trisurf-ng.git - Gitblit

continuation s working. now reset counter is needed

Samo Penic

2014-03-08 62681163a4c47fc6dbd6b2b96f84171b20cba3ed

commit \| author \| age
f74313	1	#include "general.h"
d7639a	2	#include<stdio.h>
SP	3	#include "io.h"
f74313	4	#include <confuse.h>
SP	5	#include "vertex.h"
	6	#include "bond.h"
d7639a	7	#include<string.h>
a6b1b5	8	#include<stdlib.h>
d7639a	9	#include <sys/types.h>
SP	10	#include <dirent.h>
b14a8d	11	#include "initial_distribution.h"
a2db52	12	#include "poly.h"
d7639a	13
083e03	14	#include <getopt.h>
SP	15	#include <sys/stat.h>
	16	#include <sys/types.h>
	17	#include <dirent.h>
	18	#include <errno.h>
e9eab4	19	/ DUMP STATE TO DISK DRIVE /
SP	20
1ab449	21	ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
e9eab4	22
SP	23	/* save current state with wrong pointers. Will fix that later */
	24	ts_uint i,j,k;
	25	FILE *fh=fopen("dump.bin","wb");
	26
	27	/* dump vesicle */
86f5e7	28	fwrite(vesicle, sizeof(ts_vesicle),1,fh);
e9eab4	29	/* dump vertex list */
SP	30	fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	31	/* dump bond list */
	32	fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
	33	/* dump triangle list */
	34	fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	35	/* dump cell list */
	36	fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
	37	/* dump poly list */
	38	fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
	39	/* level 1 complete */
	40
	41	/dump vertices/
	42	for(i=0;i<vesicle->vlist->n;i++){
	43	fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
	44	/* dump pointer offsets for:
	45	neigh
	46	bond
	47	tria
	48	cell is ignored
	49	*/
	50	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	51	fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	52	}
SP	53	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	54	fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	55	}
SP	56	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	57	fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	58	}
SP	59	}
	60
	61	/dump bonds/
	62	for(i=0;i<vesicle->blist->n;i++){
	63	fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
	64	/* dump pointer offsets for vtx1 and vtx2 */
3c1ac1	65	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
SP	66	fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
	67	//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
	68	fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	69	}
SP	70
	71	/dump triangles/
	72	for(i=0;i<vesicle->tlist->n;i++){
	73	fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
	74	/* dump pointer offsets for vertex */
3c1ac1	75	fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
SP	76	fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
	77	fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
e9eab4	78	/* dump pointer offsets for neigh */
SP	79	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	80	fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
e9eab4	81	}
SP	82	}
	83
	84
	85	/dump polymeres /
	86	for(i=0;i<vesicle->poly_list->n;i++){
	87	fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	88	fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
SP	89	fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
e9eab4	90	}
SP	91
	92	/* dump poly vertex(monomer) list*/
	93	for(i=0;i<vesicle->poly_list->n;i++){
	94	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	95	fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
	96	/* dump offset for neigh and bond */
	97	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	98	// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	99	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	100	}
SP	101	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	102	//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
SP	103	fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
e9eab4	104	}
SP	105	}
3c1ac1	106	// grafted vtx on vesicle data dump
SP	107	fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
e9eab4	108	}
SP	109	/* dump poly bonds between monomers list*/
	110	for(i=0;i<vesicle->poly_list->n;i++){
	111	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	112	fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
	113	/* dump vtx1 and vtx2 offsets */
3c1ac1	114	//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
SP	115	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
	116	// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
	117	fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
e9eab4	118	}
SP	119	}
	120
	121	/* pointer offsets for fixing the restored pointers */
	122	/* need pointers for
	123	vlist->vtx
	124	blist->bond
	125	tlist->tria
	126	clist->cell
	127	poly_list->poly
	128	and for each poly:
	129	poly_list->poly->vtx
	130	poly_list->poly->bond
	131	*/
	132
063289	133	fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
1ab449	134
SP	135	fwrite(&iteration, sizeof(ts_uint),1,fh);
e9eab4	136	fclose(fh);
SP	137	return TS_SUCCESS;
	138	}
	139
	140
	141	/ RESTORE DUMP FROM DISK /
1ab449	142	ts_vesicle restore_state(ts_uint iteration){
e9eab4	143	ts_uint i,j,k;
SP	144	FILE *fh=fopen("dump.bin","rb");
	145	ts_uint retval;
3c1ac1	146	ts_uint idx;
e9eab4	147
SP	148	/* we restore all the data from the dump */
	149	/* restore vesicle */
	150	ts_vesicle vesicle=(ts_vesicle )calloc(1,sizeof(ts_vesicle));
86f5e7	151	retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
SP	152	// fprintf(stderr,"was here! %e\n",vesicle->dmax);
	153
e9eab4	154	/* restore vertex list */
SP	155	vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
	156	retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
	157	/* restore bond list */
	158	vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
	159	retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
	160	/* restore triangle list */
	161	vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
	162	retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
	163	/* restore cell list */
	164	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	165	retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
	166	/* restore poly list */
	167	vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
	168	retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
	169	/* level 1 complete */
	170
3c1ac1	171	/* prerequisity. Bonds must be malloced before vertexes are recreated */
SP	172	vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond ));
	173	for(i=0;i<vesicle->blist->n;i++){
	174	vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
	175	}
	176	/* prerequisity. Triangles must be malloced before vertexes are recreated */
	177	vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle ));
	178	for(i=0;i<vesicle->tlist->n;i++){
	179	vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
	180	}
a37ba2	181	/* prerequisity. Vertices must be malloced before vertexes are recreated */
e9eab4	182	vesicle->vlist->vtx=(ts_vertex *)calloc(vesicle->vlist->n,sizeof(ts_vertex ));
a37ba2	183	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	184	vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
a37ba2	185	}
SP	186	/restore vertices/
	187	for(i=0;i<vesicle->vlist->n;i++){
e9eab4	188	retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
SP	189	/restore neigh, bond, tristar. Ignoring cell /
	190	vesicle->vlist->vtx[i]->neigh=(ts_vertex *)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex ));
	191	for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
3c1ac1	192	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	193	vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
e9eab4	194	}
SP	195	vesicle->vlist->vtx[i]->bond=(ts_bond *)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond ));
	196	for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
3c1ac1	197	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	198	/* 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 */
	199	vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
e9eab4	200	}
SP	201
	202	vesicle->vlist->vtx[i]->tristar=(ts_triangle *)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle ));
	203	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
3c1ac1	204	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	205	/* same comment as above */
	206	vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
e9eab4	207	}
SP	208
	209	}
	210
	211	/restore bonds/
3c1ac1	212	// vesicle->blist->bond=(ts_bond *)calloc(vesicle->blist->n,sizeof(ts_bond )); // done before.
e9eab4	213	for(i=0;i<vesicle->blist->n;i++){
3c1ac1	214	// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
e9eab4	215	retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
SP	216	/* restore vtx1 and vtx2 */
3c1ac1	217	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	218	vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
	219	retval=fread(&idx,sizeof(ts_uint),1,fh);
	220	vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
e9eab4	221	}
SP	222
	223	/restore triangles/
3c1ac1	224	// vesicle->tlist->tria=(ts_triangle *)calloc(vesicle->tlist->n,sizeof(ts_triangle )); // done before
e9eab4	225	for(i=0;i<vesicle->tlist->n;i++){
3c1ac1	226	// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
e9eab4	227	retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
SP	228	/* restore pointers for vertices */
3c1ac1	229	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	230	vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
	231	retval=fread(&idx,sizeof(ts_uint),1,fh);
	232	vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
	233	retval=fread(&idx,sizeof(ts_uint),1,fh);
	234	vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
e9eab4	235	/* restore pointers for neigh */
3c1ac1	236	vesicle->tlist->tria[i]->neigh=(ts_triangle *)malloc(vesicle->tlist->tria[i]->neigh_nosizeof(ts_triangle *));
e9eab4	237	for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
3c1ac1	238	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	239	vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
e9eab4	240	}
SP	241
	242	}
	243
	244	/restore cells /
	245	/TODO: do we need to recalculate cells here? /
	246	/* vesicle->clist->cell=(ts_cell *)malloc(vesicle->clist->cellnosizeof(ts_cell *));
	247	for(i=0;i<vesicle->clist->cellno;i++){
	248	vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
	249	retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
	250	}
	251	*/
	252	/restore polymeres /
	253	vesicle->poly_list->poly = (ts_poly *)calloc(vesicle->poly_list->n,sizeof(ts_poly ));
	254	for(i=0;i<vesicle->poly_list->n;i++){
	255	vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
	256	retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
3c1ac1	257	vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
SP	258	retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
	259	vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
	260	retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
	261	/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
	262	vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex *)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex ));
	263	vesicle->poly_list->poly[i]->blist->bond=(ts_bond *)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond ));
	264	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	265	vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
	266	}
	267	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	268	vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
	269	}
	270
e9eab4	271	}
3c1ac1	272
e9eab4	273
SP	274	/* restore poly vertex(monomer) list*/
	275	for(i=0;i<vesicle->poly_list->n;i++){
	276	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	277	retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
3c1ac1	278
e9eab4	279	/* restore neigh and bonds */
SP	280	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 ));
	281	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
3c1ac1	282	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	283	vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	284	}
SP	285	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 ));
	286	for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
3c1ac1	287	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	288	vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
e9eab4	289	}
SP	290
	291	}
3c1ac1	292	/* restore grafted vtx on vesicle and grafted_poly */
SP	293	retval=fread(&idx,sizeof(ts_uint),1,fh);
	294	vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
	295	vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
e9eab4	296	}
3c1ac1	297
e9eab4	298	/* restore poly bonds between monomers list*/
SP	299	for(i=0;i<vesicle->poly_list->n;i++){
	300	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	301	// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
e9eab4	302	retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
SP	303	/* restore vtx1 and vtx2 */
3c1ac1	304	retval=fread(&idx,sizeof(ts_uint),1,fh);
SP	305	vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
	306	retval=fread(&idx,sizeof(ts_uint),1,fh);
	307	vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
e9eab4	308	}
SP	309	}
	310
063289	311	// recreating space for cells //
SP	312	vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
	313	retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
	314	vesicle->clist->cell=(ts_cell *)malloc(sizeof(ts_cell )vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
	315	for(i=0;i<vesicle->clist->ncmax[0]vesicle->clist->ncmax[1]vesicle->clist->ncmax[2];i++){
	316	vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
	317	vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
	318	}
e9eab4	319
1ab449	320	retval=fread(iteration,sizeof(ts_uint),1,fh);
e9eab4	321	if(retval);
SP	322	fclose(fh);
	323	return vesicle;
	324	}
	325
	326
	327
083e03	328	ts_bool parse_args(int argc, char **argv){
SP	329	int c, retval;
	330	DIR *dir;
	331	path[0]=0;
	332	while (1)
	333	{
	334	static struct option long_options[] =
	335	{
	336	{"force-from-tape", no_argument, &force_from_tape, 1},
	337	{"tape", no_argument, 0, 't'},
	338	{"output-file", required_argument, 0, 'o'},
	339	{"directory", required_argument, 0, 'd'},
	340	{"dump-file", required_argument,0, 'f'},
	341	{0, 0, 0, 0}
	342	};
	343	/* getopt_long stores the option index here. */
	344	int option_index = 0;
	345
	346	c = getopt_long (argc, argv, "d:fot",
	347	long_options, &option_index);
	348
	349	/* Detect the end of the options. */
	350	if (c == -1)
	351	break;
	352
	353	switch (c)
	354	{
	355	case 0:
	356	/* If this option set a flag, do nothing else now. */
	357	if (long_options[option_index].flag != 0)
	358	break;
	359	printf ("option %s", long_options[option_index].name);
	360	if (optarg)
	361	printf (" with arg %s", optarg);
	362	printf ("\n");
	363	break;
	364
	365	case 't':
	366	//check if tape exists. If not, fail immediately.
	367	puts ("option -t\n");
	368	break;
	369
	370	case 'o':
	371	//set filename of master output file
	372	printf ("option -o with value `%s'\n", optarg);
	373	break;
	374
	375	case 'd':
	376	//check if directory exists. If not create one. If creation is
	377	//successful, set directory for output files.
	378	//printf ("option -d with value `%s'\n", optarg);
	379	dir = opendir(optarg);
	380	if (dir)
	381	{
	382	/* Directory exists. */
	383	closedir(dir);
	384	}
	385	else if (ENOENT == errno)
	386	{
	387	/* Directory does not exist. */
	388	retval=mkdir(optarg, 0700);
	389	if(retval){
	390	fatal("Could not create requested directory. Check if you have permissions",1);
	391	}
	392	}
	393	else
	394	{
	395	/* opendir() failed for some other reason. */
	396	fatal("Could not check if directory exists. Reason unknown",1);
	397	}
	398	ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
	399	// sprintf(path,"%s", optarg);
	400	strcpy(path, optarg);
	401	// ts_fprintf(stdout,"ok!\n");
	402
	403	break;
	404
	405	case 'f':
	406	//check if dump file specified exists. Defaults to dump.bin
	407	break;
	408
	409	case '?':
	410	/* getopt_long already printed an error message. */
	411
	412	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	413	fatal("Ooops, read help first",1);
	414	break;
	415
	416	default:
	417	exit (1);
	418	}
	419	}
	420
	421	return TS_SUCCESS;
	422
	423	}
	424
	425
	426
	427
d7639a	428	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	429	ts_uint i;
	430	printf("Number of vertices: %u\n",vlist->n);
	431	for(i=0;i<vlist->n;i++){
a6b1b5	432	printf("%u: %f %f %f\n",
8f6a69	433	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	434	}
SP	435	return TS_SUCCESS;
	436	}
	437
	438	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	439	ts_uint i,j;
a6b1b5	440	ts_vertex **vtx=vlist->vtx;
d7639a	441	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	442	for(i=0;i<vlist->n;i++){
8f6a69	443	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	444	for(j=0;j<vtx[i]->neigh_no;j++){
	445	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	446	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	447	}
SP	448	printf("\n");
	449	}
	450
	451	return TS_SUCCESS;
	452	}
	453
	454	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	455	ts_vertex **vtx=vlist->vtx;
d7639a	456	ts_uint i;
SP	457	FILE *fh;
	458
	459	fh=fopen(filename, "w");
	460	if(fh==NULL){
	461	err("Cannot open file %s for writing");
	462	return TS_FAIL;
	463	}
	464	for(i=0;i<vlist->n;i++)
8f6a69	465	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	466
SP	467	fclose(fh);
	468	return TS_SUCCESS;
	469	}
	470
	471
	472	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	473	ts_uint i,j;
	474	for(i=0;i<vlist->n;i++){
8f6a69	475	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	476	vlist->vtx[i]->y, vlist->vtx[i]->z,
	477	vlist->vtx[i]->neigh_no);
	478	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	479	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	480	//-vlist->vtx+1));
d7639a	481	}
SP	482	fprintf(fh,"\n");
	483	}
	484	return TS_SUCCESS;
	485	}
	486
	487	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	488	ts_uint i,j;
a6b1b5	489	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	490	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	491	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	492	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	493	}
SP	494	fprintf(fh,"\n");
	495	}
	496	return TS_SUCCESS;
	497	}
	498
	499	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	500	ts_triangle_list *tlist=vesicle->tlist;
d7639a	501	ts_uint i,j;
SP	502	for(i=0;i<tlist->n;i++){
41a035	503	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	504	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	505	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	506	}
SP	507	fprintf(fh,"\n");
	508	for(j=0;j<3;j++){
41a035	509	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	510	}
SP	511	fprintf(fh,"\n");
41a035	512	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	513	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	514	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	515	}
	516	return TS_SUCCESS;
	517	}
	518
	519	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	520	ts_uint i,j;
	521	for(i=0;i<vlist->n;i++){
	522	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	523	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	524	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	525	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	526	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	527	}
SP	528	fprintf(fh,"\n");
cef6ca	529	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	530	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	531	}
SP	532	fprintf(fh,"\n");
	533	}
	534	return TS_SUCCESS;
	535	}
	536
	537	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	538	ts_uint i;
a6b1b5	539	for(i=0;i<vesicle->blist->n;i++){
e016c4	540	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	541	//-vesicle->vlist->vtx+1),
e016c4	542	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	543	//-vesicle->vlist.vtx+1));
d7639a	544	}
SP	545	return TS_SUCCESS;
	546	}
	547
	548
	549	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	550	FILE *fh;
	551	fh=fopen(filename, "w");
	552	if(fh==NULL){
	553	err("Cannot open file %s for writing");
	554	return TS_FAIL;
	555	}
	556	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	557	fprint_vertex_list(fh,vesicle->vlist);
d7639a	558	fprint_tristar(fh,vesicle);
SP	559	fprint_triangle_list(fh,vesicle);
a6b1b5	560	fprint_vertex_data(fh,vesicle->vlist);
d7639a	561	fprint_bonds(fh,vesicle);
SP	562	fclose(fh);
	563	return TS_SUCCESS;
	564	}
	565
	566	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	567	FILE *fh;
	568	char line[255];
	569	fh=fopen(filename, "r");
	570	if(fh==NULL){
	571	err("Cannot open file for reading... Nonexistant file?");
	572	return TS_FAIL;
	573	}
a6b1b5	574	ts_uint retval=1;
d7639a	575	while(retval!=EOF){
SP	576	retval=fscanf(fh,"%s",line);
	577
	578	fprintf(stderr,"%s",line);
	579	}
	580	fclose(fh);
	581	return TS_SUCCESS;
	582	}
	583
	584	ts_bool write_master_xml_file(ts_char *filename){
	585	FILE *fh;
	586	ts_char i,j;
	587	ts_uint tstep;
	588	ts_char *number;
	589	fh=fopen(filename, "w");
	590	if(fh==NULL){
	591	err("Cannot open file %s for writing");
	592	return TS_FAIL;
	593	}
	594
	595	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	596	DIR *dir = opendir(".");
	597	if(dir){
	598	struct dirent *ent;
	599	tstep=0;
	600	while((ent = readdir(dir)) != NULL)
	601	{
	602	i=rindex(ent->d_name,'.');
	603	if(i==NULL) continue;
	604	if(strcmp(i+1,"vtu")==0){
	605	j=rindex(ent->d_name,'_');
	606	if(j==NULL) continue;
	607	number=strndup(j+1,j-i);
a6b1b5	608	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	609	tstep++;
SP	610	free(number);
	611	}
	612	}
	613	}
f74313	614	free(dir);
d7639a	615	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	616	fclose(fh);
	617	return TS_SUCCESS;
	618	}
	619
	620	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	621	ts_vertex_list *vlist=vesicle->vlist;
SP	622	ts_bond_list *blist=vesicle->blist;
	623	ts_vertex **vtx=vlist->vtx;
40aa5b	624	ts_uint i,j;
d7639a	625	char filename[255];
SP	626	FILE *fh;
	627
	628	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	629	fh=fopen(filename, "w");
	630	if(fh==NULL){
	631	err("Cannot open file %s for writing");
	632	return TS_FAIL;
	633	}
	634	/* Here comes header of the file */
40aa5b	635
SP	636	//find number of extra vtxs and bonds of polymeres
3c1ac1	637	ts_uint monono=0, polyno=0, poly_idx=0;
40aa5b	638	ts_bool poly=0;
SP	639	if(vesicle->poly_list!=NULL){
	640	if(vesicle->poly_list->poly[0]!=NULL){
	641	polyno=vesicle->poly_list->n;
	642	monono=vesicle->poly_list->poly[0]->vlist->n;
	643	poly=1;
	644	}
	645	}
d7639a	646	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
40aa5b	647	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno, blist->n+mononopolyno);
d7639a	648	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	649	for(i=0;i<vlist->n;i++){
a6b1b5	650	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	651	}
40aa5b	652	//polymeres
SP	653	if(poly){
3c1ac1	654	poly_idx=vlist->n;
40aa5b	655	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	656	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
SP	657	fprintf(fh,"%u ", poly_idx);
40aa5b	658	}
SP	659	}
	660	}
d7639a	661
SP	662	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	663	for(i=0;i<vlist->n;i++){
8f6a69	664	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	665	}
SP	666	//polymeres
	667	if(poly){
	668	for(i=0;i<vesicle->poly_list->n;i++){
	669	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	670	fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
	671	}
	672	}
d7639a	673	}
SP	674
	675	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	676	for(i=0;i<blist->n;i++){
e016c4	677	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	678	}
40aa5b	679	//polymeres
SP	680	if(poly){
3c1ac1	681	poly_idx=vlist->n;
40aa5b	682	for(i=0;i<vesicle->poly_list->n;i++){
SP	683	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	684	// 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	685	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	686	}
SP	687	//grafted bonds
3c1ac1	688	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	689	}
SP	690
	691	}
	692
	693
d7639a	694	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
40aa5b	695	for (i=2;i<(blist->n+mononopolyno)2+1;i+=2){
d7639a	696	fprintf(fh,"%u ",i);
SP	697	}
	698	fprintf(fh,"\n");
	699	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
40aa5b	700	for (i=0;i<blist->n+monono*polyno;i++){
d7639a	701	fprintf(fh,"3 ");
SP	702	}
	703
	704	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	705	fclose(fh);
	706	return TS_SUCCESS;
	707
	708	}
	709
	710	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	711	ts_vertex_list *vlist=vesicle->vlist;
SP	712	ts_bond_list *blist=vesicle->blist;
	713	ts_vertex **vtx=vlist->vtx;
	714	ts_uint i;
d7639a	715	FILE *fh;
SP	716
	717	fh=fopen(filename, "w");
	718	if(fh==NULL){
	719	err("Cannot open file %s for writing");
	720	return TS_FAIL;
	721	}
	722	/* Here comes header of the file */
	723	// fprintf(stderr,"NSHELL=%u\n",nshell);
	724	fprintf(fh, "# vtk DataFile Version 2.0\n");
	725	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	726	fprintf(fh, "%s\n", text);
	727	fprintf(fh,"ASCII\n");
	728	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	729	fprintf(fh,"POINTS %u double\n", vlist->n);
	730	for(i=0;i<vlist->n;i++){
8f6a69	731	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	732	}
SP	733
	734	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	735	for(i=0;i<blist->n;i++){
e016c4	736	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	737	}
SP	738	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	739	for(i=0;i<blist->n;i++)
	740	fprintf(fh,"3\n");
	741
	742	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	743	fprintf(fh,"SCALARS scalars long 1\n");
	744	fprintf(fh,"LOOKUP_TABLE default\n");
	745
	746	for(i=0;i<vlist->n;i++)
8f6a69	747	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	748
SP	749	fclose(fh);
	750	return TS_SUCCESS;
	751	}
	752
	753
	754
1ab449	755	ts_tape parsetape(char filename){
SP	756	// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
	757	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	758	tape->multiprocessing=calloc(255,sizeof(char));
	759	/* long int brezveze0=1;
b14a8d	760	long int brezveze1=1;
SP	761	long int brezveze2=1;
e86357	762	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	763	long int iter=1000, init=1000, mcsw=1000;
1ab449	764	*/
40aa5b	765
d7639a	766	cfg_opt_t opts[] = {
1ab449	767	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	768	CFG_SIMPLE_INT("npoly", &tape->npoly),
	769	CFG_SIMPLE_INT("nmono", &tape->nmono),
	770	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
	771	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
	772	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
	773	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
	774	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
	775	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
	776	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	777	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	778	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	779	CFG_SIMPLE_INT("iterations",&tape->iterations),
	780	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	781	CFG_SIMPLE_INT("inititer", &tape->inititer),
	782	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	783	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	784	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	785	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	786	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
d7639a	787	CFG_END()
SP	788	};
	789	cfg_t *cfg;
	790	ts_uint retval;
	791	cfg = cfg_init(opts, 0);
1ab449	792	retval=cfg_parse(cfg, filename);
d7639a	793	if(retval==CFG_FILE_ERROR){
a6b1b5	794	fatal("No tape file.",100);
d7639a	795	}
SP	796	else if(retval==CFG_PARSE_ERROR){
	797	fatal("Invalid tape!",100);
	798	}
a2db52	799
d7639a	800	cfg_free(cfg);
40aa5b	801
SP	802
1ab449	803	/* global variables are set automatically */
SP	804	quiet=tape->quiet;
	805	return tape;
	806	}
d7639a	807
1ab449	808	ts_bool tape_free(ts_tape *tape){
SP	809	free(tape->multiprocessing);
	810	free(tape);
	811	return TS_SUCCESS;
d7639a	812	}
f74313	813
SP	814
	815	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	816	FILE *fh;
	817	ts_uint i, nvtx,nedges,ntria;
	818	ts_uint vtxi1,vtxi2;
	819	float x,y,z;
	820	ts_vertex_list *vlist;
	821	fh=fopen(fname, "r");
	822	if(fh==NULL){
	823	err("Cannot open file for reading... Nonexistant file?");
	824	return TS_FAIL;
	825	}
	826	ts_uint retval;
	827	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	828	vesicle->vlist=init_vertex_list(nvtx);
	829	vlist=vesicle->vlist;
	830	for(i=0;i<nvtx;i++){
8f6a69	831	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	832	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	833	vlist->vtx[i]->x=x;
SP	834	vlist->vtx[i]->y=y;
	835	vlist->vtx[i]->z=z;
f74313	836	}
SP	837	for(i=0;i<nedges;i++){
	838	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	839	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	840	}
	841	//TODO: neighbours from bonds,
	842	//TODO: triangles from neigbours
	843
	844	// Don't need to read triangles. Already have enough data
	845	/*
	846	for(i=0;i<ntria;i++){
	847	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	848	vtxi1=vesicle->blist->vertex1->idx;
SP	849	vtxi2=vesicle->blist->vertex1->idx;
f74313	850
SP	851	}
	852	*/
41a035	853	if(retval);
f74313	854	fclose(fh);
SP	855
	856
	857
	858	return TS_SUCCESS;
	859	}