trisurf-ng.git - Gitblit

mihaf

2014-03-19 b30f45332934a27d267bac995eb6a94cc7cf5d9d

commit \| author \| age
f74313	1	#include "general.h"
d7639a	2	#include<stdio.h>
SP	3	#include "io.h"
f74313	4	#include <confuse.h>
SP	5	#include "vertex.h"
	6	#include "bond.h"
d7639a	7	#include<string.h>
a6b1b5	8	#include<stdlib.h>
d7639a	9	#include <sys/types.h>
SP	10	#include <dirent.h>
b14a8d	11	#include "initial_distribution.h"
a2db52	12	#include "poly.h"
d7639a	13
083e03	14	#include <getopt.h>
SP	15	#include <sys/stat.h>
	16	#include <sys/types.h>
	17	#include <dirent.h>
	18	#include <errno.h>
e9eab4	19	/ DUMP STATE TO DISK DRIVE /
SP	20
1ab449	21	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	22
SP	23	/* save current state with wrong pointers. Will fix that later */
	24	ts_uint i,j,k;
	25	FILE *fh=fopen("dump.bin","wb");
	26
	27	/* dump vesicle */
86f5e7	28	fwrite(vesicle, sizeof(ts_vesicle),1,fh);
e9eab4	29	/* dump vertex list */
SP	30	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	31	/* dump bond list */
	32	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	33	/* dump triangle list */
	34	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	35	/* dump cell list */
	36	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	37	/* dump poly list */
	38	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
	39	/* level 1 complete */
	40
	41	/dump vertices/
	42	for(i=0;i<vesicle->vlist->n;i++){
	43	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	44	/* dump pointer offsets for:
	45	neigh
	46	bond
	47	tria
	48	cell is ignored
	49	*/
	50	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	51	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	52	}
SP	53	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	54	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	55	}
SP	56	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	57	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	58	}
SP	59	}
	60
	61	/dump bonds/
	62	for(i=0;i<vesicle->blist->n;i++){
	63	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	64	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	65	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	66	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	67	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	68	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	69	}
SP	70
	71	/dump triangles/
	72	for(i=0;i<vesicle->tlist->n;i++){
	73	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	74	/* dump pointer offsets for vertex */
3c1ac1	75	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	76	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	77	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	78	/* dump pointer offsets for neigh */
SP	79	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	80	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	81	}
SP	82	}
	83
	84
	85	/dump polymeres /
	86	for(i=0;i<vesicle->poly_list->n;i++){
	87	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	88	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	89	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	90	}
SP	91
	92	/* dump poly vertex(monomer) list*/
	93	for(i=0;i<vesicle->poly_list->n;i++){
	94	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	95	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	96	/* dump offset for neigh and bond */
	97	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	98	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	99	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	100	}
SP	101	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	102	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	103	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	104	}
SP	105	}
3c1ac1	106	// grafted vtx on vesicle data dump
SP	107	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	108	}
SP	109	/* dump poly bonds between monomers list*/
	110	for(i=0;i<vesicle->poly_list->n;i++){
	111	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	112	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	113	/* dump vtx1 and vtx2 offsets */
3c1ac1	114	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	115	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	116	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	117	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	118	}
SP	119	}
	120
	121	/* pointer offsets for fixing the restored pointers */
	122	/* need pointers for
	123	vlist->vtx
	124	blist->bond
	125	tlist->tria
	126	clist->cell
	127	poly_list->poly
	128	and for each poly:
	129	poly_list->poly->vtx
	130	poly_list->poly->bond
	131	*/
	132
063289	133	fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
1ab449	134
SP	135	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	136	fclose(fh);
SP	137	return TS_SUCCESS;
	138	}
	139
	140
	141	/ RESTORE DUMP FROM DISK /
1ab449	142	ts_vesicle restore_state(ts_uint iteration){
e9eab4	143	ts_uint i,j,k;
SP	144	FILE *fh=fopen("dump.bin","rb");
3f5c83	145
SP	146	struct stat sb;
	147	if (stat("dump.bin", &sb) == -1) {
	148	//dump file does not exist.
	149	return NULL;
	150	}
	151
	152	//check if it is regular file
	153	if((sb.st_mode & S_IFMT) != S_IFREG) {
	154	//dump file is not a regular file.
	155	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	156	return NULL;
	157	}
	158
e9eab4	159	ts_uint retval;
3c1ac1	160	ts_uint idx;
e9eab4	161
SP	162	/* we restore all the data from the dump */
	163	/* restore vesicle */
	164	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
86f5e7	165	retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
SP	166	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
	167
e9eab4	168	/* restore vertex list */
SP	169	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	170	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	171	/* restore bond list */
	172	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	173	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	174	/* restore triangle list */
	175	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	176	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	177	/* restore cell list */
	178	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	179	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	180	/* restore poly list */
	181	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	182	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
	183	/* level 1 complete */
	184
3c1ac1	185	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	186	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	187	for(i=0;i<vesicle->blist->n;i++){
	188	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	189	}
	190	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	191	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	192	for(i=0;i<vesicle->tlist->n;i++){
	193	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	194	}
a37ba2	195	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	196	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	197	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	198	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	199	}
SP	200	/restore vertices/
	201	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	202	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	203	/restore neigh, bond, tristar. Ignoring cell /
	204	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	205	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	206	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	207	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	208	}
SP	209	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	210	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	211	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	212	/* 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 */
	213	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	214	}
SP	215
	216	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	217	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	218	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	219	/* same comment as above */
	220	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	221	}
SP	222
	223	}
	224
	225	/restore bonds/
3c1ac1	226	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	227	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	228	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	229	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	230	/* restore vtx1 and vtx2 */
3c1ac1	231	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	232	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	233	retval=fread(&idx,sizeof(ts_uint),1,fh);
	234	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	235	}
SP	236
	237	/restore triangles/
3c1ac1	238	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	239	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	240	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	241	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	242	/* restore pointers for vertices */
3c1ac1	243	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	244	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	245	retval=fread(&idx,sizeof(ts_uint),1,fh);
	246	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	247	retval=fread(&idx,sizeof(ts_uint),1,fh);
	248	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	249	/* restore pointers for neigh */
3c1ac1	250	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	251	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	252	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	253	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	254	}
SP	255
	256	}
	257
	258	/restore cells /
	259	/TODO: do we need to recalculate cells here? /
	260	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	261	for(i=0;i<vesicle->clist->cellno;i++){
	262	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	263	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	264	}
	265	*/
	266	/restore polymeres /
	267	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	268	for(i=0;i<vesicle->poly_list->n;i++){
	269	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	270	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	271	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	272	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	273	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	274	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	275	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	276	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	277	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	278	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	279	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	280	}
	281	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	282	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	283	}
	284
e9eab4	285	}
3c1ac1	286
e9eab4	287
SP	288	/* restore poly vertex(monomer) list*/
	289	for(i=0;i<vesicle->poly_list->n;i++){
	290	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	291	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	292
e9eab4	293	/* restore neigh and bonds */
SP	294	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 ));
	295	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	296	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	297	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	298	}
SP	299	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 ));
	300	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	301	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	302	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	303	}
SP	304
	305	}
3c1ac1	306	/* restore grafted vtx on vesicle and grafted_poly */
SP	307	retval=fread(&idx,sizeof(ts_uint),1,fh);
	308	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	309	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	310	}
3c1ac1	311
e9eab4	312	/* restore poly bonds between monomers list*/
SP	313	for(i=0;i<vesicle->poly_list->n;i++){
	314	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	315	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	316	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	317	/* restore vtx1 and vtx2 */
3c1ac1	318	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	319	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	320	retval=fread(&idx,sizeof(ts_uint),1,fh);
	321	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	322	}
SP	323	}
	324
063289	325	// recreating space for cells //
SP	326	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	327	retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
	328	vesicle->clist->cell=(ts_cell *)malloc(sizeof(ts_cell )vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
	329	for(i=0;i<vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]vesicle->clist->ncmax[2];i++){
	330	vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
	331	vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
	332	}
e9eab4	333
1ab449	334	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	335	if(retval);
SP	336	fclose(fh);
	337	return vesicle;
	338	}
	339
	340
	341
083e03	342	ts_bool parse_args(int argc, char **argv){
3f5c83	343	int c, retval;
SP	344	struct stat sb;
	345	sprintf(command_line_args.path, "./"); //clear string;
	346	sprintf(command_line_args.output_fullfilename,"./output.pvd");
	347	sprintf(command_line_args.dump_fullfilename,"./dump.bin");
	348	sprintf(command_line_args.tape_fullfilename,"./tape");
	349	FILE *file;
	350
083e03	351	while (1)
SP	352	{
	353	static struct option long_options[] =
	354	{
8a6614	355	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	356	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	357	{"tape", no_argument, 0, 't'},
SP	358	{"output-file", required_argument, 0, 'o'},
	359	{"directory", required_argument, 0, 'd'},
3f5c83	360	{"dump-filename", required_argument,0, 'f'},
083e03	361	{0, 0, 0, 0}
SP	362	};
	363	/* getopt_long stores the option index here. */
	364	int option_index = 0;
	365
3f5c83	366	c = getopt_long (argc, argv, "d:f:o:t:",
083e03	367	long_options, &option_index);
SP	368
	369	/* Detect the end of the options. */
	370	if (c == -1)
	371	break;
	372
	373	switch (c)
	374	{
	375	case 0:
	376	/* If this option set a flag, do nothing else now. */
	377	if (long_options[option_index].flag != 0)
	378	break;
	379	printf ("option %s", long_options[option_index].name);
	380	if (optarg)
	381	printf (" with arg %s", optarg);
	382	printf ("\n");
	383	break;
	384
	385	case 't':
	386	//check if tape exists. If not, fail immediately.
3f5c83	387	if (stat(optarg, &sb) == -1) {
SP	388	ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
	389	fatal("Please select correct tape",1);
	390	} else {
	391	strcpy(command_line_args.tape_fullfilename,optarg);
	392	}
083e03	393	break;
SP	394
	395	case 'o':
	396	//set filename of master output file
3f5c83	397	if ((file = fopen(optarg, "w")) == NULL) {
SP	398	fprintf(stderr,"Could not create output file!\n");
	399	fatal("Please specify correct output file",1);
	400
	401	} else {
	402	fclose(file);
	403	}
	404	strcpy(command_line_args.output_fullfilename, optarg);
	405	break;
083e03	406
SP	407	case 'd':
	408	//check if directory exists. If not create one. If creation is
	409	//successful, set directory for output files.
	410	//printf ("option -d with value `%s'\n", optarg);
3f5c83	411	if (stat(optarg, &sb) == -1) {
SP	412	//directory does not exist
083e03	413	retval=mkdir(optarg, 0700);
SP	414	if(retval){
3f5c83	415	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	416	}
SP	417	}
3f5c83	418	//check if is a proper directory
SP	419	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	420	//it is not a directory. fatal error.
	421	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	422	fatal("Cannot continue",1);
083e03	423	}
3f5c83	424	strcpy(command_line_args.path, optarg);
083e03	425	break;
SP	426
	427	case 'f':
	428	//check if dump file specified exists. Defaults to dump.bin
3f5c83	429	if ((file = fopen(optarg, "w")) == NULL) {
SP	430	fprintf(stderr,"Could not create dump file!\n");
	431	fatal("Please specify correct dump file",1);
	432
	433	} else {
	434	fclose(file);
	435	}
	436	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	437	break;
SP	438
	439	case '?':
	440	/* getopt_long already printed an error message. */
	441
	442	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	443	fatal("Ooops, read help first",1);
	444	break;
	445
	446	default:
	447	exit (1);
	448	}
	449	}
	450
	451	return TS_SUCCESS;
	452
	453	}
	454
	455
	456
	457
d7639a	458	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	459	ts_uint i;
	460	printf("Number of vertices: %u\n",vlist->n);
	461	for(i=0;i<vlist->n;i++){
a6b1b5	462	printf("%u: %f %f %f\n",
8f6a69	463	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	464	}
SP	465	return TS_SUCCESS;
	466	}
	467
	468	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	469	ts_uint i,j;
a6b1b5	470	ts_vertex **vtx=vlist->vtx;
d7639a	471	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	472	for(i=0;i<vlist->n;i++){
8f6a69	473	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	474	for(j=0;j<vtx[i]->neigh_no;j++){
	475	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	476	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	477	}
SP	478	printf("\n");
	479	}
	480
	481	return TS_SUCCESS;
	482	}
	483
	484	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	485	ts_vertex **vtx=vlist->vtx;
d7639a	486	ts_uint i;
SP	487	FILE *fh;
	488
	489	fh=fopen(filename, "w");
	490	if(fh==NULL){
	491	err("Cannot open file %s for writing");
	492	return TS_FAIL;
	493	}
	494	for(i=0;i<vlist->n;i++)
8f6a69	495	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	496
SP	497	fclose(fh);
	498	return TS_SUCCESS;
	499	}
	500
	501
	502	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	503	ts_uint i,j;
	504	for(i=0;i<vlist->n;i++){
8f6a69	505	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	506	vlist->vtx[i]->y, vlist->vtx[i]->z,
	507	vlist->vtx[i]->neigh_no);
	508	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	509	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	510	//-vlist->vtx+1));
d7639a	511	}
SP	512	fprintf(fh,"\n");
	513	}
	514	return TS_SUCCESS;
	515	}
	516
	517	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	518	ts_uint i,j;
a6b1b5	519	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	520	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	521	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	522	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	523	}
SP	524	fprintf(fh,"\n");
	525	}
	526	return TS_SUCCESS;
	527	}
	528
	529	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	530	ts_triangle_list *tlist=vesicle->tlist;
d7639a	531	ts_uint i,j;
SP	532	for(i=0;i<tlist->n;i++){
41a035	533	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	534	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	535	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	536	}
SP	537	fprintf(fh,"\n");
	538	for(j=0;j<3;j++){
41a035	539	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	540	}
SP	541	fprintf(fh,"\n");
41a035	542	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	543	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	544	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	545	}
	546	return TS_SUCCESS;
	547	}
	548
	549	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	550	ts_uint i,j;
	551	for(i=0;i<vlist->n;i++){
	552	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	553	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	554	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	555	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	556	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	557	}
SP	558	fprintf(fh,"\n");
cef6ca	559	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	560	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	561	}
SP	562	fprintf(fh,"\n");
	563	}
	564	return TS_SUCCESS;
	565	}
	566
	567	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	568	ts_uint i;
a6b1b5	569	for(i=0;i<vesicle->blist->n;i++){
e016c4	570	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	571	//-vesicle->vlist->vtx+1),
e016c4	572	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	573	//-vesicle->vlist.vtx+1));
d7639a	574	}
SP	575	return TS_SUCCESS;
	576	}
	577
	578
	579	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	580	FILE *fh;
	581	fh=fopen(filename, "w");
	582	if(fh==NULL){
	583	err("Cannot open file %s for writing");
	584	return TS_FAIL;
	585	}
	586	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	587	fprint_vertex_list(fh,vesicle->vlist);
d7639a	588	fprint_tristar(fh,vesicle);
SP	589	fprint_triangle_list(fh,vesicle);
a6b1b5	590	fprint_vertex_data(fh,vesicle->vlist);
d7639a	591	fprint_bonds(fh,vesicle);
SP	592	fclose(fh);
	593	return TS_SUCCESS;
	594	}
	595
	596	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	597	FILE *fh;
	598	char line[255];
	599	fh=fopen(filename, "r");
	600	if(fh==NULL){
	601	err("Cannot open file for reading... Nonexistant file?");
	602	return TS_FAIL;
	603	}
a6b1b5	604	ts_uint retval=1;
d7639a	605	while(retval!=EOF){
SP	606	retval=fscanf(fh,"%s",line);
	607
	608	fprintf(stderr,"%s",line);
	609	}
	610	fclose(fh);
	611	return TS_SUCCESS;
	612	}
	613
	614	ts_bool write_master_xml_file(ts_char *filename){
	615	FILE *fh;
	616	ts_char i,j;
	617	ts_uint tstep;
	618	ts_char *number;
	619	fh=fopen(filename, "w");
	620	if(fh==NULL){
	621	err("Cannot open file %s for writing");
	622	return TS_FAIL;
	623	}
	624
	625	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	626	DIR *dir = opendir(".");
	627	if(dir){
	628	struct dirent *ent;
	629	tstep=0;
	630	while((ent = readdir(dir)) != NULL)
	631	{
	632	i=rindex(ent->d_name,'.');
	633	if(i==NULL) continue;
	634	if(strcmp(i+1,"vtu")==0){
	635	j=rindex(ent->d_name,'_');
	636	if(j==NULL) continue;
	637	number=strndup(j+1,j-i);
a6b1b5	638	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	639	tstep++;
SP	640	free(number);
	641	}
	642	}
	643	}
f74313	644	free(dir);
d7639a	645	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	646	fclose(fh);
	647	return TS_SUCCESS;
	648	}
	649
	650	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	651	ts_vertex_list *vlist=vesicle->vlist;
SP	652	ts_bond_list *blist=vesicle->blist;
	653	ts_vertex **vtx=vlist->vtx;
40aa5b	654	ts_uint i,j;
d7639a	655	char filename[255];
SP	656	FILE *fh;
	657
	658	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	659	fh=fopen(filename, "w");
	660	if(fh==NULL){
	661	err("Cannot open file %s for writing");
	662	return TS_FAIL;
	663	}
	664	/* Here comes header of the file */
40aa5b	665
SP	666	//find number of extra vtxs and bonds of polymeres
58230a	667	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	668	ts_bool poly=0, fil=0;
40aa5b	669	if(vesicle->poly_list!=NULL){
SP	670	if(vesicle->poly_list->poly[0]!=NULL){
	671	polyno=vesicle->poly_list->n;
	672	monono=vesicle->poly_list->poly[0]->vlist->n;
	673	poly=1;
	674	}
	675	}
58230a	676
M	677	if(vesicle->filament_list!=NULL){
	678	if(vesicle->filament_list->poly[0]!=NULL){
	679	filno=vesicle->filament_list->n;
	680	fonono=vesicle->filament_list->poly[0]->vlist->n;
	681	fil=1;
	682	}
	683	}
	684
d7639a	685	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
58230a	686	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	687	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	688	for(i=0;i<vlist->n;i++){
a6b1b5	689	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	690	}
40aa5b	691	//polymeres
SP	692	if(poly){
3c1ac1	693	poly_idx=vlist->n;
40aa5b	694	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	695	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	696	fprintf(fh,"%u ", poly_idx);
M	697	}
	698	}
	699	}
	700	//filaments
	701	if(fil){
	702	poly_idx=vlist->n+monono*polyno;
	703	for(i=0;i<vesicle->filament_list->n;i++){
	704	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	705	// fprintf(stderr,"was here\n");
3c1ac1	706	fprintf(fh,"%u ", poly_idx);
40aa5b	707	}
SP	708	}
	709	}
d7639a	710
SP	711	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	712	for(i=0;i<vlist->n;i++){
8f6a69	713	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	714	}
SP	715	//polymeres
	716	if(poly){
	717	for(i=0;i<vesicle->poly_list->n;i++){
	718	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	719	fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
58230a	720	}
M	721	}
	722	}
	723	//filaments
	724	if(fil){
	725	for(i=0;i<vesicle->filament_list->n;i++){
	726	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	727	fprintf(fh,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
40aa5b	728	}
SP	729	}
d7639a	730	}
SP	731
	732	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	733	for(i=0;i<blist->n;i++){
e016c4	734	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	735	}
40aa5b	736	//polymeres
SP	737	if(poly){
3c1ac1	738	poly_idx=vlist->n;
40aa5b	739	for(i=0;i<vesicle->poly_list->n;i++){
SP	740	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	741	// 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	742	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	743	}
SP	744	//grafted bonds
3c1ac1	745	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	746	}
SP	747
	748	}
	749
58230a	750	//filaments
M	751	if(fil){
	752	poly_idx=vlist->n+monono*polyno;
	753	for(i=0;i<vesicle->filament_list->n;i++){
	754	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	755	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);
	756	// fprintf(stderr,"was here\n");
	757
	758	}
	759	}
	760
	761	}
40aa5b	762
d7639a	763	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	764	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	765	fprintf(fh,"%u ",i);
SP	766	}
	767	fprintf(fh,"\n");
	768	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	769	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	770	fprintf(fh,"3 ");
SP	771	}
	772
	773	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	774	fclose(fh);
	775	return TS_SUCCESS;
	776
	777	}
	778
	779	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	780	ts_vertex_list *vlist=vesicle->vlist;
SP	781	ts_bond_list *blist=vesicle->blist;
	782	ts_vertex **vtx=vlist->vtx;
	783	ts_uint i;
d7639a	784	FILE *fh;
SP	785
	786	fh=fopen(filename, "w");
	787	if(fh==NULL){
	788	err("Cannot open file %s for writing");
	789	return TS_FAIL;
	790	}
	791	/* Here comes header of the file */
	792	// fprintf(stderr,"NSHELL=%u\n",nshell);
	793	fprintf(fh, "# vtk DataFile Version 2.0\n");
	794	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	795	fprintf(fh, "%s\n", text);
	796	fprintf(fh,"ASCII\n");
	797	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	798	fprintf(fh,"POINTS %u double\n", vlist->n);
	799	for(i=0;i<vlist->n;i++){
8f6a69	800	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	801	}
SP	802
	803	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	804	for(i=0;i<blist->n;i++){
e016c4	805	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	806	}
SP	807	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	808	for(i=0;i<blist->n;i++)
	809	fprintf(fh,"3\n");
	810
	811	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	812	fprintf(fh,"SCALARS scalars long 1\n");
	813	fprintf(fh,"LOOKUP_TABLE default\n");
	814
	815	for(i=0;i<vlist->n;i++)
8f6a69	816	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	817
SP	818	fclose(fh);
	819	return TS_SUCCESS;
	820	}
	821
	822
	823
1ab449	824	ts_tape parsetape(char filename){
SP	825	// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
	826	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	827	tape->multiprocessing=calloc(255,sizeof(char));
	828	/* long int brezveze0=1;
b14a8d	829	long int brezveze1=1;
SP	830	long int brezveze2=1;
e86357	831	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	832	long int iter=1000, init=1000, mcsw=1000;
1ab449	833	*/
40aa5b	834
d7639a	835	cfg_opt_t opts[] = {
1ab449	836	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	837	CFG_SIMPLE_INT("npoly", &tape->npoly),
	838	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	839	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	840	CFG_SIMPLE_INT("nfono",&tape->nfono),
	841	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
	842	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
1ab449	843	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	844	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
	845	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
	846	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	847	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	848	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	849	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	850	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	851	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	852	CFG_SIMPLE_INT("iterations",&tape->iterations),
	853	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	854	CFG_SIMPLE_INT("inititer", &tape->inititer),
	855	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	856	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	857	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	858	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	859	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
d7639a	860	CFG_END()
SP	861	};
	862	cfg_t *cfg;
	863	ts_uint retval;
	864	cfg = cfg_init(opts, 0);
1ab449	865	retval=cfg_parse(cfg, filename);
d7639a	866	if(retval==CFG_FILE_ERROR){
a6b1b5	867	fatal("No tape file.",100);
d7639a	868	}
SP	869	else if(retval==CFG_PARSE_ERROR){
	870	fatal("Invalid tape!",100);
	871	}
a2db52	872
d7639a	873	cfg_free(cfg);
40aa5b	874
SP	875
1ab449	876	/* global variables are set automatically */
SP	877	quiet=tape->quiet;
	878	return tape;
	879	}
d7639a	880
1ab449	881	ts_bool tape_free(ts_tape *tape){
SP	882	free(tape->multiprocessing);
	883	free(tape);
	884	return TS_SUCCESS;
d7639a	885	}
f74313	886
SP	887
	888	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	889	FILE *fh;
	890	ts_uint i, nvtx,nedges,ntria;
	891	ts_uint vtxi1,vtxi2;
	892	float x,y,z;
	893	ts_vertex_list *vlist;
	894	fh=fopen(fname, "r");
	895	if(fh==NULL){
	896	err("Cannot open file for reading... Nonexistant file?");
	897	return TS_FAIL;
	898	}
	899	ts_uint retval;
	900	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	901	vesicle->vlist=init_vertex_list(nvtx);
	902	vlist=vesicle->vlist;
	903	for(i=0;i<nvtx;i++){
8f6a69	904	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	905	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	906	vlist->vtx[i]->x=x;
SP	907	vlist->vtx[i]->y=y;
	908	vlist->vtx[i]->z=z;
f74313	909	}
SP	910	for(i=0;i<nedges;i++){
	911	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	912	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	913	}
	914	//TODO: neighbours from bonds,
	915	//TODO: triangles from neigbours
	916
	917	// Don't need to read triangles. Already have enough data
	918	/*
	919	for(i=0;i<ntria;i++){
	920	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	921	vtxi1=vesicle->blist->vertex1->idx;
SP	922	vtxi2=vesicle->blist->vertex1->idx;
f74313	923
SP	924	}
	925	*/
41a035	926	if(retval);
f74313	927	fclose(fh);
SP	928
	929
	930
	931	return TS_SUCCESS;
	932	}