trisurf-ng.git - Gitblit

Samo Penic

2020-04-13 2a1e3d528265c3d366dab9ad4b0c4d3d65e1c4ed

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);
2a1e3d	427	//THIS IS HARDCODED IN CELL.C NOW
SP	428	// vesicle->clist->max_occupancy=16;
47a7ac	429	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	430	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	431	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	432	if(retval);
SP	433	fclose(fh);
	434	return vesicle;
	435	}
	436
	437
	438
083e03	439	ts_bool parse_args(int argc, char **argv){
3f5c83	440	int c, retval;
SP	441	struct stat sb;
	442	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	443	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	444	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	445	sprintf(command_line_args.tape_fullfilename,"tape");
1bf3c3	446	sprintf(command_line_args.tape_templatefull,"./tape");
3f5c83	447	FILE *file;
SP	448
083e03	449	while (1)
SP	450	{
	451	static struct option long_options[] =
	452	{
8a6614	453	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	454	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	455	{"tape", no_argument, 0, 't'},
fd8126	456	{"version", no_argument, 0, 'v'},
083e03	457	{"output-file", required_argument, 0, 'o'},
SP	458	{"directory", required_argument, 0, 'd'},
3f5c83	459	{"dump-filename", required_argument,0, 'f'},
7b0c07	460	{"tape-options",required_argument,0,'c'},
1bf3c3	461	{"tape-template", required_argument,0,0},
ab798b	462	{"restore-from-vtk",required_argument,0,0},
083e03	463	{0, 0, 0, 0}
SP	464	};
	465	/* getopt_long stores the option index here. */
	466	int option_index = 0;
	467
fd8126	468	c = getopt_long (argc, argv, "d:f:o:t:c:v",
083e03	469	long_options, &option_index);
SP	470
	471	/* Detect the end of the options. */
	472	if (c == -1)
	473	break;
	474
	475	switch (c)
	476	{
	477	case 0:
	478	/* If this option set a flag, do nothing else now. */
	479	if (long_options[option_index].flag != 0)
	480	break;
1bf3c3	481	/* printf ("option %s", long_options[option_index].name);
083e03	482	if (optarg)
1bf3c3	483	printf (" with arg %s", optarg);
SP	484	printf ("\n"); */
	485	//TODO: find a better way.
	486	if(strcmp(long_options[option_index].name,"tape-template")==0){
	487	strcpy(command_line_args.tape_templatefull,optarg);
	488	}
ab798b	489	if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
ee84bd	490	strcpy(command_line_args.dump_from_vtk,optarg);
SP	491	}
083e03	492	break;
fd8126	493	case 'v':
SP	494	fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	495	fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
	496	fprintf(stdout,"Released under terms of GPLv3\n");
	497	exit(0);
083e03	498
7b0c07	499	case 'c':
SP	500	strcpy(command_line_args.tape_opts,optarg);
	501	break;
	502	case 't': //tape
3f5c83	503	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	504	break;
SP	505
7b0c07	506	case 'o': //set filename of master pvd output file
3f5c83	507	strcpy(command_line_args.output_fullfilename, optarg);
SP	508	break;
083e03	509
SP	510	case 'd':
	511	//check if directory exists. If not create one. If creation is
	512	//successful, set directory for output files.
	513	//printf ("option -d with value `%s'\n", optarg);
3f5c83	514	if (stat(optarg, &sb) == -1) {
SP	515	//directory does not exist
083e03	516	retval=mkdir(optarg, 0700);
SP	517	if(retval){
3f5c83	518	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	519	}
SP	520	}
3f5c83	521	//check if is a proper directory
SP	522	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	523	//it is not a directory. fatal error.
	524	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	525	fatal("Cannot continue",1);
083e03	526	}
3f5c83	527	strcpy(command_line_args.path, optarg);
083e03	528	break;
SP	529
	530	case 'f':
3f5c83	531	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	532	break;
SP	533
	534	case '?':
	535	/* getopt_long already printed an error message. */
ba73ab	536	print_help(stdout);
SP	537	//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
083e03	538	fatal("Ooops, read help first",1);
SP	539	break;
	540
	541	default:
	542	exit (1);
	543	}
	544	}
	545
7b0c07	546	//Here we set correct values for full filenames!
SP	547	char buffer=(char )malloc(10000*sizeof(char));
	548	//correct the path and add trailing /
	549	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	550
	551	/* master pvd output file */
	552	strcpy(buffer,command_line_args.path);
	553	strcat(buffer,command_line_args.output_fullfilename);
	554	if ((file = fopen(buffer, "w")) == NULL) {
	555	fprintf(stderr,"Could not create output file %s!\n", buffer);
	556	fatal("Please specify correct output file or check permissions of the file",1);
1bf3c3	557	//there is a tape template. make a copy into desired directory
7b0c07	558
SP	559	} else {
	560	fclose(file);
	561	strcpy(command_line_args.output_fullfilename,buffer);
	562	}
	563
	564	/* tape file */
	565	strcpy(buffer,command_line_args.path);
	566	strcat(buffer,command_line_args.tape_fullfilename);
	567	if (stat(buffer, &sb) == -1) {
1bf3c3	568
SP	569	//tape does not exist. does tape template exist?
	570	if(stat(command_line_args.tape_templatefull, &sb)==-1){
	571	ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
	572	fatal("Please select correct tape or check permissions of the file",1);
	573	} else {
	574	//tape template found
	575	fatal("Samo did not program template copy yet",1);
	576	}
7b0c07	577	} else {
SP	578	strcpy(command_line_args.tape_fullfilename,buffer);
	579	}
	580
	581
	582	/* dump file */
	583	strcpy(buffer,command_line_args.path);
	584	strcat(buffer,command_line_args.dump_fullfilename);
	585	//check if dump file exist first.
	586	if (stat(buffer, &sb) == -1) {
	587	//no dump file. check if we can create one.
	588	if ((file = fopen(buffer, "w")) == NULL) {
	589	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	590	fatal("Please specify correct dump file or check permissions of the file",1);
	591	} else {
	592	fclose(file);
	593	//good, file is writeable. delete it for now.
	594	remove(buffer);
	595	}
	596	}
	597	strcpy(command_line_args.dump_fullfilename, buffer);
	598
	599
	600	free(buffer);
083e03	601	return TS_SUCCESS;
SP	602
	603	}
	604
	605
ba73ab	606	ts_bool print_help(FILE *fd){
SP	607	fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	608	fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
	609	fprintf(fd,"Released under terms of GPLv3\n\n");
	610
	611	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");
	612	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");
	613	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");
	614	fprintf(fd,"Flags:\n\n");
	615	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");
	616	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	617	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
ba73ab	618	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
SP	619	fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
	620	fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
c4178c	621	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
SP	622	fprintf(fd,"Examples:\n\n");
	623	fprintf(fd,"trisurf --force-from-tape\n");
	624	fprintf(fd,"trisurf --reset-iteration-count\n");
	625	fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
	626	fprintf(fd,"\n\n");
	627
ba73ab	628	return TS_SUCCESS;
SP	629	}
	630
	631
083e03	632
d7639a	633	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	634	ts_uint i;
	635	printf("Number of vertices: %u\n",vlist->n);
	636	for(i=0;i<vlist->n;i++){
a6b1b5	637	printf("%u: %f %f %f\n",
8f6a69	638	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	639	}
SP	640	return TS_SUCCESS;
	641	}
	642
	643	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	644	ts_uint i,j;
a6b1b5	645	ts_vertex **vtx=vlist->vtx;
d7639a	646	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	647	for(i=0;i<vlist->n;i++){
8f6a69	648	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	649	for(j=0;j<vtx[i]->neigh_no;j++){
	650	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	651	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	652	}
SP	653	printf("\n");
	654	}
	655
	656	return TS_SUCCESS;
	657	}
	658
	659	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	660	ts_vertex **vtx=vlist->vtx;
d7639a	661	ts_uint i;
SP	662	FILE *fh;
	663
	664	fh=fopen(filename, "w");
	665	if(fh==NULL){
	666	err("Cannot open file %s for writing");
	667	return TS_FAIL;
	668	}
	669	for(i=0;i<vlist->n;i++)
8f6a69	670	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	671
SP	672	fclose(fh);
	673	return TS_SUCCESS;
	674	}
	675
	676
	677	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	678	ts_uint i,j;
	679	for(i=0;i<vlist->n;i++){
8f6a69	680	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	681	vlist->vtx[i]->y, vlist->vtx[i]->z,
	682	vlist->vtx[i]->neigh_no);
	683	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	684	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	685	//-vlist->vtx+1));
d7639a	686	}
SP	687	fprintf(fh,"\n");
	688	}
	689	return TS_SUCCESS;
	690	}
	691
	692	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	693	ts_uint i,j;
a6b1b5	694	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	695	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	696	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	697	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	698	}
SP	699	fprintf(fh,"\n");
	700	}
	701	return TS_SUCCESS;
	702	}
	703
	704	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	705	ts_triangle_list *tlist=vesicle->tlist;
d7639a	706	ts_uint i,j;
SP	707	for(i=0;i<tlist->n;i++){
41a035	708	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	709	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	710	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	711	}
SP	712	fprintf(fh,"\n");
	713	for(j=0;j<3;j++){
41a035	714	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	715	}
SP	716	fprintf(fh,"\n");
41a035	717	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	718	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	719	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	720	}
	721	return TS_SUCCESS;
	722	}
	723
	724	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	725	ts_uint i,j;
	726	for(i=0;i<vlist->n;i++){
	727	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	728	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	729	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	730	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	731	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	732	}
SP	733	fprintf(fh,"\n");
cef6ca	734	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	735	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	736	}
SP	737	fprintf(fh,"\n");
	738	}
	739	return TS_SUCCESS;
	740	}
	741
	742	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	743	ts_uint i;
a6b1b5	744	for(i=0;i<vesicle->blist->n;i++){
e016c4	745	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	746	//-vesicle->vlist->vtx+1),
e016c4	747	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	748	//-vesicle->vlist.vtx+1));
d7639a	749	}
SP	750	return TS_SUCCESS;
	751	}
	752
	753
	754
	755	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	756	FILE *fh;
	757	char line[255];
	758	fh=fopen(filename, "r");
	759	if(fh==NULL){
	760	err("Cannot open file for reading... Nonexistant file?");
	761	return TS_FAIL;
	762	}
a6b1b5	763	ts_uint retval=1;
d7639a	764	while(retval!=EOF){
SP	765	retval=fscanf(fh,"%s",line);
	766
	767	fprintf(stderr,"%s",line);
	768	}
	769	fclose(fh);
	770	return TS_SUCCESS;
	771	}
	772
	773	ts_bool write_master_xml_file(ts_char *filename){
	774	FILE *fh;
	775	ts_char i,j;
	776	ts_uint tstep;
	777	ts_char *number;
	778	fh=fopen(filename, "w");
	779	if(fh==NULL){
	780	err("Cannot open file %s for writing");
	781	return TS_FAIL;
	782	}
	783
	784	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
267db5	785	DIR *dir = opendir(command_line_args.path);
d7639a	786	if(dir){
SP	787	struct dirent *ent;
	788	tstep=0;
	789	while((ent = readdir(dir)) != NULL)
	790	{
	791	i=rindex(ent->d_name,'.');
	792	if(i==NULL) continue;
	793	if(strcmp(i+1,"vtu")==0){
	794	j=rindex(ent->d_name,'_');
	795	if(j==NULL) continue;
	796	number=strndup(j+1,j-i);
a6b1b5	797	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	798	tstep++;
SP	799	free(number);
	800	}
	801	}
	802	}
f74313	803	free(dir);
d7639a	804	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	805	fclose(fh);
	806	return TS_SUCCESS;
	807	}
	808
0a2c81	809	ts_bool write_vertex_xml_file(ts_vesicle vesicle, ts_uint timestepno, ts_cluster_list cstlist){
a6b1b5	810	ts_vertex_list *vlist=vesicle->vlist;
SP	811	ts_bond_list *blist=vesicle->blist;
	812	ts_vertex **vtx=vlist->vtx;
40aa5b	813	ts_uint i,j;
13d445	814	//ts_double senergy=0.0;
267db5	815	char filename[10000];
SP	816	char just_name[255];
d7639a	817	FILE *fh;
267db5	818	strcpy(filename,command_line_args.path);
SP	819	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	820	strcat(filename,just_name);
d7639a	821
SP	822	fh=fopen(filename, "w");
	823	if(fh==NULL){
	824	err("Cannot open file %s for writing");
	825	return TS_FAIL;
	826	}
	827	/* Here comes header of the file */
40aa5b	828
SP	829	//find number of extra vtxs and bonds of polymeres
58230a	830	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	831	ts_bool poly=0, fil=0;
40aa5b	832	if(vesicle->poly_list!=NULL){
2a1e3d	833	if(vesicle->poly_list->n!=0){
SP	834	//if(vesicle->poly_list->poly[0]!=NULL){
40aa5b	835	polyno=vesicle->poly_list->n;
SP	836	monono=vesicle->poly_list->poly[0]->vlist->n;
	837	poly=1;
	838	}
	839	}
58230a	840
M	841	if(vesicle->filament_list!=NULL){
2a1e3d	842	if(vesicle->filament_list->n!=0){
SP	843	//if(vesicle->filament_list->poly[0]!=NULL){
58230a	844	filno=vesicle->filament_list->n;
M	845	fonono=vesicle->filament_list->poly[0]->vlist->n;
	846	fil=1;
	847	}
	848	}
	849
854cb6	850	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	851	xml_trisurf_data(fh,vesicle);
	852	fprintf(fh, " <UnstructuredGrid>\n");
8db203	853	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n);
5c64e2	854	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
d7639a	855	for(i=0;i<vlist->n;i++){
a6b1b5	856	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	857	}
40aa5b	858	//polymeres
SP	859	if(poly){
3c1ac1	860	poly_idx=vlist->n;
40aa5b	861	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	862	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	863	fprintf(fh,"%u ", poly_idx);
M	864	}
	865	}
	866	}
	867	//filaments
	868	if(fil){
	869	poly_idx=vlist->n+monono*polyno;
	870	for(i=0;i<vesicle->filament_list->n;i++){
	871	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	872	// fprintf(stderr,"was here\n");
3c1ac1	873	fprintf(fh,"%u ", poly_idx);
40aa5b	874	}
SP	875	}
	876	}
d7639a	877
45c708	878	fprintf(fh,"</DataArray>\n");
0a2c81	879	if(cstlist!=NULL){
SP	880	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	881	for(i=0;i<vlist->n;i++){
	882	if(vtx[i]->cluster!=NULL){
	883	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	884	} else {
	885	fprintf(fh,"-1 ");
	886	}
	887	}
	888	//polymeres
	889	if(poly){
	890	poly_idx=vlist->n;
	891	for(i=0;i<vesicle->poly_list->n;i++){
	892	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	893	fprintf(fh,"-1 ");
	894	}
	895	}
	896	}
	897	//filaments
	898	if(fil){
	899	poly_idx=vlist->n+monono*polyno;
	900	for(i=0;i<vesicle->filament_list->n;i++){
	901	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	902	// fprintf(stderr,"was here\n");
	903	fprintf(fh,"-1 ");
	904	}
	905	}
	906	}
	907
	908	fprintf(fh,"</DataArray>\n");
	909
	910
	911	}
	912
45c708	913	//here comes additional data as needed. Currently only spontaneous curvature
SP	914	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	915	for(i=0;i<vlist->n;i++){
	916	fprintf(fh,"%.17e ",vtx[i]->c);
	917	}
	918	//polymeres
	919	if(poly){
	920	poly_idx=vlist->n;
	921	for(i=0;i<vesicle->poly_list->n;i++){
	922	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	923	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	924	}
	925	}
	926	}
	927	//filaments
	928	if(fil){
	929	poly_idx=vlist->n+monono*polyno;
	930	for(i=0;i<vesicle->filament_list->n;i++){
	931	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	932	// fprintf(stderr,"was here\n");
	933	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	934	}
	935	}
	936	}
	937	fprintf(fh,"</DataArray>\n");
	938
5c64e2	939	//here comes additional data. Energy!
SP	940	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	941	for(i=0;i<vlist->n;i++){
	942	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	943	}
	944	//polymeres
	945	if(poly){
	946	poly_idx=vlist->n;
	947	for(i=0;i<vesicle->poly_list->n;i++){
	948	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	949	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	950	}
	951	}
	952	}
	953	//filaments
	954	if(fil){
	955	poly_idx=vlist->n+monono*polyno;
	956	for(i=0;i<vesicle->filament_list->n;i++){
	957	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	958	// fprintf(stderr,"was here\n");
	959	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	960	}
	961	}
	962	}
	963	fprintf(fh,"</DataArray>\n");
	964
45c708	965
13d445	966	fprintf(fh,"</PointData>\n<CellData>\n");
SP	967
7ec6fb	968	if(vesicle->tape->stretchswitch==1){
SP	969	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	970	for(i=0;i<blist->n;i++){
SP	971	fprintf(fh, "0.0 ");
	972	}
	973	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	974	fprintf(fh,"0.0 ");
7ec6fb	975	}
13d445	976	for(i=0;i<vesicle->tlist->n;i++){
SP	977	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	978	}
7ec6fb	979	fprintf(fh,"</DataArray>\n");
SP	980	}
45c708	981
13d445	982
SP	983
	984	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	985	for(i=0;i<vlist->n;i++){
aad500	986	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	987	}
SP	988	//polymeres
	989	if(poly){
	990	for(i=0;i<vesicle->poly_list->n;i++){
	991	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	992	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	993	}
M	994	}
	995	}
	996	//filaments
	997	if(fil){
	998	for(i=0;i<vesicle->filament_list->n;i++){
	999	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	1000	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	1001	}
SP	1002	}
d7639a	1003	}
SP	1004
	1005	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	1006	for(i=0;i<blist->n;i++){
e016c4	1007	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1008	}
40aa5b	1009	//polymeres
SP	1010	if(poly){
3c1ac1	1011	poly_idx=vlist->n;
40aa5b	1012	for(i=0;i<vesicle->poly_list->n;i++){
SP	1013	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	1014	// 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	1015	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	1016	}
SP	1017	//grafted bonds
3c1ac1	1018	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	1019	}
SP	1020
	1021	}
	1022
58230a	1023	//filaments
M	1024	if(fil){
	1025	poly_idx=vlist->n+monono*polyno;
	1026	for(i=0;i<vesicle->filament_list->n;i++){
	1027	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	1028	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);
	1029	// fprintf(stderr,"was here\n");
	1030
	1031	}
	1032	}
	1033
	1034	}
8db203	1035	for(i=0;i<vesicle->tlist->n;i++){
SP	1036	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);
	1037	}
d7639a	1038	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	1039	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	1040	fprintf(fh,"%u ",i);
SP	1041	}
8db203	1042	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	1043	fprintf(fh,"%u ", j);
	1044	}
d7639a	1045	fprintf(fh,"\n");
SP	1046	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	1047	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	1048	fprintf(fh,"3 ");
SP	1049	}
8db203	1050	for(i=0;i<vesicle->tlist->n;i++){
SP	1051	fprintf(fh,"5 ");
	1052	}
d7639a	1053	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	1054	fclose(fh);
	1055	return TS_SUCCESS;
	1056
	1057	}
	1058
	1059	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	1060	ts_vertex_list *vlist=vesicle->vlist;
SP	1061	ts_bond_list *blist=vesicle->blist;
	1062	ts_vertex **vtx=vlist->vtx;
	1063	ts_uint i;
d7639a	1064	FILE *fh;
SP	1065
	1066	fh=fopen(filename, "w");
	1067	if(fh==NULL){
	1068	err("Cannot open file %s for writing");
	1069	return TS_FAIL;
	1070	}
	1071	/* Here comes header of the file */
	1072	// fprintf(stderr,"NSHELL=%u\n",nshell);
	1073	fprintf(fh, "# vtk DataFile Version 2.0\n");
	1074	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	1075	fprintf(fh, "%s\n", text);
	1076	fprintf(fh,"ASCII\n");
	1077	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	1078	fprintf(fh,"POINTS %u double\n", vlist->n);
	1079	for(i=0;i<vlist->n;i++){
8f6a69	1080	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	1081	}
SP	1082
	1083	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	1084	for(i=0;i<blist->n;i++){
e016c4	1085	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1086	}
SP	1087	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	1088	for(i=0;i<blist->n;i++)
	1089	fprintf(fh,"3\n");
	1090
	1091	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	1092	fprintf(fh,"SCALARS scalars long 1\n");
	1093	fprintf(fh,"LOOKUP_TABLE default\n");
	1094
	1095	for(i=0;i<vlist->n;i++)
8f6a69	1096	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	1097
SP	1098	fclose(fh);
	1099	return TS_SUCCESS;
	1100	}
	1101
	1102
	1103
144784	1104	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	1105	FILE *fh;
	1106	ts_uint i;
	1107
	1108	fh=fopen(filename, "w");
	1109	if(fh==NULL){
	1110	err("Cannot open file %s for writing");
	1111	return TS_FAIL;
	1112	}
	1113
	1114	for(i=0;i<vesicle->tlist->n;i++){
	1115
	1116	fprintf(fh,"\ttriangle {");
	1117	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1118	vesicle->tlist->tria[i]->vertex[0]->x,
	1119	vesicle->tlist->tria[i]->vertex[0]->y,
	1120	vesicle->tlist->tria[i]->vertex[0]->z,
	1121
	1122	vesicle->tlist->tria[i]->vertex[1]->x,
	1123	vesicle->tlist->tria[i]->vertex[1]->y,
	1124	vesicle->tlist->tria[i]->vertex[1]->z,
	1125
	1126	vesicle->tlist->tria[i]->vertex[2]->x,
	1127	vesicle->tlist->tria[i]->vertex[2]->y,
	1128	vesicle->tlist->tria[i]->vertex[2]->z
	1129	);
	1130	}
	1131
	1132	fclose(fh);
	1133	return TS_SUCCESS;
	1134	}
	1135
	1136
1ab449	1137	ts_tape parsetape(char filename){
698ae1	1138	FILE *fd = fopen (filename, "r");
SP	1139	long length;
	1140	size_t size;
	1141	fseek (fd, 0, SEEK_END);
	1142	length = ftell (fd);
	1143	fseek (fd, 0, SEEK_SET);
	1144	size=fread (tapetxt, 1, length, fd);
	1145	fclose(fd);
	1146	if(size);
	1147	ts_tape *tape=parsetapebuffer(tapetxt);
	1148	return tape;
	1149	}
	1150
	1151	ts_tape parsetapebuffer(char buffer){
1ab449	1152	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1153	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1154
d7639a	1155	cfg_opt_t opts[] = {
1ab449	1156	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1157	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1158	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1159	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1160	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	1161	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	1162	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1163	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1164	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1165	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1166	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1167	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1168	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1169	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1170	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1171	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1172	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	1173	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	1174	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	1175	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1176	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1177	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1178	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1179	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1180	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1181	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1182	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1183	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1184	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	1185	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	1186	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	1187	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	1188	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1189	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1190	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	1191	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	1192	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	1193	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	1194	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	1195	/* Variables related to plane confinement */
514ebc	1196	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	1197	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	1198	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	1199	/* Variables related to stretching */
36bc6d	1200	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	1201	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	1202	CFG_END()
SP	1203	};
	1204	cfg_t *cfg;
	1205	ts_uint retval;
	1206	cfg = cfg_init(opts, 0);
698ae1	1207	retval=cfg_parse_buf(cfg, buffer);
514ebc	1208	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	1209	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	1210	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	1211
d7639a	1212	if(retval==CFG_FILE_ERROR){
a6b1b5	1213	fatal("No tape file.",100);
d7639a	1214	}
SP	1215	else if(retval==CFG_PARSE_ERROR){
	1216	fatal("Invalid tape!",100);
	1217	}
a2db52	1218
7b0c07	1219	/* here we override all values read from tape with values from commandline*/
SP	1220	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1221	cfg_free(cfg);
40aa5b	1222
SP	1223
1ab449	1224	/* global variables are set automatically */
SP	1225	quiet=tape->quiet;
	1226	return tape;
	1227	}
d7639a	1228
1ab449	1229	ts_bool tape_free(ts_tape *tape){
SP	1230	free(tape->multiprocessing);
	1231	free(tape);
	1232	return TS_SUCCESS;
d7639a	1233	}
f74313	1234
SP	1235
7b0c07	1236
SP	1237	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1238
	1239	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	1240	operator[0]=0;
SP	1241	operator[1]=0;
7b0c07	1242	ts_uint i,j;
SP	1243	commands=(char )malloc(10000sizeof(char));
	1244	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1245	strcpy(commands,opts);
	1246	for(i=0; ;i++, commands=NULL){
	1247	//breaks comma separated list of commands into specific commands.
	1248	command=strtok_r(commands,",",&saveptr);
	1249	if(command==NULL) break;
	1250	// fprintf(stdout,"Command %d: %s\n",i,command);
	1251	//extracts name of command and value of command into operator[2] array.
	1252	for(j=0; j<2;j++,command=NULL){
	1253	operator[j]=strtok_r(command,"=",&saveopptr);
	1254	if(operator[j]==NULL) break;
	1255	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1256	}
	1257	//1. check: must have 2 operators.
	1258	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1259
	1260	// cfg_setstr(cfg,operator[0],operator[1]);
	1261	cmdline_to_tape(cfg,operator[0],operator[1]);
	1262	//2. check: must be named properly.
	1263	//3. check: must be of right format (integer, double, string, ...)
	1264
	1265	}
	1266	free(backup);
	1267	return TS_SUCCESS;
	1268	}
	1269
	1270
	1271	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1272
	1273	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1274	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1275	switch (cfg_opt->type){
	1276	case CFGT_INT:
	1277	cfg_setint(cfg,key,atol(val));
	1278	break;
	1279	case CFGT_FLOAT:
	1280	cfg_setfloat(cfg,key,atof(val));
	1281	break;
	1282	/* case CFGT_BOOL:
	1283	cfg_setbool(cfg,operator[0],operator[1]);
	1284	break; */
	1285	case CFGT_STR:
	1286	cfg_setstr(cfg,key,val);
	1287	break;
	1288	default:
	1289	break;
	1290
	1291	}
	1292	return TS_SUCCESS;
	1293	}
	1294
	1295
	1296
f74313	1297	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1298	FILE *fh;
	1299	ts_uint i, nvtx,nedges,ntria;
	1300	ts_uint vtxi1,vtxi2;
	1301	float x,y,z;
	1302	ts_vertex_list *vlist;
	1303	fh=fopen(fname, "r");
	1304	if(fh==NULL){
	1305	err("Cannot open file for reading... Nonexistant file?");
	1306	return TS_FAIL;
	1307	}
	1308	ts_uint retval;
	1309	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1310	vesicle->vlist=init_vertex_list(nvtx);
	1311	vlist=vesicle->vlist;
	1312	for(i=0;i<nvtx;i++){
8f6a69	1313	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1314	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1315	vlist->vtx[i]->x=x;
SP	1316	vlist->vtx[i]->y=y;
	1317	vlist->vtx[i]->z=z;
f74313	1318	}
SP	1319	for(i=0;i<nedges;i++){
	1320	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1321	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1322	}
	1323	//TODO: neighbours from bonds,
	1324	//TODO: triangles from neigbours
	1325
	1326	// Don't need to read triangles. Already have enough data
	1327	/*
	1328	for(i=0;i<ntria;i++){
	1329	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1330	vtxi1=vesicle->blist->vertex1->idx;
SP	1331	vtxi2=vesicle->blist->vertex1->idx;
f74313	1332
SP	1333	}
	1334	*/
41a035	1335	if(retval);
f74313	1336	fclose(fh);
SP	1337
	1338
	1339
	1340	return TS_SUCCESS;
	1341	}