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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 1445 by chuckv, Tue Jun 8 20:26:50 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
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 23 | Line 23 | const char *gengetopt_args_info_purpose = "";
23
24		const char *gengetopt_args_info_purpose = "";
25
26	<	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
26	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
27
28		const char *gengetopt_args_info_description = "";
29
#	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')",
40	–	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
41		"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
43	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
44		"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
45		"      --sele1=selection script  select the first stuntdouble set",
46		"      --sele2=selection script  select the second stuntdouble set",
47		"      --sele3=selection script  select the third stuntdouble set",
48		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
49	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
50		"      --molname=STRING          molecule name",
51		"      --begin=INT               begin internal index",
52		"      --end=INT                 end internal index",
#	Line 51 | Line 54 | const char *gengetopt_args_info_help[] = {
54		"\n Group: staticProps\n   an option of this group is required",
55		"      --bo                      bond order parameter (--rcut must be specified)",
56		"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
57	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
58		"  -g, --gofr                    g(r)",
59	+	"      --gofz                    g(z)",
60		"      --r_theta                 g(r, cos(theta))",
61		"      --r_omega                 g(r, cos(omega))",
62	+	"      --r_z                     g(r, z)",
63		"      --theta_omega             g(cos(theta), cos(omega))",
64		"      --gxyz                    g(x, y, z)",
65		"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
#	Line 61 | Line 67 | const char *gengetopt_args_info_help[] = {
67		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
68		"  -d, --density                 density plot",
69		"      --slab_density            slab density",
70	+	"      --p_angle                 p(cos(theta))",
71		"      --hxy                     hxy",
72		"      --rho_r                   rho of R",
73	+	"      --hullvol                 hull volume of nanoparticle",
74		0
75		};
76
77	+	typedef enum {ARG_NO
78	+	, ARG_STRING
79	+	, ARG_INT
80	+	, ARG_DOUBLE
81	+	} cmdline_parser_arg_type;
82	+
83		static
84		void clear_given (struct gengetopt_args_info *args_info);
85		static
86		void clear_args (struct gengetopt_args_info *args_info);
87
88		static int
89	<	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);
89	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
90	>	struct cmdline_parser_params *params, const char *additional_error);
91
92		static int
93		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 91 | Line 106 | void clear_given (struct gengetopt_args_info *args_inf
106		args_info->nbins_given = 0 ;
107		args_info->nbins_x_given = 0 ;
108		args_info->nbins_y_given = 0 ;
109	+	args_info->nbins_z_given = 0 ;
110		args_info->nanglebins_given = 0 ;
95	–	args_info->length_given = 0 ;
111		args_info->rcut_given = 0 ;
112	+	args_info->length_given = 0 ;
113	+	args_info->zlength_given = 0 ;
114		args_info->zoffset_given = 0 ;
115		args_info->sele1_given = 0 ;
116		args_info->sele2_given = 0 ;
117		args_info->sele3_given = 0 ;
118		args_info->refsele_given = 0 ;
119	+	args_info->comsele_given = 0 ;
120		args_info->molname_given = 0 ;
121		args_info->begin_given = 0 ;
122		args_info->end_given = 0 ;
123		args_info->radius_given = 0 ;
124		args_info->bo_given = 0 ;
125		args_info->bor_given = 0 ;
126	+	args_info->bad_given = 0 ;
127		args_info->gofr_given = 0 ;
128	+	args_info->gofz_given = 0 ;
129		args_info->r_theta_given = 0 ;
130		args_info->r_omega_given = 0 ;
131	+	args_info->r_z_given = 0 ;
132		args_info->theta_omega_given = 0 ;
133		args_info->gxyz_given = 0 ;
134		args_info->p2_given = 0 ;
#	Line 115 | Line 136 | void clear_given (struct gengetopt_args_info *args_inf
136		args_info->scd_given = 0 ;
137		args_info->density_given = 0 ;
138		args_info->slab_density_given = 0 ;
139	+	args_info->p_angle_given = 0 ;
140		args_info->hxy_given = 0 ;
141		args_info->rho_r_given = 0 ;
142	+	args_info->hullvol_given = 0 ;
143		args_info->staticProps_group_counter = 0 ;
144		}
145
#	Line 135 | Line 158 | void clear_args (struct gengetopt_args_info *args_info
158		args_info->nbins_x_orig = NULL;
159		args_info->nbins_y_arg = 100;
160		args_info->nbins_y_orig = NULL;
161	+	args_info->nbins_z_arg = 100;
162	+	args_info->nbins_z_orig = NULL;
163		args_info->nanglebins_arg = 50;
164		args_info->nanglebins_orig = NULL;
140	–	args_info->length_orig = NULL;
165		args_info->rcut_orig = NULL;
166	+	args_info->length_orig = NULL;
167	+	args_info->zlength_orig = NULL;
168		args_info->zoffset_arg = 0;
169		args_info->zoffset_orig = NULL;
170		args_info->sele1_arg = NULL;
#	Line 149 | Line 175 | void clear_args (struct gengetopt_args_info *args_info
175		args_info->sele3_orig = NULL;
176		args_info->refsele_arg = NULL;
177		args_info->refsele_orig = NULL;
178	+	args_info->comsele_arg = NULL;
179	+	args_info->comsele_orig = NULL;
180		args_info->molname_arg = NULL;
181		args_info->molname_orig = NULL;
182		args_info->begin_orig = NULL;
#	Line 160 | Line 188 | void init_args_info(struct gengetopt_args_info *args_i
188		static
189		void init_args_info(struct gengetopt_args_info *args_info)
190		{
191	+
192	+
193		args_info->help_help = gengetopt_args_info_help[0] ;
194		args_info->version_help = gengetopt_args_info_help[1] ;
195		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 168 | Line 198 | void init_args_info(struct gengetopt_args_info *args_i
198		args_info->nbins_help = gengetopt_args_info_help[5] ;
199		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
200		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
201	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
202	<	args_info->length_help = gengetopt_args_info_help[9] ;
201	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
202	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
203		args_info->rcut_help = gengetopt_args_info_help[10] ;
204	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
205	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
206	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
207	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
208	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
209	<	args_info->molname_help = gengetopt_args_info_help[16] ;
210	<	args_info->begin_help = gengetopt_args_info_help[17] ;
211	<	args_info->end_help = gengetopt_args_info_help[18] ;
212	<	args_info->radius_help = gengetopt_args_info_help[19] ;
213	<	args_info->bo_help = gengetopt_args_info_help[20] ;
214	<	args_info->bor_help = gengetopt_args_info_help[21] ;
215	<	args_info->gofr_help = gengetopt_args_info_help[22] ;
216	<	args_info->r_theta_help = gengetopt_args_info_help[23] ;
217	<	args_info->r_omega_help = gengetopt_args_info_help[24] ;
218	<	args_info->theta_omega_help = gengetopt_args_info_help[25] ;
219	<	args_info->gxyz_help = gengetopt_args_info_help[26] ;
220	<	args_info->p2_help = gengetopt_args_info_help[27] ;
221	<	args_info->rp2_help = gengetopt_args_info_help[28] ;
222	<	args_info->scd_help = gengetopt_args_info_help[29] ;
223	<	args_info->density_help = gengetopt_args_info_help[30] ;
224	<	args_info->slab_density_help = gengetopt_args_info_help[31] ;
225	<	args_info->hxy_help = gengetopt_args_info_help[32] ;
226	<	args_info->rho_r_help = gengetopt_args_info_help[33] ;
204	>	args_info->length_help = gengetopt_args_info_help[11] ;
205	>	args_info->zlength_help = gengetopt_args_info_help[12] ;
206	>	args_info->zoffset_help = gengetopt_args_info_help[13] ;
207	>	args_info->sele1_help = gengetopt_args_info_help[14] ;
208	>	args_info->sele2_help = gengetopt_args_info_help[15] ;
209	>	args_info->sele3_help = gengetopt_args_info_help[16] ;
210	>	args_info->refsele_help = gengetopt_args_info_help[17] ;
211	>	args_info->comsele_help = gengetopt_args_info_help[18] ;
212	>	args_info->molname_help = gengetopt_args_info_help[19] ;
213	>	args_info->begin_help = gengetopt_args_info_help[20] ;
214	>	args_info->end_help = gengetopt_args_info_help[21] ;
215	>	args_info->radius_help = gengetopt_args_info_help[22] ;
216	>	args_info->bo_help = gengetopt_args_info_help[24] ;
217	>	args_info->bor_help = gengetopt_args_info_help[25] ;
218	>	args_info->bad_help = gengetopt_args_info_help[26] ;
219	>	args_info->gofr_help = gengetopt_args_info_help[27] ;
220	>	args_info->gofz_help = gengetopt_args_info_help[28] ;
221	>	args_info->r_theta_help = gengetopt_args_info_help[29] ;
222	>	args_info->r_omega_help = gengetopt_args_info_help[30] ;
223	>	args_info->r_z_help = gengetopt_args_info_help[31] ;
224	>	args_info->theta_omega_help = gengetopt_args_info_help[32] ;
225	>	args_info->gxyz_help = gengetopt_args_info_help[33] ;
226	>	args_info->p2_help = gengetopt_args_info_help[34] ;
227	>	args_info->rp2_help = gengetopt_args_info_help[35] ;
228	>	args_info->scd_help = gengetopt_args_info_help[36] ;
229	>	args_info->density_help = gengetopt_args_info_help[37] ;
230	>	args_info->slab_density_help = gengetopt_args_info_help[38] ;
231	>	args_info->p_angle_help = gengetopt_args_info_help[39] ;
232	>	args_info->hxy_help = gengetopt_args_info_help[40] ;
233	>	args_info->rho_r_help = gengetopt_args_info_help[41] ;
234	>	args_info->hullvol_help = gengetopt_args_info_help[42] ;
235
236		}
237
#	Line 203 | Line 241 | cmdline_parser_print_version (void)
241		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
242		}
243
244	<	void
207	<	cmdline_parser_print_help (void)
208	<	{
209	<	int i = 0;
244	>	static void print_help_common(void) {
245		cmdline_parser_print_version ();
246
247		if (strlen(gengetopt_args_info_purpose) > 0)
248		printf("\n%s\n", gengetopt_args_info_purpose);
249
250	<	printf("\n%s\n\n", gengetopt_args_info_usage);
250	>	if (strlen(gengetopt_args_info_usage) > 0)
251	>	printf("\n%s\n", gengetopt_args_info_usage);
252	>
253	>	printf("\n");
254
255		if (strlen(gengetopt_args_info_description) > 0)
256		printf("%s\n", gengetopt_args_info_description);
257	+	}
258
259	+	void
260	+	cmdline_parser_print_help (void)
261	+	{
262	+	int i = 0;
263	+	print_help_common();
264		while (gengetopt_args_info_help[i])
265		printf("%s\n", gengetopt_args_info_help[i++]);
266		}
#	Line 227 | Line 271 | cmdline_parser_init (struct gengetopt_args_info *args_
271		clear_given (args_info);
272		clear_args (args_info);
273		init_args_info (args_info);
274	+	}
275
276	<	args_info->inputs = NULL;
277	<	args_info->inputs_num = 0;
276	>	void
277	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
278	>	{
279	>	if (params)
280	>	{
281	>	params->override = 0;
282	>	params->initialize = 1;
283	>	params->check_required = 1;
284	>	params->check_ambiguity = 0;
285	>	params->print_errors = 1;
286	>	}
287		}
288
289	+	struct cmdline_parser_params *
290	+	cmdline_parser_params_create(void)
291	+	{
292	+	struct cmdline_parser_params *params =
293	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
294	+	cmdline_parser_params_init(params);
295	+	return params;
296	+	}
297	+
298		static void
299	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
299	>	free_string_field (char **s)
300		{
301	<
239	<	unsigned int i;
240	<	if (args_info->input_arg)
301	>	if (*s)
302		{
303	<	free (args_info->input_arg); /* free previous argument */
304	<	args_info->input_arg = 0;
303	>	free (*s);
304	>	*s = 0;
305		}
306	<	if (args_info->input_orig)
307	<	{
308	<	free (args_info->input_orig); /* free previous argument */
309	<	args_info->input_orig = 0;
310	<	}
311	<	if (args_info->output_arg)
312	<	{
313	<	free (args_info->output_arg); /* free previous argument */
314	<	args_info->output_arg = 0;
315	<	}
316	<	if (args_info->output_orig)
317	<	{
318	<	free (args_info->output_orig); /* free previous argument */
319	<	args_info->output_orig = 0;
320	<	}
321	<	if (args_info->step_orig)
322	<	{
323	<	free (args_info->step_orig); /* free previous argument */
324	<	args_info->step_orig = 0;
325	<	}
326	<	if (args_info->nbins_orig)
327	<	{
328	<	free (args_info->nbins_orig); /* free previous argument */
329	<	args_info->nbins_orig = 0;
330	<	}
331	<	if (args_info->nbins_x_orig)
332	<	{
333	<	free (args_info->nbins_x_orig); /* free previous argument */
334	<	args_info->nbins_x_orig = 0;
335	<	}
336	<	if (args_info->nbins_y_orig)
337	<	{
338	<	free (args_info->nbins_y_orig); /* free previous argument */
339	<	args_info->nbins_y_orig = 0;
340	<	}
341	<	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	<	}
306	>	}
307	>
308	>
309	>	static void
310	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
311	>	{
312	>
313	>	free_string_field (&(args_info->input_arg));
314	>	free_string_field (&(args_info->input_orig));
315	>	free_string_field (&(args_info->output_arg));
316	>	free_string_field (&(args_info->output_orig));
317	>	free_string_field (&(args_info->step_orig));
318	>	free_string_field (&(args_info->nbins_orig));
319	>	free_string_field (&(args_info->nbins_x_orig));
320	>	free_string_field (&(args_info->nbins_y_orig));
321	>	free_string_field (&(args_info->nbins_z_orig));
322	>	free_string_field (&(args_info->nanglebins_orig));
323	>	free_string_field (&(args_info->rcut_orig));
324	>	free_string_field (&(args_info->length_orig));
325	>	free_string_field (&(args_info->zlength_orig));
326	>	free_string_field (&(args_info->zoffset_orig));
327	>	free_string_field (&(args_info->sele1_arg));
328	>	free_string_field (&(args_info->sele1_orig));
329	>	free_string_field (&(args_info->sele2_arg));
330	>	free_string_field (&(args_info->sele2_orig));
331	>	free_string_field (&(args_info->sele3_arg));
332	>	free_string_field (&(args_info->sele3_orig));
333	>	free_string_field (&(args_info->refsele_arg));
334	>	free_string_field (&(args_info->refsele_orig));
335	>	free_string_field (&(args_info->comsele_arg));
336	>	free_string_field (&(args_info->comsele_orig));
337	>	free_string_field (&(args_info->molname_arg));
338	>	free_string_field (&(args_info->molname_orig));
339	>	free_string_field (&(args_info->begin_orig));
340	>	free_string_field (&(args_info->end_orig));
341	>	free_string_field (&(args_info->radius_orig));
342
366	–	for (i = 0; i < args_info->inputs_num; ++i)
367	–	free (args_info->inputs [i]);
343
344	<	if (args_info->inputs_num)
370	<	free (args_info->inputs);
371	<
344	>
345		clear_given (args_info);
346		}
347
348	+
349	+	static void
350	+	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
351	+	{
352	+	if (arg) {
353	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
354	+	} else {
355	+	fprintf(outfile, "%s\n", opt);
356	+	}
357	+	}
358	+
359	+
360		int
361	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
362	+	{
363	+	int i = 0;
364	+
365	+	if (!outfile)
366	+	{
367	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
368	+	return EXIT_FAILURE;
369	+	}
370	+
371	+	if (args_info->help_given)
372	+	write_into_file(outfile, "help", 0, 0 );
373	+	if (args_info->version_given)
374	+	write_into_file(outfile, "version", 0, 0 );
375	+	if (args_info->input_given)
376	+	write_into_file(outfile, "input", args_info->input_orig, 0);
377	+	if (args_info->output_given)
378	+	write_into_file(outfile, "output", args_info->output_orig, 0);
379	+	if (args_info->step_given)
380	+	write_into_file(outfile, "step", args_info->step_orig, 0);
381	+	if (args_info->nbins_given)
382	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
383	+	if (args_info->nbins_x_given)
384	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
385	+	if (args_info->nbins_y_given)
386	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
387	+	if (args_info->nbins_z_given)
388	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
389	+	if (args_info->nanglebins_given)
390	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
391	+	if (args_info->rcut_given)
392	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
393	+	if (args_info->length_given)
394	+	write_into_file(outfile, "length", args_info->length_orig, 0);
395	+	if (args_info->zlength_given)
396	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
397	+	if (args_info->zoffset_given)
398	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
399	+	if (args_info->sele1_given)
400	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
401	+	if (args_info->sele2_given)
402	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
403	+	if (args_info->sele3_given)
404	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
405	+	if (args_info->refsele_given)
406	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
407	+	if (args_info->comsele_given)
408	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
409	+	if (args_info->molname_given)
410	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
411	+	if (args_info->begin_given)
412	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
413	+	if (args_info->end_given)
414	+	write_into_file(outfile, "end", args_info->end_orig, 0);
415	+	if (args_info->radius_given)
416	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
417	+	if (args_info->bo_given)
418	+	write_into_file(outfile, "bo", 0, 0 );
419	+	if (args_info->bor_given)
420	+	write_into_file(outfile, "bor", 0, 0 );
421	+	if (args_info->bad_given)
422	+	write_into_file(outfile, "bad", 0, 0 );
423	+	if (args_info->gofr_given)
424	+	write_into_file(outfile, "gofr", 0, 0 );
425	+	if (args_info->gofz_given)
426	+	write_into_file(outfile, "gofz", 0, 0 );
427	+	if (args_info->r_theta_given)
428	+	write_into_file(outfile, "r_theta", 0, 0 );
429	+	if (args_info->r_omega_given)
430	+	write_into_file(outfile, "r_omega", 0, 0 );
431	+	if (args_info->r_z_given)
432	+	write_into_file(outfile, "r_z", 0, 0 );
433	+	if (args_info->theta_omega_given)
434	+	write_into_file(outfile, "theta_omega", 0, 0 );
435	+	if (args_info->gxyz_given)
436	+	write_into_file(outfile, "gxyz", 0, 0 );
437	+	if (args_info->p2_given)
438	+	write_into_file(outfile, "p2", 0, 0 );
439	+	if (args_info->rp2_given)
440	+	write_into_file(outfile, "rp2", 0, 0 );
441	+	if (args_info->scd_given)
442	+	write_into_file(outfile, "scd", 0, 0 );
443	+	if (args_info->density_given)
444	+	write_into_file(outfile, "density", 0, 0 );
445	+	if (args_info->slab_density_given)
446	+	write_into_file(outfile, "slab_density", 0, 0 );
447	+	if (args_info->p_angle_given)
448	+	write_into_file(outfile, "p_angle", 0, 0 );
449	+	if (args_info->hxy_given)
450	+	write_into_file(outfile, "hxy", 0, 0 );
451	+	if (args_info->rho_r_given)
452	+	write_into_file(outfile, "rho_r", 0, 0 );
453	+	if (args_info->hullvol_given)
454	+	write_into_file(outfile, "hullvol", 0, 0 );
455	+
456	+
457	+	i = EXIT_SUCCESS;
458	+	return i;
459	+	}
460	+
461	+	int
462		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
463		{
464		FILE *outfile;
#	Line 386 | Line 472 | cmdline_parser_file_save(const char *filename, struct
472		return EXIT_FAILURE;
473		}
474
475	<	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	<
475	>	i = cmdline_parser_dump(outfile, args_info);
476		fclose (outfile);
477
566	–	i = EXIT_SUCCESS;
478		return i;
479		}
480
#	Line 573 | Line 484 | cmdline_parser_free (struct gengetopt_args_info *args_
484		cmdline_parser_release (args_info);
485		}
486
487	<
577	<	/* gengetopt_strdup() */
578	<	/* strdup.c replacement of strdup, which is not standard */
487	>	/** @brief replacement of strdup, which is not standard */
488		char *
489		gengetopt_strdup (const char *s)
490		{
#	Line 591 | Line 500 | static void
500		}
501
502		static void
594	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
595	–
596	–	static void
503		reset_group_staticProps(struct gengetopt_args_info *args_info)
504		{
505		if (! args_info->staticProps_group_counter)
#	Line 601 | Line 507 | reset_group_staticProps(struct gengetopt_args_info *ar
507
508		args_info->bo_given = 0 ;
509		args_info->bor_given = 0 ;
510	+	args_info->bad_given = 0 ;
511		args_info->gofr_given = 0 ;
512	+	args_info->gofz_given = 0 ;
513		args_info->r_theta_given = 0 ;
514		args_info->r_omega_given = 0 ;
515	+	args_info->r_z_given = 0 ;
516		args_info->theta_omega_given = 0 ;
517		args_info->gxyz_given = 0 ;
518		args_info->p2_given = 0 ;
#	Line 611 | Line 520 | reset_group_staticProps(struct gengetopt_args_info *ar
520		args_info->scd_given = 0 ;
521		args_info->density_given = 0 ;
522		args_info->slab_density_given = 0 ;
523	+	args_info->p_angle_given = 0 ;
524		args_info->hxy_given = 0 ;
525		args_info->rho_r_given = 0 ;
526	+	args_info->hullvol_given = 0 ;
527
528		args_info->staticProps_group_counter = 0;
529		}
#	Line 624 | Line 535 | int
535		}
536
537		int
538	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
539	+	struct cmdline_parser_params *params)
540	+	{
541	+	int result;
542	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
543	+
544	+	if (result == EXIT_FAILURE)
545	+	{
546	+	cmdline_parser_free (args_info);
547	+	exit (EXIT_FAILURE);
548	+	}
549	+
550	+	return result;
551	+	}
552	+
553	+	int
554		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
555		{
556		int result;
557	+	struct cmdline_parser_params params;
558	+
559	+	params.override = override;
560	+	params.initialize = initialize;
561	+	params.check_required = check_required;
562	+	params.check_ambiguity = 0;
563	+	params.print_errors = 1;
564
565	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
565	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
566
567		if (result == EXIT_FAILURE)
568		{
#	Line 678 | Line 612 | cmdline_parser_required2 (struct gengetopt_args_info *
612		/* checks for dependences among options */
613
614		return error;
615	+	}
616	+
617	+
618	+	static char *package_name = 0;
619	+
620	+	/**
621	+	* @brief updates an option
622	+	* @param field the generic pointer to the field to update
623	+	* @param orig_field the pointer to the orig field
624	+	* @param field_given the pointer to the number of occurrence of this option
625	+	* @param prev_given the pointer to the number of occurrence already seen
626	+	* @param value the argument for this option (if null no arg was specified)
627	+	* @param possible_values the possible values for this option (if specified)
628	+	* @param default_value the default value (in case the option only accepts fixed values)
629	+	* @param arg_type the type of this option
630	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
631	+	* @param override @see cmdline_parser_params.override
632	+	* @param no_free whether to free a possible previous value
633	+	* @param multiple_option whether this is a multiple option
634	+	* @param long_opt the corresponding long option
635	+	* @param short_opt the corresponding short option (or '-' if none)
636	+	* @param additional_error possible further error specification
637	+	*/
638	+	static
639	+	int update_arg(void *field, char **orig_field,
640	+	unsigned int *field_given, unsigned int *prev_given,
641	+	char *value, char *possible_values[], const char *default_value,
642	+	cmdline_parser_arg_type arg_type,
643	+	int check_ambiguity, int override,
644	+	int no_free, int multiple_option,
645	+	const char *long_opt, char short_opt,
646	+	const char *additional_error)
647	+	{
648	+	char *stop_char = 0;
649	+	const char *val = value;
650	+	int found;
651	+	char **string_field;
652	+
653	+	stop_char = 0;
654	+	found = 0;
655	+
656	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
657	+	{
658	+	if (short_opt != '-')
659	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
660	+	package_name, long_opt, short_opt,
661	+	(additional_error ? additional_error : ""));
662	+	else
663	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
664	+	package_name, long_opt,
665	+	(additional_error ? additional_error : ""));
666	+	return 1; /* failure */
667	+	}
668	+
669	+
670	+	if (field_given && *field_given && ! override)
671	+	return 0;
672	+	if (prev_given)
673	+	(*prev_given)++;
674	+	if (field_given)
675	+	(*field_given)++;
676	+	if (possible_values)
677	+	val = possible_values[found];
678	+
679	+	switch(arg_type) {
680	+	case ARG_INT:
681	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
682	+	break;
683	+	case ARG_DOUBLE:
684	+	if (val) *((double *)field) = strtod (val, &stop_char);
685	+	break;
686	+	case ARG_STRING:
687	+	if (val) {
688	+	string_field = (char **)field;
689	+	if (!no_free && *string_field)
690	+	free (*string_field); /* free previous string */
691	+	*string_field = gengetopt_strdup (val);
692	+	}
693	+	break;
694	+	default:
695	+	break;
696	+	};
697	+
698	+	/* check numeric conversion */
699	+	switch(arg_type) {
700	+	case ARG_INT:
701	+	case ARG_DOUBLE:
702	+	if (val && !(stop_char && *stop_char == '\0')) {
703	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
704	+	return 1; /* failure */
705	+	}
706	+	break;
707	+	default:
708	+	;
709	+	};
710	+
711	+	/* store the original value */
712	+	switch(arg_type) {
713	+	case ARG_NO:
714	+	break;
715	+	default:
716	+	if (value && orig_field) {
717	+	if (no_free) {
718	+	*orig_field = value;
719	+	} else {
720	+	if (*orig_field)
721	+	free (*orig_field); /* free previous string */
722	+	*orig_field = gengetopt_strdup (value);
723	+	}
724	+	}
725	+	};
726	+
727	+	return 0; /* OK */
728		}
729
730	+
731		int
732	<	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)
732	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
733	>	struct cmdline_parser_params *params, const char *additional_error)
734		{
735		int c;        /* Character of the parsed option.  */
736
737		int error = 0;
738		struct gengetopt_args_info local_args_info;
739	+
740	+	int override;
741	+	int initialize;
742	+	int check_required;
743	+	int check_ambiguity;
744	+
745	+	package_name = argv[0];
746	+
747	+	override = params->override;
748	+	initialize = params->initialize;
749	+	check_required = params->check_required;
750	+	check_ambiguity = params->check_ambiguity;
751
752		if (initialize)
753		cmdline_parser_init (args_info);
#	Line 695 | Line 756 | cmdline_parser_internal (int argc, char * const *argv,
756
757		optarg = 0;
758		optind = 0;
759	<	opterr = 1;
759	>	opterr = params->print_errors;
760		optopt = '?';
761
762		while (1)
763		{
764		int option_index = 0;
704	–	char *stop_char;
765
766		static struct option long_options[] = {
767		{ "help",       0, NULL, 'h' },
#	Line 712 | Line 772 | cmdline_parser_internal (int argc, char * const *argv,
772		{ "nbins",      1, NULL, 'b' },
773		{ "nbins_x",    1, NULL, 'x' },
774		{ "nbins_y",    1, NULL, 'y' },
775	+	{ "nbins_z",    1, NULL, 0 },
776		{ "nanglebins", 1, NULL, 'a' },
716	–	{ "length",     1, NULL, 0 },
777		{ "rcut",       1, NULL, 'c' },
778	+	{ "length",     1, NULL, 0 },
779	+	{ "zlength",    1, NULL, 0 },
780		{ "zoffset",    1, NULL, 'z' },
781		{ "sele1",      1, NULL, 0 },
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;
849	<	args_info->output_given = 1;
850	<	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);
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	>
851		break;
796	–
852		case 'n':       /* process every n frame.  */
853	<	if (local_args_info.step_given)
854	<	{
855	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
856	<	goto failure;
857	<	}
858	<	if (args_info->step_given && ! override)
859	<	continue;
860	<	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);
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	<	}
812	<	if (args_info->step_orig)
813	<	free (args_info->step_orig); /* free previous string */
814	<	args_info->step_orig = gengetopt_strdup (optarg);
862	>
863		break;
816	–
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	+
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	–
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	<	break;
972	<
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		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	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1027	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1028	+	{
1029	+
1030	+
1031	+	if (update_arg( (void *)&(args_info->zlength_arg),
1032	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1033	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1034	+	check_ambiguity, override, 0, 0,
1035	+	"zlength", '-',
1036	+	additional_error))
1037	+	goto failure;
1038	+
1039	+	}
1040		/* select the first stuntdouble set.  */
1041		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1042		{
1043	<	if (local_args_info.sele1_given)
1044	<	{
1045	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1046	<	goto failure;
1047	<	}
1048	<	if (args_info->sele1_given && ! override)
1049	<	continue;
1050	<	local_args_info.sele1_given = 1;
1051	<	args_info->sele1_given = 1;
1052	<	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);
1043	>
1044	>
1045	>	if (update_arg( (void *)&(args_info->sele1_arg),
1046	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1047	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1048	>	check_ambiguity, override, 0, 0,
1049	>	"sele1", '-',
1050	>	additional_error))
1051	>	goto failure;
1052	>
1053		}
1054		/* select the second stuntdouble set.  */
1055		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1056		{
1057	<	if (local_args_info.sele2_given)
1058	<	{
1059	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1060	<	goto failure;
1061	<	}
1062	<	if (args_info->sele2_given && ! override)
1063	<	continue;
1064	<	local_args_info.sele2_given = 1;
1065	<	args_info->sele2_given = 1;
1066	<	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);
1057	>
1058	>
1059	>	if (update_arg( (void *)&(args_info->sele2_arg),
1060	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1061	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1062	>	check_ambiguity, override, 0, 0,
1063	>	"sele2", '-',
1064	>	additional_error))
1065	>	goto failure;
1066	>
1067		}
1068		/* select the third stuntdouble set.  */
1069		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1070		{
1071	<	if (local_args_info.sele3_given)
1072	<	{
1073	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1074	<	goto failure;
1075	<	}
1076	<	if (args_info->sele3_given && ! override)
1077	<	continue;
1078	<	local_args_info.sele3_given = 1;
1079	<	args_info->sele3_given = 1;
1080	<	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);
1071	>
1072	>
1073	>	if (update_arg( (void *)&(args_info->sele3_arg),
1074	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1075	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1076	>	check_ambiguity, override, 0, 0,
1077	>	"sele3", '-',
1078	>	additional_error))
1079	>	goto failure;
1080	>
1081		}
1082		/* select reference (use and only use with --gxyz).  */
1083		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1084		{
1085	<	if (local_args_info.refsele_given)
1086	<	{
1087	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1088	<	goto failure;
1089	<	}
1090	<	if (args_info->refsele_given && ! override)
1091	<	continue;
1092	<	local_args_info.refsele_given = 1;
1093	<	args_info->refsele_given = 1;
1094	<	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);
1085	>
1086	>
1087	>	if (update_arg( (void *)&(args_info->refsele_arg),
1088	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1089	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1090	>	check_ambiguity, override, 0, 0,
1091	>	"refsele", '-',
1092	>	additional_error))
1093	>	goto failure;
1094	>
1095		}
1096	+	/* select stunt doubles for center-of-mass reference point.  */
1097	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1098	+	{
1099	+
1100	+
1101	+	if (update_arg( (void *)&(args_info->comsele_arg),
1102	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1103	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1104	+	check_ambiguity, override, 0, 0,
1105	+	"comsele", '-',
1106	+	additional_error))
1107	+	goto failure;
1108	+
1109	+	}
1110		/* molecule name.  */
1111		else if (strcmp (long_options[option_index].name, "molname") == 0)
1112		{
1113	<	if (local_args_info.molname_given)
1114	<	{
1115	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1116	<	goto failure;
1117	<	}
1118	<	if (args_info->molname_given && ! override)
1119	<	continue;
1120	<	local_args_info.molname_given = 1;
1121	<	args_info->molname_given = 1;
1122	<	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);
1113	>
1114	>
1115	>	if (update_arg( (void *)&(args_info->molname_arg),
1116	>	&(args_info->molname_orig), &(args_info->molname_given),
1117	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"molname", '-',
1120	>	additional_error))
1121	>	goto failure;
1122	>
1123		}
1124		/* begin internal index.  */
1125		else if (strcmp (long_options[option_index].name, "begin") == 0)
1126		{
1127	<	if (local_args_info.begin_given)
1128	<	{
1129	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1130	<	goto failure;
1131	<	}
1132	<	if (args_info->begin_given && ! override)
1133	<	continue;
1134	<	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);
1127	>
1128	>
1129	>	if (update_arg( (void *)&(args_info->begin_arg),
1130	>	&(args_info->begin_orig), &(args_info->begin_given),
1131	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1132	>	check_ambiguity, override, 0, 0,
1133	>	"begin", '-',
1134	>	additional_error))
1135		goto failure;
1136	<	}
1132	<	if (args_info->begin_orig)
1133	<	free (args_info->begin_orig); /* free previous string */
1134	<	args_info->begin_orig = gengetopt_strdup (optarg);
1136	>
1137		}
1138		/* end internal index.  */
1139		else if (strcmp (long_options[option_index].name, "end") == 0)
1140		{
1141	<	if (local_args_info.end_given)
1142	<	{
1143	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1144	<	goto failure;
1145	<	}
1146	<	if (args_info->end_given && ! override)
1147	<	continue;
1148	<	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);
1141	>
1142	>
1143	>	if (update_arg( (void *)&(args_info->end_arg),
1144	>	&(args_info->end_orig), &(args_info->end_given),
1145	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1146	>	check_ambiguity, override, 0, 0,
1147	>	"end", '-',
1148	>	additional_error))
1149		goto failure;
1150	<	}
1153	<	if (args_info->end_orig)
1154	<	free (args_info->end_orig); /* free previous string */
1155	<	args_info->end_orig = gengetopt_strdup (optarg);
1150	>
1151		}
1152		/* nanoparticle radius.  */
1153		else if (strcmp (long_options[option_index].name, "radius") == 0)
1154		{
1155	<	if (local_args_info.radius_given)
1156	<	{
1157	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1158	<	goto failure;
1159	<	}
1160	<	if (args_info->radius_given && ! override)
1161	<	continue;
1162	<	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);
1155	>
1156	>
1157	>	if (update_arg( (void *)&(args_info->radius_arg),
1158	>	&(args_info->radius_orig), &(args_info->radius_given),
1159	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1160	>	check_ambiguity, override, 0, 0,
1161	>	"radius", '-',
1162	>	additional_error))
1163		goto failure;
1164	<	}
1174	<	if (args_info->radius_orig)
1175	<	free (args_info->radius_orig); /* free previous string */
1176	<	args_info->radius_orig = gengetopt_strdup (optarg);
1164	>
1165		}
1166		/* bond order parameter (--rcut must be specified).  */
1167		else if (strcmp (long_options[option_index].name, "bo") == 0)
1168		{
1169	<	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;
1169	>
1170		if (args_info->staticProps_group_counter && override)
1171		reset_group_staticProps (args_info);
1172		args_info->staticProps_group_counter += 1;
1173	<	break;
1173	>
1174	>	if (update_arg( 0 ,
1175	>	0 , &(args_info->bo_given),
1176	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1177	>	check_ambiguity, override, 0, 0,
1178	>	"bo", '-',
1179	>	additional_error))
1180	>	goto failure;
1181	>
1182		}
1183		/* bond order parameter as a function of radius (--rcut must be specified).  */
1184		else if (strcmp (long_options[option_index].name, "bor") == 0)
1185		{
1186	<	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;
1186	>
1187		if (args_info->staticProps_group_counter && override)
1188		reset_group_staticProps (args_info);
1189		args_info->staticProps_group_counter += 1;
1190	<	break;
1190	>
1191	>	if (update_arg( 0 ,
1192	>	0 , &(args_info->bor_given),
1193	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1194	>	check_ambiguity, override, 0, 0,
1195	>	"bor", '-',
1196	>	additional_error))
1197	>	goto failure;
1198	>
1199		}
1200	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1201	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1202	+	{
1203	+
1204	+	if (args_info->staticProps_group_counter && override)
1205	+	reset_group_staticProps (args_info);
1206	+	args_info->staticProps_group_counter += 1;
1207	+
1208	+	if (update_arg( 0 ,
1209	+	0 , &(args_info->bad_given),
1210	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1211	+	check_ambiguity, override, 0, 0,
1212	+	"bad", '-',
1213	+	additional_error))
1214	+	goto failure;
1215	+
1216	+	}
1217	+	/* g(z).  */
1218	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1219	+	{
1220	+
1221	+	if (args_info->staticProps_group_counter && override)
1222	+	reset_group_staticProps (args_info);
1223	+	args_info->staticProps_group_counter += 1;
1224	+
1225	+	if (update_arg( 0 ,
1226	+	0 , &(args_info->gofz_given),
1227	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1228	+	check_ambiguity, override, 0, 0,
1229	+	"gofz", '-',
1230	+	additional_error))
1231	+	goto failure;
1232	+
1233	+	}
1234		/* g(r, cos(theta)).  */
1235		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1236		{
1237	<	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;
1237	>
1238		if (args_info->staticProps_group_counter && override)
1239		reset_group_staticProps (args_info);
1240		args_info->staticProps_group_counter += 1;
1241	<	break;
1241	>
1242	>	if (update_arg( 0 ,
1243	>	0 , &(args_info->r_theta_given),
1244	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1245	>	check_ambiguity, override, 0, 0,
1246	>	"r_theta", '-',
1247	>	additional_error))
1248	>	goto failure;
1249	>
1250		}
1251		/* g(r, cos(omega)).  */
1252		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1253		{
1254	<	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;
1254	>
1255		if (args_info->staticProps_group_counter && override)
1256		reset_group_staticProps (args_info);
1257		args_info->staticProps_group_counter += 1;
1258	<	break;
1258	>
1259	>	if (update_arg( 0 ,
1260	>	0 , &(args_info->r_omega_given),
1261	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1262	>	check_ambiguity, override, 0, 0,
1263	>	"r_omega", '-',
1264	>	additional_error))
1265	>	goto failure;
1266	>
1267		}
1268	+	/* g(r, z).  */
1269	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1270	+	{
1271	+
1272	+	if (args_info->staticProps_group_counter && override)
1273	+	reset_group_staticProps (args_info);
1274	+	args_info->staticProps_group_counter += 1;
1275	+
1276	+	if (update_arg( 0 ,
1277	+	0 , &(args_info->r_z_given),
1278	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1279	+	check_ambiguity, override, 0, 0,
1280	+	"r_z", '-',
1281	+	additional_error))
1282	+	goto failure;
1283	+
1284	+	}
1285		/* g(cos(theta), cos(omega)).  */
1286		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1287		{
1288	<	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;
1288	>
1289		if (args_info->staticProps_group_counter && override)
1290		reset_group_staticProps (args_info);
1291		args_info->staticProps_group_counter += 1;
1292	<	break;
1292	>
1293	>	if (update_arg( 0 ,
1294	>	0 , &(args_info->theta_omega_given),
1295	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1296	>	check_ambiguity, override, 0, 0,
1297	>	"theta_omega", '-',
1298	>	additional_error))
1299	>	goto failure;
1300	>
1301		}
1302		/* g(x, y, z).  */
1303		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1304		{
1305	<	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;
1305	>
1306		if (args_info->staticProps_group_counter && override)
1307		reset_group_staticProps (args_info);
1308		args_info->staticProps_group_counter += 1;
1309	<	break;
1309	>
1310	>	if (update_arg( 0 ,
1311	>	0 , &(args_info->gxyz_given),
1312	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1313	>	check_ambiguity, override, 0, 0,
1314	>	"gxyz", '-',
1315	>	additional_error))
1316	>	goto failure;
1317	>
1318		}
1319		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1320		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1321		{
1322	<	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;
1322	>
1323		if (args_info->staticProps_group_counter && override)
1324		reset_group_staticProps (args_info);
1325		args_info->staticProps_group_counter += 1;
1326	<	break;
1326	>
1327	>	if (update_arg( 0 ,
1328	>	0 , &(args_info->rp2_given),
1329	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1330	>	check_ambiguity, override, 0, 0,
1331	>	"rp2", '-',
1332	>	additional_error))
1333	>	goto failure;
1334	>
1335		}
1336		/* slab density.  */
1337		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1338		{
1339	<	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;
1339	>
1340		if (args_info->staticProps_group_counter && override)
1341		reset_group_staticProps (args_info);
1342		args_info->staticProps_group_counter += 1;
1343	<	break;
1343	>
1344	>	if (update_arg( 0 ,
1345	>	0 , &(args_info->slab_density_given),
1346	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1347	>	check_ambiguity, override, 0, 0,
1348	>	"slab_density", '-',
1349	>	additional_error))
1350	>	goto failure;
1351	>
1352		}
1353	+	/* p(cos(theta)).  */
1354	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1355	+	{
1356	+
1357	+	if (args_info->staticProps_group_counter && override)
1358	+	reset_group_staticProps (args_info);
1359	+	args_info->staticProps_group_counter += 1;
1360	+
1361	+	if (update_arg( 0 ,
1362	+	0 , &(args_info->p_angle_given),
1363	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1364	+	check_ambiguity, override, 0, 0,
1365	+	"p_angle", '-',
1366	+	additional_error))
1367	+	goto failure;
1368	+
1369	+	}
1370		/* hxy.  */
1371		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1372		{
1373	<	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;
1373	>
1374		if (args_info->staticProps_group_counter && override)
1375		reset_group_staticProps (args_info);
1376		args_info->staticProps_group_counter += 1;
1377	<	break;
1377	>
1378	>	if (update_arg( 0 ,
1379	>	0 , &(args_info->hxy_given),
1380	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1381	>	check_ambiguity, override, 0, 0,
1382	>	"hxy", '-',
1383	>	additional_error))
1384	>	goto failure;
1385	>
1386		}
1387		/* rho of R.  */
1388		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1389		{
1390	<	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;
1390	>
1391		if (args_info->staticProps_group_counter && override)
1392		reset_group_staticProps (args_info);
1393		args_info->staticProps_group_counter += 1;
1394	<	break;
1394	>
1395	>	if (update_arg( 0 ,
1396	>	0 , &(args_info->rho_r_given),
1397	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1398	>	check_ambiguity, override, 0, 0,
1399	>	"rho_r", '-',
1400	>	additional_error))
1401	>	goto failure;
1402	>
1403		}
1404	+	/* hull volume of nanoparticle.  */
1405	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1406	+	{
1407
1408	+	if (args_info->staticProps_group_counter && override)
1409	+	reset_group_staticProps (args_info);
1410	+	args_info->staticProps_group_counter += 1;
1411	+
1412	+	if (update_arg( 0 ,
1413	+	0 , &(args_info->hullvol_given),
1414	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1415	+	check_ambiguity, override, 0, 0,
1416	+	"hullvol", '-',
1417	+	additional_error))
1418	+	goto failure;
1419	+
1420	+	}
1421	+
1422		break;
1423		case '?':       /* Invalid option.  */
1424		/* `getopt_long' already printed an error message.  */
#	Line 1375 | Line 1448 | cmdline_parser_internal (int argc, char * const *argv,
1448		if ( error )
1449		return (EXIT_FAILURE);
1450
1378	–	if (optind < argc)
1379	–	{
1380	–	int i = 0 ;
1381	–	int found_prog_name = 0;
1382	–	/* whether program name, i.e., argv[0], is in the remaining args
1383	–	(this may happen with some implementations of getopt,
1384	–	but surely not with the one included by gengetopt) */
1385	–
1386	–	i = optind;
1387	–	while (i < argc)
1388	–	if (argv[i++] == argv[0]) {
1389	–	found_prog_name = 1;
1390	–	break;
1391	–	}
1392	–	i = 0;
1393	–
1394	–	args_info->inputs_num = argc - optind - found_prog_name;
1395	–	args_info->inputs =
1396	–	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1397	–	while (optind < argc)
1398	–	if (argv[optind++] != argv[0])
1399	–	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1400	–	}
1401	–
1451		return 0;
1452
1453		failure:

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords):
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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+	Added lines
<	Changed lines
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