trisurf-ng.git - Gitblit

Fix: the number of cell total must be updated from new tape aswell.

mihaf

2014-07-08 a5e543120d541f47fe0a2e9841d02151dd3e693a

commit \| author \| age
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
083e03	14	#include <getopt.h>
SP	15	#include <sys/stat.h>
	16	#include <sys/types.h>
	17	#include <dirent.h>
	18	#include <errno.h>
e9eab4	19	/ DUMP STATE TO DISK DRIVE /
SP	20
1ab449	21	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	22
SP	23	/* save current state with wrong pointers. Will fix that later */
	24	ts_uint i,j,k;
	25	FILE *fh=fopen("dump.bin","wb");
	26
	27	/* dump vesicle */
86f5e7	28	fwrite(vesicle, sizeof(ts_vesicle),1,fh);
e9eab4	29	/* dump vertex list */
SP	30	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	31	/* dump bond list */
	32	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	33	/* dump triangle list */
	34	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	35	/* dump cell list */
	36	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	37	/* dump poly list */
	38	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	39	/* dump filament list */
M	40	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	41	/* level 1 complete */
SP	42
	43	/dump vertices/
	44	for(i=0;i<vesicle->vlist->n;i++){
	45	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	46	/* dump pointer offsets for:
	47	neigh
	48	bond
	49	tria
	50	cell is ignored
	51	*/
	52	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	53	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	54	}
SP	55	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	56	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	57	}
SP	58	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	59	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	60	}
SP	61	}
	62
	63	/dump bonds/
	64	for(i=0;i<vesicle->blist->n;i++){
	65	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	66	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	67	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	68	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	69	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	70	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	71	}
SP	72
	73	/dump triangles/
	74	for(i=0;i<vesicle->tlist->n;i++){
	75	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	76	/* dump pointer offsets for vertex */
3c1ac1	77	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	78	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	79	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	80	/* dump pointer offsets for neigh */
SP	81	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	82	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	83	}
SP	84	}
	85
	86
	87	/dump polymeres /
	88	for(i=0;i<vesicle->poly_list->n;i++){
	89	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	90	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	91	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	92	}
SP	93
	94	/* dump poly vertex(monomer) list*/
	95	for(i=0;i<vesicle->poly_list->n;i++){
	96	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	97	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	98	/* dump offset for neigh and bond */
	99	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	100	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	101	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	102	}
SP	103	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	104	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	105	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	106	}
SP	107	}
3c1ac1	108	// grafted vtx on vesicle data dump
SP	109	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	110	}
SP	111	/* dump poly bonds between monomers list*/
	112	for(i=0;i<vesicle->poly_list->n;i++){
	113	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	114	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	115	/* dump vtx1 and vtx2 offsets */
3c1ac1	116	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	117	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	118	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	119	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	120	}
SP	121	}
	122
bcf455	123
M	124	/dump filamentes grandes svinjas /
	125	for(i=0;i<vesicle->filament_list->n;i++){
	126	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	127	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	128	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	129	}
	130
	131	/* dump filamentes vertex(monomer) list*/
	132	for(i=0;i<vesicle->filament_list->n;i++){
	133	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	134	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	135	/* dump offset for neigh and bond */
	136	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	137	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	138	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	139	}
	140	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	141	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	142	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	143	}
	144	}
	145	}
	146	/* dump poly bonds between monomers list*/
	147	for(i=0;i<vesicle->filament_list->n;i++){
	148	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	149	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	150	/* dump vtx1 and vtx2 offsets */
	151	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	152	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	153	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	154	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	155	}
	156	}
	157
	158
	159
e9eab4	160	/* pointer offsets for fixing the restored pointers */
SP	161	/* need pointers for
	162	vlist->vtx
	163	blist->bond
	164	tlist->tria
	165	clist->cell
	166	poly_list->poly
	167	and for each poly:
	168	poly_list->poly->vtx
	169	poly_list->poly->bond
	170	*/
	171
063289	172	fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	173	/* write tape information on vesicle */
SP	174	fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	175	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	176	fclose(fh);
SP	177	return TS_SUCCESS;
	178	}
	179
	180
	181	/ RESTORE DUMP FROM DISK /
1ab449	182	ts_vesicle restore_state(ts_uint iteration){
e9eab4	183	ts_uint i,j,k;
SP	184	FILE *fh=fopen("dump.bin","rb");
3f5c83	185
SP	186	struct stat sb;
	187	if (stat("dump.bin", &sb) == -1) {
	188	//dump file does not exist.
	189	return NULL;
	190	}
	191
	192	//check if it is regular file
	193	if((sb.st_mode & S_IFMT) != S_IFREG) {
	194	//dump file is not a regular file.
	195	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	196	return NULL;
	197	}
	198
e9eab4	199	ts_uint retval;
3c1ac1	200	ts_uint idx;
e9eab4	201
SP	202	/* we restore all the data from the dump */
	203	/* restore vesicle */
	204	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
86f5e7	205	retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
SP	206	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
	207
e9eab4	208	/* restore vertex list */
SP	209	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	210	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	211	/* restore bond list */
	212	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	213	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	214	/* restore triangle list */
	215	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	216	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	217	/* restore cell list */
	218	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	219	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	220	/* restore poly list */
	221	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	222	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	223	/* restore filament list */
M	224	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	225	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	226	/* level 1 complete */
SP	227
3c1ac1	228	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	229	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	230	for(i=0;i<vesicle->blist->n;i++){
	231	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	232	}
	233	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	234	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	235	for(i=0;i<vesicle->tlist->n;i++){
	236	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	237	}
a37ba2	238	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	239	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	240	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	241	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	242	}
SP	243	/restore vertices/
	244	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	245	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	246	/restore neigh, bond, tristar. Ignoring cell /
	247	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	248	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	249	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	250	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	251	}
SP	252	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	253	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	254	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	255	/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
	256	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	257	}
SP	258
	259	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	260	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	261	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	262	/* same comment as above */
	263	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	264	}
SP	265
	266	}
	267
	268	/restore bonds/
3c1ac1	269	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	270	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	271	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	272	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	273	/* restore vtx1 and vtx2 */
3c1ac1	274	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	275	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	276	retval=fread(&idx,sizeof(ts_uint),1,fh);
	277	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	278	}
SP	279
	280	/restore triangles/
3c1ac1	281	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	282	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	283	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	284	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	285	/* restore pointers for vertices */
3c1ac1	286	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	287	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	288	retval=fread(&idx,sizeof(ts_uint),1,fh);
	289	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	290	retval=fread(&idx,sizeof(ts_uint),1,fh);
	291	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	292	/* restore pointers for neigh */
3c1ac1	293	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	294	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	295	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	296	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	297	}
SP	298
	299	}
	300
	301	/restore cells /
	302	/TODO: do we need to recalculate cells here? /
	303	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	304	for(i=0;i<vesicle->clist->cellno;i++){
	305	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	306	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	307	}
	308	*/
	309	/restore polymeres /
	310	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	311	for(i=0;i<vesicle->poly_list->n;i++){
	312	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	313	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	314	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	315	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	316	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	317	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	318	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	319	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	320	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	321	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	322	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	323	}
	324	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	325	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	326	}
	327
e9eab4	328	}
3c1ac1	329
e9eab4	330
SP	331	/* restore poly vertex(monomer) list*/
	332	for(i=0;i<vesicle->poly_list->n;i++){
	333	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	334	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	335
e9eab4	336	/* restore neigh and bonds */
SP	337	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 ));
	338	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	339	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	340	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	341	}
SP	342	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 ));
	343	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	344	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	345	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	346	}
SP	347
	348	}
3c1ac1	349	/* restore grafted vtx on vesicle and grafted_poly */
SP	350	retval=fread(&idx,sizeof(ts_uint),1,fh);
	351	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	352	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	353	}
3c1ac1	354
e9eab4	355	/* restore poly bonds between monomers list*/
SP	356	for(i=0;i<vesicle->poly_list->n;i++){
	357	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	358	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	359	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	360	/* restore vtx1 and vtx2 */
3c1ac1	361	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	362	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	363	retval=fread(&idx,sizeof(ts_uint),1,fh);
	364	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	365	}
SP	366	}
	367
bcf455	368	/restore filaments /
M	369	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	370	for(i=0;i<vesicle->filament_list->n;i++){
	371	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	372	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	373	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	374	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	375	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	376	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	377	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	378	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	379	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	380	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	381	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	382	}
	383	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	384	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	385	}
	386
	387	}
	388
	389
	390	/* restore poly vertex(monomer) list*/
	391	for(i=0;i<vesicle->filament_list->n;i++){
	392	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	393	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	394
	395	/* restore neigh and bonds */
	396	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex ));
	397	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	398	retval=fread(&idx,sizeof(ts_uint),1,fh);
	399	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	400	}
	401	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond ));
	402	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	403	retval=fread(&idx,sizeof(ts_uint),1,fh);
	404	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	405	}
	406
	407	}
	408	}
	409
	410	/* restore poly bonds between monomers list*/
	411	for(i=0;i<vesicle->filament_list->n;i++){
	412	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	413	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	414	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	415	/* restore vtx1 and vtx2 */
	416	retval=fread(&idx,sizeof(ts_uint),1,fh);
	417	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	418	retval=fread(&idx,sizeof(ts_uint),1,fh);
	419	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	420	}
	421	}
47a7ac	422	vesicle->tape=parsetape("tape");
063289	423	// recreating space for cells //
SP	424	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
47a7ac	425	retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
SP	426	vesicle->clist->ncmax[0]=vesicle->tape->ncxmax;
	427	vesicle->clist->ncmax[1]=vesicle->tape->ncymax;
	428	vesicle->clist->ncmax[2]=vesicle->tape->nczmax;
a5e543	429	vesicle->clist->cellno=vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]vesicle->clist->ncmax[2];
063289	430	vesicle->clist->cell=(ts_cell *)malloc(sizeof(ts_cell )vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
SP	431	for(i=0;i<vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]vesicle->clist->ncmax[2];i++){
	432	vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
	433	vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
	434	}
9166cb	435	//recreating stored tape information//
47a7ac	436	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	437	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	438	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	439	if(retval);
SP	440	fclose(fh);
	441	return vesicle;
	442	}
	443
	444
	445
083e03	446	ts_bool parse_args(int argc, char **argv){
3f5c83	447	int c, retval;
SP	448	struct stat sb;
	449	sprintf(command_line_args.path, "./"); //clear string;
	450	sprintf(command_line_args.output_fullfilename,"./output.pvd");
	451	sprintf(command_line_args.dump_fullfilename,"./dump.bin");
	452	sprintf(command_line_args.tape_fullfilename,"./tape");
	453	FILE *file;
	454
083e03	455	while (1)
SP	456	{
	457	static struct option long_options[] =
	458	{
8a6614	459	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	460	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	461	{"tape", no_argument, 0, 't'},
SP	462	{"output-file", required_argument, 0, 'o'},
	463	{"directory", required_argument, 0, 'd'},
3f5c83	464	{"dump-filename", required_argument,0, 'f'},
083e03	465	{0, 0, 0, 0}
SP	466	};
	467	/* getopt_long stores the option index here. */
	468	int option_index = 0;
	469
3f5c83	470	c = getopt_long (argc, argv, "d:f:o:t:",
083e03	471	long_options, &option_index);
SP	472
	473	/* Detect the end of the options. */
	474	if (c == -1)
	475	break;
	476
	477	switch (c)
	478	{
	479	case 0:
	480	/* If this option set a flag, do nothing else now. */
	481	if (long_options[option_index].flag != 0)
	482	break;
	483	printf ("option %s", long_options[option_index].name);
	484	if (optarg)
	485	printf (" with arg %s", optarg);
	486	printf ("\n");
	487	break;
	488
	489	case 't':
	490	//check if tape exists. If not, fail immediately.
3f5c83	491	if (stat(optarg, &sb) == -1) {
SP	492	ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
	493	fatal("Please select correct tape",1);
	494	} else {
	495	strcpy(command_line_args.tape_fullfilename,optarg);
	496	}
083e03	497	break;
SP	498
	499	case 'o':
	500	//set filename of master output file
3f5c83	501	if ((file = fopen(optarg, "w")) == NULL) {
SP	502	fprintf(stderr,"Could not create output file!\n");
	503	fatal("Please specify correct output file",1);
	504
	505	} else {
	506	fclose(file);
	507	}
	508	strcpy(command_line_args.output_fullfilename, optarg);
	509	break;
083e03	510
SP	511	case 'd':
	512	//check if directory exists. If not create one. If creation is
	513	//successful, set directory for output files.
	514	//printf ("option -d with value `%s'\n", optarg);
3f5c83	515	if (stat(optarg, &sb) == -1) {
SP	516	//directory does not exist
083e03	517	retval=mkdir(optarg, 0700);
SP	518	if(retval){
3f5c83	519	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	520	}
SP	521	}
3f5c83	522	//check if is a proper directory
SP	523	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	524	//it is not a directory. fatal error.
	525	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	526	fatal("Cannot continue",1);
083e03	527	}
3f5c83	528	strcpy(command_line_args.path, optarg);
083e03	529	break;
SP	530
	531	case 'f':
	532	//check if dump file specified exists. Defaults to dump.bin
3f5c83	533	if ((file = fopen(optarg, "w")) == NULL) {
SP	534	fprintf(stderr,"Could not create dump file!\n");
	535	fatal("Please specify correct dump file",1);
	536
	537	} else {
	538	fclose(file);
	539	}
	540	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	541	break;
SP	542
	543	case '?':
	544	/* getopt_long already printed an error message. */
	545
	546	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	547	fatal("Ooops, read help first",1);
	548	break;
	549
	550	default:
	551	exit (1);
	552	}
	553	}
	554
	555	return TS_SUCCESS;
	556
	557	}
	558
	559
	560
	561
d7639a	562	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	563	ts_uint i;
	564	printf("Number of vertices: %u\n",vlist->n);
	565	for(i=0;i<vlist->n;i++){
a6b1b5	566	printf("%u: %f %f %f\n",
8f6a69	567	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	568	}
SP	569	return TS_SUCCESS;
	570	}
	571
	572	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	573	ts_uint i,j;
a6b1b5	574	ts_vertex **vtx=vlist->vtx;
d7639a	575	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	576	for(i=0;i<vlist->n;i++){
8f6a69	577	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	578	for(j=0;j<vtx[i]->neigh_no;j++){
	579	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	580	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	581	}
SP	582	printf("\n");
	583	}
	584
	585	return TS_SUCCESS;
	586	}
	587
	588	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	589	ts_vertex **vtx=vlist->vtx;
d7639a	590	ts_uint i;
SP	591	FILE *fh;
	592
	593	fh=fopen(filename, "w");
	594	if(fh==NULL){
	595	err("Cannot open file %s for writing");
	596	return TS_FAIL;
	597	}
	598	for(i=0;i<vlist->n;i++)
8f6a69	599	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	600
SP	601	fclose(fh);
	602	return TS_SUCCESS;
	603	}
	604
	605
	606	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	607	ts_uint i,j;
	608	for(i=0;i<vlist->n;i++){
8f6a69	609	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	610	vlist->vtx[i]->y, vlist->vtx[i]->z,
	611	vlist->vtx[i]->neigh_no);
	612	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	613	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	614	//-vlist->vtx+1));
d7639a	615	}
SP	616	fprintf(fh,"\n");
	617	}
	618	return TS_SUCCESS;
	619	}
	620
	621	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	622	ts_uint i,j;
a6b1b5	623	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	624	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	625	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	626	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	627	}
SP	628	fprintf(fh,"\n");
	629	}
	630	return TS_SUCCESS;
	631	}
	632
	633	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	634	ts_triangle_list *tlist=vesicle->tlist;
d7639a	635	ts_uint i,j;
SP	636	for(i=0;i<tlist->n;i++){
41a035	637	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	638	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	639	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	640	}
SP	641	fprintf(fh,"\n");
	642	for(j=0;j<3;j++){
41a035	643	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	644	}
SP	645	fprintf(fh,"\n");
41a035	646	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	647	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	648	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	649	}
	650	return TS_SUCCESS;
	651	}
	652
	653	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	654	ts_uint i,j;
	655	for(i=0;i<vlist->n;i++){
	656	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	657	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	658	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	659	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	660	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	661	}
SP	662	fprintf(fh,"\n");
cef6ca	663	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	664	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	665	}
SP	666	fprintf(fh,"\n");
	667	}
	668	return TS_SUCCESS;
	669	}
	670
	671	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	672	ts_uint i;
a6b1b5	673	for(i=0;i<vesicle->blist->n;i++){
e016c4	674	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	675	//-vesicle->vlist->vtx+1),
e016c4	676	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	677	//-vesicle->vlist.vtx+1));
d7639a	678	}
SP	679	return TS_SUCCESS;
	680	}
	681
	682
	683	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	684	FILE *fh;
	685	fh=fopen(filename, "w");
	686	if(fh==NULL){
	687	err("Cannot open file %s for writing");
	688	return TS_FAIL;
	689	}
	690	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	691	fprint_vertex_list(fh,vesicle->vlist);
d7639a	692	fprint_tristar(fh,vesicle);
SP	693	fprint_triangle_list(fh,vesicle);
a6b1b5	694	fprint_vertex_data(fh,vesicle->vlist);
d7639a	695	fprint_bonds(fh,vesicle);
SP	696	fclose(fh);
	697	return TS_SUCCESS;
	698	}
	699
	700	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	701	FILE *fh;
	702	char line[255];
	703	fh=fopen(filename, "r");
	704	if(fh==NULL){
	705	err("Cannot open file for reading... Nonexistant file?");
	706	return TS_FAIL;
	707	}
a6b1b5	708	ts_uint retval=1;
d7639a	709	while(retval!=EOF){
SP	710	retval=fscanf(fh,"%s",line);
	711
	712	fprintf(stderr,"%s",line);
	713	}
	714	fclose(fh);
	715	return TS_SUCCESS;
	716	}
	717
	718	ts_bool write_master_xml_file(ts_char *filename){
	719	FILE *fh;
	720	ts_char i,j;
	721	ts_uint tstep;
	722	ts_char *number;
	723	fh=fopen(filename, "w");
	724	if(fh==NULL){
	725	err("Cannot open file %s for writing");
	726	return TS_FAIL;
	727	}
	728
	729	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	730	DIR *dir = opendir(".");
	731	if(dir){
	732	struct dirent *ent;
	733	tstep=0;
	734	while((ent = readdir(dir)) != NULL)
	735	{
	736	i=rindex(ent->d_name,'.');
	737	if(i==NULL) continue;
	738	if(strcmp(i+1,"vtu")==0){
	739	j=rindex(ent->d_name,'_');
	740	if(j==NULL) continue;
	741	number=strndup(j+1,j-i);
a6b1b5	742	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	743	tstep++;
SP	744	free(number);
	745	}
	746	}
	747	}
f74313	748	free(dir);
d7639a	749	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	750	fclose(fh);
	751	return TS_SUCCESS;
	752	}
	753
	754	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	755	ts_vertex_list *vlist=vesicle->vlist;
SP	756	ts_bond_list *blist=vesicle->blist;
	757	ts_vertex **vtx=vlist->vtx;
40aa5b	758	ts_uint i,j;
d7639a	759	char filename[255];
SP	760	FILE *fh;
	761
	762	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	763	fh=fopen(filename, "w");
	764	if(fh==NULL){
	765	err("Cannot open file %s for writing");
	766	return TS_FAIL;
	767	}
	768	/* Here comes header of the file */
40aa5b	769
SP	770	//find number of extra vtxs and bonds of polymeres
58230a	771	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	772	ts_bool poly=0, fil=0;
40aa5b	773	if(vesicle->poly_list!=NULL){
SP	774	if(vesicle->poly_list->poly[0]!=NULL){
	775	polyno=vesicle->poly_list->n;
	776	monono=vesicle->poly_list->poly[0]->vlist->n;
	777	poly=1;
	778	}
	779	}
58230a	780
M	781	if(vesicle->filament_list!=NULL){
	782	if(vesicle->filament_list->poly[0]!=NULL){
	783	filno=vesicle->filament_list->n;
	784	fonono=vesicle->filament_list->poly[0]->vlist->n;
	785	fil=1;
	786	}
	787	}
	788
d7639a	789	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
58230a	790	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	791	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	792	for(i=0;i<vlist->n;i++){
a6b1b5	793	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	794	}
40aa5b	795	//polymeres
SP	796	if(poly){
3c1ac1	797	poly_idx=vlist->n;
40aa5b	798	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	799	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	800	fprintf(fh,"%u ", poly_idx);
M	801	}
	802	}
	803	}
	804	//filaments
	805	if(fil){
	806	poly_idx=vlist->n+monono*polyno;
	807	for(i=0;i<vesicle->filament_list->n;i++){
	808	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	809	// fprintf(stderr,"was here\n");
3c1ac1	810	fprintf(fh,"%u ", poly_idx);
40aa5b	811	}
SP	812	}
	813	}
d7639a	814
SP	815	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	816	for(i=0;i<vlist->n;i++){
8f6a69	817	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	818	}
SP	819	//polymeres
	820	if(poly){
	821	for(i=0;i<vesicle->poly_list->n;i++){
	822	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	823	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 );
58230a	824	}
M	825	}
	826	}
	827	//filaments
	828	if(fil){
	829	for(i=0;i<vesicle->filament_list->n;i++){
	830	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	831	fprintf(fh,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
40aa5b	832	}
SP	833	}
d7639a	834	}
SP	835
	836	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	837	for(i=0;i<blist->n;i++){
e016c4	838	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	839	}
40aa5b	840	//polymeres
SP	841	if(poly){
3c1ac1	842	poly_idx=vlist->n;
40aa5b	843	for(i=0;i<vesicle->poly_list->n;i++){
SP	844	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	845	// 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);
SP	846	fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+imonono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+imonono);
40aa5b	847	}
SP	848	//grafted bonds
3c1ac1	849	fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
40aa5b	850	}
SP	851
	852	}
	853
58230a	854	//filaments
M	855	if(fil){
	856	poly_idx=vlist->n+monono*polyno;
	857	for(i=0;i<vesicle->filament_list->n;i++){
	858	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	859	fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+mononopolyno+ifonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+mononopolyno+ifonono);
	860	// fprintf(stderr,"was here\n");
	861
	862	}
	863	}
	864
	865	}
40aa5b	866
d7639a	867	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	868	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	869	fprintf(fh,"%u ",i);
SP	870	}
	871	fprintf(fh,"\n");
	872	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	873	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	874	fprintf(fh,"3 ");
SP	875	}
	876
	877	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	878	fclose(fh);
	879	return TS_SUCCESS;
	880
	881	}
	882
	883	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	884	ts_vertex_list *vlist=vesicle->vlist;
SP	885	ts_bond_list *blist=vesicle->blist;
	886	ts_vertex **vtx=vlist->vtx;
	887	ts_uint i;
d7639a	888	FILE *fh;
SP	889
	890	fh=fopen(filename, "w");
	891	if(fh==NULL){
	892	err("Cannot open file %s for writing");
	893	return TS_FAIL;
	894	}
	895	/* Here comes header of the file */
	896	// fprintf(stderr,"NSHELL=%u\n",nshell);
	897	fprintf(fh, "# vtk DataFile Version 2.0\n");
	898	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	899	fprintf(fh, "%s\n", text);
	900	fprintf(fh,"ASCII\n");
	901	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	902	fprintf(fh,"POINTS %u double\n", vlist->n);
	903	for(i=0;i<vlist->n;i++){
8f6a69	904	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	905	}
SP	906
	907	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	908	for(i=0;i<blist->n;i++){
e016c4	909	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	910	}
SP	911	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	912	for(i=0;i<blist->n;i++)
	913	fprintf(fh,"3\n");
	914
	915	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	916	fprintf(fh,"SCALARS scalars long 1\n");
	917	fprintf(fh,"LOOKUP_TABLE default\n");
	918
	919	for(i=0;i<vlist->n;i++)
8f6a69	920	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	921
SP	922	fclose(fh);
	923	return TS_SUCCESS;
	924	}
	925
	926
	927
144784	928	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	929	FILE *fh;
	930	ts_uint i;
	931
	932	fh=fopen(filename, "w");
	933	if(fh==NULL){
	934	err("Cannot open file %s for writing");
	935	return TS_FAIL;
	936	}
	937
	938	for(i=0;i<vesicle->tlist->n;i++){
	939
	940	fprintf(fh,"\ttriangle {");
	941	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	942	vesicle->tlist->tria[i]->vertex[0]->x,
	943	vesicle->tlist->tria[i]->vertex[0]->y,
	944	vesicle->tlist->tria[i]->vertex[0]->z,
	945
	946	vesicle->tlist->tria[i]->vertex[1]->x,
	947	vesicle->tlist->tria[i]->vertex[1]->y,
	948	vesicle->tlist->tria[i]->vertex[1]->z,
	949
	950	vesicle->tlist->tria[i]->vertex[2]->x,
	951	vesicle->tlist->tria[i]->vertex[2]->y,
	952	vesicle->tlist->tria[i]->vertex[2]->z
	953	);
	954	}
	955
	956	fclose(fh);
	957	return TS_SUCCESS;
	958	}
	959
	960
1ab449	961	ts_tape parsetape(char filename){
SP	962	// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
	963	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	964	tape->multiprocessing=calloc(255,sizeof(char));
	965	/* long int brezveze0=1;
b14a8d	966	long int brezveze1=1;
SP	967	long int brezveze2=1;
e86357	968	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	969	long int iter=1000, init=1000, mcsw=1000;
1ab449	970	*/
40aa5b	971
d7639a	972	cfg_opt_t opts[] = {
1ab449	973	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	974	CFG_SIMPLE_INT("npoly", &tape->npoly),
	975	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	976	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	977	CFG_SIMPLE_INT("nfono",&tape->nfono),
	978	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
	979	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	980	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	981	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	982	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	983	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
43c042	984	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	985	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	986	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	987	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	988	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	989	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	990	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	991	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	992	CFG_SIMPLE_INT("iterations",&tape->iterations),
	993	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	994	CFG_SIMPLE_INT("inititer", &tape->inititer),
	995	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	996	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	997	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	998	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	999	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1000	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	1001	CFG_END()
SP	1002	};
	1003	cfg_t *cfg;
	1004	ts_uint retval;
	1005	cfg = cfg_init(opts, 0);
1ab449	1006	retval=cfg_parse(cfg, filename);
d7639a	1007	if(retval==CFG_FILE_ERROR){
a6b1b5	1008	fatal("No tape file.",100);
d7639a	1009	}
SP	1010	else if(retval==CFG_PARSE_ERROR){
	1011	fatal("Invalid tape!",100);
	1012	}
a2db52	1013
d7639a	1014	cfg_free(cfg);
40aa5b	1015
SP	1016
1ab449	1017	/* global variables are set automatically */
SP	1018	quiet=tape->quiet;
	1019	return tape;
	1020	}
d7639a	1021
1ab449	1022	ts_bool tape_free(ts_tape *tape){
SP	1023	free(tape->multiprocessing);
	1024	free(tape);
	1025	return TS_SUCCESS;
d7639a	1026	}
f74313	1027
SP	1028
	1029	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	1030	FILE *fh;
	1031	ts_uint i, nvtx,nedges,ntria;
	1032	ts_uint vtxi1,vtxi2;
	1033	float x,y,z;
	1034	ts_vertex_list *vlist;
	1035	fh=fopen(fname, "r");
	1036	if(fh==NULL){
	1037	err("Cannot open file for reading... Nonexistant file?");
	1038	return TS_FAIL;
	1039	}
	1040	ts_uint retval;
	1041	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1042	vesicle->vlist=init_vertex_list(nvtx);
	1043	vlist=vesicle->vlist;
	1044	for(i=0;i<nvtx;i++){
8f6a69	1045	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1046	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1047	vlist->vtx[i]->x=x;
SP	1048	vlist->vtx[i]->y=y;
	1049	vlist->vtx[i]->z=z;
f74313	1050	}
SP	1051	for(i=0;i<nedges;i++){
	1052	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1053	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1054	}
	1055	//TODO: neighbours from bonds,
	1056	//TODO: triangles from neigbours
	1057
	1058	// Don't need to read triangles. Already have enough data
	1059	/*
	1060	for(i=0;i<ntria;i++){
	1061	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1062	vtxi1=vesicle->blist->vertex1->idx;
SP	1063	vtxi2=vesicle->blist->vertex1->idx;
f74313	1064
SP	1065	}
	1066	*/
41a035	1067	if(retval);
f74313	1068	fclose(fh);
SP	1069
	1070
	1071
	1072	return TS_SUCCESS;
	1073	}