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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
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Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1999 by gezelter, Sat May 31 21:00:46 2014 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.19.1
2 >  File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt --file-name=StaticPropsCmd -u
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:
# Line 17 | Line 17
17   #include <stdlib.h>
18   #include <string.h>
19  
20 < #include "getopt.h"
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 = "";
# Line 36 | Line 44 | const char *gengetopt_args_info_help[] = {
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')",
40 –  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
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 +  "      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
61    "      --molname=STRING          molecule name",
62    "      --begin=INT               begin internal index",
63    "      --end=INT                 end internal index",
64    "      --radius=DOUBLE           nanoparticle radius",
65    "\n Group: staticProps\n   an option of this group is required",
66    "      --bo                      bond order parameter (--rcut must be specified)",
67 <  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67 >  "      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
68 >  "      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
69    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
70 +  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
71    "  -g, --gofr                    g(r)",
72    "      --gofz                    g(z)",
73    "      --r_theta                 g(r, cos(theta))",
74    "      --r_omega                 g(r, cos(omega))",
75 +  "      --r_z                     g(r, z)",
76    "      --theta_omega             g(cos(theta), cos(omega))",
77    "      --gxyz                    g(x, y, z)",
78 <  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
78 >  "      --twodgofr                2D g(r) (Slab width --dz must be specified)",
79 >  "  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
80    "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
81    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
82    "  -d, --density                 density plot",
83    "      --slab_density            slab density",
84 +  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
85    "      --hxy                     hxy",
86    "      --rho_r                   rho of R",
87 +  "      --angle_r                 angle of R",
88    "      --hullvol                 hull volume of nanoparticle",
89 +  "      --rodlength               length of nanorod",
90 +  "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
91 +  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
92 +  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
93 +  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
94 +  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
95 +  "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96 +  "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
97      0
98   };
99  
100 + typedef enum {ARG_NO
101 +  , ARG_STRING
102 +  , ARG_INT
103 +  , ARG_DOUBLE
104 + } cmdline_parser_arg_type;
105 +
106   static
107   void clear_given (struct gengetopt_args_info *args_info);
108   static
109   void clear_args (struct gengetopt_args_info *args_info);
110  
111   static int
112 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
112 > cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
113 >                        struct cmdline_parser_params *params, const char *additional_error);
114  
115   static int
116   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
# Line 94 | Line 129 | void clear_given (struct gengetopt_args_info *args_inf
129    args_info->nbins_given = 0 ;
130    args_info->nbins_x_given = 0 ;
131    args_info->nbins_y_given = 0 ;
132 +  args_info->nbins_z_given = 0 ;
133    args_info->nanglebins_given = 0 ;
98 –  args_info->length_given = 0 ;
134    args_info->rcut_given = 0 ;
135 +  args_info->dz_given = 0 ;
136 +  args_info->length_given = 0 ;
137 +  args_info->zlength_given = 0 ;
138    args_info->zoffset_given = 0 ;
139    args_info->sele1_given = 0 ;
140    args_info->sele2_given = 0 ;
141    args_info->sele3_given = 0 ;
142    args_info->refsele_given = 0 ;
143 +  args_info->comsele_given = 0 ;
144 +  args_info->seleoffset_given = 0 ;
145 +  args_info->seleoffset2_given = 0 ;
146    args_info->molname_given = 0 ;
147    args_info->begin_given = 0 ;
148    args_info->end_given = 0 ;
149    args_info->radius_given = 0 ;
150    args_info->bo_given = 0 ;
151 <  args_info->bor_given = 0 ;
151 >  args_info->ior_given = 0 ;
152 >  args_info->for_given = 0 ;
153    args_info->bad_given = 0 ;
154 +  args_info->count_given = 0 ;
155    args_info->gofr_given = 0 ;
156    args_info->gofz_given = 0 ;
157    args_info->r_theta_given = 0 ;
158    args_info->r_omega_given = 0 ;
159 +  args_info->r_z_given = 0 ;
160    args_info->theta_omega_given = 0 ;
161    args_info->gxyz_given = 0 ;
162 +  args_info->twodgofr_given = 0 ;
163    args_info->p2_given = 0 ;
164    args_info->rp2_given = 0 ;
165    args_info->scd_given = 0 ;
166    args_info->density_given = 0 ;
167    args_info->slab_density_given = 0 ;
168 +  args_info->p_angle_given = 0 ;
169    args_info->hxy_given = 0 ;
170    args_info->rho_r_given = 0 ;
171 +  args_info->angle_r_given = 0 ;
172    args_info->hullvol_given = 0 ;
173 +  args_info->rodlength_given = 0 ;
174 +  args_info->tet_param_given = 0 ;
175 +  args_info->tet_param_z_given = 0 ;
176 +  args_info->rnemdz_given = 0 ;
177 +  args_info->rnemdr_given = 0 ;
178 +  args_info->rnemdrt_given = 0 ;
179 +  args_info->nitrile_given = 0 ;
180 +  args_info->multipole_given = 0 ;
181    args_info->staticProps_group_counter = 0 ;
182   }
183  
184   static
185   void clear_args (struct gengetopt_args_info *args_info)
186   {
187 +  FIX_UNUSED (args_info);
188    args_info->input_arg = NULL;
189    args_info->input_orig = NULL;
190    args_info->output_arg = NULL;
# Line 141 | Line 197 | void clear_args (struct gengetopt_args_info *args_info
197    args_info->nbins_x_orig = NULL;
198    args_info->nbins_y_arg = 100;
199    args_info->nbins_y_orig = NULL;
200 +  args_info->nbins_z_arg = 100;
201 +  args_info->nbins_z_orig = NULL;
202    args_info->nanglebins_arg = 50;
203    args_info->nanglebins_orig = NULL;
146 –  args_info->length_orig = NULL;
204    args_info->rcut_orig = NULL;
205 +  args_info->dz_orig = NULL;
206 +  args_info->length_orig = NULL;
207 +  args_info->zlength_orig = NULL;
208    args_info->zoffset_arg = 0;
209    args_info->zoffset_orig = NULL;
210    args_info->sele1_arg = NULL;
# Line 155 | Line 215 | void clear_args (struct gengetopt_args_info *args_info
215    args_info->sele3_orig = NULL;
216    args_info->refsele_arg = NULL;
217    args_info->refsele_orig = NULL;
218 +  args_info->comsele_arg = NULL;
219 +  args_info->comsele_orig = NULL;
220 +  args_info->seleoffset_orig = NULL;
221 +  args_info->seleoffset2_orig = NULL;
222    args_info->molname_arg = NULL;
223    args_info->molname_orig = NULL;
224    args_info->begin_orig = NULL;
# Line 166 | Line 230 | void init_args_info(struct gengetopt_args_info *args_i
230   static
231   void init_args_info(struct gengetopt_args_info *args_info)
232   {
233 +
234 +
235    args_info->help_help = gengetopt_args_info_help[0] ;
236    args_info->version_help = gengetopt_args_info_help[1] ;
237    args_info->input_help = gengetopt_args_info_help[2] ;
# Line 174 | Line 240 | void init_args_info(struct gengetopt_args_info *args_i
240    args_info->nbins_help = gengetopt_args_info_help[5] ;
241    args_info->nbins_x_help = gengetopt_args_info_help[6] ;
242    args_info->nbins_y_help = gengetopt_args_info_help[7] ;
243 <  args_info->nanglebins_help = gengetopt_args_info_help[8] ;
244 <  args_info->length_help = gengetopt_args_info_help[9] ;
243 >  args_info->nbins_z_help = gengetopt_args_info_help[8] ;
244 >  args_info->nanglebins_help = gengetopt_args_info_help[9] ;
245    args_info->rcut_help = gengetopt_args_info_help[10] ;
246 <  args_info->zoffset_help = gengetopt_args_info_help[11] ;
247 <  args_info->sele1_help = gengetopt_args_info_help[12] ;
248 <  args_info->sele2_help = gengetopt_args_info_help[13] ;
249 <  args_info->sele3_help = gengetopt_args_info_help[14] ;
250 <  args_info->refsele_help = gengetopt_args_info_help[15] ;
251 <  args_info->molname_help = gengetopt_args_info_help[16] ;
252 <  args_info->begin_help = gengetopt_args_info_help[17] ;
253 <  args_info->end_help = gengetopt_args_info_help[18] ;
254 <  args_info->radius_help = gengetopt_args_info_help[19] ;
255 <  args_info->bo_help = gengetopt_args_info_help[20] ;
256 <  args_info->bor_help = gengetopt_args_info_help[21] ;
257 <  args_info->bad_help = gengetopt_args_info_help[22] ;
258 <  args_info->gofr_help = gengetopt_args_info_help[23] ;
259 <  args_info->gofz_help = gengetopt_args_info_help[24] ;
260 <  args_info->r_theta_help = gengetopt_args_info_help[25] ;
261 <  args_info->r_omega_help = gengetopt_args_info_help[26] ;
262 <  args_info->theta_omega_help = gengetopt_args_info_help[27] ;
263 <  args_info->gxyz_help = gengetopt_args_info_help[28] ;
264 <  args_info->p2_help = gengetopt_args_info_help[29] ;
265 <  args_info->rp2_help = gengetopt_args_info_help[30] ;
266 <  args_info->scd_help = gengetopt_args_info_help[31] ;
267 <  args_info->density_help = gengetopt_args_info_help[32] ;
268 <  args_info->slab_density_help = gengetopt_args_info_help[33] ;
269 <  args_info->hxy_help = gengetopt_args_info_help[34] ;
270 <  args_info->rho_r_help = gengetopt_args_info_help[35] ;
271 <  args_info->hullvol_help = gengetopt_args_info_help[36] ;
246 >  args_info->dz_help = gengetopt_args_info_help[11] ;
247 >  args_info->length_help = gengetopt_args_info_help[12] ;
248 >  args_info->zlength_help = gengetopt_args_info_help[13] ;
249 >  args_info->zoffset_help = gengetopt_args_info_help[14] ;
250 >  args_info->sele1_help = gengetopt_args_info_help[15] ;
251 >  args_info->sele2_help = gengetopt_args_info_help[16] ;
252 >  args_info->sele3_help = gengetopt_args_info_help[17] ;
253 >  args_info->refsele_help = gengetopt_args_info_help[18] ;
254 >  args_info->comsele_help = gengetopt_args_info_help[19] ;
255 >  args_info->seleoffset_help = gengetopt_args_info_help[20] ;
256 >  args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
257 >  args_info->molname_help = gengetopt_args_info_help[22] ;
258 >  args_info->begin_help = gengetopt_args_info_help[23] ;
259 >  args_info->end_help = gengetopt_args_info_help[24] ;
260 >  args_info->radius_help = gengetopt_args_info_help[25] ;
261 >  args_info->bo_help = gengetopt_args_info_help[27] ;
262 >  args_info->ior_help = gengetopt_args_info_help[28] ;
263 >  args_info->for_help = gengetopt_args_info_help[29] ;
264 >  args_info->bad_help = gengetopt_args_info_help[30] ;
265 >  args_info->count_help = gengetopt_args_info_help[31] ;
266 >  args_info->gofr_help = gengetopt_args_info_help[32] ;
267 >  args_info->gofz_help = gengetopt_args_info_help[33] ;
268 >  args_info->r_theta_help = gengetopt_args_info_help[34] ;
269 >  args_info->r_omega_help = gengetopt_args_info_help[35] ;
270 >  args_info->r_z_help = gengetopt_args_info_help[36] ;
271 >  args_info->theta_omega_help = gengetopt_args_info_help[37] ;
272 >  args_info->gxyz_help = gengetopt_args_info_help[38] ;
273 >  args_info->twodgofr_help = gengetopt_args_info_help[39] ;
274 >  args_info->p2_help = gengetopt_args_info_help[40] ;
275 >  args_info->rp2_help = gengetopt_args_info_help[41] ;
276 >  args_info->scd_help = gengetopt_args_info_help[42] ;
277 >  args_info->density_help = gengetopt_args_info_help[43] ;
278 >  args_info->slab_density_help = gengetopt_args_info_help[44] ;
279 >  args_info->p_angle_help = gengetopt_args_info_help[45] ;
280 >  args_info->hxy_help = gengetopt_args_info_help[46] ;
281 >  args_info->rho_r_help = gengetopt_args_info_help[47] ;
282 >  args_info->angle_r_help = gengetopt_args_info_help[48] ;
283 >  args_info->hullvol_help = gengetopt_args_info_help[49] ;
284 >  args_info->rodlength_help = gengetopt_args_info_help[50] ;
285 >  args_info->tet_param_help = gengetopt_args_info_help[51] ;
286 >  args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
287 >  args_info->rnemdz_help = gengetopt_args_info_help[53] ;
288 >  args_info->rnemdr_help = gengetopt_args_info_help[54] ;
289 >  args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
290 >  args_info->nitrile_help = gengetopt_args_info_help[56] ;
291 >  args_info->multipole_help = gengetopt_args_info_help[57] ;
292    
293   }
294  
295   void
296   cmdline_parser_print_version (void)
297   {
298 <  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
298 >  printf ("%s %s\n",
299 >     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
300 >     CMDLINE_PARSER_VERSION);
301   }
302  
303 < void
216 < cmdline_parser_print_help (void)
217 < {
218 <  int i = 0;
303 > static void print_help_common(void) {
304    cmdline_parser_print_version ();
305  
306    if (strlen(gengetopt_args_info_purpose) > 0)
307      printf("\n%s\n", gengetopt_args_info_purpose);
308  
309 <  printf("\n%s\n\n", gengetopt_args_info_usage);
309 >  if (strlen(gengetopt_args_info_usage) > 0)
310 >    printf("\n%s\n", gengetopt_args_info_usage);
311  
312 +  printf("\n");
313 +
314    if (strlen(gengetopt_args_info_description) > 0)
315 <    printf("%s\n", gengetopt_args_info_description);
315 >    printf("%s\n\n", gengetopt_args_info_description);
316 > }
317  
318 + void
319 + cmdline_parser_print_help (void)
320 + {
321 +  int i = 0;
322 +  print_help_common();
323    while (gengetopt_args_info_help[i])
324      printf("%s\n", gengetopt_args_info_help[i++]);
325   }
# Line 237 | Line 331 | cmdline_parser_init (struct gengetopt_args_info *args_
331    clear_args (args_info);
332    init_args_info (args_info);
333  
334 <  args_info->inputs = NULL;
334 >  args_info->inputs = 0;
335    args_info->inputs_num = 0;
336   }
337  
338 + void
339 + cmdline_parser_params_init(struct cmdline_parser_params *params)
340 + {
341 +  if (params)
342 +    {
343 +      params->override = 0;
344 +      params->initialize = 1;
345 +      params->check_required = 1;
346 +      params->check_ambiguity = 0;
347 +      params->print_errors = 1;
348 +    }
349 + }
350 +
351 + struct cmdline_parser_params *
352 + cmdline_parser_params_create(void)
353 + {
354 +  struct cmdline_parser_params *params =
355 +    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
356 +  cmdline_parser_params_init(params);  
357 +  return params;
358 + }
359 +
360   static void
361 < cmdline_parser_release (struct gengetopt_args_info *args_info)
361 > free_string_field (char **s)
362   {
363 <  
248 <  unsigned int i;
249 <  if (args_info->input_arg)
363 >  if (*s)
364      {
365 <      free (args_info->input_arg); /* free previous argument */
366 <      args_info->input_arg = 0;
253 <    }
254 <  if (args_info->input_orig)
255 <    {
256 <      free (args_info->input_orig); /* free previous argument */
257 <      args_info->input_orig = 0;
258 <    }
259 <  if (args_info->output_arg)
260 <    {
261 <      free (args_info->output_arg); /* free previous argument */
262 <      args_info->output_arg = 0;
263 <    }
264 <  if (args_info->output_orig)
265 <    {
266 <      free (args_info->output_orig); /* free previous argument */
267 <      args_info->output_orig = 0;
268 <    }
269 <  if (args_info->step_orig)
270 <    {
271 <      free (args_info->step_orig); /* free previous argument */
272 <      args_info->step_orig = 0;
273 <    }
274 <  if (args_info->nbins_orig)
275 <    {
276 <      free (args_info->nbins_orig); /* free previous argument */
277 <      args_info->nbins_orig = 0;
278 <    }
279 <  if (args_info->nbins_x_orig)
280 <    {
281 <      free (args_info->nbins_x_orig); /* free previous argument */
282 <      args_info->nbins_x_orig = 0;
283 <    }
284 <  if (args_info->nbins_y_orig)
285 <    {
286 <      free (args_info->nbins_y_orig); /* free previous argument */
287 <      args_info->nbins_y_orig = 0;
288 <    }
289 <  if (args_info->nanglebins_orig)
290 <    {
291 <      free (args_info->nanglebins_orig); /* free previous argument */
292 <      args_info->nanglebins_orig = 0;
293 <    }
294 <  if (args_info->length_orig)
295 <    {
296 <      free (args_info->length_orig); /* free previous argument */
297 <      args_info->length_orig = 0;
365 >      free (*s);
366 >      *s = 0;
367      }
368 <  if (args_info->rcut_orig)
369 <    {
370 <      free (args_info->rcut_orig); /* free previous argument */
371 <      args_info->rcut_orig = 0;
372 <    }
373 <  if (args_info->zoffset_orig)
374 <    {
375 <      free (args_info->zoffset_orig); /* free previous argument */
376 <      args_info->zoffset_orig = 0;
377 <    }
378 <  if (args_info->sele1_arg)
379 <    {
380 <      free (args_info->sele1_arg); /* free previous argument */
381 <      args_info->sele1_arg = 0;
382 <    }
383 <  if (args_info->sele1_orig)
384 <    {
385 <      free (args_info->sele1_orig); /* free previous argument */
386 <      args_info->sele1_orig = 0;
387 <    }
388 <  if (args_info->sele2_arg)
389 <    {
390 <      free (args_info->sele2_arg); /* free previous argument */
391 <      args_info->sele2_arg = 0;
392 <    }
393 <  if (args_info->sele2_orig)
394 <    {
395 <      free (args_info->sele2_orig); /* free previous argument */
396 <      args_info->sele2_orig = 0;
397 <    }
398 <  if (args_info->sele3_arg)
399 <    {
400 <      free (args_info->sele3_arg); /* free previous argument */
401 <      args_info->sele3_arg = 0;
402 <    }
403 <  if (args_info->sele3_orig)
404 <    {
405 <      free (args_info->sele3_orig); /* free previous argument */
406 <      args_info->sele3_orig = 0;
338 <    }
339 <  if (args_info->refsele_arg)
340 <    {
341 <      free (args_info->refsele_arg); /* free previous argument */
342 <      args_info->refsele_arg = 0;
343 <    }
344 <  if (args_info->refsele_orig)
345 <    {
346 <      free (args_info->refsele_orig); /* free previous argument */
347 <      args_info->refsele_orig = 0;
348 <    }
349 <  if (args_info->molname_arg)
350 <    {
351 <      free (args_info->molname_arg); /* free previous argument */
352 <      args_info->molname_arg = 0;
353 <    }
354 <  if (args_info->molname_orig)
355 <    {
356 <      free (args_info->molname_orig); /* free previous argument */
357 <      args_info->molname_orig = 0;
358 <    }
359 <  if (args_info->begin_orig)
360 <    {
361 <      free (args_info->begin_orig); /* free previous argument */
362 <      args_info->begin_orig = 0;
363 <    }
364 <  if (args_info->end_orig)
365 <    {
366 <      free (args_info->end_orig); /* free previous argument */
367 <      args_info->end_orig = 0;
368 <    }
369 <  if (args_info->radius_orig)
370 <    {
371 <      free (args_info->radius_orig); /* free previous argument */
372 <      args_info->radius_orig = 0;
373 <    }
368 > }
369 >
370 >
371 > static void
372 > cmdline_parser_release (struct gengetopt_args_info *args_info)
373 > {
374 >  unsigned int i;
375 >  free_string_field (&(args_info->input_arg));
376 >  free_string_field (&(args_info->input_orig));
377 >  free_string_field (&(args_info->output_arg));
378 >  free_string_field (&(args_info->output_orig));
379 >  free_string_field (&(args_info->step_orig));
380 >  free_string_field (&(args_info->nbins_orig));
381 >  free_string_field (&(args_info->nbins_x_orig));
382 >  free_string_field (&(args_info->nbins_y_orig));
383 >  free_string_field (&(args_info->nbins_z_orig));
384 >  free_string_field (&(args_info->nanglebins_orig));
385 >  free_string_field (&(args_info->rcut_orig));
386 >  free_string_field (&(args_info->dz_orig));
387 >  free_string_field (&(args_info->length_orig));
388 >  free_string_field (&(args_info->zlength_orig));
389 >  free_string_field (&(args_info->zoffset_orig));
390 >  free_string_field (&(args_info->sele1_arg));
391 >  free_string_field (&(args_info->sele1_orig));
392 >  free_string_field (&(args_info->sele2_arg));
393 >  free_string_field (&(args_info->sele2_orig));
394 >  free_string_field (&(args_info->sele3_arg));
395 >  free_string_field (&(args_info->sele3_orig));
396 >  free_string_field (&(args_info->refsele_arg));
397 >  free_string_field (&(args_info->refsele_orig));
398 >  free_string_field (&(args_info->comsele_arg));
399 >  free_string_field (&(args_info->comsele_orig));
400 >  free_string_field (&(args_info->seleoffset_orig));
401 >  free_string_field (&(args_info->seleoffset2_orig));
402 >  free_string_field (&(args_info->molname_arg));
403 >  free_string_field (&(args_info->molname_orig));
404 >  free_string_field (&(args_info->begin_orig));
405 >  free_string_field (&(args_info->end_orig));
406 >  free_string_field (&(args_info->radius_orig));
407    
408 +  
409    for (i = 0; i < args_info->inputs_num; ++i)
410      free (args_info->inputs [i]);
411 <  
411 >
412    if (args_info->inputs_num)
413      free (args_info->inputs);
414 <  
414 >
415    clear_given (args_info);
416   }
417  
418 +
419 + static void
420 + write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
421 + {
422 +  FIX_UNUSED (values);
423 +  if (arg) {
424 +    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
425 +  } else {
426 +    fprintf(outfile, "%s\n", opt);
427 +  }
428 + }
429 +
430 +
431   int
432 + cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
433 + {
434 +  int i = 0;
435 +
436 +  if (!outfile)
437 +    {
438 +      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
439 +      return EXIT_FAILURE;
440 +    }
441 +
442 +  if (args_info->help_given)
443 +    write_into_file(outfile, "help", 0, 0 );
444 +  if (args_info->version_given)
445 +    write_into_file(outfile, "version", 0, 0 );
446 +  if (args_info->input_given)
447 +    write_into_file(outfile, "input", args_info->input_orig, 0);
448 +  if (args_info->output_given)
449 +    write_into_file(outfile, "output", args_info->output_orig, 0);
450 +  if (args_info->step_given)
451 +    write_into_file(outfile, "step", args_info->step_orig, 0);
452 +  if (args_info->nbins_given)
453 +    write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
454 +  if (args_info->nbins_x_given)
455 +    write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
456 +  if (args_info->nbins_y_given)
457 +    write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
458 +  if (args_info->nbins_z_given)
459 +    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
460 +  if (args_info->nanglebins_given)
461 +    write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
462 +  if (args_info->rcut_given)
463 +    write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
464 +  if (args_info->dz_given)
465 +    write_into_file(outfile, "dz", args_info->dz_orig, 0);
466 +  if (args_info->length_given)
467 +    write_into_file(outfile, "length", args_info->length_orig, 0);
468 +  if (args_info->zlength_given)
469 +    write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
470 +  if (args_info->zoffset_given)
471 +    write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
472 +  if (args_info->sele1_given)
473 +    write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
474 +  if (args_info->sele2_given)
475 +    write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
476 +  if (args_info->sele3_given)
477 +    write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
478 +  if (args_info->refsele_given)
479 +    write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
480 +  if (args_info->comsele_given)
481 +    write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
482 +  if (args_info->seleoffset_given)
483 +    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
484 +  if (args_info->seleoffset2_given)
485 +    write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
486 +  if (args_info->molname_given)
487 +    write_into_file(outfile, "molname", args_info->molname_orig, 0);
488 +  if (args_info->begin_given)
489 +    write_into_file(outfile, "begin", args_info->begin_orig, 0);
490 +  if (args_info->end_given)
491 +    write_into_file(outfile, "end", args_info->end_orig, 0);
492 +  if (args_info->radius_given)
493 +    write_into_file(outfile, "radius", args_info->radius_orig, 0);
494 +  if (args_info->bo_given)
495 +    write_into_file(outfile, "bo", 0, 0 );
496 +  if (args_info->ior_given)
497 +    write_into_file(outfile, "ior", 0, 0 );
498 +  if (args_info->for_given)
499 +    write_into_file(outfile, "for", 0, 0 );
500 +  if (args_info->bad_given)
501 +    write_into_file(outfile, "bad", 0, 0 );
502 +  if (args_info->count_given)
503 +    write_into_file(outfile, "count", 0, 0 );
504 +  if (args_info->gofr_given)
505 +    write_into_file(outfile, "gofr", 0, 0 );
506 +  if (args_info->gofz_given)
507 +    write_into_file(outfile, "gofz", 0, 0 );
508 +  if (args_info->r_theta_given)
509 +    write_into_file(outfile, "r_theta", 0, 0 );
510 +  if (args_info->r_omega_given)
511 +    write_into_file(outfile, "r_omega", 0, 0 );
512 +  if (args_info->r_z_given)
513 +    write_into_file(outfile, "r_z", 0, 0 );
514 +  if (args_info->theta_omega_given)
515 +    write_into_file(outfile, "theta_omega", 0, 0 );
516 +  if (args_info->gxyz_given)
517 +    write_into_file(outfile, "gxyz", 0, 0 );
518 +  if (args_info->twodgofr_given)
519 +    write_into_file(outfile, "twodgofr", 0, 0 );
520 +  if (args_info->p2_given)
521 +    write_into_file(outfile, "p2", 0, 0 );
522 +  if (args_info->rp2_given)
523 +    write_into_file(outfile, "rp2", 0, 0 );
524 +  if (args_info->scd_given)
525 +    write_into_file(outfile, "scd", 0, 0 );
526 +  if (args_info->density_given)
527 +    write_into_file(outfile, "density", 0, 0 );
528 +  if (args_info->slab_density_given)
529 +    write_into_file(outfile, "slab_density", 0, 0 );
530 +  if (args_info->p_angle_given)
531 +    write_into_file(outfile, "p_angle", 0, 0 );
532 +  if (args_info->hxy_given)
533 +    write_into_file(outfile, "hxy", 0, 0 );
534 +  if (args_info->rho_r_given)
535 +    write_into_file(outfile, "rho_r", 0, 0 );
536 +  if (args_info->angle_r_given)
537 +    write_into_file(outfile, "angle_r", 0, 0 );
538 +  if (args_info->hullvol_given)
539 +    write_into_file(outfile, "hullvol", 0, 0 );
540 +  if (args_info->rodlength_given)
541 +    write_into_file(outfile, "rodlength", 0, 0 );
542 +  if (args_info->tet_param_given)
543 +    write_into_file(outfile, "tet_param", 0, 0 );
544 +  if (args_info->tet_param_z_given)
545 +    write_into_file(outfile, "tet_param_z", 0, 0 );
546 +  if (args_info->rnemdz_given)
547 +    write_into_file(outfile, "rnemdz", 0, 0 );
548 +  if (args_info->rnemdr_given)
549 +    write_into_file(outfile, "rnemdr", 0, 0 );
550 +  if (args_info->rnemdrt_given)
551 +    write_into_file(outfile, "rnemdrt", 0, 0 );
552 +  if (args_info->nitrile_given)
553 +    write_into_file(outfile, "nitrile", 0, 0 );
554 +  if (args_info->multipole_given)
555 +    write_into_file(outfile, "multipole", 0, 0 );
556 +  
557 +
558 +  i = EXIT_SUCCESS;
559 +  return i;
560 + }
561 +
562 + int
563   cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
564   {
565    FILE *outfile;
# Line 395 | Line 573 | cmdline_parser_file_save(const char *filename, struct
573        return EXIT_FAILURE;
574      }
575  
576 <  if (args_info->help_given) {
399 <    fprintf(outfile, "%s\n", "help");
400 <  }
401 <  if (args_info->version_given) {
402 <    fprintf(outfile, "%s\n", "version");
403 <  }
404 <  if (args_info->input_given) {
405 <    if (args_info->input_orig) {
406 <      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
407 <    } else {
408 <      fprintf(outfile, "%s\n", "input");
409 <    }
410 <  }
411 <  if (args_info->output_given) {
412 <    if (args_info->output_orig) {
413 <      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
414 <    } else {
415 <      fprintf(outfile, "%s\n", "output");
416 <    }
417 <  }
418 <  if (args_info->step_given) {
419 <    if (args_info->step_orig) {
420 <      fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
421 <    } else {
422 <      fprintf(outfile, "%s\n", "step");
423 <    }
424 <  }
425 <  if (args_info->nbins_given) {
426 <    if (args_info->nbins_orig) {
427 <      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
428 <    } else {
429 <      fprintf(outfile, "%s\n", "nbins");
430 <    }
431 <  }
432 <  if (args_info->nbins_x_given) {
433 <    if (args_info->nbins_x_orig) {
434 <      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
435 <    } else {
436 <      fprintf(outfile, "%s\n", "nbins_x");
437 <    }
438 <  }
439 <  if (args_info->nbins_y_given) {
440 <    if (args_info->nbins_y_orig) {
441 <      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
442 <    } else {
443 <      fprintf(outfile, "%s\n", "nbins_y");
444 <    }
445 <  }
446 <  if (args_info->nanglebins_given) {
447 <    if (args_info->nanglebins_orig) {
448 <      fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
449 <    } else {
450 <      fprintf(outfile, "%s\n", "nanglebins");
451 <    }
452 <  }
453 <  if (args_info->length_given) {
454 <    if (args_info->length_orig) {
455 <      fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
456 <    } else {
457 <      fprintf(outfile, "%s\n", "length");
458 <    }
459 <  }
460 <  if (args_info->rcut_given) {
461 <    if (args_info->rcut_orig) {
462 <      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
463 <    } else {
464 <      fprintf(outfile, "%s\n", "rcut");
465 <    }
466 <  }
467 <  if (args_info->zoffset_given) {
468 <    if (args_info->zoffset_orig) {
469 <      fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
470 <    } else {
471 <      fprintf(outfile, "%s\n", "zoffset");
472 <    }
473 <  }
474 <  if (args_info->sele1_given) {
475 <    if (args_info->sele1_orig) {
476 <      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
477 <    } else {
478 <      fprintf(outfile, "%s\n", "sele1");
479 <    }
480 <  }
481 <  if (args_info->sele2_given) {
482 <    if (args_info->sele2_orig) {
483 <      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
484 <    } else {
485 <      fprintf(outfile, "%s\n", "sele2");
486 <    }
487 <  }
488 <  if (args_info->sele3_given) {
489 <    if (args_info->sele3_orig) {
490 <      fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
491 <    } else {
492 <      fprintf(outfile, "%s\n", "sele3");
493 <    }
494 <  }
495 <  if (args_info->refsele_given) {
496 <    if (args_info->refsele_orig) {
497 <      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
498 <    } else {
499 <      fprintf(outfile, "%s\n", "refsele");
500 <    }
501 <  }
502 <  if (args_info->molname_given) {
503 <    if (args_info->molname_orig) {
504 <      fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
505 <    } else {
506 <      fprintf(outfile, "%s\n", "molname");
507 <    }
508 <  }
509 <  if (args_info->begin_given) {
510 <    if (args_info->begin_orig) {
511 <      fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
512 <    } else {
513 <      fprintf(outfile, "%s\n", "begin");
514 <    }
515 <  }
516 <  if (args_info->end_given) {
517 <    if (args_info->end_orig) {
518 <      fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
519 <    } else {
520 <      fprintf(outfile, "%s\n", "end");
521 <    }
522 <  }
523 <  if (args_info->radius_given) {
524 <    if (args_info->radius_orig) {
525 <      fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
526 <    } else {
527 <      fprintf(outfile, "%s\n", "radius");
528 <    }
529 <  }
530 <  if (args_info->bo_given) {
531 <    fprintf(outfile, "%s\n", "bo");
532 <  }
533 <  if (args_info->bor_given) {
534 <    fprintf(outfile, "%s\n", "bor");
535 <  }
536 <  if (args_info->bad_given) {
537 <    fprintf(outfile, "%s\n", "bad");
538 <  }
539 <  if (args_info->gofr_given) {
540 <    fprintf(outfile, "%s\n", "gofr");
541 <  }
542 <  if (args_info->gofz_given) {
543 <    fprintf(outfile, "%s\n", "gofz");
544 <  }
545 <  if (args_info->r_theta_given) {
546 <    fprintf(outfile, "%s\n", "r_theta");
547 <  }
548 <  if (args_info->r_omega_given) {
549 <    fprintf(outfile, "%s\n", "r_omega");
550 <  }
551 <  if (args_info->theta_omega_given) {
552 <    fprintf(outfile, "%s\n", "theta_omega");
553 <  }
554 <  if (args_info->gxyz_given) {
555 <    fprintf(outfile, "%s\n", "gxyz");
556 <  }
557 <  if (args_info->p2_given) {
558 <    fprintf(outfile, "%s\n", "p2");
559 <  }
560 <  if (args_info->rp2_given) {
561 <    fprintf(outfile, "%s\n", "rp2");
562 <  }
563 <  if (args_info->scd_given) {
564 <    fprintf(outfile, "%s\n", "scd");
565 <  }
566 <  if (args_info->density_given) {
567 <    fprintf(outfile, "%s\n", "density");
568 <  }
569 <  if (args_info->slab_density_given) {
570 <    fprintf(outfile, "%s\n", "slab_density");
571 <  }
572 <  if (args_info->hxy_given) {
573 <    fprintf(outfile, "%s\n", "hxy");
574 <  }
575 <  if (args_info->rho_r_given) {
576 <    fprintf(outfile, "%s\n", "rho_r");
577 <  }
578 <  if (args_info->hullvol_given) {
579 <    fprintf(outfile, "%s\n", "hullvol");
580 <  }
581 <  
576 >  i = cmdline_parser_dump(outfile, args_info);
577    fclose (outfile);
578  
584 –  i = EXIT_SUCCESS;
579    return i;
580   }
581  
# Line 591 | Line 585 | cmdline_parser_free (struct gengetopt_args_info *args_
585    cmdline_parser_release (args_info);
586   }
587  
588 <
595 < /* gengetopt_strdup() */
596 < /* strdup.c replacement of strdup, which is not standard */
588 > /** @brief replacement of strdup, which is not standard */
589   char *
590   gengetopt_strdup (const char *s)
591   {
592 <  char *result = NULL;
592 >  char *result = 0;
593    if (!s)
594      return result;
595  
# Line 609 | Line 601 | static void
601   }
602  
603   static void
612 – reset_group_staticProps(struct gengetopt_args_info *args_info);
613 –
614 – static void
604   reset_group_staticProps(struct gengetopt_args_info *args_info)
605   {
606    if (! args_info->staticProps_group_counter)
607      return;
608    
609    args_info->bo_given = 0 ;
610 <  args_info->bor_given = 0 ;
610 >  args_info->ior_given = 0 ;
611 >  args_info->for_given = 0 ;
612    args_info->bad_given = 0 ;
613 +  args_info->count_given = 0 ;
614    args_info->gofr_given = 0 ;
615    args_info->gofz_given = 0 ;
616    args_info->r_theta_given = 0 ;
617    args_info->r_omega_given = 0 ;
618 +  args_info->r_z_given = 0 ;
619    args_info->theta_omega_given = 0 ;
620    args_info->gxyz_given = 0 ;
621 +  args_info->twodgofr_given = 0 ;
622    args_info->p2_given = 0 ;
623    args_info->rp2_given = 0 ;
624    args_info->scd_given = 0 ;
625    args_info->density_given = 0 ;
626    args_info->slab_density_given = 0 ;
627 +  args_info->p_angle_given = 0 ;
628    args_info->hxy_given = 0 ;
629    args_info->rho_r_given = 0 ;
630 +  args_info->angle_r_given = 0 ;
631    args_info->hullvol_given = 0 ;
632 +  args_info->rodlength_given = 0 ;
633 +  args_info->tet_param_given = 0 ;
634 +  args_info->tet_param_z_given = 0 ;
635 +  args_info->rnemdz_given = 0 ;
636 +  args_info->rnemdr_given = 0 ;
637 +  args_info->rnemdrt_given = 0 ;
638 +  args_info->nitrile_given = 0 ;
639 +  args_info->multipole_given = 0 ;
640  
641    args_info->staticProps_group_counter = 0;
642   }
643  
644   int
645 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
645 > cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
646   {
647    return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
648   }
649  
650   int
651 < cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
651 > cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
652 >                   struct cmdline_parser_params *params)
653   {
654    int result;
655 +  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
656  
657 <  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
657 >  if (result == EXIT_FAILURE)
658 >    {
659 >      cmdline_parser_free (args_info);
660 >      exit (EXIT_FAILURE);
661 >    }
662 >  
663 >  return result;
664 > }
665  
666 + int
667 + cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
668 + {
669 +  int result;
670 +  struct cmdline_parser_params params;
671 +  
672 +  params.override = override;
673 +  params.initialize = initialize;
674 +  params.check_required = check_required;
675 +  params.check_ambiguity = 0;
676 +  params.print_errors = 1;
677 +
678 +  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
679 +
680    if (result == EXIT_FAILURE)
681      {
682        cmdline_parser_free (args_info);
# Line 665 | Line 691 | cmdline_parser_required (struct gengetopt_args_info *a
691   {
692    int result = EXIT_SUCCESS;
693  
694 <  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
694 >  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
695      result = EXIT_FAILURE;
696  
697    if (result == EXIT_FAILURE)
# Line 681 | Line 707 | cmdline_parser_required2 (struct gengetopt_args_info *
707   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
708   {
709    int error = 0;
710 +  FIX_UNUSED (additional_error);
711  
712    /* checks for required options */
713    if (! args_info->input_given)
# Line 691 | Line 718 | cmdline_parser_required2 (struct gengetopt_args_info *
718    
719    if (args_info->staticProps_group_counter == 0)
720      {
721 <      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 : ""));
721 >      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 : ""));
722        error = 1;
723      }
724    
# Line 701 | Line 728 | cmdline_parser_required2 (struct gengetopt_args_info *
728    return error;
729   }
730  
731 +
732 + static char *package_name = 0;
733 +
734 + /**
735 + * @brief updates an option
736 + * @param field the generic pointer to the field to update
737 + * @param orig_field the pointer to the orig field
738 + * @param field_given the pointer to the number of occurrence of this option
739 + * @param prev_given the pointer to the number of occurrence already seen
740 + * @param value the argument for this option (if null no arg was specified)
741 + * @param possible_values the possible values for this option (if specified)
742 + * @param default_value the default value (in case the option only accepts fixed values)
743 + * @param arg_type the type of this option
744 + * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
745 + * @param override @see cmdline_parser_params.override
746 + * @param no_free whether to free a possible previous value
747 + * @param multiple_option whether this is a multiple option
748 + * @param long_opt the corresponding long option
749 + * @param short_opt the corresponding short option (or '-' if none)
750 + * @param additional_error possible further error specification
751 + */
752 + static
753 + int update_arg(void *field, char **orig_field,
754 +               unsigned int *field_given, unsigned int *prev_given,
755 +               char *value, const char *possible_values[],
756 +               const char *default_value,
757 +               cmdline_parser_arg_type arg_type,
758 +               int check_ambiguity, int override,
759 +               int no_free, int multiple_option,
760 +               const char *long_opt, char short_opt,
761 +               const char *additional_error)
762 + {
763 +  char *stop_char = 0;
764 +  const char *val = value;
765 +  int found;
766 +  char **string_field;
767 +  FIX_UNUSED (field);
768 +
769 +  stop_char = 0;
770 +  found = 0;
771 +
772 +  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
773 +    {
774 +      if (short_opt != '-')
775 +        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
776 +               package_name, long_opt, short_opt,
777 +               (additional_error ? additional_error : ""));
778 +      else
779 +        fprintf (stderr, "%s: `--%s' option given more than once%s\n",
780 +               package_name, long_opt,
781 +               (additional_error ? additional_error : ""));
782 +      return 1; /* failure */
783 +    }
784 +
785 +  FIX_UNUSED (default_value);
786 +    
787 +  if (field_given && *field_given && ! override)
788 +    return 0;
789 +  if (prev_given)
790 +    (*prev_given)++;
791 +  if (field_given)
792 +    (*field_given)++;
793 +  if (possible_values)
794 +    val = possible_values[found];
795 +
796 +  switch(arg_type) {
797 +  case ARG_INT:
798 +    if (val) *((int *)field) = strtol (val, &stop_char, 0);
799 +    break;
800 +  case ARG_DOUBLE:
801 +    if (val) *((double *)field) = strtod (val, &stop_char);
802 +    break;
803 +  case ARG_STRING:
804 +    if (val) {
805 +      string_field = (char **)field;
806 +      if (!no_free && *string_field)
807 +        free (*string_field); /* free previous string */
808 +      *string_field = gengetopt_strdup (val);
809 +    }
810 +    break;
811 +  default:
812 +    break;
813 +  };
814 +
815 +  /* check numeric conversion */
816 +  switch(arg_type) {
817 +  case ARG_INT:
818 +  case ARG_DOUBLE:
819 +    if (val && !(stop_char && *stop_char == '\0')) {
820 +      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
821 +      return 1; /* failure */
822 +    }
823 +    break;
824 +  default:
825 +    ;
826 +  };
827 +
828 +  /* store the original value */
829 +  switch(arg_type) {
830 +  case ARG_NO:
831 +    break;
832 +  default:
833 +    if (value && orig_field) {
834 +      if (no_free) {
835 +        *orig_field = value;
836 +      } else {
837 +        if (*orig_field)
838 +          free (*orig_field); /* free previous string */
839 +        *orig_field = gengetopt_strdup (value);
840 +      }
841 +    }
842 +  };
843 +
844 +  return 0; /* OK */
845 + }
846 +
847 +
848   int
849 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
849 > cmdline_parser_internal (
850 >  int argc, char **argv, struct gengetopt_args_info *args_info,
851 >                        struct cmdline_parser_params *params, const char *additional_error)
852   {
853    int c;        /* Character of the parsed option.  */
854  
855    int error = 0;
856    struct gengetopt_args_info local_args_info;
857 +  
858 +  int override;
859 +  int initialize;
860 +  int check_required;
861 +  int check_ambiguity;
862 +  
863 +  package_name = argv[0];
864 +  
865 +  override = params->override;
866 +  initialize = params->initialize;
867 +  check_required = params->check_required;
868 +  check_ambiguity = params->check_ambiguity;
869  
870    if (initialize)
871      cmdline_parser_init (args_info);
# Line 716 | Line 874 | cmdline_parser_internal (int argc, char * const *argv,
874  
875    optarg = 0;
876    optind = 0;
877 <  opterr = 1;
877 >  opterr = params->print_errors;
878    optopt = '?';
879  
880    while (1)
881      {
882        int option_index = 0;
725 –      char *stop_char;
883  
884        static struct option long_options[] = {
885          { "help",       0, NULL, 'h' },
# Line 733 | Line 890 | cmdline_parser_internal (int argc, char * const *argv,
890          { "nbins",      1, NULL, 'b' },
891          { "nbins_x",    1, NULL, 'x' },
892          { "nbins_y",    1, NULL, 'y' },
893 +        { "nbins_z",    1, NULL, 0 },
894          { "nanglebins", 1, NULL, 'a' },
737 –        { "length",     1, NULL, 0 },
895          { "rcut",       1, NULL, 'c' },
896 +        { "dz", 1, NULL, 0 },
897 +        { "length",     1, NULL, 0 },
898 +        { "zlength",    1, NULL, 0 },
899          { "zoffset",    1, NULL, 'z' },
900          { "sele1",      1, NULL, 0 },
901          { "sele2",      1, NULL, 0 },
902          { "sele3",      1, NULL, 0 },
903          { "refsele",    1, NULL, 0 },
904 +        { "comsele",    1, NULL, 0 },
905 +        { "seleoffset", 1, NULL, 0 },
906 +        { "seleoffset2",        1, NULL, 0 },
907          { "molname",    1, NULL, 0 },
908          { "begin",      1, NULL, 0 },
909          { "end",        1, NULL, 0 },
910          { "radius",     1, NULL, 0 },
911          { "bo", 0, NULL, 0 },
912 <        { "bor",        0, NULL, 0 },
912 >        { "ior",        0, NULL, 0 },
913 >        { "for",        0, NULL, 0 },
914          { "bad",        0, NULL, 0 },
915 +        { "count",      0, NULL, 0 },
916          { "gofr",       0, NULL, 'g' },
917          { "gofz",       0, NULL, 0 },
918          { "r_theta",    0, NULL, 0 },
919          { "r_omega",    0, NULL, 0 },
920 +        { "r_z",        0, NULL, 0 },
921          { "theta_omega",        0, NULL, 0 },
922          { "gxyz",       0, NULL, 0 },
923 +        { "twodgofr",   0, NULL, 0 },
924          { "p2", 0, NULL, 'p' },
925          { "rp2",        0, NULL, 0 },
926          { "scd",        0, NULL, 's' },
927          { "density",    0, NULL, 'd' },
928          { "slab_density",       0, NULL, 0 },
929 +        { "p_angle",    0, NULL, 0 },
930          { "hxy",        0, NULL, 0 },
931          { "rho_r",      0, NULL, 0 },
932 +        { "angle_r",    0, NULL, 0 },
933          { "hullvol",    0, NULL, 0 },
934 <        { NULL, 0, NULL, 0 }
934 >        { "rodlength",  0, NULL, 0 },
935 >        { "tet_param",  0, NULL, 'Q' },
936 >        { "tet_param_z",        0, NULL, 0 },
937 >        { "rnemdz",     0, NULL, 0 },
938 >        { "rnemdr",     0, NULL, 0 },
939 >        { "rnemdrt",    0, NULL, 0 },
940 >        { "nitrile",    0, NULL, 0 },
941 >        { "multipole",  0, NULL, 'm' },
942 >        { 0,  0, 0, 0 }
943        };
944  
945 <      stop_char = 0;
769 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
945 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQm", long_options, &option_index);
946  
947        if (c == -1) break;       /* Exit from `while (1)' loop.  */
948  
# Line 783 | Line 959 | cmdline_parser_internal (int argc, char * const *argv,
959            exit (EXIT_SUCCESS);
960  
961          case 'i':       /* input dump file.  */
962 <          if (local_args_info.input_given)
963 <            {
964 <              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
965 <              goto failure;
966 <            }
967 <          if (args_info->input_given && ! override)
968 <            continue;
969 <          local_args_info.input_given = 1;
970 <          args_info->input_given = 1;
971 <          if (args_info->input_arg)
796 <            free (args_info->input_arg); /* free previous string */
797 <          args_info->input_arg = gengetopt_strdup (optarg);
798 <          if (args_info->input_orig)
799 <            free (args_info->input_orig); /* free previous string */
800 <          args_info->input_orig = gengetopt_strdup (optarg);
962 >        
963 >        
964 >          if (update_arg( (void *)&(args_info->input_arg),
965 >               &(args_info->input_orig), &(args_info->input_given),
966 >              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
967 >              check_ambiguity, override, 0, 0,
968 >              "input", 'i',
969 >              additional_error))
970 >            goto failure;
971 >        
972            break;
802 –
973          case 'o':       /* output file name.  */
974 <          if (local_args_info.output_given)
975 <            {
976 <              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
977 <              goto failure;
978 <            }
979 <          if (args_info->output_given && ! override)
980 <            continue;
981 <          local_args_info.output_given = 1;
982 <          args_info->output_given = 1;
983 <          if (args_info->output_arg)
814 <            free (args_info->output_arg); /* free previous string */
815 <          args_info->output_arg = gengetopt_strdup (optarg);
816 <          if (args_info->output_orig)
817 <            free (args_info->output_orig); /* free previous string */
818 <          args_info->output_orig = gengetopt_strdup (optarg);
974 >        
975 >        
976 >          if (update_arg( (void *)&(args_info->output_arg),
977 >               &(args_info->output_orig), &(args_info->output_given),
978 >              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
979 >              check_ambiguity, override, 0, 0,
980 >              "output", 'o',
981 >              additional_error))
982 >            goto failure;
983 >        
984            break;
820 –
985          case 'n':       /* process every n frame.  */
986 <          if (local_args_info.step_given)
987 <            {
988 <              fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
989 <              goto failure;
990 <            }
991 <          if (args_info->step_given && ! override)
992 <            continue;
993 <          local_args_info.step_given = 1;
830 <          args_info->step_given = 1;
831 <          args_info->step_arg = strtol (optarg, &stop_char, 0);
832 <          if (!(stop_char && *stop_char == '\0')) {
833 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
986 >        
987 >        
988 >          if (update_arg( (void *)&(args_info->step_arg),
989 >               &(args_info->step_orig), &(args_info->step_given),
990 >              &(local_args_info.step_given), optarg, 0, "1", ARG_INT,
991 >              check_ambiguity, override, 0, 0,
992 >              "step", 'n',
993 >              additional_error))
994              goto failure;
995 <          }
836 <          if (args_info->step_orig)
837 <            free (args_info->step_orig); /* free previous string */
838 <          args_info->step_orig = gengetopt_strdup (optarg);
995 >        
996            break;
840 –
997          case 'b':       /* number of bins (general purpose).  */
998 <          if (local_args_info.nbins_given)
999 <            {
1000 <              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001 <              goto failure;
1002 <            }
1003 <          if (args_info->nbins_given && ! override)
1004 <            continue;
1005 <          local_args_info.nbins_given = 1;
850 <          args_info->nbins_given = 1;
851 <          args_info->nbins_arg = strtol (optarg, &stop_char, 0);
852 <          if (!(stop_char && *stop_char == '\0')) {
853 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
998 >        
999 >        
1000 >          if (update_arg( (void *)&(args_info->nbins_arg),
1001 >               &(args_info->nbins_orig), &(args_info->nbins_given),
1002 >              &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
1003 >              check_ambiguity, override, 0, 0,
1004 >              "nbins", 'b',
1005 >              additional_error))
1006              goto failure;
1007 <          }
856 <          if (args_info->nbins_orig)
857 <            free (args_info->nbins_orig); /* free previous string */
858 <          args_info->nbins_orig = gengetopt_strdup (optarg);
1007 >        
1008            break;
860 –
1009          case 'x':       /* number of bins in x axis.  */
1010 <          if (local_args_info.nbins_x_given)
1011 <            {
1012 <              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1013 <              goto failure;
1014 <            }
1015 <          if (args_info->nbins_x_given && ! override)
1016 <            continue;
1017 <          local_args_info.nbins_x_given = 1;
870 <          args_info->nbins_x_given = 1;
871 <          args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
872 <          if (!(stop_char && *stop_char == '\0')) {
873 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1010 >        
1011 >        
1012 >          if (update_arg( (void *)&(args_info->nbins_x_arg),
1013 >               &(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1014 >              &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1015 >              check_ambiguity, override, 0, 0,
1016 >              "nbins_x", 'x',
1017 >              additional_error))
1018              goto failure;
1019 <          }
876 <          if (args_info->nbins_x_orig)
877 <            free (args_info->nbins_x_orig); /* free previous string */
878 <          args_info->nbins_x_orig = gengetopt_strdup (optarg);
1019 >        
1020            break;
880 –
1021          case 'y':       /* number of bins in y axis.  */
1022 <          if (local_args_info.nbins_y_given)
1023 <            {
1024 <              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1025 <              goto failure;
1026 <            }
1027 <          if (args_info->nbins_y_given && ! override)
1028 <            continue;
1029 <          local_args_info.nbins_y_given = 1;
890 <          args_info->nbins_y_given = 1;
891 <          args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
892 <          if (!(stop_char && *stop_char == '\0')) {
893 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1022 >        
1023 >        
1024 >          if (update_arg( (void *)&(args_info->nbins_y_arg),
1025 >               &(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1026 >              &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1027 >              check_ambiguity, override, 0, 0,
1028 >              "nbins_y", 'y',
1029 >              additional_error))
1030              goto failure;
1031 <          }
896 <          if (args_info->nbins_y_orig)
897 <            free (args_info->nbins_y_orig); /* free previous string */
898 <          args_info->nbins_y_orig = gengetopt_strdup (optarg);
1031 >        
1032            break;
900 –
1033          case 'a':       /* number of bins for cos(angle).  */
1034 <          if (local_args_info.nanglebins_given)
1035 <            {
1036 <              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1037 <              goto failure;
1038 <            }
1039 <          if (args_info->nanglebins_given && ! override)
1040 <            continue;
1041 <          local_args_info.nanglebins_given = 1;
910 <          args_info->nanglebins_given = 1;
911 <          args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
912 <          if (!(stop_char && *stop_char == '\0')) {
913 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1034 >        
1035 >        
1036 >          if (update_arg( (void *)&(args_info->nanglebins_arg),
1037 >               &(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1038 >              &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1039 >              check_ambiguity, override, 0, 0,
1040 >              "nanglebins", 'a',
1041 >              additional_error))
1042              goto failure;
1043 <          }
916 <          if (args_info->nanglebins_orig)
917 <            free (args_info->nanglebins_orig); /* free previous string */
918 <          args_info->nanglebins_orig = gengetopt_strdup (optarg);
1043 >        
1044            break;
920 –
1045          case 'c':       /* cutoff radius (rcut).  */
1046 <          if (local_args_info.rcut_given)
1047 <            {
1048 <              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1049 <              goto failure;
1050 <            }
1051 <          if (args_info->rcut_given && ! override)
1052 <            continue;
1053 <          local_args_info.rcut_given = 1;
930 <          args_info->rcut_given = 1;
931 <          args_info->rcut_arg = strtod (optarg, &stop_char);
932 <          if (!(stop_char && *stop_char == '\0')) {
933 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1046 >        
1047 >        
1048 >          if (update_arg( (void *)&(args_info->rcut_arg),
1049 >               &(args_info->rcut_orig), &(args_info->rcut_given),
1050 >              &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1051 >              check_ambiguity, override, 0, 0,
1052 >              "rcut", 'c',
1053 >              additional_error))
1054              goto failure;
1055 <          }
936 <          if (args_info->rcut_orig)
937 <            free (args_info->rcut_orig); /* free previous string */
938 <          args_info->rcut_orig = gengetopt_strdup (optarg);
1055 >        
1056            break;
940 –
1057          case 'z':       /* Where to set the zero for the slab_density calculation.  */
1058 <          if (local_args_info.zoffset_given)
1059 <            {
1060 <              fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1061 <              goto failure;
1062 <            }
1063 <          if (args_info->zoffset_given && ! override)
1064 <            continue;
1065 <          local_args_info.zoffset_given = 1;
950 <          args_info->zoffset_given = 1;
951 <          args_info->zoffset_arg = strtod (optarg, &stop_char);
952 <          if (!(stop_char && *stop_char == '\0')) {
953 <            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1058 >        
1059 >        
1060 >          if (update_arg( (void *)&(args_info->zoffset_arg),
1061 >               &(args_info->zoffset_orig), &(args_info->zoffset_given),
1062 >              &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1063 >              check_ambiguity, override, 0, 0,
1064 >              "zoffset", 'z',
1065 >              additional_error))
1066              goto failure;
1067 <          }
956 <          if (args_info->zoffset_orig)
957 <            free (args_info->zoffset_orig); /* free previous string */
958 <          args_info->zoffset_orig = gengetopt_strdup (optarg);
1067 >        
1068            break;
960 –
1069          case 'g':       /* g(r).  */
1070 <          if (local_args_info.gofr_given)
963 <            {
964 <              fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
965 <              goto failure;
966 <            }
967 <          if (args_info->gofr_given && ! override)
968 <            continue;
969 <          local_args_info.gofr_given = 1;
970 <          args_info->gofr_given = 1;
1070 >        
1071            if (args_info->staticProps_group_counter && override)
1072              reset_group_staticProps (args_info);
1073            args_info->staticProps_group_counter += 1;
1074 +        
1075 +          if (update_arg( 0 ,
1076 +               0 , &(args_info->gofr_given),
1077 +              &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1078 +              check_ambiguity, override, 0, 0,
1079 +              "gofr", 'g',
1080 +              additional_error))
1081 +            goto failure;
1082 +        
1083            break;
1084 <
1085 <        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
977 <          if (local_args_info.p2_given)
978 <            {
979 <              fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
980 <              goto failure;
981 <            }
982 <          if (args_info->p2_given && ! override)
983 <            continue;
984 <          local_args_info.p2_given = 1;
985 <          args_info->p2_given = 1;
1084 >        case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1085 >        
1086            if (args_info->staticProps_group_counter && override)
1087              reset_group_staticProps (args_info);
1088            args_info->staticProps_group_counter += 1;
1089 +        
1090 +          if (update_arg( 0 ,
1091 +               0 , &(args_info->p2_given),
1092 +              &(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1093 +              check_ambiguity, override, 0, 0,
1094 +              "p2", 'p',
1095 +              additional_error))
1096 +            goto failure;
1097 +        
1098            break;
990 –
1099          case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1100 <          if (local_args_info.scd_given)
993 <            {
994 <              fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
995 <              goto failure;
996 <            }
997 <          if (args_info->scd_given && ! override)
998 <            continue;
999 <          local_args_info.scd_given = 1;
1000 <          args_info->scd_given = 1;
1100 >        
1101            if (args_info->staticProps_group_counter && override)
1102              reset_group_staticProps (args_info);
1103            args_info->staticProps_group_counter += 1;
1104 +        
1105 +          if (update_arg( 0 ,
1106 +               0 , &(args_info->scd_given),
1107 +              &(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1108 +              check_ambiguity, override, 0, 0,
1109 +              "scd", 's',
1110 +              additional_error))
1111 +            goto failure;
1112 +        
1113            break;
1005 –
1114          case 'd':       /* density plot.  */
1115 <          if (local_args_info.density_given)
1008 <            {
1009 <              fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1010 <              goto failure;
1011 <            }
1012 <          if (args_info->density_given && ! override)
1013 <            continue;
1014 <          local_args_info.density_given = 1;
1015 <          args_info->density_given = 1;
1115 >        
1116            if (args_info->staticProps_group_counter && override)
1117              reset_group_staticProps (args_info);
1118            args_info->staticProps_group_counter += 1;
1119 +        
1120 +          if (update_arg( 0 ,
1121 +               0 , &(args_info->density_given),
1122 +              &(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1123 +              check_ambiguity, override, 0, 0,
1124 +              "density", 'd',
1125 +              additional_error))
1126 +            goto failure;
1127 +        
1128            break;
1129 +        case 'Q':       /* tetrahedrality order parameter (Qk).  */
1130 +        
1131 +          if (args_info->staticProps_group_counter && override)
1132 +            reset_group_staticProps (args_info);
1133 +          args_info->staticProps_group_counter += 1;
1134 +        
1135 +          if (update_arg( 0 ,
1136 +               0 , &(args_info->tet_param_given),
1137 +              &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1138 +              check_ambiguity, override, 0, 0,
1139 +              "tet_param", 'Q',
1140 +              additional_error))
1141 +            goto failure;
1142 +        
1143 +          break;
1144 +        case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1145 +        
1146 +          if (args_info->staticProps_group_counter && override)
1147 +            reset_group_staticProps (args_info);
1148 +          args_info->staticProps_group_counter += 1;
1149 +        
1150 +          if (update_arg( 0 ,
1151 +               0 , &(args_info->multipole_given),
1152 +              &(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1153 +              check_ambiguity, override, 0, 0,
1154 +              "multipole", 'm',
1155 +              additional_error))
1156 +            goto failure;
1157 +        
1158 +          break;
1159  
1021 –
1160          case 0: /* Long option with no short option */
1161 <          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1162 <          if (strcmp (long_options[option_index].name, "length") == 0)
1161 >          /* number of bins in z axis.  */
1162 >          if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1163            {
1164 <            if (local_args_info.length_given)
1165 <              {
1166 <                fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1167 <                goto failure;
1168 <              }
1169 <            if (args_info->length_given && ! override)
1170 <              continue;
1171 <            local_args_info.length_given = 1;
1034 <            args_info->length_given = 1;
1035 <            args_info->length_arg = strtod (optarg, &stop_char);
1036 <            if (!(stop_char && *stop_char == '\0')) {
1037 <              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1164 >          
1165 >          
1166 >            if (update_arg( (void *)&(args_info->nbins_z_arg),
1167 >                 &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1168 >                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1169 >                check_ambiguity, override, 0, 0,
1170 >                "nbins_z", '-',
1171 >                additional_error))
1172                goto failure;
1173 <            }
1040 <            if (args_info->length_orig)
1041 <              free (args_info->length_orig); /* free previous string */
1042 <            args_info->length_orig = gengetopt_strdup (optarg);
1173 >          
1174            }
1175 +          /* slab width (dz).  */
1176 +          else if (strcmp (long_options[option_index].name, "dz") == 0)
1177 +          {
1178 +          
1179 +          
1180 +            if (update_arg( (void *)&(args_info->dz_arg),
1181 +                 &(args_info->dz_orig), &(args_info->dz_given),
1182 +                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1183 +                check_ambiguity, override, 0, 0,
1184 +                "dz", '-',
1185 +                additional_error))
1186 +              goto failure;
1187 +          
1188 +          }
1189 +          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1190 +          else if (strcmp (long_options[option_index].name, "length") == 0)
1191 +          {
1192 +          
1193 +          
1194 +            if (update_arg( (void *)&(args_info->length_arg),
1195 +                 &(args_info->length_orig), &(args_info->length_given),
1196 +                &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1197 +                check_ambiguity, override, 0, 0,
1198 +                "length", '-',
1199 +                additional_error))
1200 +              goto failure;
1201 +          
1202 +          }
1203 +          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1204 +          else if (strcmp (long_options[option_index].name, "zlength") == 0)
1205 +          {
1206 +          
1207 +          
1208 +            if (update_arg( (void *)&(args_info->zlength_arg),
1209 +                 &(args_info->zlength_orig), &(args_info->zlength_given),
1210 +                &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1211 +                check_ambiguity, override, 0, 0,
1212 +                "zlength", '-',
1213 +                additional_error))
1214 +              goto failure;
1215 +          
1216 +          }
1217            /* select the first stuntdouble set.  */
1218            else if (strcmp (long_options[option_index].name, "sele1") == 0)
1219            {
1220 <            if (local_args_info.sele1_given)
1221 <              {
1222 <                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1223 <                goto failure;
1224 <              }
1225 <            if (args_info->sele1_given && ! override)
1226 <              continue;
1227 <            local_args_info.sele1_given = 1;
1228 <            args_info->sele1_given = 1;
1229 <            if (args_info->sele1_arg)
1057 <              free (args_info->sele1_arg); /* free previous string */
1058 <            args_info->sele1_arg = gengetopt_strdup (optarg);
1059 <            if (args_info->sele1_orig)
1060 <              free (args_info->sele1_orig); /* free previous string */
1061 <            args_info->sele1_orig = gengetopt_strdup (optarg);
1220 >          
1221 >          
1222 >            if (update_arg( (void *)&(args_info->sele1_arg),
1223 >                 &(args_info->sele1_orig), &(args_info->sele1_given),
1224 >                &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1225 >                check_ambiguity, override, 0, 0,
1226 >                "sele1", '-',
1227 >                additional_error))
1228 >              goto failure;
1229 >          
1230            }
1231            /* select the second stuntdouble set.  */
1232            else if (strcmp (long_options[option_index].name, "sele2") == 0)
1233            {
1234 <            if (local_args_info.sele2_given)
1235 <              {
1236 <                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1237 <                goto failure;
1238 <              }
1239 <            if (args_info->sele2_given && ! override)
1240 <              continue;
1241 <            local_args_info.sele2_given = 1;
1242 <            args_info->sele2_given = 1;
1243 <            if (args_info->sele2_arg)
1076 <              free (args_info->sele2_arg); /* free previous string */
1077 <            args_info->sele2_arg = gengetopt_strdup (optarg);
1078 <            if (args_info->sele2_orig)
1079 <              free (args_info->sele2_orig); /* free previous string */
1080 <            args_info->sele2_orig = gengetopt_strdup (optarg);
1234 >          
1235 >          
1236 >            if (update_arg( (void *)&(args_info->sele2_arg),
1237 >                 &(args_info->sele2_orig), &(args_info->sele2_given),
1238 >                &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1239 >                check_ambiguity, override, 0, 0,
1240 >                "sele2", '-',
1241 >                additional_error))
1242 >              goto failure;
1243 >          
1244            }
1245            /* select the third stuntdouble set.  */
1246            else if (strcmp (long_options[option_index].name, "sele3") == 0)
1247            {
1248 <            if (local_args_info.sele3_given)
1249 <              {
1250 <                fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1251 <                goto failure;
1252 <              }
1253 <            if (args_info->sele3_given && ! override)
1254 <              continue;
1255 <            local_args_info.sele3_given = 1;
1256 <            args_info->sele3_given = 1;
1257 <            if (args_info->sele3_arg)
1095 <              free (args_info->sele3_arg); /* free previous string */
1096 <            args_info->sele3_arg = gengetopt_strdup (optarg);
1097 <            if (args_info->sele3_orig)
1098 <              free (args_info->sele3_orig); /* free previous string */
1099 <            args_info->sele3_orig = gengetopt_strdup (optarg);
1248 >          
1249 >          
1250 >            if (update_arg( (void *)&(args_info->sele3_arg),
1251 >                 &(args_info->sele3_orig), &(args_info->sele3_given),
1252 >                &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1253 >                check_ambiguity, override, 0, 0,
1254 >                "sele3", '-',
1255 >                additional_error))
1256 >              goto failure;
1257 >          
1258            }
1259            /* select reference (use and only use with --gxyz).  */
1260            else if (strcmp (long_options[option_index].name, "refsele") == 0)
1261            {
1262 <            if (local_args_info.refsele_given)
1263 <              {
1264 <                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1265 <                goto failure;
1266 <              }
1267 <            if (args_info->refsele_given && ! override)
1268 <              continue;
1269 <            local_args_info.refsele_given = 1;
1270 <            args_info->refsele_given = 1;
1271 <            if (args_info->refsele_arg)
1114 <              free (args_info->refsele_arg); /* free previous string */
1115 <            args_info->refsele_arg = gengetopt_strdup (optarg);
1116 <            if (args_info->refsele_orig)
1117 <              free (args_info->refsele_orig); /* free previous string */
1118 <            args_info->refsele_orig = gengetopt_strdup (optarg);
1262 >          
1263 >          
1264 >            if (update_arg( (void *)&(args_info->refsele_arg),
1265 >                 &(args_info->refsele_orig), &(args_info->refsele_given),
1266 >                &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1267 >                check_ambiguity, override, 0, 0,
1268 >                "refsele", '-',
1269 >                additional_error))
1270 >              goto failure;
1271 >          
1272            }
1273 +          /* select stunt doubles for center-of-mass reference point.  */
1274 +          else if (strcmp (long_options[option_index].name, "comsele") == 0)
1275 +          {
1276 +          
1277 +          
1278 +            if (update_arg( (void *)&(args_info->comsele_arg),
1279 +                 &(args_info->comsele_orig), &(args_info->comsele_given),
1280 +                &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1281 +                check_ambiguity, override, 0, 0,
1282 +                "comsele", '-',
1283 +                additional_error))
1284 +              goto failure;
1285 +          
1286 +          }
1287 +          /* global index offset for a second object (used to define a vector between sites in molecule).  */
1288 +          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1289 +          {
1290 +          
1291 +          
1292 +            if (update_arg( (void *)&(args_info->seleoffset_arg),
1293 +                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1294 +                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1295 +                check_ambiguity, override, 0, 0,
1296 +                "seleoffset", '-',
1297 +                additional_error))
1298 +              goto failure;
1299 +          
1300 +          }
1301 +          /* global index offset for a third object (used to define a vector between sites in molecule).  */
1302 +          else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1303 +          {
1304 +          
1305 +          
1306 +            if (update_arg( (void *)&(args_info->seleoffset2_arg),
1307 +                 &(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1308 +                &(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1309 +                check_ambiguity, override, 0, 0,
1310 +                "seleoffset2", '-',
1311 +                additional_error))
1312 +              goto failure;
1313 +          
1314 +          }
1315            /* molecule name.  */
1316            else if (strcmp (long_options[option_index].name, "molname") == 0)
1317            {
1318 <            if (local_args_info.molname_given)
1319 <              {
1320 <                fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1321 <                goto failure;
1322 <              }
1323 <            if (args_info->molname_given && ! override)
1324 <              continue;
1325 <            local_args_info.molname_given = 1;
1326 <            args_info->molname_given = 1;
1327 <            if (args_info->molname_arg)
1133 <              free (args_info->molname_arg); /* free previous string */
1134 <            args_info->molname_arg = gengetopt_strdup (optarg);
1135 <            if (args_info->molname_orig)
1136 <              free (args_info->molname_orig); /* free previous string */
1137 <            args_info->molname_orig = gengetopt_strdup (optarg);
1318 >          
1319 >          
1320 >            if (update_arg( (void *)&(args_info->molname_arg),
1321 >                 &(args_info->molname_orig), &(args_info->molname_given),
1322 >                &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1323 >                check_ambiguity, override, 0, 0,
1324 >                "molname", '-',
1325 >                additional_error))
1326 >              goto failure;
1327 >          
1328            }
1329            /* begin internal index.  */
1330            else if (strcmp (long_options[option_index].name, "begin") == 0)
1331            {
1332 <            if (local_args_info.begin_given)
1333 <              {
1334 <                fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1335 <                goto failure;
1336 <              }
1337 <            if (args_info->begin_given && ! override)
1338 <              continue;
1339 <            local_args_info.begin_given = 1;
1150 <            args_info->begin_given = 1;
1151 <            args_info->begin_arg = strtol (optarg, &stop_char, 0);
1152 <            if (!(stop_char && *stop_char == '\0')) {
1153 <              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1332 >          
1333 >          
1334 >            if (update_arg( (void *)&(args_info->begin_arg),
1335 >                 &(args_info->begin_orig), &(args_info->begin_given),
1336 >                &(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1337 >                check_ambiguity, override, 0, 0,
1338 >                "begin", '-',
1339 >                additional_error))
1340                goto failure;
1341 <            }
1156 <            if (args_info->begin_orig)
1157 <              free (args_info->begin_orig); /* free previous string */
1158 <            args_info->begin_orig = gengetopt_strdup (optarg);
1341 >          
1342            }
1343            /* end internal index.  */
1344            else if (strcmp (long_options[option_index].name, "end") == 0)
1345            {
1346 <            if (local_args_info.end_given)
1347 <              {
1348 <                fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1349 <                goto failure;
1350 <              }
1351 <            if (args_info->end_given && ! override)
1352 <              continue;
1353 <            local_args_info.end_given = 1;
1171 <            args_info->end_given = 1;
1172 <            args_info->end_arg = strtol (optarg, &stop_char, 0);
1173 <            if (!(stop_char && *stop_char == '\0')) {
1174 <              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1346 >          
1347 >          
1348 >            if (update_arg( (void *)&(args_info->end_arg),
1349 >                 &(args_info->end_orig), &(args_info->end_given),
1350 >                &(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1351 >                check_ambiguity, override, 0, 0,
1352 >                "end", '-',
1353 >                additional_error))
1354                goto failure;
1355 <            }
1177 <            if (args_info->end_orig)
1178 <              free (args_info->end_orig); /* free previous string */
1179 <            args_info->end_orig = gengetopt_strdup (optarg);
1355 >          
1356            }
1357            /* nanoparticle radius.  */
1358            else if (strcmp (long_options[option_index].name, "radius") == 0)
1359            {
1360 <            if (local_args_info.radius_given)
1361 <              {
1362 <                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1363 <                goto failure;
1364 <              }
1365 <            if (args_info->radius_given && ! override)
1366 <              continue;
1367 <            local_args_info.radius_given = 1;
1192 <            args_info->radius_given = 1;
1193 <            args_info->radius_arg = strtod (optarg, &stop_char);
1194 <            if (!(stop_char && *stop_char == '\0')) {
1195 <              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1360 >          
1361 >          
1362 >            if (update_arg( (void *)&(args_info->radius_arg),
1363 >                 &(args_info->radius_orig), &(args_info->radius_given),
1364 >                &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1365 >                check_ambiguity, override, 0, 0,
1366 >                "radius", '-',
1367 >                additional_error))
1368                goto failure;
1369 <            }
1198 <            if (args_info->radius_orig)
1199 <              free (args_info->radius_orig); /* free previous string */
1200 <            args_info->radius_orig = gengetopt_strdup (optarg);
1369 >          
1370            }
1371            /* bond order parameter (--rcut must be specified).  */
1372            else if (strcmp (long_options[option_index].name, "bo") == 0)
1373            {
1374 <            if (local_args_info.bo_given)
1206 <              {
1207 <                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1208 <                goto failure;
1209 <              }
1210 <            if (args_info->bo_given && ! override)
1211 <              continue;
1212 <            local_args_info.bo_given = 1;
1213 <            args_info->bo_given = 1;
1374 >          
1375              if (args_info->staticProps_group_counter && override)
1376                reset_group_staticProps (args_info);
1377              args_info->staticProps_group_counter += 1;
1378 <            break;
1378 >          
1379 >            if (update_arg( 0 ,
1380 >                 0 , &(args_info->bo_given),
1381 >                &(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1382 >                check_ambiguity, override, 0, 0,
1383 >                "bo", '-',
1384 >                additional_error))
1385 >              goto failure;
1386 >          
1387            }
1388 <          /* bond order parameter as a function of radius (--rcut must be specified).  */
1389 <          else if (strcmp (long_options[option_index].name, "bor") == 0)
1388 >          /* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1389 >          else if (strcmp (long_options[option_index].name, "ior") == 0)
1390            {
1391 <            if (local_args_info.bor_given)
1223 <              {
1224 <                fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1225 <                goto failure;
1226 <              }
1227 <            if (args_info->bor_given && ! override)
1228 <              continue;
1229 <            local_args_info.bor_given = 1;
1230 <            args_info->bor_given = 1;
1391 >          
1392              if (args_info->staticProps_group_counter && override)
1393                reset_group_staticProps (args_info);
1394              args_info->staticProps_group_counter += 1;
1395 <            break;
1395 >          
1396 >            if (update_arg( 0 ,
1397 >                 0 , &(args_info->ior_given),
1398 >                &(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1399 >                check_ambiguity, override, 0, 0,
1400 >                "ior", '-',
1401 >                additional_error))
1402 >              goto failure;
1403 >          
1404            }
1405 +          /* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1406 +          else if (strcmp (long_options[option_index].name, "for") == 0)
1407 +          {
1408 +          
1409 +            if (args_info->staticProps_group_counter && override)
1410 +              reset_group_staticProps (args_info);
1411 +            args_info->staticProps_group_counter += 1;
1412 +          
1413 +            if (update_arg( 0 ,
1414 +                 0 , &(args_info->for_given),
1415 +                &(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1416 +                check_ambiguity, override, 0, 0,
1417 +                "for", '-',
1418 +                additional_error))
1419 +              goto failure;
1420 +          
1421 +          }
1422            /* N(theta) bond angle density within (--rcut must be specified).  */
1423            else if (strcmp (long_options[option_index].name, "bad") == 0)
1424            {
1425 <            if (local_args_info.bad_given)
1240 <              {
1241 <                fprintf (stderr, "%s: `--bad' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1242 <                goto failure;
1243 <              }
1244 <            if (args_info->bad_given && ! override)
1245 <              continue;
1246 <            local_args_info.bad_given = 1;
1247 <            args_info->bad_given = 1;
1425 >          
1426              if (args_info->staticProps_group_counter && override)
1427                reset_group_staticProps (args_info);
1428              args_info->staticProps_group_counter += 1;
1429 <            break;
1429 >          
1430 >            if (update_arg( 0 ,
1431 >                 0 , &(args_info->bad_given),
1432 >                &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1433 >                check_ambiguity, override, 0, 0,
1434 >                "bad", '-',
1435 >                additional_error))
1436 >              goto failure;
1437 >          
1438            }
1439 +          /* count of molecules matching selection criteria (and associated statistics).  */
1440 +          else if (strcmp (long_options[option_index].name, "count") == 0)
1441 +          {
1442 +          
1443 +            if (args_info->staticProps_group_counter && override)
1444 +              reset_group_staticProps (args_info);
1445 +            args_info->staticProps_group_counter += 1;
1446 +          
1447 +            if (update_arg( 0 ,
1448 +                 0 , &(args_info->count_given),
1449 +                &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1450 +                check_ambiguity, override, 0, 0,
1451 +                "count", '-',
1452 +                additional_error))
1453 +              goto failure;
1454 +          
1455 +          }
1456            /* g(z).  */
1457            else if (strcmp (long_options[option_index].name, "gofz") == 0)
1458            {
1459 <            if (local_args_info.gofz_given)
1257 <              {
1258 <                fprintf (stderr, "%s: `--gofz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1259 <                goto failure;
1260 <              }
1261 <            if (args_info->gofz_given && ! override)
1262 <              continue;
1263 <            local_args_info.gofz_given = 1;
1264 <            args_info->gofz_given = 1;
1459 >          
1460              if (args_info->staticProps_group_counter && override)
1461                reset_group_staticProps (args_info);
1462              args_info->staticProps_group_counter += 1;
1463 <            break;
1463 >          
1464 >            if (update_arg( 0 ,
1465 >                 0 , &(args_info->gofz_given),
1466 >                &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1467 >                check_ambiguity, override, 0, 0,
1468 >                "gofz", '-',
1469 >                additional_error))
1470 >              goto failure;
1471 >          
1472            }
1473            /* g(r, cos(theta)).  */
1474            else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1475            {
1476 <            if (local_args_info.r_theta_given)
1274 <              {
1275 <                fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1276 <                goto failure;
1277 <              }
1278 <            if (args_info->r_theta_given && ! override)
1279 <              continue;
1280 <            local_args_info.r_theta_given = 1;
1281 <            args_info->r_theta_given = 1;
1476 >          
1477              if (args_info->staticProps_group_counter && override)
1478                reset_group_staticProps (args_info);
1479              args_info->staticProps_group_counter += 1;
1480 <            break;
1480 >          
1481 >            if (update_arg( 0 ,
1482 >                 0 , &(args_info->r_theta_given),
1483 >                &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1484 >                check_ambiguity, override, 0, 0,
1485 >                "r_theta", '-',
1486 >                additional_error))
1487 >              goto failure;
1488 >          
1489            }
1490            /* g(r, cos(omega)).  */
1491            else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1492            {
1493 <            if (local_args_info.r_omega_given)
1291 <              {
1292 <                fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1293 <                goto failure;
1294 <              }
1295 <            if (args_info->r_omega_given && ! override)
1296 <              continue;
1297 <            local_args_info.r_omega_given = 1;
1298 <            args_info->r_omega_given = 1;
1493 >          
1494              if (args_info->staticProps_group_counter && override)
1495                reset_group_staticProps (args_info);
1496              args_info->staticProps_group_counter += 1;
1497 <            break;
1497 >          
1498 >            if (update_arg( 0 ,
1499 >                 0 , &(args_info->r_omega_given),
1500 >                &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1501 >                check_ambiguity, override, 0, 0,
1502 >                "r_omega", '-',
1503 >                additional_error))
1504 >              goto failure;
1505 >          
1506            }
1507 +          /* g(r, z).  */
1508 +          else if (strcmp (long_options[option_index].name, "r_z") == 0)
1509 +          {
1510 +          
1511 +            if (args_info->staticProps_group_counter && override)
1512 +              reset_group_staticProps (args_info);
1513 +            args_info->staticProps_group_counter += 1;
1514 +          
1515 +            if (update_arg( 0 ,
1516 +                 0 , &(args_info->r_z_given),
1517 +                &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1518 +                check_ambiguity, override, 0, 0,
1519 +                "r_z", '-',
1520 +                additional_error))
1521 +              goto failure;
1522 +          
1523 +          }
1524            /* g(cos(theta), cos(omega)).  */
1525            else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1526            {
1527 <            if (local_args_info.theta_omega_given)
1308 <              {
1309 <                fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1310 <                goto failure;
1311 <              }
1312 <            if (args_info->theta_omega_given && ! override)
1313 <              continue;
1314 <            local_args_info.theta_omega_given = 1;
1315 <            args_info->theta_omega_given = 1;
1527 >          
1528              if (args_info->staticProps_group_counter && override)
1529                reset_group_staticProps (args_info);
1530              args_info->staticProps_group_counter += 1;
1531 <            break;
1531 >          
1532 >            if (update_arg( 0 ,
1533 >                 0 , &(args_info->theta_omega_given),
1534 >                &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1535 >                check_ambiguity, override, 0, 0,
1536 >                "theta_omega", '-',
1537 >                additional_error))
1538 >              goto failure;
1539 >          
1540            }
1541            /* g(x, y, z).  */
1542            else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1543            {
1544 <            if (local_args_info.gxyz_given)
1325 <              {
1326 <                fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1327 <                goto failure;
1328 <              }
1329 <            if (args_info->gxyz_given && ! override)
1330 <              continue;
1331 <            local_args_info.gxyz_given = 1;
1332 <            args_info->gxyz_given = 1;
1544 >          
1545              if (args_info->staticProps_group_counter && override)
1546                reset_group_staticProps (args_info);
1547              args_info->staticProps_group_counter += 1;
1548 <            break;
1548 >          
1549 >            if (update_arg( 0 ,
1550 >                 0 , &(args_info->gxyz_given),
1551 >                &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1552 >                check_ambiguity, override, 0, 0,
1553 >                "gxyz", '-',
1554 >                additional_error))
1555 >              goto failure;
1556 >          
1557            }
1558 +          /* 2D g(r) (Slab width --dz must be specified).  */
1559 +          else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1560 +          {
1561 +          
1562 +            if (args_info->staticProps_group_counter && override)
1563 +              reset_group_staticProps (args_info);
1564 +            args_info->staticProps_group_counter += 1;
1565 +          
1566 +            if (update_arg( 0 ,
1567 +                 0 , &(args_info->twodgofr_given),
1568 +                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1569 +                check_ambiguity, override, 0, 0,
1570 +                "twodgofr", '-',
1571 +                additional_error))
1572 +              goto failure;
1573 +          
1574 +          }
1575            /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1576            else if (strcmp (long_options[option_index].name, "rp2") == 0)
1577            {
1578 <            if (local_args_info.rp2_given)
1342 <              {
1343 <                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1344 <                goto failure;
1345 <              }
1346 <            if (args_info->rp2_given && ! override)
1347 <              continue;
1348 <            local_args_info.rp2_given = 1;
1349 <            args_info->rp2_given = 1;
1578 >          
1579              if (args_info->staticProps_group_counter && override)
1580                reset_group_staticProps (args_info);
1581              args_info->staticProps_group_counter += 1;
1582 <            break;
1582 >          
1583 >            if (update_arg( 0 ,
1584 >                 0 , &(args_info->rp2_given),
1585 >                &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1586 >                check_ambiguity, override, 0, 0,
1587 >                "rp2", '-',
1588 >                additional_error))
1589 >              goto failure;
1590 >          
1591            }
1592            /* slab density.  */
1593            else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1594            {
1595 <            if (local_args_info.slab_density_given)
1359 <              {
1360 <                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1361 <                goto failure;
1362 <              }
1363 <            if (args_info->slab_density_given && ! override)
1364 <              continue;
1365 <            local_args_info.slab_density_given = 1;
1366 <            args_info->slab_density_given = 1;
1595 >          
1596              if (args_info->staticProps_group_counter && override)
1597                reset_group_staticProps (args_info);
1598              args_info->staticProps_group_counter += 1;
1599 <            break;
1599 >          
1600 >            if (update_arg( 0 ,
1601 >                 0 , &(args_info->slab_density_given),
1602 >                &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1603 >                check_ambiguity, override, 0, 0,
1604 >                "slab_density", '-',
1605 >                additional_error))
1606 >              goto failure;
1607 >          
1608            }
1609 +          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1610 +          else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1611 +          {
1612 +          
1613 +            if (args_info->staticProps_group_counter && override)
1614 +              reset_group_staticProps (args_info);
1615 +            args_info->staticProps_group_counter += 1;
1616 +          
1617 +            if (update_arg( 0 ,
1618 +                 0 , &(args_info->p_angle_given),
1619 +                &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1620 +                check_ambiguity, override, 0, 0,
1621 +                "p_angle", '-',
1622 +                additional_error))
1623 +              goto failure;
1624 +          
1625 +          }
1626            /* hxy.  */
1627            else if (strcmp (long_options[option_index].name, "hxy") == 0)
1628            {
1629 <            if (local_args_info.hxy_given)
1376 <              {
1377 <                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1378 <                goto failure;
1379 <              }
1380 <            if (args_info->hxy_given && ! override)
1381 <              continue;
1382 <            local_args_info.hxy_given = 1;
1383 <            args_info->hxy_given = 1;
1629 >          
1630              if (args_info->staticProps_group_counter && override)
1631                reset_group_staticProps (args_info);
1632              args_info->staticProps_group_counter += 1;
1633 <            break;
1633 >          
1634 >            if (update_arg( 0 ,
1635 >                 0 , &(args_info->hxy_given),
1636 >                &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1637 >                check_ambiguity, override, 0, 0,
1638 >                "hxy", '-',
1639 >                additional_error))
1640 >              goto failure;
1641 >          
1642            }
1643            /* rho of R.  */
1644            else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1645            {
1646 <            if (local_args_info.rho_r_given)
1393 <              {
1394 <                fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1395 <                goto failure;
1396 <              }
1397 <            if (args_info->rho_r_given && ! override)
1398 <              continue;
1399 <            local_args_info.rho_r_given = 1;
1400 <            args_info->rho_r_given = 1;
1646 >          
1647              if (args_info->staticProps_group_counter && override)
1648                reset_group_staticProps (args_info);
1649              args_info->staticProps_group_counter += 1;
1650 <            break;
1650 >          
1651 >            if (update_arg( 0 ,
1652 >                 0 , &(args_info->rho_r_given),
1653 >                &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1654 >                check_ambiguity, override, 0, 0,
1655 >                "rho_r", '-',
1656 >                additional_error))
1657 >              goto failure;
1658 >          
1659            }
1660 +          /* angle of R.  */
1661 +          else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1662 +          {
1663 +          
1664 +            if (args_info->staticProps_group_counter && override)
1665 +              reset_group_staticProps (args_info);
1666 +            args_info->staticProps_group_counter += 1;
1667 +          
1668 +            if (update_arg( 0 ,
1669 +                 0 , &(args_info->angle_r_given),
1670 +                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1671 +                check_ambiguity, override, 0, 0,
1672 +                "angle_r", '-',
1673 +                additional_error))
1674 +              goto failure;
1675 +          
1676 +          }
1677            /* hull volume of nanoparticle.  */
1678            else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1679            {
1680 <            if (local_args_info.hullvol_given)
1410 <              {
1411 <                fprintf (stderr, "%s: `--hullvol' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1412 <                goto failure;
1413 <              }
1414 <            if (args_info->hullvol_given && ! override)
1415 <              continue;
1416 <            local_args_info.hullvol_given = 1;
1417 <            args_info->hullvol_given = 1;
1680 >          
1681              if (args_info->staticProps_group_counter && override)
1682                reset_group_staticProps (args_info);
1683              args_info->staticProps_group_counter += 1;
1684 <            break;
1684 >          
1685 >            if (update_arg( 0 ,
1686 >                 0 , &(args_info->hullvol_given),
1687 >                &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1688 >                check_ambiguity, override, 0, 0,
1689 >                "hullvol", '-',
1690 >                additional_error))
1691 >              goto failure;
1692 >          
1693            }
1694 +          /* length of nanorod.  */
1695 +          else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1696 +          {
1697            
1698 +            if (args_info->staticProps_group_counter && override)
1699 +              reset_group_staticProps (args_info);
1700 +            args_info->staticProps_group_counter += 1;
1701 +          
1702 +            if (update_arg( 0 ,
1703 +                 0 , &(args_info->rodlength_given),
1704 +                &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1705 +                check_ambiguity, override, 0, 0,
1706 +                "rodlength", '-',
1707 +                additional_error))
1708 +              goto failure;
1709 +          
1710 +          }
1711 +          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
1712 +          else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1713 +          {
1714 +          
1715 +            if (args_info->staticProps_group_counter && override)
1716 +              reset_group_staticProps (args_info);
1717 +            args_info->staticProps_group_counter += 1;
1718 +          
1719 +            if (update_arg( 0 ,
1720 +                 0 , &(args_info->tet_param_z_given),
1721 +                &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1722 +                check_ambiguity, override, 0, 0,
1723 +                "tet_param_z", '-',
1724 +                additional_error))
1725 +              goto failure;
1726 +          
1727 +          }
1728 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1729 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1730 +          {
1731 +          
1732 +            if (args_info->staticProps_group_counter && override)
1733 +              reset_group_staticProps (args_info);
1734 +            args_info->staticProps_group_counter += 1;
1735 +          
1736 +            if (update_arg( 0 ,
1737 +                 0 , &(args_info->rnemdz_given),
1738 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1739 +                check_ambiguity, override, 0, 0,
1740 +                "rnemdz", '-',
1741 +                additional_error))
1742 +              goto failure;
1743 +          
1744 +          }
1745 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1746 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1747 +          {
1748 +          
1749 +            if (args_info->staticProps_group_counter && override)
1750 +              reset_group_staticProps (args_info);
1751 +            args_info->staticProps_group_counter += 1;
1752 +          
1753 +            if (update_arg( 0 ,
1754 +                 0 , &(args_info->rnemdr_given),
1755 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1756 +                check_ambiguity, override, 0, 0,
1757 +                "rnemdr", '-',
1758 +                additional_error))
1759 +              goto failure;
1760 +          
1761 +          }
1762 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1763 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1764 +          {
1765 +          
1766 +            if (args_info->staticProps_group_counter && override)
1767 +              reset_group_staticProps (args_info);
1768 +            args_info->staticProps_group_counter += 1;
1769 +          
1770 +            if (update_arg( 0 ,
1771 +                 0 , &(args_info->rnemdrt_given),
1772 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1773 +                check_ambiguity, override, 0, 0,
1774 +                "rnemdrt", '-',
1775 +                additional_error))
1776 +              goto failure;
1777 +          
1778 +          }
1779 +          /* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1780 +          else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1781 +          {
1782 +          
1783 +            if (args_info->staticProps_group_counter && override)
1784 +              reset_group_staticProps (args_info);
1785 +            args_info->staticProps_group_counter += 1;
1786 +          
1787 +            if (update_arg( 0 ,
1788 +                 0 , &(args_info->nitrile_given),
1789 +                &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1790 +                check_ambiguity, override, 0, 0,
1791 +                "nitrile", '-',
1792 +                additional_error))
1793 +              goto failure;
1794 +          
1795 +          }
1796 +          
1797            break;
1798          case '?':       /* Invalid option.  */
1799            /* `getopt_long' already printed an error message.  */
# Line 1434 | Line 1807 | cmdline_parser_internal (int argc, char * const *argv,
1807  
1808    if (args_info->staticProps_group_counter > 1)
1809      {
1810 <      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 : ""));
1810 >      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 : ""));
1811        error = 1;
1812      }
1813    

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1999 by gezelter, Sat May 31 21:00:46 2014 UTC

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