--- branches/development/src/applications/staticProps/StaticPropsCmd.cpp 2011/10/03 20:32:45 1655 +++ trunk/src/applications/staticProps/StaticPropsCmd.cpp 2013/01/29 20:58:08 1843 @@ -1,7 +1,7 @@ /* File autogenerated by gengetopt version 2.22.4 generated with the following command: - gengetopt -F StaticPropsCmd -u + gengetopt --file-name=StaticPropsCmd --unamed-opts The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: @@ -52,6 +52,7 @@ const char *gengetopt_args_info_help[] = { " --sele3=selection script select the third stuntdouble set", " --refsele=selection script\n select reference (use and only use with --gxyz)", " --comsele=selection script\n select stunt doubles for center-of-mass \n reference point", + " --seleoffset=INT global index offset for a second object (used \n to define a vector between sites in molecule)", " --molname=STRING molecule name", " --begin=INT begin internal index", " --end=INT end internal index", @@ -80,7 +81,8 @@ const char *gengetopt_args_info_help[] = { " --angle_r angle of R", " --hullvol hull volume of nanoparticle", " --rodlength length of nanorod", - " -Q, --tet_param tetrahedrality order parameter", + " -Q, --tet_param tetrahedrality order parameter (Qk)", + " --tet_param_z spatially-resolved tetrahedrality order \n parameter Qk(z)", 0 }; @@ -128,6 +130,7 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->sele3_given = 0 ; args_info->refsele_given = 0 ; args_info->comsele_given = 0 ; + args_info->seleoffset_given = 0 ; args_info->molname_given = 0 ; args_info->begin_given = 0 ; args_info->end_given = 0 ; @@ -156,6 +159,7 @@ void clear_given (struct gengetopt_args_info *args_inf args_info->hullvol_given = 0 ; args_info->rodlength_given = 0 ; args_info->tet_param_given = 0 ; + args_info->tet_param_z_given = 0 ; args_info->staticProps_group_counter = 0 ; } @@ -195,6 +199,7 @@ void clear_args (struct gengetopt_args_info *args_info args_info->refsele_orig = NULL; args_info->comsele_arg = NULL; args_info->comsele_orig = NULL; + args_info->seleoffset_orig = NULL; args_info->molname_arg = NULL; args_info->molname_orig = NULL; args_info->begin_orig = NULL; @@ -228,34 +233,36 @@ void init_args_info(struct gengetopt_args_info *args_i args_info->sele3_help = gengetopt_args_info_help[17] ; args_info->refsele_help = gengetopt_args_info_help[18] ; args_info->comsele_help = gengetopt_args_info_help[19] ; - args_info->molname_help = gengetopt_args_info_help[20] ; - args_info->begin_help = gengetopt_args_info_help[21] ; - args_info->end_help = gengetopt_args_info_help[22] ; - args_info->radius_help = gengetopt_args_info_help[23] ; - args_info->bo_help = gengetopt_args_info_help[25] ; - args_info->bor_help = gengetopt_args_info_help[26] ; - args_info->bad_help = gengetopt_args_info_help[27] ; - args_info->count_help = gengetopt_args_info_help[28] ; - args_info->gofr_help = gengetopt_args_info_help[29] ; - args_info->gofz_help = gengetopt_args_info_help[30] ; - args_info->r_theta_help = gengetopt_args_info_help[31] ; - args_info->r_omega_help = gengetopt_args_info_help[32] ; - args_info->r_z_help = gengetopt_args_info_help[33] ; - args_info->theta_omega_help = gengetopt_args_info_help[34] ; - args_info->gxyz_help = gengetopt_args_info_help[35] ; - args_info->twodgofr_help = gengetopt_args_info_help[36] ; - args_info->p2_help = gengetopt_args_info_help[37] ; - args_info->rp2_help = gengetopt_args_info_help[38] ; - args_info->scd_help = gengetopt_args_info_help[39] ; - args_info->density_help = gengetopt_args_info_help[40] ; - args_info->slab_density_help = gengetopt_args_info_help[41] ; - args_info->p_angle_help = gengetopt_args_info_help[42] ; - args_info->hxy_help = gengetopt_args_info_help[43] ; - args_info->rho_r_help = gengetopt_args_info_help[44] ; - args_info->angle_r_help = gengetopt_args_info_help[45] ; - args_info->hullvol_help = gengetopt_args_info_help[46] ; - args_info->rodlength_help = gengetopt_args_info_help[47] ; - args_info->tet_param_help = gengetopt_args_info_help[48] ; + args_info->seleoffset_help = gengetopt_args_info_help[20] ; + args_info->molname_help = gengetopt_args_info_help[21] ; + args_info->begin_help = gengetopt_args_info_help[22] ; + args_info->end_help = gengetopt_args_info_help[23] ; + args_info->radius_help = gengetopt_args_info_help[24] ; + args_info->bo_help = gengetopt_args_info_help[26] ; + args_info->bor_help = gengetopt_args_info_help[27] ; + args_info->bad_help = gengetopt_args_info_help[28] ; + args_info->count_help = gengetopt_args_info_help[29] ; + args_info->gofr_help = gengetopt_args_info_help[30] ; + args_info->gofz_help = gengetopt_args_info_help[31] ; + args_info->r_theta_help = gengetopt_args_info_help[32] ; + args_info->r_omega_help = gengetopt_args_info_help[33] ; + args_info->r_z_help = gengetopt_args_info_help[34] ; + args_info->theta_omega_help = gengetopt_args_info_help[35] ; + args_info->gxyz_help = gengetopt_args_info_help[36] ; + args_info->twodgofr_help = gengetopt_args_info_help[37] ; + args_info->p2_help = gengetopt_args_info_help[38] ; + args_info->rp2_help = gengetopt_args_info_help[39] ; + args_info->scd_help = gengetopt_args_info_help[40] ; + args_info->density_help = gengetopt_args_info_help[41] ; + args_info->slab_density_help = gengetopt_args_info_help[42] ; + args_info->p_angle_help = gengetopt_args_info_help[43] ; + args_info->hxy_help = gengetopt_args_info_help[44] ; + args_info->rho_r_help = gengetopt_args_info_help[45] ; + args_info->angle_r_help = gengetopt_args_info_help[46] ; + args_info->hullvol_help = gengetopt_args_info_help[47] ; + args_info->rodlength_help = gengetopt_args_info_help[48] ; + args_info->tet_param_help = gengetopt_args_info_help[49] ; + args_info->tet_param_z_help = gengetopt_args_info_help[50] ; } @@ -364,6 +371,7 @@ cmdline_parser_release (struct gengetopt_args_info *ar free_string_field (&(args_info->refsele_orig)); free_string_field (&(args_info->comsele_arg)); free_string_field (&(args_info->comsele_orig)); + free_string_field (&(args_info->seleoffset_orig)); free_string_field (&(args_info->molname_arg)); free_string_field (&(args_info->molname_orig)); free_string_field (&(args_info->begin_orig)); @@ -444,6 +452,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "refsele", args_info->refsele_orig, 0); if (args_info->comsele_given) write_into_file(outfile, "comsele", args_info->comsele_orig, 0); + if (args_info->seleoffset_given) + write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0); if (args_info->molname_given) write_into_file(outfile, "molname", args_info->molname_orig, 0); if (args_info->begin_given) @@ -500,6 +510,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar write_into_file(outfile, "rodlength", 0, 0 ); if (args_info->tet_param_given) write_into_file(outfile, "tet_param", 0, 0 ); + if (args_info->tet_param_z_given) + write_into_file(outfile, "tet_param_z", 0, 0 ); i = EXIT_SUCCESS; @@ -577,6 +589,7 @@ reset_group_staticProps(struct gengetopt_args_info *ar args_info->hullvol_given = 0 ; args_info->rodlength_given = 0 ; args_info->tet_param_given = 0 ; + args_info->tet_param_z_given = 0 ; args_info->staticProps_group_counter = 0; } @@ -842,6 +855,7 @@ cmdline_parser_internal ( { "sele3", 1, NULL, 0 }, { "refsele", 1, NULL, 0 }, { "comsele", 1, NULL, 0 }, + { "seleoffset", 1, NULL, 0 }, { "molname", 1, NULL, 0 }, { "begin", 1, NULL, 0 }, { "end", 1, NULL, 0 }, @@ -870,6 +884,7 @@ cmdline_parser_internal ( { "hullvol", 0, NULL, 0 }, { "rodlength", 0, NULL, 0 }, { "tet_param", 0, NULL, 'Q' }, + { "tet_param_z", 0, NULL, 0 }, { 0, 0, 0, 0 } }; @@ -1057,7 +1072,7 @@ cmdline_parser_internal ( goto failure; break; - case 'Q': /* tetrahedrality order parameter. */ + case 'Q': /* tetrahedrality order parameter (Qk). */ if (args_info->staticProps_group_counter && override) reset_group_staticProps (args_info); @@ -1200,6 +1215,20 @@ cmdline_parser_internal ( goto failure; } + /* global index offset for a second object (used to define a vector between sites in molecule). */ + else if (strcmp (long_options[option_index].name, "seleoffset") == 0) + { + + + if (update_arg( (void *)&(args_info->seleoffset_arg), + &(args_info->seleoffset_orig), &(args_info->seleoffset_given), + &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT, + check_ambiguity, override, 0, 0, + "seleoffset", '-', + additional_error)) + goto failure; + + } /* molecule name. */ else if (strcmp (long_options[option_index].name, "molname") == 0) { @@ -1575,6 +1604,23 @@ cmdline_parser_internal ( &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "rodlength", '-', + additional_error)) + goto failure; + + } + /* spatially-resolved tetrahedrality order parameter Qk(z). */ + else if (strcmp (long_options[option_index].name, "tet_param_z") == 0) + { + + if (args_info->staticProps_group_counter && override) + reset_group_staticProps (args_info); + args_info->staticProps_group_counter += 1; + + if (update_arg( 0 , + 0 , &(args_info->tet_param_z_given), + &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO, + check_ambiguity, override, 0, 0, + "tet_param_z", '-', additional_error)) goto failure;