/[escript]/branches/domexper/dudley/src/Mesh_readGmsh.c
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Annotation of /branches/domexper/dudley/src/Mesh_readGmsh.c

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Revision 2243 - (hide annotations)
Wed Feb 4 05:22:28 2009 UTC (10 years, 2 months ago) by gross
Original Path: trunk/finley/src/Mesh_readGmsh.c
File MIME type: text/plain
File size: 16391 byte(s)
small bug fixed which could lead to a seg fault
1 gross 935
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
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 gross 935
14 ksteube 1811
15 gross 935 /**************************************************************/
16    
17 ksteube 1312 /* Finley: read mesh */
18 gross 935
19     /**************************************************************/
20    
21     #include "Mesh.h"
22     #include <stdio.h>
23    
24 gross 1896 #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 gross 935
26     /**************************************************************/
27    
28     /* reads a mesh from a Finley file of name fname */
29    
30     #define MAX_numNodes_gmsh 10
31    
32 ksteube 1312 Finley_Mesh* Finley_Mesh_readGmsh(char* fname ,index_t numDim, index_t order, index_t reduced_order, bool_t optimize) {
33 gross 935
34     double version = 1.0;
35 ksteube 1887 int format = 0, size = sizeof(double), scan_ret;
36 jfenwick 1986 dim_t numNodes, totalNumElements=0, numTags=0, numNodesPerElement=0, numNodesPerElement2, element_dim=0;
37 phornby 1628 index_t e, i0, j, gmsh_type, partition_id, itmp, elementary_id;
38 gross 1028 index_t numElements=0, numFaceElements=0, *id=NULL, *tag=NULL, *vertices=NULL;
39 gross 935 Finley_Mesh *mesh_p=NULL;
40 gross 1028 char line[LenString_MAX+1];
41 gross 935 char error_msg[LenErrorMsg_MAX];
42     double rtmp0, rtmp1;
43 jfenwick 1986 #ifdef Finley_TRACE
44 gross 935 double time0=Finley_timer();
45 jfenwick 1986 #endif
46 gross 1028 FILE * fileHandle_p = NULL;
47     ElementTypeId* element_type=NULL;
48 gross 935
49 ksteube 1312 Paso_MPIInfo *mpi_info = Paso_MPIInfo_alloc( MPI_COMM_WORLD );
50 gross 935 Finley_resetError();
51 ksteube 1312 if (mpi_info->size>1) {
52     Finley_setError(IO_ERROR,"reading GMSH with MPI is not supported yet.");
53     Paso_MPIInfo_free( mpi_info );
54 gross 935 return NULL;
55 ksteube 1312 } else {
56 gross 997
57 ksteube 1312 /* allocate mesh */
58 gross 935
59 ksteube 1312 mesh_p = Finley_Mesh_alloc(fname,numDim,order, reduced_order, mpi_info);
60     if (! Finley_noError()) return NULL;
61    
62     /* get file handle */
63     fileHandle_p = fopen(fname, "r");
64     if (fileHandle_p==NULL) {
65     sprintf(error_msg,"Opening Gmsh file %s for reading failed.",fname);
66     Finley_setError(IO_ERROR,error_msg);
67     Paso_MPIInfo_free( mpi_info );
68     return NULL;
69     }
70    
71     /* start reading */
72     while(1) {
73     if (! Finley_noError()) break;
74     /* find line staring with $ */
75     do {
76     if( ! fgets(line, sizeof(line), fileHandle_p) ) break;
77     if(feof(fileHandle_p)) break;
78     } while(line[0] != '$');
79    
80     if (feof(fileHandle_p)) break;
81    
82    
83     /* format */
84     if (!strncmp(&line[1], "MeshFormat", 10)) {
85 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%lf %d %d\n", &version, &format, &size);
86     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
87 ksteube 1312 }
88     /* nodes are read */
89     if ( !strncmp(&line[1], "NOD", 3) ||
90     !strncmp(&line[1], "NOE", 3) ||
91     !strncmp(&line[1], "Nodes", 5) ) {
92    
93 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &numNodes);
94     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
95 ksteube 1312 if (! Finley_noError()) break;
96     Finley_NodeFile_allocTable(mesh_p->Nodes, numNodes);
97     if (! Finley_noError()) break;
98     for (i0 = 0; i0 < numNodes; i0++) {
99     if (1 == numDim) {
100 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
101 ksteube 1312 &mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)],
102     &rtmp0,
103     &rtmp1);
104 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
105 ksteube 1312 } else if (2 == numDim) {
106 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
107 ksteube 1312 &mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)],
108     &mesh_p->Nodes->Coordinates[INDEX2(1,i0,numDim)],
109     &rtmp0);
110 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
111 ksteube 1312 } else if (3 == numDim) {
112 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
113 ksteube 1312 &mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)],
114     &mesh_p->Nodes->Coordinates[INDEX2(1,i0,numDim)],
115     &mesh_p->Nodes->Coordinates[INDEX2(2,i0,numDim)]);
116 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
117 ksteube 1312 }
118     mesh_p->Nodes->globalDegreesOfFreedom[i0]=mesh_p->Nodes->Id[i0];
119     mesh_p->Nodes->Tag[i0]=0;
120 gross 935 }
121 ksteube 1312 }
122     /* elements */
123     else if(!strncmp(&line[1], "ELM", 3) ||
124     !strncmp(&line[1], "Elements", 8)) {
125    
126     ElementTypeId final_element_type = NoType;
127     ElementTypeId final_face_element_type = NoType;
128 gross 1814 ElementTypeId contact_element_type = NoType;
129 ksteube 1312 numElements=0;
130     numFaceElements=0;
131 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &totalNumElements);
132     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
133 ksteube 1312
134     id=TMPMEMALLOC(totalNumElements,index_t);
135     tag=TMPMEMALLOC(totalNumElements,index_t);
136    
137    
138     element_type=TMPMEMALLOC(totalNumElements,ElementTypeId);
139     vertices=TMPMEMALLOC(totalNumElements*MAX_numNodes_gmsh,index_t);
140     if (! (Finley_checkPtr(id) || Finley_checkPtr(tag) || Finley_checkPtr(element_type) || Finley_checkPtr(vertices) ) ) {
141     /* read all in */
142     for(e = 0; e < totalNumElements; e++) {
143 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %d", &id[e], &gmsh_type);
144     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
145 ksteube 1312 switch (gmsh_type) {
146     case 1: /* line order 1 */
147     element_type[e]=Line2;
148     element_dim=1;
149     numNodesPerElement=2;
150     break;
151     case 2: /* traingle order 1 */
152     element_type[e]=Tri3;
153     numNodesPerElement= 3;
154     element_dim=2;
155     break;
156     case 3: /* quadrilateral order 1 */
157     element_type[e]=Rec4;
158     numNodesPerElement= 4;
159     element_dim=2;
160     break;
161     case 4: /* tetrahedron order 1 */
162     element_type[e]=Tet4;
163     numNodesPerElement= 4;
164     element_dim=3;
165     break;
166     case 5: /* hexahedron order 1 */
167     element_type[e]=Hex8;
168     numNodesPerElement= 8;
169     element_dim=3;
170     break;
171     case 8: /* line order 2 */
172     element_type[e]=Line3;
173     numNodesPerElement= 3;
174     element_dim=1;
175     break;
176     case 9: /* traingle order 2 */
177     element_type[e]=Tri6;
178     numNodesPerElement= 6;
179     element_dim=2;
180     break;
181     case 10: /* quadrilateral order 2 */
182     element_type[e]=Rec9;
183     numNodesPerElement= 9;
184     element_dim=2;
185     break;
186     case 11: /* tetrahedron order 2 */
187     element_type[e]=Tet10;
188     numNodesPerElement= 10;
189     element_dim=3;
190     break;
191     case 15 : /* point */
192     element_type[e]=Point1;
193     numNodesPerElement= 1;
194     element_dim=0;
195     break;
196     default:
197     element_type[e]=NoType;
198     sprintf(error_msg,"Unexected gmsh element type %d in mesh file %s.",gmsh_type,fname);
199     Finley_setError(IO_ERROR,error_msg);
200     }
201     if (element_dim == numDim) {
202     if (final_element_type == NoType) {
203     final_element_type = element_type[e];
204     } else if (final_element_type != element_type[e]) {
205     sprintf(error_msg,"Finley can handle a single type of internal elements only.");
206     Finley_setError(IO_ERROR,error_msg);
207     break;
208     }
209     numElements++;
210     } else if (element_dim == numDim-1) {
211     if (final_face_element_type == NoType) {
212     final_face_element_type = element_type[e];
213     } else if (final_face_element_type != element_type[e]) {
214     sprintf(error_msg,"Finley can handle a single type of face elements only.");
215     Finley_setError(IO_ERROR,error_msg);
216     break;
217     }
218     numFaceElements++;
219     }
220    
221     if(version <= 1.0){
222 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %d %d", &tag[e], &elementary_id, &numNodesPerElement2);
223     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
224 ksteube 1312 partition_id = 1;
225     if (numNodesPerElement2 != numNodesPerElement) {
226     sprintf(error_msg,"Illegal number of nodes for element %d in mesh file %s.",id[e],fname);
227     Finley_setError(IO_ERROR,error_msg);
228     }
229     } else {
230 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &numTags);
231     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
232 ksteube 1312 elementary_id = tag[e] = partition_id = 1;
233     numNodesPerElement2=-1;
234     for(j = 0; j < numTags; j++){
235 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &itmp);
236     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
237 ksteube 1312 if (j == 0) {
238     tag[e] = itmp;
239     } else if (j == 1) {
240     elementary_id = itmp;
241     } else if (j == 2) {
242     partition_id = itmp;
243     }
244     /* ignore any other tags */
245     }
246     }
247     if (! Finley_noError()) break;
248 ksteube 1887 for(j = 0; j < numNodesPerElement; j++) {
249     scan_ret = fscanf(fileHandle_p, "%d", &vertices[INDEX2(j,e,MAX_numNodes_gmsh)]);
250     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
251     }
252 ksteube 1312 /* for tet10 the last two nodes need to be swapped */
253     if (element_type[e]==Tet10) {
254     itmp=vertices[INDEX2(9,e,MAX_numNodes_gmsh)];
255     vertices[INDEX2(9,e,MAX_numNodes_gmsh)]=vertices[INDEX2(8,e,MAX_numNodes_gmsh)];
256     vertices[INDEX2(8,e,MAX_numNodes_gmsh)]=itmp;
257     }
258     }
259     /* all elements have been read, now we have to identify the elements for finley */
260    
261     if (Finley_noError()) {
262     /* first we have to identify the elements to define Elementis and FaceElements */
263 gross 935 if (final_element_type == NoType) {
264 ksteube 1312 if (numDim==1) {
265     final_element_type=Line2;
266     } else if (numDim==2) {
267     final_element_type=Tri3;
268     } else if (numDim==3) {
269     final_element_type=Tet4;
270     }
271 gross 935 }
272     if (final_face_element_type == NoType) {
273 ksteube 1312 if (numDim==1) {
274     final_face_element_type=Point1;
275     } else if (numDim==2) {
276     final_face_element_type=Line2;
277     } else if (numDim==3) {
278     final_face_element_type=Tri3;
279     }
280 gross 935 }
281 gross 1814 if (final_face_element_type == Line2) {
282     contact_element_type=Line2_Contact;
283     } else if (final_face_element_type == Line3) {
284     contact_element_type=Line3_Contact;
285     } else if (final_face_element_type == Tri3) {
286     contact_element_type=Tri3_Contact;
287     } else if (final_face_element_type == Tri6) {
288     contact_element_type=Tri6_Contact;
289     } else {
290     contact_element_type=Point1_Contact;
291     }
292    
293 ksteube 1312 mesh_p->Elements=Finley_ElementFile_alloc(final_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info);
294     mesh_p->FaceElements=Finley_ElementFile_alloc(final_face_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info);
295 gross 1814 mesh_p->ContactElements=Finley_ElementFile_alloc(contact_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info);
296 ksteube 1312 mesh_p->Points=Finley_ElementFile_alloc(Point1,mesh_p->order, mesh_p->reduced_order, mpi_info);
297     if (Finley_noError()) {
298     Finley_ElementFile_allocTable(mesh_p->Elements, numElements);
299     Finley_ElementFile_allocTable(mesh_p->FaceElements, numFaceElements);
300     Finley_ElementFile_allocTable(mesh_p->ContactElements, 0);
301     Finley_ElementFile_allocTable(mesh_p->Points, 0);
302     if (Finley_noError()) {
303     mesh_p->Elements->minColor=0;
304     mesh_p->Elements->maxColor=numElements-1;
305     mesh_p->FaceElements->minColor=0;
306     mesh_p->FaceElements->maxColor=numFaceElements-1;
307     mesh_p->ContactElements->minColor=0;
308     mesh_p->ContactElements->maxColor=0;
309     mesh_p->Points->minColor=0;
310     mesh_p->Points->maxColor=0;
311     numElements=0;
312     numFaceElements=0;
313     for(e = 0; e < totalNumElements; e++) {
314     if (element_type[e] == final_element_type) {
315     mesh_p->Elements->Id[numElements]=id[e];
316     mesh_p->Elements->Tag[numElements]=tag[e];
317     mesh_p->Elements->Color[numElements]=numElements;
318 gross 1740 mesh_p->Elements->Owner[numElements]=0;
319 ksteube 1312 for (j = 0; j< mesh_p->Elements->ReferenceElement->Type->numNodes; ++j) {
320     mesh_p->Elements->Nodes[INDEX2(j, numElements, mesh_p->Elements->ReferenceElement->Type->numNodes)]=vertices[INDEX2(j,e,MAX_numNodes_gmsh)];
321     }
322     numElements++;
323     } else if (element_type[e] == final_face_element_type) {
324     mesh_p->FaceElements->Id[numFaceElements]=id[e];
325     mesh_p->FaceElements->Tag[numFaceElements]=tag[e];
326     mesh_p->FaceElements->Color[numFaceElements]=numFaceElements;
327 gross 2243 mesh_p->FaceElements->Owner[numFaceElements]=0;
328 ksteube 1312 for (j = 0; j< mesh_p->FaceElements->ReferenceElement->Type->numNodes; ++j) {
329     mesh_p->FaceElements->Nodes[INDEX2(j, numFaceElements, mesh_p->FaceElements->ReferenceElement->Type->numNodes)]=vertices[INDEX2(j,e,MAX_numNodes_gmsh)];
330     }
331     numFaceElements++;
332     }
333 gross 935 }
334 ksteube 1312 }
335 gross 935 }
336 ksteube 1312 }
337 gross 935 }
338 ksteube 1312 /* and clean up */
339     TMPMEMFREE(id);
340     TMPMEMFREE(tag);
341     TMPMEMFREE(element_type);
342     TMPMEMFREE(vertices);
343 gross 935 }
344 ksteube 1312 /* serach for end of data block */
345     do {
346     if (!fgets(line, sizeof(line), fileHandle_p)) {
347     sprintf(error_msg,"Unexected end of file in %s",fname);
348     Finley_setError(IO_ERROR,error_msg);
349     }
350     if (feof(fileHandle_p)) {
351     sprintf(error_msg,"Unexected end of file in %s",fname);
352     Finley_setError(IO_ERROR,error_msg);
353     }
354     if (! Finley_noError()) break;
355     } while(line[0] != '$');
356     }
357    
358     /* close file */
359     fclose(fileHandle_p);
360     /* clean up */
361     if (! Finley_noError()) {
362     Finley_Mesh_free(mesh_p);
363     return NULL;
364     }
365     /* resolve id's : */
366     Finley_Mesh_resolveNodeIds(mesh_p);
367     /* rearrange elements: */
368     Finley_Mesh_prepare(mesh_p, optimize);
369     /* that's it */
370     #ifdef Finley_TRACE
371     printf("timing: reading mesh: %.4e sec\n",Finley_timer()-time0);
372     #endif
373     Paso_MPIInfo_free( mpi_info );
374     return mesh_p;
375 gross 935 }
376     }

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