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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1413 by gezelter, Mon Mar 22 19:21:22 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.16
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4	<	gengetopt -F StaticPropsCmd
4	>	gengetopt -F StaticPropsCmd -u
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 21 | Line 21
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -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)",
41	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
43	+	"      --sele1=selection script  select the first stuntdouble set",
44	+	"      --sele2=selection script  select the second stuntdouble set",
45	+	"      --sele3=selection script  select the third stuntdouble set",
46	+	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
47	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
48	+	"      --molname=STRING          molecule name",
49	+	"      --begin=INT               begin internal index",
50	+	"      --end=INT                 end internal index",
51	+	"      --radius=DOUBLE           nanoparticle radius",
52	+	"\n Group: staticProps\n   an option of this group is required",
53	+	"      --bo                      bond order parameter (--rcut must be specified)",
54	+	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
55	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
56	+	"  -g, --gofr                    g(r)",
57	+	"      --gofz                    g(z)",
58	+	"      --r_theta                 g(r, cos(theta))",
59	+	"      --r_omega                 g(r, cos(omega))",
60	+	"      --theta_omega             g(cos(theta), cos(omega))",
61	+	"      --gxyz                    g(x, y, z)",
62	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
63	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
64	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
65	+	"  -d, --density                 density plot",
66	+	"      --slab_density            slab density",
67	+	"      --p_angle                 p(cos(theta))",
68	+	"      --hxy                     hxy",
69	+	"      --rho_r                   rho of R",
70	+	"      --hullvol                 hull volume of nanoparticle",
71	+	0
72	+	};
73	+
74	+	typedef enum {ARG_NO
75	+	, ARG_STRING
76	+	, ARG_INT
77	+	, ARG_DOUBLE
78	+	} cmdline_parser_arg_type;
79	+
80		static
81		void clear_given (struct gengetopt_args_info *args_info);
82		static
83		void clear_args (struct gengetopt_args_info *args_info);
84
85		static int
86	<	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);
86	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
87	>	struct cmdline_parser_params *params, const char *additional_error);
88
89		static int
90		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 43 | Line 100 | void clear_given (struct gengetopt_args_info *args_inf
100		args_info->input_given = 0 ;
101		args_info->output_given = 0 ;
102		args_info->step_given = 0 ;
103	<	args_info->nrbins_given = 0 ;
103	>	args_info->nbins_given = 0 ;
104		args_info->nbins_x_given = 0 ;
105		args_info->nbins_y_given = 0 ;
106		args_info->nanglebins_given = 0 ;
107		args_info->length_given = 0 ;
51	–	args_info->LegendreL_given = 0 ;
108		args_info->rcut_given = 0 ;
109		args_info->zoffset_given = 0 ;
110		args_info->sele1_given = 0 ;
111		args_info->sele2_given = 0 ;
112		args_info->sele3_given = 0 ;
113		args_info->refsele_given = 0 ;
114	+	args_info->comsele_given = 0 ;
115		args_info->molname_given = 0 ;
116		args_info->begin_given = 0 ;
117		args_info->end_given = 0 ;
118	+	args_info->radius_given = 0 ;
119		args_info->bo_given = 0 ;
120	+	args_info->bor_given = 0 ;
121	+	args_info->bad_given = 0 ;
122		args_info->gofr_given = 0 ;
123	+	args_info->gofz_given = 0 ;
124		args_info->r_theta_given = 0 ;
125		args_info->r_omega_given = 0 ;
126		args_info->theta_omega_given = 0 ;
#	Line 69 | Line 130 | void clear_given (struct gengetopt_args_info *args_inf
130		args_info->scd_given = 0 ;
131		args_info->density_given = 0 ;
132		args_info->slab_density_given = 0 ;
133	+	args_info->p_angle_given = 0 ;
134		args_info->hxy_given = 0 ;
135	+	args_info->rho_r_given = 0 ;
136	+	args_info->hullvol_given = 0 ;
137		args_info->staticProps_group_counter = 0 ;
138		}
139
#	Line 82 | Line 146 | void clear_args (struct gengetopt_args_info *args_info
146		args_info->output_orig = NULL;
147		args_info->step_arg = 1;
148		args_info->step_orig = NULL;
149	<	args_info->nrbins_arg = 100;
150	<	args_info->nrbins_orig = NULL;
149	>	args_info->nbins_arg = 100;
150	>	args_info->nbins_orig = NULL;
151		args_info->nbins_x_arg = 100;
152		args_info->nbins_x_orig = NULL;
153		args_info->nbins_y_arg = 100;
#	Line 91 | Line 155 | void clear_args (struct gengetopt_args_info *args_info
155		args_info->nanglebins_arg = 50;
156		args_info->nanglebins_orig = NULL;
157		args_info->length_orig = NULL;
94	–	args_info->LegendreL_orig = NULL;
158		args_info->rcut_orig = NULL;
159		args_info->zoffset_arg = 0;
160		args_info->zoffset_orig = NULL;
#	Line 103 | Line 166 | void clear_args (struct gengetopt_args_info *args_info
166		args_info->sele3_orig = NULL;
167		args_info->refsele_arg = NULL;
168		args_info->refsele_orig = NULL;
169	+	args_info->comsele_arg = NULL;
170	+	args_info->comsele_orig = NULL;
171		args_info->molname_arg = NULL;
172		args_info->molname_orig = NULL;
173		args_info->begin_orig = NULL;
174		args_info->end_orig = NULL;
175	+	args_info->radius_orig = NULL;
176
177		}
178
179	+	static
180	+	void init_args_info(struct gengetopt_args_info *args_info)
181	+	{
182	+
183	+
184	+	args_info->help_help = gengetopt_args_info_help[0] ;
185	+	args_info->version_help = gengetopt_args_info_help[1] ;
186	+	args_info->input_help = gengetopt_args_info_help[2] ;
187	+	args_info->output_help = gengetopt_args_info_help[3] ;
188	+	args_info->step_help = gengetopt_args_info_help[4] ;
189	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
190	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
191	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
192	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
193	+	args_info->length_help = gengetopt_args_info_help[9] ;
194	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
195	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
196	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
197	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
198	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
199	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
200	+	args_info->comsele_help = gengetopt_args_info_help[16] ;
201	+	args_info->molname_help = gengetopt_args_info_help[17] ;
202	+	args_info->begin_help = gengetopt_args_info_help[18] ;
203	+	args_info->end_help = gengetopt_args_info_help[19] ;
204	+	args_info->radius_help = gengetopt_args_info_help[20] ;
205	+	args_info->bo_help = gengetopt_args_info_help[22] ;
206	+	args_info->bor_help = gengetopt_args_info_help[23] ;
207	+	args_info->bad_help = gengetopt_args_info_help[24] ;
208	+	args_info->gofr_help = gengetopt_args_info_help[25] ;
209	+	args_info->gofz_help = gengetopt_args_info_help[26] ;
210	+	args_info->r_theta_help = gengetopt_args_info_help[27] ;
211	+	args_info->r_omega_help = gengetopt_args_info_help[28] ;
212	+	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
213	+	args_info->gxyz_help = gengetopt_args_info_help[30] ;
214	+	args_info->p2_help = gengetopt_args_info_help[31] ;
215	+	args_info->rp2_help = gengetopt_args_info_help[32] ;
216	+	args_info->scd_help = gengetopt_args_info_help[33] ;
217	+	args_info->density_help = gengetopt_args_info_help[34] ;
218	+	args_info->slab_density_help = gengetopt_args_info_help[35] ;
219	+	args_info->p_angle_help = gengetopt_args_info_help[36] ;
220	+	args_info->hxy_help = gengetopt_args_info_help[37] ;
221	+	args_info->rho_r_help = gengetopt_args_info_help[38] ;
222	+	args_info->hullvol_help = gengetopt_args_info_help[39] ;
223	+
224	+	}
225	+
226		void
227		cmdline_parser_print_version (void)
228		{
229		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
230		}
231
232	+	static void print_help_common(void) {
233	+	cmdline_parser_print_version ();
234	+
235	+	if (strlen(gengetopt_args_info_purpose) > 0)
236	+	printf("\n%s\n", gengetopt_args_info_purpose);
237	+
238	+	if (strlen(gengetopt_args_info_usage) > 0)
239	+	printf("\n%s\n", gengetopt_args_info_usage);
240	+
241	+	printf("\n");
242	+
243	+	if (strlen(gengetopt_args_info_description) > 0)
244	+	printf("%s\n", gengetopt_args_info_description);
245	+	}
246	+
247		void
248		cmdline_parser_print_help (void)
249		{
250	<	cmdline_parser_print_version ();
251	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
252	<	printf("%s\n","  -h, --help                    Print help and exit");
253	<	printf("%s\n","  -V, --version                 Print version and exit");
126	<	printf("%s\n","  -i, --input=filename          input dump file");
127	<	printf("%s\n","  -o, --output=filename         output file name");
128	<	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
129	<	printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
130	<	printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
131	<	printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
132	<	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
133	<	printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
134	<	printf("%s\n","  -l, --LegendreL=INT           Order of Legendre Polynomial (used for Bond \n                                  Order calculations)");
135	<	printf("%s\n","  -c, --rcut=DOUBLE             cutoff radius (rcut)");
136	<	printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
137	<	printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
138	<	printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
139	<	printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
140	<	printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
141	<	printf("%s\n","      --molname=STRING          molecule name");
142	<	printf("%s\n","      --begin=INT               begin internal index");
143	<	printf("%s\n","      --end=INT                 end internal index");
144	<	printf("%s\n","\n Group: staticProps\n   an option of this group is required");
145	<	printf("%s\n","  -b, --bo                      bond order parameter (--rcut and --LegendreL \n                                  must be specified");
146	<	printf("%s\n","  -g, --gofr                    g(r)");
147	<	printf("%s\n","      --r_theta                 g(r, cos(theta))");
148	<	printf("%s\n","      --r_omega                 g(r, cos(omega))");
149	<	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
150	<	printf("%s\n","      --gxyz                    g(x, y, z)");
151	<	printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
152	<	printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
153	<	printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
154	<	printf("%s\n","  -d, --density                 density plot");
155	<	printf("%s\n","      --slab_density            slab density");
156	<	printf("%s\n","      --hxy                     hxy");
157	<
250	>	int i = 0;
251	>	print_help_common();
252	>	while (gengetopt_args_info_help[i])
253	>	printf("%s\n", gengetopt_args_info_help[i++]);
254		}
255
256		void
#	Line 162 | Line 258 | cmdline_parser_init (struct gengetopt_args_info *args_
258		{
259		clear_given (args_info);
260		clear_args (args_info);
261	+	init_args_info (args_info);
262	+
263	+	args_info->inputs = NULL;
264	+	args_info->inputs_num = 0;
265		}
266
267	+	void
268	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
269	+	{
270	+	if (params)
271	+	{
272	+	params->override = 0;
273	+	params->initialize = 1;
274	+	params->check_required = 1;
275	+	params->check_ambiguity = 0;
276	+	params->print_errors = 1;
277	+	}
278	+	}
279	+
280	+	struct cmdline_parser_params *
281	+	cmdline_parser_params_create(void)
282	+	{
283	+	struct cmdline_parser_params *params =
284	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
285	+	cmdline_parser_params_init(params);
286	+	return params;
287	+	}
288	+
289		static void
290	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
290	>	free_string_field (char **s)
291		{
292	<
171	<	if (args_info->input_arg)
292	>	if (*s)
293		{
294	<	free (args_info->input_arg); /* free previous argument */
295	<	args_info->input_arg = 0;
294	>	free (*s);
295	>	*s = 0;
296		}
297	<	if (args_info->input_orig)
297	>	}
298	>
299	>
300	>	static void
301	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
302	>	{
303	>	unsigned int i;
304	>	free_string_field (&(args_info->input_arg));
305	>	free_string_field (&(args_info->input_orig));
306	>	free_string_field (&(args_info->output_arg));
307	>	free_string_field (&(args_info->output_orig));
308	>	free_string_field (&(args_info->step_orig));
309	>	free_string_field (&(args_info->nbins_orig));
310	>	free_string_field (&(args_info->nbins_x_orig));
311	>	free_string_field (&(args_info->nbins_y_orig));
312	>	free_string_field (&(args_info->nanglebins_orig));
313	>	free_string_field (&(args_info->length_orig));
314	>	free_string_field (&(args_info->rcut_orig));
315	>	free_string_field (&(args_info->zoffset_orig));
316	>	free_string_field (&(args_info->sele1_arg));
317	>	free_string_field (&(args_info->sele1_orig));
318	>	free_string_field (&(args_info->sele2_arg));
319	>	free_string_field (&(args_info->sele2_orig));
320	>	free_string_field (&(args_info->sele3_arg));
321	>	free_string_field (&(args_info->sele3_orig));
322	>	free_string_field (&(args_info->refsele_arg));
323	>	free_string_field (&(args_info->refsele_orig));
324	>	free_string_field (&(args_info->comsele_arg));
325	>	free_string_field (&(args_info->comsele_orig));
326	>	free_string_field (&(args_info->molname_arg));
327	>	free_string_field (&(args_info->molname_orig));
328	>	free_string_field (&(args_info->begin_orig));
329	>	free_string_field (&(args_info->end_orig));
330	>	free_string_field (&(args_info->radius_orig));
331	>
332	>
333	>	for (i = 0; i < args_info->inputs_num; ++i)
334	>	free (args_info->inputs [i]);
335	>
336	>	if (args_info->inputs_num)
337	>	free (args_info->inputs);
338	>
339	>	clear_given (args_info);
340	>	}
341	>
342	>
343	>	static void
344	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
345	>	{
346	>	if (arg) {
347	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
348	>	} else {
349	>	fprintf(outfile, "%s\n", opt);
350	>	}
351	>	}
352	>
353	>
354	>	int
355	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
356	>	{
357	>	int i = 0;
358	>
359	>	if (!outfile)
360		{
361	<	free (args_info->input_orig); /* free previous argument */
362	<	args_info->input_orig = 0;
361	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
362	>	return EXIT_FAILURE;
363		}
364	<	if (args_info->output_arg)
365	<	{
366	<	free (args_info->output_arg); /* free previous argument */
367	<	args_info->output_arg = 0;
368	<	}
369	<	if (args_info->output_orig)
370	<	{
371	<	free (args_info->output_orig); /* free previous argument */
372	<	args_info->output_orig = 0;
373	<	}
374	<	if (args_info->step_orig)
375	<	{
376	<	free (args_info->step_orig); /* free previous argument */
377	<	args_info->step_orig = 0;
378	<	}
379	<	if (args_info->nrbins_orig)
380	<	{
381	<	free (args_info->nrbins_orig); /* free previous argument */
382	<	args_info->nrbins_orig = 0;
383	<	}
384	<	if (args_info->nbins_x_orig)
385	<	{
386	<	free (args_info->nbins_x_orig); /* free previous argument */
387	<	args_info->nbins_x_orig = 0;
388	<	}
389	<	if (args_info->nbins_y_orig)
390	<	{
391	<	free (args_info->nbins_y_orig); /* free previous argument */
392	<	args_info->nbins_y_orig = 0;
393	<	}
394	<	if (args_info->nanglebins_orig)
395	<	{
396	<	free (args_info->nanglebins_orig); /* free previous argument */
397	<	args_info->nanglebins_orig = 0;
398	<	}
399	<	if (args_info->length_orig)
400	<	{
401	<	free (args_info->length_orig); /* free previous argument */
402	<	args_info->length_orig = 0;
403	<	}
404	<	if (args_info->LegendreL_orig)
405	<	{
406	<	free (args_info->LegendreL_orig); /* free previous argument */
407	<	args_info->LegendreL_orig = 0;
408	<	}
409	<	if (args_info->rcut_orig)
410	<	{
411	<	free (args_info->rcut_orig); /* free previous argument */
412	<	args_info->rcut_orig = 0;
413	<	}
414	<	if (args_info->zoffset_orig)
415	<	{
416	<	free (args_info->zoffset_orig); /* free previous argument */
417	<	args_info->zoffset_orig = 0;
418	<	}
419	<	if (args_info->sele1_arg)
420	<	{
421	<	free (args_info->sele1_arg); /* free previous argument */
422	<	args_info->sele1_arg = 0;
423	<	}
424	<	if (args_info->sele1_orig)
425	<	{
426	<	free (args_info->sele1_orig); /* free previous argument */
427	<	args_info->sele1_orig = 0;
428	<	}
429	<	if (args_info->sele2_arg)
430	<	{
431	<	free (args_info->sele2_arg); /* free previous argument */
432	<	args_info->sele2_arg = 0;
433	<	}
434	<	if (args_info->sele2_orig)
435	<	{
436	<	free (args_info->sele2_orig); /* free previous argument */
437	<	args_info->sele2_orig = 0;
438	<	}
439	<	if (args_info->sele3_arg)
440	<	{
441	<	free (args_info->sele3_arg); /* free previous argument */
442	<	args_info->sele3_arg = 0;
260	<	}
261	<	if (args_info->sele3_orig)
262	<	{
263	<	free (args_info->sele3_orig); /* free previous argument */
264	<	args_info->sele3_orig = 0;
265	<	}
266	<	if (args_info->refsele_arg)
267	<	{
268	<	free (args_info->refsele_arg); /* free previous argument */
269	<	args_info->refsele_arg = 0;
270	<	}
271	<	if (args_info->refsele_orig)
272	<	{
273	<	free (args_info->refsele_orig); /* free previous argument */
274	<	args_info->refsele_orig = 0;
275	<	}
276	<	if (args_info->molname_arg)
277	<	{
278	<	free (args_info->molname_arg); /* free previous argument */
279	<	args_info->molname_arg = 0;
280	<	}
281	<	if (args_info->molname_orig)
282	<	{
283	<	free (args_info->molname_orig); /* free previous argument */
284	<	args_info->molname_orig = 0;
285	<	}
286	<	if (args_info->begin_orig)
287	<	{
288	<	free (args_info->begin_orig); /* free previous argument */
289	<	args_info->begin_orig = 0;
290	<	}
291	<	if (args_info->end_orig)
292	<	{
293	<	free (args_info->end_orig); /* free previous argument */
294	<	args_info->end_orig = 0;
295	<	}
364	>
365	>	if (args_info->help_given)
366	>	write_into_file(outfile, "help", 0, 0 );
367	>	if (args_info->version_given)
368	>	write_into_file(outfile, "version", 0, 0 );
369	>	if (args_info->input_given)
370	>	write_into_file(outfile, "input", args_info->input_orig, 0);
371	>	if (args_info->output_given)
372	>	write_into_file(outfile, "output", args_info->output_orig, 0);
373	>	if (args_info->step_given)
374	>	write_into_file(outfile, "step", args_info->step_orig, 0);
375	>	if (args_info->nbins_given)
376	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
377	>	if (args_info->nbins_x_given)
378	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
379	>	if (args_info->nbins_y_given)
380	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
381	>	if (args_info->nanglebins_given)
382	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
383	>	if (args_info->length_given)
384	>	write_into_file(outfile, "length", args_info->length_orig, 0);
385	>	if (args_info->rcut_given)
386	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
387	>	if (args_info->zoffset_given)
388	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
389	>	if (args_info->sele1_given)
390	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
391	>	if (args_info->sele2_given)
392	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
393	>	if (args_info->sele3_given)
394	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
395	>	if (args_info->refsele_given)
396	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
397	>	if (args_info->comsele_given)
398	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
399	>	if (args_info->molname_given)
400	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
401	>	if (args_info->begin_given)
402	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
403	>	if (args_info->end_given)
404	>	write_into_file(outfile, "end", args_info->end_orig, 0);
405	>	if (args_info->radius_given)
406	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
407	>	if (args_info->bo_given)
408	>	write_into_file(outfile, "bo", 0, 0 );
409	>	if (args_info->bor_given)
410	>	write_into_file(outfile, "bor", 0, 0 );
411	>	if (args_info->bad_given)
412	>	write_into_file(outfile, "bad", 0, 0 );
413	>	if (args_info->gofr_given)
414	>	write_into_file(outfile, "gofr", 0, 0 );
415	>	if (args_info->gofz_given)
416	>	write_into_file(outfile, "gofz", 0, 0 );
417	>	if (args_info->r_theta_given)
418	>	write_into_file(outfile, "r_theta", 0, 0 );
419	>	if (args_info->r_omega_given)
420	>	write_into_file(outfile, "r_omega", 0, 0 );
421	>	if (args_info->theta_omega_given)
422	>	write_into_file(outfile, "theta_omega", 0, 0 );
423	>	if (args_info->gxyz_given)
424	>	write_into_file(outfile, "gxyz", 0, 0 );
425	>	if (args_info->p2_given)
426	>	write_into_file(outfile, "p2", 0, 0 );
427	>	if (args_info->rp2_given)
428	>	write_into_file(outfile, "rp2", 0, 0 );
429	>	if (args_info->scd_given)
430	>	write_into_file(outfile, "scd", 0, 0 );
431	>	if (args_info->density_given)
432	>	write_into_file(outfile, "density", 0, 0 );
433	>	if (args_info->slab_density_given)
434	>	write_into_file(outfile, "slab_density", 0, 0 );
435	>	if (args_info->p_angle_given)
436	>	write_into_file(outfile, "p_angle", 0, 0 );
437	>	if (args_info->hxy_given)
438	>	write_into_file(outfile, "hxy", 0, 0 );
439	>	if (args_info->rho_r_given)
440	>	write_into_file(outfile, "rho_r", 0, 0 );
441	>	if (args_info->hullvol_given)
442	>	write_into_file(outfile, "hullvol", 0, 0 );
443
444	<	clear_given (args_info);
444	>
445	>	i = EXIT_SUCCESS;
446	>	return i;
447		}
448
449		int
#	Line 311 | Line 460 | cmdline_parser_file_save(const char *filename, struct
460		return EXIT_FAILURE;
461		}
462
463	<	if (args_info->help_given) {
315	<	fprintf(outfile, "%s\n", "help");
316	<	}
317	<	if (args_info->version_given) {
318	<	fprintf(outfile, "%s\n", "version");
319	<	}
320	<	if (args_info->input_given) {
321	<	if (args_info->input_orig) {
322	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
323	<	} else {
324	<	fprintf(outfile, "%s\n", "input");
325	<	}
326	<	}
327	<	if (args_info->output_given) {
328	<	if (args_info->output_orig) {
329	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
330	<	} else {
331	<	fprintf(outfile, "%s\n", "output");
332	<	}
333	<	}
334	<	if (args_info->step_given) {
335	<	if (args_info->step_orig) {
336	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
337	<	} else {
338	<	fprintf(outfile, "%s\n", "step");
339	<	}
340	<	}
341	<	if (args_info->nrbins_given) {
342	<	if (args_info->nrbins_orig) {
343	<	fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
344	<	} else {
345	<	fprintf(outfile, "%s\n", "nrbins");
346	<	}
347	<	}
348	<	if (args_info->nbins_x_given) {
349	<	if (args_info->nbins_x_orig) {
350	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
351	<	} else {
352	<	fprintf(outfile, "%s\n", "nbins_x");
353	<	}
354	<	}
355	<	if (args_info->nbins_y_given) {
356	<	if (args_info->nbins_y_orig) {
357	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
358	<	} else {
359	<	fprintf(outfile, "%s\n", "nbins_y");
360	<	}
361	<	}
362	<	if (args_info->nanglebins_given) {
363	<	if (args_info->nanglebins_orig) {
364	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
365	<	} else {
366	<	fprintf(outfile, "%s\n", "nanglebins");
367	<	}
368	<	}
369	<	if (args_info->length_given) {
370	<	if (args_info->length_orig) {
371	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
372	<	} else {
373	<	fprintf(outfile, "%s\n", "length");
374	<	}
375	<	}
376	<	if (args_info->LegendreL_given) {
377	<	if (args_info->LegendreL_orig) {
378	<	fprintf(outfile, "%s=\"%s\"\n", "LegendreL", args_info->LegendreL_orig);
379	<	} else {
380	<	fprintf(outfile, "%s\n", "LegendreL");
381	<	}
382	<	}
383	<	if (args_info->rcut_given) {
384	<	if (args_info->rcut_orig) {
385	<	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
386	<	} else {
387	<	fprintf(outfile, "%s\n", "rcut");
388	<	}
389	<	}
390	<	if (args_info->zoffset_given) {
391	<	if (args_info->zoffset_orig) {
392	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
393	<	} else {
394	<	fprintf(outfile, "%s\n", "zoffset");
395	<	}
396	<	}
397	<	if (args_info->sele1_given) {
398	<	if (args_info->sele1_orig) {
399	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
400	<	} else {
401	<	fprintf(outfile, "%s\n", "sele1");
402	<	}
403	<	}
404	<	if (args_info->sele2_given) {
405	<	if (args_info->sele2_orig) {
406	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
407	<	} else {
408	<	fprintf(outfile, "%s\n", "sele2");
409	<	}
410	<	}
411	<	if (args_info->sele3_given) {
412	<	if (args_info->sele3_orig) {
413	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
414	<	} else {
415	<	fprintf(outfile, "%s\n", "sele3");
416	<	}
417	<	}
418	<	if (args_info->refsele_given) {
419	<	if (args_info->refsele_orig) {
420	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
421	<	} else {
422	<	fprintf(outfile, "%s\n", "refsele");
423	<	}
424	<	}
425	<	if (args_info->molname_given) {
426	<	if (args_info->molname_orig) {
427	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
428	<	} else {
429	<	fprintf(outfile, "%s\n", "molname");
430	<	}
431	<	}
432	<	if (args_info->begin_given) {
433	<	if (args_info->begin_orig) {
434	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
435	<	} else {
436	<	fprintf(outfile, "%s\n", "begin");
437	<	}
438	<	}
439	<	if (args_info->end_given) {
440	<	if (args_info->end_orig) {
441	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
442	<	} else {
443	<	fprintf(outfile, "%s\n", "end");
444	<	}
445	<	}
446	<	if (args_info->bo_given) {
447	<	fprintf(outfile, "%s\n", "bo");
448	<	}
449	<	if (args_info->gofr_given) {
450	<	fprintf(outfile, "%s\n", "gofr");
451	<	}
452	<	if (args_info->r_theta_given) {
453	<	fprintf(outfile, "%s\n", "r_theta");
454	<	}
455	<	if (args_info->r_omega_given) {
456	<	fprintf(outfile, "%s\n", "r_omega");
457	<	}
458	<	if (args_info->theta_omega_given) {
459	<	fprintf(outfile, "%s\n", "theta_omega");
460	<	}
461	<	if (args_info->gxyz_given) {
462	<	fprintf(outfile, "%s\n", "gxyz");
463	<	}
464	<	if (args_info->p2_given) {
465	<	fprintf(outfile, "%s\n", "p2");
466	<	}
467	<	if (args_info->rp2_given) {
468	<	fprintf(outfile, "%s\n", "rp2");
469	<	}
470	<	if (args_info->scd_given) {
471	<	fprintf(outfile, "%s\n", "scd");
472	<	}
473	<	if (args_info->density_given) {
474	<	fprintf(outfile, "%s\n", "density");
475	<	}
476	<	if (args_info->slab_density_given) {
477	<	fprintf(outfile, "%s\n", "slab_density");
478	<	}
479	<	if (args_info->hxy_given) {
480	<	fprintf(outfile, "%s\n", "hxy");
481	<	}
482	<
463	>	i = cmdline_parser_dump(outfile, args_info);
464		fclose (outfile);
465
485	–	i = EXIT_SUCCESS;
466		return i;
467		}
468
#	Line 492 | Line 472 | cmdline_parser_free (struct gengetopt_args_info *args_
472		cmdline_parser_release (args_info);
473		}
474
475	<
496	<	/* gengetopt_strdup() */
497	<	/* strdup.c replacement of strdup, which is not standard */
475	>	/** @brief replacement of strdup, which is not standard */
476		char *
477		gengetopt_strdup (const char *s)
478		{
#	Line 510 | Line 488 | static void
488		}
489
490		static void
513	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
514	–
515	–	static void
491		reset_group_staticProps(struct gengetopt_args_info *args_info)
492		{
493		if (! args_info->staticProps_group_counter)
494		return;
495
496		args_info->bo_given = 0 ;
497	+	args_info->bor_given = 0 ;
498	+	args_info->bad_given = 0 ;
499		args_info->gofr_given = 0 ;
500	+	args_info->gofz_given = 0 ;
501		args_info->r_theta_given = 0 ;
502		args_info->r_omega_given = 0 ;
503		args_info->theta_omega_given = 0 ;
#	Line 529 | Line 507 | reset_group_staticProps(struct gengetopt_args_info *ar
507		args_info->scd_given = 0 ;
508		args_info->density_given = 0 ;
509		args_info->slab_density_given = 0 ;
510	+	args_info->p_angle_given = 0 ;
511		args_info->hxy_given = 0 ;
512	+	args_info->rho_r_given = 0 ;
513	+	args_info->hullvol_given = 0 ;
514
515		args_info->staticProps_group_counter = 0;
516		}
#	Line 541 | Line 522 | int
522		}
523
524		int
525	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
526	+	struct cmdline_parser_params *params)
527	+	{
528	+	int result;
529	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
530	+
531	+	if (result == EXIT_FAILURE)
532	+	{
533	+	cmdline_parser_free (args_info);
534	+	exit (EXIT_FAILURE);
535	+	}
536	+
537	+	return result;
538	+	}
539	+
540	+	int
541		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
542		{
543		int result;
544	+	struct cmdline_parser_params params;
545	+
546	+	params.override = override;
547	+	params.initialize = initialize;
548	+	params.check_required = check_required;
549	+	params.check_ambiguity = 0;
550	+	params.print_errors = 1;
551
552	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
552	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
553
554		if (result == EXIT_FAILURE)
555		{
#	Line 578 | Line 582 | cmdline_parser_required2 (struct gengetopt_args_info *
582		{
583		int error = 0;
584
585	+	/* checks for required options */
586		if (! args_info->input_given)
587		{
588		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
589		error = 1;
590		}
591	+
592		if (args_info->staticProps_group_counter == 0)
593		{
594		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 : ""));
#	Line 590 | Line 596 | cmdline_parser_required2 (struct gengetopt_args_info *
596		}
597
598
599	+	/* checks for dependences among options */
600	+
601		return error;
602		}
603
604	+
605	+	static char *package_name = 0;
606	+
607	+	/**
608	+	* @brief updates an option
609	+	* @param field the generic pointer to the field to update
610	+	* @param orig_field the pointer to the orig field
611	+	* @param field_given the pointer to the number of occurrence of this option
612	+	* @param prev_given the pointer to the number of occurrence already seen
613	+	* @param value the argument for this option (if null no arg was specified)
614	+	* @param possible_values the possible values for this option (if specified)
615	+	* @param default_value the default value (in case the option only accepts fixed values)
616	+	* @param arg_type the type of this option
617	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
618	+	* @param override @see cmdline_parser_params.override
619	+	* @param no_free whether to free a possible previous value
620	+	* @param multiple_option whether this is a multiple option
621	+	* @param long_opt the corresponding long option
622	+	* @param short_opt the corresponding short option (or '-' if none)
623	+	* @param additional_error possible further error specification
624	+	*/
625	+	static
626	+	int update_arg(void *field, char **orig_field,
627	+	unsigned int *field_given, unsigned int *prev_given,
628	+	char *value, char *possible_values[], const char *default_value,
629	+	cmdline_parser_arg_type arg_type,
630	+	int check_ambiguity, int override,
631	+	int no_free, int multiple_option,
632	+	const char *long_opt, char short_opt,
633	+	const char *additional_error)
634	+	{
635	+	char *stop_char = 0;
636	+	const char *val = value;
637	+	int found;
638	+	char **string_field;
639	+
640	+	stop_char = 0;
641	+	found = 0;
642	+
643	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
644	+	{
645	+	if (short_opt != '-')
646	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
647	+	package_name, long_opt, short_opt,
648	+	(additional_error ? additional_error : ""));
649	+	else
650	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
651	+	package_name, long_opt,
652	+	(additional_error ? additional_error : ""));
653	+	return 1; /* failure */
654	+	}
655	+
656	+
657	+	if (field_given && *field_given && ! override)
658	+	return 0;
659	+	if (prev_given)
660	+	(*prev_given)++;
661	+	if (field_given)
662	+	(*field_given)++;
663	+	if (possible_values)
664	+	val = possible_values[found];
665	+
666	+	switch(arg_type) {
667	+	case ARG_INT:
668	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
669	+	break;
670	+	case ARG_DOUBLE:
671	+	if (val) *((double *)field) = strtod (val, &stop_char);
672	+	break;
673	+	case ARG_STRING:
674	+	if (val) {
675	+	string_field = (char **)field;
676	+	if (!no_free && *string_field)
677	+	free (*string_field); /* free previous string */
678	+	*string_field = gengetopt_strdup (val);
679	+	}
680	+	break;
681	+	default:
682	+	break;
683	+	};
684	+
685	+	/* check numeric conversion */
686	+	switch(arg_type) {
687	+	case ARG_INT:
688	+	case ARG_DOUBLE:
689	+	if (val && !(stop_char && *stop_char == '\0')) {
690	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
691	+	return 1; /* failure */
692	+	}
693	+	break;
694	+	default:
695	+	;
696	+	};
697	+
698	+	/* store the original value */
699	+	switch(arg_type) {
700	+	case ARG_NO:
701	+	break;
702	+	default:
703	+	if (value && orig_field) {
704	+	if (no_free) {
705	+	*orig_field = value;
706	+	} else {
707	+	if (*orig_field)
708	+	free (*orig_field); /* free previous string */
709	+	*orig_field = gengetopt_strdup (value);
710	+	}
711	+	}
712	+	};
713	+
714	+	return 0; /* OK */
715	+	}
716	+
717	+
718		int
719	<	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)
719	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
720	>	struct cmdline_parser_params *params, const char *additional_error)
721		{
722		int c;        /* Character of the parsed option.  */
723
724		int error = 0;
725		struct gengetopt_args_info local_args_info;
726	+
727	+	int override;
728	+	int initialize;
729	+	int check_required;
730	+	int check_ambiguity;
731	+
732	+	package_name = argv[0];
733	+
734	+	override = params->override;
735	+	initialize = params->initialize;
736	+	check_required = params->check_required;
737	+	check_ambiguity = params->check_ambiguity;
738
739		if (initialize)
740		cmdline_parser_init (args_info);
#	Line 608 | Line 743 | cmdline_parser_internal (int argc, char * const *argv,
743
744		optarg = 0;
745		optind = 0;
746	<	opterr = 1;
746	>	opterr = params->print_errors;
747		optopt = '?';
748
749		while (1)
750		{
751		int option_index = 0;
617	–	char *stop_char;
752
753		static struct option long_options[] = {
754		{ "help",       0, NULL, 'h' },
#	Line 622 | Line 756 | cmdline_parser_internal (int argc, char * const *argv,
756		{ "input",      1, NULL, 'i' },
757		{ "output",     1, NULL, 'o' },
758		{ "step",       1, NULL, 'n' },
759	<	{ "nrbins",     1, NULL, 'r' },
759	>	{ "nbins",      1, NULL, 'b' },
760		{ "nbins_x",    1, NULL, 'x' },
761		{ "nbins_y",    1, NULL, 'y' },
762		{ "nanglebins", 1, NULL, 'a' },
763		{ "length",     1, NULL, 0 },
630	–	{ "LegendreL",  1, NULL, 'l' },
764		{ "rcut",       1, NULL, 'c' },
765		{ "zoffset",    1, NULL, 'z' },
766		{ "sele1",      1, NULL, 0 },
767		{ "sele2",      1, NULL, 0 },
768		{ "sele3",      1, NULL, 0 },
769		{ "refsele",    1, NULL, 0 },
770	+	{ "comsele",    1, NULL, 0 },
771		{ "molname",    1, NULL, 0 },
772		{ "begin",      1, NULL, 0 },
773		{ "end",        1, NULL, 0 },
774	<	{ "bo", 0, NULL, 'b' },
774	>	{ "radius",     1, NULL, 0 },
775	>	{ "bo", 0, NULL, 0 },
776	>	{ "bor",        0, NULL, 0 },
777	>	{ "bad",        0, NULL, 0 },
778		{ "gofr",       0, NULL, 'g' },
779	+	{ "gofz",       0, NULL, 0 },
780		{ "r_theta",    0, NULL, 0 },
781		{ "r_omega",    0, NULL, 0 },
782		{ "theta_omega",        0, NULL, 0 },
#	Line 648 | Line 786 | cmdline_parser_internal (int argc, char * const *argv,
786		{ "scd",        0, NULL, 's' },
787		{ "density",    0, NULL, 'd' },
788		{ "slab_density",       0, NULL, 0 },
789	+	{ "p_angle",    0, NULL, 0 },
790		{ "hxy",        0, NULL, 0 },
791	+	{ "rho_r",      0, NULL, 0 },
792	+	{ "hullvol",    0, NULL, 0 },
793		{ NULL, 0, NULL, 0 }
794		};
795
796	<	stop_char = 0;
656	<	c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:c:z:bgpsd", long_options, &option_index);
796	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
797
798		if (c == -1) break;       /* Exit from `while (1)' loop.  */
799
#	Line 670 | Line 810 | cmdline_parser_internal (int argc, char * const *argv,
810		exit (EXIT_SUCCESS);
811
812		case 'i':       /* input dump file.  */
813	<	if (local_args_info.input_given)
814	<	{
815	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
816	<	goto failure;
817	<	}
818	<	if (args_info->input_given && ! override)
819	<	continue;
820	<	local_args_info.input_given = 1;
821	<	args_info->input_given = 1;
822	<	if (args_info->input_arg)
683	<	free (args_info->input_arg); /* free previous string */
684	<	args_info->input_arg = gengetopt_strdup (optarg);
685	<	if (args_info->input_orig)
686	<	free (args_info->input_orig); /* free previous string */
687	<	args_info->input_orig = gengetopt_strdup (optarg);
813	>
814	>
815	>	if (update_arg( (void *)&(args_info->input_arg),
816	>	&(args_info->input_orig), &(args_info->input_given),
817	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
818	>	check_ambiguity, override, 0, 0,
819	>	"input", 'i',
820	>	additional_error))
821	>	goto failure;
822	>
823		break;
689	–
824		case 'o':       /* output file name.  */
825	<	if (local_args_info.output_given)
826	<	{
827	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
828	<	goto failure;
829	<	}
830	<	if (args_info->output_given && ! override)
831	<	continue;
832	<	local_args_info.output_given = 1;
833	<	args_info->output_given = 1;
834	<	if (args_info->output_arg)
701	<	free (args_info->output_arg); /* free previous string */
702	<	args_info->output_arg = gengetopt_strdup (optarg);
703	<	if (args_info->output_orig)
704	<	free (args_info->output_orig); /* free previous string */
705	<	args_info->output_orig = gengetopt_strdup (optarg);
825	>
826	>
827	>	if (update_arg( (void *)&(args_info->output_arg),
828	>	&(args_info->output_orig), &(args_info->output_given),
829	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
830	>	check_ambiguity, override, 0, 0,
831	>	"output", 'o',
832	>	additional_error))
833	>	goto failure;
834	>
835		break;
707	–
836		case 'n':       /* process every n frame.  */
837	<	if (local_args_info.step_given)
838	<	{
839	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
840	<	goto failure;
841	<	}
842	<	if (args_info->step_given && ! override)
843	<	continue;
844	<	local_args_info.step_given = 1;
717	<	args_info->step_given = 1;
718	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
719	<	if (!(stop_char && *stop_char == '\0')) {
720	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
837	>
838	>
839	>	if (update_arg( (void *)&(args_info->step_arg),
840	>	&(args_info->step_orig), &(args_info->step_given),
841	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
842	>	check_ambiguity, override, 0, 0,
843	>	"step", 'n',
844	>	additional_error))
845		goto failure;
846	<	}
723	<	if (args_info->step_orig)
724	<	free (args_info->step_orig); /* free previous string */
725	<	args_info->step_orig = gengetopt_strdup (optarg);
846	>
847		break;
848	<
849	<	case 'r':       /* number of bins for distance.  */
850	<	if (local_args_info.nrbins_given)
851	<	{
852	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
853	<	goto failure;
854	<	}
855	<	if (args_info->nrbins_given && ! override)
856	<	continue;
736	<	local_args_info.nrbins_given = 1;
737	<	args_info->nrbins_given = 1;
738	<	args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
739	<	if (!(stop_char && *stop_char == '\0')) {
740	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
848	>	case 'b':       /* number of bins (general purpose).  */
849	>
850	>
851	>	if (update_arg( (void *)&(args_info->nbins_arg),
852	>	&(args_info->nbins_orig), &(args_info->nbins_given),
853	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
854	>	check_ambiguity, override, 0, 0,
855	>	"nbins", 'b',
856	>	additional_error))
857		goto failure;
858	<	}
743	<	if (args_info->nrbins_orig)
744	<	free (args_info->nrbins_orig); /* free previous string */
745	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
858	>
859		break;
747	–
860		case 'x':       /* number of bins in x axis.  */
861	<	if (local_args_info.nbins_x_given)
862	<	{
863	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
864	<	goto failure;
865	<	}
866	<	if (args_info->nbins_x_given && ! override)
867	<	continue;
868	<	local_args_info.nbins_x_given = 1;
757	<	args_info->nbins_x_given = 1;
758	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
759	<	if (!(stop_char && *stop_char == '\0')) {
760	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
861	>
862	>
863	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
864	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
865	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
866	>	check_ambiguity, override, 0, 0,
867	>	"nbins_x", 'x',
868	>	additional_error))
869		goto failure;
870	<	}
763	<	if (args_info->nbins_x_orig)
764	<	free (args_info->nbins_x_orig); /* free previous string */
765	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
870	>
871		break;
767	–
872		case 'y':       /* number of bins in y axis.  */
873	<	if (local_args_info.nbins_y_given)
874	<	{
875	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
876	<	goto failure;
877	<	}
878	<	if (args_info->nbins_y_given && ! override)
879	<	continue;
880	<	local_args_info.nbins_y_given = 1;
777	<	args_info->nbins_y_given = 1;
778	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
779	<	if (!(stop_char && *stop_char == '\0')) {
780	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
873	>
874	>
875	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
876	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
877	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
878	>	check_ambiguity, override, 0, 0,
879	>	"nbins_y", 'y',
880	>	additional_error))
881		goto failure;
882	<	}
783	<	if (args_info->nbins_y_orig)
784	<	free (args_info->nbins_y_orig); /* free previous string */
785	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
882	>
883		break;
787	–
884		case 'a':       /* number of bins for cos(angle).  */
885	<	if (local_args_info.nanglebins_given)
886	<	{
887	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
888	<	goto failure;
889	<	}
890	<	if (args_info->nanglebins_given && ! override)
891	<	continue;
892	<	local_args_info.nanglebins_given = 1;
797	<	args_info->nanglebins_given = 1;
798	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
799	<	if (!(stop_char && *stop_char == '\0')) {
800	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
885	>
886	>
887	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
888	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
889	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
890	>	check_ambiguity, override, 0, 0,
891	>	"nanglebins", 'a',
892	>	additional_error))
893		goto failure;
894	<	}
803	<	if (args_info->nanglebins_orig)
804	<	free (args_info->nanglebins_orig); /* free previous string */
805	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
894	>
895		break;
807	–
808	–	case 'l':       /* Order of Legendre Polynomial (used for Bond Order calculations).  */
809	–	if (local_args_info.LegendreL_given)
810	–	{
811	–	fprintf (stderr, "%s: `--LegendreL' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
812	–	goto failure;
813	–	}
814	–	if (args_info->LegendreL_given && ! override)
815	–	continue;
816	–	local_args_info.LegendreL_given = 1;
817	–	args_info->LegendreL_given = 1;
818	–	args_info->LegendreL_arg = strtol (optarg, &stop_char, 0);
819	–	if (!(stop_char && *stop_char == '\0')) {
820	–	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
821	–	goto failure;
822	–	}
823	–	if (args_info->LegendreL_orig)
824	–	free (args_info->LegendreL_orig); /* free previous string */
825	–	args_info->LegendreL_orig = gengetopt_strdup (optarg);
826	–	break;
827	–
896		case 'c':       /* cutoff radius (rcut).  */
897	<	if (local_args_info.rcut_given)
898	<	{
899	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
900	<	goto failure;
901	<	}
902	<	if (args_info->rcut_given && ! override)
903	<	continue;
904	<	local_args_info.rcut_given = 1;
837	<	args_info->rcut_given = 1;
838	<	args_info->rcut_arg = strtod (optarg, &stop_char);
839	<	if (!(stop_char && *stop_char == '\0')) {
840	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
897	>
898	>
899	>	if (update_arg( (void *)&(args_info->rcut_arg),
900	>	&(args_info->rcut_orig), &(args_info->rcut_given),
901	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
902	>	check_ambiguity, override, 0, 0,
903	>	"rcut", 'c',
904	>	additional_error))
905		goto failure;
906	<	}
843	<	if (args_info->rcut_orig)
844	<	free (args_info->rcut_orig); /* free previous string */
845	<	args_info->rcut_orig = gengetopt_strdup (optarg);
906	>
907		break;
847	–
908		case 'z':       /* Where to set the zero for the slab_density calculation.  */
909	<	if (local_args_info.zoffset_given)
910	<	{
911	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
912	<	goto failure;
913	<	}
914	<	if (args_info->zoffset_given && ! override)
915	<	continue;
916	<	local_args_info.zoffset_given = 1;
917	<	args_info->zoffset_given = 1;
918	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
859	<	if (!(stop_char && *stop_char == '\0')) {
860	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
861	<	goto failure;
862	<	}
863	<	if (args_info->zoffset_orig)
864	<	free (args_info->zoffset_orig); /* free previous string */
865	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
909	>
910	>
911	>	if (update_arg( (void *)&(args_info->zoffset_arg),
912	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
913	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
914	>	check_ambiguity, override, 0, 0,
915	>	"zoffset", 'z',
916	>	additional_error))
917	>	goto failure;
918	>
919		break;
867	–
868	–	case 'b':       /* bond order parameter (--rcut and --LegendreL must be specified.  */
869	–	if (local_args_info.bo_given)
870	–	{
871	–	fprintf (stderr, "%s: `--bo' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
872	–	goto failure;
873	–	}
874	–	if (args_info->bo_given && ! override)
875	–	continue;
876	–	local_args_info.bo_given = 1;
877	–	args_info->bo_given = 1;
878	–	if (args_info->staticProps_group_counter && override)
879	–	reset_group_staticProps (args_info);
880	–	args_info->staticProps_group_counter += 1;
881	–	break;
882	–
920		case 'g':       /* g(r).  */
921	<	if (local_args_info.gofr_given)
885	<	{
886	<	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
887	<	goto failure;
888	<	}
889	<	if (args_info->gofr_given && ! override)
890	<	continue;
891	<	local_args_info.gofr_given = 1;
892	<	args_info->gofr_given = 1;
921	>
922		if (args_info->staticProps_group_counter && override)
923		reset_group_staticProps (args_info);
924		args_info->staticProps_group_counter += 1;
925	+
926	+	if (update_arg( 0 ,
927	+	0 , &(args_info->gofr_given),
928	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
929	+	check_ambiguity, override, 0, 0,
930	+	"gofr", 'g',
931	+	additional_error))
932	+	goto failure;
933	+
934		break;
897	–
935		case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
936	<	if (local_args_info.p2_given)
900	<	{
901	<	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
902	<	goto failure;
903	<	}
904	<	if (args_info->p2_given && ! override)
905	<	continue;
906	<	local_args_info.p2_given = 1;
907	<	args_info->p2_given = 1;
936	>
937		if (args_info->staticProps_group_counter && override)
938		reset_group_staticProps (args_info);
939		args_info->staticProps_group_counter += 1;
940	+
941	+	if (update_arg( 0 ,
942	+	0 , &(args_info->p2_given),
943	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
944	+	check_ambiguity, override, 0, 0,
945	+	"p2", 'p',
946	+	additional_error))
947	+	goto failure;
948	+
949		break;
912	–
950		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
951	<	if (local_args_info.scd_given)
915	<	{
916	<	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	<	goto failure;
918	<	}
919	<	if (args_info->scd_given && ! override)
920	<	continue;
921	<	local_args_info.scd_given = 1;
922	<	args_info->scd_given = 1;
951	>
952		if (args_info->staticProps_group_counter && override)
953		reset_group_staticProps (args_info);
954		args_info->staticProps_group_counter += 1;
955	+
956	+	if (update_arg( 0 ,
957	+	0 , &(args_info->scd_given),
958	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
959	+	check_ambiguity, override, 0, 0,
960	+	"scd", 's',
961	+	additional_error))
962	+	goto failure;
963	+
964		break;
927	–
965		case 'd':       /* density plot.  */
966	<	if (local_args_info.density_given)
930	<	{
931	<	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
932	<	goto failure;
933	<	}
934	<	if (args_info->density_given && ! override)
935	<	continue;
936	<	local_args_info.density_given = 1;
937	<	args_info->density_given = 1;
966	>
967		if (args_info->staticProps_group_counter && override)
968		reset_group_staticProps (args_info);
969		args_info->staticProps_group_counter += 1;
970	+
971	+	if (update_arg( 0 ,
972	+	0 , &(args_info->density_given),
973	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
974	+	check_ambiguity, override, 0, 0,
975	+	"density", 'd',
976	+	additional_error))
977	+	goto failure;
978	+
979		break;
980
943	–
981		case 0: /* Long option with no short option */
982		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
983		if (strcmp (long_options[option_index].name, "length") == 0)
984		{
985	<	if (local_args_info.length_given)
986	<	{
987	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
988	<	goto failure;
989	<	}
990	<	if (args_info->length_given && ! override)
991	<	continue;
992	<	local_args_info.length_given = 1;
956	<	args_info->length_given = 1;
957	<	args_info->length_arg = strtod (optarg, &stop_char);
958	<	if (!(stop_char && *stop_char == '\0')) {
959	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
985	>
986	>
987	>	if (update_arg( (void *)&(args_info->length_arg),
988	>	&(args_info->length_orig), &(args_info->length_given),
989	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
990	>	check_ambiguity, override, 0, 0,
991	>	"length", '-',
992	>	additional_error))
993		goto failure;
994	<	}
962	<	if (args_info->length_orig)
963	<	free (args_info->length_orig); /* free previous string */
964	<	args_info->length_orig = gengetopt_strdup (optarg);
994	>
995		}
996		/* select the first stuntdouble set.  */
997		else if (strcmp (long_options[option_index].name, "sele1") == 0)
998		{
999	<	if (local_args_info.sele1_given)
1000	<	{
1001	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1002	<	goto failure;
1003	<	}
1004	<	if (args_info->sele1_given && ! override)
1005	<	continue;
1006	<	local_args_info.sele1_given = 1;
1007	<	args_info->sele1_given = 1;
1008	<	if (args_info->sele1_arg)
979	<	free (args_info->sele1_arg); /* free previous string */
980	<	args_info->sele1_arg = gengetopt_strdup (optarg);
981	<	if (args_info->sele1_orig)
982	<	free (args_info->sele1_orig); /* free previous string */
983	<	args_info->sele1_orig = gengetopt_strdup (optarg);
999	>
1000	>
1001	>	if (update_arg( (void *)&(args_info->sele1_arg),
1002	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1003	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1004	>	check_ambiguity, override, 0, 0,
1005	>	"sele1", '-',
1006	>	additional_error))
1007	>	goto failure;
1008	>
1009		}
1010		/* select the second stuntdouble set.  */
1011		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1012		{
1013	<	if (local_args_info.sele2_given)
1014	<	{
1015	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1016	<	goto failure;
1017	<	}
1018	<	if (args_info->sele2_given && ! override)
1019	<	continue;
1020	<	local_args_info.sele2_given = 1;
1021	<	args_info->sele2_given = 1;
1022	<	if (args_info->sele2_arg)
998	<	free (args_info->sele2_arg); /* free previous string */
999	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1000	<	if (args_info->sele2_orig)
1001	<	free (args_info->sele2_orig); /* free previous string */
1002	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1013	>
1014	>
1015	>	if (update_arg( (void *)&(args_info->sele2_arg),
1016	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1017	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1018	>	check_ambiguity, override, 0, 0,
1019	>	"sele2", '-',
1020	>	additional_error))
1021	>	goto failure;
1022	>
1023		}
1024		/* select the third stuntdouble set.  */
1025		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1026		{
1027	<	if (local_args_info.sele3_given)
1028	<	{
1029	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1030	<	goto failure;
1031	<	}
1032	<	if (args_info->sele3_given && ! override)
1033	<	continue;
1034	<	local_args_info.sele3_given = 1;
1035	<	args_info->sele3_given = 1;
1036	<	if (args_info->sele3_arg)
1017	<	free (args_info->sele3_arg); /* free previous string */
1018	<	args_info->sele3_arg = gengetopt_strdup (optarg);
1019	<	if (args_info->sele3_orig)
1020	<	free (args_info->sele3_orig); /* free previous string */
1021	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1027	>
1028	>
1029	>	if (update_arg( (void *)&(args_info->sele3_arg),
1030	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1031	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1032	>	check_ambiguity, override, 0, 0,
1033	>	"sele3", '-',
1034	>	additional_error))
1035	>	goto failure;
1036	>
1037		}
1038		/* select reference (use and only use with --gxyz).  */
1039		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1040		{
1041	<	if (local_args_info.refsele_given)
1042	<	{
1043	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1044	<	goto failure;
1045	<	}
1046	<	if (args_info->refsele_given && ! override)
1047	<	continue;
1048	<	local_args_info.refsele_given = 1;
1049	<	args_info->refsele_given = 1;
1050	<	if (args_info->refsele_arg)
1036	<	free (args_info->refsele_arg); /* free previous string */
1037	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1038	<	if (args_info->refsele_orig)
1039	<	free (args_info->refsele_orig); /* free previous string */
1040	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1041	>
1042	>
1043	>	if (update_arg( (void *)&(args_info->refsele_arg),
1044	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1045	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1046	>	check_ambiguity, override, 0, 0,
1047	>	"refsele", '-',
1048	>	additional_error))
1049	>	goto failure;
1050	>
1051		}
1052	+	/* select stunt doubles for center-of-mass reference point.  */
1053	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1054	+	{
1055	+
1056	+
1057	+	if (update_arg( (void *)&(args_info->comsele_arg),
1058	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1059	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1060	+	check_ambiguity, override, 0, 0,
1061	+	"comsele", '-',
1062	+	additional_error))
1063	+	goto failure;
1064	+
1065	+	}
1066		/* molecule name.  */
1067		else if (strcmp (long_options[option_index].name, "molname") == 0)
1068		{
1069	<	if (local_args_info.molname_given)
1070	<	{
1071	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1072	<	goto failure;
1073	<	}
1074	<	if (args_info->molname_given && ! override)
1075	<	continue;
1076	<	local_args_info.molname_given = 1;
1077	<	args_info->molname_given = 1;
1078	<	if (args_info->molname_arg)
1055	<	free (args_info->molname_arg); /* free previous string */
1056	<	args_info->molname_arg = gengetopt_strdup (optarg);
1057	<	if (args_info->molname_orig)
1058	<	free (args_info->molname_orig); /* free previous string */
1059	<	args_info->molname_orig = gengetopt_strdup (optarg);
1069	>
1070	>
1071	>	if (update_arg( (void *)&(args_info->molname_arg),
1072	>	&(args_info->molname_orig), &(args_info->molname_given),
1073	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1074	>	check_ambiguity, override, 0, 0,
1075	>	"molname", '-',
1076	>	additional_error))
1077	>	goto failure;
1078	>
1079		}
1080		/* begin internal index.  */
1081		else if (strcmp (long_options[option_index].name, "begin") == 0)
1082		{
1083	<	if (local_args_info.begin_given)
1084	<	{
1085	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1086	<	goto failure;
1087	<	}
1088	<	if (args_info->begin_given && ! override)
1089	<	continue;
1090	<	local_args_info.begin_given = 1;
1072	<	args_info->begin_given = 1;
1073	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1074	<	if (!(stop_char && *stop_char == '\0')) {
1075	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1083	>
1084	>
1085	>	if (update_arg( (void *)&(args_info->begin_arg),
1086	>	&(args_info->begin_orig), &(args_info->begin_given),
1087	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1088	>	check_ambiguity, override, 0, 0,
1089	>	"begin", '-',
1090	>	additional_error))
1091		goto failure;
1092	<	}
1078	<	if (args_info->begin_orig)
1079	<	free (args_info->begin_orig); /* free previous string */
1080	<	args_info->begin_orig = gengetopt_strdup (optarg);
1092	>
1093		}
1094		/* end internal index.  */
1095		else if (strcmp (long_options[option_index].name, "end") == 0)
1096		{
1097	<	if (local_args_info.end_given)
1098	<	{
1099	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1100	<	goto failure;
1101	<	}
1102	<	if (args_info->end_given && ! override)
1103	<	continue;
1104	<	local_args_info.end_given = 1;
1093	<	args_info->end_given = 1;
1094	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
1095	<	if (!(stop_char && *stop_char == '\0')) {
1096	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1097	>
1098	>
1099	>	if (update_arg( (void *)&(args_info->end_arg),
1100	>	&(args_info->end_orig), &(args_info->end_given),
1101	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1102	>	check_ambiguity, override, 0, 0,
1103	>	"end", '-',
1104	>	additional_error))
1105		goto failure;
1106	<	}
1099	<	if (args_info->end_orig)
1100	<	free (args_info->end_orig); /* free previous string */
1101	<	args_info->end_orig = gengetopt_strdup (optarg);
1106	>
1107		}
1108	+	/* nanoparticle radius.  */
1109	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1110	+	{
1111	+
1112	+
1113	+	if (update_arg( (void *)&(args_info->radius_arg),
1114	+	&(args_info->radius_orig), &(args_info->radius_given),
1115	+	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1116	+	check_ambiguity, override, 0, 0,
1117	+	"radius", '-',
1118	+	additional_error))
1119	+	goto failure;
1120	+
1121	+	}
1122	+	/* bond order parameter (--rcut must be specified).  */
1123	+	else if (strcmp (long_options[option_index].name, "bo") == 0)
1124	+	{
1125	+
1126	+	if (args_info->staticProps_group_counter && override)
1127	+	reset_group_staticProps (args_info);
1128	+	args_info->staticProps_group_counter += 1;
1129	+
1130	+	if (update_arg( 0 ,
1131	+	0 , &(args_info->bo_given),
1132	+	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1133	+	check_ambiguity, override, 0, 0,
1134	+	"bo", '-',
1135	+	additional_error))
1136	+	goto failure;
1137	+
1138	+	}
1139	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1140	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1141	+	{
1142	+
1143	+	if (args_info->staticProps_group_counter && override)
1144	+	reset_group_staticProps (args_info);
1145	+	args_info->staticProps_group_counter += 1;
1146	+
1147	+	if (update_arg( 0 ,
1148	+	0 , &(args_info->bor_given),
1149	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1150	+	check_ambiguity, override, 0, 0,
1151	+	"bor", '-',
1152	+	additional_error))
1153	+	goto failure;
1154	+
1155	+	}
1156	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1157	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1158	+	{
1159	+
1160	+	if (args_info->staticProps_group_counter && override)
1161	+	reset_group_staticProps (args_info);
1162	+	args_info->staticProps_group_counter += 1;
1163	+
1164	+	if (update_arg( 0 ,
1165	+	0 , &(args_info->bad_given),
1166	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1167	+	check_ambiguity, override, 0, 0,
1168	+	"bad", '-',
1169	+	additional_error))
1170	+	goto failure;
1171	+
1172	+	}
1173	+	/* g(z).  */
1174	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1175	+	{
1176	+
1177	+	if (args_info->staticProps_group_counter && override)
1178	+	reset_group_staticProps (args_info);
1179	+	args_info->staticProps_group_counter += 1;
1180	+
1181	+	if (update_arg( 0 ,
1182	+	0 , &(args_info->gofz_given),
1183	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1184	+	check_ambiguity, override, 0, 0,
1185	+	"gofz", '-',
1186	+	additional_error))
1187	+	goto failure;
1188	+
1189	+	}
1190		/* g(r, cos(theta)).  */
1191		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1192		{
1193	<	if (local_args_info.r_theta_given)
1107	<	{
1108	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1109	<	goto failure;
1110	<	}
1111	<	if (args_info->r_theta_given && ! override)
1112	<	continue;
1113	<	local_args_info.r_theta_given = 1;
1114	<	args_info->r_theta_given = 1;
1193	>
1194		if (args_info->staticProps_group_counter && override)
1195		reset_group_staticProps (args_info);
1196		args_info->staticProps_group_counter += 1;
1197	<	break;
1197	>
1198	>	if (update_arg( 0 ,
1199	>	0 , &(args_info->r_theta_given),
1200	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1201	>	check_ambiguity, override, 0, 0,
1202	>	"r_theta", '-',
1203	>	additional_error))
1204	>	goto failure;
1205	>
1206		}
1207		/* g(r, cos(omega)).  */
1208		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1209		{
1210	<	if (local_args_info.r_omega_given)
1124	<	{
1125	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1126	<	goto failure;
1127	<	}
1128	<	if (args_info->r_omega_given && ! override)
1129	<	continue;
1130	<	local_args_info.r_omega_given = 1;
1131	<	args_info->r_omega_given = 1;
1210	>
1211		if (args_info->staticProps_group_counter && override)
1212		reset_group_staticProps (args_info);
1213		args_info->staticProps_group_counter += 1;
1214	<	break;
1214	>
1215	>	if (update_arg( 0 ,
1216	>	0 , &(args_info->r_omega_given),
1217	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1218	>	check_ambiguity, override, 0, 0,
1219	>	"r_omega", '-',
1220	>	additional_error))
1221	>	goto failure;
1222	>
1223		}
1224		/* g(cos(theta), cos(omega)).  */
1225		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1226		{
1227	<	if (local_args_info.theta_omega_given)
1141	<	{
1142	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1143	<	goto failure;
1144	<	}
1145	<	if (args_info->theta_omega_given && ! override)
1146	<	continue;
1147	<	local_args_info.theta_omega_given = 1;
1148	<	args_info->theta_omega_given = 1;
1227	>
1228		if (args_info->staticProps_group_counter && override)
1229		reset_group_staticProps (args_info);
1230		args_info->staticProps_group_counter += 1;
1231	<	break;
1231	>
1232	>	if (update_arg( 0 ,
1233	>	0 , &(args_info->theta_omega_given),
1234	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1235	>	check_ambiguity, override, 0, 0,
1236	>	"theta_omega", '-',
1237	>	additional_error))
1238	>	goto failure;
1239	>
1240		}
1241		/* g(x, y, z).  */
1242		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1243		{
1244	<	if (local_args_info.gxyz_given)
1158	<	{
1159	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1160	<	goto failure;
1161	<	}
1162	<	if (args_info->gxyz_given && ! override)
1163	<	continue;
1164	<	local_args_info.gxyz_given = 1;
1165	<	args_info->gxyz_given = 1;
1244	>
1245		if (args_info->staticProps_group_counter && override)
1246		reset_group_staticProps (args_info);
1247		args_info->staticProps_group_counter += 1;
1248	<	break;
1248	>
1249	>	if (update_arg( 0 ,
1250	>	0 , &(args_info->gxyz_given),
1251	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1252	>	check_ambiguity, override, 0, 0,
1253	>	"gxyz", '-',
1254	>	additional_error))
1255	>	goto failure;
1256	>
1257		}
1258		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1259		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1260		{
1261	<	if (local_args_info.rp2_given)
1175	<	{
1176	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1177	<	goto failure;
1178	<	}
1179	<	if (args_info->rp2_given && ! override)
1180	<	continue;
1181	<	local_args_info.rp2_given = 1;
1182	<	args_info->rp2_given = 1;
1261	>
1262		if (args_info->staticProps_group_counter && override)
1263		reset_group_staticProps (args_info);
1264		args_info->staticProps_group_counter += 1;
1265	<	break;
1265	>
1266	>	if (update_arg( 0 ,
1267	>	0 , &(args_info->rp2_given),
1268	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1269	>	check_ambiguity, override, 0, 0,
1270	>	"rp2", '-',
1271	>	additional_error))
1272	>	goto failure;
1273	>
1274		}
1275		/* slab density.  */
1276		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1277		{
1278	<	if (local_args_info.slab_density_given)
1192	<	{
1193	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1194	<	goto failure;
1195	<	}
1196	<	if (args_info->slab_density_given && ! override)
1197	<	continue;
1198	<	local_args_info.slab_density_given = 1;
1199	<	args_info->slab_density_given = 1;
1278	>
1279		if (args_info->staticProps_group_counter && override)
1280		reset_group_staticProps (args_info);
1281		args_info->staticProps_group_counter += 1;
1282	<	break;
1282	>
1283	>	if (update_arg( 0 ,
1284	>	0 , &(args_info->slab_density_given),
1285	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1286	>	check_ambiguity, override, 0, 0,
1287	>	"slab_density", '-',
1288	>	additional_error))
1289	>	goto failure;
1290	>
1291		}
1292	+	/* p(cos(theta)).  */
1293	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1294	+	{
1295	+
1296	+	if (args_info->staticProps_group_counter && override)
1297	+	reset_group_staticProps (args_info);
1298	+	args_info->staticProps_group_counter += 1;
1299	+
1300	+	if (update_arg( 0 ,
1301	+	0 , &(args_info->p_angle_given),
1302	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1303	+	check_ambiguity, override, 0, 0,
1304	+	"p_angle", '-',
1305	+	additional_error))
1306	+	goto failure;
1307	+
1308	+	}
1309		/* hxy.  */
1310		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1311		{
1312	<	if (local_args_info.hxy_given)
1209	<	{
1210	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1211	<	goto failure;
1212	<	}
1213	<	if (args_info->hxy_given && ! override)
1214	<	continue;
1215	<	local_args_info.hxy_given = 1;
1216	<	args_info->hxy_given = 1;
1312	>
1313		if (args_info->staticProps_group_counter && override)
1314		reset_group_staticProps (args_info);
1315		args_info->staticProps_group_counter += 1;
1316	<	break;
1316	>
1317	>	if (update_arg( 0 ,
1318	>	0 , &(args_info->hxy_given),
1319	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1320	>	check_ambiguity, override, 0, 0,
1321	>	"hxy", '-',
1322	>	additional_error))
1323	>	goto failure;
1324	>
1325		}
1326	+	/* rho of R.  */
1327	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1328	+	{
1329
1330	+	if (args_info->staticProps_group_counter && override)
1331	+	reset_group_staticProps (args_info);
1332	+	args_info->staticProps_group_counter += 1;
1333	+
1334	+	if (update_arg( 0 ,
1335	+	0 , &(args_info->rho_r_given),
1336	+	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1337	+	check_ambiguity, override, 0, 0,
1338	+	"rho_r", '-',
1339	+	additional_error))
1340	+	goto failure;
1341	+
1342	+	}
1343	+	/* hull volume of nanoparticle.  */
1344	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1345	+	{
1346	+
1347	+	if (args_info->staticProps_group_counter && override)
1348	+	reset_group_staticProps (args_info);
1349	+	args_info->staticProps_group_counter += 1;
1350	+
1351	+	if (update_arg( 0 ,
1352	+	0 , &(args_info->hullvol_given),
1353	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1354	+	check_ambiguity, override, 0, 0,
1355	+	"hullvol", '-',
1356	+	additional_error))
1357	+	goto failure;
1358	+
1359	+	}
1360	+
1361		break;
1362		case '?':       /* Invalid option.  */
1363		/* `getopt_long' already printed an error message.  */
#	Line 1249 | Line 1387 | cmdline_parser_internal (int argc, char * const *argv,
1387		if ( error )
1388		return (EXIT_FAILURE);
1389
1390	+	if (optind < argc)
1391	+	{
1392	+	int i = 0 ;
1393	+	int found_prog_name = 0;
1394	+	/* whether program name, i.e., argv[0], is in the remaining args
1395	+	(this may happen with some implementations of getopt,
1396	+	but surely not with the one included by gengetopt) */
1397	+
1398	+	i = optind;
1399	+	while (i < argc)
1400	+	if (argv[i++] == argv[0]) {
1401	+	found_prog_name = 1;
1402	+	break;
1403	+	}
1404	+	i = 0;
1405	+
1406	+	args_info->inputs_num = argc - optind - found_prog_name;
1407	+	args_info->inputs =
1408	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1409	+	while (optind < argc)
1410	+	if (argv[optind++] != argv[0])
1411	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1412	+	}
1413	+
1414		return 0;
1415
1416		failure:

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