Trisurf Monte Carlo simulator
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Samo Penic
2022-05-04 06afc729f9061c1cfa14c78728d61d518324c2f0
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7f6076 1 /* vim: set ts=4 sts=4 sw=4 noet : */
8c1bb1 2 #include <stdio.h>
SP 3 #include <string.h>
4 #include <stdlib.h>
5 #include <libxml/xmlmemory.h>
6 #include <libxml/parser.h>
7 #include <general.h>
8 #include <restore.h>
9 #include <snapshot.h>
10 #include <zlib.h>
11 #include "vesicle.h"
487968 12 #include "vertex.h"
a011d2 13 #include "triangle.h"
a3dbf0 14 #include "bond.h"
SP 15 #include "energy.h"
bb4033 16 #include "poly.h"
a3dbf0 17 #include "initial_distribution.h"
698ae1 18 #include "io.h"
002513 19 #include <math.h>
06afc7 20 #include "globals.h"
a011d2 21
ab798b 22 ts_vesicle *parseDump(char *dumpfname) {
8c1bb1 23     xmlDocPtr doc;
8fa1c0 24     xmlNodePtr cur, cur1,cur2;
SP 25     ts_vesicle *vesicle=NULL;
8c1bb1 26     doc = xmlParseFile(dumpfname);
002513 27     int i;
8c1bb1 28     if (doc == NULL ) {
SP 29         fatal("Dump file could not be found or parsed. It is correct file?",1);
30     }
31     
32     cur = xmlDocGetRootElement(doc);
33     
34     if (cur == NULL) {
35         fatal("Dump file is empty.",1);
36     }
37     
38     if (xmlStrcmp(cur->name, (const xmlChar *) "VTKFile")) {
39         fatal("document of the wrong type, root node != story",1);
40     }
41     
42     cur = cur->xmlChildrenNode;
43     while (cur != NULL) {
698ae1 44
SP 45         if ((!xmlStrcmp(cur->name, (const xmlChar *)"tape"))){
46             setGlobalTapeTXTfromTapeTag(doc, cur);
47         }
48
8c1bb1 49         if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
3c772b 50             vesicle=parseTrisurfTag(doc, cur);
8c1bb1 51         }
8fa1c0 52         // START Point Position data &  Bonds
SP 53         if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){
54             cur1 = cur->xmlChildrenNode;
55             while(cur1!=NULL){
56                 if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
57                     cur2=cur1->xmlChildrenNode;
58                     while(cur2!=NULL){
def8b5 59                         if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){
SP 60                             if(vesicle!=NULL)
61                                 parseXMLPointData(vesicle,doc,cur2);
62                         }
8fa1c0 63                         if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
720bd4 64                             //fprintf(stderr,"Found point data\n");
8fa1c0 65                             if(vesicle!=NULL)
f62178 66                                 //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
28efdb 67                                 parseXMLVertexPosition(vesicle, doc, cur2);
8fa1c0 68                         }
SP 69                         if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
720bd4 70                         //fprintf(stderr,"Found cell(Bonds) data\n");
a3dbf0 71                             if(vesicle!=NULL)
28efdb 72                                 parseXMLBonds(vesicle, doc, cur2);
8fa1c0 73                         }
SP 74                         cur2=cur2->next;
75                     }    
76                 }
77                 cur1 = cur1->next;
78             }
79         }
80         // END Point Position data & Bonds
8c1bb1 81     cur = cur->next;
SP 82     }
83     xmlFreeDoc(doc);
bb4033 84
86b69b 85 //    vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
d43116 86     set_vesicle_values_from_tape(vesicle);
a3dbf0 87     init_normal_vectors(vesicle->tlist);
SP 88     mean_curvature_and_energy(vesicle);
89434d 89     sweep_attraction_bond_energy(vesicle);
002513 90     if(vesicle->tape->stretchswitch==1){
699ac4 91         vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2);  
002513 92         for(i=0;i<vesicle->tlist->n;i++){
SP 93             stretchenergy(vesicle, vesicle->tlist->tria[i]);
94         }
95     }
ab798b 96 /* TODO: filaments */
a3dbf0 97
f4d6ca 98 //    ts_fprintf(stdout,"Restoration completed\n");
ab798b 99 //    write_vertex_xml_file(vesicle,999);
SP 100 //    vesicle_free(vesicle);
101 //    exit(0);
102     return vesicle;
8c1bb1 103 }
SP 104
698ae1 105 ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
SP 106     xmlChar *tape = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
107     strcpy(tapetxt,(char *)tape);
108     xmlFree(tape);
109     return TS_SUCCESS;
110 }
8fa1c0 111
SP 112
113 /* this is a parser of additional data in xml */
8c1bb1 114 ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){
720bd4 115     //fprintf(stderr,"Parsing trisurf tag\n");
487968 116     xmlNodePtr child;
SP 117
118 #ifdef COMPRESS
8c1bb1 119     /* base64decode */
SP 120     size_t cLen;
121     /*size_t tLen;
122     const unsigned char test[]="Test";
123     char *cTest=base64_encode(test, 4,&tLen);
124     unsigned char *cuTest=base64_decode((char *)cTest,tLen,&tLen);
125     cuTest[tLen]=0;
126     fprintf(stderr,"%s\n",cuTest);
127     */
128     xmlChar *b64=xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
129     unsigned char *compressed=base64_decode((char *)b64,strlen((char *)b64)-1,&cLen);
130     /* uncompress */
131     unsigned char *subtree=(unsigned char *)malloc(512000*sizeof(unsigned char)); /* TODO: again, the uncompressed string must not exceed this */
132     z_stream infstream;
133     infstream.zalloc = Z_NULL;
134     infstream.zfree = Z_NULL;
135     infstream.opaque = Z_NULL;
136     infstream.avail_in = (ts_uint)cLen; // size of input
137         infstream.next_in = compressed; // input char array
138         infstream.avail_out = (ts_uint)512000; // size of output
139         infstream.next_out = subtree; // output char array
140      
141         // the actual DE-compression work.
142         inflateInit(&infstream);
143         inflate(&infstream, Z_NO_FLUSH);
144         inflateEnd(&infstream);    
720bd4 145     //fprintf(stderr,"%lu\n",cLen);
8c1bb1 146     subtree[infstream.total_out]='\0'; //zero terminate string    
720bd4 147     //fprintf(stderr,"%s\n",subtree);
8c1bb1 148     
SP 149     free(subtree);
487968 150 #endif
8c1bb1 151     /*parse xml subtree */
86b69b 152     xmlChar *nvtx, *npoly, *nmono;
8c1bb1 153     nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
SP 154     npoly=xmlGetProp(cur, (xmlChar *)"npoly");
86b69b 155     nmono=xmlGetProp(cur, (xmlChar *)"nmono");
698ae1 156     ts_tape *tape=parsetapebuffer(tapetxt);
SP 157     //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
158     //TODO: check if nvtx is in agreement with nshell from tape
159     ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
d43116 160 //    vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
SP 161     vesicle->poly_list=init_empty_poly_list(atoi((char *)npoly),atoi((char *)nmono));
8c1bb1 162     xmlFree(nvtx);
SP 163     xmlFree(npoly);
86b69b 164     xmlFree(nmono);
487968 165
SP 166     child = cur->xmlChildrenNode;
167     while (child != NULL) {
168         if ((!xmlStrcmp(child->name, (const xmlChar *)"vtxn"))){
169             parseTrisurfVtxn(vesicle->vlist, doc, child);
170         }
a011d2 171         if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
SP 172             parseTrisurfTria(vesicle, doc, child);
173         }
e9ac7b 174         if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
SP 175             parseTrisurfTriaNeigh(vesicle, doc, child);
176         }
a011d2 177          if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
SP 178             parseTrisurfTristar(vesicle, doc, child);
179         }
4891eb 180          if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
SP 181             parseTrisurfNucleus(vesicle, doc, child);
182         }
49981c 183           if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
SP 184             parseTrisurfConstantVolume(doc, child);
185         }
186           if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
187             parseTrisurfConstantArea(doc, child);
188         }
189
a011d2 190
487968 191     child = child->next;
SP 192     }
193
698ae1 194     vesicle->tape=tape;
d43116 195 //    set_vesicle_values_from_tape(vesicle);
8c1bb1 196     return vesicle;
SP 197 }
487968 198
a011d2 199
SP 200
201 /* Low level tags parsers */
49981c 202 ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
SP 203     xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
204     char *n=(char *)cvol;
205     V0=atof(n);
206     xmlFree(cvol);
207     return TS_SUCCESS;
208 }
209 ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
210     xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
211     char *n=(char *)carea;
212     A0=atof(n);
213     xmlFree(carea);
214     return TS_SUCCESS;
215 }
216
4891eb 217 ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP 218     xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
219     char *n=(char *)coords;
220     char *token=strtok(n," ");
221     ts_uint i;
222     for(i=0;i<3;i++){
223         vesicle->nucleus_center[i]=atof(token);
224         token=strtok(NULL," ");
225     }
226     xmlFree(coords);
227     return TS_SUCCESS;
228 }
a011d2 229
SP 230 ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){
487968 231
SP 232     xmlChar *chari;
233     xmlChar *neighs;
234     char *n;
235     char *token;
236     ts_uint neighi;
237     ts_uint i;
238     chari = xmlGetProp(cur, (xmlChar *)"idx");
239     i=atoi((char *)chari);
240     xmlFree(chari);
241     ts_vertex *vtx=vlist->vtx[i];
242     neighs = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
243     //fprintf(stderr,"Found neigh for vtx %u that seems to have index %u with neighs=%s\n",i,vtx->idx,neighs);
244
245     n=(char *)neighs;
246     token=strtok(n," ");
247     while(token!=NULL){
248         neighi=atoi(token);
249         //fprintf(stderr,"%u", neighi);
250         vtx_add_neighbour(vtx,vlist->vtx[neighi]);
251         token=strtok(NULL," ");
252     }    
253     xmlFree(neighs);
254     return TS_SUCCESS;
255 }
256
a011d2 257 ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP 258     xmlChar *triangles;
259     char *tria;
260     char *vtx[3];
261     
e87e4e 262     ts_uint i,j;
a011d2 263     triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
SP 264     tria=(char *)triangles;
e87e4e 265     vtx[0]=strtok(tria," ");
SP 266     for(i=1;i<3;i++)    vtx[i]=strtok(NULL," ");
267     j=0;
a011d2 268     while(vtx[2]!=NULL){
SP 269         triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
270         for(i=0;i<3;i++)    vtx[i]=strtok(NULL," ");
e87e4e 271         j++;
a011d2 272     }    
720bd4 273     //fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);    
a011d2 274
SP 275     xmlFree(triangles);
276     return TS_SUCCESS;
277 }
278
279
e9ac7b 280 ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP 281     xmlChar *triangles;
282     char *tria;
283     char *ntria[3];
284     ts_uint i,j;
285     triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
286     tria=(char *)triangles;
e87e4e 287     ntria[0]=strtok(tria," ");
SP 288     for(i=1;i<3;i++)    ntria[i]=strtok(NULL," ");
e9ac7b 289     j=0;
SP 290     while(ntria[2]!=NULL){
291         triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
292         triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
293         triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
294         j++;
295         for(i=0;i<3;i++)    ntria[i]=strtok(NULL," ");
296     }    
720bd4 297     //fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);    
e9ac7b 298
SP 299     xmlFree(triangles);
300     return TS_SUCCESS;
301 }
302
303
a011d2 304 ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP 305
306     xmlChar *chari;
307     xmlChar *tristar;
308     char *t;
309     char *token;
310     ts_uint neighi;
311     ts_uint i;
312     chari = xmlGetProp(cur, (xmlChar *)"idx");
313     i=atoi((char *)chari);
314     xmlFree(chari);
315     ts_vertex *vtx=vesicle->vlist->vtx[i];
316     tristar = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
317 //    fprintf(stderr,"Found tristar for vtx %u that seems to have index %u with tristar=%s\n",i,vtx->idx,tristar);
318
319     t=(char *)tristar;
320     token=strtok(t," ");
321     while(token!=NULL){
322         neighi=atoi(token);
323         //fprintf(stderr,"%u", neighi);
324         vertex_add_tristar(vtx,vesicle->tlist->tria[neighi]);
325         token=strtok(NULL," ");
326     }    
327     xmlFree(tristar);
328     return TS_SUCCESS;
329 }
330
def8b5 331 /* this parses the data for vertices (like spontaneous curvature, etc.) */
SP 332 ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
333     xmlNodePtr child = cur->xmlChildrenNode;
334     xmlChar *property_name;
335     xmlChar *values;
336     char *vals;
337     char *token;
338     int idx, polyidx, monoidx, filidx, fonoidx;
339     while (child != NULL) {
340         if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
341             property_name=xmlGetProp(child, (xmlChar *)"Name");
342         //    fprintf(stderr,"Name: %s\n", property_name);
343             if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
344                 values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
345                 vals=(char *)values;
346                 token=strtok(vals," ");
347                 idx=0;
348                 while(token!=NULL){
349                     if(idx<vesicle->vlist->n){
350                         vesicle->vlist->vtx[idx]->c=atof(token);
351                     } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
352                         polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
353                         monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
354                         vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=atof(token);
355                     } else {
356                         filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
357                         fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
358                         //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
359                         vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=atof(token);
360                     }
361                     idx++;
362                     token=strtok(NULL," ");
363                 }
364                 xmlFree(values);        
365             }
6487a0 366             if(!xmlStrcmp(property_name,(const xmlChar *)"direct_interaction_force")){
SP 367                 values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
368                 vals=(char *)values;
369                 token=strtok(vals," ");
370                 idx=0;
371                 while(token!=NULL){
372                     if(idx<vesicle->vlist->n){
373                         vesicle->vlist->vtx[idx]->direct_interaction_force=atof(token);
374                     } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
375                         polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
376                         monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
377                         vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->direct_interaction_force=atof(token);
378                     } else {
379                         filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
380                         fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
381                         //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
382                         vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->direct_interaction_force=atof(token);
383                     }
384                     idx++;
385                     token=strtok(NULL," ");
386                 }
387                 xmlFree(values);        
388             }
def8b5 389             xmlFree(property_name);
SP 390         }
391         
392         child=child->next;
393     }
394     return TS_SUCCESS;
395 }
8fa1c0 396 /* this is a parser of vertex positions and bonds from main xml data */
SP 397 ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
398     xmlNodePtr child = cur->xmlChildrenNode;
399     xmlChar *points;
400     char *pts;
301c87 401     int i, idx, polyidx, monoidx, filidx, fonoidx;
8fa1c0 402     char *token[3];
SP 403     while (child != NULL) {
404         if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
405             points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
406             pts=(char *)points;
e87e4e 407             token[0]=strtok(pts," ");
ecdd71 408             token[1]=strtok(NULL," ");
SP 409             token[2]=strtok(NULL,"\n");
8fa1c0 410             idx=0;
SP 411             while(token[0]!=NULL){
86b69b 412                 if(idx<vesicle->vlist->n){
SP 413                     vesicle->vlist->vtx[idx]->x=atof(token[0]);
414                     vesicle->vlist->vtx[idx]->y=atof(token[1]);
415                     vesicle->vlist->vtx[idx]->z=atof(token[2]);
301c87 416                 } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
86b69b 417                     polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
SP 418                     monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
419                     vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=atof(token[0]);
420                     vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]);
421                     vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=atof(token[2]);
301c87 422                 } else {
SP 423                     filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
424                     fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
f62178 425                     //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
301c87 426                     vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=atof(token[0]);
SP 427                     vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]);
428                     vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]);
86b69b 429                 }
ecdd71 430                 for(i=0;i<2;i++)    token[i]=strtok(NULL," ");    
SP 431                 token[2]=strtok(NULL,"\n");
8fa1c0 432                 idx++;
SP 433             }
434             xmlFree(points);
435         }
436         child=child->next;
437     }
f62178 438     //fprintf(stderr,"Came here\n");
720bd4 439     //fprintf(stderr,"Vertices position j=%d\n",idx);    
28efdb 440
8fa1c0 441     return TS_SUCCESS;
SP 442 }
a3dbf0 443 ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
SP 444     xmlNodePtr child = cur->xmlChildrenNode;
bb4033 445     xmlChar *bonds, *conname;
a3dbf0 446     char *b;
86b69b 447     int idx, polyidx;
a3dbf0 448     char *token[2];
3cd5f4 449     int temp_cnt=0;
a3dbf0 450     while (child != NULL) {
bb4033 451         conname=xmlGetProp(child, (xmlChar *)"Name");
SP 452         if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
a3dbf0 453             bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
SP 454             b=(char *)bonds;
e87e4e 455             token[0]=strtok(b," ");
ecdd71 456             token[1]=strtok(NULL,"\n");
a3dbf0 457             idx=0;
SP 458             while(token[0]!=NULL){
86b69b 459                 if(idx<3*(vesicle->vlist->n-2)){
SP 460                     bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
3cd5f4 461                     //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
86b69b 462                 }
SP 463                 else {
464                 //find grafted vtx
301c87 465                     if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
3cd5f4 466                         && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly)){
SP 467                         temp_cnt++;
468                         //fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]);
469                         
86b69b 470                         polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
720bd4 471                         //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
86b69b 472                         vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];
SP 473                         vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
474                     }
475                 }
ecdd71 476                 token[0]=strtok(NULL," ");    
SP 477                 token[1]=strtok(NULL,"\n");    
a3dbf0 478                 idx++;
SP 479             }
480             xmlFree(bonds);
481         }
bb4033 482         xmlFree(conname);
a3dbf0 483         child=child->next;
SP 484     }
720bd4 485     //fprintf(stderr,"Bond data j=%d\n",idx);    
a3dbf0 486     return TS_SUCCESS;
SP 487 }
488
8fa1c0 489
SP 490