1 #define PETSCDM_DLL 2 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 4 #undef __FUNCT__ 5 #define __FUNCT__ "DMPlexCreateGmsh" 6 /*@ 7 DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file. 8 9 Collective on comm 10 11 Input Parameters: 12 + comm - The MPI communicator 13 . viewer - The Viewer associated with a Gmsh file 14 - interpolate - Create faces and edges in the mesh 15 16 Output Parameter: 17 . dm - The DM object representing the mesh 18 19 Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format 20 21 Level: beginner 22 23 .keywords: mesh,Gmsh 24 .seealso: DMPLEX, DMCreate() 25 @*/ 26 PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm) 27 { 28 FILE *fd; 29 PetscSection coordSection; 30 Vec coordinates; 31 PetscScalar *coords, *coordsIn = NULL; 32 PetscInt dim = 0, tdim = 0, coordSize, c, v, d, cellNum, numCorners, numTags; 33 int numVertices = 0, numCells = 0, trueNumCells = 0, numFacets = 0, cone[8], tags[2], snum; 34 long fpos = 0; 35 PetscMPIInt num_proc, rank; 36 char line[PETSC_MAX_PATH_LEN]; 37 PetscBool match; 38 PetscErrorCode ierr; 39 40 PetscFunctionBegin; 41 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 42 ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); 43 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 44 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 45 if (!rank) { 46 PetscBool match; 47 int fileType, dataSize; 48 49 ierr = PetscViewerASCIIGetPointer(viewer, &fd);CHKERRQ(ierr); 50 /* Read header */ 51 fgets(line, PETSC_MAX_PATH_LEN, fd); 52 ierr = PetscStrncmp(line, "$MeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 53 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 54 snum = fscanf(fd, "2.2 %d %d\n", &fileType, &dataSize);CHKERRQ(snum != 2); 55 if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType); 56 if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize); 57 fgets(line, PETSC_MAX_PATH_LEN, fd); 58 ierr = PetscStrncmp(line, "$EndMeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 59 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 60 /* Read vertices */ 61 fgets(line, PETSC_MAX_PATH_LEN, fd); 62 ierr = PetscStrncmp(line, "$Nodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 63 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 64 snum = fscanf(fd, "%d\n", &numVertices);CHKERRQ(snum != 1); 65 ierr = PetscMalloc(numVertices*3 * sizeof(PetscScalar), &coordsIn);CHKERRQ(ierr); 66 for (v = 0; v < numVertices; ++v) { 67 double x, y, z; 68 int i; 69 70 snum = fscanf(fd, "%d %lg %lg %lg\n", &i, &x, &y, &z);CHKERRQ(snum != 4); 71 coordsIn[v*3+0] = x; coordsIn[v*3+1] = y; coordsIn[v*3+2] = z; 72 if (i != v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1); 73 } 74 fgets(line, PETSC_MAX_PATH_LEN, fd); 75 ierr = PetscStrncmp(line, "$EndNodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 76 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 77 /* Read cells */ 78 fgets(line, PETSC_MAX_PATH_LEN, fd); 79 ierr = PetscStrncmp(line, "$Elements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 80 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 81 snum = fscanf(fd, "%d\n", &numCells);CHKERRQ(snum != 1); 82 } 83 84 if (!rank) { 85 fpos = ftell(fd); 86 /* The Gmsh format disguises facets as elements, so we have to run through all "element" entries 87 to get the correct numCells and decide the topological dimension of the mesh */ 88 trueNumCells = 0; 89 for (c = 0; c < numCells; ++c) { 90 ierr = DMPlexCreateGmsh_ReadElement(fd, &dim, &cellNum, &numCorners, cone, &numTags, tags);CHKERRQ(ierr); 91 if (dim > tdim) { 92 tdim = dim; 93 trueNumCells = 0; 94 } 95 trueNumCells++; 96 } 97 } 98 ierr = DMPlexSetChart(*dm, 0, trueNumCells+numVertices);CHKERRQ(ierr); 99 numFacets = numCells - trueNumCells; 100 if (!rank) { 101 ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr); 102 for (c = 0; c < numCells; ++c) { 103 ierr = DMPlexCreateGmsh_ReadElement(fd, &dim, &cellNum, &numCorners, cone, &numTags, tags);CHKERRQ(ierr); 104 if (dim == tdim) { 105 ierr = DMPlexSetConeSize(*dm, c-numFacets, numCorners);CHKERRQ(ierr); 106 } 107 if (cellNum != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", cellNum, c+1); 108 } 109 } 110 ierr = DMSetUp(*dm);CHKERRQ(ierr); 111 if (!rank) { 112 ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr); 113 PetscInt pcone[8], corner; 114 for (c = 0; c < numCells; ++c) { 115 ierr = DMPlexCreateGmsh_ReadElement(fd, &dim, &cellNum, &numCorners, cone, &numTags, tags);CHKERRQ(ierr); 116 if (dim == tdim) { 117 for (corner = 0; corner < numCorners; ++corner) pcone[corner] = cone[corner] + trueNumCells-1; 118 ierr = DMPlexSetCone(*dm, c-numFacets, pcone);CHKERRQ(ierr); 119 } 120 if (cellNum != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", cellNum, c+1); 121 } 122 fgets(line, PETSC_MAX_PATH_LEN, fd); 123 ierr = PetscStrncmp(line, "$EndElements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 124 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 125 } 126 ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 127 ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); 128 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 129 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 130 if (interpolate) { 131 DM idm; 132 133 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 134 ierr = DMDestroy(dm);CHKERRQ(ierr); 135 *dm = idm; 136 } 137 138 if (!rank) { 139 ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr); 140 /* Apply boundary IDs by finding the relevant facets with vertex joins */ 141 PetscInt pcone[8], corner, vStart, vEnd; 142 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 143 for (c = 0; c < numCells; ++c) { 144 ierr = DMPlexCreateGmsh_ReadElement(fd, &dim, &cellNum, &numCorners, cone, &numTags, tags);CHKERRQ(ierr); 145 if (dim == tdim-1) { 146 PetscInt joinSize; 147 const PetscInt *join; 148 for (corner = 0; corner < numCorners; ++corner) pcone[corner] = cone[corner] + vStart - 1; 149 ierr = DMPlexGetFullJoin(*dm, numCorners, pcone, &joinSize, &join);CHKERRQ(ierr); 150 if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for element %d", cellNum); 151 ierr = DMPlexSetLabelValue(*dm, "Face Sets", join[0], tags[0]);CHKERRQ(ierr); 152 ierr = DMPlexRestoreJoin(*dm, numCorners, pcone, &joinSize, &join);CHKERRQ(ierr); 153 } 154 if (cellNum != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", cellNum, c+1); 155 } 156 fgets(line, PETSC_MAX_PATH_LEN, fd); 157 ierr = PetscStrncmp(line, "$EndElements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr); 158 if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file"); 159 } 160 161 /* Read coordinates */ 162 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 163 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 164 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 165 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 166 for (v = numCells; v < numCells+numVertices; ++v) { 167 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 168 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 169 } 170 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 171 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 172 ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr); 173 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 174 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 175 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 176 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 177 if (!rank) { 178 for (v = 0; v < numVertices; ++v) { 179 for (d = 0; d < dim; ++d) { 180 coords[v*dim+d] = coordsIn[v*3+d]; 181 } 182 } 183 } 184 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 185 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 186 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 187 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 188 PetscFunctionReturn(0); 189 } 190 191 #undef __FUNCT__ 192 #define __FUNCT__ "DMPlexCreateGmsh_ReadElement" 193 PetscErrorCode DMPlexCreateGmsh_ReadElement(FILE *fd, PetscInt *dim, PetscInt *cellNum, PetscInt *numCorners, int cone[], PetscInt *numTags, int tags[]) 194 { 195 PetscInt t; 196 int snum, cellType; 197 198 PetscFunctionBegin; 199 snum = fscanf(fd, "%d %d %d", cellNum, &cellType, numTags);CHKERRQ(snum != 3); 200 if (numTags) for (t = 0; t < *numTags; ++t) {snum = fscanf(fd, "%d", &tags[t]);CHKERRQ(snum != 1);} 201 switch (cellType) { 202 case 1: /* 2-node line */ 203 *dim = 1; 204 *numCorners = 2; 205 snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != *numCorners); 206 break; 207 case 2: /* 3-node triangle */ 208 *dim = 2; 209 *numCorners = 3; 210 snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != *numCorners); 211 break; 212 case 3: /* 4-node quadrangle */ 213 *dim = 2; 214 *numCorners = 4; 215 snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != *numCorners); 216 break; 217 case 4: /* 4-node tetrahedron */ 218 *dim = 3; 219 *numCorners = 4; 220 snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != *numCorners); 221 break; 222 case 5: /* 8-node hexahedron */ 223 *dim = 3; 224 *numCorners = 8; 225 snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != *numCorners); 226 break; 227 default: 228 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType); 229 } 230 PetscFunctionReturn(0); 231 } 232