--- trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp 2012/09/07 18:13:55 1795 +++ trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp 2013/10/31 18:18:57 1939 @@ -1,7 +1,7 @@ /* File autogenerated by gengetopt version 2.22.4 generated with the following command: - gengetopt -F DynamicPropsCmd -u + gengetopt --file-name=DynamicPropsCmd --unamed-opts The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: @@ -43,13 +43,17 @@ const char *gengetopt_args_info_help[] = { " --sele1=selection script select first stuntdouble set", " --sele2=selection script select second stuntdouble set (if sele2 is not \n set, use script from sele1)", " --order=INT Lengendre Polynomial Order", + " -z, --nzbins=INT Number of Z bins (default=`100')", " -m, --memory=memory specification\n Available memory (defaults to 2G) \n (default=`2G')", "\n Group: dynamicProps\n an option of this group is required", + " -s, --selecorr selection correlation function", " -r, --rcorr rmsd", " -v, --vcorr velocity correlation function", " -d, --dcorr dipole correlation function", " -l, --lcorr Lengendre correlation function", - " -s, --sdcorr System dipole correlation function", + " --lcorrZ Lengendre correlation function binned by Z", + " --cohZ Lengendre correlation function for OH bond \n vectors binned by Z", + " -M, --sdcorr System dipole correlation function", " --r_rcorr Radial rmsd", " --thetacorr Angular rmsd", " --drcorr Directional rmsd for particles with unit \n vectors", @@ -89,11 +93,15 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->sele1_given = 0 ; args_info->sele2_given = 0 ; args_info->order_given = 0 ; + args_info->nzbins_given = 0 ; args_info->memory_given = 0 ; + args_info->selecorr_given = 0 ; args_info->rcorr_given = 0 ; args_info->vcorr_given = 0 ; args_info->dcorr_given = 0 ; args_info->lcorr_given = 0 ; + args_info->lcorrZ_given = 0 ; + args_info->cohZ_given = 0 ; args_info->sdcorr_given = 0 ; args_info->r_rcorr_given = 0 ; args_info->thetacorr_given = 0 ; @@ -117,6 +125,8 @@ void clear_args (struct gengetopt_args_info *args_info args_info->sele2_arg = NULL; args_info->sele2_orig = NULL; args_info->order_orig = NULL; + args_info->nzbins_arg = 100; + args_info->nzbins_orig = NULL; args_info->memory_arg = gengetopt_strdup ("2G"); args_info->memory_orig = NULL; @@ -134,18 +144,22 @@ void init_args_info(struct gengetopt_args_info *args_i args_info->sele1_help = gengetopt_args_info_help[4] ; args_info->sele2_help = gengetopt_args_info_help[5] ; args_info->order_help = gengetopt_args_info_help[6] ; - args_info->memory_help = gengetopt_args_info_help[7] ; - args_info->rcorr_help = gengetopt_args_info_help[9] ; - args_info->vcorr_help = gengetopt_args_info_help[10] ; - args_info->dcorr_help = gengetopt_args_info_help[11] ; - args_info->lcorr_help = gengetopt_args_info_help[12] ; - args_info->sdcorr_help = gengetopt_args_info_help[13] ; - args_info->r_rcorr_help = gengetopt_args_info_help[14] ; - args_info->thetacorr_help = gengetopt_args_info_help[15] ; - args_info->drcorr_help = gengetopt_args_info_help[16] ; - args_info->helfandEcorr_help = gengetopt_args_info_help[17] ; - args_info->momentum_help = gengetopt_args_info_help[18] ; - args_info->stresscorr_help = gengetopt_args_info_help[19] ; + args_info->nzbins_help = gengetopt_args_info_help[7] ; + args_info->memory_help = gengetopt_args_info_help[8] ; + args_info->selecorr_help = gengetopt_args_info_help[10] ; + args_info->rcorr_help = gengetopt_args_info_help[11] ; + args_info->vcorr_help = gengetopt_args_info_help[12] ; + args_info->dcorr_help = gengetopt_args_info_help[13] ; + args_info->lcorr_help = gengetopt_args_info_help[14] ; + args_info->lcorrZ_help = gengetopt_args_info_help[15] ; + args_info->cohZ_help = gengetopt_args_info_help[16] ; + args_info->sdcorr_help = gengetopt_args_info_help[17] ; + args_info->r_rcorr_help = gengetopt_args_info_help[18] ; + args_info->thetacorr_help = gengetopt_args_info_help[19] ; + args_info->drcorr_help = gengetopt_args_info_help[20] ; + args_info->helfandEcorr_help = gengetopt_args_info_help[21] ; + args_info->momentum_help = gengetopt_args_info_help[22] ; + args_info->stresscorr_help = gengetopt_args_info_help[23] ; } @@ -238,6 +252,7 @@ cmdline_parser_release (struct gengetopt_args_info *ar free_string_field (&(args_info->sele2_arg)); free_string_field (&(args_info->sele2_orig)); free_string_field (&(args_info->order_orig)); + free_string_field (&(args_info->nzbins_orig)); free_string_field (&(args_info->memory_arg)); free_string_field (&(args_info->memory_orig)); @@ -289,8 +304,12 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "sele2", args_info->sele2_orig, 0); if (args_info->order_given) write_into_file(outfile, "order", args_info->order_orig, 0); + if (args_info->nzbins_given) + write_into_file(outfile, "nzbins", args_info->nzbins_orig, 0); if (args_info->memory_given) write_into_file(outfile, "memory", args_info->memory_orig, 0); + if (args_info->selecorr_given) + write_into_file(outfile, "selecorr", 0, 0 ); if (args_info->rcorr_given) write_into_file(outfile, "rcorr", 0, 0 ); if (args_info->vcorr_given) @@ -299,6 +318,10 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "dcorr", 0, 0 ); if (args_info->lcorr_given) write_into_file(outfile, "lcorr", 0, 0 ); + if (args_info->lcorrZ_given) + write_into_file(outfile, "lcorrZ", 0, 0 ); + if (args_info->cohZ_given) + write_into_file(outfile, "cohZ", 0, 0 ); if (args_info->sdcorr_given) write_into_file(outfile, "sdcorr", 0, 0 ); if (args_info->r_rcorr_given) @@ -366,10 +389,13 @@ reset_group_dynamicProps(struct gengetopt_args_info *a if (! args_info->dynamicProps_group_counter) return; + args_info->selecorr_given = 0 ; args_info->rcorr_given = 0 ; args_info->vcorr_given = 0 ; args_info->dcorr_given = 0 ; args_info->lcorr_given = 0 ; + args_info->lcorrZ_given = 0 ; + args_info->cohZ_given = 0 ; args_info->sdcorr_given = 0 ; args_info->r_rcorr_given = 0 ; args_info->thetacorr_given = 0 ; @@ -625,12 +651,16 @@ cmdline_parser_internal ( { "sele1", 1, NULL, 0 }, { "sele2", 1, NULL, 0 }, { "order", 1, NULL, 0 }, + { "nzbins", 1, NULL, 'z' }, { "memory", 1, NULL, 'm' }, + { "selecorr", 0, NULL, 's' }, { "rcorr", 0, NULL, 'r' }, { "vcorr", 0, NULL, 'v' }, { "dcorr", 0, NULL, 'd' }, { "lcorr", 0, NULL, 'l' }, - { "sdcorr", 0, NULL, 's' }, + { "lcorrZ", 0, NULL, 0 }, + { "cohZ", 0, NULL, 0 }, + { "sdcorr", 0, NULL, 'M' }, { "r_rcorr", 0, NULL, 0 }, { "thetacorr", 0, NULL, 0 }, { "drcorr", 0, NULL, 0 }, @@ -640,7 +670,7 @@ cmdline_parser_internal ( { 0, 0, 0, 0 } }; - c = getopt_long (argc, argv, "hVi:o:m:rvdlsp", long_options, &option_index); + c = getopt_long (argc, argv, "hVi:o:z:m:srvdlMp", long_options, &option_index); if (c == -1) break; /* Exit from `while (1)' loop. */ @@ -680,6 +710,18 @@ cmdline_parser_internal ( goto failure; break; + case 'z': /* Number of Z bins. */ + + + if (update_arg( (void *)&(args_info->nzbins_arg), + &(args_info->nzbins_orig), &(args_info->nzbins_given), + &(local_args_info.nzbins_given), optarg, 0, "100", ARG_INT, + check_ambiguity, override, 0, 0, + "nzbins", 'z', + additional_error)) + goto failure; + + break; case 'm': /* Available memory (defaults to 2G). */ @@ -692,6 +734,21 @@ cmdline_parser_internal ( goto failure; break; + case 's': /* selection correlation function. */ + + if (args_info->dynamicProps_group_counter && override) + reset_group_dynamicProps (args_info); + args_info->dynamicProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->selecorr_given), + &(local_args_info.selecorr_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "selecorr", 's', + additional_error)) + goto failure; + + break; case 'r': /* rmsd. */ if (args_info->dynamicProps_group_counter && override) @@ -752,7 +809,7 @@ cmdline_parser_internal ( goto failure; break; - case 's': /* System dipole correlation function. */ + case 'M': /* System dipole correlation function. */ if (args_info->dynamicProps_group_counter && override) reset_group_dynamicProps (args_info); @@ -762,7 +819,7 @@ cmdline_parser_internal ( 0 , &(args_info->sdcorr_given), &(local_args_info.sdcorr_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, - "sdcorr", 's', + "sdcorr", 'M', additional_error)) goto failure; @@ -826,6 +883,40 @@ cmdline_parser_internal ( goto failure; } + /* Lengendre correlation function binned by Z. */ + else if (strcmp (long_options[option_index].name, "lcorrZ") == 0) + { + + if (args_info->dynamicProps_group_counter && override) + reset_group_dynamicProps (args_info); + args_info->dynamicProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->lcorrZ_given), + &(local_args_info.lcorrZ_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "lcorrZ", '-', + additional_error)) + goto failure; + + } + /* Lengendre correlation function for OH bond vectors binned by Z. */ + else if (strcmp (long_options[option_index].name, "cohZ") == 0) + { + + if (args_info->dynamicProps_group_counter && override) + reset_group_dynamicProps (args_info); + args_info->dynamicProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->cohZ_given), + &(local_args_info.cohZ_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "cohZ", '-', + additional_error)) + goto failure; + + } /* Radial rmsd. */ else if (strcmp (long_options[option_index].name, "r_rcorr") == 0) {