| 1 | 
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/* | 
| 2 | 
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  File autogenerated by gengetopt version 2.22 | 
| 3 | 
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  generated with the following command: | 
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< | 
  gengetopt -F StaticPropsCmd  | 
| 4 | 
> | 
  gengetopt -F StaticPropsCmd -u  | 
| 5 | 
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 | 
| 6 | 
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  The developers of gengetopt consider the fixed text that goes in all | 
| 7 | 
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  gengetopt output files to be in the public domain: | 
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 | 
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const char *gengetopt_args_info_purpose = ""; | 
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 | 
| 26 | 
< | 
const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]..."; | 
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> | 
const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]..."; | 
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 | 
| 28 | 
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const char *gengetopt_args_info_description = ""; | 
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 | 
| 36 | 
  | 
  "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')", | 
| 37 | 
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  "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')", | 
| 38 | 
  | 
  "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')", | 
| 39 | 
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  "      --nbins_z=INT             number of bins in z axis  (default=`100')", | 
| 39 | 
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  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')", | 
| 40 | 
  | 
  "  -c, --rcut=DOUBLE             cutoff radius (rcut)", | 
| 41 | 
+ | 
  "      --dz=DOUBLE               slab width (dz)", | 
| 42 | 
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  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
| 43 | 
  | 
  "      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
| 44 | 
  | 
  "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')", | 
| 55 | 
  | 
  "      --bo                      bond order parameter (--rcut must be specified)", | 
| 56 | 
  | 
  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)", | 
| 57 | 
  | 
  "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)", | 
| 58 | 
+ | 
  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)", | 
| 59 | 
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  "  -g, --gofr                    g(r)", | 
| 60 | 
  | 
  "      --gofz                    g(z)", | 
| 61 | 
  | 
  "      --r_theta                 g(r, cos(theta))", | 
| 62 | 
  | 
  "      --r_omega                 g(r, cos(omega))", | 
| 62 | 
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  "      --r_z                     g(r, z)", | 
| 63 | 
  | 
  "      --theta_omega             g(cos(theta), cos(omega))", | 
| 64 | 
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  "      --gxyz                    g(x, y, z)", | 
| 65 | 
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  "      --twodgofr                2D g(r) (Slab width --dz must be specified)", | 
| 66 | 
  | 
  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)", | 
| 67 | 
  | 
  "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)", | 
| 68 | 
  | 
  "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)", | 
| 71 | 
  | 
  "      --p_angle                 p(cos(theta))", | 
| 72 | 
  | 
  "      --hxy                     hxy", | 
| 73 | 
  | 
  "      --rho_r                   rho of R", | 
| 74 | 
+ | 
  "      --angle_r                 angle of R", | 
| 75 | 
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  "      --hullvol                 hull volume of nanoparticle", | 
| 76 | 
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    0 | 
| 77 | 
  | 
}; | 
| 108 | 
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  args_info->nbins_given = 0 ; | 
| 109 | 
  | 
  args_info->nbins_x_given = 0 ; | 
| 110 | 
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  args_info->nbins_y_given = 0 ; | 
| 109 | 
– | 
  args_info->nbins_z_given = 0 ; | 
| 111 | 
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  args_info->nanglebins_given = 0 ; | 
| 112 | 
  | 
  args_info->rcut_given = 0 ; | 
| 113 | 
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  args_info->dz_given = 0 ; | 
| 114 | 
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  args_info->length_given = 0 ; | 
| 115 | 
  | 
  args_info->zlength_given = 0 ; | 
| 116 | 
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  args_info->zoffset_given = 0 ; | 
| 126 | 
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  args_info->bo_given = 0 ; | 
| 127 | 
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  args_info->bor_given = 0 ; | 
| 128 | 
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  args_info->bad_given = 0 ; | 
| 129 | 
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  args_info->count_given = 0 ; | 
| 130 | 
  | 
  args_info->gofr_given = 0 ; | 
| 131 | 
  | 
  args_info->gofz_given = 0 ; | 
| 132 | 
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  args_info->r_theta_given = 0 ; | 
| 133 | 
  | 
  args_info->r_omega_given = 0 ; | 
| 131 | 
– | 
  args_info->r_z_given = 0 ; | 
| 134 | 
  | 
  args_info->theta_omega_given = 0 ; | 
| 135 | 
  | 
  args_info->gxyz_given = 0 ; | 
| 136 | 
+ | 
  args_info->twodgofr_given = 0 ; | 
| 137 | 
  | 
  args_info->p2_given = 0 ; | 
| 138 | 
  | 
  args_info->rp2_given = 0 ; | 
| 139 | 
  | 
  args_info->scd_given = 0 ; | 
| 142 | 
  | 
  args_info->p_angle_given = 0 ; | 
| 143 | 
  | 
  args_info->hxy_given = 0 ; | 
| 144 | 
  | 
  args_info->rho_r_given = 0 ; | 
| 145 | 
+ | 
  args_info->angle_r_given = 0 ; | 
| 146 | 
  | 
  args_info->hullvol_given = 0 ; | 
| 147 | 
  | 
  args_info->staticProps_group_counter = 0 ; | 
| 148 | 
  | 
} | 
| 162 | 
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  args_info->nbins_x_orig = NULL; | 
| 163 | 
  | 
  args_info->nbins_y_arg = 100; | 
| 164 | 
  | 
  args_info->nbins_y_orig = NULL; | 
| 161 | 
– | 
  args_info->nbins_z_arg = 100; | 
| 162 | 
– | 
  args_info->nbins_z_orig = NULL; | 
| 165 | 
  | 
  args_info->nanglebins_arg = 50; | 
| 166 | 
  | 
  args_info->nanglebins_orig = NULL; | 
| 167 | 
  | 
  args_info->rcut_orig = NULL; | 
| 168 | 
+ | 
  args_info->dz_orig = NULL; | 
| 169 | 
  | 
  args_info->length_orig = NULL; | 
| 170 | 
  | 
  args_info->zlength_orig = NULL; | 
| 171 | 
  | 
  args_info->zoffset_arg = 0; | 
| 204 | 
  | 
  args_info->nbins_z_help = gengetopt_args_info_help[8] ; | 
| 205 | 
  | 
  args_info->nanglebins_help = gengetopt_args_info_help[9] ; | 
| 206 | 
  | 
  args_info->rcut_help = gengetopt_args_info_help[10] ; | 
| 207 | 
< | 
  args_info->length_help = gengetopt_args_info_help[11] ; | 
| 208 | 
< | 
  args_info->zlength_help = gengetopt_args_info_help[12] ; | 
| 209 | 
< | 
  args_info->zoffset_help = gengetopt_args_info_help[13] ; | 
| 210 | 
< | 
  args_info->sele1_help = gengetopt_args_info_help[14] ; | 
| 211 | 
< | 
  args_info->sele2_help = gengetopt_args_info_help[15] ; | 
| 212 | 
< | 
  args_info->sele3_help = gengetopt_args_info_help[16] ; | 
| 213 | 
< | 
  args_info->refsele_help = gengetopt_args_info_help[17] ; | 
| 214 | 
< | 
  args_info->comsele_help = gengetopt_args_info_help[18] ; | 
| 215 | 
< | 
  args_info->molname_help = gengetopt_args_info_help[19] ; | 
| 216 | 
< | 
  args_info->begin_help = gengetopt_args_info_help[20] ; | 
| 217 | 
< | 
  args_info->end_help = gengetopt_args_info_help[21] ; | 
| 218 | 
< | 
  args_info->radius_help = gengetopt_args_info_help[22] ; | 
| 219 | 
< | 
  args_info->bo_help = gengetopt_args_info_help[24] ; | 
| 220 | 
< | 
  args_info->bor_help = gengetopt_args_info_help[25] ; | 
| 221 | 
< | 
  args_info->bad_help = gengetopt_args_info_help[26] ; | 
| 222 | 
< | 
  args_info->gofr_help = gengetopt_args_info_help[27] ; | 
| 223 | 
< | 
  args_info->gofz_help = gengetopt_args_info_help[28] ; | 
| 224 | 
< | 
  args_info->r_theta_help = gengetopt_args_info_help[29] ; | 
| 225 | 
< | 
  args_info->r_omega_help = gengetopt_args_info_help[30] ; | 
| 226 | 
< | 
  args_info->r_z_help = gengetopt_args_info_help[31] ; | 
| 227 | 
< | 
  args_info->theta_omega_help = gengetopt_args_info_help[32] ; | 
| 228 | 
< | 
  args_info->gxyz_help = gengetopt_args_info_help[33] ; | 
| 229 | 
< | 
  args_info->p2_help = gengetopt_args_info_help[34] ; | 
| 230 | 
< | 
  args_info->rp2_help = gengetopt_args_info_help[35] ; | 
| 231 | 
< | 
  args_info->scd_help = gengetopt_args_info_help[36] ; | 
| 232 | 
< | 
  args_info->density_help = gengetopt_args_info_help[37] ; | 
| 233 | 
< | 
  args_info->slab_density_help = gengetopt_args_info_help[38] ; | 
| 234 | 
< | 
  args_info->p_angle_help = gengetopt_args_info_help[39] ; | 
| 235 | 
< | 
  args_info->hxy_help = gengetopt_args_info_help[40] ; | 
| 236 | 
< | 
  args_info->rho_r_help = gengetopt_args_info_help[41] ; | 
| 237 | 
< | 
  args_info->hullvol_help = gengetopt_args_info_help[42] ; | 
| 207 | 
> | 
  args_info->dz_help = gengetopt_args_info_help[11] ; | 
| 208 | 
> | 
  args_info->length_help = gengetopt_args_info_help[12] ; | 
| 209 | 
> | 
  args_info->zlength_help = gengetopt_args_info_help[13] ; | 
| 210 | 
> | 
  args_info->zoffset_help = gengetopt_args_info_help[14] ; | 
| 211 | 
> | 
  args_info->sele1_help = gengetopt_args_info_help[15] ; | 
| 212 | 
> | 
  args_info->sele2_help = gengetopt_args_info_help[16] ; | 
| 213 | 
> | 
  args_info->sele3_help = gengetopt_args_info_help[17] ; | 
| 214 | 
> | 
  args_info->refsele_help = gengetopt_args_info_help[18] ; | 
| 215 | 
> | 
  args_info->comsele_help = gengetopt_args_info_help[19] ; | 
| 216 | 
> | 
  args_info->molname_help = gengetopt_args_info_help[20] ; | 
| 217 | 
> | 
  args_info->begin_help = gengetopt_args_info_help[21] ; | 
| 218 | 
> | 
  args_info->end_help = gengetopt_args_info_help[22] ; | 
| 219 | 
> | 
  args_info->radius_help = gengetopt_args_info_help[23] ; | 
| 220 | 
> | 
  args_info->bo_help = gengetopt_args_info_help[25] ; | 
| 221 | 
> | 
  args_info->bor_help = gengetopt_args_info_help[26] ; | 
| 222 | 
> | 
  args_info->bad_help = gengetopt_args_info_help[27] ; | 
| 223 | 
> | 
  args_info->count_help = gengetopt_args_info_help[28] ; | 
| 224 | 
> | 
  args_info->gofr_help = gengetopt_args_info_help[29] ; | 
| 225 | 
> | 
  args_info->gofz_help = gengetopt_args_info_help[30] ; | 
| 226 | 
> | 
  args_info->r_theta_help = gengetopt_args_info_help[31] ; | 
| 227 | 
> | 
  args_info->r_omega_help = gengetopt_args_info_help[32] ; | 
| 228 | 
> | 
  args_info->r_z_help = gengetopt_args_info_help[33] ; | 
| 229 | 
> | 
  args_info->theta_omega_help = gengetopt_args_info_help[34] ; | 
| 230 | 
> | 
  args_info->gxyz_help = gengetopt_args_info_help[35] ; | 
| 231 | 
> | 
  args_info->twodgofr_help = gengetopt_args_info_help[36] ; | 
| 232 | 
> | 
  args_info->p2_help = gengetopt_args_info_help[37] ; | 
| 233 | 
> | 
  args_info->rp2_help = gengetopt_args_info_help[38] ; | 
| 234 | 
> | 
  args_info->scd_help = gengetopt_args_info_help[39] ; | 
| 235 | 
> | 
  args_info->density_help = gengetopt_args_info_help[40] ; | 
| 236 | 
> | 
  args_info->slab_density_help = gengetopt_args_info_help[41] ; | 
| 237 | 
> | 
  args_info->p_angle_help = gengetopt_args_info_help[42] ; | 
| 238 | 
> | 
  args_info->hxy_help = gengetopt_args_info_help[43] ; | 
| 239 | 
> | 
  args_info->rho_r_help = gengetopt_args_info_help[44] ; | 
| 240 | 
> | 
  args_info->hullvol_help = gengetopt_args_info_help[45] ; | 
| 241 | 
  | 
   | 
| 242 | 
  | 
} | 
| 243 | 
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 | 
| 277 | 
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  clear_given (args_info); | 
| 278 | 
  | 
  clear_args (args_info); | 
| 279 | 
  | 
  init_args_info (args_info); | 
| 280 | 
+ | 
 | 
| 281 | 
+ | 
  args_info->inputs = NULL; | 
| 282 | 
+ | 
  args_info->inputs_num = 0; | 
| 283 | 
  | 
} | 
| 284 | 
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 | 
| 285 | 
  | 
void | 
| 318 | 
  | 
static void | 
| 319 | 
  | 
cmdline_parser_release (struct gengetopt_args_info *args_info) | 
| 320 | 
  | 
{ | 
| 321 | 
< | 
 | 
| 321 | 
> | 
  unsigned int i; | 
| 322 | 
  | 
  free_string_field (&(args_info->input_arg)); | 
| 323 | 
  | 
  free_string_field (&(args_info->input_orig)); | 
| 324 | 
  | 
  free_string_field (&(args_info->output_arg)); | 
| 327 | 
  | 
  free_string_field (&(args_info->nbins_orig)); | 
| 328 | 
  | 
  free_string_field (&(args_info->nbins_x_orig)); | 
| 329 | 
  | 
  free_string_field (&(args_info->nbins_y_orig)); | 
| 321 | 
– | 
  free_string_field (&(args_info->nbins_z_orig)); | 
| 330 | 
  | 
  free_string_field (&(args_info->nanglebins_orig)); | 
| 331 | 
  | 
  free_string_field (&(args_info->rcut_orig)); | 
| 332 | 
+ | 
  free_string_field (&(args_info->dz_orig)); | 
| 333 | 
  | 
  free_string_field (&(args_info->length_orig)); | 
| 334 | 
  | 
  free_string_field (&(args_info->zlength_orig)); | 
| 335 | 
  | 
  free_string_field (&(args_info->zoffset_orig)); | 
| 350 | 
  | 
  free_string_field (&(args_info->radius_orig)); | 
| 351 | 
  | 
   | 
| 352 | 
  | 
   | 
| 353 | 
+ | 
  for (i = 0; i < args_info->inputs_num; ++i) | 
| 354 | 
+ | 
    free (args_info->inputs [i]); | 
| 355 | 
  | 
 | 
| 356 | 
+ | 
  if (args_info->inputs_num) | 
| 357 | 
+ | 
    free (args_info->inputs); | 
| 358 | 
+ | 
 | 
| 359 | 
  | 
  clear_given (args_info); | 
| 360 | 
  | 
} | 
| 361 | 
  | 
 | 
| 398 | 
  | 
    write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0); | 
| 399 | 
  | 
  if (args_info->nbins_y_given) | 
| 400 | 
  | 
    write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0); | 
| 387 | 
– | 
  if (args_info->nbins_z_given) | 
| 388 | 
– | 
    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); | 
| 401 | 
  | 
  if (args_info->nanglebins_given) | 
| 402 | 
  | 
    write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); | 
| 403 | 
  | 
  if (args_info->rcut_given) | 
| 404 | 
  | 
    write_into_file(outfile, "rcut", args_info->rcut_orig, 0); | 
| 405 | 
+ | 
  if (args_info->dz_given) | 
| 406 | 
+ | 
    write_into_file(outfile, "dz", args_info->dz_orig, 0); | 
| 407 | 
  | 
  if (args_info->length_given) | 
| 408 | 
  | 
    write_into_file(outfile, "length", args_info->length_orig, 0); | 
| 409 | 
  | 
  if (args_info->zlength_given) | 
| 434 | 
  | 
    write_into_file(outfile, "bor", 0, 0 ); | 
| 435 | 
  | 
  if (args_info->bad_given) | 
| 436 | 
  | 
    write_into_file(outfile, "bad", 0, 0 ); | 
| 437 | 
+ | 
  if (args_info->count_given) | 
| 438 | 
+ | 
    write_into_file(outfile, "count", 0, 0 ); | 
| 439 | 
  | 
  if (args_info->gofr_given) | 
| 440 | 
  | 
    write_into_file(outfile, "gofr", 0, 0 ); | 
| 441 | 
  | 
  if (args_info->gofz_given) | 
| 444 | 
  | 
    write_into_file(outfile, "r_theta", 0, 0 ); | 
| 445 | 
  | 
  if (args_info->r_omega_given) | 
| 446 | 
  | 
    write_into_file(outfile, "r_omega", 0, 0 ); | 
| 431 | 
– | 
  if (args_info->r_z_given) | 
| 432 | 
– | 
    write_into_file(outfile, "r_z", 0, 0 ); | 
| 447 | 
  | 
  if (args_info->theta_omega_given) | 
| 448 | 
  | 
    write_into_file(outfile, "theta_omega", 0, 0 ); | 
| 449 | 
  | 
  if (args_info->gxyz_given) | 
| 450 | 
  | 
    write_into_file(outfile, "gxyz", 0, 0 ); | 
| 451 | 
+ | 
  if (args_info->twodgofr_given) | 
| 452 | 
+ | 
    write_into_file(outfile, "twodgofr", 0, 0 ); | 
| 453 | 
  | 
  if (args_info->p2_given) | 
| 454 | 
  | 
    write_into_file(outfile, "p2", 0, 0 ); | 
| 455 | 
  | 
  if (args_info->rp2_given) | 
| 466 | 
  | 
    write_into_file(outfile, "hxy", 0, 0 ); | 
| 467 | 
  | 
  if (args_info->rho_r_given) | 
| 468 | 
  | 
    write_into_file(outfile, "rho_r", 0, 0 ); | 
| 469 | 
+ | 
  if (args_info->angle_r_given) | 
| 470 | 
+ | 
    write_into_file(outfile, "angle_r", 0, 0 ); | 
| 471 | 
  | 
  if (args_info->hullvol_given) | 
| 472 | 
  | 
    write_into_file(outfile, "hullvol", 0, 0 ); | 
| 473 | 
  | 
   | 
| 526 | 
  | 
  args_info->bo_given = 0 ; | 
| 527 | 
  | 
  args_info->bor_given = 0 ; | 
| 528 | 
  | 
  args_info->bad_given = 0 ; | 
| 529 | 
+ | 
  args_info->count_given = 0 ; | 
| 530 | 
  | 
  args_info->gofr_given = 0 ; | 
| 531 | 
  | 
  args_info->gofz_given = 0 ; | 
| 532 | 
  | 
  args_info->r_theta_given = 0 ; | 
| 533 | 
  | 
  args_info->r_omega_given = 0 ; | 
| 515 | 
– | 
  args_info->r_z_given = 0 ; | 
| 534 | 
  | 
  args_info->theta_omega_given = 0 ; | 
| 535 | 
  | 
  args_info->gxyz_given = 0 ; | 
| 536 | 
+ | 
  args_info->twodgofr_given = 0 ; | 
| 537 | 
  | 
  args_info->p2_given = 0 ; | 
| 538 | 
  | 
  args_info->rp2_given = 0 ; | 
| 539 | 
  | 
  args_info->scd_given = 0 ; | 
| 542 | 
  | 
  args_info->p_angle_given = 0 ; | 
| 543 | 
  | 
  args_info->hxy_given = 0 ; | 
| 544 | 
  | 
  args_info->rho_r_given = 0 ; | 
| 545 | 
+ | 
  args_info->angle_r_given = 0 ; | 
| 546 | 
  | 
  args_info->hullvol_given = 0 ; | 
| 547 | 
  | 
 | 
| 548 | 
  | 
  args_info->staticProps_group_counter = 0; | 
| 792 | 
  | 
        { "nbins",      1, NULL, 'b' }, | 
| 793 | 
  | 
        { "nbins_x",    1, NULL, 'x' }, | 
| 794 | 
  | 
        { "nbins_y",    1, NULL, 'y' }, | 
| 775 | 
– | 
        { "nbins_z",    1, NULL, 0 }, | 
| 795 | 
  | 
        { "nanglebins", 1, NULL, 'a' }, | 
| 796 | 
  | 
        { "rcut",       1, NULL, 'c' }, | 
| 797 | 
+ | 
        { "dz", 1, NULL, 0 }, | 
| 798 | 
  | 
        { "length",     1, NULL, 0 }, | 
| 799 | 
  | 
        { "zlength",    1, NULL, 0 }, | 
| 800 | 
  | 
        { "zoffset",    1, NULL, 'z' }, | 
| 810 | 
  | 
        { "bo", 0, NULL, 0 }, | 
| 811 | 
  | 
        { "bor",        0, NULL, 0 }, | 
| 812 | 
  | 
        { "bad",        0, NULL, 0 }, | 
| 813 | 
+ | 
        { "count",      0, NULL, 0 }, | 
| 814 | 
  | 
        { "gofr",       0, NULL, 'g' }, | 
| 815 | 
  | 
        { "gofz",       0, NULL, 0 }, | 
| 816 | 
  | 
        { "r_theta",    0, NULL, 0 }, | 
| 817 | 
  | 
        { "r_omega",    0, NULL, 0 }, | 
| 797 | 
– | 
        { "r_z",        0, NULL, 0 }, | 
| 818 | 
  | 
        { "theta_omega",        0, NULL, 0 }, | 
| 819 | 
  | 
        { "gxyz",       0, NULL, 0 }, | 
| 820 | 
+ | 
        { "twodgofr",   0, NULL, 0 }, | 
| 821 | 
  | 
        { "p2", 0, NULL, 'p' }, | 
| 822 | 
  | 
        { "rp2",        0, NULL, 0 }, | 
| 823 | 
  | 
        { "scd",        0, NULL, 's' }, | 
| 826 | 
  | 
        { "p_angle",    0, NULL, 0 }, | 
| 827 | 
  | 
        { "hxy",        0, NULL, 0 }, | 
| 828 | 
  | 
        { "rho_r",      0, NULL, 0 }, | 
| 829 | 
+ | 
        { "angle_r",    0, NULL, 0 }, | 
| 830 | 
  | 
        { "hullvol",    0, NULL, 0 }, | 
| 831 | 
  | 
        { NULL, 0, NULL, 0 } | 
| 832 | 
  | 
      }; | 
| 905 | 
  | 
              "nbins_x", 'x', | 
| 906 | 
  | 
              additional_error)) | 
| 907 | 
  | 
            goto failure; | 
| 908 | 
< | 
         | 
| 908 | 
> | 
          | 
| 909 | 
  | 
          break; | 
| 910 | 
  | 
        case 'y':       /* number of bins in y axis.  */ | 
| 911 | 
  | 
         | 
| 1017 | 
  | 
          break; | 
| 1018 | 
  | 
 | 
| 1019 | 
  | 
        case 0: /* Long option with no short option */ | 
| 1020 | 
< | 
          /* number of bins in z axis.  */ | 
| 1021 | 
< | 
          if (strcmp (long_options[option_index].name, "nbins_z") == 0) | 
| 1020 | 
> | 
          /* number of bins in z axis.  */ | 
| 1021 | 
> | 
          if (strcmp (long_options[option_index].name, "nbins_z") == 0) | 
| 1022 | 
> | 
          {         | 
| 1023 | 
> | 
                   | 
| 1024 | 
> | 
            if (update_arg( (void *)&(args_info->nbins_z_arg),  | 
| 1025 | 
> | 
                &(args_info->nbins_z_orig), &(args_info->nbins_z_given), | 
| 1026 | 
> | 
                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, | 
| 1027 | 
> | 
                check_ambiguity, override, 0, 0, | 
| 1028 | 
> | 
                "nbins_z", '-', | 
| 1029 | 
> | 
                 additional_error)) | 
| 1030 | 
> | 
               goto failure; | 
| 1031 | 
> | 
                   | 
| 1032 | 
> | 
          } | 
| 1033 | 
> | 
 | 
| 1034 | 
> | 
 | 
| 1035 | 
> | 
          /* slab width (dz).  */ | 
| 1036 | 
> | 
          else if (strcmp (long_options[option_index].name, "dz") == 0) | 
| 1037 | 
  | 
          { | 
| 1038 | 
  | 
           | 
| 1039 | 
  | 
           | 
| 1040 | 
< | 
            if (update_arg( (void *)&(args_info->nbins_z_arg),  | 
| 1041 | 
< | 
                 &(args_info->nbins_z_orig), &(args_info->nbins_z_given), | 
| 1042 | 
< | 
                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, | 
| 1040 | 
> | 
            if (update_arg( (void *)&(args_info->dz_arg),  | 
| 1041 | 
> | 
                 &(args_info->dz_orig), &(args_info->dz_given), | 
| 1042 | 
> | 
                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, | 
| 1043 | 
  | 
                check_ambiguity, override, 0, 0, | 
| 1044 | 
< | 
                "nbins_z", '-', | 
| 1044 | 
> | 
                "dz", '-', | 
| 1045 | 
  | 
                additional_error)) | 
| 1046 | 
  | 
              goto failure; | 
| 1047 | 
  | 
           | 
| 1048 | 
  | 
          } | 
| 1049 | 
  | 
          /* maximum length (Defaults to 1/2 smallest length of first frame).  */ | 
| 1050 | 
< | 
          else if (strcmp (long_options[option_index].name, "length") == 0) | 
| 1050 | 
> | 
          if (strcmp (long_options[option_index].name, "length") == 0) | 
| 1051 | 
  | 
          { | 
| 1052 | 
  | 
           | 
| 1053 | 
  | 
           | 
| 1251 | 
  | 
              goto failure; | 
| 1252 | 
  | 
           | 
| 1253 | 
  | 
          } | 
| 1254 | 
+ | 
          /* count of molecules matching selection criteria (and associated statistics).  */ | 
| 1255 | 
+ | 
          else if (strcmp (long_options[option_index].name, "count") == 0) | 
| 1256 | 
+ | 
          { | 
| 1257 | 
+ | 
           | 
| 1258 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1259 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1260 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1261 | 
+ | 
           | 
| 1262 | 
+ | 
            if (update_arg( 0 ,  | 
| 1263 | 
+ | 
                 0 , &(args_info->count_given), | 
| 1264 | 
+ | 
                &(local_args_info.count_given), optarg, 0, 0, ARG_NO, | 
| 1265 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1266 | 
+ | 
                "count", '-', | 
| 1267 | 
+ | 
                additional_error)) | 
| 1268 | 
+ | 
              goto failure; | 
| 1269 | 
+ | 
           | 
| 1270 | 
+ | 
          } | 
| 1271 | 
  | 
          /* g(z).  */ | 
| 1272 | 
  | 
          else if (strcmp (long_options[option_index].name, "gofz") == 0) | 
| 1273 | 
  | 
          { | 
| 1319 | 
  | 
              goto failure; | 
| 1320 | 
  | 
           | 
| 1321 | 
  | 
          } | 
| 1268 | 
– | 
          /* g(r, z).  */ | 
| 1269 | 
– | 
          else if (strcmp (long_options[option_index].name, "r_z") == 0) | 
| 1270 | 
– | 
          { | 
| 1271 | 
– | 
           | 
| 1272 | 
– | 
            if (args_info->staticProps_group_counter && override) | 
| 1273 | 
– | 
              reset_group_staticProps (args_info); | 
| 1274 | 
– | 
            args_info->staticProps_group_counter += 1; | 
| 1275 | 
– | 
           | 
| 1276 | 
– | 
            if (update_arg( 0 ,  | 
| 1277 | 
– | 
                 0 , &(args_info->r_z_given), | 
| 1278 | 
– | 
                &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO, | 
| 1279 | 
– | 
                check_ambiguity, override, 0, 0, | 
| 1280 | 
– | 
                "r_z", '-', | 
| 1281 | 
– | 
                additional_error)) | 
| 1282 | 
– | 
              goto failure; | 
| 1283 | 
– | 
           | 
| 1284 | 
– | 
          } | 
| 1322 | 
  | 
          /* g(cos(theta), cos(omega)).  */ | 
| 1323 | 
  | 
          else if (strcmp (long_options[option_index].name, "theta_omega") == 0) | 
| 1324 | 
  | 
          { | 
| 1353 | 
  | 
              goto failure; | 
| 1354 | 
  | 
           | 
| 1355 | 
  | 
          } | 
| 1356 | 
+ | 
          /* 2D g(r) (Slab width --dz must be specified).  */ | 
| 1357 | 
+ | 
          else if (strcmp (long_options[option_index].name, "twodgofr") == 0) | 
| 1358 | 
+ | 
          { | 
| 1359 | 
+ | 
           | 
| 1360 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1361 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1362 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1363 | 
+ | 
           | 
| 1364 | 
+ | 
            if (update_arg( 0 ,  | 
| 1365 | 
+ | 
                 0 , &(args_info->twodgofr_given), | 
| 1366 | 
+ | 
                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, | 
| 1367 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1368 | 
+ | 
                "twodgofr", '-', | 
| 1369 | 
+ | 
                additional_error)) | 
| 1370 | 
+ | 
              goto failure; | 
| 1371 | 
+ | 
           | 
| 1372 | 
+ | 
          } | 
| 1373 | 
  | 
          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 1374 | 
  | 
          else if (strcmp (long_options[option_index].name, "rp2") == 0) | 
| 1375 | 
  | 
          { | 
| 1455 | 
  | 
              goto failure; | 
| 1456 | 
  | 
           | 
| 1457 | 
  | 
          } | 
| 1458 | 
+ | 
          /* angle of R.  */ | 
| 1459 | 
+ | 
          else if (strcmp (long_options[option_index].name, "angle_r") == 0) | 
| 1460 | 
+ | 
          { | 
| 1461 | 
+ | 
           | 
| 1462 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1463 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1464 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1465 | 
+ | 
           | 
| 1466 | 
+ | 
            if (update_arg( 0 ,  | 
| 1467 | 
+ | 
                 0 , &(args_info->angle_r_given), | 
| 1468 | 
+ | 
                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, | 
| 1469 | 
+ | 
                check_ambiguity, override, 0, 0, | 
| 1470 | 
+ | 
                "angle_r", '-', | 
| 1471 | 
+ | 
                additional_error)) | 
| 1472 | 
+ | 
              goto failure; | 
| 1473 | 
+ | 
           | 
| 1474 | 
+ | 
          } | 
| 1475 | 
  | 
          /* hull volume of nanoparticle.  */ | 
| 1476 | 
  | 
          else if (strcmp (long_options[option_index].name, "hullvol") == 0) | 
| 1477 | 
  | 
          { | 
| 1519 | 
  | 
  if ( error ) | 
| 1520 | 
  | 
    return (EXIT_FAILURE); | 
| 1521 | 
  | 
 | 
| 1522 | 
+ | 
  if (optind < argc) | 
| 1523 | 
+ | 
    { | 
| 1524 | 
+ | 
      int i = 0 ; | 
| 1525 | 
+ | 
      int found_prog_name = 0; | 
| 1526 | 
+ | 
      /* whether program name, i.e., argv[0], is in the remaining args | 
| 1527 | 
+ | 
         (this may happen with some implementations of getopt, | 
| 1528 | 
+ | 
          but surely not with the one included by gengetopt) */ | 
| 1529 | 
+ | 
 | 
| 1530 | 
+ | 
      i = optind; | 
| 1531 | 
+ | 
      while (i < argc) | 
| 1532 | 
+ | 
        if (argv[i++] == argv[0]) { | 
| 1533 | 
+ | 
          found_prog_name = 1; | 
| 1534 | 
+ | 
          break; | 
| 1535 | 
+ | 
        } | 
| 1536 | 
+ | 
      i = 0; | 
| 1537 | 
+ | 
 | 
| 1538 | 
+ | 
      args_info->inputs_num = argc - optind - found_prog_name; | 
| 1539 | 
+ | 
      args_info->inputs = | 
| 1540 | 
+ | 
        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; | 
| 1541 | 
+ | 
      while (optind < argc) | 
| 1542 | 
+ | 
        if (argv[optind++] != argv[0]) | 
| 1543 | 
+ | 
          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; | 
| 1544 | 
+ | 
    } | 
| 1545 | 
+ | 
 | 
| 1546 | 
  | 
  return 0; | 
| 1547 | 
  | 
 | 
| 1548 | 
  | 
failure: |