s.index == 2010) { /* Vertices */ if (s.zoneID == 0) { numVertices = s.last; PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found number of vertices: %" PetscInt_FMT "\n", numVertices)); } else { PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found vertex coordinates\n")); PetscCheck(!coordsIn, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Currently no support for multiple coordinate sets in Fluent files"); coordsIn = (PetscScalar *)s.data; } } else if (s.index == 12 || s.index == 2012) { /* Cells */ if (s.zoneID == 0) { numCells = s.last; PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found number of cells %" PetscInt_FMT "\n", numCells)); } else { PetscCall(PetscMalloc2(numCells, &cellSizes, numCells, &cellTypes)); for (PetscInt c = 0; c < numCells; ++c) PetscCall(GetNumCellFaces(s.nd ? s.nd : (int)((PetscInt *)s.data)[c], &cellSizes[c], &cellTypes[c])); PetscCall(PetscFree(s.data)); PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found number of cell faces %" PetscInt_FMT "\n", numCells && s.nd ? cellSizes[0] : 0)); } } else if (s.index == 13 || s.index == 2013) { /* Facets */ if (s.zoneID == 0) { /* Header section */ numFaces = (PetscInt)(s.last - s.first + 1); PetscCall(PetscInfo((PetscObject)viewer, "CASE: Found number of faces %" PetscInt_FMT " face vertices: %d\n", numFaces, s.nd)); } else { /* Data section */ PetscInt *tmp; PetscInt totSize = 0, offset = 0, doffset; PetscCheck(numFaces >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No header section for facets in Fluent file"); if (!faceZoneIDs) PetscCall(PetscMalloc3(numFaces, &faceSizes, numFaces * 2, &faceAdjCell, numFaces, &faceZoneIDs)); // Record the zoneID and face size for each face set for (unsigned int z = s.first - 1; z < s.last; z++) { faceZoneIDs[z] = s.zoneID; if (s.nd) { faceSizes[z] = s.nd; } else { faceSizes[z] = ((PetscInt *)s.data)[offset]; offset += faceSizes[z] + 3; } totSize += faceSizes[z]; maxFaceSize = PetscMax(maxFaceSize, faceSizes[z]); } offset = totFaceVert; doffset = s.nd ? 0 : 1; PetscCall(PetscMalloc1(totFaceVert + totSize, &tmp)); if (faces) PetscCall(PetscArraycpy(tmp, faces, totFaceVert)); PetscCall(PetscFree(faces)); totFaceVert += totSize; faces = tmp; // Record face vertices and adjacent faces const PetscInt Nfz = s.last - s.first + 1; for (PetscInt f = 0; f < Nfz; ++f) { const PetscInt face = f + s.first - 1; const PetscInt faceSize = faceSizes[face]; for (PetscInt v = 0; v < faceSize; ++v) faces[offset + v] = ((PetscInt *)s.data)[doffset + v]; faceAdjCell[face * 2 + 0] = ((PetscInt *)s.data)[doffset + faceSize + 0]; faceAdjCell[face * 2 + 1] = ((PetscInt *)s.data)[doffset + faceSize + 1]; offset += faceSize; doffset += faceSize + (s.nd ? 2 : 3); } PetscCall(PetscFree(s.data)); } } else if (s.index == 39) { /* Label information */ if (s.zoneID >= maxZoneID) { DMLabel *tmpL; const char **tmp; unsigned int newmax = maxZoneID + 1; while (newmax < s.zoneID + 1) newmax *= 2; PetscCall(PetscCalloc2(newmax, &tmp, newmax, &tmpL)); for (PetscInt i = 0; i < (PetscInt)maxZoneID; ++i) { tmp[i] = zoneNames[i]; tmpL[i] = zoneLabels[i]; } maxZoneID = newmax; PetscCall(PetscFree2(zoneNames, zoneLabels)); zoneNames = tmp; zoneLabels = tmpL; } zoneNames[s.zoneID] = (const char *)s.data; } } while (s.index >= 0); } PetscCallMPI(MPI_Bcast(&dim, 1, MPIU_INT, 0, comm)); PetscCheck(dim >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Fluent file does not include dimension"); /* Allocate cell-vertex mesh */ PetscCall(DMCreate(comm, dm)); PetscCall(DMSetType(*dm, DMPLEX)); PetscCall(DMSetDimension(*dm, dim)); // We do not want this label automatically computed, instead we fill it here PetscCall(DMCreateLabel(*dm, "celltype")); PetscCall(DMPlexSetChart(*dm, 0, numCells + numFaces + numVertices)); if (rank == 0) { PetscCheck(numCells >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown number of cells in Fluent file"); for (PetscInt c = 0; c < numCells; ++c) { PetscCall(DMPlexSetConeSize(*dm, c, cellSizes[c])); PetscCall(DMPlexSetCellType(*dm, c, cellTypes[c])); } for (PetscInt v = numCells; v < numCells + numVertices; ++v) PetscCall(DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT)); for (PetscInt f = 0; f < numFaces; ++f) { DMPolytopeType ct; switch (faceSizes[f]) { case 2: ct = DM_POLYTOPE_SEGMENT; break; case 3: ct = DM_POLYTOPE_TRIANGLE; break; case 4: ct = DM_POLYTOPE_QUADRILATERAL; break; default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown face type in Fluent file with cone size %" PetscInt_FMT, faceSizes[f]); } PetscCall(DMPlexSetConeSize(*dm, f + numCells + numVertices, faceSizes[f])); PetscCall(DMPlexSetCellType(*dm, f + numCells + numVertices, ct)); } } PetscCall(DMSetUp(*dm)); if (rank == 0 && faces) { PetscSection s; PetscInt *cones, csize, foffset = 0; PetscCall(DMPlexGetCones(*dm, &cones)); PetscCall(DMPlexGetConeSection(*dm, &s)); PetscCall(PetscSectionGetConstrainedStorageSize(s, &csize)); for (PetscInt c = 0; c < csize; ++c) cones[c] = -1; for (PetscInt f = 0; f < numFaces; f++) { const PetscInt cl = faceAdjCell[f * 2 + 0] - 1; const PetscInt cr = faceAdjCell[f * 2 + 1] - 1; const PetscInt face = f + numCells + numVertices; PetscInt fcone[16]; // How could Fluent define the outward normal differently? Is there no end to the pain? if (dim == 3) { if (cl >= 0) PetscCall(InsertFace(*dm, cl, face, -1)); if (cr >= 0) PetscCall(InsertFace(*dm, cr, face, 0)); } else { if (cl >= 0) PetscCall(InsertFace(*dm, cl, face, 0)); if (cr >= 0) PetscCall(InsertFace(*dm, cr, face, -1)); } PetscCheck(faceSizes[f] < 16, PETSC_COMM_SELF, PETSC_ERR_SUP, "Number of face vertices %" PetscInt_FMT " exceeds temporary storage", faceSizes[f]); for (PetscInt v = 0; v < faceSizes[f]; ++v) fcone[v] = faces[foffset + v] + numCells - 1; foffset += faceSizes[f]; PetscCall(DMPlexSetCone(*dm, face, fcone)); } } PetscCall(DMPlexSymmetrize(*dm)); PetscCall(DMPlexStratify(*dm)); if (dim == 3) { DM idm; PetscCall(DMCreate(PetscObjectComm((PetscObject)*dm), &idm)); PetscCall(DMSetType(idm, DMPLEX)); PetscCall(DMSetDimension(idm, dim)); PetscCall(DMPlexInterpolateFaces_Internal(*dm, 1, idm)); PetscCall(DMDestroy(dm)); *dm = idm; } PetscCall(DMViewFromOptions(*dm, NULL, "-cas_dm_view")); if (rank == 0 && faces) { for (PetscInt c = 0; c < numCells; ++c) PetscCall(ReorderCell(viewer, *dm, c, cellTypes[c])); } if (rank == 0 && faces) { PetscInt joinSize, meetSize, *fverts, cells[2]; const PetscInt *join, *meet; PetscInt foffset = 0; PetscCall(PetscMalloc1(maxFaceSize, &fverts)); /* Mark facets by finding the full join of all adjacent vertices */ for (f = 0; f < numFaces; f++) { const PetscInt cl = faceAdjCell[f * 2 + 0] - 1; const PetscInt cr = faceAdjCell[f * 2 + 1] - 1; const PetscInt id = (PetscInt)faceZoneIDs[f]; if (cl > 0 && cr > 0) { /* If we know both adjoining cells we can use a single-level meet */ cells[0] = cl; cells[1] = cr; PetscCall(DMPlexGetMeet(*dm, 2, cells, &meetSize, &meet)); PetscCheck(meetSize == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %" PetscInt_FMT " cells: %" PetscInt_FMT ", %" PetscInt_FMT, f, cl, cr); PetscCall(DMSetLabelValue_Fast(*dm, &faceSets, "Face Sets", meet[0], id)); if (zoneNames && zoneNames[id]) PetscCall(DMSetLabelValue_Fast(*dm, &zoneLabels[id], zoneNames[id], meet[0], 1)); PetscCall(DMPlexRestoreMeet(*dm, meetSize, fverts, &meetSize, &meet)); } else { for (PetscInt fi = 0; fi < faceSizes[f]; fi++) fverts[fi] = faces[foffset + fi] + numCells - 1; PetscCall(DMPlexGetFullJoin(*dm, faceSizes[f], fverts, &joinSize, &join)); PetscCheck(joinSize == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %" PetscInt_FMT, f); PetscCall(DMSetLabelValue_Fast(*dm, &faceSets, "Face Sets", join[0], id)); if (zoneNames && zoneNames[id]) PetscCall(DMSetLabelValue_Fast(*dm, &zoneLabels[id], zoneNames[id], join[0], 1)); PetscCall(DMPlexRestoreJoin(*dm, joinSize, fverts, &joinSize, &join)); } foffset += faceSizes[f]; } PetscCall(PetscFree(fverts)); } { /* Create Face Sets label at all processes */ enum { n = 1 }; PetscBool flag[n]; flag[0] = faceSets ? PETSC_TRUE : PETSC_FALSE; PetscCallMPI(MPI_Bcast(flag, n, MPI_C_BOOL, 0, comm)); if (flag[0]) PetscCall(DMCreateLabel(*dm, "Face Sets")); // TODO Code to create all the zone labels on each process } if (!interpolate) { DM udm; PetscCall(DMPlexUninterpolate(*dm, &udm)); PetscCall(DMDestroy(dm)); *dm = udm; } /* Read coordinates */ PetscCall(DMGetCoordinateSection(*dm, &coordSection)); PetscCall(PetscSectionSetNumFields(coordSection, 1)); PetscCall(PetscSectionSetFieldComponents(coordSection, 0, dim)); PetscCall(PetscSectionSetChart(coordSection, numCells, numCells + numVertices)); for (PetscInt v = numCells; v < numCells + numVertices; ++v) { PetscCall(PetscSectionSetDof(coordSection, v, dim)); PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, dim)); } PetscCall(PetscSectionSetUp(coordSection)); PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates")); PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); PetscCall(VecSetType(coordinates, VECSTANDARD)); PetscCall(VecGetArray(coordinates, &coords)); if (rank == 0 && coordsIn) { for (PetscInt v = 0; v < numVertices; ++v) { for (PetscInt d = 0; d < dim; ++d) coords[v * dim + d] = coordsIn[v * dim + d]; } } PetscCall(VecRestoreArray(coordinates, &coords)); PetscCall(DMSetCoordinatesLocal(*dm, coordinates)); PetscCall(VecDestroy(&coordinates)); if (rank == 0) { PetscCall(PetscFree(cellVertices)); PetscCall(PetscFree2(cellSizes, cellTypes)); PetscCall(PetscFree(faces)); PetscCall(PetscFree3(faceSizes, faceAdjCell, faceZoneIDs)); PetscCall(PetscFree(coordsIn)); if (zoneNames) for (PetscInt i = 0; i < (PetscInt)maxZoneID; ++i) PetscCall(PetscFree(zoneNames[i])); PetscCall(PetscFree2(zoneNames, zoneLabels)); } PetscFunctionReturn(PETSC_SUCCESS); }