trisurf-ng.git - Gitblit

Samo Penic

2019-10-16 3c6e26add4550990dc81446b2aea00a6e4d2feeb

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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);
5c64e2	257	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
d7639a	258	for(i=0;i<vlist->n;i++){
a6b1b5	259	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	260	}
40aa5b	261	//polymeres
SP	262	if(poly){
3c1ac1	263	poly_idx=vlist->n;
40aa5b	264	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	265	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
58230a	266	fprintf(fh,"%u ", poly_idx);
M	267	}
	268	}
	269	}
	270	//filaments
	271	if(fil){
	272	poly_idx=vlist->n+monono*polyno;
	273	for(i=0;i<vesicle->filament_list->n;i++){
	274	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	275	// fprintf(stderr,"was here\n");
3c1ac1	276	fprintf(fh,"%u ", poly_idx);
40aa5b	277	}
SP	278	}
	279	}
d7639a	280
45c708	281	fprintf(fh,"</DataArray>\n");
0a2c81	282	if(cstlist!=NULL){
SP	283	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	284	for(i=0;i<vlist->n;i++){
	285	if(vtx[i]->cluster!=NULL){
	286	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	287	} else {
	288	fprintf(fh,"-1 ");
	289	}
	290	}
	291	//polymeres
	292	if(poly){
	293	poly_idx=vlist->n;
	294	for(i=0;i<vesicle->poly_list->n;i++){
	295	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	296	fprintf(fh,"-1 ");
	297	}
	298	}
	299	}
	300	//filaments
	301	if(fil){
	302	poly_idx=vlist->n+monono*polyno;
	303	for(i=0;i<vesicle->filament_list->n;i++){
	304	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	305	// fprintf(stderr,"was here\n");
	306	fprintf(fh,"-1 ");
	307	}
	308	}
	309	}
	310
	311	fprintf(fh,"</DataArray>\n");
	312
	313
	314	}
	315
45c708	316	//here comes additional data as needed. Currently only spontaneous curvature
SP	317	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	318	for(i=0;i<vlist->n;i++){
	319	fprintf(fh,"%.17e ",vtx[i]->c);
	320	}
	321	//polymeres
	322	if(poly){
	323	poly_idx=vlist->n;
	324	for(i=0;i<vesicle->poly_list->n;i++){
	325	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	326	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	327	}
	328	}
	329	}
	330	//filaments
	331	if(fil){
	332	poly_idx=vlist->n+monono*polyno;
	333	for(i=0;i<vesicle->filament_list->n;i++){
	334	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	335	// fprintf(stderr,"was here\n");
	336	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	337	}
	338	}
	339	}
	340	fprintf(fh,"</DataArray>\n");
	341
5c64e2	342	//here comes additional data. Energy!
SP	343	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	344	for(i=0;i<vlist->n;i++){
	345	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	346	}
	347	//polymeres
	348	if(poly){
	349	poly_idx=vlist->n;
	350	for(i=0;i<vesicle->poly_list->n;i++){
	351	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	352	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	353	}
	354	}
	355	}
	356	//filaments
	357	if(fil){
	358	poly_idx=vlist->n+monono*polyno;
	359	for(i=0;i<vesicle->filament_list->n;i++){
	360	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	361	// fprintf(stderr,"was here\n");
	362	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	363	}
	364	}
	365	}
	366	fprintf(fh,"</DataArray>\n");
	367
45c708	368
13d445	369	fprintf(fh,"</PointData>\n<CellData>\n");
SP	370
7ec6fb	371	if(vesicle->tape->stretchswitch==1){
SP	372	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	373	for(i=0;i<blist->n;i++){
SP	374	fprintf(fh, "0.0 ");
	375	}
	376	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	377	fprintf(fh,"0.0 ");
7ec6fb	378	}
13d445	379	for(i=0;i<vesicle->tlist->n;i++){
SP	380	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	381	}
7ec6fb	382	fprintf(fh,"</DataArray>\n");
SP	383	}
45c708	384
13d445	385
SP	386
	387	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	388	for(i=0;i<vlist->n;i++){
aad500	389	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	390	}
SP	391	//polymeres
	392	if(poly){
	393	for(i=0;i<vesicle->poly_list->n;i++){
	394	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	395	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	396	}
M	397	}
	398	}
	399	//filaments
	400	if(fil){
	401	for(i=0;i<vesicle->filament_list->n;i++){
	402	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	403	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	404	}
SP	405	}
d7639a	406	}
SP	407
	408	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	409	for(i=0;i<blist->n;i++){
e016c4	410	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	411	}
40aa5b	412	//polymeres
SP	413	if(poly){
3c1ac1	414	poly_idx=vlist->n;
40aa5b	415	for(i=0;i<vesicle->poly_list->n;i++){
SP	416	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	417	// 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	418	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	419	}
SP	420	//grafted bonds
3c1ac1	421	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	422	}
SP	423
	424	}
	425
58230a	426	//filaments
M	427	if(fil){
	428	poly_idx=vlist->n+monono*polyno;
	429	for(i=0;i<vesicle->filament_list->n;i++){
	430	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	431	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);
	432	// fprintf(stderr,"was here\n");
	433
	434	}
	435	}
	436
	437	}
8db203	438	for(i=0;i<vesicle->tlist->n;i++){
SP	439	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);
	440	}
d7639a	441	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	442	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	443	fprintf(fh,"%u ",i);
SP	444	}
8db203	445	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	446	fprintf(fh,"%u ", j);
	447	}
d7639a	448	fprintf(fh,"\n");
SP	449	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	450	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	451	fprintf(fh,"3 ");
SP	452	}
8db203	453	for(i=0;i<vesicle->tlist->n;i++){
SP	454	fprintf(fh,"5 ");
	455	}
d7639a	456	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	457	fclose(fh);
	458	return TS_SUCCESS;
	459
	460	}
	461
144784	462	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	463	FILE *fh;
	464	ts_uint i;
	465
	466	fh=fopen(filename, "w");
	467	if(fh==NULL){
	468	err("Cannot open file %s for writing");
	469	return TS_FAIL;
	470	}
	471
	472	for(i=0;i<vesicle->tlist->n;i++){
	473
	474	fprintf(fh,"\ttriangle {");
	475	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	476	vesicle->tlist->tria[i]->vertex[0]->x,
	477	vesicle->tlist->tria[i]->vertex[0]->y,
	478	vesicle->tlist->tria[i]->vertex[0]->z,
	479
	480	vesicle->tlist->tria[i]->vertex[1]->x,
	481	vesicle->tlist->tria[i]->vertex[1]->y,
	482	vesicle->tlist->tria[i]->vertex[1]->z,
	483
	484	vesicle->tlist->tria[i]->vertex[2]->x,
	485	vesicle->tlist->tria[i]->vertex[2]->y,
	486	vesicle->tlist->tria[i]->vertex[2]->z
	487	);
	488	}
	489
	490	fclose(fh);
	491	return TS_SUCCESS;
	492	}
	493
	494
1ab449	495	ts_tape parsetape(char filename){
698ae1	496	FILE *fd = fopen (filename, "r");
SP	497	long length;
	498	size_t size;
	499	fseek (fd, 0, SEEK_END);
	500	length = ftell (fd);
	501	fseek (fd, 0, SEEK_SET);
	502	size=fread (tapetxt, 1, length, fd);
	503	fclose(fd);
	504	if(size);
	505	ts_tape *tape=parsetapebuffer(tapetxt);
	506	return tape;
	507	}
	508
	509	ts_tape parsetapebuffer(char buffer){
1ab449	510	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	511	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	512
d7639a	513	cfg_opt_t opts[] = {
1ab449	514	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	515	CFG_SIMPLE_INT("npoly", &tape->npoly),
	516	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	517	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	518	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	519	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	520	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	521	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	522	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	523	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	524	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	525	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	526	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	527	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	528	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	529	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	530	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	531	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	532	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	533	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	534	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	535	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	536	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	537	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	538	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	539	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	540	CFG_SIMPLE_INT("iterations",&tape->iterations),
	541	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	542	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	543	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	544	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	545	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	546	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	547	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	548	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	549	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	550	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	551	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	552	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	553	/* Variables related to plane confinement */
514ebc	554	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	555	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	556	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	557	/* Variables related to stretching */
36bc6d	558	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	559	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	560	CFG_END()
SP	561	};
	562	cfg_t *cfg;
	563	ts_uint retval;
	564	cfg = cfg_init(opts, 0);
698ae1	565	retval=cfg_parse_buf(cfg, buffer);
514ebc	566	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	567	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	568	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	569
d7639a	570	if(retval==CFG_FILE_ERROR){
a6b1b5	571	fatal("No tape file.",100);
d7639a	572	}
SP	573	else if(retval==CFG_PARSE_ERROR){
	574	fatal("Invalid tape!",100);
	575	}
a2db52	576
7b0c07	577	/* here we override all values read from tape with values from commandline*/
SP	578	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	579	cfg_free(cfg);
40aa5b	580
SP	581
1ab449	582	/* global variables are set automatically */
SP	583	quiet=tape->quiet;
	584	return tape;
	585	}
d7639a	586
1ab449	587	ts_bool tape_free(ts_tape *tape){
SP	588	free(tape->multiprocessing);
	589	free(tape);
	590	return TS_SUCCESS;
d7639a	591	}
f74313	592
SP	593
7b0c07	594
SP	595	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	596
	597	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	598	operator[0]=0;
SP	599	operator[1]=0;
7b0c07	600	ts_uint i,j;
SP	601	commands=(char )malloc(10000sizeof(char));
	602	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	603	strcpy(commands,opts);
	604	for(i=0; ;i++, commands=NULL){
	605	//breaks comma separated list of commands into specific commands.
	606	command=strtok_r(commands,",",&saveptr);
	607	if(command==NULL) break;
	608	// fprintf(stdout,"Command %d: %s\n",i,command);
	609	//extracts name of command and value of command into operator[2] array.
	610	for(j=0; j<2;j++,command=NULL){
	611	operator[j]=strtok_r(command,"=",&saveopptr);
	612	if(operator[j]==NULL) break;
	613	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	614	}
	615	//1. check: must have 2 operators.
	616	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	617
	618	// cfg_setstr(cfg,operator[0],operator[1]);
	619	cmdline_to_tape(cfg,operator[0],operator[1]);
	620	//2. check: must be named properly.
	621	//3. check: must be of right format (integer, double, string, ...)
	622
	623	}
	624	free(backup);
	625	return TS_SUCCESS;
	626	}
	627
	628
	629	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	630
	631	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	632	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	633	switch (cfg_opt->type){
	634	case CFGT_INT:
	635	cfg_setint(cfg,key,atol(val));
	636	break;
	637	case CFGT_FLOAT:
	638	cfg_setfloat(cfg,key,atof(val));
	639	break;
	640	/* case CFGT_BOOL:
	641	cfg_setbool(cfg,operator[0],operator[1]);
	642	break; */
	643	case CFGT_STR:
	644	cfg_setstr(cfg,key,val);
	645	break;
	646	default:
	647	break;
	648
	649	}
f74313	650	return TS_SUCCESS;
SP	651	}