| 1 |
/* |
| 2 |
File autogenerated by gengetopt version 2.22.4 |
| 3 |
generated with the following command: |
| 4 |
gengetopt -i StaticProps.ggo -F StaticPropsCmd -c cpp |
| 5 |
|
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The developers of gengetopt consider the fixed text that goes in all |
| 7 |
gengetopt output files to be in the public domain: |
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we make no copyright claims on it. |
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*/ |
| 10 |
|
| 11 |
/* If we use autoconf. */ |
| 12 |
#ifdef HAVE_CONFIG_H |
| 13 |
#include "config.h" |
| 14 |
#endif |
| 15 |
|
| 16 |
#include <stdio.h> |
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#include <stdlib.h> |
| 18 |
#include <string.h> |
| 19 |
|
| 20 |
#ifndef FIX_UNUSED |
| 21 |
#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ |
| 22 |
#endif |
| 23 |
|
| 24 |
#include <getopt.h> |
| 25 |
|
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#include "StaticPropsCmd.h" |
| 27 |
|
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const char *gengetopt_args_info_purpose = ""; |
| 29 |
|
| 30 |
const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]..."; |
| 31 |
|
| 32 |
const char *gengetopt_args_info_description = ""; |
| 33 |
|
| 34 |
const char *gengetopt_args_info_help[] = { |
| 35 |
" -h, --help Print help and exit", |
| 36 |
" -V, --version Print version and exit", |
| 37 |
" -i, --input=filename input dump file", |
| 38 |
" -o, --output=filename output file name", |
| 39 |
" -n, --step=INT process every n frame (default=`1')", |
| 40 |
" -b, --nbins=INT number of bins (general purpose) \n (default=`100')", |
| 41 |
" -x, --nbins_x=INT number of bins in x axis (default=`100')", |
| 42 |
" -y, --nbins_y=INT number of bins in y axis (default=`100')", |
| 43 |
" --nbins_z=INT number of bins in z axis (default=`100')", |
| 44 |
" -a, --nanglebins=INT number of bins for cos(angle) (default=`50')", |
| 45 |
" -c, --rcut=DOUBLE cutoff radius (rcut)", |
| 46 |
" --dz=DOUBLE slab width (dz)", |
| 47 |
" --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", |
| 48 |
" --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", |
| 49 |
" -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')", |
| 50 |
" --sele1=selection script select the first stuntdouble set", |
| 51 |
" --sele2=selection script select the second stuntdouble set", |
| 52 |
" --sele3=selection script select the third stuntdouble set", |
| 53 |
" --refsele=selection script\n select reference (use and only use with --gxyz)", |
| 54 |
" --comsele=selection script\n select stunt doubles for center-of-mass \n reference point", |
| 55 |
" --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 |
" --begin=INT begin internal index", |
| 59 |
" --end=INT end internal index", |
| 60 |
" --radius=DOUBLE nanoparticle radius", |
| 61 |
" -v, --voxelSize=DOUBLE voxel size (angstroms)", |
| 62 |
" --gaussWidth=DOUBLE Gaussian width (angstroms)", |
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"\n Group: staticProps\n an option of this group is required", |
| 64 |
" --bo bond order parameter (--rcut must be specified)", |
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" --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)", |
| 67 |
" --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)", |
| 70 |
" --gofz g(z)", |
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" --r_theta g(r, cos(theta))", |
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" --r_omega g(r, cos(omega))", |
| 73 |
" --r_z g(r, z)", |
| 74 |
" --theta_omega g(cos(theta), cos(omega))", |
| 75 |
" --gxyz g(x, y, z)", |
| 76 |
" --twodgofr 2D g(r) (Slab width --dz must be specified)", |
| 77 |
" -p, --p2 p2 order parameter (--sele1 must be specified, \n --sele2 is optional)", |
| 78 |
" --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)", |
| 80 |
" -d, --density density plot", |
| 81 |
" --slab_density slab density", |
| 82 |
" --p_angle p(cos(theta)) (--sele1 must be specified, \n --sele2 is optional)", |
| 83 |
" --hxy hxy", |
| 84 |
" --rho_r rho of R", |
| 85 |
" --angle_r angle of R", |
| 86 |
" --hullvol hull volume of nanoparticle", |
| 87 |
" --rodlength length of nanorod", |
| 88 |
" -Q, --tet_param tetrahedrality order parameter (Qk)", |
| 89 |
" --tet_param_z spatially-resolved tetrahedrality order \n parameter Qk(z)", |
| 90 |
" --tet_param_xyz volume-resolved tetrahedrality order parameter \n Qk(x,y,z). (voxelSize, rcut, and gaussWidth \n must be specified)", |
| 91 |
" --rnemdz slab-resolved RNEMD statistics (temperature, \n density, velocity)", |
| 92 |
" --rnemdr shell-resolved RNEMD statistics (temperature, \n density, angular velocity)", |
| 93 |
" --rnemdrt shell and angle-resolved RNEMD statistics \n (temperature, density, angular velocity)", |
| 94 |
" --nitrile electrostatic potential to frequency map based \n on the Cho nitrile fits", |
| 95 |
" -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", |
| 97 |
0 |
| 98 |
}; |
| 99 |
|
| 100 |
typedef enum {ARG_NO |
| 101 |
, ARG_STRING |
| 102 |
, ARG_INT |
| 103 |
, ARG_DOUBLE |
| 104 |
} cmdline_parser_arg_type; |
| 105 |
|
| 106 |
static |
| 107 |
void clear_given (struct gengetopt_args_info *args_info); |
| 108 |
static |
| 109 |
void clear_args (struct gengetopt_args_info *args_info); |
| 110 |
|
| 111 |
static int |
| 112 |
cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info, |
| 113 |
struct cmdline_parser_params *params, const char *additional_error); |
| 114 |
|
| 115 |
static int |
| 116 |
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error); |
| 117 |
|
| 118 |
static char * |
| 119 |
gengetopt_strdup (const char *s); |
| 120 |
|
| 121 |
static |
| 122 |
void clear_given (struct gengetopt_args_info *args_info) |
| 123 |
{ |
| 124 |
args_info->help_given = 0 ; |
| 125 |
args_info->version_given = 0 ; |
| 126 |
args_info->input_given = 0 ; |
| 127 |
args_info->output_given = 0 ; |
| 128 |
args_info->step_given = 0 ; |
| 129 |
args_info->nbins_given = 0 ; |
| 130 |
args_info->nbins_x_given = 0 ; |
| 131 |
args_info->nbins_y_given = 0 ; |
| 132 |
args_info->nbins_z_given = 0 ; |
| 133 |
args_info->nanglebins_given = 0 ; |
| 134 |
args_info->rcut_given = 0 ; |
| 135 |
args_info->dz_given = 0 ; |
| 136 |
args_info->length_given = 0 ; |
| 137 |
args_info->zlength_given = 0 ; |
| 138 |
args_info->zoffset_given = 0 ; |
| 139 |
args_info->sele1_given = 0 ; |
| 140 |
args_info->sele2_given = 0 ; |
| 141 |
args_info->sele3_given = 0 ; |
| 142 |
args_info->refsele_given = 0 ; |
| 143 |
args_info->comsele_given = 0 ; |
| 144 |
args_info->seleoffset_given = 0 ; |
| 145 |
args_info->seleoffset2_given = 0 ; |
| 146 |
args_info->molname_given = 0 ; |
| 147 |
args_info->begin_given = 0 ; |
| 148 |
args_info->end_given = 0 ; |
| 149 |
args_info->radius_given = 0 ; |
| 150 |
args_info->voxelSize_given = 0 ; |
| 151 |
args_info->gaussWidth_given = 0 ; |
| 152 |
args_info->bo_given = 0 ; |
| 153 |
args_info->ior_given = 0 ; |
| 154 |
args_info->for_given = 0 ; |
| 155 |
args_info->bad_given = 0 ; |
| 156 |
args_info->count_given = 0 ; |
| 157 |
args_info->gofr_given = 0 ; |
| 158 |
args_info->gofz_given = 0 ; |
| 159 |
args_info->r_theta_given = 0 ; |
| 160 |
args_info->r_omega_given = 0 ; |
| 161 |
args_info->r_z_given = 0 ; |
| 162 |
args_info->theta_omega_given = 0 ; |
| 163 |
args_info->gxyz_given = 0 ; |
| 164 |
args_info->twodgofr_given = 0 ; |
| 165 |
args_info->p2_given = 0 ; |
| 166 |
args_info->rp2_given = 0 ; |
| 167 |
args_info->scd_given = 0 ; |
| 168 |
args_info->density_given = 0 ; |
| 169 |
args_info->slab_density_given = 0 ; |
| 170 |
args_info->p_angle_given = 0 ; |
| 171 |
args_info->hxy_given = 0 ; |
| 172 |
args_info->rho_r_given = 0 ; |
| 173 |
args_info->angle_r_given = 0 ; |
| 174 |
args_info->hullvol_given = 0 ; |
| 175 |
args_info->rodlength_given = 0 ; |
| 176 |
args_info->tet_param_given = 0 ; |
| 177 |
args_info->tet_param_z_given = 0 ; |
| 178 |
args_info->tet_param_xyz_given = 0 ; |
| 179 |
args_info->rnemdz_given = 0 ; |
| 180 |
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 |
args_info->staticProps_group_counter = 0 ; |
| 186 |
} |
| 187 |
|
| 188 |
static |
| 189 |
void clear_args (struct gengetopt_args_info *args_info) |
| 190 |
{ |
| 191 |
FIX_UNUSED (args_info); |
| 192 |
args_info->input_arg = NULL; |
| 193 |
args_info->input_orig = NULL; |
| 194 |
args_info->output_arg = NULL; |
| 195 |
args_info->output_orig = NULL; |
| 196 |
args_info->step_arg = 1; |
| 197 |
args_info->step_orig = NULL; |
| 198 |
args_info->nbins_arg = 100; |
| 199 |
args_info->nbins_orig = NULL; |
| 200 |
args_info->nbins_x_arg = 100; |
| 201 |
args_info->nbins_x_orig = NULL; |
| 202 |
args_info->nbins_y_arg = 100; |
| 203 |
args_info->nbins_y_orig = NULL; |
| 204 |
args_info->nbins_z_arg = 100; |
| 205 |
args_info->nbins_z_orig = NULL; |
| 206 |
args_info->nanglebins_arg = 50; |
| 207 |
args_info->nanglebins_orig = NULL; |
| 208 |
args_info->rcut_orig = NULL; |
| 209 |
args_info->dz_orig = NULL; |
| 210 |
args_info->length_orig = NULL; |
| 211 |
args_info->zlength_orig = NULL; |
| 212 |
args_info->zoffset_arg = 0; |
| 213 |
args_info->zoffset_orig = NULL; |
| 214 |
args_info->sele1_arg = NULL; |
| 215 |
args_info->sele1_orig = NULL; |
| 216 |
args_info->sele2_arg = NULL; |
| 217 |
args_info->sele2_orig = NULL; |
| 218 |
args_info->sele3_arg = NULL; |
| 219 |
args_info->sele3_orig = NULL; |
| 220 |
args_info->refsele_arg = NULL; |
| 221 |
args_info->refsele_orig = NULL; |
| 222 |
args_info->comsele_arg = NULL; |
| 223 |
args_info->comsele_orig = NULL; |
| 224 |
args_info->seleoffset_orig = NULL; |
| 225 |
args_info->seleoffset2_orig = NULL; |
| 226 |
args_info->molname_arg = NULL; |
| 227 |
args_info->molname_orig = NULL; |
| 228 |
args_info->begin_orig = NULL; |
| 229 |
args_info->end_orig = NULL; |
| 230 |
args_info->radius_orig = NULL; |
| 231 |
args_info->voxelSize_orig = NULL; |
| 232 |
args_info->gaussWidth_orig = NULL; |
| 233 |
|
| 234 |
} |
| 235 |
|
| 236 |
static |
| 237 |
void init_args_info(struct gengetopt_args_info *args_info) |
| 238 |
{ |
| 239 |
|
| 240 |
|
| 241 |
args_info->help_help = gengetopt_args_info_help[0] ; |
| 242 |
args_info->version_help = gengetopt_args_info_help[1] ; |
| 243 |
args_info->input_help = gengetopt_args_info_help[2] ; |
| 244 |
args_info->output_help = gengetopt_args_info_help[3] ; |
| 245 |
args_info->step_help = gengetopt_args_info_help[4] ; |
| 246 |
args_info->nbins_help = gengetopt_args_info_help[5] ; |
| 247 |
args_info->nbins_x_help = gengetopt_args_info_help[6] ; |
| 248 |
args_info->nbins_y_help = gengetopt_args_info_help[7] ; |
| 249 |
args_info->nbins_z_help = gengetopt_args_info_help[8] ; |
| 250 |
args_info->nanglebins_help = gengetopt_args_info_help[9] ; |
| 251 |
args_info->rcut_help = gengetopt_args_info_help[10] ; |
| 252 |
args_info->dz_help = gengetopt_args_info_help[11] ; |
| 253 |
args_info->length_help = gengetopt_args_info_help[12] ; |
| 254 |
args_info->zlength_help = gengetopt_args_info_help[13] ; |
| 255 |
args_info->zoffset_help = gengetopt_args_info_help[14] ; |
| 256 |
args_info->sele1_help = gengetopt_args_info_help[15] ; |
| 257 |
args_info->sele2_help = gengetopt_args_info_help[16] ; |
| 258 |
args_info->sele3_help = gengetopt_args_info_help[17] ; |
| 259 |
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->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 |
} |
| 304 |
|
| 305 |
void |
| 306 |
cmdline_parser_print_version (void) |
| 307 |
{ |
| 308 |
printf ("%s %s\n", |
| 309 |
(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE), |
| 310 |
CMDLINE_PARSER_VERSION); |
| 311 |
} |
| 312 |
|
| 313 |
static void print_help_common(void) { |
| 314 |
cmdline_parser_print_version (); |
| 315 |
|
| 316 |
if (strlen(gengetopt_args_info_purpose) > 0) |
| 317 |
printf("\n%s\n", gengetopt_args_info_purpose); |
| 318 |
|
| 319 |
if (strlen(gengetopt_args_info_usage) > 0) |
| 320 |
printf("\n%s\n", gengetopt_args_info_usage); |
| 321 |
|
| 322 |
printf("\n"); |
| 323 |
|
| 324 |
if (strlen(gengetopt_args_info_description) > 0) |
| 325 |
printf("%s\n\n", gengetopt_args_info_description); |
| 326 |
} |
| 327 |
|
| 328 |
void |
| 329 |
cmdline_parser_print_help (void) |
| 330 |
{ |
| 331 |
int i = 0; |
| 332 |
print_help_common(); |
| 333 |
while (gengetopt_args_info_help[i]) |
| 334 |
printf("%s\n", gengetopt_args_info_help[i++]); |
| 335 |
} |
| 336 |
|
| 337 |
void |
| 338 |
cmdline_parser_init (struct gengetopt_args_info *args_info) |
| 339 |
{ |
| 340 |
clear_given (args_info); |
| 341 |
clear_args (args_info); |
| 342 |
init_args_info (args_info); |
| 343 |
} |
| 344 |
|
| 345 |
void |
| 346 |
cmdline_parser_params_init(struct cmdline_parser_params *params) |
| 347 |
{ |
| 348 |
if (params) |
| 349 |
{ |
| 350 |
params->override = 0; |
| 351 |
params->initialize = 1; |
| 352 |
params->check_required = 1; |
| 353 |
params->check_ambiguity = 0; |
| 354 |
params->print_errors = 1; |
| 355 |
} |
| 356 |
} |
| 357 |
|
| 358 |
struct cmdline_parser_params * |
| 359 |
cmdline_parser_params_create(void) |
| 360 |
{ |
| 361 |
struct cmdline_parser_params *params = |
| 362 |
(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params)); |
| 363 |
cmdline_parser_params_init(params); |
| 364 |
return params; |
| 365 |
} |
| 366 |
|
| 367 |
static void |
| 368 |
free_string_field (char **s) |
| 369 |
{ |
| 370 |
if (*s) |
| 371 |
{ |
| 372 |
free (*s); |
| 373 |
*s = 0; |
| 374 |
} |
| 375 |
} |
| 376 |
|
| 377 |
|
| 378 |
static void |
| 379 |
cmdline_parser_release (struct gengetopt_args_info *args_info) |
| 380 |
{ |
| 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)); |
| 385 |
free_string_field (&(args_info->output_orig)); |
| 386 |
free_string_field (&(args_info->step_orig)); |
| 387 |
free_string_field (&(args_info->nbins_orig)); |
| 388 |
free_string_field (&(args_info->nbins_x_orig)); |
| 389 |
free_string_field (&(args_info->nbins_y_orig)); |
| 390 |
free_string_field (&(args_info->nbins_z_orig)); |
| 391 |
free_string_field (&(args_info->nanglebins_orig)); |
| 392 |
free_string_field (&(args_info->rcut_orig)); |
| 393 |
free_string_field (&(args_info->dz_orig)); |
| 394 |
free_string_field (&(args_info->length_orig)); |
| 395 |
free_string_field (&(args_info->zlength_orig)); |
| 396 |
free_string_field (&(args_info->zoffset_orig)); |
| 397 |
free_string_field (&(args_info->sele1_arg)); |
| 398 |
free_string_field (&(args_info->sele1_orig)); |
| 399 |
free_string_field (&(args_info->sele2_arg)); |
| 400 |
free_string_field (&(args_info->sele2_orig)); |
| 401 |
free_string_field (&(args_info->sele3_arg)); |
| 402 |
free_string_field (&(args_info->sele3_orig)); |
| 403 |
free_string_field (&(args_info->refsele_arg)); |
| 404 |
free_string_field (&(args_info->refsele_orig)); |
| 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 |
|
| 418 |
|
| 419 |
clear_given (args_info); |
| 420 |
} |
| 421 |
|
| 422 |
|
| 423 |
static void |
| 424 |
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) |
| 425 |
{ |
| 426 |
FIX_UNUSED (values); |
| 427 |
if (arg) { |
| 428 |
fprintf(outfile, "%s=\"%s\"\n", opt, arg); |
| 429 |
} else { |
| 430 |
fprintf(outfile, "%s\n", opt); |
| 431 |
} |
| 432 |
} |
| 433 |
|
| 434 |
|
| 435 |
int |
| 436 |
cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info) |
| 437 |
{ |
| 438 |
int i = 0; |
| 439 |
|
| 440 |
if (!outfile) |
| 441 |
{ |
| 442 |
fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE); |
| 443 |
return EXIT_FAILURE; |
| 444 |
} |
| 445 |
|
| 446 |
if (args_info->help_given) |
| 447 |
write_into_file(outfile, "help", 0, 0 ); |
| 448 |
if (args_info->version_given) |
| 449 |
write_into_file(outfile, "version", 0, 0 ); |
| 450 |
if (args_info->input_given) |
| 451 |
write_into_file(outfile, "input", args_info->input_orig, 0); |
| 452 |
if (args_info->output_given) |
| 453 |
write_into_file(outfile, "output", args_info->output_orig, 0); |
| 454 |
if (args_info->step_given) |
| 455 |
write_into_file(outfile, "step", args_info->step_orig, 0); |
| 456 |
if (args_info->nbins_given) |
| 457 |
write_into_file(outfile, "nbins", args_info->nbins_orig, 0); |
| 458 |
if (args_info->nbins_x_given) |
| 459 |
write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0); |
| 460 |
if (args_info->nbins_y_given) |
| 461 |
write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0); |
| 462 |
if (args_info->nbins_z_given) |
| 463 |
write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); |
| 464 |
if (args_info->nanglebins_given) |
| 465 |
write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); |
| 466 |
if (args_info->rcut_given) |
| 467 |
write_into_file(outfile, "rcut", args_info->rcut_orig, 0); |
| 468 |
if (args_info->dz_given) |
| 469 |
write_into_file(outfile, "dz", args_info->dz_orig, 0); |
| 470 |
if (args_info->length_given) |
| 471 |
write_into_file(outfile, "length", args_info->length_orig, 0); |
| 472 |
if (args_info->zlength_given) |
| 473 |
write_into_file(outfile, "zlength", args_info->zlength_orig, 0); |
| 474 |
if (args_info->zoffset_given) |
| 475 |
write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); |
| 476 |
if (args_info->sele1_given) |
| 477 |
write_into_file(outfile, "sele1", args_info->sele1_orig, 0); |
| 478 |
if (args_info->sele2_given) |
| 479 |
write_into_file(outfile, "sele2", args_info->sele2_orig, 0); |
| 480 |
if (args_info->sele3_given) |
| 481 |
write_into_file(outfile, "sele3", args_info->sele3_orig, 0); |
| 482 |
if (args_info->refsele_given) |
| 483 |
write_into_file(outfile, "refsele", args_info->refsele_orig, 0); |
| 484 |
if (args_info->comsele_given) |
| 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) |
| 493 |
write_into_file(outfile, "begin", args_info->begin_orig, 0); |
| 494 |
if (args_info->end_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->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) |
| 511 |
write_into_file(outfile, "count", 0, 0 ); |
| 512 |
if (args_info->gofr_given) |
| 513 |
write_into_file(outfile, "gofr", 0, 0 ); |
| 514 |
if (args_info->gofz_given) |
| 515 |
write_into_file(outfile, "gofz", 0, 0 ); |
| 516 |
if (args_info->r_theta_given) |
| 517 |
write_into_file(outfile, "r_theta", 0, 0 ); |
| 518 |
if (args_info->r_omega_given) |
| 519 |
write_into_file(outfile, "r_omega", 0, 0 ); |
| 520 |
if (args_info->r_z_given) |
| 521 |
write_into_file(outfile, "r_z", 0, 0 ); |
| 522 |
if (args_info->theta_omega_given) |
| 523 |
write_into_file(outfile, "theta_omega", 0, 0 ); |
| 524 |
if (args_info->gxyz_given) |
| 525 |
write_into_file(outfile, "gxyz", 0, 0 ); |
| 526 |
if (args_info->twodgofr_given) |
| 527 |
write_into_file(outfile, "twodgofr", 0, 0 ); |
| 528 |
if (args_info->p2_given) |
| 529 |
write_into_file(outfile, "p2", 0, 0 ); |
| 530 |
if (args_info->rp2_given) |
| 531 |
write_into_file(outfile, "rp2", 0, 0 ); |
| 532 |
if (args_info->scd_given) |
| 533 |
write_into_file(outfile, "scd", 0, 0 ); |
| 534 |
if (args_info->density_given) |
| 535 |
write_into_file(outfile, "density", 0, 0 ); |
| 536 |
if (args_info->slab_density_given) |
| 537 |
write_into_file(outfile, "slab_density", 0, 0 ); |
| 538 |
if (args_info->p_angle_given) |
| 539 |
write_into_file(outfile, "p_angle", 0, 0 ); |
| 540 |
if (args_info->hxy_given) |
| 541 |
write_into_file(outfile, "hxy", 0, 0 ); |
| 542 |
if (args_info->rho_r_given) |
| 543 |
write_into_file(outfile, "rho_r", 0, 0 ); |
| 544 |
if (args_info->angle_r_given) |
| 545 |
write_into_file(outfile, "angle_r", 0, 0 ); |
| 546 |
if (args_info->hullvol_given) |
| 547 |
write_into_file(outfile, "hullvol", 0, 0 ); |
| 548 |
if (args_info->rodlength_given) |
| 549 |
write_into_file(outfile, "rodlength", 0, 0 ); |
| 550 |
if (args_info->tet_param_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; |
| 571 |
return i; |
| 572 |
} |
| 573 |
|
| 574 |
int |
| 575 |
cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) |
| 576 |
{ |
| 577 |
FILE *outfile; |
| 578 |
int i = 0; |
| 579 |
|
| 580 |
outfile = fopen(filename, "w"); |
| 581 |
|
| 582 |
if (!outfile) |
| 583 |
{ |
| 584 |
fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename); |
| 585 |
return EXIT_FAILURE; |
| 586 |
} |
| 587 |
|
| 588 |
i = cmdline_parser_dump(outfile, args_info); |
| 589 |
fclose (outfile); |
| 590 |
|
| 591 |
return i; |
| 592 |
} |
| 593 |
|
| 594 |
void |
| 595 |
cmdline_parser_free (struct gengetopt_args_info *args_info) |
| 596 |
{ |
| 597 |
cmdline_parser_release (args_info); |
| 598 |
} |
| 599 |
|
| 600 |
/** @brief replacement of strdup, which is not standard */ |
| 601 |
char * |
| 602 |
gengetopt_strdup (const char *s) |
| 603 |
{ |
| 604 |
char *result = 0; |
| 605 |
if (!s) |
| 606 |
return result; |
| 607 |
|
| 608 |
result = (char*)malloc(strlen(s) + 1); |
| 609 |
if (result == (char*)0) |
| 610 |
return (char*)0; |
| 611 |
strcpy(result, s); |
| 612 |
return result; |
| 613 |
} |
| 614 |
|
| 615 |
static void |
| 616 |
reset_group_staticProps(struct gengetopt_args_info *args_info) |
| 617 |
{ |
| 618 |
if (! args_info->staticProps_group_counter) |
| 619 |
return; |
| 620 |
|
| 621 |
args_info->bo_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 ; |
| 627 |
args_info->gofz_given = 0 ; |
| 628 |
args_info->r_theta_given = 0 ; |
| 629 |
args_info->r_omega_given = 0 ; |
| 630 |
args_info->r_z_given = 0 ; |
| 631 |
args_info->theta_omega_given = 0 ; |
| 632 |
args_info->gxyz_given = 0 ; |
| 633 |
args_info->twodgofr_given = 0 ; |
| 634 |
args_info->p2_given = 0 ; |
| 635 |
args_info->rp2_given = 0 ; |
| 636 |
args_info->scd_given = 0 ; |
| 637 |
args_info->density_given = 0 ; |
| 638 |
args_info->slab_density_given = 0 ; |
| 639 |
args_info->p_angle_given = 0 ; |
| 640 |
args_info->hxy_given = 0 ; |
| 641 |
args_info->rho_r_given = 0 ; |
| 642 |
args_info->angle_r_given = 0 ; |
| 643 |
args_info->hullvol_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 |
} |
| 657 |
|
| 658 |
int |
| 659 |
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info) |
| 660 |
{ |
| 661 |
return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); |
| 662 |
} |
| 663 |
|
| 664 |
int |
| 665 |
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, |
| 666 |
struct cmdline_parser_params *params) |
| 667 |
{ |
| 668 |
int result; |
| 669 |
result = cmdline_parser_internal (argc, argv, args_info, params, 0); |
| 670 |
|
| 671 |
if (result == EXIT_FAILURE) |
| 672 |
{ |
| 673 |
cmdline_parser_free (args_info); |
| 674 |
exit (EXIT_FAILURE); |
| 675 |
} |
| 676 |
|
| 677 |
return result; |
| 678 |
} |
| 679 |
|
| 680 |
int |
| 681 |
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
| 682 |
{ |
| 683 |
int result; |
| 684 |
struct cmdline_parser_params params; |
| 685 |
|
| 686 |
params.override = override; |
| 687 |
params.initialize = initialize; |
| 688 |
params.check_required = check_required; |
| 689 |
params.check_ambiguity = 0; |
| 690 |
params.print_errors = 1; |
| 691 |
|
| 692 |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); |
| 693 |
|
| 694 |
if (result == EXIT_FAILURE) |
| 695 |
{ |
| 696 |
cmdline_parser_free (args_info); |
| 697 |
exit (EXIT_FAILURE); |
| 698 |
} |
| 699 |
|
| 700 |
return result; |
| 701 |
} |
| 702 |
|
| 703 |
int |
| 704 |
cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name) |
| 705 |
{ |
| 706 |
int result = EXIT_SUCCESS; |
| 707 |
|
| 708 |
if (cmdline_parser_required2(args_info, prog_name, 0) > 0) |
| 709 |
result = EXIT_FAILURE; |
| 710 |
|
| 711 |
if (result == EXIT_FAILURE) |
| 712 |
{ |
| 713 |
cmdline_parser_free (args_info); |
| 714 |
exit (EXIT_FAILURE); |
| 715 |
} |
| 716 |
|
| 717 |
return result; |
| 718 |
} |
| 719 |
|
| 720 |
int |
| 721 |
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) |
| 722 |
{ |
| 723 |
int error = 0; |
| 724 |
FIX_UNUSED (additional_error); |
| 725 |
|
| 726 |
/* checks for required options */ |
| 727 |
if (! args_info->input_given) |
| 728 |
{ |
| 729 |
fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : "")); |
| 730 |
error = 1; |
| 731 |
} |
| 732 |
|
| 733 |
if (args_info->staticProps_group_counter == 0) |
| 734 |
{ |
| 735 |
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 : "")); |
| 736 |
error = 1; |
| 737 |
} |
| 738 |
|
| 739 |
|
| 740 |
/* checks for dependences among options */ |
| 741 |
|
| 742 |
return error; |
| 743 |
} |
| 744 |
|
| 745 |
|
| 746 |
static char *package_name = 0; |
| 747 |
|
| 748 |
/** |
| 749 |
* @brief updates an option |
| 750 |
* @param field the generic pointer to the field to update |
| 751 |
* @param orig_field the pointer to the orig field |
| 752 |
* @param field_given the pointer to the number of occurrence of this option |
| 753 |
* @param prev_given the pointer to the number of occurrence already seen |
| 754 |
* @param value the argument for this option (if null no arg was specified) |
| 755 |
* @param possible_values the possible values for this option (if specified) |
| 756 |
* @param default_value the default value (in case the option only accepts fixed values) |
| 757 |
* @param arg_type the type of this option |
| 758 |
* @param check_ambiguity @see cmdline_parser_params.check_ambiguity |
| 759 |
* @param override @see cmdline_parser_params.override |
| 760 |
* @param no_free whether to free a possible previous value |
| 761 |
* @param multiple_option whether this is a multiple option |
| 762 |
* @param long_opt the corresponding long option |
| 763 |
* @param short_opt the corresponding short option (or '-' if none) |
| 764 |
* @param additional_error possible further error specification |
| 765 |
*/ |
| 766 |
static |
| 767 |
int update_arg(void *field, char **orig_field, |
| 768 |
unsigned int *field_given, unsigned int *prev_given, |
| 769 |
char *value, const char *possible_values[], |
| 770 |
const char *default_value, |
| 771 |
cmdline_parser_arg_type arg_type, |
| 772 |
int check_ambiguity, int override, |
| 773 |
int no_free, int multiple_option, |
| 774 |
const char *long_opt, char short_opt, |
| 775 |
const char *additional_error) |
| 776 |
{ |
| 777 |
char *stop_char = 0; |
| 778 |
const char *val = value; |
| 779 |
int found; |
| 780 |
char **string_field; |
| 781 |
FIX_UNUSED (field); |
| 782 |
|
| 783 |
stop_char = 0; |
| 784 |
found = 0; |
| 785 |
|
| 786 |
if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) |
| 787 |
{ |
| 788 |
if (short_opt != '-') |
| 789 |
fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", |
| 790 |
package_name, long_opt, short_opt, |
| 791 |
(additional_error ? additional_error : "")); |
| 792 |
else |
| 793 |
fprintf (stderr, "%s: `--%s' option given more than once%s\n", |
| 794 |
package_name, long_opt, |
| 795 |
(additional_error ? additional_error : "")); |
| 796 |
return 1; /* failure */ |
| 797 |
} |
| 798 |
|
| 799 |
FIX_UNUSED (default_value); |
| 800 |
|
| 801 |
if (field_given && *field_given && ! override) |
| 802 |
return 0; |
| 803 |
if (prev_given) |
| 804 |
(*prev_given)++; |
| 805 |
if (field_given) |
| 806 |
(*field_given)++; |
| 807 |
if (possible_values) |
| 808 |
val = possible_values[found]; |
| 809 |
|
| 810 |
switch(arg_type) { |
| 811 |
case ARG_INT: |
| 812 |
if (val) *((int *)field) = strtol (val, &stop_char, 0); |
| 813 |
break; |
| 814 |
case ARG_DOUBLE: |
| 815 |
if (val) *((double *)field) = strtod (val, &stop_char); |
| 816 |
break; |
| 817 |
case ARG_STRING: |
| 818 |
if (val) { |
| 819 |
string_field = (char **)field; |
| 820 |
if (!no_free && *string_field) |
| 821 |
free (*string_field); /* free previous string */ |
| 822 |
*string_field = gengetopt_strdup (val); |
| 823 |
} |
| 824 |
break; |
| 825 |
default: |
| 826 |
break; |
| 827 |
}; |
| 828 |
|
| 829 |
/* check numeric conversion */ |
| 830 |
switch(arg_type) { |
| 831 |
case ARG_INT: |
| 832 |
case ARG_DOUBLE: |
| 833 |
if (val && !(stop_char && *stop_char == '\0')) { |
| 834 |
fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val); |
| 835 |
return 1; /* failure */ |
| 836 |
} |
| 837 |
break; |
| 838 |
default: |
| 839 |
; |
| 840 |
}; |
| 841 |
|
| 842 |
/* store the original value */ |
| 843 |
switch(arg_type) { |
| 844 |
case ARG_NO: |
| 845 |
break; |
| 846 |
default: |
| 847 |
if (value && orig_field) { |
| 848 |
if (no_free) { |
| 849 |
*orig_field = value; |
| 850 |
} else { |
| 851 |
if (*orig_field) |
| 852 |
free (*orig_field); /* free previous string */ |
| 853 |
*orig_field = gengetopt_strdup (value); |
| 854 |
} |
| 855 |
} |
| 856 |
}; |
| 857 |
|
| 858 |
return 0; /* OK */ |
| 859 |
} |
| 860 |
|
| 861 |
|
| 862 |
int |
| 863 |
cmdline_parser_internal ( |
| 864 |
int argc, char **argv, struct gengetopt_args_info *args_info, |
| 865 |
struct cmdline_parser_params *params, const char *additional_error) |
| 866 |
{ |
| 867 |
int c; /* Character of the parsed option. */ |
| 868 |
|
| 869 |
int error = 0; |
| 870 |
struct gengetopt_args_info local_args_info; |
| 871 |
|
| 872 |
int override; |
| 873 |
int initialize; |
| 874 |
int check_required; |
| 875 |
int check_ambiguity; |
| 876 |
|
| 877 |
package_name = argv[0]; |
| 878 |
|
| 879 |
override = params->override; |
| 880 |
initialize = params->initialize; |
| 881 |
check_required = params->check_required; |
| 882 |
check_ambiguity = params->check_ambiguity; |
| 883 |
|
| 884 |
if (initialize) |
| 885 |
cmdline_parser_init (args_info); |
| 886 |
|
| 887 |
cmdline_parser_init (&local_args_info); |
| 888 |
|
| 889 |
optarg = 0; |
| 890 |
optind = 0; |
| 891 |
opterr = params->print_errors; |
| 892 |
optopt = '?'; |
| 893 |
|
| 894 |
while (1) |
| 895 |
{ |
| 896 |
int option_index = 0; |
| 897 |
|
| 898 |
static struct option long_options[] = { |
| 899 |
{ "help", 0, NULL, 'h' }, |
| 900 |
{ "version", 0, NULL, 'V' }, |
| 901 |
{ "input", 1, NULL, 'i' }, |
| 902 |
{ "output", 1, NULL, 'o' }, |
| 903 |
{ "step", 1, NULL, 'n' }, |
| 904 |
{ "nbins", 1, NULL, 'b' }, |
| 905 |
{ "nbins_x", 1, NULL, 'x' }, |
| 906 |
{ "nbins_y", 1, NULL, 'y' }, |
| 907 |
{ "nbins_z", 1, NULL, 0 }, |
| 908 |
{ "nanglebins", 1, NULL, 'a' }, |
| 909 |
{ "rcut", 1, NULL, 'c' }, |
| 910 |
{ "dz", 1, NULL, 0 }, |
| 911 |
{ "length", 1, NULL, 0 }, |
| 912 |
{ "zlength", 1, NULL, 0 }, |
| 913 |
{ "zoffset", 1, NULL, 'z' }, |
| 914 |
{ "sele1", 1, NULL, 0 }, |
| 915 |
{ "sele2", 1, NULL, 0 }, |
| 916 |
{ "sele3", 1, NULL, 0 }, |
| 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 |
{ "ior", 0, NULL, 0 }, |
| 929 |
{ "for", 0, NULL, 0 }, |
| 930 |
{ "bad", 0, NULL, 0 }, |
| 931 |
{ "count", 0, NULL, 0 }, |
| 932 |
{ "gofr", 0, NULL, 'g' }, |
| 933 |
{ "gofz", 0, NULL, 0 }, |
| 934 |
{ "r_theta", 0, NULL, 0 }, |
| 935 |
{ "r_omega", 0, NULL, 0 }, |
| 936 |
{ "r_z", 0, NULL, 0 }, |
| 937 |
{ "theta_omega", 0, NULL, 0 }, |
| 938 |
{ "gxyz", 0, NULL, 0 }, |
| 939 |
{ "twodgofr", 0, NULL, 0 }, |
| 940 |
{ "p2", 0, NULL, 'p' }, |
| 941 |
{ "rp2", 0, NULL, 0 }, |
| 942 |
{ "scd", 0, NULL, 's' }, |
| 943 |
{ "density", 0, NULL, 'd' }, |
| 944 |
{ "slab_density", 0, NULL, 0 }, |
| 945 |
{ "p_angle", 0, NULL, 0 }, |
| 946 |
{ "hxy", 0, NULL, 0 }, |
| 947 |
{ "rho_r", 0, NULL, 0 }, |
| 948 |
{ "angle_r", 0, NULL, 0 }, |
| 949 |
{ "hullvol", 0, NULL, 0 }, |
| 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:v:gpsdQm", long_options, &option_index); |
| 964 |
|
| 965 |
if (c == -1) break; /* Exit from `while (1)' loop. */ |
| 966 |
|
| 967 |
switch (c) |
| 968 |
{ |
| 969 |
case 'h': /* Print help and exit. */ |
| 970 |
cmdline_parser_print_help (); |
| 971 |
cmdline_parser_free (&local_args_info); |
| 972 |
exit (EXIT_SUCCESS); |
| 973 |
|
| 974 |
case 'V': /* Print version and exit. */ |
| 975 |
cmdline_parser_print_version (); |
| 976 |
cmdline_parser_free (&local_args_info); |
| 977 |
exit (EXIT_SUCCESS); |
| 978 |
|
| 979 |
case 'i': /* input dump file. */ |
| 980 |
|
| 981 |
|
| 982 |
if (update_arg( (void *)&(args_info->input_arg), |
| 983 |
&(args_info->input_orig), &(args_info->input_given), |
| 984 |
&(local_args_info.input_given), optarg, 0, 0, ARG_STRING, |
| 985 |
check_ambiguity, override, 0, 0, |
| 986 |
"input", 'i', |
| 987 |
additional_error)) |
| 988 |
goto failure; |
| 989 |
|
| 990 |
break; |
| 991 |
case 'o': /* output file name. */ |
| 992 |
|
| 993 |
|
| 994 |
if (update_arg( (void *)&(args_info->output_arg), |
| 995 |
&(args_info->output_orig), &(args_info->output_given), |
| 996 |
&(local_args_info.output_given), optarg, 0, 0, ARG_STRING, |
| 997 |
check_ambiguity, override, 0, 0, |
| 998 |
"output", 'o', |
| 999 |
additional_error)) |
| 1000 |
goto failure; |
| 1001 |
|
| 1002 |
break; |
| 1003 |
case 'n': /* process every n frame. */ |
| 1004 |
|
| 1005 |
|
| 1006 |
if (update_arg( (void *)&(args_info->step_arg), |
| 1007 |
&(args_info->step_orig), &(args_info->step_given), |
| 1008 |
&(local_args_info.step_given), optarg, 0, "1", ARG_INT, |
| 1009 |
check_ambiguity, override, 0, 0, |
| 1010 |
"step", 'n', |
| 1011 |
additional_error)) |
| 1012 |
goto failure; |
| 1013 |
|
| 1014 |
break; |
| 1015 |
case 'b': /* number of bins (general purpose). */ |
| 1016 |
|
| 1017 |
|
| 1018 |
if (update_arg( (void *)&(args_info->nbins_arg), |
| 1019 |
&(args_info->nbins_orig), &(args_info->nbins_given), |
| 1020 |
&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT, |
| 1021 |
check_ambiguity, override, 0, 0, |
| 1022 |
"nbins", 'b', |
| 1023 |
additional_error)) |
| 1024 |
goto failure; |
| 1025 |
|
| 1026 |
break; |
| 1027 |
case 'x': /* number of bins in x axis. */ |
| 1028 |
|
| 1029 |
|
| 1030 |
if (update_arg( (void *)&(args_info->nbins_x_arg), |
| 1031 |
&(args_info->nbins_x_orig), &(args_info->nbins_x_given), |
| 1032 |
&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT, |
| 1033 |
check_ambiguity, override, 0, 0, |
| 1034 |
"nbins_x", 'x', |
| 1035 |
additional_error)) |
| 1036 |
goto failure; |
| 1037 |
|
| 1038 |
break; |
| 1039 |
case 'y': /* number of bins in y axis. */ |
| 1040 |
|
| 1041 |
|
| 1042 |
if (update_arg( (void *)&(args_info->nbins_y_arg), |
| 1043 |
&(args_info->nbins_y_orig), &(args_info->nbins_y_given), |
| 1044 |
&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT, |
| 1045 |
check_ambiguity, override, 0, 0, |
| 1046 |
"nbins_y", 'y', |
| 1047 |
additional_error)) |
| 1048 |
goto failure; |
| 1049 |
|
| 1050 |
break; |
| 1051 |
case 'a': /* number of bins for cos(angle). */ |
| 1052 |
|
| 1053 |
|
| 1054 |
if (update_arg( (void *)&(args_info->nanglebins_arg), |
| 1055 |
&(args_info->nanglebins_orig), &(args_info->nanglebins_given), |
| 1056 |
&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT, |
| 1057 |
check_ambiguity, override, 0, 0, |
| 1058 |
"nanglebins", 'a', |
| 1059 |
additional_error)) |
| 1060 |
goto failure; |
| 1061 |
|
| 1062 |
break; |
| 1063 |
case 'c': /* cutoff radius (rcut). */ |
| 1064 |
|
| 1065 |
|
| 1066 |
if (update_arg( (void *)&(args_info->rcut_arg), |
| 1067 |
&(args_info->rcut_orig), &(args_info->rcut_given), |
| 1068 |
&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE, |
| 1069 |
check_ambiguity, override, 0, 0, |
| 1070 |
"rcut", 'c', |
| 1071 |
additional_error)) |
| 1072 |
goto failure; |
| 1073 |
|
| 1074 |
break; |
| 1075 |
case 'z': /* Where to set the zero for the slab_density calculation. */ |
| 1076 |
|
| 1077 |
|
| 1078 |
if (update_arg( (void *)&(args_info->zoffset_arg), |
| 1079 |
&(args_info->zoffset_orig), &(args_info->zoffset_given), |
| 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 |
|
| 1098 |
break; |
| 1099 |
case 'g': /* g(r). */ |
| 1100 |
|
| 1101 |
if (args_info->staticProps_group_counter && override) |
| 1102 |
reset_group_staticProps (args_info); |
| 1103 |
args_info->staticProps_group_counter += 1; |
| 1104 |
|
| 1105 |
if (update_arg( 0 , |
| 1106 |
0 , &(args_info->gofr_given), |
| 1107 |
&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO, |
| 1108 |
check_ambiguity, override, 0, 0, |
| 1109 |
"gofr", 'g', |
| 1110 |
additional_error)) |
| 1111 |
goto failure; |
| 1112 |
|
| 1113 |
break; |
| 1114 |
case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */ |
| 1115 |
|
| 1116 |
if (args_info->staticProps_group_counter && override) |
| 1117 |
reset_group_staticProps (args_info); |
| 1118 |
args_info->staticProps_group_counter += 1; |
| 1119 |
|
| 1120 |
if (update_arg( 0 , |
| 1121 |
0 , &(args_info->p2_given), |
| 1122 |
&(local_args_info.p2_given), optarg, 0, 0, ARG_NO, |
| 1123 |
check_ambiguity, override, 0, 0, |
| 1124 |
"p2", 'p', |
| 1125 |
additional_error)) |
| 1126 |
goto failure; |
| 1127 |
|
| 1128 |
break; |
| 1129 |
case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */ |
| 1130 |
|
| 1131 |
if (args_info->staticProps_group_counter && override) |
| 1132 |
reset_group_staticProps (args_info); |
| 1133 |
args_info->staticProps_group_counter += 1; |
| 1134 |
|
| 1135 |
if (update_arg( 0 , |
| 1136 |
0 , &(args_info->scd_given), |
| 1137 |
&(local_args_info.scd_given), optarg, 0, 0, ARG_NO, |
| 1138 |
check_ambiguity, override, 0, 0, |
| 1139 |
"scd", 's', |
| 1140 |
additional_error)) |
| 1141 |
goto failure; |
| 1142 |
|
| 1143 |
break; |
| 1144 |
case 'd': /* density plot. */ |
| 1145 |
|
| 1146 |
if (args_info->staticProps_group_counter && override) |
| 1147 |
reset_group_staticProps (args_info); |
| 1148 |
args_info->staticProps_group_counter += 1; |
| 1149 |
|
| 1150 |
if (update_arg( 0 , |
| 1151 |
0 , &(args_info->density_given), |
| 1152 |
&(local_args_info.density_given), optarg, 0, 0, ARG_NO, |
| 1153 |
check_ambiguity, override, 0, 0, |
| 1154 |
"density", 'd', |
| 1155 |
additional_error)) |
| 1156 |
goto failure; |
| 1157 |
|
| 1158 |
break; |
| 1159 |
case 'Q': /* tetrahedrality order parameter (Qk). */ |
| 1160 |
|
| 1161 |
if (args_info->staticProps_group_counter && override) |
| 1162 |
reset_group_staticProps (args_info); |
| 1163 |
args_info->staticProps_group_counter += 1; |
| 1164 |
|
| 1165 |
if (update_arg( 0 , |
| 1166 |
0 , &(args_info->tet_param_given), |
| 1167 |
&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO, |
| 1168 |
check_ambiguity, override, 0, 0, |
| 1169 |
"tet_param", 'Q', |
| 1170 |
additional_error)) |
| 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. */ |
| 1192 |
if (strcmp (long_options[option_index].name, "nbins_z") == 0) |
| 1193 |
{ |
| 1194 |
|
| 1195 |
|
| 1196 |
if (update_arg( (void *)&(args_info->nbins_z_arg), |
| 1197 |
&(args_info->nbins_z_orig), &(args_info->nbins_z_given), |
| 1198 |
&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, |
| 1199 |
check_ambiguity, override, 0, 0, |
| 1200 |
"nbins_z", '-', |
| 1201 |
additional_error)) |
| 1202 |
goto failure; |
| 1203 |
|
| 1204 |
} |
| 1205 |
/* slab width (dz). */ |
| 1206 |
else if (strcmp (long_options[option_index].name, "dz") == 0) |
| 1207 |
{ |
| 1208 |
|
| 1209 |
|
| 1210 |
if (update_arg( (void *)&(args_info->dz_arg), |
| 1211 |
&(args_info->dz_orig), &(args_info->dz_given), |
| 1212 |
&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, |
| 1213 |
check_ambiguity, override, 0, 0, |
| 1214 |
"dz", '-', |
| 1215 |
additional_error)) |
| 1216 |
goto failure; |
| 1217 |
|
| 1218 |
} |
| 1219 |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1220 |
else if (strcmp (long_options[option_index].name, "length") == 0) |
| 1221 |
{ |
| 1222 |
|
| 1223 |
|
| 1224 |
if (update_arg( (void *)&(args_info->length_arg), |
| 1225 |
&(args_info->length_orig), &(args_info->length_given), |
| 1226 |
&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE, |
| 1227 |
check_ambiguity, override, 0, 0, |
| 1228 |
"length", '-', |
| 1229 |
additional_error)) |
| 1230 |
goto failure; |
| 1231 |
|
| 1232 |
} |
| 1233 |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
| 1234 |
else if (strcmp (long_options[option_index].name, "zlength") == 0) |
| 1235 |
{ |
| 1236 |
|
| 1237 |
|
| 1238 |
if (update_arg( (void *)&(args_info->zlength_arg), |
| 1239 |
&(args_info->zlength_orig), &(args_info->zlength_given), |
| 1240 |
&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, |
| 1241 |
check_ambiguity, override, 0, 0, |
| 1242 |
"zlength", '-', |
| 1243 |
additional_error)) |
| 1244 |
goto failure; |
| 1245 |
|
| 1246 |
} |
| 1247 |
/* select the first stuntdouble set. */ |
| 1248 |
else if (strcmp (long_options[option_index].name, "sele1") == 0) |
| 1249 |
{ |
| 1250 |
|
| 1251 |
|
| 1252 |
if (update_arg( (void *)&(args_info->sele1_arg), |
| 1253 |
&(args_info->sele1_orig), &(args_info->sele1_given), |
| 1254 |
&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING, |
| 1255 |
check_ambiguity, override, 0, 0, |
| 1256 |
"sele1", '-', |
| 1257 |
additional_error)) |
| 1258 |
goto failure; |
| 1259 |
|
| 1260 |
} |
| 1261 |
/* select the second stuntdouble set. */ |
| 1262 |
else if (strcmp (long_options[option_index].name, "sele2") == 0) |
| 1263 |
{ |
| 1264 |
|
| 1265 |
|
| 1266 |
if (update_arg( (void *)&(args_info->sele2_arg), |
| 1267 |
&(args_info->sele2_orig), &(args_info->sele2_given), |
| 1268 |
&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING, |
| 1269 |
check_ambiguity, override, 0, 0, |
| 1270 |
"sele2", '-', |
| 1271 |
additional_error)) |
| 1272 |
goto failure; |
| 1273 |
|
| 1274 |
} |
| 1275 |
/* select the third stuntdouble set. */ |
| 1276 |
else if (strcmp (long_options[option_index].name, "sele3") == 0) |
| 1277 |
{ |
| 1278 |
|
| 1279 |
|
| 1280 |
if (update_arg( (void *)&(args_info->sele3_arg), |
| 1281 |
&(args_info->sele3_orig), &(args_info->sele3_given), |
| 1282 |
&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING, |
| 1283 |
check_ambiguity, override, 0, 0, |
| 1284 |
"sele3", '-', |
| 1285 |
additional_error)) |
| 1286 |
goto failure; |
| 1287 |
|
| 1288 |
} |
| 1289 |
/* select reference (use and only use with --gxyz). */ |
| 1290 |
else if (strcmp (long_options[option_index].name, "refsele") == 0) |
| 1291 |
{ |
| 1292 |
|
| 1293 |
|
| 1294 |
if (update_arg( (void *)&(args_info->refsele_arg), |
| 1295 |
&(args_info->refsele_orig), &(args_info->refsele_given), |
| 1296 |
&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING, |
| 1297 |
check_ambiguity, override, 0, 0, |
| 1298 |
"refsele", '-', |
| 1299 |
additional_error)) |
| 1300 |
goto failure; |
| 1301 |
|
| 1302 |
} |
| 1303 |
/* select stunt doubles for center-of-mass reference point. */ |
| 1304 |
else if (strcmp (long_options[option_index].name, "comsele") == 0) |
| 1305 |
{ |
| 1306 |
|
| 1307 |
|
| 1308 |
if (update_arg( (void *)&(args_info->comsele_arg), |
| 1309 |
&(args_info->comsele_orig), &(args_info->comsele_given), |
| 1310 |
&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING, |
| 1311 |
check_ambiguity, override, 0, 0, |
| 1312 |
"comsele", '-', |
| 1313 |
additional_error)) |
| 1314 |
goto failure; |
| 1315 |
|
| 1316 |
} |
| 1317 |
/* global index offset for a second object (used to define a vector between sites in molecule). */ |
| 1318 |
else if (strcmp (long_options[option_index].name, "seleoffset") == 0) |
| 1319 |
{ |
| 1320 |
|
| 1321 |
|
| 1322 |
if (update_arg( (void *)&(args_info->seleoffset_arg), |
| 1323 |
&(args_info->seleoffset_orig), &(args_info->seleoffset_given), |
| 1324 |
&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT, |
| 1325 |
check_ambiguity, override, 0, 0, |
| 1326 |
"seleoffset", '-', |
| 1327 |
additional_error)) |
| 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 |
{ |
| 1348 |
|
| 1349 |
|
| 1350 |
if (update_arg( (void *)&(args_info->molname_arg), |
| 1351 |
&(args_info->molname_orig), &(args_info->molname_given), |
| 1352 |
&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING, |
| 1353 |
check_ambiguity, override, 0, 0, |
| 1354 |
"molname", '-', |
| 1355 |
additional_error)) |
| 1356 |
goto failure; |
| 1357 |
|
| 1358 |
} |
| 1359 |
/* begin internal index. */ |
| 1360 |
else if (strcmp (long_options[option_index].name, "begin") == 0) |
| 1361 |
{ |
| 1362 |
|
| 1363 |
|
| 1364 |
if (update_arg( (void *)&(args_info->begin_arg), |
| 1365 |
&(args_info->begin_orig), &(args_info->begin_given), |
| 1366 |
&(local_args_info.begin_given), optarg, 0, 0, ARG_INT, |
| 1367 |
check_ambiguity, override, 0, 0, |
| 1368 |
"begin", '-', |
| 1369 |
additional_error)) |
| 1370 |
goto failure; |
| 1371 |
|
| 1372 |
} |
| 1373 |
/* end internal index. */ |
| 1374 |
else if (strcmp (long_options[option_index].name, "end") == 0) |
| 1375 |
{ |
| 1376 |
|
| 1377 |
|
| 1378 |
if (update_arg( (void *)&(args_info->end_arg), |
| 1379 |
&(args_info->end_orig), &(args_info->end_given), |
| 1380 |
&(local_args_info.end_given), optarg, 0, 0, ARG_INT, |
| 1381 |
check_ambiguity, override, 0, 0, |
| 1382 |
"end", '-', |
| 1383 |
additional_error)) |
| 1384 |
goto failure; |
| 1385 |
|
| 1386 |
} |
| 1387 |
/* nanoparticle radius. */ |
| 1388 |
else if (strcmp (long_options[option_index].name, "radius") == 0) |
| 1389 |
{ |
| 1390 |
|
| 1391 |
|
| 1392 |
if (update_arg( (void *)&(args_info->radius_arg), |
| 1393 |
&(args_info->radius_orig), &(args_info->radius_given), |
| 1394 |
&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE, |
| 1395 |
check_ambiguity, override, 0, 0, |
| 1396 |
"radius", '-', |
| 1397 |
additional_error)) |
| 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 |
{ |
| 1418 |
|
| 1419 |
if (args_info->staticProps_group_counter && override) |
| 1420 |
reset_group_staticProps (args_info); |
| 1421 |
args_info->staticProps_group_counter += 1; |
| 1422 |
|
| 1423 |
if (update_arg( 0 , |
| 1424 |
0 , &(args_info->bo_given), |
| 1425 |
&(local_args_info.bo_given), optarg, 0, 0, ARG_NO, |
| 1426 |
check_ambiguity, override, 0, 0, |
| 1427 |
"bo", '-', |
| 1428 |
additional_error)) |
| 1429 |
goto failure; |
| 1430 |
|
| 1431 |
} |
| 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) |
| 1437 |
reset_group_staticProps (args_info); |
| 1438 |
args_info->staticProps_group_counter += 1; |
| 1439 |
|
| 1440 |
if (update_arg( 0 , |
| 1441 |
0 , &(args_info->ior_given), |
| 1442 |
&(local_args_info.ior_given), optarg, 0, 0, ARG_NO, |
| 1443 |
check_ambiguity, override, 0, 0, |
| 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 |
|
| 1465 |
} |
| 1466 |
/* N(theta) bond angle density within (--rcut must be specified). */ |
| 1467 |
else if (strcmp (long_options[option_index].name, "bad") == 0) |
| 1468 |
{ |
| 1469 |
|
| 1470 |
if (args_info->staticProps_group_counter && override) |
| 1471 |
reset_group_staticProps (args_info); |
| 1472 |
args_info->staticProps_group_counter += 1; |
| 1473 |
|
| 1474 |
if (update_arg( 0 , |
| 1475 |
0 , &(args_info->bad_given), |
| 1476 |
&(local_args_info.bad_given), optarg, 0, 0, ARG_NO, |
| 1477 |
check_ambiguity, override, 0, 0, |
| 1478 |
"bad", '-', |
| 1479 |
additional_error)) |
| 1480 |
goto failure; |
| 1481 |
|
| 1482 |
} |
| 1483 |
/* count of molecules matching selection criteria (and associated statistics). */ |
| 1484 |
else if (strcmp (long_options[option_index].name, "count") == 0) |
| 1485 |
{ |
| 1486 |
|
| 1487 |
if (args_info->staticProps_group_counter && override) |
| 1488 |
reset_group_staticProps (args_info); |
| 1489 |
args_info->staticProps_group_counter += 1; |
| 1490 |
|
| 1491 |
if (update_arg( 0 , |
| 1492 |
0 , &(args_info->count_given), |
| 1493 |
&(local_args_info.count_given), optarg, 0, 0, ARG_NO, |
| 1494 |
check_ambiguity, override, 0, 0, |
| 1495 |
"count", '-', |
| 1496 |
additional_error)) |
| 1497 |
goto failure; |
| 1498 |
|
| 1499 |
} |
| 1500 |
/* g(z). */ |
| 1501 |
else if (strcmp (long_options[option_index].name, "gofz") == 0) |
| 1502 |
{ |
| 1503 |
|
| 1504 |
if (args_info->staticProps_group_counter && override) |
| 1505 |
reset_group_staticProps (args_info); |
| 1506 |
args_info->staticProps_group_counter += 1; |
| 1507 |
|
| 1508 |
if (update_arg( 0 , |
| 1509 |
0 , &(args_info->gofz_given), |
| 1510 |
&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO, |
| 1511 |
check_ambiguity, override, 0, 0, |
| 1512 |
"gofz", '-', |
| 1513 |
additional_error)) |
| 1514 |
goto failure; |
| 1515 |
|
| 1516 |
} |
| 1517 |
/* g(r, cos(theta)). */ |
| 1518 |
else if (strcmp (long_options[option_index].name, "r_theta") == 0) |
| 1519 |
{ |
| 1520 |
|
| 1521 |
if (args_info->staticProps_group_counter && override) |
| 1522 |
reset_group_staticProps (args_info); |
| 1523 |
args_info->staticProps_group_counter += 1; |
| 1524 |
|
| 1525 |
if (update_arg( 0 , |
| 1526 |
0 , &(args_info->r_theta_given), |
| 1527 |
&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO, |
| 1528 |
check_ambiguity, override, 0, 0, |
| 1529 |
"r_theta", '-', |
| 1530 |
additional_error)) |
| 1531 |
goto failure; |
| 1532 |
|
| 1533 |
} |
| 1534 |
/* g(r, cos(omega)). */ |
| 1535 |
else if (strcmp (long_options[option_index].name, "r_omega") == 0) |
| 1536 |
{ |
| 1537 |
|
| 1538 |
if (args_info->staticProps_group_counter && override) |
| 1539 |
reset_group_staticProps (args_info); |
| 1540 |
args_info->staticProps_group_counter += 1; |
| 1541 |
|
| 1542 |
if (update_arg( 0 , |
| 1543 |
0 , &(args_info->r_omega_given), |
| 1544 |
&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO, |
| 1545 |
check_ambiguity, override, 0, 0, |
| 1546 |
"r_omega", '-', |
| 1547 |
additional_error)) |
| 1548 |
goto failure; |
| 1549 |
|
| 1550 |
} |
| 1551 |
/* g(r, z). */ |
| 1552 |
else if (strcmp (long_options[option_index].name, "r_z") == 0) |
| 1553 |
{ |
| 1554 |
|
| 1555 |
if (args_info->staticProps_group_counter && override) |
| 1556 |
reset_group_staticProps (args_info); |
| 1557 |
args_info->staticProps_group_counter += 1; |
| 1558 |
|
| 1559 |
if (update_arg( 0 , |
| 1560 |
0 , &(args_info->r_z_given), |
| 1561 |
&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO, |
| 1562 |
check_ambiguity, override, 0, 0, |
| 1563 |
"r_z", '-', |
| 1564 |
additional_error)) |
| 1565 |
goto failure; |
| 1566 |
|
| 1567 |
} |
| 1568 |
/* g(cos(theta), cos(omega)). */ |
| 1569 |
else if (strcmp (long_options[option_index].name, "theta_omega") == 0) |
| 1570 |
{ |
| 1571 |
|
| 1572 |
if (args_info->staticProps_group_counter && override) |
| 1573 |
reset_group_staticProps (args_info); |
| 1574 |
args_info->staticProps_group_counter += 1; |
| 1575 |
|
| 1576 |
if (update_arg( 0 , |
| 1577 |
0 , &(args_info->theta_omega_given), |
| 1578 |
&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, |
| 1579 |
check_ambiguity, override, 0, 0, |
| 1580 |
"theta_omega", '-', |
| 1581 |
additional_error)) |
| 1582 |
goto failure; |
| 1583 |
|
| 1584 |
} |
| 1585 |
/* g(x, y, z). */ |
| 1586 |
else if (strcmp (long_options[option_index].name, "gxyz") == 0) |
| 1587 |
{ |
| 1588 |
|
| 1589 |
if (args_info->staticProps_group_counter && override) |
| 1590 |
reset_group_staticProps (args_info); |
| 1591 |
args_info->staticProps_group_counter += 1; |
| 1592 |
|
| 1593 |
if (update_arg( 0 , |
| 1594 |
0 , &(args_info->gxyz_given), |
| 1595 |
&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, |
| 1596 |
check_ambiguity, override, 0, 0, |
| 1597 |
"gxyz", '-', |
| 1598 |
additional_error)) |
| 1599 |
goto failure; |
| 1600 |
|
| 1601 |
} |
| 1602 |
/* 2D g(r) (Slab width --dz must be specified). */ |
| 1603 |
else if (strcmp (long_options[option_index].name, "twodgofr") == 0) |
| 1604 |
{ |
| 1605 |
|
| 1606 |
if (args_info->staticProps_group_counter && override) |
| 1607 |
reset_group_staticProps (args_info); |
| 1608 |
args_info->staticProps_group_counter += 1; |
| 1609 |
|
| 1610 |
if (update_arg( 0 , |
| 1611 |
0 , &(args_info->twodgofr_given), |
| 1612 |
&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, |
| 1613 |
check_ambiguity, override, 0, 0, |
| 1614 |
"twodgofr", '-', |
| 1615 |
additional_error)) |
| 1616 |
goto failure; |
| 1617 |
|
| 1618 |
} |
| 1619 |
/* rp2 order parameter (--sele1 and --sele2 must be specified). */ |
| 1620 |
else if (strcmp (long_options[option_index].name, "rp2") == 0) |
| 1621 |
{ |
| 1622 |
|
| 1623 |
if (args_info->staticProps_group_counter && override) |
| 1624 |
reset_group_staticProps (args_info); |
| 1625 |
args_info->staticProps_group_counter += 1; |
| 1626 |
|
| 1627 |
if (update_arg( 0 , |
| 1628 |
0 , &(args_info->rp2_given), |
| 1629 |
&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO, |
| 1630 |
check_ambiguity, override, 0, 0, |
| 1631 |
"rp2", '-', |
| 1632 |
additional_error)) |
| 1633 |
goto failure; |
| 1634 |
|
| 1635 |
} |
| 1636 |
/* slab density. */ |
| 1637 |
else if (strcmp (long_options[option_index].name, "slab_density") == 0) |
| 1638 |
{ |
| 1639 |
|
| 1640 |
if (args_info->staticProps_group_counter && override) |
| 1641 |
reset_group_staticProps (args_info); |
| 1642 |
args_info->staticProps_group_counter += 1; |
| 1643 |
|
| 1644 |
if (update_arg( 0 , |
| 1645 |
0 , &(args_info->slab_density_given), |
| 1646 |
&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO, |
| 1647 |
check_ambiguity, override, 0, 0, |
| 1648 |
"slab_density", '-', |
| 1649 |
additional_error)) |
| 1650 |
goto failure; |
| 1651 |
|
| 1652 |
} |
| 1653 |
/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional). */ |
| 1654 |
else if (strcmp (long_options[option_index].name, "p_angle") == 0) |
| 1655 |
{ |
| 1656 |
|
| 1657 |
if (args_info->staticProps_group_counter && override) |
| 1658 |
reset_group_staticProps (args_info); |
| 1659 |
args_info->staticProps_group_counter += 1; |
| 1660 |
|
| 1661 |
if (update_arg( 0 , |
| 1662 |
0 , &(args_info->p_angle_given), |
| 1663 |
&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO, |
| 1664 |
check_ambiguity, override, 0, 0, |
| 1665 |
"p_angle", '-', |
| 1666 |
additional_error)) |
| 1667 |
goto failure; |
| 1668 |
|
| 1669 |
} |
| 1670 |
/* hxy. */ |
| 1671 |
else if (strcmp (long_options[option_index].name, "hxy") == 0) |
| 1672 |
{ |
| 1673 |
|
| 1674 |
if (args_info->staticProps_group_counter && override) |
| 1675 |
reset_group_staticProps (args_info); |
| 1676 |
args_info->staticProps_group_counter += 1; |
| 1677 |
|
| 1678 |
if (update_arg( 0 , |
| 1679 |
0 , &(args_info->hxy_given), |
| 1680 |
&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO, |
| 1681 |
check_ambiguity, override, 0, 0, |
| 1682 |
"hxy", '-', |
| 1683 |
additional_error)) |
| 1684 |
goto failure; |
| 1685 |
|
| 1686 |
} |
| 1687 |
/* rho of R. */ |
| 1688 |
else if (strcmp (long_options[option_index].name, "rho_r") == 0) |
| 1689 |
{ |
| 1690 |
|
| 1691 |
if (args_info->staticProps_group_counter && override) |
| 1692 |
reset_group_staticProps (args_info); |
| 1693 |
args_info->staticProps_group_counter += 1; |
| 1694 |
|
| 1695 |
if (update_arg( 0 , |
| 1696 |
0 , &(args_info->rho_r_given), |
| 1697 |
&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO, |
| 1698 |
check_ambiguity, override, 0, 0, |
| 1699 |
"rho_r", '-', |
| 1700 |
additional_error)) |
| 1701 |
goto failure; |
| 1702 |
|
| 1703 |
} |
| 1704 |
/* angle of R. */ |
| 1705 |
else if (strcmp (long_options[option_index].name, "angle_r") == 0) |
| 1706 |
{ |
| 1707 |
|
| 1708 |
if (args_info->staticProps_group_counter && override) |
| 1709 |
reset_group_staticProps (args_info); |
| 1710 |
args_info->staticProps_group_counter += 1; |
| 1711 |
|
| 1712 |
if (update_arg( 0 , |
| 1713 |
0 , &(args_info->angle_r_given), |
| 1714 |
&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, |
| 1715 |
check_ambiguity, override, 0, 0, |
| 1716 |
"angle_r", '-', |
| 1717 |
additional_error)) |
| 1718 |
goto failure; |
| 1719 |
|
| 1720 |
} |
| 1721 |
/* hull volume of nanoparticle. */ |
| 1722 |
else if (strcmp (long_options[option_index].name, "hullvol") == 0) |
| 1723 |
{ |
| 1724 |
|
| 1725 |
if (args_info->staticProps_group_counter && override) |
| 1726 |
reset_group_staticProps (args_info); |
| 1727 |
args_info->staticProps_group_counter += 1; |
| 1728 |
|
| 1729 |
if (update_arg( 0 , |
| 1730 |
0 , &(args_info->hullvol_given), |
| 1731 |
&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO, |
| 1732 |
check_ambiguity, override, 0, 0, |
| 1733 |
"hullvol", '-', |
| 1734 |
additional_error)) |
| 1735 |
goto failure; |
| 1736 |
|
| 1737 |
} |
| 1738 |
/* length of nanorod. */ |
| 1739 |
else if (strcmp (long_options[option_index].name, "rodlength") == 0) |
| 1740 |
{ |
| 1741 |
|
| 1742 |
if (args_info->staticProps_group_counter && override) |
| 1743 |
reset_group_staticProps (args_info); |
| 1744 |
args_info->staticProps_group_counter += 1; |
| 1745 |
|
| 1746 |
if (update_arg( 0 , |
| 1747 |
0 , &(args_info->rodlength_given), |
| 1748 |
&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO, |
| 1749 |
check_ambiguity, override, 0, 0, |
| 1750 |
"rodlength", '-', |
| 1751 |
additional_error)) |
| 1752 |
goto failure; |
| 1753 |
|
| 1754 |
} |
| 1755 |
/* spatially-resolved tetrahedrality order parameter Qk(z). */ |
| 1756 |
else if (strcmp (long_options[option_index].name, "tet_param_z") == 0) |
| 1757 |
{ |
| 1758 |
|
| 1759 |
if (args_info->staticProps_group_counter && override) |
| 1760 |
reset_group_staticProps (args_info); |
| 1761 |
args_info->staticProps_group_counter += 1; |
| 1762 |
|
| 1763 |
if (update_arg( 0 , |
| 1764 |
0 , &(args_info->tet_param_z_given), |
| 1765 |
&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO, |
| 1766 |
check_ambiguity, override, 0, 0, |
| 1767 |
"tet_param_z", '-', |
| 1768 |
additional_error)) |
| 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 |
{ |
| 1792 |
|
| 1793 |
if (args_info->staticProps_group_counter && override) |
| 1794 |
reset_group_staticProps (args_info); |
| 1795 |
args_info->staticProps_group_counter += 1; |
| 1796 |
|
| 1797 |
if (update_arg( 0 , |
| 1798 |
0 , &(args_info->rnemdz_given), |
| 1799 |
&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO, |
| 1800 |
check_ambiguity, override, 0, 0, |
| 1801 |
"rnemdz", '-', |
| 1802 |
additional_error)) |
| 1803 |
goto failure; |
| 1804 |
|
| 1805 |
} |
| 1806 |
/* shell-resolved RNEMD statistics (temperature, density, angular velocity). */ |
| 1807 |
else if (strcmp (long_options[option_index].name, "rnemdr") == 0) |
| 1808 |
{ |
| 1809 |
|
| 1810 |
if (args_info->staticProps_group_counter && override) |
| 1811 |
reset_group_staticProps (args_info); |
| 1812 |
args_info->staticProps_group_counter += 1; |
| 1813 |
|
| 1814 |
if (update_arg( 0 , |
| 1815 |
0 , &(args_info->rnemdr_given), |
| 1816 |
&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO, |
| 1817 |
check_ambiguity, override, 0, 0, |
| 1818 |
"rnemdr", '-', |
| 1819 |
additional_error)) |
| 1820 |
goto failure; |
| 1821 |
|
| 1822 |
} |
| 1823 |
/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity). */ |
| 1824 |
else if (strcmp (long_options[option_index].name, "rnemdrt") == 0) |
| 1825 |
{ |
| 1826 |
|
| 1827 |
if (args_info->staticProps_group_counter && override) |
| 1828 |
reset_group_staticProps (args_info); |
| 1829 |
args_info->staticProps_group_counter += 1; |
| 1830 |
|
| 1831 |
if (update_arg( 0 , |
| 1832 |
0 , &(args_info->rnemdrt_given), |
| 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 |
|
| 1873 |
} |
| 1874 |
|
| 1875 |
break; |
| 1876 |
case '?': /* Invalid option. */ |
| 1877 |
/* `getopt_long' already printed an error message. */ |
| 1878 |
goto failure; |
| 1879 |
|
| 1880 |
default: /* bug: option not considered. */ |
| 1881 |
fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); |
| 1882 |
abort (); |
| 1883 |
} /* switch */ |
| 1884 |
} /* while */ |
| 1885 |
|
| 1886 |
if (args_info->staticProps_group_counter > 1) |
| 1887 |
{ |
| 1888 |
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 : "")); |
| 1889 |
error = 1; |
| 1890 |
} |
| 1891 |
|
| 1892 |
|
| 1893 |
|
| 1894 |
if (check_required) |
| 1895 |
{ |
| 1896 |
error += cmdline_parser_required2 (args_info, argv[0], additional_error); |
| 1897 |
} |
| 1898 |
|
| 1899 |
cmdline_parser_release (&local_args_info); |
| 1900 |
|
| 1901 |
if ( error ) |
| 1902 |
return (EXIT_FAILURE); |
| 1903 |
|
| 1904 |
return 0; |
| 1905 |
|
| 1906 |
failure: |
| 1907 |
|
| 1908 |
cmdline_parser_release (&local_args_info); |
| 1909 |
return (EXIT_FAILURE); |
| 1910 |
} |
