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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
Revision: 1979
Committed: Sat Apr 5 20:56:01 2014 UTC (11 years ago) by gezelter
File size: 62939 byte(s)
Log Message: 
* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals
* Added the ability to specify non-bonded constraints in a molecule
* Added the ability to do selection offsets in the pAngle staticProps module

File Contents

# Content
1 /*
2 File autogenerated by gengetopt version 2.22.4
3 generated with the following command:
4 gengetopt --file-name=StaticPropsCmd --unamed-opts
5
6 The developers of gengetopt consider the fixed text that goes in all
7 gengetopt output files to be in the public domain:
8 we make no copyright claims on it.
9 */
10
11 /* If we use autoconf. */
12 #ifdef HAVE_CONFIG_H
13 #include "config.h"
14 #endif
15
16 #include <stdio.h>
17 #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 #ifdef WIN32
25 #include "utils/wingetopt.h"
26 #else
27 #include <getopt.h>
28 #endif
29
30 #include "StaticPropsCmd.h"
31
32 const char *gengetopt_args_info_purpose = "";
33
34 const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35
36 const char *gengetopt_args_info_description = "";
37
38 const char *gengetopt_args_info_help[] = {
39 " -h, --help Print help and exit",
40 " -V, --version Print version and exit",
41 " -i, --input=filename input dump file",
42 " -o, --output=filename output file name",
43 " -n, --step=INT process every n frame (default=`1')",
44 " -b, --nbins=INT number of bins (general purpose) \n (default=`100')",
45 " -x, --nbins_x=INT number of bins in x axis (default=`100')",
46 " -y, --nbins_y=INT number of bins in y axis (default=`100')",
47 " --nbins_z=INT number of bins in z axis (default=`100')",
48 " -a, --nanglebins=INT number of bins for cos(angle) (default=`50')",
49 " -c, --rcut=DOUBLE cutoff radius (rcut)",
50 " --dz=DOUBLE slab width (dz)",
51 " --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
52 " --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
53 " -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')",
54 " --sele1=selection script select the first stuntdouble set",
55 " --sele2=selection script select the second stuntdouble set",
56 " --sele3=selection script select the third stuntdouble set",
57 " --refsele=selection script\n select reference (use and only use with --gxyz)",
58 " --comsele=selection script\n select stunt doubles for center-of-mass \n reference point",
59 " --seleoffset=INT global index offset for a second object (used \n to define a vector between sites in molecule)",
60 " --molname=STRING molecule name",
61 " --begin=INT begin internal index",
62 " --end=INT end internal index",
63 " --radius=DOUBLE nanoparticle radius",
64 "\n Group: staticProps\n an option of this group is required",
65 " --bo bond order parameter (--rcut must be specified)",
66 " --bor bond order parameter as a function of radius \n (--rcut must be specified)",
67 " --bad N(theta) bond angle density within (--rcut must \n be specified)",
68 " --count count of molecules matching selection criteria \n (and associated statistics)",
69 " -g, --gofr g(r)",
70 " --gofz g(z)",
71 " --r_theta g(r, cos(theta))",
72 " --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)",
79 " -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 " --rnemdz slab-resolved RNEMD statistics (temperature, \n density, velocity)",
91 " --rnemdr shell-resolved RNEMD statistics (temperature, \n density, angular velocity)",
92 " --rnemdrt shell and angle-resolved RNEMD statistics \n (temperature, density, angular velocity)",
93 0
94 };
95
96 typedef enum {ARG_NO
97 , ARG_STRING
98 , ARG_INT
99 , ARG_DOUBLE
100 } cmdline_parser_arg_type;
101
102 static
103 void clear_given (struct gengetopt_args_info *args_info);
104 static
105 void clear_args (struct gengetopt_args_info *args_info);
106
107 static int
108 cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
109 struct cmdline_parser_params *params, const char *additional_error);
110
111 static int
112 cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
113
114 static char *
115 gengetopt_strdup (const char *s);
116
117 static
118 void clear_given (struct gengetopt_args_info *args_info)
119 {
120 args_info->help_given = 0 ;
121 args_info->version_given = 0 ;
122 args_info->input_given = 0 ;
123 args_info->output_given = 0 ;
124 args_info->step_given = 0 ;
125 args_info->nbins_given = 0 ;
126 args_info->nbins_x_given = 0 ;
127 args_info->nbins_y_given = 0 ;
128 args_info->nbins_z_given = 0 ;
129 args_info->nanglebins_given = 0 ;
130 args_info->rcut_given = 0 ;
131 args_info->dz_given = 0 ;
132 args_info->length_given = 0 ;
133 args_info->zlength_given = 0 ;
134 args_info->zoffset_given = 0 ;
135 args_info->sele1_given = 0 ;
136 args_info->sele2_given = 0 ;
137 args_info->sele3_given = 0 ;
138 args_info->refsele_given = 0 ;
139 args_info->comsele_given = 0 ;
140 args_info->seleoffset_given = 0 ;
141 args_info->molname_given = 0 ;
142 args_info->begin_given = 0 ;
143 args_info->end_given = 0 ;
144 args_info->radius_given = 0 ;
145 args_info->bo_given = 0 ;
146 args_info->bor_given = 0 ;
147 args_info->bad_given = 0 ;
148 args_info->count_given = 0 ;
149 args_info->gofr_given = 0 ;
150 args_info->gofz_given = 0 ;
151 args_info->r_theta_given = 0 ;
152 args_info->r_omega_given = 0 ;
153 args_info->r_z_given = 0 ;
154 args_info->theta_omega_given = 0 ;
155 args_info->gxyz_given = 0 ;
156 args_info->twodgofr_given = 0 ;
157 args_info->p2_given = 0 ;
158 args_info->rp2_given = 0 ;
159 args_info->scd_given = 0 ;
160 args_info->density_given = 0 ;
161 args_info->slab_density_given = 0 ;
162 args_info->p_angle_given = 0 ;
163 args_info->hxy_given = 0 ;
164 args_info->rho_r_given = 0 ;
165 args_info->angle_r_given = 0 ;
166 args_info->hullvol_given = 0 ;
167 args_info->rodlength_given = 0 ;
168 args_info->tet_param_given = 0 ;
169 args_info->tet_param_z_given = 0 ;
170 args_info->rnemdz_given = 0 ;
171 args_info->rnemdr_given = 0 ;
172 args_info->rnemdrt_given = 0 ;
173 args_info->staticProps_group_counter = 0 ;
174 }
175
176 static
177 void clear_args (struct gengetopt_args_info *args_info)
178 {
179 FIX_UNUSED (args_info);
180 args_info->input_arg = NULL;
181 args_info->input_orig = NULL;
182 args_info->output_arg = NULL;
183 args_info->output_orig = NULL;
184 args_info->step_arg = 1;
185 args_info->step_orig = NULL;
186 args_info->nbins_arg = 100;
187 args_info->nbins_orig = NULL;
188 args_info->nbins_x_arg = 100;
189 args_info->nbins_x_orig = NULL;
190 args_info->nbins_y_arg = 100;
191 args_info->nbins_y_orig = NULL;
192 args_info->nbins_z_arg = 100;
193 args_info->nbins_z_orig = NULL;
194 args_info->nanglebins_arg = 50;
195 args_info->nanglebins_orig = NULL;
196 args_info->rcut_orig = NULL;
197 args_info->dz_orig = NULL;
198 args_info->length_orig = NULL;
199 args_info->zlength_orig = NULL;
200 args_info->zoffset_arg = 0;
201 args_info->zoffset_orig = NULL;
202 args_info->sele1_arg = NULL;
203 args_info->sele1_orig = NULL;
204 args_info->sele2_arg = NULL;
205 args_info->sele2_orig = NULL;
206 args_info->sele3_arg = NULL;
207 args_info->sele3_orig = NULL;
208 args_info->refsele_arg = NULL;
209 args_info->refsele_orig = NULL;
210 args_info->comsele_arg = NULL;
211 args_info->comsele_orig = NULL;
212 args_info->seleoffset_orig = NULL;
213 args_info->molname_arg = NULL;
214 args_info->molname_orig = NULL;
215 args_info->begin_orig = NULL;
216 args_info->end_orig = NULL;
217 args_info->radius_orig = NULL;
218
219 }
220
221 static
222 void init_args_info(struct gengetopt_args_info *args_info)
223 {
224
225
226 args_info->help_help = gengetopt_args_info_help[0] ;
227 args_info->version_help = gengetopt_args_info_help[1] ;
228 args_info->input_help = gengetopt_args_info_help[2] ;
229 args_info->output_help = gengetopt_args_info_help[3] ;
230 args_info->step_help = gengetopt_args_info_help[4] ;
231 args_info->nbins_help = gengetopt_args_info_help[5] ;
232 args_info->nbins_x_help = gengetopt_args_info_help[6] ;
233 args_info->nbins_y_help = gengetopt_args_info_help[7] ;
234 args_info->nbins_z_help = gengetopt_args_info_help[8] ;
235 args_info->nanglebins_help = gengetopt_args_info_help[9] ;
236 args_info->rcut_help = gengetopt_args_info_help[10] ;
237 args_info->dz_help = gengetopt_args_info_help[11] ;
238 args_info->length_help = gengetopt_args_info_help[12] ;
239 args_info->zlength_help = gengetopt_args_info_help[13] ;
240 args_info->zoffset_help = gengetopt_args_info_help[14] ;
241 args_info->sele1_help = gengetopt_args_info_help[15] ;
242 args_info->sele2_help = gengetopt_args_info_help[16] ;
243 args_info->sele3_help = gengetopt_args_info_help[17] ;
244 args_info->refsele_help = gengetopt_args_info_help[18] ;
245 args_info->comsele_help = gengetopt_args_info_help[19] ;
246 args_info->seleoffset_help = gengetopt_args_info_help[20] ;
247 args_info->molname_help = gengetopt_args_info_help[21] ;
248 args_info->begin_help = gengetopt_args_info_help[22] ;
249 args_info->end_help = gengetopt_args_info_help[23] ;
250 args_info->radius_help = gengetopt_args_info_help[24] ;
251 args_info->bo_help = gengetopt_args_info_help[26] ;
252 args_info->bor_help = gengetopt_args_info_help[27] ;
253 args_info->bad_help = gengetopt_args_info_help[28] ;
254 args_info->count_help = gengetopt_args_info_help[29] ;
255 args_info->gofr_help = gengetopt_args_info_help[30] ;
256 args_info->gofz_help = gengetopt_args_info_help[31] ;
257 args_info->r_theta_help = gengetopt_args_info_help[32] ;
258 args_info->r_omega_help = gengetopt_args_info_help[33] ;
259 args_info->r_z_help = gengetopt_args_info_help[34] ;
260 args_info->theta_omega_help = gengetopt_args_info_help[35] ;
261 args_info->gxyz_help = gengetopt_args_info_help[36] ;
262 args_info->twodgofr_help = gengetopt_args_info_help[37] ;
263 args_info->p2_help = gengetopt_args_info_help[38] ;
264 args_info->rp2_help = gengetopt_args_info_help[39] ;
265 args_info->scd_help = gengetopt_args_info_help[40] ;
266 args_info->density_help = gengetopt_args_info_help[41] ;
267 args_info->slab_density_help = gengetopt_args_info_help[42] ;
268 args_info->p_angle_help = gengetopt_args_info_help[43] ;
269 args_info->hxy_help = gengetopt_args_info_help[44] ;
270 args_info->rho_r_help = gengetopt_args_info_help[45] ;
271 args_info->angle_r_help = gengetopt_args_info_help[46] ;
272 args_info->hullvol_help = gengetopt_args_info_help[47] ;
273 args_info->rodlength_help = gengetopt_args_info_help[48] ;
274 args_info->tet_param_help = gengetopt_args_info_help[49] ;
275 args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
276 args_info->rnemdz_help = gengetopt_args_info_help[51] ;
277 args_info->rnemdr_help = gengetopt_args_info_help[52] ;
278 args_info->rnemdrt_help = gengetopt_args_info_help[53] ;
279
280 }
281
282 void
283 cmdline_parser_print_version (void)
284 {
285 printf ("%s %s\n",
286 (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
287 CMDLINE_PARSER_VERSION);
288 }
289
290 static void print_help_common(void) {
291 cmdline_parser_print_version ();
292
293 if (strlen(gengetopt_args_info_purpose) > 0)
294 printf("\n%s\n", gengetopt_args_info_purpose);
295
296 if (strlen(gengetopt_args_info_usage) > 0)
297 printf("\n%s\n", gengetopt_args_info_usage);
298
299 printf("\n");
300
301 if (strlen(gengetopt_args_info_description) > 0)
302 printf("%s\n\n", gengetopt_args_info_description);
303 }
304
305 void
306 cmdline_parser_print_help (void)
307 {
308 int i = 0;
309 print_help_common();
310 while (gengetopt_args_info_help[i])
311 printf("%s\n", gengetopt_args_info_help[i++]);
312 }
313
314 void
315 cmdline_parser_init (struct gengetopt_args_info *args_info)
316 {
317 clear_given (args_info);
318 clear_args (args_info);
319 init_args_info (args_info);
320
321 args_info->inputs = 0;
322 args_info->inputs_num = 0;
323 }
324
325 void
326 cmdline_parser_params_init(struct cmdline_parser_params *params)
327 {
328 if (params)
329 {
330 params->override = 0;
331 params->initialize = 1;
332 params->check_required = 1;
333 params->check_ambiguity = 0;
334 params->print_errors = 1;
335 }
336 }
337
338 struct cmdline_parser_params *
339 cmdline_parser_params_create(void)
340 {
341 struct cmdline_parser_params *params =
342 (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
343 cmdline_parser_params_init(params);
344 return params;
345 }
346
347 static void
348 free_string_field (char **s)
349 {
350 if (*s)
351 {
352 free (*s);
353 *s = 0;
354 }
355 }
356
357
358 static void
359 cmdline_parser_release (struct gengetopt_args_info *args_info)
360 {
361 unsigned int i;
362 free_string_field (&(args_info->input_arg));
363 free_string_field (&(args_info->input_orig));
364 free_string_field (&(args_info->output_arg));
365 free_string_field (&(args_info->output_orig));
366 free_string_field (&(args_info->step_orig));
367 free_string_field (&(args_info->nbins_orig));
368 free_string_field (&(args_info->nbins_x_orig));
369 free_string_field (&(args_info->nbins_y_orig));
370 free_string_field (&(args_info->nbins_z_orig));
371 free_string_field (&(args_info->nanglebins_orig));
372 free_string_field (&(args_info->rcut_orig));
373 free_string_field (&(args_info->dz_orig));
374 free_string_field (&(args_info->length_orig));
375 free_string_field (&(args_info->zlength_orig));
376 free_string_field (&(args_info->zoffset_orig));
377 free_string_field (&(args_info->sele1_arg));
378 free_string_field (&(args_info->sele1_orig));
379 free_string_field (&(args_info->sele2_arg));
380 free_string_field (&(args_info->sele2_orig));
381 free_string_field (&(args_info->sele3_arg));
382 free_string_field (&(args_info->sele3_orig));
383 free_string_field (&(args_info->refsele_arg));
384 free_string_field (&(args_info->refsele_orig));
385 free_string_field (&(args_info->comsele_arg));
386 free_string_field (&(args_info->comsele_orig));
387 free_string_field (&(args_info->seleoffset_orig));
388 free_string_field (&(args_info->molname_arg));
389 free_string_field (&(args_info->molname_orig));
390 free_string_field (&(args_info->begin_orig));
391 free_string_field (&(args_info->end_orig));
392 free_string_field (&(args_info->radius_orig));
393
394
395 for (i = 0; i < args_info->inputs_num; ++i)
396 free (args_info->inputs [i]);
397
398 if (args_info->inputs_num)
399 free (args_info->inputs);
400
401 clear_given (args_info);
402 }
403
404
405 static void
406 write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
407 {
408 FIX_UNUSED (values);
409 if (arg) {
410 fprintf(outfile, "%s=\"%s\"\n", opt, arg);
411 } else {
412 fprintf(outfile, "%s\n", opt);
413 }
414 }
415
416
417 int
418 cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
419 {
420 int i = 0;
421
422 if (!outfile)
423 {
424 fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
425 return EXIT_FAILURE;
426 }
427
428 if (args_info->help_given)
429 write_into_file(outfile, "help", 0, 0 );
430 if (args_info->version_given)
431 write_into_file(outfile, "version", 0, 0 );
432 if (args_info->input_given)
433 write_into_file(outfile, "input", args_info->input_orig, 0);
434 if (args_info->output_given)
435 write_into_file(outfile, "output", args_info->output_orig, 0);
436 if (args_info->step_given)
437 write_into_file(outfile, "step", args_info->step_orig, 0);
438 if (args_info->nbins_given)
439 write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
440 if (args_info->nbins_x_given)
441 write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
442 if (args_info->nbins_y_given)
443 write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
444 if (args_info->nbins_z_given)
445 write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
446 if (args_info->nanglebins_given)
447 write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
448 if (args_info->rcut_given)
449 write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
450 if (args_info->dz_given)
451 write_into_file(outfile, "dz", args_info->dz_orig, 0);
452 if (args_info->length_given)
453 write_into_file(outfile, "length", args_info->length_orig, 0);
454 if (args_info->zlength_given)
455 write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
456 if (args_info->zoffset_given)
457 write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
458 if (args_info->sele1_given)
459 write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
460 if (args_info->sele2_given)
461 write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
462 if (args_info->sele3_given)
463 write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
464 if (args_info->refsele_given)
465 write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
466 if (args_info->comsele_given)
467 write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
468 if (args_info->seleoffset_given)
469 write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
470 if (args_info->molname_given)
471 write_into_file(outfile, "molname", args_info->molname_orig, 0);
472 if (args_info->begin_given)
473 write_into_file(outfile, "begin", args_info->begin_orig, 0);
474 if (args_info->end_given)
475 write_into_file(outfile, "end", args_info->end_orig, 0);
476 if (args_info->radius_given)
477 write_into_file(outfile, "radius", args_info->radius_orig, 0);
478 if (args_info->bo_given)
479 write_into_file(outfile, "bo", 0, 0 );
480 if (args_info->bor_given)
481 write_into_file(outfile, "bor", 0, 0 );
482 if (args_info->bad_given)
483 write_into_file(outfile, "bad", 0, 0 );
484 if (args_info->count_given)
485 write_into_file(outfile, "count", 0, 0 );
486 if (args_info->gofr_given)
487 write_into_file(outfile, "gofr", 0, 0 );
488 if (args_info->gofz_given)
489 write_into_file(outfile, "gofz", 0, 0 );
490 if (args_info->r_theta_given)
491 write_into_file(outfile, "r_theta", 0, 0 );
492 if (args_info->r_omega_given)
493 write_into_file(outfile, "r_omega", 0, 0 );
494 if (args_info->r_z_given)
495 write_into_file(outfile, "r_z", 0, 0 );
496 if (args_info->theta_omega_given)
497 write_into_file(outfile, "theta_omega", 0, 0 );
498 if (args_info->gxyz_given)
499 write_into_file(outfile, "gxyz", 0, 0 );
500 if (args_info->twodgofr_given)
501 write_into_file(outfile, "twodgofr", 0, 0 );
502 if (args_info->p2_given)
503 write_into_file(outfile, "p2", 0, 0 );
504 if (args_info->rp2_given)
505 write_into_file(outfile, "rp2", 0, 0 );
506 if (args_info->scd_given)
507 write_into_file(outfile, "scd", 0, 0 );
508 if (args_info->density_given)
509 write_into_file(outfile, "density", 0, 0 );
510 if (args_info->slab_density_given)
511 write_into_file(outfile, "slab_density", 0, 0 );
512 if (args_info->p_angle_given)
513 write_into_file(outfile, "p_angle", 0, 0 );
514 if (args_info->hxy_given)
515 write_into_file(outfile, "hxy", 0, 0 );
516 if (args_info->rho_r_given)
517 write_into_file(outfile, "rho_r", 0, 0 );
518 if (args_info->angle_r_given)
519 write_into_file(outfile, "angle_r", 0, 0 );
520 if (args_info->hullvol_given)
521 write_into_file(outfile, "hullvol", 0, 0 );
522 if (args_info->rodlength_given)
523 write_into_file(outfile, "rodlength", 0, 0 );
524 if (args_info->tet_param_given)
525 write_into_file(outfile, "tet_param", 0, 0 );
526 if (args_info->tet_param_z_given)
527 write_into_file(outfile, "tet_param_z", 0, 0 );
528 if (args_info->rnemdz_given)
529 write_into_file(outfile, "rnemdz", 0, 0 );
530 if (args_info->rnemdr_given)
531 write_into_file(outfile, "rnemdr", 0, 0 );
532 if (args_info->rnemdrt_given)
533 write_into_file(outfile, "rnemdrt", 0, 0 );
534
535
536 i = EXIT_SUCCESS;
537 return i;
538 }
539
540 int
541 cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
542 {
543 FILE *outfile;
544 int i = 0;
545
546 outfile = fopen(filename, "w");
547
548 if (!outfile)
549 {
550 fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
551 return EXIT_FAILURE;
552 }
553
554 i = cmdline_parser_dump(outfile, args_info);
555 fclose (outfile);
556
557 return i;
558 }
559
560 void
561 cmdline_parser_free (struct gengetopt_args_info *args_info)
562 {
563 cmdline_parser_release (args_info);
564 }
565
566 /** @brief replacement of strdup, which is not standard */
567 char *
568 gengetopt_strdup (const char *s)
569 {
570 char *result = 0;
571 if (!s)
572 return result;
573
574 result = (char*)malloc(strlen(s) + 1);
575 if (result == (char*)0)
576 return (char*)0;
577 strcpy(result, s);
578 return result;
579 }
580
581 static void
582 reset_group_staticProps(struct gengetopt_args_info *args_info)
583 {
584 if (! args_info->staticProps_group_counter)
585 return;
586
587 args_info->bo_given = 0 ;
588 args_info->bor_given = 0 ;
589 args_info->bad_given = 0 ;
590 args_info->count_given = 0 ;
591 args_info->gofr_given = 0 ;
592 args_info->gofz_given = 0 ;
593 args_info->r_theta_given = 0 ;
594 args_info->r_omega_given = 0 ;
595 args_info->r_z_given = 0 ;
596 args_info->theta_omega_given = 0 ;
597 args_info->gxyz_given = 0 ;
598 args_info->twodgofr_given = 0 ;
599 args_info->p2_given = 0 ;
600 args_info->rp2_given = 0 ;
601 args_info->scd_given = 0 ;
602 args_info->density_given = 0 ;
603 args_info->slab_density_given = 0 ;
604 args_info->p_angle_given = 0 ;
605 args_info->hxy_given = 0 ;
606 args_info->rho_r_given = 0 ;
607 args_info->angle_r_given = 0 ;
608 args_info->hullvol_given = 0 ;
609 args_info->rodlength_given = 0 ;
610 args_info->tet_param_given = 0 ;
611 args_info->tet_param_z_given = 0 ;
612 args_info->rnemdz_given = 0 ;
613 args_info->rnemdr_given = 0 ;
614 args_info->rnemdrt_given = 0 ;
615
616 args_info->staticProps_group_counter = 0;
617 }
618
619 int
620 cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
621 {
622 return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
623 }
624
625 int
626 cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
627 struct cmdline_parser_params *params)
628 {
629 int result;
630 result = cmdline_parser_internal (argc, argv, args_info, params, 0);
631
632 if (result == EXIT_FAILURE)
633 {
634 cmdline_parser_free (args_info);
635 exit (EXIT_FAILURE);
636 }
637
638 return result;
639 }
640
641 int
642 cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
643 {
644 int result;
645 struct cmdline_parser_params params;
646
647 params.override = override;
648 params.initialize = initialize;
649 params.check_required = check_required;
650 params.check_ambiguity = 0;
651 params.print_errors = 1;
652
653 result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
654
655 if (result == EXIT_FAILURE)
656 {
657 cmdline_parser_free (args_info);
658 exit (EXIT_FAILURE);
659 }
660
661 return result;
662 }
663
664 int
665 cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
666 {
667 int result = EXIT_SUCCESS;
668
669 if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
670 result = EXIT_FAILURE;
671
672 if (result == EXIT_FAILURE)
673 {
674 cmdline_parser_free (args_info);
675 exit (EXIT_FAILURE);
676 }
677
678 return result;
679 }
680
681 int
682 cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
683 {
684 int error = 0;
685 FIX_UNUSED (additional_error);
686
687 /* checks for required options */
688 if (! args_info->input_given)
689 {
690 fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
691 error = 1;
692 }
693
694 if (args_info->staticProps_group_counter == 0)
695 {
696 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 : ""));
697 error = 1;
698 }
699
700
701 /* checks for dependences among options */
702
703 return error;
704 }
705
706
707 static char *package_name = 0;
708
709 /**
710 * @brief updates an option
711 * @param field the generic pointer to the field to update
712 * @param orig_field the pointer to the orig field
713 * @param field_given the pointer to the number of occurrence of this option
714 * @param prev_given the pointer to the number of occurrence already seen
715 * @param value the argument for this option (if null no arg was specified)
716 * @param possible_values the possible values for this option (if specified)
717 * @param default_value the default value (in case the option only accepts fixed values)
718 * @param arg_type the type of this option
719 * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
720 * @param override @see cmdline_parser_params.override
721 * @param no_free whether to free a possible previous value
722 * @param multiple_option whether this is a multiple option
723 * @param long_opt the corresponding long option
724 * @param short_opt the corresponding short option (or '-' if none)
725 * @param additional_error possible further error specification
726 */
727 static
728 int update_arg(void *field, char **orig_field,
729 unsigned int *field_given, unsigned int *prev_given,
730 char *value, const char *possible_values[],
731 const char *default_value,
732 cmdline_parser_arg_type arg_type,
733 int check_ambiguity, int override,
734 int no_free, int multiple_option,
735 const char *long_opt, char short_opt,
736 const char *additional_error)
737 {
738 char *stop_char = 0;
739 const char *val = value;
740 int found;
741 char **string_field;
742 FIX_UNUSED (field);
743
744 stop_char = 0;
745 found = 0;
746
747 if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
748 {
749 if (short_opt != '-')
750 fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
751 package_name, long_opt, short_opt,
752 (additional_error ? additional_error : ""));
753 else
754 fprintf (stderr, "%s: `--%s' option given more than once%s\n",
755 package_name, long_opt,
756 (additional_error ? additional_error : ""));
757 return 1; /* failure */
758 }
759
760 FIX_UNUSED (default_value);
761
762 if (field_given && *field_given && ! override)
763 return 0;
764 if (prev_given)
765 (*prev_given)++;
766 if (field_given)
767 (*field_given)++;
768 if (possible_values)
769 val = possible_values[found];
770
771 switch(arg_type) {
772 case ARG_INT:
773 if (val) *((int *)field) = strtol (val, &stop_char, 0);
774 break;
775 case ARG_DOUBLE:
776 if (val) *((double *)field) = strtod (val, &stop_char);
777 break;
778 case ARG_STRING:
779 if (val) {
780 string_field = (char **)field;
781 if (!no_free && *string_field)
782 free (*string_field); /* free previous string */
783 *string_field = gengetopt_strdup (val);
784 }
785 break;
786 default:
787 break;
788 };
789
790 /* check numeric conversion */
791 switch(arg_type) {
792 case ARG_INT:
793 case ARG_DOUBLE:
794 if (val && !(stop_char && *stop_char == '\0')) {
795 fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
796 return 1; /* failure */
797 }
798 break;
799 default:
800 ;
801 };
802
803 /* store the original value */
804 switch(arg_type) {
805 case ARG_NO:
806 break;
807 default:
808 if (value && orig_field) {
809 if (no_free) {
810 *orig_field = value;
811 } else {
812 if (*orig_field)
813 free (*orig_field); /* free previous string */
814 *orig_field = gengetopt_strdup (value);
815 }
816 }
817 };
818
819 return 0; /* OK */
820 }
821
822
823 int
824 cmdline_parser_internal (
825 int argc, char **argv, struct gengetopt_args_info *args_info,
826 struct cmdline_parser_params *params, const char *additional_error)
827 {
828 int c; /* Character of the parsed option. */
829
830 int error = 0;
831 struct gengetopt_args_info local_args_info;
832
833 int override;
834 int initialize;
835 int check_required;
836 int check_ambiguity;
837
838 package_name = argv[0];
839
840 override = params->override;
841 initialize = params->initialize;
842 check_required = params->check_required;
843 check_ambiguity = params->check_ambiguity;
844
845 if (initialize)
846 cmdline_parser_init (args_info);
847
848 cmdline_parser_init (&local_args_info);
849
850 optarg = 0;
851 optind = 0;
852 opterr = params->print_errors;
853 optopt = '?';
854
855 while (1)
856 {
857 int option_index = 0;
858
859 static struct option long_options[] = {
860 { "help", 0, NULL, 'h' },
861 { "version", 0, NULL, 'V' },
862 { "input", 1, NULL, 'i' },
863 { "output", 1, NULL, 'o' },
864 { "step", 1, NULL, 'n' },
865 { "nbins", 1, NULL, 'b' },
866 { "nbins_x", 1, NULL, 'x' },
867 { "nbins_y", 1, NULL, 'y' },
868 { "nbins_z", 1, NULL, 0 },
869 { "nanglebins", 1, NULL, 'a' },
870 { "rcut", 1, NULL, 'c' },
871 { "dz", 1, NULL, 0 },
872 { "length", 1, NULL, 0 },
873 { "zlength", 1, NULL, 0 },
874 { "zoffset", 1, NULL, 'z' },
875 { "sele1", 1, NULL, 0 },
876 { "sele2", 1, NULL, 0 },
877 { "sele3", 1, NULL, 0 },
878 { "refsele", 1, NULL, 0 },
879 { "comsele", 1, NULL, 0 },
880 { "seleoffset", 1, NULL, 0 },
881 { "molname", 1, NULL, 0 },
882 { "begin", 1, NULL, 0 },
883 { "end", 1, NULL, 0 },
884 { "radius", 1, NULL, 0 },
885 { "bo", 0, NULL, 0 },
886 { "bor", 0, NULL, 0 },
887 { "bad", 0, NULL, 0 },
888 { "count", 0, NULL, 0 },
889 { "gofr", 0, NULL, 'g' },
890 { "gofz", 0, NULL, 0 },
891 { "r_theta", 0, NULL, 0 },
892 { "r_omega", 0, NULL, 0 },
893 { "r_z", 0, NULL, 0 },
894 { "theta_omega", 0, NULL, 0 },
895 { "gxyz", 0, NULL, 0 },
896 { "twodgofr", 0, NULL, 0 },
897 { "p2", 0, NULL, 'p' },
898 { "rp2", 0, NULL, 0 },
899 { "scd", 0, NULL, 's' },
900 { "density", 0, NULL, 'd' },
901 { "slab_density", 0, NULL, 0 },
902 { "p_angle", 0, NULL, 0 },
903 { "hxy", 0, NULL, 0 },
904 { "rho_r", 0, NULL, 0 },
905 { "angle_r", 0, NULL, 0 },
906 { "hullvol", 0, NULL, 0 },
907 { "rodlength", 0, NULL, 0 },
908 { "tet_param", 0, NULL, 'Q' },
909 { "tet_param_z", 0, NULL, 0 },
910 { "rnemdz", 0, NULL, 0 },
911 { "rnemdr", 0, NULL, 0 },
912 { "rnemdrt", 0, NULL, 0 },
913 { 0, 0, 0, 0 }
914 };
915
916 c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
917
918 if (c == -1) break; /* Exit from `while (1)' loop. */
919
920 switch (c)
921 {
922 case 'h': /* Print help and exit. */
923 cmdline_parser_print_help ();
924 cmdline_parser_free (&local_args_info);
925 exit (EXIT_SUCCESS);
926
927 case 'V': /* Print version and exit. */
928 cmdline_parser_print_version ();
929 cmdline_parser_free (&local_args_info);
930 exit (EXIT_SUCCESS);
931
932 case 'i': /* input dump file. */
933
934
935 if (update_arg( (void *)&(args_info->input_arg),
936 &(args_info->input_orig), &(args_info->input_given),
937 &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
938 check_ambiguity, override, 0, 0,
939 "input", 'i',
940 additional_error))
941 goto failure;
942
943 break;
944 case 'o': /* output file name. */
945
946
947 if (update_arg( (void *)&(args_info->output_arg),
948 &(args_info->output_orig), &(args_info->output_given),
949 &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
950 check_ambiguity, override, 0, 0,
951 "output", 'o',
952 additional_error))
953 goto failure;
954
955 break;
956 case 'n': /* process every n frame. */
957
958
959 if (update_arg( (void *)&(args_info->step_arg),
960 &(args_info->step_orig), &(args_info->step_given),
961 &(local_args_info.step_given), optarg, 0, "1", ARG_INT,
962 check_ambiguity, override, 0, 0,
963 "step", 'n',
964 additional_error))
965 goto failure;
966
967 break;
968 case 'b': /* number of bins (general purpose). */
969
970
971 if (update_arg( (void *)&(args_info->nbins_arg),
972 &(args_info->nbins_orig), &(args_info->nbins_given),
973 &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
974 check_ambiguity, override, 0, 0,
975 "nbins", 'b',
976 additional_error))
977 goto failure;
978
979 break;
980 case 'x': /* number of bins in x axis. */
981
982
983 if (update_arg( (void *)&(args_info->nbins_x_arg),
984 &(args_info->nbins_x_orig), &(args_info->nbins_x_given),
985 &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
986 check_ambiguity, override, 0, 0,
987 "nbins_x", 'x',
988 additional_error))
989 goto failure;
990
991 break;
992 case 'y': /* number of bins in y axis. */
993
994
995 if (update_arg( (void *)&(args_info->nbins_y_arg),
996 &(args_info->nbins_y_orig), &(args_info->nbins_y_given),
997 &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
998 check_ambiguity, override, 0, 0,
999 "nbins_y", 'y',
1000 additional_error))
1001 goto failure;
1002
1003 break;
1004 case 'a': /* number of bins for cos(angle). */
1005
1006
1007 if (update_arg( (void *)&(args_info->nanglebins_arg),
1008 &(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1009 &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1010 check_ambiguity, override, 0, 0,
1011 "nanglebins", 'a',
1012 additional_error))
1013 goto failure;
1014
1015 break;
1016 case 'c': /* cutoff radius (rcut). */
1017
1018
1019 if (update_arg( (void *)&(args_info->rcut_arg),
1020 &(args_info->rcut_orig), &(args_info->rcut_given),
1021 &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1022 check_ambiguity, override, 0, 0,
1023 "rcut", 'c',
1024 additional_error))
1025 goto failure;
1026
1027 break;
1028 case 'z': /* Where to set the zero for the slab_density calculation. */
1029
1030
1031 if (update_arg( (void *)&(args_info->zoffset_arg),
1032 &(args_info->zoffset_orig), &(args_info->zoffset_given),
1033 &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1034 check_ambiguity, override, 0, 0,
1035 "zoffset", 'z',
1036 additional_error))
1037 goto failure;
1038
1039 break;
1040 case 'g': /* g(r). */
1041
1042 if (args_info->staticProps_group_counter && override)
1043 reset_group_staticProps (args_info);
1044 args_info->staticProps_group_counter += 1;
1045
1046 if (update_arg( 0 ,
1047 0 , &(args_info->gofr_given),
1048 &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1049 check_ambiguity, override, 0, 0,
1050 "gofr", 'g',
1051 additional_error))
1052 goto failure;
1053
1054 break;
1055 case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */
1056
1057 if (args_info->staticProps_group_counter && override)
1058 reset_group_staticProps (args_info);
1059 args_info->staticProps_group_counter += 1;
1060
1061 if (update_arg( 0 ,
1062 0 , &(args_info->p2_given),
1063 &(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1064 check_ambiguity, override, 0, 0,
1065 "p2", 'p',
1066 additional_error))
1067 goto failure;
1068
1069 break;
1070 case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */
1071
1072 if (args_info->staticProps_group_counter && override)
1073 reset_group_staticProps (args_info);
1074 args_info->staticProps_group_counter += 1;
1075
1076 if (update_arg( 0 ,
1077 0 , &(args_info->scd_given),
1078 &(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1079 check_ambiguity, override, 0, 0,
1080 "scd", 's',
1081 additional_error))
1082 goto failure;
1083
1084 break;
1085 case 'd': /* density plot. */
1086
1087 if (args_info->staticProps_group_counter && override)
1088 reset_group_staticProps (args_info);
1089 args_info->staticProps_group_counter += 1;
1090
1091 if (update_arg( 0 ,
1092 0 , &(args_info->density_given),
1093 &(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1094 check_ambiguity, override, 0, 0,
1095 "density", 'd',
1096 additional_error))
1097 goto failure;
1098
1099 break;
1100 case 'Q': /* tetrahedrality order parameter (Qk). */
1101
1102 if (args_info->staticProps_group_counter && override)
1103 reset_group_staticProps (args_info);
1104 args_info->staticProps_group_counter += 1;
1105
1106 if (update_arg( 0 ,
1107 0 , &(args_info->tet_param_given),
1108 &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1109 check_ambiguity, override, 0, 0,
1110 "tet_param", 'Q',
1111 additional_error))
1112 goto failure;
1113
1114 break;
1115
1116 case 0: /* Long option with no short option */
1117 /* number of bins in z axis. */
1118 if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1119 {
1120
1121
1122 if (update_arg( (void *)&(args_info->nbins_z_arg),
1123 &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1124 &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1125 check_ambiguity, override, 0, 0,
1126 "nbins_z", '-',
1127 additional_error))
1128 goto failure;
1129
1130 }
1131 /* slab width (dz). */
1132 else if (strcmp (long_options[option_index].name, "dz") == 0)
1133 {
1134
1135
1136 if (update_arg( (void *)&(args_info->dz_arg),
1137 &(args_info->dz_orig), &(args_info->dz_given),
1138 &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1139 check_ambiguity, override, 0, 0,
1140 "dz", '-',
1141 additional_error))
1142 goto failure;
1143
1144 }
1145 /* maximum length (Defaults to 1/2 smallest length of first frame). */
1146 else if (strcmp (long_options[option_index].name, "length") == 0)
1147 {
1148
1149
1150 if (update_arg( (void *)&(args_info->length_arg),
1151 &(args_info->length_orig), &(args_info->length_given),
1152 &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1153 check_ambiguity, override, 0, 0,
1154 "length", '-',
1155 additional_error))
1156 goto failure;
1157
1158 }
1159 /* maximum length (Defaults to 1/2 smallest length of first frame). */
1160 else if (strcmp (long_options[option_index].name, "zlength") == 0)
1161 {
1162
1163
1164 if (update_arg( (void *)&(args_info->zlength_arg),
1165 &(args_info->zlength_orig), &(args_info->zlength_given),
1166 &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1167 check_ambiguity, override, 0, 0,
1168 "zlength", '-',
1169 additional_error))
1170 goto failure;
1171
1172 }
1173 /* select the first stuntdouble set. */
1174 else if (strcmp (long_options[option_index].name, "sele1") == 0)
1175 {
1176
1177
1178 if (update_arg( (void *)&(args_info->sele1_arg),
1179 &(args_info->sele1_orig), &(args_info->sele1_given),
1180 &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1181 check_ambiguity, override, 0, 0,
1182 "sele1", '-',
1183 additional_error))
1184 goto failure;
1185
1186 }
1187 /* select the second stuntdouble set. */
1188 else if (strcmp (long_options[option_index].name, "sele2") == 0)
1189 {
1190
1191
1192 if (update_arg( (void *)&(args_info->sele2_arg),
1193 &(args_info->sele2_orig), &(args_info->sele2_given),
1194 &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1195 check_ambiguity, override, 0, 0,
1196 "sele2", '-',
1197 additional_error))
1198 goto failure;
1199
1200 }
1201 /* select the third stuntdouble set. */
1202 else if (strcmp (long_options[option_index].name, "sele3") == 0)
1203 {
1204
1205
1206 if (update_arg( (void *)&(args_info->sele3_arg),
1207 &(args_info->sele3_orig), &(args_info->sele3_given),
1208 &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1209 check_ambiguity, override, 0, 0,
1210 "sele3", '-',
1211 additional_error))
1212 goto failure;
1213
1214 }
1215 /* select reference (use and only use with --gxyz). */
1216 else if (strcmp (long_options[option_index].name, "refsele") == 0)
1217 {
1218
1219
1220 if (update_arg( (void *)&(args_info->refsele_arg),
1221 &(args_info->refsele_orig), &(args_info->refsele_given),
1222 &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1223 check_ambiguity, override, 0, 0,
1224 "refsele", '-',
1225 additional_error))
1226 goto failure;
1227
1228 }
1229 /* select stunt doubles for center-of-mass reference point. */
1230 else if (strcmp (long_options[option_index].name, "comsele") == 0)
1231 {
1232
1233
1234 if (update_arg( (void *)&(args_info->comsele_arg),
1235 &(args_info->comsele_orig), &(args_info->comsele_given),
1236 &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1237 check_ambiguity, override, 0, 0,
1238 "comsele", '-',
1239 additional_error))
1240 goto failure;
1241
1242 }
1243 /* global index offset for a second object (used to define a vector between sites in molecule). */
1244 else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1245 {
1246
1247
1248 if (update_arg( (void *)&(args_info->seleoffset_arg),
1249 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1250 &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1251 check_ambiguity, override, 0, 0,
1252 "seleoffset", '-',
1253 additional_error))
1254 goto failure;
1255
1256 }
1257 /* molecule name. */
1258 else if (strcmp (long_options[option_index].name, "molname") == 0)
1259 {
1260
1261
1262 if (update_arg( (void *)&(args_info->molname_arg),
1263 &(args_info->molname_orig), &(args_info->molname_given),
1264 &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1265 check_ambiguity, override, 0, 0,
1266 "molname", '-',
1267 additional_error))
1268 goto failure;
1269
1270 }
1271 /* begin internal index. */
1272 else if (strcmp (long_options[option_index].name, "begin") == 0)
1273 {
1274
1275
1276 if (update_arg( (void *)&(args_info->begin_arg),
1277 &(args_info->begin_orig), &(args_info->begin_given),
1278 &(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1279 check_ambiguity, override, 0, 0,
1280 "begin", '-',
1281 additional_error))
1282 goto failure;
1283
1284 }
1285 /* end internal index. */
1286 else if (strcmp (long_options[option_index].name, "end") == 0)
1287 {
1288
1289
1290 if (update_arg( (void *)&(args_info->end_arg),
1291 &(args_info->end_orig), &(args_info->end_given),
1292 &(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1293 check_ambiguity, override, 0, 0,
1294 "end", '-',
1295 additional_error))
1296 goto failure;
1297
1298 }
1299 /* nanoparticle radius. */
1300 else if (strcmp (long_options[option_index].name, "radius") == 0)
1301 {
1302
1303
1304 if (update_arg( (void *)&(args_info->radius_arg),
1305 &(args_info->radius_orig), &(args_info->radius_given),
1306 &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1307 check_ambiguity, override, 0, 0,
1308 "radius", '-',
1309 additional_error))
1310 goto failure;
1311
1312 }
1313 /* bond order parameter (--rcut must be specified). */
1314 else if (strcmp (long_options[option_index].name, "bo") == 0)
1315 {
1316
1317 if (args_info->staticProps_group_counter && override)
1318 reset_group_staticProps (args_info);
1319 args_info->staticProps_group_counter += 1;
1320
1321 if (update_arg( 0 ,
1322 0 , &(args_info->bo_given),
1323 &(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1324 check_ambiguity, override, 0, 0,
1325 "bo", '-',
1326 additional_error))
1327 goto failure;
1328
1329 }
1330 /* bond order parameter as a function of radius (--rcut must be specified). */
1331 else if (strcmp (long_options[option_index].name, "bor") == 0)
1332 {
1333
1334 if (args_info->staticProps_group_counter && override)
1335 reset_group_staticProps (args_info);
1336 args_info->staticProps_group_counter += 1;
1337
1338 if (update_arg( 0 ,
1339 0 , &(args_info->bor_given),
1340 &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1341 check_ambiguity, override, 0, 0,
1342 "bor", '-',
1343 additional_error))
1344 goto failure;
1345
1346 }
1347 /* N(theta) bond angle density within (--rcut must be specified). */
1348 else if (strcmp (long_options[option_index].name, "bad") == 0)
1349 {
1350
1351 if (args_info->staticProps_group_counter && override)
1352 reset_group_staticProps (args_info);
1353 args_info->staticProps_group_counter += 1;
1354
1355 if (update_arg( 0 ,
1356 0 , &(args_info->bad_given),
1357 &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1358 check_ambiguity, override, 0, 0,
1359 "bad", '-',
1360 additional_error))
1361 goto failure;
1362
1363 }
1364 /* count of molecules matching selection criteria (and associated statistics). */
1365 else if (strcmp (long_options[option_index].name, "count") == 0)
1366 {
1367
1368 if (args_info->staticProps_group_counter && override)
1369 reset_group_staticProps (args_info);
1370 args_info->staticProps_group_counter += 1;
1371
1372 if (update_arg( 0 ,
1373 0 , &(args_info->count_given),
1374 &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1375 check_ambiguity, override, 0, 0,
1376 "count", '-',
1377 additional_error))
1378 goto failure;
1379
1380 }
1381 /* g(z). */
1382 else if (strcmp (long_options[option_index].name, "gofz") == 0)
1383 {
1384
1385 if (args_info->staticProps_group_counter && override)
1386 reset_group_staticProps (args_info);
1387 args_info->staticProps_group_counter += 1;
1388
1389 if (update_arg( 0 ,
1390 0 , &(args_info->gofz_given),
1391 &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1392 check_ambiguity, override, 0, 0,
1393 "gofz", '-',
1394 additional_error))
1395 goto failure;
1396
1397 }
1398 /* g(r, cos(theta)). */
1399 else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1400 {
1401
1402 if (args_info->staticProps_group_counter && override)
1403 reset_group_staticProps (args_info);
1404 args_info->staticProps_group_counter += 1;
1405
1406 if (update_arg( 0 ,
1407 0 , &(args_info->r_theta_given),
1408 &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1409 check_ambiguity, override, 0, 0,
1410 "r_theta", '-',
1411 additional_error))
1412 goto failure;
1413
1414 }
1415 /* g(r, cos(omega)). */
1416 else if (strcmp (long_options[option_index].name, "r_omega") == 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->r_omega_given),
1425 &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1426 check_ambiguity, override, 0, 0,
1427 "r_omega", '-',
1428 additional_error))
1429 goto failure;
1430
1431 }
1432 /* g(r, z). */
1433 else if (strcmp (long_options[option_index].name, "r_z") == 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->r_z_given),
1442 &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1443 check_ambiguity, override, 0, 0,
1444 "r_z", '-',
1445 additional_error))
1446 goto failure;
1447
1448 }
1449 /* g(cos(theta), cos(omega)). */
1450 else if (strcmp (long_options[option_index].name, "theta_omega") == 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->theta_omega_given),
1459 &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1460 check_ambiguity, override, 0, 0,
1461 "theta_omega", '-',
1462 additional_error))
1463 goto failure;
1464
1465 }
1466 /* g(x, y, z). */
1467 else if (strcmp (long_options[option_index].name, "gxyz") == 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->gxyz_given),
1476 &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1477 check_ambiguity, override, 0, 0,
1478 "gxyz", '-',
1479 additional_error))
1480 goto failure;
1481
1482 }
1483 /* 2D g(r) (Slab width --dz must be specified). */
1484 else if (strcmp (long_options[option_index].name, "twodgofr") == 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->twodgofr_given),
1493 &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1494 check_ambiguity, override, 0, 0,
1495 "twodgofr", '-',
1496 additional_error))
1497 goto failure;
1498
1499 }
1500 /* rp2 order parameter (--sele1 and --sele2 must be specified). */
1501 else if (strcmp (long_options[option_index].name, "rp2") == 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->rp2_given),
1510 &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1511 check_ambiguity, override, 0, 0,
1512 "rp2", '-',
1513 additional_error))
1514 goto failure;
1515
1516 }
1517 /* slab density. */
1518 else if (strcmp (long_options[option_index].name, "slab_density") == 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->slab_density_given),
1527 &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1528 check_ambiguity, override, 0, 0,
1529 "slab_density", '-',
1530 additional_error))
1531 goto failure;
1532
1533 }
1534 /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional). */
1535 else if (strcmp (long_options[option_index].name, "p_angle") == 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->p_angle_given),
1544 &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1545 check_ambiguity, override, 0, 0,
1546 "p_angle", '-',
1547 additional_error))
1548 goto failure;
1549
1550 }
1551 /* hxy. */
1552 else if (strcmp (long_options[option_index].name, "hxy") == 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->hxy_given),
1561 &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1562 check_ambiguity, override, 0, 0,
1563 "hxy", '-',
1564 additional_error))
1565 goto failure;
1566
1567 }
1568 /* rho of R. */
1569 else if (strcmp (long_options[option_index].name, "rho_r") == 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->rho_r_given),
1578 &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1579 check_ambiguity, override, 0, 0,
1580 "rho_r", '-',
1581 additional_error))
1582 goto failure;
1583
1584 }
1585 /* angle of R. */
1586 else if (strcmp (long_options[option_index].name, "angle_r") == 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->angle_r_given),
1595 &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1596 check_ambiguity, override, 0, 0,
1597 "angle_r", '-',
1598 additional_error))
1599 goto failure;
1600
1601 }
1602 /* hull volume of nanoparticle. */
1603 else if (strcmp (long_options[option_index].name, "hullvol") == 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->hullvol_given),
1612 &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1613 check_ambiguity, override, 0, 0,
1614 "hullvol", '-',
1615 additional_error))
1616 goto failure;
1617
1618 }
1619 /* length of nanorod. */
1620 else if (strcmp (long_options[option_index].name, "rodlength") == 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->rodlength_given),
1629 &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1630 check_ambiguity, override, 0, 0,
1631 "rodlength", '-',
1632 additional_error))
1633 goto failure;
1634
1635 }
1636 /* spatially-resolved tetrahedrality order parameter Qk(z). */
1637 else if (strcmp (long_options[option_index].name, "tet_param_z") == 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->tet_param_z_given),
1646 &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1647 check_ambiguity, override, 0, 0,
1648 "tet_param_z", '-',
1649 additional_error))
1650 goto failure;
1651
1652 }
1653 /* slab-resolved RNEMD statistics (temperature, density, velocity). */
1654 else if (strcmp (long_options[option_index].name, "rnemdz") == 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->rnemdz_given),
1663 &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1664 check_ambiguity, override, 0, 0,
1665 "rnemdz", '-',
1666 additional_error))
1667 goto failure;
1668
1669 }
1670 /* shell-resolved RNEMD statistics (temperature, density, angular velocity). */
1671 else if (strcmp (long_options[option_index].name, "rnemdr") == 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->rnemdr_given),
1680 &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1681 check_ambiguity, override, 0, 0,
1682 "rnemdr", '-',
1683 additional_error))
1684 goto failure;
1685
1686 }
1687 /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity). */
1688 else if (strcmp (long_options[option_index].name, "rnemdrt") == 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->rnemdrt_given),
1697 &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1698 check_ambiguity, override, 0, 0,
1699 "rnemdrt", '-',
1700 additional_error))
1701 goto failure;
1702
1703 }
1704
1705 break;
1706 case '?': /* Invalid option. */
1707 /* `getopt_long' already printed an error message. */
1708 goto failure;
1709
1710 default: /* bug: option not considered. */
1711 fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1712 abort ();
1713 } /* switch */
1714 } /* while */
1715
1716 if (args_info->staticProps_group_counter > 1)
1717 {
1718 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 : ""));
1719 error = 1;
1720 }
1721
1722
1723
1724 if (check_required)
1725 {
1726 error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1727 }
1728
1729 cmdline_parser_release (&local_args_info);
1730
1731 if ( error )
1732 return (EXIT_FAILURE);
1733
1734 if (optind < argc)
1735 {
1736 int i = 0 ;
1737 int found_prog_name = 0;
1738 /* whether program name, i.e., argv[0], is in the remaining args
1739 (this may happen with some implementations of getopt,
1740 but surely not with the one included by gengetopt) */
1741
1742 i = optind;
1743 while (i < argc)
1744 if (argv[i++] == argv[0]) {
1745 found_prog_name = 1;
1746 break;
1747 }
1748 i = 0;
1749
1750 args_info->inputs_num = argc - optind - found_prog_name;
1751 args_info->inputs =
1752 (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1753 while (optind < argc)
1754 if (argv[optind++] != argv[0])
1755 args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1756 }
1757
1758 return 0;
1759
1760 failure:
1761
1762 cmdline_parser_release (&local_args_info);
1763 return (EXIT_FAILURE);
1764 }

Properties

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