trisurf-ng.git - Gitblit

added assigning new values to restore from dump

mihaf

2014-03-10 d9cb01f2bbcaf704b11d7d8c926f2634c04db928

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	{
8a6614	336	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	337	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	338	{"tape", no_argument, 0, 't'},
SP	339	{"output-file", required_argument, 0, 'o'},
	340	{"directory", required_argument, 0, 'd'},
	341	{"dump-file", required_argument,0, 'f'},
	342	{0, 0, 0, 0}
	343	};
	344	/* getopt_long stores the option index here. */
	345	int option_index = 0;
	346
	347	c = getopt_long (argc, argv, "d:fot",
	348	long_options, &option_index);
	349
	350	/* Detect the end of the options. */
	351	if (c == -1)
	352	break;
	353
	354	switch (c)
	355	{
	356	case 0:
	357	/* If this option set a flag, do nothing else now. */
	358	if (long_options[option_index].flag != 0)
	359	break;
	360	printf ("option %s", long_options[option_index].name);
	361	if (optarg)
	362	printf (" with arg %s", optarg);
	363	printf ("\n");
	364	break;
	365
	366	case 't':
	367	//check if tape exists. If not, fail immediately.
	368	puts ("option -t\n");
	369	break;
	370
	371	case 'o':
	372	//set filename of master output file
	373	printf ("option -o with value `%s'\n", optarg);
	374	break;
	375
	376	case 'd':
	377	//check if directory exists. If not create one. If creation is
	378	//successful, set directory for output files.
	379	//printf ("option -d with value `%s'\n", optarg);
	380	dir = opendir(optarg);
	381	if (dir)
	382	{
	383	/* Directory exists. */
	384	closedir(dir);
	385	}
	386	else if (ENOENT == errno)
	387	{
	388	/* Directory does not exist. */
	389	retval=mkdir(optarg, 0700);
	390	if(retval){
	391	fatal("Could not create requested directory. Check if you have permissions",1);
	392	}
	393	}
	394	else
	395	{
	396	/* opendir() failed for some other reason. */
	397	fatal("Could not check if directory exists. Reason unknown",1);
	398	}
	399	ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
	400	// sprintf(path,"%s", optarg);
	401	strcpy(path, optarg);
	402	// ts_fprintf(stdout,"ok!\n");
	403
	404	break;
	405
	406	case 'f':
	407	//check if dump file specified exists. Defaults to dump.bin
	408	break;
	409
	410	case '?':
	411	/* getopt_long already printed an error message. */
	412
	413	ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
	414	fatal("Ooops, read help first",1);
	415	break;
	416
	417	default:
	418	exit (1);
	419	}
	420	}
	421
	422	return TS_SUCCESS;
	423
	424	}
	425
	426
	427
	428
d7639a	429	ts_bool print_vertex_list(ts_vertex_list *vlist){
SP	430	ts_uint i;
	431	printf("Number of vertices: %u\n",vlist->n);
	432	for(i=0;i<vlist->n;i++){
a6b1b5	433	printf("%u: %f %f %f\n",
8f6a69	434	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	435	}
SP	436	return TS_SUCCESS;
	437	}
	438
	439	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	440	ts_uint i,j;
a6b1b5	441	ts_vertex **vtx=vlist->vtx;
d7639a	442	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	443	for(i=0;i<vlist->n;i++){
8f6a69	444	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	445	for(j=0;j<vtx[i]->neigh_no;j++){
	446	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	447	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	448	}
SP	449	printf("\n");
	450	}
	451
	452	return TS_SUCCESS;
	453	}
	454
	455	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	456	ts_vertex **vtx=vlist->vtx;
d7639a	457	ts_uint i;
SP	458	FILE *fh;
	459
	460	fh=fopen(filename, "w");
	461	if(fh==NULL){
	462	err("Cannot open file %s for writing");
	463	return TS_FAIL;
	464	}
	465	for(i=0;i<vlist->n;i++)
8f6a69	466	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	467
SP	468	fclose(fh);
	469	return TS_SUCCESS;
	470	}
	471
	472
	473	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	474	ts_uint i,j;
	475	for(i=0;i<vlist->n;i++){
8f6a69	476	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	477	vlist->vtx[i]->y, vlist->vtx[i]->z,
	478	vlist->vtx[i]->neigh_no);
	479	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	480	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	481	//-vlist->vtx+1));
d7639a	482	}
SP	483	fprintf(fh,"\n");
	484	}
	485	return TS_SUCCESS;
	486	}
	487
	488	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	489	ts_uint i,j;
a6b1b5	490	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	491	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	492	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	493	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	494	}
SP	495	fprintf(fh,"\n");
	496	}
	497	return TS_SUCCESS;
	498	}
	499
	500	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	501	ts_triangle_list *tlist=vesicle->tlist;
d7639a	502	ts_uint i,j;
SP	503	for(i=0;i<tlist->n;i++){
41a035	504	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	505	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	506	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	507	}
SP	508	fprintf(fh,"\n");
	509	for(j=0;j<3;j++){
41a035	510	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	511	}
SP	512	fprintf(fh,"\n");
41a035	513	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	514	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	515	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	516	}
	517	return TS_SUCCESS;
	518	}
	519
	520	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	521	ts_uint i,j;
	522	for(i=0;i<vlist->n;i++){
	523	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	524	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	525	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
cef6ca	526	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	527	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	528	}
SP	529	fprintf(fh,"\n");
cef6ca	530	for(j=0;j<vlist->vtx[i]->bond_no;j++){
8f6a69	531	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	532	}
SP	533	fprintf(fh,"\n");
	534	}
	535	return TS_SUCCESS;
	536	}
	537
	538	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	539	ts_uint i;
a6b1b5	540	for(i=0;i<vesicle->blist->n;i++){
e016c4	541	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	542	//-vesicle->vlist->vtx+1),
e016c4	543	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	544	//-vesicle->vlist.vtx+1));
d7639a	545	}
SP	546	return TS_SUCCESS;
	547	}
	548
	549
	550	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	551	FILE *fh;
	552	fh=fopen(filename, "w");
	553	if(fh==NULL){
	554	err("Cannot open file %s for writing");
	555	return TS_FAIL;
	556	}
	557	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	558	fprint_vertex_list(fh,vesicle->vlist);
d7639a	559	fprint_tristar(fh,vesicle);
SP	560	fprint_triangle_list(fh,vesicle);
a6b1b5	561	fprint_vertex_data(fh,vesicle->vlist);
d7639a	562	fprint_bonds(fh,vesicle);
SP	563	fclose(fh);
	564	return TS_SUCCESS;
	565	}
	566
	567	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	568	FILE *fh;
	569	char line[255];
	570	fh=fopen(filename, "r");
	571	if(fh==NULL){
	572	err("Cannot open file for reading... Nonexistant file?");
	573	return TS_FAIL;
	574	}
a6b1b5	575	ts_uint retval=1;
d7639a	576	while(retval!=EOF){
SP	577	retval=fscanf(fh,"%s",line);
	578
	579	fprintf(stderr,"%s",line);
	580	}
	581	fclose(fh);
	582	return TS_SUCCESS;
	583	}
	584
	585	ts_bool write_master_xml_file(ts_char *filename){
	586	FILE *fh;
	587	ts_char i,j;
	588	ts_uint tstep;
	589	ts_char *number;
	590	fh=fopen(filename, "w");
	591	if(fh==NULL){
	592	err("Cannot open file %s for writing");
	593	return TS_FAIL;
	594	}
	595
	596	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	597	DIR *dir = opendir(".");
	598	if(dir){
	599	struct dirent *ent;
	600	tstep=0;
	601	while((ent = readdir(dir)) != NULL)
	602	{
	603	i=rindex(ent->d_name,'.');
	604	if(i==NULL) continue;
	605	if(strcmp(i+1,"vtu")==0){
	606	j=rindex(ent->d_name,'_');
	607	if(j==NULL) continue;
	608	number=strndup(j+1,j-i);
a6b1b5	609	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	610	tstep++;
SP	611	free(number);
	612	}
	613	}
	614	}
f74313	615	free(dir);
d7639a	616	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	617	fclose(fh);
	618	return TS_SUCCESS;
	619	}
	620
	621	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	622	ts_vertex_list *vlist=vesicle->vlist;
SP	623	ts_bond_list *blist=vesicle->blist;
	624	ts_vertex **vtx=vlist->vtx;
40aa5b	625	ts_uint i,j;
d7639a	626	char filename[255];
SP	627	FILE *fh;
	628
	629	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	630	fh=fopen(filename, "w");
	631	if(fh==NULL){
	632	err("Cannot open file %s for writing");
	633	return TS_FAIL;
	634	}
	635	/* Here comes header of the file */
40aa5b	636
SP	637	//find number of extra vtxs and bonds of polymeres
3c1ac1	638	ts_uint monono=0, polyno=0, poly_idx=0;
40aa5b	639	ts_bool poly=0;
SP	640	if(vesicle->poly_list!=NULL){
	641	if(vesicle->poly_list->poly[0]!=NULL){
	642	polyno=vesicle->poly_list->n;
	643	monono=vesicle->poly_list->poly[0]->vlist->n;
	644	poly=1;
	645	}
	646	}
d7639a	647	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
40aa5b	648	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno, blist->n+mononopolyno);
d7639a	649	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	650	for(i=0;i<vlist->n;i++){
a6b1b5	651	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	652	}
40aa5b	653	//polymeres
SP	654	if(poly){
3c1ac1	655	poly_idx=vlist->n;
40aa5b	656	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	657	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
SP	658	fprintf(fh,"%u ", poly_idx);
40aa5b	659	}
SP	660	}
	661	}
d7639a	662
SP	663	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	664	for(i=0;i<vlist->n;i++){
8f6a69	665	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	666	}
SP	667	//polymeres
	668	if(poly){
	669	for(i=0;i<vesicle->poly_list->n;i++){
	670	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	671	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 );
	672	}
	673	}
d7639a	674	}
SP	675
	676	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	677	for(i=0;i<blist->n;i++){
e016c4	678	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	679	}
40aa5b	680	//polymeres
SP	681	if(poly){
3c1ac1	682	poly_idx=vlist->n;
40aa5b	683	for(i=0;i<vesicle->poly_list->n;i++){
SP	684	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	685	// 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	686	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	687	}
SP	688	//grafted bonds
3c1ac1	689	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	690	}
SP	691
	692	}
	693
	694
d7639a	695	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
40aa5b	696	for (i=2;i<(blist->n+mononopolyno)2+1;i+=2){
d7639a	697	fprintf(fh,"%u ",i);
SP	698	}
	699	fprintf(fh,"\n");
	700	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
40aa5b	701	for (i=0;i<blist->n+monono*polyno;i++){
d7639a	702	fprintf(fh,"3 ");
SP	703	}
	704
	705	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	706	fclose(fh);
	707	return TS_SUCCESS;
	708
	709	}
	710
	711	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	712	ts_vertex_list *vlist=vesicle->vlist;
SP	713	ts_bond_list *blist=vesicle->blist;
	714	ts_vertex **vtx=vlist->vtx;
	715	ts_uint i;
d7639a	716	FILE *fh;
SP	717
	718	fh=fopen(filename, "w");
	719	if(fh==NULL){
	720	err("Cannot open file %s for writing");
	721	return TS_FAIL;
	722	}
	723	/* Here comes header of the file */
	724	// fprintf(stderr,"NSHELL=%u\n",nshell);
	725	fprintf(fh, "# vtk DataFile Version 2.0\n");
	726	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	727	fprintf(fh, "%s\n", text);
	728	fprintf(fh,"ASCII\n");
	729	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	730	fprintf(fh,"POINTS %u double\n", vlist->n);
	731	for(i=0;i<vlist->n;i++){
8f6a69	732	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	733	}
SP	734
	735	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	736	for(i=0;i<blist->n;i++){
e016c4	737	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	738	}
SP	739	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	740	for(i=0;i<blist->n;i++)
	741	fprintf(fh,"3\n");
	742
	743	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	744	fprintf(fh,"SCALARS scalars long 1\n");
	745	fprintf(fh,"LOOKUP_TABLE default\n");
	746
	747	for(i=0;i<vlist->n;i++)
8f6a69	748	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	749
SP	750	fclose(fh);
	751	return TS_SUCCESS;
	752	}
	753
	754
	755
1ab449	756	ts_tape parsetape(char filename){
SP	757	// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
	758	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
	759	tape->multiprocessing=calloc(255,sizeof(char));
	760	/* long int brezveze0=1;
b14a8d	761	long int brezveze1=1;
SP	762	long int brezveze2=1;
e86357	763	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	764	long int iter=1000, init=1000, mcsw=1000;
1ab449	765	*/
40aa5b	766
d7639a	767	cfg_opt_t opts[] = {
1ab449	768	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	769	CFG_SIMPLE_INT("npoly", &tape->npoly),
	770	CFG_SIMPLE_INT("nmono", &tape->nmono),
	771	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
	772	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
	773	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
	774	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
	775	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
	776	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
	777	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	778	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	779	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	780	CFG_SIMPLE_INT("iterations",&tape->iterations),
	781	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	782	CFG_SIMPLE_INT("inititer", &tape->inititer),
	783	CFG_SIMPLE_BOOL("quiet",&tape->quiet),
	784	CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
	785	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
	786	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	787	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
d7639a	788	CFG_END()
SP	789	};
	790	cfg_t *cfg;
	791	ts_uint retval;
	792	cfg = cfg_init(opts, 0);
1ab449	793	retval=cfg_parse(cfg, filename);
d7639a	794	if(retval==CFG_FILE_ERROR){
a6b1b5	795	fatal("No tape file.",100);
d7639a	796	}
SP	797	else if(retval==CFG_PARSE_ERROR){
	798	fatal("Invalid tape!",100);
	799	}
a2db52	800
d7639a	801	cfg_free(cfg);
40aa5b	802
SP	803
1ab449	804	/* global variables are set automatically */
SP	805	quiet=tape->quiet;
	806	return tape;
	807	}
d7639a	808
1ab449	809	ts_bool tape_free(ts_tape *tape){
SP	810	free(tape->multiprocessing);
	811	free(tape);
	812	return TS_SUCCESS;
d7639a	813	}
f74313	814
SP	815
	816	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	817	FILE *fh;
	818	ts_uint i, nvtx,nedges,ntria;
	819	ts_uint vtxi1,vtxi2;
	820	float x,y,z;
	821	ts_vertex_list *vlist;
	822	fh=fopen(fname, "r");
	823	if(fh==NULL){
	824	err("Cannot open file for reading... Nonexistant file?");
	825	return TS_FAIL;
	826	}
	827	ts_uint retval;
	828	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	829	vesicle->vlist=init_vertex_list(nvtx);
	830	vlist=vesicle->vlist;
	831	for(i=0;i<nvtx;i++){
8f6a69	832	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	833	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	834	vlist->vtx[i]->x=x;
SP	835	vlist->vtx[i]->y=y;
	836	vlist->vtx[i]->z=z;
f74313	837	}
SP	838	for(i=0;i<nedges;i++){
	839	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	840	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	841	}
	842	//TODO: neighbours from bonds,
	843	//TODO: triangles from neigbours
	844
	845	// Don't need to read triangles. Already have enough data
	846	/*
	847	for(i=0;i<ntria;i++){
	848	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	849	vtxi1=vesicle->blist->vertex1->idx;
SP	850	vtxi2=vesicle->blist->vertex1->idx;
f74313	851
SP	852	}
	853	*/
41a035	854	if(retval);
f74313	855	fclose(fh);
SP	856
	857
	858
	859	return TS_SUCCESS;
	860	}