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Nucleus translates with the vesicle. Dump and restore includes optional <nu...

Samo Penic

2016-05-31 4891eb093f61d37056c50c572e669349dd49a65a

commit \| author \| age
7f6076	1	/* vim: set ts=4 sts=4 sw=4 noet : */
f74313	2	#include "general.h"
d7639a	3	#include<stdio.h>
SP	4	#include "io.h"
f74313	5	#include "vertex.h"
SP	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>
854cb6	19	#include <snapshot.h>
e9eab4	20	/ DUMP STATE TO DISK DRIVE /
SP	21
1ab449	22	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	23
SP	24	/* save current state with wrong pointers. Will fix that later */
	25	ts_uint i,j,k;
267db5	26	FILE *fh=fopen(command_line_args.dump_fullfilename,"wb");
e9eab4	27
SP	28	/* dump vesicle */
d0a1d3	29	fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
e9eab4	30	/* dump vertex list */
SP	31	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	32	/* dump bond list */
	33	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	34	/* dump triangle list */
	35	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	36	/* dump cell list */
	37	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	38	/* dump poly list */
	39	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	40	/* dump filament list */
M	41	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	42	/* level 1 complete */
SP	43
	44	/dump vertices/
	45	for(i=0;i<vesicle->vlist->n;i++){
	46	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	47	/* dump pointer offsets for:
	48	neigh
	49	bond
	50	tria
	51	cell is ignored
	52	*/
	53	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	54	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	55	}
SP	56	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	57	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	58	}
SP	59	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	60	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	61	}
SP	62	}
	63
	64	/dump bonds/
	65	for(i=0;i<vesicle->blist->n;i++){
	66	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	67	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	68	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	69	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	70	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	71	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	72	}
SP	73
	74	/dump triangles/
	75	for(i=0;i<vesicle->tlist->n;i++){
	76	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	77	/* dump pointer offsets for vertex */
3c1ac1	78	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	79	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	80	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	81	/* dump pointer offsets for neigh */
SP	82	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	83	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	84	}
SP	85	}
	86
	87
	88	/dump polymeres /
	89	for(i=0;i<vesicle->poly_list->n;i++){
	90	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	91	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	92	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	93	}
SP	94
	95	/* dump poly vertex(monomer) list*/
	96	for(i=0;i<vesicle->poly_list->n;i++){
	97	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	98	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	99	/* dump offset for neigh and bond */
	100	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	101	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	102	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	103	}
SP	104	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	105	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	106	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	107	}
SP	108	}
3c1ac1	109	// grafted vtx on vesicle data dump
SP	110	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	111	}
SP	112	/* dump poly bonds between monomers list*/
	113	for(i=0;i<vesicle->poly_list->n;i++){
	114	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	115	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	116	/* dump vtx1 and vtx2 offsets */
3c1ac1	117	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	118	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	119	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	120	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	121	}
SP	122	}
	123
bcf455	124
M	125	/dump filamentes grandes svinjas /
	126	for(i=0;i<vesicle->filament_list->n;i++){
	127	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	128	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	129	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	130	}
	131
	132	/* dump filamentes vertex(monomer) list*/
	133	for(i=0;i<vesicle->filament_list->n;i++){
	134	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	135	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	136	/* dump offset for neigh and bond */
	137	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	138	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	139	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	140	}
	141	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	142	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	143	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	144	}
	145	}
	146	}
	147	/* dump poly bonds between monomers list*/
	148	for(i=0;i<vesicle->filament_list->n;i++){
	149	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	150	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	151	/* dump vtx1 and vtx2 offsets */
	152	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	153	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	154	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	155	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	156	}
	157	}
	158
	159
	160
e9eab4	161	/* pointer offsets for fixing the restored pointers */
SP	162	/* need pointers for
	163	vlist->vtx
	164	blist->bond
	165	tlist->tria
	166	clist->cell
	167	poly_list->poly
	168	and for each poly:
	169	poly_list->poly->vtx
	170	poly_list->poly->bond
	171	*/
	172
bd2210	173	// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	174	/* write tape information on vesicle */
bd2210	175	// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	176	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	177	fclose(fh);
SP	178	return TS_SUCCESS;
	179	}
	180
	181
	182	/ RESTORE DUMP FROM DISK /
1ab449	183	ts_vesicle restore_state(ts_uint iteration){
e9eab4	184	ts_uint i,j,k;
267db5	185	FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
3f5c83	186
SP	187	struct stat sb;
267db5	188	if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
3f5c83	189	//dump file does not exist.
SP	190	return NULL;
	191	}
	192
	193	//check if it is regular file
	194	if((sb.st_mode & S_IFMT) != S_IFREG) {
	195	//dump file is not a regular file.
	196	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	197	return NULL;
	198	}
	199
e9eab4	200	ts_uint retval;
3c1ac1	201	ts_uint idx;
e9eab4	202
SP	203	/* we restore all the data from the dump */
	204	/* restore vesicle */
	205	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
d0a1d3	206	retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
86f5e7	207	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
SP	208
e9eab4	209	/* restore vertex list */
SP	210	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	211	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	212	/* restore bond list */
	213	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	214	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	215	/* restore triangle list */
	216	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	217	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	218	/* restore cell list */
	219	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	220	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	221	/* restore poly list */
	222	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	223	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	224	/* restore filament list */
M	225	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	226	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	227	/* level 1 complete */
SP	228
3c1ac1	229	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	230	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	231	for(i=0;i<vesicle->blist->n;i++){
	232	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	233	}
	234	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	235	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	236	for(i=0;i<vesicle->tlist->n;i++){
	237	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	238	}
a37ba2	239	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	240	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	241	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	242	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	243	}
SP	244	/restore vertices/
	245	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	246	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	247	/restore neigh, bond, tristar. Ignoring cell /
	248	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	249	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	250	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	251	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	252	}
SP	253	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	254	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	255	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	256	/* 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 */
	257	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	258	}
SP	259
	260	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	261	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	262	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	263	/* same comment as above */
	264	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	265	}
SP	266
	267	}
	268
	269	/restore bonds/
3c1ac1	270	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	271	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	272	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	273	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	274	/* restore vtx1 and vtx2 */
3c1ac1	275	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	276	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	277	retval=fread(&idx,sizeof(ts_uint),1,fh);
	278	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	279	}
SP	280
	281	/restore triangles/
3c1ac1	282	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	283	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	284	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	285	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	286	/* restore pointers for vertices */
3c1ac1	287	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	288	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	289	retval=fread(&idx,sizeof(ts_uint),1,fh);
	290	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	291	retval=fread(&idx,sizeof(ts_uint),1,fh);
	292	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	293	/* restore pointers for neigh */
3c1ac1	294	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	295	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	296	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	297	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	298	}
SP	299
	300	}
	301
	302	/restore cells /
	303	/TODO: do we need to recalculate cells here? /
	304	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	305	for(i=0;i<vesicle->clist->cellno;i++){
	306	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	307	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	308	}
	309	*/
	310	/restore polymeres /
	311	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	312	for(i=0;i<vesicle->poly_list->n;i++){
	313	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	314	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	315	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	316	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	317	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	318	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	319	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	320	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	321	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	322	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	323	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	324	}
	325	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	326	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	327	}
	328
e9eab4	329	}
3c1ac1	330
e9eab4	331
SP	332	/* restore poly vertex(monomer) list*/
	333	for(i=0;i<vesicle->poly_list->n;i++){
	334	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	335	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	336
e9eab4	337	/* restore neigh and bonds */
SP	338	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 ));
	339	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	340	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	341	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	342	}
SP	343	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 ));
	344	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	345	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	346	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	347	}
SP	348
	349	}
3c1ac1	350	/* restore grafted vtx on vesicle and grafted_poly */
SP	351	retval=fread(&idx,sizeof(ts_uint),1,fh);
	352	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	353	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	354	}
3c1ac1	355
e9eab4	356	/* restore poly bonds between monomers list*/
SP	357	for(i=0;i<vesicle->poly_list->n;i++){
	358	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	359	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	360	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	361	/* restore vtx1 and vtx2 */
3c1ac1	362	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	363	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	364	retval=fread(&idx,sizeof(ts_uint),1,fh);
	365	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	366	}
SP	367	}
	368
bcf455	369	/restore filaments /
M	370	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	371	for(i=0;i<vesicle->filament_list->n;i++){
	372	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	373	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	374	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	375	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	376	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	377	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	378	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	379	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	380	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	381	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	382	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	383	}
	384	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	385	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	386	}
	387
	388	}
	389
	390
	391	/* restore poly vertex(monomer) list*/
	392	for(i=0;i<vesicle->filament_list->n;i++){
	393	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	394	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	395
	396	/* restore neigh and bonds */
	397	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 ));
	398	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	399	retval=fread(&idx,sizeof(ts_uint),1,fh);
	400	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	401	}
	402	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 ));
	403	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	404	retval=fread(&idx,sizeof(ts_uint),1,fh);
	405	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	406	}
	407
	408	}
	409	}
	410
	411	/* restore poly bonds between monomers list*/
	412	for(i=0;i<vesicle->filament_list->n;i++){
	413	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	414	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	415	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	416	/* restore vtx1 and vtx2 */
	417	retval=fread(&idx,sizeof(ts_uint),1,fh);
	418	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	419	retval=fread(&idx,sizeof(ts_uint),1,fh);
	420	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	421	}
	422	}
267db5	423	vesicle->tape=parsetape(command_line_args.tape_fullfilename);
063289	424	// recreating space for cells //
055dd7	425	vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
364c30	426	vesicle->clist->max_occupancy=8;
47a7ac	427	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	428	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	429	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	430	if(retval);
SP	431	fclose(fh);
	432	return vesicle;
	433	}
	434
	435
	436
083e03	437	ts_bool parse_args(int argc, char **argv){
3f5c83	438	int c, retval;
SP	439	struct stat sb;
	440	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	441	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	442	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	443	sprintf(command_line_args.tape_fullfilename,"tape");
1bf3c3	444	sprintf(command_line_args.tape_templatefull,"./tape");
3f5c83	445	FILE *file;
SP	446
083e03	447	while (1)
SP	448	{
	449	static struct option long_options[] =
	450	{
8a6614	451	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	452	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	453	{"tape", no_argument, 0, 't'},
fd8126	454	{"version", no_argument, 0, 'v'},
083e03	455	{"output-file", required_argument, 0, 'o'},
SP	456	{"directory", required_argument, 0, 'd'},
3f5c83	457	{"dump-filename", required_argument,0, 'f'},
7b0c07	458	{"tape-options",required_argument,0,'c'},
1bf3c3	459	{"tape-template", required_argument,0,0},
ab798b	460	{"restore-from-vtk",required_argument,0,0},
083e03	461	{0, 0, 0, 0}
SP	462	};
	463	/* getopt_long stores the option index here. */
	464	int option_index = 0;
	465
fd8126	466	c = getopt_long (argc, argv, "d:f:o:t:c:v",
083e03	467	long_options, &option_index);
SP	468
	469	/* Detect the end of the options. */
	470	if (c == -1)
	471	break;
	472
	473	switch (c)
	474	{
	475	case 0:
	476	/* If this option set a flag, do nothing else now. */
	477	if (long_options[option_index].flag != 0)
	478	break;
1bf3c3	479	/* printf ("option %s", long_options[option_index].name);
083e03	480	if (optarg)
1bf3c3	481	printf (" with arg %s", optarg);
SP	482	printf ("\n"); */
	483	//TODO: find a better way.
	484	if(strcmp(long_options[option_index].name,"tape-template")==0){
	485	strcpy(command_line_args.tape_templatefull,optarg);
	486	}
ab798b	487	if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
ee84bd	488	strcpy(command_line_args.dump_from_vtk,optarg);
SP	489	}
083e03	490	break;
fd8126	491	case 'v':
SP	492	fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	493	fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
	494	fprintf(stdout,"Released under terms of GPLv3\n");
	495	exit(0);
083e03	496
7b0c07	497	case 'c':
SP	498	strcpy(command_line_args.tape_opts,optarg);
	499	break;
	500	case 't': //tape
3f5c83	501	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	502	break;
SP	503
7b0c07	504	case 'o': //set filename of master pvd output file
3f5c83	505	strcpy(command_line_args.output_fullfilename, optarg);
SP	506	break;
083e03	507
SP	508	case 'd':
	509	//check if directory exists. If not create one. If creation is
	510	//successful, set directory for output files.
	511	//printf ("option -d with value `%s'\n", optarg);
3f5c83	512	if (stat(optarg, &sb) == -1) {
SP	513	//directory does not exist
083e03	514	retval=mkdir(optarg, 0700);
SP	515	if(retval){
3f5c83	516	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	517	}
SP	518	}
3f5c83	519	//check if is a proper directory
SP	520	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	521	//it is not a directory. fatal error.
	522	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	523	fatal("Cannot continue",1);
083e03	524	}
3f5c83	525	strcpy(command_line_args.path, optarg);
083e03	526	break;
SP	527
	528	case 'f':
3f5c83	529	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	530	break;
SP	531
	532	case '?':
	533	/* getopt_long already printed an error message. */
ba73ab	534	print_help(stdout);
SP	535	//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
083e03	536	fatal("Ooops, read help first",1);
SP	537	break;
	538
	539	default:
	540	exit (1);
	541	}
	542	}
	543
7b0c07	544	//Here we set correct values for full filenames!
SP	545	char buffer=(char )malloc(10000*sizeof(char));
	546	//correct the path and add trailing /
	547	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	548
	549	/* master pvd output file */
	550	strcpy(buffer,command_line_args.path);
	551	strcat(buffer,command_line_args.output_fullfilename);
	552	if ((file = fopen(buffer, "w")) == NULL) {
	553	fprintf(stderr,"Could not create output file %s!\n", buffer);
	554	fatal("Please specify correct output file or check permissions of the file",1);
1bf3c3	555	//there is a tape template. make a copy into desired directory
7b0c07	556
SP	557	} else {
	558	fclose(file);
	559	strcpy(command_line_args.output_fullfilename,buffer);
	560	}
	561
	562	/* tape file */
	563	strcpy(buffer,command_line_args.path);
	564	strcat(buffer,command_line_args.tape_fullfilename);
	565	if (stat(buffer, &sb) == -1) {
1bf3c3	566
SP	567	//tape does not exist. does tape template exist?
	568	if(stat(command_line_args.tape_templatefull, &sb)==-1){
	569	ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
	570	fatal("Please select correct tape or check permissions of the file",1);
	571	} else {
	572	//tape template found
	573	fatal("Samo did not program template copy yet",1);
	574	}
7b0c07	575	} else {
SP	576	strcpy(command_line_args.tape_fullfilename,buffer);
	577	}
	578
	579
	580	/* dump file */
	581	strcpy(buffer,command_line_args.path);
	582	strcat(buffer,command_line_args.dump_fullfilename);
	583	//check if dump file exist first.
	584	if (stat(buffer, &sb) == -1) {
	585	//no dump file. check if we can create one.
	586	if ((file = fopen(buffer, "w")) == NULL) {
	587	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	588	fatal("Please specify correct dump file or check permissions of the file",1);
	589	} else {
	590	fclose(file);
	591	//good, file is writeable. delete it for now.
	592	remove(buffer);
	593	}
	594	}
	595	strcpy(command_line_args.dump_fullfilename, buffer);
	596
	597
	598	free(buffer);
083e03	599	return TS_SUCCESS;
SP	600
	601	}
	602
	603
ba73ab	604	ts_bool print_help(FILE *fd){
SP	605	fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	606	fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
	607	fprintf(fd,"Released under terms of GPLv3\n\n");
	608
	609	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");
	610	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");
	611	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");
	612	fprintf(fd,"Flags:\n\n");
	613	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");
	614	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	615	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
ba73ab	616	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
SP	617	fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
	618	fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
c4178c	619	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
SP	620	fprintf(fd,"Examples:\n\n");
	621	fprintf(fd,"trisurf --force-from-tape\n");
	622	fprintf(fd,"trisurf --reset-iteration-count\n");
	623	fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
	624	fprintf(fd,"\n\n");
	625
ba73ab	626	return TS_SUCCESS;
SP	627	}
	628
	629
083e03	630
d7639a	631	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	632	ts_uint i;
	633	printf("Number of vertices: %u\n",vlist->n);
	634	for(i=0;i<vlist->n;i++){
a6b1b5	635	printf("%u: %f %f %f\n",
8f6a69	636	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	637	}
SP	638	return TS_SUCCESS;
	639	}
	640
	641	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	642	ts_uint i,j;
a6b1b5	643	ts_vertex **vtx=vlist->vtx;
d7639a	644	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	645	for(i=0;i<vlist->n;i++){
8f6a69	646	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	647	for(j=0;j<vtx[i]->neigh_no;j++){
	648	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	649	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	650	}
SP	651	printf("\n");
	652	}
	653
	654	return TS_SUCCESS;
	655	}
	656
	657	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	658	ts_vertex **vtx=vlist->vtx;
d7639a	659	ts_uint i;
SP	660	FILE *fh;
	661
	662	fh=fopen(filename, "w");
	663	if(fh==NULL){
	664	err("Cannot open file %s for writing");
	665	return TS_FAIL;
	666	}
	667	for(i=0;i<vlist->n;i++)
8f6a69	668	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	669
SP	670	fclose(fh);
	671	return TS_SUCCESS;
	672	}
	673
	674
	675	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	676	ts_uint i,j;
	677	for(i=0;i<vlist->n;i++){
8f6a69	678	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	679	vlist->vtx[i]->y, vlist->vtx[i]->z,
	680	vlist->vtx[i]->neigh_no);
	681	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	682	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	683	//-vlist->vtx+1));
d7639a	684	}
SP	685	fprintf(fh,"\n");
	686	}
	687	return TS_SUCCESS;
	688	}
	689
	690	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	691	ts_uint i,j;
a6b1b5	692	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	693	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	694	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	695	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	696	}
SP	697	fprintf(fh,"\n");
	698	}
	699	return TS_SUCCESS;
	700	}
	701
	702	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	703	ts_triangle_list *tlist=vesicle->tlist;
d7639a	704	ts_uint i,j;
SP	705	for(i=0;i<tlist->n;i++){
41a035	706	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	707	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	708	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	709	}
SP	710	fprintf(fh,"\n");
	711	for(j=0;j<3;j++){
41a035	712	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	713	}
SP	714	fprintf(fh,"\n");
41a035	715	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	716	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	717	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	718	}
	719	return TS_SUCCESS;
	720	}
	721
	722	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	723	ts_uint i,j;
	724	for(i=0;i<vlist->n;i++){
	725	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	726	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	727	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	728	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	729	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	730	}
SP	731	fprintf(fh,"\n");
cef6ca	732	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	733	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	734	}
SP	735	fprintf(fh,"\n");
	736	}
	737	return TS_SUCCESS;
	738	}
	739
	740	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	741	ts_uint i;
a6b1b5	742	for(i=0;i<vesicle->blist->n;i++){
e016c4	743	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	744	//-vesicle->vlist->vtx+1),
e016c4	745	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	746	//-vesicle->vlist.vtx+1));
d7639a	747	}
SP	748	return TS_SUCCESS;
	749	}
	750
	751
	752	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	753	FILE *fh;
	754	fh=fopen(filename, "w");
	755	if(fh==NULL){
	756	err("Cannot open file %s for writing");
	757	return TS_FAIL;
	758	}
	759	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	760	fprint_vertex_list(fh,vesicle->vlist);
d7639a	761	fprint_tristar(fh,vesicle);
SP	762	fprint_triangle_list(fh,vesicle);
a6b1b5	763	fprint_vertex_data(fh,vesicle->vlist);
d7639a	764	fprint_bonds(fh,vesicle);
SP	765	fclose(fh);
	766	return TS_SUCCESS;
	767	}
	768
	769	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	770	FILE *fh;
	771	char line[255];
	772	fh=fopen(filename, "r");
	773	if(fh==NULL){
	774	err("Cannot open file for reading... Nonexistant file?");
	775	return TS_FAIL;
	776	}
a6b1b5	777	ts_uint retval=1;
d7639a	778	while(retval!=EOF){
SP	779	retval=fscanf(fh,"%s",line);
	780
	781	fprintf(stderr,"%s",line);
	782	}
	783	fclose(fh);
	784	return TS_SUCCESS;
	785	}
	786
	787	ts_bool write_master_xml_file(ts_char *filename){
	788	FILE *fh;
	789	ts_char i,j;
	790	ts_uint tstep;
	791	ts_char *number;
	792	fh=fopen(filename, "w");
	793	if(fh==NULL){
	794	err("Cannot open file %s for writing");
	795	return TS_FAIL;
	796	}
	797
	798	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
267db5	799	DIR *dir = opendir(command_line_args.path);
d7639a	800	if(dir){
SP	801	struct dirent *ent;
	802	tstep=0;
	803	while((ent = readdir(dir)) != NULL)
	804	{
	805	i=rindex(ent->d_name,'.');
	806	if(i==NULL) continue;
	807	if(strcmp(i+1,"vtu")==0){
	808	j=rindex(ent->d_name,'_');
	809	if(j==NULL) continue;
	810	number=strndup(j+1,j-i);
a6b1b5	811	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	812	tstep++;
SP	813	free(number);
	814	}
	815	}
	816	}
f74313	817	free(dir);
d7639a	818	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	819	fclose(fh);
	820	return TS_SUCCESS;
	821	}
	822
	823	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	824	ts_vertex_list *vlist=vesicle->vlist;
SP	825	ts_bond_list *blist=vesicle->blist;
	826	ts_vertex **vtx=vlist->vtx;
40aa5b	827	ts_uint i,j;
267db5	828	char filename[10000];
SP	829	char just_name[255];
d7639a	830	FILE *fh;
267db5	831	strcpy(filename,command_line_args.path);
SP	832	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	833	strcat(filename,just_name);
d7639a	834
SP	835	fh=fopen(filename, "w");
	836	if(fh==NULL){
	837	err("Cannot open file %s for writing");
	838	return TS_FAIL;
	839	}
	840	/* Here comes header of the file */
40aa5b	841
SP	842	//find number of extra vtxs and bonds of polymeres
58230a	843	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	844	ts_bool poly=0, fil=0;
40aa5b	845	if(vesicle->poly_list!=NULL){
SP	846	if(vesicle->poly_list->poly[0]!=NULL){
	847	polyno=vesicle->poly_list->n;
	848	monono=vesicle->poly_list->poly[0]->vlist->n;
	849	poly=1;
	850	}
	851	}
58230a	852
M	853	if(vesicle->filament_list!=NULL){
	854	if(vesicle->filament_list->poly[0]!=NULL){
	855	filno=vesicle->filament_list->n;
	856	fonono=vesicle->filament_list->poly[0]->vlist->n;
	857	fil=1;
	858	}
	859	}
	860
854cb6	861	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	862	xml_trisurf_data(fh,vesicle);
	863	fprintf(fh, " <UnstructuredGrid>\n");
58230a	864	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	865	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	866	for(i=0;i<vlist->n;i++){
a6b1b5	867	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	868	}
40aa5b	869	//polymeres
SP	870	if(poly){
3c1ac1	871	poly_idx=vlist->n;
40aa5b	872	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	873	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	874	fprintf(fh,"%u ", poly_idx);
M	875	}
	876	}
	877	}
	878	//filaments
	879	if(fil){
	880	poly_idx=vlist->n+monono*polyno;
	881	for(i=0;i<vesicle->filament_list->n;i++){
	882	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	883	// fprintf(stderr,"was here\n");
3c1ac1	884	fprintf(fh,"%u ", poly_idx);
40aa5b	885	}
SP	886	}
	887	}
d7639a	888
SP	889	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	890	for(i=0;i<vlist->n;i++){
aad500	891	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	892	}
SP	893	//polymeres
	894	if(poly){
	895	for(i=0;i<vesicle->poly_list->n;i++){
	896	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	897	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	898	}
M	899	}
	900	}
	901	//filaments
	902	if(fil){
	903	for(i=0;i<vesicle->filament_list->n;i++){
	904	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	905	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	906	}
SP	907	}
d7639a	908	}
SP	909
	910	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	911	for(i=0;i<blist->n;i++){
e016c4	912	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	913	}
40aa5b	914	//polymeres
SP	915	if(poly){
3c1ac1	916	poly_idx=vlist->n;
40aa5b	917	for(i=0;i<vesicle->poly_list->n;i++){
SP	918	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	919	// 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	920	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	921	}
SP	922	//grafted bonds
3c1ac1	923	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	924	}
SP	925
	926	}
	927
58230a	928	//filaments
M	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]->blist->n;j++){
	933	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);
	934	// fprintf(stderr,"was here\n");
	935
	936	}
	937	}
	938
	939	}
40aa5b	940
d7639a	941	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	942	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	943	fprintf(fh,"%u ",i);
SP	944	}
	945	fprintf(fh,"\n");
	946	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	947	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	948	fprintf(fh,"3 ");
SP	949	}
	950
	951	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	952	fclose(fh);
	953	return TS_SUCCESS;
	954
	955	}
	956
	957	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	958	ts_vertex_list *vlist=vesicle->vlist;
SP	959	ts_bond_list *blist=vesicle->blist;
	960	ts_vertex **vtx=vlist->vtx;
	961	ts_uint i;
d7639a	962	FILE *fh;
SP	963
	964	fh=fopen(filename, "w");
	965	if(fh==NULL){
	966	err("Cannot open file %s for writing");
	967	return TS_FAIL;
	968	}
	969	/* Here comes header of the file */
	970	// fprintf(stderr,"NSHELL=%u\n",nshell);
	971	fprintf(fh, "# vtk DataFile Version 2.0\n");
	972	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	973	fprintf(fh, "%s\n", text);
	974	fprintf(fh,"ASCII\n");
	975	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	976	fprintf(fh,"POINTS %u double\n", vlist->n);
	977	for(i=0;i<vlist->n;i++){
8f6a69	978	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	979	}
SP	980
	981	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	982	for(i=0;i<blist->n;i++){
e016c4	983	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	984	}
SP	985	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	986	for(i=0;i<blist->n;i++)
	987	fprintf(fh,"3\n");
	988
	989	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	990	fprintf(fh,"SCALARS scalars long 1\n");
	991	fprintf(fh,"LOOKUP_TABLE default\n");
	992
	993	for(i=0;i<vlist->n;i++)
8f6a69	994	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	995
SP	996	fclose(fh);
	997	return TS_SUCCESS;
	998	}
	999
	1000
	1001
144784	1002	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	1003	FILE *fh;
	1004	ts_uint i;
	1005
	1006	fh=fopen(filename, "w");
	1007	if(fh==NULL){
	1008	err("Cannot open file %s for writing");
	1009	return TS_FAIL;
	1010	}
	1011
	1012	for(i=0;i<vesicle->tlist->n;i++){
	1013
	1014	fprintf(fh,"\ttriangle {");
	1015	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1016	vesicle->tlist->tria[i]->vertex[0]->x,
	1017	vesicle->tlist->tria[i]->vertex[0]->y,
	1018	vesicle->tlist->tria[i]->vertex[0]->z,
	1019
	1020	vesicle->tlist->tria[i]->vertex[1]->x,
	1021	vesicle->tlist->tria[i]->vertex[1]->y,
	1022	vesicle->tlist->tria[i]->vertex[1]->z,
	1023
	1024	vesicle->tlist->tria[i]->vertex[2]->x,
	1025	vesicle->tlist->tria[i]->vertex[2]->y,
	1026	vesicle->tlist->tria[i]->vertex[2]->z
	1027	);
	1028	}
	1029
	1030	fclose(fh);
	1031	return TS_SUCCESS;
	1032	}
	1033
	1034
1ab449	1035	ts_tape parsetape(char filename){
698ae1	1036	FILE *fd = fopen (filename, "r");
SP	1037	long length;
	1038	size_t size;
	1039	fseek (fd, 0, SEEK_END);
	1040	length = ftell (fd);
	1041	fseek (fd, 0, SEEK_SET);
	1042	size=fread (tapetxt, 1, length, fd);
	1043	fclose(fd);
	1044	if(size);
	1045	ts_tape *tape=parsetapebuffer(tapetxt);
	1046	return tape;
	1047	}
	1048
	1049	ts_tape parsetapebuffer(char buffer){
1ab449	1050	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1051	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1052
d7639a	1053	cfg_opt_t opts[] = {
1ab449	1054	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1055	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1056	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1057	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1058	CFG_SIMPLE_INT("nfono",&tape->nfono),
	1059	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1060	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1061	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1062	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1063	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1064	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1065	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1066	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1067	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1068	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1069	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	1070	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1071	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1072	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1073	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1074	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1075	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1076	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1077	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1078	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1079	CFG_SIMPLE_INT("inititer", &tape->inititer),
	1080	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	1081	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	1082	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	1083	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1084	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1085	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	1086	CFG_END()
SP	1087	};
	1088	cfg_t *cfg;
	1089	ts_uint retval;
	1090	cfg = cfg_init(opts, 0);
698ae1	1091	retval=cfg_parse_buf(cfg, buffer);
d7639a	1092	if(retval==CFG_FILE_ERROR){
a6b1b5	1093	fatal("No tape file.",100);
d7639a	1094	}
SP	1095	else if(retval==CFG_PARSE_ERROR){
	1096	fatal("Invalid tape!",100);
	1097	}
a2db52	1098
7b0c07	1099	/* here we override all values read from tape with values from commandline*/
SP	1100	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1101	cfg_free(cfg);
40aa5b	1102
SP	1103
1ab449	1104	/* global variables are set automatically */
SP	1105	quiet=tape->quiet;
	1106	return tape;
	1107	}
d7639a	1108
1ab449	1109	ts_bool tape_free(ts_tape *tape){
SP	1110	free(tape->multiprocessing);
	1111	free(tape);
	1112	return TS_SUCCESS;
d7639a	1113	}
f74313	1114
SP	1115
7b0c07	1116
SP	1117	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1118
	1119	char commands, backup, saveptr, saveopptr, command, operator[2];
	1120	ts_uint i,j;
	1121	commands=(char )malloc(10000sizeof(char));
	1122	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1123	strcpy(commands,opts);
	1124	for(i=0; ;i++, commands=NULL){
	1125	//breaks comma separated list of commands into specific commands.
	1126	command=strtok_r(commands,",",&saveptr);
	1127	if(command==NULL) break;
	1128	// fprintf(stdout,"Command %d: %s\n",i,command);
	1129	//extracts name of command and value of command into operator[2] array.
	1130	for(j=0; j<2;j++,command=NULL){
	1131	operator[j]=strtok_r(command,"=",&saveopptr);
	1132	if(operator[j]==NULL) break;
	1133	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1134	}
	1135	//1. check: must have 2 operators.
	1136	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1137
	1138	// cfg_setstr(cfg,operator[0],operator[1]);
	1139	cmdline_to_tape(cfg,operator[0],operator[1]);
	1140	//2. check: must be named properly.
	1141	//3. check: must be of right format (integer, double, string, ...)
	1142
	1143	}
	1144	free(backup);
	1145	return TS_SUCCESS;
	1146	}
	1147
	1148
	1149	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1150
	1151	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1152	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1153	switch (cfg_opt->type){
	1154	case CFGT_INT:
	1155	cfg_setint(cfg,key,atol(val));
	1156	break;
	1157	case CFGT_FLOAT:
	1158	cfg_setfloat(cfg,key,atof(val));
	1159	break;
	1160	/* case CFGT_BOOL:
	1161	cfg_setbool(cfg,operator[0],operator[1]);
	1162	break; */
	1163	case CFGT_STR:
	1164	cfg_setstr(cfg,key,val);
	1165	break;
	1166	default:
	1167	break;
	1168
	1169	}
	1170	return TS_SUCCESS;
	1171	}
	1172
	1173
	1174
f74313	1175	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1176	FILE *fh;
	1177	ts_uint i, nvtx,nedges,ntria;
	1178	ts_uint vtxi1,vtxi2;
	1179	float x,y,z;
	1180	ts_vertex_list *vlist;
	1181	fh=fopen(fname, "r");
	1182	if(fh==NULL){
	1183	err("Cannot open file for reading... Nonexistant file?");
	1184	return TS_FAIL;
	1185	}
	1186	ts_uint retval;
	1187	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1188	vesicle->vlist=init_vertex_list(nvtx);
	1189	vlist=vesicle->vlist;
	1190	for(i=0;i<nvtx;i++){
8f6a69	1191	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1192	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1193	vlist->vtx[i]->x=x;
SP	1194	vlist->vtx[i]->y=y;
	1195	vlist->vtx[i]->z=z;
f74313	1196	}
SP	1197	for(i=0;i<nedges;i++){
	1198	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1199	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1200	}
	1201	//TODO: neighbours from bonds,
	1202	//TODO: triangles from neigbours
	1203
	1204	// Don't need to read triangles. Already have enough data
	1205	/*
	1206	for(i=0;i<ntria;i++){
	1207	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1208	vtxi1=vesicle->blist->vertex1->idx;
SP	1209	vtxi2=vesicle->blist->vertex1->idx;
f74313	1210
SP	1211	}
	1212	*/
41a035	1213	if(retval);
f74313	1214	fclose(fh);
SP	1215
	1216
	1217
	1218	return TS_SUCCESS;
	1219	}