trisurf-ng.git - Gitblit

Added some basic help on flags. Unformatted.

Samo Penic

2016-05-27 ba73ab71fa4df14cbf55bf4111c791eea21a85c8

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");
	615	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump or tape).\n");
	616	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
	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");
	619	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n");
	620	return TS_SUCCESS;
	621	}
	622
	623
083e03	624
d7639a	625	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	626	ts_uint i;
	627	printf("Number of vertices: %u\n",vlist->n);
	628	for(i=0;i<vlist->n;i++){
a6b1b5	629	printf("%u: %f %f %f\n",
8f6a69	630	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	631	}
SP	632	return TS_SUCCESS;
	633	}
	634
	635	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	636	ts_uint i,j;
a6b1b5	637	ts_vertex **vtx=vlist->vtx;
d7639a	638	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	639	for(i=0;i<vlist->n;i++){
8f6a69	640	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	641	for(j=0;j<vtx[i]->neigh_no;j++){
	642	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	643	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	644	}
SP	645	printf("\n");
	646	}
	647
	648	return TS_SUCCESS;
	649	}
	650
	651	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	652	ts_vertex **vtx=vlist->vtx;
d7639a	653	ts_uint i;
SP	654	FILE *fh;
	655
	656	fh=fopen(filename, "w");
	657	if(fh==NULL){
	658	err("Cannot open file %s for writing");
	659	return TS_FAIL;
	660	}
	661	for(i=0;i<vlist->n;i++)
8f6a69	662	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	663
SP	664	fclose(fh);
	665	return TS_SUCCESS;
	666	}
	667
	668
	669	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	670	ts_uint i,j;
	671	for(i=0;i<vlist->n;i++){
8f6a69	672	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	673	vlist->vtx[i]->y, vlist->vtx[i]->z,
	674	vlist->vtx[i]->neigh_no);
	675	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	676	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	677	//-vlist->vtx+1));
d7639a	678	}
SP	679	fprintf(fh,"\n");
	680	}
	681	return TS_SUCCESS;
	682	}
	683
	684	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	685	ts_uint i,j;
a6b1b5	686	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	687	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	688	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	689	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	690	}
SP	691	fprintf(fh,"\n");
	692	}
	693	return TS_SUCCESS;
	694	}
	695
	696	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	697	ts_triangle_list *tlist=vesicle->tlist;
d7639a	698	ts_uint i,j;
SP	699	for(i=0;i<tlist->n;i++){
41a035	700	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	701	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	702	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	703	}
SP	704	fprintf(fh,"\n");
	705	for(j=0;j<3;j++){
41a035	706	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	707	}
SP	708	fprintf(fh,"\n");
41a035	709	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	710	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	711	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	712	}
	713	return TS_SUCCESS;
	714	}
	715
	716	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	717	ts_uint i,j;
	718	for(i=0;i<vlist->n;i++){
	719	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	720	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	721	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	722	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	723	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	724	}
SP	725	fprintf(fh,"\n");
cef6ca	726	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	727	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	728	}
SP	729	fprintf(fh,"\n");
	730	}
	731	return TS_SUCCESS;
	732	}
	733
	734	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	735	ts_uint i;
a6b1b5	736	for(i=0;i<vesicle->blist->n;i++){
e016c4	737	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	738	//-vesicle->vlist->vtx+1),
e016c4	739	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	740	//-vesicle->vlist.vtx+1));
d7639a	741	}
SP	742	return TS_SUCCESS;
	743	}
	744
	745
	746	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	747	FILE *fh;
	748	fh=fopen(filename, "w");
	749	if(fh==NULL){
	750	err("Cannot open file %s for writing");
	751	return TS_FAIL;
	752	}
	753	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	754	fprint_vertex_list(fh,vesicle->vlist);
d7639a	755	fprint_tristar(fh,vesicle);
SP	756	fprint_triangle_list(fh,vesicle);
a6b1b5	757	fprint_vertex_data(fh,vesicle->vlist);
d7639a	758	fprint_bonds(fh,vesicle);
SP	759	fclose(fh);
	760	return TS_SUCCESS;
	761	}
	762
	763	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	764	FILE *fh;
	765	char line[255];
	766	fh=fopen(filename, "r");
	767	if(fh==NULL){
	768	err("Cannot open file for reading... Nonexistant file?");
	769	return TS_FAIL;
	770	}
a6b1b5	771	ts_uint retval=1;
d7639a	772	while(retval!=EOF){
SP	773	retval=fscanf(fh,"%s",line);
	774
	775	fprintf(stderr,"%s",line);
	776	}
	777	fclose(fh);
	778	return TS_SUCCESS;
	779	}
	780
	781	ts_bool write_master_xml_file(ts_char *filename){
	782	FILE *fh;
	783	ts_char i,j;
	784	ts_uint tstep;
	785	ts_char *number;
	786	fh=fopen(filename, "w");
	787	if(fh==NULL){
	788	err("Cannot open file %s for writing");
	789	return TS_FAIL;
	790	}
	791
	792	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
267db5	793	DIR *dir = opendir(command_line_args.path);
d7639a	794	if(dir){
SP	795	struct dirent *ent;
	796	tstep=0;
	797	while((ent = readdir(dir)) != NULL)
	798	{
	799	i=rindex(ent->d_name,'.');
	800	if(i==NULL) continue;
	801	if(strcmp(i+1,"vtu")==0){
	802	j=rindex(ent->d_name,'_');
	803	if(j==NULL) continue;
	804	number=strndup(j+1,j-i);
a6b1b5	805	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	806	tstep++;
SP	807	free(number);
	808	}
	809	}
	810	}
f74313	811	free(dir);
d7639a	812	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	813	fclose(fh);
	814	return TS_SUCCESS;
	815	}
	816
	817	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	818	ts_vertex_list *vlist=vesicle->vlist;
SP	819	ts_bond_list *blist=vesicle->blist;
	820	ts_vertex **vtx=vlist->vtx;
40aa5b	821	ts_uint i,j;
267db5	822	char filename[10000];
SP	823	char just_name[255];
d7639a	824	FILE *fh;
267db5	825	strcpy(filename,command_line_args.path);
SP	826	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	827	strcat(filename,just_name);
d7639a	828
SP	829	fh=fopen(filename, "w");
	830	if(fh==NULL){
	831	err("Cannot open file %s for writing");
	832	return TS_FAIL;
	833	}
	834	/* Here comes header of the file */
40aa5b	835
SP	836	//find number of extra vtxs and bonds of polymeres
58230a	837	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	838	ts_bool poly=0, fil=0;
40aa5b	839	if(vesicle->poly_list!=NULL){
SP	840	if(vesicle->poly_list->poly[0]!=NULL){
	841	polyno=vesicle->poly_list->n;
	842	monono=vesicle->poly_list->poly[0]->vlist->n;
	843	poly=1;
	844	}
	845	}
58230a	846
M	847	if(vesicle->filament_list!=NULL){
	848	if(vesicle->filament_list->poly[0]!=NULL){
	849	filno=vesicle->filament_list->n;
	850	fonono=vesicle->filament_list->poly[0]->vlist->n;
	851	fil=1;
	852	}
	853	}
	854
854cb6	855	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	856	xml_trisurf_data(fh,vesicle);
	857	fprintf(fh, " <UnstructuredGrid>\n");
58230a	858	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1));
d7639a	859	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	860	for(i=0;i<vlist->n;i++){
a6b1b5	861	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	862	}
40aa5b	863	//polymeres
SP	864	if(poly){
3c1ac1	865	poly_idx=vlist->n;
40aa5b	866	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	867	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	868	fprintf(fh,"%u ", poly_idx);
M	869	}
	870	}
	871	}
	872	//filaments
	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]->vlist->n;j++,poly_idx++){
	877	// fprintf(stderr,"was here\n");
3c1ac1	878	fprintf(fh,"%u ", poly_idx);
40aa5b	879	}
SP	880	}
	881	}
d7639a	882
SP	883	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	884	for(i=0;i<vlist->n;i++){
aad500	885	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	886	}
SP	887	//polymeres
	888	if(poly){
	889	for(i=0;i<vesicle->poly_list->n;i++){
	890	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	891	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	892	}
M	893	}
	894	}
	895	//filaments
	896	if(fil){
	897	for(i=0;i<vesicle->filament_list->n;i++){
	898	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	899	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	900	}
SP	901	}
d7639a	902	}
SP	903
	904	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	905	for(i=0;i<blist->n;i++){
e016c4	906	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	907	}
40aa5b	908	//polymeres
SP	909	if(poly){
3c1ac1	910	poly_idx=vlist->n;
40aa5b	911	for(i=0;i<vesicle->poly_list->n;i++){
SP	912	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	913	// 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	914	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	915	}
SP	916	//grafted bonds
3c1ac1	917	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	918	}
SP	919
	920	}
	921
58230a	922	//filaments
M	923	if(fil){
	924	poly_idx=vlist->n+monono*polyno;
	925	for(i=0;i<vesicle->filament_list->n;i++){
	926	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	927	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);
	928	// fprintf(stderr,"was here\n");
	929
	930	}
	931	}
	932
	933	}
40aa5b	934
d7639a	935	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	936	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	937	fprintf(fh,"%u ",i);
SP	938	}
	939	fprintf(fh,"\n");
	940	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
58230a	941	for (i=0;i<blist->n+mononopolyno+fononofilno;i++){
d7639a	942	fprintf(fh,"3 ");
SP	943	}
	944
	945	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	946	fclose(fh);
	947	return TS_SUCCESS;
	948
	949	}
	950
	951	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	952	ts_vertex_list *vlist=vesicle->vlist;
SP	953	ts_bond_list *blist=vesicle->blist;
	954	ts_vertex **vtx=vlist->vtx;
	955	ts_uint i;
d7639a	956	FILE *fh;
SP	957
	958	fh=fopen(filename, "w");
	959	if(fh==NULL){
	960	err("Cannot open file %s for writing");
	961	return TS_FAIL;
	962	}
	963	/* Here comes header of the file */
	964	// fprintf(stderr,"NSHELL=%u\n",nshell);
	965	fprintf(fh, "# vtk DataFile Version 2.0\n");
	966	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	967	fprintf(fh, "%s\n", text);
	968	fprintf(fh,"ASCII\n");
	969	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	970	fprintf(fh,"POINTS %u double\n", vlist->n);
	971	for(i=0;i<vlist->n;i++){
8f6a69	972	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	973	}
SP	974
	975	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	976	for(i=0;i<blist->n;i++){
e016c4	977	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	978	}
SP	979	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	980	for(i=0;i<blist->n;i++)
	981	fprintf(fh,"3\n");
	982
	983	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	984	fprintf(fh,"SCALARS scalars long 1\n");
	985	fprintf(fh,"LOOKUP_TABLE default\n");
	986
	987	for(i=0;i<vlist->n;i++)
8f6a69	988	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	989
SP	990	fclose(fh);
	991	return TS_SUCCESS;
	992	}
	993
	994
	995
144784	996	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	997	FILE *fh;
	998	ts_uint i;
	999
	1000	fh=fopen(filename, "w");
	1001	if(fh==NULL){
	1002	err("Cannot open file %s for writing");
	1003	return TS_FAIL;
	1004	}
	1005
	1006	for(i=0;i<vesicle->tlist->n;i++){
	1007
	1008	fprintf(fh,"\ttriangle {");
	1009	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	1010	vesicle->tlist->tria[i]->vertex[0]->x,
	1011	vesicle->tlist->tria[i]->vertex[0]->y,
	1012	vesicle->tlist->tria[i]->vertex[0]->z,
	1013
	1014	vesicle->tlist->tria[i]->vertex[1]->x,
	1015	vesicle->tlist->tria[i]->vertex[1]->y,
	1016	vesicle->tlist->tria[i]->vertex[1]->z,
	1017
	1018	vesicle->tlist->tria[i]->vertex[2]->x,
	1019	vesicle->tlist->tria[i]->vertex[2]->y,
	1020	vesicle->tlist->tria[i]->vertex[2]->z
	1021	);
	1022	}
	1023
	1024	fclose(fh);
	1025	return TS_SUCCESS;
	1026	}
	1027
	1028
1ab449	1029	ts_tape parsetape(char filename){
698ae1	1030	FILE *fd = fopen (filename, "r");
SP	1031	long length;
	1032	size_t size;
	1033	fseek (fd, 0, SEEK_END);
	1034	length = ftell (fd);
	1035	fseek (fd, 0, SEEK_SET);
	1036	size=fread (tapetxt, 1, length, fd);
	1037	fclose(fd);
	1038	if(size);
	1039	ts_tape *tape=parsetapebuffer(tapetxt);
	1040	return tape;
	1041	}
	1042
	1043	ts_tape parsetapebuffer(char buffer){
1ab449	1044	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	1045	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	1046
d7639a	1047	cfg_opt_t opts[] = {
1ab449	1048	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	1049	CFG_SIMPLE_INT("npoly", &tape->npoly),
	1050	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	1051	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	1052	CFG_SIMPLE_INT("nfono",&tape->nfono),
	1053	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	1054	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	1055	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	1056	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	1057	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	1058	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	1059	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	1060	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	1061	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	1062	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	1063	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
1ab449	1064	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	1065	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	1066	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	1067	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	1068	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	1069	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	1070	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	1071	CFG_SIMPLE_INT("iterations",&tape->iterations),
	1072	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	1073	CFG_SIMPLE_INT("inititer", &tape->inititer),
	1074	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	1075	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	1076	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	1077	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	1078	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	1079	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
d7639a	1080	CFG_END()
SP	1081	};
	1082	cfg_t *cfg;
	1083	ts_uint retval;
	1084	cfg = cfg_init(opts, 0);
698ae1	1085	retval=cfg_parse_buf(cfg, buffer);
d7639a	1086	if(retval==CFG_FILE_ERROR){
a6b1b5	1087	fatal("No tape file.",100);
d7639a	1088	}
SP	1089	else if(retval==CFG_PARSE_ERROR){
	1090	fatal("Invalid tape!",100);
	1091	}
a2db52	1092
7b0c07	1093	/* here we override all values read from tape with values from commandline*/
SP	1094	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	1095	cfg_free(cfg);
40aa5b	1096
SP	1097
1ab449	1098	/* global variables are set automatically */
SP	1099	quiet=tape->quiet;
	1100	return tape;
	1101	}
d7639a	1102
1ab449	1103	ts_bool tape_free(ts_tape *tape){
SP	1104	free(tape->multiprocessing);
	1105	free(tape);
	1106	return TS_SUCCESS;
d7639a	1107	}
f74313	1108
SP	1109
7b0c07	1110
SP	1111	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	1112
	1113	char commands, backup, saveptr, saveopptr, command, operator[2];
	1114	ts_uint i,j;
	1115	commands=(char )malloc(10000sizeof(char));
	1116	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	1117	strcpy(commands,opts);
	1118	for(i=0; ;i++, commands=NULL){
	1119	//breaks comma separated list of commands into specific commands.
	1120	command=strtok_r(commands,",",&saveptr);
	1121	if(command==NULL) break;
	1122	// fprintf(stdout,"Command %d: %s\n",i,command);
	1123	//extracts name of command and value of command into operator[2] array.
	1124	for(j=0; j<2;j++,command=NULL){
	1125	operator[j]=strtok_r(command,"=",&saveopptr);
	1126	if(operator[j]==NULL) break;
	1127	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	1128	}
	1129	//1. check: must have 2 operators.
	1130	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	1131
	1132	// cfg_setstr(cfg,operator[0],operator[1]);
	1133	cmdline_to_tape(cfg,operator[0],operator[1]);
	1134	//2. check: must be named properly.
	1135	//3. check: must be of right format (integer, double, string, ...)
	1136
	1137	}
	1138	free(backup);
	1139	return TS_SUCCESS;
	1140	}
	1141
	1142
	1143	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	1144
	1145	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	1146	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	1147	switch (cfg_opt->type){
	1148	case CFGT_INT:
	1149	cfg_setint(cfg,key,atol(val));
	1150	break;
	1151	case CFGT_FLOAT:
	1152	cfg_setfloat(cfg,key,atof(val));
	1153	break;
	1154	/* case CFGT_BOOL:
	1155	cfg_setbool(cfg,operator[0],operator[1]);
	1156	break; */
	1157	case CFGT_STR:
	1158	cfg_setstr(cfg,key,val);
	1159	break;
	1160	default:
	1161	break;
	1162
	1163	}
	1164	return TS_SUCCESS;
	1165	}
	1166
	1167
	1168
f74313	1169	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
SP	1170	FILE *fh;
	1171	ts_uint i, nvtx,nedges,ntria;
	1172	ts_uint vtxi1,vtxi2;
	1173	float x,y,z;
	1174	ts_vertex_list *vlist;
	1175	fh=fopen(fname, "r");
	1176	if(fh==NULL){
	1177	err("Cannot open file for reading... Nonexistant file?");
	1178	return TS_FAIL;
	1179	}
	1180	ts_uint retval;
	1181	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	1182	vesicle->vlist=init_vertex_list(nvtx);
	1183	vlist=vesicle->vlist;
	1184	for(i=0;i<nvtx;i++){
8f6a69	1185	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	1186	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	1187	vlist->vtx[i]->x=x;
SP	1188	vlist->vtx[i]->y=y;
	1189	vlist->vtx[i]->z=z;
f74313	1190	}
SP	1191	for(i=0;i<nedges;i++){
	1192	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	1193	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	1194	}
	1195	//TODO: neighbours from bonds,
	1196	//TODO: triangles from neigbours
	1197
	1198	// Don't need to read triangles. Already have enough data
	1199	/*
	1200	for(i=0;i<ntria;i++){
	1201	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	1202	vtxi1=vesicle->blist->vertex1->idx;
SP	1203	vtxi2=vesicle->blist->vertex1->idx;
f74313	1204
SP	1205	}
	1206	*/
41a035	1207	if(retval);
f74313	1208	fclose(fh);
SP	1209
	1210
	1211
	1212	return TS_SUCCESS;
	1213	}