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/* |
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File autogenerated by gengetopt version 2.22 |
3 |
generated with the following command: |
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gengetopt -F StaticPropsCmd -u |
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|
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The developers of gengetopt consider the fixed text that goes in all |
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gengetopt output files to be in the public domain: |
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we make no copyright claims on it. |
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*/ |
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|
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/* If we use autoconf. */ |
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#ifdef HAVE_CONFIG_H |
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#include "config.h" |
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#endif |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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|
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#include "getopt.h" |
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|
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#include "StaticPropsCmd.h" |
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|
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const char *gengetopt_args_info_purpose = ""; |
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|
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const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]..."; |
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|
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const char *gengetopt_args_info_description = ""; |
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|
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const char *gengetopt_args_info_help[] = { |
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" -h, --help Print help and exit", |
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" -V, --version Print version and exit", |
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" -i, --input=filename input dump file", |
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" -o, --output=filename output file name", |
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" -n, --step=INT process every n frame (default=`1')", |
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" -b, --nbins=INT number of bins (general purpose) \n (default=`100')", |
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" -x, --nbins_x=INT number of bins in x axis (default=`100')", |
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" -y, --nbins_y=INT number of bins in y axis (default=`100')", |
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" -a, --nanglebins=INT number of bins for cos(angle) (default=`50')", |
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" -c, --rcut=DOUBLE cutoff radius (rcut)", |
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" --dz=DOUBLE slab width (dz)", |
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" --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", |
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" --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)", |
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" -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')", |
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" --sele1=selection script select the first stuntdouble set", |
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" --sele2=selection script select the second stuntdouble set", |
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" --sele3=selection script select the third stuntdouble set", |
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" --refsele=selection script\n select reference (use and only use with --gxyz)", |
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" --comsele=selection script\n select stunt doubles for center-of-mass \n reference point", |
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" --molname=STRING molecule name", |
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" --begin=INT begin internal index", |
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" --end=INT end internal index", |
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" --radius=DOUBLE nanoparticle radius", |
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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)", |
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" --bor bond order parameter as a function of radius \n (--rcut must be specified)", |
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" --bad N(theta) bond angle density within (--rcut must \n be specified)", |
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" --count count of molecules matching selection criteria \n (and associated statistics)", |
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" -g, --gofr g(r)", |
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" --gofz g(z)", |
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" --r_theta g(r, cos(theta))", |
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" --r_omega g(r, cos(omega))", |
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" --theta_omega g(cos(theta), cos(omega))", |
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" --gxyz g(x, y, z)", |
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" --twodgofr 2D g(r) (Slab width --dz must be specified)", |
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" -p, --p2 p2 order parameter (--sele1 and --sele2 must be \n specified)", |
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" --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)", |
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" -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)", |
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" -d, --density density plot", |
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" --slab_density slab density", |
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" --p_angle p(cos(theta))", |
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" --hxy hxy", |
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" --rho_r rho of R", |
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" --angle_r angle of R", |
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" --hullvol hull volume of nanoparticle", |
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0 |
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}; |
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|
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typedef enum {ARG_NO |
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, ARG_STRING |
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, ARG_INT |
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, ARG_DOUBLE |
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} cmdline_parser_arg_type; |
84 |
|
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static |
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void clear_given (struct gengetopt_args_info *args_info); |
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static |
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void clear_args (struct gengetopt_args_info *args_info); |
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|
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static int |
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cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
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struct cmdline_parser_params *params, const char *additional_error); |
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|
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static int |
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cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error); |
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|
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static char * |
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gengetopt_strdup (const char *s); |
99 |
|
100 |
static |
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void clear_given (struct gengetopt_args_info *args_info) |
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{ |
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args_info->help_given = 0 ; |
104 |
args_info->version_given = 0 ; |
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args_info->input_given = 0 ; |
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args_info->output_given = 0 ; |
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args_info->step_given = 0 ; |
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args_info->nbins_given = 0 ; |
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args_info->nbins_x_given = 0 ; |
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args_info->nbins_y_given = 0 ; |
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args_info->nanglebins_given = 0 ; |
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args_info->rcut_given = 0 ; |
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args_info->dz_given = 0 ; |
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args_info->length_given = 0 ; |
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args_info->zlength_given = 0 ; |
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args_info->zoffset_given = 0 ; |
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args_info->sele1_given = 0 ; |
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args_info->sele2_given = 0 ; |
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args_info->sele3_given = 0 ; |
120 |
args_info->refsele_given = 0 ; |
121 |
args_info->comsele_given = 0 ; |
122 |
args_info->molname_given = 0 ; |
123 |
args_info->begin_given = 0 ; |
124 |
args_info->end_given = 0 ; |
125 |
args_info->radius_given = 0 ; |
126 |
args_info->bo_given = 0 ; |
127 |
args_info->bor_given = 0 ; |
128 |
args_info->bad_given = 0 ; |
129 |
args_info->count_given = 0 ; |
130 |
args_info->gofr_given = 0 ; |
131 |
args_info->gofz_given = 0 ; |
132 |
args_info->r_theta_given = 0 ; |
133 |
args_info->r_omega_given = 0 ; |
134 |
args_info->theta_omega_given = 0 ; |
135 |
args_info->gxyz_given = 0 ; |
136 |
args_info->twodgofr_given = 0 ; |
137 |
args_info->p2_given = 0 ; |
138 |
args_info->rp2_given = 0 ; |
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args_info->scd_given = 0 ; |
140 |
args_info->density_given = 0 ; |
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args_info->slab_density_given = 0 ; |
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args_info->p_angle_given = 0 ; |
143 |
args_info->hxy_given = 0 ; |
144 |
args_info->rho_r_given = 0 ; |
145 |
args_info->angle_r_given = 0 ; |
146 |
args_info->hullvol_given = 0 ; |
147 |
args_info->staticProps_group_counter = 0 ; |
148 |
} |
149 |
|
150 |
static |
151 |
void clear_args (struct gengetopt_args_info *args_info) |
152 |
{ |
153 |
args_info->input_arg = NULL; |
154 |
args_info->input_orig = NULL; |
155 |
args_info->output_arg = NULL; |
156 |
args_info->output_orig = NULL; |
157 |
args_info->step_arg = 1; |
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args_info->step_orig = NULL; |
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args_info->nbins_arg = 100; |
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args_info->nbins_orig = NULL; |
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args_info->nbins_x_arg = 100; |
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args_info->nbins_x_orig = NULL; |
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args_info->nbins_y_arg = 100; |
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args_info->nbins_y_orig = NULL; |
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args_info->nanglebins_arg = 50; |
166 |
args_info->nanglebins_orig = NULL; |
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args_info->rcut_orig = NULL; |
168 |
args_info->dz_orig = NULL; |
169 |
args_info->length_orig = NULL; |
170 |
args_info->zlength_orig = NULL; |
171 |
args_info->zoffset_arg = 0; |
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args_info->zoffset_orig = NULL; |
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args_info->sele1_arg = NULL; |
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args_info->sele1_orig = NULL; |
175 |
args_info->sele2_arg = NULL; |
176 |
args_info->sele2_orig = NULL; |
177 |
args_info->sele3_arg = NULL; |
178 |
args_info->sele3_orig = NULL; |
179 |
args_info->refsele_arg = NULL; |
180 |
args_info->refsele_orig = NULL; |
181 |
args_info->comsele_arg = NULL; |
182 |
args_info->comsele_orig = NULL; |
183 |
args_info->molname_arg = NULL; |
184 |
args_info->molname_orig = NULL; |
185 |
args_info->begin_orig = NULL; |
186 |
args_info->end_orig = NULL; |
187 |
args_info->radius_orig = NULL; |
188 |
|
189 |
} |
190 |
|
191 |
static |
192 |
void init_args_info(struct gengetopt_args_info *args_info) |
193 |
{ |
194 |
|
195 |
|
196 |
args_info->help_help = gengetopt_args_info_help[0] ; |
197 |
args_info->version_help = gengetopt_args_info_help[1] ; |
198 |
args_info->input_help = gengetopt_args_info_help[2] ; |
199 |
args_info->output_help = gengetopt_args_info_help[3] ; |
200 |
args_info->step_help = gengetopt_args_info_help[4] ; |
201 |
args_info->nbins_help = gengetopt_args_info_help[5] ; |
202 |
args_info->nbins_x_help = gengetopt_args_info_help[6] ; |
203 |
args_info->nbins_y_help = gengetopt_args_info_help[7] ; |
204 |
args_info->nbins_z_help = gengetopt_args_info_help[8] ; |
205 |
args_info->nanglebins_help = gengetopt_args_info_help[9] ; |
206 |
args_info->rcut_help = gengetopt_args_info_help[10] ; |
207 |
args_info->dz_help = gengetopt_args_info_help[11] ; |
208 |
args_info->length_help = gengetopt_args_info_help[12] ; |
209 |
args_info->zlength_help = gengetopt_args_info_help[13] ; |
210 |
args_info->zoffset_help = gengetopt_args_info_help[14] ; |
211 |
args_info->sele1_help = gengetopt_args_info_help[15] ; |
212 |
args_info->sele2_help = gengetopt_args_info_help[16] ; |
213 |
args_info->sele3_help = gengetopt_args_info_help[17] ; |
214 |
args_info->refsele_help = gengetopt_args_info_help[18] ; |
215 |
args_info->comsele_help = gengetopt_args_info_help[19] ; |
216 |
args_info->molname_help = gengetopt_args_info_help[20] ; |
217 |
args_info->begin_help = gengetopt_args_info_help[21] ; |
218 |
args_info->end_help = gengetopt_args_info_help[22] ; |
219 |
args_info->radius_help = gengetopt_args_info_help[23] ; |
220 |
args_info->bo_help = gengetopt_args_info_help[25] ; |
221 |
args_info->bor_help = gengetopt_args_info_help[26] ; |
222 |
args_info->bad_help = gengetopt_args_info_help[27] ; |
223 |
args_info->count_help = gengetopt_args_info_help[28] ; |
224 |
args_info->gofr_help = gengetopt_args_info_help[29] ; |
225 |
args_info->gofz_help = gengetopt_args_info_help[30] ; |
226 |
args_info->r_theta_help = gengetopt_args_info_help[31] ; |
227 |
args_info->r_omega_help = gengetopt_args_info_help[32] ; |
228 |
args_info->r_z_help = gengetopt_args_info_help[33] ; |
229 |
args_info->theta_omega_help = gengetopt_args_info_help[34] ; |
230 |
args_info->gxyz_help = gengetopt_args_info_help[35] ; |
231 |
args_info->twodgofr_help = gengetopt_args_info_help[36] ; |
232 |
args_info->p2_help = gengetopt_args_info_help[37] ; |
233 |
args_info->rp2_help = gengetopt_args_info_help[38] ; |
234 |
args_info->scd_help = gengetopt_args_info_help[39] ; |
235 |
args_info->density_help = gengetopt_args_info_help[40] ; |
236 |
args_info->slab_density_help = gengetopt_args_info_help[41] ; |
237 |
args_info->p_angle_help = gengetopt_args_info_help[42] ; |
238 |
args_info->hxy_help = gengetopt_args_info_help[43] ; |
239 |
args_info->rho_r_help = gengetopt_args_info_help[44] ; |
240 |
args_info->hullvol_help = gengetopt_args_info_help[45] ; |
241 |
|
242 |
} |
243 |
|
244 |
void |
245 |
cmdline_parser_print_version (void) |
246 |
{ |
247 |
printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); |
248 |
} |
249 |
|
250 |
static void print_help_common(void) { |
251 |
cmdline_parser_print_version (); |
252 |
|
253 |
if (strlen(gengetopt_args_info_purpose) > 0) |
254 |
printf("\n%s\n", gengetopt_args_info_purpose); |
255 |
|
256 |
if (strlen(gengetopt_args_info_usage) > 0) |
257 |
printf("\n%s\n", gengetopt_args_info_usage); |
258 |
|
259 |
printf("\n"); |
260 |
|
261 |
if (strlen(gengetopt_args_info_description) > 0) |
262 |
printf("%s\n", gengetopt_args_info_description); |
263 |
} |
264 |
|
265 |
void |
266 |
cmdline_parser_print_help (void) |
267 |
{ |
268 |
int i = 0; |
269 |
print_help_common(); |
270 |
while (gengetopt_args_info_help[i]) |
271 |
printf("%s\n", gengetopt_args_info_help[i++]); |
272 |
} |
273 |
|
274 |
void |
275 |
cmdline_parser_init (struct gengetopt_args_info *args_info) |
276 |
{ |
277 |
clear_given (args_info); |
278 |
clear_args (args_info); |
279 |
init_args_info (args_info); |
280 |
|
281 |
args_info->inputs = NULL; |
282 |
args_info->inputs_num = 0; |
283 |
} |
284 |
|
285 |
void |
286 |
cmdline_parser_params_init(struct cmdline_parser_params *params) |
287 |
{ |
288 |
if (params) |
289 |
{ |
290 |
params->override = 0; |
291 |
params->initialize = 1; |
292 |
params->check_required = 1; |
293 |
params->check_ambiguity = 0; |
294 |
params->print_errors = 1; |
295 |
} |
296 |
} |
297 |
|
298 |
struct cmdline_parser_params * |
299 |
cmdline_parser_params_create(void) |
300 |
{ |
301 |
struct cmdline_parser_params *params = |
302 |
(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params)); |
303 |
cmdline_parser_params_init(params); |
304 |
return params; |
305 |
} |
306 |
|
307 |
static void |
308 |
free_string_field (char **s) |
309 |
{ |
310 |
if (*s) |
311 |
{ |
312 |
free (*s); |
313 |
*s = 0; |
314 |
} |
315 |
} |
316 |
|
317 |
|
318 |
static void |
319 |
cmdline_parser_release (struct gengetopt_args_info *args_info) |
320 |
{ |
321 |
unsigned int i; |
322 |
free_string_field (&(args_info->input_arg)); |
323 |
free_string_field (&(args_info->input_orig)); |
324 |
free_string_field (&(args_info->output_arg)); |
325 |
free_string_field (&(args_info->output_orig)); |
326 |
free_string_field (&(args_info->step_orig)); |
327 |
free_string_field (&(args_info->nbins_orig)); |
328 |
free_string_field (&(args_info->nbins_x_orig)); |
329 |
free_string_field (&(args_info->nbins_y_orig)); |
330 |
free_string_field (&(args_info->nanglebins_orig)); |
331 |
free_string_field (&(args_info->rcut_orig)); |
332 |
free_string_field (&(args_info->dz_orig)); |
333 |
free_string_field (&(args_info->length_orig)); |
334 |
free_string_field (&(args_info->zlength_orig)); |
335 |
free_string_field (&(args_info->zoffset_orig)); |
336 |
free_string_field (&(args_info->sele1_arg)); |
337 |
free_string_field (&(args_info->sele1_orig)); |
338 |
free_string_field (&(args_info->sele2_arg)); |
339 |
free_string_field (&(args_info->sele2_orig)); |
340 |
free_string_field (&(args_info->sele3_arg)); |
341 |
free_string_field (&(args_info->sele3_orig)); |
342 |
free_string_field (&(args_info->refsele_arg)); |
343 |
free_string_field (&(args_info->refsele_orig)); |
344 |
free_string_field (&(args_info->comsele_arg)); |
345 |
free_string_field (&(args_info->comsele_orig)); |
346 |
free_string_field (&(args_info->molname_arg)); |
347 |
free_string_field (&(args_info->molname_orig)); |
348 |
free_string_field (&(args_info->begin_orig)); |
349 |
free_string_field (&(args_info->end_orig)); |
350 |
free_string_field (&(args_info->radius_orig)); |
351 |
|
352 |
|
353 |
for (i = 0; i < args_info->inputs_num; ++i) |
354 |
free (args_info->inputs [i]); |
355 |
|
356 |
if (args_info->inputs_num) |
357 |
free (args_info->inputs); |
358 |
|
359 |
clear_given (args_info); |
360 |
} |
361 |
|
362 |
|
363 |
static void |
364 |
write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) |
365 |
{ |
366 |
if (arg) { |
367 |
fprintf(outfile, "%s=\"%s\"\n", opt, arg); |
368 |
} else { |
369 |
fprintf(outfile, "%s\n", opt); |
370 |
} |
371 |
} |
372 |
|
373 |
|
374 |
int |
375 |
cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info) |
376 |
{ |
377 |
int i = 0; |
378 |
|
379 |
if (!outfile) |
380 |
{ |
381 |
fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE); |
382 |
return EXIT_FAILURE; |
383 |
} |
384 |
|
385 |
if (args_info->help_given) |
386 |
write_into_file(outfile, "help", 0, 0 ); |
387 |
if (args_info->version_given) |
388 |
write_into_file(outfile, "version", 0, 0 ); |
389 |
if (args_info->input_given) |
390 |
write_into_file(outfile, "input", args_info->input_orig, 0); |
391 |
if (args_info->output_given) |
392 |
write_into_file(outfile, "output", args_info->output_orig, 0); |
393 |
if (args_info->step_given) |
394 |
write_into_file(outfile, "step", args_info->step_orig, 0); |
395 |
if (args_info->nbins_given) |
396 |
write_into_file(outfile, "nbins", args_info->nbins_orig, 0); |
397 |
if (args_info->nbins_x_given) |
398 |
write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0); |
399 |
if (args_info->nbins_y_given) |
400 |
write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0); |
401 |
if (args_info->nanglebins_given) |
402 |
write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); |
403 |
if (args_info->rcut_given) |
404 |
write_into_file(outfile, "rcut", args_info->rcut_orig, 0); |
405 |
if (args_info->dz_given) |
406 |
write_into_file(outfile, "dz", args_info->dz_orig, 0); |
407 |
if (args_info->length_given) |
408 |
write_into_file(outfile, "length", args_info->length_orig, 0); |
409 |
if (args_info->zlength_given) |
410 |
write_into_file(outfile, "zlength", args_info->zlength_orig, 0); |
411 |
if (args_info->zoffset_given) |
412 |
write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); |
413 |
if (args_info->sele1_given) |
414 |
write_into_file(outfile, "sele1", args_info->sele1_orig, 0); |
415 |
if (args_info->sele2_given) |
416 |
write_into_file(outfile, "sele2", args_info->sele2_orig, 0); |
417 |
if (args_info->sele3_given) |
418 |
write_into_file(outfile, "sele3", args_info->sele3_orig, 0); |
419 |
if (args_info->refsele_given) |
420 |
write_into_file(outfile, "refsele", args_info->refsele_orig, 0); |
421 |
if (args_info->comsele_given) |
422 |
write_into_file(outfile, "comsele", args_info->comsele_orig, 0); |
423 |
if (args_info->molname_given) |
424 |
write_into_file(outfile, "molname", args_info->molname_orig, 0); |
425 |
if (args_info->begin_given) |
426 |
write_into_file(outfile, "begin", args_info->begin_orig, 0); |
427 |
if (args_info->end_given) |
428 |
write_into_file(outfile, "end", args_info->end_orig, 0); |
429 |
if (args_info->radius_given) |
430 |
write_into_file(outfile, "radius", args_info->radius_orig, 0); |
431 |
if (args_info->bo_given) |
432 |
write_into_file(outfile, "bo", 0, 0 ); |
433 |
if (args_info->bor_given) |
434 |
write_into_file(outfile, "bor", 0, 0 ); |
435 |
if (args_info->bad_given) |
436 |
write_into_file(outfile, "bad", 0, 0 ); |
437 |
if (args_info->count_given) |
438 |
write_into_file(outfile, "count", 0, 0 ); |
439 |
if (args_info->gofr_given) |
440 |
write_into_file(outfile, "gofr", 0, 0 ); |
441 |
if (args_info->gofz_given) |
442 |
write_into_file(outfile, "gofz", 0, 0 ); |
443 |
if (args_info->r_theta_given) |
444 |
write_into_file(outfile, "r_theta", 0, 0 ); |
445 |
if (args_info->r_omega_given) |
446 |
write_into_file(outfile, "r_omega", 0, 0 ); |
447 |
if (args_info->theta_omega_given) |
448 |
write_into_file(outfile, "theta_omega", 0, 0 ); |
449 |
if (args_info->gxyz_given) |
450 |
write_into_file(outfile, "gxyz", 0, 0 ); |
451 |
if (args_info->twodgofr_given) |
452 |
write_into_file(outfile, "twodgofr", 0, 0 ); |
453 |
if (args_info->p2_given) |
454 |
write_into_file(outfile, "p2", 0, 0 ); |
455 |
if (args_info->rp2_given) |
456 |
write_into_file(outfile, "rp2", 0, 0 ); |
457 |
if (args_info->scd_given) |
458 |
write_into_file(outfile, "scd", 0, 0 ); |
459 |
if (args_info->density_given) |
460 |
write_into_file(outfile, "density", 0, 0 ); |
461 |
if (args_info->slab_density_given) |
462 |
write_into_file(outfile, "slab_density", 0, 0 ); |
463 |
if (args_info->p_angle_given) |
464 |
write_into_file(outfile, "p_angle", 0, 0 ); |
465 |
if (args_info->hxy_given) |
466 |
write_into_file(outfile, "hxy", 0, 0 ); |
467 |
if (args_info->rho_r_given) |
468 |
write_into_file(outfile, "rho_r", 0, 0 ); |
469 |
if (args_info->angle_r_given) |
470 |
write_into_file(outfile, "angle_r", 0, 0 ); |
471 |
if (args_info->hullvol_given) |
472 |
write_into_file(outfile, "hullvol", 0, 0 ); |
473 |
|
474 |
|
475 |
i = EXIT_SUCCESS; |
476 |
return i; |
477 |
} |
478 |
|
479 |
int |
480 |
cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) |
481 |
{ |
482 |
FILE *outfile; |
483 |
int i = 0; |
484 |
|
485 |
outfile = fopen(filename, "w"); |
486 |
|
487 |
if (!outfile) |
488 |
{ |
489 |
fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename); |
490 |
return EXIT_FAILURE; |
491 |
} |
492 |
|
493 |
i = cmdline_parser_dump(outfile, args_info); |
494 |
fclose (outfile); |
495 |
|
496 |
return i; |
497 |
} |
498 |
|
499 |
void |
500 |
cmdline_parser_free (struct gengetopt_args_info *args_info) |
501 |
{ |
502 |
cmdline_parser_release (args_info); |
503 |
} |
504 |
|
505 |
/** @brief replacement of strdup, which is not standard */ |
506 |
char * |
507 |
gengetopt_strdup (const char *s) |
508 |
{ |
509 |
char *result = NULL; |
510 |
if (!s) |
511 |
return result; |
512 |
|
513 |
result = (char*)malloc(strlen(s) + 1); |
514 |
if (result == (char*)0) |
515 |
return (char*)0; |
516 |
strcpy(result, s); |
517 |
return result; |
518 |
} |
519 |
|
520 |
static void |
521 |
reset_group_staticProps(struct gengetopt_args_info *args_info) |
522 |
{ |
523 |
if (! args_info->staticProps_group_counter) |
524 |
return; |
525 |
|
526 |
args_info->bo_given = 0 ; |
527 |
args_info->bor_given = 0 ; |
528 |
args_info->bad_given = 0 ; |
529 |
args_info->count_given = 0 ; |
530 |
args_info->gofr_given = 0 ; |
531 |
args_info->gofz_given = 0 ; |
532 |
args_info->r_theta_given = 0 ; |
533 |
args_info->r_omega_given = 0 ; |
534 |
args_info->theta_omega_given = 0 ; |
535 |
args_info->gxyz_given = 0 ; |
536 |
args_info->twodgofr_given = 0 ; |
537 |
args_info->p2_given = 0 ; |
538 |
args_info->rp2_given = 0 ; |
539 |
args_info->scd_given = 0 ; |
540 |
args_info->density_given = 0 ; |
541 |
args_info->slab_density_given = 0 ; |
542 |
args_info->p_angle_given = 0 ; |
543 |
args_info->hxy_given = 0 ; |
544 |
args_info->rho_r_given = 0 ; |
545 |
args_info->angle_r_given = 0 ; |
546 |
args_info->hullvol_given = 0 ; |
547 |
|
548 |
args_info->staticProps_group_counter = 0; |
549 |
} |
550 |
|
551 |
int |
552 |
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) |
553 |
{ |
554 |
return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); |
555 |
} |
556 |
|
557 |
int |
558 |
cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
559 |
struct cmdline_parser_params *params) |
560 |
{ |
561 |
int result; |
562 |
result = cmdline_parser_internal (argc, argv, args_info, params, NULL); |
563 |
|
564 |
if (result == EXIT_FAILURE) |
565 |
{ |
566 |
cmdline_parser_free (args_info); |
567 |
exit (EXIT_FAILURE); |
568 |
} |
569 |
|
570 |
return result; |
571 |
} |
572 |
|
573 |
int |
574 |
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) |
575 |
{ |
576 |
int result; |
577 |
struct cmdline_parser_params params; |
578 |
|
579 |
params.override = override; |
580 |
params.initialize = initialize; |
581 |
params.check_required = check_required; |
582 |
params.check_ambiguity = 0; |
583 |
params.print_errors = 1; |
584 |
|
585 |
result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); |
586 |
|
587 |
if (result == EXIT_FAILURE) |
588 |
{ |
589 |
cmdline_parser_free (args_info); |
590 |
exit (EXIT_FAILURE); |
591 |
} |
592 |
|
593 |
return result; |
594 |
} |
595 |
|
596 |
int |
597 |
cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name) |
598 |
{ |
599 |
int result = EXIT_SUCCESS; |
600 |
|
601 |
if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) |
602 |
result = EXIT_FAILURE; |
603 |
|
604 |
if (result == EXIT_FAILURE) |
605 |
{ |
606 |
cmdline_parser_free (args_info); |
607 |
exit (EXIT_FAILURE); |
608 |
} |
609 |
|
610 |
return result; |
611 |
} |
612 |
|
613 |
int |
614 |
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) |
615 |
{ |
616 |
int error = 0; |
617 |
|
618 |
/* checks for required options */ |
619 |
if (! args_info->input_given) |
620 |
{ |
621 |
fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : "")); |
622 |
error = 1; |
623 |
} |
624 |
|
625 |
if (args_info->staticProps_group_counter == 0) |
626 |
{ |
627 |
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 : "")); |
628 |
error = 1; |
629 |
} |
630 |
|
631 |
|
632 |
/* checks for dependences among options */ |
633 |
|
634 |
return error; |
635 |
} |
636 |
|
637 |
|
638 |
static char *package_name = 0; |
639 |
|
640 |
/** |
641 |
* @brief updates an option |
642 |
* @param field the generic pointer to the field to update |
643 |
* @param orig_field the pointer to the orig field |
644 |
* @param field_given the pointer to the number of occurrence of this option |
645 |
* @param prev_given the pointer to the number of occurrence already seen |
646 |
* @param value the argument for this option (if null no arg was specified) |
647 |
* @param possible_values the possible values for this option (if specified) |
648 |
* @param default_value the default value (in case the option only accepts fixed values) |
649 |
* @param arg_type the type of this option |
650 |
* @param check_ambiguity @see cmdline_parser_params.check_ambiguity |
651 |
* @param override @see cmdline_parser_params.override |
652 |
* @param no_free whether to free a possible previous value |
653 |
* @param multiple_option whether this is a multiple option |
654 |
* @param long_opt the corresponding long option |
655 |
* @param short_opt the corresponding short option (or '-' if none) |
656 |
* @param additional_error possible further error specification |
657 |
*/ |
658 |
static |
659 |
int update_arg(void *field, char **orig_field, |
660 |
unsigned int *field_given, unsigned int *prev_given, |
661 |
char *value, char *possible_values[], const char *default_value, |
662 |
cmdline_parser_arg_type arg_type, |
663 |
int check_ambiguity, int override, |
664 |
int no_free, int multiple_option, |
665 |
const char *long_opt, char short_opt, |
666 |
const char *additional_error) |
667 |
{ |
668 |
char *stop_char = 0; |
669 |
const char *val = value; |
670 |
int found; |
671 |
char **string_field; |
672 |
|
673 |
stop_char = 0; |
674 |
found = 0; |
675 |
|
676 |
if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) |
677 |
{ |
678 |
if (short_opt != '-') |
679 |
fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", |
680 |
package_name, long_opt, short_opt, |
681 |
(additional_error ? additional_error : "")); |
682 |
else |
683 |
fprintf (stderr, "%s: `--%s' option given more than once%s\n", |
684 |
package_name, long_opt, |
685 |
(additional_error ? additional_error : "")); |
686 |
return 1; /* failure */ |
687 |
} |
688 |
|
689 |
|
690 |
if (field_given && *field_given && ! override) |
691 |
return 0; |
692 |
if (prev_given) |
693 |
(*prev_given)++; |
694 |
if (field_given) |
695 |
(*field_given)++; |
696 |
if (possible_values) |
697 |
val = possible_values[found]; |
698 |
|
699 |
switch(arg_type) { |
700 |
case ARG_INT: |
701 |
if (val) *((int *)field) = strtol (val, &stop_char, 0); |
702 |
break; |
703 |
case ARG_DOUBLE: |
704 |
if (val) *((double *)field) = strtod (val, &stop_char); |
705 |
break; |
706 |
case ARG_STRING: |
707 |
if (val) { |
708 |
string_field = (char **)field; |
709 |
if (!no_free && *string_field) |
710 |
free (*string_field); /* free previous string */ |
711 |
*string_field = gengetopt_strdup (val); |
712 |
} |
713 |
break; |
714 |
default: |
715 |
break; |
716 |
}; |
717 |
|
718 |
/* check numeric conversion */ |
719 |
switch(arg_type) { |
720 |
case ARG_INT: |
721 |
case ARG_DOUBLE: |
722 |
if (val && !(stop_char && *stop_char == '\0')) { |
723 |
fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val); |
724 |
return 1; /* failure */ |
725 |
} |
726 |
break; |
727 |
default: |
728 |
; |
729 |
}; |
730 |
|
731 |
/* store the original value */ |
732 |
switch(arg_type) { |
733 |
case ARG_NO: |
734 |
break; |
735 |
default: |
736 |
if (value && orig_field) { |
737 |
if (no_free) { |
738 |
*orig_field = value; |
739 |
} else { |
740 |
if (*orig_field) |
741 |
free (*orig_field); /* free previous string */ |
742 |
*orig_field = gengetopt_strdup (value); |
743 |
} |
744 |
} |
745 |
}; |
746 |
|
747 |
return 0; /* OK */ |
748 |
} |
749 |
|
750 |
|
751 |
int |
752 |
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, |
753 |
struct cmdline_parser_params *params, const char *additional_error) |
754 |
{ |
755 |
int c; /* Character of the parsed option. */ |
756 |
|
757 |
int error = 0; |
758 |
struct gengetopt_args_info local_args_info; |
759 |
|
760 |
int override; |
761 |
int initialize; |
762 |
int check_required; |
763 |
int check_ambiguity; |
764 |
|
765 |
package_name = argv[0]; |
766 |
|
767 |
override = params->override; |
768 |
initialize = params->initialize; |
769 |
check_required = params->check_required; |
770 |
check_ambiguity = params->check_ambiguity; |
771 |
|
772 |
if (initialize) |
773 |
cmdline_parser_init (args_info); |
774 |
|
775 |
cmdline_parser_init (&local_args_info); |
776 |
|
777 |
optarg = 0; |
778 |
optind = 0; |
779 |
opterr = params->print_errors; |
780 |
optopt = '?'; |
781 |
|
782 |
while (1) |
783 |
{ |
784 |
int option_index = 0; |
785 |
|
786 |
static struct option long_options[] = { |
787 |
{ "help", 0, NULL, 'h' }, |
788 |
{ "version", 0, NULL, 'V' }, |
789 |
{ "input", 1, NULL, 'i' }, |
790 |
{ "output", 1, NULL, 'o' }, |
791 |
{ "step", 1, NULL, 'n' }, |
792 |
{ "nbins", 1, NULL, 'b' }, |
793 |
{ "nbins_x", 1, NULL, 'x' }, |
794 |
{ "nbins_y", 1, NULL, 'y' }, |
795 |
{ "nanglebins", 1, NULL, 'a' }, |
796 |
{ "rcut", 1, NULL, 'c' }, |
797 |
{ "dz", 1, NULL, 0 }, |
798 |
{ "length", 1, NULL, 0 }, |
799 |
{ "zlength", 1, NULL, 0 }, |
800 |
{ "zoffset", 1, NULL, 'z' }, |
801 |
{ "sele1", 1, NULL, 0 }, |
802 |
{ "sele2", 1, NULL, 0 }, |
803 |
{ "sele3", 1, NULL, 0 }, |
804 |
{ "refsele", 1, NULL, 0 }, |
805 |
{ "comsele", 1, NULL, 0 }, |
806 |
{ "molname", 1, NULL, 0 }, |
807 |
{ "begin", 1, NULL, 0 }, |
808 |
{ "end", 1, NULL, 0 }, |
809 |
{ "radius", 1, NULL, 0 }, |
810 |
{ "bo", 0, NULL, 0 }, |
811 |
{ "bor", 0, NULL, 0 }, |
812 |
{ "bad", 0, NULL, 0 }, |
813 |
{ "count", 0, NULL, 0 }, |
814 |
{ "gofr", 0, NULL, 'g' }, |
815 |
{ "gofz", 0, NULL, 0 }, |
816 |
{ "r_theta", 0, NULL, 0 }, |
817 |
{ "r_omega", 0, NULL, 0 }, |
818 |
{ "theta_omega", 0, NULL, 0 }, |
819 |
{ "gxyz", 0, NULL, 0 }, |
820 |
{ "twodgofr", 0, NULL, 0 }, |
821 |
{ "p2", 0, NULL, 'p' }, |
822 |
{ "rp2", 0, NULL, 0 }, |
823 |
{ "scd", 0, NULL, 's' }, |
824 |
{ "density", 0, NULL, 'd' }, |
825 |
{ "slab_density", 0, NULL, 0 }, |
826 |
{ "p_angle", 0, NULL, 0 }, |
827 |
{ "hxy", 0, NULL, 0 }, |
828 |
{ "rho_r", 0, NULL, 0 }, |
829 |
{ "angle_r", 0, NULL, 0 }, |
830 |
{ "hullvol", 0, NULL, 0 }, |
831 |
{ NULL, 0, NULL, 0 } |
832 |
}; |
833 |
|
834 |
c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); |
835 |
|
836 |
if (c == -1) break; /* Exit from `while (1)' loop. */ |
837 |
|
838 |
switch (c) |
839 |
{ |
840 |
case 'h': /* Print help and exit. */ |
841 |
cmdline_parser_print_help (); |
842 |
cmdline_parser_free (&local_args_info); |
843 |
exit (EXIT_SUCCESS); |
844 |
|
845 |
case 'V': /* Print version and exit. */ |
846 |
cmdline_parser_print_version (); |
847 |
cmdline_parser_free (&local_args_info); |
848 |
exit (EXIT_SUCCESS); |
849 |
|
850 |
case 'i': /* input dump file. */ |
851 |
|
852 |
|
853 |
if (update_arg( (void *)&(args_info->input_arg), |
854 |
&(args_info->input_orig), &(args_info->input_given), |
855 |
&(local_args_info.input_given), optarg, 0, 0, ARG_STRING, |
856 |
check_ambiguity, override, 0, 0, |
857 |
"input", 'i', |
858 |
additional_error)) |
859 |
goto failure; |
860 |
|
861 |
break; |
862 |
case 'o': /* output file name. */ |
863 |
|
864 |
|
865 |
if (update_arg( (void *)&(args_info->output_arg), |
866 |
&(args_info->output_orig), &(args_info->output_given), |
867 |
&(local_args_info.output_given), optarg, 0, 0, ARG_STRING, |
868 |
check_ambiguity, override, 0, 0, |
869 |
"output", 'o', |
870 |
additional_error)) |
871 |
goto failure; |
872 |
|
873 |
break; |
874 |
case 'n': /* process every n frame. */ |
875 |
|
876 |
|
877 |
if (update_arg( (void *)&(args_info->step_arg), |
878 |
&(args_info->step_orig), &(args_info->step_given), |
879 |
&(local_args_info.step_given), optarg, 0, "1", ARG_INT, |
880 |
check_ambiguity, override, 0, 0, |
881 |
"step", 'n', |
882 |
additional_error)) |
883 |
goto failure; |
884 |
|
885 |
break; |
886 |
case 'b': /* number of bins (general purpose). */ |
887 |
|
888 |
|
889 |
if (update_arg( (void *)&(args_info->nbins_arg), |
890 |
&(args_info->nbins_orig), &(args_info->nbins_given), |
891 |
&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT, |
892 |
check_ambiguity, override, 0, 0, |
893 |
"nbins", 'b', |
894 |
additional_error)) |
895 |
goto failure; |
896 |
|
897 |
break; |
898 |
case 'x': /* number of bins in x axis. */ |
899 |
|
900 |
|
901 |
if (update_arg( (void *)&(args_info->nbins_x_arg), |
902 |
&(args_info->nbins_x_orig), &(args_info->nbins_x_given), |
903 |
&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT, |
904 |
check_ambiguity, override, 0, 0, |
905 |
"nbins_x", 'x', |
906 |
additional_error)) |
907 |
goto failure; |
908 |
|
909 |
break; |
910 |
case 'y': /* number of bins in y axis. */ |
911 |
|
912 |
|
913 |
if (update_arg( (void *)&(args_info->nbins_y_arg), |
914 |
&(args_info->nbins_y_orig), &(args_info->nbins_y_given), |
915 |
&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT, |
916 |
check_ambiguity, override, 0, 0, |
917 |
"nbins_y", 'y', |
918 |
additional_error)) |
919 |
goto failure; |
920 |
|
921 |
break; |
922 |
case 'a': /* number of bins for cos(angle). */ |
923 |
|
924 |
|
925 |
if (update_arg( (void *)&(args_info->nanglebins_arg), |
926 |
&(args_info->nanglebins_orig), &(args_info->nanglebins_given), |
927 |
&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT, |
928 |
check_ambiguity, override, 0, 0, |
929 |
"nanglebins", 'a', |
930 |
additional_error)) |
931 |
goto failure; |
932 |
|
933 |
break; |
934 |
case 'c': /* cutoff radius (rcut). */ |
935 |
|
936 |
|
937 |
if (update_arg( (void *)&(args_info->rcut_arg), |
938 |
&(args_info->rcut_orig), &(args_info->rcut_given), |
939 |
&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE, |
940 |
check_ambiguity, override, 0, 0, |
941 |
"rcut", 'c', |
942 |
additional_error)) |
943 |
goto failure; |
944 |
|
945 |
break; |
946 |
case 'z': /* Where to set the zero for the slab_density calculation. */ |
947 |
|
948 |
|
949 |
if (update_arg( (void *)&(args_info->zoffset_arg), |
950 |
&(args_info->zoffset_orig), &(args_info->zoffset_given), |
951 |
&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE, |
952 |
check_ambiguity, override, 0, 0, |
953 |
"zoffset", 'z', |
954 |
additional_error)) |
955 |
goto failure; |
956 |
|
957 |
break; |
958 |
case 'g': /* g(r). */ |
959 |
|
960 |
if (args_info->staticProps_group_counter && override) |
961 |
reset_group_staticProps (args_info); |
962 |
args_info->staticProps_group_counter += 1; |
963 |
|
964 |
if (update_arg( 0 , |
965 |
0 , &(args_info->gofr_given), |
966 |
&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO, |
967 |
check_ambiguity, override, 0, 0, |
968 |
"gofr", 'g', |
969 |
additional_error)) |
970 |
goto failure; |
971 |
|
972 |
break; |
973 |
case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */ |
974 |
|
975 |
if (args_info->staticProps_group_counter && override) |
976 |
reset_group_staticProps (args_info); |
977 |
args_info->staticProps_group_counter += 1; |
978 |
|
979 |
if (update_arg( 0 , |
980 |
0 , &(args_info->p2_given), |
981 |
&(local_args_info.p2_given), optarg, 0, 0, ARG_NO, |
982 |
check_ambiguity, override, 0, 0, |
983 |
"p2", 'p', |
984 |
additional_error)) |
985 |
goto failure; |
986 |
|
987 |
break; |
988 |
case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */ |
989 |
|
990 |
if (args_info->staticProps_group_counter && override) |
991 |
reset_group_staticProps (args_info); |
992 |
args_info->staticProps_group_counter += 1; |
993 |
|
994 |
if (update_arg( 0 , |
995 |
0 , &(args_info->scd_given), |
996 |
&(local_args_info.scd_given), optarg, 0, 0, ARG_NO, |
997 |
check_ambiguity, override, 0, 0, |
998 |
"scd", 's', |
999 |
additional_error)) |
1000 |
goto failure; |
1001 |
|
1002 |
break; |
1003 |
case 'd': /* density plot. */ |
1004 |
|
1005 |
if (args_info->staticProps_group_counter && override) |
1006 |
reset_group_staticProps (args_info); |
1007 |
args_info->staticProps_group_counter += 1; |
1008 |
|
1009 |
if (update_arg( 0 , |
1010 |
0 , &(args_info->density_given), |
1011 |
&(local_args_info.density_given), optarg, 0, 0, ARG_NO, |
1012 |
check_ambiguity, override, 0, 0, |
1013 |
"density", 'd', |
1014 |
additional_error)) |
1015 |
goto failure; |
1016 |
|
1017 |
break; |
1018 |
|
1019 |
case 0: /* Long option with no short option */ |
1020 |
/* number of bins in z axis. */ |
1021 |
if (strcmp (long_options[option_index].name, "nbins_z") == 0) |
1022 |
{ |
1023 |
|
1024 |
if (update_arg( (void *)&(args_info->nbins_z_arg), |
1025 |
&(args_info->nbins_z_orig), &(args_info->nbins_z_given), |
1026 |
&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, |
1027 |
check_ambiguity, override, 0, 0, |
1028 |
"nbins_z", '-', |
1029 |
additional_error)) |
1030 |
goto failure; |
1031 |
|
1032 |
} |
1033 |
|
1034 |
|
1035 |
/* slab width (dz). */ |
1036 |
else if (strcmp (long_options[option_index].name, "dz") == 0) |
1037 |
{ |
1038 |
|
1039 |
|
1040 |
if (update_arg( (void *)&(args_info->dz_arg), |
1041 |
&(args_info->dz_orig), &(args_info->dz_given), |
1042 |
&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE, |
1043 |
check_ambiguity, override, 0, 0, |
1044 |
"dz", '-', |
1045 |
additional_error)) |
1046 |
goto failure; |
1047 |
|
1048 |
} |
1049 |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
1050 |
if (strcmp (long_options[option_index].name, "length") == 0) |
1051 |
{ |
1052 |
|
1053 |
|
1054 |
if (update_arg( (void *)&(args_info->length_arg), |
1055 |
&(args_info->length_orig), &(args_info->length_given), |
1056 |
&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE, |
1057 |
check_ambiguity, override, 0, 0, |
1058 |
"length", '-', |
1059 |
additional_error)) |
1060 |
goto failure; |
1061 |
|
1062 |
} |
1063 |
/* maximum length (Defaults to 1/2 smallest length of first frame). */ |
1064 |
else if (strcmp (long_options[option_index].name, "zlength") == 0) |
1065 |
{ |
1066 |
|
1067 |
|
1068 |
if (update_arg( (void *)&(args_info->zlength_arg), |
1069 |
&(args_info->zlength_orig), &(args_info->zlength_given), |
1070 |
&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE, |
1071 |
check_ambiguity, override, 0, 0, |
1072 |
"zlength", '-', |
1073 |
additional_error)) |
1074 |
goto failure; |
1075 |
|
1076 |
} |
1077 |
/* select the first stuntdouble set. */ |
1078 |
else if (strcmp (long_options[option_index].name, "sele1") == 0) |
1079 |
{ |
1080 |
|
1081 |
|
1082 |
if (update_arg( (void *)&(args_info->sele1_arg), |
1083 |
&(args_info->sele1_orig), &(args_info->sele1_given), |
1084 |
&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING, |
1085 |
check_ambiguity, override, 0, 0, |
1086 |
"sele1", '-', |
1087 |
additional_error)) |
1088 |
goto failure; |
1089 |
|
1090 |
} |
1091 |
/* select the second stuntdouble set. */ |
1092 |
else if (strcmp (long_options[option_index].name, "sele2") == 0) |
1093 |
{ |
1094 |
|
1095 |
|
1096 |
if (update_arg( (void *)&(args_info->sele2_arg), |
1097 |
&(args_info->sele2_orig), &(args_info->sele2_given), |
1098 |
&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING, |
1099 |
check_ambiguity, override, 0, 0, |
1100 |
"sele2", '-', |
1101 |
additional_error)) |
1102 |
goto failure; |
1103 |
|
1104 |
} |
1105 |
/* select the third stuntdouble set. */ |
1106 |
else if (strcmp (long_options[option_index].name, "sele3") == 0) |
1107 |
{ |
1108 |
|
1109 |
|
1110 |
if (update_arg( (void *)&(args_info->sele3_arg), |
1111 |
&(args_info->sele3_orig), &(args_info->sele3_given), |
1112 |
&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING, |
1113 |
check_ambiguity, override, 0, 0, |
1114 |
"sele3", '-', |
1115 |
additional_error)) |
1116 |
goto failure; |
1117 |
|
1118 |
} |
1119 |
/* select reference (use and only use with --gxyz). */ |
1120 |
else if (strcmp (long_options[option_index].name, "refsele") == 0) |
1121 |
{ |
1122 |
|
1123 |
|
1124 |
if (update_arg( (void *)&(args_info->refsele_arg), |
1125 |
&(args_info->refsele_orig), &(args_info->refsele_given), |
1126 |
&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING, |
1127 |
check_ambiguity, override, 0, 0, |
1128 |
"refsele", '-', |
1129 |
additional_error)) |
1130 |
goto failure; |
1131 |
|
1132 |
} |
1133 |
/* select stunt doubles for center-of-mass reference point. */ |
1134 |
else if (strcmp (long_options[option_index].name, "comsele") == 0) |
1135 |
{ |
1136 |
|
1137 |
|
1138 |
if (update_arg( (void *)&(args_info->comsele_arg), |
1139 |
&(args_info->comsele_orig), &(args_info->comsele_given), |
1140 |
&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING, |
1141 |
check_ambiguity, override, 0, 0, |
1142 |
"comsele", '-', |
1143 |
additional_error)) |
1144 |
goto failure; |
1145 |
|
1146 |
} |
1147 |
/* molecule name. */ |
1148 |
else if (strcmp (long_options[option_index].name, "molname") == 0) |
1149 |
{ |
1150 |
|
1151 |
|
1152 |
if (update_arg( (void *)&(args_info->molname_arg), |
1153 |
&(args_info->molname_orig), &(args_info->molname_given), |
1154 |
&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING, |
1155 |
check_ambiguity, override, 0, 0, |
1156 |
"molname", '-', |
1157 |
additional_error)) |
1158 |
goto failure; |
1159 |
|
1160 |
} |
1161 |
/* begin internal index. */ |
1162 |
else if (strcmp (long_options[option_index].name, "begin") == 0) |
1163 |
{ |
1164 |
|
1165 |
|
1166 |
if (update_arg( (void *)&(args_info->begin_arg), |
1167 |
&(args_info->begin_orig), &(args_info->begin_given), |
1168 |
&(local_args_info.begin_given), optarg, 0, 0, ARG_INT, |
1169 |
check_ambiguity, override, 0, 0, |
1170 |
"begin", '-', |
1171 |
additional_error)) |
1172 |
goto failure; |
1173 |
|
1174 |
} |
1175 |
/* end internal index. */ |
1176 |
else if (strcmp (long_options[option_index].name, "end") == 0) |
1177 |
{ |
1178 |
|
1179 |
|
1180 |
if (update_arg( (void *)&(args_info->end_arg), |
1181 |
&(args_info->end_orig), &(args_info->end_given), |
1182 |
&(local_args_info.end_given), optarg, 0, 0, ARG_INT, |
1183 |
check_ambiguity, override, 0, 0, |
1184 |
"end", '-', |
1185 |
additional_error)) |
1186 |
goto failure; |
1187 |
|
1188 |
} |
1189 |
/* nanoparticle radius. */ |
1190 |
else if (strcmp (long_options[option_index].name, "radius") == 0) |
1191 |
{ |
1192 |
|
1193 |
|
1194 |
if (update_arg( (void *)&(args_info->radius_arg), |
1195 |
&(args_info->radius_orig), &(args_info->radius_given), |
1196 |
&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE, |
1197 |
check_ambiguity, override, 0, 0, |
1198 |
"radius", '-', |
1199 |
additional_error)) |
1200 |
goto failure; |
1201 |
|
1202 |
} |
1203 |
/* bond order parameter (--rcut must be specified). */ |
1204 |
else if (strcmp (long_options[option_index].name, "bo") == 0) |
1205 |
{ |
1206 |
|
1207 |
if (args_info->staticProps_group_counter && override) |
1208 |
reset_group_staticProps (args_info); |
1209 |
args_info->staticProps_group_counter += 1; |
1210 |
|
1211 |
if (update_arg( 0 , |
1212 |
0 , &(args_info->bo_given), |
1213 |
&(local_args_info.bo_given), optarg, 0, 0, ARG_NO, |
1214 |
check_ambiguity, override, 0, 0, |
1215 |
"bo", '-', |
1216 |
additional_error)) |
1217 |
goto failure; |
1218 |
|
1219 |
} |
1220 |
/* bond order parameter as a function of radius (--rcut must be specified). */ |
1221 |
else if (strcmp (long_options[option_index].name, "bor") == 0) |
1222 |
{ |
1223 |
|
1224 |
if (args_info->staticProps_group_counter && override) |
1225 |
reset_group_staticProps (args_info); |
1226 |
args_info->staticProps_group_counter += 1; |
1227 |
|
1228 |
if (update_arg( 0 , |
1229 |
0 , &(args_info->bor_given), |
1230 |
&(local_args_info.bor_given), optarg, 0, 0, ARG_NO, |
1231 |
check_ambiguity, override, 0, 0, |
1232 |
"bor", '-', |
1233 |
additional_error)) |
1234 |
goto failure; |
1235 |
|
1236 |
} |
1237 |
/* N(theta) bond angle density within (--rcut must be specified). */ |
1238 |
else if (strcmp (long_options[option_index].name, "bad") == 0) |
1239 |
{ |
1240 |
|
1241 |
if (args_info->staticProps_group_counter && override) |
1242 |
reset_group_staticProps (args_info); |
1243 |
args_info->staticProps_group_counter += 1; |
1244 |
|
1245 |
if (update_arg( 0 , |
1246 |
0 , &(args_info->bad_given), |
1247 |
&(local_args_info.bad_given), optarg, 0, 0, ARG_NO, |
1248 |
check_ambiguity, override, 0, 0, |
1249 |
"bad", '-', |
1250 |
additional_error)) |
1251 |
goto failure; |
1252 |
|
1253 |
} |
1254 |
/* count of molecules matching selection criteria (and associated statistics). */ |
1255 |
else if (strcmp (long_options[option_index].name, "count") == 0) |
1256 |
{ |
1257 |
|
1258 |
if (args_info->staticProps_group_counter && override) |
1259 |
reset_group_staticProps (args_info); |
1260 |
args_info->staticProps_group_counter += 1; |
1261 |
|
1262 |
if (update_arg( 0 , |
1263 |
0 , &(args_info->count_given), |
1264 |
&(local_args_info.count_given), optarg, 0, 0, ARG_NO, |
1265 |
check_ambiguity, override, 0, 0, |
1266 |
"count", '-', |
1267 |
additional_error)) |
1268 |
goto failure; |
1269 |
|
1270 |
} |
1271 |
/* g(z). */ |
1272 |
else if (strcmp (long_options[option_index].name, "gofz") == 0) |
1273 |
{ |
1274 |
|
1275 |
if (args_info->staticProps_group_counter && override) |
1276 |
reset_group_staticProps (args_info); |
1277 |
args_info->staticProps_group_counter += 1; |
1278 |
|
1279 |
if (update_arg( 0 , |
1280 |
0 , &(args_info->gofz_given), |
1281 |
&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO, |
1282 |
check_ambiguity, override, 0, 0, |
1283 |
"gofz", '-', |
1284 |
additional_error)) |
1285 |
goto failure; |
1286 |
|
1287 |
} |
1288 |
/* g(r, cos(theta)). */ |
1289 |
else if (strcmp (long_options[option_index].name, "r_theta") == 0) |
1290 |
{ |
1291 |
|
1292 |
if (args_info->staticProps_group_counter && override) |
1293 |
reset_group_staticProps (args_info); |
1294 |
args_info->staticProps_group_counter += 1; |
1295 |
|
1296 |
if (update_arg( 0 , |
1297 |
0 , &(args_info->r_theta_given), |
1298 |
&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO, |
1299 |
check_ambiguity, override, 0, 0, |
1300 |
"r_theta", '-', |
1301 |
additional_error)) |
1302 |
goto failure; |
1303 |
|
1304 |
} |
1305 |
/* g(r, cos(omega)). */ |
1306 |
else if (strcmp (long_options[option_index].name, "r_omega") == 0) |
1307 |
{ |
1308 |
|
1309 |
if (args_info->staticProps_group_counter && override) |
1310 |
reset_group_staticProps (args_info); |
1311 |
args_info->staticProps_group_counter += 1; |
1312 |
|
1313 |
if (update_arg( 0 , |
1314 |
0 , &(args_info->r_omega_given), |
1315 |
&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO, |
1316 |
check_ambiguity, override, 0, 0, |
1317 |
"r_omega", '-', |
1318 |
additional_error)) |
1319 |
goto failure; |
1320 |
|
1321 |
} |
1322 |
/* g(cos(theta), cos(omega)). */ |
1323 |
else if (strcmp (long_options[option_index].name, "theta_omega") == 0) |
1324 |
{ |
1325 |
|
1326 |
if (args_info->staticProps_group_counter && override) |
1327 |
reset_group_staticProps (args_info); |
1328 |
args_info->staticProps_group_counter += 1; |
1329 |
|
1330 |
if (update_arg( 0 , |
1331 |
0 , &(args_info->theta_omega_given), |
1332 |
&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, |
1333 |
check_ambiguity, override, 0, 0, |
1334 |
"theta_omega", '-', |
1335 |
additional_error)) |
1336 |
goto failure; |
1337 |
|
1338 |
} |
1339 |
/* g(x, y, z). */ |
1340 |
else if (strcmp (long_options[option_index].name, "gxyz") == 0) |
1341 |
{ |
1342 |
|
1343 |
if (args_info->staticProps_group_counter && override) |
1344 |
reset_group_staticProps (args_info); |
1345 |
args_info->staticProps_group_counter += 1; |
1346 |
|
1347 |
if (update_arg( 0 , |
1348 |
0 , &(args_info->gxyz_given), |
1349 |
&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, |
1350 |
check_ambiguity, override, 0, 0, |
1351 |
"gxyz", '-', |
1352 |
additional_error)) |
1353 |
goto failure; |
1354 |
|
1355 |
} |
1356 |
/* 2D g(r) (Slab width --dz must be specified). */ |
1357 |
else if (strcmp (long_options[option_index].name, "twodgofr") == 0) |
1358 |
{ |
1359 |
|
1360 |
if (args_info->staticProps_group_counter && override) |
1361 |
reset_group_staticProps (args_info); |
1362 |
args_info->staticProps_group_counter += 1; |
1363 |
|
1364 |
if (update_arg( 0 , |
1365 |
0 , &(args_info->twodgofr_given), |
1366 |
&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO, |
1367 |
check_ambiguity, override, 0, 0, |
1368 |
"twodgofr", '-', |
1369 |
additional_error)) |
1370 |
goto failure; |
1371 |
|
1372 |
} |
1373 |
/* rp2 order parameter (--sele1 and --sele2 must be specified). */ |
1374 |
else if (strcmp (long_options[option_index].name, "rp2") == 0) |
1375 |
{ |
1376 |
|
1377 |
if (args_info->staticProps_group_counter && override) |
1378 |
reset_group_staticProps (args_info); |
1379 |
args_info->staticProps_group_counter += 1; |
1380 |
|
1381 |
if (update_arg( 0 , |
1382 |
0 , &(args_info->rp2_given), |
1383 |
&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO, |
1384 |
check_ambiguity, override, 0, 0, |
1385 |
"rp2", '-', |
1386 |
additional_error)) |
1387 |
goto failure; |
1388 |
|
1389 |
} |
1390 |
/* slab density. */ |
1391 |
else if (strcmp (long_options[option_index].name, "slab_density") == 0) |
1392 |
{ |
1393 |
|
1394 |
if (args_info->staticProps_group_counter && override) |
1395 |
reset_group_staticProps (args_info); |
1396 |
args_info->staticProps_group_counter += 1; |
1397 |
|
1398 |
if (update_arg( 0 , |
1399 |
0 , &(args_info->slab_density_given), |
1400 |
&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO, |
1401 |
check_ambiguity, override, 0, 0, |
1402 |
"slab_density", '-', |
1403 |
additional_error)) |
1404 |
goto failure; |
1405 |
|
1406 |
} |
1407 |
/* p(cos(theta)). */ |
1408 |
else if (strcmp (long_options[option_index].name, "p_angle") == 0) |
1409 |
{ |
1410 |
|
1411 |
if (args_info->staticProps_group_counter && override) |
1412 |
reset_group_staticProps (args_info); |
1413 |
args_info->staticProps_group_counter += 1; |
1414 |
|
1415 |
if (update_arg( 0 , |
1416 |
0 , &(args_info->p_angle_given), |
1417 |
&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO, |
1418 |
check_ambiguity, override, 0, 0, |
1419 |
"p_angle", '-', |
1420 |
additional_error)) |
1421 |
goto failure; |
1422 |
|
1423 |
} |
1424 |
/* hxy. */ |
1425 |
else if (strcmp (long_options[option_index].name, "hxy") == 0) |
1426 |
{ |
1427 |
|
1428 |
if (args_info->staticProps_group_counter && override) |
1429 |
reset_group_staticProps (args_info); |
1430 |
args_info->staticProps_group_counter += 1; |
1431 |
|
1432 |
if (update_arg( 0 , |
1433 |
0 , &(args_info->hxy_given), |
1434 |
&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO, |
1435 |
check_ambiguity, override, 0, 0, |
1436 |
"hxy", '-', |
1437 |
additional_error)) |
1438 |
goto failure; |
1439 |
|
1440 |
} |
1441 |
/* rho of R. */ |
1442 |
else if (strcmp (long_options[option_index].name, "rho_r") == 0) |
1443 |
{ |
1444 |
|
1445 |
if (args_info->staticProps_group_counter && override) |
1446 |
reset_group_staticProps (args_info); |
1447 |
args_info->staticProps_group_counter += 1; |
1448 |
|
1449 |
if (update_arg( 0 , |
1450 |
0 , &(args_info->rho_r_given), |
1451 |
&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO, |
1452 |
check_ambiguity, override, 0, 0, |
1453 |
"rho_r", '-', |
1454 |
additional_error)) |
1455 |
goto failure; |
1456 |
|
1457 |
} |
1458 |
/* angle of R. */ |
1459 |
else if (strcmp (long_options[option_index].name, "angle_r") == 0) |
1460 |
{ |
1461 |
|
1462 |
if (args_info->staticProps_group_counter && override) |
1463 |
reset_group_staticProps (args_info); |
1464 |
args_info->staticProps_group_counter += 1; |
1465 |
|
1466 |
if (update_arg( 0 , |
1467 |
0 , &(args_info->angle_r_given), |
1468 |
&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO, |
1469 |
check_ambiguity, override, 0, 0, |
1470 |
"angle_r", '-', |
1471 |
additional_error)) |
1472 |
goto failure; |
1473 |
|
1474 |
} |
1475 |
/* hull volume of nanoparticle. */ |
1476 |
else if (strcmp (long_options[option_index].name, "hullvol") == 0) |
1477 |
{ |
1478 |
|
1479 |
if (args_info->staticProps_group_counter && override) |
1480 |
reset_group_staticProps (args_info); |
1481 |
args_info->staticProps_group_counter += 1; |
1482 |
|
1483 |
if (update_arg( 0 , |
1484 |
0 , &(args_info->hullvol_given), |
1485 |
&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO, |
1486 |
check_ambiguity, override, 0, 0, |
1487 |
"hullvol", '-', |
1488 |
additional_error)) |
1489 |
goto failure; |
1490 |
|
1491 |
} |
1492 |
|
1493 |
break; |
1494 |
case '?': /* Invalid option. */ |
1495 |
/* `getopt_long' already printed an error message. */ |
1496 |
goto failure; |
1497 |
|
1498 |
default: /* bug: option not considered. */ |
1499 |
fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); |
1500 |
abort (); |
1501 |
} /* switch */ |
1502 |
} /* while */ |
1503 |
|
1504 |
if (args_info->staticProps_group_counter > 1) |
1505 |
{ |
1506 |
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 : "")); |
1507 |
error = 1; |
1508 |
} |
1509 |
|
1510 |
|
1511 |
|
1512 |
if (check_required) |
1513 |
{ |
1514 |
error += cmdline_parser_required2 (args_info, argv[0], additional_error); |
1515 |
} |
1516 |
|
1517 |
cmdline_parser_release (&local_args_info); |
1518 |
|
1519 |
if ( error ) |
1520 |
return (EXIT_FAILURE); |
1521 |
|
1522 |
if (optind < argc) |
1523 |
{ |
1524 |
int i = 0 ; |
1525 |
int found_prog_name = 0; |
1526 |
/* whether program name, i.e., argv[0], is in the remaining args |
1527 |
(this may happen with some implementations of getopt, |
1528 |
but surely not with the one included by gengetopt) */ |
1529 |
|
1530 |
i = optind; |
1531 |
while (i < argc) |
1532 |
if (argv[i++] == argv[0]) { |
1533 |
found_prog_name = 1; |
1534 |
break; |
1535 |
} |
1536 |
i = 0; |
1537 |
|
1538 |
args_info->inputs_num = argc - optind - found_prog_name; |
1539 |
args_info->inputs = |
1540 |
(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; |
1541 |
while (optind < argc) |
1542 |
if (argv[optind++] != argv[0]) |
1543 |
args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; |
1544 |
} |
1545 |
|
1546 |
return 0; |
1547 |
|
1548 |
failure: |
1549 |
|
1550 |
cmdline_parser_release (&local_args_info); |
1551 |
return (EXIT_FAILURE); |
1552 |
} |