| 1 |
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/* |
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File autogenerated by gengetopt version 2.22.4 |
| 3 |
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generated with the following command: |
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< |
gengetopt --file-name=StaticPropsCmd --unamed-opts |
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> |
gengetopt -i StaticProps.ggo -F StaticPropsCmd -c cpp |
| 5 |
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|
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The developers of gengetopt consider the fixed text that goes in all |
| 7 |
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gengetopt output files to be in the public domain: |
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#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ |
| 22 |
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#endif |
| 23 |
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|
| 24 |
– |
#ifdef WIN32 |
| 25 |
– |
#include "utils/wingetopt.h" |
| 26 |
– |
#else |
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#include <getopt.h> |
| 28 |
– |
#endif |
| 25 |
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|
| 26 |
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#include "StaticPropsCmd.h" |
| 27 |
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|
| 28 |
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const char *gengetopt_args_info_purpose = ""; |
| 29 |
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|
| 30 |
< |
const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]..."; |
| 30 |
> |
const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]..."; |
| 31 |
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|
| 32 |
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const char *gengetopt_args_info_description = ""; |
| 33 |
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|
| 53 |
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" --refsele=selection script\n select reference (use and only use with --gxyz)", |
| 54 |
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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)", |
| 56 |
+ |
" --seleoffset2=INT global index offset for a third object (used to \n define a vector between sites in molecule)", |
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" --molname=STRING molecule name", |
| 58 |
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" --begin=INT begin internal index", |
| 59 |
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" --end=INT end internal index", |
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" --radius=DOUBLE nanoparticle radius", |
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+ |
" -v, --voxelSize=DOUBLE voxel size (angstroms)", |
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+ |
" --gaussWidth=DOUBLE Gaussian width (angstroms)", |
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"\n Group: staticProps\n an option of this group is required", |
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" --bo bond order parameter (--rcut must be specified)", |
| 65 |
< |
" --bor bond order parameter as a function of radius \n (--rcut must be specified)", |
| 65 |
> |
" --ior icosahedral bond order parameter as a function \n of radius (--rcut must be specified)", |
| 66 |
> |
" --for FCC bond order parameter as a function of \n radius (--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)", |
| 69 |
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" -g, --gofr g(r)", |
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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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" --tet_param_xyz volume-resolved tetrahedrality order parameter \n Qk(x,y,z). (voxelSize, rcut, and gaussWidth \n must be specified)", |
| 91 |
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" --rnemdz slab-resolved RNEMD statistics (temperature, \n density, velocity)", |
| 92 |
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" --rnemdr shell-resolved RNEMD statistics (temperature, \n density, angular velocity)", |
| 93 |
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" --rnemdrt shell and angle-resolved RNEMD statistics \n (temperature, density, angular velocity)", |
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+ |
" --nitrile electrostatic potential to frequency map based \n on the Cho nitrile fits", |
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+ |
" -m, --multipole average multipole moments contained within \n cutoff spheres as a function of radius", |
| 96 |
+ |
" --surfDiffusion X, Y, and R (surface diffusion if Z exposed and \n bulk immobile) diffusion", |
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0 |
| 98 |
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}; |
| 99 |
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|
| 142 |
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args_info->refsele_given = 0 ; |
| 143 |
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args_info->comsele_given = 0 ; |
| 144 |
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args_info->seleoffset_given = 0 ; |
| 145 |
+ |
args_info->seleoffset2_given = 0 ; |
| 146 |
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args_info->molname_given = 0 ; |
| 147 |
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args_info->begin_given = 0 ; |
| 148 |
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args_info->end_given = 0 ; |
| 149 |
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args_info->radius_given = 0 ; |
| 150 |
+ |
args_info->voxelSize_given = 0 ; |
| 151 |
+ |
args_info->gaussWidth_given = 0 ; |
| 152 |
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args_info->bo_given = 0 ; |
| 153 |
< |
args_info->bor_given = 0 ; |
| 153 |
> |
args_info->ior_given = 0 ; |
| 154 |
> |
args_info->for_given = 0 ; |
| 155 |
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args_info->bad_given = 0 ; |
| 156 |
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args_info->count_given = 0 ; |
| 157 |
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args_info->gofr_given = 0 ; |
| 175 |
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args_info->rodlength_given = 0 ; |
| 176 |
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args_info->tet_param_given = 0 ; |
| 177 |
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args_info->tet_param_z_given = 0 ; |
| 178 |
+ |
args_info->tet_param_xyz_given = 0 ; |
| 179 |
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args_info->rnemdz_given = 0 ; |
| 180 |
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args_info->rnemdr_given = 0 ; |
| 181 |
|
args_info->rnemdrt_given = 0 ; |
| 182 |
+ |
args_info->nitrile_given = 0 ; |
| 183 |
+ |
args_info->multipole_given = 0 ; |
| 184 |
+ |
args_info->surfDiffusion_given = 0 ; |
| 185 |
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args_info->staticProps_group_counter = 0 ; |
| 186 |
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} |
| 187 |
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|
| 222 |
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args_info->comsele_arg = NULL; |
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args_info->comsele_orig = NULL; |
| 224 |
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args_info->seleoffset_orig = NULL; |
| 225 |
+ |
args_info->seleoffset2_orig = NULL; |
| 226 |
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args_info->molname_arg = NULL; |
| 227 |
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args_info->molname_orig = NULL; |
| 228 |
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args_info->begin_orig = NULL; |
| 229 |
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args_info->end_orig = NULL; |
| 230 |
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args_info->radius_orig = NULL; |
| 231 |
+ |
args_info->voxelSize_orig = NULL; |
| 232 |
+ |
args_info->gaussWidth_orig = NULL; |
| 233 |
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|
| 234 |
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} |
| 235 |
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|
| 259 |
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args_info->refsele_help = gengetopt_args_info_help[18] ; |
| 260 |
|
args_info->comsele_help = gengetopt_args_info_help[19] ; |
| 261 |
|
args_info->seleoffset_help = gengetopt_args_info_help[20] ; |
| 262 |
< |
args_info->molname_help = gengetopt_args_info_help[21] ; |
| 263 |
< |
args_info->begin_help = gengetopt_args_info_help[22] ; |
| 264 |
< |
args_info->end_help = gengetopt_args_info_help[23] ; |
| 265 |
< |
args_info->radius_help = gengetopt_args_info_help[24] ; |
| 266 |
< |
args_info->bo_help = gengetopt_args_info_help[26] ; |
| 267 |
< |
args_info->bor_help = gengetopt_args_info_help[27] ; |
| 268 |
< |
args_info->bad_help = gengetopt_args_info_help[28] ; |
| 269 |
< |
args_info->count_help = gengetopt_args_info_help[29] ; |
| 270 |
< |
args_info->gofr_help = gengetopt_args_info_help[30] ; |
| 271 |
< |
args_info->gofz_help = gengetopt_args_info_help[31] ; |
| 272 |
< |
args_info->r_theta_help = gengetopt_args_info_help[32] ; |
| 273 |
< |
args_info->r_omega_help = gengetopt_args_info_help[33] ; |
| 274 |
< |
args_info->r_z_help = gengetopt_args_info_help[34] ; |
| 275 |
< |
args_info->theta_omega_help = gengetopt_args_info_help[35] ; |
| 276 |
< |
args_info->gxyz_help = gengetopt_args_info_help[36] ; |
| 277 |
< |
args_info->twodgofr_help = gengetopt_args_info_help[37] ; |
| 278 |
< |
args_info->p2_help = gengetopt_args_info_help[38] ; |
| 279 |
< |
args_info->rp2_help = gengetopt_args_info_help[39] ; |
| 280 |
< |
args_info->scd_help = gengetopt_args_info_help[40] ; |
| 281 |
< |
args_info->density_help = gengetopt_args_info_help[41] ; |
| 282 |
< |
args_info->slab_density_help = gengetopt_args_info_help[42] ; |
| 283 |
< |
args_info->p_angle_help = gengetopt_args_info_help[43] ; |
| 284 |
< |
args_info->hxy_help = gengetopt_args_info_help[44] ; |
| 285 |
< |
args_info->rho_r_help = gengetopt_args_info_help[45] ; |
| 286 |
< |
args_info->angle_r_help = gengetopt_args_info_help[46] ; |
| 287 |
< |
args_info->hullvol_help = gengetopt_args_info_help[47] ; |
| 288 |
< |
args_info->rodlength_help = gengetopt_args_info_help[48] ; |
| 289 |
< |
args_info->tet_param_help = gengetopt_args_info_help[49] ; |
| 290 |
< |
args_info->tet_param_z_help = gengetopt_args_info_help[50] ; |
| 291 |
< |
args_info->rnemdz_help = gengetopt_args_info_help[51] ; |
| 292 |
< |
args_info->rnemdr_help = gengetopt_args_info_help[52] ; |
| 293 |
< |
args_info->rnemdrt_help = gengetopt_args_info_help[53] ; |
| 262 |
> |
args_info->seleoffset2_help = gengetopt_args_info_help[21] ; |
| 263 |
> |
args_info->molname_help = gengetopt_args_info_help[22] ; |
| 264 |
> |
args_info->begin_help = gengetopt_args_info_help[23] ; |
| 265 |
> |
args_info->end_help = gengetopt_args_info_help[24] ; |
| 266 |
> |
args_info->radius_help = gengetopt_args_info_help[25] ; |
| 267 |
> |
args_info->voxelSize_help = gengetopt_args_info_help[26] ; |
| 268 |
> |
args_info->gaussWidth_help = gengetopt_args_info_help[27] ; |
| 269 |
> |
args_info->bo_help = gengetopt_args_info_help[29] ; |
| 270 |
> |
args_info->ior_help = gengetopt_args_info_help[30] ; |
| 271 |
> |
args_info->for_help = gengetopt_args_info_help[31] ; |
| 272 |
> |
args_info->bad_help = gengetopt_args_info_help[32] ; |
| 273 |
> |
args_info->count_help = gengetopt_args_info_help[33] ; |
| 274 |
> |
args_info->gofr_help = gengetopt_args_info_help[34] ; |
| 275 |
> |
args_info->gofz_help = gengetopt_args_info_help[35] ; |
| 276 |
> |
args_info->r_theta_help = gengetopt_args_info_help[36] ; |
| 277 |
> |
args_info->r_omega_help = gengetopt_args_info_help[37] ; |
| 278 |
> |
args_info->r_z_help = gengetopt_args_info_help[38] ; |
| 279 |
> |
args_info->theta_omega_help = gengetopt_args_info_help[39] ; |
| 280 |
> |
args_info->gxyz_help = gengetopt_args_info_help[40] ; |
| 281 |
> |
args_info->twodgofr_help = gengetopt_args_info_help[41] ; |
| 282 |
> |
args_info->p2_help = gengetopt_args_info_help[42] ; |
| 283 |
> |
args_info->rp2_help = gengetopt_args_info_help[43] ; |
| 284 |
> |
args_info->scd_help = gengetopt_args_info_help[44] ; |
| 285 |
> |
args_info->density_help = gengetopt_args_info_help[45] ; |
| 286 |
> |
args_info->slab_density_help = gengetopt_args_info_help[46] ; |
| 287 |
> |
args_info->p_angle_help = gengetopt_args_info_help[47] ; |
| 288 |
> |
args_info->hxy_help = gengetopt_args_info_help[48] ; |
| 289 |
> |
args_info->rho_r_help = gengetopt_args_info_help[49] ; |
| 290 |
> |
args_info->angle_r_help = gengetopt_args_info_help[50] ; |
| 291 |
> |
args_info->hullvol_help = gengetopt_args_info_help[51] ; |
| 292 |
> |
args_info->rodlength_help = gengetopt_args_info_help[52] ; |
| 293 |
> |
args_info->tet_param_help = gengetopt_args_info_help[53] ; |
| 294 |
> |
args_info->tet_param_z_help = gengetopt_args_info_help[54] ; |
| 295 |
> |
args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ; |
| 296 |
> |
args_info->rnemdz_help = gengetopt_args_info_help[56] ; |
| 297 |
> |
args_info->rnemdr_help = gengetopt_args_info_help[57] ; |
| 298 |
> |
args_info->rnemdrt_help = gengetopt_args_info_help[58] ; |
| 299 |
> |
args_info->nitrile_help = gengetopt_args_info_help[59] ; |
| 300 |
> |
args_info->multipole_help = gengetopt_args_info_help[60] ; |
| 301 |
> |
args_info->surfDiffusion_help = gengetopt_args_info_help[61] ; |
| 302 |
|
|
| 303 |
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} |
| 304 |
|
|
| 340 |
|
clear_given (args_info); |
| 341 |
|
clear_args (args_info); |
| 342 |
|
init_args_info (args_info); |
| 320 |
– |
|
| 321 |
– |
args_info->inputs = 0; |
| 322 |
– |
args_info->inputs_num = 0; |
| 343 |
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} |
| 344 |
|
|
| 345 |
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void |
| 378 |
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static void |
| 379 |
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cmdline_parser_release (struct gengetopt_args_info *args_info) |
| 380 |
|
{ |
| 381 |
< |
unsigned int i; |
| 381 |
> |
|
| 382 |
|
free_string_field (&(args_info->input_arg)); |
| 383 |
|
free_string_field (&(args_info->input_orig)); |
| 384 |
|
free_string_field (&(args_info->output_arg)); |
| 405 |
|
free_string_field (&(args_info->comsele_arg)); |
| 406 |
|
free_string_field (&(args_info->comsele_orig)); |
| 407 |
|
free_string_field (&(args_info->seleoffset_orig)); |
| 408 |
+ |
free_string_field (&(args_info->seleoffset2_orig)); |
| 409 |
|
free_string_field (&(args_info->molname_arg)); |
| 410 |
|
free_string_field (&(args_info->molname_orig)); |
| 411 |
|
free_string_field (&(args_info->begin_orig)); |
| 412 |
|
free_string_field (&(args_info->end_orig)); |
| 413 |
|
free_string_field (&(args_info->radius_orig)); |
| 414 |
+ |
free_string_field (&(args_info->voxelSize_orig)); |
| 415 |
+ |
free_string_field (&(args_info->gaussWidth_orig)); |
| 416 |
|
|
| 417 |
|
|
| 395 |
– |
for (i = 0; i < args_info->inputs_num; ++i) |
| 396 |
– |
free (args_info->inputs [i]); |
| 418 |
|
|
| 398 |
– |
if (args_info->inputs_num) |
| 399 |
– |
free (args_info->inputs); |
| 400 |
– |
|
| 419 |
|
clear_given (args_info); |
| 420 |
|
} |
| 421 |
|
|
| 485 |
|
write_into_file(outfile, "comsele", args_info->comsele_orig, 0); |
| 486 |
|
if (args_info->seleoffset_given) |
| 487 |
|
write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0); |
| 488 |
+ |
if (args_info->seleoffset2_given) |
| 489 |
+ |
write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0); |
| 490 |
|
if (args_info->molname_given) |
| 491 |
|
write_into_file(outfile, "molname", args_info->molname_orig, 0); |
| 492 |
|
if (args_info->begin_given) |
| 495 |
|
write_into_file(outfile, "end", args_info->end_orig, 0); |
| 496 |
|
if (args_info->radius_given) |
| 497 |
|
write_into_file(outfile, "radius", args_info->radius_orig, 0); |
| 498 |
+ |
if (args_info->voxelSize_given) |
| 499 |
+ |
write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0); |
| 500 |
+ |
if (args_info->gaussWidth_given) |
| 501 |
+ |
write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0); |
| 502 |
|
if (args_info->bo_given) |
| 503 |
|
write_into_file(outfile, "bo", 0, 0 ); |
| 504 |
< |
if (args_info->bor_given) |
| 505 |
< |
write_into_file(outfile, "bor", 0, 0 ); |
| 504 |
> |
if (args_info->ior_given) |
| 505 |
> |
write_into_file(outfile, "ior", 0, 0 ); |
| 506 |
> |
if (args_info->for_given) |
| 507 |
> |
write_into_file(outfile, "for", 0, 0 ); |
| 508 |
|
if (args_info->bad_given) |
| 509 |
|
write_into_file(outfile, "bad", 0, 0 ); |
| 510 |
|
if (args_info->count_given) |
| 551 |
|
write_into_file(outfile, "tet_param", 0, 0 ); |
| 552 |
|
if (args_info->tet_param_z_given) |
| 553 |
|
write_into_file(outfile, "tet_param_z", 0, 0 ); |
| 554 |
+ |
if (args_info->tet_param_xyz_given) |
| 555 |
+ |
write_into_file(outfile, "tet_param_xyz", 0, 0 ); |
| 556 |
|
if (args_info->rnemdz_given) |
| 557 |
|
write_into_file(outfile, "rnemdz", 0, 0 ); |
| 558 |
|
if (args_info->rnemdr_given) |
| 559 |
|
write_into_file(outfile, "rnemdr", 0, 0 ); |
| 560 |
|
if (args_info->rnemdrt_given) |
| 561 |
|
write_into_file(outfile, "rnemdrt", 0, 0 ); |
| 562 |
+ |
if (args_info->nitrile_given) |
| 563 |
+ |
write_into_file(outfile, "nitrile", 0, 0 ); |
| 564 |
+ |
if (args_info->multipole_given) |
| 565 |
+ |
write_into_file(outfile, "multipole", 0, 0 ); |
| 566 |
+ |
if (args_info->surfDiffusion_given) |
| 567 |
+ |
write_into_file(outfile, "surfDiffusion", 0, 0 ); |
| 568 |
|
|
| 569 |
|
|
| 570 |
|
i = EXIT_SUCCESS; |
| 619 |
|
return; |
| 620 |
|
|
| 621 |
|
args_info->bo_given = 0 ; |
| 622 |
< |
args_info->bor_given = 0 ; |
| 622 |
> |
args_info->ior_given = 0 ; |
| 623 |
> |
args_info->for_given = 0 ; |
| 624 |
|
args_info->bad_given = 0 ; |
| 625 |
|
args_info->count_given = 0 ; |
| 626 |
|
args_info->gofr_given = 0 ; |
| 644 |
|
args_info->rodlength_given = 0 ; |
| 645 |
|
args_info->tet_param_given = 0 ; |
| 646 |
|
args_info->tet_param_z_given = 0 ; |
| 647 |
+ |
args_info->tet_param_xyz_given = 0 ; |
| 648 |
|
args_info->rnemdz_given = 0 ; |
| 649 |
|
args_info->rnemdr_given = 0 ; |
| 650 |
|
args_info->rnemdrt_given = 0 ; |
| 651 |
+ |
args_info->nitrile_given = 0 ; |
| 652 |
+ |
args_info->multipole_given = 0 ; |
| 653 |
+ |
args_info->surfDiffusion_given = 0 ; |
| 654 |
|
|
| 655 |
|
args_info->staticProps_group_counter = 0; |
| 656 |
|
} |
| 917 |
|
{ "refsele", 1, NULL, 0 }, |
| 918 |
|
{ "comsele", 1, NULL, 0 }, |
| 919 |
|
{ "seleoffset", 1, NULL, 0 }, |
| 920 |
+ |
{ "seleoffset2", 1, NULL, 0 }, |
| 921 |
|
{ "molname", 1, NULL, 0 }, |
| 922 |
|
{ "begin", 1, NULL, 0 }, |
| 923 |
|
{ "end", 1, NULL, 0 }, |
| 924 |
|
{ "radius", 1, NULL, 0 }, |
| 925 |
+ |
{ "voxelSize", 1, NULL, 'v' }, |
| 926 |
+ |
{ "gaussWidth", 1, NULL, 0 }, |
| 927 |
|
{ "bo", 0, NULL, 0 }, |
| 928 |
< |
{ "bor", 0, NULL, 0 }, |
| 928 |
> |
{ "ior", 0, NULL, 0 }, |
| 929 |
> |
{ "for", 0, NULL, 0 }, |
| 930 |
|
{ "bad", 0, NULL, 0 }, |
| 931 |
|
{ "count", 0, NULL, 0 }, |
| 932 |
|
{ "gofr", 0, NULL, 'g' }, |
| 950 |
|
{ "rodlength", 0, NULL, 0 }, |
| 951 |
|
{ "tet_param", 0, NULL, 'Q' }, |
| 952 |
|
{ "tet_param_z", 0, NULL, 0 }, |
| 953 |
+ |
{ "tet_param_xyz", 0, NULL, 0 }, |
| 954 |
|
{ "rnemdz", 0, NULL, 0 }, |
| 955 |
|
{ "rnemdr", 0, NULL, 0 }, |
| 956 |
|
{ "rnemdrt", 0, NULL, 0 }, |
| 957 |
+ |
{ "nitrile", 0, NULL, 0 }, |
| 958 |
+ |
{ "multipole", 0, NULL, 'm' }, |
| 959 |
+ |
{ "surfDiffusion", 0, NULL, 0 }, |
| 960 |
|
{ 0, 0, 0, 0 } |
| 961 |
|
}; |
| 962 |
|
|
| 963 |
< |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index); |
| 963 |
> |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index); |
| 964 |
|
|
| 965 |
|
if (c == -1) break; /* Exit from `while (1)' loop. */ |
| 966 |
|
|
| 1080 |
|
&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE, |
| 1081 |
|
check_ambiguity, override, 0, 0, |
| 1082 |
|
"zoffset", 'z', |
| 1083 |
+ |
additional_error)) |
| 1084 |
+ |
goto failure; |
| 1085 |
+ |
|
| 1086 |
+ |
break; |
| 1087 |
+ |
case 'v': /* voxel size (angstroms). */ |
| 1088 |
+ |
|
| 1089 |
+ |
|
| 1090 |
+ |
if (update_arg( (void *)&(args_info->voxelSize_arg), |
| 1091 |
+ |
&(args_info->voxelSize_orig), &(args_info->voxelSize_given), |
| 1092 |
+ |
&(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE, |
| 1093 |
+ |
check_ambiguity, override, 0, 0, |
| 1094 |
+ |
"voxelSize", 'v', |
| 1095 |
|
additional_error)) |
| 1096 |
|
goto failure; |
| 1097 |
|
|
| 1171 |
|
goto failure; |
| 1172 |
|
|
| 1173 |
|
break; |
| 1174 |
+ |
case 'm': /* average multipole moments contained within cutoff spheres as a function of radius. */ |
| 1175 |
+ |
|
| 1176 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1177 |
+ |
reset_group_staticProps (args_info); |
| 1178 |
+ |
args_info->staticProps_group_counter += 1; |
| 1179 |
+ |
|
| 1180 |
+ |
if (update_arg( 0 , |
| 1181 |
+ |
0 , &(args_info->multipole_given), |
| 1182 |
+ |
&(local_args_info.multipole_given), optarg, 0, 0, ARG_NO, |
| 1183 |
+ |
check_ambiguity, override, 0, 0, |
| 1184 |
+ |
"multipole", 'm', |
| 1185 |
+ |
additional_error)) |
| 1186 |
+ |
goto failure; |
| 1187 |
+ |
|
| 1188 |
+ |
break; |
| 1189 |
|
|
| 1190 |
|
case 0: /* Long option with no short option */ |
| 1191 |
|
/* number of bins in z axis. */ |
| 1328 |
|
goto failure; |
| 1329 |
|
|
| 1330 |
|
} |
| 1331 |
+ |
/* global index offset for a third object (used to define a vector between sites in molecule). */ |
| 1332 |
+ |
else if (strcmp (long_options[option_index].name, "seleoffset2") == 0) |
| 1333 |
+ |
{ |
| 1334 |
+ |
|
| 1335 |
+ |
|
| 1336 |
+ |
if (update_arg( (void *)&(args_info->seleoffset2_arg), |
| 1337 |
+ |
&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given), |
| 1338 |
+ |
&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT, |
| 1339 |
+ |
check_ambiguity, override, 0, 0, |
| 1340 |
+ |
"seleoffset2", '-', |
| 1341 |
+ |
additional_error)) |
| 1342 |
+ |
goto failure; |
| 1343 |
+ |
|
| 1344 |
+ |
} |
| 1345 |
|
/* molecule name. */ |
| 1346 |
|
else if (strcmp (long_options[option_index].name, "molname") == 0) |
| 1347 |
|
{ |
| 1398 |
|
goto failure; |
| 1399 |
|
|
| 1400 |
|
} |
| 1401 |
+ |
/* Gaussian width (angstroms). */ |
| 1402 |
+ |
else if (strcmp (long_options[option_index].name, "gaussWidth") == 0) |
| 1403 |
+ |
{ |
| 1404 |
+ |
|
| 1405 |
+ |
|
| 1406 |
+ |
if (update_arg( (void *)&(args_info->gaussWidth_arg), |
| 1407 |
+ |
&(args_info->gaussWidth_orig), &(args_info->gaussWidth_given), |
| 1408 |
+ |
&(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE, |
| 1409 |
+ |
check_ambiguity, override, 0, 0, |
| 1410 |
+ |
"gaussWidth", '-', |
| 1411 |
+ |
additional_error)) |
| 1412 |
+ |
goto failure; |
| 1413 |
+ |
|
| 1414 |
+ |
} |
| 1415 |
|
/* bond order parameter (--rcut must be specified). */ |
| 1416 |
|
else if (strcmp (long_options[option_index].name, "bo") == 0) |
| 1417 |
|
{ |
| 1429 |
|
goto failure; |
| 1430 |
|
|
| 1431 |
|
} |
| 1432 |
< |
/* bond order parameter as a function of radius (--rcut must be specified). */ |
| 1433 |
< |
else if (strcmp (long_options[option_index].name, "bor") == 0) |
| 1432 |
> |
/* icosahedral bond order parameter as a function of radius (--rcut must be specified). */ |
| 1433 |
> |
else if (strcmp (long_options[option_index].name, "ior") == 0) |
| 1434 |
|
{ |
| 1435 |
|
|
| 1436 |
|
if (args_info->staticProps_group_counter && override) |
| 1438 |
|
args_info->staticProps_group_counter += 1; |
| 1439 |
|
|
| 1440 |
|
if (update_arg( 0 , |
| 1441 |
< |
0 , &(args_info->bor_given), |
| 1442 |
< |
&(local_args_info.bor_given), optarg, 0, 0, ARG_NO, |
| 1441 |
> |
0 , &(args_info->ior_given), |
| 1442 |
> |
&(local_args_info.ior_given), optarg, 0, 0, ARG_NO, |
| 1443 |
|
check_ambiguity, override, 0, 0, |
| 1444 |
< |
"bor", '-', |
| 1444 |
> |
"ior", '-', |
| 1445 |
> |
additional_error)) |
| 1446 |
> |
goto failure; |
| 1447 |
> |
|
| 1448 |
> |
} |
| 1449 |
> |
/* FCC bond order parameter as a function of radius (--rcut must be specified). */ |
| 1450 |
> |
else if (strcmp (long_options[option_index].name, "for") == 0) |
| 1451 |
> |
{ |
| 1452 |
> |
|
| 1453 |
> |
if (args_info->staticProps_group_counter && override) |
| 1454 |
> |
reset_group_staticProps (args_info); |
| 1455 |
> |
args_info->staticProps_group_counter += 1; |
| 1456 |
> |
|
| 1457 |
> |
if (update_arg( 0 , |
| 1458 |
> |
0 , &(args_info->for_given), |
| 1459 |
> |
&(local_args_info.for_given), optarg, 0, 0, ARG_NO, |
| 1460 |
> |
check_ambiguity, override, 0, 0, |
| 1461 |
> |
"for", '-', |
| 1462 |
|
additional_error)) |
| 1463 |
|
goto failure; |
| 1464 |
|
|
| 1769 |
|
goto failure; |
| 1770 |
|
|
| 1771 |
|
} |
| 1772 |
+ |
/* volume-resolved tetrahedrality order parameter Qk(x,y,z). (voxelSize, rcut, and gaussWidth must be specified). */ |
| 1773 |
+ |
else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0) |
| 1774 |
+ |
{ |
| 1775 |
+ |
|
| 1776 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1777 |
+ |
reset_group_staticProps (args_info); |
| 1778 |
+ |
args_info->staticProps_group_counter += 1; |
| 1779 |
+ |
|
| 1780 |
+ |
if (update_arg( 0 , |
| 1781 |
+ |
0 , &(args_info->tet_param_xyz_given), |
| 1782 |
+ |
&(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO, |
| 1783 |
+ |
check_ambiguity, override, 0, 0, |
| 1784 |
+ |
"tet_param_xyz", '-', |
| 1785 |
+ |
additional_error)) |
| 1786 |
+ |
goto failure; |
| 1787 |
+ |
|
| 1788 |
+ |
} |
| 1789 |
|
/* slab-resolved RNEMD statistics (temperature, density, velocity). */ |
| 1790 |
|
else if (strcmp (long_options[option_index].name, "rnemdz") == 0) |
| 1791 |
|
{ |
| 1833 |
|
&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO, |
| 1834 |
|
check_ambiguity, override, 0, 0, |
| 1835 |
|
"rnemdrt", '-', |
| 1836 |
+ |
additional_error)) |
| 1837 |
+ |
goto failure; |
| 1838 |
+ |
|
| 1839 |
+ |
} |
| 1840 |
+ |
/* electrostatic potential to frequency map based on the Cho nitrile fits. */ |
| 1841 |
+ |
else if (strcmp (long_options[option_index].name, "nitrile") == 0) |
| 1842 |
+ |
{ |
| 1843 |
+ |
|
| 1844 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1845 |
+ |
reset_group_staticProps (args_info); |
| 1846 |
+ |
args_info->staticProps_group_counter += 1; |
| 1847 |
+ |
|
| 1848 |
+ |
if (update_arg( 0 , |
| 1849 |
+ |
0 , &(args_info->nitrile_given), |
| 1850 |
+ |
&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO, |
| 1851 |
+ |
check_ambiguity, override, 0, 0, |
| 1852 |
+ |
"nitrile", '-', |
| 1853 |
+ |
additional_error)) |
| 1854 |
+ |
goto failure; |
| 1855 |
+ |
|
| 1856 |
+ |
} |
| 1857 |
+ |
/* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion. */ |
| 1858 |
+ |
else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0) |
| 1859 |
+ |
{ |
| 1860 |
+ |
|
| 1861 |
+ |
if (args_info->staticProps_group_counter && override) |
| 1862 |
+ |
reset_group_staticProps (args_info); |
| 1863 |
+ |
args_info->staticProps_group_counter += 1; |
| 1864 |
+ |
|
| 1865 |
+ |
if (update_arg( 0 , |
| 1866 |
+ |
0 , &(args_info->surfDiffusion_given), |
| 1867 |
+ |
&(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO, |
| 1868 |
+ |
check_ambiguity, override, 0, 0, |
| 1869 |
+ |
"surfDiffusion", '-', |
| 1870 |
|
additional_error)) |
| 1871 |
|
goto failure; |
| 1872 |
|
|
| 1901 |
|
if ( error ) |
| 1902 |
|
return (EXIT_FAILURE); |
| 1903 |
|
|
| 1734 |
– |
if (optind < argc) |
| 1735 |
– |
{ |
| 1736 |
– |
int i = 0 ; |
| 1737 |
– |
int found_prog_name = 0; |
| 1738 |
– |
/* whether program name, i.e., argv[0], is in the remaining args |
| 1739 |
– |
(this may happen with some implementations of getopt, |
| 1740 |
– |
but surely not with the one included by gengetopt) */ |
| 1741 |
– |
|
| 1742 |
– |
i = optind; |
| 1743 |
– |
while (i < argc) |
| 1744 |
– |
if (argv[i++] == argv[0]) { |
| 1745 |
– |
found_prog_name = 1; |
| 1746 |
– |
break; |
| 1747 |
– |
} |
| 1748 |
– |
i = 0; |
| 1749 |
– |
|
| 1750 |
– |
args_info->inputs_num = argc - optind - found_prog_name; |
| 1751 |
– |
args_info->inputs = |
| 1752 |
– |
(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; |
| 1753 |
– |
while (optind < argc) |
| 1754 |
– |
if (argv[optind++] != argv[0]) |
| 1755 |
– |
args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; |
| 1756 |
– |
} |
| 1757 |
– |
|
| 1904 |
|
return 0; |
| 1905 |
|
|
| 1906 |
|
failure: |
