/[escript]/trunk/finley/src/Mesh_readGmsh.c
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Annotation of /trunk/finley/src/Mesh_readGmsh.c

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Revision 1896 - (hide annotations)
Sun Oct 19 23:16:21 2008 UTC (11 years, 4 months ago) by gross
File MIME type: text/plain
File size: 16356 byte(s)
small fixes.
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 gross 935 dim_t numNodes, totalNumElements=0, numTags=0, numNodesPerElement, numNodesPerElement2, element_dim;
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     double time0=Finley_timer();
44 gross 1028 FILE * fileHandle_p = NULL;
45     ElementTypeId* element_type=NULL;
46 gross 935
47 ksteube 1312 Paso_MPIInfo *mpi_info = Paso_MPIInfo_alloc( MPI_COMM_WORLD );
48 gross 935 Finley_resetError();
49 ksteube 1312 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 gross 935 return NULL;
53 ksteube 1312 } else {
54 gross 997
55 ksteube 1312 /* allocate mesh */
56 gross 935
57 ksteube 1312 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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%lf %d %d\n", &version, &format, &size);
84     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
85 ksteube 1312 }
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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &numNodes);
92     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
93 ksteube 1312 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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
99 ksteube 1312 &mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)],
100     &rtmp0,
101     &rtmp1);
102 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
103 ksteube 1312 } else if (2 == numDim) {
104 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
105 ksteube 1312 &mesh_p->Nodes->Coordinates[INDEX2(0,i0,numDim)],
106     &mesh_p->Nodes->Coordinates[INDEX2(1,i0,numDim)],
107     &rtmp0);
108 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
109 ksteube 1312 } else if (3 == numDim) {
110 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %le %le %le\n", &mesh_p->Nodes->Id[i0],
111 ksteube 1312 &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 ksteube 1887 FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
115 ksteube 1312 }
116     mesh_p->Nodes->globalDegreesOfFreedom[i0]=mesh_p->Nodes->Id[i0];
117     mesh_p->Nodes->Tag[i0]=0;
118 gross 935 }
119 ksteube 1312 }
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 gross 1814 ElementTypeId contact_element_type = NoType;
127 ksteube 1312 numElements=0;
128     numFaceElements=0;
129 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &totalNumElements);
130     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
131 ksteube 1312
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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %d", &id[e], &gmsh_type);
142     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
143 ksteube 1312 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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d %d %d", &tag[e], &elementary_id, &numNodesPerElement2);
221     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
222 ksteube 1312 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 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &numTags);
229     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
230 ksteube 1312 elementary_id = tag[e] = partition_id = 1;
231     numNodesPerElement2=-1;
232     for(j = 0; j < numTags; j++){
233 ksteube 1887 scan_ret = fscanf(fileHandle_p, "%d", &itmp);
234     FSCANF_CHECK(scan_ret, "fscanf: Finley_Mesh_readGmsh");
235 ksteube 1312 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 ksteube 1887 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 ksteube 1312 /* 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 gross 935 if (final_element_type == NoType) {
262 ksteube 1312 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 gross 935 }
270     if (final_face_element_type == NoType) {
271 ksteube 1312 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 gross 935 }
279 gross 1814 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 ksteube 1312 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 gross 1814 mesh_p->ContactElements=Finley_ElementFile_alloc(contact_element_type,mesh_p->order, mesh_p->reduced_order, mpi_info);
294 ksteube 1312 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 gross 1740 mesh_p->Elements->Owner[numElements]=0;
317 ksteube 1312 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 gross 1740 mesh_p->FaceElements->Owner[numElements]=0;
326 ksteube 1312 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 gross 935 }
332 ksteube 1312 }
333 gross 935 }
334 ksteube 1312 }
335 gross 935 }
336 ksteube 1312 /* and clean up */
337     TMPMEMFREE(id);
338     TMPMEMFREE(tag);
339     TMPMEMFREE(element_type);
340     TMPMEMFREE(vertices);
341 gross 935 }
342 ksteube 1312 /* 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 gross 935 }
374     }

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