trisurf-ng.git - Gitblit

Constant volume and constant area fix. Removed spherical harmonics calculat...

Samo Penic

2019-09-25 d5d78a49c6b51fb1f6f0661d063034eaf65e02f7

commit \| author \| age
819a09	1
7f6076	2	/* vim: set ts=4 sts=4 sw=4 noet : */
f74313	3	#include "general.h"
d7639a	4	#include<stdio.h>
SP	5	#include "io.h"
f74313	6	#include "vertex.h"
SP	7	#include "bond.h"
d7639a	8	#include<string.h>
a6b1b5	9	#include<stdlib.h>
d7639a	10	#include <sys/types.h>
SP	11	#include <dirent.h>
b14a8d	12	#include "initial_distribution.h"
a2db52	13	#include "poly.h"
055dd7	14	#include "cell.h"
083e03	15	#include <getopt.h>
SP	16	#include <sys/stat.h>
	17	#include <sys/types.h>
	18	#include <dirent.h>
	19	#include <errno.h>
854cb6	20	#include <snapshot.h>
e9eab4	21	/ DUMP STATE TO DISK DRIVE /
SP	22
1ab449	23	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	24
SP	25	/* save current state with wrong pointers. Will fix that later */
	26	ts_uint i,j,k;
267db5	27	FILE *fh=fopen(command_line_args.dump_fullfilename,"wb");
e9eab4	28
SP	29	/* dump vesicle */
d0a1d3	30	fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
e9eab4	31	/* dump vertex list */
SP	32	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	33	/* dump bond list */
	34	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	35	/* dump triangle list */
	36	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	37	/* dump cell list */
	38	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	39	/* dump poly list */
	40	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	41	/* dump filament list */
M	42	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	43	/* level 1 complete */
SP	44
	45	/dump vertices/
	46	for(i=0;i<vesicle->vlist->n;i++){
	47	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	48	/* dump pointer offsets for:
	49	neigh
	50	bond
	51	tria
	52	cell is ignored
	53	*/
	54	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	55	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	56	}
SP	57	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	58	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	59	}
SP	60	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	61	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	62	}
SP	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 */
3c1ac1	69	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	70	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	71	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	72	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	73	}
SP	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 */
3c1ac1	79	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	80	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	81	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	82	/* dump pointer offsets for neigh */
SP	83	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	84	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	85	}
SP	86	}
	87
	88
	89	/dump polymeres /
	90	for(i=0;i<vesicle->poly_list->n;i++){
	91	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	92	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	93	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	94	}
SP	95
	96	/* dump poly vertex(monomer) list*/
	97	for(i=0;i<vesicle->poly_list->n;i++){
	98	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	99	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	100	/* dump offset for neigh and bond */
	101	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	102	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	103	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	104	}
SP	105	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	106	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	107	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	108	}
SP	109	}
3c1ac1	110	// grafted vtx on vesicle data dump
SP	111	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	112	}
SP	113	/* dump poly bonds between monomers list*/
	114	for(i=0;i<vesicle->poly_list->n;i++){
	115	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	116	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	117	/* dump vtx1 and vtx2 offsets */
3c1ac1	118	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	119	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	120	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	121	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	122	}
SP	123	}
	124
bcf455	125
M	126	/dump filamentes grandes svinjas /
	127	for(i=0;i<vesicle->filament_list->n;i++){
	128	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	129	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	130	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	131	}
	132
	133	/* dump filamentes vertex(monomer) list*/
	134	for(i=0;i<vesicle->filament_list->n;i++){
	135	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	136	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	137	/* dump offset for neigh and bond */
	138	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	139	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	140	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	141	}
	142	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	143	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	144	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	145	}
	146	}
	147	}
	148	/* dump poly bonds between monomers list*/
	149	for(i=0;i<vesicle->filament_list->n;i++){
	150	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	151	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	152	/* dump vtx1 and vtx2 offsets */
	153	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	154	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	155	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	156	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	157	}
	158	}
	159
	160
	161
e9eab4	162	/* pointer offsets for fixing the restored pointers */
SP	163	/* need pointers for
	164	vlist->vtx
	165	blist->bond
	166	tlist->tria
	167	clist->cell
	168	poly_list->poly
	169	and for each poly:
	170	poly_list->poly->vtx
	171	poly_list->poly->bond
	172	*/
	173
bd2210	174	// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	175	/* write tape information on vesicle */
bd2210	176	// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	177	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	178	fclose(fh);
SP	179	return TS_SUCCESS;
	180	}
	181
	182
	183	/ RESTORE DUMP FROM DISK /
1ab449	184	ts_vesicle restore_state(ts_uint iteration){
e9eab4	185	ts_uint i,j,k;
267db5	186	FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
3f5c83	187
SP	188	struct stat sb;
267db5	189	if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
3f5c83	190	//dump file does not exist.
SP	191	return NULL;
	192	}
	193
	194	//check if it is regular file
	195	if((sb.st_mode & S_IFMT) != S_IFREG) {
	196	//dump file is not a regular file.
	197	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	198	return NULL;
	199	}
	200
e9eab4	201	ts_uint retval;
3c1ac1	202	ts_uint idx;
e9eab4	203
SP	204	/* we restore all the data from the dump */
	205	/* restore vesicle */
	206	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
d0a1d3	207	retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
86f5e7	208	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
SP	209
e9eab4	210	/* restore vertex list */
SP	211	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	212	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	213	/* restore bond list */
	214	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	215	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	216	/* restore triangle list */
	217	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	218	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	219	/* restore cell list */
	220	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	221	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	222	/* restore poly list */
	223	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	224	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	225	/* restore filament list */
M	226	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	227	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	228	/* level 1 complete */
SP	229
3c1ac1	230	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	231	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	232	for(i=0;i<vesicle->blist->n;i++){
	233	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	234	}
	235	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	236	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	237	for(i=0;i<vesicle->tlist->n;i++){
	238	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	239	}
a37ba2	240	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	241	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	242	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	243	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	244	}
SP	245	/restore vertices/
	246	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	247	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	248	/restore neigh, bond, tristar. Ignoring cell /
	249	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	250	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	251	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	252	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	253	}
SP	254	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	255	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	256	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	257	/* 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 */
	258	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	259	}
SP	260
	261	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	262	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	263	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	264	/* same comment as above */
	265	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	266	}
SP	267
	268	}
	269
	270	/restore bonds/
3c1ac1	271	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	272	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	273	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	274	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	275	/* restore vtx1 and vtx2 */
3c1ac1	276	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	277	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	278	retval=fread(&idx,sizeof(ts_uint),1,fh);
	279	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	280	}
SP	281
	282	/restore triangles/
3c1ac1	283	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	284	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	285	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	286	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	287	/* restore pointers for vertices */
3c1ac1	288	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	289	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	290	retval=fread(&idx,sizeof(ts_uint),1,fh);
	291	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	292	retval=fread(&idx,sizeof(ts_uint),1,fh);
	293	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	294	/* restore pointers for neigh */
3c1ac1	295	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	296	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	297	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	298	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	299	}
SP	300
	301	}
	302
	303	/restore cells /
	304	/TODO: do we need to recalculate cells here? /
	305	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	306	for(i=0;i<vesicle->clist->cellno;i++){
	307	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	308	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	309	}
	310	*/
	311	/restore polymeres /
	312	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	313	for(i=0;i<vesicle->poly_list->n;i++){
	314	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	315	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	316	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	317	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	318	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	319	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	320	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	321	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	322	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	323	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	324	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	325	}
	326	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	327	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	328	}
	329
e9eab4	330	}
3c1ac1	331
e9eab4	332
SP	333	/* restore poly vertex(monomer) list*/
	334	for(i=0;i<vesicle->poly_list->n;i++){
	335	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	336	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	337
e9eab4	338	/* restore neigh and bonds */
SP	339	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 ));
	340	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	341	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	342	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	343	}
SP	344	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 ));
	345	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	346	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	347	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	348	}
SP	349
	350	}
3c1ac1	351	/* restore grafted vtx on vesicle and grafted_poly */
SP	352	retval=fread(&idx,sizeof(ts_uint),1,fh);
	353	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	354	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	355	}
3c1ac1	356
e9eab4	357	/* restore poly bonds between monomers list*/
SP	358	for(i=0;i<vesicle->poly_list->n;i++){
	359	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	360	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	361	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	362	/* restore vtx1 and vtx2 */
3c1ac1	363	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	364	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	365	retval=fread(&idx,sizeof(ts_uint),1,fh);
	366	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	367	}
SP	368	}
	369
bcf455	370	/restore filaments /
M	371	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	372	for(i=0;i<vesicle->filament_list->n;i++){
	373	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	374	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	375	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	376	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	377	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	378	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	379	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	380	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	381	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	382	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	383	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	384	}
	385	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	386	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	387	}
	388
	389	}
	390
	391
	392	/* restore poly vertex(monomer) list*/
	393	for(i=0;i<vesicle->filament_list->n;i++){
	394	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	395	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	396
	397	/* restore neigh and bonds */
	398	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 ));
	399	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	400	retval=fread(&idx,sizeof(ts_uint),1,fh);
	401	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	402	}
	403	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 ));
	404	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	405	retval=fread(&idx,sizeof(ts_uint),1,fh);
	406	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	407	}
	408
	409	}
	410	}
	411
	412	/* restore poly bonds between monomers list*/
	413	for(i=0;i<vesicle->filament_list->n;i++){
	414	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	415	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	416	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	417	/* restore vtx1 and vtx2 */
	418	retval=fread(&idx,sizeof(ts_uint),1,fh);
	419	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	420	retval=fread(&idx,sizeof(ts_uint),1,fh);
	421	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	422	}
	423	}
267db5	424	vesicle->tape=parsetape(command_line_args.tape_fullfilename);
063289	425	// recreating space for cells //
055dd7	426	vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
90882f	427	vesicle->clist->max_occupancy=16;
47a7ac	428	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	429	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	430	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	431	if(retval);
SP	432	fclose(fh);
	433	return vesicle;
	434	}
	435
	436
	437
083e03	438	ts_bool parse_args(int argc, char **argv){
3f5c83	439	int c, retval;
SP	440	struct stat sb;
	441	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	442	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	443	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	444	sprintf(command_line_args.tape_fullfilename,"tape");
1bf3c3	445	sprintf(command_line_args.tape_templatefull,"./tape");
3f5c83	446	FILE *file;
SP	447
083e03	448	while (1)
SP	449	{
	450	static struct option long_options[] =
	451	{
8a6614	452	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	453	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	454	{"tape", no_argument, 0, 't'},
fd8126	455	{"version", no_argument, 0, 'v'},
083e03	456	{"output-file", required_argument, 0, 'o'},
SP	457	{"directory", required_argument, 0, 'd'},
3f5c83	458	{"dump-filename", required_argument,0, 'f'},
7b0c07	459	{"tape-options",required_argument,0,'c'},
1bf3c3	460	{"tape-template", required_argument,0,0},
ab798b	461	{"restore-from-vtk",required_argument,0,0},
083e03	462	{0, 0, 0, 0}
SP	463	};
	464	/* getopt_long stores the option index here. */
	465	int option_index = 0;
	466
fd8126	467	c = getopt_long (argc, argv, "d:f:o:t:c:v",
083e03	468	long_options, &option_index);
SP	469
	470	/* Detect the end of the options. */
	471	if (c == -1)
	472	break;
	473
	474	switch (c)
	475	{
	476	case 0:
	477	/* If this option set a flag, do nothing else now. */
	478	if (long_options[option_index].flag != 0)
	479	break;
1bf3c3	480	/* printf ("option %s", long_options[option_index].name);
083e03	481	if (optarg)
1bf3c3	482	printf (" with arg %s", optarg);
SP	483	printf ("\n"); */
	484	//TODO: find a better way.
	485	if(strcmp(long_options[option_index].name,"tape-template")==0){
	486	strcpy(command_line_args.tape_templatefull,optarg);
	487	}
ab798b	488	if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
ee84bd	489	strcpy(command_line_args.dump_from_vtk,optarg);
SP	490	}
083e03	491	break;
fd8126	492	case 'v':
SP	493	fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	494	fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
	495	fprintf(stdout,"Released under terms of GPLv3\n");
	496	exit(0);
083e03	497
7b0c07	498	case 'c':
SP	499	strcpy(command_line_args.tape_opts,optarg);
	500	break;
	501	case 't': //tape
3f5c83	502	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	503	break;
SP	504
7b0c07	505	case 'o': //set filename of master pvd output file
3f5c83	506	strcpy(command_line_args.output_fullfilename, optarg);
SP	507	break;
083e03	508
SP	509	case 'd':
	510	//check if directory exists. If not create one. If creation is
	511	//successful, set directory for output files.
	512	//printf ("option -d with value `%s'\n", optarg);
3f5c83	513	if (stat(optarg, &sb) == -1) {
SP	514	//directory does not exist
083e03	515	retval=mkdir(optarg, 0700);
SP	516	if(retval){
3f5c83	517	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	518	}
SP	519	}
3f5c83	520	//check if is a proper directory
SP	521	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	522	//it is not a directory. fatal error.
	523	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	524	fatal("Cannot continue",1);
083e03	525	}
3f5c83	526	strcpy(command_line_args.path, optarg);
083e03	527	break;
SP	528
	529	case 'f':
3f5c83	530	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	531	break;
SP	532
	533	case '?':
	534	/* getopt_long already printed an error message. */
ba73ab	535	print_help(stdout);
SP	536	//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
083e03	537	fatal("Ooops, read help first",1);
SP	538	break;
	539
	540	default:
	541	exit (1);
	542	}
	543	}
	544
7b0c07	545	//Here we set correct values for full filenames!
SP	546	char buffer=(char )malloc(10000*sizeof(char));
	547	//correct the path and add trailing /
	548	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	549
	550	/* master pvd output file */
	551	strcpy(buffer,command_line_args.path);
	552	strcat(buffer,command_line_args.output_fullfilename);
	553	if ((file = fopen(buffer, "w")) == NULL) {
	554	fprintf(stderr,"Could not create output file %s!\n", buffer);
	555	fatal("Please specify correct output file or check permissions of the file",1);
1bf3c3	556	//there is a tape template. make a copy into desired directory
7b0c07	557
SP	558	} else {
	559	fclose(file);
	560	strcpy(command_line_args.output_fullfilename,buffer);
	561	}
	562
	563	/* tape file */
	564	strcpy(buffer,command_line_args.path);
	565	strcat(buffer,command_line_args.tape_fullfilename);
	566	if (stat(buffer, &sb) == -1) {
1bf3c3	567
SP	568	//tape does not exist. does tape template exist?
	569	if(stat(command_line_args.tape_templatefull, &sb)==-1){
	570	ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
	571	fatal("Please select correct tape or check permissions of the file",1);
	572	} else {
	573	//tape template found
	574	fatal("Samo did not program template copy yet",1);
	575	}
7b0c07	576	} else {
SP	577	strcpy(command_line_args.tape_fullfilename,buffer);
	578	}
	579
	580
	581	/* dump file */
	582	strcpy(buffer,command_line_args.path);
	583	strcat(buffer,command_line_args.dump_fullfilename);
	584	//check if dump file exist first.
	585	if (stat(buffer, &sb) == -1) {
	586	//no dump file. check if we can create one.
	587	if ((file = fopen(buffer, "w")) == NULL) {
	588	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	589	fatal("Please specify correct dump file or check permissions of the file",1);
	590	} else {
	591	fclose(file);
	592	//good, file is writeable. delete it for now.
	593	remove(buffer);
	594	}
	595	}
	596	strcpy(command_line_args.dump_fullfilename, buffer);
	597
	598
	599	free(buffer);
083e03	600	return TS_SUCCESS;
SP	601
	602	}
	603
	604
ba73ab	605	ts_bool print_help(FILE *fd){
SP	606	fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	607	fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
	608	fprintf(fd,"Released under terms of GPLv3\n\n");
	609
	610	fprintf(fd, "Invoking trisurf-ng without any flags results in default operation. Program reads 'tape' file and 'dump.bin' binary representation of the vesicle from disk and continues the simulation where it was aborted (as specified in 'dump.bin').\n\n");
	611	fprintf(fd,"If 'tape' has different values than binary dump, those are used (if possible -- some values in tape, such as nshell cannot be modified).\n\n\n");
	612	fprintf(fd,"However, if dump.bin is not present, user is notified to specify --force-from-tape flag. The vesicle will be created from specifications in tape.\n\n\n");
	613	fprintf(fd,"Flags:\n\n");
	614	fprintf(fd,"--force-from-tape\t\t makes initial shape of the vesicle from tape. Ignores already existing binary dump and possible simulation results.\n");
	615	fprintf(fd,"--restore-from-vtk\t\t VTK's file ending with '.vtu' are preferred way to make state snapshots for restoration. With this flag the restoration of the vesicle from vtk is possible. The simulation will continue if hidden '.status' file with last iteration done is present. Otherwise it will start simulation from timestep 0.\n");
c4178c	616	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
ba73ab	617	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
SP	618	fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
	619	fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
c4178c	620	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
SP	621	fprintf(fd,"Examples:\n\n");
	622	fprintf(fd,"trisurf --force-from-tape\n");
	623	fprintf(fd,"trisurf --reset-iteration-count\n");
	624	fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
	625	fprintf(fd,"\n\n");
	626
ba73ab	627	return TS_SUCCESS;
SP	628	}
	629
	630
083e03	631
d7639a	632	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	633	ts_uint i;
	634	printf("Number of vertices: %u\n",vlist->n);
	635	for(i=0;i<vlist->n;i++){
a6b1b5	636	printf("%u: %f %f %f\n",
8f6a69	637	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	638	}
SP	639	return TS_SUCCESS;
	640	}
	641
	642	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	643	ts_uint i,j;
a6b1b5	644	ts_vertex **vtx=vlist->vtx;
d7639a	645	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	646	for(i=0;i<vlist->n;i++){
8f6a69	647	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	648	for(j=0;j<vtx[i]->neigh_no;j++){
	649	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	650	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	651	}
SP	652	printf("\n");
	653	}
	654
	655	return TS_SUCCESS;
	656	}
	657
	658	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	659	ts_vertex **vtx=vlist->vtx;
d7639a	660	ts_uint i;
SP	661	FILE *fh;
	662
	663	fh=fopen(filename, "w");
	664	if(fh==NULL){
	665	err("Cannot open file %s for writing");
	666	return TS_FAIL;
	667	}
	668	for(i=0;i<vlist->n;i++)
8f6a69	669	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	670
SP	671	fclose(fh);
	672	return TS_SUCCESS;
	673	}
	674
	675
	676	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	677	ts_uint i,j;
	678	for(i=0;i<vlist->n;i++){
8f6a69	679	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	680	vlist->vtx[i]->y, vlist->vtx[i]->z,
	681	vlist->vtx[i]->neigh_no);
	682	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	683	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	684	//-vlist->vtx+1));
d7639a	685	}
SP	686	fprintf(fh,"\n");
	687	}
	688	return TS_SUCCESS;
	689	}
	690
	691	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	692	ts_uint i,j;
a6b1b5	693	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	694	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	695	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	696	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	697	}
SP	698	fprintf(fh,"\n");
	699	}
	700	return TS_SUCCESS;
	701	}
	702
	703	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	704	ts_triangle_list *tlist=vesicle->tlist;
d7639a	705	ts_uint i,j;
SP	706	for(i=0;i<tlist->n;i++){
41a035	707	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	708	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	709	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	710	}
SP	711	fprintf(fh,"\n");
	712	for(j=0;j<3;j++){
41a035	713	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	714	}
SP	715	fprintf(fh,"\n");
41a035	716	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	717	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	718	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	719	}
	720	return TS_SUCCESS;
	721	}
	722
	723	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	724	ts_uint i,j;
	725	for(i=0;i<vlist->n;i++){
	726	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	727	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	728	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	729	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	730	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	731	}
SP	732	fprintf(fh,"\n");
cef6ca	733	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	734	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	735	}
SP	736	fprintf(fh,"\n");
	737	}
	738	return TS_SUCCESS;
	739	}
	740
	741	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	742	ts_uint i;
a6b1b5	743	for(i=0;i<vesicle->blist->n;i++){
e016c4	744	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	745	//-vesicle->vlist->vtx+1),
e016c4	746	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	747	//-vesicle->vlist.vtx+1));
d7639a	748	}
SP	749	return TS_SUCCESS;
	750	}
	751
	752
	753	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	754	FILE *fh;
	755	fh=fopen(filename, "w");
	756	if(fh==NULL){
	757	err("Cannot open file %s for writing");
	758	return TS_FAIL;
	759	}
	760	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	761	fprint_vertex_list(fh,vesicle->vlist);
d7639a	762	fprint_tristar(fh,vesicle);
SP	763	fprint_triangle_list(fh,vesicle);
a6b1b5	764	fprint_vertex_data(fh,vesicle->vlist);
d7639a	765	fprint_bonds(fh,vesicle);
SP	766	fclose(fh);
	767	return TS_SUCCESS;
	768	}
	769
	770	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	771	FILE *fh;
	772	char line[255];
	773	fh=fopen(filename, "r");
	774	if(fh==NULL){
	775	err("Cannot open file for reading... Nonexistant file?");
	776	return TS_FAIL;
	777	}
a6b1b5	778	ts_uint retval=1;
d7639a	779	while(retval!=EOF){
SP	780	retval=fscanf(fh,"%s",line);
	781
	782	fprintf(stderr,"%s",line);
	783	}
	784	fclose(fh);
	785	return TS_SUCCESS;
	786	}
	787
	788	ts_bool write_master_xml_file(ts_char *filename){
	789	FILE *fh;
	790	ts_char i,j;
	791	ts_uint tstep;
	792	ts_char *number;
	793	fh=fopen(filename, "w");
	794	if(fh==NULL){
	795	err("Cannot open file %s for writing");
	796	return TS_FAIL;
	797	}
	798
	799	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
267db5	800	DIR *dir = opendir(command_line_args.path);
d7639a	801	if(dir){
SP	802	struct dirent *ent;
	803	tstep=0;
	804	while((ent = readdir(dir)) != NULL)
	805	{
	806	i=rindex(ent->d_name,'.');
	807	if(i==NULL) continue;
	808	if(strcmp(i+1,"vtu")==0){
	809	j=rindex(ent->d_name,'_');
	810	if(j==NULL) continue;
	811	number=strndup(j+1,j-i);
a6b1b5	812	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	813	tstep++;
SP	814	free(number);
	815	}
	816	}
	817	}
f74313	818	free(dir);
d7639a	819	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	820	fclose(fh);
	821	return TS_SUCCESS;
	822	}
	823
0a2c81	824	ts_bool write_vertex_xml_file(ts_vesicle vesicle, ts_uint timestepno, ts_cluster_list cstlist){
a6b1b5	825	ts_vertex_list *vlist=vesicle->vlist;
SP	826	ts_bond_list *blist=vesicle->blist;
	827	ts_vertex **vtx=vlist->vtx;
40aa5b	828	ts_uint i,j;
13d445	829	//ts_double senergy=0.0;
267db5	830	char filename[10000];
SP	831	char just_name[255];
d7639a	832	FILE *fh;
267db5	833	strcpy(filename,command_line_args.path);
SP	834	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	835	strcat(filename,just_name);
d7639a	836
SP	837	fh=fopen(filename, "w");
	838	if(fh==NULL){
	839	err("Cannot open file %s for writing");
	840	return TS_FAIL;
	841	}
	842	/* Here comes header of the file */
40aa5b	843
SP	844	//find number of extra vtxs and bonds of polymeres
58230a	845	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	846	ts_bool poly=0, fil=0;
40aa5b	847	if(vesicle->poly_list!=NULL){
SP	848	if(vesicle->poly_list->poly[0]!=NULL){
	849	polyno=vesicle->poly_list->n;
	850	monono=vesicle->poly_list->poly[0]->vlist->n;
	851	poly=1;
	852	}
	853	}
58230a	854
M	855	if(vesicle->filament_list!=NULL){
	856	if(vesicle->filament_list->poly[0]!=NULL){
	857	filno=vesicle->filament_list->n;
	858	fonono=vesicle->filament_list->poly[0]->vlist->n;
	859	fil=1;
	860	}
	861	}
	862
854cb6	863	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	864	xml_trisurf_data(fh,vesicle);
	865	fprintf(fh, " <UnstructuredGrid>\n");
8db203	866	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n);
5c64e2	867	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
d7639a	868	for(i=0;i<vlist->n;i++){
a6b1b5	869	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	870	}
40aa5b	871	//polymeres
SP	872	if(poly){
3c1ac1	873	poly_idx=vlist->n;
40aa5b	874	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	875	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	876	fprintf(fh,"%u ", poly_idx);
M	877	}
	878	}
	879	}
	880	//filaments
	881	if(fil){
	882	poly_idx=vlist->n+monono*polyno;
	883	for(i=0;i<vesicle->filament_list->n;i++){
	884	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	885	// fprintf(stderr,"was here\n");
3c1ac1	886	fprintf(fh,"%u ", poly_idx);
40aa5b	887	}
SP	888	}
	889	}
d7639a	890
45c708	891	fprintf(fh,"</DataArray>\n");
0a2c81	892	if(cstlist!=NULL){
SP	893	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	894	for(i=0;i<vlist->n;i++){
	895	if(vtx[i]->cluster!=NULL){
	896	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	897	} else {
	898	fprintf(fh,"-1 ");
	899	}
	900	}
	901	//polymeres
	902	if(poly){
	903	poly_idx=vlist->n;
	904	for(i=0;i<vesicle->poly_list->n;i++){
	905	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	906	fprintf(fh,"-1 ");
	907	}
	908	}
	909	}
	910	//filaments
	911	if(fil){
	912	poly_idx=vlist->n+monono*polyno;
	913	for(i=0;i<vesicle->filament_list->n;i++){
	914	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	915	// fprintf(stderr,"was here\n");
	916	fprintf(fh,"-1 ");
	917	}
	918	}
	919	}
	920
	921	fprintf(fh,"</DataArray>\n");
	922
	923
	924	}
	925
45c708	926	//here comes additional data as needed. Currently only spontaneous curvature
SP	927	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	928	for(i=0;i<vlist->n;i++){
	929	fprintf(fh,"%.17e ",vtx[i]->c);
	930	}
	931	//polymeres
	932	if(poly){
	933	poly_idx=vlist->n;
	934	for(i=0;i<vesicle->poly_list->n;i++){
	935	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	936	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	937	}
	938	}
	939	}
	940	//filaments
	941	if(fil){
	942	poly_idx=vlist->n+monono*polyno;
	943	for(i=0;i<vesicle->filament_list->n;i++){
	944	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	945	// fprintf(stderr,"was here\n");
	946	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	947	}
	948	}
	949	}
	950	fprintf(fh,"</DataArray>\n");
	951
5c64e2	952	//here comes additional data. Energy!
SP	953	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	954	for(i=0;i<vlist->n;i++){
	955	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	956	}
	957	//polymeres
	958	if(poly){
	959	poly_idx=vlist->n;
	960	for(i=0;i<vesicle->poly_list->n;i++){
	961	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	962	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	963	}
	964	}
	965	}
	966	//filaments
	967	if(fil){
	968	poly_idx=vlist->n+monono*polyno;
	969	for(i=0;i<vesicle->filament_list->n;i++){
	970	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	971	// fprintf(stderr,"was here\n");
	972	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	973	}
	974	}
	975	}
	976	fprintf(fh,"</DataArray>\n");
	977
45c708	978
13d445	979	fprintf(fh,"</PointData>\n<CellData>\n");
SP	980
7ec6fb	981	if(vesicle->tape->stretchswitch==1){
SP	982	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	983	for(i=0;i<blist->n;i++){
SP	984	fprintf(fh, "0.0 ");
	985	}
	986	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	987	fprintf(fh,"0.0 ");
7ec6fb	988	}
13d445	989	for(i=0;i<vesicle->tlist->n;i++){
SP	990	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	991	}
7ec6fb	992	fprintf(fh,"</DataArray>\n");
SP	993	}
45c708	994
13d445	995
SP	996
	997	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	998	for(i=0;i<vlist->n;i++){
aad500	999	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	1000	}
SP	1001	//polymeres
	1002	if(poly){
	1003	for(i=0;i<vesicle->poly_list->n;i++){
	1004	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	1005	fprintf(fh,"%.17e %.17e %.17e\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	1006	}
M	1007	}
	1008	}
	1009	//filaments
	1010	if(fil){
	1011	for(i=0;i<vesicle->filament_list->n;i++){
	1012	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	1013	fprintf(fh,"%.17e %.17e %.17e\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	1014	}
SP	1015	}
d7639a	1016	}
SP	1017
	1018	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	1019	for(i=0;i<blist->n;i++){
e016c4	1020	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1021	}
40aa5b	1022	//polymeres
SP	1023	if(poly){
3c1ac1	1024	poly_idx=vlist->n;
40aa5b	1025	for(i=0;i<vesicle->poly_list->n;i++){
SP	1026	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	1027	// 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	1028	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	1029	}
SP	1030	//grafted bonds
3c1ac1	1031	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	1032	}
SP	1033
	1034	}
	1035
58230a	1036	//filaments
M	1037	if(fil){
	1038	poly_idx=vlist->n+monono*polyno;
	1039	for(i=0;i<vesicle->filament_list->n;i++){
	1040	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	1041	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);
	1042	// fprintf(stderr,"was here\n");
	1043
	1044	}
	1045	}
	1046
	1047	}
8db203	1048	for(i=0;i<vesicle->tlist->n;i++){
SP	1049	fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
	1050	}
d7639a	1051	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	1052	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	1053	fprintf(fh,"%u ",i);
SP	1054	}
8db203	1055	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	1056	fprintf(fh,"%u ", j);
	1057	}
d7639a	1058	fprintf(fh,"\n");
SP	1059	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	1060	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	1061	fprintf(fh,"3 ");
SP	1062	}
8db203	1063	for(i=0;i<vesicle->tlist->n;i++){
SP	1064	fprintf(fh,"5 ");
	1065	}
d7639a	1066	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	1067	fclose(fh);
	1068	return TS_SUCCESS;
	1069
	1070	}
	1071
	1072	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	1073	ts_vertex_list *vlist=vesicle->vlist;
SP	1074	ts_bond_list *blist=vesicle->blist;
	1075	ts_vertex **vtx=vlist->vtx;
	1076	ts_uint i;
d7639a	1077	FILE *fh;
SP	1078
	1079	fh=fopen(filename, "w");
	1080	if(fh==NULL){
	1081	err("Cannot open file %s for writing");
	1082	return TS_FAIL;
	1083	}
	1084	/* Here comes header of the file */
	1085	// fprintf(stderr,"NSHELL=%u\n",nshell);
	1086	fprintf(fh, "# vtk DataFile Version 2.0\n");
	1087	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	1088	fprintf(fh, "%s\n", text);
	1089	fprintf(fh,"ASCII\n");
	1090	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	1091	fprintf(fh,"POINTS %u double\n", vlist->n);
	1092	for(i=0;i<vlist->n;i++){
8f6a69	1093	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	1094	}
SP	1095
	1096	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	1097	for(i=0;i<blist->n;i++){
e016c4	1098	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1099	}
SP	1100	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	1101	for(i=0;i<blist->n;i++)
	1102	fprintf(fh,"3\n");
	1103
	1104	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	1105	fprintf(fh,"SCALARS scalars long 1\n");
	1106	fprintf(fh,"LOOKUP_TABLE default\n");
	1107
	1108	for(i=0;i<vlist->n;i++)
8f6a69	1109	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	1110
SP	1111	fclose(fh);
	1112	return TS_SUCCESS;
	1113	}
	1114
	1115
	1116
144784	1117	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	1118	FILE *fh;
	1119	ts_uint i;
	1120
	1121	fh=fopen(filename, "w");
	1122	if(fh==NULL){
	1123	err("Cannot open file %s for writing");
	1124	return TS_FAIL;
	1125	}
	1126
	1127	for(i=0;i<vesicle->tlist->n;i++){
	1128
	1129	fprintf(fh,"\ttriangle {");
	1130	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1131	vesicle->tlist->tria[i]->vertex[0]->x,
	1132	vesicle->tlist->tria[i]->vertex[0]->y,
	1133	vesicle->tlist->tria[i]->vertex[0]->z,
	1134
	1135	vesicle->tlist->tria[i]->vertex[1]->x,
	1136	vesicle->tlist->tria[i]->vertex[1]->y,
	1137	vesicle->tlist->tria[i]->vertex[1]->z,
	1138
	1139	vesicle->tlist->tria[i]->vertex[2]->x,
	1140	vesicle->tlist->tria[i]->vertex[2]->y,
	1141	vesicle->tlist->tria[i]->vertex[2]->z
	1142	);
	1143	}
	1144
	1145	fclose(fh);
	1146	return TS_SUCCESS;
	1147	}
	1148
	1149
1ab449	1150	ts_tape parsetape(char filename){
698ae1	1151	FILE *fd = fopen (filename, "r");
SP	1152	long length;
	1153	size_t size;
	1154	fseek (fd, 0, SEEK_END);
	1155	length = ftell (fd);
	1156	fseek (fd, 0, SEEK_SET);
	1157	size=fread (tapetxt, 1, length, fd);
	1158	fclose(fd);
	1159	if(size);
	1160	ts_tape *tape=parsetapebuffer(tapetxt);
	1161	return tape;
	1162	}
	1163
	1164	ts_tape parsetapebuffer(char buffer){
1ab449	1165	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1166	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1167
d7639a	1168	cfg_opt_t opts[] = {
1ab449	1169	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1170	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1171	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1172	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1173	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	1174	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	1175	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1176	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1177	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1178	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1179	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1180	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1181	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1182	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1183	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1184	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1185	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	1186	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	1187	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	1188	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1189	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1190	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1191	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1192	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1193	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1194	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1195	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1196	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1197	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	1198	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	1199	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	1200	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	1201	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1202	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1203	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	1204	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	1205	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	1206	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	1207	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	1208	/* Variables related to plane confinement */
514ebc	1209	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	1210	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	1211	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	1212	/* Variables related to stretching */
36bc6d	1213	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	1214	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	1215	CFG_END()
SP	1216	};
	1217	cfg_t *cfg;
	1218	ts_uint retval;
	1219	cfg = cfg_init(opts, 0);
698ae1	1220	retval=cfg_parse_buf(cfg, buffer);
514ebc	1221	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	1222	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	1223	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	1224
d7639a	1225	if(retval==CFG_FILE_ERROR){
a6b1b5	1226	fatal("No tape file.",100);
d7639a	1227	}
SP	1228	else if(retval==CFG_PARSE_ERROR){
	1229	fatal("Invalid tape!",100);
	1230	}
a2db52	1231
7b0c07	1232	/* here we override all values read from tape with values from commandline*/
SP	1233	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1234	cfg_free(cfg);
40aa5b	1235
SP	1236
1ab449	1237	/* global variables are set automatically */
SP	1238	quiet=tape->quiet;
	1239	return tape;
	1240	}
d7639a	1241
1ab449	1242	ts_bool tape_free(ts_tape *tape){
SP	1243	free(tape->multiprocessing);
	1244	free(tape);
	1245	return TS_SUCCESS;
d7639a	1246	}
f74313	1247
SP	1248
7b0c07	1249
SP	1250	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1251
	1252	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	1253	operator[0]=0;
SP	1254	operator[1]=0;
7b0c07	1255	ts_uint i,j;
SP	1256	commands=(char )malloc(10000sizeof(char));
	1257	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1258	strcpy(commands,opts);
	1259	for(i=0; ;i++, commands=NULL){
	1260	//breaks comma separated list of commands into specific commands.
	1261	command=strtok_r(commands,",",&saveptr);
	1262	if(command==NULL) break;
	1263	// fprintf(stdout,"Command %d: %s\n",i,command);
	1264	//extracts name of command and value of command into operator[2] array.
	1265	for(j=0; j<2;j++,command=NULL){
	1266	operator[j]=strtok_r(command,"=",&saveopptr);
	1267	if(operator[j]==NULL) break;
	1268	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1269	}
	1270	//1. check: must have 2 operators.
	1271	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1272
	1273	// cfg_setstr(cfg,operator[0],operator[1]);
	1274	cmdline_to_tape(cfg,operator[0],operator[1]);
	1275	//2. check: must be named properly.
	1276	//3. check: must be of right format (integer, double, string, ...)
	1277
	1278	}
	1279	free(backup);
	1280	return TS_SUCCESS;
	1281	}
	1282
	1283
	1284	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1285
	1286	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1287	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1288	switch (cfg_opt->type){
	1289	case CFGT_INT:
	1290	cfg_setint(cfg,key,atol(val));
	1291	break;
	1292	case CFGT_FLOAT:
	1293	cfg_setfloat(cfg,key,atof(val));
	1294	break;
	1295	/* case CFGT_BOOL:
	1296	cfg_setbool(cfg,operator[0],operator[1]);
	1297	break; */
	1298	case CFGT_STR:
	1299	cfg_setstr(cfg,key,val);
	1300	break;
	1301	default:
	1302	break;
	1303
	1304	}
	1305	return TS_SUCCESS;
	1306	}
	1307
	1308
	1309
f74313	1310	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1311	FILE *fh;
	1312	ts_uint i, nvtx,nedges,ntria;
	1313	ts_uint vtxi1,vtxi2;
	1314	float x,y,z;
	1315	ts_vertex_list *vlist;
	1316	fh=fopen(fname, "r");
	1317	if(fh==NULL){
	1318	err("Cannot open file for reading... Nonexistant file?");
	1319	return TS_FAIL;
	1320	}
	1321	ts_uint retval;
	1322	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1323	vesicle->vlist=init_vertex_list(nvtx);
	1324	vlist=vesicle->vlist;
	1325	for(i=0;i<nvtx;i++){
8f6a69	1326	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1327	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1328	vlist->vtx[i]->x=x;
SP	1329	vlist->vtx[i]->y=y;
	1330	vlist->vtx[i]->z=z;
f74313	1331	}
SP	1332	for(i=0;i<nedges;i++){
	1333	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1334	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1335	}
	1336	//TODO: neighbours from bonds,
	1337	//TODO: triangles from neigbours
	1338
	1339	// Don't need to read triangles. Already have enough data
	1340	/*
	1341	for(i=0;i<ntria;i++){
	1342	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1343	vtxi1=vesicle->blist->vertex1->idx;
SP	1344	vtxi2=vesicle->blist->vertex1->idx;
f74313	1345
SP	1346	}
	1347	*/
41a035	1348	if(retval);
f74313	1349	fclose(fh);
SP	1350
	1351
	1352
	1353	return TS_SUCCESS;
	1354	}