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/* | 
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  File autogenerated by gengetopt version 2.22 | 
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  File autogenerated by gengetopt version 2.22.4 | 
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  generated with the following command: | 
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  gengetopt -F StaticPropsCmd -u  | 
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  gengetopt --file-name=StaticPropsCmd --unamed-opts  | 
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 | 
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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 <stdlib.h> | 
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#include <string.h> | 
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 | 
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#include "getopt.h" | 
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#ifndef FIX_UNUSED | 
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#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ | 
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#endif | 
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 | 
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#ifdef WIN32 | 
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#include "utils/wingetopt.h" | 
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#else | 
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#include <getopt.h> | 
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#endif | 
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 | 
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#include "StaticPropsCmd.h" | 
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 | 
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const char *gengetopt_args_info_purpose = ""; | 
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  "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')", | 
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  "      --nbins_z=INT             number of bins in z axis  (default=`100')", | 
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  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')", | 
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  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
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  "  -c, --rcut=DOUBLE             cutoff radius (rcut)", | 
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  "      --dz=DOUBLE               slab width (dz)", | 
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  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
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  "      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
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  "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')", | 
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  "      --sele1=selection script  select the first stuntdouble set", | 
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  "      --sele2=selection script  select the second stuntdouble set", | 
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  "      --sele3=selection script  select the third stuntdouble set", | 
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  "      --refsele=selection script\n                                select reference (use and only use with --gxyz)", | 
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  "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point", | 
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  "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)", | 
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  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)", | 
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  "      --molname=STRING          molecule name", | 
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  "      --begin=INT               begin internal index", | 
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  "      --end=INT                 end internal index", | 
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  "      --bo                      bond order parameter (--rcut must be specified)", | 
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  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)", | 
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  "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)", | 
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  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)", | 
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  "  -g, --gofr                    g(r)", | 
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  "      --gofz                    g(z)", | 
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  "      --r_theta                 g(r, cos(theta))", | 
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  "      --r_z                     g(r, z)", | 
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  "      --theta_omega             g(cos(theta), cos(omega))", | 
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  "      --gxyz                    g(x, y, z)", | 
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  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)", | 
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  "      --twodgofr                2D g(r) (Slab width --dz must be specified)", | 
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  "  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)", | 
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  "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)", | 
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  "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)", | 
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  "  -d, --density                 density plot", | 
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  "      --slab_density            slab density", | 
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  "      --p_angle                 p(cos(theta))", | 
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  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)", | 
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  "      --hxy                     hxy", | 
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  "      --rho_r                   rho of R", | 
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  "      --angle_r                 angle of R", | 
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  "      --hullvol                 hull volume of nanoparticle", | 
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  "      --rodlength               length of nanorod", | 
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  "  -Q, --tet_param               tetrahedrality order parameter (Qk)", | 
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  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)", | 
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  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)", | 
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  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)", | 
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  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)", | 
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    0 | 
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}; | 
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 | 
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void clear_args (struct gengetopt_args_info *args_info); | 
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static int | 
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cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
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cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info, | 
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                        struct cmdline_parser_params *params, const char *additional_error); | 
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static int | 
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  args_info->nbins_y_given = 0 ; | 
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  args_info->nbins_z_given = 0 ; | 
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  args_info->nanglebins_given = 0 ; | 
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  args_info->length_given = 0 ; | 
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  args_info->rcut_given = 0 ; | 
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  args_info->dz_given = 0 ; | 
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  args_info->length_given = 0 ; | 
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  args_info->zlength_given = 0 ; | 
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  args_info->zoffset_given = 0 ; | 
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  args_info->sele1_given = 0 ; | 
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  args_info->sele2_given = 0 ; | 
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  args_info->sele3_given = 0 ; | 
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  args_info->refsele_given = 0 ; | 
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  args_info->comsele_given = 0 ; | 
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  args_info->seleoffset_given = 0 ; | 
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  args_info->seleoffset2_given = 0 ; | 
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  args_info->molname_given = 0 ; | 
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  args_info->begin_given = 0 ; | 
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  args_info->end_given = 0 ; | 
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  args_info->bo_given = 0 ; | 
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  args_info->bor_given = 0 ; | 
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  args_info->bad_given = 0 ; | 
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  args_info->count_given = 0 ; | 
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  args_info->gofr_given = 0 ; | 
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  args_info->gofz_given = 0 ; | 
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  args_info->r_theta_given = 0 ; | 
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  args_info->r_z_given = 0 ; | 
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  args_info->theta_omega_given = 0 ; | 
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  args_info->gxyz_given = 0 ; | 
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  args_info->twodgofr_given = 0 ; | 
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  args_info->p2_given = 0 ; | 
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  args_info->rp2_given = 0 ; | 
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  args_info->scd_given = 0 ; | 
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  args_info->p_angle_given = 0 ; | 
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  args_info->hxy_given = 0 ; | 
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  args_info->rho_r_given = 0 ; | 
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  args_info->angle_r_given = 0 ; | 
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  args_info->hullvol_given = 0 ; | 
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  args_info->rodlength_given = 0 ; | 
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  args_info->tet_param_given = 0 ; | 
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  args_info->tet_param_z_given = 0 ; | 
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  args_info->rnemdz_given = 0 ; | 
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  args_info->rnemdr_given = 0 ; | 
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  args_info->rnemdrt_given = 0 ; | 
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  args_info->staticProps_group_counter = 0 ; | 
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} | 
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static | 
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void clear_args (struct gengetopt_args_info *args_info) | 
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{ | 
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  FIX_UNUSED (args_info); | 
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  args_info->input_arg = NULL; | 
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  args_info->input_orig = NULL; | 
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  args_info->output_arg = NULL; | 
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  args_info->nbins_z_orig = NULL; | 
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  args_info->nanglebins_arg = 50; | 
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  args_info->nanglebins_orig = NULL; | 
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  args_info->length_orig = NULL; | 
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  args_info->rcut_orig = NULL; | 
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  args_info->dz_orig = NULL; | 
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  args_info->length_orig = NULL; | 
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  args_info->zlength_orig = NULL; | 
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  args_info->zoffset_arg = 0; | 
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  args_info->zoffset_orig = NULL; | 
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  args_info->sele1_arg = NULL; | 
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  args_info->refsele_orig = NULL; | 
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  args_info->comsele_arg = NULL; | 
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  args_info->comsele_orig = NULL; | 
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  args_info->seleoffset_orig = NULL; | 
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  args_info->seleoffset2_orig = NULL; | 
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  args_info->molname_arg = NULL; | 
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  args_info->molname_orig = NULL; | 
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  args_info->begin_orig = NULL; | 
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  args_info->nbins_y_help = gengetopt_args_info_help[7] ; | 
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  args_info->nbins_z_help = gengetopt_args_info_help[8] ; | 
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  args_info->nanglebins_help = gengetopt_args_info_help[9] ; | 
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  args_info->length_help = gengetopt_args_info_help[10] ; | 
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  args_info->rcut_help = gengetopt_args_info_help[11] ; | 
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  args_info->zoffset_help = gengetopt_args_info_help[12] ; | 
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  args_info->sele1_help = gengetopt_args_info_help[13] ; | 
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  args_info->sele2_help = gengetopt_args_info_help[14] ; | 
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  args_info->sele3_help = gengetopt_args_info_help[15] ; | 
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  args_info->refsele_help = gengetopt_args_info_help[16] ; | 
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  args_info->comsele_help = gengetopt_args_info_help[17] ; | 
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  args_info->molname_help = gengetopt_args_info_help[18] ; | 
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  args_info->begin_help = gengetopt_args_info_help[19] ; | 
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  args_info->end_help = gengetopt_args_info_help[20] ; | 
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  args_info->radius_help = gengetopt_args_info_help[21] ; | 
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  args_info->bo_help = gengetopt_args_info_help[23] ; | 
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  args_info->bor_help = gengetopt_args_info_help[24] ; | 
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  args_info->bad_help = gengetopt_args_info_help[25] ; | 
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  args_info->gofr_help = gengetopt_args_info_help[26] ; | 
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  args_info->gofz_help = gengetopt_args_info_help[27] ; | 
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  args_info->r_theta_help = gengetopt_args_info_help[28] ; | 
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  args_info->r_omega_help = gengetopt_args_info_help[29] ; | 
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  args_info->r_z_help = gengetopt_args_info_help[30] ; | 
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  args_info->theta_omega_help = gengetopt_args_info_help[31] ; | 
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  args_info->gxyz_help = gengetopt_args_info_help[32] ; | 
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  args_info->p2_help = gengetopt_args_info_help[33] ; | 
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  args_info->rp2_help = gengetopt_args_info_help[34] ; | 
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  args_info->scd_help = gengetopt_args_info_help[35] ; | 
| 264 | 
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  args_info->density_help = gengetopt_args_info_help[36] ; | 
| 265 | 
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  args_info->slab_density_help = gengetopt_args_info_help[37] ; | 
| 266 | 
< | 
  args_info->p_angle_help = gengetopt_args_info_help[38] ; | 
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  args_info->hxy_help = gengetopt_args_info_help[39] ; | 
| 268 | 
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  args_info->rho_r_help = gengetopt_args_info_help[40] ; | 
| 269 | 
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  args_info->hullvol_help = gengetopt_args_info_help[41] ; | 
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  args_info->rcut_help = gengetopt_args_info_help[10] ; | 
| 240 | 
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  args_info->dz_help = gengetopt_args_info_help[11] ; | 
| 241 | 
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  args_info->length_help = gengetopt_args_info_help[12] ; | 
| 242 | 
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  args_info->zlength_help = gengetopt_args_info_help[13] ; | 
| 243 | 
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  args_info->zoffset_help = gengetopt_args_info_help[14] ; | 
| 244 | 
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  args_info->sele1_help = gengetopt_args_info_help[15] ; | 
| 245 | 
> | 
  args_info->sele2_help = gengetopt_args_info_help[16] ; | 
| 246 | 
> | 
  args_info->sele3_help = gengetopt_args_info_help[17] ; | 
| 247 | 
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  args_info->refsele_help = gengetopt_args_info_help[18] ; | 
| 248 | 
> | 
  args_info->comsele_help = gengetopt_args_info_help[19] ; | 
| 249 | 
> | 
  args_info->seleoffset_help = gengetopt_args_info_help[20] ; | 
| 250 | 
> | 
  args_info->seleoffset2_help = gengetopt_args_info_help[21] ; | 
| 251 | 
> | 
  args_info->molname_help = gengetopt_args_info_help[22] ; | 
| 252 | 
> | 
  args_info->begin_help = gengetopt_args_info_help[23] ; | 
| 253 | 
> | 
  args_info->end_help = gengetopt_args_info_help[24] ; | 
| 254 | 
> | 
  args_info->radius_help = gengetopt_args_info_help[25] ; | 
| 255 | 
> | 
  args_info->bo_help = gengetopt_args_info_help[27] ; | 
| 256 | 
> | 
  args_info->bor_help = gengetopt_args_info_help[28] ; | 
| 257 | 
> | 
  args_info->bad_help = gengetopt_args_info_help[29] ; | 
| 258 | 
> | 
  args_info->count_help = gengetopt_args_info_help[30] ; | 
| 259 | 
> | 
  args_info->gofr_help = gengetopt_args_info_help[31] ; | 
| 260 | 
> | 
  args_info->gofz_help = gengetopt_args_info_help[32] ; | 
| 261 | 
> | 
  args_info->r_theta_help = gengetopt_args_info_help[33] ; | 
| 262 | 
> | 
  args_info->r_omega_help = gengetopt_args_info_help[34] ; | 
| 263 | 
> | 
  args_info->r_z_help = gengetopt_args_info_help[35] ; | 
| 264 | 
> | 
  args_info->theta_omega_help = gengetopt_args_info_help[36] ; | 
| 265 | 
> | 
  args_info->gxyz_help = gengetopt_args_info_help[37] ; | 
| 266 | 
> | 
  args_info->twodgofr_help = gengetopt_args_info_help[38] ; | 
| 267 | 
> | 
  args_info->p2_help = gengetopt_args_info_help[39] ; | 
| 268 | 
> | 
  args_info->rp2_help = gengetopt_args_info_help[40] ; | 
| 269 | 
> | 
  args_info->scd_help = gengetopt_args_info_help[41] ; | 
| 270 | 
> | 
  args_info->density_help = gengetopt_args_info_help[42] ; | 
| 271 | 
> | 
  args_info->slab_density_help = gengetopt_args_info_help[43] ; | 
| 272 | 
> | 
  args_info->p_angle_help = gengetopt_args_info_help[44] ; | 
| 273 | 
> | 
  args_info->hxy_help = gengetopt_args_info_help[45] ; | 
| 274 | 
> | 
  args_info->rho_r_help = gengetopt_args_info_help[46] ; | 
| 275 | 
> | 
  args_info->angle_r_help = gengetopt_args_info_help[47] ; | 
| 276 | 
> | 
  args_info->hullvol_help = gengetopt_args_info_help[48] ; | 
| 277 | 
> | 
  args_info->rodlength_help = gengetopt_args_info_help[49] ; | 
| 278 | 
> | 
  args_info->tet_param_help = gengetopt_args_info_help[50] ; | 
| 279 | 
> | 
  args_info->tet_param_z_help = gengetopt_args_info_help[51] ; | 
| 280 | 
> | 
  args_info->rnemdz_help = gengetopt_args_info_help[52] ; | 
| 281 | 
> | 
  args_info->rnemdr_help = gengetopt_args_info_help[53] ; | 
| 282 | 
> | 
  args_info->rnemdrt_help = gengetopt_args_info_help[54] ; | 
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   | 
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} | 
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 | 
| 286 | 
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void | 
| 287 | 
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cmdline_parser_print_version (void) | 
| 288 | 
  | 
{ | 
| 289 | 
< | 
  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); | 
| 289 | 
> | 
  printf ("%s %s\n", | 
| 290 | 
> | 
     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), | 
| 291 | 
> | 
     CMDLINE_PARSER_VERSION); | 
| 292 | 
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} | 
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 | 
| 294 | 
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static void print_help_common(void) { | 
| 303 | 
  | 
  printf("\n"); | 
| 304 | 
  | 
 | 
| 305 | 
  | 
  if (strlen(gengetopt_args_info_description) > 0) | 
| 306 | 
< | 
    printf("%s\n", gengetopt_args_info_description); | 
| 306 | 
> | 
    printf("%s\n\n", gengetopt_args_info_description); | 
| 307 | 
  | 
} | 
| 308 | 
  | 
 | 
| 309 | 
  | 
void | 
| 322 | 
  | 
  clear_args (args_info); | 
| 323 | 
  | 
  init_args_info (args_info); | 
| 324 | 
  | 
 | 
| 325 | 
< | 
  args_info->inputs = NULL; | 
| 325 | 
> | 
  args_info->inputs = 0; | 
| 326 | 
  | 
  args_info->inputs_num = 0; | 
| 327 | 
  | 
} | 
| 328 | 
  | 
 | 
| 373 | 
  | 
  free_string_field (&(args_info->nbins_y_orig)); | 
| 374 | 
  | 
  free_string_field (&(args_info->nbins_z_orig)); | 
| 375 | 
  | 
  free_string_field (&(args_info->nanglebins_orig)); | 
| 322 | 
– | 
  free_string_field (&(args_info->length_orig)); | 
| 376 | 
  | 
  free_string_field (&(args_info->rcut_orig)); | 
| 377 | 
+ | 
  free_string_field (&(args_info->dz_orig)); | 
| 378 | 
+ | 
  free_string_field (&(args_info->length_orig)); | 
| 379 | 
+ | 
  free_string_field (&(args_info->zlength_orig)); | 
| 380 | 
  | 
  free_string_field (&(args_info->zoffset_orig)); | 
| 381 | 
  | 
  free_string_field (&(args_info->sele1_arg)); | 
| 382 | 
  | 
  free_string_field (&(args_info->sele1_orig)); | 
| 388 | 
  | 
  free_string_field (&(args_info->refsele_orig)); | 
| 389 | 
  | 
  free_string_field (&(args_info->comsele_arg)); | 
| 390 | 
  | 
  free_string_field (&(args_info->comsele_orig)); | 
| 391 | 
+ | 
  free_string_field (&(args_info->seleoffset_orig)); | 
| 392 | 
+ | 
  free_string_field (&(args_info->seleoffset2_orig)); | 
| 393 | 
  | 
  free_string_field (&(args_info->molname_arg)); | 
| 394 | 
  | 
  free_string_field (&(args_info->molname_orig)); | 
| 395 | 
  | 
  free_string_field (&(args_info->begin_orig)); | 
| 408 | 
  | 
 | 
| 409 | 
  | 
 | 
| 410 | 
  | 
static void | 
| 411 | 
< | 
write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) | 
| 411 | 
> | 
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) | 
| 412 | 
  | 
{ | 
| 413 | 
+ | 
  FIX_UNUSED (values); | 
| 414 | 
  | 
  if (arg) { | 
| 415 | 
  | 
    fprintf(outfile, "%s=\"%s\"\n", opt, arg); | 
| 416 | 
  | 
  } else { | 
| 450 | 
  | 
    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); | 
| 451 | 
  | 
  if (args_info->nanglebins_given) | 
| 452 | 
  | 
    write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); | 
| 394 | 
– | 
  if (args_info->length_given) | 
| 395 | 
– | 
    write_into_file(outfile, "length", args_info->length_orig, 0); | 
| 453 | 
  | 
  if (args_info->rcut_given) | 
| 454 | 
  | 
    write_into_file(outfile, "rcut", args_info->rcut_orig, 0); | 
| 455 | 
+ | 
  if (args_info->dz_given) | 
| 456 | 
+ | 
    write_into_file(outfile, "dz", args_info->dz_orig, 0); | 
| 457 | 
+ | 
  if (args_info->length_given) | 
| 458 | 
+ | 
    write_into_file(outfile, "length", args_info->length_orig, 0); | 
| 459 | 
+ | 
  if (args_info->zlength_given) | 
| 460 | 
+ | 
    write_into_file(outfile, "zlength", args_info->zlength_orig, 0); | 
| 461 | 
  | 
  if (args_info->zoffset_given) | 
| 462 | 
  | 
    write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); | 
| 463 | 
  | 
  if (args_info->sele1_given) | 
| 470 | 
  | 
    write_into_file(outfile, "refsele", args_info->refsele_orig, 0); | 
| 471 | 
  | 
  if (args_info->comsele_given) | 
| 472 | 
  | 
    write_into_file(outfile, "comsele", args_info->comsele_orig, 0); | 
| 473 | 
+ | 
  if (args_info->seleoffset_given) | 
| 474 | 
+ | 
    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0); | 
| 475 | 
+ | 
  if (args_info->seleoffset2_given) | 
| 476 | 
+ | 
    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0); | 
| 477 | 
  | 
  if (args_info->molname_given) | 
| 478 | 
  | 
    write_into_file(outfile, "molname", args_info->molname_orig, 0); | 
| 479 | 
  | 
  if (args_info->begin_given) | 
| 488 | 
  | 
    write_into_file(outfile, "bor", 0, 0 ); | 
| 489 | 
  | 
  if (args_info->bad_given) | 
| 490 | 
  | 
    write_into_file(outfile, "bad", 0, 0 ); | 
| 491 | 
+ | 
  if (args_info->count_given) | 
| 492 | 
+ | 
    write_into_file(outfile, "count", 0, 0 ); | 
| 493 | 
  | 
  if (args_info->gofr_given) | 
| 494 | 
  | 
    write_into_file(outfile, "gofr", 0, 0 ); | 
| 495 | 
  | 
  if (args_info->gofz_given) | 
| 504 | 
  | 
    write_into_file(outfile, "theta_omega", 0, 0 ); | 
| 505 | 
  | 
  if (args_info->gxyz_given) | 
| 506 | 
  | 
    write_into_file(outfile, "gxyz", 0, 0 ); | 
| 507 | 
+ | 
  if (args_info->twodgofr_given) | 
| 508 | 
+ | 
    write_into_file(outfile, "twodgofr", 0, 0 ); | 
| 509 | 
  | 
  if (args_info->p2_given) | 
| 510 | 
  | 
    write_into_file(outfile, "p2", 0, 0 ); | 
| 511 | 
  | 
  if (args_info->rp2_given) | 
| 522 | 
  | 
    write_into_file(outfile, "hxy", 0, 0 ); | 
| 523 | 
  | 
  if (args_info->rho_r_given) | 
| 524 | 
  | 
    write_into_file(outfile, "rho_r", 0, 0 ); | 
| 525 | 
+ | 
  if (args_info->angle_r_given) | 
| 526 | 
+ | 
    write_into_file(outfile, "angle_r", 0, 0 ); | 
| 527 | 
  | 
  if (args_info->hullvol_given) | 
| 528 | 
  | 
    write_into_file(outfile, "hullvol", 0, 0 ); | 
| 529 | 
+ | 
  if (args_info->rodlength_given) | 
| 530 | 
+ | 
    write_into_file(outfile, "rodlength", 0, 0 ); | 
| 531 | 
+ | 
  if (args_info->tet_param_given) | 
| 532 | 
+ | 
    write_into_file(outfile, "tet_param", 0, 0 ); | 
| 533 | 
+ | 
  if (args_info->tet_param_z_given) | 
| 534 | 
+ | 
    write_into_file(outfile, "tet_param_z", 0, 0 ); | 
| 535 | 
+ | 
  if (args_info->rnemdz_given) | 
| 536 | 
+ | 
    write_into_file(outfile, "rnemdz", 0, 0 ); | 
| 537 | 
+ | 
  if (args_info->rnemdr_given) | 
| 538 | 
+ | 
    write_into_file(outfile, "rnemdr", 0, 0 ); | 
| 539 | 
+ | 
  if (args_info->rnemdrt_given) | 
| 540 | 
+ | 
    write_into_file(outfile, "rnemdrt", 0, 0 ); | 
| 541 | 
  | 
   | 
| 542 | 
  | 
 | 
| 543 | 
  | 
  i = EXIT_SUCCESS; | 
| 574 | 
  | 
char * | 
| 575 | 
  | 
gengetopt_strdup (const char *s) | 
| 576 | 
  | 
{ | 
| 577 | 
< | 
  char *result = NULL; | 
| 577 | 
> | 
  char *result = 0; | 
| 578 | 
  | 
  if (!s) | 
| 579 | 
  | 
    return result; | 
| 580 | 
  | 
 | 
| 594 | 
  | 
  args_info->bo_given = 0 ; | 
| 595 | 
  | 
  args_info->bor_given = 0 ; | 
| 596 | 
  | 
  args_info->bad_given = 0 ; | 
| 597 | 
+ | 
  args_info->count_given = 0 ; | 
| 598 | 
  | 
  args_info->gofr_given = 0 ; | 
| 599 | 
  | 
  args_info->gofz_given = 0 ; | 
| 600 | 
  | 
  args_info->r_theta_given = 0 ; | 
| 602 | 
  | 
  args_info->r_z_given = 0 ; | 
| 603 | 
  | 
  args_info->theta_omega_given = 0 ; | 
| 604 | 
  | 
  args_info->gxyz_given = 0 ; | 
| 605 | 
+ | 
  args_info->twodgofr_given = 0 ; | 
| 606 | 
  | 
  args_info->p2_given = 0 ; | 
| 607 | 
  | 
  args_info->rp2_given = 0 ; | 
| 608 | 
  | 
  args_info->scd_given = 0 ; | 
| 611 | 
  | 
  args_info->p_angle_given = 0 ; | 
| 612 | 
  | 
  args_info->hxy_given = 0 ; | 
| 613 | 
  | 
  args_info->rho_r_given = 0 ; | 
| 614 | 
+ | 
  args_info->angle_r_given = 0 ; | 
| 615 | 
  | 
  args_info->hullvol_given = 0 ; | 
| 616 | 
+ | 
  args_info->rodlength_given = 0 ; | 
| 617 | 
+ | 
  args_info->tet_param_given = 0 ; | 
| 618 | 
+ | 
  args_info->tet_param_z_given = 0 ; | 
| 619 | 
+ | 
  args_info->rnemdz_given = 0 ; | 
| 620 | 
+ | 
  args_info->rnemdr_given = 0 ; | 
| 621 | 
+ | 
  args_info->rnemdrt_given = 0 ; | 
| 622 | 
  | 
 | 
| 623 | 
  | 
  args_info->staticProps_group_counter = 0; | 
| 624 | 
  | 
} | 
| 625 | 
  | 
 | 
| 626 | 
  | 
int | 
| 627 | 
< | 
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) | 
| 627 | 
> | 
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) | 
| 628 | 
  | 
{ | 
| 629 | 
  | 
  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); | 
| 630 | 
  | 
} | 
| 631 | 
  | 
 | 
| 632 | 
  | 
int | 
| 633 | 
< | 
cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
| 633 | 
> | 
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, | 
| 634 | 
  | 
                   struct cmdline_parser_params *params) | 
| 635 | 
  | 
{ | 
| 636 | 
  | 
  int result; | 
| 637 | 
< | 
  result = cmdline_parser_internal (argc, argv, args_info, params, NULL); | 
| 637 | 
> | 
  result = cmdline_parser_internal (argc, argv, args_info, params, 0); | 
| 638 | 
  | 
 | 
| 639 | 
  | 
  if (result == EXIT_FAILURE) | 
| 640 | 
  | 
    { | 
| 646 | 
  | 
} | 
| 647 | 
  | 
 | 
| 648 | 
  | 
int | 
| 649 | 
< | 
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) | 
| 649 | 
> | 
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) | 
| 650 | 
  | 
{ | 
| 651 | 
  | 
  int result; | 
| 652 | 
  | 
  struct cmdline_parser_params params; | 
| 657 | 
  | 
  params.check_ambiguity = 0; | 
| 658 | 
  | 
  params.print_errors = 1; | 
| 659 | 
  | 
 | 
| 660 | 
< | 
  result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); | 
| 660 | 
> | 
  result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); | 
| 661 | 
  | 
 | 
| 662 | 
  | 
  if (result == EXIT_FAILURE) | 
| 663 | 
  | 
    { | 
| 673 | 
  | 
{ | 
| 674 | 
  | 
  int result = EXIT_SUCCESS; | 
| 675 | 
  | 
 | 
| 676 | 
< | 
  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) | 
| 676 | 
> | 
  if (cmdline_parser_required2(args_info, prog_name, 0) > 0) | 
| 677 | 
  | 
    result = EXIT_FAILURE; | 
| 678 | 
  | 
 | 
| 679 | 
  | 
  if (result == EXIT_FAILURE) | 
| 689 | 
  | 
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) | 
| 690 | 
  | 
{ | 
| 691 | 
  | 
  int error = 0; | 
| 692 | 
+ | 
  FIX_UNUSED (additional_error); | 
| 693 | 
  | 
 | 
| 694 | 
  | 
  /* checks for required options */ | 
| 695 | 
  | 
  if (! args_info->input_given) | 
| 700 | 
  | 
   | 
| 701 | 
  | 
  if (args_info->staticProps_group_counter == 0) | 
| 702 | 
  | 
    { | 
| 703 | 
< | 
      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 703 | 
> | 
      fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 704 | 
  | 
      error = 1; | 
| 705 | 
  | 
    } | 
| 706 | 
  | 
   | 
| 734 | 
  | 
static | 
| 735 | 
  | 
int update_arg(void *field, char **orig_field, | 
| 736 | 
  | 
               unsigned int *field_given, unsigned int *prev_given,  | 
| 737 | 
< | 
               char *value, char *possible_values[], const char *default_value, | 
| 737 | 
> | 
               char *value, const char *possible_values[], | 
| 738 | 
> | 
               const char *default_value, | 
| 739 | 
  | 
               cmdline_parser_arg_type arg_type, | 
| 740 | 
  | 
               int check_ambiguity, int override, | 
| 741 | 
  | 
               int no_free, int multiple_option, | 
| 746 | 
  | 
  const char *val = value; | 
| 747 | 
  | 
  int found; | 
| 748 | 
  | 
  char **string_field; | 
| 749 | 
+ | 
  FIX_UNUSED (field); | 
| 750 | 
  | 
 | 
| 751 | 
  | 
  stop_char = 0; | 
| 752 | 
  | 
  found = 0; | 
| 764 | 
  | 
      return 1; /* failure */ | 
| 765 | 
  | 
    } | 
| 766 | 
  | 
 | 
| 767 | 
+ | 
  FIX_UNUSED (default_value); | 
| 768 | 
  | 
     | 
| 769 | 
  | 
  if (field_given && *field_given && ! override) | 
| 770 | 
  | 
    return 0; | 
| 828 | 
  | 
 | 
| 829 | 
  | 
 | 
| 830 | 
  | 
int | 
| 831 | 
< | 
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
| 831 | 
> | 
cmdline_parser_internal ( | 
| 832 | 
> | 
  int argc, char **argv, struct gengetopt_args_info *args_info, | 
| 833 | 
  | 
                        struct cmdline_parser_params *params, const char *additional_error) | 
| 834 | 
  | 
{ | 
| 835 | 
  | 
  int c;        /* Character of the parsed option.  */ | 
| 874 | 
  | 
        { "nbins_y",    1, NULL, 'y' }, | 
| 875 | 
  | 
        { "nbins_z",    1, NULL, 0 }, | 
| 876 | 
  | 
        { "nanglebins", 1, NULL, 'a' }, | 
| 778 | 
– | 
        { "length",     1, NULL, 0 }, | 
| 877 | 
  | 
        { "rcut",       1, NULL, 'c' }, | 
| 878 | 
+ | 
        { "dz", 1, NULL, 0 }, | 
| 879 | 
+ | 
        { "length",     1, NULL, 0 }, | 
| 880 | 
+ | 
        { "zlength",    1, NULL, 0 }, | 
| 881 | 
  | 
        { "zoffset",    1, NULL, 'z' }, | 
| 882 | 
  | 
        { "sele1",      1, NULL, 0 }, | 
| 883 | 
  | 
        { "sele2",      1, NULL, 0 }, | 
| 884 | 
  | 
        { "sele3",      1, NULL, 0 }, | 
| 885 | 
  | 
        { "refsele",    1, NULL, 0 }, | 
| 886 | 
  | 
        { "comsele",    1, NULL, 0 }, | 
| 887 | 
+ | 
        { "seleoffset", 1, NULL, 0 }, | 
| 888 | 
+ | 
        { "seleoffset2",        1, NULL, 0 }, | 
| 889 | 
  | 
        { "molname",    1, NULL, 0 }, | 
| 890 | 
  | 
        { "begin",      1, NULL, 0 }, | 
| 891 | 
  | 
        { "end",        1, NULL, 0 }, | 
| 893 | 
  | 
        { "bo", 0, NULL, 0 }, | 
| 894 | 
  | 
        { "bor",        0, NULL, 0 }, | 
| 895 | 
  | 
        { "bad",        0, NULL, 0 }, | 
| 896 | 
+ | 
        { "count",      0, NULL, 0 }, | 
| 897 | 
  | 
        { "gofr",       0, NULL, 'g' }, | 
| 898 | 
  | 
        { "gofz",       0, NULL, 0 }, | 
| 899 | 
  | 
        { "r_theta",    0, NULL, 0 }, | 
| 901 | 
  | 
        { "r_z",        0, NULL, 0 }, | 
| 902 | 
  | 
        { "theta_omega",        0, NULL, 0 }, | 
| 903 | 
  | 
        { "gxyz",       0, NULL, 0 }, | 
| 904 | 
+ | 
        { "twodgofr",   0, NULL, 0 }, | 
| 905 | 
  | 
        { "p2", 0, NULL, 'p' }, | 
| 906 | 
  | 
        { "rp2",        0, NULL, 0 }, | 
| 907 | 
  | 
        { "scd",        0, NULL, 's' }, | 
| 910 | 
  | 
        { "p_angle",    0, NULL, 0 }, | 
| 911 | 
  | 
        { "hxy",        0, NULL, 0 }, | 
| 912 | 
  | 
        { "rho_r",      0, NULL, 0 }, | 
| 913 | 
+ | 
        { "angle_r",    0, NULL, 0 }, | 
| 914 | 
  | 
        { "hullvol",    0, NULL, 0 }, | 
| 915 | 
< | 
        { NULL, 0, NULL, 0 } | 
| 915 | 
> | 
        { "rodlength",  0, NULL, 0 }, | 
| 916 | 
> | 
        { "tet_param",  0, NULL, 'Q' }, | 
| 917 | 
> | 
        { "tet_param_z",        0, NULL, 0 }, | 
| 918 | 
> | 
        { "rnemdz",     0, NULL, 0 }, | 
| 919 | 
> | 
        { "rnemdr",     0, NULL, 0 }, | 
| 920 | 
> | 
        { "rnemdrt",    0, NULL, 0 }, | 
| 921 | 
> | 
        { 0,  0, 0, 0 } | 
| 922 | 
  | 
      }; | 
| 923 | 
  | 
 | 
| 924 | 
< | 
      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); | 
| 924 | 
> | 
      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); | 
| 925 | 
  | 
 | 
| 926 | 
  | 
      if (c == -1) break;       /* Exit from `while (1)' loop.  */ | 
| 927 | 
  | 
 | 
| 1060 | 
  | 
            goto failure; | 
| 1061 | 
  | 
         | 
| 1062 | 
  | 
          break; | 
| 1063 | 
< | 
        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 1063 | 
> | 
        case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */ | 
| 1064 | 
  | 
         | 
| 1065 | 
  | 
          if (args_info->staticProps_group_counter && override) | 
| 1066 | 
  | 
            reset_group_staticProps (args_info); | 
| 1105 | 
  | 
            goto failure; | 
| 1106 | 
  | 
         | 
| 1107 | 
  | 
          break; | 
| 1108 | 
+ | 
        case 'Q':       /* tetrahedrality order parameter (Qk).  */ | 
| 1109 | 
+ | 
         | 
| 1110 | 
+ | 
          if (args_info->staticProps_group_counter && override) | 
| 1111 | 
+ | 
            reset_group_staticProps (args_info); | 
| 1112 | 
+ | 
          args_info->staticProps_group_counter += 1; | 
| 1113 | 
+ | 
         | 
| 1114 | 
+ | 
          if (update_arg( 0 ,  | 
| 1115 | 
+ | 
               0 , &(args_info->tet_param_given), | 
| 1116 | 
+ | 
              &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, | 
| 1117 | 
+ | 
              check_ambiguity, override, 0, 0, | 
| 1118 | 
+ | 
              "tet_param", 'Q', | 
| 1119 | 
+ | 
              additional_error)) | 
| 1120 | 
+ | 
            goto failure; | 
| 1121 | 
+ | 
         | 
| 1122 | 
+ | 
          break; | 
| 1123 | 
  | 
 | 
| 1124 | 
  | 
        case 0: /* Long option with no short option */ | 
| 1125 | 
  | 
          /* number of bins in z axis.  */ | 
| 1136 | 
  | 
              goto failure; | 
| 1137 | 
  | 
           | 
| 1138 | 
  | 
          } | 
| 1139 | 
+ | 
          /* slab width (dz).  */ | 
| 1140 | 
+ | 
          else if (strcmp (long_options[option_index].name, "dz") == 0) | 
| 1141 | 
+ | 
          { | 
| 1142 | 
+ | 
           | 
| 1143 | 
+ | 
           | 
| 1144 | 
+ | 
            if (update_arg( (void *)&(args_info->dz_arg),  | 
| 1145 | 
+ | 
                 &(args_info->dz_orig), &(args_info->dz_given), | 
| 1146 | 
+ | 
                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, | 
| 1147 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1148 | 
+ | 
                "dz", '-', | 
| 1149 | 
+ | 
                additional_error)) | 
| 1150 | 
+ | 
              goto failure; | 
| 1151 | 
+ | 
           | 
| 1152 | 
+ | 
          } | 
| 1153 | 
  | 
          /* maximum length (Defaults to 1/2 smallest length of first frame).  */ | 
| 1154 | 
  | 
          else if (strcmp (long_options[option_index].name, "length") == 0) | 
| 1155 | 
  | 
          { | 
| 1164 | 
  | 
              goto failure; | 
| 1165 | 
  | 
           | 
| 1166 | 
  | 
          } | 
| 1167 | 
+ | 
          /* maximum length (Defaults to 1/2 smallest length of first frame).  */ | 
| 1168 | 
+ | 
          else if (strcmp (long_options[option_index].name, "zlength") == 0) | 
| 1169 | 
+ | 
          { | 
| 1170 | 
+ | 
           | 
| 1171 | 
+ | 
           | 
| 1172 | 
+ | 
            if (update_arg( (void *)&(args_info->zlength_arg),  | 
| 1173 | 
+ | 
                 &(args_info->zlength_orig), &(args_info->zlength_given), | 
| 1174 | 
+ | 
                &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, | 
| 1175 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1176 | 
+ | 
                "zlength", '-', | 
| 1177 | 
+ | 
                additional_error)) | 
| 1178 | 
+ | 
              goto failure; | 
| 1179 | 
+ | 
           | 
| 1180 | 
+ | 
          } | 
| 1181 | 
  | 
          /* select the first stuntdouble set.  */ | 
| 1182 | 
  | 
          else if (strcmp (long_options[option_index].name, "sele1") == 0) | 
| 1183 | 
  | 
          { | 
| 1248 | 
  | 
              goto failure; | 
| 1249 | 
  | 
           | 
| 1250 | 
  | 
          } | 
| 1251 | 
+ | 
          /* global index offset for a second object (used to define a vector between sites in molecule).  */ | 
| 1252 | 
+ | 
          else if (strcmp (long_options[option_index].name, "seleoffset") == 0) | 
| 1253 | 
+ | 
          { | 
| 1254 | 
+ | 
           | 
| 1255 | 
+ | 
           | 
| 1256 | 
+ | 
            if (update_arg( (void *)&(args_info->seleoffset_arg),  | 
| 1257 | 
+ | 
                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given), | 
| 1258 | 
+ | 
                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT, | 
| 1259 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1260 | 
+ | 
                "seleoffset", '-', | 
| 1261 | 
+ | 
                additional_error)) | 
| 1262 | 
+ | 
              goto failure; | 
| 1263 | 
+ | 
           | 
| 1264 | 
+ | 
          } | 
| 1265 | 
+ | 
          /* global index offset for a third object (used to define a vector between sites in molecule).  */ | 
| 1266 | 
+ | 
          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0) | 
| 1267 | 
+ | 
          { | 
| 1268 | 
+ | 
           | 
| 1269 | 
+ | 
           | 
| 1270 | 
+ | 
            if (update_arg( (void *)&(args_info->seleoffset2_arg),  | 
| 1271 | 
+ | 
                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given), | 
| 1272 | 
+ | 
                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT, | 
| 1273 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1274 | 
+ | 
                "seleoffset2", '-', | 
| 1275 | 
+ | 
                additional_error)) | 
| 1276 | 
+ | 
              goto failure; | 
| 1277 | 
+ | 
           | 
| 1278 | 
+ | 
          } | 
| 1279 | 
  | 
          /* molecule name.  */ | 
| 1280 | 
  | 
          else if (strcmp (long_options[option_index].name, "molname") == 0) | 
| 1281 | 
  | 
          { | 
| 1383 | 
  | 
              goto failure; | 
| 1384 | 
  | 
           | 
| 1385 | 
  | 
          } | 
| 1386 | 
+ | 
          /* count of molecules matching selection criteria (and associated statistics).  */ | 
| 1387 | 
+ | 
          else if (strcmp (long_options[option_index].name, "count") == 0) | 
| 1388 | 
+ | 
          { | 
| 1389 | 
+ | 
           | 
| 1390 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1391 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1392 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1393 | 
+ | 
           | 
| 1394 | 
+ | 
            if (update_arg( 0 ,  | 
| 1395 | 
+ | 
                 0 , &(args_info->count_given), | 
| 1396 | 
+ | 
                &(local_args_info.count_given), optarg, 0, 0, ARG_NO, | 
| 1397 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1398 | 
+ | 
                "count", '-', | 
| 1399 | 
+ | 
                additional_error)) | 
| 1400 | 
+ | 
              goto failure; | 
| 1401 | 
+ | 
           | 
| 1402 | 
+ | 
          } | 
| 1403 | 
  | 
          /* g(z).  */ | 
| 1404 | 
  | 
          else if (strcmp (long_options[option_index].name, "gofz") == 0) | 
| 1405 | 
  | 
          { | 
| 1498 | 
  | 
                &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, | 
| 1499 | 
  | 
                check_ambiguity, override, 0, 0, | 
| 1500 | 
  | 
                "gxyz", '-', | 
| 1501 | 
+ | 
                additional_error)) | 
| 1502 | 
+ | 
              goto failure; | 
| 1503 | 
+ | 
           | 
| 1504 | 
+ | 
          } | 
| 1505 | 
+ | 
          /* 2D g(r) (Slab width --dz must be specified).  */ | 
| 1506 | 
+ | 
          else if (strcmp (long_options[option_index].name, "twodgofr") == 0) | 
| 1507 | 
+ | 
          { | 
| 1508 | 
+ | 
           | 
| 1509 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1510 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1511 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1512 | 
+ | 
           | 
| 1513 | 
+ | 
            if (update_arg( 0 ,  | 
| 1514 | 
+ | 
                 0 , &(args_info->twodgofr_given), | 
| 1515 | 
+ | 
                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, | 
| 1516 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1517 | 
+ | 
                "twodgofr", '-', | 
| 1518 | 
  | 
                additional_error)) | 
| 1519 | 
  | 
              goto failure; | 
| 1520 | 
  | 
           | 
| 1553 | 
  | 
              goto failure; | 
| 1554 | 
  | 
           | 
| 1555 | 
  | 
          } | 
| 1556 | 
< | 
          /* p(cos(theta)).  */ | 
| 1556 | 
> | 
          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */ | 
| 1557 | 
  | 
          else if (strcmp (long_options[option_index].name, "p_angle") == 0) | 
| 1558 | 
  | 
          { | 
| 1559 | 
  | 
           | 
| 1604 | 
  | 
              goto failure; | 
| 1605 | 
  | 
           | 
| 1606 | 
  | 
          } | 
| 1607 | 
+ | 
          /* angle of R.  */ | 
| 1608 | 
+ | 
          else if (strcmp (long_options[option_index].name, "angle_r") == 0) | 
| 1609 | 
+ | 
          { | 
| 1610 | 
+ | 
           | 
| 1611 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1612 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1613 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1614 | 
+ | 
           | 
| 1615 | 
+ | 
            if (update_arg( 0 ,  | 
| 1616 | 
+ | 
                 0 , &(args_info->angle_r_given), | 
| 1617 | 
+ | 
                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, | 
| 1618 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1619 | 
+ | 
                "angle_r", '-', | 
| 1620 | 
+ | 
                additional_error)) | 
| 1621 | 
+ | 
              goto failure; | 
| 1622 | 
+ | 
           | 
| 1623 | 
+ | 
          } | 
| 1624 | 
  | 
          /* hull volume of nanoparticle.  */ | 
| 1625 | 
  | 
          else if (strcmp (long_options[option_index].name, "hullvol") == 0) | 
| 1626 | 
  | 
          { | 
| 1638 | 
  | 
              goto failure; | 
| 1639 | 
  | 
           | 
| 1640 | 
  | 
          } | 
| 1641 | 
+ | 
          /* length of nanorod.  */ | 
| 1642 | 
+ | 
          else if (strcmp (long_options[option_index].name, "rodlength") == 0) | 
| 1643 | 
+ | 
          { | 
| 1644 | 
  | 
           | 
| 1645 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1646 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1647 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1648 | 
+ | 
           | 
| 1649 | 
+ | 
            if (update_arg( 0 ,  | 
| 1650 | 
+ | 
                 0 , &(args_info->rodlength_given), | 
| 1651 | 
+ | 
                &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, | 
| 1652 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1653 | 
+ | 
                "rodlength", '-', | 
| 1654 | 
+ | 
                additional_error)) | 
| 1655 | 
+ | 
              goto failure; | 
| 1656 | 
+ | 
           | 
| 1657 | 
+ | 
          } | 
| 1658 | 
+ | 
          /* spatially-resolved tetrahedrality order parameter Qk(z).  */ | 
| 1659 | 
+ | 
          else if (strcmp (long_options[option_index].name, "tet_param_z") == 0) | 
| 1660 | 
+ | 
          { | 
| 1661 | 
+ | 
           | 
| 1662 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1663 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1664 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1665 | 
+ | 
           | 
| 1666 | 
+ | 
            if (update_arg( 0 ,  | 
| 1667 | 
+ | 
                 0 , &(args_info->tet_param_z_given), | 
| 1668 | 
+ | 
                &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO, | 
| 1669 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1670 | 
+ | 
                "tet_param_z", '-', | 
| 1671 | 
+ | 
                additional_error)) | 
| 1672 | 
+ | 
              goto failure; | 
| 1673 | 
+ | 
           | 
| 1674 | 
+ | 
          } | 
| 1675 | 
+ | 
          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */ | 
| 1676 | 
+ | 
          else if (strcmp (long_options[option_index].name, "rnemdz") == 0) | 
| 1677 | 
+ | 
          { | 
| 1678 | 
+ | 
           | 
| 1679 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1680 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1681 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1682 | 
+ | 
           | 
| 1683 | 
+ | 
            if (update_arg( 0 ,  | 
| 1684 | 
+ | 
                 0 , &(args_info->rnemdz_given), | 
| 1685 | 
+ | 
                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO, | 
| 1686 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1687 | 
+ | 
                "rnemdz", '-', | 
| 1688 | 
+ | 
                additional_error)) | 
| 1689 | 
+ | 
              goto failure; | 
| 1690 | 
+ | 
           | 
| 1691 | 
+ | 
          } | 
| 1692 | 
+ | 
          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */ | 
| 1693 | 
+ | 
          else if (strcmp (long_options[option_index].name, "rnemdr") == 0) | 
| 1694 | 
+ | 
          { | 
| 1695 | 
+ | 
           | 
| 1696 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1697 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1698 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1699 | 
+ | 
           | 
| 1700 | 
+ | 
            if (update_arg( 0 ,  | 
| 1701 | 
+ | 
                 0 , &(args_info->rnemdr_given), | 
| 1702 | 
+ | 
                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO, | 
| 1703 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1704 | 
+ | 
                "rnemdr", '-', | 
| 1705 | 
+ | 
                additional_error)) | 
| 1706 | 
+ | 
              goto failure; | 
| 1707 | 
+ | 
           | 
| 1708 | 
+ | 
          } | 
| 1709 | 
+ | 
          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */ | 
| 1710 | 
+ | 
          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0) | 
| 1711 | 
+ | 
          { | 
| 1712 | 
+ | 
           | 
| 1713 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1714 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1715 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1716 | 
+ | 
           | 
| 1717 | 
+ | 
            if (update_arg( 0 ,  | 
| 1718 | 
+ | 
                 0 , &(args_info->rnemdrt_given), | 
| 1719 | 
+ | 
                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO, | 
| 1720 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1721 | 
+ | 
                "rnemdrt", '-', | 
| 1722 | 
+ | 
                additional_error)) | 
| 1723 | 
+ | 
              goto failure; | 
| 1724 | 
+ | 
           | 
| 1725 | 
+ | 
          } | 
| 1726 | 
+ | 
           | 
| 1727 | 
  | 
          break; | 
| 1728 | 
  | 
        case '?':       /* Invalid option.  */ | 
| 1729 | 
  | 
          /* `getopt_long' already printed an error message.  */ | 
| 1737 | 
  | 
 | 
| 1738 | 
  | 
  if (args_info->staticProps_group_counter > 1) | 
| 1739 | 
  | 
    { | 
| 1740 | 
< | 
      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 1740 | 
> | 
      fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 1741 | 
  | 
      error = 1; | 
| 1742 | 
  | 
    } | 
| 1743 | 
  | 
   |