| 1 |
|
| 2 |
/******************************************************* |
| 3 |
* |
| 4 |
* Copyright (c) 2003-2008 by University of Queensland |
| 5 |
* Earth Systems Science Computational Center (ESSCC) |
| 6 |
* http://www.uq.edu.au/esscc |
| 7 |
* |
| 8 |
* Primary Business: Queensland, Australia |
| 9 |
* Licensed under the Open Software License version 3.0 |
| 10 |
* http://www.opensource.org/licenses/osl-3.0.php |
| 11 |
* |
| 12 |
*******************************************************/ |
| 13 |
|
| 14 |
|
| 15 |
/**************************************************************/ |
| 16 |
|
| 17 |
/* Finley: read mesh */ |
| 18 |
|
| 19 |
/**************************************************************/ |
| 20 |
|
| 21 |
#include "Mesh.h" |
| 22 |
#include <stdio.h> |
| 23 |
|
| 24 |
#define FSCANF_CHECK(scan_ret, reason) { if (scan_ret == EOF) { perror(reason); Finley_setError(IO_ERROR,"scan error while reading finley file"); return NULL;} } |
| 25 |
|
| 26 |
/**************************************************************/ |
| 27 |
|
| 28 |
/* reads a mesh from a Finley file of name fname */ |
| 29 |
|
| 30 |
#define MAX_numNodes_gmsh 10 |
| 31 |
|
| 32 |
Finley_Mesh* Finley_Mesh_readGmsh(char* fname ,index_t numDim, index_t order, index_t reduced_order, bool_t optimize) { |
| 33 |
|
| 34 |
double version = 1.0; |
| 35 |
int format = 0, size = sizeof(double), scan_ret; |
| 36 |
dim_t numNodes, totalNumElements=0, numTags=0, numNodesPerElement, numNodesPerElement2, element_dim; |
| 37 |
index_t e, i0, j, gmsh_type, partition_id, itmp, elementary_id; |
| 38 |
index_t numElements=0, numFaceElements=0, *id=NULL, *tag=NULL, *vertices=NULL; |
| 39 |
Finley_Mesh *mesh_p=NULL; |
| 40 |
char line[LenString_MAX+1]; |
| 41 |
char error_msg[LenErrorMsg_MAX]; |
| 42 |
double rtmp0, rtmp1; |
| 43 |
double time0=Finley_timer(); |
| 44 |
FILE * fileHandle_p = NULL; |
| 45 |
ElementTypeId* element_type=NULL; |
| 46 |
|
| 47 |
Paso_MPIInfo *mpi_info = Paso_MPIInfo_alloc( MPI_COMM_WORLD ); |
| 48 |
Finley_resetError(); |
| 49 |
if (mpi_info->size>1) { |
| 50 |
Finley_setError(IO_ERROR,"reading GMSH with MPI is not supported yet."); |
| 51 |
Paso_MPIInfo_free( mpi_info ); |
| 52 |
return NULL; |
| 53 |
} else { |
| 54 |
|
| 55 |
/* allocate mesh */ |
| 56 |
|
| 57 |
mesh_p = Finley_Mesh_alloc(fname,numDim,order, reduced_order, mpi_info); |
| 58 |
if (! Finley_noError()) return NULL; |
| 59 |
|
| 60 |
/* get file handle */ |
| 61 |
fileHandle_p = fopen(fname, "r"); |
| 62 |
if (fileHandle_p==NULL) { |
| 63 |
sprintf(error_msg,"Opening Gmsh file %s for reading failed.",fname); |
| 64 |
Finley_setError(IO_ERROR,error_msg); |
| 65 |
Paso_MPIInfo_free( mpi_info ); |
| 66 |
return NULL; |
| 67 |
} |
| 68 |
|
| 69 |
/* start reading */ |
| 70 |
while(1) { |
| 71 |
if (! Finley_noError()) break; |
| 72 |
/* find line staring with $ */ |
| 73 |
do { |
| 74 |
if( ! fgets(line, sizeof(line), fileHandle_p) ) break; |
| 75 |
if(feof(fileHandle_p)) break; |
| 76 |
} while(line[0] != '$'); |
| 77 |
|
| 78 |
if (feof(fileHandle_p)) break; |
| 79 |
|
| 80 |
|
| 81 |
/* format */ |
| 82 |
if (!strncmp(&line[1], "MeshFormat", 10)) { |
| 83 |
scan_ret = fscanf(fileHandle_p, "%lf %d %d\n", &version, &format, &size); |
| 84 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 85 |
} |
| 86 |
/* nodes are read */ |
| 87 |
if ( !strncmp(&line[1], "NOD", 3) || |
| 88 |
!strncmp(&line[1], "NOE", 3) || |
| 89 |
!strncmp(&line[1], "Nodes", 5) ) { |
| 90 |
|
| 91 |
scan_ret = fscanf(fileHandle_p, "%d", &numNodes); |
| 92 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 93 |
if (! Finley_noError()) break; |
| 94 |
Finley_NodeFile_allocTable(mesh_p->Nodes, numNodes); |
| 95 |
if (! Finley_noError()) break; |
| 96 |
for (i0 = 0; i0 < numNodes; i0++) { |
| 97 |
if (1 == numDim) { |
| 98 |
scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0], |
| 99 |
&mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)], |
| 100 |
&rtmp0, |
| 101 |
&rtmp1); |
| 102 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 103 |
} else if (2 == numDim) { |
| 104 |
scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0], |
| 105 |
&mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)], |
| 106 |
&mesh_p->Nodes->Coordinates[INDEX2(1,i0,numDim)], |
| 107 |
&rtmp0); |
| 108 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 109 |
} else if (3 == numDim) { |
| 110 |
scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0], |
| 111 |
&mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)], |
| 112 |
&mesh_p->Nodes->Coordinates[INDEX2(1,i0,numDim)], |
| 113 |
&mesh_p->Nodes->Coordinates[INDEX2(2,i0,numDim)]); |
| 114 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 115 |
} |
| 116 |
mesh_p->Nodes->globalDegreesOfFreedom[i0]=mesh_p->Nodes->Id[i0]; |
| 117 |
mesh_p->Nodes->Tag[i0]=0; |
| 118 |
} |
| 119 |
} |
| 120 |
/* elements */ |
| 121 |
else if(!strncmp(&line[1], "ELM", 3) || |
| 122 |
!strncmp(&line[1], "Elements", 8)) { |
| 123 |
|
| 124 |
ElementTypeId final_element_type = NoType; |
| 125 |
ElementTypeId final_face_element_type = NoType; |
| 126 |
ElementTypeId contact_element_type = NoType; |
| 127 |
numElements=0; |
| 128 |
numFaceElements=0; |
| 129 |
scan_ret = fscanf(fileHandle_p, "%d", &totalNumElements); |
| 130 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 131 |
|
| 132 |
id=TMPMEMALLOC(totalNumElements,index_t); |
| 133 |
tag=TMPMEMALLOC(totalNumElements,index_t); |
| 134 |
|
| 135 |
|
| 136 |
element_type=TMPMEMALLOC(totalNumElements,ElementTypeId); |
| 137 |
vertices=TMPMEMALLOC(totalNumElements*MAX_numNodes_gmsh,index_t); |
| 138 |
if (! (Finley_checkPtr(id) || Finley_checkPtr(tag) || Finley_checkPtr(element_type) || Finley_checkPtr(vertices) ) ) { |
| 139 |
/* read all in */ |
| 140 |
for(e = 0; e < totalNumElements; e++) { |
| 141 |
scan_ret = fscanf(fileHandle_p, "%d %d", &id[e], &gmsh_type); |
| 142 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 143 |
switch (gmsh_type) { |
| 144 |
case 1: /* line order 1 */ |
| 145 |
element_type[e]=Line2; |
| 146 |
element_dim=1; |
| 147 |
numNodesPerElement=2; |
| 148 |
break; |
| 149 |
case 2: /* traingle order 1 */ |
| 150 |
element_type[e]=Tri3; |
| 151 |
numNodesPerElement= 3; |
| 152 |
element_dim=2; |
| 153 |
break; |
| 154 |
case 3: /* quadrilateral order 1 */ |
| 155 |
element_type[e]=Rec4; |
| 156 |
numNodesPerElement= 4; |
| 157 |
element_dim=2; |
| 158 |
break; |
| 159 |
case 4: /* tetrahedron order 1 */ |
| 160 |
element_type[e]=Tet4; |
| 161 |
numNodesPerElement= 4; |
| 162 |
element_dim=3; |
| 163 |
break; |
| 164 |
case 5: /* hexahedron order 1 */ |
| 165 |
element_type[e]=Hex8; |
| 166 |
numNodesPerElement= 8; |
| 167 |
element_dim=3; |
| 168 |
break; |
| 169 |
case 8: /* line order 2 */ |
| 170 |
element_type[e]=Line3; |
| 171 |
numNodesPerElement= 3; |
| 172 |
element_dim=1; |
| 173 |
break; |
| 174 |
case 9: /* traingle order 2 */ |
| 175 |
element_type[e]=Tri6; |
| 176 |
numNodesPerElement= 6; |
| 177 |
element_dim=2; |
| 178 |
break; |
| 179 |
case 10: /* quadrilateral order 2 */ |
| 180 |
element_type[e]=Rec9; |
| 181 |
numNodesPerElement= 9; |
| 182 |
element_dim=2; |
| 183 |
break; |
| 184 |
case 11: /* tetrahedron order 2 */ |
| 185 |
element_type[e]=Tet10; |
| 186 |
numNodesPerElement= 10; |
| 187 |
element_dim=3; |
| 188 |
break; |
| 189 |
case 15 : /* point */ |
| 190 |
element_type[e]=Point1; |
| 191 |
numNodesPerElement= 1; |
| 192 |
element_dim=0; |
| 193 |
break; |
| 194 |
default: |
| 195 |
element_type[e]=NoType; |
| 196 |
sprintf(error_msg,"Unexected gmsh element type %d in mesh file %s.",gmsh_type,fname); |
| 197 |
Finley_setError(IO_ERROR,error_msg); |
| 198 |
} |
| 199 |
if (element_dim == numDim) { |
| 200 |
if (final_element_type == NoType) { |
| 201 |
final_element_type = element_type[e]; |
| 202 |
} else if (final_element_type != element_type[e]) { |
| 203 |
sprintf(error_msg,"Finley can handle a single type of internal elements only."); |
| 204 |
Finley_setError(IO_ERROR,error_msg); |
| 205 |
break; |
| 206 |
} |
| 207 |
numElements++; |
| 208 |
} else if (element_dim == numDim-1) { |
| 209 |
if (final_face_element_type == NoType) { |
| 210 |
final_face_element_type = element_type[e]; |
| 211 |
} else if (final_face_element_type != element_type[e]) { |
| 212 |
sprintf(error_msg,"Finley can handle a single type of face elements only."); |
| 213 |
Finley_setError(IO_ERROR,error_msg); |
| 214 |
break; |
| 215 |
} |
| 216 |
numFaceElements++; |
| 217 |
} |
| 218 |
|
| 219 |
if(version <= 1.0){ |
| 220 |
scan_ret = fscanf(fileHandle_p, "%d %d %d", &tag[e], &elementary_id, &numNodesPerElement2); |
| 221 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 222 |
partition_id = 1; |
| 223 |
if (numNodesPerElement2 != numNodesPerElement) { |
| 224 |
sprintf(error_msg,"Illegal number of nodes for element %d in mesh file %s.",id[e],fname); |
| 225 |
Finley_setError(IO_ERROR,error_msg); |
| 226 |
} |
| 227 |
} else { |
| 228 |
scan_ret = fscanf(fileHandle_p, "%d", &numTags); |
| 229 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 230 |
elementary_id = tag[e] = partition_id = 1; |
| 231 |
numNodesPerElement2=-1; |
| 232 |
for(j = 0; j < numTags; j++){ |
| 233 |
scan_ret = fscanf(fileHandle_p, "%d", &itmp); |
| 234 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 235 |
if (j == 0) { |
| 236 |
tag[e] = itmp; |
| 237 |
} else if (j == 1) { |
| 238 |
elementary_id = itmp; |
| 239 |
} else if (j == 2) { |
| 240 |
partition_id = itmp; |
| 241 |
} |
| 242 |
/* ignore any other tags */ |
| 243 |
} |
| 244 |
} |
| 245 |
if (! Finley_noError()) break; |
| 246 |
for(j = 0; j < numNodesPerElement; j++) { |
| 247 |
scan_ret = fscanf(fileHandle_p, "%d", &vertices[INDEX2(j,e,MAX_numNodes_gmsh)]); |
| 248 |
FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh"); |
| 249 |
} |
| 250 |
/* for tet10 the last two nodes need to be swapped */ |
| 251 |
if (element_type[e]==Tet10) { |
| 252 |
itmp=vertices[INDEX2(9,e,MAX_numNodes_gmsh)]; |
| 253 |
vertices[INDEX2(9,e,MAX_numNodes_gmsh)]=vertices[INDEX2(8,e,MAX_numNodes_gmsh)]; |
| 254 |
vertices[INDEX2(8,e,MAX_numNodes_gmsh)]=itmp; |
| 255 |
} |
| 256 |
} |
| 257 |
/* all elements have been read, now we have to identify the elements for finley */ |
| 258 |
|
| 259 |
if (Finley_noError()) { |
| 260 |
/* first we have to identify the elements to define Elementis and FaceElements */ |
| 261 |
if (final_element_type == NoType) { |
| 262 |
if (numDim==1) { |
| 263 |
final_element_type=Line2; |
| 264 |
} else if (numDim==2) { |
| 265 |
final_element_type=Tri3; |
| 266 |
} else if (numDim==3) { |
| 267 |
final_element_type=Tet4; |
| 268 |
} |
| 269 |
} |
| 270 |
if (final_face_element_type == NoType) { |
| 271 |
if (numDim==1) { |
| 272 |
final_face_element_type=Point1; |
| 273 |
} else if (numDim==2) { |
| 274 |
final_face_element_type=Line2; |
| 275 |
} else if (numDim==3) { |
| 276 |
final_face_element_type=Tri3; |
| 277 |
} |
| 278 |
} |
| 279 |
if (final_face_element_type == Line2) { |
| 280 |
contact_element_type=Line2_Contact; |
| 281 |
} else if (final_face_element_type == Line3) { |
| 282 |
contact_element_type=Line3_Contact; |
| 283 |
} else if (final_face_element_type == Tri3) { |
| 284 |
contact_element_type=Tri3_Contact; |
| 285 |
} else if (final_face_element_type == Tri6) { |
| 286 |
contact_element_type=Tri6_Contact; |
| 287 |
} else { |
| 288 |
contact_element_type=Point1_Contact; |
| 289 |
} |
| 290 |
|
| 291 |
mesh_p->Elements=Finley_ElementFile_alloc(final_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info); |
| 292 |
mesh_p->FaceElements=Finley_ElementFile_alloc(final_face_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info); |
| 293 |
mesh_p->ContactElements=Finley_ElementFile_alloc(contact_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info); |
| 294 |
mesh_p->Points=Finley_ElementFile_alloc(Point1,mesh_p->order, mesh_p->reduced_order, mpi_info); |
| 295 |
if (Finley_noError()) { |
| 296 |
Finley_ElementFile_allocTable(mesh_p->Elements, numElements); |
| 297 |
Finley_ElementFile_allocTable(mesh_p->FaceElements, numFaceElements); |
| 298 |
Finley_ElementFile_allocTable(mesh_p->ContactElements, 0); |
| 299 |
Finley_ElementFile_allocTable(mesh_p->Points, 0); |
| 300 |
if (Finley_noError()) { |
| 301 |
mesh_p->Elements->minColor=0; |
| 302 |
mesh_p->Elements->maxColor=numElements-1; |
| 303 |
mesh_p->FaceElements->minColor=0; |
| 304 |
mesh_p->FaceElements->maxColor=numFaceElements-1; |
| 305 |
mesh_p->ContactElements->minColor=0; |
| 306 |
mesh_p->ContactElements->maxColor=0; |
| 307 |
mesh_p->Points->minColor=0; |
| 308 |
mesh_p->Points->maxColor=0; |
| 309 |
numElements=0; |
| 310 |
numFaceElements=0; |
| 311 |
for(e = 0; e < totalNumElements; e++) { |
| 312 |
if (element_type[e] == final_element_type) { |
| 313 |
mesh_p->Elements->Id[numElements]=id[e]; |
| 314 |
mesh_p->Elements->Tag[numElements]=tag[e]; |
| 315 |
mesh_p->Elements->Color[numElements]=numElements; |
| 316 |
mesh_p->Elements->Owner[numElements]=0; |
| 317 |
for (j = 0; j< mesh_p->Elements->ReferenceElement->Type->numNodes; ++j) { |
| 318 |
mesh_p->Elements->Nodes[INDEX2(j, numElements, mesh_p->Elements->ReferenceElement->Type->numNodes)]=vertices[INDEX2(j,e,MAX_numNodes_gmsh)]; |
| 319 |
} |
| 320 |
numElements++; |
| 321 |
} else if (element_type[e] == final_face_element_type) { |
| 322 |
mesh_p->FaceElements->Id[numFaceElements]=id[e]; |
| 323 |
mesh_p->FaceElements->Tag[numFaceElements]=tag[e]; |
| 324 |
mesh_p->FaceElements->Color[numFaceElements]=numFaceElements; |
| 325 |
mesh_p->FaceElements->Owner[numElements]=0; |
| 326 |
for (j = 0; j< mesh_p->FaceElements->ReferenceElement->Type->numNodes; ++j) { |
| 327 |
mesh_p->FaceElements->Nodes[INDEX2(j, numFaceElements, mesh_p->FaceElements->ReferenceElement->Type->numNodes)]=vertices[INDEX2(j,e,MAX_numNodes_gmsh)]; |
| 328 |
} |
| 329 |
numFaceElements++; |
| 330 |
} |
| 331 |
} |
| 332 |
} |
| 333 |
} |
| 334 |
} |
| 335 |
} |
| 336 |
/* and clean up */ |
| 337 |
TMPMEMFREE(id); |
| 338 |
TMPMEMFREE(tag); |
| 339 |
TMPMEMFREE(element_type); |
| 340 |
TMPMEMFREE(vertices); |
| 341 |
} |
| 342 |
/* serach for end of data block */ |
| 343 |
do { |
| 344 |
if (!fgets(line, sizeof(line), fileHandle_p)) { |
| 345 |
sprintf(error_msg,"Unexected end of file in %s",fname); |
| 346 |
Finley_setError(IO_ERROR,error_msg); |
| 347 |
} |
| 348 |
if (feof(fileHandle_p)) { |
| 349 |
sprintf(error_msg,"Unexected end of file in %s",fname); |
| 350 |
Finley_setError(IO_ERROR,error_msg); |
| 351 |
} |
| 352 |
if (! Finley_noError()) break; |
| 353 |
} while(line[0] != '$'); |
| 354 |
} |
| 355 |
|
| 356 |
/* close file */ |
| 357 |
fclose(fileHandle_p); |
| 358 |
/* clean up */ |
| 359 |
if (! Finley_noError()) { |
| 360 |
Finley_Mesh_free(mesh_p); |
| 361 |
return NULL; |
| 362 |
} |
| 363 |
/* resolve id's : */ |
| 364 |
Finley_Mesh_resolveNodeIds(mesh_p); |
| 365 |
/* rearrange elements: */ |
| 366 |
Finley_Mesh_prepare(mesh_p, optimize); |
| 367 |
/* that's it */ |
| 368 |
#ifdef Finley_TRACE |
| 369 |
printf("timing: reading mesh: %.4e sec\n",Finley_timer()-time0); |
| 370 |
#endif |
| 371 |
Paso_MPIInfo_free( mpi_info ); |
| 372 |
return mesh_p; |
| 373 |
} |
| 374 |
} |
Parent Directory
| 
Revision Log