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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1440 by gezelter, Thu Apr 29 14:41:48 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.19.1
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4	<	gengetopt -i StaticProps.ggo -F StaticPropsCmd -u
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 36 | Line 36 | const char *gengetopt_args_info_help[] = {
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	+	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
40		"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
41		"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
42		"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
#	Line 44 | Line 45 | const char *gengetopt_args_info_help[] = {
45		"      --sele2=selection script  select the second stuntdouble set",
46		"      --sele3=selection script  select the third stuntdouble set",
47		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
48	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
49		"      --molname=STRING          molecule name",
50		"      --begin=INT               begin internal index",
51		"      --end=INT                 end internal index",
#	Line 51 | Line 53 | const char *gengetopt_args_info_help[] = {
53		"\n Group: staticProps\n   an option of this group is required",
54		"      --bo                      bond order parameter (--rcut must be specified)",
55		"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
56	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
57		"  -g, --gofr                    g(r)",
58	+	"      --gofz                    g(z)",
59		"      --r_theta                 g(r, cos(theta))",
60		"      --r_omega                 g(r, cos(omega))",
61	+	"      --r_z                     g(r, z)",
62		"      --theta_omega             g(cos(theta), cos(omega))",
63		"      --gxyz                    g(x, y, z)",
64		"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
#	Line 61 | Line 66 | const char *gengetopt_args_info_help[] = {
66		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
67		"  -d, --density                 density plot",
68		"      --slab_density            slab density",
69	+	"      --p_angle                 p(cos(theta))",
70		"      --hxy                     hxy",
71		"      --rho_r                   rho of R",
72	+	"      --hullvol                 hull volume of nanoparticle",
73		0
74		};
75
76	+	typedef enum {ARG_NO
77	+	, ARG_STRING
78	+	, ARG_INT
79	+	, ARG_DOUBLE
80	+	} cmdline_parser_arg_type;
81	+
82		static
83		void clear_given (struct gengetopt_args_info *args_info);
84		static
85		void clear_args (struct gengetopt_args_info *args_info);
86
87		static int
88	<	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);
88	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
89	>	struct cmdline_parser_params *params, const char *additional_error);
90
91		static int
92		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 91 | Line 105 | void clear_given (struct gengetopt_args_info *args_inf
105		args_info->nbins_given = 0 ;
106		args_info->nbins_x_given = 0 ;
107		args_info->nbins_y_given = 0 ;
108	+	args_info->nbins_z_given = 0 ;
109		args_info->nanglebins_given = 0 ;
110		args_info->length_given = 0 ;
111		args_info->rcut_given = 0 ;
#	Line 99 | Line 114 | void clear_given (struct gengetopt_args_info *args_inf
114		args_info->sele2_given = 0 ;
115		args_info->sele3_given = 0 ;
116		args_info->refsele_given = 0 ;
117	+	args_info->comsele_given = 0 ;
118		args_info->molname_given = 0 ;
119		args_info->begin_given = 0 ;
120		args_info->end_given = 0 ;
121		args_info->radius_given = 0 ;
122		args_info->bo_given = 0 ;
123		args_info->bor_given = 0 ;
124	+	args_info->bad_given = 0 ;
125		args_info->gofr_given = 0 ;
126	+	args_info->gofz_given = 0 ;
127		args_info->r_theta_given = 0 ;
128		args_info->r_omega_given = 0 ;
129	+	args_info->r_z_given = 0 ;
130		args_info->theta_omega_given = 0 ;
131		args_info->gxyz_given = 0 ;
132		args_info->p2_given = 0 ;
#	Line 115 | Line 134 | void clear_given (struct gengetopt_args_info *args_inf
134		args_info->scd_given = 0 ;
135		args_info->density_given = 0 ;
136		args_info->slab_density_given = 0 ;
137	+	args_info->p_angle_given = 0 ;
138		args_info->hxy_given = 0 ;
139		args_info->rho_r_given = 0 ;
140	+	args_info->hullvol_given = 0 ;
141		args_info->staticProps_group_counter = 0 ;
142		}
143
#	Line 135 | Line 156 | void clear_args (struct gengetopt_args_info *args_info
156		args_info->nbins_x_orig = NULL;
157		args_info->nbins_y_arg = 100;
158		args_info->nbins_y_orig = NULL;
159	+	args_info->nbins_z_arg = 100;
160	+	args_info->nbins_z_orig = NULL;
161		args_info->nanglebins_arg = 50;
162		args_info->nanglebins_orig = NULL;
163		args_info->length_orig = NULL;
#	Line 149 | Line 172 | void clear_args (struct gengetopt_args_info *args_info
172		args_info->sele3_orig = NULL;
173		args_info->refsele_arg = NULL;
174		args_info->refsele_orig = NULL;
175	+	args_info->comsele_arg = NULL;
176	+	args_info->comsele_orig = NULL;
177		args_info->molname_arg = NULL;
178		args_info->molname_orig = NULL;
179		args_info->begin_orig = NULL;
#	Line 160 | Line 185 | void init_args_info(struct gengetopt_args_info *args_i
185		static
186		void init_args_info(struct gengetopt_args_info *args_info)
187		{
188	+
189	+
190		args_info->help_help = gengetopt_args_info_help[0] ;
191		args_info->version_help = gengetopt_args_info_help[1] ;
192		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 168 | Line 195 | void init_args_info(struct gengetopt_args_info *args_i
195		args_info->nbins_help = gengetopt_args_info_help[5] ;
196		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
197		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
198	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
199	<	args_info->length_help = gengetopt_args_info_help[9] ;
200	<	args_info->rcut_help = gengetopt_args_info_help[10] ;
201	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
202	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
203	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
204	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
205	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
206	<	args_info->molname_help = gengetopt_args_info_help[16] ;
207	<	args_info->begin_help = gengetopt_args_info_help[17] ;
208	<	args_info->end_help = gengetopt_args_info_help[18] ;
209	<	args_info->radius_help = gengetopt_args_info_help[19] ;
210	<	args_info->bo_help = gengetopt_args_info_help[20] ;
211	<	args_info->bor_help = gengetopt_args_info_help[21] ;
212	<	args_info->gofr_help = gengetopt_args_info_help[22] ;
213	<	args_info->r_theta_help = gengetopt_args_info_help[23] ;
214	<	args_info->r_omega_help = gengetopt_args_info_help[24] ;
215	<	args_info->theta_omega_help = gengetopt_args_info_help[25] ;
216	<	args_info->gxyz_help = gengetopt_args_info_help[26] ;
217	<	args_info->p2_help = gengetopt_args_info_help[27] ;
218	<	args_info->rp2_help = gengetopt_args_info_help[28] ;
219	<	args_info->scd_help = gengetopt_args_info_help[29] ;
220	<	args_info->density_help = gengetopt_args_info_help[30] ;
221	<	args_info->slab_density_help = gengetopt_args_info_help[31] ;
222	<	args_info->hxy_help = gengetopt_args_info_help[32] ;
223	<	args_info->rho_r_help = gengetopt_args_info_help[33] ;
198	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
199	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
200	>	args_info->length_help = gengetopt_args_info_help[10] ;
201	>	args_info->rcut_help = gengetopt_args_info_help[11] ;
202	>	args_info->zoffset_help = gengetopt_args_info_help[12] ;
203	>	args_info->sele1_help = gengetopt_args_info_help[13] ;
204	>	args_info->sele2_help = gengetopt_args_info_help[14] ;
205	>	args_info->sele3_help = gengetopt_args_info_help[15] ;
206	>	args_info->refsele_help = gengetopt_args_info_help[16] ;
207	>	args_info->comsele_help = gengetopt_args_info_help[17] ;
208	>	args_info->molname_help = gengetopt_args_info_help[18] ;
209	>	args_info->begin_help = gengetopt_args_info_help[19] ;
210	>	args_info->end_help = gengetopt_args_info_help[20] ;
211	>	args_info->radius_help = gengetopt_args_info_help[21] ;
212	>	args_info->bo_help = gengetopt_args_info_help[23] ;
213	>	args_info->bor_help = gengetopt_args_info_help[24] ;
214	>	args_info->bad_help = gengetopt_args_info_help[25] ;
215	>	args_info->gofr_help = gengetopt_args_info_help[26] ;
216	>	args_info->gofz_help = gengetopt_args_info_help[27] ;
217	>	args_info->r_theta_help = gengetopt_args_info_help[28] ;
218	>	args_info->r_omega_help = gengetopt_args_info_help[29] ;
219	>	args_info->r_z_help = gengetopt_args_info_help[30] ;
220	>	args_info->theta_omega_help = gengetopt_args_info_help[31] ;
221	>	args_info->gxyz_help = gengetopt_args_info_help[32] ;
222	>	args_info->p2_help = gengetopt_args_info_help[33] ;
223	>	args_info->rp2_help = gengetopt_args_info_help[34] ;
224	>	args_info->scd_help = gengetopt_args_info_help[35] ;
225	>	args_info->density_help = gengetopt_args_info_help[36] ;
226	>	args_info->slab_density_help = gengetopt_args_info_help[37] ;
227	>	args_info->p_angle_help = gengetopt_args_info_help[38] ;
228	>	args_info->hxy_help = gengetopt_args_info_help[39] ;
229	>	args_info->rho_r_help = gengetopt_args_info_help[40] ;
230	>	args_info->hullvol_help = gengetopt_args_info_help[41] ;
231
232		}
233
#	Line 203 | Line 237 | cmdline_parser_print_version (void)
237		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
238		}
239
240	<	void
207	<	cmdline_parser_print_help (void)
208	<	{
209	<	int i = 0;
240	>	static void print_help_common(void) {
241		cmdline_parser_print_version ();
242
243		if (strlen(gengetopt_args_info_purpose) > 0)
244		printf("\n%s\n", gengetopt_args_info_purpose);
245
246	<	printf("\n%s\n\n", gengetopt_args_info_usage);
246	>	if (strlen(gengetopt_args_info_usage) > 0)
247	>	printf("\n%s\n", gengetopt_args_info_usage);
248
249	+	printf("\n");
250	+
251		if (strlen(gengetopt_args_info_description) > 0)
252		printf("%s\n", gengetopt_args_info_description);
253	+	}
254
255	+	void
256	+	cmdline_parser_print_help (void)
257	+	{
258	+	int i = 0;
259	+	print_help_common();
260		while (gengetopt_args_info_help[i])
261		printf("%s\n", gengetopt_args_info_help[i++]);
262		}
#	Line 232 | Line 272 | cmdline_parser_init (struct gengetopt_args_info *args_
272		args_info->inputs_num = 0;
273		}
274
275	+	void
276	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
277	+	{
278	+	if (params)
279	+	{
280	+	params->override = 0;
281	+	params->initialize = 1;
282	+	params->check_required = 1;
283	+	params->check_ambiguity = 0;
284	+	params->print_errors = 1;
285	+	}
286	+	}
287	+
288	+	struct cmdline_parser_params *
289	+	cmdline_parser_params_create(void)
290	+	{
291	+	struct cmdline_parser_params *params =
292	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
293	+	cmdline_parser_params_init(params);
294	+	return params;
295	+	}
296	+
297		static void
298	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
298	>	free_string_field (char **s)
299		{
300	<
239	<	unsigned int i;
240	<	if (args_info->input_arg)
300	>	if (*s)
301		{
302	<	free (args_info->input_arg); /* free previous argument */
303	<	args_info->input_arg = 0;
302	>	free (*s);
303	>	*s = 0;
304		}
305	<	if (args_info->input_orig)
306	<	{
307	<	free (args_info->input_orig); /* free previous argument */
308	<	args_info->input_orig = 0;
309	<	}
310	<	if (args_info->output_arg)
311	<	{
312	<	free (args_info->output_arg); /* free previous argument */
313	<	args_info->output_arg = 0;
314	<	}
315	<	if (args_info->output_orig)
316	<	{
317	<	free (args_info->output_orig); /* free previous argument */
318	<	args_info->output_orig = 0;
319	<	}
320	<	if (args_info->step_orig)
321	<	{
322	<	free (args_info->step_orig); /* free previous argument */
323	<	args_info->step_orig = 0;
324	<	}
325	<	if (args_info->nbins_orig)
326	<	{
327	<	free (args_info->nbins_orig); /* free previous argument */
328	<	args_info->nbins_orig = 0;
329	<	}
330	<	if (args_info->nbins_x_orig)
331	<	{
332	<	free (args_info->nbins_x_orig); /* free previous argument */
333	<	args_info->nbins_x_orig = 0;
334	<	}
335	<	if (args_info->nbins_y_orig)
336	<	{
337	<	free (args_info->nbins_y_orig); /* free previous argument */
338	<	args_info->nbins_y_orig = 0;
339	<	}
280	<	if (args_info->nanglebins_orig)
281	<	{
282	<	free (args_info->nanglebins_orig); /* free previous argument */
283	<	args_info->nanglebins_orig = 0;
284	<	}
285	<	if (args_info->length_orig)
286	<	{
287	<	free (args_info->length_orig); /* free previous argument */
288	<	args_info->length_orig = 0;
289	<	}
290	<	if (args_info->rcut_orig)
291	<	{
292	<	free (args_info->rcut_orig); /* free previous argument */
293	<	args_info->rcut_orig = 0;
294	<	}
295	<	if (args_info->zoffset_orig)
296	<	{
297	<	free (args_info->zoffset_orig); /* free previous argument */
298	<	args_info->zoffset_orig = 0;
299	<	}
300	<	if (args_info->sele1_arg)
301	<	{
302	<	free (args_info->sele1_arg); /* free previous argument */
303	<	args_info->sele1_arg = 0;
304	<	}
305	<	if (args_info->sele1_orig)
306	<	{
307	<	free (args_info->sele1_orig); /* free previous argument */
308	<	args_info->sele1_orig = 0;
309	<	}
310	<	if (args_info->sele2_arg)
311	<	{
312	<	free (args_info->sele2_arg); /* free previous argument */
313	<	args_info->sele2_arg = 0;
314	<	}
315	<	if (args_info->sele2_orig)
316	<	{
317	<	free (args_info->sele2_orig); /* free previous argument */
318	<	args_info->sele2_orig = 0;
319	<	}
320	<	if (args_info->sele3_arg)
321	<	{
322	<	free (args_info->sele3_arg); /* free previous argument */
323	<	args_info->sele3_arg = 0;
324	<	}
325	<	if (args_info->sele3_orig)
326	<	{
327	<	free (args_info->sele3_orig); /* free previous argument */
328	<	args_info->sele3_orig = 0;
329	<	}
330	<	if (args_info->refsele_arg)
331	<	{
332	<	free (args_info->refsele_arg); /* free previous argument */
333	<	args_info->refsele_arg = 0;
334	<	}
335	<	if (args_info->refsele_orig)
336	<	{
337	<	free (args_info->refsele_orig); /* free previous argument */
338	<	args_info->refsele_orig = 0;
339	<	}
340	<	if (args_info->molname_arg)
341	<	{
342	<	free (args_info->molname_arg); /* free previous argument */
343	<	args_info->molname_arg = 0;
344	<	}
345	<	if (args_info->molname_orig)
346	<	{
347	<	free (args_info->molname_orig); /* free previous argument */
348	<	args_info->molname_orig = 0;
349	<	}
350	<	if (args_info->begin_orig)
351	<	{
352	<	free (args_info->begin_orig); /* free previous argument */
353	<	args_info->begin_orig = 0;
354	<	}
355	<	if (args_info->end_orig)
356	<	{
357	<	free (args_info->end_orig); /* free previous argument */
358	<	args_info->end_orig = 0;
359	<	}
360	<	if (args_info->radius_orig)
361	<	{
362	<	free (args_info->radius_orig); /* free previous argument */
363	<	args_info->radius_orig = 0;
364	<	}
305	>	}
306	>
307	>
308	>	static void
309	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
310	>	{
311	>	unsigned int i;
312	>	free_string_field (&(args_info->input_arg));
313	>	free_string_field (&(args_info->input_orig));
314	>	free_string_field (&(args_info->output_arg));
315	>	free_string_field (&(args_info->output_orig));
316	>	free_string_field (&(args_info->step_orig));
317	>	free_string_field (&(args_info->nbins_orig));
318	>	free_string_field (&(args_info->nbins_x_orig));
319	>	free_string_field (&(args_info->nbins_y_orig));
320	>	free_string_field (&(args_info->nbins_z_orig));
321	>	free_string_field (&(args_info->nanglebins_orig));
322	>	free_string_field (&(args_info->length_orig));
323	>	free_string_field (&(args_info->rcut_orig));
324	>	free_string_field (&(args_info->zoffset_orig));
325	>	free_string_field (&(args_info->sele1_arg));
326	>	free_string_field (&(args_info->sele1_orig));
327	>	free_string_field (&(args_info->sele2_arg));
328	>	free_string_field (&(args_info->sele2_orig));
329	>	free_string_field (&(args_info->sele3_arg));
330	>	free_string_field (&(args_info->sele3_orig));
331	>	free_string_field (&(args_info->refsele_arg));
332	>	free_string_field (&(args_info->refsele_orig));
333	>	free_string_field (&(args_info->comsele_arg));
334	>	free_string_field (&(args_info->comsele_orig));
335	>	free_string_field (&(args_info->molname_arg));
336	>	free_string_field (&(args_info->molname_orig));
337	>	free_string_field (&(args_info->begin_orig));
338	>	free_string_field (&(args_info->end_orig));
339	>	free_string_field (&(args_info->radius_orig));
340
341	+
342		for (i = 0; i < args_info->inputs_num; ++i)
343		free (args_info->inputs [i]);
344	<
344	>
345		if (args_info->inputs_num)
346		free (args_info->inputs);
347	<
347	>
348		clear_given (args_info);
349		}
350
351	+
352	+	static void
353	+	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
354	+	{
355	+	if (arg) {
356	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
357	+	} else {
358	+	fprintf(outfile, "%s\n", opt);
359	+	}
360	+	}
361	+
362	+
363		int
364	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
365	+	{
366	+	int i = 0;
367	+
368	+	if (!outfile)
369	+	{
370	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
371	+	return EXIT_FAILURE;
372	+	}
373	+
374	+	if (args_info->help_given)
375	+	write_into_file(outfile, "help", 0, 0 );
376	+	if (args_info->version_given)
377	+	write_into_file(outfile, "version", 0, 0 );
378	+	if (args_info->input_given)
379	+	write_into_file(outfile, "input", args_info->input_orig, 0);
380	+	if (args_info->output_given)
381	+	write_into_file(outfile, "output", args_info->output_orig, 0);
382	+	if (args_info->step_given)
383	+	write_into_file(outfile, "step", args_info->step_orig, 0);
384	+	if (args_info->nbins_given)
385	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
386	+	if (args_info->nbins_x_given)
387	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
388	+	if (args_info->nbins_y_given)
389	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
390	+	if (args_info->nbins_z_given)
391	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
392	+	if (args_info->nanglebins_given)
393	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
394	+	if (args_info->length_given)
395	+	write_into_file(outfile, "length", args_info->length_orig, 0);
396	+	if (args_info->rcut_given)
397	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
398	+	if (args_info->zoffset_given)
399	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
400	+	if (args_info->sele1_given)
401	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
402	+	if (args_info->sele2_given)
403	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
404	+	if (args_info->sele3_given)
405	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
406	+	if (args_info->refsele_given)
407	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
408	+	if (args_info->comsele_given)
409	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
410	+	if (args_info->molname_given)
411	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
412	+	if (args_info->begin_given)
413	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
414	+	if (args_info->end_given)
415	+	write_into_file(outfile, "end", args_info->end_orig, 0);
416	+	if (args_info->radius_given)
417	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
418	+	if (args_info->bo_given)
419	+	write_into_file(outfile, "bo", 0, 0 );
420	+	if (args_info->bor_given)
421	+	write_into_file(outfile, "bor", 0, 0 );
422	+	if (args_info->bad_given)
423	+	write_into_file(outfile, "bad", 0, 0 );
424	+	if (args_info->gofr_given)
425	+	write_into_file(outfile, "gofr", 0, 0 );
426	+	if (args_info->gofz_given)
427	+	write_into_file(outfile, "gofz", 0, 0 );
428	+	if (args_info->r_theta_given)
429	+	write_into_file(outfile, "r_theta", 0, 0 );
430	+	if (args_info->r_omega_given)
431	+	write_into_file(outfile, "r_omega", 0, 0 );
432	+	if (args_info->r_z_given)
433	+	write_into_file(outfile, "r_z", 0, 0 );
434	+	if (args_info->theta_omega_given)
435	+	write_into_file(outfile, "theta_omega", 0, 0 );
436	+	if (args_info->gxyz_given)
437	+	write_into_file(outfile, "gxyz", 0, 0 );
438	+	if (args_info->p2_given)
439	+	write_into_file(outfile, "p2", 0, 0 );
440	+	if (args_info->rp2_given)
441	+	write_into_file(outfile, "rp2", 0, 0 );
442	+	if (args_info->scd_given)
443	+	write_into_file(outfile, "scd", 0, 0 );
444	+	if (args_info->density_given)
445	+	write_into_file(outfile, "density", 0, 0 );
446	+	if (args_info->slab_density_given)
447	+	write_into_file(outfile, "slab_density", 0, 0 );
448	+	if (args_info->p_angle_given)
449	+	write_into_file(outfile, "p_angle", 0, 0 );
450	+	if (args_info->hxy_given)
451	+	write_into_file(outfile, "hxy", 0, 0 );
452	+	if (args_info->rho_r_given)
453	+	write_into_file(outfile, "rho_r", 0, 0 );
454	+	if (args_info->hullvol_given)
455	+	write_into_file(outfile, "hullvol", 0, 0 );
456	+
457	+
458	+	i = EXIT_SUCCESS;
459	+	return i;
460	+	}
461	+
462	+	int
463		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
464		{
465		FILE *outfile;
#	Line 386 | Line 473 | cmdline_parser_file_save(const char *filename, struct
473		return EXIT_FAILURE;
474		}
475
476	<	if (args_info->help_given) {
390	<	fprintf(outfile, "%s\n", "help");
391	<	}
392	<	if (args_info->version_given) {
393	<	fprintf(outfile, "%s\n", "version");
394	<	}
395	<	if (args_info->input_given) {
396	<	if (args_info->input_orig) {
397	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
398	<	} else {
399	<	fprintf(outfile, "%s\n", "input");
400	<	}
401	<	}
402	<	if (args_info->output_given) {
403	<	if (args_info->output_orig) {
404	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
405	<	} else {
406	<	fprintf(outfile, "%s\n", "output");
407	<	}
408	<	}
409	<	if (args_info->step_given) {
410	<	if (args_info->step_orig) {
411	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
412	<	} else {
413	<	fprintf(outfile, "%s\n", "step");
414	<	}
415	<	}
416	<	if (args_info->nbins_given) {
417	<	if (args_info->nbins_orig) {
418	<	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
419	<	} else {
420	<	fprintf(outfile, "%s\n", "nbins");
421	<	}
422	<	}
423	<	if (args_info->nbins_x_given) {
424	<	if (args_info->nbins_x_orig) {
425	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
426	<	} else {
427	<	fprintf(outfile, "%s\n", "nbins_x");
428	<	}
429	<	}
430	<	if (args_info->nbins_y_given) {
431	<	if (args_info->nbins_y_orig) {
432	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
433	<	} else {
434	<	fprintf(outfile, "%s\n", "nbins_y");
435	<	}
436	<	}
437	<	if (args_info->nanglebins_given) {
438	<	if (args_info->nanglebins_orig) {
439	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
440	<	} else {
441	<	fprintf(outfile, "%s\n", "nanglebins");
442	<	}
443	<	}
444	<	if (args_info->length_given) {
445	<	if (args_info->length_orig) {
446	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
447	<	} else {
448	<	fprintf(outfile, "%s\n", "length");
449	<	}
450	<	}
451	<	if (args_info->rcut_given) {
452	<	if (args_info->rcut_orig) {
453	<	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
454	<	} else {
455	<	fprintf(outfile, "%s\n", "rcut");
456	<	}
457	<	}
458	<	if (args_info->zoffset_given) {
459	<	if (args_info->zoffset_orig) {
460	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
461	<	} else {
462	<	fprintf(outfile, "%s\n", "zoffset");
463	<	}
464	<	}
465	<	if (args_info->sele1_given) {
466	<	if (args_info->sele1_orig) {
467	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
468	<	} else {
469	<	fprintf(outfile, "%s\n", "sele1");
470	<	}
471	<	}
472	<	if (args_info->sele2_given) {
473	<	if (args_info->sele2_orig) {
474	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
475	<	} else {
476	<	fprintf(outfile, "%s\n", "sele2");
477	<	}
478	<	}
479	<	if (args_info->sele3_given) {
480	<	if (args_info->sele3_orig) {
481	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
482	<	} else {
483	<	fprintf(outfile, "%s\n", "sele3");
484	<	}
485	<	}
486	<	if (args_info->refsele_given) {
487	<	if (args_info->refsele_orig) {
488	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
489	<	} else {
490	<	fprintf(outfile, "%s\n", "refsele");
491	<	}
492	<	}
493	<	if (args_info->molname_given) {
494	<	if (args_info->molname_orig) {
495	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
496	<	} else {
497	<	fprintf(outfile, "%s\n", "molname");
498	<	}
499	<	}
500	<	if (args_info->begin_given) {
501	<	if (args_info->begin_orig) {
502	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
503	<	} else {
504	<	fprintf(outfile, "%s\n", "begin");
505	<	}
506	<	}
507	<	if (args_info->end_given) {
508	<	if (args_info->end_orig) {
509	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
510	<	} else {
511	<	fprintf(outfile, "%s\n", "end");
512	<	}
513	<	}
514	<	if (args_info->radius_given) {
515	<	if (args_info->radius_orig) {
516	<	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
517	<	} else {
518	<	fprintf(outfile, "%s\n", "radius");
519	<	}
520	<	}
521	<	if (args_info->bo_given) {
522	<	fprintf(outfile, "%s\n", "bo");
523	<	}
524	<	if (args_info->bor_given) {
525	<	fprintf(outfile, "%s\n", "bor");
526	<	}
527	<	if (args_info->gofr_given) {
528	<	fprintf(outfile, "%s\n", "gofr");
529	<	}
530	<	if (args_info->r_theta_given) {
531	<	fprintf(outfile, "%s\n", "r_theta");
532	<	}
533	<	if (args_info->r_omega_given) {
534	<	fprintf(outfile, "%s\n", "r_omega");
535	<	}
536	<	if (args_info->theta_omega_given) {
537	<	fprintf(outfile, "%s\n", "theta_omega");
538	<	}
539	<	if (args_info->gxyz_given) {
540	<	fprintf(outfile, "%s\n", "gxyz");
541	<	}
542	<	if (args_info->p2_given) {
543	<	fprintf(outfile, "%s\n", "p2");
544	<	}
545	<	if (args_info->rp2_given) {
546	<	fprintf(outfile, "%s\n", "rp2");
547	<	}
548	<	if (args_info->scd_given) {
549	<	fprintf(outfile, "%s\n", "scd");
550	<	}
551	<	if (args_info->density_given) {
552	<	fprintf(outfile, "%s\n", "density");
553	<	}
554	<	if (args_info->slab_density_given) {
555	<	fprintf(outfile, "%s\n", "slab_density");
556	<	}
557	<	if (args_info->hxy_given) {
558	<	fprintf(outfile, "%s\n", "hxy");
559	<	}
560	<	if (args_info->rho_r_given) {
561	<	fprintf(outfile, "%s\n", "rho_r");
562	<	}
563	<
476	>	i = cmdline_parser_dump(outfile, args_info);
477		fclose (outfile);
478
566	–	i = EXIT_SUCCESS;
479		return i;
480		}
481
#	Line 573 | Line 485 | cmdline_parser_free (struct gengetopt_args_info *args_
485		cmdline_parser_release (args_info);
486		}
487
488	<
577	<	/* gengetopt_strdup() */
578	<	/* strdup.c replacement of strdup, which is not standard */
488	>	/** @brief replacement of strdup, which is not standard */
489		char *
490		gengetopt_strdup (const char *s)
491		{
#	Line 591 | Line 501 | static void
501		}
502
503		static void
594	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
595	–
596	–	static void
504		reset_group_staticProps(struct gengetopt_args_info *args_info)
505		{
506		if (! args_info->staticProps_group_counter)
#	Line 601 | Line 508 | reset_group_staticProps(struct gengetopt_args_info *ar
508
509		args_info->bo_given = 0 ;
510		args_info->bor_given = 0 ;
511	+	args_info->bad_given = 0 ;
512		args_info->gofr_given = 0 ;
513	+	args_info->gofz_given = 0 ;
514		args_info->r_theta_given = 0 ;
515		args_info->r_omega_given = 0 ;
516	+	args_info->r_z_given = 0 ;
517		args_info->theta_omega_given = 0 ;
518		args_info->gxyz_given = 0 ;
519		args_info->p2_given = 0 ;
#	Line 611 | Line 521 | reset_group_staticProps(struct gengetopt_args_info *ar
521		args_info->scd_given = 0 ;
522		args_info->density_given = 0 ;
523		args_info->slab_density_given = 0 ;
524	+	args_info->p_angle_given = 0 ;
525		args_info->hxy_given = 0 ;
526		args_info->rho_r_given = 0 ;
527	+	args_info->hullvol_given = 0 ;
528
529		args_info->staticProps_group_counter = 0;
530		}
#	Line 624 | Line 536 | int
536		}
537
538		int
539	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
540	+	struct cmdline_parser_params *params)
541	+	{
542	+	int result;
543	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
544	+
545	+	if (result == EXIT_FAILURE)
546	+	{
547	+	cmdline_parser_free (args_info);
548	+	exit (EXIT_FAILURE);
549	+	}
550	+
551	+	return result;
552	+	}
553	+
554	+	int
555		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
556		{
557		int result;
558	+	struct cmdline_parser_params params;
559	+
560	+	params.override = override;
561	+	params.initialize = initialize;
562	+	params.check_required = check_required;
563	+	params.check_ambiguity = 0;
564	+	params.print_errors = 1;
565
566	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
566	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
567
568		if (result == EXIT_FAILURE)
569		{
#	Line 678 | Line 613 | cmdline_parser_required2 (struct gengetopt_args_info *
613		/* checks for dependences among options */
614
615		return error;
616	+	}
617	+
618	+
619	+	static char *package_name = 0;
620	+
621	+	/**
622	+	* @brief updates an option
623	+	* @param field the generic pointer to the field to update
624	+	* @param orig_field the pointer to the orig field
625	+	* @param field_given the pointer to the number of occurrence of this option
626	+	* @param prev_given the pointer to the number of occurrence already seen
627	+	* @param value the argument for this option (if null no arg was specified)
628	+	* @param possible_values the possible values for this option (if specified)
629	+	* @param default_value the default value (in case the option only accepts fixed values)
630	+	* @param arg_type the type of this option
631	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
632	+	* @param override @see cmdline_parser_params.override
633	+	* @param no_free whether to free a possible previous value
634	+	* @param multiple_option whether this is a multiple option
635	+	* @param long_opt the corresponding long option
636	+	* @param short_opt the corresponding short option (or '-' if none)
637	+	* @param additional_error possible further error specification
638	+	*/
639	+	static
640	+	int update_arg(void *field, char **orig_field,
641	+	unsigned int *field_given, unsigned int *prev_given,
642	+	char *value, char *possible_values[], const char *default_value,
643	+	cmdline_parser_arg_type arg_type,
644	+	int check_ambiguity, int override,
645	+	int no_free, int multiple_option,
646	+	const char *long_opt, char short_opt,
647	+	const char *additional_error)
648	+	{
649	+	char *stop_char = 0;
650	+	const char *val = value;
651	+	int found;
652	+	char **string_field;
653	+
654	+	stop_char = 0;
655	+	found = 0;
656	+
657	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
658	+	{
659	+	if (short_opt != '-')
660	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
661	+	package_name, long_opt, short_opt,
662	+	(additional_error ? additional_error : ""));
663	+	else
664	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
665	+	package_name, long_opt,
666	+	(additional_error ? additional_error : ""));
667	+	return 1; /* failure */
668	+	}
669	+
670	+
671	+	if (field_given && *field_given && ! override)
672	+	return 0;
673	+	if (prev_given)
674	+	(*prev_given)++;
675	+	if (field_given)
676	+	(*field_given)++;
677	+	if (possible_values)
678	+	val = possible_values[found];
679	+
680	+	switch(arg_type) {
681	+	case ARG_INT:
682	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
683	+	break;
684	+	case ARG_DOUBLE:
685	+	if (val) *((double *)field) = strtod (val, &stop_char);
686	+	break;
687	+	case ARG_STRING:
688	+	if (val) {
689	+	string_field = (char **)field;
690	+	if (!no_free && *string_field)
691	+	free (*string_field); /* free previous string */
692	+	*string_field = gengetopt_strdup (val);
693	+	}
694	+	break;
695	+	default:
696	+	break;
697	+	};
698	+
699	+	/* check numeric conversion */
700	+	switch(arg_type) {
701	+	case ARG_INT:
702	+	case ARG_DOUBLE:
703	+	if (val && !(stop_char && *stop_char == '\0')) {
704	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
705	+	return 1; /* failure */
706	+	}
707	+	break;
708	+	default:
709	+	;
710	+	};
711	+
712	+	/* store the original value */
713	+	switch(arg_type) {
714	+	case ARG_NO:
715	+	break;
716	+	default:
717	+	if (value && orig_field) {
718	+	if (no_free) {
719	+	*orig_field = value;
720	+	} else {
721	+	if (*orig_field)
722	+	free (*orig_field); /* free previous string */
723	+	*orig_field = gengetopt_strdup (value);
724	+	}
725	+	}
726	+	};
727	+
728	+	return 0; /* OK */
729		}
730
731	+
732		int
733	<	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)
733	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
734	>	struct cmdline_parser_params *params, const char *additional_error)
735		{
736		int c;        /* Character of the parsed option.  */
737
738		int error = 0;
739		struct gengetopt_args_info local_args_info;
740	+
741	+	int override;
742	+	int initialize;
743	+	int check_required;
744	+	int check_ambiguity;
745	+
746	+	package_name = argv[0];
747	+
748	+	override = params->override;
749	+	initialize = params->initialize;
750	+	check_required = params->check_required;
751	+	check_ambiguity = params->check_ambiguity;
752
753		if (initialize)
754		cmdline_parser_init (args_info);
#	Line 695 | Line 757 | cmdline_parser_internal (int argc, char * const *argv,
757
758		optarg = 0;
759		optind = 0;
760	<	opterr = 1;
760	>	opterr = params->print_errors;
761		optopt = '?';
762
763		while (1)
764		{
765		int option_index = 0;
704	–	char *stop_char;
766
767		static struct option long_options[] = {
768		{ "help",       0, NULL, 'h' },
#	Line 712 | Line 773 | cmdline_parser_internal (int argc, char * const *argv,
773		{ "nbins",      1, NULL, 'b' },
774		{ "nbins_x",    1, NULL, 'x' },
775		{ "nbins_y",    1, NULL, 'y' },
776	+	{ "nbins_z",    1, NULL, 0 },
777		{ "nanglebins", 1, NULL, 'a' },
778		{ "length",     1, NULL, 0 },
779		{ "rcut",       1, NULL, 'c' },
#	Line 720 | Line 782 | cmdline_parser_internal (int argc, char * const *argv,
782		{ "sele2",      1, NULL, 0 },
783		{ "sele3",      1, NULL, 0 },
784		{ "refsele",    1, NULL, 0 },
785	+	{ "comsele",    1, NULL, 0 },
786		{ "molname",    1, NULL, 0 },
787		{ "begin",      1, NULL, 0 },
788		{ "end",        1, NULL, 0 },
789		{ "radius",     1, NULL, 0 },
790		{ "bo", 0, NULL, 0 },
791		{ "bor",        0, NULL, 0 },
792	+	{ "bad",        0, NULL, 0 },
793		{ "gofr",       0, NULL, 'g' },
794	+	{ "gofz",       0, NULL, 0 },
795		{ "r_theta",    0, NULL, 0 },
796		{ "r_omega",    0, NULL, 0 },
797	+	{ "r_z",        0, NULL, 0 },
798		{ "theta_omega",        0, NULL, 0 },
799		{ "gxyz",       0, NULL, 0 },
800		{ "p2", 0, NULL, 'p' },
#	Line 736 | Line 802 | cmdline_parser_internal (int argc, char * const *argv,
802		{ "scd",        0, NULL, 's' },
803		{ "density",    0, NULL, 'd' },
804		{ "slab_density",       0, NULL, 0 },
805	+	{ "p_angle",    0, NULL, 0 },
806		{ "hxy",        0, NULL, 0 },
807		{ "rho_r",      0, NULL, 0 },
808	+	{ "hullvol",    0, NULL, 0 },
809		{ NULL, 0, NULL, 0 }
810		};
811
744	–	stop_char = 0;
812		c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
813
814		if (c == -1) break;       /* Exit from `while (1)' loop.  */
#	Line 759 | Line 826 | cmdline_parser_internal (int argc, char * const *argv,
826		exit (EXIT_SUCCESS);
827
828		case 'i':       /* input dump file.  */
829	<	if (local_args_info.input_given)
830	<	{
831	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
832	<	goto failure;
833	<	}
834	<	if (args_info->input_given && ! override)
835	<	continue;
836	<	local_args_info.input_given = 1;
837	<	args_info->input_given = 1;
838	<	if (args_info->input_arg)
772	<	free (args_info->input_arg); /* free previous string */
773	<	args_info->input_arg = gengetopt_strdup (optarg);
774	<	if (args_info->input_orig)
775	<	free (args_info->input_orig); /* free previous string */
776	<	args_info->input_orig = gengetopt_strdup (optarg);
829	>
830	>
831	>	if (update_arg( (void *)&(args_info->input_arg),
832	>	&(args_info->input_orig), &(args_info->input_given),
833	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
834	>	check_ambiguity, override, 0, 0,
835	>	"input", 'i',
836	>	additional_error))
837	>	goto failure;
838	>
839		break;
778	–
840		case 'o':       /* output file name.  */
841	<	if (local_args_info.output_given)
842	<	{
843	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
844	<	goto failure;
845	<	}
846	<	if (args_info->output_given && ! override)
847	<	continue;
848	<	local_args_info.output_given = 1;
788	<	args_info->output_given = 1;
789	<	if (args_info->output_arg)
790	<	free (args_info->output_arg); /* free previous string */
791	<	args_info->output_arg = gengetopt_strdup (optarg);
792	<	if (args_info->output_orig)
793	<	free (args_info->output_orig); /* free previous string */
794	<	args_info->output_orig = gengetopt_strdup (optarg);
795	<	break;
796	<
797	<	case 'n':       /* process every n frame.  */
798	<	if (local_args_info.step_given)
799	<	{
800	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
801	<	goto failure;
802	<	}
803	<	if (args_info->step_given && ! override)
804	<	continue;
805	<	local_args_info.step_given = 1;
806	<	args_info->step_given = 1;
807	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
808	<	if (!(stop_char && *stop_char == '\0')) {
809	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
841	>
842	>
843	>	if (update_arg( (void *)&(args_info->output_arg),
844	>	&(args_info->output_orig), &(args_info->output_given),
845	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
846	>	check_ambiguity, override, 0, 0,
847	>	"output", 'o',
848	>	additional_error))
849		goto failure;
850	<	}
812	<	if (args_info->step_orig)
813	<	free (args_info->step_orig); /* free previous string */
814	<	args_info->step_orig = gengetopt_strdup (optarg);
850	>
851		break;
852	<
852	>	case 'n':       /* process every n frame.  */
853	>
854	>
855	>	if (update_arg( (void *)&(args_info->step_arg),
856	>	&(args_info->step_orig), &(args_info->step_given),
857	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
858	>	check_ambiguity, override, 0, 0,
859	>	"step", 'n',
860	>	additional_error))
861	>	goto failure;
862	>
863	>	break;
864		case 'b':       /* number of bins (general purpose).  */
865	<	if (local_args_info.nbins_given)
866	<	{
867	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
868	<	goto failure;
869	<	}
870	<	if (args_info->nbins_given && ! override)
871	<	continue;
872	<	local_args_info.nbins_given = 1;
826	<	args_info->nbins_given = 1;
827	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
828	<	if (!(stop_char && *stop_char == '\0')) {
829	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
865	>
866	>
867	>	if (update_arg( (void *)&(args_info->nbins_arg),
868	>	&(args_info->nbins_orig), &(args_info->nbins_given),
869	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
870	>	check_ambiguity, override, 0, 0,
871	>	"nbins", 'b',
872	>	additional_error))
873		goto failure;
874	<	}
832	<	if (args_info->nbins_orig)
833	<	free (args_info->nbins_orig); /* free previous string */
834	<	args_info->nbins_orig = gengetopt_strdup (optarg);
874	>
875		break;
836	–
876		case 'x':       /* number of bins in x axis.  */
877	<	if (local_args_info.nbins_x_given)
878	<	{
879	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
880	<	goto failure;
881	<	}
882	<	if (args_info->nbins_x_given && ! override)
883	<	continue;
884	<	local_args_info.nbins_x_given = 1;
846	<	args_info->nbins_x_given = 1;
847	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
848	<	if (!(stop_char && *stop_char == '\0')) {
849	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
877	>
878	>
879	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
880	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
881	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
882	>	check_ambiguity, override, 0, 0,
883	>	"nbins_x", 'x',
884	>	additional_error))
885		goto failure;
886	<	}
852	<	if (args_info->nbins_x_orig)
853	<	free (args_info->nbins_x_orig); /* free previous string */
854	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
886	>
887		break;
856	–
888		case 'y':       /* number of bins in y axis.  */
889	<	if (local_args_info.nbins_y_given)
890	<	{
891	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
892	<	goto failure;
893	<	}
894	<	if (args_info->nbins_y_given && ! override)
895	<	continue;
896	<	local_args_info.nbins_y_given = 1;
866	<	args_info->nbins_y_given = 1;
867	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
868	<	if (!(stop_char && *stop_char == '\0')) {
869	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
889	>
890	>
891	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
892	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
893	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
894	>	check_ambiguity, override, 0, 0,
895	>	"nbins_y", 'y',
896	>	additional_error))
897		goto failure;
898	<	}
872	<	if (args_info->nbins_y_orig)
873	<	free (args_info->nbins_y_orig); /* free previous string */
874	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
898	>
899		break;
876	–
900		case 'a':       /* number of bins for cos(angle).  */
901	<	if (local_args_info.nanglebins_given)
902	<	{
903	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
904	<	goto failure;
905	<	}
906	<	if (args_info->nanglebins_given && ! override)
907	<	continue;
908	<	local_args_info.nanglebins_given = 1;
886	<	args_info->nanglebins_given = 1;
887	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
888	<	if (!(stop_char && *stop_char == '\0')) {
889	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
901	>
902	>
903	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
904	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
905	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
906	>	check_ambiguity, override, 0, 0,
907	>	"nanglebins", 'a',
908	>	additional_error))
909		goto failure;
910	<	}
892	<	if (args_info->nanglebins_orig)
893	<	free (args_info->nanglebins_orig); /* free previous string */
894	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
910	>
911		break;
896	–
912		case 'c':       /* cutoff radius (rcut).  */
913	<	if (local_args_info.rcut_given)
914	<	{
915	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
916	<	goto failure;
917	<	}
918	<	if (args_info->rcut_given && ! override)
919	<	continue;
920	<	local_args_info.rcut_given = 1;
906	<	args_info->rcut_given = 1;
907	<	args_info->rcut_arg = strtod (optarg, &stop_char);
908	<	if (!(stop_char && *stop_char == '\0')) {
909	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
913	>
914	>
915	>	if (update_arg( (void *)&(args_info->rcut_arg),
916	>	&(args_info->rcut_orig), &(args_info->rcut_given),
917	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
918	>	check_ambiguity, override, 0, 0,
919	>	"rcut", 'c',
920	>	additional_error))
921		goto failure;
922	<	}
912	<	if (args_info->rcut_orig)
913	<	free (args_info->rcut_orig); /* free previous string */
914	<	args_info->rcut_orig = gengetopt_strdup (optarg);
922	>
923		break;
916	–
924		case 'z':       /* Where to set the zero for the slab_density calculation.  */
925	<	if (local_args_info.zoffset_given)
926	<	{
927	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
928	<	goto failure;
929	<	}
930	<	if (args_info->zoffset_given && ! override)
931	<	continue;
932	<	local_args_info.zoffset_given = 1;
926	<	args_info->zoffset_given = 1;
927	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
928	<	if (!(stop_char && *stop_char == '\0')) {
929	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
925	>
926	>
927	>	if (update_arg( (void *)&(args_info->zoffset_arg),
928	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
929	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
930	>	check_ambiguity, override, 0, 0,
931	>	"zoffset", 'z',
932	>	additional_error))
933		goto failure;
934	<	}
932	<	if (args_info->zoffset_orig)
933	<	free (args_info->zoffset_orig); /* free previous string */
934	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
934	>
935		break;
936	–
936		case 'g':       /* g(r).  */
937	<	if (local_args_info.gofr_given)
939	<	{
940	<	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
941	<	goto failure;
942	<	}
943	<	if (args_info->gofr_given && ! override)
944	<	continue;
945	<	local_args_info.gofr_given = 1;
946	<	args_info->gofr_given = 1;
937	>
938		if (args_info->staticProps_group_counter && override)
939		reset_group_staticProps (args_info);
940		args_info->staticProps_group_counter += 1;
941	+
942	+	if (update_arg( 0 ,
943	+	0 , &(args_info->gofr_given),
944	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
945	+	check_ambiguity, override, 0, 0,
946	+	"gofr", 'g',
947	+	additional_error))
948	+	goto failure;
949	+
950		break;
951	–
951		case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
952	<	if (local_args_info.p2_given)
954	<	{
955	<	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
956	<	goto failure;
957	<	}
958	<	if (args_info->p2_given && ! override)
959	<	continue;
960	<	local_args_info.p2_given = 1;
961	<	args_info->p2_given = 1;
952	>
953		if (args_info->staticProps_group_counter && override)
954		reset_group_staticProps (args_info);
955		args_info->staticProps_group_counter += 1;
956	<	break;
957	<
956	>
957	>	if (update_arg( 0 ,
958	>	0 , &(args_info->p2_given),
959	>	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
960	>	check_ambiguity, override, 0, 0,
961	>	"p2", 'p',
962	>	additional_error))
963	>	goto failure;
964	>
965	>	break;
966		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
967	<	if (local_args_info.scd_given)
969	<	{
970	<	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	<	goto failure;
972	<	}
973	<	if (args_info->scd_given && ! override)
974	<	continue;
975	<	local_args_info.scd_given = 1;
976	<	args_info->scd_given = 1;
967	>
968		if (args_info->staticProps_group_counter && override)
969		reset_group_staticProps (args_info);
970		args_info->staticProps_group_counter += 1;
971	+
972	+	if (update_arg( 0 ,
973	+	0 , &(args_info->scd_given),
974	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
975	+	check_ambiguity, override, 0, 0,
976	+	"scd", 's',
977	+	additional_error))
978	+	goto failure;
979	+
980		break;
981	–
981		case 'd':       /* density plot.  */
982	<	if (local_args_info.density_given)
984	<	{
985	<	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
986	<	goto failure;
987	<	}
988	<	if (args_info->density_given && ! override)
989	<	continue;
990	<	local_args_info.density_given = 1;
991	<	args_info->density_given = 1;
982	>
983		if (args_info->staticProps_group_counter && override)
984		reset_group_staticProps (args_info);
985		args_info->staticProps_group_counter += 1;
986	+
987	+	if (update_arg( 0 ,
988	+	0 , &(args_info->density_given),
989	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
990	+	check_ambiguity, override, 0, 0,
991	+	"density", 'd',
992	+	additional_error))
993	+	goto failure;
994	+
995		break;
996
997	–
997		case 0: /* Long option with no short option */
998	+	/* number of bins in z axis.  */
999	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1000	+	{
1001	+
1002	+
1003	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1004	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1005	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1006	+	check_ambiguity, override, 0, 0,
1007	+	"nbins_z", '-',
1008	+	additional_error))
1009	+	goto failure;
1010	+
1011	+	}
1012		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1013	<	if (strcmp (long_options[option_index].name, "length") == 0)
1013	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1014		{
1015	<	if (local_args_info.length_given)
1016	<	{
1017	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1018	<	goto failure;
1019	<	}
1020	<	if (args_info->length_given && ! override)
1021	<	continue;
1022	<	local_args_info.length_given = 1;
1010	<	args_info->length_given = 1;
1011	<	args_info->length_arg = strtod (optarg, &stop_char);
1012	<	if (!(stop_char && *stop_char == '\0')) {
1013	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1015	>
1016	>
1017	>	if (update_arg( (void *)&(args_info->length_arg),
1018	>	&(args_info->length_orig), &(args_info->length_given),
1019	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1020	>	check_ambiguity, override, 0, 0,
1021	>	"length", '-',
1022	>	additional_error))
1023		goto failure;
1024	<	}
1016	<	if (args_info->length_orig)
1017	<	free (args_info->length_orig); /* free previous string */
1018	<	args_info->length_orig = gengetopt_strdup (optarg);
1024	>
1025		}
1026		/* select the first stuntdouble set.  */
1027		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1028		{
1029	<	if (local_args_info.sele1_given)
1030	<	{
1031	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1032	<	goto failure;
1033	<	}
1034	<	if (args_info->sele1_given && ! override)
1035	<	continue;
1036	<	local_args_info.sele1_given = 1;
1037	<	args_info->sele1_given = 1;
1038	<	if (args_info->sele1_arg)
1033	<	free (args_info->sele1_arg); /* free previous string */
1034	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1035	<	if (args_info->sele1_orig)
1036	<	free (args_info->sele1_orig); /* free previous string */
1037	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1029	>
1030	>
1031	>	if (update_arg( (void *)&(args_info->sele1_arg),
1032	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1033	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1034	>	check_ambiguity, override, 0, 0,
1035	>	"sele1", '-',
1036	>	additional_error))
1037	>	goto failure;
1038	>
1039		}
1040		/* select the second stuntdouble set.  */
1041		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1042		{
1043	<	if (local_args_info.sele2_given)
1044	<	{
1045	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1046	<	goto failure;
1047	<	}
1048	<	if (args_info->sele2_given && ! override)
1049	<	continue;
1050	<	local_args_info.sele2_given = 1;
1051	<	args_info->sele2_given = 1;
1052	<	if (args_info->sele2_arg)
1052	<	free (args_info->sele2_arg); /* free previous string */
1053	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1054	<	if (args_info->sele2_orig)
1055	<	free (args_info->sele2_orig); /* free previous string */
1056	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1043	>
1044	>
1045	>	if (update_arg( (void *)&(args_info->sele2_arg),
1046	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1047	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1048	>	check_ambiguity, override, 0, 0,
1049	>	"sele2", '-',
1050	>	additional_error))
1051	>	goto failure;
1052	>
1053		}
1054		/* select the third stuntdouble set.  */
1055		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1056		{
1057	<	if (local_args_info.sele3_given)
1058	<	{
1059	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1060	<	goto failure;
1061	<	}
1062	<	if (args_info->sele3_given && ! override)
1063	<	continue;
1064	<	local_args_info.sele3_given = 1;
1065	<	args_info->sele3_given = 1;
1066	<	if (args_info->sele3_arg)
1071	<	free (args_info->sele3_arg); /* free previous string */
1072	<	args_info->sele3_arg = gengetopt_strdup (optarg);
1073	<	if (args_info->sele3_orig)
1074	<	free (args_info->sele3_orig); /* free previous string */
1075	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1057	>
1058	>
1059	>	if (update_arg( (void *)&(args_info->sele3_arg),
1060	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1061	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1062	>	check_ambiguity, override, 0, 0,
1063	>	"sele3", '-',
1064	>	additional_error))
1065	>	goto failure;
1066	>
1067		}
1068		/* select reference (use and only use with --gxyz).  */
1069		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1070		{
1071	<	if (local_args_info.refsele_given)
1072	<	{
1073	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1074	<	goto failure;
1075	<	}
1076	<	if (args_info->refsele_given && ! override)
1077	<	continue;
1078	<	local_args_info.refsele_given = 1;
1079	<	args_info->refsele_given = 1;
1080	<	if (args_info->refsele_arg)
1090	<	free (args_info->refsele_arg); /* free previous string */
1091	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1092	<	if (args_info->refsele_orig)
1093	<	free (args_info->refsele_orig); /* free previous string */
1094	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1071	>
1072	>
1073	>	if (update_arg( (void *)&(args_info->refsele_arg),
1074	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1075	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1076	>	check_ambiguity, override, 0, 0,
1077	>	"refsele", '-',
1078	>	additional_error))
1079	>	goto failure;
1080	>
1081		}
1082	+	/* select stunt doubles for center-of-mass reference point.  */
1083	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1084	+	{
1085	+
1086	+
1087	+	if (update_arg( (void *)&(args_info->comsele_arg),
1088	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1089	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1090	+	check_ambiguity, override, 0, 0,
1091	+	"comsele", '-',
1092	+	additional_error))
1093	+	goto failure;
1094	+
1095	+	}
1096		/* molecule name.  */
1097		else if (strcmp (long_options[option_index].name, "molname") == 0)
1098		{
1099	<	if (local_args_info.molname_given)
1100	<	{
1101	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1102	<	goto failure;
1103	<	}
1104	<	if (args_info->molname_given && ! override)
1105	<	continue;
1106	<	local_args_info.molname_given = 1;
1107	<	args_info->molname_given = 1;
1108	<	if (args_info->molname_arg)
1109	<	free (args_info->molname_arg); /* free previous string */
1110	<	args_info->molname_arg = gengetopt_strdup (optarg);
1111	<	if (args_info->molname_orig)
1112	<	free (args_info->molname_orig); /* free previous string */
1113	<	args_info->molname_orig = gengetopt_strdup (optarg);
1099	>
1100	>
1101	>	if (update_arg( (void *)&(args_info->molname_arg),
1102	>	&(args_info->molname_orig), &(args_info->molname_given),
1103	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1104	>	check_ambiguity, override, 0, 0,
1105	>	"molname", '-',
1106	>	additional_error))
1107	>	goto failure;
1108	>
1109		}
1110		/* begin internal index.  */
1111		else if (strcmp (long_options[option_index].name, "begin") == 0)
1112		{
1113	<	if (local_args_info.begin_given)
1114	<	{
1115	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1116	<	goto failure;
1117	<	}
1118	<	if (args_info->begin_given && ! override)
1119	<	continue;
1120	<	local_args_info.begin_given = 1;
1126	<	args_info->begin_given = 1;
1127	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1128	<	if (!(stop_char && *stop_char == '\0')) {
1129	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1113	>
1114	>
1115	>	if (update_arg( (void *)&(args_info->begin_arg),
1116	>	&(args_info->begin_orig), &(args_info->begin_given),
1117	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"begin", '-',
1120	>	additional_error))
1121		goto failure;
1122	<	}
1132	<	if (args_info->begin_orig)
1133	<	free (args_info->begin_orig); /* free previous string */
1134	<	args_info->begin_orig = gengetopt_strdup (optarg);
1122	>
1123		}
1124		/* end internal index.  */
1125		else if (strcmp (long_options[option_index].name, "end") == 0)
1126		{
1127	<	if (local_args_info.end_given)
1128	<	{
1129	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1130	<	goto failure;
1131	<	}
1132	<	if (args_info->end_given && ! override)
1133	<	continue;
1134	<	local_args_info.end_given = 1;
1147	<	args_info->end_given = 1;
1148	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
1149	<	if (!(stop_char && *stop_char == '\0')) {
1150	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1127	>
1128	>
1129	>	if (update_arg( (void *)&(args_info->end_arg),
1130	>	&(args_info->end_orig), &(args_info->end_given),
1131	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1132	>	check_ambiguity, override, 0, 0,
1133	>	"end", '-',
1134	>	additional_error))
1135		goto failure;
1136	<	}
1153	<	if (args_info->end_orig)
1154	<	free (args_info->end_orig); /* free previous string */
1155	<	args_info->end_orig = gengetopt_strdup (optarg);
1136	>
1137		}
1138		/* nanoparticle radius.  */
1139		else if (strcmp (long_options[option_index].name, "radius") == 0)
1140		{
1141	<	if (local_args_info.radius_given)
1142	<	{
1143	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1144	<	goto failure;
1145	<	}
1146	<	if (args_info->radius_given && ! override)
1147	<	continue;
1148	<	local_args_info.radius_given = 1;
1168	<	args_info->radius_given = 1;
1169	<	args_info->radius_arg = strtod (optarg, &stop_char);
1170	<	if (!(stop_char && *stop_char == '\0')) {
1171	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1141	>
1142	>
1143	>	if (update_arg( (void *)&(args_info->radius_arg),
1144	>	&(args_info->radius_orig), &(args_info->radius_given),
1145	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1146	>	check_ambiguity, override, 0, 0,
1147	>	"radius", '-',
1148	>	additional_error))
1149		goto failure;
1150	<	}
1174	<	if (args_info->radius_orig)
1175	<	free (args_info->radius_orig); /* free previous string */
1176	<	args_info->radius_orig = gengetopt_strdup (optarg);
1150	>
1151		}
1152		/* bond order parameter (--rcut must be specified).  */
1153		else if (strcmp (long_options[option_index].name, "bo") == 0)
1154		{
1155	<	if (local_args_info.bo_given)
1182	<	{
1183	<	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1184	<	goto failure;
1185	<	}
1186	<	if (args_info->bo_given && ! override)
1187	<	continue;
1188	<	local_args_info.bo_given = 1;
1189	<	args_info->bo_given = 1;
1155	>
1156		if (args_info->staticProps_group_counter && override)
1157		reset_group_staticProps (args_info);
1158		args_info->staticProps_group_counter += 1;
1159	<	break;
1159	>
1160	>	if (update_arg( 0 ,
1161	>	0 , &(args_info->bo_given),
1162	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1163	>	check_ambiguity, override, 0, 0,
1164	>	"bo", '-',
1165	>	additional_error))
1166	>	goto failure;
1167	>
1168		}
1169		/* bond order parameter as a function of radius (--rcut must be specified).  */
1170		else if (strcmp (long_options[option_index].name, "bor") == 0)
1171		{
1172	<	if (local_args_info.bor_given)
1199	<	{
1200	<	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1201	<	goto failure;
1202	<	}
1203	<	if (args_info->bor_given && ! override)
1204	<	continue;
1205	<	local_args_info.bor_given = 1;
1206	<	args_info->bor_given = 1;
1172	>
1173		if (args_info->staticProps_group_counter && override)
1174		reset_group_staticProps (args_info);
1175		args_info->staticProps_group_counter += 1;
1176	<	break;
1176	>
1177	>	if (update_arg( 0 ,
1178	>	0 , &(args_info->bor_given),
1179	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1180	>	check_ambiguity, override, 0, 0,
1181	>	"bor", '-',
1182	>	additional_error))
1183	>	goto failure;
1184	>
1185		}
1186	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1187	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1188	+	{
1189	+
1190	+	if (args_info->staticProps_group_counter && override)
1191	+	reset_group_staticProps (args_info);
1192	+	args_info->staticProps_group_counter += 1;
1193	+
1194	+	if (update_arg( 0 ,
1195	+	0 , &(args_info->bad_given),
1196	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1197	+	check_ambiguity, override, 0, 0,
1198	+	"bad", '-',
1199	+	additional_error))
1200	+	goto failure;
1201	+
1202	+	}
1203	+	/* g(z).  */
1204	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1205	+	{
1206	+
1207	+	if (args_info->staticProps_group_counter && override)
1208	+	reset_group_staticProps (args_info);
1209	+	args_info->staticProps_group_counter += 1;
1210	+
1211	+	if (update_arg( 0 ,
1212	+	0 , &(args_info->gofz_given),
1213	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1214	+	check_ambiguity, override, 0, 0,
1215	+	"gofz", '-',
1216	+	additional_error))
1217	+	goto failure;
1218	+
1219	+	}
1220		/* g(r, cos(theta)).  */
1221		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1222		{
1223	<	if (local_args_info.r_theta_given)
1216	<	{
1217	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1218	<	goto failure;
1219	<	}
1220	<	if (args_info->r_theta_given && ! override)
1221	<	continue;
1222	<	local_args_info.r_theta_given = 1;
1223	<	args_info->r_theta_given = 1;
1223	>
1224		if (args_info->staticProps_group_counter && override)
1225		reset_group_staticProps (args_info);
1226		args_info->staticProps_group_counter += 1;
1227	<	break;
1227	>
1228	>	if (update_arg( 0 ,
1229	>	0 , &(args_info->r_theta_given),
1230	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1231	>	check_ambiguity, override, 0, 0,
1232	>	"r_theta", '-',
1233	>	additional_error))
1234	>	goto failure;
1235	>
1236		}
1237		/* g(r, cos(omega)).  */
1238		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1239		{
1240	<	if (local_args_info.r_omega_given)
1233	<	{
1234	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1235	<	goto failure;
1236	<	}
1237	<	if (args_info->r_omega_given && ! override)
1238	<	continue;
1239	<	local_args_info.r_omega_given = 1;
1240	<	args_info->r_omega_given = 1;
1240	>
1241		if (args_info->staticProps_group_counter && override)
1242		reset_group_staticProps (args_info);
1243		args_info->staticProps_group_counter += 1;
1244	<	break;
1244	>
1245	>	if (update_arg( 0 ,
1246	>	0 , &(args_info->r_omega_given),
1247	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1248	>	check_ambiguity, override, 0, 0,
1249	>	"r_omega", '-',
1250	>	additional_error))
1251	>	goto failure;
1252	>
1253		}
1254	+	/* g(r, z).  */
1255	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1256	+	{
1257	+
1258	+	if (args_info->staticProps_group_counter && override)
1259	+	reset_group_staticProps (args_info);
1260	+	args_info->staticProps_group_counter += 1;
1261	+
1262	+	if (update_arg( 0 ,
1263	+	0 , &(args_info->r_z_given),
1264	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1265	+	check_ambiguity, override, 0, 0,
1266	+	"r_z", '-',
1267	+	additional_error))
1268	+	goto failure;
1269	+
1270	+	}
1271		/* g(cos(theta), cos(omega)).  */
1272		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1273		{
1274	<	if (local_args_info.theta_omega_given)
1250	<	{
1251	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	<	goto failure;
1253	<	}
1254	<	if (args_info->theta_omega_given && ! override)
1255	<	continue;
1256	<	local_args_info.theta_omega_given = 1;
1257	<	args_info->theta_omega_given = 1;
1274	>
1275		if (args_info->staticProps_group_counter && override)
1276		reset_group_staticProps (args_info);
1277		args_info->staticProps_group_counter += 1;
1278	<	break;
1278	>
1279	>	if (update_arg( 0 ,
1280	>	0 , &(args_info->theta_omega_given),
1281	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1282	>	check_ambiguity, override, 0, 0,
1283	>	"theta_omega", '-',
1284	>	additional_error))
1285	>	goto failure;
1286	>
1287		}
1288		/* g(x, y, z).  */
1289		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1290		{
1291	<	if (local_args_info.gxyz_given)
1267	<	{
1268	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1269	<	goto failure;
1270	<	}
1271	<	if (args_info->gxyz_given && ! override)
1272	<	continue;
1273	<	local_args_info.gxyz_given = 1;
1274	<	args_info->gxyz_given = 1;
1291	>
1292		if (args_info->staticProps_group_counter && override)
1293		reset_group_staticProps (args_info);
1294		args_info->staticProps_group_counter += 1;
1295	<	break;
1295	>
1296	>	if (update_arg( 0 ,
1297	>	0 , &(args_info->gxyz_given),
1298	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1299	>	check_ambiguity, override, 0, 0,
1300	>	"gxyz", '-',
1301	>	additional_error))
1302	>	goto failure;
1303	>
1304		}
1305		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1306		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1307		{
1308	<	if (local_args_info.rp2_given)
1284	<	{
1285	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1286	<	goto failure;
1287	<	}
1288	<	if (args_info->rp2_given && ! override)
1289	<	continue;
1290	<	local_args_info.rp2_given = 1;
1291	<	args_info->rp2_given = 1;
1308	>
1309		if (args_info->staticProps_group_counter && override)
1310		reset_group_staticProps (args_info);
1311		args_info->staticProps_group_counter += 1;
1312	<	break;
1312	>
1313	>	if (update_arg( 0 ,
1314	>	0 , &(args_info->rp2_given),
1315	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1316	>	check_ambiguity, override, 0, 0,
1317	>	"rp2", '-',
1318	>	additional_error))
1319	>	goto failure;
1320	>
1321		}
1322		/* slab density.  */
1323		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1324		{
1325	<	if (local_args_info.slab_density_given)
1301	<	{
1302	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1303	<	goto failure;
1304	<	}
1305	<	if (args_info->slab_density_given && ! override)
1306	<	continue;
1307	<	local_args_info.slab_density_given = 1;
1308	<	args_info->slab_density_given = 1;
1325	>
1326		if (args_info->staticProps_group_counter && override)
1327		reset_group_staticProps (args_info);
1328		args_info->staticProps_group_counter += 1;
1329	<	break;
1329	>
1330	>	if (update_arg( 0 ,
1331	>	0 , &(args_info->slab_density_given),
1332	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1333	>	check_ambiguity, override, 0, 0,
1334	>	"slab_density", '-',
1335	>	additional_error))
1336	>	goto failure;
1337	>
1338		}
1339	+	/* p(cos(theta)).  */
1340	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1341	+	{
1342	+
1343	+	if (args_info->staticProps_group_counter && override)
1344	+	reset_group_staticProps (args_info);
1345	+	args_info->staticProps_group_counter += 1;
1346	+
1347	+	if (update_arg( 0 ,
1348	+	0 , &(args_info->p_angle_given),
1349	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1350	+	check_ambiguity, override, 0, 0,
1351	+	"p_angle", '-',
1352	+	additional_error))
1353	+	goto failure;
1354	+
1355	+	}
1356		/* hxy.  */
1357		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1358		{
1359	<	if (local_args_info.hxy_given)
1318	<	{
1319	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1320	<	goto failure;
1321	<	}
1322	<	if (args_info->hxy_given && ! override)
1323	<	continue;
1324	<	local_args_info.hxy_given = 1;
1325	<	args_info->hxy_given = 1;
1359	>
1360		if (args_info->staticProps_group_counter && override)
1361		reset_group_staticProps (args_info);
1362		args_info->staticProps_group_counter += 1;
1363	<	break;
1363	>
1364	>	if (update_arg( 0 ,
1365	>	0 , &(args_info->hxy_given),
1366	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1367	>	check_ambiguity, override, 0, 0,
1368	>	"hxy", '-',
1369	>	additional_error))
1370	>	goto failure;
1371	>
1372		}
1373		/* rho of R.  */
1374		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1375		{
1376	<	if (local_args_info.rho_r_given)
1335	<	{
1336	<	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1337	<	goto failure;
1338	<	}
1339	<	if (args_info->rho_r_given && ! override)
1340	<	continue;
1341	<	local_args_info.rho_r_given = 1;
1342	<	args_info->rho_r_given = 1;
1376	>
1377		if (args_info->staticProps_group_counter && override)
1378		reset_group_staticProps (args_info);
1379		args_info->staticProps_group_counter += 1;
1380	<	break;
1380	>
1381	>	if (update_arg( 0 ,
1382	>	0 , &(args_info->rho_r_given),
1383	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1384	>	check_ambiguity, override, 0, 0,
1385	>	"rho_r", '-',
1386	>	additional_error))
1387	>	goto failure;
1388	>
1389		}
1390	+	/* hull volume of nanoparticle.  */
1391	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1392	+	{
1393
1394	+	if (args_info->staticProps_group_counter && override)
1395	+	reset_group_staticProps (args_info);
1396	+	args_info->staticProps_group_counter += 1;
1397	+
1398	+	if (update_arg( 0 ,
1399	+	0 , &(args_info->hullvol_given),
1400	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1401	+	check_ambiguity, override, 0, 0,
1402	+	"hullvol", '-',
1403	+	additional_error))
1404	+	goto failure;
1405	+
1406	+	}
1407	+
1408		break;
1409		case '?':       /* Invalid option.  */
1410		/* `getopt_long' already printed an error message.  */

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