trisurf-ng.git - Gitblit

Command line tape options, directories and files are parsed correctly. Comm...

Samo Penic

2014-09-11 7b0c077e18af45b1312c35aa52efb0211d1378c5

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f74313	1	#include "general.h"
d7639a	2	#include<stdio.h>
SP	3	#include "io.h"
f74313	4	#include "vertex.h"
SP	5	#include "bond.h"
d7639a	6	#include<string.h>
a6b1b5	7	#include<stdlib.h>
d7639a	8	#include <sys/types.h>
SP	9	#include <dirent.h>
b14a8d	10	#include "initial_distribution.h"
a2db52	11	#include "poly.h"
055dd7	12	#include "cell.h"
083e03	13	#include <getopt.h>
SP	14	#include <sys/stat.h>
	15	#include <sys/types.h>
	16	#include <dirent.h>
	17	#include <errno.h>
e9eab4	18	/ DUMP STATE TO DISK DRIVE /
SP	19
1ab449	20	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	21
SP	22	/* save current state with wrong pointers. Will fix that later */
	23	ts_uint i,j,k;
	24	FILE *fh=fopen("dump.bin","wb");
	25
	26	/* dump vesicle */
86f5e7	27	fwrite(vesicle, sizeof(ts_vesicle),1,fh);
e9eab4	28	/* dump vertex list */
SP	29	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	30	/* dump bond list */
	31	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	32	/* dump triangle list */
	33	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	34	/* dump cell list */
	35	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	36	/* dump poly list */
	37	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	38	/* dump filament list */
M	39	fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	40	/* level 1 complete */
SP	41
	42	/dump vertices/
	43	for(i=0;i<vesicle->vlist->n;i++){
	44	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	45	/* dump pointer offsets for:
	46	neigh
	47	bond
	48	tria
	49	cell is ignored
	50	*/
	51	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	52	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	53	}
SP	54	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	55	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	56	}
SP	57	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	58	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	59	}
SP	60	}
	61
	62	/dump bonds/
	63	for(i=0;i<vesicle->blist->n;i++){
	64	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	65	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	66	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	67	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	68	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	69	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	70	}
SP	71
	72	/dump triangles/
	73	for(i=0;i<vesicle->tlist->n;i++){
	74	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	75	/* dump pointer offsets for vertex */
3c1ac1	76	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	77	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	78	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	79	/* dump pointer offsets for neigh */
SP	80	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	81	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	82	}
SP	83	}
	84
	85
	86	/dump polymeres /
	87	for(i=0;i<vesicle->poly_list->n;i++){
	88	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	89	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	90	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	91	}
SP	92
	93	/* dump poly vertex(monomer) list*/
	94	for(i=0;i<vesicle->poly_list->n;i++){
	95	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	96	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	97	/* dump offset for neigh and bond */
	98	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	99	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	100	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	101	}
SP	102	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	103	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	104	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	105	}
SP	106	}
3c1ac1	107	// grafted vtx on vesicle data dump
SP	108	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	109	}
SP	110	/* dump poly bonds between monomers list*/
	111	for(i=0;i<vesicle->poly_list->n;i++){
	112	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	113	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	114	/* dump vtx1 and vtx2 offsets */
3c1ac1	115	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	116	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	117	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	118	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	119	}
SP	120	}
	121
bcf455	122
M	123	/dump filamentes grandes svinjas /
	124	for(i=0;i<vesicle->filament_list->n;i++){
	125	fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	126	fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	127	fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	128	}
	129
	130	/* dump filamentes vertex(monomer) list*/
	131	for(i=0;i<vesicle->filament_list->n;i++){
	132	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	133	fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	134	/* dump offset for neigh and bond */
	135	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	136	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	137	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
	138	}
	139	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	140	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
	141	fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
	142	}
	143	}
	144	}
	145	/* dump poly bonds between monomers list*/
	146	for(i=0;i<vesicle->filament_list->n;i++){
	147	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	148	fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	149	/* dump vtx1 and vtx2 offsets */
	150	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	151	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	152	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	153	fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
	154	}
	155	}
	156
	157
	158
e9eab4	159	/* pointer offsets for fixing the restored pointers */
SP	160	/* need pointers for
	161	vlist->vtx
	162	blist->bond
	163	tlist->tria
	164	clist->cell
	165	poly_list->poly
	166	and for each poly:
	167	poly_list->poly->vtx
	168	poly_list->poly->bond
	169	*/
	170
bd2210	171	// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
9166cb	172	/* write tape information on vesicle */
bd2210	173	// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
1ab449	174	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	175	fclose(fh);
SP	176	return TS_SUCCESS;
	177	}
	178
	179
	180	/ RESTORE DUMP FROM DISK /
1ab449	181	ts_vesicle restore_state(ts_uint iteration){
e9eab4	182	ts_uint i,j,k;
SP	183	FILE *fh=fopen("dump.bin","rb");
3f5c83	184
SP	185	struct stat sb;
	186	if (stat("dump.bin", &sb) == -1) {
	187	//dump file does not exist.
	188	return NULL;
	189	}
	190
	191	//check if it is regular file
	192	if((sb.st_mode & S_IFMT) != S_IFREG) {
	193	//dump file is not a regular file.
	194	ts_fprintf(stderr,"Dump file is not a regular file!\n");
	195	return NULL;
	196	}
	197
e9eab4	198	ts_uint retval;
3c1ac1	199	ts_uint idx;
e9eab4	200
SP	201	/* we restore all the data from the dump */
	202	/* restore vesicle */
	203	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
86f5e7	204	retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
SP	205	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
	206
e9eab4	207	/* restore vertex list */
SP	208	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	209	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	210	/* restore bond list */
	211	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	212	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	213	/* restore triangle list */
	214	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	215	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	216	/* restore cell list */
	217	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	218	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	219	/* restore poly list */
	220	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	221	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
bcf455	222	/* restore filament list */
M	223	vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	224	retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
e9eab4	225	/* level 1 complete */
SP	226
3c1ac1	227	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	228	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	229	for(i=0;i<vesicle->blist->n;i++){
	230	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	231	}
	232	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	233	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	234	for(i=0;i<vesicle->tlist->n;i++){
	235	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	236	}
a37ba2	237	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	238	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	239	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	240	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	241	}
SP	242	/restore vertices/
	243	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	244	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	245	/restore neigh, bond, tristar. Ignoring cell /
	246	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	247	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	248	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	249	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	250	}
SP	251	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	252	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	253	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	254	/* 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 */
	255	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	256	}
SP	257
	258	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	259	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	260	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	261	/* same comment as above */
	262	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	263	}
SP	264
	265	}
	266
	267	/restore bonds/
3c1ac1	268	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	269	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	270	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	271	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	272	/* restore vtx1 and vtx2 */
3c1ac1	273	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	274	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	275	retval=fread(&idx,sizeof(ts_uint),1,fh);
	276	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	277	}
SP	278
	279	/restore triangles/
3c1ac1	280	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	281	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	282	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	283	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	284	/* restore pointers for vertices */
3c1ac1	285	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	286	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	287	retval=fread(&idx,sizeof(ts_uint),1,fh);
	288	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	289	retval=fread(&idx,sizeof(ts_uint),1,fh);
	290	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	291	/* restore pointers for neigh */
3c1ac1	292	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	293	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	294	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	295	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	296	}
SP	297
	298	}
	299
	300	/restore cells /
	301	/TODO: do we need to recalculate cells here? /
	302	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	303	for(i=0;i<vesicle->clist->cellno;i++){
	304	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	305	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	306	}
	307	*/
	308	/restore polymeres /
	309	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	310	for(i=0;i<vesicle->poly_list->n;i++){
	311	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	312	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	313	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	314	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	315	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	316	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	317	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	318	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	319	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	320	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	321	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	322	}
	323	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	324	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	325	}
	326
e9eab4	327	}
3c1ac1	328
e9eab4	329
SP	330	/* restore poly vertex(monomer) list*/
	331	for(i=0;i<vesicle->poly_list->n;i++){
	332	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	333	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	334
e9eab4	335	/* restore neigh and bonds */
SP	336	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 ));
	337	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	338	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	339	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	340	}
SP	341	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 ));
	342	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	343	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	344	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	345	}
SP	346
	347	}
3c1ac1	348	/* restore grafted vtx on vesicle and grafted_poly */
SP	349	retval=fread(&idx,sizeof(ts_uint),1,fh);
	350	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	351	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	352	}
3c1ac1	353
e9eab4	354	/* restore poly bonds between monomers list*/
SP	355	for(i=0;i<vesicle->poly_list->n;i++){
	356	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	357	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	358	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	359	/* restore vtx1 and vtx2 */
3c1ac1	360	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	361	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	362	retval=fread(&idx,sizeof(ts_uint),1,fh);
	363	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	364	}
SP	365	}
	366
bcf455	367	/restore filaments /
M	368	vesicle->filament_list->poly = (ts_poly *)calloc(vesicle->filament_list->n,sizeof(ts_poly ));
	369	for(i=0;i<vesicle->filament_list->n;i++){
	370	vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	371	retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
	372	vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
	373	retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	374	vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	375	retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	376	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	377	vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	378	vesicle->filament_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond ));
	379	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	380	vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	381	}
	382	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	383	vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	384	}
	385
	386	}
	387
	388
	389	/* restore poly vertex(monomer) list*/
	390	for(i=0;i<vesicle->filament_list->n;i++){
	391	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	392	retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	393
	394	/* restore neigh and bonds */
	395	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 ));
	396	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
	397	retval=fread(&idx,sizeof(ts_uint),1,fh);
	398	vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	399	}
	400	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 ));
	401	for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
	402	retval=fread(&idx,sizeof(ts_uint),1,fh);
	403	vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
	404	}
	405
	406	}
	407	}
	408
	409	/* restore poly bonds between monomers list*/
	410	for(i=0;i<vesicle->filament_list->n;i++){
	411	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	412	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	413	retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	414	/* restore vtx1 and vtx2 */
	415	retval=fread(&idx,sizeof(ts_uint),1,fh);
	416	vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	417	retval=fread(&idx,sizeof(ts_uint),1,fh);
	418	vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
	419	}
	420	}
47a7ac	421	vesicle->tape=parsetape("tape");
063289	422	// recreating space for cells //
055dd7	423	vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
364c30	424	vesicle->clist->max_occupancy=8;
47a7ac	425	// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
SP	426	// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
1ab449	427	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	428	if(retval);
SP	429	fclose(fh);
	430	return vesicle;
	431	}
	432
	433
	434
083e03	435	ts_bool parse_args(int argc, char **argv){
3f5c83	436	int c, retval;
SP	437	struct stat sb;
	438	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	439	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	440	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	441	sprintf(command_line_args.tape_fullfilename,"tape");
3f5c83	442	FILE *file;
SP	443
083e03	444	while (1)
SP	445	{
	446	static struct option long_options[] =
	447	{
8a6614	448	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	449	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	450	{"tape", no_argument, 0, 't'},
SP	451	{"output-file", required_argument, 0, 'o'},
	452	{"directory", required_argument, 0, 'd'},
3f5c83	453	{"dump-filename", required_argument,0, 'f'},
7b0c07	454	{"tape-options",required_argument,0,'c'},
083e03	455	{0, 0, 0, 0}
SP	456	};
	457	/* getopt_long stores the option index here. */
	458	int option_index = 0;
	459
7b0c07	460	c = getopt_long (argc, argv, "d:f:o:t:c:",
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
7b0c07	479	case 'c':
SP	480	strcpy(command_line_args.tape_opts,optarg);
	481	break;
	482	case 't': //tape
3f5c83	483	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	484	break;
SP	485
7b0c07	486	case 'o': //set filename of master pvd output file
3f5c83	487	strcpy(command_line_args.output_fullfilename, optarg);
SP	488	break;
083e03	489
SP	490	case 'd':
	491	//check if directory exists. If not create one. If creation is
	492	//successful, set directory for output files.
	493	//printf ("option -d with value `%s'\n", optarg);
3f5c83	494	if (stat(optarg, &sb) == -1) {
SP	495	//directory does not exist
083e03	496	retval=mkdir(optarg, 0700);
SP	497	if(retval){
3f5c83	498	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	499	}
SP	500	}
3f5c83	501	//check if is a proper directory
SP	502	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	503	//it is not a directory. fatal error.
	504	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	505	fatal("Cannot continue",1);
083e03	506	}
3f5c83	507	strcpy(command_line_args.path, optarg);
083e03	508	break;
SP	509
	510	case 'f':
3f5c83	511	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	512	break;
SP	513
	514	case '?':
	515	/* getopt_long already printed an error message. */
	516
	517	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	518	fatal("Ooops, read help first",1);
	519	break;
	520
	521	default:
	522	exit (1);
	523	}
	524	}
	525
7b0c07	526	//Here we set correct values for full filenames!
SP	527	char buffer=(char )malloc(10000*sizeof(char));
	528	//correct the path and add trailing /
	529	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	530
	531	/* master pvd output file */
	532	strcpy(buffer,command_line_args.path);
	533	strcat(buffer,command_line_args.output_fullfilename);
	534	if ((file = fopen(buffer, "w")) == NULL) {
	535	fprintf(stderr,"Could not create output file %s!\n", buffer);
	536	fatal("Please specify correct output file or check permissions of the file",1);
	537
	538	} else {
	539	fclose(file);
	540	strcpy(command_line_args.output_fullfilename,buffer);
	541	}
	542
	543	/* tape file */
	544	strcpy(buffer,command_line_args.path);
	545	strcat(buffer,command_line_args.tape_fullfilename);
	546	if (stat(buffer, &sb) == -1) {
	547	ts_fprintf(stderr,"Tape '%s' does not exist!\n",buffer);
	548	fatal("Please select correct tape or check permissions of the file",1);
	549	} else {
	550	strcpy(command_line_args.tape_fullfilename,buffer);
	551	}
	552
	553
	554	/* dump file */
	555	strcpy(buffer,command_line_args.path);
	556	strcat(buffer,command_line_args.dump_fullfilename);
	557	//check if dump file exist first.
	558	if (stat(buffer, &sb) == -1) {
	559	//no dump file. check if we can create one.
	560	if ((file = fopen(buffer, "w")) == NULL) {
	561	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	562	fatal("Please specify correct dump file or check permissions of the file",1);
	563	} else {
	564	fclose(file);
	565	//good, file is writeable. delete it for now.
	566	remove(buffer);
	567	}
	568	}
	569	strcpy(command_line_args.dump_fullfilename, buffer);
	570
	571
	572	free(buffer);
083e03	573	return TS_SUCCESS;
SP	574
	575	}
	576
	577
	578
	579
d7639a	580	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	581	ts_uint i;
	582	printf("Number of vertices: %u\n",vlist->n);
	583	for(i=0;i<vlist->n;i++){
a6b1b5	584	printf("%u: %f %f %f\n",
8f6a69	585	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	586	}
SP	587	return TS_SUCCESS;
	588	}
	589
	590	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	591	ts_uint i,j;
a6b1b5	592	ts_vertex **vtx=vlist->vtx;
d7639a	593	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	594	for(i=0;i<vlist->n;i++){
8f6a69	595	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	596	for(j=0;j<vtx[i]->neigh_no;j++){
	597	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	598	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	599	}
SP	600	printf("\n");
	601	}
	602
	603	return TS_SUCCESS;
	604	}
	605
	606	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	607	ts_vertex **vtx=vlist->vtx;
d7639a	608	ts_uint i;
SP	609	FILE *fh;
	610
	611	fh=fopen(filename, "w");
	612	if(fh==NULL){
	613	err("Cannot open file %s for writing");
	614	return TS_FAIL;
	615	}
	616	for(i=0;i<vlist->n;i++)
8f6a69	617	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	618
SP	619	fclose(fh);
	620	return TS_SUCCESS;
	621	}
	622
	623
	624	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	625	ts_uint i,j;
	626	for(i=0;i<vlist->n;i++){
8f6a69	627	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	628	vlist->vtx[i]->y, vlist->vtx[i]->z,
	629	vlist->vtx[i]->neigh_no);
	630	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	631	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	632	//-vlist->vtx+1));
d7639a	633	}
SP	634	fprintf(fh,"\n");
	635	}
	636	return TS_SUCCESS;
	637	}
	638
	639	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	640	ts_uint i,j;
a6b1b5	641	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	642	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	643	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	644	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	645	}
SP	646	fprintf(fh,"\n");
	647	}
	648	return TS_SUCCESS;
	649	}
	650
	651	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	652	ts_triangle_list *tlist=vesicle->tlist;
d7639a	653	ts_uint i,j;
SP	654	for(i=0;i<tlist->n;i++){
41a035	655	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	656	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	657	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	658	}
SP	659	fprintf(fh,"\n");
	660	for(j=0;j<3;j++){
41a035	661	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	662	}
SP	663	fprintf(fh,"\n");
41a035	664	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	665	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	666	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	667	}
	668	return TS_SUCCESS;
	669	}
	670
	671	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	672	ts_uint i,j;
	673	for(i=0;i<vlist->n;i++){
	674	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	675	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	676	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	677	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	678	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	679	}
SP	680	fprintf(fh,"\n");
cef6ca	681	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	682	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	683	}
SP	684	fprintf(fh,"\n");
	685	}
	686	return TS_SUCCESS;
	687	}
	688
	689	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	690	ts_uint i;
a6b1b5	691	for(i=0;i<vesicle->blist->n;i++){
e016c4	692	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	693	//-vesicle->vlist->vtx+1),
e016c4	694	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	695	//-vesicle->vlist.vtx+1));
d7639a	696	}
SP	697	return TS_SUCCESS;
	698	}
	699
	700
	701	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	702	FILE *fh;
	703	fh=fopen(filename, "w");
	704	if(fh==NULL){
	705	err("Cannot open file %s for writing");
	706	return TS_FAIL;
	707	}
	708	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	709	fprint_vertex_list(fh,vesicle->vlist);
d7639a	710	fprint_tristar(fh,vesicle);
SP	711	fprint_triangle_list(fh,vesicle);
a6b1b5	712	fprint_vertex_data(fh,vesicle->vlist);
d7639a	713	fprint_bonds(fh,vesicle);
SP	714	fclose(fh);
	715	return TS_SUCCESS;
	716	}
	717
	718	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	719	FILE *fh;
	720	char line[255];
	721	fh=fopen(filename, "r");
	722	if(fh==NULL){
	723	err("Cannot open file for reading... Nonexistant file?");
	724	return TS_FAIL;
	725	}
a6b1b5	726	ts_uint retval=1;
d7639a	727	while(retval!=EOF){
SP	728	retval=fscanf(fh,"%s",line);
	729
	730	fprintf(stderr,"%s",line);
	731	}
	732	fclose(fh);
	733	return TS_SUCCESS;
	734	}
	735
	736	ts_bool write_master_xml_file(ts_char *filename){
	737	FILE *fh;
	738	ts_char i,j;
	739	ts_uint tstep;
	740	ts_char *number;
	741	fh=fopen(filename, "w");
	742	if(fh==NULL){
	743	err("Cannot open file %s for writing");
	744	return TS_FAIL;
	745	}
	746
	747	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	748	DIR *dir = opendir(".");
	749	if(dir){
	750	struct dirent *ent;
	751	tstep=0;
	752	while((ent = readdir(dir)) != NULL)
	753	{
	754	i=rindex(ent->d_name,'.');
	755	if(i==NULL) continue;
	756	if(strcmp(i+1,"vtu")==0){
	757	j=rindex(ent->d_name,'_');
	758	if(j==NULL) continue;
	759	number=strndup(j+1,j-i);
a6b1b5	760	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	761	tstep++;
SP	762	free(number);
	763	}
	764	}
	765	}
f74313	766	free(dir);
d7639a	767	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	768	fclose(fh);
	769	return TS_SUCCESS;
	770	}
	771
	772	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	773	ts_vertex_list *vlist=vesicle->vlist;
SP	774	ts_bond_list *blist=vesicle->blist;
	775	ts_vertex **vtx=vlist->vtx;
40aa5b	776	ts_uint i,j;
d7639a	777	char filename[255];
SP	778	FILE *fh;
	779
	780	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	781	fh=fopen(filename, "w");
	782	if(fh==NULL){
	783	err("Cannot open file %s for writing");
	784	return TS_FAIL;
	785	}
	786	/* Here comes header of the file */
40aa5b	787
SP	788	//find number of extra vtxs and bonds of polymeres
58230a	789	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	790	ts_bool poly=0, fil=0;
40aa5b	791	if(vesicle->poly_list!=NULL){
SP	792	if(vesicle->poly_list->poly[0]!=NULL){
	793	polyno=vesicle->poly_list->n;
	794	monono=vesicle->poly_list->poly[0]->vlist->n;
	795	poly=1;
	796	}
	797	}
58230a	798
M	799	if(vesicle->filament_list!=NULL){
	800	if(vesicle->filament_list->poly[0]!=NULL){
	801	filno=vesicle->filament_list->n;
	802	fonono=vesicle->filament_list->poly[0]->vlist->n;
	803	fil=1;
	804	}
	805	}
	806
d7639a	807	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
58230a	808	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	809	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	810	for(i=0;i<vlist->n;i++){
a6b1b5	811	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	812	}
40aa5b	813	//polymeres
SP	814	if(poly){
3c1ac1	815	poly_idx=vlist->n;
40aa5b	816	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	817	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	818	fprintf(fh,"%u ", poly_idx);
M	819	}
	820	}
	821	}
	822	//filaments
	823	if(fil){
	824	poly_idx=vlist->n+monono*polyno;
	825	for(i=0;i<vesicle->filament_list->n;i++){
	826	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	827	// fprintf(stderr,"was here\n");
3c1ac1	828	fprintf(fh,"%u ", poly_idx);
40aa5b	829	}
SP	830	}
	831	}
d7639a	832
SP	833	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	834	for(i=0;i<vlist->n;i++){
8f6a69	835	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	836	}
SP	837	//polymeres
	838	if(poly){
	839	for(i=0;i<vesicle->poly_list->n;i++){
	840	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	841	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	842	}
M	843	}
	844	}
	845	//filaments
	846	if(fil){
	847	for(i=0;i<vesicle->filament_list->n;i++){
	848	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	849	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	850	}
SP	851	}
d7639a	852	}
SP	853
	854	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	855	for(i=0;i<blist->n;i++){
e016c4	856	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	857	}
40aa5b	858	//polymeres
SP	859	if(poly){
3c1ac1	860	poly_idx=vlist->n;
40aa5b	861	for(i=0;i<vesicle->poly_list->n;i++){
SP	862	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	863	// 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	864	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	865	}
SP	866	//grafted bonds
3c1ac1	867	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	868	}
SP	869
	870	}
	871
58230a	872	//filaments
M	873	if(fil){
	874	poly_idx=vlist->n+monono*polyno;
	875	for(i=0;i<vesicle->filament_list->n;i++){
	876	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	877	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);
	878	// fprintf(stderr,"was here\n");
	879
	880	}
	881	}
	882
	883	}
40aa5b	884
d7639a	885	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	886	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	887	fprintf(fh,"%u ",i);
SP	888	}
	889	fprintf(fh,"\n");
	890	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	891	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	892	fprintf(fh,"3 ");
SP	893	}
	894
	895	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	896	fclose(fh);
	897	return TS_SUCCESS;
	898
	899	}
	900
	901	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	902	ts_vertex_list *vlist=vesicle->vlist;
SP	903	ts_bond_list *blist=vesicle->blist;
	904	ts_vertex **vtx=vlist->vtx;
	905	ts_uint i;
d7639a	906	FILE *fh;
SP	907
	908	fh=fopen(filename, "w");
	909	if(fh==NULL){
	910	err("Cannot open file %s for writing");
	911	return TS_FAIL;
	912	}
	913	/* Here comes header of the file */
	914	// fprintf(stderr,"NSHELL=%u\n",nshell);
	915	fprintf(fh, "# vtk DataFile Version 2.0\n");
	916	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	917	fprintf(fh, "%s\n", text);
	918	fprintf(fh,"ASCII\n");
	919	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	920	fprintf(fh,"POINTS %u double\n", vlist->n);
	921	for(i=0;i<vlist->n;i++){
8f6a69	922	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	923	}
SP	924
	925	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	926	for(i=0;i<blist->n;i++){
e016c4	927	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	928	}
SP	929	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	930	for(i=0;i<blist->n;i++)
	931	fprintf(fh,"3\n");
	932
	933	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	934	fprintf(fh,"SCALARS scalars long 1\n");
	935	fprintf(fh,"LOOKUP_TABLE default\n");
	936
	937	for(i=0;i<vlist->n;i++)
8f6a69	938	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	939
SP	940	fclose(fh);
	941	return TS_SUCCESS;
	942	}
	943
	944
	945
144784	946	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	947	FILE *fh;
	948	ts_uint i;
	949
	950	fh=fopen(filename, "w");
	951	if(fh==NULL){
	952	err("Cannot open file %s for writing");
	953	return TS_FAIL;
	954	}
	955
	956	for(i=0;i<vesicle->tlist->n;i++){
	957
	958	fprintf(fh,"\ttriangle {");
	959	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	960	vesicle->tlist->tria[i]->vertex[0]->x,
	961	vesicle->tlist->tria[i]->vertex[0]->y,
	962	vesicle->tlist->tria[i]->vertex[0]->z,
	963
	964	vesicle->tlist->tria[i]->vertex[1]->x,
	965	vesicle->tlist->tria[i]->vertex[1]->y,
	966	vesicle->tlist->tria[i]->vertex[1]->z,
	967
	968	vesicle->tlist->tria[i]->vertex[2]->x,
	969	vesicle->tlist->tria[i]->vertex[2]->y,
	970	vesicle->tlist->tria[i]->vertex[2]->z
	971	);
	972	}
	973
	974	fclose(fh);
	975	return TS_SUCCESS;
	976	}
	977
	978
1ab449	979	ts_tape parsetape(char filename){
SP	980	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	981	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	982
d7639a	983	cfg_opt_t opts[] = {
1ab449	984	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	985	CFG_SIMPLE_INT("npoly", &tape->npoly),
	986	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	987	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	988	CFG_SIMPLE_INT("nfono",&tape->nfono),
	989	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
	990	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	991	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	992	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	993	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	994	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
43c042	995	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	996	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	997	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	998	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	999	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1000	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1001	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1002	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1003	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1004	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1005	CFG_SIMPLE_INT("inititer", &tape->inititer),
	1006	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	1007	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	1008	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	1009	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1010	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1011	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	1012	CFG_END()
SP	1013	};
	1014	cfg_t *cfg;
	1015	ts_uint retval;
	1016	cfg = cfg_init(opts, 0);
1ab449	1017	retval=cfg_parse(cfg, filename);
d7639a	1018	if(retval==CFG_FILE_ERROR){
a6b1b5	1019	fatal("No tape file.",100);
d7639a	1020	}
SP	1021	else if(retval==CFG_PARSE_ERROR){
	1022	fatal("Invalid tape!",100);
	1023	}
a2db52	1024
7b0c07	1025	/* here we override all values read from tape with values from commandline*/
SP	1026	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1027	cfg_free(cfg);
40aa5b	1028
SP	1029
1ab449	1030	/* global variables are set automatically */
SP	1031	quiet=tape->quiet;
	1032	return tape;
	1033	}
d7639a	1034
1ab449	1035	ts_bool tape_free(ts_tape *tape){
SP	1036	free(tape->multiprocessing);
	1037	free(tape);
	1038	return TS_SUCCESS;
d7639a	1039	}
f74313	1040
SP	1041
7b0c07	1042
SP	1043	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1044
	1045	char commands, backup, saveptr, saveopptr, command, operator[2];
	1046	ts_uint i,j;
	1047	commands=(char )malloc(10000sizeof(char));
	1048	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1049	strcpy(commands,opts);
	1050	for(i=0; ;i++, commands=NULL){
	1051	//breaks comma separated list of commands into specific commands.
	1052	command=strtok_r(commands,",",&saveptr);
	1053	if(command==NULL) break;
	1054	// fprintf(stdout,"Command %d: %s\n",i,command);
	1055	//extracts name of command and value of command into operator[2] array.
	1056	for(j=0; j<2;j++,command=NULL){
	1057	operator[j]=strtok_r(command,"=",&saveopptr);
	1058	if(operator[j]==NULL) break;
	1059	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1060	}
	1061	//1. check: must have 2 operators.
	1062	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1063
	1064	// cfg_setstr(cfg,operator[0],operator[1]);
	1065	cmdline_to_tape(cfg,operator[0],operator[1]);
	1066	//2. check: must be named properly.
	1067	//3. check: must be of right format (integer, double, string, ...)
	1068
	1069	}
	1070	free(backup);
	1071	return TS_SUCCESS;
	1072	}
	1073
	1074
	1075	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1076
	1077	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1078	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1079	switch (cfg_opt->type){
	1080	case CFGT_INT:
	1081	cfg_setint(cfg,key,atol(val));
	1082	break;
	1083	case CFGT_FLOAT:
	1084	cfg_setfloat(cfg,key,atof(val));
	1085	break;
	1086	/* case CFGT_BOOL:
	1087	cfg_setbool(cfg,operator[0],operator[1]);
	1088	break; */
	1089	case CFGT_STR:
	1090	cfg_setstr(cfg,key,val);
	1091	break;
	1092	default:
	1093	break;
	1094
	1095	}
	1096	return TS_SUCCESS;
	1097	}
	1098
	1099
	1100
f74313	1101	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1102	FILE *fh;
	1103	ts_uint i, nvtx,nedges,ntria;
	1104	ts_uint vtxi1,vtxi2;
	1105	float x,y,z;
	1106	ts_vertex_list *vlist;
	1107	fh=fopen(fname, "r");
	1108	if(fh==NULL){
	1109	err("Cannot open file for reading... Nonexistant file?");
	1110	return TS_FAIL;
	1111	}
	1112	ts_uint retval;
	1113	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1114	vesicle->vlist=init_vertex_list(nvtx);
	1115	vlist=vesicle->vlist;
	1116	for(i=0;i<nvtx;i++){
8f6a69	1117	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1118	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1119	vlist->vtx[i]->x=x;
SP	1120	vlist->vtx[i]->y=y;
	1121	vlist->vtx[i]->z=z;
f74313	1122	}
SP	1123	for(i=0;i<nedges;i++){
	1124	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1125	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1126	}
	1127	//TODO: neighbours from bonds,
	1128	//TODO: triangles from neigbours
	1129
	1130	// Don't need to read triangles. Already have enough data
	1131	/*
	1132	for(i=0;i<ntria;i++){
	1133	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1134	vtxi1=vesicle->blist->vertex1->idx;
SP	1135	vtxi2=vesicle->blist->vertex1->idx;
f74313	1136
SP	1137	}
	1138	*/
41a035	1139	if(retval);
f74313	1140	fclose(fh);
SP	1141
	1142
	1143
	1144	return TS_SUCCESS;
	1145	}