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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 967 by xsun, Mon May 22 15:30:42 2006 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.16
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4	<	gengetopt -F StaticPropsCmd
4	>	gengetopt -F StaticPropsCmd -u
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
#	Line 21 | Line 21
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
41	+	"      --dz=DOUBLE               slab width (dz)",
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",
53	+	"      --radius=DOUBLE           nanoparticle radius",
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	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
59	+	"  -g, --gofr                    g(r)",
60	+	"      --gofz                    g(z)",
61	+	"      --r_theta                 g(r, cos(theta))",
62	+	"      --r_omega                 g(r, cos(omega))",
63	+	"      --theta_omega             g(cos(theta), cos(omega))",
64	+	"      --gxyz                    g(x, y, z)",
65	+	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
66	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
67	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
68	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
69	+	"  -d, --density                 density plot",
70	+	"      --slab_density            slab density",
71	+	"      --p_angle                 p(cos(theta))",
72	+	"      --hxy                     hxy",
73	+	"      --rho_r                   rho of R",
74	+	"      --angle_r                 angle of R",
75	+	"      --hullvol                 hull volume of nanoparticle",
76	+	0
77	+	};
78	+
79	+	typedef enum {ARG_NO
80	+	, ARG_STRING
81	+	, ARG_INT
82	+	, ARG_DOUBLE
83	+	} cmdline_parser_arg_type;
84	+
85		static
86		void clear_given (struct gengetopt_args_info *args_info);
87		static
88		void clear_args (struct gengetopt_args_info *args_info);
89
90		static int
91	<	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);
91	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
92	>	struct cmdline_parser_params *params, const char *additional_error);
93
94		static int
95		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 43 | Line 105 | void clear_given (struct gengetopt_args_info *args_inf
105		args_info->input_given = 0 ;
106		args_info->output_given = 0 ;
107		args_info->step_given = 0 ;
108	<	args_info->nrbins_given = 0 ;
108	>	args_info->nbins_given = 0 ;
109		args_info->nbins_x_given = 0 ;
110		args_info->nbins_y_given = 0 ;
111		args_info->nanglebins_given = 0 ;
112	+	args_info->rcut_given = 0 ;
113	+	args_info->dz_given = 0 ;
114		args_info->length_given = 0 ;
115	+	args_info->zlength_given = 0 ;
116		args_info->zoffset_given = 0 ;
117		args_info->sele1_given = 0 ;
118		args_info->sele2_given = 0 ;
119		args_info->sele3_given = 0 ;
120		args_info->refsele_given = 0 ;
121	+	args_info->comsele_given = 0 ;
122		args_info->molname_given = 0 ;
123		args_info->begin_given = 0 ;
124		args_info->end_given = 0 ;
125	+	args_info->radius_given = 0 ;
126	+	args_info->bo_given = 0 ;
127	+	args_info->bor_given = 0 ;
128	+	args_info->bad_given = 0 ;
129	+	args_info->count_given = 0 ;
130		args_info->gofr_given = 0 ;
131	+	args_info->gofz_given = 0 ;
132		args_info->r_theta_given = 0 ;
133		args_info->r_omega_given = 0 ;
134		args_info->theta_omega_given = 0 ;
135		args_info->gxyz_given = 0 ;
136	+	args_info->twodgofr_given = 0 ;
137		args_info->p2_given = 0 ;
138	+	args_info->rp2_given = 0 ;
139		args_info->scd_given = 0 ;
140		args_info->density_given = 0 ;
141		args_info->slab_density_given = 0 ;
142	+	args_info->p_angle_given = 0 ;
143		args_info->hxy_given = 0 ;
144	+	args_info->rho_r_given = 0 ;
145	+	args_info->angle_r_given = 0 ;
146	+	args_info->hullvol_given = 0 ;
147		args_info->staticProps_group_counter = 0 ;
148		}
149
#	Line 78 | Line 156 | void clear_args (struct gengetopt_args_info *args_info
156		args_info->output_orig = NULL;
157		args_info->step_arg = 1;
158		args_info->step_orig = NULL;
159	<	args_info->nrbins_arg = 100;
160	<	args_info->nrbins_orig = NULL;
159	>	args_info->nbins_arg = 100;
160	>	args_info->nbins_orig = NULL;
161		args_info->nbins_x_arg = 100;
162		args_info->nbins_x_orig = NULL;
163		args_info->nbins_y_arg = 100;
164		args_info->nbins_y_orig = NULL;
165		args_info->nanglebins_arg = 50;
166		args_info->nanglebins_orig = NULL;
167	+	args_info->rcut_orig = NULL;
168	+	args_info->dz_orig = NULL;
169		args_info->length_orig = NULL;
170	+	args_info->zlength_orig = NULL;
171		args_info->zoffset_arg = 0;
172		args_info->zoffset_orig = NULL;
173		args_info->sele1_arg = NULL;
#	Line 97 | Line 178 | void clear_args (struct gengetopt_args_info *args_info
178		args_info->sele3_orig = NULL;
179		args_info->refsele_arg = NULL;
180		args_info->refsele_orig = NULL;
181	+	args_info->comsele_arg = NULL;
182	+	args_info->comsele_orig = NULL;
183		args_info->molname_arg = NULL;
184		args_info->molname_orig = NULL;
185		args_info->begin_orig = NULL;
186		args_info->end_orig = NULL;
187	+	args_info->radius_orig = NULL;
188
189		}
190
191	+	static
192	+	void init_args_info(struct gengetopt_args_info *args_info)
193	+	{
194	+
195	+
196	+	args_info->help_help = gengetopt_args_info_help[0] ;
197	+	args_info->version_help = gengetopt_args_info_help[1] ;
198	+	args_info->input_help = gengetopt_args_info_help[2] ;
199	+	args_info->output_help = gengetopt_args_info_help[3] ;
200	+	args_info->step_help = gengetopt_args_info_help[4] ;
201	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
202	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
203	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
204	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
205	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
206	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
207	+	args_info->dz_help = gengetopt_args_info_help[11] ;
208	+	args_info->length_help = gengetopt_args_info_help[12] ;
209	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
210	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
211	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
212	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
213	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
214	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
215	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
216	+	args_info->molname_help = gengetopt_args_info_help[20] ;
217	+	args_info->begin_help = gengetopt_args_info_help[21] ;
218	+	args_info->end_help = gengetopt_args_info_help[22] ;
219	+	args_info->radius_help = gengetopt_args_info_help[23] ;
220	+	args_info->bo_help = gengetopt_args_info_help[25] ;
221	+	args_info->bor_help = gengetopt_args_info_help[26] ;
222	+	args_info->bad_help = gengetopt_args_info_help[27] ;
223	+	args_info->count_help = gengetopt_args_info_help[28] ;
224	+	args_info->gofr_help = gengetopt_args_info_help[29] ;
225	+	args_info->gofz_help = gengetopt_args_info_help[30] ;
226	+	args_info->r_theta_help = gengetopt_args_info_help[31] ;
227	+	args_info->r_omega_help = gengetopt_args_info_help[32] ;
228	+	args_info->r_z_help = gengetopt_args_info_help[33] ;
229	+	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
230	+	args_info->gxyz_help = gengetopt_args_info_help[35] ;
231	+	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
232	+	args_info->p2_help = gengetopt_args_info_help[37] ;
233	+	args_info->rp2_help = gengetopt_args_info_help[38] ;
234	+	args_info->scd_help = gengetopt_args_info_help[39] ;
235	+	args_info->density_help = gengetopt_args_info_help[40] ;
236	+	args_info->slab_density_help = gengetopt_args_info_help[41] ;
237	+	args_info->p_angle_help = gengetopt_args_info_help[42] ;
238	+	args_info->hxy_help = gengetopt_args_info_help[43] ;
239	+	args_info->rho_r_help = gengetopt_args_info_help[44] ;
240	+	args_info->hullvol_help = gengetopt_args_info_help[45] ;
241	+
242	+	}
243	+
244		void
245		cmdline_parser_print_version (void)
246		{
247		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
248		}
249
250	+	static void print_help_common(void) {
251	+	cmdline_parser_print_version ();
252	+
253	+	if (strlen(gengetopt_args_info_purpose) > 0)
254	+	printf("\n%s\n", gengetopt_args_info_purpose);
255	+
256	+	if (strlen(gengetopt_args_info_usage) > 0)
257	+	printf("\n%s\n", gengetopt_args_info_usage);
258	+
259	+	printf("\n");
260	+
261	+	if (strlen(gengetopt_args_info_description) > 0)
262	+	printf("%s\n", gengetopt_args_info_description);
263	+	}
264	+
265		void
266		cmdline_parser_print_help (void)
267		{
268	<	cmdline_parser_print_version ();
269	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
270	<	printf("%s\n","  -h, --help                    Print help and exit");
271	<	printf("%s\n","  -V, --version                 Print version and exit");
120	<	printf("%s\n","  -i, --input=filename          input dump file");
121	<	printf("%s\n","  -o, --output=filename         output file name");
122	<	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
123	<	printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
124	<	printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
125	<	printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
126	<	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
127	<	printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
128	<	printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
129	<	printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
130	<	printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
131	<	printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
132	<	printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
133	<	printf("%s\n","      --molname=STRING          molecule name");
134	<	printf("%s\n","      --begin=INT               begin interanl index");
135	<	printf("%s\n","      --end=INT                 end internal index");
136	<	printf("%s\n","\n Group: staticProps\n   an option of this group is required");
137	<	printf("%s\n","      --gofr                    g(r)");
138	<	printf("%s\n","      --r_theta                 g(r, cos(theta))");
139	<	printf("%s\n","      --r_omega                 g(r, cos(omega))");
140	<	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
141	<	printf("%s\n","      --gxyz                    g(x, y, z)");
142	<	printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
143	<	printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
144	<	printf("%s\n","      --density                 density plot (--sele1 must be specified)");
145	<	printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
146	<	printf("%s\n","      --hxy                     hxy (--sele1 must be specified)");
147	<
268	>	int i = 0;
269	>	print_help_common();
270	>	while (gengetopt_args_info_help[i])
271	>	printf("%s\n", gengetopt_args_info_help[i++]);
272		}
273
274		void
#	Line 152 | Line 276 | cmdline_parser_init (struct gengetopt_args_info *args_
276		{
277		clear_given (args_info);
278		clear_args (args_info);
279	+	init_args_info (args_info);
280	+
281	+	args_info->inputs = NULL;
282	+	args_info->inputs_num = 0;
283		}
284
285	+	void
286	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
287	+	{
288	+	if (params)
289	+	{
290	+	params->override = 0;
291	+	params->initialize = 1;
292	+	params->check_required = 1;
293	+	params->check_ambiguity = 0;
294	+	params->print_errors = 1;
295	+	}
296	+	}
297	+
298	+	struct cmdline_parser_params *
299	+	cmdline_parser_params_create(void)
300	+	{
301	+	struct cmdline_parser_params *params =
302	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
303	+	cmdline_parser_params_init(params);
304	+	return params;
305	+	}
306	+
307		static void
308	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
308	>	free_string_field (char **s)
309		{
310	<
161	<	if (args_info->input_arg)
310	>	if (*s)
311		{
312	<	free (args_info->input_arg); /* free previous argument */
313	<	args_info->input_arg = 0;
312	>	free (*s);
313	>	*s = 0;
314		}
315	<	if (args_info->input_orig)
315	>	}
316	>
317	>
318	>	static void
319	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
320	>	{
321	>	unsigned int i;
322	>	free_string_field (&(args_info->input_arg));
323	>	free_string_field (&(args_info->input_orig));
324	>	free_string_field (&(args_info->output_arg));
325	>	free_string_field (&(args_info->output_orig));
326	>	free_string_field (&(args_info->step_orig));
327	>	free_string_field (&(args_info->nbins_orig));
328	>	free_string_field (&(args_info->nbins_x_orig));
329	>	free_string_field (&(args_info->nbins_y_orig));
330	>	free_string_field (&(args_info->nanglebins_orig));
331	>	free_string_field (&(args_info->rcut_orig));
332	>	free_string_field (&(args_info->dz_orig));
333	>	free_string_field (&(args_info->length_orig));
334	>	free_string_field (&(args_info->zlength_orig));
335	>	free_string_field (&(args_info->zoffset_orig));
336	>	free_string_field (&(args_info->sele1_arg));
337	>	free_string_field (&(args_info->sele1_orig));
338	>	free_string_field (&(args_info->sele2_arg));
339	>	free_string_field (&(args_info->sele2_orig));
340	>	free_string_field (&(args_info->sele3_arg));
341	>	free_string_field (&(args_info->sele3_orig));
342	>	free_string_field (&(args_info->refsele_arg));
343	>	free_string_field (&(args_info->refsele_orig));
344	>	free_string_field (&(args_info->comsele_arg));
345	>	free_string_field (&(args_info->comsele_orig));
346	>	free_string_field (&(args_info->molname_arg));
347	>	free_string_field (&(args_info->molname_orig));
348	>	free_string_field (&(args_info->begin_orig));
349	>	free_string_field (&(args_info->end_orig));
350	>	free_string_field (&(args_info->radius_orig));
351	>
352	>
353	>	for (i = 0; i < args_info->inputs_num; ++i)
354	>	free (args_info->inputs [i]);
355	>
356	>	if (args_info->inputs_num)
357	>	free (args_info->inputs);
358	>
359	>	clear_given (args_info);
360	>	}
361	>
362	>
363	>	static void
364	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
365	>	{
366	>	if (arg) {
367	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
368	>	} else {
369	>	fprintf(outfile, "%s\n", opt);
370	>	}
371	>	}
372	>
373	>
374	>	int
375	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
376	>	{
377	>	int i = 0;
378	>
379	>	if (!outfile)
380		{
381	<	free (args_info->input_orig); /* free previous argument */
382	<	args_info->input_orig = 0;
381	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
382	>	return EXIT_FAILURE;
383		}
384	<	if (args_info->output_arg)
385	<	{
386	<	free (args_info->output_arg); /* free previous argument */
387	<	args_info->output_arg = 0;
388	<	}
389	<	if (args_info->output_orig)
390	<	{
391	<	free (args_info->output_orig); /* free previous argument */
392	<	args_info->output_orig = 0;
393	<	}
394	<	if (args_info->step_orig)
395	<	{
396	<	free (args_info->step_orig); /* free previous argument */
397	<	args_info->step_orig = 0;
398	<	}
399	<	if (args_info->nrbins_orig)
400	<	{
401	<	free (args_info->nrbins_orig); /* free previous argument */
402	<	args_info->nrbins_orig = 0;
403	<	}
404	<	if (args_info->nbins_x_orig)
405	<	{
406	<	free (args_info->nbins_x_orig); /* free previous argument */
407	<	args_info->nbins_x_orig = 0;
408	<	}
409	<	if (args_info->nbins_y_orig)
410	<	{
411	<	free (args_info->nbins_y_orig); /* free previous argument */
412	<	args_info->nbins_y_orig = 0;
413	<	}
414	<	if (args_info->nanglebins_orig)
415	<	{
416	<	free (args_info->nanglebins_orig); /* free previous argument */
417	<	args_info->nanglebins_orig = 0;
418	<	}
419	<	if (args_info->length_orig)
420	<	{
421	<	free (args_info->length_orig); /* free previous argument */
422	<	args_info->length_orig = 0;
423	<	}
424	<	if (args_info->zoffset_orig)
425	<	{
426	<	free (args_info->zoffset_orig); /* free previous argument */
427	<	args_info->zoffset_orig = 0;
428	<	}
429	<	if (args_info->sele1_arg)
430	<	{
431	<	free (args_info->sele1_arg); /* free previous argument */
432	<	args_info->sele1_arg = 0;
433	<	}
434	<	if (args_info->sele1_orig)
435	<	{
436	<	free (args_info->sele1_orig); /* free previous argument */
437	<	args_info->sele1_orig = 0;
438	<	}
439	<	if (args_info->sele2_arg)
440	<	{
441	<	free (args_info->sele2_arg); /* free previous argument */
442	<	args_info->sele2_arg = 0;
443	<	}
444	<	if (args_info->sele2_orig)
445	<	{
446	<	free (args_info->sele2_orig); /* free previous argument */
447	<	args_info->sele2_orig = 0;
448	<	}
449	<	if (args_info->sele3_arg)
450	<	{
451	<	free (args_info->sele3_arg); /* free previous argument */
452	<	args_info->sele3_arg = 0;
453	<	}
454	<	if (args_info->sele3_orig)
455	<	{
456	<	free (args_info->sele3_orig); /* free previous argument */
457	<	args_info->sele3_orig = 0;
458	<	}
459	<	if (args_info->refsele_arg)
460	<	{
461	<	free (args_info->refsele_arg); /* free previous argument */
462	<	args_info->refsele_arg = 0;
463	<	}
464	<	if (args_info->refsele_orig)
465	<	{
466	<	free (args_info->refsele_orig); /* free previous argument */
467	<	args_info->refsele_orig = 0;
468	<	}
469	<	if (args_info->molname_arg)
470	<	{
471	<	free (args_info->molname_arg); /* free previous argument */
472	<	args_info->molname_arg = 0;
260	<	}
261	<	if (args_info->molname_orig)
262	<	{
263	<	free (args_info->molname_orig); /* free previous argument */
264	<	args_info->molname_orig = 0;
265	<	}
266	<	if (args_info->begin_orig)
267	<	{
268	<	free (args_info->begin_orig); /* free previous argument */
269	<	args_info->begin_orig = 0;
270	<	}
271	<	if (args_info->end_orig)
272	<	{
273	<	free (args_info->end_orig); /* free previous argument */
274	<	args_info->end_orig = 0;
275	<	}
384	>
385	>	if (args_info->help_given)
386	>	write_into_file(outfile, "help", 0, 0 );
387	>	if (args_info->version_given)
388	>	write_into_file(outfile, "version", 0, 0 );
389	>	if (args_info->input_given)
390	>	write_into_file(outfile, "input", args_info->input_orig, 0);
391	>	if (args_info->output_given)
392	>	write_into_file(outfile, "output", args_info->output_orig, 0);
393	>	if (args_info->step_given)
394	>	write_into_file(outfile, "step", args_info->step_orig, 0);
395	>	if (args_info->nbins_given)
396	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
397	>	if (args_info->nbins_x_given)
398	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
399	>	if (args_info->nbins_y_given)
400	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
401	>	if (args_info->nanglebins_given)
402	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
403	>	if (args_info->rcut_given)
404	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
405	>	if (args_info->dz_given)
406	>	write_into_file(outfile, "dz", args_info->dz_orig, 0);
407	>	if (args_info->length_given)
408	>	write_into_file(outfile, "length", args_info->length_orig, 0);
409	>	if (args_info->zlength_given)
410	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
411	>	if (args_info->zoffset_given)
412	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
413	>	if (args_info->sele1_given)
414	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
415	>	if (args_info->sele2_given)
416	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
417	>	if (args_info->sele3_given)
418	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
419	>	if (args_info->refsele_given)
420	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
421	>	if (args_info->comsele_given)
422	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
423	>	if (args_info->molname_given)
424	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
425	>	if (args_info->begin_given)
426	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
427	>	if (args_info->end_given)
428	>	write_into_file(outfile, "end", args_info->end_orig, 0);
429	>	if (args_info->radius_given)
430	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
431	>	if (args_info->bo_given)
432	>	write_into_file(outfile, "bo", 0, 0 );
433	>	if (args_info->bor_given)
434	>	write_into_file(outfile, "bor", 0, 0 );
435	>	if (args_info->bad_given)
436	>	write_into_file(outfile, "bad", 0, 0 );
437	>	if (args_info->count_given)
438	>	write_into_file(outfile, "count", 0, 0 );
439	>	if (args_info->gofr_given)
440	>	write_into_file(outfile, "gofr", 0, 0 );
441	>	if (args_info->gofz_given)
442	>	write_into_file(outfile, "gofz", 0, 0 );
443	>	if (args_info->r_theta_given)
444	>	write_into_file(outfile, "r_theta", 0, 0 );
445	>	if (args_info->r_omega_given)
446	>	write_into_file(outfile, "r_omega", 0, 0 );
447	>	if (args_info->theta_omega_given)
448	>	write_into_file(outfile, "theta_omega", 0, 0 );
449	>	if (args_info->gxyz_given)
450	>	write_into_file(outfile, "gxyz", 0, 0 );
451	>	if (args_info->twodgofr_given)
452	>	write_into_file(outfile, "twodgofr", 0, 0 );
453	>	if (args_info->p2_given)
454	>	write_into_file(outfile, "p2", 0, 0 );
455	>	if (args_info->rp2_given)
456	>	write_into_file(outfile, "rp2", 0, 0 );
457	>	if (args_info->scd_given)
458	>	write_into_file(outfile, "scd", 0, 0 );
459	>	if (args_info->density_given)
460	>	write_into_file(outfile, "density", 0, 0 );
461	>	if (args_info->slab_density_given)
462	>	write_into_file(outfile, "slab_density", 0, 0 );
463	>	if (args_info->p_angle_given)
464	>	write_into_file(outfile, "p_angle", 0, 0 );
465	>	if (args_info->hxy_given)
466	>	write_into_file(outfile, "hxy", 0, 0 );
467	>	if (args_info->rho_r_given)
468	>	write_into_file(outfile, "rho_r", 0, 0 );
469	>	if (args_info->angle_r_given)
470	>	write_into_file(outfile, "angle_r", 0, 0 );
471	>	if (args_info->hullvol_given)
472	>	write_into_file(outfile, "hullvol", 0, 0 );
473
474	<	clear_given (args_info);
474	>
475	>	i = EXIT_SUCCESS;
476	>	return i;
477		}
478
479		int
#	Line 291 | Line 490 | cmdline_parser_file_save(const char *filename, struct
490		return EXIT_FAILURE;
491		}
492
493	<	if (args_info->help_given) {
295	<	fprintf(outfile, "%s\n", "help");
296	<	}
297	<	if (args_info->version_given) {
298	<	fprintf(outfile, "%s\n", "version");
299	<	}
300	<	if (args_info->input_given) {
301	<	if (args_info->input_orig) {
302	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
303	<	} else {
304	<	fprintf(outfile, "%s\n", "input");
305	<	}
306	<	}
307	<	if (args_info->output_given) {
308	<	if (args_info->output_orig) {
309	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
310	<	} else {
311	<	fprintf(outfile, "%s\n", "output");
312	<	}
313	<	}
314	<	if (args_info->step_given) {
315	<	if (args_info->step_orig) {
316	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
317	<	} else {
318	<	fprintf(outfile, "%s\n", "step");
319	<	}
320	<	}
321	<	if (args_info->nrbins_given) {
322	<	if (args_info->nrbins_orig) {
323	<	fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
324	<	} else {
325	<	fprintf(outfile, "%s\n", "nrbins");
326	<	}
327	<	}
328	<	if (args_info->nbins_x_given) {
329	<	if (args_info->nbins_x_orig) {
330	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
331	<	} else {
332	<	fprintf(outfile, "%s\n", "nbins_x");
333	<	}
334	<	}
335	<	if (args_info->nbins_y_given) {
336	<	if (args_info->nbins_y_orig) {
337	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
338	<	} else {
339	<	fprintf(outfile, "%s\n", "nbins_y");
340	<	}
341	<	}
342	<	if (args_info->nanglebins_given) {
343	<	if (args_info->nanglebins_orig) {
344	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
345	<	} else {
346	<	fprintf(outfile, "%s\n", "nanglebins");
347	<	}
348	<	}
349	<	if (args_info->length_given) {
350	<	if (args_info->length_orig) {
351	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
352	<	} else {
353	<	fprintf(outfile, "%s\n", "length");
354	<	}
355	<	}
356	<	if (args_info->zoffset_given) {
357	<	if (args_info->zoffset_orig) {
358	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
359	<	} else {
360	<	fprintf(outfile, "%s\n", "zoffset");
361	<	}
362	<	}
363	<	if (args_info->sele1_given) {
364	<	if (args_info->sele1_orig) {
365	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
366	<	} else {
367	<	fprintf(outfile, "%s\n", "sele1");
368	<	}
369	<	}
370	<	if (args_info->sele2_given) {
371	<	if (args_info->sele2_orig) {
372	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
373	<	} else {
374	<	fprintf(outfile, "%s\n", "sele2");
375	<	}
376	<	}
377	<	if (args_info->sele3_given) {
378	<	if (args_info->sele3_orig) {
379	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
380	<	} else {
381	<	fprintf(outfile, "%s\n", "sele3");
382	<	}
383	<	}
384	<	if (args_info->refsele_given) {
385	<	if (args_info->refsele_orig) {
386	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
387	<	} else {
388	<	fprintf(outfile, "%s\n", "refsele");
389	<	}
390	<	}
391	<	if (args_info->molname_given) {
392	<	if (args_info->molname_orig) {
393	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
394	<	} else {
395	<	fprintf(outfile, "%s\n", "molname");
396	<	}
397	<	}
398	<	if (args_info->begin_given) {
399	<	if (args_info->begin_orig) {
400	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
401	<	} else {
402	<	fprintf(outfile, "%s\n", "begin");
403	<	}
404	<	}
405	<	if (args_info->end_given) {
406	<	if (args_info->end_orig) {
407	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
408	<	} else {
409	<	fprintf(outfile, "%s\n", "end");
410	<	}
411	<	}
412	<	if (args_info->gofr_given) {
413	<	fprintf(outfile, "%s\n", "gofr");
414	<	}
415	<	if (args_info->r_theta_given) {
416	<	fprintf(outfile, "%s\n", "r_theta");
417	<	}
418	<	if (args_info->r_omega_given) {
419	<	fprintf(outfile, "%s\n", "r_omega");
420	<	}
421	<	if (args_info->theta_omega_given) {
422	<	fprintf(outfile, "%s\n", "theta_omega");
423	<	}
424	<	if (args_info->gxyz_given) {
425	<	fprintf(outfile, "%s\n", "gxyz");
426	<	}
427	<	if (args_info->p2_given) {
428	<	fprintf(outfile, "%s\n", "p2");
429	<	}
430	<	if (args_info->scd_given) {
431	<	fprintf(outfile, "%s\n", "scd");
432	<	}
433	<	if (args_info->density_given) {
434	<	fprintf(outfile, "%s\n", "density");
435	<	}
436	<	if (args_info->slab_density_given) {
437	<	fprintf(outfile, "%s\n", "slab_density");
438	<	}
439	<	if (args_info->hxy_given) {
440	<	fprintf(outfile, "%s\n", "hxy");
441	<	}
442	<
493	>	i = cmdline_parser_dump(outfile, args_info);
494		fclose (outfile);
495
445	–	i = EXIT_SUCCESS;
496		return i;
497		}
498
#	Line 452 | Line 502 | cmdline_parser_free (struct gengetopt_args_info *args_
502		cmdline_parser_release (args_info);
503		}
504
505	<
456	<	/* gengetopt_strdup() */
457	<	/* strdup.c replacement of strdup, which is not standard */
505	>	/** @brief replacement of strdup, which is not standard */
506		char *
507		gengetopt_strdup (const char *s)
508		{
#	Line 470 | Line 518 | static void
518		}
519
520		static void
473	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
474	–
475	–	static void
521		reset_group_staticProps(struct gengetopt_args_info *args_info)
522		{
523		if (! args_info->staticProps_group_counter)
524		return;
525
526	+	args_info->bo_given = 0 ;
527	+	args_info->bor_given = 0 ;
528	+	args_info->bad_given = 0 ;
529	+	args_info->count_given = 0 ;
530		args_info->gofr_given = 0 ;
531	+	args_info->gofz_given = 0 ;
532		args_info->r_theta_given = 0 ;
533		args_info->r_omega_given = 0 ;
534		args_info->theta_omega_given = 0 ;
535		args_info->gxyz_given = 0 ;
536	+	args_info->twodgofr_given = 0 ;
537		args_info->p2_given = 0 ;
538	+	args_info->rp2_given = 0 ;
539		args_info->scd_given = 0 ;
540		args_info->density_given = 0 ;
541		args_info->slab_density_given = 0 ;
542	+	args_info->p_angle_given = 0 ;
543		args_info->hxy_given = 0 ;
544	+	args_info->rho_r_given = 0 ;
545	+	args_info->angle_r_given = 0 ;
546	+	args_info->hullvol_given = 0 ;
547
548		args_info->staticProps_group_counter = 0;
549		}
#	Line 499 | Line 555 | int
555		}
556
557		int
558	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
559	+	struct cmdline_parser_params *params)
560	+	{
561	+	int result;
562	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
563	+
564	+	if (result == EXIT_FAILURE)
565	+	{
566	+	cmdline_parser_free (args_info);
567	+	exit (EXIT_FAILURE);
568	+	}
569	+
570	+	return result;
571	+	}
572	+
573	+	int
574		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
575		{
576		int result;
577	+	struct cmdline_parser_params params;
578	+
579	+	params.override = override;
580	+	params.initialize = initialize;
581	+	params.check_required = check_required;
582	+	params.check_ambiguity = 0;
583	+	params.print_errors = 1;
584
585	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
585	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
586
587		if (result == EXIT_FAILURE)
588		{
#	Line 536 | Line 615 | cmdline_parser_required2 (struct gengetopt_args_info *
615		{
616		int error = 0;
617
618	+	/* checks for required options */
619		if (! args_info->input_given)
620		{
621		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
622		error = 1;
623		}
624	+
625		if (args_info->staticProps_group_counter == 0)
626		{
627		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 548 | Line 629 | cmdline_parser_required2 (struct gengetopt_args_info *
629		}
630
631
632	+	/* checks for dependences among options */
633	+
634		return error;
635		}
636
637	+
638	+	static char *package_name = 0;
639	+
640	+	/**
641	+	* @brief updates an option
642	+	* @param field the generic pointer to the field to update
643	+	* @param orig_field the pointer to the orig field
644	+	* @param field_given the pointer to the number of occurrence of this option
645	+	* @param prev_given the pointer to the number of occurrence already seen
646	+	* @param value the argument for this option (if null no arg was specified)
647	+	* @param possible_values the possible values for this option (if specified)
648	+	* @param default_value the default value (in case the option only accepts fixed values)
649	+	* @param arg_type the type of this option
650	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
651	+	* @param override @see cmdline_parser_params.override
652	+	* @param no_free whether to free a possible previous value
653	+	* @param multiple_option whether this is a multiple option
654	+	* @param long_opt the corresponding long option
655	+	* @param short_opt the corresponding short option (or '-' if none)
656	+	* @param additional_error possible further error specification
657	+	*/
658	+	static
659	+	int update_arg(void *field, char **orig_field,
660	+	unsigned int *field_given, unsigned int *prev_given,
661	+	char *value, char *possible_values[], const char *default_value,
662	+	cmdline_parser_arg_type arg_type,
663	+	int check_ambiguity, int override,
664	+	int no_free, int multiple_option,
665	+	const char *long_opt, char short_opt,
666	+	const char *additional_error)
667	+	{
668	+	char *stop_char = 0;
669	+	const char *val = value;
670	+	int found;
671	+	char **string_field;
672	+
673	+	stop_char = 0;
674	+	found = 0;
675	+
676	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
677	+	{
678	+	if (short_opt != '-')
679	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
680	+	package_name, long_opt, short_opt,
681	+	(additional_error ? additional_error : ""));
682	+	else
683	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
684	+	package_name, long_opt,
685	+	(additional_error ? additional_error : ""));
686	+	return 1; /* failure */
687	+	}
688	+
689	+
690	+	if (field_given && *field_given && ! override)
691	+	return 0;
692	+	if (prev_given)
693	+	(*prev_given)++;
694	+	if (field_given)
695	+	(*field_given)++;
696	+	if (possible_values)
697	+	val = possible_values[found];
698	+
699	+	switch(arg_type) {
700	+	case ARG_INT:
701	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
702	+	break;
703	+	case ARG_DOUBLE:
704	+	if (val) *((double *)field) = strtod (val, &stop_char);
705	+	break;
706	+	case ARG_STRING:
707	+	if (val) {
708	+	string_field = (char **)field;
709	+	if (!no_free && *string_field)
710	+	free (*string_field); /* free previous string */
711	+	*string_field = gengetopt_strdup (val);
712	+	}
713	+	break;
714	+	default:
715	+	break;
716	+	};
717	+
718	+	/* check numeric conversion */
719	+	switch(arg_type) {
720	+	case ARG_INT:
721	+	case ARG_DOUBLE:
722	+	if (val && !(stop_char && *stop_char == '\0')) {
723	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
724	+	return 1; /* failure */
725	+	}
726	+	break;
727	+	default:
728	+	;
729	+	};
730	+
731	+	/* store the original value */
732	+	switch(arg_type) {
733	+	case ARG_NO:
734	+	break;
735	+	default:
736	+	if (value && orig_field) {
737	+	if (no_free) {
738	+	*orig_field = value;
739	+	} else {
740	+	if (*orig_field)
741	+	free (*orig_field); /* free previous string */
742	+	*orig_field = gengetopt_strdup (value);
743	+	}
744	+	}
745	+	};
746	+
747	+	return 0; /* OK */
748	+	}
749	+
750	+
751		int
752	<	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)
752	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
753	>	struct cmdline_parser_params *params, const char *additional_error)
754		{
755		int c;        /* Character of the parsed option.  */
756
757		int error = 0;
758		struct gengetopt_args_info local_args_info;
759	+
760	+	int override;
761	+	int initialize;
762	+	int check_required;
763	+	int check_ambiguity;
764	+
765	+	package_name = argv[0];
766	+
767	+	override = params->override;
768	+	initialize = params->initialize;
769	+	check_required = params->check_required;
770	+	check_ambiguity = params->check_ambiguity;
771
772		if (initialize)
773		cmdline_parser_init (args_info);
#	Line 566 | Line 776 | cmdline_parser_internal (int argc, char * const *argv,
776
777		optarg = 0;
778		optind = 0;
779	<	opterr = 1;
779	>	opterr = params->print_errors;
780		optopt = '?';
781
782		while (1)
783		{
784		int option_index = 0;
575	–	char *stop_char;
785
786		static struct option long_options[] = {
787		{ "help",       0, NULL, 'h' },
#	Line 580 | Line 789 | cmdline_parser_internal (int argc, char * const *argv,
789		{ "input",      1, NULL, 'i' },
790		{ "output",     1, NULL, 'o' },
791		{ "step",       1, NULL, 'n' },
792	<	{ "nrbins",     1, NULL, 'r' },
792	>	{ "nbins",      1, NULL, 'b' },
793		{ "nbins_x",    1, NULL, 'x' },
794		{ "nbins_y",    1, NULL, 'y' },
795		{ "nanglebins", 1, NULL, 'a' },
796	<	{ "length",     1, NULL, 'l' },
796	>	{ "rcut",       1, NULL, 'c' },
797	>	{ "dz", 1, NULL, 0 },
798	>	{ "length",     1, NULL, 0 },
799	>	{ "zlength",    1, NULL, 0 },
800		{ "zoffset",    1, NULL, 'z' },
801		{ "sele1",      1, NULL, 0 },
802		{ "sele2",      1, NULL, 0 },
803		{ "sele3",      1, NULL, 0 },
804		{ "refsele",    1, NULL, 0 },
805	+	{ "comsele",    1, NULL, 0 },
806		{ "molname",    1, NULL, 0 },
807		{ "begin",      1, NULL, 0 },
808		{ "end",        1, NULL, 0 },
809	<	{ "gofr",       0, NULL, 0 },
809	>	{ "radius",     1, NULL, 0 },
810	>	{ "bo", 0, NULL, 0 },
811	>	{ "bor",        0, NULL, 0 },
812	>	{ "bad",        0, NULL, 0 },
813	>	{ "count",      0, NULL, 0 },
814	>	{ "gofr",       0, NULL, 'g' },
815	>	{ "gofz",       0, NULL, 0 },
816		{ "r_theta",    0, NULL, 0 },
817		{ "r_omega",    0, NULL, 0 },
818		{ "theta_omega",        0, NULL, 0 },
819		{ "gxyz",       0, NULL, 0 },
820	<	{ "p2", 0, NULL, 0 },
821	<	{ "scd",        0, NULL, 0 },
822	<	{ "density",    0, NULL, 0 },
820	>	{ "twodgofr",   0, NULL, 0 },
821	>	{ "p2", 0, NULL, 'p' },
822	>	{ "rp2",        0, NULL, 0 },
823	>	{ "scd",        0, NULL, 's' },
824	>	{ "density",    0, NULL, 'd' },
825		{ "slab_density",       0, NULL, 0 },
826	+	{ "p_angle",    0, NULL, 0 },
827		{ "hxy",        0, NULL, 0 },
828	+	{ "rho_r",      0, NULL, 0 },
829	+	{ "angle_r",    0, NULL, 0 },
830	+	{ "hullvol",    0, NULL, 0 },
831		{ NULL, 0, NULL, 0 }
832		};
833
834	<	stop_char = 0;
610	<	c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index);
834	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
835
836		if (c == -1) break;       /* Exit from `while (1)' loop.  */
837
#	Line 624 | Line 848 | cmdline_parser_internal (int argc, char * const *argv,
848		exit (EXIT_SUCCESS);
849
850		case 'i':       /* input dump file.  */
851	<	if (local_args_info.input_given)
852	<	{
853	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
854	<	goto failure;
855	<	}
856	<	if (args_info->input_given && ! override)
857	<	continue;
858	<	local_args_info.input_given = 1;
859	<	args_info->input_given = 1;
860	<	if (args_info->input_arg)
637	<	free (args_info->input_arg); /* free previous string */
638	<	args_info->input_arg = gengetopt_strdup (optarg);
639	<	if (args_info->input_orig)
640	<	free (args_info->input_orig); /* free previous string */
641	<	args_info->input_orig = gengetopt_strdup (optarg);
851	>
852	>
853	>	if (update_arg( (void *)&(args_info->input_arg),
854	>	&(args_info->input_orig), &(args_info->input_given),
855	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
856	>	check_ambiguity, override, 0, 0,
857	>	"input", 'i',
858	>	additional_error))
859	>	goto failure;
860	>
861		break;
643	–
862		case 'o':       /* output file name.  */
863	<	if (local_args_info.output_given)
864	<	{
865	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
866	<	goto failure;
867	<	}
868	<	if (args_info->output_given && ! override)
869	<	continue;
870	<	local_args_info.output_given = 1;
871	<	args_info->output_given = 1;
872	<	if (args_info->output_arg)
655	<	free (args_info->output_arg); /* free previous string */
656	<	args_info->output_arg = gengetopt_strdup (optarg);
657	<	if (args_info->output_orig)
658	<	free (args_info->output_orig); /* free previous string */
659	<	args_info->output_orig = gengetopt_strdup (optarg);
863	>
864	>
865	>	if (update_arg( (void *)&(args_info->output_arg),
866	>	&(args_info->output_orig), &(args_info->output_given),
867	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
868	>	check_ambiguity, override, 0, 0,
869	>	"output", 'o',
870	>	additional_error))
871	>	goto failure;
872	>
873		break;
661	–
874		case 'n':       /* process every n frame.  */
875	<	if (local_args_info.step_given)
876	<	{
877	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
878	<	goto failure;
879	<	}
880	<	if (args_info->step_given && ! override)
881	<	continue;
882	<	local_args_info.step_given = 1;
671	<	args_info->step_given = 1;
672	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
673	<	if (!(stop_char && *stop_char == '\0')) {
674	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
875	>
876	>
877	>	if (update_arg( (void *)&(args_info->step_arg),
878	>	&(args_info->step_orig), &(args_info->step_given),
879	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
880	>	check_ambiguity, override, 0, 0,
881	>	"step", 'n',
882	>	additional_error))
883		goto failure;
884	<	}
677	<	if (args_info->step_orig)
678	<	free (args_info->step_orig); /* free previous string */
679	<	args_info->step_orig = gengetopt_strdup (optarg);
884	>
885		break;
886	<
887	<	case 'r':       /* number of bins for distance.  */
888	<	if (local_args_info.nrbins_given)
889	<	{
890	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
891	<	goto failure;
892	<	}
893	<	if (args_info->nrbins_given && ! override)
894	<	continue;
690	<	local_args_info.nrbins_given = 1;
691	<	args_info->nrbins_given = 1;
692	<	args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
693	<	if (!(stop_char && *stop_char == '\0')) {
694	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
886	>	case 'b':       /* number of bins (general purpose).  */
887	>
888	>
889	>	if (update_arg( (void *)&(args_info->nbins_arg),
890	>	&(args_info->nbins_orig), &(args_info->nbins_given),
891	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
892	>	check_ambiguity, override, 0, 0,
893	>	"nbins", 'b',
894	>	additional_error))
895		goto failure;
896	<	}
697	<	if (args_info->nrbins_orig)
698	<	free (args_info->nrbins_orig); /* free previous string */
699	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
896	>
897		break;
701	–
898		case 'x':       /* number of bins in x axis.  */
899	<	if (local_args_info.nbins_x_given)
900	<	{
901	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
902	<	goto failure;
903	<	}
904	<	if (args_info->nbins_x_given && ! override)
905	<	continue;
906	<	local_args_info.nbins_x_given = 1;
711	<	args_info->nbins_x_given = 1;
712	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
713	<	if (!(stop_char && *stop_char == '\0')) {
714	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
899	>
900	>
901	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
902	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
903	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
904	>	check_ambiguity, override, 0, 0,
905	>	"nbins_x", 'x',
906	>	additional_error))
907		goto failure;
908	<	}
717	<	if (args_info->nbins_x_orig)
718	<	free (args_info->nbins_x_orig); /* free previous string */
719	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
908	>
909		break;
721	–
910		case 'y':       /* number of bins in y axis.  */
911	<	if (local_args_info.nbins_y_given)
912	<	{
913	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
914	<	goto failure;
915	<	}
916	<	if (args_info->nbins_y_given && ! override)
917	<	continue;
918	<	local_args_info.nbins_y_given = 1;
731	<	args_info->nbins_y_given = 1;
732	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
733	<	if (!(stop_char && *stop_char == '\0')) {
734	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
911	>
912	>
913	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
914	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
915	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
916	>	check_ambiguity, override, 0, 0,
917	>	"nbins_y", 'y',
918	>	additional_error))
919		goto failure;
920	<	}
737	<	if (args_info->nbins_y_orig)
738	<	free (args_info->nbins_y_orig); /* free previous string */
739	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
920	>
921		break;
741	–
922		case 'a':       /* number of bins for cos(angle).  */
923	<	if (local_args_info.nanglebins_given)
924	<	{
925	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
926	<	goto failure;
927	<	}
928	<	if (args_info->nanglebins_given && ! override)
929	<	continue;
930	<	local_args_info.nanglebins_given = 1;
751	<	args_info->nanglebins_given = 1;
752	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
753	<	if (!(stop_char && *stop_char == '\0')) {
754	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
923	>
924	>
925	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
926	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
927	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
928	>	check_ambiguity, override, 0, 0,
929	>	"nanglebins", 'a',
930	>	additional_error))
931		goto failure;
932	<	}
757	<	if (args_info->nanglebins_orig)
758	<	free (args_info->nanglebins_orig); /* free previous string */
759	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
932	>
933		break;
934	<
935	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
936	<	if (local_args_info.length_given)
937	<	{
938	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
939	<	goto failure;
940	<	}
941	<	if (args_info->length_given && ! override)
942	<	continue;
770	<	local_args_info.length_given = 1;
771	<	args_info->length_given = 1;
772	<	args_info->length_arg = strtod (optarg, &stop_char);
773	<	if (!(stop_char && *stop_char == '\0')) {
774	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
934	>	case 'c':       /* cutoff radius (rcut).  */
935	>
936	>
937	>	if (update_arg( (void *)&(args_info->rcut_arg),
938	>	&(args_info->rcut_orig), &(args_info->rcut_given),
939	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
940	>	check_ambiguity, override, 0, 0,
941	>	"rcut", 'c',
942	>	additional_error))
943		goto failure;
944	<	}
777	<	if (args_info->length_orig)
778	<	free (args_info->length_orig); /* free previous string */
779	<	args_info->length_orig = gengetopt_strdup (optarg);
944	>
945		break;
781	–
946		case 'z':       /* Where to set the zero for the slab_density calculation.  */
947	<	if (local_args_info.zoffset_given)
948	<	{
949	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
950	<	goto failure;
951	<	}
952	<	if (args_info->zoffset_given && ! override)
953	<	continue;
954	<	local_args_info.zoffset_given = 1;
791	<	args_info->zoffset_given = 1;
792	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
793	<	if (!(stop_char && *stop_char == '\0')) {
794	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
947	>
948	>
949	>	if (update_arg( (void *)&(args_info->zoffset_arg),
950	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
951	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
952	>	check_ambiguity, override, 0, 0,
953	>	"zoffset", 'z',
954	>	additional_error))
955		goto failure;
956	<	}
797	<	if (args_info->zoffset_orig)
798	<	free (args_info->zoffset_orig); /* free previous string */
799	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
956	>
957		break;
958	<
958	>	case 'g':       /* g(r).  */
959	>
960	>	if (args_info->staticProps_group_counter && override)
961	>	reset_group_staticProps (args_info);
962	>	args_info->staticProps_group_counter += 1;
963	>
964	>	if (update_arg( 0 ,
965	>	0 , &(args_info->gofr_given),
966	>	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
967	>	check_ambiguity, override, 0, 0,
968	>	"gofr", 'g',
969	>	additional_error))
970	>	goto failure;
971	>
972	>	break;
973	>	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
974	>
975	>	if (args_info->staticProps_group_counter && override)
976	>	reset_group_staticProps (args_info);
977	>	args_info->staticProps_group_counter += 1;
978	>
979	>	if (update_arg( 0 ,
980	>	0 , &(args_info->p2_given),
981	>	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
982	>	check_ambiguity, override, 0, 0,
983	>	"p2", 'p',
984	>	additional_error))
985	>	goto failure;
986	>
987	>	break;
988	>	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
989	>
990	>	if (args_info->staticProps_group_counter && override)
991	>	reset_group_staticProps (args_info);
992	>	args_info->staticProps_group_counter += 1;
993	>
994	>	if (update_arg( 0 ,
995	>	0 , &(args_info->scd_given),
996	>	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
997	>	check_ambiguity, override, 0, 0,
998	>	"scd", 's',
999	>	additional_error))
1000	>	goto failure;
1001	>
1002	>	break;
1003	>	case 'd':       /* density plot.  */
1004	>
1005	>	if (args_info->staticProps_group_counter && override)
1006	>	reset_group_staticProps (args_info);
1007	>	args_info->staticProps_group_counter += 1;
1008	>
1009	>	if (update_arg( 0 ,
1010	>	0 , &(args_info->density_given),
1011	>	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1012	>	check_ambiguity, override, 0, 0,
1013	>	"density", 'd',
1014	>	additional_error))
1015	>	goto failure;
1016	>
1017	>	break;
1018
1019		case 0: /* Long option with no short option */
1020	+	/* slab width (dz).  */
1021	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1022	+	{
1023	+
1024	+
1025	+	if (update_arg( (void *)&(args_info->dz_arg),
1026	+	&(args_info->dz_orig), &(args_info->dz_given),
1027	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1028	+	check_ambiguity, override, 0, 0,
1029	+	"dz", '-',
1030	+	additional_error))
1031	+	goto failure;
1032	+
1033	+	}
1034	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1035	+	if (strcmp (long_options[option_index].name, "length") == 0)
1036	+	{
1037	+
1038	+
1039	+	if (update_arg( (void *)&(args_info->length_arg),
1040	+	&(args_info->length_orig), &(args_info->length_given),
1041	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1042	+	check_ambiguity, override, 0, 0,
1043	+	"length", '-',
1044	+	additional_error))
1045	+	goto failure;
1046	+
1047	+	}
1048	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1049	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1050	+	{
1051	+
1052	+
1053	+	if (update_arg( (void *)&(args_info->zlength_arg),
1054	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1055	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1056	+	check_ambiguity, override, 0, 0,
1057	+	"zlength", '-',
1058	+	additional_error))
1059	+	goto failure;
1060	+
1061	+	}
1062		/* select the first stuntdouble set.  */
1063	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1063	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1064		{
1065	<	if (local_args_info.sele1_given)
1066	<	{
1067	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1068	<	goto failure;
1069	<	}
1070	<	if (args_info->sele1_given && ! override)
1071	<	continue;
1072	<	local_args_info.sele1_given = 1;
1073	<	args_info->sele1_given = 1;
1074	<	if (args_info->sele1_arg)
817	<	free (args_info->sele1_arg); /* free previous string */
818	<	args_info->sele1_arg = gengetopt_strdup (optarg);
819	<	if (args_info->sele1_orig)
820	<	free (args_info->sele1_orig); /* free previous string */
821	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1065	>
1066	>
1067	>	if (update_arg( (void *)&(args_info->sele1_arg),
1068	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1069	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1070	>	check_ambiguity, override, 0, 0,
1071	>	"sele1", '-',
1072	>	additional_error))
1073	>	goto failure;
1074	>
1075		}
1076		/* select the second stuntdouble set.  */
1077		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1078		{
1079	<	if (local_args_info.sele2_given)
1080	<	{
1081	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1082	<	goto failure;
1083	<	}
1084	<	if (args_info->sele2_given && ! override)
1085	<	continue;
1086	<	local_args_info.sele2_given = 1;
1087	<	args_info->sele2_given = 1;
1088	<	if (args_info->sele2_arg)
836	<	free (args_info->sele2_arg); /* free previous string */
837	<	args_info->sele2_arg = gengetopt_strdup (optarg);
838	<	if (args_info->sele2_orig)
839	<	free (args_info->sele2_orig); /* free previous string */
840	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1079	>
1080	>
1081	>	if (update_arg( (void *)&(args_info->sele2_arg),
1082	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1083	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1084	>	check_ambiguity, override, 0, 0,
1085	>	"sele2", '-',
1086	>	additional_error))
1087	>	goto failure;
1088	>
1089		}
1090		/* select the third stuntdouble set.  */
1091		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1092		{
1093	<	if (local_args_info.sele3_given)
1094	<	{
1095	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1096	<	goto failure;
1097	<	}
1098	<	if (args_info->sele3_given && ! override)
1099	<	continue;
1100	<	local_args_info.sele3_given = 1;
1101	<	args_info->sele3_given = 1;
1102	<	if (args_info->sele3_arg)
855	<	free (args_info->sele3_arg); /* free previous string */
856	<	args_info->sele3_arg = gengetopt_strdup (optarg);
857	<	if (args_info->sele3_orig)
858	<	free (args_info->sele3_orig); /* free previous string */
859	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1093	>
1094	>
1095	>	if (update_arg( (void *)&(args_info->sele3_arg),
1096	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1097	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1098	>	check_ambiguity, override, 0, 0,
1099	>	"sele3", '-',
1100	>	additional_error))
1101	>	goto failure;
1102	>
1103		}
1104		/* select reference (use and only use with --gxyz).  */
1105		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1106		{
1107	<	if (local_args_info.refsele_given)
1108	<	{
1109	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1110	<	goto failure;
1111	<	}
1112	<	if (args_info->refsele_given && ! override)
1113	<	continue;
1114	<	local_args_info.refsele_given = 1;
1115	<	args_info->refsele_given = 1;
1116	<	if (args_info->refsele_arg)
874	<	free (args_info->refsele_arg); /* free previous string */
875	<	args_info->refsele_arg = gengetopt_strdup (optarg);
876	<	if (args_info->refsele_orig)
877	<	free (args_info->refsele_orig); /* free previous string */
878	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1107	>
1108	>
1109	>	if (update_arg( (void *)&(args_info->refsele_arg),
1110	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1111	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1112	>	check_ambiguity, override, 0, 0,
1113	>	"refsele", '-',
1114	>	additional_error))
1115	>	goto failure;
1116	>
1117		}
1118	+	/* select stunt doubles for center-of-mass reference point.  */
1119	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1120	+	{
1121	+
1122	+
1123	+	if (update_arg( (void *)&(args_info->comsele_arg),
1124	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1125	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1126	+	check_ambiguity, override, 0, 0,
1127	+	"comsele", '-',
1128	+	additional_error))
1129	+	goto failure;
1130	+
1131	+	}
1132		/* molecule name.  */
1133		else if (strcmp (long_options[option_index].name, "molname") == 0)
1134		{
1135	<	if (local_args_info.molname_given)
1136	<	{
1137	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1138	<	goto failure;
1139	<	}
1140	<	if (args_info->molname_given && ! override)
1141	<	continue;
1142	<	local_args_info.molname_given = 1;
1143	<	args_info->molname_given = 1;
1144	<	if (args_info->molname_arg)
893	<	free (args_info->molname_arg); /* free previous string */
894	<	args_info->molname_arg = gengetopt_strdup (optarg);
895	<	if (args_info->molname_orig)
896	<	free (args_info->molname_orig); /* free previous string */
897	<	args_info->molname_orig = gengetopt_strdup (optarg);
1135	>
1136	>
1137	>	if (update_arg( (void *)&(args_info->molname_arg),
1138	>	&(args_info->molname_orig), &(args_info->molname_given),
1139	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1140	>	check_ambiguity, override, 0, 0,
1141	>	"molname", '-',
1142	>	additional_error))
1143	>	goto failure;
1144	>
1145		}
1146	<	/* begin interanl index.  */
1146	>	/* begin internal index.  */
1147		else if (strcmp (long_options[option_index].name, "begin") == 0)
1148		{
1149	<	if (local_args_info.begin_given)
1150	<	{
1151	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1152	<	goto failure;
1153	<	}
1154	<	if (args_info->begin_given && ! override)
1155	<	continue;
1156	<	local_args_info.begin_given = 1;
910	<	args_info->begin_given = 1;
911	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
912	<	if (!(stop_char && *stop_char == '\0')) {
913	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1149	>
1150	>
1151	>	if (update_arg( (void *)&(args_info->begin_arg),
1152	>	&(args_info->begin_orig), &(args_info->begin_given),
1153	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1154	>	check_ambiguity, override, 0, 0,
1155	>	"begin", '-',
1156	>	additional_error))
1157		goto failure;
1158	<	}
916	<	if (args_info->begin_orig)
917	<	free (args_info->begin_orig); /* free previous string */
918	<	args_info->begin_orig = gengetopt_strdup (optarg);
1158	>
1159		}
1160		/* end internal index.  */
1161		else if (strcmp (long_options[option_index].name, "end") == 0)
1162		{
1163	<	if (local_args_info.end_given)
1164	<	{
1165	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1166	<	goto failure;
1167	<	}
1168	<	if (args_info->end_given && ! override)
1169	<	continue;
1170	<	local_args_info.end_given = 1;
931	<	args_info->end_given = 1;
932	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
933	<	if (!(stop_char && *stop_char == '\0')) {
934	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1163	>
1164	>
1165	>	if (update_arg( (void *)&(args_info->end_arg),
1166	>	&(args_info->end_orig), &(args_info->end_given),
1167	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1168	>	check_ambiguity, override, 0, 0,
1169	>	"end", '-',
1170	>	additional_error))
1171		goto failure;
1172	<	}
937	<	if (args_info->end_orig)
938	<	free (args_info->end_orig); /* free previous string */
939	<	args_info->end_orig = gengetopt_strdup (optarg);
1172	>
1173		}
1174	<	/* g(r).  */
1175	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1174	>	/* nanoparticle radius.  */
1175	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1176		{
1177	<	if (local_args_info.gofr_given)
1178	<	{
1179	<	fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1180	<	goto failure;
1181	<	}
1182	<	if (args_info->gofr_given && ! override)
1183	<	continue;
1184	<	local_args_info.gofr_given = 1;
1185	<	args_info->gofr_given = 1;
1177	>
1178	>
1179	>	if (update_arg( (void *)&(args_info->radius_arg),
1180	>	&(args_info->radius_orig), &(args_info->radius_given),
1181	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1182	>	check_ambiguity, override, 0, 0,
1183	>	"radius", '-',
1184	>	additional_error))
1185	>	goto failure;
1186	>
1187	>	}
1188	>	/* bond order parameter (--rcut must be specified).  */
1189	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1190	>	{
1191	>
1192		if (args_info->staticProps_group_counter && override)
1193		reset_group_staticProps (args_info);
1194		args_info->staticProps_group_counter += 1;
1195	<	break;
1195	>
1196	>	if (update_arg( 0 ,
1197	>	0 , &(args_info->bo_given),
1198	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1199	>	check_ambiguity, override, 0, 0,
1200	>	"bo", '-',
1201	>	additional_error))
1202	>	goto failure;
1203	>
1204		}
1205	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1206	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1207	+	{
1208	+
1209	+	if (args_info->staticProps_group_counter && override)
1210	+	reset_group_staticProps (args_info);
1211	+	args_info->staticProps_group_counter += 1;
1212	+
1213	+	if (update_arg( 0 ,
1214	+	0 , &(args_info->bor_given),
1215	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1216	+	check_ambiguity, override, 0, 0,
1217	+	"bor", '-',
1218	+	additional_error))
1219	+	goto failure;
1220	+
1221	+	}
1222	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1223	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1224	+	{
1225	+
1226	+	if (args_info->staticProps_group_counter && override)
1227	+	reset_group_staticProps (args_info);
1228	+	args_info->staticProps_group_counter += 1;
1229	+
1230	+	if (update_arg( 0 ,
1231	+	0 , &(args_info->bad_given),
1232	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1233	+	check_ambiguity, override, 0, 0,
1234	+	"bad", '-',
1235	+	additional_error))
1236	+	goto failure;
1237	+
1238	+	}
1239	+	/* count of molecules matching selection criteria (and associated statistics).  */
1240	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1241	+	{
1242	+
1243	+	if (args_info->staticProps_group_counter && override)
1244	+	reset_group_staticProps (args_info);
1245	+	args_info->staticProps_group_counter += 1;
1246	+
1247	+	if (update_arg( 0 ,
1248	+	0 , &(args_info->count_given),
1249	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1250	+	check_ambiguity, override, 0, 0,
1251	+	"count", '-',
1252	+	additional_error))
1253	+	goto failure;
1254	+
1255	+	}
1256	+	/* g(z).  */
1257	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1258	+	{
1259	+
1260	+	if (args_info->staticProps_group_counter && override)
1261	+	reset_group_staticProps (args_info);
1262	+	args_info->staticProps_group_counter += 1;
1263	+
1264	+	if (update_arg( 0 ,
1265	+	0 , &(args_info->gofz_given),
1266	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1267	+	check_ambiguity, override, 0, 0,
1268	+	"gofz", '-',
1269	+	additional_error))
1270	+	goto failure;
1271	+
1272	+	}
1273		/* g(r, cos(theta)).  */
1274		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1275		{
1276	<	if (local_args_info.r_theta_given)
962	<	{
963	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
964	<	goto failure;
965	<	}
966	<	if (args_info->r_theta_given && ! override)
967	<	continue;
968	<	local_args_info.r_theta_given = 1;
969	<	args_info->r_theta_given = 1;
1276	>
1277		if (args_info->staticProps_group_counter && override)
1278		reset_group_staticProps (args_info);
1279		args_info->staticProps_group_counter += 1;
1280	<	break;
1280	>
1281	>	if (update_arg( 0 ,
1282	>	0 , &(args_info->r_theta_given),
1283	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1284	>	check_ambiguity, override, 0, 0,
1285	>	"r_theta", '-',
1286	>	additional_error))
1287	>	goto failure;
1288	>
1289		}
1290		/* g(r, cos(omega)).  */
1291		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1292		{
1293	<	if (local_args_info.r_omega_given)
979	<	{
980	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
981	<	goto failure;
982	<	}
983	<	if (args_info->r_omega_given && ! override)
984	<	continue;
985	<	local_args_info.r_omega_given = 1;
986	<	args_info->r_omega_given = 1;
1293	>
1294		if (args_info->staticProps_group_counter && override)
1295		reset_group_staticProps (args_info);
1296		args_info->staticProps_group_counter += 1;
1297	<	break;
1297	>
1298	>	if (update_arg( 0 ,
1299	>	0 , &(args_info->r_omega_given),
1300	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1301	>	check_ambiguity, override, 0, 0,
1302	>	"r_omega", '-',
1303	>	additional_error))
1304	>	goto failure;
1305	>
1306		}
1307		/* g(cos(theta), cos(omega)).  */
1308		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1309		{
1310	<	if (local_args_info.theta_omega_given)
996	<	{
997	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
998	<	goto failure;
999	<	}
1000	<	if (args_info->theta_omega_given && ! override)
1001	<	continue;
1002	<	local_args_info.theta_omega_given = 1;
1003	<	args_info->theta_omega_given = 1;
1310	>
1311		if (args_info->staticProps_group_counter && override)
1312		reset_group_staticProps (args_info);
1313		args_info->staticProps_group_counter += 1;
1314	<	break;
1314	>
1315	>	if (update_arg( 0 ,
1316	>	0 , &(args_info->theta_omega_given),
1317	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1318	>	check_ambiguity, override, 0, 0,
1319	>	"theta_omega", '-',
1320	>	additional_error))
1321	>	goto failure;
1322	>
1323		}
1324		/* g(x, y, z).  */
1325		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1326		{
1327	<	if (local_args_info.gxyz_given)
1013	<	{
1014	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1015	<	goto failure;
1016	<	}
1017	<	if (args_info->gxyz_given && ! override)
1018	<	continue;
1019	<	local_args_info.gxyz_given = 1;
1020	<	args_info->gxyz_given = 1;
1327	>
1328		if (args_info->staticProps_group_counter && override)
1329		reset_group_staticProps (args_info);
1330		args_info->staticProps_group_counter += 1;
1331	<	break;
1332	<	}
1333	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1334	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1331	>
1332	>	if (update_arg( 0 ,
1333	>	0 , &(args_info->gxyz_given),
1334	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1335	>	check_ambiguity, override, 0, 0,
1336	>	"gxyz", '-',
1337	>	additional_error))
1338	>	goto failure;
1339	>
1340	>	}
1341	>	/* 2D g(r) (Slab width --dz must be specified).  */
1342	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1343		{
1344	<	if (local_args_info.p2_given)
1030	<	{
1031	<	fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1032	<	goto failure;
1033	<	}
1034	<	if (args_info->p2_given && ! override)
1035	<	continue;
1036	<	local_args_info.p2_given = 1;
1037	<	args_info->p2_given = 1;
1344	>
1345		if (args_info->staticProps_group_counter && override)
1346		reset_group_staticProps (args_info);
1347		args_info->staticProps_group_counter += 1;
1348	<	break;
1348	>
1349	>	if (update_arg( 0 ,
1350	>	0 , &(args_info->twodgofr_given),
1351	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1352	>	check_ambiguity, override, 0, 0,
1353	>	"twodgofr", '-',
1354	>	additional_error))
1355	>	goto failure;
1356	>
1357		}
1358	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1359	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1358	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1359	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1360		{
1361	<	if (local_args_info.scd_given)
1047	<	{
1048	<	fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1049	<	goto failure;
1050	<	}
1051	<	if (args_info->scd_given && ! override)
1052	<	continue;
1053	<	local_args_info.scd_given = 1;
1054	<	args_info->scd_given = 1;
1361	>
1362		if (args_info->staticProps_group_counter && override)
1363		reset_group_staticProps (args_info);
1364		args_info->staticProps_group_counter += 1;
1365	<	break;
1365	>
1366	>	if (update_arg( 0 ,
1367	>	0 , &(args_info->rp2_given),
1368	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1369	>	check_ambiguity, override, 0, 0,
1370	>	"rp2", '-',
1371	>	additional_error))
1372	>	goto failure;
1373	>
1374		}
1375	<	/* density plot (--sele1 must be specified).  */
1376	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1375	>	/* slab density.  */
1376	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1377		{
1378	<	if (local_args_info.density_given)
1064	<	{
1065	<	fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1066	<	goto failure;
1067	<	}
1068	<	if (args_info->density_given && ! override)
1069	<	continue;
1070	<	local_args_info.density_given = 1;
1071	<	args_info->density_given = 1;
1378	>
1379		if (args_info->staticProps_group_counter && override)
1380		reset_group_staticProps (args_info);
1381		args_info->staticProps_group_counter += 1;
1382	<	break;
1382	>
1383	>	if (update_arg( 0 ,
1384	>	0 , &(args_info->slab_density_given),
1385	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1386	>	check_ambiguity, override, 0, 0,
1387	>	"slab_density", '-',
1388	>	additional_error))
1389	>	goto failure;
1390	>
1391		}
1392	<	/* slab density (--sele1 must be specified).  */
1393	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1392	>	/* p(cos(theta)).  */
1393	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1394		{
1395	<	if (local_args_info.slab_density_given)
1081	<	{
1082	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1083	<	goto failure;
1084	<	}
1085	<	if (args_info->slab_density_given && ! override)
1086	<	continue;
1087	<	local_args_info.slab_density_given = 1;
1088	<	args_info->slab_density_given = 1;
1395	>
1396		if (args_info->staticProps_group_counter && override)
1397		reset_group_staticProps (args_info);
1398		args_info->staticProps_group_counter += 1;
1399	<	break;
1399	>
1400	>	if (update_arg( 0 ,
1401	>	0 , &(args_info->p_angle_given),
1402	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1403	>	check_ambiguity, override, 0, 0,
1404	>	"p_angle", '-',
1405	>	additional_error))
1406	>	goto failure;
1407	>
1408		}
1409	<	/* hxy (--sele1 must be specified).  */
1409	>	/* hxy.  */
1410		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1411		{
1412	<	if (local_args_info.hxy_given)
1098	<	{
1099	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1100	<	goto failure;
1101	<	}
1102	<	if (args_info->hxy_given && ! override)
1103	<	continue;
1104	<	local_args_info.hxy_given = 1;
1105	<	args_info->hxy_given = 1;
1412	>
1413		if (args_info->staticProps_group_counter && override)
1414		reset_group_staticProps (args_info);
1415		args_info->staticProps_group_counter += 1;
1416	<	break;
1416	>
1417	>	if (update_arg( 0 ,
1418	>	0 , &(args_info->hxy_given),
1419	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1420	>	check_ambiguity, override, 0, 0,
1421	>	"hxy", '-',
1422	>	additional_error))
1423	>	goto failure;
1424	>
1425		}
1426	+	/* rho of R.  */
1427	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1428	+	{
1429
1430	+	if (args_info->staticProps_group_counter && override)
1431	+	reset_group_staticProps (args_info);
1432	+	args_info->staticProps_group_counter += 1;
1433	+
1434	+	if (update_arg( 0 ,
1435	+	0 , &(args_info->rho_r_given),
1436	+	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1437	+	check_ambiguity, override, 0, 0,
1438	+	"rho_r", '-',
1439	+	additional_error))
1440	+	goto failure;
1441	+
1442	+	}
1443	+	/* angle of R.  */
1444	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1445	+	{
1446	+
1447	+	if (args_info->staticProps_group_counter && override)
1448	+	reset_group_staticProps (args_info);
1449	+	args_info->staticProps_group_counter += 1;
1450	+
1451	+	if (update_arg( 0 ,
1452	+	0 , &(args_info->angle_r_given),
1453	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1454	+	check_ambiguity, override, 0, 0,
1455	+	"angle_r", '-',
1456	+	additional_error))
1457	+	goto failure;
1458	+
1459	+	}
1460	+	/* hull volume of nanoparticle.  */
1461	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1462	+	{
1463	+
1464	+	if (args_info->staticProps_group_counter && override)
1465	+	reset_group_staticProps (args_info);
1466	+	args_info->staticProps_group_counter += 1;
1467	+
1468	+	if (update_arg( 0 ,
1469	+	0 , &(args_info->hullvol_given),
1470	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1471	+	check_ambiguity, override, 0, 0,
1472	+	"hullvol", '-',
1473	+	additional_error))
1474	+	goto failure;
1475	+
1476	+	}
1477	+
1478		break;
1479		case '?':       /* Invalid option.  */
1480		/* `getopt_long' already printed an error message.  */
#	Line 1138 | Line 1504 | cmdline_parser_internal (int argc, char * const *argv,
1504		if ( error )
1505		return (EXIT_FAILURE);
1506
1507	+	if (optind < argc)
1508	+	{
1509	+	int i = 0 ;
1510	+	int found_prog_name = 0;
1511	+	/* whether program name, i.e., argv[0], is in the remaining args
1512	+	(this may happen with some implementations of getopt,
1513	+	but surely not with the one included by gengetopt) */
1514	+
1515	+	i = optind;
1516	+	while (i < argc)
1517	+	if (argv[i++] == argv[0]) {
1518	+	found_prog_name = 1;
1519	+	break;
1520	+	}
1521	+	i = 0;
1522	+
1523	+	args_info->inputs_num = argc - optind - found_prog_name;
1524	+	args_info->inputs =
1525	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1526	+	while (optind < argc)
1527	+	if (argv[optind++] != argv[0])
1528	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1529	+	}
1530	+
1531		return 0;
1532
1533		failure:

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords):
Revision 967 by xsun, Mon May 22 15:30:42 2006 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC

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

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