trisurf-ng.git - Gitblit

Fixed cell from dump with new tape. Take 2.

Samo Penic

2014-07-08 055dd7840f6926f3b4b41a04a86b7fac0a8fec26

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"
055dd7	13	#include "cell.h"
083e03	14	#include <getopt.h>
SP	15	#include <sys/stat.h>
	16	#include <sys/types.h>
	17	#include <dirent.h>
	18	#include <errno.h>
e9eab4	19	/ DUMP STATE TO DISK DRIVE /
SP	20
1ab449	21	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	22
SP	23	/* save current state with wrong pointers. Will fix that later */
	24	ts_uint i,j,k;
	25	FILE *fh=fopen("dump.bin","wb");
	26
	27	/* dump vesicle */
86f5e7	28	fwrite(vesicle, sizeof(ts_vesicle),1,fh);
e9eab4	29	/* dump vertex list */
SP	30	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	31	/* dump bond list */
	32	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	33	/* dump triangle list */
	34	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	35	/* dump cell list */
	36	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	37	/* dump poly list */
	38	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	39	/* dump filament list */
M	40	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	41	/* level 1 complete */
SP	42
	43	/dump vertices/
	44	for(i=0;i<vesicle->vlist->n;i++){
	45	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	46	/* dump pointer offsets for:
	47	neigh
	48	bond
	49	tria
	50	cell is ignored
	51	*/
	52	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	53	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	54	}
SP	55	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	56	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	57	}
SP	58	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	59	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	60	}
SP	61	}
	62
	63	/dump bonds/
	64	for(i=0;i<vesicle->blist->n;i++){
	65	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	66	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	67	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	68	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	69	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	70	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	71	}
SP	72
	73	/dump triangles/
	74	for(i=0;i<vesicle->tlist->n;i++){
	75	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	76	/* dump pointer offsets for vertex */
3c1ac1	77	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	78	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	79	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	80	/* dump pointer offsets for neigh */
SP	81	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	82	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	83	}
SP	84	}
	85
	86
	87	/dump polymeres /
	88	for(i=0;i<vesicle->poly_list->n;i++){
	89	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	90	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	91	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	92	}
SP	93
	94	/* dump poly vertex(monomer) list*/
	95	for(i=0;i<vesicle->poly_list->n;i++){
	96	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	97	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	98	/* dump offset for neigh and bond */
	99	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	100	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	101	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	102	}
SP	103	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	104	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	105	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	106	}
SP	107	}
3c1ac1	108	// grafted vtx on vesicle data dump
SP	109	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	110	}
SP	111	/* dump poly bonds between monomers list*/
	112	for(i=0;i<vesicle->poly_list->n;i++){
	113	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	114	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	115	/* dump vtx1 and vtx2 offsets */
3c1ac1	116	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	117	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	118	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	119	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	120	}
SP	121	}
	122
bcf455	123
M	124	/dump filamentes grandes svinjas /
	125	for(i=0;i<vesicle->filament_list->n;i++){
	126	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	127	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	128	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	129	}
	130
	131	/* dump filamentes vertex(monomer) list*/
	132	for(i=0;i<vesicle->filament_list->n;i++){
	133	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	134	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	135	/* dump offset for neigh and bond */
	136	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	137	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	138	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	139	}
	140	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	141	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	142	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	143	}
	144	}
	145	}
	146	/* dump poly bonds between monomers list*/
	147	for(i=0;i<vesicle->filament_list->n;i++){
	148	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	149	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	150	/* dump vtx1 and vtx2 offsets */
	151	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	152	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	153	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	154	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	155	}
	156	}
	157
	158
	159
e9eab4	160	/* pointer offsets for fixing the restored pointers */
SP	161	/* need pointers for
	162	vlist->vtx
	163	blist->bond
	164	tlist->tria
	165	clist->cell
	166	poly_list->poly
	167	and for each poly:
	168	poly_list->poly->vtx
	169	poly_list->poly->bond
	170	*/
	171
063289	172	fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	173	/* write tape information on vesicle */
SP	174	fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	175	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	176	fclose(fh);
SP	177	return TS_SUCCESS;
	178	}
	179
	180
	181	/ RESTORE DUMP FROM DISK /
1ab449	182	ts_vesicle restore_state(ts_uint iteration){
e9eab4	183	ts_uint i,j,k;
SP	184	FILE *fh=fopen("dump.bin","rb");
3f5c83	185
SP	186	struct stat sb;
	187	if (stat("dump.bin", &sb) == -1) {
	188	//dump file does not exist.
	189	return NULL;
	190	}
	191
	192	//check if it is regular file
	193	if((sb.st_mode & S_IFMT) != S_IFREG) {
	194	//dump file is not a regular file.
	195	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	196	return NULL;
	197	}
	198
e9eab4	199	ts_uint retval;
3c1ac1	200	ts_uint idx;
e9eab4	201
SP	202	/* we restore all the data from the dump */
	203	/* restore vesicle */
	204	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
86f5e7	205	retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
SP	206	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
	207
e9eab4	208	/* restore vertex list */
SP	209	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	210	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	211	/* restore bond list */
	212	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	213	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	214	/* restore triangle list */
	215	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	216	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	217	/* restore cell list */
	218	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	219	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	220	/* restore poly list */
	221	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	222	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	223	/* restore filament list */
M	224	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	225	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	226	/* level 1 complete */
SP	227
3c1ac1	228	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	229	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	230	for(i=0;i<vesicle->blist->n;i++){
	231	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	232	}
	233	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	234	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	235	for(i=0;i<vesicle->tlist->n;i++){
	236	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	237	}
a37ba2	238	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	239	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	240	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	241	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	242	}
SP	243	/restore vertices/
	244	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	245	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	246	/restore neigh, bond, tristar. Ignoring cell /
	247	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	248	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	249	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	250	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	251	}
SP	252	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	253	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	254	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	255	/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
	256	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	257	}
SP	258
	259	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	260	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	261	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	262	/* same comment as above */
	263	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	264	}
SP	265
	266	}
	267
	268	/restore bonds/
3c1ac1	269	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	270	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	271	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	272	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	273	/* restore vtx1 and vtx2 */
3c1ac1	274	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	275	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	276	retval=fread(&idx,sizeof(ts_uint),1,fh);
	277	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	278	}
SP	279
	280	/restore triangles/
3c1ac1	281	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	282	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	283	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	284	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	285	/* restore pointers for vertices */
3c1ac1	286	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	287	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	288	retval=fread(&idx,sizeof(ts_uint),1,fh);
	289	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	290	retval=fread(&idx,sizeof(ts_uint),1,fh);
	291	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	292	/* restore pointers for neigh */
3c1ac1	293	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	294	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	295	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	296	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	297	}
SP	298
	299	}
	300
	301	/restore cells /
	302	/TODO: do we need to recalculate cells here? /
	303	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	304	for(i=0;i<vesicle->clist->cellno;i++){
	305	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	306	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	307	}
	308	*/
	309	/restore polymeres /
	310	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	311	for(i=0;i<vesicle->poly_list->n;i++){
	312	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	313	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	314	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	315	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	316	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	317	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	318	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	319	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	320	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	321	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	322	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	323	}
	324	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	325	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	326	}
	327
e9eab4	328	}
3c1ac1	329
e9eab4	330
SP	331	/* restore poly vertex(monomer) list*/
	332	for(i=0;i<vesicle->poly_list->n;i++){
	333	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	334	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	335
e9eab4	336	/* restore neigh and bonds */
SP	337	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex ));
	338	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	339	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	340	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	341	}
SP	342	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond ));
	343	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	344	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	345	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	346	}
SP	347
	348	}
3c1ac1	349	/* restore grafted vtx on vesicle and grafted_poly */
SP	350	retval=fread(&idx,sizeof(ts_uint),1,fh);
	351	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	352	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	353	}
3c1ac1	354
e9eab4	355	/* restore poly bonds between monomers list*/
SP	356	for(i=0;i<vesicle->poly_list->n;i++){
	357	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	358	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	359	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	360	/* restore vtx1 and vtx2 */
3c1ac1	361	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	362	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	363	retval=fread(&idx,sizeof(ts_uint),1,fh);
	364	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	365	}
SP	366	}
	367
bcf455	368	/restore filaments /
M	369	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	370	for(i=0;i<vesicle->filament_list->n;i++){
	371	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	372	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	373	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	374	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	375	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	376	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	377	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	378	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	379	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	380	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	381	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	382	}
	383	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	384	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	385	}
	386
	387	}
	388
	389
	390	/* restore poly vertex(monomer) list*/
	391	for(i=0;i<vesicle->filament_list->n;i++){
	392	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	393	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	394
	395	/* restore neigh and bonds */
	396	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex ));
	397	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	398	retval=fread(&idx,sizeof(ts_uint),1,fh);
	399	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	400	}
	401	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond ));
	402	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	403	retval=fread(&idx,sizeof(ts_uint),1,fh);
	404	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	405	}
	406
	407	}
	408	}
	409
	410	/* restore poly bonds between monomers list*/
	411	for(i=0;i<vesicle->filament_list->n;i++){
	412	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	413	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	414	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	415	/* restore vtx1 and vtx2 */
	416	retval=fread(&idx,sizeof(ts_uint),1,fh);
	417	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	418	retval=fread(&idx,sizeof(ts_uint),1,fh);
	419	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	420	}
	421	}
47a7ac	422	vesicle->tape=parsetape("tape");
063289	423	// recreating space for cells //
055dd7	424	vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
SP	425
47a7ac	426	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	427	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	428	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	429	if(retval);
SP	430	fclose(fh);
	431	return vesicle;
	432	}
	433
	434
	435
083e03	436	ts_bool parse_args(int argc, char **argv){
3f5c83	437	int c, retval;
SP	438	struct stat sb;
	439	sprintf(command_line_args.path, "./"); //clear string;
	440	sprintf(command_line_args.output_fullfilename,"./output.pvd");
	441	sprintf(command_line_args.dump_fullfilename,"./dump.bin");
	442	sprintf(command_line_args.tape_fullfilename,"./tape");
	443	FILE *file;
	444
083e03	445	while (1)
SP	446	{
	447	static struct option long_options[] =
	448	{
8a6614	449	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	450	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	451	{"tape", no_argument, 0, 't'},
SP	452	{"output-file", required_argument, 0, 'o'},
	453	{"directory", required_argument, 0, 'd'},
3f5c83	454	{"dump-filename", required_argument,0, 'f'},
083e03	455	{0, 0, 0, 0}
SP	456	};
	457	/* getopt_long stores the option index here. */
	458	int option_index = 0;
	459
3f5c83	460	c = getopt_long (argc, argv, "d:f:o:t:",
083e03	461	long_options, &option_index);
SP	462
	463	/* Detect the end of the options. */
	464	if (c == -1)
	465	break;
	466
	467	switch (c)
	468	{
	469	case 0:
	470	/* If this option set a flag, do nothing else now. */
	471	if (long_options[option_index].flag != 0)
	472	break;
	473	printf ("option %s", long_options[option_index].name);
	474	if (optarg)
	475	printf (" with arg %s", optarg);
	476	printf ("\n");
	477	break;
	478
	479	case 't':
	480	//check if tape exists. If not, fail immediately.
3f5c83	481	if (stat(optarg, &sb) == -1) {
SP	482	ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
	483	fatal("Please select correct tape",1);
	484	} else {
	485	strcpy(command_line_args.tape_fullfilename,optarg);
	486	}
083e03	487	break;
SP	488
	489	case 'o':
	490	//set filename of master output file
3f5c83	491	if ((file = fopen(optarg, "w")) == NULL) {
SP	492	fprintf(stderr,"Could not create output file!\n");
	493	fatal("Please specify correct output file",1);
	494
	495	} else {
	496	fclose(file);
	497	}
	498	strcpy(command_line_args.output_fullfilename, optarg);
	499	break;
083e03	500
SP	501	case 'd':
	502	//check if directory exists. If not create one. If creation is
	503	//successful, set directory for output files.
	504	//printf ("option -d with value `%s'\n", optarg);
3f5c83	505	if (stat(optarg, &sb) == -1) {
SP	506	//directory does not exist
083e03	507	retval=mkdir(optarg, 0700);
SP	508	if(retval){
3f5c83	509	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	510	}
SP	511	}
3f5c83	512	//check if is a proper directory
SP	513	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	514	//it is not a directory. fatal error.
	515	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	516	fatal("Cannot continue",1);
083e03	517	}
3f5c83	518	strcpy(command_line_args.path, optarg);
083e03	519	break;
SP	520
	521	case 'f':
	522	//check if dump file specified exists. Defaults to dump.bin
3f5c83	523	if ((file = fopen(optarg, "w")) == NULL) {
SP	524	fprintf(stderr,"Could not create dump file!\n");
	525	fatal("Please specify correct dump file",1);
	526
	527	} else {
	528	fclose(file);
	529	}
	530	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	531	break;
SP	532
	533	case '?':
	534	/* getopt_long already printed an error message. */
	535
	536	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	537	fatal("Ooops, read help first",1);
	538	break;
	539
	540	default:
	541	exit (1);
	542	}
	543	}
	544
	545	return TS_SUCCESS;
	546
	547	}
	548
	549
	550
	551
d7639a	552	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	553	ts_uint i;
	554	printf("Number of vertices: %u\n",vlist->n);
	555	for(i=0;i<vlist->n;i++){
a6b1b5	556	printf("%u: %f %f %f\n",
8f6a69	557	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	558	}
SP	559	return TS_SUCCESS;
	560	}
	561
	562	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	563	ts_uint i,j;
a6b1b5	564	ts_vertex **vtx=vlist->vtx;
d7639a	565	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	566	for(i=0;i<vlist->n;i++){
8f6a69	567	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	568	for(j=0;j<vtx[i]->neigh_no;j++){
	569	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	570	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	571	}
SP	572	printf("\n");
	573	}
	574
	575	return TS_SUCCESS;
	576	}
	577
	578	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	579	ts_vertex **vtx=vlist->vtx;
d7639a	580	ts_uint i;
SP	581	FILE *fh;
	582
	583	fh=fopen(filename, "w");
	584	if(fh==NULL){
	585	err("Cannot open file %s for writing");
	586	return TS_FAIL;
	587	}
	588	for(i=0;i<vlist->n;i++)
8f6a69	589	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	590
SP	591	fclose(fh);
	592	return TS_SUCCESS;
	593	}
	594
	595
	596	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	597	ts_uint i,j;
	598	for(i=0;i<vlist->n;i++){
8f6a69	599	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	600	vlist->vtx[i]->y, vlist->vtx[i]->z,
	601	vlist->vtx[i]->neigh_no);
	602	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	603	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	604	//-vlist->vtx+1));
d7639a	605	}
SP	606	fprintf(fh,"\n");
	607	}
	608	return TS_SUCCESS;
	609	}
	610
	611	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	612	ts_uint i,j;
a6b1b5	613	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	614	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	615	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	616	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	617	}
SP	618	fprintf(fh,"\n");
	619	}
	620	return TS_SUCCESS;
	621	}
	622
	623	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	624	ts_triangle_list *tlist=vesicle->tlist;
d7639a	625	ts_uint i,j;
SP	626	for(i=0;i<tlist->n;i++){
41a035	627	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	628	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	629	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	630	}
SP	631	fprintf(fh,"\n");
	632	for(j=0;j<3;j++){
41a035	633	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	634	}
SP	635	fprintf(fh,"\n");
41a035	636	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	637	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	638	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	639	}
	640	return TS_SUCCESS;
	641	}
	642
	643	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	644	ts_uint i,j;
	645	for(i=0;i<vlist->n;i++){
	646	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	647	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	648	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	649	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	650	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	651	}
SP	652	fprintf(fh,"\n");
cef6ca	653	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	654	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	655	}
SP	656	fprintf(fh,"\n");
	657	}
	658	return TS_SUCCESS;
	659	}
	660
	661	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	662	ts_uint i;
a6b1b5	663	for(i=0;i<vesicle->blist->n;i++){
e016c4	664	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	665	//-vesicle->vlist->vtx+1),
e016c4	666	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	667	//-vesicle->vlist.vtx+1));
d7639a	668	}
SP	669	return TS_SUCCESS;
	670	}
	671
	672
	673	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	674	FILE *fh;
	675	fh=fopen(filename, "w");
	676	if(fh==NULL){
	677	err("Cannot open file %s for writing");
	678	return TS_FAIL;
	679	}
	680	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	681	fprint_vertex_list(fh,vesicle->vlist);
d7639a	682	fprint_tristar(fh,vesicle);
SP	683	fprint_triangle_list(fh,vesicle);
a6b1b5	684	fprint_vertex_data(fh,vesicle->vlist);
d7639a	685	fprint_bonds(fh,vesicle);
SP	686	fclose(fh);
	687	return TS_SUCCESS;
	688	}
	689
	690	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	691	FILE *fh;
	692	char line[255];
	693	fh=fopen(filename, "r");
	694	if(fh==NULL){
	695	err("Cannot open file for reading... Nonexistant file?");
	696	return TS_FAIL;
	697	}
a6b1b5	698	ts_uint retval=1;
d7639a	699	while(retval!=EOF){
SP	700	retval=fscanf(fh,"%s",line);
	701
	702	fprintf(stderr,"%s",line);
	703	}
	704	fclose(fh);
	705	return TS_SUCCESS;
	706	}
	707
	708	ts_bool write_master_xml_file(ts_char *filename){
	709	FILE *fh;
	710	ts_char i,j;
	711	ts_uint tstep;
	712	ts_char *number;
	713	fh=fopen(filename, "w");
	714	if(fh==NULL){
	715	err("Cannot open file %s for writing");
	716	return TS_FAIL;
	717	}
	718
	719	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	720	DIR *dir = opendir(".");
	721	if(dir){
	722	struct dirent *ent;
	723	tstep=0;
	724	while((ent = readdir(dir)) != NULL)
	725	{
	726	i=rindex(ent->d_name,'.');
	727	if(i==NULL) continue;
	728	if(strcmp(i+1,"vtu")==0){
	729	j=rindex(ent->d_name,'_');
	730	if(j==NULL) continue;
	731	number=strndup(j+1,j-i);
a6b1b5	732	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	733	tstep++;
SP	734	free(number);
	735	}
	736	}
	737	}
f74313	738	free(dir);
d7639a	739	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	740	fclose(fh);
	741	return TS_SUCCESS;
	742	}
	743
	744	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	745	ts_vertex_list *vlist=vesicle->vlist;
SP	746	ts_bond_list *blist=vesicle->blist;
	747	ts_vertex **vtx=vlist->vtx;
40aa5b	748	ts_uint i,j;
d7639a	749	char filename[255];
SP	750	FILE *fh;
	751
	752	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	753	fh=fopen(filename, "w");
	754	if(fh==NULL){
	755	err("Cannot open file %s for writing");
	756	return TS_FAIL;
	757	}
	758	/* Here comes header of the file */
40aa5b	759
SP	760	//find number of extra vtxs and bonds of polymeres
58230a	761	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	762	ts_bool poly=0, fil=0;
40aa5b	763	if(vesicle->poly_list!=NULL){
SP	764	if(vesicle->poly_list->poly[0]!=NULL){
	765	polyno=vesicle->poly_list->n;
	766	monono=vesicle->poly_list->poly[0]->vlist->n;
	767	poly=1;
	768	}
	769	}
58230a	770
M	771	if(vesicle->filament_list!=NULL){
	772	if(vesicle->filament_list->poly[0]!=NULL){
	773	filno=vesicle->filament_list->n;
	774	fonono=vesicle->filament_list->poly[0]->vlist->n;
	775	fil=1;
	776	}
	777	}
	778
d7639a	779	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
58230a	780	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	781	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	782	for(i=0;i<vlist->n;i++){
a6b1b5	783	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	784	}
40aa5b	785	//polymeres
SP	786	if(poly){
3c1ac1	787	poly_idx=vlist->n;
40aa5b	788	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	789	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	790	fprintf(fh,"%u ", poly_idx);
M	791	}
	792	}
	793	}
	794	//filaments
	795	if(fil){
	796	poly_idx=vlist->n+monono*polyno;
	797	for(i=0;i<vesicle->filament_list->n;i++){
	798	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	799	// fprintf(stderr,"was here\n");
3c1ac1	800	fprintf(fh,"%u ", poly_idx);
40aa5b	801	}
SP	802	}
	803	}
d7639a	804
SP	805	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	806	for(i=0;i<vlist->n;i++){
8f6a69	807	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	808	}
SP	809	//polymeres
	810	if(poly){
	811	for(i=0;i<vesicle->poly_list->n;i++){
	812	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	813	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	814	}
M	815	}
	816	}
	817	//filaments
	818	if(fil){
	819	for(i=0;i<vesicle->filament_list->n;i++){
	820	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	821	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	822	}
SP	823	}
d7639a	824	}
SP	825
	826	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	827	for(i=0;i<blist->n;i++){
e016c4	828	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	829	}
40aa5b	830	//polymeres
SP	831	if(poly){
3c1ac1	832	poly_idx=vlist->n;
40aa5b	833	for(i=0;i<vesicle->poly_list->n;i++){
SP	834	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	835	// 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	836	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	837	}
SP	838	//grafted bonds
3c1ac1	839	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	840	}
SP	841
	842	}
	843
58230a	844	//filaments
M	845	if(fil){
	846	poly_idx=vlist->n+monono*polyno;
	847	for(i=0;i<vesicle->filament_list->n;i++){
	848	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	849	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);
	850	// fprintf(stderr,"was here\n");
	851
	852	}
	853	}
	854
	855	}
40aa5b	856
d7639a	857	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	858	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	859	fprintf(fh,"%u ",i);
SP	860	}
	861	fprintf(fh,"\n");
	862	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	863	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	864	fprintf(fh,"3 ");
SP	865	}
	866
	867	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	868	fclose(fh);
	869	return TS_SUCCESS;
	870
	871	}
	872
	873	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	874	ts_vertex_list *vlist=vesicle->vlist;
SP	875	ts_bond_list *blist=vesicle->blist;
	876	ts_vertex **vtx=vlist->vtx;
	877	ts_uint i;
d7639a	878	FILE *fh;
SP	879
	880	fh=fopen(filename, "w");
	881	if(fh==NULL){
	882	err("Cannot open file %s for writing");
	883	return TS_FAIL;
	884	}
	885	/* Here comes header of the file */
	886	// fprintf(stderr,"NSHELL=%u\n",nshell);
	887	fprintf(fh, "# vtk DataFile Version 2.0\n");
	888	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	889	fprintf(fh, "%s\n", text);
	890	fprintf(fh,"ASCII\n");
	891	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	892	fprintf(fh,"POINTS %u double\n", vlist->n);
	893	for(i=0;i<vlist->n;i++){
8f6a69	894	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	895	}
SP	896
	897	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	898	for(i=0;i<blist->n;i++){
e016c4	899	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	900	}
SP	901	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	902	for(i=0;i<blist->n;i++)
	903	fprintf(fh,"3\n");
	904
	905	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	906	fprintf(fh,"SCALARS scalars long 1\n");
	907	fprintf(fh,"LOOKUP_TABLE default\n");
	908
	909	for(i=0;i<vlist->n;i++)
8f6a69	910	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	911
SP	912	fclose(fh);
	913	return TS_SUCCESS;
	914	}
	915
	916
	917
144784	918	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	919	FILE *fh;
	920	ts_uint i;
	921
	922	fh=fopen(filename, "w");
	923	if(fh==NULL){
	924	err("Cannot open file %s for writing");
	925	return TS_FAIL;
	926	}
	927
	928	for(i=0;i<vesicle->tlist->n;i++){
	929
	930	fprintf(fh,"\ttriangle {");
	931	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	932	vesicle->tlist->tria[i]->vertex[0]->x,
	933	vesicle->tlist->tria[i]->vertex[0]->y,
	934	vesicle->tlist->tria[i]->vertex[0]->z,
	935
	936	vesicle->tlist->tria[i]->vertex[1]->x,
	937	vesicle->tlist->tria[i]->vertex[1]->y,
	938	vesicle->tlist->tria[i]->vertex[1]->z,
	939
	940	vesicle->tlist->tria[i]->vertex[2]->x,
	941	vesicle->tlist->tria[i]->vertex[2]->y,
	942	vesicle->tlist->tria[i]->vertex[2]->z
	943	);
	944	}
	945
	946	fclose(fh);
	947	return TS_SUCCESS;
	948	}
	949
	950
1ab449	951	ts_tape parsetape(char filename){
SP	952	// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
	953	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	954	tape->multiprocessing=calloc(255,sizeof(char));
	955	/* long int brezveze0=1;
b14a8d	956	long int brezveze1=1;
SP	957	long int brezveze2=1;
e86357	958	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	959	long int iter=1000, init=1000, mcsw=1000;
1ab449	960	*/
40aa5b	961
d7639a	962	cfg_opt_t opts[] = {
1ab449	963	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	964	CFG_SIMPLE_INT("npoly", &tape->npoly),
	965	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	966	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	967	CFG_SIMPLE_INT("nfono",&tape->nfono),
	968	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
	969	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	970	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	971	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	972	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	973	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
43c042	974	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	975	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	976	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	977	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	978	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	979	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	980	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	981	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	982	CFG_SIMPLE_INT("iterations",&tape->iterations),
	983	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	984	CFG_SIMPLE_INT("inititer", &tape->inititer),
	985	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	986	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	987	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	988	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	989	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	990	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	991	CFG_END()
SP	992	};
	993	cfg_t *cfg;
	994	ts_uint retval;
	995	cfg = cfg_init(opts, 0);
1ab449	996	retval=cfg_parse(cfg, filename);
d7639a	997	if(retval==CFG_FILE_ERROR){
a6b1b5	998	fatal("No tape file.",100);
d7639a	999	}
SP	1000	else if(retval==CFG_PARSE_ERROR){
	1001	fatal("Invalid tape!",100);
	1002	}
a2db52	1003
d7639a	1004	cfg_free(cfg);
40aa5b	1005
SP	1006
1ab449	1007	/* global variables are set automatically */
SP	1008	quiet=tape->quiet;
	1009	return tape;
	1010	}
d7639a	1011
1ab449	1012	ts_bool tape_free(ts_tape *tape){
SP	1013	free(tape->multiprocessing);
	1014	free(tape);
	1015	return TS_SUCCESS;
d7639a	1016	}
f74313	1017
SP	1018
	1019	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	1020	FILE *fh;
	1021	ts_uint i, nvtx,nedges,ntria;
	1022	ts_uint vtxi1,vtxi2;
	1023	float x,y,z;
	1024	ts_vertex_list *vlist;
	1025	fh=fopen(fname, "r");
	1026	if(fh==NULL){
	1027	err("Cannot open file for reading... Nonexistant file?");
	1028	return TS_FAIL;
	1029	}
	1030	ts_uint retval;
	1031	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1032	vesicle->vlist=init_vertex_list(nvtx);
	1033	vlist=vesicle->vlist;
	1034	for(i=0;i<nvtx;i++){
8f6a69	1035	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1036	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1037	vlist->vtx[i]->x=x;
SP	1038	vlist->vtx[i]->y=y;
	1039	vlist->vtx[i]->z=z;
f74313	1040	}
SP	1041	for(i=0;i<nedges;i++){
	1042	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1043	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1044	}
	1045	//TODO: neighbours from bonds,
	1046	//TODO: triangles from neigbours
	1047
	1048	// Don't need to read triangles. Already have enough data
	1049	/*
	1050	for(i=0;i<ntria;i++){
	1051	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1052	vtxi1=vesicle->blist->vertex1->idx;
SP	1053	vtxi2=vesicle->blist->vertex1->idx;
f74313	1054
SP	1055	}
	1056	*/
41a035	1057	if(retval);
f74313	1058	fclose(fh);
SP	1059
	1060
	1061
	1062	return TS_SUCCESS;
	1063	}