trisurf-ng.git - Gitblit

Samo Penic

2016-06-07 45c708286ecd53ef5db3c76f4d0eb1e1379d628d

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
45c708	889	fprintf(fh,"</DataArray>\n");
SP	890
	891	//here comes additional data as needed. Currently only spontaneous curvature
	892	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	893	for(i=0;i<vlist->n;i++){
	894	fprintf(fh,"%.17e ",vtx[i]->c);
	895	}
	896	//polymeres
	897	if(poly){
	898	poly_idx=vlist->n;
	899	for(i=0;i<vesicle->poly_list->n;i++){
	900	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	901	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	902	}
	903	}
	904	}
	905	//filaments
	906	if(fil){
	907	poly_idx=vlist->n+monono*polyno;
	908	for(i=0;i<vesicle->filament_list->n;i++){
	909	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	910	// fprintf(stderr,"was here\n");
	911	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	912	}
	913	}
	914	}
	915	fprintf(fh,"</DataArray>\n");
	916
	917
	918
	919	fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	920	for(i=0;i<vlist->n;i++){
aad500	921	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	922	}
SP	923	//polymeres
	924	if(poly){
	925	for(i=0;i<vesicle->poly_list->n;i++){
	926	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	927	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	928	}
M	929	}
	930	}
	931	//filaments
	932	if(fil){
	933	for(i=0;i<vesicle->filament_list->n;i++){
	934	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	935	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	936	}
SP	937	}
d7639a	938	}
SP	939
	940	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	941	for(i=0;i<blist->n;i++){
e016c4	942	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	943	}
40aa5b	944	//polymeres
SP	945	if(poly){
3c1ac1	946	poly_idx=vlist->n;
40aa5b	947	for(i=0;i<vesicle->poly_list->n;i++){
SP	948	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	949	// 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	950	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	951	}
SP	952	//grafted bonds
3c1ac1	953	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	954	}
SP	955
	956	}
	957
58230a	958	//filaments
M	959	if(fil){
	960	poly_idx=vlist->n+monono*polyno;
	961	for(i=0;i<vesicle->filament_list->n;i++){
	962	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	963	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);
	964	// fprintf(stderr,"was here\n");
	965
	966	}
	967	}
	968
	969	}
40aa5b	970
d7639a	971	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	972	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	973	fprintf(fh,"%u ",i);
SP	974	}
	975	fprintf(fh,"\n");
	976	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	977	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	978	fprintf(fh,"3 ");
SP	979	}
	980
	981	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	982	fclose(fh);
	983	return TS_SUCCESS;
	984
	985	}
	986
	987	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	988	ts_vertex_list *vlist=vesicle->vlist;
SP	989	ts_bond_list *blist=vesicle->blist;
	990	ts_vertex **vtx=vlist->vtx;
	991	ts_uint i;
d7639a	992	FILE *fh;
SP	993
	994	fh=fopen(filename, "w");
	995	if(fh==NULL){
	996	err("Cannot open file %s for writing");
	997	return TS_FAIL;
	998	}
	999	/* Here comes header of the file */
	1000	// fprintf(stderr,"NSHELL=%u\n",nshell);
	1001	fprintf(fh, "# vtk DataFile Version 2.0\n");
	1002	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	1003	fprintf(fh, "%s\n", text);
	1004	fprintf(fh,"ASCII\n");
	1005	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	1006	fprintf(fh,"POINTS %u double\n", vlist->n);
	1007	for(i=0;i<vlist->n;i++){
8f6a69	1008	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	1009	}
SP	1010
	1011	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	1012	for(i=0;i<blist->n;i++){
e016c4	1013	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	1014	}
SP	1015	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	1016	for(i=0;i<blist->n;i++)
	1017	fprintf(fh,"3\n");
	1018
	1019	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	1020	fprintf(fh,"SCALARS scalars long 1\n");
	1021	fprintf(fh,"LOOKUP_TABLE default\n");
	1022
	1023	for(i=0;i<vlist->n;i++)
8f6a69	1024	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	1025
SP	1026	fclose(fh);
	1027	return TS_SUCCESS;
	1028	}
	1029
	1030
	1031
144784	1032	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	1033	FILE *fh;
	1034	ts_uint i;
	1035
	1036	fh=fopen(filename, "w");
	1037	if(fh==NULL){
	1038	err("Cannot open file %s for writing");
	1039	return TS_FAIL;
	1040	}
	1041
	1042	for(i=0;i<vesicle->tlist->n;i++){
	1043
	1044	fprintf(fh,"\ttriangle {");
	1045	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1046	vesicle->tlist->tria[i]->vertex[0]->x,
	1047	vesicle->tlist->tria[i]->vertex[0]->y,
	1048	vesicle->tlist->tria[i]->vertex[0]->z,
	1049
	1050	vesicle->tlist->tria[i]->vertex[1]->x,
	1051	vesicle->tlist->tria[i]->vertex[1]->y,
	1052	vesicle->tlist->tria[i]->vertex[1]->z,
	1053
	1054	vesicle->tlist->tria[i]->vertex[2]->x,
	1055	vesicle->tlist->tria[i]->vertex[2]->y,
	1056	vesicle->tlist->tria[i]->vertex[2]->z
	1057	);
	1058	}
	1059
	1060	fclose(fh);
	1061	return TS_SUCCESS;
	1062	}
	1063
	1064
1ab449	1065	ts_tape parsetape(char filename){
698ae1	1066	FILE *fd = fopen (filename, "r");
SP	1067	long length;
	1068	size_t size;
	1069	fseek (fd, 0, SEEK_END);
	1070	length = ftell (fd);
	1071	fseek (fd, 0, SEEK_SET);
	1072	size=fread (tapetxt, 1, length, fd);
	1073	fclose(fd);
	1074	if(size);
	1075	ts_tape *tape=parsetapebuffer(tapetxt);
	1076	return tape;
	1077	}
	1078
	1079	ts_tape parsetapebuffer(char buffer){
1ab449	1080	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1081	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1082
d7639a	1083	cfg_opt_t opts[] = {
1ab449	1084	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1085	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1086	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1087	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1088	CFG_SIMPLE_INT("nfono",&tape->nfono),
	1089	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1090	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1091	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1092	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1093	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1094	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1095	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1096	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1097	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1098	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1099	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	1100	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1101	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1102	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1103	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1104	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1105	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1106	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1107	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1108	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1109	CFG_SIMPLE_INT("inititer", &tape->inititer),
	1110	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	1111	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	1112	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	1113	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1114	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1115	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	1116	CFG_END()
SP	1117	};
	1118	cfg_t *cfg;
	1119	ts_uint retval;
	1120	cfg = cfg_init(opts, 0);
698ae1	1121	retval=cfg_parse_buf(cfg, buffer);
d7639a	1122	if(retval==CFG_FILE_ERROR){
a6b1b5	1123	fatal("No tape file.",100);
d7639a	1124	}
SP	1125	else if(retval==CFG_PARSE_ERROR){
	1126	fatal("Invalid tape!",100);
	1127	}
a2db52	1128
7b0c07	1129	/* here we override all values read from tape with values from commandline*/
SP	1130	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1131	cfg_free(cfg);
40aa5b	1132
SP	1133
1ab449	1134	/* global variables are set automatically */
SP	1135	quiet=tape->quiet;
	1136	return tape;
	1137	}
d7639a	1138
1ab449	1139	ts_bool tape_free(ts_tape *tape){
SP	1140	free(tape->multiprocessing);
	1141	free(tape);
	1142	return TS_SUCCESS;
d7639a	1143	}
f74313	1144
SP	1145
7b0c07	1146
SP	1147	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1148
	1149	char commands, backup, saveptr, saveopptr, command, operator[2];
	1150	ts_uint i,j;
	1151	commands=(char )malloc(10000sizeof(char));
	1152	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1153	strcpy(commands,opts);
	1154	for(i=0; ;i++, commands=NULL){
	1155	//breaks comma separated list of commands into specific commands.
	1156	command=strtok_r(commands,",",&saveptr);
	1157	if(command==NULL) break;
	1158	// fprintf(stdout,"Command %d: %s\n",i,command);
	1159	//extracts name of command and value of command into operator[2] array.
	1160	for(j=0; j<2;j++,command=NULL){
	1161	operator[j]=strtok_r(command,"=",&saveopptr);
	1162	if(operator[j]==NULL) break;
	1163	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1164	}
	1165	//1. check: must have 2 operators.
	1166	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1167
	1168	// cfg_setstr(cfg,operator[0],operator[1]);
	1169	cmdline_to_tape(cfg,operator[0],operator[1]);
	1170	//2. check: must be named properly.
	1171	//3. check: must be of right format (integer, double, string, ...)
	1172
	1173	}
	1174	free(backup);
	1175	return TS_SUCCESS;
	1176	}
	1177
	1178
	1179	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1180
	1181	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1182	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1183	switch (cfg_opt->type){
	1184	case CFGT_INT:
	1185	cfg_setint(cfg,key,atol(val));
	1186	break;
	1187	case CFGT_FLOAT:
	1188	cfg_setfloat(cfg,key,atof(val));
	1189	break;
	1190	/* case CFGT_BOOL:
	1191	cfg_setbool(cfg,operator[0],operator[1]);
	1192	break; */
	1193	case CFGT_STR:
	1194	cfg_setstr(cfg,key,val);
	1195	break;
	1196	default:
	1197	break;
	1198
	1199	}
	1200	return TS_SUCCESS;
	1201	}
	1202
	1203
	1204
f74313	1205	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1206	FILE *fh;
	1207	ts_uint i, nvtx,nedges,ntria;
	1208	ts_uint vtxi1,vtxi2;
	1209	float x,y,z;
	1210	ts_vertex_list *vlist;
	1211	fh=fopen(fname, "r");
	1212	if(fh==NULL){
	1213	err("Cannot open file for reading... Nonexistant file?");
	1214	return TS_FAIL;
	1215	}
	1216	ts_uint retval;
	1217	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1218	vesicle->vlist=init_vertex_list(nvtx);
	1219	vlist=vesicle->vlist;
	1220	for(i=0;i<nvtx;i++){
8f6a69	1221	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1222	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1223	vlist->vtx[i]->x=x;
SP	1224	vlist->vtx[i]->y=y;
	1225	vlist->vtx[i]->z=z;
f74313	1226	}
SP	1227	for(i=0;i<nedges;i++){
	1228	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1229	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1230	}
	1231	//TODO: neighbours from bonds,
	1232	//TODO: triangles from neigbours
	1233
	1234	// Don't need to read triangles. Already have enough data
	1235	/*
	1236	for(i=0;i<ntria;i++){
	1237	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1238	vtxi1=vesicle->blist->vertex1->idx;
SP	1239	vtxi2=vesicle->blist->vertex1->idx;
f74313	1240
SP	1241	}
	1242	*/
41a035	1243	if(retval);
f74313	1244	fclose(fh);
SP	1245
	1246
	1247
	1248	return TS_SUCCESS;
	1249	}