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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 929 by gezelter, Tue Apr 11 15:33:27 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.16
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4		gengetopt -F StaticPropsCmd
5
#	Line 21 | Line 21
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
41	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
43	+	"      --sele1=selection script  select the first stuntdouble set",
44	+	"      --sele2=selection script  select the second stuntdouble set",
45	+	"      --sele3=selection script  select the third stuntdouble set",
46	+	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
47	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
48	+	"      --molname=STRING          molecule name",
49	+	"      --begin=INT               begin internal index",
50	+	"      --end=INT                 end internal index",
51	+	"      --radius=DOUBLE           nanoparticle radius",
52	+	"\n Group: staticProps\n   an option of this group is required",
53	+	"      --bo                      bond order parameter (--rcut must be specified)",
54	+	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
55	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
56	+	"  -g, --gofr                    g(r)",
57	+	"      --gofz                    g(z)",
58	+	"      --r_theta                 g(r, cos(theta))",
59	+	"      --r_omega                 g(r, cos(omega))",
60	+	"      --theta_omega             g(cos(theta), cos(omega))",
61	+	"      --gxyz                    g(x, y, z)",
62	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
63	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
64	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
65	+	"  -d, --density                 density plot",
66	+	"      --slab_density            slab density",
67	+	"      --hxy                     hxy",
68	+	"      --rho_r                   rho of R",
69	+	"      --hullvol                 hull volume of nanoparticle",
70	+	0
71	+	};
72	+
73	+	typedef enum {ARG_NO
74	+	, ARG_STRING
75	+	, ARG_INT
76	+	, ARG_DOUBLE
77	+	} cmdline_parser_arg_type;
78	+
79		static
80		void clear_given (struct gengetopt_args_info *args_info);
81		static
82		void clear_args (struct gengetopt_args_info *args_info);
83
84		static int
85	<	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);
85	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
86	>	struct cmdline_parser_params *params, const char *additional_error);
87
88		static int
89		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 43 | Line 99 | void clear_given (struct gengetopt_args_info *args_inf
99		args_info->input_given = 0 ;
100		args_info->output_given = 0 ;
101		args_info->step_given = 0 ;
102	<	args_info->nrbins_given = 0 ;
102	>	args_info->nbins_given = 0 ;
103	>	args_info->nbins_x_given = 0 ;
104	>	args_info->nbins_y_given = 0 ;
105		args_info->nanglebins_given = 0 ;
106		args_info->length_given = 0 ;
107	+	args_info->rcut_given = 0 ;
108		args_info->zoffset_given = 0 ;
109		args_info->sele1_given = 0 ;
110		args_info->sele2_given = 0 ;
111		args_info->sele3_given = 0 ;
112		args_info->refsele_given = 0 ;
113	+	args_info->comsele_given = 0 ;
114		args_info->molname_given = 0 ;
115		args_info->begin_given = 0 ;
116		args_info->end_given = 0 ;
117	+	args_info->radius_given = 0 ;
118	+	args_info->bo_given = 0 ;
119	+	args_info->bor_given = 0 ;
120	+	args_info->bad_given = 0 ;
121		args_info->gofr_given = 0 ;
122	+	args_info->gofz_given = 0 ;
123		args_info->r_theta_given = 0 ;
124		args_info->r_omega_given = 0 ;
125		args_info->theta_omega_given = 0 ;
126		args_info->gxyz_given = 0 ;
127		args_info->p2_given = 0 ;
128	+	args_info->rp2_given = 0 ;
129		args_info->scd_given = 0 ;
130		args_info->density_given = 0 ;
131		args_info->slab_density_given = 0 ;
132	+	args_info->hxy_given = 0 ;
133	+	args_info->rho_r_given = 0 ;
134	+	args_info->hullvol_given = 0 ;
135		args_info->staticProps_group_counter = 0 ;
136		}
137
#	Line 75 | Line 144 | void clear_args (struct gengetopt_args_info *args_info
144		args_info->output_orig = NULL;
145		args_info->step_arg = 1;
146		args_info->step_orig = NULL;
147	<	args_info->nrbins_arg = 100;
148	<	args_info->nrbins_orig = NULL;
147	>	args_info->nbins_arg = 100;
148	>	args_info->nbins_orig = NULL;
149	>	args_info->nbins_x_arg = 100;
150	>	args_info->nbins_x_orig = NULL;
151	>	args_info->nbins_y_arg = 100;
152	>	args_info->nbins_y_orig = NULL;
153		args_info->nanglebins_arg = 50;
154		args_info->nanglebins_orig = NULL;
155		args_info->length_orig = NULL;
156	+	args_info->rcut_orig = NULL;
157		args_info->zoffset_arg = 0;
158		args_info->zoffset_orig = NULL;
159		args_info->sele1_arg = NULL;
#	Line 90 | Line 164 | void clear_args (struct gengetopt_args_info *args_info
164		args_info->sele3_orig = NULL;
165		args_info->refsele_arg = NULL;
166		args_info->refsele_orig = NULL;
167	+	args_info->comsele_arg = NULL;
168	+	args_info->comsele_orig = NULL;
169		args_info->molname_arg = NULL;
170		args_info->molname_orig = NULL;
171		args_info->begin_orig = NULL;
172		args_info->end_orig = NULL;
173	+	args_info->radius_orig = NULL;
174
175		}
176
177	+	static
178	+	void init_args_info(struct gengetopt_args_info *args_info)
179	+	{
180	+
181	+
182	+	args_info->help_help = gengetopt_args_info_help[0] ;
183	+	args_info->version_help = gengetopt_args_info_help[1] ;
184	+	args_info->input_help = gengetopt_args_info_help[2] ;
185	+	args_info->output_help = gengetopt_args_info_help[3] ;
186	+	args_info->step_help = gengetopt_args_info_help[4] ;
187	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
188	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
189	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
190	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
191	+	args_info->length_help = gengetopt_args_info_help[9] ;
192	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
193	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
194	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
195	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
196	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
197	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
198	+	args_info->comsele_help = gengetopt_args_info_help[16] ;
199	+	args_info->molname_help = gengetopt_args_info_help[17] ;
200	+	args_info->begin_help = gengetopt_args_info_help[18] ;
201	+	args_info->end_help = gengetopt_args_info_help[19] ;
202	+	args_info->radius_help = gengetopt_args_info_help[20] ;
203	+	args_info->bo_help = gengetopt_args_info_help[22] ;
204	+	args_info->bor_help = gengetopt_args_info_help[23] ;
205	+	args_info->bad_help = gengetopt_args_info_help[24] ;
206	+	args_info->gofr_help = gengetopt_args_info_help[25] ;
207	+	args_info->gofz_help = gengetopt_args_info_help[26] ;
208	+	args_info->r_theta_help = gengetopt_args_info_help[27] ;
209	+	args_info->r_omega_help = gengetopt_args_info_help[28] ;
210	+	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
211	+	args_info->gxyz_help = gengetopt_args_info_help[30] ;
212	+	args_info->p2_help = gengetopt_args_info_help[31] ;
213	+	args_info->rp2_help = gengetopt_args_info_help[32] ;
214	+	args_info->scd_help = gengetopt_args_info_help[33] ;
215	+	args_info->density_help = gengetopt_args_info_help[34] ;
216	+	args_info->slab_density_help = gengetopt_args_info_help[35] ;
217	+	args_info->hxy_help = gengetopt_args_info_help[36] ;
218	+	args_info->rho_r_help = gengetopt_args_info_help[37] ;
219	+	args_info->hullvol_help = gengetopt_args_info_help[38] ;
220	+
221	+	}
222	+
223		void
224		cmdline_parser_print_version (void)
225		{
226		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
227		}
228
229	+	static void print_help_common(void) {
230	+	cmdline_parser_print_version ();
231	+
232	+	if (strlen(gengetopt_args_info_purpose) > 0)
233	+	printf("\n%s\n", gengetopt_args_info_purpose);
234	+
235	+	if (strlen(gengetopt_args_info_usage) > 0)
236	+	printf("\n%s\n", gengetopt_args_info_usage);
237	+
238	+	printf("\n");
239	+
240	+	if (strlen(gengetopt_args_info_description) > 0)
241	+	printf("%s\n", gengetopt_args_info_description);
242	+	}
243	+
244		void
245		cmdline_parser_print_help (void)
246		{
247	<	cmdline_parser_print_version ();
248	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
249	<	printf("%s\n","  -h, --help                    Print help and exit");
250	<	printf("%s\n","  -V, --version                 Print version and exit");
113	<	printf("%s\n","  -i, --input=filename          input dump file");
114	<	printf("%s\n","  -o, --output=filename         output file name");
115	<	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
116	<	printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
117	<	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
118	<	printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
119	<	printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
120	<	printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
121	<	printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
122	<	printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
123	<	printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
124	<	printf("%s\n","      --molname=STRING          molecule name");
125	<	printf("%s\n","      --begin=INT               begin interanl index");
126	<	printf("%s\n","      --end=INT                 end internal index");
127	<	printf("%s\n","\n Group: staticProps\n   an option of this group is required");
128	<	printf("%s\n","      --gofr                    g(r)");
129	<	printf("%s\n","      --r_theta                 g(r, cos(theta))");
130	<	printf("%s\n","      --r_omega                 g(r, cos(omega))");
131	<	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
132	<	printf("%s\n","      --gxyz                    g(x, y, z)");
133	<	printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
134	<	printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
135	<	printf("%s\n","      --density                 density plot (--sele1 must be specified)");
136	<	printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
137	<
247	>	int i = 0;
248	>	print_help_common();
249	>	while (gengetopt_args_info_help[i])
250	>	printf("%s\n", gengetopt_args_info_help[i++]);
251		}
252
253		void
#	Line 142 | Line 255 | cmdline_parser_init (struct gengetopt_args_info *args_
255		{
256		clear_given (args_info);
257		clear_args (args_info);
258	+	init_args_info (args_info);
259		}
260
261	+	void
262	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
263	+	{
264	+	if (params)
265	+	{
266	+	params->override = 0;
267	+	params->initialize = 1;
268	+	params->check_required = 1;
269	+	params->check_ambiguity = 0;
270	+	params->print_errors = 1;
271	+	}
272	+	}
273	+
274	+	struct cmdline_parser_params *
275	+	cmdline_parser_params_create(void)
276	+	{
277	+	struct cmdline_parser_params *params =
278	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
279	+	cmdline_parser_params_init(params);
280	+	return params;
281	+	}
282	+
283		static void
284	+	free_string_field (char **s)
285	+	{
286	+	if (*s)
287	+	{
288	+	free (*s);
289	+	*s = 0;
290	+	}
291	+	}
292	+
293	+
294	+	static void
295		cmdline_parser_release (struct gengetopt_args_info *args_info)
296		{
297	+
298	+	free_string_field (&(args_info->input_arg));
299	+	free_string_field (&(args_info->input_orig));
300	+	free_string_field (&(args_info->output_arg));
301	+	free_string_field (&(args_info->output_orig));
302	+	free_string_field (&(args_info->step_orig));
303	+	free_string_field (&(args_info->nbins_orig));
304	+	free_string_field (&(args_info->nbins_x_orig));
305	+	free_string_field (&(args_info->nbins_y_orig));
306	+	free_string_field (&(args_info->nanglebins_orig));
307	+	free_string_field (&(args_info->length_orig));
308	+	free_string_field (&(args_info->rcut_orig));
309	+	free_string_field (&(args_info->zoffset_orig));
310	+	free_string_field (&(args_info->sele1_arg));
311	+	free_string_field (&(args_info->sele1_orig));
312	+	free_string_field (&(args_info->sele2_arg));
313	+	free_string_field (&(args_info->sele2_orig));
314	+	free_string_field (&(args_info->sele3_arg));
315	+	free_string_field (&(args_info->sele3_orig));
316	+	free_string_field (&(args_info->refsele_arg));
317	+	free_string_field (&(args_info->refsele_orig));
318	+	free_string_field (&(args_info->comsele_arg));
319	+	free_string_field (&(args_info->comsele_orig));
320	+	free_string_field (&(args_info->molname_arg));
321	+	free_string_field (&(args_info->molname_orig));
322	+	free_string_field (&(args_info->begin_orig));
323	+	free_string_field (&(args_info->end_orig));
324	+	free_string_field (&(args_info->radius_orig));
325
326	<	if (args_info->input_arg)
326	>
327	>
328	>	clear_given (args_info);
329	>	}
330	>
331	>
332	>	static void
333	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
334	>	{
335	>	if (arg) {
336	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
337	>	} else {
338	>	fprintf(outfile, "%s\n", opt);
339	>	}
340	>	}
341	>
342	>
343	>	int
344	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
345	>	{
346	>	int i = 0;
347	>
348	>	if (!outfile)
349		{
350	<	free (args_info->input_arg); /* free previous argument */
351	<	args_info->input_arg = 0;
350	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
351	>	return EXIT_FAILURE;
352		}
353	<	if (args_info->input_orig)
354	<	{
355	<	free (args_info->input_orig); /* free previous argument */
356	<	args_info->input_orig = 0;
357	<	}
358	<	if (args_info->output_arg)
359	<	{
360	<	free (args_info->output_arg); /* free previous argument */
361	<	args_info->output_arg = 0;
362	<	}
363	<	if (args_info->output_orig)
364	<	{
365	<	free (args_info->output_orig); /* free previous argument */
366	<	args_info->output_orig = 0;
367	<	}
368	<	if (args_info->step_orig)
369	<	{
370	<	free (args_info->step_orig); /* free previous argument */
371	<	args_info->step_orig = 0;
372	<	}
373	<	if (args_info->nrbins_orig)
374	<	{
375	<	free (args_info->nrbins_orig); /* free previous argument */
376	<	args_info->nrbins_orig = 0;
377	<	}
378	<	if (args_info->nanglebins_orig)
379	<	{
380	<	free (args_info->nanglebins_orig); /* free previous argument */
381	<	args_info->nanglebins_orig = 0;
382	<	}
383	<	if (args_info->length_orig)
384	<	{
385	<	free (args_info->length_orig); /* free previous argument */
386	<	args_info->length_orig = 0;
387	<	}
388	<	if (args_info->zoffset_orig)
389	<	{
390	<	free (args_info->zoffset_orig); /* free previous argument */
391	<	args_info->zoffset_orig = 0;
392	<	}
393	<	if (args_info->sele1_arg)
394	<	{
395	<	free (args_info->sele1_arg); /* free previous argument */
396	<	args_info->sele1_arg = 0;
397	<	}
398	<	if (args_info->sele1_orig)
399	<	{
400	<	free (args_info->sele1_orig); /* free previous argument */
401	<	args_info->sele1_orig = 0;
402	<	}
403	<	if (args_info->sele2_arg)
404	<	{
405	<	free (args_info->sele2_arg); /* free previous argument */
406	<	args_info->sele2_arg = 0;
407	<	}
408	<	if (args_info->sele2_orig)
409	<	{
410	<	free (args_info->sele2_orig); /* free previous argument */
411	<	args_info->sele2_orig = 0;
412	<	}
413	<	if (args_info->sele3_arg)
414	<	{
415	<	free (args_info->sele3_arg); /* free previous argument */
416	<	args_info->sele3_arg = 0;
417	<	}
418	<	if (args_info->sele3_orig)
419	<	{
420	<	free (args_info->sele3_orig); /* free previous argument */
421	<	args_info->sele3_orig = 0;
422	<	}
423	<	if (args_info->refsele_arg)
424	<	{
425	<	free (args_info->refsele_arg); /* free previous argument */
426	<	args_info->refsele_arg = 0;
427	<	}
428	<	if (args_info->refsele_orig)
429	<	{
233	<	free (args_info->refsele_orig); /* free previous argument */
234	<	args_info->refsele_orig = 0;
235	<	}
236	<	if (args_info->molname_arg)
237	<	{
238	<	free (args_info->molname_arg); /* free previous argument */
239	<	args_info->molname_arg = 0;
240	<	}
241	<	if (args_info->molname_orig)
242	<	{
243	<	free (args_info->molname_orig); /* free previous argument */
244	<	args_info->molname_orig = 0;
245	<	}
246	<	if (args_info->begin_orig)
247	<	{
248	<	free (args_info->begin_orig); /* free previous argument */
249	<	args_info->begin_orig = 0;
250	<	}
251	<	if (args_info->end_orig)
252	<	{
253	<	free (args_info->end_orig); /* free previous argument */
254	<	args_info->end_orig = 0;
255	<	}
353	>
354	>	if (args_info->help_given)
355	>	write_into_file(outfile, "help", 0, 0 );
356	>	if (args_info->version_given)
357	>	write_into_file(outfile, "version", 0, 0 );
358	>	if (args_info->input_given)
359	>	write_into_file(outfile, "input", args_info->input_orig, 0);
360	>	if (args_info->output_given)
361	>	write_into_file(outfile, "output", args_info->output_orig, 0);
362	>	if (args_info->step_given)
363	>	write_into_file(outfile, "step", args_info->step_orig, 0);
364	>	if (args_info->nbins_given)
365	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
366	>	if (args_info->nbins_x_given)
367	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
368	>	if (args_info->nbins_y_given)
369	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
370	>	if (args_info->nanglebins_given)
371	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
372	>	if (args_info->length_given)
373	>	write_into_file(outfile, "length", args_info->length_orig, 0);
374	>	if (args_info->rcut_given)
375	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
376	>	if (args_info->zoffset_given)
377	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
378	>	if (args_info->sele1_given)
379	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
380	>	if (args_info->sele2_given)
381	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
382	>	if (args_info->sele3_given)
383	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
384	>	if (args_info->refsele_given)
385	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
386	>	if (args_info->comsele_given)
387	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
388	>	if (args_info->molname_given)
389	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
390	>	if (args_info->begin_given)
391	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
392	>	if (args_info->end_given)
393	>	write_into_file(outfile, "end", args_info->end_orig, 0);
394	>	if (args_info->radius_given)
395	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
396	>	if (args_info->bo_given)
397	>	write_into_file(outfile, "bo", 0, 0 );
398	>	if (args_info->bor_given)
399	>	write_into_file(outfile, "bor", 0, 0 );
400	>	if (args_info->bad_given)
401	>	write_into_file(outfile, "bad", 0, 0 );
402	>	if (args_info->gofr_given)
403	>	write_into_file(outfile, "gofr", 0, 0 );
404	>	if (args_info->gofz_given)
405	>	write_into_file(outfile, "gofz", 0, 0 );
406	>	if (args_info->r_theta_given)
407	>	write_into_file(outfile, "r_theta", 0, 0 );
408	>	if (args_info->r_omega_given)
409	>	write_into_file(outfile, "r_omega", 0, 0 );
410	>	if (args_info->theta_omega_given)
411	>	write_into_file(outfile, "theta_omega", 0, 0 );
412	>	if (args_info->gxyz_given)
413	>	write_into_file(outfile, "gxyz", 0, 0 );
414	>	if (args_info->p2_given)
415	>	write_into_file(outfile, "p2", 0, 0 );
416	>	if (args_info->rp2_given)
417	>	write_into_file(outfile, "rp2", 0, 0 );
418	>	if (args_info->scd_given)
419	>	write_into_file(outfile, "scd", 0, 0 );
420	>	if (args_info->density_given)
421	>	write_into_file(outfile, "density", 0, 0 );
422	>	if (args_info->slab_density_given)
423	>	write_into_file(outfile, "slab_density", 0, 0 );
424	>	if (args_info->hxy_given)
425	>	write_into_file(outfile, "hxy", 0, 0 );
426	>	if (args_info->rho_r_given)
427	>	write_into_file(outfile, "rho_r", 0, 0 );
428	>	if (args_info->hullvol_given)
429	>	write_into_file(outfile, "hullvol", 0, 0 );
430
431	<	clear_given (args_info);
431	>
432	>	i = EXIT_SUCCESS;
433	>	return i;
434		}
435
436		int
#	Line 271 | Line 447 | cmdline_parser_file_save(const char *filename, struct
447		return EXIT_FAILURE;
448		}
449
450	<	if (args_info->help_given) {
275	<	fprintf(outfile, "%s\n", "help");
276	<	}
277	<	if (args_info->version_given) {
278	<	fprintf(outfile, "%s\n", "version");
279	<	}
280	<	if (args_info->input_given) {
281	<	if (args_info->input_orig) {
282	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
283	<	} else {
284	<	fprintf(outfile, "%s\n", "input");
285	<	}
286	<	}
287	<	if (args_info->output_given) {
288	<	if (args_info->output_orig) {
289	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
290	<	} else {
291	<	fprintf(outfile, "%s\n", "output");
292	<	}
293	<	}
294	<	if (args_info->step_given) {
295	<	if (args_info->step_orig) {
296	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
297	<	} else {
298	<	fprintf(outfile, "%s\n", "step");
299	<	}
300	<	}
301	<	if (args_info->nrbins_given) {
302	<	if (args_info->nrbins_orig) {
303	<	fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
304	<	} else {
305	<	fprintf(outfile, "%s\n", "nrbins");
306	<	}
307	<	}
308	<	if (args_info->nanglebins_given) {
309	<	if (args_info->nanglebins_orig) {
310	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
311	<	} else {
312	<	fprintf(outfile, "%s\n", "nanglebins");
313	<	}
314	<	}
315	<	if (args_info->length_given) {
316	<	if (args_info->length_orig) {
317	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
318	<	} else {
319	<	fprintf(outfile, "%s\n", "length");
320	<	}
321	<	}
322	<	if (args_info->zoffset_given) {
323	<	if (args_info->zoffset_orig) {
324	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
325	<	} else {
326	<	fprintf(outfile, "%s\n", "zoffset");
327	<	}
328	<	}
329	<	if (args_info->sele1_given) {
330	<	if (args_info->sele1_orig) {
331	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
332	<	} else {
333	<	fprintf(outfile, "%s\n", "sele1");
334	<	}
335	<	}
336	<	if (args_info->sele2_given) {
337	<	if (args_info->sele2_orig) {
338	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
339	<	} else {
340	<	fprintf(outfile, "%s\n", "sele2");
341	<	}
342	<	}
343	<	if (args_info->sele3_given) {
344	<	if (args_info->sele3_orig) {
345	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
346	<	} else {
347	<	fprintf(outfile, "%s\n", "sele3");
348	<	}
349	<	}
350	<	if (args_info->refsele_given) {
351	<	if (args_info->refsele_orig) {
352	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
353	<	} else {
354	<	fprintf(outfile, "%s\n", "refsele");
355	<	}
356	<	}
357	<	if (args_info->molname_given) {
358	<	if (args_info->molname_orig) {
359	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
360	<	} else {
361	<	fprintf(outfile, "%s\n", "molname");
362	<	}
363	<	}
364	<	if (args_info->begin_given) {
365	<	if (args_info->begin_orig) {
366	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
367	<	} else {
368	<	fprintf(outfile, "%s\n", "begin");
369	<	}
370	<	}
371	<	if (args_info->end_given) {
372	<	if (args_info->end_orig) {
373	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
374	<	} else {
375	<	fprintf(outfile, "%s\n", "end");
376	<	}
377	<	}
378	<	if (args_info->gofr_given) {
379	<	fprintf(outfile, "%s\n", "gofr");
380	<	}
381	<	if (args_info->r_theta_given) {
382	<	fprintf(outfile, "%s\n", "r_theta");
383	<	}
384	<	if (args_info->r_omega_given) {
385	<	fprintf(outfile, "%s\n", "r_omega");
386	<	}
387	<	if (args_info->theta_omega_given) {
388	<	fprintf(outfile, "%s\n", "theta_omega");
389	<	}
390	<	if (args_info->gxyz_given) {
391	<	fprintf(outfile, "%s\n", "gxyz");
392	<	}
393	<	if (args_info->p2_given) {
394	<	fprintf(outfile, "%s\n", "p2");
395	<	}
396	<	if (args_info->scd_given) {
397	<	fprintf(outfile, "%s\n", "scd");
398	<	}
399	<	if (args_info->density_given) {
400	<	fprintf(outfile, "%s\n", "density");
401	<	}
402	<	if (args_info->slab_density_given) {
403	<	fprintf(outfile, "%s\n", "slab_density");
404	<	}
405	<
450	>	i = cmdline_parser_dump(outfile, args_info);
451		fclose (outfile);
452
408	–	i = EXIT_SUCCESS;
453		return i;
454		}
455
#	Line 415 | Line 459 | cmdline_parser_free (struct gengetopt_args_info *args_
459		cmdline_parser_release (args_info);
460		}
461
462	<
419	<	/* gengetopt_strdup() */
420	<	/* strdup.c replacement of strdup, which is not standard */
462	>	/** @brief replacement of strdup, which is not standard */
463		char *
464		gengetopt_strdup (const char *s)
465		{
#	Line 433 | Line 475 | static void
475		}
476
477		static void
436	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
437	–
438	–	static void
478		reset_group_staticProps(struct gengetopt_args_info *args_info)
479		{
480		if (! args_info->staticProps_group_counter)
481		return;
482
483	+	args_info->bo_given = 0 ;
484	+	args_info->bor_given = 0 ;
485	+	args_info->bad_given = 0 ;
486		args_info->gofr_given = 0 ;
487	+	args_info->gofz_given = 0 ;
488		args_info->r_theta_given = 0 ;
489		args_info->r_omega_given = 0 ;
490		args_info->theta_omega_given = 0 ;
491		args_info->gxyz_given = 0 ;
492		args_info->p2_given = 0 ;
493	+	args_info->rp2_given = 0 ;
494		args_info->scd_given = 0 ;
495		args_info->density_given = 0 ;
496		args_info->slab_density_given = 0 ;
497	+	args_info->hxy_given = 0 ;
498	+	args_info->rho_r_given = 0 ;
499	+	args_info->hullvol_given = 0 ;
500
501		args_info->staticProps_group_counter = 0;
502		}
#	Line 461 | Line 508 | int
508		}
509
510		int
511	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
512	+	struct cmdline_parser_params *params)
513	+	{
514	+	int result;
515	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
516	+
517	+	if (result == EXIT_FAILURE)
518	+	{
519	+	cmdline_parser_free (args_info);
520	+	exit (EXIT_FAILURE);
521	+	}
522	+
523	+	return result;
524	+	}
525	+
526	+	int
527		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
528		{
529		int result;
530	+	struct cmdline_parser_params params;
531	+
532	+	params.override = override;
533	+	params.initialize = initialize;
534	+	params.check_required = check_required;
535	+	params.check_ambiguity = 0;
536	+	params.print_errors = 1;
537
538	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
538	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
539
540		if (result == EXIT_FAILURE)
541		{
#	Line 498 | Line 568 | cmdline_parser_required2 (struct gengetopt_args_info *
568		{
569		int error = 0;
570
571	+	/* checks for required options */
572		if (! args_info->input_given)
573		{
574		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
575		error = 1;
576		}
577	+
578		if (args_info->staticProps_group_counter == 0)
579		{
580		fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
#	Line 510 | Line 582 | cmdline_parser_required2 (struct gengetopt_args_info *
582		}
583
584
585	+	/* checks for dependences among options */
586	+
587		return error;
588		}
589
590	+
591	+	static char *package_name = 0;
592	+
593	+	/**
594	+	* @brief updates an option
595	+	* @param field the generic pointer to the field to update
596	+	* @param orig_field the pointer to the orig field
597	+	* @param field_given the pointer to the number of occurrence of this option
598	+	* @param prev_given the pointer to the number of occurrence already seen
599	+	* @param value the argument for this option (if null no arg was specified)
600	+	* @param possible_values the possible values for this option (if specified)
601	+	* @param default_value the default value (in case the option only accepts fixed values)
602	+	* @param arg_type the type of this option
603	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
604	+	* @param override @see cmdline_parser_params.override
605	+	* @param no_free whether to free a possible previous value
606	+	* @param multiple_option whether this is a multiple option
607	+	* @param long_opt the corresponding long option
608	+	* @param short_opt the corresponding short option (or '-' if none)
609	+	* @param additional_error possible further error specification
610	+	*/
611	+	static
612	+	int update_arg(void *field, char **orig_field,
613	+	unsigned int *field_given, unsigned int *prev_given,
614	+	char *value, char *possible_values[], const char *default_value,
615	+	cmdline_parser_arg_type arg_type,
616	+	int check_ambiguity, int override,
617	+	int no_free, int multiple_option,
618	+	const char *long_opt, char short_opt,
619	+	const char *additional_error)
620	+	{
621	+	char *stop_char = 0;
622	+	const char *val = value;
623	+	int found;
624	+	char **string_field;
625	+
626	+	stop_char = 0;
627	+	found = 0;
628	+
629	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
630	+	{
631	+	if (short_opt != '-')
632	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
633	+	package_name, long_opt, short_opt,
634	+	(additional_error ? additional_error : ""));
635	+	else
636	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
637	+	package_name, long_opt,
638	+	(additional_error ? additional_error : ""));
639	+	return 1; /* failure */
640	+	}
641	+
642	+
643	+	if (field_given && *field_given && ! override)
644	+	return 0;
645	+	if (prev_given)
646	+	(*prev_given)++;
647	+	if (field_given)
648	+	(*field_given)++;
649	+	if (possible_values)
650	+	val = possible_values[found];
651	+
652	+	switch(arg_type) {
653	+	case ARG_INT:
654	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
655	+	break;
656	+	case ARG_DOUBLE:
657	+	if (val) *((double *)field) = strtod (val, &stop_char);
658	+	break;
659	+	case ARG_STRING:
660	+	if (val) {
661	+	string_field = (char **)field;
662	+	if (!no_free && *string_field)
663	+	free (*string_field); /* free previous string */
664	+	*string_field = gengetopt_strdup (val);
665	+	}
666	+	break;
667	+	default:
668	+	break;
669	+	};
670	+
671	+	/* check numeric conversion */
672	+	switch(arg_type) {
673	+	case ARG_INT:
674	+	case ARG_DOUBLE:
675	+	if (val && !(stop_char && *stop_char == '\0')) {
676	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
677	+	return 1; /* failure */
678	+	}
679	+	break;
680	+	default:
681	+	;
682	+	};
683	+
684	+	/* store the original value */
685	+	switch(arg_type) {
686	+	case ARG_NO:
687	+	break;
688	+	default:
689	+	if (value && orig_field) {
690	+	if (no_free) {
691	+	*orig_field = value;
692	+	} else {
693	+	if (*orig_field)
694	+	free (*orig_field); /* free previous string */
695	+	*orig_field = gengetopt_strdup (value);
696	+	}
697	+	}
698	+	};
699	+
700	+	return 0; /* OK */
701	+	}
702	+
703	+
704		int
705	<	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)
705	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
706	>	struct cmdline_parser_params *params, const char *additional_error)
707		{
708		int c;        /* Character of the parsed option.  */
709
710		int error = 0;
711		struct gengetopt_args_info local_args_info;
712	+
713	+	int override;
714	+	int initialize;
715	+	int check_required;
716	+	int check_ambiguity;
717	+
718	+	package_name = argv[0];
719	+
720	+	override = params->override;
721	+	initialize = params->initialize;
722	+	check_required = params->check_required;
723	+	check_ambiguity = params->check_ambiguity;
724
725		if (initialize)
726		cmdline_parser_init (args_info);
#	Line 528 | Line 729 | cmdline_parser_internal (int argc, char * const *argv,
729
730		optarg = 0;
731		optind = 0;
732	<	opterr = 1;
732	>	opterr = params->print_errors;
733		optopt = '?';
734
735		while (1)
736		{
737		int option_index = 0;
537	–	char *stop_char;
738
739		static struct option long_options[] = {
740		{ "help",       0, NULL, 'h' },
#	Line 542 | Line 742 | cmdline_parser_internal (int argc, char * const *argv,
742		{ "input",      1, NULL, 'i' },
743		{ "output",     1, NULL, 'o' },
744		{ "step",       1, NULL, 'n' },
745	<	{ "nrbins",     1, NULL, 'r' },
745	>	{ "nbins",      1, NULL, 'b' },
746	>	{ "nbins_x",    1, NULL, 'x' },
747	>	{ "nbins_y",    1, NULL, 'y' },
748		{ "nanglebins", 1, NULL, 'a' },
749	<	{ "length",     1, NULL, 'l' },
749	>	{ "length",     1, NULL, 0 },
750	>	{ "rcut",       1, NULL, 'c' },
751		{ "zoffset",    1, NULL, 'z' },
752		{ "sele1",      1, NULL, 0 },
753		{ "sele2",      1, NULL, 0 },
754		{ "sele3",      1, NULL, 0 },
755		{ "refsele",    1, NULL, 0 },
756	+	{ "comsele",    1, NULL, 0 },
757		{ "molname",    1, NULL, 0 },
758		{ "begin",      1, NULL, 0 },
759		{ "end",        1, NULL, 0 },
760	<	{ "gofr",       0, NULL, 0 },
760	>	{ "radius",     1, NULL, 0 },
761	>	{ "bo", 0, NULL, 0 },
762	>	{ "bor",        0, NULL, 0 },
763	>	{ "bad",        0, NULL, 0 },
764	>	{ "gofr",       0, NULL, 'g' },
765	>	{ "gofz",       0, NULL, 0 },
766		{ "r_theta",    0, NULL, 0 },
767		{ "r_omega",    0, NULL, 0 },
768		{ "theta_omega",        0, NULL, 0 },
769		{ "gxyz",       0, NULL, 0 },
770	<	{ "p2", 0, NULL, 0 },
771	<	{ "scd",        0, NULL, 0 },
772	<	{ "density",    0, NULL, 0 },
770	>	{ "p2", 0, NULL, 'p' },
771	>	{ "rp2",        0, NULL, 0 },
772	>	{ "scd",        0, NULL, 's' },
773	>	{ "density",    0, NULL, 'd' },
774		{ "slab_density",       0, NULL, 0 },
775	+	{ "hxy",        0, NULL, 0 },
776	+	{ "rho_r",      0, NULL, 0 },
777	+	{ "hullvol",    0, NULL, 0 },
778		{ NULL, 0, NULL, 0 }
779		};
780
781	<	stop_char = 0;
569	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:z:", long_options, &option_index);
781	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
782
783		if (c == -1) break;       /* Exit from `while (1)' loop.  */
784
#	Line 583 | Line 795 | cmdline_parser_internal (int argc, char * const *argv,
795		exit (EXIT_SUCCESS);
796
797		case 'i':       /* input dump file.  */
798	<	if (local_args_info.input_given)
799	<	{
800	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
801	<	goto failure;
802	<	}
803	<	if (args_info->input_given && ! override)
804	<	continue;
805	<	local_args_info.input_given = 1;
806	<	args_info->input_given = 1;
807	<	if (args_info->input_arg)
596	<	free (args_info->input_arg); /* free previous string */
597	<	args_info->input_arg = gengetopt_strdup (optarg);
598	<	if (args_info->input_orig)
599	<	free (args_info->input_orig); /* free previous string */
600	<	args_info->input_orig = gengetopt_strdup (optarg);
798	>
799	>
800	>	if (update_arg( (void *)&(args_info->input_arg),
801	>	&(args_info->input_orig), &(args_info->input_given),
802	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
803	>	check_ambiguity, override, 0, 0,
804	>	"input", 'i',
805	>	additional_error))
806	>	goto failure;
807	>
808		break;
602	–
809		case 'o':       /* output file name.  */
810	<	if (local_args_info.output_given)
811	<	{
812	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
813	<	goto failure;
814	<	}
815	<	if (args_info->output_given && ! override)
816	<	continue;
817	<	local_args_info.output_given = 1;
818	<	args_info->output_given = 1;
819	<	if (args_info->output_arg)
614	<	free (args_info->output_arg); /* free previous string */
615	<	args_info->output_arg = gengetopt_strdup (optarg);
616	<	if (args_info->output_orig)
617	<	free (args_info->output_orig); /* free previous string */
618	<	args_info->output_orig = gengetopt_strdup (optarg);
810	>
811	>
812	>	if (update_arg( (void *)&(args_info->output_arg),
813	>	&(args_info->output_orig), &(args_info->output_given),
814	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
815	>	check_ambiguity, override, 0, 0,
816	>	"output", 'o',
817	>	additional_error))
818	>	goto failure;
819	>
820		break;
620	–
821		case 'n':       /* process every n frame.  */
822	<	if (local_args_info.step_given)
823	<	{
824	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
825	<	goto failure;
826	<	}
827	<	if (args_info->step_given && ! override)
828	<	continue;
829	<	local_args_info.step_given = 1;
630	<	args_info->step_given = 1;
631	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
632	<	if (!(stop_char && *stop_char == '\0')) {
633	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
822	>
823	>
824	>	if (update_arg( (void *)&(args_info->step_arg),
825	>	&(args_info->step_orig), &(args_info->step_given),
826	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
827	>	check_ambiguity, override, 0, 0,
828	>	"step", 'n',
829	>	additional_error))
830		goto failure;
831	<	}
636	<	if (args_info->step_orig)
637	<	free (args_info->step_orig); /* free previous string */
638	<	args_info->step_orig = gengetopt_strdup (optarg);
831	>
832		break;
833	<
834	<	case 'r':       /* number of bins for distance.  */
835	<	if (local_args_info.nrbins_given)
836	<	{
837	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
838	<	goto failure;
839	<	}
840	<	if (args_info->nrbins_given && ! override)
841	<	continue;
649	<	local_args_info.nrbins_given = 1;
650	<	args_info->nrbins_given = 1;
651	<	args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
652	<	if (!(stop_char && *stop_char == '\0')) {
653	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
833	>	case 'b':       /* number of bins (general purpose).  */
834	>
835	>
836	>	if (update_arg( (void *)&(args_info->nbins_arg),
837	>	&(args_info->nbins_orig), &(args_info->nbins_given),
838	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
839	>	check_ambiguity, override, 0, 0,
840	>	"nbins", 'b',
841	>	additional_error))
842		goto failure;
843	<	}
656	<	if (args_info->nrbins_orig)
657	<	free (args_info->nrbins_orig); /* free previous string */
658	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
843	>
844		break;
845	<
845	>	case 'x':       /* number of bins in x axis.  */
846	>
847	>
848	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
849	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
850	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
851	>	check_ambiguity, override, 0, 0,
852	>	"nbins_x", 'x',
853	>	additional_error))
854	>	goto failure;
855	>
856	>	break;
857	>	case 'y':       /* number of bins in y axis.  */
858	>
859	>
860	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
861	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
862	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
863	>	check_ambiguity, override, 0, 0,
864	>	"nbins_y", 'y',
865	>	additional_error))
866	>	goto failure;
867	>
868	>	break;
869		case 'a':       /* number of bins for cos(angle).  */
870	<	if (local_args_info.nanglebins_given)
871	<	{
872	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
873	<	goto failure;
874	<	}
875	<	if (args_info->nanglebins_given && ! override)
876	<	continue;
877	<	local_args_info.nanglebins_given = 1;
670	<	args_info->nanglebins_given = 1;
671	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
672	<	if (!(stop_char && *stop_char == '\0')) {
673	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
870	>
871	>
872	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
873	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
874	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
875	>	check_ambiguity, override, 0, 0,
876	>	"nanglebins", 'a',
877	>	additional_error))
878		goto failure;
879	<	}
676	<	if (args_info->nanglebins_orig)
677	<	free (args_info->nanglebins_orig); /* free previous string */
678	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
879	>
880		break;
881	<
882	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
883	<	if (local_args_info.length_given)
884	<	{
885	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
886	<	goto failure;
887	<	}
888	<	if (args_info->length_given && ! override)
889	<	continue;
689	<	local_args_info.length_given = 1;
690	<	args_info->length_given = 1;
691	<	args_info->length_arg = strtod (optarg, &stop_char);
692	<	if (!(stop_char && *stop_char == '\0')) {
693	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
881	>	case 'c':       /* cutoff radius (rcut).  */
882	>
883	>
884	>	if (update_arg( (void *)&(args_info->rcut_arg),
885	>	&(args_info->rcut_orig), &(args_info->rcut_given),
886	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
887	>	check_ambiguity, override, 0, 0,
888	>	"rcut", 'c',
889	>	additional_error))
890		goto failure;
891	<	}
696	<	if (args_info->length_orig)
697	<	free (args_info->length_orig); /* free previous string */
698	<	args_info->length_orig = gengetopt_strdup (optarg);
891	>
892		break;
700	–
893		case 'z':       /* Where to set the zero for the slab_density calculation.  */
894	<	if (local_args_info.zoffset_given)
895	<	{
896	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
897	<	goto failure;
898	<	}
899	<	if (args_info->zoffset_given && ! override)
900	<	continue;
901	<	local_args_info.zoffset_given = 1;
710	<	args_info->zoffset_given = 1;
711	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
712	<	if (!(stop_char && *stop_char == '\0')) {
713	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
894	>
895	>
896	>	if (update_arg( (void *)&(args_info->zoffset_arg),
897	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
898	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
899	>	check_ambiguity, override, 0, 0,
900	>	"zoffset", 'z',
901	>	additional_error))
902		goto failure;
903	<	}
716	<	if (args_info->zoffset_orig)
717	<	free (args_info->zoffset_orig); /* free previous string */
718	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
903	>
904		break;
905	+	case 'g':       /* g(r).  */
906	+
907	+	if (args_info->staticProps_group_counter && override)
908	+	reset_group_staticProps (args_info);
909	+	args_info->staticProps_group_counter += 1;
910	+
911	+	if (update_arg( 0 ,
912	+	0 , &(args_info->gofr_given),
913	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
914	+	check_ambiguity, override, 0, 0,
915	+	"gofr", 'g',
916	+	additional_error))
917	+	goto failure;
918	+
919	+	break;
920	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
921	+
922	+	if (args_info->staticProps_group_counter && override)
923	+	reset_group_staticProps (args_info);
924	+	args_info->staticProps_group_counter += 1;
925	+
926	+	if (update_arg( 0 ,
927	+	0 , &(args_info->p2_given),
928	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
929	+	check_ambiguity, override, 0, 0,
930	+	"p2", 'p',
931	+	additional_error))
932	+	goto failure;
933	+
934	+	break;
935	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
936	+
937	+	if (args_info->staticProps_group_counter && override)
938	+	reset_group_staticProps (args_info);
939	+	args_info->staticProps_group_counter += 1;
940	+
941	+	if (update_arg( 0 ,
942	+	0 , &(args_info->scd_given),
943	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
944	+	check_ambiguity, override, 0, 0,
945	+	"scd", 's',
946	+	additional_error))
947	+	goto failure;
948	+
949	+	break;
950	+	case 'd':       /* density plot.  */
951	+
952	+	if (args_info->staticProps_group_counter && override)
953	+	reset_group_staticProps (args_info);
954	+	args_info->staticProps_group_counter += 1;
955	+
956	+	if (update_arg( 0 ,
957	+	0 , &(args_info->density_given),
958	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
959	+	check_ambiguity, override, 0, 0,
960	+	"density", 'd',
961	+	additional_error))
962	+	goto failure;
963	+
964	+	break;
965
721	–
966		case 0: /* Long option with no short option */
967	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
968	+	if (strcmp (long_options[option_index].name, "length") == 0)
969	+	{
970	+
971	+
972	+	if (update_arg( (void *)&(args_info->length_arg),
973	+	&(args_info->length_orig), &(args_info->length_given),
974	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
975	+	check_ambiguity, override, 0, 0,
976	+	"length", '-',
977	+	additional_error))
978	+	goto failure;
979	+
980	+	}
981		/* select the first stuntdouble set.  */
982	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
982	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
983		{
984	<	if (local_args_info.sele1_given)
985	<	{
986	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
987	<	goto failure;
988	<	}
989	<	if (args_info->sele1_given && ! override)
990	<	continue;
991	<	local_args_info.sele1_given = 1;
992	<	args_info->sele1_given = 1;
993	<	if (args_info->sele1_arg)
736	<	free (args_info->sele1_arg); /* free previous string */
737	<	args_info->sele1_arg = gengetopt_strdup (optarg);
738	<	if (args_info->sele1_orig)
739	<	free (args_info->sele1_orig); /* free previous string */
740	<	args_info->sele1_orig = gengetopt_strdup (optarg);
984	>
985	>
986	>	if (update_arg( (void *)&(args_info->sele1_arg),
987	>	&(args_info->sele1_orig), &(args_info->sele1_given),
988	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
989	>	check_ambiguity, override, 0, 0,
990	>	"sele1", '-',
991	>	additional_error))
992	>	goto failure;
993	>
994		}
995		/* select the second stuntdouble set.  */
996		else if (strcmp (long_options[option_index].name, "sele2") == 0)
997		{
998	<	if (local_args_info.sele2_given)
999	<	{
1000	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001	<	goto failure;
1002	<	}
1003	<	if (args_info->sele2_given && ! override)
1004	<	continue;
1005	<	local_args_info.sele2_given = 1;
1006	<	args_info->sele2_given = 1;
1007	<	if (args_info->sele2_arg)
755	<	free (args_info->sele2_arg); /* free previous string */
756	<	args_info->sele2_arg = gengetopt_strdup (optarg);
757	<	if (args_info->sele2_orig)
758	<	free (args_info->sele2_orig); /* free previous string */
759	<	args_info->sele2_orig = gengetopt_strdup (optarg);
998	>
999	>
1000	>	if (update_arg( (void *)&(args_info->sele2_arg),
1001	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1002	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1003	>	check_ambiguity, override, 0, 0,
1004	>	"sele2", '-',
1005	>	additional_error))
1006	>	goto failure;
1007	>
1008		}
1009		/* select the third stuntdouble set.  */
1010		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1011		{
1012	<	if (local_args_info.sele3_given)
1013	<	{
1014	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1015	<	goto failure;
1016	<	}
1017	<	if (args_info->sele3_given && ! override)
1018	<	continue;
1019	<	local_args_info.sele3_given = 1;
1020	<	args_info->sele3_given = 1;
1021	<	if (args_info->sele3_arg)
774	<	free (args_info->sele3_arg); /* free previous string */
775	<	args_info->sele3_arg = gengetopt_strdup (optarg);
776	<	if (args_info->sele3_orig)
777	<	free (args_info->sele3_orig); /* free previous string */
778	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1012	>
1013	>
1014	>	if (update_arg( (void *)&(args_info->sele3_arg),
1015	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1016	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1017	>	check_ambiguity, override, 0, 0,
1018	>	"sele3", '-',
1019	>	additional_error))
1020	>	goto failure;
1021	>
1022		}
1023		/* select reference (use and only use with --gxyz).  */
1024		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1025		{
1026	<	if (local_args_info.refsele_given)
1027	<	{
1028	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1029	<	goto failure;
1030	<	}
1031	<	if (args_info->refsele_given && ! override)
1032	<	continue;
1033	<	local_args_info.refsele_given = 1;
1034	<	args_info->refsele_given = 1;
1035	<	if (args_info->refsele_arg)
793	<	free (args_info->refsele_arg); /* free previous string */
794	<	args_info->refsele_arg = gengetopt_strdup (optarg);
795	<	if (args_info->refsele_orig)
796	<	free (args_info->refsele_orig); /* free previous string */
797	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1026	>
1027	>
1028	>	if (update_arg( (void *)&(args_info->refsele_arg),
1029	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1030	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1031	>	check_ambiguity, override, 0, 0,
1032	>	"refsele", '-',
1033	>	additional_error))
1034	>	goto failure;
1035	>
1036		}
1037	+	/* select stunt doubles for center-of-mass reference point.  */
1038	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1039	+	{
1040	+
1041	+
1042	+	if (update_arg( (void *)&(args_info->comsele_arg),
1043	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1044	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1045	+	check_ambiguity, override, 0, 0,
1046	+	"comsele", '-',
1047	+	additional_error))
1048	+	goto failure;
1049	+
1050	+	}
1051		/* molecule name.  */
1052		else if (strcmp (long_options[option_index].name, "molname") == 0)
1053		{
1054	<	if (local_args_info.molname_given)
1055	<	{
1056	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1057	<	goto failure;
1058	<	}
1059	<	if (args_info->molname_given && ! override)
1060	<	continue;
1061	<	local_args_info.molname_given = 1;
1062	<	args_info->molname_given = 1;
1063	<	if (args_info->molname_arg)
812	<	free (args_info->molname_arg); /* free previous string */
813	<	args_info->molname_arg = gengetopt_strdup (optarg);
814	<	if (args_info->molname_orig)
815	<	free (args_info->molname_orig); /* free previous string */
816	<	args_info->molname_orig = gengetopt_strdup (optarg);
1054	>
1055	>
1056	>	if (update_arg( (void *)&(args_info->molname_arg),
1057	>	&(args_info->molname_orig), &(args_info->molname_given),
1058	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1059	>	check_ambiguity, override, 0, 0,
1060	>	"molname", '-',
1061	>	additional_error))
1062	>	goto failure;
1063	>
1064		}
1065	<	/* begin interanl index.  */
1065	>	/* begin internal index.  */
1066		else if (strcmp (long_options[option_index].name, "begin") == 0)
1067		{
1068	<	if (local_args_info.begin_given)
1069	<	{
1070	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1071	<	goto failure;
1072	<	}
1073	<	if (args_info->begin_given && ! override)
1074	<	continue;
1075	<	local_args_info.begin_given = 1;
829	<	args_info->begin_given = 1;
830	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
831	<	if (!(stop_char && *stop_char == '\0')) {
832	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1068	>
1069	>
1070	>	if (update_arg( (void *)&(args_info->begin_arg),
1071	>	&(args_info->begin_orig), &(args_info->begin_given),
1072	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1073	>	check_ambiguity, override, 0, 0,
1074	>	"begin", '-',
1075	>	additional_error))
1076		goto failure;
1077	<	}
835	<	if (args_info->begin_orig)
836	<	free (args_info->begin_orig); /* free previous string */
837	<	args_info->begin_orig = gengetopt_strdup (optarg);
1077	>
1078		}
1079		/* end internal index.  */
1080		else if (strcmp (long_options[option_index].name, "end") == 0)
1081		{
1082	<	if (local_args_info.end_given)
1083	<	{
1084	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1085	<	goto failure;
1086	<	}
1087	<	if (args_info->end_given && ! override)
1088	<	continue;
1089	<	local_args_info.end_given = 1;
850	<	args_info->end_given = 1;
851	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
852	<	if (!(stop_char && *stop_char == '\0')) {
853	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1082	>
1083	>
1084	>	if (update_arg( (void *)&(args_info->end_arg),
1085	>	&(args_info->end_orig), &(args_info->end_given),
1086	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1087	>	check_ambiguity, override, 0, 0,
1088	>	"end", '-',
1089	>	additional_error))
1090		goto failure;
1091	<	}
856	<	if (args_info->end_orig)
857	<	free (args_info->end_orig); /* free previous string */
858	<	args_info->end_orig = gengetopt_strdup (optarg);
1091	>
1092		}
1093	<	/* g(r).  */
1094	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1093	>	/* nanoparticle radius.  */
1094	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1095		{
1096	<	if (local_args_info.gofr_given)
1097	<	{
1098	<	fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1099	<	goto failure;
1100	<	}
1101	<	if (args_info->gofr_given && ! override)
1102	<	continue;
1103	<	local_args_info.gofr_given = 1;
1104	<	args_info->gofr_given = 1;
1096	>
1097	>
1098	>	if (update_arg( (void *)&(args_info->radius_arg),
1099	>	&(args_info->radius_orig), &(args_info->radius_given),
1100	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1101	>	check_ambiguity, override, 0, 0,
1102	>	"radius", '-',
1103	>	additional_error))
1104	>	goto failure;
1105	>
1106	>	}
1107	>	/* bond order parameter (--rcut must be specified).  */
1108	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1109	>	{
1110	>
1111		if (args_info->staticProps_group_counter && override)
1112		reset_group_staticProps (args_info);
1113		args_info->staticProps_group_counter += 1;
1114	<	break;
1114	>
1115	>	if (update_arg( 0 ,
1116	>	0 , &(args_info->bo_given),
1117	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"bo", '-',
1120	>	additional_error))
1121	>	goto failure;
1122	>
1123		}
1124	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1125	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1126	+	{
1127	+
1128	+	if (args_info->staticProps_group_counter && override)
1129	+	reset_group_staticProps (args_info);
1130	+	args_info->staticProps_group_counter += 1;
1131	+
1132	+	if (update_arg( 0 ,
1133	+	0 , &(args_info->bor_given),
1134	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1135	+	check_ambiguity, override, 0, 0,
1136	+	"bor", '-',
1137	+	additional_error))
1138	+	goto failure;
1139	+
1140	+	}
1141	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1142	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1143	+	{
1144	+
1145	+	if (args_info->staticProps_group_counter && override)
1146	+	reset_group_staticProps (args_info);
1147	+	args_info->staticProps_group_counter += 1;
1148	+
1149	+	if (update_arg( 0 ,
1150	+	0 , &(args_info->bad_given),
1151	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1152	+	check_ambiguity, override, 0, 0,
1153	+	"bad", '-',
1154	+	additional_error))
1155	+	goto failure;
1156	+
1157	+	}
1158	+	/* g(z).  */
1159	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1160	+	{
1161	+
1162	+	if (args_info->staticProps_group_counter && override)
1163	+	reset_group_staticProps (args_info);
1164	+	args_info->staticProps_group_counter += 1;
1165	+
1166	+	if (update_arg( 0 ,
1167	+	0 , &(args_info->gofz_given),
1168	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1169	+	check_ambiguity, override, 0, 0,
1170	+	"gofz", '-',
1171	+	additional_error))
1172	+	goto failure;
1173	+
1174	+	}
1175		/* g(r, cos(theta)).  */
1176		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1177		{
1178	<	if (local_args_info.r_theta_given)
881	<	{
882	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
883	<	goto failure;
884	<	}
885	<	if (args_info->r_theta_given && ! override)
886	<	continue;
887	<	local_args_info.r_theta_given = 1;
888	<	args_info->r_theta_given = 1;
1178	>
1179		if (args_info->staticProps_group_counter && override)
1180		reset_group_staticProps (args_info);
1181		args_info->staticProps_group_counter += 1;
1182	<	break;
1182	>
1183	>	if (update_arg( 0 ,
1184	>	0 , &(args_info->r_theta_given),
1185	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1186	>	check_ambiguity, override, 0, 0,
1187	>	"r_theta", '-',
1188	>	additional_error))
1189	>	goto failure;
1190	>
1191		}
1192		/* g(r, cos(omega)).  */
1193		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1194		{
1195	<	if (local_args_info.r_omega_given)
898	<	{
899	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
900	<	goto failure;
901	<	}
902	<	if (args_info->r_omega_given && ! override)
903	<	continue;
904	<	local_args_info.r_omega_given = 1;
905	<	args_info->r_omega_given = 1;
1195	>
1196		if (args_info->staticProps_group_counter && override)
1197		reset_group_staticProps (args_info);
1198		args_info->staticProps_group_counter += 1;
1199	<	break;
1199	>
1200	>	if (update_arg( 0 ,
1201	>	0 , &(args_info->r_omega_given),
1202	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1203	>	check_ambiguity, override, 0, 0,
1204	>	"r_omega", '-',
1205	>	additional_error))
1206	>	goto failure;
1207	>
1208		}
1209		/* g(cos(theta), cos(omega)).  */
1210		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1211		{
1212	<	if (local_args_info.theta_omega_given)
915	<	{
916	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	<	goto failure;
918	<	}
919	<	if (args_info->theta_omega_given && ! override)
920	<	continue;
921	<	local_args_info.theta_omega_given = 1;
922	<	args_info->theta_omega_given = 1;
1212	>
1213		if (args_info->staticProps_group_counter && override)
1214		reset_group_staticProps (args_info);
1215		args_info->staticProps_group_counter += 1;
1216	<	break;
1216	>
1217	>	if (update_arg( 0 ,
1218	>	0 , &(args_info->theta_omega_given),
1219	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1220	>	check_ambiguity, override, 0, 0,
1221	>	"theta_omega", '-',
1222	>	additional_error))
1223	>	goto failure;
1224	>
1225		}
1226		/* g(x, y, z).  */
1227		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1228		{
1229	<	if (local_args_info.gxyz_given)
932	<	{
933	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
934	<	goto failure;
935	<	}
936	<	if (args_info->gxyz_given && ! override)
937	<	continue;
938	<	local_args_info.gxyz_given = 1;
939	<	args_info->gxyz_given = 1;
1229	>
1230		if (args_info->staticProps_group_counter && override)
1231		reset_group_staticProps (args_info);
1232		args_info->staticProps_group_counter += 1;
1233	<	break;
1233	>
1234	>	if (update_arg( 0 ,
1235	>	0 , &(args_info->gxyz_given),
1236	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1237	>	check_ambiguity, override, 0, 0,
1238	>	"gxyz", '-',
1239	>	additional_error))
1240	>	goto failure;
1241	>
1242		}
1243	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1244	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1243	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1244	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1245		{
1246	<	if (local_args_info.p2_given)
949	<	{
950	<	fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
951	<	goto failure;
952	<	}
953	<	if (args_info->p2_given && ! override)
954	<	continue;
955	<	local_args_info.p2_given = 1;
956	<	args_info->p2_given = 1;
1246	>
1247		if (args_info->staticProps_group_counter && override)
1248		reset_group_staticProps (args_info);
1249		args_info->staticProps_group_counter += 1;
1250	<	break;
1250	>
1251	>	if (update_arg( 0 ,
1252	>	0 , &(args_info->rp2_given),
1253	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1254	>	check_ambiguity, override, 0, 0,
1255	>	"rp2", '-',
1256	>	additional_error))
1257	>	goto failure;
1258	>
1259		}
1260	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1261	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1260	>	/* slab density.  */
1261	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1262		{
1263	<	if (local_args_info.scd_given)
966	<	{
967	<	fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
968	<	goto failure;
969	<	}
970	<	if (args_info->scd_given && ! override)
971	<	continue;
972	<	local_args_info.scd_given = 1;
973	<	args_info->scd_given = 1;
1263	>
1264		if (args_info->staticProps_group_counter && override)
1265		reset_group_staticProps (args_info);
1266		args_info->staticProps_group_counter += 1;
1267	<	break;
1267	>
1268	>	if (update_arg( 0 ,
1269	>	0 , &(args_info->slab_density_given),
1270	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1271	>	check_ambiguity, override, 0, 0,
1272	>	"slab_density", '-',
1273	>	additional_error))
1274	>	goto failure;
1275	>
1276		}
1277	<	/* density plot (--sele1 must be specified).  */
1278	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1277	>	/* hxy.  */
1278	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1279		{
1280	<	if (local_args_info.density_given)
983	<	{
984	<	fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
985	<	goto failure;
986	<	}
987	<	if (args_info->density_given && ! override)
988	<	continue;
989	<	local_args_info.density_given = 1;
990	<	args_info->density_given = 1;
1280	>
1281		if (args_info->staticProps_group_counter && override)
1282		reset_group_staticProps (args_info);
1283		args_info->staticProps_group_counter += 1;
1284	<	break;
1284	>
1285	>	if (update_arg( 0 ,
1286	>	0 , &(args_info->hxy_given),
1287	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1288	>	check_ambiguity, override, 0, 0,
1289	>	"hxy", '-',
1290	>	additional_error))
1291	>	goto failure;
1292	>
1293		}
1294	<	/* slab density (--sele1 must be specified).  */
1295	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1294	>	/* rho of R.  */
1295	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1296		{
1297	<	if (local_args_info.slab_density_given)
1000	<	{
1001	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1002	<	goto failure;
1003	<	}
1004	<	if (args_info->slab_density_given && ! override)
1005	<	continue;
1006	<	local_args_info.slab_density_given = 1;
1007	<	args_info->slab_density_given = 1;
1297	>
1298		if (args_info->staticProps_group_counter && override)
1299		reset_group_staticProps (args_info);
1300		args_info->staticProps_group_counter += 1;
1301	<	break;
1301	>
1302	>	if (update_arg( 0 ,
1303	>	0 , &(args_info->rho_r_given),
1304	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1305	>	check_ambiguity, override, 0, 0,
1306	>	"rho_r", '-',
1307	>	additional_error))
1308	>	goto failure;
1309	>
1310		}
1311	+	/* hull volume of nanoparticle.  */
1312	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1313	+	{
1314
1315	+	if (args_info->staticProps_group_counter && override)
1316	+	reset_group_staticProps (args_info);
1317	+	args_info->staticProps_group_counter += 1;
1318	+
1319	+	if (update_arg( 0 ,
1320	+	0 , &(args_info->hullvol_given),
1321	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1322	+	check_ambiguity, override, 0, 0,
1323	+	"hullvol", '-',
1324	+	additional_error))
1325	+	goto failure;
1326	+
1327	+	}
1328	+
1329		break;
1330		case '?':       /* Invalid option.  */
1331		/* `getopt_long' already printed an error message.  */

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