Trisurf Monte Carlo simulator
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Samo Penic
2014-03-05 e9eab4fb2f72383a1a2adbe5f09f7bbd1fd45768
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f74313 1 #include "general.h"
d7639a 2 #include<stdio.h>
SP 3 #include "io.h"
f74313 4 #include <confuse.h>
SP 5 #include "vertex.h"
6 #include "bond.h"
d7639a 7 #include<string.h>
a6b1b5 8 #include<stdlib.h>
d7639a 9 #include <sys/types.h>
SP 10 #include <dirent.h>
b14a8d 11 #include "initial_distribution.h"
a2db52 12 #include "poly.h"
d7639a 13
e9eab4 14
SP 15
16 /** DUMP STATE TO DISK DRIVE **/
17
18 ts_bool dump_state(ts_vesicle *vesicle){
19
20     /* save current state with wrong pointers. Will fix that later */
21     ts_uint i,j,k;
22     ts_ulong off;
23     FILE *fh=fopen("dump.bin","wb");
24
25     /* dump vesicle */
26     fwrite(vesicle, sizeof(vesicle),1,fh);
27     /* dump vertex list */
28     fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
29     /* dump bond list */
30     fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
31     /* dump triangle list */
32     fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
33     /* dump cell list */
34     fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
35     /* dump poly list */
36     fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
37     /* level 1 complete */
38
39     /*dump vertices*/
40     for(i=0;i<vesicle->vlist->n;i++){
41         fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
42         /* dump pointer offsets for:
43                     neigh
44                     bond
45                     tria
46                     cell is ignored
47         */
48         for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
49             off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
50             fwrite(&off,sizeof(ts_ulong),1,fh); 
51         }
52         for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
53             off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
54             fwrite(&off,sizeof(ts_ulong),1,fh); 
55         }
56         for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
57             off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
58             fwrite(&off,sizeof(ts_ulong),1,fh); 
59         }
60 //        off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
61 //        fwrite(&off,sizeof(ts_ulong),1,fh); 
62
63     }
64
65     /*dump bonds*/
66     for(i=0;i<vesicle->blist->n;i++){
67         fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
68         /* dump pointer offsets for vtx1 and vtx2 */
69         off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
70         fwrite(&off,sizeof(ts_ulong),1,fh); 
71         off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
72         fwrite(&off,sizeof(ts_ulong),1,fh); 
73     }
74
75     /*dump triangles*/
76     for(i=0;i<vesicle->tlist->n;i++){
77         fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
78         /* dump pointer offsets for vertex */
79         off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
80         fwrite(&off,sizeof(ts_ulong),1,fh); 
81         off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
82         fwrite(&off,sizeof(ts_ulong),1,fh); 
83         off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
84         fwrite(&off,sizeof(ts_ulong),1,fh); 
85         /* dump pointer offsets for neigh */
86         for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
87             off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
88             fwrite(&off,sizeof(ts_ulong),1,fh); 
89         }
90     }
91    
92     /*dump cells and its contents is not dumped but recalculated on restore*/
93
94 /*    for(i=0;i<vesicle->clist->cellno;i++){
95         fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
96         for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
97             off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
98             fwrite(&off,sizeof(ts_ulong),1,fh);
99         }
100     }
101 */
102
103
104     /*dump polymeres */
105     for(i=0;i<vesicle->poly_list->n;i++){
106         fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
107     } 
108      
109     /* dump poly vertex(monomer) list*/
110     for(i=0;i<vesicle->poly_list->n;i++){
111         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
112             fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
113             /* dump offset for neigh and bond */
114             for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
115                 off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
116                 fwrite(&off,sizeof(ts_ulong),1,fh); 
117             }
118             for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
119                 off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
120                 fwrite(&off,sizeof(ts_ulong),1,fh); 
121             }
122         }
123     }
124     /* dump poly bonds between monomers list*/
125     for(i=0;i<vesicle->poly_list->n;i++){
126         for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
127             fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
128             /* dump vtx1 and vtx2 offsets */
129             off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
130             fwrite(&off,sizeof(ts_ulong),1,fh); 
131             off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
132             fwrite(&off,sizeof(ts_ulong),1,fh); 
133         }
134     }
135
136 /* pointer offsets for fixing the restored pointers */
137 /* need pointers for 
138     vlist->vtx
139     blist->bond
140     tlist->tria
141     clist->cell
142     poly_list->poly
143     and for each poly:
144         poly_list->poly->vtx
145         poly_list->poly->bond
146 */
147
148     fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
149     fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
150     fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
151     fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
152     fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
153     for(i=0;i<vesicle->poly_list->n;i++){
154         fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
155         fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
156     }
157     fclose(fh);
158     return TS_SUCCESS;
159 }
160
161
162 /** RESTORE DUMP FROM DISK **/
163 ts_vesicle *restore_state(){
164     ts_uint i,j,k;
165     FILE *fh=fopen("dump.bin","rb");
166     ts_uint retval;
167     ts_ulong off;
168
169 /* we restore all the data from the dump */
170     /* restore vesicle */
171     ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
172     retval=fread(vesicle, sizeof(vesicle),1,fh);
173     /* restore vertex list */
174     vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
175     retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
176     /* restore bond list */
177     vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
178     retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
179     /* restore triangle list */
180     vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
181     retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
182     /* restore cell list */
183     vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
184     retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
185     /* restore poly list */
186     vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
187     retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
188     /* level 1 complete */
189
190   /*restore vertices*/
191     vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
192     for(i=0;i<vesicle->vlist->n;i++){
193         vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
194         retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
195         /*restore neigh, bond, tristar. Ignoring cell */
196         vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
197         for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
198             retval=fread(&off,sizeof(ts_ulong),1,fh);
199             vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
200         }
201         vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
202         for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
203             retval=fread(&off,sizeof(ts_ulong),1,fh);
204             vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;    
205         }
206
207         vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
208         for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
209             retval=fread(&off,sizeof(ts_ulong),1,fh);
210             vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
211         }
212
213     }
214
215     /*restore bonds*/
216     vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
217     for(i=0;i<vesicle->blist->n;i++){
218         vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
219         retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
220         /* restore vtx1 and vtx2 */
221         retval=fread(&off,sizeof(ts_ulong),1,fh);
222         vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
223         retval=fread(&off,sizeof(ts_ulong),1,fh);
224         vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
225     }
226
227     /*restore triangles*/
228     vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
229     for(i=0;i<vesicle->tlist->n;i++){
230         vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
231         retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
232         /* restore pointers for vertices */
233         retval=fread(&off,sizeof(ts_ulong),1,fh);
234         vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
235         retval=fread(&off,sizeof(ts_ulong),1,fh);
236         vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
237         retval=fread(&off,sizeof(ts_ulong),1,fh);
238         vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
239         /* restore pointers for neigh */
240         for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
241             retval=fread(&off,sizeof(ts_ulong),1,fh);
242             vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
243         }
244
245     }
246    
247     /*restore cells */
248 /*TODO: do we need to recalculate cells here? */
249 /*    vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
250     for(i=0;i<vesicle->clist->cellno;i++){
251         vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
252         retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
253     }
254 */
255     /*restore polymeres */
256     vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
257     for(i=0;i<vesicle->poly_list->n;i++){
258         vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
259         retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
260     } 
261      
262     /* restore poly vertex(monomer) list*/
263     for(i=0;i<vesicle->poly_list->n;i++){
264         vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
265         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
266             vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
267             retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
268             
269             /* restore neigh and bonds */
270             vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
271             for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
272                 retval=fread(&off,sizeof(ts_ulong),1,fh);
273                 vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
274             }
275             vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
276             for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
277                 retval=fread(&off,sizeof(ts_ulong),1,fh);
278                 vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
279             }
280
281         }
282     }
283     /* restore poly bonds between monomers list*/
284     for(i=0;i<vesicle->poly_list->n;i++){
285         vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
286         for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
287             vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
288             retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
289             /* restore vtx1 and vtx2 */
290                 retval=fread(&off,sizeof(ts_ulong),1,fh);
291                 vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
292                 retval=fread(&off,sizeof(ts_ulong),1,fh);
293                 vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
294         }
295     }
296
297
298     /* recalculate pointers using saved information on pointer addresses */
299     /* following pointers need to be recalculated:
300         all vtx->neigh
301         all vtx->tristar
302         all vtx->bond
303         vtx->cell
304         vtx->grafted_poly
305         bond->vtx1
306         bond->vtx2
307         tria->vertex[*]
308         tria->neigh
309         cell->vertex
310         poly->grafted_vtx
311         poly->vlist->vtx->neigh
312         poly->vlist->vtx->bond
313         poly->vlist->vtx->cell
314     */
315
316     /* read pointers from disk */
317 /*    fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
318     fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
319     fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
320     fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
321     fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
322     for(i=0;i<vesicle->poly_list->n;i++){
323         fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
324         fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
325     }
326 */
327
328
329     if(retval); 
330     fclose(fh);
331     return vesicle;
332 }
333
334
335
d7639a 336 ts_bool print_vertex_list(ts_vertex_list *vlist){
SP 337     ts_uint i;
338     printf("Number of vertices: %u\n",vlist->n);
339     for(i=0;i<vlist->n;i++){
a6b1b5 340         printf("%u: %f %f %f\n",
8f6a69 341 vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a 342     }
SP 343     return TS_SUCCESS;
344 }
345
346 ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
347     ts_uint i,j;
a6b1b5 348     ts_vertex **vtx=vlist->vtx;
d7639a 349     printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP 350     for(i=0;i<vlist->n;i++){
8f6a69 351         printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP 352         for(j=0;j<vtx[i]->neigh_no;j++){
353             printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
354 vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a 355         }
SP 356         printf("\n");
357     }
358
359 return TS_SUCCESS;
360 }
361
362 ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
a6b1b5 363     ts_vertex **vtx=vlist->vtx;
d7639a 364     ts_uint i;
SP 365     FILE *fh;
366     
367     fh=fopen(filename, "w");
368     if(fh==NULL){
369         err("Cannot open file %s for writing");
370         return TS_FAIL;
371     }
372     for(i=0;i<vlist->n;i++)
8f6a69 373         fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a 374
SP 375     fclose(fh);
376 return TS_SUCCESS;
377 }
378
379
380 ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
381     ts_uint i,j;
382     for(i=0;i<vlist->n;i++){
8f6a69 383         fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP 384             vlist->vtx[i]->y, vlist->vtx[i]->z,
385             vlist->vtx[i]->neigh_no);
386         for(j=0;j<vlist->vtx[i]->neigh_no;j++){
387             fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5 388         //-vlist->vtx+1));
d7639a 389         }
SP 390         fprintf(fh,"\n");
391     }
392     return TS_SUCCESS;
393 }
394
395 ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
396     ts_uint i,j;
a6b1b5 397     for(i=0;i<vesicle->vlist->n;i++){
8f6a69 398         fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP 399         for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
400             fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a 401         }
SP 402         fprintf(fh,"\n");
403     }
404     return TS_SUCCESS;
405 }
406
407 ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
a6b1b5 408         ts_triangle_list *tlist=vesicle->tlist;
d7639a 409       ts_uint i,j;
SP 410     for(i=0;i<tlist->n;i++){
41a035 411         fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP 412         for(j=0;j<tlist->tria[i]->neigh_no;j++){
413             fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1)); 
d7639a 414         }
SP 415         fprintf(fh,"\n");
416             for(j=0;j<3;j++){
41a035 417             fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1)); 
d7639a 418             }
SP 419         fprintf(fh,"\n");
41a035 420         fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP 421 tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a 422         fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP 423     }
424     return TS_SUCCESS;
425 }
426
427 ts_bool fprint_vertex_data(FILE *fh,ts_vertex_list *vlist){
428     ts_uint i,j;
429     for(i=0;i<vlist->n;i++){
430         fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69 431         vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP 432         vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
433         for(j=0;j<vlist->vtx[i]->neigh_no;j++){
434             fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a 435         }
SP 436             fprintf(fh,"\n");
8f6a69 437         for(j=0;j<vlist->vtx[i]->neigh_no;j++){
SP 438             fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a 439         }
SP 440             fprintf(fh,"\n");
441     }
442     return TS_SUCCESS;
443 }
444
445 ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
446     ts_uint i;
a6b1b5 447     for(i=0;i<vesicle->blist->n;i++){
e016c4 448         fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5 449 //-vesicle->vlist->vtx+1),
e016c4 450         (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5 451     //-vesicle->vlist.vtx+1));
d7639a 452     }
SP 453     return TS_SUCCESS;
454 }
455
456
457 ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
458     FILE *fh;
459     fh=fopen(filename, "w");
460     if(fh==NULL){
461         err("Cannot open file %s for writing");
462         return TS_FAIL;
463     }
464     fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5 465     fprint_vertex_list(fh,vesicle->vlist);
d7639a 466     fprint_tristar(fh,vesicle);
SP 467     fprint_triangle_list(fh,vesicle);
a6b1b5 468     fprint_vertex_data(fh,vesicle->vlist);
d7639a 469     fprint_bonds(fh,vesicle);
SP 470     fclose(fh);    
471     return TS_SUCCESS;
472 }
473
474 ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
475     FILE *fh;
476     char line[255];
477     fh=fopen(filename, "r");
478         if(fh==NULL){
479                 err("Cannot open file for reading... Nonexistant file?");
480                 return TS_FAIL;
481         }
a6b1b5 482     ts_uint retval=1;
d7639a 483     while(retval!=EOF){
SP 484         retval=fscanf(fh,"%s",line);
485         
486         fprintf(stderr,"%s",line);
487     }    
488     fclose(fh);    
489     return TS_SUCCESS;
490 }
491
492 ts_bool write_master_xml_file(ts_char *filename){
493      FILE *fh;
494     ts_char *i,*j;
495     ts_uint tstep;
496     ts_char *number;
497         fh=fopen(filename, "w");
498         if(fh==NULL){
499                 err("Cannot open file %s for writing");
500                 return TS_FAIL;
501         }
502
503     fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
504     DIR *dir = opendir(".");
505     if(dir){
506         struct dirent *ent;
507         tstep=0;
508         while((ent = readdir(dir)) != NULL)
509         {
510             i=rindex(ent->d_name,'.');
511             if(i==NULL) continue;
512             if(strcmp(i+1,"vtu")==0){
513                     j=rindex(ent->d_name,'_');
514                     if(j==NULL) continue;
515                     number=strndup(j+1,j-i); 
a6b1b5 516                 fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a 517                 tstep++;
SP 518                     free(number);
519             }  
520         }
521     }
f74313 522     free(dir);
d7639a 523     fprintf(fh,"</Collection>\n</VTKFile>\n");
SP 524     fclose(fh);
525     return TS_SUCCESS;
526 }
527
528 ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5 529     ts_vertex_list *vlist=vesicle->vlist;
SP 530     ts_bond_list *blist=vesicle->blist;
531     ts_vertex **vtx=vlist->vtx;
40aa5b 532     ts_uint i,j;
d7639a 533         char filename[255];
SP 534     FILE *fh;
535
536         sprintf(filename,"timestep_%.6u.vtu",timestepno);
537     fh=fopen(filename, "w");
538     if(fh==NULL){
539         err("Cannot open file %s for writing");
540         return TS_FAIL;
541     }
542     /* Here comes header of the file */
40aa5b 543
SP 544     //find number of extra vtxs and bonds of polymeres
545     ts_uint monono=0, polyno=0;
546     ts_bool poly=0;
547     if(vesicle->poly_list!=NULL){
548         if(vesicle->poly_list->poly[0]!=NULL){
549         polyno=vesicle->poly_list->n;
550         monono=vesicle->poly_list->poly[0]->vlist->n;
551         poly=1;
552         }
553     }
d7639a 554     fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
40aa5b 555     fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
d7639a 556     fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP 557        for(i=0;i<vlist->n;i++){
a6b1b5 558         fprintf(fh,"%u ",vtx[i]->idx);
d7639a 559     }
40aa5b 560     //polymeres
SP 561     if(poly){
562         for(i=0;i<vesicle->poly_list->n;i++){
563             for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
564                 fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
565             }
566         }
567     }
d7639a 568
SP 569     fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
570     for(i=0;i<vlist->n;i++){
8f6a69 571         fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b 572     }
SP 573     //polymeres
574     if(poly){
575         for(i=0;i<vesicle->poly_list->n;i++){
576             for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
577                 fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
578             }
579         }
d7639a 580     }
SP 581
582     fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
583     for(i=0;i<blist->n;i++){
e016c4 584             fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a 585     }
40aa5b 586     //polymeres
SP 587     if(poly){
588         for(i=0;i<vesicle->poly_list->n;i++){
589             for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
590                 fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
591             }
592     //grafted bonds
593         fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
594         }
595
596     }
597     
598
d7639a 599     fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
40aa5b 600     for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
d7639a 601     fprintf(fh,"%u ",i);
SP 602     }
603     fprintf(fh,"\n");
604     fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
40aa5b 605      for (i=0;i<blist->n+monono*polyno;i++){
d7639a 606         fprintf(fh,"3 ");
SP 607     }
608
609     fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
610     fclose(fh);
611     return TS_SUCCESS;
612
613 }
614
615 ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
a6b1b5 616     ts_vertex_list *vlist=vesicle->vlist;
SP 617     ts_bond_list *blist=vesicle->blist;
618     ts_vertex **vtx=vlist->vtx;
619     ts_uint i;
d7639a 620     FILE *fh;
SP 621     
622     fh=fopen(filename, "w");
623     if(fh==NULL){
624         err("Cannot open file %s for writing");
625         return TS_FAIL;
626     }
627     /* Here comes header of the file */
628 //    fprintf(stderr,"NSHELL=%u\n",nshell);
629     fprintf(fh, "# vtk DataFile Version 2.0\n");
630     /* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */ 
631     fprintf(fh, "%s\n", text);
632     fprintf(fh,"ASCII\n");
633     fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
634     fprintf(fh,"POINTS %u double\n", vlist->n);
635     for(i=0;i<vlist->n;i++){
8f6a69 636         fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a 637     }
SP 638     
639     fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
640     for(i=0;i<blist->n;i++){
e016c4 641             fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a 642     }
SP 643     fprintf(fh,"CELL_TYPES %u\n",blist->n);
644     for(i=0;i<blist->n;i++)
645         fprintf(fh,"3\n");
646
647     fprintf(fh,"POINT_DATA %u\n", vlist->n);
648     fprintf(fh,"SCALARS scalars long 1\n");
649     fprintf(fh,"LOOKUP_TABLE default\n");
650
651     for(i=0;i<vlist->n;i++)
8f6a69 652         fprintf(fh,"%u\n",vtx[i]->idx);
d7639a 653
SP 654     fclose(fh);
655     return TS_SUCCESS;
656 }
657
658
659
d7a113 660 ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
a2db52 661     long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20;  // THIS IS DUE TO CONFUSE BUG!
b14a8d 662     char *buf=malloc(255*sizeof(char));
SP 663     long int brezveze0=1;
664     long int brezveze1=1;
665     long int brezveze2=1;
48bb92 666     ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
d7a113 667     long int iter=1000, init=1000, mcsw=1000;
40aa5b 668
SP 669
d7639a 670     cfg_opt_t opts[] = {
SP 671         CFG_SIMPLE_INT("nshell", &nshell),
a2db52 672         CFG_SIMPLE_INT("npoly", &npoly),
SP 673         CFG_SIMPLE_INT("nmono", &nmono),
d7639a 674         CFG_SIMPLE_FLOAT("dmax", &dmax),
SP 675         CFG_SIMPLE_FLOAT("xk0",&xk0),
48bb92 676         CFG_SIMPLE_FLOAT("k_spring",&kspring),
d7639a 677         CFG_SIMPLE_FLOAT("stepsize",&stepsize),
SP 678         CFG_SIMPLE_INT("nxmax", &ncxmax),
679         CFG_SIMPLE_INT("nymax", &ncymax),
680         CFG_SIMPLE_INT("nzmax", &nczmax),
d7a113 681         CFG_SIMPLE_INT("iterations",&iter),
SP 682     CFG_SIMPLE_INT("mcsweeps",&mcsw),
683     CFG_SIMPLE_INT("inititer", &init),
d7639a 684         CFG_SIMPLE_BOOL("quiet",&quiet),
314f2d 685         CFG_SIMPLE_STR("multiprocessing",buf),
b14a8d 686         CFG_SIMPLE_INT("smp_cores",&brezveze0),
SP 687         CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
688         CFG_SIMPLE_INT("distributed_processes",&brezveze2),
d7639a 689         CFG_END()
SP 690     };
691     cfg_t *cfg;    
692     ts_uint retval;
693     cfg = cfg_init(opts, 0);
a6b1b5 694     retval=cfg_parse(cfg, "tape");
d7639a 695     if(retval==CFG_FILE_ERROR){
a6b1b5 696     fatal("No tape file.",100);
d7639a 697     }
SP 698     else if(retval==CFG_PARSE_ERROR){
699     fatal("Invalid tape!",100);
700     }
b14a8d 701     ts_vesicle *vesicle;
d7a113 702         *iterations=iter;
SP 703     *inititer=init;
704     *mcsweeps=mcsw;
b14a8d 705     vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
a2db52 706     vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
48bb92 707     vesicle->spring_constant=kspring;
M 708     poly_assign_spring_const(vesicle);
709     
a2db52 710
d7639a 711     vesicle->nshell=nshell;
SP 712     vesicle->dmax=dmax*dmax;
713     vesicle->bending_rigidity=xk0;
714     vesicle->stepsize=stepsize;
a6b1b5 715     vesicle->clist->ncmax[0]=ncxmax;
SP 716     vesicle->clist->ncmax[1]=ncymax;
717     vesicle->clist->ncmax[2]=nczmax;
718     vesicle->clist->max_occupancy=8;
b14a8d 719
d7639a 720     cfg_free(cfg);
b14a8d 721     free(buf);
SP 722   //  fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
40aa5b 723
SP 724             
725
b14a8d 726     return vesicle;
d7639a 727
SP 728 }
f74313 729
SP 730
731 ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
732     FILE *fh;
733     ts_uint i, nvtx,nedges,ntria;
734     ts_uint vtxi1,vtxi2;
735     float x,y,z;
736     ts_vertex_list *vlist;
737     fh=fopen(fname, "r");
738         if(fh==NULL){
739                 err("Cannot open file for reading... Nonexistant file?");
740                 return TS_FAIL;
741         }
742     ts_uint retval;
743     retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
744     vesicle->vlist=init_vertex_list(nvtx);
745     vlist=vesicle->vlist;
746     for(i=0;i<nvtx;i++){
8f6a69 747    //     fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313 748        retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69 749         vlist->vtx[i]->x=x;
SP 750         vlist->vtx[i]->y=y;
751         vlist->vtx[i]->z=z;
f74313 752     }
SP 753     for(i=0;i<nedges;i++){
754         retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
755         bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
756     }
757     //TODO: neighbours from bonds,
758     //TODO: triangles from neigbours
759
760 //    Don't need to read triangles. Already have enough data
761     /*
762     for(i=0;i<ntria;i++){
763         retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69 764         vtxi1=vesicle->blist->vertex1->idx;
SP 765         vtxi2=vesicle->blist->vertex1->idx;
f74313 766         
SP 767     }
768     */
41a035 769     if(retval);
f74313 770     fclose(fh);    
SP 771
772
773
774     return TS_SUCCESS;
775 }