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/* |
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File autogenerated by gengetopt version 2.11 |
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generated with the following command: |
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/home/maul/gezelter/tim/program/gengetopt-2.11/src/gengetopt --file-name=Dump2XYZCmd |
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/home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd |
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The developers of gengetopt consider the fixed text that goes in all |
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gengetopt output files to be in the public domain: |
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#include "config.h" |
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#endif |
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#include "getopt.h" |
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#include "applications/dump2Xyz/Dump2XYZCmd.h" |
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#include "Dump2XYZCmd.h" |
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void |
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cmdline_parser_print_version (void) |
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printf("\n" |
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"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE); |
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printf("\n"); |
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printf(" -h, --help Print help and exit\n"); |
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printf(" -V, --version Print version and exit\n"); |
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printf(" -i, --input=filename input dump file\n"); |
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printf(" -o, --output=filename output file name\n"); |
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printf(" -n, --frame=INT print every n frame (default=`1')\n"); |
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printf(" -d, --dipole print the dipole moments (default=off)\n"); |
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printf(" -w, --water skip the the waters (default=off)\n"); |
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printf(" -m, --periodicBox map to the periodic box (default=off)\n"); |
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printf(" -z, --zconstraint replace the atom types of zconstraint molecules \n (default=off)\n"); |
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printf(" -r, --rigidbody add a pseudo COM atom to rigidbody (default=off)\n"); |
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printf(" -t, --watertype replace the atom type of water model (default=on)\n"); |
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printf(" -s, --ignore=atomtype ignore the atom types\n"); |
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printf(" --repeatX=INT The number of images to repeat in the x direction \n (default=`0')\n"); |
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printf(" --repeatY=INT The number of images to repeat in the y direction \n (default=`0')\n"); |
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printf(" --repeatZ=INT The number of images to repeat in the z direction \n (default=`0')\n"); |
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printf(" -h, --help Print help and exit\n"); |
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printf(" -V, --version Print version and exit\n"); |
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printf(" -i, --input=filename input dump file\n"); |
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printf(" -o, --output=filename output file name\n"); |
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printf(" -n, --frame=INT print every n frame (default=`1')\n"); |
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printf(" -d, --dipole print the dipole moments (default=off)\n"); |
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printf(" -w, --water skip the the waters (default=off)\n"); |
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printf(" -m, --periodicBox map to the periodic box (default=off)\n"); |
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printf(" -z, --zconstraint replace the atom types of zconstraint \n molecules (default=off)\n"); |
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printf(" -r, --rigidbody add a pseudo COM atom to rigidbody \n (default=off)\n"); |
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printf(" -t, --watertype replace the atom type of water model \n (default=on)\n"); |
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printf(" -g, --ignore=atomtype ignore the atom types\n"); |
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printf(" -s, --selection=selection script selection syntax:\n" |
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" select DMPC -- select DMPC molecule\n" |
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" select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n" |
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" select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n" |
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" select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n" |
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" select 5 -- select stuntdobule whose global index is 5\n" |
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" select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n" |
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" select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n"); |
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printf(" --repeatX=INT The number of images to repeat in the x \n direction (default=`0')\n"); |
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printf(" --repeatY=INT The number of images to repeat in the y \n direction (default=`0')\n"); |
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printf(" --repeatZ=INT The number of images to repeat in the z \n direction (default=`0')\n"); |
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} |
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args_info->rigidbody_given = 0 ; |
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args_info->watertype_given = 0 ; |
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args_info->ignore_given = 0 ; |
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args_info->selection_given = 0 ; |
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args_info->repeatX_given = 0 ; |
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args_info->repeatY_given = 0 ; |
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args_info->repeatZ_given = 0 ; |
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args_info->rigidbody_flag = 0;\ |
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args_info->watertype_flag = 1;\ |
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args_info->ignore_arg = NULL; \ |
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args_info->selection_arg = NULL; \ |
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args_info->repeatX_arg = 0 ;\ |
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args_info->repeatY_arg = 0 ;\ |
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args_info->repeatZ_arg = 0 ;\ |
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{ "zconstraint", 0, NULL, 'z' }, |
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{ "rigidbody", 0, NULL, 'r' }, |
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{ "watertype", 0, NULL, 't' }, |
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{ "ignore", 1, NULL, 's' }, |
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{ "ignore", 1, NULL, 'g' }, |
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{ "selection", 1, NULL, 's' }, |
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{ "repeatX", 1, NULL, 0 }, |
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{ "repeatY", 1, NULL, 0 }, |
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{ "repeatZ", 1, NULL, 0 }, |
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}; |
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stop_char = 0; |
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c = getopt_long (argc, argv, "hVi:o:n:dwmzrts:", long_options, &option_index); |
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c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index); |
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if (c == -1) break; /* Exit from `while (1)' loop. */ |
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args_info->watertype_flag = !(args_info->watertype_flag); |
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break; |
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case 's': /* ignore the atom types. */ |
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case 'g': /* ignore the atom types. */ |
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args_info->ignore_given++; |
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ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list)); |
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ignore_new->next = ignore_list; |
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ignore_new->ignore_arg = gengetopt_strdup (optarg); |
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break; |
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case 's': /* general selection syntax:\n |
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select DMPC -- select DMPC molecule\n \ |
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select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \ |
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select 5 -- select stuntdobule whose global index is 5\n \ |
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select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \ |
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select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule . */ |
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if (args_info->selection_given) |
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{ |
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fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE); |
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clear_args (); |
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exit (EXIT_FAILURE); |
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} |
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args_info->selection_given = 1; |
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args_info->selection_arg = gengetopt_strdup (optarg); |
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break; |
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case 0: /* Long option with no short option */ |
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/* The number of images to repeat in the x direction. */ |
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if (strcmp (long_options[option_index].name, "repeatX") == 0) |