trisurf-ng.git - Gitblit

Samo Penic

2020-04-09 4f5ffcfd5ba38b6b7dd6d3b15de8bb8677537b9f

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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>
dba66b	20	#include <b64zlib_compression.h>
e9eab4	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;
4f5ffc	248	fprintf(stderr,"WAS HERE AND I SHOULDNT BE\n");
58230a	249	fonono=vesicle->filament_list->poly[0]->vlist->n;
M	250	fil=1;
	251	}
	252	}
	253
854cb6	254	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
SP	255	xml_trisurf_data(fh,vesicle);
	256	fprintf(fh, " <UnstructuredGrid>\n");
8db203	257	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno+fononofilno, blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n);
80ebbe	258	fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"binary\">");
a69203	259	long int_vector=(long )malloc((vlist->n+mononopolyno+fononofilno)*sizeof(long));
842378	260	ts_double float_vector=(double )malloc((vlist->n+mononopolyno+fononofilno)*sizeof(double));
SP	261	ts_double float_cell_vector=(double )malloc((blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n)*sizeof(double));
	262	ts_double coordinate_vector=(double )malloc(3(vlist->n+mononopolyno+fononofilno)sizeof(double));
a69203	263	// sizes are as expected 4 bytes for int and 1 byte for char
SP	264	// printf("size of ts_uint %ld, of int %ld, of char %ld",sizeof(ts_uint), sizeof(int), sizeof(char));
80ebbe	265	int offset=0;
d7639a	266	for(i=0;i<vlist->n;i++){
80ebbe	267	// fprintf(fh,"%u ",vtx[i]->idx);
SP	268	int_vector[i+offset]=vtx[i]->idx;
d7639a	269	}
a69203	270	offset=offset+i;
40aa5b	271	//polymeres
SP	272	if(poly){
3c1ac1	273	poly_idx=vlist->n;
40aa5b	274	for(i=0;i<vesicle->poly_list->n;i++){
3c1ac1	275	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
80ebbe	276	//fprintf(fh,"%u ", poly_idx);
SP	277	int_vector[j+offset]=poly_idx;
58230a	278	}
80ebbe	279	offset=offset+j;
58230a	280	}
M	281	}
	282	//filaments
	283	if(fil){
	284	poly_idx=vlist->n+monono*polyno;
	285	for(i=0;i<vesicle->filament_list->n;i++){
	286	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
	287	// fprintf(stderr,"was here\n");
80ebbe	288	//fprintf(fh,"%u ", poly_idx);
SP	289	int_vector[j+offset]=poly_idx;
40aa5b	290	}
80ebbe	291	offset=offset+j;
40aa5b	292	}
SP	293	}
a69203	294	printf("Offset in the end is %d, should be %d",offset,(vlist->n+mononopolyno+fononofilno) );
842378	295	char printout=ts_compress((char )int_vector,offset*sizeof(long));
80ebbe	296	fprintf(fh,"%s",printout);
SP	297	free(printout);
d7639a	298
45c708	299	fprintf(fh,"</DataArray>\n");
0a2c81	300	if(cstlist!=NULL){
842378	301	fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"binary\">");
SP	302	offset=0;
	303	for(i=0;i<vlist->n;i++,offset++){
0a2c81	304	if(vtx[i]->cluster!=NULL){
842378	305	// fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
SP	306	int_vector[offset]=vtx[i]->cluster->nvtx;
0a2c81	307	} else {
842378	308	// fprintf(fh,"-1 ");
SP	309	int_vector[offset]=-1;
0a2c81	310	}
SP	311	}
	312	//polymeres
	313	if(poly){
	314	poly_idx=vlist->n;
	315	for(i=0;i<vesicle->poly_list->n;i++){
842378	316	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
SP	317	//fprintf(fh,"-1 ");
	318	int_vector[offset]=-1;
0a2c81	319	}
SP	320	}
	321	}
	322	//filaments
	323	if(fil){
	324	poly_idx=vlist->n+monono*polyno;
	325	for(i=0;i<vesicle->filament_list->n;i++){
842378	326	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
SP	327	// fprintf(fh,"-1 ");
	328	int_vector[offset]=-1;
0a2c81	329	}
SP	330	}
	331	}
842378	332	char printout=ts_compress((char )int_vector,offset*sizeof(long));
SP	333	fprintf(fh,"%s",printout);
	334	free(printout);
0a2c81	335
SP	336	fprintf(fh,"</DataArray>\n");
	337
	338
	339	}
	340
45c708	341	//here comes additional data as needed. Currently only spontaneous curvature
842378	342	fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"binary\">");
SP	343	offset=0;
	344	for(i=0;i<vlist->n;i++, offset++){
	345	// fprintf(fh,"%.17e ",vtx[i]->c);
	346	float_vector[offset]=vtx[i]->c;
45c708	347	}
SP	348	//polymeres
	349	if(poly){
	350	poly_idx=vlist->n;
	351	for(i=0;i<vesicle->poly_list->n;i++){
842378	352	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
SP	353	//fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
	354	float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->c;
45c708	355	}
SP	356	}
	357	}
	358	//filaments
	359	if(fil){
	360	poly_idx=vlist->n+monono*polyno;
	361	for(i=0;i<vesicle->filament_list->n;i++){
842378	362	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
45c708	363	// fprintf(stderr,"was here\n");
842378	364	//fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
SP	365	float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->c;
45c708	366	}
SP	367	}
	368	}
842378	369	printout=ts_compress((char )float_vector,offsetsizeof(double));
SP	370	fprintf(fh,"%s",printout);
	371	free(printout);
	372
	373
45c708	374	fprintf(fh,"</DataArray>\n");
SP	375
5c64e2	376	//here comes additional data. Energy!
842378	377	fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"binary\">");
SP	378	offset=0;
	379	for(i=0;i<vlist->n;i++,offset++){
	380	// fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
	381	float_vector[offset]=vtx[i]->energy*vtx[i]->xk;
5c64e2	382	}
SP	383	//polymeres
	384	if(poly){
	385	poly_idx=vlist->n;
	386	for(i=0;i<vesicle->poly_list->n;i++){
842378	387	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
SP	388	//fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
	389	float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k;
5c64e2	390	}
SP	391	}
	392	}
	393	//filaments
	394	if(fil){
	395	poly_idx=vlist->n+monono*polyno;
	396	for(i=0;i<vesicle->filament_list->n;i++){
842378	397	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
5c64e2	398	// fprintf(stderr,"was here\n");
842378	399	// fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
SP	400	float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k;
5c64e2	401	}
SP	402	}
	403	}
842378	404
SP	405	printout=ts_compress((char )float_vector,offsetsizeof(double));
	406	fprintf(fh,"%s",printout);
	407	free(printout);
	408
5c64e2	409	fprintf(fh,"</DataArray>\n");
SP	410
45c708	411
13d445	412	fprintf(fh,"</PointData>\n<CellData>\n");
SP	413
7ec6fb	414	if(vesicle->tape->stretchswitch==1){
842378	415	fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"binary\">");
SP	416	offset=0;
	417	for(i=0;i<blist->n;i++,offset++){
	418	//fprintf(fh, "0.0 ");
	419	float_cell_vector[offset]=0.0;
cf7aba	420	}
842378	421	for(i=0;i<mononopolyno+filno(fonono-1);i++,offset++){
SP	422	float_cell_vector[offset]=0.0;
	423	//fprintf(fh,"0.0 ");
7ec6fb	424	}
842378	425	for(i=0;i<vesicle->tlist->n;i++,offset++){
SP	426	float_cell_vector[offset]=vesicle->tlist->tria[i]->energy;
	427	//fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
13d445	428	}
842378	429
SP	430	printout=ts_compress((char )float_cell_vector,offsetsizeof(double));
	431	fprintf(fh,"%s",printout);
	432	free(printout);
	433
7ec6fb	434	fprintf(fh,"</DataArray>\n");
SP	435	}
45c708	436
13d445	437
SP	438
201659	439	fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"binary\">");
842378	440	offset=0;
SP	441	for(i=0;i<vlist->n;i++,offset+=3){
	442	//fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
	443	coordinate_vector[offset]=vtx[i]->x;
	444	coordinate_vector[offset+1]=vtx[i]->y;
	445	coordinate_vector[offset+2]=vtx[i]->z;
40aa5b	446	}
SP	447	//polymeres
	448	if(poly){
	449	for(i=0;i<vesicle->poly_list->n;i++){
842378	450	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,offset+=3){
SP	451	//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 );
	452	coordinate_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->x;
	453	coordinate_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[j]->y;
	454	coordinate_vector[offset+2]=vesicle->poly_list->poly[i]->vlist->vtx[j]->z;
58230a	455	}
M	456	}
	457	}
	458	//filaments
	459	if(fil){
842378	460	for(i=0;i<vesicle->filament_list->n;i++,offset+=3){
58230a	461	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
842378	462	// 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 );
SP	463	coordinate_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->x;
	464	coordinate_vector[offset+1]=vesicle->filament_list->poly[i]->vlist->vtx[j]->y;
	465	coordinate_vector[offset+2]=vesicle->filament_list->poly[i]->vlist->vtx[j]->z;
40aa5b	466	}
SP	467	}
d7639a	468	}
842378	469	printout=ts_compress((char )coordinate_vector,offsetsizeof(double));
SP	470	fprintf(fh,"%s",printout);
	471	free(printout);
d7639a	472
842378	473
SP	474
	475	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"binary\">");
	476	free(int_vector);
	477	int_vector=(long )malloc(((blist->n+mononopolyno+filno(fonono-1))2+vesicle->tlist->n3)sizeof(long));
	478	offset=0;
	479	for(i=0;i<blist->n;i++,offset+=2){
	480	// fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
	481	int_vector[offset]=blist->bond[i]->vtx1->idx;
	482	int_vector[offset+1]=blist->bond[i]->vtx2->idx;
d7639a	483	}
40aa5b	484	//polymeres
SP	485	if(poly){
3c1ac1	486	poly_idx=vlist->n;
40aa5b	487	for(i=0;i<vesicle->poly_list->n;i++){
842378	488	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++,offset+=2){
SP	489	//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);
	490	int_vector[offset]= vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono;
	491	int_vector[offset+1]=vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono;
	492
40aa5b	493	}
SP	494	//grafted bonds
842378	495	//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);
SP	496	int_vector[offset]=vesicle->poly_list->poly[i]->grafted_vtx->idx;
	497	int_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono;
	498	offset+=2;
40aa5b	499	}
SP	500
	501	}
	502
58230a	503	//filaments
M	504	if(fil){
	505	poly_idx=vlist->n+monono*polyno;
	506	for(i=0;i<vesicle->filament_list->n;i++){
842378	507	for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++,offset+=2){
SP	508	// 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);
	509	int_vector[offset]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+mononopolyno+ifonono;
	510	int_vector[offset+1]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+mononopolyno+ifonono;
58230a	511	// fprintf(stderr,"was here\n");
M	512
	513	}
	514	}
	515
	516	}
842378	517	for(i=0;i<vesicle->tlist->n;i++,offset+=3){
SP	518	// 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);
	519	int_vector[offset]=vesicle->tlist->tria[i]->vertex[0]->idx;
	520	int_vector[offset+1]=vesicle->tlist->tria[i]->vertex[1]->idx;
	521	int_vector[offset+2]=vesicle->tlist->tria[i]->vertex[2]->idx;
	522
8db203	523	}
842378	524	printout=ts_compress((char )int_vector,offsetsizeof(long));
SP	525	fprintf(fh,"%s",printout);
	526	free(printout);
	527
	528
	529	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"binary\">");
	530	offset=0;
	531	for (i=2;i<(blist->n+mononopolyno+(fonono-1)filno)*2+1;i+=2,offset++){
	532	// fprintf(fh,"%u ",i);
	533	int_vector[offset]=i;
d7639a	534	}
842378	535	for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3,offset++){ //let's continue counting from where we left of
SP	536	// fprintf(fh,"%u ", j);
	537	int_vector[offset]=j;
8db203	538	}
842378	539	// fprintf(fh,"\n");
SP	540	printout=ts_compress((char )int_vector,offsetsizeof(long));
	541	fprintf(fh,"%s",printout);
	542	free(printout);
201659	543	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"binary\">");
842378	544	free(int_vector);
SP	545	free(float_vector);
	546	free(float_cell_vector);
	547	free(coordinate_vector);
	548	unsigned char char_vector=(unsigned char )malloc((blist->n+mononopolyno+filno(fonono-1)+vesicle->tlist->n)*sizeof(char));
	549	offset=0;
	550	for (i=0;i<blist->n+mononopolyno+(fonono-1)filno;i++,offset++){
	551	//fprintf(fh,"3 ");
	552	char_vector[offset]=3;
d7639a	553	}
842378	554	for(i=0;i<vesicle->tlist->n;i++,offset++){
SP	555	// fprintf(fh,"5 ");
	556	char_vector[offset]=5;
8db203	557	}
842378	558	printout=ts_compress((char )char_vector,offsetsizeof(char));
SP	559	fprintf(fh,"%s",printout);
	560	free(printout);
	561	free(char_vector);
	562
d7639a	563	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
SP	564	fclose(fh);
	565	return TS_SUCCESS;
	566
	567	}
	568
144784	569	ts_bool write_pov_file(ts_vesicle vesicle, char filename){
SP	570	FILE *fh;
	571	ts_uint i;
	572
	573	fh=fopen(filename, "w");
	574	if(fh==NULL){
	575	err("Cannot open file %s for writing");
	576	return TS_FAIL;
	577	}
	578
	579	for(i=0;i<vesicle->tlist->n;i++){
	580
	581	fprintf(fh,"\ttriangle {");
	582	fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
	583	vesicle->tlist->tria[i]->vertex[0]->x,
	584	vesicle->tlist->tria[i]->vertex[0]->y,
	585	vesicle->tlist->tria[i]->vertex[0]->z,
	586
	587	vesicle->tlist->tria[i]->vertex[1]->x,
	588	vesicle->tlist->tria[i]->vertex[1]->y,
	589	vesicle->tlist->tria[i]->vertex[1]->z,
	590
	591	vesicle->tlist->tria[i]->vertex[2]->x,
	592	vesicle->tlist->tria[i]->vertex[2]->y,
	593	vesicle->tlist->tria[i]->vertex[2]->z
	594	);
	595	}
	596
	597	fclose(fh);
	598	return TS_SUCCESS;
	599	}
	600
	601
1ab449	602	ts_tape parsetape(char filename){
698ae1	603	FILE *fd = fopen (filename, "r");
SP	604	long length;
	605	size_t size;
	606	fseek (fd, 0, SEEK_END);
	607	length = ftell (fd);
	608	fseek (fd, 0, SEEK_SET);
	609	size=fread (tapetxt, 1, length, fd);
	610	fclose(fd);
	611	if(size);
	612	ts_tape *tape=parsetapebuffer(tapetxt);
	613	return tape;
	614	}
	615
	616	ts_tape parsetapebuffer(char buffer){
1ab449	617	ts_tape tape=(ts_tape )calloc(1,sizeof(ts_tape));
SP	618	tape->multiprocessing=calloc(255,sizeof(char));
40aa5b	619
d7639a	620	cfg_opt_t opts[] = {
1ab449	621	CFG_SIMPLE_INT("nshell", &tape->nshell),
SP	622	CFG_SIMPLE_INT("npoly", &tape->npoly),
	623	CFG_SIMPLE_INT("nmono", &tape->nmono),
58230a	624	CFG_SIMPLE_INT("nfil",&tape->nfil),
M	625	CFG_SIMPLE_INT("nfono",&tape->nfono),
e98482	626	CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
58230a	627	CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
37791b	628	CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
SP	629	CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
	630	CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
58230a	631	CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
ea1cce	632	CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
1ab449	633	CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
SP	634	CFG_SIMPLE_INT("pswitch",&tape->pswitch),
9166cb	635	CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
c0ae90	636	CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
43c042	637	CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
2ae815	638	CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
SP	639	CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
1ab449	640	CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
SP	641	CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
b30f45	642	CFG_SIMPLE_FLOAT("xi",&tape->xi),
1ab449	643	CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
SP	644	CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
	645	CFG_SIMPLE_INT("nymax", &tape->ncymax),
	646	CFG_SIMPLE_INT("nzmax", &tape->nczmax),
	647	CFG_SIMPLE_INT("iterations",&tape->iterations),
	648	CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
	649	CFG_SIMPLE_INT("inititer", &tape->inititer),
819a09	650	CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
S	651	CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
1ab449	652	CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
SP	653	CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
	654	CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
dc77e8	655	CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
e5858f	656	CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
SP	657	CFG_SIMPLE_FLOAT("c0",&tape->c0),
	658	CFG_SIMPLE_FLOAT("w",&tape->w),
250de4	659	CFG_SIMPLE_FLOAT("F",&tape->F),
6c274d	660	/* Variables related to plane confinement */
514ebc	661	CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
SP	662	CFG_FLOAT("plane_d", 15, CFGF_NONE),
	663	CFG_FLOAT("plane_F", 1000, CFGF_NONE),
6c274d	664	/* Variables related to stretching */
36bc6d	665	// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
SP	666	// CFG_FLOAT("xkA0",0,CFGF_NONE),
d7639a	667	CFG_END()
SP	668	};
	669	cfg_t *cfg;
	670	ts_uint retval;
	671	cfg = cfg_init(opts, 0);
698ae1	672	retval=cfg_parse_buf(cfg, buffer);
514ebc	673	tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
88bdd7	674	tape->plane_d=cfg_getfloat(cfg,"plane_d");
SP	675	tape->plane_F=cfg_getfloat(cfg,"plane_F");
514ebc	676
d7639a	677	if(retval==CFG_FILE_ERROR){
a6b1b5	678	fatal("No tape file.",100);
d7639a	679	}
SP	680	else if(retval==CFG_PARSE_ERROR){
	681	fatal("Invalid tape!",100);
	682	}
a2db52	683
7b0c07	684	/* here we override all values read from tape with values from commandline*/
SP	685	getcmdline_tape(cfg,command_line_args.tape_opts);
d7639a	686	cfg_free(cfg);
40aa5b	687
SP	688
1ab449	689	/* global variables are set automatically */
SP	690	quiet=tape->quiet;
	691	return tape;
	692	}
d7639a	693
1ab449	694	ts_bool tape_free(ts_tape *tape){
SP	695	free(tape->multiprocessing);
	696	free(tape);
	697	return TS_SUCCESS;
d7639a	698	}
f74313	699
SP	700
7b0c07	701
SP	702	ts_bool getcmdline_tape(cfg_t cfg, char opts){
	703
	704	char commands, backup, saveptr, saveopptr, command, operator[2];
07e3de	705	operator[0]=0;
SP	706	operator[1]=0;
7b0c07	707	ts_uint i,j;
SP	708	commands=(char )malloc(10000sizeof(char));
	709	backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
	710	strcpy(commands,opts);
	711	for(i=0; ;i++, commands=NULL){
	712	//breaks comma separated list of commands into specific commands.
	713	command=strtok_r(commands,",",&saveptr);
	714	if(command==NULL) break;
	715	// fprintf(stdout,"Command %d: %s\n",i,command);
	716	//extracts name of command and value of command into operator[2] array.
	717	for(j=0; j<2;j++,command=NULL){
	718	operator[j]=strtok_r(command,"=",&saveopptr);
	719	if(operator[j]==NULL) break;
	720	// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
	721	}
	722	//1. check: must have 2 operators.
	723	if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
	724
	725	// cfg_setstr(cfg,operator[0],operator[1]);
	726	cmdline_to_tape(cfg,operator[0],operator[1]);
	727	//2. check: must be named properly.
	728	//3. check: must be of right format (integer, double, string, ...)
	729
	730	}
	731	free(backup);
	732	return TS_SUCCESS;
	733	}
	734
	735
	736	ts_bool cmdline_to_tape(cfg_t cfg, char key, char *val){
	737
	738	cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
	739	if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
	740	switch (cfg_opt->type){
	741	case CFGT_INT:
	742	cfg_setint(cfg,key,atol(val));
	743	break;
	744	case CFGT_FLOAT:
	745	cfg_setfloat(cfg,key,atof(val));
	746	break;
	747	/* case CFGT_BOOL:
	748	cfg_setbool(cfg,operator[0],operator[1]);
	749	break; */
	750	case CFGT_STR:
	751	cfg_setstr(cfg,key,val);
	752	break;
	753	default:
	754	break;
	755
	756	}
f74313	757	return TS_SUCCESS;
SP	758	}