/* vim: set ts=4 sts=4 sw=4 noet : */
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#include "general.h"
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#include<stdio.h>
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#include "io.h"
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#include "vertex.h"
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#include "bond.h"
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#include<string.h>
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#include<stdlib.h>
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#include <sys/types.h>
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#include <dirent.h>
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#include "initial_distribution.h"
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#include "poly.h"
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#include "cell.h"
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#include <getopt.h>
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#include <sys/stat.h>
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#include <sys/types.h>
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#include <dirent.h>
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#include <errno.h>
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#include <snapshot.h>
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#include <b64zlib_compression.h>
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ts_bool parse_args(int argc, char **argv){
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int c, retval;
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struct stat sb;
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sprintf(command_line_args.path, "./"); //clear string;
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sprintf(command_line_args.output_fullfilename,"output.pvd");
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sprintf(command_line_args.dump_fullfilename,"dump.bin");
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sprintf(command_line_args.tape_fullfilename,"tape");
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sprintf(command_line_args.tape_templatefull,"./tape");
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FILE *file;
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while (1)
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{
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static struct option long_options[] =
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{
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{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
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{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
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{"tape", no_argument, 0, 't'},
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{"version", no_argument, 0, 'v'},
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{"output-file", required_argument, 0, 'o'},
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{"directory", required_argument, 0, 'd'},
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{"dump-filename", required_argument,0, 'f'},
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{"tape-options",required_argument,0,'c'},
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{"tape-template", required_argument,0,0},
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{"restore-from-vtk",required_argument,0,0},
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{0, 0, 0, 0}
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};
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/* getopt_long stores the option index here. */
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int option_index = 0;
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c = getopt_long (argc, argv, "d:f:o:t:c:v",
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long_options, &option_index);
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/* Detect the end of the options. */
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if (c == -1)
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break;
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switch (c)
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{
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case 0:
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/* If this option set a flag, do nothing else now. */
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if (long_options[option_index].flag != 0)
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break;
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/* printf ("option %s", long_options[option_index].name);
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if (optarg)
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printf (" with arg %s", optarg);
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printf ("\n"); */
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//TODO: find a better way.
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if(strcmp(long_options[option_index].name,"tape-template")==0){
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strcpy(command_line_args.tape_templatefull,optarg);
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}
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if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
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strcpy(command_line_args.dump_from_vtk,optarg);
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}
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break;
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case 'v':
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fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
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fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
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fprintf(stdout,"Released under terms of GPLv3\n");
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exit(0);
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case 'c':
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strcpy(command_line_args.tape_opts,optarg);
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break;
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case 't': //tape
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strcpy(command_line_args.tape_fullfilename,optarg);
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break;
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case 'o': //set filename of master pvd output file
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strcpy(command_line_args.output_fullfilename, optarg);
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break;
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case 'd':
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//check if directory exists. If not create one. If creation is
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//successful, set directory for output files.
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//printf ("option -d with value `%s'\n", optarg);
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if (stat(optarg, &sb) == -1) {
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//directory does not exist
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retval=mkdir(optarg, 0700);
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if(retval){
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fatal("Could not create requested directory. Check if you have permissions",1);
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}
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}
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//check if is a proper directory
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else if((sb.st_mode & S_IFMT) != S_IFDIR) {
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//it is not a directory. fatal error.
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ts_fprintf(stderr,"%s is not a directory!\n",optarg);
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fatal("Cannot continue",1);
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}
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strcpy(command_line_args.path, optarg);
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break;
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case 'f':
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strcpy(command_line_args.dump_fullfilename, optarg);
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break;
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case '?':
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/* getopt_long already printed an error message. */
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print_help(stdout);
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//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
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fatal("Ooops, read help first",1);
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break;
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default:
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exit (1);
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}
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}
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//Here we set correct values for full filenames!
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char *buffer=(char *)malloc(10000*sizeof(char));
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//correct the path and add trailing /
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if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
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/* master pvd output file */
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strcpy(buffer,command_line_args.path);
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strcat(buffer,command_line_args.output_fullfilename);
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if ((file = fopen(buffer, "w")) == NULL) {
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fprintf(stderr,"Could not create output file %s!\n", buffer);
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fatal("Please specify correct output file or check permissions of the file",1);
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//there is a tape template. make a copy into desired directory
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} else {
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fclose(file);
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strcpy(command_line_args.output_fullfilename,buffer);
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}
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/* tape file */
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strcpy(buffer,command_line_args.path);
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strcat(buffer,command_line_args.tape_fullfilename);
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if (stat(buffer, &sb) == -1) {
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//tape does not exist. does tape template exist?
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if(stat(command_line_args.tape_templatefull, &sb)==-1){
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ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
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fatal("Please select correct tape or check permissions of the file",1);
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} else {
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//tape template found
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fatal("Samo did not program template copy yet",1);
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}
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} else {
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strcpy(command_line_args.tape_fullfilename,buffer);
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}
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/* dump file */
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strcpy(buffer,command_line_args.path);
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strcat(buffer,command_line_args.dump_fullfilename);
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//check if dump file exist first.
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if (stat(buffer, &sb) == -1) {
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//no dump file. check if we can create one.
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if ((file = fopen(buffer, "w")) == NULL) {
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fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
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fatal("Please specify correct dump file or check permissions of the file",1);
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} else {
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fclose(file);
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//good, file is writeable. delete it for now.
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remove(buffer);
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}
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}
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strcpy(command_line_args.dump_fullfilename, buffer);
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free(buffer);
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return TS_SUCCESS;
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}
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ts_bool print_help(FILE *fd){
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fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
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fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
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fprintf(fd,"Released under terms of GPLv3\n\n");
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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");
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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");
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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");
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fprintf(fd,"Flags:\n\n");
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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");
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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");
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fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
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fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
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fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
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fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
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fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
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fprintf(fd,"Examples:\n\n");
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fprintf(fd,"trisurf --force-from-tape\n");
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fprintf(fd,"trisurf --reset-iteration-count\n");
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fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
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fprintf(fd,"\n\n");
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return TS_SUCCESS;
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}
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ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno, ts_cluster_list *cstlist){
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ts_vertex_list *vlist=vesicle->vlist;
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ts_bond_list *blist=vesicle->blist;
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ts_vertex **vtx=vlist->vtx;
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ts_uint i,j;
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//ts_double senergy=0.0;
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char filename[10000];
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char just_name[255];
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FILE *fh;
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strcpy(filename,command_line_args.path);
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sprintf(just_name,"timestep_%.6u.vtu",timestepno);
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strcat(filename,just_name);
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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/* Here comes header of the file */
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//find number of extra vtxs and bonds of polymeres
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ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
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ts_bool poly=0, fil=0;
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if(vesicle->poly_list!=NULL){
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if(vesicle->poly_list->poly[0]!=NULL){
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polyno=vesicle->poly_list->n;
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monono=vesicle->poly_list->poly[0]->vlist->n;
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poly=1;
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}
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}
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if(vesicle->filament_list!=NULL){
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if(vesicle->filament_list->poly[0]!=NULL){
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filno=vesicle->filament_list->n;
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fprintf(stderr,"WAS HERE AND I SHOULDNT BE\n");
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fonono=vesicle->filament_list->poly[0]->vlist->n;
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fil=1;
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}
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}
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fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
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xml_trisurf_data(fh,vesicle);
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fprintf(fh, " <UnstructuredGrid>\n");
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fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
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fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"binary\">");
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long *int_vector=(long *)malloc((vlist->n+monono*polyno+fonono*filno)*sizeof(long));
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ts_double *float_vector=(double *)malloc((vlist->n+monono*polyno+fonono*filno)*sizeof(double));
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ts_double *float_cell_vector=(double *)malloc((blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n)*sizeof(double));
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ts_double *coordinate_vector=(double *)malloc(3*(vlist->n+monono*polyno+fonono*filno)*sizeof(double));
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// sizes are as expected 4 bytes for int and 1 byte for char
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// printf("size of ts_uint %ld, of int %ld, of char %ld",sizeof(ts_uint), sizeof(int), sizeof(char));
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int offset=0;
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for(i=0;i<vlist->n;i++){
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// fprintf(fh,"%u ",vtx[i]->idx);
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int_vector[i+offset]=vtx[i]->idx;
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}
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offset=offset+i;
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//polymeres
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if(poly){
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poly_idx=vlist->n;
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
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//fprintf(fh,"%u ", poly_idx);
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int_vector[j+offset]=poly_idx;
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}
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offset=offset+j;
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}
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}
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//filaments
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if(fil){
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poly_idx=vlist->n+monono*polyno;
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
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// fprintf(stderr,"was here\n");
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//fprintf(fh,"%u ", poly_idx);
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int_vector[j+offset]=poly_idx;
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}
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offset=offset+j;
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}
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}
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printf("Offset in the end is %d, should be %d",offset,(vlist->n+monono*polyno+fonono*filno) );
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char *printout=ts_compress((char *)int_vector,offset*sizeof(long));
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fprintf(fh,"%s",printout);
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free(printout);
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fprintf(fh,"</DataArray>\n");
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if(cstlist!=NULL){
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fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"binary\">");
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offset=0;
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for(i=0;i<vlist->n;i++,offset++){
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if(vtx[i]->cluster!=NULL){
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// fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
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int_vector[offset]=vtx[i]->cluster->nvtx;
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} else {
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// fprintf(fh,"-1 ");
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int_vector[offset]=-1;
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}
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}
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//polymeres
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if(poly){
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poly_idx=vlist->n;
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
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//fprintf(fh,"-1 ");
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int_vector[offset]=-1;
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}
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}
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}
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//filaments
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if(fil){
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poly_idx=vlist->n+monono*polyno;
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
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// fprintf(fh,"-1 ");
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int_vector[offset]=-1;
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}
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}
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}
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char *printout=ts_compress((char *)int_vector,offset*sizeof(long));
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fprintf(fh,"%s",printout);
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free(printout);
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fprintf(fh,"</DataArray>\n");
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}
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//here comes additional data as needed. Currently only spontaneous curvature
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fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"binary\">");
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offset=0;
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for(i=0;i<vlist->n;i++, offset++){
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// fprintf(fh,"%.17e ",vtx[i]->c);
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float_vector[offset]=vtx[i]->c;
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}
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//polymeres
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if(poly){
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poly_idx=vlist->n;
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
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//fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
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float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->c;
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}
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}
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}
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//filaments
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if(fil){
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poly_idx=vlist->n+monono*polyno;
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
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// fprintf(stderr,"was here\n");
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//fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
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float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->c;
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}
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}
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}
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printout=ts_compress((char *)float_vector,offset*sizeof(double));
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fprintf(fh,"%s",printout);
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free(printout);
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fprintf(fh,"</DataArray>\n");
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//here comes additional data. Energy!
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fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"binary\">");
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offset=0;
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for(i=0;i<vlist->n;i++,offset++){
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// fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
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float_vector[offset]=vtx[i]->energy*vtx[i]->xk;
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}
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//polymeres
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if(poly){
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poly_idx=vlist->n;
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
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//fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
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float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k;
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}
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}
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}
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//filaments
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if(fil){
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poly_idx=vlist->n+monono*polyno;
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
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// fprintf(stderr,"was here\n");
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// fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
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float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k;
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}
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}
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}
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printout=ts_compress((char *)float_vector,offset*sizeof(double));
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fprintf(fh,"%s",printout);
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free(printout);
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fprintf(fh,"</DataArray>\n");
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|
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fprintf(fh,"</PointData>\n<CellData>\n");
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if(vesicle->tape->stretchswitch==1){
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fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"binary\">");
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offset=0;
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for(i=0;i<blist->n;i++,offset++){
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//fprintf(fh, "0.0 ");
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float_cell_vector[offset]=0.0;
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}
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for(i=0;i<monono*polyno+filno*(fonono-1);i++,offset++){
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float_cell_vector[offset]=0.0;
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//fprintf(fh,"0.0 ");
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}
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for(i=0;i<vesicle->tlist->n;i++,offset++){
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float_cell_vector[offset]=vesicle->tlist->tria[i]->energy;
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//fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
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}
|
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printout=ts_compress((char *)float_cell_vector,offset*sizeof(double));
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fprintf(fh,"%s",printout);
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free(printout);
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fprintf(fh,"</DataArray>\n");
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}
|
|
|
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fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"binary\">");
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offset=0;
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for(i=0;i<vlist->n;i++,offset+=3){
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//fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
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coordinate_vector[offset]=vtx[i]->x;
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coordinate_vector[offset+1]=vtx[i]->y;
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coordinate_vector[offset+2]=vtx[i]->z;
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}
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//polymeres
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if(poly){
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,offset+=3){
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//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 );
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coordinate_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->x;
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coordinate_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[j]->y;
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coordinate_vector[offset+2]=vesicle->poly_list->poly[i]->vlist->vtx[j]->z;
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}
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}
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}
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//filaments
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if(fil){
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for(i=0;i<vesicle->filament_list->n;i++,offset+=3){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
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// 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 );
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coordinate_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->x;
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coordinate_vector[offset+1]=vesicle->filament_list->poly[i]->vlist->vtx[j]->y;
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coordinate_vector[offset+2]=vesicle->filament_list->poly[i]->vlist->vtx[j]->z;
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}
|
}
|
}
|
printout=ts_compress((char *)coordinate_vector,offset*sizeof(double));
|
fprintf(fh,"%s",printout);
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free(printout);
|
|
|
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fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"binary\">");
|
free(int_vector);
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int_vector=(long *)malloc(((blist->n+monono*polyno+filno*(fonono-1))*2+vesicle->tlist->n*3)*sizeof(long));
|
offset=0;
|
for(i=0;i<blist->n;i++,offset+=2){
|
// fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
|
int_vector[offset]=blist->bond[i]->vtx1->idx;
|
int_vector[offset+1]=blist->bond[i]->vtx2->idx;
|
}
|
//polymeres
|
if(poly){
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poly_idx=vlist->n;
|
for(i=0;i<vesicle->poly_list->n;i++){
|
for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++,offset+=2){
|
//fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
|
int_vector[offset]= vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono;
|
int_vector[offset+1]=vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono;
|
|
}
|
//grafted bonds
|
//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);
|
int_vector[offset]=vesicle->poly_list->poly[i]->grafted_vtx->idx;
|
int_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono;
|
offset+=2;
|
}
|
|
}
|
|
//filaments
|
if(fil){
|
poly_idx=vlist->n+monono*polyno;
|
for(i=0;i<vesicle->filament_list->n;i++){
|
for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++,offset+=2){
|
// fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
|
int_vector[offset]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono;
|
int_vector[offset+1]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono;
|
// fprintf(stderr,"was here\n");
|
|
}
|
}
|
|
}
|
for(i=0;i<vesicle->tlist->n;i++,offset+=3){
|
// 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);
|
int_vector[offset]=vesicle->tlist->tria[i]->vertex[0]->idx;
|
int_vector[offset+1]=vesicle->tlist->tria[i]->vertex[1]->idx;
|
int_vector[offset+2]=vesicle->tlist->tria[i]->vertex[2]->idx;
|
|
}
|
printout=ts_compress((char *)int_vector,offset*sizeof(long));
|
fprintf(fh,"%s",printout);
|
free(printout);
|
|
|
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"binary\">");
|
offset=0;
|
for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2,offset++){
|
// fprintf(fh,"%u ",i);
|
int_vector[offset]=i;
|
}
|
for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3,offset++){ //let's continue counting from where we left of
|
// fprintf(fh,"%u ", j);
|
int_vector[offset]=j;
|
}
|
// fprintf(fh,"\n");
|
printout=ts_compress((char *)int_vector,offset*sizeof(long));
|
fprintf(fh,"%s",printout);
|
free(printout);
|
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"binary\">");
|
free(int_vector);
|
free(float_vector);
|
free(float_cell_vector);
|
free(coordinate_vector);
|
unsigned char *char_vector=(unsigned char *)malloc((blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n)*sizeof(char));
|
offset=0;
|
for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++,offset++){
|
//fprintf(fh,"3 ");
|
char_vector[offset]=3;
|
}
|
for(i=0;i<vesicle->tlist->n;i++,offset++){
|
// fprintf(fh,"5 ");
|
char_vector[offset]=5;
|
}
|
printout=ts_compress((char *)char_vector,offset*sizeof(char));
|
fprintf(fh,"%s",printout);
|
free(printout);
|
free(char_vector);
|
|
fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
|
fclose(fh);
|
return TS_SUCCESS;
|
|
}
|
|
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
|
FILE *fh;
|
ts_uint i;
|
|
fh=fopen(filename, "w");
|
if(fh==NULL){
|
err("Cannot open file %s for writing");
|
return TS_FAIL;
|
}
|
|
for(i=0;i<vesicle->tlist->n;i++){
|
|
fprintf(fh,"\ttriangle {");
|
fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
|
vesicle->tlist->tria[i]->vertex[0]->x,
|
vesicle->tlist->tria[i]->vertex[0]->y,
|
vesicle->tlist->tria[i]->vertex[0]->z,
|
|
vesicle->tlist->tria[i]->vertex[1]->x,
|
vesicle->tlist->tria[i]->vertex[1]->y,
|
vesicle->tlist->tria[i]->vertex[1]->z,
|
|
vesicle->tlist->tria[i]->vertex[2]->x,
|
vesicle->tlist->tria[i]->vertex[2]->y,
|
vesicle->tlist->tria[i]->vertex[2]->z
|
);
|
}
|
|
fclose(fh);
|
return TS_SUCCESS;
|
}
|
|
|
ts_tape *parsetape(char *filename){
|
FILE *fd = fopen (filename, "r");
|
long length;
|
size_t size;
|
fseek (fd, 0, SEEK_END);
|
length = ftell (fd);
|
fseek (fd, 0, SEEK_SET);
|
size=fread (tapetxt, 1, length, fd);
|
fclose(fd);
|
if(size);
|
ts_tape *tape=parsetapebuffer(tapetxt);
|
return tape;
|
}
|
|
ts_tape *parsetapebuffer(char *buffer){
|
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
|
tape->multiprocessing=calloc(255,sizeof(char));
|
|
cfg_opt_t opts[] = {
|
CFG_SIMPLE_INT("nshell", &tape->nshell),
|
CFG_SIMPLE_INT("npoly", &tape->npoly),
|
CFG_SIMPLE_INT("nmono", &tape->nmono),
|
CFG_SIMPLE_INT("nfil",&tape->nfil),
|
CFG_SIMPLE_INT("nfono",&tape->nfono),
|
CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
|
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
|
CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
|
CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
|
CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
|
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
|
CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
|
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
|
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
|
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
|
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
|
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
|
CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
|
CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
|
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
|
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
|
CFG_SIMPLE_FLOAT("xi",&tape->xi),
|
CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
|
CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
|
CFG_SIMPLE_INT("nymax", &tape->ncymax),
|
CFG_SIMPLE_INT("nzmax", &tape->nczmax),
|
CFG_SIMPLE_INT("iterations",&tape->iterations),
|
CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
|
CFG_SIMPLE_INT("inititer", &tape->inititer),
|
CFG_SIMPLE_BOOL("quiet",(cfg_bool_t *)&tape->quiet),
|
CFG_SIMPLE_STR("multiprocessing",&tape->multiprocessing),
|
CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
|
CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
|
CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
|
CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
|
CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
|
CFG_SIMPLE_FLOAT("c0",&tape->c0),
|
CFG_SIMPLE_FLOAT("w",&tape->w),
|
CFG_SIMPLE_FLOAT("F",&tape->F),
|
/* Variables related to plane confinement */
|
CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
|
CFG_FLOAT("plane_d", 15, CFGF_NONE),
|
CFG_FLOAT("plane_F", 1000, CFGF_NONE),
|
/* Variables related to stretching */
|
// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
|
// CFG_FLOAT("xkA0",0,CFGF_NONE),
|
CFG_END()
|
};
|
cfg_t *cfg;
|
ts_uint retval;
|
cfg = cfg_init(opts, 0);
|
retval=cfg_parse_buf(cfg, buffer);
|
tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
|
tape->plane_d=cfg_getfloat(cfg,"plane_d");
|
tape->plane_F=cfg_getfloat(cfg,"plane_F");
|
|
if(retval==CFG_FILE_ERROR){
|
fatal("No tape file.",100);
|
}
|
else if(retval==CFG_PARSE_ERROR){
|
fatal("Invalid tape!",100);
|
}
|
|
/* here we override all values read from tape with values from commandline*/
|
getcmdline_tape(cfg,command_line_args.tape_opts);
|
cfg_free(cfg);
|
|
|
/* global variables are set automatically */
|
quiet=tape->quiet;
|
return tape;
|
}
|
|
ts_bool tape_free(ts_tape *tape){
|
free(tape->multiprocessing);
|
free(tape);
|
return TS_SUCCESS;
|
}
|
|
|
|
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
|
|
char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
|
operator[0]=0;
|
operator[1]=0;
|
ts_uint i,j;
|
commands=(char *)malloc(10000*sizeof(char));
|
backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
|
strcpy(commands,opts);
|
for(i=0; ;i++, commands=NULL){
|
//breaks comma separated list of commands into specific commands.
|
command=strtok_r(commands,",",&saveptr);
|
if(command==NULL) break;
|
// fprintf(stdout,"Command %d: %s\n",i,command);
|
//extracts name of command and value of command into operator[2] array.
|
for(j=0; j<2;j++,command=NULL){
|
operator[j]=strtok_r(command,"=",&saveopptr);
|
if(operator[j]==NULL) break;
|
// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
|
}
|
//1. check: must have 2 operators.
|
if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
|
|
// cfg_setstr(cfg,operator[0],operator[1]);
|
cmdline_to_tape(cfg,operator[0],operator[1]);
|
//2. check: must be named properly.
|
//3. check: must be of right format (integer, double, string, ...)
|
|
}
|
free(backup);
|
return TS_SUCCESS;
|
}
|
|
|
ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val){
|
|
cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
|
if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
|
switch (cfg_opt->type){
|
case CFGT_INT:
|
cfg_setint(cfg,key,atol(val));
|
break;
|
case CFGT_FLOAT:
|
cfg_setfloat(cfg,key,atof(val));
|
break;
|
/* case CFGT_BOOL:
|
cfg_setbool(cfg,operator[0],operator[1]);
|
break; */
|
case CFGT_STR:
|
cfg_setstr(cfg,key,val);
|
break;
|
default:
|
break;
|
|
}
|
return TS_SUCCESS;
|
}
|
