| 36 |
|
" -b, --nbins=INT number of bins (general purpose) \n (default=`100')", |
| 37 |
|
" -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 |
– |
" --nbins_z=INT number of bins in z axis (default=`100')", |
| 39 |
|
" -a, --nanglebins=INT number of bins for cos(angle) (default=`50')", |
| 41 |
– |
" --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", |
| 40 |
|
" -c, --rcut=DOUBLE cutoff radius (rcut)", |
| 41 |
+ |
" --dz=DOUBLE slab width (dz)", |
| 42 |
+ |
" --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')", |
| 45 |
|
" --sele1=selection script select the first stuntdouble set", |
| 46 |
|
" --sele2=selection script select the second stuntdouble set", |
| 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 |
|
" -g, --gofr g(r)", |
| 60 |
|
" --gofz g(z)", |
| 61 |
|
" --r_theta g(r, cos(theta))", |
| 62 |
|
" --r_omega g(r, cos(omega))", |
| 61 |
– |
" --r_z g(r, z)", |
| 63 |
|
" --theta_omega g(cos(theta), cos(omega))", |
| 64 |
|
" --gxyz g(x, y, z)", |
| 65 |
+ |
" --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 |
|
" --hullvol hull volume of nanoparticle", |
| 76 |
|
0 |
| 77 |
|
}; |
| 108 |
|
args_info->nbins_given = 0 ; |
| 109 |
|
args_info->nbins_x_given = 0 ; |
| 110 |
|
args_info->nbins_y_given = 0 ; |
| 108 |
– |
args_info->nbins_z_given = 0 ; |
| 111 |
|
args_info->nanglebins_given = 0 ; |
| 110 |
– |
args_info->length_given = 0 ; |
| 112 |
|
args_info->rcut_given = 0 ; |
| 113 |
+ |
args_info->dz_given = 0 ; |
| 114 |
+ |
args_info->length_given = 0 ; |
| 115 |
+ |
args_info->zlength_given = 0 ; |
| 116 |
|
args_info->zoffset_given = 0 ; |
| 117 |
|
args_info->sele1_given = 0 ; |
| 118 |
|
args_info->sele2_given = 0 ; |
| 126 |
|
args_info->bo_given = 0 ; |
| 127 |
|
args_info->bor_given = 0 ; |
| 128 |
|
args_info->bad_given = 0 ; |
| 129 |
+ |
args_info->count_given = 0 ; |
| 130 |
|
args_info->gofr_given = 0 ; |
| 131 |
|
args_info->gofz_given = 0 ; |
| 132 |
|
args_info->r_theta_given = 0 ; |
| 133 |
|
args_info->r_omega_given = 0 ; |
| 129 |
– |
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 |
|
args_info->nbins_x_orig = NULL; |
| 163 |
|
args_info->nbins_y_arg = 100; |
| 164 |
|
args_info->nbins_y_orig = NULL; |
| 159 |
– |
args_info->nbins_z_arg = 100; |
| 160 |
– |
args_info->nbins_z_orig = NULL; |
| 165 |
|
args_info->nanglebins_arg = 50; |
| 166 |
|
args_info->nanglebins_orig = NULL; |
| 163 |
– |
args_info->length_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; |
| 172 |
|
args_info->zoffset_orig = NULL; |
| 173 |
|
args_info->sele1_arg = NULL; |
| 203 |
|
args_info->nbins_y_help = gengetopt_args_info_help[7] ; |
| 204 |
|
args_info->nbins_z_help = gengetopt_args_info_help[8] ; |
| 205 |
|
args_info->nanglebins_help = gengetopt_args_info_help[9] ; |
| 206 |
< |
args_info->length_help = gengetopt_args_info_help[10] ; |
| 207 |
< |
args_info->rcut_help = gengetopt_args_info_help[11] ; |
| 208 |
< |
args_info->zoffset_help = gengetopt_args_info_help[12] ; |
| 209 |
< |
args_info->sele1_help = gengetopt_args_info_help[13] ; |
| 210 |
< |
args_info->sele2_help = gengetopt_args_info_help[14] ; |
| 211 |
< |
args_info->sele3_help = gengetopt_args_info_help[15] ; |
| 212 |
< |
args_info->refsele_help = gengetopt_args_info_help[16] ; |
| 213 |
< |
args_info->comsele_help = gengetopt_args_info_help[17] ; |
| 214 |
< |
args_info->molname_help = gengetopt_args_info_help[18] ; |
| 215 |
< |
args_info->begin_help = gengetopt_args_info_help[19] ; |
| 216 |
< |
args_info->end_help = gengetopt_args_info_help[20] ; |
| 217 |
< |
args_info->radius_help = gengetopt_args_info_help[21] ; |
| 218 |
< |
args_info->bo_help = gengetopt_args_info_help[23] ; |
| 219 |
< |
args_info->bor_help = gengetopt_args_info_help[24] ; |
| 220 |
< |
args_info->bad_help = gengetopt_args_info_help[25] ; |
| 221 |
< |
args_info->gofr_help = gengetopt_args_info_help[26] ; |
| 222 |
< |
args_info->gofz_help = gengetopt_args_info_help[27] ; |
| 223 |
< |
args_info->r_theta_help = gengetopt_args_info_help[28] ; |
| 224 |
< |
args_info->r_omega_help = gengetopt_args_info_help[29] ; |
| 225 |
< |
args_info->r_z_help = gengetopt_args_info_help[30] ; |
| 226 |
< |
args_info->theta_omega_help = gengetopt_args_info_help[31] ; |
| 227 |
< |
args_info->gxyz_help = gengetopt_args_info_help[32] ; |
| 228 |
< |
args_info->p2_help = gengetopt_args_info_help[33] ; |
| 229 |
< |
args_info->rp2_help = gengetopt_args_info_help[34] ; |
| 230 |
< |
args_info->scd_help = gengetopt_args_info_help[35] ; |
| 231 |
< |
args_info->density_help = gengetopt_args_info_help[36] ; |
| 232 |
< |
args_info->slab_density_help = gengetopt_args_info_help[37] ; |
| 233 |
< |
args_info->p_angle_help = gengetopt_args_info_help[38] ; |
| 234 |
< |
args_info->hxy_help = gengetopt_args_info_help[39] ; |
| 235 |
< |
args_info->rho_r_help = gengetopt_args_info_help[40] ; |
| 236 |
< |
args_info->hullvol_help = gengetopt_args_info_help[41] ; |
| 206 |
> |
args_info->rcut_help = gengetopt_args_info_help[10] ; |
| 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 |
|
|
| 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)); |
| 320 |
– |
free_string_field (&(args_info->nbins_z_orig)); |
| 330 |
|
free_string_field (&(args_info->nanglebins_orig)); |
| 322 |
– |
free_string_field (&(args_info->length_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)); |
| 336 |
|
free_string_field (&(args_info->sele1_arg)); |
| 337 |
|
free_string_field (&(args_info->sele1_orig)); |
| 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); |
| 390 |
– |
if (args_info->nbins_z_given) |
| 391 |
– |
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); |
| 394 |
– |
if (args_info->length_given) |
| 395 |
– |
write_into_file(outfile, "length", args_info->length_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) |
| 410 |
+ |
write_into_file(outfile, "zlength", args_info->zlength_orig, 0); |
| 411 |
|
if (args_info->zoffset_given) |
| 412 |
|
write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); |
| 413 |
|
if (args_info->sele1_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 ); |
| 432 |
– |
if (args_info->r_z_given) |
| 433 |
– |
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 ; |
| 516 |
– |
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' }, |
| 776 |
– |
{ "nbins_z", 1, NULL, 0 }, |
| 795 |
|
{ "nanglebins", 1, NULL, 'a' }, |
| 778 |
– |
{ "length", 1, NULL, 0 }, |
| 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' }, |
| 801 |
|
{ "sele1", 1, NULL, 0 }, |
| 802 |
|
{ "sele2", 1, NULL, 0 }, |
| 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 |
|
|
| 1060 |
|
goto failure; |
| 1061 |
|
|
| 1062 |
|
} |
| 1063 |
+ |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1064 |
+ |
else if (strcmp (long_options[option_index].name, "zlength") == 0) |
| 1065 |
+ |
{ |
| 1066 |
+ |
|
| 1067 |
+ |
|
| 1068 |
+ |
if (update_arg( (void *)&(args_info->zlength_arg), |
| 1069 |
+ |
&(args_info->zlength_orig), &(args_info->zlength_given), |
| 1070 |
+ |
&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, |
| 1071 |
+ |
check_ambiguity, override, 0, 0, |
| 1072 |
+ |
"zlength", '-', |
| 1073 |
+ |
additional_error)) |
| 1074 |
+ |
goto failure; |
| 1075 |
+ |
|
| 1076 |
+ |
} |
| 1077 |
|
/* select the first stuntdouble set. */ |
| 1078 |
|
else if (strcmp (long_options[option_index].name, "sele1") == 0) |
| 1079 |
|
{ |
| 1247 |
|
&(local_args_info.bad_given), optarg, 0, 0, ARG_NO, |
| 1248 |
|
check_ambiguity, override, 0, 0, |
| 1249 |
|
"bad", '-', |
| 1250 |
+ |
additional_error)) |
| 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 |
|
|
| 1319 |
|
goto failure; |
| 1320 |
|
|
| 1321 |
|
} |
| 1322 |
< |
/* g(r, z). */ |
| 1323 |
< |
else if (strcmp (long_options[option_index].name, "r_z") == 0) |
| 1322 |
> |
/* g(cos(theta), cos(omega)). */ |
| 1323 |
> |
else if (strcmp (long_options[option_index].name, "theta_omega") == 0) |
| 1324 |
|
{ |
| 1325 |
|
|
| 1326 |
|
if (args_info->staticProps_group_counter && override) |
| 1328 |
|
args_info->staticProps_group_counter += 1; |
| 1329 |
|
|
| 1330 |
|
if (update_arg( 0 , |
| 1331 |
< |
0 , &(args_info->r_z_given), |
| 1332 |
< |
&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO, |
| 1331 |
> |
0 , &(args_info->theta_omega_given), |
| 1332 |
> |
&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, |
| 1333 |
|
check_ambiguity, override, 0, 0, |
| 1334 |
< |
"r_z", '-', |
| 1334 |
> |
"theta_omega", '-', |
| 1335 |
|
additional_error)) |
| 1336 |
|
goto failure; |
| 1337 |
|
|
| 1338 |
|
} |
| 1339 |
< |
/* g(cos(theta), cos(omega)). */ |
| 1340 |
< |
else if (strcmp (long_options[option_index].name, "theta_omega") == 0) |
| 1339 |
> |
/* g(x, y, z). */ |
| 1340 |
> |
else if (strcmp (long_options[option_index].name, "gxyz") == 0) |
| 1341 |
|
{ |
| 1342 |
|
|
| 1343 |
|
if (args_info->staticProps_group_counter && override) |
| 1345 |
|
args_info->staticProps_group_counter += 1; |
| 1346 |
|
|
| 1347 |
|
if (update_arg( 0 , |
| 1348 |
< |
0 , &(args_info->theta_omega_given), |
| 1349 |
< |
&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, |
| 1348 |
> |
0 , &(args_info->gxyz_given), |
| 1349 |
> |
&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, |
| 1350 |
|
check_ambiguity, override, 0, 0, |
| 1351 |
< |
"theta_omega", '-', |
| 1351 |
> |
"gxyz", '-', |
| 1352 |
|
additional_error)) |
| 1353 |
|
goto failure; |
| 1354 |
|
|
| 1355 |
|
} |
| 1356 |
< |
/* g(x, y, z). */ |
| 1357 |
< |
else if (strcmp (long_options[option_index].name, "gxyz") == 0) |
| 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) |
| 1362 |
|
args_info->staticProps_group_counter += 1; |
| 1363 |
|
|
| 1364 |
|
if (update_arg( 0 , |
| 1365 |
< |
0 , &(args_info->gxyz_given), |
| 1366 |
< |
&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, |
| 1365 |
> |
0 , &(args_info->twodgofr_given), |
| 1366 |
> |
&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, |
| 1367 |
|
check_ambiguity, override, 0, 0, |
| 1368 |
< |
"gxyz", '-', |
| 1368 |
> |
"twodgofr", '-', |
| 1369 |
|
additional_error)) |
| 1370 |
|
goto failure; |
| 1371 |
|
|
| 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 |
|
{ |
