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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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+ |
#include <getopt.h> |
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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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" --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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" --p_angle p(cos(theta))", |
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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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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->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->staticProps_group_counter = 0 ; |
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} |
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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->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] ; |
| 226 |
< |
args_info->length_help = gengetopt_args_info_help[10] ; |
| 227 |
< |
args_info->rcut_help = gengetopt_args_info_help[11] ; |
| 228 |
< |
args_info->zoffset_help = gengetopt_args_info_help[12] ; |
| 229 |
< |
args_info->sele1_help = gengetopt_args_info_help[13] ; |
| 230 |
< |
args_info->sele2_help = gengetopt_args_info_help[14] ; |
| 231 |
< |
args_info->sele3_help = gengetopt_args_info_help[15] ; |
| 232 |
< |
args_info->refsele_help = gengetopt_args_info_help[16] ; |
| 233 |
< |
args_info->comsele_help = gengetopt_args_info_help[17] ; |
| 234 |
< |
args_info->molname_help = gengetopt_args_info_help[18] ; |
| 235 |
< |
args_info->begin_help = gengetopt_args_info_help[19] ; |
| 236 |
< |
args_info->end_help = gengetopt_args_info_help[20] ; |
| 237 |
< |
args_info->radius_help = gengetopt_args_info_help[21] ; |
| 238 |
< |
args_info->bo_help = gengetopt_args_info_help[23] ; |
| 239 |
< |
args_info->bor_help = gengetopt_args_info_help[24] ; |
| 240 |
< |
args_info->bad_help = gengetopt_args_info_help[25] ; |
| 241 |
< |
args_info->gofr_help = gengetopt_args_info_help[26] ; |
| 242 |
< |
args_info->gofz_help = gengetopt_args_info_help[27] ; |
| 243 |
< |
args_info->r_theta_help = gengetopt_args_info_help[28] ; |
| 244 |
< |
args_info->r_omega_help = gengetopt_args_info_help[29] ; |
| 245 |
< |
args_info->r_z_help = gengetopt_args_info_help[30] ; |
| 246 |
< |
args_info->theta_omega_help = gengetopt_args_info_help[31] ; |
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< |
args_info->gxyz_help = gengetopt_args_info_help[32] ; |
| 248 |
< |
args_info->p2_help = gengetopt_args_info_help[33] ; |
| 249 |
< |
args_info->rp2_help = gengetopt_args_info_help[34] ; |
| 250 |
< |
args_info->scd_help = gengetopt_args_info_help[35] ; |
| 251 |
< |
args_info->density_help = gengetopt_args_info_help[36] ; |
| 252 |
< |
args_info->slab_density_help = gengetopt_args_info_help[37] ; |
| 253 |
< |
args_info->p_angle_help = gengetopt_args_info_help[38] ; |
| 254 |
< |
args_info->hxy_help = gengetopt_args_info_help[39] ; |
| 255 |
< |
args_info->rho_r_help = gengetopt_args_info_help[40] ; |
| 256 |
< |
args_info->hullvol_help = gengetopt_args_info_help[41] ; |
| 226 |
> |
args_info->rcut_help = gengetopt_args_info_help[10] ; |
| 227 |
> |
args_info->dz_help = gengetopt_args_info_help[11] ; |
| 228 |
> |
args_info->length_help = gengetopt_args_info_help[12] ; |
| 229 |
> |
args_info->zlength_help = gengetopt_args_info_help[13] ; |
| 230 |
> |
args_info->zoffset_help = gengetopt_args_info_help[14] ; |
| 231 |
> |
args_info->sele1_help = gengetopt_args_info_help[15] ; |
| 232 |
> |
args_info->sele2_help = gengetopt_args_info_help[16] ; |
| 233 |
> |
args_info->sele3_help = gengetopt_args_info_help[17] ; |
| 234 |
> |
args_info->refsele_help = gengetopt_args_info_help[18] ; |
| 235 |
> |
args_info->comsele_help = gengetopt_args_info_help[19] ; |
| 236 |
> |
args_info->seleoffset_help = gengetopt_args_info_help[20] ; |
| 237 |
> |
args_info->molname_help = gengetopt_args_info_help[21] ; |
| 238 |
> |
args_info->begin_help = gengetopt_args_info_help[22] ; |
| 239 |
> |
args_info->end_help = gengetopt_args_info_help[23] ; |
| 240 |
> |
args_info->radius_help = gengetopt_args_info_help[24] ; |
| 241 |
> |
args_info->bo_help = gengetopt_args_info_help[26] ; |
| 242 |
> |
args_info->bor_help = gengetopt_args_info_help[27] ; |
| 243 |
> |
args_info->bad_help = gengetopt_args_info_help[28] ; |
| 244 |
> |
args_info->count_help = gengetopt_args_info_help[29] ; |
| 245 |
> |
args_info->gofr_help = gengetopt_args_info_help[30] ; |
| 246 |
> |
args_info->gofz_help = gengetopt_args_info_help[31] ; |
| 247 |
> |
args_info->r_theta_help = gengetopt_args_info_help[32] ; |
| 248 |
> |
args_info->r_omega_help = gengetopt_args_info_help[33] ; |
| 249 |
> |
args_info->r_z_help = gengetopt_args_info_help[34] ; |
| 250 |
> |
args_info->theta_omega_help = gengetopt_args_info_help[35] ; |
| 251 |
> |
args_info->gxyz_help = gengetopt_args_info_help[36] ; |
| 252 |
> |
args_info->twodgofr_help = gengetopt_args_info_help[37] ; |
| 253 |
> |
args_info->p2_help = gengetopt_args_info_help[38] ; |
| 254 |
> |
args_info->rp2_help = gengetopt_args_info_help[39] ; |
| 255 |
> |
args_info->scd_help = gengetopt_args_info_help[40] ; |
| 256 |
> |
args_info->density_help = gengetopt_args_info_help[41] ; |
| 257 |
> |
args_info->slab_density_help = gengetopt_args_info_help[42] ; |
| 258 |
> |
args_info->p_angle_help = gengetopt_args_info_help[43] ; |
| 259 |
> |
args_info->hxy_help = gengetopt_args_info_help[44] ; |
| 260 |
> |
args_info->rho_r_help = gengetopt_args_info_help[45] ; |
| 261 |
> |
args_info->angle_r_help = gengetopt_args_info_help[46] ; |
| 262 |
> |
args_info->hullvol_help = gengetopt_args_info_help[47] ; |
| 263 |
> |
args_info->rodlength_help = gengetopt_args_info_help[48] ; |
| 264 |
> |
args_info->tet_param_help = gengetopt_args_info_help[49] ; |
| 265 |
> |
args_info->tet_param_z_help = gengetopt_args_info_help[50] ; |
| 266 |
|
|
| 267 |
|
} |
| 268 |
|
|
| 269 |
|
void |
| 270 |
|
cmdline_parser_print_version (void) |
| 271 |
|
{ |
| 272 |
< |
printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); |
| 272 |
> |
printf ("%s %s\n", |
| 273 |
> |
(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), |
| 274 |
> |
CMDLINE_PARSER_VERSION); |
| 275 |
|
} |
| 276 |
|
|
| 277 |
|
static void print_help_common(void) { |
| 286 |
|
printf("\n"); |
| 287 |
|
|
| 288 |
|
if (strlen(gengetopt_args_info_description) > 0) |
| 289 |
< |
printf("%s\n", gengetopt_args_info_description); |
| 289 |
> |
printf("%s\n\n", gengetopt_args_info_description); |
| 290 |
|
} |
| 291 |
|
|
| 292 |
|
void |
| 305 |
|
clear_args (args_info); |
| 306 |
|
init_args_info (args_info); |
| 307 |
|
|
| 308 |
< |
args_info->inputs = NULL; |
| 308 |
> |
args_info->inputs = 0; |
| 309 |
|
args_info->inputs_num = 0; |
| 310 |
|
} |
| 311 |
|
|
| 356 |
|
free_string_field (&(args_info->nbins_y_orig)); |
| 357 |
|
free_string_field (&(args_info->nbins_z_orig)); |
| 358 |
|
free_string_field (&(args_info->nanglebins_orig)); |
| 322 |
– |
free_string_field (&(args_info->length_orig)); |
| 359 |
|
free_string_field (&(args_info->rcut_orig)); |
| 360 |
+ |
free_string_field (&(args_info->dz_orig)); |
| 361 |
+ |
free_string_field (&(args_info->length_orig)); |
| 362 |
+ |
free_string_field (&(args_info->zlength_orig)); |
| 363 |
|
free_string_field (&(args_info->zoffset_orig)); |
| 364 |
|
free_string_field (&(args_info->sele1_arg)); |
| 365 |
|
free_string_field (&(args_info->sele1_orig)); |
| 371 |
|
free_string_field (&(args_info->refsele_orig)); |
| 372 |
|
free_string_field (&(args_info->comsele_arg)); |
| 373 |
|
free_string_field (&(args_info->comsele_orig)); |
| 374 |
+ |
free_string_field (&(args_info->seleoffset_orig)); |
| 375 |
|
free_string_field (&(args_info->molname_arg)); |
| 376 |
|
free_string_field (&(args_info->molname_orig)); |
| 377 |
|
free_string_field (&(args_info->begin_orig)); |
| 390 |
|
|
| 391 |
|
|
| 392 |
|
static void |
| 393 |
< |
write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) |
| 393 |
> |
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) |
| 394 |
|
{ |
| 395 |
+ |
FIX_UNUSED (values); |
| 396 |
|
if (arg) { |
| 397 |
|
fprintf(outfile, "%s=\"%s\"\n", opt, arg); |
| 398 |
|
} else { |
| 432 |
|
write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); |
| 433 |
|
if (args_info->nanglebins_given) |
| 434 |
|
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); |
| 435 |
|
if (args_info->rcut_given) |
| 436 |
|
write_into_file(outfile, "rcut", args_info->rcut_orig, 0); |
| 437 |
+ |
if (args_info->dz_given) |
| 438 |
+ |
write_into_file(outfile, "dz", args_info->dz_orig, 0); |
| 439 |
+ |
if (args_info->length_given) |
| 440 |
+ |
write_into_file(outfile, "length", args_info->length_orig, 0); |
| 441 |
+ |
if (args_info->zlength_given) |
| 442 |
+ |
write_into_file(outfile, "zlength", args_info->zlength_orig, 0); |
| 443 |
|
if (args_info->zoffset_given) |
| 444 |
|
write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); |
| 445 |
|
if (args_info->sele1_given) |
| 452 |
|
write_into_file(outfile, "refsele", args_info->refsele_orig, 0); |
| 453 |
|
if (args_info->comsele_given) |
| 454 |
|
write_into_file(outfile, "comsele", args_info->comsele_orig, 0); |
| 455 |
+ |
if (args_info->seleoffset_given) |
| 456 |
+ |
write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0); |
| 457 |
|
if (args_info->molname_given) |
| 458 |
|
write_into_file(outfile, "molname", args_info->molname_orig, 0); |
| 459 |
|
if (args_info->begin_given) |
| 468 |
|
write_into_file(outfile, "bor", 0, 0 ); |
| 469 |
|
if (args_info->bad_given) |
| 470 |
|
write_into_file(outfile, "bad", 0, 0 ); |
| 471 |
+ |
if (args_info->count_given) |
| 472 |
+ |
write_into_file(outfile, "count", 0, 0 ); |
| 473 |
|
if (args_info->gofr_given) |
| 474 |
|
write_into_file(outfile, "gofr", 0, 0 ); |
| 475 |
|
if (args_info->gofz_given) |
| 484 |
|
write_into_file(outfile, "theta_omega", 0, 0 ); |
| 485 |
|
if (args_info->gxyz_given) |
| 486 |
|
write_into_file(outfile, "gxyz", 0, 0 ); |
| 487 |
+ |
if (args_info->twodgofr_given) |
| 488 |
+ |
write_into_file(outfile, "twodgofr", 0, 0 ); |
| 489 |
|
if (args_info->p2_given) |
| 490 |
|
write_into_file(outfile, "p2", 0, 0 ); |
| 491 |
|
if (args_info->rp2_given) |
| 502 |
|
write_into_file(outfile, "hxy", 0, 0 ); |
| 503 |
|
if (args_info->rho_r_given) |
| 504 |
|
write_into_file(outfile, "rho_r", 0, 0 ); |
| 505 |
+ |
if (args_info->angle_r_given) |
| 506 |
+ |
write_into_file(outfile, "angle_r", 0, 0 ); |
| 507 |
|
if (args_info->hullvol_given) |
| 508 |
|
write_into_file(outfile, "hullvol", 0, 0 ); |
| 509 |
+ |
if (args_info->rodlength_given) |
| 510 |
+ |
write_into_file(outfile, "rodlength", 0, 0 ); |
| 511 |
+ |
if (args_info->tet_param_given) |
| 512 |
+ |
write_into_file(outfile, "tet_param", 0, 0 ); |
| 513 |
+ |
if (args_info->tet_param_z_given) |
| 514 |
+ |
write_into_file(outfile, "tet_param_z", 0, 0 ); |
| 515 |
|
|
| 516 |
|
|
| 517 |
|
i = EXIT_SUCCESS; |
| 548 |
|
char * |
| 549 |
|
gengetopt_strdup (const char *s) |
| 550 |
|
{ |
| 551 |
< |
char *result = NULL; |
| 551 |
> |
char *result = 0; |
| 552 |
|
if (!s) |
| 553 |
|
return result; |
| 554 |
|
|
| 568 |
|
args_info->bo_given = 0 ; |
| 569 |
|
args_info->bor_given = 0 ; |
| 570 |
|
args_info->bad_given = 0 ; |
| 571 |
+ |
args_info->count_given = 0 ; |
| 572 |
|
args_info->gofr_given = 0 ; |
| 573 |
|
args_info->gofz_given = 0 ; |
| 574 |
|
args_info->r_theta_given = 0 ; |
| 576 |
|
args_info->r_z_given = 0 ; |
| 577 |
|
args_info->theta_omega_given = 0 ; |
| 578 |
|
args_info->gxyz_given = 0 ; |
| 579 |
+ |
args_info->twodgofr_given = 0 ; |
| 580 |
|
args_info->p2_given = 0 ; |
| 581 |
|
args_info->rp2_given = 0 ; |
| 582 |
|
args_info->scd_given = 0 ; |
| 585 |
|
args_info->p_angle_given = 0 ; |
| 586 |
|
args_info->hxy_given = 0 ; |
| 587 |
|
args_info->rho_r_given = 0 ; |
| 588 |
+ |
args_info->angle_r_given = 0 ; |
| 589 |
|
args_info->hullvol_given = 0 ; |
| 590 |
+ |
args_info->rodlength_given = 0 ; |
| 591 |
+ |
args_info->tet_param_given = 0 ; |
| 592 |
+ |
args_info->tet_param_z_given = 0 ; |
| 593 |
|
|
| 594 |
|
args_info->staticProps_group_counter = 0; |
| 595 |
|
} |
| 596 |
|
|
| 597 |
|
int |
| 598 |
< |
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) |
| 598 |
> |
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) |
| 599 |
|
{ |
| 600 |
|
return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); |
| 601 |
|
} |
| 602 |
|
|
| 603 |
|
int |
| 604 |
< |
cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
| 604 |
> |
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, |
| 605 |
|
struct cmdline_parser_params *params) |
| 606 |
|
{ |
| 607 |
|
int result; |
| 608 |
< |
result = cmdline_parser_internal (argc, argv, args_info, params, NULL); |
| 608 |
> |
result = cmdline_parser_internal (argc, argv, args_info, params, 0); |
| 609 |
|
|
| 610 |
|
if (result == EXIT_FAILURE) |
| 611 |
|
{ |
| 617 |
|
} |
| 618 |
|
|
| 619 |
|
int |
| 620 |
< |
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
| 620 |
> |
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
| 621 |
|
{ |
| 622 |
|
int result; |
| 623 |
|
struct cmdline_parser_params params; |
| 628 |
|
params.check_ambiguity = 0; |
| 629 |
|
params.print_errors = 1; |
| 630 |
|
|
| 631 |
< |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); |
| 631 |
> |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); |
| 632 |
|
|
| 633 |
|
if (result == EXIT_FAILURE) |
| 634 |
|
{ |
| 644 |
|
{ |
| 645 |
|
int result = EXIT_SUCCESS; |
| 646 |
|
|
| 647 |
< |
if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) |
| 647 |
> |
if (cmdline_parser_required2(args_info, prog_name, 0) > 0) |
| 648 |
|
result = EXIT_FAILURE; |
| 649 |
|
|
| 650 |
|
if (result == EXIT_FAILURE) |
| 660 |
|
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) |
| 661 |
|
{ |
| 662 |
|
int error = 0; |
| 663 |
+ |
FIX_UNUSED (additional_error); |
| 664 |
|
|
| 665 |
|
/* checks for required options */ |
| 666 |
|
if (! args_info->input_given) |
| 671 |
|
|
| 672 |
|
if (args_info->staticProps_group_counter == 0) |
| 673 |
|
{ |
| 674 |
< |
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 : "")); |
| 674 |
> |
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 : "")); |
| 675 |
|
error = 1; |
| 676 |
|
} |
| 677 |
|
|
| 705 |
|
static |
| 706 |
|
int update_arg(void *field, char **orig_field, |
| 707 |
|
unsigned int *field_given, unsigned int *prev_given, |
| 708 |
< |
char *value, char *possible_values[], const char *default_value, |
| 708 |
> |
char *value, const char *possible_values[], |
| 709 |
> |
const char *default_value, |
| 710 |
|
cmdline_parser_arg_type arg_type, |
| 711 |
|
int check_ambiguity, int override, |
| 712 |
|
int no_free, int multiple_option, |
| 717 |
|
const char *val = value; |
| 718 |
|
int found; |
| 719 |
|
char **string_field; |
| 720 |
+ |
FIX_UNUSED (field); |
| 721 |
|
|
| 722 |
|
stop_char = 0; |
| 723 |
|
found = 0; |
| 735 |
|
return 1; /* failure */ |
| 736 |
|
} |
| 737 |
|
|
| 738 |
+ |
FIX_UNUSED (default_value); |
| 739 |
|
|
| 740 |
|
if (field_given && *field_given && ! override) |
| 741 |
|
return 0; |
| 799 |
|
|
| 800 |
|
|
| 801 |
|
int |
| 802 |
< |
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
| 802 |
> |
cmdline_parser_internal ( |
| 803 |
> |
int argc, char **argv, struct gengetopt_args_info *args_info, |
| 804 |
|
struct cmdline_parser_params *params, const char *additional_error) |
| 805 |
|
{ |
| 806 |
|
int c; /* Character of the parsed option. */ |
| 845 |
|
{ "nbins_y", 1, NULL, 'y' }, |
| 846 |
|
{ "nbins_z", 1, NULL, 0 }, |
| 847 |
|
{ "nanglebins", 1, NULL, 'a' }, |
| 778 |
– |
{ "length", 1, NULL, 0 }, |
| 848 |
|
{ "rcut", 1, NULL, 'c' }, |
| 849 |
+ |
{ "dz", 1, NULL, 0 }, |
| 850 |
+ |
{ "length", 1, NULL, 0 }, |
| 851 |
+ |
{ "zlength", 1, NULL, 0 }, |
| 852 |
|
{ "zoffset", 1, NULL, 'z' }, |
| 853 |
|
{ "sele1", 1, NULL, 0 }, |
| 854 |
|
{ "sele2", 1, NULL, 0 }, |
| 855 |
|
{ "sele3", 1, NULL, 0 }, |
| 856 |
|
{ "refsele", 1, NULL, 0 }, |
| 857 |
|
{ "comsele", 1, NULL, 0 }, |
| 858 |
+ |
{ "seleoffset", 1, NULL, 0 }, |
| 859 |
|
{ "molname", 1, NULL, 0 }, |
| 860 |
|
{ "begin", 1, NULL, 0 }, |
| 861 |
|
{ "end", 1, NULL, 0 }, |
| 863 |
|
{ "bo", 0, NULL, 0 }, |
| 864 |
|
{ "bor", 0, NULL, 0 }, |
| 865 |
|
{ "bad", 0, NULL, 0 }, |
| 866 |
+ |
{ "count", 0, NULL, 0 }, |
| 867 |
|
{ "gofr", 0, NULL, 'g' }, |
| 868 |
|
{ "gofz", 0, NULL, 0 }, |
| 869 |
|
{ "r_theta", 0, NULL, 0 }, |
| 871 |
|
{ "r_z", 0, NULL, 0 }, |
| 872 |
|
{ "theta_omega", 0, NULL, 0 }, |
| 873 |
|
{ "gxyz", 0, NULL, 0 }, |
| 874 |
+ |
{ "twodgofr", 0, NULL, 0 }, |
| 875 |
|
{ "p2", 0, NULL, 'p' }, |
| 876 |
|
{ "rp2", 0, NULL, 0 }, |
| 877 |
|
{ "scd", 0, NULL, 's' }, |
| 880 |
|
{ "p_angle", 0, NULL, 0 }, |
| 881 |
|
{ "hxy", 0, NULL, 0 }, |
| 882 |
|
{ "rho_r", 0, NULL, 0 }, |
| 883 |
+ |
{ "angle_r", 0, NULL, 0 }, |
| 884 |
|
{ "hullvol", 0, NULL, 0 }, |
| 885 |
< |
{ NULL, 0, NULL, 0 } |
| 885 |
> |
{ "rodlength", 0, NULL, 0 }, |
| 886 |
> |
{ "tet_param", 0, NULL, 'Q' }, |
| 887 |
> |
{ "tet_param_z", 0, NULL, 0 }, |
| 888 |
> |
{ 0, 0, 0, 0 } |
| 889 |
|
}; |
| 890 |
|
|
| 891 |
< |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); |
| 891 |
> |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); |
| 892 |
|
|
| 893 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
| 894 |
|
|
| 1027 |
|
goto failure; |
| 1028 |
|
|
| 1029 |
|
break; |
| 1030 |
< |
case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */ |
| 1030 |
> |
case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */ |
| 1031 |
|
|
| 1032 |
|
if (args_info->staticProps_group_counter && override) |
| 1033 |
|
reset_group_staticProps (args_info); |
| 1072 |
|
goto failure; |
| 1073 |
|
|
| 1074 |
|
break; |
| 1075 |
+ |
case 'Q': /* tetrahedrality order parameter (Qk). */ |
| 1076 |
+ |
|
| 1077 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1078 |
+ |
reset_group_staticProps (args_info); |
| 1079 |
+ |
args_info->staticProps_group_counter += 1; |
| 1080 |
+ |
|
| 1081 |
+ |
if (update_arg( 0 , |
| 1082 |
+ |
0 , &(args_info->tet_param_given), |
| 1083 |
+ |
&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, |
| 1084 |
+ |
check_ambiguity, override, 0, 0, |
| 1085 |
+ |
"tet_param", 'Q', |
| 1086 |
+ |
additional_error)) |
| 1087 |
+ |
goto failure; |
| 1088 |
+ |
|
| 1089 |
+ |
break; |
| 1090 |
|
|
| 1091 |
|
case 0: /* Long option with no short option */ |
| 1092 |
|
/* number of bins in z axis. */ |
| 1103 |
|
goto failure; |
| 1104 |
|
|
| 1105 |
|
} |
| 1106 |
+ |
/* slab width (dz). */ |
| 1107 |
+ |
else if (strcmp (long_options[option_index].name, "dz") == 0) |
| 1108 |
+ |
{ |
| 1109 |
+ |
|
| 1110 |
+ |
|
| 1111 |
+ |
if (update_arg( (void *)&(args_info->dz_arg), |
| 1112 |
+ |
&(args_info->dz_orig), &(args_info->dz_given), |
| 1113 |
+ |
&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, |
| 1114 |
+ |
check_ambiguity, override, 0, 0, |
| 1115 |
+ |
"dz", '-', |
| 1116 |
+ |
additional_error)) |
| 1117 |
+ |
goto failure; |
| 1118 |
+ |
|
| 1119 |
+ |
} |
| 1120 |
|
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1121 |
|
else if (strcmp (long_options[option_index].name, "length") == 0) |
| 1122 |
|
{ |
| 1131 |
|
goto failure; |
| 1132 |
|
|
| 1133 |
|
} |
| 1134 |
+ |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1135 |
+ |
else if (strcmp (long_options[option_index].name, "zlength") == 0) |
| 1136 |
+ |
{ |
| 1137 |
+ |
|
| 1138 |
+ |
|
| 1139 |
+ |
if (update_arg( (void *)&(args_info->zlength_arg), |
| 1140 |
+ |
&(args_info->zlength_orig), &(args_info->zlength_given), |
| 1141 |
+ |
&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, |
| 1142 |
+ |
check_ambiguity, override, 0, 0, |
| 1143 |
+ |
"zlength", '-', |
| 1144 |
+ |
additional_error)) |
| 1145 |
+ |
goto failure; |
| 1146 |
+ |
|
| 1147 |
+ |
} |
| 1148 |
|
/* select the first stuntdouble set. */ |
| 1149 |
|
else if (strcmp (long_options[option_index].name, "sele1") == 0) |
| 1150 |
|
{ |
| 1215 |
|
goto failure; |
| 1216 |
|
|
| 1217 |
|
} |
| 1218 |
+ |
/* global index offset for a second object (used to define a vector between sites in molecule). */ |
| 1219 |
+ |
else if (strcmp (long_options[option_index].name, "seleoffset") == 0) |
| 1220 |
+ |
{ |
| 1221 |
+ |
|
| 1222 |
+ |
|
| 1223 |
+ |
if (update_arg( (void *)&(args_info->seleoffset_arg), |
| 1224 |
+ |
&(args_info->seleoffset_orig), &(args_info->seleoffset_given), |
| 1225 |
+ |
&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT, |
| 1226 |
+ |
check_ambiguity, override, 0, 0, |
| 1227 |
+ |
"seleoffset", '-', |
| 1228 |
+ |
additional_error)) |
| 1229 |
+ |
goto failure; |
| 1230 |
+ |
|
| 1231 |
+ |
} |
| 1232 |
|
/* molecule name. */ |
| 1233 |
|
else if (strcmp (long_options[option_index].name, "molname") == 0) |
| 1234 |
|
{ |
| 1336 |
|
goto failure; |
| 1337 |
|
|
| 1338 |
|
} |
| 1339 |
+ |
/* count of molecules matching selection criteria (and associated statistics). */ |
| 1340 |
+ |
else if (strcmp (long_options[option_index].name, "count") == 0) |
| 1341 |
+ |
{ |
| 1342 |
+ |
|
| 1343 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1344 |
+ |
reset_group_staticProps (args_info); |
| 1345 |
+ |
args_info->staticProps_group_counter += 1; |
| 1346 |
+ |
|
| 1347 |
+ |
if (update_arg( 0 , |
| 1348 |
+ |
0 , &(args_info->count_given), |
| 1349 |
+ |
&(local_args_info.count_given), optarg, 0, 0, ARG_NO, |
| 1350 |
+ |
check_ambiguity, override, 0, 0, |
| 1351 |
+ |
"count", '-', |
| 1352 |
+ |
additional_error)) |
| 1353 |
+ |
goto failure; |
| 1354 |
+ |
|
| 1355 |
+ |
} |
| 1356 |
|
/* g(z). */ |
| 1357 |
|
else if (strcmp (long_options[option_index].name, "gofz") == 0) |
| 1358 |
|
{ |
| 1455 |
|
goto failure; |
| 1456 |
|
|
| 1457 |
|
} |
| 1458 |
+ |
/* 2D g(r) (Slab width --dz must be specified). */ |
| 1459 |
+ |
else if (strcmp (long_options[option_index].name, "twodgofr") == 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->twodgofr_given), |
| 1468 |
+ |
&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, |
| 1469 |
+ |
check_ambiguity, override, 0, 0, |
| 1470 |
+ |
"twodgofr", '-', |
| 1471 |
+ |
additional_error)) |
| 1472 |
+ |
goto failure; |
| 1473 |
+ |
|
| 1474 |
+ |
} |
| 1475 |
|
/* rp2 order parameter (--sele1 and --sele2 must be specified). */ |
| 1476 |
|
else if (strcmp (long_options[option_index].name, "rp2") == 0) |
| 1477 |
|
{ |
| 1557 |
|
goto failure; |
| 1558 |
|
|
| 1559 |
|
} |
| 1560 |
+ |
/* angle of R. */ |
| 1561 |
+ |
else if (strcmp (long_options[option_index].name, "angle_r") == 0) |
| 1562 |
+ |
{ |
| 1563 |
+ |
|
| 1564 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1565 |
+ |
reset_group_staticProps (args_info); |
| 1566 |
+ |
args_info->staticProps_group_counter += 1; |
| 1567 |
+ |
|
| 1568 |
+ |
if (update_arg( 0 , |
| 1569 |
+ |
0 , &(args_info->angle_r_given), |
| 1570 |
+ |
&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, |
| 1571 |
+ |
check_ambiguity, override, 0, 0, |
| 1572 |
+ |
"angle_r", '-', |
| 1573 |
+ |
additional_error)) |
| 1574 |
+ |
goto failure; |
| 1575 |
+ |
|
| 1576 |
+ |
} |
| 1577 |
|
/* hull volume of nanoparticle. */ |
| 1578 |
|
else if (strcmp (long_options[option_index].name, "hullvol") == 0) |
| 1579 |
|
{ |
| 1591 |
|
goto failure; |
| 1592 |
|
|
| 1593 |
|
} |
| 1594 |
+ |
/* length of nanorod. */ |
| 1595 |
+ |
else if (strcmp (long_options[option_index].name, "rodlength") == 0) |
| 1596 |
+ |
{ |
| 1597 |
|
|
| 1598 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1599 |
+ |
reset_group_staticProps (args_info); |
| 1600 |
+ |
args_info->staticProps_group_counter += 1; |
| 1601 |
+ |
|
| 1602 |
+ |
if (update_arg( 0 , |
| 1603 |
+ |
0 , &(args_info->rodlength_given), |
| 1604 |
+ |
&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, |
| 1605 |
+ |
check_ambiguity, override, 0, 0, |
| 1606 |
+ |
"rodlength", '-', |
| 1607 |
+ |
additional_error)) |
| 1608 |
+ |
goto failure; |
| 1609 |
+ |
|
| 1610 |
+ |
} |
| 1611 |
+ |
/* spatially-resolved tetrahedrality order parameter Qk(z). */ |
| 1612 |
+ |
else if (strcmp (long_options[option_index].name, "tet_param_z") == 0) |
| 1613 |
+ |
{ |
| 1614 |
+ |
|
| 1615 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1616 |
+ |
reset_group_staticProps (args_info); |
| 1617 |
+ |
args_info->staticProps_group_counter += 1; |
| 1618 |
+ |
|
| 1619 |
+ |
if (update_arg( 0 , |
| 1620 |
+ |
0 , &(args_info->tet_param_z_given), |
| 1621 |
+ |
&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO, |
| 1622 |
+ |
check_ambiguity, override, 0, 0, |
| 1623 |
+ |
"tet_param_z", '-', |
| 1624 |
+ |
additional_error)) |
| 1625 |
+ |
goto failure; |
| 1626 |
+ |
|
| 1627 |
+ |
} |
| 1628 |
+ |
|
| 1629 |
|
break; |
| 1630 |
|
case '?': /* Invalid option. */ |
| 1631 |
|
/* `getopt_long' already printed an error message. */ |
| 1639 |
|
|
| 1640 |
|
if (args_info->staticProps_group_counter > 1) |
| 1641 |
|
{ |
| 1642 |
< |
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 : "")); |
| 1642 |
> |
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 : "")); |
| 1643 |
|
error = 1; |
| 1644 |
|
} |
| 1645 |
|
|
