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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
Revision: 1843
Committed: Tue Jan 29 20:58:08 2013 UTC (12 years, 9 months ago) by gezelter
File size: 59522 byte(s)
Log Message: 
Simplified the Tetrahedrality [Qk(z)] analysis code.

File Contents

# User Rev Content
1 tim 310 /*
2 gezelter 1629 File autogenerated by gengetopt version 2.22.4
3 tim 310 generated with the following command:
4 gezelter 1819 gengetopt --file-name=StaticPropsCmd --unamed-opts
5 tim 310
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 gezelter 929 /* If we use autoconf. */
12     #ifdef HAVE_CONFIG_H
13     #include "config.h"
14     #endif
15 tim 310
16     #include <stdio.h>
17     #include <stdlib.h>
18     #include <string.h>
19    
20 gezelter 1629 #ifndef FIX_UNUSED
21     #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22     #endif
23 tim 310
24 gezelter 1629 #include <getopt.h>
25    
26 tim 311 #include "StaticPropsCmd.h"
27 tim 310
28 chuckv 1128 const char *gengetopt_args_info_purpose = "";
29    
30 gezelter 1454 const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
31 chuckv 1128
32     const char *gengetopt_args_info_description = "";
33    
34     const char *gengetopt_args_info_help[] = {
35     " -h, --help Print help and exit",
36     " -V, --version Print version and exit",
37     " -i, --input=filename input dump file",
38     " -o, --output=filename output file name",
39     " -n, --step=INT process every n frame (default=`1')",
40     " -b, --nbins=INT number of bins (general purpose) \n (default=`100')",
41     " -x, --nbins_x=INT number of bins in x axis (default=`100')",
42     " -y, --nbins_y=INT number of bins in y axis (default=`100')",
43 gezelter 1440 " --nbins_z=INT number of bins in z axis (default=`100')",
44 chuckv 1128 " -a, --nanglebins=INT number of bins for cos(angle) (default=`50')",
45 chuckv 1445 " -c, --rcut=DOUBLE cutoff radius (rcut)",
46 gezelter 1454 " --dz=DOUBLE slab width (dz)",
47 chuckv 1128 " --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
48 chuckv 1445 " --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
49 chuckv 1128 " -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')",
50     " --sele1=selection script select the first stuntdouble set",
51     " --sele2=selection script select the second stuntdouble set",
52     " --sele3=selection script select the third stuntdouble set",
53     " --refsele=selection script\n select reference (use and only use with --gxyz)",
54 gezelter 1390 " --comsele=selection script\n select stunt doubles for center-of-mass \n reference point",
55 gezelter 1819 " --seleoffset=INT global index offset for a second object (used \n to define a vector between sites in molecule)",
56 chuckv 1128 " --molname=STRING molecule name",
57     " --begin=INT begin internal index",
58     " --end=INT end internal index",
59     " --radius=DOUBLE nanoparticle radius",
60     "\n Group: staticProps\n an option of this group is required",
61     " --bo bond order parameter (--rcut must be specified)",
62     " --bor bond order parameter as a function of radius \n (--rcut must be specified)",
63 chuckv 1180 " --bad N(theta) bond angle density within (--rcut must \n be specified)",
64 gezelter 1629 " --count count of molecules matching selection criteria \n (and associated statistics)",
65 chuckv 1128 " -g, --gofr g(r)",
66 xsun 1213 " --gofz g(z)",
67 chuckv 1128 " --r_theta g(r, cos(theta))",
68     " --r_omega g(r, cos(omega))",
69 gezelter 1440 " --r_z g(r, z)",
70 chuckv 1128 " --theta_omega g(cos(theta), cos(omega))",
71     " --gxyz g(x, y, z)",
72 gezelter 1454 " --twodgofr 2D g(r) (Slab width --dz must be specified)",
73 gezelter 1629 " -p, --p2 p2 order parameter (--sele1 must be specified, \n --sele2 is optional)",
74 chuckv 1128 " --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)",
75     " -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)",
76     " -d, --density density plot",
77     " --slab_density slab density",
78 gezelter 1413 " --p_angle p(cos(theta))",
79 chuckv 1128 " --hxy hxy",
80     " --rho_r rho of R",
81 gezelter 1629 " --angle_r angle of R",
82 chuckv 1180 " --hullvol hull volume of nanoparticle",
83 gezelter 1629 " --rodlength length of nanorod",
84 gezelter 1843 " -Q, --tet_param tetrahedrality order parameter (Qk)",
85     " --tet_param_z spatially-resolved tetrahedrality order \n parameter Qk(z)",
86 chuckv 1128 0
87     };
88    
89 gezelter 1390 typedef enum {ARG_NO
90     , ARG_STRING
91     , ARG_INT
92     , ARG_DOUBLE
93     } cmdline_parser_arg_type;
94    
95 gezelter 929 static
96     void clear_given (struct gengetopt_args_info *args_info);
97     static
98     void clear_args (struct gengetopt_args_info *args_info);
99    
100     static int
101 gezelter 1629 cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
102 gezelter 1390 struct cmdline_parser_params *params, const char *additional_error);
103 gezelter 929
104     static int
105     cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
106    
107     static char *
108     gengetopt_strdup (const char *s);
109    
110     static
111     void clear_given (struct gengetopt_args_info *args_info)
112     {
113     args_info->help_given = 0 ;
114     args_info->version_given = 0 ;
115     args_info->input_given = 0 ;
116     args_info->output_given = 0 ;
117     args_info->step_given = 0 ;
118 gezelter 1041 args_info->nbins_given = 0 ;
119 xsun 955 args_info->nbins_x_given = 0 ;
120     args_info->nbins_y_given = 0 ;
121 gezelter 1440 args_info->nbins_z_given = 0 ;
122 gezelter 929 args_info->nanglebins_given = 0 ;
123 chuckv 1445 args_info->rcut_given = 0 ;
124 gezelter 1454 args_info->dz_given = 0 ;
125 gezelter 929 args_info->length_given = 0 ;
126 chuckv 1445 args_info->zlength_given = 0 ;
127 gezelter 929 args_info->zoffset_given = 0 ;
128     args_info->sele1_given = 0 ;
129     args_info->sele2_given = 0 ;
130     args_info->sele3_given = 0 ;
131     args_info->refsele_given = 0 ;
132 gezelter 1390 args_info->comsele_given = 0 ;
133 gezelter 1819 args_info->seleoffset_given = 0 ;
134 gezelter 929 args_info->molname_given = 0 ;
135     args_info->begin_given = 0 ;
136     args_info->end_given = 0 ;
137 chuckv 1091 args_info->radius_given = 0 ;
138 gezelter 1039 args_info->bo_given = 0 ;
139 chuckv 1128 args_info->bor_given = 0 ;
140 chuckv 1180 args_info->bad_given = 0 ;
141 gezelter 1629 args_info->count_given = 0 ;
142 gezelter 929 args_info->gofr_given = 0 ;
143 xsun 1213 args_info->gofz_given = 0 ;
144 gezelter 929 args_info->r_theta_given = 0 ;
145     args_info->r_omega_given = 0 ;
146 gezelter 1440 args_info->r_z_given = 0 ;
147 gezelter 929 args_info->theta_omega_given = 0 ;
148     args_info->gxyz_given = 0 ;
149 gezelter 1454 args_info->twodgofr_given = 0 ;
150 gezelter 929 args_info->p2_given = 0 ;
151 xsun 980 args_info->rp2_given = 0 ;
152 gezelter 929 args_info->scd_given = 0 ;
153     args_info->density_given = 0 ;
154     args_info->slab_density_given = 0 ;
155 gezelter 1413 args_info->p_angle_given = 0 ;
156 xsun 955 args_info->hxy_given = 0 ;
157 chuckv 1091 args_info->rho_r_given = 0 ;
158 gezelter 1629 args_info->angle_r_given = 0 ;
159 chuckv 1180 args_info->hullvol_given = 0 ;
160 gezelter 1629 args_info->rodlength_given = 0 ;
161     args_info->tet_param_given = 0 ;
162 plouden 1762 args_info->tet_param_z_given = 0 ;
163 gezelter 929 args_info->staticProps_group_counter = 0 ;
164     }
165    
166     static
167     void clear_args (struct gengetopt_args_info *args_info)
168     {
169 gezelter 1629 FIX_UNUSED (args_info);
170 gezelter 929 args_info->input_arg = NULL;
171     args_info->input_orig = NULL;
172     args_info->output_arg = NULL;
173     args_info->output_orig = NULL;
174     args_info->step_arg = 1;
175     args_info->step_orig = NULL;
176 gezelter 1041 args_info->nbins_arg = 100;
177     args_info->nbins_orig = NULL;
178 xsun 955 args_info->nbins_x_arg = 100;
179     args_info->nbins_x_orig = NULL;
180     args_info->nbins_y_arg = 100;
181     args_info->nbins_y_orig = NULL;
182 gezelter 1440 args_info->nbins_z_arg = 100;
183     args_info->nbins_z_orig = NULL;
184 gezelter 929 args_info->nanglebins_arg = 50;
185     args_info->nanglebins_orig = NULL;
186 chuckv 1445 args_info->rcut_orig = NULL;
187 gezelter 1454 args_info->dz_orig = NULL;
188 gezelter 929 args_info->length_orig = NULL;
189 chuckv 1445 args_info->zlength_orig = NULL;
190 gezelter 929 args_info->zoffset_arg = 0;
191     args_info->zoffset_orig = NULL;
192     args_info->sele1_arg = NULL;
193     args_info->sele1_orig = NULL;
194     args_info->sele2_arg = NULL;
195     args_info->sele2_orig = NULL;
196     args_info->sele3_arg = NULL;
197     args_info->sele3_orig = NULL;
198     args_info->refsele_arg = NULL;
199     args_info->refsele_orig = NULL;
200 gezelter 1390 args_info->comsele_arg = NULL;
201     args_info->comsele_orig = NULL;
202 gezelter 1819 args_info->seleoffset_orig = NULL;
203 gezelter 929 args_info->molname_arg = NULL;
204     args_info->molname_orig = NULL;
205     args_info->begin_orig = NULL;
206     args_info->end_orig = NULL;
207 chuckv 1091 args_info->radius_orig = NULL;
208 gezelter 929
209     }
210    
211 chuckv 1128 static
212     void init_args_info(struct gengetopt_args_info *args_info)
213     {
214 gezelter 1390
215    
216 chuckv 1128 args_info->help_help = gengetopt_args_info_help[0] ;
217     args_info->version_help = gengetopt_args_info_help[1] ;
218     args_info->input_help = gengetopt_args_info_help[2] ;
219     args_info->output_help = gengetopt_args_info_help[3] ;
220     args_info->step_help = gengetopt_args_info_help[4] ;
221     args_info->nbins_help = gengetopt_args_info_help[5] ;
222     args_info->nbins_x_help = gengetopt_args_info_help[6] ;
223     args_info->nbins_y_help = gengetopt_args_info_help[7] ;
224 gezelter 1440 args_info->nbins_z_help = gengetopt_args_info_help[8] ;
225     args_info->nanglebins_help = gengetopt_args_info_help[9] ;
226 chuckv 1445 args_info->rcut_help = gengetopt_args_info_help[10] ;
227 gezelter 1454 args_info->dz_help = gengetopt_args_info_help[11] ;
228     args_info->length_help = gengetopt_args_info_help[12] ;
229     args_info->zlength_help = gengetopt_args_info_help[13] ;
230     args_info->zoffset_help = gengetopt_args_info_help[14] ;
231     args_info->sele1_help = gengetopt_args_info_help[15] ;
232     args_info->sele2_help = gengetopt_args_info_help[16] ;
233     args_info->sele3_help = gengetopt_args_info_help[17] ;
234     args_info->refsele_help = gengetopt_args_info_help[18] ;
235     args_info->comsele_help = gengetopt_args_info_help[19] ;
236 gezelter 1819 args_info->seleoffset_help = gengetopt_args_info_help[20] ;
237     args_info->molname_help = gengetopt_args_info_help[21] ;
238     args_info->begin_help = gengetopt_args_info_help[22] ;
239     args_info->end_help = gengetopt_args_info_help[23] ;
240     args_info->radius_help = gengetopt_args_info_help[24] ;
241     args_info->bo_help = gengetopt_args_info_help[26] ;
242     args_info->bor_help = gengetopt_args_info_help[27] ;
243     args_info->bad_help = gengetopt_args_info_help[28] ;
244     args_info->count_help = gengetopt_args_info_help[29] ;
245     args_info->gofr_help = gengetopt_args_info_help[30] ;
246     args_info->gofz_help = gengetopt_args_info_help[31] ;
247     args_info->r_theta_help = gengetopt_args_info_help[32] ;
248     args_info->r_omega_help = gengetopt_args_info_help[33] ;
249     args_info->r_z_help = gengetopt_args_info_help[34] ;
250     args_info->theta_omega_help = gengetopt_args_info_help[35] ;
251     args_info->gxyz_help = gengetopt_args_info_help[36] ;
252     args_info->twodgofr_help = gengetopt_args_info_help[37] ;
253     args_info->p2_help = gengetopt_args_info_help[38] ;
254     args_info->rp2_help = gengetopt_args_info_help[39] ;
255     args_info->scd_help = gengetopt_args_info_help[40] ;
256     args_info->density_help = gengetopt_args_info_help[41] ;
257     args_info->slab_density_help = gengetopt_args_info_help[42] ;
258     args_info->p_angle_help = gengetopt_args_info_help[43] ;
259     args_info->hxy_help = gengetopt_args_info_help[44] ;
260     args_info->rho_r_help = gengetopt_args_info_help[45] ;
261     args_info->angle_r_help = gengetopt_args_info_help[46] ;
262     args_info->hullvol_help = gengetopt_args_info_help[47] ;
263     args_info->rodlength_help = gengetopt_args_info_help[48] ;
264     args_info->tet_param_help = gengetopt_args_info_help[49] ;
265     args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
266 chuckv 1128
267     }
268    
269 tim 310 void
270     cmdline_parser_print_version (void)
271     {
272 gezelter 1629 printf ("%s %s\n",
273     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
274     CMDLINE_PARSER_VERSION);
275 tim 310 }
276    
277 gezelter 1390 static void print_help_common(void) {
278 tim 310 cmdline_parser_print_version ();
279 chuckv 1128
280     if (strlen(gengetopt_args_info_purpose) > 0)
281     printf("\n%s\n", gengetopt_args_info_purpose);
282    
283 gezelter 1390 if (strlen(gengetopt_args_info_usage) > 0)
284     printf("\n%s\n", gengetopt_args_info_usage);
285 chuckv 1128
286 gezelter 1390 printf("\n");
287    
288 chuckv 1128 if (strlen(gengetopt_args_info_description) > 0)
289 gezelter 1629 printf("%s\n\n", gengetopt_args_info_description);
290 gezelter 1390 }
291 chuckv 1128
292 gezelter 1390 void
293     cmdline_parser_print_help (void)
294     {
295     int i = 0;
296     print_help_common();
297 chuckv 1128 while (gengetopt_args_info_help[i])
298     printf("%s\n", gengetopt_args_info_help[i++]);
299 tim 310 }
300    
301 gezelter 929 void
302     cmdline_parser_init (struct gengetopt_args_info *args_info)
303     {
304     clear_given (args_info);
305     clear_args (args_info);
306 chuckv 1128 init_args_info (args_info);
307 gezelter 1454
308 gezelter 1629 args_info->inputs = 0;
309 gezelter 1454 args_info->inputs_num = 0;
310 gezelter 1390 }
311 chuckv 1128
312 gezelter 1390 void
313     cmdline_parser_params_init(struct cmdline_parser_params *params)
314     {
315     if (params)
316     {
317     params->override = 0;
318     params->initialize = 1;
319     params->check_required = 1;
320     params->check_ambiguity = 0;
321     params->print_errors = 1;
322     }
323 gezelter 929 }
324 tim 310
325 gezelter 1390 struct cmdline_parser_params *
326     cmdline_parser_params_create(void)
327     {
328     struct cmdline_parser_params *params =
329     (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
330     cmdline_parser_params_init(params);
331     return params;
332     }
333    
334 gezelter 929 static void
335 gezelter 1390 free_string_field (char **s)
336 gezelter 929 {
337 gezelter 1390 if (*s)
338 gezelter 929 {
339 gezelter 1390 free (*s);
340     *s = 0;
341 gezelter 929 }
342 gezelter 1390 }
343    
344    
345     static void
346     cmdline_parser_release (struct gengetopt_args_info *args_info)
347     {
348 gezelter 1454 unsigned int i;
349 gezelter 1390 free_string_field (&(args_info->input_arg));
350     free_string_field (&(args_info->input_orig));
351     free_string_field (&(args_info->output_arg));
352     free_string_field (&(args_info->output_orig));
353     free_string_field (&(args_info->step_orig));
354     free_string_field (&(args_info->nbins_orig));
355     free_string_field (&(args_info->nbins_x_orig));
356     free_string_field (&(args_info->nbins_y_orig));
357 gezelter 1440 free_string_field (&(args_info->nbins_z_orig));
358 gezelter 1390 free_string_field (&(args_info->nanglebins_orig));
359 chuckv 1445 free_string_field (&(args_info->rcut_orig));
360 gezelter 1454 free_string_field (&(args_info->dz_orig));
361 gezelter 1390 free_string_field (&(args_info->length_orig));
362 chuckv 1445 free_string_field (&(args_info->zlength_orig));
363 gezelter 1390 free_string_field (&(args_info->zoffset_orig));
364     free_string_field (&(args_info->sele1_arg));
365     free_string_field (&(args_info->sele1_orig));
366     free_string_field (&(args_info->sele2_arg));
367     free_string_field (&(args_info->sele2_orig));
368     free_string_field (&(args_info->sele3_arg));
369     free_string_field (&(args_info->sele3_orig));
370     free_string_field (&(args_info->refsele_arg));
371     free_string_field (&(args_info->refsele_orig));
372     free_string_field (&(args_info->comsele_arg));
373     free_string_field (&(args_info->comsele_orig));
374 gezelter 1819 free_string_field (&(args_info->seleoffset_orig));
375 gezelter 1390 free_string_field (&(args_info->molname_arg));
376     free_string_field (&(args_info->molname_orig));
377     free_string_field (&(args_info->begin_orig));
378     free_string_field (&(args_info->end_orig));
379     free_string_field (&(args_info->radius_orig));
380 gezelter 929
381 chuckv 1128
382 gezelter 1454 for (i = 0; i < args_info->inputs_num; ++i)
383     free (args_info->inputs [i]);
384 gezelter 1390
385 gezelter 1454 if (args_info->inputs_num)
386     free (args_info->inputs);
387    
388 gezelter 929 clear_given (args_info);
389     }
390 tim 310
391 gezelter 1390
392     static void
393 gezelter 1629 write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
394 gezelter 1390 {
395 gezelter 1629 FIX_UNUSED (values);
396 gezelter 1390 if (arg) {
397     fprintf(outfile, "%s=\"%s\"\n", opt, arg);
398     } else {
399     fprintf(outfile, "%s\n", opt);
400     }
401     }
402    
403    
404 gezelter 929 int
405 gezelter 1390 cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
406     {
407     int i = 0;
408    
409     if (!outfile)
410     {
411     fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
412     return EXIT_FAILURE;
413     }
414    
415     if (args_info->help_given)
416     write_into_file(outfile, "help", 0, 0 );
417     if (args_info->version_given)
418     write_into_file(outfile, "version", 0, 0 );
419     if (args_info->input_given)
420     write_into_file(outfile, "input", args_info->input_orig, 0);
421     if (args_info->output_given)
422     write_into_file(outfile, "output", args_info->output_orig, 0);
423     if (args_info->step_given)
424     write_into_file(outfile, "step", args_info->step_orig, 0);
425     if (args_info->nbins_given)
426     write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
427     if (args_info->nbins_x_given)
428     write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
429     if (args_info->nbins_y_given)
430     write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
431 gezelter 1440 if (args_info->nbins_z_given)
432     write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
433 gezelter 1390 if (args_info->nanglebins_given)
434     write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
435 chuckv 1445 if (args_info->rcut_given)
436     write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
437 gezelter 1454 if (args_info->dz_given)
438     write_into_file(outfile, "dz", args_info->dz_orig, 0);
439 gezelter 1390 if (args_info->length_given)
440     write_into_file(outfile, "length", args_info->length_orig, 0);
441 chuckv 1445 if (args_info->zlength_given)
442     write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
443 gezelter 1390 if (args_info->zoffset_given)
444     write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
445     if (args_info->sele1_given)
446     write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
447     if (args_info->sele2_given)
448     write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
449     if (args_info->sele3_given)
450     write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
451     if (args_info->refsele_given)
452     write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
453     if (args_info->comsele_given)
454     write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
455 gezelter 1819 if (args_info->seleoffset_given)
456     write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
457 gezelter 1390 if (args_info->molname_given)
458     write_into_file(outfile, "molname", args_info->molname_orig, 0);
459     if (args_info->begin_given)
460     write_into_file(outfile, "begin", args_info->begin_orig, 0);
461     if (args_info->end_given)
462     write_into_file(outfile, "end", args_info->end_orig, 0);
463     if (args_info->radius_given)
464     write_into_file(outfile, "radius", args_info->radius_orig, 0);
465     if (args_info->bo_given)
466     write_into_file(outfile, "bo", 0, 0 );
467     if (args_info->bor_given)
468     write_into_file(outfile, "bor", 0, 0 );
469     if (args_info->bad_given)
470     write_into_file(outfile, "bad", 0, 0 );
471 gezelter 1629 if (args_info->count_given)
472     write_into_file(outfile, "count", 0, 0 );
473 gezelter 1390 if (args_info->gofr_given)
474     write_into_file(outfile, "gofr", 0, 0 );
475     if (args_info->gofz_given)
476     write_into_file(outfile, "gofz", 0, 0 );
477     if (args_info->r_theta_given)
478     write_into_file(outfile, "r_theta", 0, 0 );
479     if (args_info->r_omega_given)
480     write_into_file(outfile, "r_omega", 0, 0 );
481 gezelter 1440 if (args_info->r_z_given)
482     write_into_file(outfile, "r_z", 0, 0 );
483 gezelter 1390 if (args_info->theta_omega_given)
484     write_into_file(outfile, "theta_omega", 0, 0 );
485     if (args_info->gxyz_given)
486     write_into_file(outfile, "gxyz", 0, 0 );
487 gezelter 1454 if (args_info->twodgofr_given)
488     write_into_file(outfile, "twodgofr", 0, 0 );
489 gezelter 1390 if (args_info->p2_given)
490     write_into_file(outfile, "p2", 0, 0 );
491     if (args_info->rp2_given)
492     write_into_file(outfile, "rp2", 0, 0 );
493     if (args_info->scd_given)
494     write_into_file(outfile, "scd", 0, 0 );
495     if (args_info->density_given)
496     write_into_file(outfile, "density", 0, 0 );
497     if (args_info->slab_density_given)
498     write_into_file(outfile, "slab_density", 0, 0 );
499 gezelter 1413 if (args_info->p_angle_given)
500     write_into_file(outfile, "p_angle", 0, 0 );
501 gezelter 1390 if (args_info->hxy_given)
502     write_into_file(outfile, "hxy", 0, 0 );
503     if (args_info->rho_r_given)
504     write_into_file(outfile, "rho_r", 0, 0 );
505 gezelter 1629 if (args_info->angle_r_given)
506     write_into_file(outfile, "angle_r", 0, 0 );
507 gezelter 1390 if (args_info->hullvol_given)
508     write_into_file(outfile, "hullvol", 0, 0 );
509 gezelter 1629 if (args_info->rodlength_given)
510     write_into_file(outfile, "rodlength", 0, 0 );
511     if (args_info->tet_param_given)
512     write_into_file(outfile, "tet_param", 0, 0 );
513 plouden 1762 if (args_info->tet_param_z_given)
514     write_into_file(outfile, "tet_param_z", 0, 0 );
515 gezelter 1390
516    
517     i = EXIT_SUCCESS;
518     return i;
519     }
520    
521     int
522 gezelter 929 cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
523     {
524     FILE *outfile;
525     int i = 0;
526    
527     outfile = fopen(filename, "w");
528    
529     if (!outfile)
530     {
531     fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
532     return EXIT_FAILURE;
533     }
534    
535 gezelter 1390 i = cmdline_parser_dump(outfile, args_info);
536 gezelter 929 fclose (outfile);
537    
538     return i;
539     }
540    
541     void
542     cmdline_parser_free (struct gengetopt_args_info *args_info)
543     {
544     cmdline_parser_release (args_info);
545     }
546    
547 gezelter 1390 /** @brief replacement of strdup, which is not standard */
548 tim 310 char *
549     gengetopt_strdup (const char *s)
550     {
551 gezelter 1629 char *result = 0;
552 gezelter 929 if (!s)
553     return result;
554    
555     result = (char*)malloc(strlen(s) + 1);
556 tim 310 if (result == (char*)0)
557     return (char*)0;
558     strcpy(result, s);
559     return result;
560     }
561    
562 gezelter 929 static void
563     reset_group_staticProps(struct gengetopt_args_info *args_info)
564 tim 310 {
565 gezelter 929 if (! args_info->staticProps_group_counter)
566     return;
567 tim 310
568 gezelter 1039 args_info->bo_given = 0 ;
569 chuckv 1128 args_info->bor_given = 0 ;
570 chuckv 1180 args_info->bad_given = 0 ;
571 gezelter 1629 args_info->count_given = 0 ;
572 tim 310 args_info->gofr_given = 0 ;
573 xsun 1213 args_info->gofz_given = 0 ;
574 tim 310 args_info->r_theta_given = 0 ;
575     args_info->r_omega_given = 0 ;
576 gezelter 1440 args_info->r_z_given = 0 ;
577 tim 310 args_info->theta_omega_given = 0 ;
578 tim 369 args_info->gxyz_given = 0 ;
579 gezelter 1454 args_info->twodgofr_given = 0 ;
580 tim 543 args_info->p2_given = 0 ;
581 xsun 980 args_info->rp2_given = 0 ;
582 tim 544 args_info->scd_given = 0 ;
583 tim 545 args_info->density_given = 0 ;
584 tim 840 args_info->slab_density_given = 0 ;
585 gezelter 1413 args_info->p_angle_given = 0 ;
586 xsun 967 args_info->hxy_given = 0 ;
587 chuckv 1091 args_info->rho_r_given = 0 ;
588 gezelter 1629 args_info->angle_r_given = 0 ;
589 chuckv 1180 args_info->hullvol_given = 0 ;
590 gezelter 1629 args_info->rodlength_given = 0 ;
591     args_info->tet_param_given = 0 ;
592 plouden 1762 args_info->tet_param_z_given = 0 ;
593 gezelter 929
594     args_info->staticProps_group_counter = 0;
595 tim 543 }
596 tim 310
597 gezelter 929 int
598 gezelter 1629 cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
599 gezelter 929 {
600     return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
601     }
602 tim 310
603 gezelter 929 int
604 gezelter 1629 cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
605 gezelter 1390 struct cmdline_parser_params *params)
606     {
607     int result;
608 gezelter 1629 result = cmdline_parser_internal (argc, argv, args_info, params, 0);
609 gezelter 1390
610     if (result == EXIT_FAILURE)
611     {
612     cmdline_parser_free (args_info);
613     exit (EXIT_FAILURE);
614     }
615    
616     return result;
617     }
618    
619     int
620 gezelter 1629 cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
621 gezelter 929 {
622     int result;
623 gezelter 1390 struct cmdline_parser_params params;
624    
625     params.override = override;
626     params.initialize = initialize;
627     params.check_required = check_required;
628     params.check_ambiguity = 0;
629     params.print_errors = 1;
630 gezelter 929
631 gezelter 1629 result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
632 gezelter 929
633     if (result == EXIT_FAILURE)
634     {
635     cmdline_parser_free (args_info);
636     exit (EXIT_FAILURE);
637     }
638    
639     return result;
640     }
641    
642     int
643     cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
644     {
645     int result = EXIT_SUCCESS;
646    
647 gezelter 1629 if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
648 gezelter 929 result = EXIT_FAILURE;
649    
650     if (result == EXIT_FAILURE)
651     {
652     cmdline_parser_free (args_info);
653     exit (EXIT_FAILURE);
654     }
655    
656     return result;
657     }
658    
659     int
660     cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
661     {
662     int error = 0;
663 gezelter 1629 FIX_UNUSED (additional_error);
664 gezelter 929
665 chuckv 1128 /* checks for required options */
666 gezelter 929 if (! args_info->input_given)
667     {
668     fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
669     error = 1;
670     }
671 chuckv 1128
672 gezelter 929 if (args_info->staticProps_group_counter == 0)
673     {
674 gezelter 1629 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 : ""));
675 gezelter 929 error = 1;
676     }
677    
678    
679 chuckv 1128 /* checks for dependences among options */
680    
681 gezelter 929 return error;
682     }
683    
684 gezelter 1390
685     static char *package_name = 0;
686    
687     /**
688     * @brief updates an option
689     * @param field the generic pointer to the field to update
690     * @param orig_field the pointer to the orig field
691     * @param field_given the pointer to the number of occurrence of this option
692     * @param prev_given the pointer to the number of occurrence already seen
693     * @param value the argument for this option (if null no arg was specified)
694     * @param possible_values the possible values for this option (if specified)
695     * @param default_value the default value (in case the option only accepts fixed values)
696     * @param arg_type the type of this option
697     * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
698     * @param override @see cmdline_parser_params.override
699     * @param no_free whether to free a possible previous value
700     * @param multiple_option whether this is a multiple option
701     * @param long_opt the corresponding long option
702     * @param short_opt the corresponding short option (or '-' if none)
703     * @param additional_error possible further error specification
704     */
705     static
706     int update_arg(void *field, char **orig_field,
707     unsigned int *field_given, unsigned int *prev_given,
708 gezelter 1629 char *value, const char *possible_values[],
709     const char *default_value,
710 gezelter 1390 cmdline_parser_arg_type arg_type,
711     int check_ambiguity, int override,
712     int no_free, int multiple_option,
713     const char *long_opt, char short_opt,
714     const char *additional_error)
715     {
716     char *stop_char = 0;
717     const char *val = value;
718     int found;
719     char **string_field;
720 gezelter 1629 FIX_UNUSED (field);
721 gezelter 1390
722     stop_char = 0;
723     found = 0;
724    
725     if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
726     {
727     if (short_opt != '-')
728     fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
729     package_name, long_opt, short_opt,
730     (additional_error ? additional_error : ""));
731     else
732     fprintf (stderr, "%s: `--%s' option given more than once%s\n",
733     package_name, long_opt,
734     (additional_error ? additional_error : ""));
735     return 1; /* failure */
736     }
737    
738 gezelter 1629 FIX_UNUSED (default_value);
739 gezelter 1390
740     if (field_given && *field_given && ! override)
741     return 0;
742     if (prev_given)
743     (*prev_given)++;
744     if (field_given)
745     (*field_given)++;
746     if (possible_values)
747     val = possible_values[found];
748    
749     switch(arg_type) {
750     case ARG_INT:
751     if (val) *((int *)field) = strtol (val, &stop_char, 0);
752     break;
753     case ARG_DOUBLE:
754     if (val) *((double *)field) = strtod (val, &stop_char);
755     break;
756     case ARG_STRING:
757     if (val) {
758     string_field = (char **)field;
759     if (!no_free && *string_field)
760     free (*string_field); /* free previous string */
761     *string_field = gengetopt_strdup (val);
762     }
763     break;
764     default:
765     break;
766     };
767    
768     /* check numeric conversion */
769     switch(arg_type) {
770     case ARG_INT:
771     case ARG_DOUBLE:
772     if (val && !(stop_char && *stop_char == '\0')) {
773     fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
774     return 1; /* failure */
775     }
776     break;
777     default:
778     ;
779     };
780    
781     /* store the original value */
782     switch(arg_type) {
783     case ARG_NO:
784     break;
785     default:
786     if (value && orig_field) {
787     if (no_free) {
788     *orig_field = value;
789     } else {
790     if (*orig_field)
791     free (*orig_field); /* free previous string */
792     *orig_field = gengetopt_strdup (value);
793     }
794     }
795     };
796    
797     return 0; /* OK */
798     }
799    
800    
801 gezelter 929 int
802 gezelter 1629 cmdline_parser_internal (
803     int argc, char **argv, struct gengetopt_args_info *args_info,
804 gezelter 1390 struct cmdline_parser_params *params, const char *additional_error)
805 gezelter 929 {
806     int c; /* Character of the parsed option. */
807    
808     int error = 0;
809     struct gengetopt_args_info local_args_info;
810 gezelter 1390
811     int override;
812     int initialize;
813     int check_required;
814     int check_ambiguity;
815    
816     package_name = argv[0];
817    
818     override = params->override;
819     initialize = params->initialize;
820     check_required = params->check_required;
821     check_ambiguity = params->check_ambiguity;
822 gezelter 929
823     if (initialize)
824     cmdline_parser_init (args_info);
825    
826     cmdline_parser_init (&local_args_info);
827    
828 tim 310 optarg = 0;
829 chuckv 1128 optind = 0;
830 gezelter 1390 opterr = params->print_errors;
831 tim 310 optopt = '?';
832    
833     while (1)
834     {
835     int option_index = 0;
836    
837     static struct option long_options[] = {
838     { "help", 0, NULL, 'h' },
839     { "version", 0, NULL, 'V' },
840     { "input", 1, NULL, 'i' },
841     { "output", 1, NULL, 'o' },
842 tim 311 { "step", 1, NULL, 'n' },
843 gezelter 1041 { "nbins", 1, NULL, 'b' },
844 xsun 967 { "nbins_x", 1, NULL, 'x' },
845     { "nbins_y", 1, NULL, 'y' },
846 gezelter 1440 { "nbins_z", 1, NULL, 0 },
847 tim 310 { "nanglebins", 1, NULL, 'a' },
848 chuckv 1445 { "rcut", 1, NULL, 'c' },
849 gezelter 1454 { "dz", 1, NULL, 0 },
850 gezelter 1039 { "length", 1, NULL, 0 },
851 chuckv 1445 { "zlength", 1, NULL, 0 },
852 gezelter 929 { "zoffset", 1, NULL, 'z' },
853 tim 310 { "sele1", 1, NULL, 0 },
854     { "sele2", 1, NULL, 0 },
855 tim 544 { "sele3", 1, NULL, 0 },
856 tim 369 { "refsele", 1, NULL, 0 },
857 gezelter 1390 { "comsele", 1, NULL, 0 },
858 gezelter 1819 { "seleoffset", 1, NULL, 0 },
859 tim 544 { "molname", 1, NULL, 0 },
860     { "begin", 1, NULL, 0 },
861     { "end", 1, NULL, 0 },
862 chuckv 1091 { "radius", 1, NULL, 0 },
863 gezelter 1041 { "bo", 0, NULL, 0 },
864 chuckv 1128 { "bor", 0, NULL, 0 },
865 chuckv 1180 { "bad", 0, NULL, 0 },
866 gezelter 1629 { "count", 0, NULL, 0 },
867 gezelter 1039 { "gofr", 0, NULL, 'g' },
868 xsun 1213 { "gofz", 0, NULL, 0 },
869 tim 310 { "r_theta", 0, NULL, 0 },
870     { "r_omega", 0, NULL, 0 },
871 gezelter 1440 { "r_z", 0, NULL, 0 },
872 tim 310 { "theta_omega", 0, NULL, 0 },
873 tim 369 { "gxyz", 0, NULL, 0 },
874 gezelter 1454 { "twodgofr", 0, NULL, 0 },
875 gezelter 1039 { "p2", 0, NULL, 'p' },
876 xsun 980 { "rp2", 0, NULL, 0 },
877 gezelter 1039 { "scd", 0, NULL, 's' },
878     { "density", 0, NULL, 'd' },
879 tim 840 { "slab_density", 0, NULL, 0 },
880 gezelter 1413 { "p_angle", 0, NULL, 0 },
881 xsun 955 { "hxy", 0, NULL, 0 },
882 chuckv 1091 { "rho_r", 0, NULL, 0 },
883 gezelter 1629 { "angle_r", 0, NULL, 0 },
884 chuckv 1180 { "hullvol", 0, NULL, 0 },
885 gezelter 1629 { "rodlength", 0, NULL, 0 },
886     { "tet_param", 0, NULL, 'Q' },
887 plouden 1762 { "tet_param_z", 0, NULL, 0 },
888 gezelter 1629 { 0, 0, 0, 0 }
889 tim 310 };
890    
891 gezelter 1629 c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
892 tim 310
893     if (c == -1) break; /* Exit from `while (1)' loop. */
894    
895     switch (c)
896     {
897     case 'h': /* Print help and exit. */
898     cmdline_parser_print_help ();
899 gezelter 929 cmdline_parser_free (&local_args_info);
900 tim 310 exit (EXIT_SUCCESS);
901    
902     case 'V': /* Print version and exit. */
903     cmdline_parser_print_version ();
904 gezelter 929 cmdline_parser_free (&local_args_info);
905 tim 310 exit (EXIT_SUCCESS);
906    
907     case 'i': /* input dump file. */
908 gezelter 1390
909    
910     if (update_arg( (void *)&(args_info->input_arg),
911     &(args_info->input_orig), &(args_info->input_given),
912     &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
913     check_ambiguity, override, 0, 0,
914     "input", 'i',
915     additional_error))
916     goto failure;
917    
918 tim 310 break;
919     case 'o': /* output file name. */
920 gezelter 1390
921    
922     if (update_arg( (void *)&(args_info->output_arg),
923     &(args_info->output_orig), &(args_info->output_given),
924     &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
925     check_ambiguity, override, 0, 0,
926     "output", 'o',
927     additional_error))
928     goto failure;
929    
930 tim 310 break;
931 tim 311 case 'n': /* process every n frame. */
932 gezelter 1390
933    
934     if (update_arg( (void *)&(args_info->step_arg),
935     &(args_info->step_orig), &(args_info->step_given),
936     &(local_args_info.step_given), optarg, 0, "1", ARG_INT,
937     check_ambiguity, override, 0, 0,
938     "step", 'n',
939     additional_error))
940 gezelter 929 goto failure;
941 gezelter 1390
942 tim 310 break;
943 gezelter 1041 case 'b': /* number of bins (general purpose). */
944 gezelter 1390
945    
946     if (update_arg( (void *)&(args_info->nbins_arg),
947     &(args_info->nbins_orig), &(args_info->nbins_given),
948     &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
949     check_ambiguity, override, 0, 0,
950     "nbins", 'b',
951     additional_error))
952 gezelter 929 goto failure;
953 gezelter 1390
954 tim 310 break;
955 xsun 955 case 'x': /* number of bins in x axis. */
956 gezelter 1390
957    
958     if (update_arg( (void *)&(args_info->nbins_x_arg),
959     &(args_info->nbins_x_orig), &(args_info->nbins_x_given),
960     &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
961     check_ambiguity, override, 0, 0,
962     "nbins_x", 'x',
963     additional_error))
964 xsun 955 goto failure;
965 gezelter 1390
966 xsun 955 break;
967     case 'y': /* number of bins in y axis. */
968 gezelter 1390
969    
970     if (update_arg( (void *)&(args_info->nbins_y_arg),
971     &(args_info->nbins_y_orig), &(args_info->nbins_y_given),
972     &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
973     check_ambiguity, override, 0, 0,
974     "nbins_y", 'y',
975     additional_error))
976 xsun 955 goto failure;
977 gezelter 1390
978 xsun 955 break;
979 tim 310 case 'a': /* number of bins for cos(angle). */
980 gezelter 1390
981    
982     if (update_arg( (void *)&(args_info->nanglebins_arg),
983     &(args_info->nanglebins_orig), &(args_info->nanglebins_given),
984     &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
985     check_ambiguity, override, 0, 0,
986     "nanglebins", 'a',
987     additional_error))
988 gezelter 929 goto failure;
989 gezelter 1390
990 tim 310 break;
991 gezelter 1039 case 'c': /* cutoff radius (rcut). */
992 gezelter 1390
993    
994     if (update_arg( (void *)&(args_info->rcut_arg),
995     &(args_info->rcut_orig), &(args_info->rcut_given),
996     &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
997     check_ambiguity, override, 0, 0,
998     "rcut", 'c',
999     additional_error))
1000 gezelter 1039 goto failure;
1001 gezelter 1390
1002 gezelter 1039 break;
1003 gezelter 929 case 'z': /* Where to set the zero for the slab_density calculation. */
1004 gezelter 1390
1005    
1006     if (update_arg( (void *)&(args_info->zoffset_arg),
1007     &(args_info->zoffset_orig), &(args_info->zoffset_given),
1008     &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1009     check_ambiguity, override, 0, 0,
1010     "zoffset", 'z',
1011     additional_error))
1012 gezelter 929 goto failure;
1013 gezelter 1390
1014 gezelter 929 break;
1015 gezelter 1039 case 'g': /* g(r). */
1016 gezelter 1390
1017 gezelter 1039 if (args_info->staticProps_group_counter && override)
1018     reset_group_staticProps (args_info);
1019     args_info->staticProps_group_counter += 1;
1020 gezelter 1390
1021     if (update_arg( 0 ,
1022     0 , &(args_info->gofr_given),
1023     &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1024     check_ambiguity, override, 0, 0,
1025     "gofr", 'g',
1026     additional_error))
1027     goto failure;
1028    
1029 gezelter 1039 break;
1030 gezelter 1629 case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */
1031 gezelter 1390
1032 gezelter 1039 if (args_info->staticProps_group_counter && override)
1033     reset_group_staticProps (args_info);
1034     args_info->staticProps_group_counter += 1;
1035 gezelter 1390
1036     if (update_arg( 0 ,
1037     0 , &(args_info->p2_given),
1038     &(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1039     check_ambiguity, override, 0, 0,
1040     "p2", 'p',
1041     additional_error))
1042     goto failure;
1043    
1044 gezelter 1039 break;
1045     case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */
1046 gezelter 1390
1047 gezelter 1039 if (args_info->staticProps_group_counter && override)
1048     reset_group_staticProps (args_info);
1049     args_info->staticProps_group_counter += 1;
1050 gezelter 1390
1051     if (update_arg( 0 ,
1052     0 , &(args_info->scd_given),
1053     &(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1054     check_ambiguity, override, 0, 0,
1055     "scd", 's',
1056     additional_error))
1057     goto failure;
1058    
1059 gezelter 1039 break;
1060     case 'd': /* density plot. */
1061 gezelter 1390
1062 gezelter 1039 if (args_info->staticProps_group_counter && override)
1063     reset_group_staticProps (args_info);
1064     args_info->staticProps_group_counter += 1;
1065 gezelter 1390
1066     if (update_arg( 0 ,
1067     0 , &(args_info->density_given),
1068     &(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1069     check_ambiguity, override, 0, 0,
1070     "density", 'd',
1071     additional_error))
1072     goto failure;
1073    
1074 gezelter 1039 break;
1075 gezelter 1843 case 'Q': /* tetrahedrality order parameter (Qk). */
1076 gezelter 1629
1077     if (args_info->staticProps_group_counter && override)
1078     reset_group_staticProps (args_info);
1079     args_info->staticProps_group_counter += 1;
1080    
1081     if (update_arg( 0 ,
1082     0 , &(args_info->tet_param_given),
1083     &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1084     check_ambiguity, override, 0, 0,
1085     "tet_param", 'Q',
1086     additional_error))
1087     goto failure;
1088    
1089     break;
1090 gezelter 1039
1091 tim 310 case 0: /* Long option with no short option */
1092 gezelter 1440 /* number of bins in z axis. */
1093     if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1094     {
1095    
1096    
1097     if (update_arg( (void *)&(args_info->nbins_z_arg),
1098     &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1099     &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1100     check_ambiguity, override, 0, 0,
1101     "nbins_z", '-',
1102     additional_error))
1103     goto failure;
1104    
1105     }
1106 gezelter 1454 /* slab width (dz). */
1107     else if (strcmp (long_options[option_index].name, "dz") == 0)
1108     {
1109    
1110    
1111     if (update_arg( (void *)&(args_info->dz_arg),
1112     &(args_info->dz_orig), &(args_info->dz_given),
1113     &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1114     check_ambiguity, override, 0, 0,
1115     "dz", '-',
1116     additional_error))
1117     goto failure;
1118    
1119     }
1120 gezelter 1039 /* maximum length (Defaults to 1/2 smallest length of first frame). */
1121 gezelter 1440 else if (strcmp (long_options[option_index].name, "length") == 0)
1122 gezelter 1039 {
1123 gezelter 1390
1124    
1125     if (update_arg( (void *)&(args_info->length_arg),
1126     &(args_info->length_orig), &(args_info->length_given),
1127     &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1128     check_ambiguity, override, 0, 0,
1129     "length", '-',
1130     additional_error))
1131 gezelter 1039 goto failure;
1132 gezelter 1390
1133 gezelter 1039 }
1134 chuckv 1445 /* maximum length (Defaults to 1/2 smallest length of first frame). */
1135     else if (strcmp (long_options[option_index].name, "zlength") == 0)
1136     {
1137    
1138    
1139     if (update_arg( (void *)&(args_info->zlength_arg),
1140     &(args_info->zlength_orig), &(args_info->zlength_given),
1141     &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1142     check_ambiguity, override, 0, 0,
1143     "zlength", '-',
1144     additional_error))
1145     goto failure;
1146    
1147     }
1148 tim 544 /* select the first stuntdouble set. */
1149 gezelter 1039 else if (strcmp (long_options[option_index].name, "sele1") == 0)
1150 tim 543 {
1151 gezelter 1390
1152    
1153     if (update_arg( (void *)&(args_info->sele1_arg),
1154     &(args_info->sele1_orig), &(args_info->sele1_given),
1155     &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1156     check_ambiguity, override, 0, 0,
1157     "sele1", '-',
1158     additional_error))
1159     goto failure;
1160    
1161 tim 543 }
1162 tim 544 /* select the second stuntdouble set. */
1163 tim 310 else if (strcmp (long_options[option_index].name, "sele2") == 0)
1164 tim 543 {
1165 gezelter 1390
1166    
1167     if (update_arg( (void *)&(args_info->sele2_arg),
1168     &(args_info->sele2_orig), &(args_info->sele2_given),
1169     &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1170     check_ambiguity, override, 0, 0,
1171     "sele2", '-',
1172     additional_error))
1173     goto failure;
1174    
1175 tim 543 }
1176 tim 544 /* select the third stuntdouble set. */
1177     else if (strcmp (long_options[option_index].name, "sele3") == 0)
1178     {
1179 gezelter 1390
1180    
1181     if (update_arg( (void *)&(args_info->sele3_arg),
1182     &(args_info->sele3_orig), &(args_info->sele3_given),
1183     &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1184     check_ambiguity, override, 0, 0,
1185     "sele3", '-',
1186     additional_error))
1187     goto failure;
1188    
1189 tim 544 }
1190 tim 369 /* select reference (use and only use with --gxyz). */
1191     else if (strcmp (long_options[option_index].name, "refsele") == 0)
1192 tim 543 {
1193 gezelter 1390
1194    
1195     if (update_arg( (void *)&(args_info->refsele_arg),
1196     &(args_info->refsele_orig), &(args_info->refsele_given),
1197     &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1198     check_ambiguity, override, 0, 0,
1199     "refsele", '-',
1200     additional_error))
1201     goto failure;
1202    
1203 tim 543 }
1204 gezelter 1390 /* select stunt doubles for center-of-mass reference point. */
1205     else if (strcmp (long_options[option_index].name, "comsele") == 0)
1206     {
1207    
1208    
1209     if (update_arg( (void *)&(args_info->comsele_arg),
1210     &(args_info->comsele_orig), &(args_info->comsele_given),
1211     &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1212     check_ambiguity, override, 0, 0,
1213     "comsele", '-',
1214     additional_error))
1215     goto failure;
1216    
1217     }
1218 gezelter 1819 /* global index offset for a second object (used to define a vector between sites in molecule). */
1219     else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1220     {
1221    
1222    
1223     if (update_arg( (void *)&(args_info->seleoffset_arg),
1224     &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1225     &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1226     check_ambiguity, override, 0, 0,
1227     "seleoffset", '-',
1228     additional_error))
1229     goto failure;
1230    
1231     }
1232 tim 544 /* molecule name. */
1233     else if (strcmp (long_options[option_index].name, "molname") == 0)
1234     {
1235 gezelter 1390
1236    
1237     if (update_arg( (void *)&(args_info->molname_arg),
1238     &(args_info->molname_orig), &(args_info->molname_given),
1239     &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1240     check_ambiguity, override, 0, 0,
1241     "molname", '-',
1242     additional_error))
1243     goto failure;
1244    
1245 tim 544 }
1246 gezelter 1039 /* begin internal index. */
1247 tim 544 else if (strcmp (long_options[option_index].name, "begin") == 0)
1248     {
1249 gezelter 1390
1250    
1251     if (update_arg( (void *)&(args_info->begin_arg),
1252     &(args_info->begin_orig), &(args_info->begin_given),
1253     &(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1254     check_ambiguity, override, 0, 0,
1255     "begin", '-',
1256     additional_error))
1257 gezelter 929 goto failure;
1258 gezelter 1390
1259 tim 544 }
1260     /* end internal index. */
1261     else if (strcmp (long_options[option_index].name, "end") == 0)
1262     {
1263 gezelter 1390
1264    
1265     if (update_arg( (void *)&(args_info->end_arg),
1266     &(args_info->end_orig), &(args_info->end_given),
1267     &(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1268     check_ambiguity, override, 0, 0,
1269     "end", '-',
1270     additional_error))
1271 gezelter 929 goto failure;
1272 gezelter 1390
1273 tim 544 }
1274 chuckv 1091 /* nanoparticle radius. */
1275     else if (strcmp (long_options[option_index].name, "radius") == 0)
1276     {
1277 gezelter 1390
1278    
1279     if (update_arg( (void *)&(args_info->radius_arg),
1280     &(args_info->radius_orig), &(args_info->radius_given),
1281     &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1282     check_ambiguity, override, 0, 0,
1283     "radius", '-',
1284     additional_error))
1285 chuckv 1091 goto failure;
1286 gezelter 1390
1287 chuckv 1091 }
1288 chuckv 1128 /* bond order parameter (--rcut must be specified). */
1289 gezelter 1041 else if (strcmp (long_options[option_index].name, "bo") == 0)
1290     {
1291 gezelter 1390
1292 gezelter 1041 if (args_info->staticProps_group_counter && override)
1293     reset_group_staticProps (args_info);
1294     args_info->staticProps_group_counter += 1;
1295 gezelter 1390
1296     if (update_arg( 0 ,
1297     0 , &(args_info->bo_given),
1298     &(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1299     check_ambiguity, override, 0, 0,
1300     "bo", '-',
1301     additional_error))
1302     goto failure;
1303    
1304 gezelter 1041 }
1305 chuckv 1128 /* bond order parameter as a function of radius (--rcut must be specified). */
1306     else if (strcmp (long_options[option_index].name, "bor") == 0)
1307     {
1308 gezelter 1390
1309 chuckv 1128 if (args_info->staticProps_group_counter && override)
1310     reset_group_staticProps (args_info);
1311     args_info->staticProps_group_counter += 1;
1312 gezelter 1390
1313     if (update_arg( 0 ,
1314     0 , &(args_info->bor_given),
1315     &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1316     check_ambiguity, override, 0, 0,
1317     "bor", '-',
1318     additional_error))
1319     goto failure;
1320    
1321 chuckv 1128 }
1322 chuckv 1180 /* N(theta) bond angle density within (--rcut must be specified). */
1323     else if (strcmp (long_options[option_index].name, "bad") == 0)
1324     {
1325 gezelter 1390
1326 chuckv 1180 if (args_info->staticProps_group_counter && override)
1327     reset_group_staticProps (args_info);
1328     args_info->staticProps_group_counter += 1;
1329 gezelter 1390
1330     if (update_arg( 0 ,
1331     0 , &(args_info->bad_given),
1332     &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1333     check_ambiguity, override, 0, 0,
1334     "bad", '-',
1335     additional_error))
1336     goto failure;
1337    
1338 chuckv 1180 }
1339 gezelter 1629 /* count of molecules matching selection criteria (and associated statistics). */
1340     else if (strcmp (long_options[option_index].name, "count") == 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->count_given),
1349     &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1350     check_ambiguity, override, 0, 0,
1351     "count", '-',
1352     additional_error))
1353     goto failure;
1354    
1355     }
1356 xsun 1213 /* g(z). */
1357     else if (strcmp (long_options[option_index].name, "gofz") == 0)
1358     {
1359 gezelter 1390
1360 xsun 1213 if (args_info->staticProps_group_counter && override)
1361     reset_group_staticProps (args_info);
1362     args_info->staticProps_group_counter += 1;
1363 gezelter 1390
1364     if (update_arg( 0 ,
1365     0 , &(args_info->gofz_given),
1366     &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1367     check_ambiguity, override, 0, 0,
1368     "gofz", '-',
1369     additional_error))
1370     goto failure;
1371    
1372 xsun 1213 }
1373 tim 310 /* g(r, cos(theta)). */
1374     else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1375 tim 543 {
1376 gezelter 1390
1377 gezelter 929 if (args_info->staticProps_group_counter && override)
1378     reset_group_staticProps (args_info);
1379     args_info->staticProps_group_counter += 1;
1380 gezelter 1390
1381     if (update_arg( 0 ,
1382     0 , &(args_info->r_theta_given),
1383     &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1384     check_ambiguity, override, 0, 0,
1385     "r_theta", '-',
1386     additional_error))
1387     goto failure;
1388    
1389 tim 543 }
1390 tim 310 /* g(r, cos(omega)). */
1391     else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1392 tim 543 {
1393 gezelter 1390
1394 gezelter 929 if (args_info->staticProps_group_counter && override)
1395     reset_group_staticProps (args_info);
1396     args_info->staticProps_group_counter += 1;
1397 gezelter 1390
1398     if (update_arg( 0 ,
1399     0 , &(args_info->r_omega_given),
1400     &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1401     check_ambiguity, override, 0, 0,
1402     "r_omega", '-',
1403     additional_error))
1404     goto failure;
1405    
1406 tim 543 }
1407 gezelter 1440 /* g(r, z). */
1408     else if (strcmp (long_options[option_index].name, "r_z") == 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->r_z_given),
1417     &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1418     check_ambiguity, override, 0, 0,
1419     "r_z", '-',
1420     additional_error))
1421     goto failure;
1422    
1423     }
1424 tim 310 /* g(cos(theta), cos(omega)). */
1425     else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1426 tim 543 {
1427 gezelter 1390
1428 gezelter 929 if (args_info->staticProps_group_counter && override)
1429     reset_group_staticProps (args_info);
1430     args_info->staticProps_group_counter += 1;
1431 gezelter 1390
1432     if (update_arg( 0 ,
1433     0 , &(args_info->theta_omega_given),
1434     &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1435     check_ambiguity, override, 0, 0,
1436     "theta_omega", '-',
1437     additional_error))
1438     goto failure;
1439    
1440 tim 543 }
1441 tim 310 /* g(x, y, z). */
1442 tim 369 else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1443 tim 543 {
1444 gezelter 1390
1445 gezelter 929 if (args_info->staticProps_group_counter && override)
1446     reset_group_staticProps (args_info);
1447     args_info->staticProps_group_counter += 1;
1448 gezelter 1390
1449     if (update_arg( 0 ,
1450     0 , &(args_info->gxyz_given),
1451     &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1452     check_ambiguity, override, 0, 0,
1453     "gxyz", '-',
1454     additional_error))
1455     goto failure;
1456    
1457 tim 543 }
1458 gezelter 1454 /* 2D g(r) (Slab width --dz must be specified). */
1459     else if (strcmp (long_options[option_index].name, "twodgofr") == 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->twodgofr_given),
1468     &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1469     check_ambiguity, override, 0, 0,
1470     "twodgofr", '-',
1471     additional_error))
1472     goto failure;
1473    
1474     }
1475 xsun 980 /* rp2 order parameter (--sele1 and --sele2 must be specified). */
1476     else if (strcmp (long_options[option_index].name, "rp2") == 0)
1477     {
1478 gezelter 1390
1479 xsun 980 if (args_info->staticProps_group_counter && override)
1480     reset_group_staticProps (args_info);
1481     args_info->staticProps_group_counter += 1;
1482 gezelter 1390
1483     if (update_arg( 0 ,
1484     0 , &(args_info->rp2_given),
1485     &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1486     check_ambiguity, override, 0, 0,
1487     "rp2", '-',
1488     additional_error))
1489     goto failure;
1490    
1491 xsun 980 }
1492 gezelter 1039 /* slab density. */
1493 tim 840 else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1494     {
1495 gezelter 1390
1496 gezelter 929 if (args_info->staticProps_group_counter && override)
1497     reset_group_staticProps (args_info);
1498     args_info->staticProps_group_counter += 1;
1499 gezelter 1390
1500     if (update_arg( 0 ,
1501     0 , &(args_info->slab_density_given),
1502     &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1503     check_ambiguity, override, 0, 0,
1504     "slab_density", '-',
1505     additional_error))
1506     goto failure;
1507    
1508 tim 840 }
1509 gezelter 1413 /* p(cos(theta)). */
1510     else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1511     {
1512    
1513     if (args_info->staticProps_group_counter && override)
1514     reset_group_staticProps (args_info);
1515     args_info->staticProps_group_counter += 1;
1516    
1517     if (update_arg( 0 ,
1518     0 , &(args_info->p_angle_given),
1519     &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1520     check_ambiguity, override, 0, 0,
1521     "p_angle", '-',
1522     additional_error))
1523     goto failure;
1524    
1525     }
1526 gezelter 1039 /* hxy. */
1527 xsun 955 else if (strcmp (long_options[option_index].name, "hxy") == 0)
1528     {
1529 gezelter 1390
1530 xsun 955 if (args_info->staticProps_group_counter && override)
1531     reset_group_staticProps (args_info);
1532     args_info->staticProps_group_counter += 1;
1533 gezelter 1390
1534     if (update_arg( 0 ,
1535     0 , &(args_info->hxy_given),
1536     &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1537     check_ambiguity, override, 0, 0,
1538     "hxy", '-',
1539     additional_error))
1540     goto failure;
1541    
1542 xsun 955 }
1543 chuckv 1091 /* rho of R. */
1544     else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1545     {
1546 gezelter 1390
1547 chuckv 1091 if (args_info->staticProps_group_counter && override)
1548     reset_group_staticProps (args_info);
1549     args_info->staticProps_group_counter += 1;
1550 gezelter 1390
1551     if (update_arg( 0 ,
1552     0 , &(args_info->rho_r_given),
1553     &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1554     check_ambiguity, override, 0, 0,
1555     "rho_r", '-',
1556     additional_error))
1557     goto failure;
1558    
1559 chuckv 1091 }
1560 gezelter 1629 /* angle of R. */
1561     else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1562     {
1563    
1564     if (args_info->staticProps_group_counter && override)
1565     reset_group_staticProps (args_info);
1566     args_info->staticProps_group_counter += 1;
1567    
1568     if (update_arg( 0 ,
1569     0 , &(args_info->angle_r_given),
1570     &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1571     check_ambiguity, override, 0, 0,
1572     "angle_r", '-',
1573     additional_error))
1574     goto failure;
1575    
1576     }
1577 chuckv 1180 /* hull volume of nanoparticle. */
1578     else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1579     {
1580 gezelter 1390
1581 chuckv 1180 if (args_info->staticProps_group_counter && override)
1582     reset_group_staticProps (args_info);
1583     args_info->staticProps_group_counter += 1;
1584 gezelter 1390
1585     if (update_arg( 0 ,
1586     0 , &(args_info->hullvol_given),
1587     &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1588     check_ambiguity, override, 0, 0,
1589     "hullvol", '-',
1590     additional_error))
1591     goto failure;
1592    
1593 chuckv 1180 }
1594 gezelter 1629 /* length of nanorod. */
1595     else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1596     {
1597 tim 840
1598 gezelter 1629 if (args_info->staticProps_group_counter && override)
1599     reset_group_staticProps (args_info);
1600     args_info->staticProps_group_counter += 1;
1601    
1602     if (update_arg( 0 ,
1603     0 , &(args_info->rodlength_given),
1604     &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1605     check_ambiguity, override, 0, 0,
1606     "rodlength", '-',
1607     additional_error))
1608     goto failure;
1609    
1610     }
1611 gezelter 1843 /* spatially-resolved tetrahedrality order parameter Qk(z). */
1612 plouden 1762 else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1613     {
1614 gezelter 1629
1615 plouden 1762 if (args_info->staticProps_group_counter && override)
1616     reset_group_staticProps (args_info);
1617     args_info->staticProps_group_counter += 1;
1618    
1619     if (update_arg( 0 ,
1620     0 , &(args_info->tet_param_z_given),
1621     &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1622     check_ambiguity, override, 0, 0,
1623     "tet_param_z", '-',
1624     additional_error))
1625     goto failure;
1626    
1627     }
1628    
1629 gezelter 929 break;
1630 tim 310 case '?': /* Invalid option. */
1631     /* `getopt_long' already printed an error message. */
1632 gezelter 929 goto failure;
1633 tim 310
1634     default: /* bug: option not considered. */
1635 gezelter 929 fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1636 tim 310 abort ();
1637     } /* switch */
1638     } /* while */
1639    
1640 gezelter 929 if (args_info->staticProps_group_counter > 1)
1641 tim 310 {
1642 gezelter 1629 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 : ""));
1643 gezelter 929 error = 1;
1644 tim 310 }
1645    
1646    
1647 gezelter 929
1648     if (check_required)
1649 tim 310 {
1650 gezelter 929 error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1651 tim 310 }
1652    
1653 gezelter 929 cmdline_parser_release (&local_args_info);
1654    
1655     if ( error )
1656     return (EXIT_FAILURE);
1657    
1658 gezelter 1454 if (optind < argc)
1659     {
1660     int i = 0 ;
1661     int found_prog_name = 0;
1662     /* whether program name, i.e., argv[0], is in the remaining args
1663     (this may happen with some implementations of getopt,
1664     but surely not with the one included by gengetopt) */
1665    
1666     i = optind;
1667     while (i < argc)
1668     if (argv[i++] == argv[0]) {
1669     found_prog_name = 1;
1670     break;
1671     }
1672     i = 0;
1673    
1674     args_info->inputs_num = argc - optind - found_prog_name;
1675     args_info->inputs =
1676     (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1677     while (optind < argc)
1678     if (argv[optind++] != argv[0])
1679     args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1680     }
1681    
1682 tim 310 return 0;
1683 gezelter 929
1684     failure:
1685    
1686     cmdline_parser_release (&local_args_info);
1687     return (EXIT_FAILURE);
1688 tim 310 }

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