trisurf-ng.git - Gitblit

have some kind of memory allocation error :(

Samo Penic

2019-10-17 80ebbe388f3e945e62f47b0141c660ee6f05c8fc

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
SP	21
083e03	22	ts_bool parse_args(int argc, char **argv){
3f5c83	23	int c, retval;
SP	24	struct stat sb;
	25	sprintf(command_line_args.path, "./"); //clear string;
7b0c07	26	sprintf(command_line_args.output_fullfilename,"output.pvd");
SP	27	sprintf(command_line_args.dump_fullfilename,"dump.bin");
	28	sprintf(command_line_args.tape_fullfilename,"tape");
1bf3c3	29	sprintf(command_line_args.tape_templatefull,"./tape");
3f5c83	30	FILE *file;
SP	31
083e03	32	while (1)
SP	33	{
	34	static struct option long_options[] =
	35	{
8a6614	36	{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
SP	37	{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
083e03	38	{"tape", no_argument, 0, 't'},
fd8126	39	{"version", no_argument, 0, 'v'},
083e03	40	{"output-file", required_argument, 0, 'o'},
SP	41	{"directory", required_argument, 0, 'd'},
3f5c83	42	{"dump-filename", required_argument,0, 'f'},
7b0c07	43	{"tape-options",required_argument,0,'c'},
1bf3c3	44	{"tape-template", required_argument,0,0},
ab798b	45	{"restore-from-vtk",required_argument,0,0},
083e03	46	{0, 0, 0, 0}
SP	47	};
	48	/* getopt_long stores the option index here. */
	49	int option_index = 0;
	50
fd8126	51	c = getopt_long (argc, argv, "d:f:o:t:c:v",
083e03	52	long_options, &option_index);
SP	53
	54	/* Detect the end of the options. */
	55	if (c == -1)
	56	break;
	57
	58	switch (c)
	59	{
	60	case 0:
	61	/* If this option set a flag, do nothing else now. */
	62	if (long_options[option_index].flag != 0)
	63	break;
1bf3c3	64	/* printf ("option %s", long_options[option_index].name);
083e03	65	if (optarg)
1bf3c3	66	printf (" with arg %s", optarg);
SP	67	printf ("\n"); */
	68	//TODO: find a better way.
	69	if(strcmp(long_options[option_index].name,"tape-template")==0){
	70	strcpy(command_line_args.tape_templatefull,optarg);
	71	}
ab798b	72	if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
ee84bd	73	strcpy(command_line_args.dump_from_vtk,optarg);
SP	74	}
083e03	75	break;
fd8126	76	case 'v':
SP	77	fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	78	fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
	79	fprintf(stdout,"Released under terms of GPLv3\n");
	80	exit(0);
083e03	81
7b0c07	82	case 'c':
SP	83	strcpy(command_line_args.tape_opts,optarg);
	84	break;
	85	case 't': //tape
3f5c83	86	strcpy(command_line_args.tape_fullfilename,optarg);
083e03	87	break;
SP	88
7b0c07	89	case 'o': //set filename of master pvd output file
3f5c83	90	strcpy(command_line_args.output_fullfilename, optarg);
SP	91	break;
083e03	92
SP	93	case 'd':
	94	//check if directory exists. If not create one. If creation is
	95	//successful, set directory for output files.
	96	//printf ("option -d with value `%s'\n", optarg);
3f5c83	97	if (stat(optarg, &sb) == -1) {
SP	98	//directory does not exist
083e03	99	retval=mkdir(optarg, 0700);
SP	100	if(retval){
3f5c83	101	fatal("Could not create requested directory. Check if you have permissions",1);
083e03	102	}
SP	103	}
3f5c83	104	//check if is a proper directory
SP	105	else if((sb.st_mode & S_IFMT) != S_IFDIR) {
	106	//it is not a directory. fatal error.
	107	ts_fprintf(stderr,"%s is not a directory!\n",optarg);
	108	fatal("Cannot continue",1);
083e03	109	}
3f5c83	110	strcpy(command_line_args.path, optarg);
083e03	111	break;
SP	112
	113	case 'f':
3f5c83	114	strcpy(command_line_args.dump_fullfilename, optarg);
083e03	115	break;
SP	116
	117	case '?':
	118	/* getopt_long already printed an error message. */
ba73ab	119	print_help(stdout);
SP	120	//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
083e03	121	fatal("Ooops, read help first",1);
SP	122	break;
	123
	124	default:
	125	exit (1);
	126	}
	127	}
	128
7b0c07	129	//Here we set correct values for full filenames!
SP	130	char buffer=(char )malloc(10000*sizeof(char));
	131	//correct the path and add trailing /
	132	if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
	133
	134	/* master pvd output file */
	135	strcpy(buffer,command_line_args.path);
	136	strcat(buffer,command_line_args.output_fullfilename);
	137	if ((file = fopen(buffer, "w")) == NULL) {
	138	fprintf(stderr,"Could not create output file %s!\n", buffer);
	139	fatal("Please specify correct output file or check permissions of the file",1);
1bf3c3	140	//there is a tape template. make a copy into desired directory
7b0c07	141
SP	142	} else {
	143	fclose(file);
	144	strcpy(command_line_args.output_fullfilename,buffer);
	145	}
	146
	147	/* tape file */
	148	strcpy(buffer,command_line_args.path);
	149	strcat(buffer,command_line_args.tape_fullfilename);
	150	if (stat(buffer, &sb) == -1) {
1bf3c3	151
SP	152	//tape does not exist. does tape template exist?
	153	if(stat(command_line_args.tape_templatefull, &sb)==-1){
	154	ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
	155	fatal("Please select correct tape or check permissions of the file",1);
	156	} else {
	157	//tape template found
	158	fatal("Samo did not program template copy yet",1);
	159	}
7b0c07	160	} else {
SP	161	strcpy(command_line_args.tape_fullfilename,buffer);
	162	}
	163
	164
	165	/* dump file */
	166	strcpy(buffer,command_line_args.path);
	167	strcat(buffer,command_line_args.dump_fullfilename);
	168	//check if dump file exist first.
	169	if (stat(buffer, &sb) == -1) {
	170	//no dump file. check if we can create one.
	171	if ((file = fopen(buffer, "w")) == NULL) {
	172	fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
	173	fatal("Please specify correct dump file or check permissions of the file",1);
	174	} else {
	175	fclose(file);
	176	//good, file is writeable. delete it for now.
	177	remove(buffer);
	178	}
	179	}
	180	strcpy(command_line_args.dump_fullfilename, buffer);
	181
	182
	183	free(buffer);
083e03	184	return TS_SUCCESS;
SP	185
	186	}
	187
	188
ba73ab	189	ts_bool print_help(FILE *fd){
SP	190	fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
	191	fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
	192	fprintf(fd,"Released under terms of GPLv3\n\n");
	193
	194	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");
	195	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");
	196	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");
	197	fprintf(fd,"Flags:\n\n");
	198	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");
	199	fprintf(fd,"--restore-from-vtk\t\t VTK's file ending with '.vtu' are preferred way to make state snapshots for restoration. With this flag the restoration of the vesicle from vtk is possible. The simulation will continue if hidden '.status' file with last iteration done is present. Otherwise it will start simulation from timestep 0.\n");
c4178c	200	fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
ba73ab	201	fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
SP	202	fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
	203	fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
c4178c	204	fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
SP	205	fprintf(fd,"Examples:\n\n");
	206	fprintf(fd,"trisurf --force-from-tape\n");
	207	fprintf(fd,"trisurf --reset-iteration-count\n");
	208	fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
	209	fprintf(fd,"\n\n");
	210
d7639a	211	return TS_SUCCESS;
SP	212	}
	213
0a2c81	214	ts_bool write_vertex_xml_file(ts_vesicle vesicle, ts_uint timestepno, ts_cluster_list cstlist){
a6b1b5	215	ts_vertex_list *vlist=vesicle->vlist;
SP	216	ts_bond_list *blist=vesicle->blist;
	217	ts_vertex **vtx=vlist->vtx;
40aa5b	218	ts_uint i,j;
13d445	219	//ts_double senergy=0.0;
267db5	220	char filename[10000];
SP	221	char just_name[255];
d7639a	222	FILE *fh;
267db5	223	strcpy(filename,command_line_args.path);
SP	224	sprintf(just_name,"timestep_%.6u.vtu",timestepno);
	225	strcat(filename,just_name);
d7639a	226
SP	227	fh=fopen(filename, "w");
	228	if(fh==NULL){
	229	err("Cannot open file %s for writing");
	230	return TS_FAIL;
	231	}
	232	/* Here comes header of the file */
40aa5b	233
SP	234	//find number of extra vtxs and bonds of polymeres
58230a	235	ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
M	236	ts_bool poly=0, fil=0;
40aa5b	237	if(vesicle->poly_list!=NULL){
SP	238	if(vesicle->poly_list->poly[0]!=NULL){
	239	polyno=vesicle->poly_list->n;
	240	monono=vesicle->poly_list->poly[0]->vlist->n;
	241	poly=1;
	242	}
	243	}
58230a	244
M	245	if(vesicle->filament_list!=NULL){
	246	if(vesicle->filament_list->poly[0]!=NULL){
	247	filno=vesicle->filament_list->n;
	248	fonono=vesicle->filament_list->poly[0]->vlist->n;
	249	fil=1;
	250	}
	251	}
	252
854cb6	253	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	254	xml_trisurf_data(fh,vesicle);
	255	fprintf(fh, " <UnstructuredGrid>\n");
8db203	256	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n);
80ebbe	257	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"binary\">");
SP	258	int int_vector=(int )malloc(vlist->n+mononopolyno+fononofilno*sizeof(ts_uint));
	259	int offset=0;
d7639a	260	for(i=0;i<vlist->n;i++){
80ebbe	261	// fprintf(fh,"%u ",vtx[i]->idx);
SP	262	int_vector[i+offset]=vtx[i]->idx;
d7639a	263	}
40aa5b	264	//polymeres
SP	265	if(poly){
3c1ac1	266	poly_idx=vlist->n;
80ebbe	267	offset=offset+i;
40aa5b	268	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	269	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
80ebbe	270	//fprintf(fh,"%u ", poly_idx);
SP	271	int_vector[j+offset]=poly_idx;
58230a	272	}
80ebbe	273	offset=offset+j;
58230a	274	}
M	275	}
	276	//filaments
	277	if(fil){
	278	poly_idx=vlist->n+monono*polyno;
	279	for(i=0;i<vesicle->filament_list->n;i++){
	280	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	281	// fprintf(stderr,"was here\n");
80ebbe	282	//fprintf(fh,"%u ", poly_idx);
SP	283	int_vector[j+offset]=poly_idx;
40aa5b	284	}
80ebbe	285	offset=offset+j;
40aa5b	286	}
SP	287	}
80ebbe	288	char printout=ts_compress_intlist(int_vector,vlist->n+mononopolyno+fononofilnosizeof(ts_uint));
SP	289	fprintf(fh,"%s",printout);
	290	free(printout);
d7639a	291
45c708	292	fprintf(fh,"</DataArray>\n");
0a2c81	293	if(cstlist!=NULL){
SP	294	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	295	for(i=0;i<vlist->n;i++){
	296	if(vtx[i]->cluster!=NULL){
	297	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	298	} else {
	299	fprintf(fh,"-1 ");
	300	}
	301	}
	302	//polymeres
	303	if(poly){
	304	poly_idx=vlist->n;
	305	for(i=0;i<vesicle->poly_list->n;i++){
	306	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	307	fprintf(fh,"-1 ");
	308	}
	309	}
	310	}
	311	//filaments
	312	if(fil){
	313	poly_idx=vlist->n+monono*polyno;
	314	for(i=0;i<vesicle->filament_list->n;i++){
	315	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	316	// fprintf(stderr,"was here\n");
	317	fprintf(fh,"-1 ");
	318	}
	319	}
	320	}
	321
	322	fprintf(fh,"</DataArray>\n");
	323
	324
	325	}
	326
45c708	327	//here comes additional data as needed. Currently only spontaneous curvature
SP	328	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	329	for(i=0;i<vlist->n;i++){
	330	fprintf(fh,"%.17e ",vtx[i]->c);
	331	}
	332	//polymeres
	333	if(poly){
	334	poly_idx=vlist->n;
	335	for(i=0;i<vesicle->poly_list->n;i++){
	336	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	337	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	338	}
	339	}
	340	}
	341	//filaments
	342	if(fil){
	343	poly_idx=vlist->n+monono*polyno;
	344	for(i=0;i<vesicle->filament_list->n;i++){
	345	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	346	// fprintf(stderr,"was here\n");
	347	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	348	}
	349	}
	350	}
	351	fprintf(fh,"</DataArray>\n");
	352
5c64e2	353	//here comes additional data. Energy!
SP	354	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	355	for(i=0;i<vlist->n;i++){
	356	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	357	}
	358	//polymeres
	359	if(poly){
	360	poly_idx=vlist->n;
	361	for(i=0;i<vesicle->poly_list->n;i++){
	362	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	363	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	364	}
	365	}
	366	}
	367	//filaments
	368	if(fil){
	369	poly_idx=vlist->n+monono*polyno;
	370	for(i=0;i<vesicle->filament_list->n;i++){
	371	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	372	// fprintf(stderr,"was here\n");
	373	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	374	}
	375	}
	376	}
	377	fprintf(fh,"</DataArray>\n");
	378
45c708	379
13d445	380	fprintf(fh,"</PointData>\n<CellData>\n");
SP	381
7ec6fb	382	if(vesicle->tape->stretchswitch==1){
SP	383	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	384	for(i=0;i<blist->n;i++){
SP	385	fprintf(fh, "0.0 ");
	386	}
	387	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	388	fprintf(fh,"0.0 ");
7ec6fb	389	}
13d445	390	for(i=0;i<vesicle->tlist->n;i++){
SP	391	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	392	}
7ec6fb	393	fprintf(fh,"</DataArray>\n");
SP	394	}
45c708	395
13d445	396
SP	397
	398	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	399	for(i=0;i<vlist->n;i++){
aad500	400	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	401	}
SP	402	//polymeres
	403	if(poly){
	404	for(i=0;i<vesicle->poly_list->n;i++){
	405	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	406	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	407	}
M	408	}
	409	}
	410	//filaments
	411	if(fil){
	412	for(i=0;i<vesicle->filament_list->n;i++){
	413	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	414	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	415	}
SP	416	}
d7639a	417	}
SP	418
	419	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	420	for(i=0;i<blist->n;i++){
e016c4	421	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	422	}
40aa5b	423	//polymeres
SP	424	if(poly){
3c1ac1	425	poly_idx=vlist->n;
40aa5b	426	for(i=0;i<vesicle->poly_list->n;i++){
SP	427	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	428	// 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	429	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	430	}
SP	431	//grafted bonds
3c1ac1	432	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	433	}
SP	434
	435	}
	436
58230a	437	//filaments
M	438	if(fil){
	439	poly_idx=vlist->n+monono*polyno;
	440	for(i=0;i<vesicle->filament_list->n;i++){
	441	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	442	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);
	443	// fprintf(stderr,"was here\n");
	444
	445	}
	446	}
	447
	448	}
8db203	449	for(i=0;i<vesicle->tlist->n;i++){
SP	450	fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
	451	}
d7639a	452	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	453	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	454	fprintf(fh,"%u ",i);
SP	455	}
8db203	456	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	457	fprintf(fh,"%u ", j);
	458	}
d7639a	459	fprintf(fh,"\n");
SP	460	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	461	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	462	fprintf(fh,"3 ");
SP	463	}
8db203	464	for(i=0;i<vesicle->tlist->n;i++){
SP	465	fprintf(fh,"5 ");
	466	}
d7639a	467	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	468	fclose(fh);
	469	return TS_SUCCESS;
	470
	471	}
	472
144784	473	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	474	FILE *fh;
	475	ts_uint i;
	476
	477	fh=fopen(filename, "w");
	478	if(fh==NULL){
	479	err("Cannot open file %s for writing");
	480	return TS_FAIL;
	481	}
	482
	483	for(i=0;i<vesicle->tlist->n;i++){
	484
	485	fprintf(fh,"\ttriangle {");
	486	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	487	vesicle->tlist->tria[i]->vertex[0]->x,
	488	vesicle->tlist->tria[i]->vertex[0]->y,
	489	vesicle->tlist->tria[i]->vertex[0]->z,
	490
	491	vesicle->tlist->tria[i]->vertex[1]->x,
	492	vesicle->tlist->tria[i]->vertex[1]->y,
	493	vesicle->tlist->tria[i]->vertex[1]->z,
	494
	495	vesicle->tlist->tria[i]->vertex[2]->x,
	496	vesicle->tlist->tria[i]->vertex[2]->y,
	497	vesicle->tlist->tria[i]->vertex[2]->z
	498	);
	499	}
	500
	501	fclose(fh);
	502	return TS_SUCCESS;
	503	}
	504
	505
1ab449	506	ts_tape parsetape(char filename){
698ae1	507	FILE *fd = fopen (filename, "r");
SP	508	long length;
	509	size_t size;
	510	fseek (fd, 0, SEEK_END);
	511	length = ftell (fd);
	512	fseek (fd, 0, SEEK_SET);
	513	size=fread (tapetxt, 1, length, fd);
	514	fclose(fd);
	515	if(size);
	516	ts_tape *tape=parsetapebuffer(tapetxt);
	517	return tape;
	518	}
	519
	520	ts_tape parsetapebuffer(char buffer){
1ab449	521	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	522	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	523
d7639a	524	cfg_opt_t opts[] = {
1ab449	525	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	526	CFG_SIMPLE_INT("npoly", &tape->npoly),
	527	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	528	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	529	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	530	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	531	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	532	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	533	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	534	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	535	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	536	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	537	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	538	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	539	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	540	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	541	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	542	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	543	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	544	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	545	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	546	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	547	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	548	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	549	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	550	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	551	CFG_SIMPLE_INT("iterations",&tape->iterations),
	552	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	553	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	554	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	555	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	556	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	557	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	558	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	559	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	560	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	561	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	562	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	563	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	564	/* Variables related to plane confinement */
514ebc	565	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	566	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	567	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	568	/* Variables related to stretching */
36bc6d	569	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	570	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	571	CFG_END()
SP	572	};
	573	cfg_t *cfg;
	574	ts_uint retval;
	575	cfg = cfg_init(opts, 0);
698ae1	576	retval=cfg_parse_buf(cfg, buffer);
514ebc	577	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	578	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	579	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	580
d7639a	581	if(retval==CFG_FILE_ERROR){
a6b1b5	582	fatal("No tape file.",100);
d7639a	583	}
SP	584	else if(retval==CFG_PARSE_ERROR){
	585	fatal("Invalid tape!",100);
	586	}
a2db52	587
7b0c07	588	/* here we override all values read from tape with values from commandline*/
SP	589	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	590	cfg_free(cfg);
40aa5b	591
SP	592
1ab449	593	/* global variables are set automatically */
SP	594	quiet=tape->quiet;
	595	return tape;
	596	}
d7639a	597
1ab449	598	ts_bool tape_free(ts_tape *tape){
SP	599	free(tape->multiprocessing);
	600	free(tape);
	601	return TS_SUCCESS;
d7639a	602	}
f74313	603
SP	604
7b0c07	605
SP	606	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	607
	608	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	609	operator[0]=0;
SP	610	operator[1]=0;
7b0c07	611	ts_uint i,j;
SP	612	commands=(char )malloc(10000sizeof(char));
	613	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	614	strcpy(commands,opts);
	615	for(i=0; ;i++, commands=NULL){
	616	//breaks comma separated list of commands into specific commands.
	617	command=strtok_r(commands,",",&saveptr);
	618	if(command==NULL) break;
	619	// fprintf(stdout,"Command %d: %s\n",i,command);
	620	//extracts name of command and value of command into operator[2] array.
	621	for(j=0; j<2;j++,command=NULL){
	622	operator[j]=strtok_r(command,"=",&saveopptr);
	623	if(operator[j]==NULL) break;
	624	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	625	}
	626	//1. check: must have 2 operators.
	627	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	628
	629	// cfg_setstr(cfg,operator[0],operator[1]);
	630	cmdline_to_tape(cfg,operator[0],operator[1]);
	631	//2. check: must be named properly.
	632	//3. check: must be of right format (integer, double, string, ...)
	633
	634	}
	635	free(backup);
	636	return TS_SUCCESS;
	637	}
	638
	639
	640	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	641
	642	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	643	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	644	switch (cfg_opt->type){
	645	case CFGT_INT:
	646	cfg_setint(cfg,key,atol(val));
	647	break;
	648	case CFGT_FLOAT:
	649	cfg_setfloat(cfg,key,atof(val));
	650	break;
	651	/* case CFGT_BOOL:
	652	cfg_setbool(cfg,operator[0],operator[1]);
	653	break; */
	654	case CFGT_STR:
	655	cfg_setstr(cfg,key,val);
	656	break;
	657	default:
	658	break;
	659
	660	}
f74313	661	return TS_SUCCESS;
SP	662	}