trisurf-ng.git - Gitblit

Debugged all the leaks. Decompression still not working

Samo Penic

2019-10-18 a69203a95d66595b80891aafc1ca8a59303290d0

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\">");
a69203	258	long int_vector=(long )malloc((vlist->n+mononopolyno+fononofilno)*sizeof(long));
SP	259	// sizes are as expected 4 bytes for int and 1 byte for char
	260	// printf("size of ts_uint %ld, of int %ld, of char %ld",sizeof(ts_uint), sizeof(int), sizeof(char));
80ebbe	261	int offset=0;
d7639a	262	for(i=0;i<vlist->n;i++){
80ebbe	263	// fprintf(fh,"%u ",vtx[i]->idx);
SP	264	int_vector[i+offset]=vtx[i]->idx;
d7639a	265	}
a69203	266	offset=offset+i;
40aa5b	267	//polymeres
SP	268	if(poly){
3c1ac1	269	poly_idx=vlist->n;
40aa5b	270	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	271	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
80ebbe	272	//fprintf(fh,"%u ", poly_idx);
SP	273	int_vector[j+offset]=poly_idx;
58230a	274	}
80ebbe	275	offset=offset+j;
58230a	276	}
M	277	}
	278	//filaments
	279	if(fil){
	280	poly_idx=vlist->n+monono*polyno;
	281	for(i=0;i<vesicle->filament_list->n;i++){
	282	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	283	// fprintf(stderr,"was here\n");
80ebbe	284	//fprintf(fh,"%u ", poly_idx);
SP	285	int_vector[j+offset]=poly_idx;
40aa5b	286	}
80ebbe	287	offset=offset+j;
40aa5b	288	}
SP	289	}
a69203	290	printf("Offset in the end is %d, should be %d",offset,(vlist->n+mononopolyno+fononofilno) );
SP	291	char printout=ts_compress((char )int_vector,offset*sizeof(long), offset);
80ebbe	292	fprintf(fh,"%s",printout);
SP	293	free(printout);
d7639a	294
45c708	295	fprintf(fh,"</DataArray>\n");
0a2c81	296	if(cstlist!=NULL){
SP	297	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
	298	for(i=0;i<vlist->n;i++){
	299	if(vtx[i]->cluster!=NULL){
	300	fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
	301	} else {
	302	fprintf(fh,"-1 ");
	303	}
	304	}
	305	//polymeres
	306	if(poly){
	307	poly_idx=vlist->n;
	308	for(i=0;i<vesicle->poly_list->n;i++){
	309	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	310	fprintf(fh,"-1 ");
	311	}
	312	}
	313	}
	314	//filaments
	315	if(fil){
	316	poly_idx=vlist->n+monono*polyno;
	317	for(i=0;i<vesicle->filament_list->n;i++){
	318	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	319	// fprintf(stderr,"was here\n");
	320	fprintf(fh,"-1 ");
	321	}
	322	}
	323	}
	324
	325	fprintf(fh,"</DataArray>\n");
	326
	327
	328	}
	329
45c708	330	//here comes additional data as needed. Currently only spontaneous curvature
SP	331	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
	332	for(i=0;i<vlist->n;i++){
	333	fprintf(fh,"%.17e ",vtx[i]->c);
	334	}
	335	//polymeres
	336	if(poly){
	337	poly_idx=vlist->n;
	338	for(i=0;i<vesicle->poly_list->n;i++){
	339	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	340	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	341	}
	342	}
	343	}
	344	//filaments
	345	if(fil){
	346	poly_idx=vlist->n+monono*polyno;
	347	for(i=0;i<vesicle->filament_list->n;i++){
	348	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	349	// fprintf(stderr,"was here\n");
	350	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
	351	}
	352	}
	353	}
	354	fprintf(fh,"</DataArray>\n");
	355
5c64e2	356	//here comes additional data. Energy!
SP	357	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
	358	for(i=0;i<vlist->n;i++){
	359	fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	360	}
	361	//polymeres
	362	if(poly){
	363	poly_idx=vlist->n;
	364	for(i=0;i<vesicle->poly_list->n;i++){
	365	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
	366	fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	367	}
	368	}
	369	}
	370	//filaments
	371	if(fil){
	372	poly_idx=vlist->n+monono*polyno;
	373	for(i=0;i<vesicle->filament_list->n;i++){
	374	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	375	// fprintf(stderr,"was here\n");
	376	fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
	377	}
	378	}
	379	}
	380	fprintf(fh,"</DataArray>\n");
	381
45c708	382
13d445	383	fprintf(fh,"</PointData>\n<CellData>\n");
SP	384
7ec6fb	385	if(vesicle->tape->stretchswitch==1){
SP	386	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
cf7aba	387	for(i=0;i<blist->n;i++){
SP	388	fprintf(fh, "0.0 ");
	389	}
	390	for(i=0;i<mononopolyno+filno(fonono-1);i++){
13d445	391	fprintf(fh,"0.0 ");
7ec6fb	392	}
13d445	393	for(i=0;i<vesicle->tlist->n;i++){
SP	394	fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
	395	}
7ec6fb	396	fprintf(fh,"</DataArray>\n");
SP	397	}
45c708	398
13d445	399
SP	400
	401	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
d7639a	402	for(i=0;i<vlist->n;i++){
aad500	403	fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	404	}
SP	405	//polymeres
	406	if(poly){
	407	for(i=0;i<vesicle->poly_list->n;i++){
	408	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
aad500	409	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	410	}
M	411	}
	412	}
	413	//filaments
	414	if(fil){
	415	for(i=0;i<vesicle->filament_list->n;i++){
	416	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
aad500	417	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	418	}
SP	419	}
d7639a	420	}
SP	421
	422	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	423	for(i=0;i<blist->n;i++){
e016c4	424	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	425	}
40aa5b	426	//polymeres
SP	427	if(poly){
3c1ac1	428	poly_idx=vlist->n;
40aa5b	429	for(i=0;i<vesicle->poly_list->n;i++){
SP	430	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
3c1ac1	431	// 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	432	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	433	}
SP	434	//grafted bonds
3c1ac1	435	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	436	}
SP	437
	438	}
	439
58230a	440	//filaments
M	441	if(fil){
	442	poly_idx=vlist->n+monono*polyno;
	443	for(i=0;i<vesicle->filament_list->n;i++){
	444	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
	445	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);
	446	// fprintf(stderr,"was here\n");
	447
	448	}
	449	}
	450
	451	}
8db203	452	for(i=0;i<vesicle->tlist->n;i++){
SP	453	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);
	454	}
d7639a	455	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
58230a	456	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2){
d7639a	457	fprintf(fh,"%u ",i);
SP	458	}
8db203	459	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
SP	460	fprintf(fh,"%u ", j);
	461	}
d7639a	462	fprintf(fh,"\n");
SP	463	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
8db203	464	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++){
d7639a	465	fprintf(fh,"3 ");
SP	466	}
8db203	467	for(i=0;i<vesicle->tlist->n;i++){
SP	468	fprintf(fh,"5 ");
	469	}
d7639a	470	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	471	fclose(fh);
	472	return TS_SUCCESS;
	473
	474	}
	475
144784	476	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	477	FILE *fh;
	478	ts_uint i;
	479
	480	fh=fopen(filename, "w");
	481	if(fh==NULL){
	482	err("Cannot open file %s for writing");
	483	return TS_FAIL;
	484	}
	485
	486	for(i=0;i<vesicle->tlist->n;i++){
	487
	488	fprintf(fh,"\ttriangle {");
	489	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	490	vesicle->tlist->tria[i]->vertex[0]->x,
	491	vesicle->tlist->tria[i]->vertex[0]->y,
	492	vesicle->tlist->tria[i]->vertex[0]->z,
	493
	494	vesicle->tlist->tria[i]->vertex[1]->x,
	495	vesicle->tlist->tria[i]->vertex[1]->y,
	496	vesicle->tlist->tria[i]->vertex[1]->z,
	497
	498	vesicle->tlist->tria[i]->vertex[2]->x,
	499	vesicle->tlist->tria[i]->vertex[2]->y,
	500	vesicle->tlist->tria[i]->vertex[2]->z
	501	);
	502	}
	503
	504	fclose(fh);
	505	return TS_SUCCESS;
	506	}
	507
	508
1ab449	509	ts_tape parsetape(char filename){
698ae1	510	FILE *fd = fopen (filename, "r");
SP	511	long length;
	512	size_t size;
	513	fseek (fd, 0, SEEK_END);
	514	length = ftell (fd);
	515	fseek (fd, 0, SEEK_SET);
	516	size=fread (tapetxt, 1, length, fd);
	517	fclose(fd);
	518	if(size);
	519	ts_tape *tape=parsetapebuffer(tapetxt);
	520	return tape;
	521	}
	522
	523	ts_tape parsetapebuffer(char buffer){
1ab449	524	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	525	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	526
d7639a	527	cfg_opt_t opts[] = {
1ab449	528	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	529	CFG_SIMPLE_INT("npoly", &tape->npoly),
	530	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	531	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	532	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	533	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	534	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	535	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	536	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	537	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	538	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	539	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	540	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	541	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	542	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	543	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	544	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	545	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	546	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	547	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	548	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	549	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	550	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	551	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	552	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	553	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	554	CFG_SIMPLE_INT("iterations",&tape->iterations),
	555	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	556	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	557	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	558	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	559	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	560	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	561	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	562	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	563	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	564	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	565	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	566	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	567	/* Variables related to plane confinement */
514ebc	568	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	569	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	570	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	571	/* Variables related to stretching */
36bc6d	572	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	573	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	574	CFG_END()
SP	575	};
	576	cfg_t *cfg;
	577	ts_uint retval;
	578	cfg = cfg_init(opts, 0);
698ae1	579	retval=cfg_parse_buf(cfg, buffer);
514ebc	580	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	581	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	582	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	583
d7639a	584	if(retval==CFG_FILE_ERROR){
a6b1b5	585	fatal("No tape file.",100);
d7639a	586	}
SP	587	else if(retval==CFG_PARSE_ERROR){
	588	fatal("Invalid tape!",100);
	589	}
a2db52	590
7b0c07	591	/* here we override all values read from tape with values from commandline*/
SP	592	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	593	cfg_free(cfg);
40aa5b	594
SP	595
1ab449	596	/* global variables are set automatically */
SP	597	quiet=tape->quiet;
	598	return tape;
	599	}
d7639a	600
1ab449	601	ts_bool tape_free(ts_tape *tape){
SP	602	free(tape->multiprocessing);
	603	free(tape);
	604	return TS_SUCCESS;
d7639a	605	}
f74313	606
SP	607
7b0c07	608
SP	609	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	610
	611	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	612	operator[0]=0;
SP	613	operator[1]=0;
7b0c07	614	ts_uint i,j;
SP	615	commands=(char )malloc(10000sizeof(char));
	616	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	617	strcpy(commands,opts);
	618	for(i=0; ;i++, commands=NULL){
	619	//breaks comma separated list of commands into specific commands.
	620	command=strtok_r(commands,",",&saveptr);
	621	if(command==NULL) break;
	622	// fprintf(stdout,"Command %d: %s\n",i,command);
	623	//extracts name of command and value of command into operator[2] array.
	624	for(j=0; j<2;j++,command=NULL){
	625	operator[j]=strtok_r(command,"=",&saveopptr);
	626	if(operator[j]==NULL) break;
	627	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	628	}
	629	//1. check: must have 2 operators.
	630	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	631
	632	// cfg_setstr(cfg,operator[0],operator[1]);
	633	cmdline_to_tape(cfg,operator[0],operator[1]);
	634	//2. check: must be named properly.
	635	//3. check: must be of right format (integer, double, string, ...)
	636
	637	}
	638	free(backup);
	639	return TS_SUCCESS;
	640	}
	641
	642
	643	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	644
	645	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	646	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	647	switch (cfg_opt->type){
	648	case CFGT_INT:
	649	cfg_setint(cfg,key,atol(val));
	650	break;
	651	case CFGT_FLOAT:
	652	cfg_setfloat(cfg,key,atof(val));
	653	break;
	654	/* case CFGT_BOOL:
	655	cfg_setbool(cfg,operator[0],operator[1]);
	656	break; */
	657	case CFGT_STR:
	658	cfg_setstr(cfg,key,val);
	659	break;
	660	default:
	661	break;
	662
	663	}
f74313	664	return TS_SUCCESS;
SP	665	}