trisurf-ng.git - Gitblit

Moved all global variables to separate file and defined extern keyword wher...

Samo Penic

2022-05-04 06afc729f9061c1cfa14c78728d61d518324c2f0

commit \| author \| age
819a09	1
7f6076	2	/* vim: set ts=4 sts=4 sw=4 noet : */
f74313	3	#include "general.h"
06afc7	4	#include "globals.h"
d7639a	5	#include<stdio.h>
SP	6	#include "io.h"
f74313	7	#include "vertex.h"
SP	8	#include "bond.h"
d7639a	9	#include<string.h>
a6b1b5	10	#include<stdlib.h>
d7639a	11	#include <sys/types.h>
SP	12	#include <dirent.h>
b14a8d	13	#include "initial_distribution.h"
a2db52	14	#include "poly.h"
055dd7	15	#include "cell.h"
083e03	16	#include <getopt.h>
SP	17	#include <sys/stat.h>
	18	#include <sys/types.h>
	19	#include <dirent.h>
	20	#include <errno.h>
854cb6	21	#include <snapshot.h>
e9eab4	22	/ DUMP STATE TO DISK DRIVE /
SP	23
1ab449	24	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	25
SP	26	/* save current state with wrong pointers. Will fix that later */
	27	ts_uint i,j,k;
267db5	28	FILE *fh=fopen(command_line_args.dump_fullfilename,"wb");
e9eab4	29
SP	30	/* dump vesicle */
d0a1d3	31	fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
e9eab4	32	/* dump vertex list */
SP	33	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	34	/* dump bond list */
	35	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	36	/* dump triangle list */
	37	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	38	/* dump cell list */
	39	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	40	/* dump poly list */
	41	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	42	/* dump filament list */
M	43	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	44	/* level 1 complete */
SP	45
	46	/dump vertices/
	47	for(i=0;i<vesicle->vlist->n;i++){
	48	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	49	/* dump pointer offsets for:
	50	neigh
	51	bond
	52	tria
	53	cell is ignored
	54	*/
	55	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	56	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	57	}
SP	58	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	59	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	60	}
SP	61	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	62	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	63	}
SP	64	}
	65
	66	/dump bonds/
	67	for(i=0;i<vesicle->blist->n;i++){
	68	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	69	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	70	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	71	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	72	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	73	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	74	}
SP	75
	76	/dump triangles/
	77	for(i=0;i<vesicle->tlist->n;i++){
	78	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	79	/* dump pointer offsets for vertex */
3c1ac1	80	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	81	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	82	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	83	/* dump pointer offsets for neigh */
SP	84	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	85	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	86	}
SP	87	}
	88
	89
	90	/dump polymeres /
	91	for(i=0;i<vesicle->poly_list->n;i++){
	92	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	93	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	94	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	95	}
SP	96
	97	/* dump poly vertex(monomer) list*/
	98	for(i=0;i<vesicle->poly_list->n;i++){
	99	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	100	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	101	/* dump offset for neigh and bond */
	102	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	103	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	104	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	105	}
SP	106	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	107	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	108	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	109	}
SP	110	}
3c1ac1	111	// grafted vtx on vesicle data dump
SP	112	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	113	}
SP	114	/* dump poly bonds between monomers list*/
	115	for(i=0;i<vesicle->poly_list->n;i++){
	116	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	117	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	118	/* dump vtx1 and vtx2 offsets */
3c1ac1	119	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	120	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	121	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	122	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	123	}
SP	124	}
	125
bcf455	126
M	127	/dump filamentes grandes svinjas /
	128	for(i=0;i<vesicle->filament_list->n;i++){
	129	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	130	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	131	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	132	}
	133
	134	/* dump filamentes vertex(monomer) list*/
	135	for(i=0;i<vesicle->filament_list->n;i++){
	136	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	137	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	138	/* dump offset for neigh and bond */
	139	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	140	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	141	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	142	}
	143	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	144	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	145	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	146	}
	147	}
	148	}
	149	/* dump poly bonds between monomers list*/
	150	for(i=0;i<vesicle->filament_list->n;i++){
	151	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	152	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	153	/* dump vtx1 and vtx2 offsets */
	154	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	155	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	156	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	157	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	158	}
	159	}
	160
	161
	162
e9eab4	163	/* pointer offsets for fixing the restored pointers */
SP	164	/* need pointers for
	165	vlist->vtx
	166	blist->bond
	167	tlist->tria
	168	clist->cell
	169	poly_list->poly
	170	and for each poly:
	171	poly_list->poly->vtx
	172	poly_list->poly->bond
	173	*/
	174
bd2210	175	// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	176	/* write tape information on vesicle */
bd2210	177	// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	178	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	179	fclose(fh);
SP	180	return TS_SUCCESS;
	181	}
	182
	183
	184	/ RESTORE DUMP FROM DISK /
1ab449	185	ts_vesicle restore_state(ts_uint iteration){
e9eab4	186	ts_uint i,j,k;
267db5	187	FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
3f5c83	188
SP	189	struct stat sb;
267db5	190	if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
3f5c83	191	//dump file does not exist.
SP	192	return NULL;
	193	}
	194
	195	//check if it is regular file
	196	if((sb.st_mode & S_IFMT) != S_IFREG) {
	197	//dump file is not a regular file.
	198	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	199	return NULL;
	200	}
	201
e9eab4	202	ts_uint retval;
3c1ac1	203	ts_uint idx;
e9eab4	204
SP	205	/* we restore all the data from the dump */
	206	/* restore vesicle */
	207	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
d0a1d3	208	retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
86f5e7	209	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
SP	210
e9eab4	211	/* restore vertex list */
SP	212	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	213	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	214	/* restore bond list */
	215	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	216	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	217	/* restore triangle list */
	218	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	219	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	220	/* restore cell list */
	221	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	222	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	223	/* restore poly list */
	224	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	225	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	226	/* restore filament list */
M	227	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	228	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	229	/* level 1 complete */
SP	230
3c1ac1	231	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	232	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	233	for(i=0;i<vesicle->blist->n;i++){
	234	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	235	}
	236	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	237	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	238	for(i=0;i<vesicle->tlist->n;i++){
	239	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	240	}
a37ba2	241	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	242	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	243	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	244	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	245	}
SP	246	/restore vertices/
	247	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	248	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	249	/restore neigh, bond, tristar. Ignoring cell /
	250	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	251	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	252	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	253	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	254	}
SP	255	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	256	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	257	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	258	/* 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 */
	259	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	260	}
SP	261
	262	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	263	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	264	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	265	/* same comment as above */
	266	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	267	}
SP	268
	269	}
	270
	271	/restore bonds/
3c1ac1	272	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	273	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	274	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	275	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	276	/* restore vtx1 and vtx2 */
3c1ac1	277	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	278	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	279	retval=fread(&idx,sizeof(ts_uint),1,fh);
	280	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	281	}
SP	282
	283	/restore triangles/
3c1ac1	284	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	285	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	286	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	287	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	288	/* restore pointers for vertices */
3c1ac1	289	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	290	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	291	retval=fread(&idx,sizeof(ts_uint),1,fh);
	292	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	293	retval=fread(&idx,sizeof(ts_uint),1,fh);
	294	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	295	/* restore pointers for neigh */
3c1ac1	296	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	297	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	298	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	299	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	300	}
SP	301
	302	}
	303
	304	/restore cells /
	305	/TODO: do we need to recalculate cells here? /
	306	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	307	for(i=0;i<vesicle->clist->cellno;i++){
	308	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	309	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	310	}
	311	*/
	312	/restore polymeres /
	313	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	314	for(i=0;i<vesicle->poly_list->n;i++){
	315	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	316	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	317	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	318	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	319	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	320	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	321	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	322	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	323	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	324	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	325	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	326	}
	327	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	328	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	329	}
	330
e9eab4	331	}
3c1ac1	332
e9eab4	333
SP	334	/* restore poly vertex(monomer) list*/
	335	for(i=0;i<vesicle->poly_list->n;i++){
	336	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	337	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	338
e9eab4	339	/* restore neigh and bonds */
SP	340	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 ));
	341	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	342	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	343	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	344	}
SP	345	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 ));
	346	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	347	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	348	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	349	}
SP	350
	351	}
3c1ac1	352	/* restore grafted vtx on vesicle and grafted_poly */
SP	353	retval=fread(&idx,sizeof(ts_uint),1,fh);
	354	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	355	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	356	}
3c1ac1	357
e9eab4	358	/* restore poly bonds between monomers list*/
SP	359	for(i=0;i<vesicle->poly_list->n;i++){
	360	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	361	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	362	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	363	/* restore vtx1 and vtx2 */
3c1ac1	364	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	365	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	366	retval=fread(&idx,sizeof(ts_uint),1,fh);
	367	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	368	}
SP	369	}
	370
bcf455	371	/restore filaments /
M	372	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	373	for(i=0;i<vesicle->filament_list->n;i++){
	374	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	375	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	376	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	377	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	378	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	379	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	380	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	381	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	382	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	383	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	384	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	385	}
	386	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	387	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	388	}
	389
	390	}
	391
	392
	393	/* restore poly vertex(monomer) list*/
	394	for(i=0;i<vesicle->filament_list->n;i++){
	395	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	396	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	397
	398	/* restore neigh and bonds */
	399	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 ));
	400	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	401	retval=fread(&idx,sizeof(ts_uint),1,fh);
	402	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	403	}
	404	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 ));
	405	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	406	retval=fread(&idx,sizeof(ts_uint),1,fh);
	407	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	408	}
	409
	410	}
	411	}
	412
	413	/* restore poly bonds between monomers list*/
	414	for(i=0;i<vesicle->filament_list->n;i++){
	415	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	416	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	417	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	418	/* restore vtx1 and vtx2 */
	419	retval=fread(&idx,sizeof(ts_uint),1,fh);
	420	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	421	retval=fread(&idx,sizeof(ts_uint),1,fh);
	422	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	423	}
	424	}
267db5	425	vesicle->tape=parsetape(command_line_args.tape_fullfilename);
063289	426	// recreating space for cells //
055dd7	427	vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
2a1e3d	428	//THIS IS HARDCODED IN CELL.C NOW
SP	429	// vesicle->clist->max_occupancy=16;
47a7ac	430	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	431	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	432	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	433	if(retval);
SP	434	fclose(fh);
	435	return vesicle;
	436	}
	437
	438
	439
083e03	440	ts_bool parse_args(int argc, char **argv){
3f5c83	441	int c, retval;
SP	442	struct stat sb;
	443	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	444	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	445	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	446	sprintf(command_line_args.tape_fullfilename,"tape");
1bf3c3	447	sprintf(command_line_args.tape_templatefull,"./tape");
3f5c83	448	FILE *file;
SP	449
083e03	450	while (1)
SP	451	{
	452	static struct option long_options[] =
	453	{
8a6614	454	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	455	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	456	{"tape", no_argument, 0, 't'},
fd8126	457	{"version", no_argument, 0, 'v'},
083e03	458	{"output-file", required_argument, 0, 'o'},
SP	459	{"directory", required_argument, 0, 'd'},
3f5c83	460	{"dump-filename", required_argument,0, 'f'},
7b0c07	461	{"tape-options",required_argument,0,'c'},
1bf3c3	462	{"tape-template", required_argument,0,0},
ab798b	463	{"restore-from-vtk",required_argument,0,0},
083e03	464	{0, 0, 0, 0}
SP	465	};
	466	/* getopt_long stores the option index here. */
	467	int option_index = 0;
	468
fd8126	469	c = getopt_long (argc, argv, "d:f:o:t:c:v",
083e03	470	long_options, &option_index);
SP	471
	472	/* Detect the end of the options. */
	473	if (c == -1)
	474	break;
	475
	476	switch (c)
	477	{
	478	case 0:
	479	/* If this option set a flag, do nothing else now. */
	480	if (long_options[option_index].flag != 0)
	481	break;
1bf3c3	482	/* printf ("option %s", long_options[option_index].name);
083e03	483	if (optarg)
1bf3c3	484	printf (" with arg %s", optarg);
SP	485	printf ("\n"); */
	486	//TODO: find a better way.
	487	if(strcmp(long_options[option_index].name,"tape-template")==0){
	488	strcpy(command_line_args.tape_templatefull,optarg);
	489	}
ab798b	490	if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
ee84bd	491	strcpy(command_line_args.dump_from_vtk,optarg);
SP	492	}
083e03	493	break;
fd8126	494	case 'v':
SP	495	fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	496	fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
	497	fprintf(stdout,"Released under terms of GPLv3\n");
	498	exit(0);
083e03	499
7b0c07	500	case 'c':
SP	501	strcpy(command_line_args.tape_opts,optarg);
	502	break;
	503	case 't': //tape
3f5c83	504	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	505	break;
SP	506
7b0c07	507	case 'o': //set filename of master pvd output file
3f5c83	508	strcpy(command_line_args.output_fullfilename, optarg);
SP	509	break;
083e03	510
SP	511	case 'd':
	512	//check if directory exists. If not create one. If creation is
	513	//successful, set directory for output files.
	514	//printf ("option -d with value `%s'\n", optarg);
3f5c83	515	if (stat(optarg, &sb) == -1) {
SP	516	//directory does not exist
083e03	517	retval=mkdir(optarg, 0700);
SP	518	if(retval){
3f5c83	519	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	520	}
SP	521	}
3f5c83	522	//check if is a proper directory
SP	523	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	524	//it is not a directory. fatal error.
	525	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	526	fatal("Cannot continue",1);
083e03	527	}
3f5c83	528	strcpy(command_line_args.path, optarg);
083e03	529	break;
SP	530
	531	case 'f':
3f5c83	532	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	533	break;
SP	534
	535	case '?':
	536	/* getopt_long already printed an error message. */
ba73ab	537	print_help(stdout);
SP	538	//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
083e03	539	fatal("Ooops, read help first",1);
SP	540	break;
	541
	542	default:
	543	exit (1);
	544	}
	545	}
	546
7b0c07	547	//Here we set correct values for full filenames!
SP	548	char buffer=(char )malloc(10000*sizeof(char));
	549	//correct the path and add trailing /
	550	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	551
	552	/* master pvd output file */
	553	strcpy(buffer,command_line_args.path);
	554	strcat(buffer,command_line_args.output_fullfilename);
	555	if ((file = fopen(buffer, "w")) == NULL) {
	556	fprintf(stderr,"Could not create output file %s!\n", buffer);
	557	fatal("Please specify correct output file or check permissions of the file",1);
1bf3c3	558	//there is a tape template. make a copy into desired directory
7b0c07	559
SP	560	} else {
	561	fclose(file);
	562	strcpy(command_line_args.output_fullfilename,buffer);
	563	}
	564
	565	/* tape file */
	566	strcpy(buffer,command_line_args.path);
	567	strcat(buffer,command_line_args.tape_fullfilename);
	568	if (stat(buffer, &sb) == -1) {
1bf3c3	569
SP	570	//tape does not exist. does tape template exist?
	571	if(stat(command_line_args.tape_templatefull, &sb)==-1){
	572	ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
	573	fatal("Please select correct tape or check permissions of the file",1);
	574	} else {
	575	//tape template found
	576	fatal("Samo did not program template copy yet",1);
	577	}
7b0c07	578	} else {
SP	579	strcpy(command_line_args.tape_fullfilename,buffer);
	580	}
	581
	582
	583	/* dump file */
	584	strcpy(buffer,command_line_args.path);
	585	strcat(buffer,command_line_args.dump_fullfilename);
	586	//check if dump file exist first.
	587	if (stat(buffer, &sb) == -1) {
	588	//no dump file. check if we can create one.
	589	if ((file = fopen(buffer, "w")) == NULL) {
	590	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	591	fatal("Please specify correct dump file or check permissions of the file",1);
	592	} else {
	593	fclose(file);
	594	//good, file is writeable. delete it for now.
	595	remove(buffer);
	596	}
	597	}
	598	strcpy(command_line_args.dump_fullfilename, buffer);
	599
	600
	601	free(buffer);
083e03	602	return TS_SUCCESS;
SP	603
	604	}
	605
	606
ba73ab	607	ts_bool print_help(FILE *fd){
SP	608	fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	609	fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
	610	fprintf(fd,"Released under terms of GPLv3\n\n");
	611
	612	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");
	613	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");
	614	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");
	615	fprintf(fd,"Flags:\n\n");
	616	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");
	617	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	618	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
ba73ab	619	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
SP	620	fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
	621	fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
c4178c	622	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
SP	623	fprintf(fd,"Examples:\n\n");
	624	fprintf(fd,"trisurf --force-from-tape\n");
	625	fprintf(fd,"trisurf --reset-iteration-count\n");
	626	fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
	627	fprintf(fd,"\n\n");
	628
ba73ab	629	return TS_SUCCESS;
SP	630	}
	631
	632
083e03	633
d7639a	634	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	635	ts_uint i;
	636	printf("Number of vertices: %u\n",vlist->n);
	637	for(i=0;i<vlist->n;i++){
a6b1b5	638	printf("%u: %f %f %f\n",
8f6a69	639	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	640	}
SP	641	return TS_SUCCESS;
	642	}
	643
	644	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	645	ts_uint i,j;
a6b1b5	646	ts_vertex **vtx=vlist->vtx;
d7639a	647	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	648	for(i=0;i<vlist->n;i++){
8f6a69	649	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	650	for(j=0;j<vtx[i]->neigh_no;j++){
	651	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	652	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	653	}
SP	654	printf("\n");
	655	}
	656
	657	return TS_SUCCESS;
	658	}
	659
	660	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	661	ts_vertex **vtx=vlist->vtx;
d7639a	662	ts_uint i;
SP	663	FILE *fh;
	664
	665	fh=fopen(filename, "w");
	666	if(fh==NULL){
	667	err("Cannot open file %s for writing");
	668	return TS_FAIL;
	669	}
	670	for(i=0;i<vlist->n;i++)
8f6a69	671	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	672
SP	673	fclose(fh);
	674	return TS_SUCCESS;
	675	}
	676
	677
	678	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	679	ts_uint i,j;
	680	for(i=0;i<vlist->n;i++){
8f6a69	681	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	682	vlist->vtx[i]->y, vlist->vtx[i]->z,
	683	vlist->vtx[i]->neigh_no);
	684	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	685	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	686	//-vlist->vtx+1));
d7639a	687	}
SP	688	fprintf(fh,"\n");
	689	}
	690	return TS_SUCCESS;
	691	}
	692
	693	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	694	ts_uint i,j;
a6b1b5	695	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	696	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	697	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	698	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	699	}
SP	700	fprintf(fh,"\n");
	701	}
	702	return TS_SUCCESS;
	703	}
	704
	705	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	706	ts_triangle_list *tlist=vesicle->tlist;
d7639a	707	ts_uint i,j;
SP	708	for(i=0;i<tlist->n;i++){
41a035	709	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	710	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	711	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	712	}
SP	713	fprintf(fh,"\n");
	714	for(j=0;j<3;j++){
41a035	715	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	716	}
SP	717	fprintf(fh,"\n");
41a035	718	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	719	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	720	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	721	}
	722	return TS_SUCCESS;
	723	}
	724
	725	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	726	ts_uint i,j;
	727	for(i=0;i<vlist->n;i++){
	728	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	729	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	730	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	731	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	732	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	733	}
SP	734	fprintf(fh,"\n");
cef6ca	735	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	736	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	737	}
SP	738	fprintf(fh,"\n");
	739	}
	740	return TS_SUCCESS;
	741	}
	742
	743	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	744	ts_uint i;
a6b1b5	745	for(i=0;i<vesicle->blist->n;i++){
e016c4	746	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	747	//-vesicle->vlist->vtx+1),
e016c4	748	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	749	//-vesicle->vlist.vtx+1));
d7639a	750	}
SP	751	return TS_SUCCESS;
	752	}
	753
	754
	755
	756	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	757	FILE *fh;
	758	char line[255];
	759	fh=fopen(filename, "r");
	760	if(fh==NULL){
	761	err("Cannot open file for reading... Nonexistant file?");
	762	return TS_FAIL;
	763	}
a6b1b5	764	ts_uint retval=1;
d7639a	765	while(retval!=EOF){
SP	766	retval=fscanf(fh,"%s",line);
	767
	768	fprintf(stderr,"%s",line);
	769	}
	770	fclose(fh);
	771	return TS_SUCCESS;
	772	}
	773
	774	ts_bool write_master_xml_file(ts_char *filename){
	775	FILE *fh;
	776	ts_char i,j;
	777	ts_uint tstep;
	778	ts_char *number;
	779	fh=fopen(filename, "w");
	780	if(fh==NULL){
	781	err("Cannot open file %s for writing");
	782	return TS_FAIL;
	783	}
	784
	785	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
267db5	786	DIR *dir = opendir(command_line_args.path);
d7639a	787	if(dir){
SP	788	struct dirent *ent;
	789	tstep=0;
	790	while((ent = readdir(dir)) != NULL)
	791	{
	792	i=rindex(ent->d_name,'.');
	793	if(i==NULL) continue;
	794	if(strcmp(i+1,"vtu")==0){
	795	j=rindex(ent->d_name,'_');
	796	if(j==NULL) continue;
	797	number=strndup(j+1,j-i);
a6b1b5	798	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	799	tstep++;
SP	800	free(number);
	801	}
	802	}
	803	}
f74313	804	free(dir);
d7639a	805	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	806	fclose(fh);
	807	return TS_SUCCESS;
	808	}
	809
0a2c81	810	ts_bool write_vertex_xml_file(ts_vesicle vesicle, ts_uint timestepno, ts_cluster_list cstlist){
a6b1b5	811	ts_vertex_list *vlist=vesicle->vlist;
SP	812	ts_bond_list *blist=vesicle->blist;
	813	ts_vertex **vtx=vlist->vtx;
40aa5b	814	ts_uint i,j;
13d445	815	//ts_double senergy=0.0;
267db5	816	char filename[10000];
SP	817	char just_name[255];
d7639a	818	FILE *fh;
267db5	819	strcpy(filename,command_line_args.path);
SP	820	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	821	strcat(filename,just_name);
d7639a	822
SP	823	fh=fopen(filename, "w");
	824	if(fh==NULL){
	825	err("Cannot open file %s for writing");
	826	return TS_FAIL;
	827	}
	828	/* Here comes header of the file */
40aa5b	829
SP	830	//find number of extra vtxs and bonds of polymeres
58230a	831	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	832	ts_bool poly=0, fil=0;
40aa5b	833	if(vesicle->poly_list!=NULL){
2a1e3d	834	if(vesicle->poly_list->n!=0){
SP	835	//if(vesicle->poly_list->poly[0]!=NULL){
40aa5b	836	polyno=vesicle->poly_list->n;
SP	837	monono=vesicle->poly_list->poly[0]->vlist->n;
	838	poly=1;
	839	}
	840	}
58230a	841
M	842	if(vesicle->filament_list!=NULL){
2a1e3d	843	if(vesicle->filament_list->n!=0){
SP	844	//if(vesicle->filament_list->poly[0]!=NULL){
58230a	845	filno=vesicle->filament_list->n;
M	846	fonono=vesicle->filament_list->poly[0]->vlist->n;
	847	fil=1;
	848	}
	849	}
	850
854cb6	851	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	852	xml_trisurf_data(fh,vesicle);
	853	fprintf(fh, " <UnstructuredGrid>\n");
8db203	854	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n);
5c64e2	855	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
d7639a	856	for(i=0;i<vlist->n;i++){
a6b1b5	857	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	858	}
40aa5b	859	//polymeres
SP	860	if(poly){
3c1ac1	861	poly_idx=vlist->n;
40aa5b	862	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	863	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	864	fprintf(fh,"%u ", poly_idx);
M	865	}
	866	}
	867	}
	868	//filaments
	869	if(fil){
	870	poly_idx=vlist->n+monono*polyno;
	871	for(i=0;i<vesicle->filament_list->n;i++){
	872	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	873	// fprintf(stderr,"was here\n");
3c1ac1	874	fprintf(fh,"%u ", poly_idx);
40aa5b	875	}
SP	876	}
	877	}
d7639a	878
45c708	879	fprintf(fh,"</DataArray>\n");
0a2c81	880	if(cstlist!=NULL){
SP	881	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	882	for(i=0;i<vlist->n;i++){
	883	if(vtx[i]->cluster!=NULL){
	884	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	885	} else {
	886	fprintf(fh,"-1 ");
	887	}
	888	}
	889	//polymeres
	890	if(poly){
	891	poly_idx=vlist->n;
	892	for(i=0;i<vesicle->poly_list->n;i++){
	893	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	894	fprintf(fh,"-1 ");
	895	}
	896	}
	897	}
	898	//filaments
	899	if(fil){
	900	poly_idx=vlist->n+monono*polyno;
	901	for(i=0;i<vesicle->filament_list->n;i++){
	902	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	903	// fprintf(stderr,"was here\n");
	904	fprintf(fh,"-1 ");
	905	}
	906	}
	907	}
	908
	909	fprintf(fh,"</DataArray>\n");
	910
	911
	912	}
	913
45c708	914	//here comes additional data as needed. Currently only spontaneous curvature
SP	915	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	916	for(i=0;i<vlist->n;i++){
	917	fprintf(fh,"%.17e ",vtx[i]->c);
	918	}
	919	//polymeres
	920	if(poly){
	921	poly_idx=vlist->n;
	922	for(i=0;i<vesicle->poly_list->n;i++){
	923	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	924	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	925	}
	926	}
	927	}
	928	//filaments
	929	if(fil){
	930	poly_idx=vlist->n+monono*polyno;
	931	for(i=0;i<vesicle->filament_list->n;i++){
	932	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	933	// fprintf(stderr,"was here\n");
	934	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	935	}
	936	}
	937	}
	938	fprintf(fh,"</DataArray>\n");
6487a0	939	fprintf(fh,"<DataArray type=\"Float64\" Name=\"direct_interaction_force\" format=\"ascii\">");
SP	940	for(i=0;i<vlist->n;i++){
	941	fprintf(fh,"%.17e ",vtx[i]->direct_interaction_force);
	942	}
	943	//polymeres
	944	if(poly){
	945	poly_idx=vlist->n;
	946	for(i=0;i<vesicle->poly_list->n;i++){
	947	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	948	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
	949	}
	950	}
	951	}
	952	//filaments
	953	if(fil){
	954	poly_idx=vlist->n+monono*polyno;
	955	for(i=0;i<vesicle->filament_list->n;i++){
	956	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	957	// fprintf(stderr,"was here\n");
	958	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
	959	}
	960	}
	961	}
	962	fprintf(fh,"</DataArray>\n");
45c708	963
5c64e2	964	//here comes additional data. Energy!
SP	965	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	966	for(i=0;i<vlist->n;i++){
	967	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	968	}
	969	//polymeres
	970	if(poly){
	971	poly_idx=vlist->n;
	972	for(i=0;i<vesicle->poly_list->n;i++){
	973	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	974	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	975	}
	976	}
	977	}
	978	//filaments
	979	if(fil){
	980	poly_idx=vlist->n+monono*polyno;
	981	for(i=0;i<vesicle->filament_list->n;i++){
	982	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	983	// fprintf(stderr,"was here\n");
	984	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	985	}
	986	}
	987	}
	988	fprintf(fh,"</DataArray>\n");
	989
45c708	990
13d445	991	fprintf(fh,"</PointData>\n<CellData>\n");
SP	992
7ec6fb	993	if(vesicle->tape->stretchswitch==1){
SP	994	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	995	for(i=0;i<blist->n;i++){
SP	996	fprintf(fh, "0.0 ");
	997	}
	998	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	999	fprintf(fh,"0.0 ");
7ec6fb	1000	}
13d445	1001	for(i=0;i<vesicle->tlist->n;i++){
SP	1002	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	1003	}
7ec6fb	1004	fprintf(fh,"</DataArray>\n");
SP	1005	}
45c708	1006
13d445	1007
SP	1008
	1009	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	1010	for(i=0;i<vlist->n;i++){
aad500	1011	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	1012	}
SP	1013	//polymeres
	1014	if(poly){
	1015	for(i=0;i<vesicle->poly_list->n;i++){
	1016	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	1017	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	1018	}
M	1019	}
	1020	}
	1021	//filaments
	1022	if(fil){
	1023	for(i=0;i<vesicle->filament_list->n;i++){
	1024	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	1025	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	1026	}
SP	1027	}
d7639a	1028	}
SP	1029
	1030	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	1031	for(i=0;i<blist->n;i++){
e016c4	1032	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1033	}
40aa5b	1034	//polymeres
SP	1035	if(poly){
3c1ac1	1036	poly_idx=vlist->n;
40aa5b	1037	for(i=0;i<vesicle->poly_list->n;i++){
SP	1038	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	1039	// 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	1040	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	1041	}
SP	1042	//grafted bonds
3c1ac1	1043	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	1044	}
SP	1045
	1046	}
	1047
58230a	1048	//filaments
M	1049	if(fil){
	1050	poly_idx=vlist->n+monono*polyno;
	1051	for(i=0;i<vesicle->filament_list->n;i++){
	1052	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	1053	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);
	1054	// fprintf(stderr,"was here\n");
	1055
	1056	}
	1057	}
	1058
	1059	}
8db203	1060	for(i=0;i<vesicle->tlist->n;i++){
SP	1061	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);
	1062	}
d7639a	1063	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	1064	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	1065	fprintf(fh,"%u ",i);
SP	1066	}
8db203	1067	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	1068	fprintf(fh,"%u ", j);
	1069	}
d7639a	1070	fprintf(fh,"\n");
SP	1071	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	1072	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	1073	fprintf(fh,"3 ");
SP	1074	}
8db203	1075	for(i=0;i<vesicle->tlist->n;i++){
SP	1076	fprintf(fh,"5 ");
	1077	}
d7639a	1078	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	1079	fclose(fh);
	1080	return TS_SUCCESS;
	1081
	1082	}
	1083
	1084	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	1085	ts_vertex_list *vlist=vesicle->vlist;
SP	1086	ts_bond_list *blist=vesicle->blist;
	1087	ts_vertex **vtx=vlist->vtx;
	1088	ts_uint i;
d7639a	1089	FILE *fh;
SP	1090
	1091	fh=fopen(filename, "w");
	1092	if(fh==NULL){
	1093	err("Cannot open file %s for writing");
	1094	return TS_FAIL;
	1095	}
	1096	/* Here comes header of the file */
	1097	// fprintf(stderr,"NSHELL=%u\n",nshell);
	1098	fprintf(fh, "# vtk DataFile Version 2.0\n");
	1099	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	1100	fprintf(fh, "%s\n", text);
	1101	fprintf(fh,"ASCII\n");
	1102	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	1103	fprintf(fh,"POINTS %u double\n", vlist->n);
	1104	for(i=0;i<vlist->n;i++){
8f6a69	1105	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	1106	}
SP	1107
	1108	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	1109	for(i=0;i<blist->n;i++){
e016c4	1110	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1111	}
SP	1112	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	1113	for(i=0;i<blist->n;i++)
	1114	fprintf(fh,"3\n");
	1115
	1116	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	1117	fprintf(fh,"SCALARS scalars long 1\n");
	1118	fprintf(fh,"LOOKUP_TABLE default\n");
	1119
	1120	for(i=0;i<vlist->n;i++)
8f6a69	1121	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	1122
SP	1123	fclose(fh);
	1124	return TS_SUCCESS;
	1125	}
	1126
	1127
	1128
144784	1129	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	1130	FILE *fh;
	1131	ts_uint i;
	1132
	1133	fh=fopen(filename, "w");
	1134	if(fh==NULL){
	1135	err("Cannot open file %s for writing");
	1136	return TS_FAIL;
	1137	}
	1138
	1139	for(i=0;i<vesicle->tlist->n;i++){
	1140
	1141	fprintf(fh,"\ttriangle {");
	1142	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1143	vesicle->tlist->tria[i]->vertex[0]->x,
	1144	vesicle->tlist->tria[i]->vertex[0]->y,
	1145	vesicle->tlist->tria[i]->vertex[0]->z,
	1146
	1147	vesicle->tlist->tria[i]->vertex[1]->x,
	1148	vesicle->tlist->tria[i]->vertex[1]->y,
	1149	vesicle->tlist->tria[i]->vertex[1]->z,
	1150
	1151	vesicle->tlist->tria[i]->vertex[2]->x,
	1152	vesicle->tlist->tria[i]->vertex[2]->y,
	1153	vesicle->tlist->tria[i]->vertex[2]->z
	1154	);
	1155	}
	1156
	1157	fclose(fh);
	1158	return TS_SUCCESS;
	1159	}
	1160
	1161
1ab449	1162	ts_tape parsetape(char filename){
698ae1	1163	FILE *fd = fopen (filename, "r");
SP	1164	long length;
	1165	size_t size;
	1166	fseek (fd, 0, SEEK_END);
	1167	length = ftell (fd);
	1168	fseek (fd, 0, SEEK_SET);
	1169	size=fread (tapetxt, 1, length, fd);
	1170	fclose(fd);
	1171	if(size);
	1172	ts_tape *tape=parsetapebuffer(tapetxt);
	1173	return tape;
	1174	}
	1175
	1176	ts_tape parsetapebuffer(char buffer){
1ab449	1177	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1178	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1179
d7639a	1180	cfg_opt_t opts[] = {
1ab449	1181	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1182	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1183	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1184	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1185	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	1186	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	1187	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1188	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1189	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1190	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1191	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1192	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1193	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1194	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1195	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1196	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1197	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	1198	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	1199	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	1200	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1201	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1202	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1203	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1204	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1205	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1206	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1207	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1208	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1209	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	1210	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	1211	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	1212	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	1213	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1214	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1215	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	1216	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	1217	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	1218	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	1219	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	1220	/* Variables related to plane confinement */
514ebc	1221	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	1222	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	1223	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	1224	/* Variables related to stretching */
36bc6d	1225	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	1226	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	1227	CFG_END()
SP	1228	};
	1229	cfg_t *cfg;
	1230	ts_uint retval;
	1231	cfg = cfg_init(opts, 0);
698ae1	1232	retval=cfg_parse_buf(cfg, buffer);
514ebc	1233	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	1234	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	1235	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	1236
d7639a	1237	if(retval==CFG_FILE_ERROR){
a6b1b5	1238	fatal("No tape file.",100);
d7639a	1239	}
SP	1240	else if(retval==CFG_PARSE_ERROR){
	1241	fatal("Invalid tape!",100);
	1242	}
a2db52	1243
7b0c07	1244	/* here we override all values read from tape with values from commandline*/
SP	1245	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1246	cfg_free(cfg);
40aa5b	1247
SP	1248
1ab449	1249	/* global variables are set automatically */
SP	1250	quiet=tape->quiet;
	1251	return tape;
	1252	}
d7639a	1253
1ab449	1254	ts_bool tape_free(ts_tape *tape){
SP	1255	free(tape->multiprocessing);
	1256	free(tape);
	1257	return TS_SUCCESS;
d7639a	1258	}
f74313	1259
SP	1260
7b0c07	1261
SP	1262	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1263
	1264	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	1265	operator[0]=0;
SP	1266	operator[1]=0;
7b0c07	1267	ts_uint i,j;
SP	1268	commands=(char )malloc(10000sizeof(char));
	1269	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1270	strcpy(commands,opts);
	1271	for(i=0; ;i++, commands=NULL){
	1272	//breaks comma separated list of commands into specific commands.
	1273	command=strtok_r(commands,",",&saveptr);
	1274	if(command==NULL) break;
	1275	// fprintf(stdout,"Command %d: %s\n",i,command);
	1276	//extracts name of command and value of command into operator[2] array.
	1277	for(j=0; j<2;j++,command=NULL){
	1278	operator[j]=strtok_r(command,"=",&saveopptr);
	1279	if(operator[j]==NULL) break;
	1280	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1281	}
	1282	//1. check: must have 2 operators.
	1283	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1284
	1285	// cfg_setstr(cfg,operator[0],operator[1]);
	1286	cmdline_to_tape(cfg,operator[0],operator[1]);
	1287	//2. check: must be named properly.
	1288	//3. check: must be of right format (integer, double, string, ...)
	1289
	1290	}
	1291	free(backup);
	1292	return TS_SUCCESS;
	1293	}
	1294
	1295
	1296	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1297
	1298	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1299	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1300	switch (cfg_opt->type){
	1301	case CFGT_INT:
	1302	cfg_setint(cfg,key,atol(val));
	1303	break;
	1304	case CFGT_FLOAT:
	1305	cfg_setfloat(cfg,key,atof(val));
	1306	break;
	1307	/* case CFGT_BOOL:
	1308	cfg_setbool(cfg,operator[0],operator[1]);
	1309	break; */
	1310	case CFGT_STR:
	1311	cfg_setstr(cfg,key,val);
	1312	break;
	1313	default:
	1314	break;
	1315
	1316	}
	1317	return TS_SUCCESS;
	1318	}
	1319
	1320
	1321
f74313	1322	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1323	FILE *fh;
	1324	ts_uint i, nvtx,nedges,ntria;
	1325	ts_uint vtxi1,vtxi2;
	1326	float x,y,z;
	1327	ts_vertex_list *vlist;
	1328	fh=fopen(fname, "r");
	1329	if(fh==NULL){
	1330	err("Cannot open file for reading... Nonexistant file?");
	1331	return TS_FAIL;
	1332	}
	1333	ts_uint retval;
	1334	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1335	vesicle->vlist=init_vertex_list(nvtx);
	1336	vlist=vesicle->vlist;
	1337	for(i=0;i<nvtx;i++){
8f6a69	1338	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1339	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1340	vlist->vtx[i]->x=x;
SP	1341	vlist->vtx[i]->y=y;
	1342	vlist->vtx[i]->z=z;
f74313	1343	}
SP	1344	for(i=0;i<nedges;i++){
	1345	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1346	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1347	}
	1348	//TODO: neighbours from bonds,
	1349	//TODO: triangles from neigbours
	1350
	1351	// Don't need to read triangles. Already have enough data
	1352	/*
	1353	for(i=0;i<ntria;i++){
	1354	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1355	vtxi1=vesicle->blist->vertex1->idx;
SP	1356	vtxi2=vesicle->blist->vertex1->idx;
f74313	1357
SP	1358	}
	1359	*/
41a035	1360	if(retval);
f74313	1361	fclose(fh);
SP	1362
	1363
	1364
	1365	return TS_SUCCESS;
	1366	}