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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 |
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> |
gengetopt -F StaticPropsCmd -u |
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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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|
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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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|
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const char *gengetopt_args_info_description = ""; |
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|
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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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" -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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" --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", |
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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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|
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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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|
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static int |
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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->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->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->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->nanglebins_arg = 50; |
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args_info->nanglebins_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->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->rcut_help = gengetopt_args_info_help[10] ; |
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< |
args_info->length_help = gengetopt_args_info_help[11] ; |
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< |
args_info->zlength_help = gengetopt_args_info_help[12] ; |
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< |
args_info->zoffset_help = gengetopt_args_info_help[13] ; |
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< |
args_info->sele1_help = gengetopt_args_info_help[14] ; |
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< |
args_info->sele2_help = gengetopt_args_info_help[15] ; |
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< |
args_info->sele3_help = gengetopt_args_info_help[16] ; |
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< |
args_info->refsele_help = gengetopt_args_info_help[17] ; |
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< |
args_info->comsele_help = gengetopt_args_info_help[18] ; |
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< |
args_info->molname_help = gengetopt_args_info_help[19] ; |
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< |
args_info->begin_help = gengetopt_args_info_help[20] ; |
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< |
args_info->end_help = gengetopt_args_info_help[21] ; |
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< |
args_info->radius_help = gengetopt_args_info_help[22] ; |
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< |
args_info->bo_help = gengetopt_args_info_help[24] ; |
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< |
args_info->bor_help = gengetopt_args_info_help[25] ; |
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< |
args_info->bad_help = gengetopt_args_info_help[26] ; |
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< |
args_info->gofr_help = gengetopt_args_info_help[27] ; |
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< |
args_info->gofz_help = gengetopt_args_info_help[28] ; |
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< |
args_info->r_theta_help = gengetopt_args_info_help[29] ; |
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< |
args_info->r_omega_help = gengetopt_args_info_help[30] ; |
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< |
args_info->r_z_help = gengetopt_args_info_help[31] ; |
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< |
args_info->theta_omega_help = gengetopt_args_info_help[32] ; |
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< |
args_info->gxyz_help = gengetopt_args_info_help[33] ; |
| 244 |
< |
args_info->p2_help = gengetopt_args_info_help[34] ; |
| 245 |
< |
args_info->rp2_help = gengetopt_args_info_help[35] ; |
| 246 |
< |
args_info->scd_help = gengetopt_args_info_help[36] ; |
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< |
args_info->density_help = gengetopt_args_info_help[37] ; |
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< |
args_info->slab_density_help = gengetopt_args_info_help[38] ; |
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< |
args_info->p_angle_help = gengetopt_args_info_help[39] ; |
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< |
args_info->hxy_help = gengetopt_args_info_help[40] ; |
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< |
args_info->rho_r_help = gengetopt_args_info_help[41] ; |
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< |
args_info->hullvol_help = gengetopt_args_info_help[42] ; |
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> |
args_info->dz_help = gengetopt_args_info_help[11] ; |
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> |
args_info->length_help = gengetopt_args_info_help[12] ; |
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> |
args_info->zlength_help = gengetopt_args_info_help[13] ; |
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> |
args_info->zoffset_help = gengetopt_args_info_help[14] ; |
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> |
args_info->sele1_help = gengetopt_args_info_help[15] ; |
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> |
args_info->sele2_help = gengetopt_args_info_help[16] ; |
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> |
args_info->sele3_help = gengetopt_args_info_help[17] ; |
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> |
args_info->refsele_help = gengetopt_args_info_help[18] ; |
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> |
args_info->comsele_help = gengetopt_args_info_help[19] ; |
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> |
args_info->molname_help = gengetopt_args_info_help[20] ; |
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> |
args_info->begin_help = gengetopt_args_info_help[21] ; |
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> |
args_info->end_help = gengetopt_args_info_help[22] ; |
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> |
args_info->radius_help = gengetopt_args_info_help[23] ; |
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> |
args_info->bo_help = gengetopt_args_info_help[25] ; |
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> |
args_info->bor_help = gengetopt_args_info_help[26] ; |
| 237 |
> |
args_info->bad_help = gengetopt_args_info_help[27] ; |
| 238 |
> |
args_info->count_help = gengetopt_args_info_help[28] ; |
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> |
args_info->gofr_help = gengetopt_args_info_help[29] ; |
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> |
args_info->gofz_help = gengetopt_args_info_help[30] ; |
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> |
args_info->r_theta_help = gengetopt_args_info_help[31] ; |
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> |
args_info->r_omega_help = gengetopt_args_info_help[32] ; |
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> |
args_info->r_z_help = gengetopt_args_info_help[33] ; |
| 244 |
> |
args_info->theta_omega_help = gengetopt_args_info_help[34] ; |
| 245 |
> |
args_info->gxyz_help = gengetopt_args_info_help[35] ; |
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> |
args_info->twodgofr_help = gengetopt_args_info_help[36] ; |
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> |
args_info->p2_help = gengetopt_args_info_help[37] ; |
| 248 |
> |
args_info->rp2_help = gengetopt_args_info_help[38] ; |
| 249 |
> |
args_info->scd_help = gengetopt_args_info_help[39] ; |
| 250 |
> |
args_info->density_help = gengetopt_args_info_help[40] ; |
| 251 |
> |
args_info->slab_density_help = gengetopt_args_info_help[41] ; |
| 252 |
> |
args_info->p_angle_help = gengetopt_args_info_help[42] ; |
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> |
args_info->hxy_help = gengetopt_args_info_help[43] ; |
| 254 |
> |
args_info->rho_r_help = gengetopt_args_info_help[44] ; |
| 255 |
> |
args_info->angle_r_help = gengetopt_args_info_help[45] ; |
| 256 |
> |
args_info->hullvol_help = gengetopt_args_info_help[46] ; |
| 257 |
> |
args_info->rodlength_help = gengetopt_args_info_help[47] ; |
| 258 |
> |
args_info->tet_param_help = gengetopt_args_info_help[48] ; |
| 259 |
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|
| 260 |
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} |
| 261 |
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|
| 262 |
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void |
| 263 |
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cmdline_parser_print_version (void) |
| 264 |
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{ |
| 265 |
< |
printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); |
| 265 |
> |
printf ("%s %s\n", |
| 266 |
> |
(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), |
| 267 |
> |
CMDLINE_PARSER_VERSION); |
| 268 |
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} |
| 269 |
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|
| 270 |
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static void print_help_common(void) { |
| 279 |
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printf("\n"); |
| 280 |
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|
| 281 |
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if (strlen(gengetopt_args_info_description) > 0) |
| 282 |
< |
printf("%s\n", gengetopt_args_info_description); |
| 282 |
> |
printf("%s\n\n", gengetopt_args_info_description); |
| 283 |
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} |
| 284 |
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|
| 285 |
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void |
| 297 |
|
clear_given (args_info); |
| 298 |
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clear_args (args_info); |
| 299 |
|
init_args_info (args_info); |
| 300 |
+ |
|
| 301 |
+ |
args_info->inputs = 0; |
| 302 |
+ |
args_info->inputs_num = 0; |
| 303 |
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} |
| 304 |
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|
| 305 |
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void |
| 338 |
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static void |
| 339 |
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cmdline_parser_release (struct gengetopt_args_info *args_info) |
| 340 |
|
{ |
| 341 |
< |
|
| 341 |
> |
unsigned int i; |
| 342 |
|
free_string_field (&(args_info->input_arg)); |
| 343 |
|
free_string_field (&(args_info->input_orig)); |
| 344 |
|
free_string_field (&(args_info->output_arg)); |
| 350 |
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free_string_field (&(args_info->nbins_z_orig)); |
| 351 |
|
free_string_field (&(args_info->nanglebins_orig)); |
| 352 |
|
free_string_field (&(args_info->rcut_orig)); |
| 353 |
+ |
free_string_field (&(args_info->dz_orig)); |
| 354 |
|
free_string_field (&(args_info->length_orig)); |
| 355 |
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free_string_field (&(args_info->zlength_orig)); |
| 356 |
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free_string_field (&(args_info->zoffset_orig)); |
| 371 |
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free_string_field (&(args_info->radius_orig)); |
| 372 |
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|
| 373 |
|
|
| 374 |
+ |
for (i = 0; i < args_info->inputs_num; ++i) |
| 375 |
+ |
free (args_info->inputs [i]); |
| 376 |
+ |
|
| 377 |
+ |
if (args_info->inputs_num) |
| 378 |
+ |
free (args_info->inputs); |
| 379 |
|
|
| 380 |
|
clear_given (args_info); |
| 381 |
|
} |
| 382 |
|
|
| 383 |
|
|
| 384 |
|
static void |
| 385 |
< |
write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) |
| 385 |
> |
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) |
| 386 |
|
{ |
| 387 |
+ |
FIX_UNUSED (values); |
| 388 |
|
if (arg) { |
| 389 |
|
fprintf(outfile, "%s=\"%s\"\n", opt, arg); |
| 390 |
|
} else { |
| 426 |
|
write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); |
| 427 |
|
if (args_info->rcut_given) |
| 428 |
|
write_into_file(outfile, "rcut", args_info->rcut_orig, 0); |
| 429 |
+ |
if (args_info->dz_given) |
| 430 |
+ |
write_into_file(outfile, "dz", args_info->dz_orig, 0); |
| 431 |
|
if (args_info->length_given) |
| 432 |
|
write_into_file(outfile, "length", args_info->length_orig, 0); |
| 433 |
|
if (args_info->zlength_given) |
| 458 |
|
write_into_file(outfile, "bor", 0, 0 ); |
| 459 |
|
if (args_info->bad_given) |
| 460 |
|
write_into_file(outfile, "bad", 0, 0 ); |
| 461 |
+ |
if (args_info->count_given) |
| 462 |
+ |
write_into_file(outfile, "count", 0, 0 ); |
| 463 |
|
if (args_info->gofr_given) |
| 464 |
|
write_into_file(outfile, "gofr", 0, 0 ); |
| 465 |
|
if (args_info->gofz_given) |
| 474 |
|
write_into_file(outfile, "theta_omega", 0, 0 ); |
| 475 |
|
if (args_info->gxyz_given) |
| 476 |
|
write_into_file(outfile, "gxyz", 0, 0 ); |
| 477 |
+ |
if (args_info->twodgofr_given) |
| 478 |
+ |
write_into_file(outfile, "twodgofr", 0, 0 ); |
| 479 |
|
if (args_info->p2_given) |
| 480 |
|
write_into_file(outfile, "p2", 0, 0 ); |
| 481 |
|
if (args_info->rp2_given) |
| 492 |
|
write_into_file(outfile, "hxy", 0, 0 ); |
| 493 |
|
if (args_info->rho_r_given) |
| 494 |
|
write_into_file(outfile, "rho_r", 0, 0 ); |
| 495 |
+ |
if (args_info->angle_r_given) |
| 496 |
+ |
write_into_file(outfile, "angle_r", 0, 0 ); |
| 497 |
|
if (args_info->hullvol_given) |
| 498 |
|
write_into_file(outfile, "hullvol", 0, 0 ); |
| 499 |
+ |
if (args_info->rodlength_given) |
| 500 |
+ |
write_into_file(outfile, "rodlength", 0, 0 ); |
| 501 |
+ |
if (args_info->tet_param_given) |
| 502 |
+ |
write_into_file(outfile, "tet_param", 0, 0 ); |
| 503 |
|
|
| 504 |
|
|
| 505 |
|
i = EXIT_SUCCESS; |
| 536 |
|
char * |
| 537 |
|
gengetopt_strdup (const char *s) |
| 538 |
|
{ |
| 539 |
< |
char *result = NULL; |
| 539 |
> |
char *result = 0; |
| 540 |
|
if (!s) |
| 541 |
|
return result; |
| 542 |
|
|
| 556 |
|
args_info->bo_given = 0 ; |
| 557 |
|
args_info->bor_given = 0 ; |
| 558 |
|
args_info->bad_given = 0 ; |
| 559 |
+ |
args_info->count_given = 0 ; |
| 560 |
|
args_info->gofr_given = 0 ; |
| 561 |
|
args_info->gofz_given = 0 ; |
| 562 |
|
args_info->r_theta_given = 0 ; |
| 564 |
|
args_info->r_z_given = 0 ; |
| 565 |
|
args_info->theta_omega_given = 0 ; |
| 566 |
|
args_info->gxyz_given = 0 ; |
| 567 |
+ |
args_info->twodgofr_given = 0 ; |
| 568 |
|
args_info->p2_given = 0 ; |
| 569 |
|
args_info->rp2_given = 0 ; |
| 570 |
|
args_info->scd_given = 0 ; |
| 573 |
|
args_info->p_angle_given = 0 ; |
| 574 |
|
args_info->hxy_given = 0 ; |
| 575 |
|
args_info->rho_r_given = 0 ; |
| 576 |
+ |
args_info->angle_r_given = 0 ; |
| 577 |
|
args_info->hullvol_given = 0 ; |
| 578 |
+ |
args_info->rodlength_given = 0 ; |
| 579 |
+ |
args_info->tet_param_given = 0 ; |
| 580 |
|
|
| 581 |
|
args_info->staticProps_group_counter = 0; |
| 582 |
|
} |
| 583 |
|
|
| 584 |
|
int |
| 585 |
< |
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) |
| 585 |
> |
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) |
| 586 |
|
{ |
| 587 |
|
return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); |
| 588 |
|
} |
| 589 |
|
|
| 590 |
|
int |
| 591 |
< |
cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
| 591 |
> |
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, |
| 592 |
|
struct cmdline_parser_params *params) |
| 593 |
|
{ |
| 594 |
|
int result; |
| 595 |
< |
result = cmdline_parser_internal (argc, argv, args_info, params, NULL); |
| 595 |
> |
result = cmdline_parser_internal (argc, argv, args_info, params, 0); |
| 596 |
|
|
| 597 |
|
if (result == EXIT_FAILURE) |
| 598 |
|
{ |
| 604 |
|
} |
| 605 |
|
|
| 606 |
|
int |
| 607 |
< |
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
| 607 |
> |
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
| 608 |
|
{ |
| 609 |
|
int result; |
| 610 |
|
struct cmdline_parser_params params; |
| 615 |
|
params.check_ambiguity = 0; |
| 616 |
|
params.print_errors = 1; |
| 617 |
|
|
| 618 |
< |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); |
| 618 |
> |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); |
| 619 |
|
|
| 620 |
|
if (result == EXIT_FAILURE) |
| 621 |
|
{ |
| 631 |
|
{ |
| 632 |
|
int result = EXIT_SUCCESS; |
| 633 |
|
|
| 634 |
< |
if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) |
| 634 |
> |
if (cmdline_parser_required2(args_info, prog_name, 0) > 0) |
| 635 |
|
result = EXIT_FAILURE; |
| 636 |
|
|
| 637 |
|
if (result == EXIT_FAILURE) |
| 647 |
|
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) |
| 648 |
|
{ |
| 649 |
|
int error = 0; |
| 650 |
+ |
FIX_UNUSED (additional_error); |
| 651 |
|
|
| 652 |
|
/* checks for required options */ |
| 653 |
|
if (! args_info->input_given) |
| 658 |
|
|
| 659 |
|
if (args_info->staticProps_group_counter == 0) |
| 660 |
|
{ |
| 661 |
< |
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 : "")); |
| 661 |
> |
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 : "")); |
| 662 |
|
error = 1; |
| 663 |
|
} |
| 664 |
|
|
| 692 |
|
static |
| 693 |
|
int update_arg(void *field, char **orig_field, |
| 694 |
|
unsigned int *field_given, unsigned int *prev_given, |
| 695 |
< |
char *value, char *possible_values[], const char *default_value, |
| 695 |
> |
char *value, const char *possible_values[], |
| 696 |
> |
const char *default_value, |
| 697 |
|
cmdline_parser_arg_type arg_type, |
| 698 |
|
int check_ambiguity, int override, |
| 699 |
|
int no_free, int multiple_option, |
| 704 |
|
const char *val = value; |
| 705 |
|
int found; |
| 706 |
|
char **string_field; |
| 707 |
+ |
FIX_UNUSED (field); |
| 708 |
|
|
| 709 |
|
stop_char = 0; |
| 710 |
|
found = 0; |
| 722 |
|
return 1; /* failure */ |
| 723 |
|
} |
| 724 |
|
|
| 725 |
+ |
FIX_UNUSED (default_value); |
| 726 |
|
|
| 727 |
|
if (field_given && *field_given && ! override) |
| 728 |
|
return 0; |
| 786 |
|
|
| 787 |
|
|
| 788 |
|
int |
| 789 |
< |
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
| 789 |
> |
cmdline_parser_internal ( |
| 790 |
> |
int argc, char **argv, struct gengetopt_args_info *args_info, |
| 791 |
|
struct cmdline_parser_params *params, const char *additional_error) |
| 792 |
|
{ |
| 793 |
|
int c; /* Character of the parsed option. */ |
| 833 |
|
{ "nbins_z", 1, NULL, 0 }, |
| 834 |
|
{ "nanglebins", 1, NULL, 'a' }, |
| 835 |
|
{ "rcut", 1, NULL, 'c' }, |
| 836 |
+ |
{ "dz", 1, NULL, 0 }, |
| 837 |
|
{ "length", 1, NULL, 0 }, |
| 838 |
|
{ "zlength", 1, NULL, 0 }, |
| 839 |
|
{ "zoffset", 1, NULL, 'z' }, |
| 849 |
|
{ "bo", 0, NULL, 0 }, |
| 850 |
|
{ "bor", 0, NULL, 0 }, |
| 851 |
|
{ "bad", 0, NULL, 0 }, |
| 852 |
+ |
{ "count", 0, NULL, 0 }, |
| 853 |
|
{ "gofr", 0, NULL, 'g' }, |
| 854 |
|
{ "gofz", 0, NULL, 0 }, |
| 855 |
|
{ "r_theta", 0, NULL, 0 }, |
| 857 |
|
{ "r_z", 0, NULL, 0 }, |
| 858 |
|
{ "theta_omega", 0, NULL, 0 }, |
| 859 |
|
{ "gxyz", 0, NULL, 0 }, |
| 860 |
+ |
{ "twodgofr", 0, NULL, 0 }, |
| 861 |
|
{ "p2", 0, NULL, 'p' }, |
| 862 |
|
{ "rp2", 0, NULL, 0 }, |
| 863 |
|
{ "scd", 0, NULL, 's' }, |
| 866 |
|
{ "p_angle", 0, NULL, 0 }, |
| 867 |
|
{ "hxy", 0, NULL, 0 }, |
| 868 |
|
{ "rho_r", 0, NULL, 0 }, |
| 869 |
+ |
{ "angle_r", 0, NULL, 0 }, |
| 870 |
|
{ "hullvol", 0, NULL, 0 }, |
| 871 |
< |
{ NULL, 0, NULL, 0 } |
| 871 |
> |
{ "rodlength", 0, NULL, 0 }, |
| 872 |
> |
{ "tet_param", 0, NULL, 'Q' }, |
| 873 |
> |
{ 0, 0, 0, 0 } |
| 874 |
|
}; |
| 875 |
|
|
| 876 |
< |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); |
| 876 |
> |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); |
| 877 |
|
|
| 878 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
| 879 |
|
|
| 1012 |
|
goto failure; |
| 1013 |
|
|
| 1014 |
|
break; |
| 1015 |
< |
case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */ |
| 1015 |
> |
case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */ |
| 1016 |
|
|
| 1017 |
|
if (args_info->staticProps_group_counter && override) |
| 1018 |
|
reset_group_staticProps (args_info); |
| 1057 |
|
goto failure; |
| 1058 |
|
|
| 1059 |
|
break; |
| 1060 |
+ |
case 'Q': /* tetrahedrality order parameter. */ |
| 1061 |
+ |
|
| 1062 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1063 |
+ |
reset_group_staticProps (args_info); |
| 1064 |
+ |
args_info->staticProps_group_counter += 1; |
| 1065 |
+ |
|
| 1066 |
+ |
if (update_arg( 0 , |
| 1067 |
+ |
0 , &(args_info->tet_param_given), |
| 1068 |
+ |
&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, |
| 1069 |
+ |
check_ambiguity, override, 0, 0, |
| 1070 |
+ |
"tet_param", 'Q', |
| 1071 |
+ |
additional_error)) |
| 1072 |
+ |
goto failure; |
| 1073 |
+ |
|
| 1074 |
+ |
break; |
| 1075 |
|
|
| 1076 |
|
case 0: /* Long option with no short option */ |
| 1077 |
|
/* number of bins in z axis. */ |
| 1088 |
|
goto failure; |
| 1089 |
|
|
| 1090 |
|
} |
| 1091 |
+ |
/* slab width (dz). */ |
| 1092 |
+ |
else if (strcmp (long_options[option_index].name, "dz") == 0) |
| 1093 |
+ |
{ |
| 1094 |
+ |
|
| 1095 |
+ |
|
| 1096 |
+ |
if (update_arg( (void *)&(args_info->dz_arg), |
| 1097 |
+ |
&(args_info->dz_orig), &(args_info->dz_given), |
| 1098 |
+ |
&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, |
| 1099 |
+ |
check_ambiguity, override, 0, 0, |
| 1100 |
+ |
"dz", '-', |
| 1101 |
+ |
additional_error)) |
| 1102 |
+ |
goto failure; |
| 1103 |
+ |
|
| 1104 |
+ |
} |
| 1105 |
|
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1106 |
|
else if (strcmp (long_options[option_index].name, "length") == 0) |
| 1107 |
|
{ |
| 1303 |
|
&(local_args_info.bad_given), optarg, 0, 0, ARG_NO, |
| 1304 |
|
check_ambiguity, override, 0, 0, |
| 1305 |
|
"bad", '-', |
| 1306 |
+ |
additional_error)) |
| 1307 |
+ |
goto failure; |
| 1308 |
+ |
|
| 1309 |
+ |
} |
| 1310 |
+ |
/* count of molecules matching selection criteria (and associated statistics). */ |
| 1311 |
+ |
else if (strcmp (long_options[option_index].name, "count") == 0) |
| 1312 |
+ |
{ |
| 1313 |
+ |
|
| 1314 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1315 |
+ |
reset_group_staticProps (args_info); |
| 1316 |
+ |
args_info->staticProps_group_counter += 1; |
| 1317 |
+ |
|
| 1318 |
+ |
if (update_arg( 0 , |
| 1319 |
+ |
0 , &(args_info->count_given), |
| 1320 |
+ |
&(local_args_info.count_given), optarg, 0, 0, ARG_NO, |
| 1321 |
+ |
check_ambiguity, override, 0, 0, |
| 1322 |
+ |
"count", '-', |
| 1323 |
|
additional_error)) |
| 1324 |
|
goto failure; |
| 1325 |
|
|
| 1426 |
|
goto failure; |
| 1427 |
|
|
| 1428 |
|
} |
| 1429 |
+ |
/* 2D g(r) (Slab width --dz must be specified). */ |
| 1430 |
+ |
else if (strcmp (long_options[option_index].name, "twodgofr") == 0) |
| 1431 |
+ |
{ |
| 1432 |
+ |
|
| 1433 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1434 |
+ |
reset_group_staticProps (args_info); |
| 1435 |
+ |
args_info->staticProps_group_counter += 1; |
| 1436 |
+ |
|
| 1437 |
+ |
if (update_arg( 0 , |
| 1438 |
+ |
0 , &(args_info->twodgofr_given), |
| 1439 |
+ |
&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, |
| 1440 |
+ |
check_ambiguity, override, 0, 0, |
| 1441 |
+ |
"twodgofr", '-', |
| 1442 |
+ |
additional_error)) |
| 1443 |
+ |
goto failure; |
| 1444 |
+ |
|
| 1445 |
+ |
} |
| 1446 |
|
/* rp2 order parameter (--sele1 and --sele2 must be specified). */ |
| 1447 |
|
else if (strcmp (long_options[option_index].name, "rp2") == 0) |
| 1448 |
|
{ |
| 1528 |
|
goto failure; |
| 1529 |
|
|
| 1530 |
|
} |
| 1531 |
+ |
/* angle of R. */ |
| 1532 |
+ |
else if (strcmp (long_options[option_index].name, "angle_r") == 0) |
| 1533 |
+ |
{ |
| 1534 |
+ |
|
| 1535 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1536 |
+ |
reset_group_staticProps (args_info); |
| 1537 |
+ |
args_info->staticProps_group_counter += 1; |
| 1538 |
+ |
|
| 1539 |
+ |
if (update_arg( 0 , |
| 1540 |
+ |
0 , &(args_info->angle_r_given), |
| 1541 |
+ |
&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, |
| 1542 |
+ |
check_ambiguity, override, 0, 0, |
| 1543 |
+ |
"angle_r", '-', |
| 1544 |
+ |
additional_error)) |
| 1545 |
+ |
goto failure; |
| 1546 |
+ |
|
| 1547 |
+ |
} |
| 1548 |
|
/* hull volume of nanoparticle. */ |
| 1549 |
|
else if (strcmp (long_options[option_index].name, "hullvol") == 0) |
| 1550 |
|
{ |
| 1562 |
|
goto failure; |
| 1563 |
|
|
| 1564 |
|
} |
| 1565 |
+ |
/* length of nanorod. */ |
| 1566 |
+ |
else if (strcmp (long_options[option_index].name, "rodlength") == 0) |
| 1567 |
+ |
{ |
| 1568 |
|
|
| 1569 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1570 |
+ |
reset_group_staticProps (args_info); |
| 1571 |
+ |
args_info->staticProps_group_counter += 1; |
| 1572 |
+ |
|
| 1573 |
+ |
if (update_arg( 0 , |
| 1574 |
+ |
0 , &(args_info->rodlength_given), |
| 1575 |
+ |
&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, |
| 1576 |
+ |
check_ambiguity, override, 0, 0, |
| 1577 |
+ |
"rodlength", '-', |
| 1578 |
+ |
additional_error)) |
| 1579 |
+ |
goto failure; |
| 1580 |
+ |
|
| 1581 |
+ |
} |
| 1582 |
+ |
|
| 1583 |
|
break; |
| 1584 |
|
case '?': /* Invalid option. */ |
| 1585 |
|
/* `getopt_long' already printed an error message. */ |
| 1593 |
|
|
| 1594 |
|
if (args_info->staticProps_group_counter > 1) |
| 1595 |
|
{ |
| 1596 |
< |
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 : "")); |
| 1596 |
> |
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 : "")); |
| 1597 |
|
error = 1; |
| 1598 |
|
} |
| 1599 |
|
|
| 1609 |
|
if ( error ) |
| 1610 |
|
return (EXIT_FAILURE); |
| 1611 |
|
|
| 1612 |
+ |
if (optind < argc) |
| 1613 |
+ |
{ |
| 1614 |
+ |
int i = 0 ; |
| 1615 |
+ |
int found_prog_name = 0; |
| 1616 |
+ |
/* whether program name, i.e., argv[0], is in the remaining args |
| 1617 |
+ |
(this may happen with some implementations of getopt, |
| 1618 |
+ |
but surely not with the one included by gengetopt) */ |
| 1619 |
+ |
|
| 1620 |
+ |
i = optind; |
| 1621 |
+ |
while (i < argc) |
| 1622 |
+ |
if (argv[i++] == argv[0]) { |
| 1623 |
+ |
found_prog_name = 1; |
| 1624 |
+ |
break; |
| 1625 |
+ |
} |
| 1626 |
+ |
i = 0; |
| 1627 |
+ |
|
| 1628 |
+ |
args_info->inputs_num = argc - optind - found_prog_name; |
| 1629 |
+ |
args_info->inputs = |
| 1630 |
+ |
(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; |
| 1631 |
+ |
while (optind < argc) |
| 1632 |
+ |
if (argv[optind++] != argv[0]) |
| 1633 |
+ |
args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; |
| 1634 |
+ |
} |
| 1635 |
+ |
|
| 1636 |
|
return 0; |
| 1637 |
|
|
| 1638 |
|
failure: |
