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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 967 by xsun, Mon May 22 15:30:42 2006 UTC vs.
Revision 1454 by gezelter, Wed Jun 23 19:25:02 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	+	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
40	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
41	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"      --dz=DOUBLE               slab width (dz)",
43	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
44	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
45	+	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
46	+	"      --sele1=selection script  select the first stuntdouble set",
47	+	"      --sele2=selection script  select the second stuntdouble set",
48	+	"      --sele3=selection script  select the third stuntdouble set",
49	+	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
50	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
51	+	"      --molname=STRING          molecule name",
52	+	"      --begin=INT               begin internal index",
53	+	"      --end=INT                 end internal index",
54	+	"      --radius=DOUBLE           nanoparticle radius",
55	+	"\n Group: staticProps\n   an option of this group is required",
56	+	"      --bo                      bond order parameter (--rcut must be specified)",
57	+	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
58	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
59	+	"  -g, --gofr                    g(r)",
60	+	"      --gofz                    g(z)",
61	+	"      --r_theta                 g(r, cos(theta))",
62	+	"      --r_omega                 g(r, cos(omega))",
63	+	"      --r_z                     g(r, z)",
64	+	"      --theta_omega             g(cos(theta), cos(omega))",
65	+	"      --gxyz                    g(x, y, z)",
66	+	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
67	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
68	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
69	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
70	+	"  -d, --density                 density plot",
71	+	"      --slab_density            slab density",
72	+	"      --p_angle                 p(cos(theta))",
73	+	"      --hxy                     hxy",
74	+	"      --rho_r                   rho 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->nbins_z_given = 0 ;
112		args_info->nanglebins_given = 0 ;
113	+	args_info->rcut_given = 0 ;
114	+	args_info->dz_given = 0 ;
115		args_info->length_given = 0 ;
116	+	args_info->zlength_given = 0 ;
117		args_info->zoffset_given = 0 ;
118		args_info->sele1_given = 0 ;
119		args_info->sele2_given = 0 ;
120		args_info->sele3_given = 0 ;
121		args_info->refsele_given = 0 ;
122	+	args_info->comsele_given = 0 ;
123		args_info->molname_given = 0 ;
124		args_info->begin_given = 0 ;
125		args_info->end_given = 0 ;
126	+	args_info->radius_given = 0 ;
127	+	args_info->bo_given = 0 ;
128	+	args_info->bor_given = 0 ;
129	+	args_info->bad_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->r_z_given = 0 ;
135		args_info->theta_omega_given = 0 ;
136		args_info->gxyz_given = 0 ;
137	+	args_info->twodgofr_given = 0 ;
138		args_info->p2_given = 0 ;
139	+	args_info->rp2_given = 0 ;
140		args_info->scd_given = 0 ;
141		args_info->density_given = 0 ;
142		args_info->slab_density_given = 0 ;
143	+	args_info->p_angle_given = 0 ;
144		args_info->hxy_given = 0 ;
145	+	args_info->rho_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->nbins_z_arg = 100;
166	+	args_info->nbins_z_orig = NULL;
167		args_info->nanglebins_arg = 50;
168		args_info->nanglebins_orig = NULL;
169	+	args_info->rcut_orig = NULL;
170	+	args_info->dz_orig = NULL;
171		args_info->length_orig = NULL;
172	+	args_info->zlength_orig = NULL;
173		args_info->zoffset_arg = 0;
174		args_info->zoffset_orig = NULL;
175		args_info->sele1_arg = NULL;
#	Line 97 | Line 180 | void clear_args (struct gengetopt_args_info *args_info
180		args_info->sele3_orig = NULL;
181		args_info->refsele_arg = NULL;
182		args_info->refsele_orig = NULL;
183	+	args_info->comsele_arg = NULL;
184	+	args_info->comsele_orig = NULL;
185		args_info->molname_arg = NULL;
186		args_info->molname_orig = NULL;
187		args_info->begin_orig = NULL;
188		args_info->end_orig = NULL;
189	+	args_info->radius_orig = NULL;
190
191		}
192
193	+	static
194	+	void init_args_info(struct gengetopt_args_info *args_info)
195	+	{
196	+
197	+
198	+	args_info->help_help = gengetopt_args_info_help[0] ;
199	+	args_info->version_help = gengetopt_args_info_help[1] ;
200	+	args_info->input_help = gengetopt_args_info_help[2] ;
201	+	args_info->output_help = gengetopt_args_info_help[3] ;
202	+	args_info->step_help = gengetopt_args_info_help[4] ;
203	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
204	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
205	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
206	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
207	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
208	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
209	+	args_info->dz_help = gengetopt_args_info_help[11] ;
210	+	args_info->length_help = gengetopt_args_info_help[12] ;
211	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
212	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
213	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
214	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
215	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
216	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
217	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
218	+	args_info->molname_help = gengetopt_args_info_help[20] ;
219	+	args_info->begin_help = gengetopt_args_info_help[21] ;
220	+	args_info->end_help = gengetopt_args_info_help[22] ;
221	+	args_info->radius_help = gengetopt_args_info_help[23] ;
222	+	args_info->bo_help = gengetopt_args_info_help[25] ;
223	+	args_info->bor_help = gengetopt_args_info_help[26] ;
224	+	args_info->bad_help = gengetopt_args_info_help[27] ;
225	+	args_info->gofr_help = gengetopt_args_info_help[28] ;
226	+	args_info->gofz_help = gengetopt_args_info_help[29] ;
227	+	args_info->r_theta_help = gengetopt_args_info_help[30] ;
228	+	args_info->r_omega_help = gengetopt_args_info_help[31] ;
229	+	args_info->r_z_help = gengetopt_args_info_help[32] ;
230	+	args_info->theta_omega_help = gengetopt_args_info_help[33] ;
231	+	args_info->gxyz_help = gengetopt_args_info_help[34] ;
232	+	args_info->twodgofr_help = gengetopt_args_info_help[35] ;
233	+	args_info->p2_help = gengetopt_args_info_help[36] ;
234	+	args_info->rp2_help = gengetopt_args_info_help[37] ;
235	+	args_info->scd_help = gengetopt_args_info_help[38] ;
236	+	args_info->density_help = gengetopt_args_info_help[39] ;
237	+	args_info->slab_density_help = gengetopt_args_info_help[40] ;
238	+	args_info->p_angle_help = gengetopt_args_info_help[41] ;
239	+	args_info->hxy_help = gengetopt_args_info_help[42] ;
240	+	args_info->rho_r_help = gengetopt_args_info_help[43] ;
241	+	args_info->hullvol_help = gengetopt_args_info_help[44] ;
242	+
243	+	}
244	+
245		void
246		cmdline_parser_print_version (void)
247		{
248		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
249		}
250
251	+	static void print_help_common(void) {
252	+	cmdline_parser_print_version ();
253	+
254	+	if (strlen(gengetopt_args_info_purpose) > 0)
255	+	printf("\n%s\n", gengetopt_args_info_purpose);
256	+
257	+	if (strlen(gengetopt_args_info_usage) > 0)
258	+	printf("\n%s\n", gengetopt_args_info_usage);
259	+
260	+	printf("\n");
261	+
262	+	if (strlen(gengetopt_args_info_description) > 0)
263	+	printf("%s\n", gengetopt_args_info_description);
264	+	}
265	+
266		void
267		cmdline_parser_print_help (void)
268		{
269	<	cmdline_parser_print_version ();
270	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
271	<	printf("%s\n","  -h, --help                    Print help and exit");
272	<	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	<
269	>	int i = 0;
270	>	print_help_common();
271	>	while (gengetopt_args_info_help[i])
272	>	printf("%s\n", gengetopt_args_info_help[i++]);
273		}
274
275		void
#	Line 152 | Line 277 | cmdline_parser_init (struct gengetopt_args_info *args_
277		{
278		clear_given (args_info);
279		clear_args (args_info);
280	+	init_args_info (args_info);
281	+
282	+	args_info->inputs = NULL;
283	+	args_info->inputs_num = 0;
284	+	}
285	+
286	+	void
287	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
288	+	{
289	+	if (params)
290	+	{
291	+	params->override = 0;
292	+	params->initialize = 1;
293	+	params->check_required = 1;
294	+	params->check_ambiguity = 0;
295	+	params->print_errors = 1;
296	+	}
297	+	}
298	+
299	+	struct cmdline_parser_params *
300	+	cmdline_parser_params_create(void)
301	+	{
302	+	struct cmdline_parser_params *params =
303	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
304	+	cmdline_parser_params_init(params);
305	+	return params;
306	+	}
307	+
308	+	static void
309	+	free_string_field (char **s)
310	+	{
311	+	if (*s)
312	+	{
313	+	free (*s);
314	+	*s = 0;
315	+	}
316		}
317
318	+
319		static void
320		cmdline_parser_release (struct gengetopt_args_info *args_info)
321		{
322	+	unsigned int i;
323	+	free_string_field (&(args_info->input_arg));
324	+	free_string_field (&(args_info->input_orig));
325	+	free_string_field (&(args_info->output_arg));
326	+	free_string_field (&(args_info->output_orig));
327	+	free_string_field (&(args_info->step_orig));
328	+	free_string_field (&(args_info->nbins_orig));
329	+	free_string_field (&(args_info->nbins_x_orig));
330	+	free_string_field (&(args_info->nbins_y_orig));
331	+	free_string_field (&(args_info->nbins_z_orig));
332	+	free_string_field (&(args_info->nanglebins_orig));
333	+	free_string_field (&(args_info->rcut_orig));
334	+	free_string_field (&(args_info->dz_orig));
335	+	free_string_field (&(args_info->length_orig));
336	+	free_string_field (&(args_info->zlength_orig));
337	+	free_string_field (&(args_info->zoffset_orig));
338	+	free_string_field (&(args_info->sele1_arg));
339	+	free_string_field (&(args_info->sele1_orig));
340	+	free_string_field (&(args_info->sele2_arg));
341	+	free_string_field (&(args_info->sele2_orig));
342	+	free_string_field (&(args_info->sele3_arg));
343	+	free_string_field (&(args_info->sele3_orig));
344	+	free_string_field (&(args_info->refsele_arg));
345	+	free_string_field (&(args_info->refsele_orig));
346	+	free_string_field (&(args_info->comsele_arg));
347	+	free_string_field (&(args_info->comsele_orig));
348	+	free_string_field (&(args_info->molname_arg));
349	+	free_string_field (&(args_info->molname_orig));
350	+	free_string_field (&(args_info->begin_orig));
351	+	free_string_field (&(args_info->end_orig));
352	+	free_string_field (&(args_info->radius_orig));
353
354	<	if (args_info->input_arg)
354	>
355	>	for (i = 0; i < args_info->inputs_num; ++i)
356	>	free (args_info->inputs [i]);
357	>
358	>	if (args_info->inputs_num)
359	>	free (args_info->inputs);
360	>
361	>	clear_given (args_info);
362	>	}
363	>
364	>
365	>	static void
366	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
367	>	{
368	>	if (arg) {
369	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
370	>	} else {
371	>	fprintf(outfile, "%s\n", opt);
372	>	}
373	>	}
374	>
375	>
376	>	int
377	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
378	>	{
379	>	int i = 0;
380	>
381	>	if (!outfile)
382		{
383	<	free (args_info->input_arg); /* free previous argument */
384	<	args_info->input_arg = 0;
383	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
384	>	return EXIT_FAILURE;
385		}
386	<	if (args_info->input_orig)
387	<	{
388	<	free (args_info->input_orig); /* free previous argument */
389	<	args_info->input_orig = 0;
390	<	}
391	<	if (args_info->output_arg)
392	<	{
393	<	free (args_info->output_arg); /* free previous argument */
394	<	args_info->output_arg = 0;
395	<	}
396	<	if (args_info->output_orig)
397	<	{
398	<	free (args_info->output_orig); /* free previous argument */
399	<	args_info->output_orig = 0;
400	<	}
401	<	if (args_info->step_orig)
402	<	{
403	<	free (args_info->step_orig); /* free previous argument */
404	<	args_info->step_orig = 0;
405	<	}
406	<	if (args_info->nrbins_orig)
407	<	{
408	<	free (args_info->nrbins_orig); /* free previous argument */
409	<	args_info->nrbins_orig = 0;
410	<	}
411	<	if (args_info->nbins_x_orig)
412	<	{
413	<	free (args_info->nbins_x_orig); /* free previous argument */
414	<	args_info->nbins_x_orig = 0;
415	<	}
416	<	if (args_info->nbins_y_orig)
417	<	{
418	<	free (args_info->nbins_y_orig); /* free previous argument */
419	<	args_info->nbins_y_orig = 0;
420	<	}
421	<	if (args_info->nanglebins_orig)
422	<	{
423	<	free (args_info->nanglebins_orig); /* free previous argument */
424	<	args_info->nanglebins_orig = 0;
425	<	}
426	<	if (args_info->length_orig)
427	<	{
428	<	free (args_info->length_orig); /* free previous argument */
429	<	args_info->length_orig = 0;
430	<	}
431	<	if (args_info->zoffset_orig)
432	<	{
433	<	free (args_info->zoffset_orig); /* free previous argument */
434	<	args_info->zoffset_orig = 0;
435	<	}
436	<	if (args_info->sele1_arg)
437	<	{
438	<	free (args_info->sele1_arg); /* free previous argument */
439	<	args_info->sele1_arg = 0;
440	<	}
441	<	if (args_info->sele1_orig)
442	<	{
443	<	free (args_info->sele1_orig); /* free previous argument */
444	<	args_info->sele1_orig = 0;
445	<	}
446	<	if (args_info->sele2_arg)
447	<	{
448	<	free (args_info->sele2_arg); /* free previous argument */
449	<	args_info->sele2_arg = 0;
450	<	}
451	<	if (args_info->sele2_orig)
452	<	{
453	<	free (args_info->sele2_orig); /* free previous argument */
454	<	args_info->sele2_orig = 0;
455	<	}
456	<	if (args_info->sele3_arg)
457	<	{
458	<	free (args_info->sele3_arg); /* free previous argument */
459	<	args_info->sele3_arg = 0;
460	<	}
461	<	if (args_info->sele3_orig)
462	<	{
463	<	free (args_info->sele3_orig); /* free previous argument */
464	<	args_info->sele3_orig = 0;
465	<	}
466	<	if (args_info->refsele_arg)
467	<	{
468	<	free (args_info->refsele_arg); /* free previous argument */
469	<	args_info->refsele_arg = 0;
470	<	}
471	<	if (args_info->refsele_orig)
472	<	{
473	<	free (args_info->refsele_orig); /* free previous argument */
474	<	args_info->refsele_orig = 0;
255	<	}
256	<	if (args_info->molname_arg)
257	<	{
258	<	free (args_info->molname_arg); /* free previous argument */
259	<	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	<	}
386	>
387	>	if (args_info->help_given)
388	>	write_into_file(outfile, "help", 0, 0 );
389	>	if (args_info->version_given)
390	>	write_into_file(outfile, "version", 0, 0 );
391	>	if (args_info->input_given)
392	>	write_into_file(outfile, "input", args_info->input_orig, 0);
393	>	if (args_info->output_given)
394	>	write_into_file(outfile, "output", args_info->output_orig, 0);
395	>	if (args_info->step_given)
396	>	write_into_file(outfile, "step", args_info->step_orig, 0);
397	>	if (args_info->nbins_given)
398	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
399	>	if (args_info->nbins_x_given)
400	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
401	>	if (args_info->nbins_y_given)
402	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
403	>	if (args_info->nbins_z_given)
404	>	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
405	>	if (args_info->nanglebins_given)
406	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
407	>	if (args_info->rcut_given)
408	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
409	>	if (args_info->dz_given)
410	>	write_into_file(outfile, "dz", args_info->dz_orig, 0);
411	>	if (args_info->length_given)
412	>	write_into_file(outfile, "length", args_info->length_orig, 0);
413	>	if (args_info->zlength_given)
414	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
415	>	if (args_info->zoffset_given)
416	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
417	>	if (args_info->sele1_given)
418	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
419	>	if (args_info->sele2_given)
420	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
421	>	if (args_info->sele3_given)
422	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
423	>	if (args_info->refsele_given)
424	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
425	>	if (args_info->comsele_given)
426	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
427	>	if (args_info->molname_given)
428	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
429	>	if (args_info->begin_given)
430	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
431	>	if (args_info->end_given)
432	>	write_into_file(outfile, "end", args_info->end_orig, 0);
433	>	if (args_info->radius_given)
434	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
435	>	if (args_info->bo_given)
436	>	write_into_file(outfile, "bo", 0, 0 );
437	>	if (args_info->bor_given)
438	>	write_into_file(outfile, "bor", 0, 0 );
439	>	if (args_info->bad_given)
440	>	write_into_file(outfile, "bad", 0, 0 );
441	>	if (args_info->gofr_given)
442	>	write_into_file(outfile, "gofr", 0, 0 );
443	>	if (args_info->gofz_given)
444	>	write_into_file(outfile, "gofz", 0, 0 );
445	>	if (args_info->r_theta_given)
446	>	write_into_file(outfile, "r_theta", 0, 0 );
447	>	if (args_info->r_omega_given)
448	>	write_into_file(outfile, "r_omega", 0, 0 );
449	>	if (args_info->r_z_given)
450	>	write_into_file(outfile, "r_z", 0, 0 );
451	>	if (args_info->theta_omega_given)
452	>	write_into_file(outfile, "theta_omega", 0, 0 );
453	>	if (args_info->gxyz_given)
454	>	write_into_file(outfile, "gxyz", 0, 0 );
455	>	if (args_info->twodgofr_given)
456	>	write_into_file(outfile, "twodgofr", 0, 0 );
457	>	if (args_info->p2_given)
458	>	write_into_file(outfile, "p2", 0, 0 );
459	>	if (args_info->rp2_given)
460	>	write_into_file(outfile, "rp2", 0, 0 );
461	>	if (args_info->scd_given)
462	>	write_into_file(outfile, "scd", 0, 0 );
463	>	if (args_info->density_given)
464	>	write_into_file(outfile, "density", 0, 0 );
465	>	if (args_info->slab_density_given)
466	>	write_into_file(outfile, "slab_density", 0, 0 );
467	>	if (args_info->p_angle_given)
468	>	write_into_file(outfile, "p_angle", 0, 0 );
469	>	if (args_info->hxy_given)
470	>	write_into_file(outfile, "hxy", 0, 0 );
471	>	if (args_info->rho_r_given)
472	>	write_into_file(outfile, "rho_r", 0, 0 );
473	>	if (args_info->hullvol_given)
474	>	write_into_file(outfile, "hullvol", 0, 0 );
475
476	<	clear_given (args_info);
476	>
477	>	i = EXIT_SUCCESS;
478	>	return i;
479		}
480
481		int
#	Line 291 | Line 492 | cmdline_parser_file_save(const char *filename, struct
492		return EXIT_FAILURE;
493		}
494
495	<	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	<
495	>	i = cmdline_parser_dump(outfile, args_info);
496		fclose (outfile);
497
445	–	i = EXIT_SUCCESS;
498		return i;
499		}
500
#	Line 452 | Line 504 | cmdline_parser_free (struct gengetopt_args_info *args_
504		cmdline_parser_release (args_info);
505		}
506
507	<
456	<	/* gengetopt_strdup() */
457	<	/* strdup.c replacement of strdup, which is not standard */
507	>	/** @brief replacement of strdup, which is not standard */
508		char *
509		gengetopt_strdup (const char *s)
510		{
#	Line 470 | Line 520 | static void
520		}
521
522		static void
473	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
474	–
475	–	static void
523		reset_group_staticProps(struct gengetopt_args_info *args_info)
524		{
525		if (! args_info->staticProps_group_counter)
526		return;
527
528	+	args_info->bo_given = 0 ;
529	+	args_info->bor_given = 0 ;
530	+	args_info->bad_given = 0 ;
531		args_info->gofr_given = 0 ;
532	+	args_info->gofz_given = 0 ;
533		args_info->r_theta_given = 0 ;
534		args_info->r_omega_given = 0 ;
535	+	args_info->r_z_given = 0 ;
536		args_info->theta_omega_given = 0 ;
537		args_info->gxyz_given = 0 ;
538	+	args_info->twodgofr_given = 0 ;
539		args_info->p2_given = 0 ;
540	+	args_info->rp2_given = 0 ;
541		args_info->scd_given = 0 ;
542		args_info->density_given = 0 ;
543		args_info->slab_density_given = 0 ;
544	+	args_info->p_angle_given = 0 ;
545		args_info->hxy_given = 0 ;
546	+	args_info->rho_r_given = 0 ;
547	+	args_info->hullvol_given = 0 ;
548
549		args_info->staticProps_group_counter = 0;
550		}
#	Line 499 | Line 556 | int
556		}
557
558		int
559	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
560	+	struct cmdline_parser_params *params)
561	+	{
562	+	int result;
563	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
564	+
565	+	if (result == EXIT_FAILURE)
566	+	{
567	+	cmdline_parser_free (args_info);
568	+	exit (EXIT_FAILURE);
569	+	}
570	+
571	+	return result;
572	+	}
573	+
574	+	int
575		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
576		{
577		int result;
578	+	struct cmdline_parser_params params;
579	+
580	+	params.override = override;
581	+	params.initialize = initialize;
582	+	params.check_required = check_required;
583	+	params.check_ambiguity = 0;
584	+	params.print_errors = 1;
585
586	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
586	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
587
588		if (result == EXIT_FAILURE)
589		{
#	Line 536 | Line 616 | cmdline_parser_required2 (struct gengetopt_args_info *
616		{
617		int error = 0;
618
619	+	/* checks for required options */
620		if (! args_info->input_given)
621		{
622		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
623		error = 1;
624		}
625	+
626		if (args_info->staticProps_group_counter == 0)
627		{
628		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 630 | cmdline_parser_required2 (struct gengetopt_args_info *
630		}
631
632
633	+	/* checks for dependences among options */
634	+
635		return error;
636		}
637
638	+
639	+	static char *package_name = 0;
640	+
641	+	/**
642	+	* @brief updates an option
643	+	* @param field the generic pointer to the field to update
644	+	* @param orig_field the pointer to the orig field
645	+	* @param field_given the pointer to the number of occurrence of this option
646	+	* @param prev_given the pointer to the number of occurrence already seen
647	+	* @param value the argument for this option (if null no arg was specified)
648	+	* @param possible_values the possible values for this option (if specified)
649	+	* @param default_value the default value (in case the option only accepts fixed values)
650	+	* @param arg_type the type of this option
651	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
652	+	* @param override @see cmdline_parser_params.override
653	+	* @param no_free whether to free a possible previous value
654	+	* @param multiple_option whether this is a multiple option
655	+	* @param long_opt the corresponding long option
656	+	* @param short_opt the corresponding short option (or '-' if none)
657	+	* @param additional_error possible further error specification
658	+	*/
659	+	static
660	+	int update_arg(void *field, char **orig_field,
661	+	unsigned int *field_given, unsigned int *prev_given,
662	+	char *value, char *possible_values[], const char *default_value,
663	+	cmdline_parser_arg_type arg_type,
664	+	int check_ambiguity, int override,
665	+	int no_free, int multiple_option,
666	+	const char *long_opt, char short_opt,
667	+	const char *additional_error)
668	+	{
669	+	char *stop_char = 0;
670	+	const char *val = value;
671	+	int found;
672	+	char **string_field;
673	+
674	+	stop_char = 0;
675	+	found = 0;
676	+
677	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
678	+	{
679	+	if (short_opt != '-')
680	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
681	+	package_name, long_opt, short_opt,
682	+	(additional_error ? additional_error : ""));
683	+	else
684	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
685	+	package_name, long_opt,
686	+	(additional_error ? additional_error : ""));
687	+	return 1; /* failure */
688	+	}
689	+
690	+
691	+	if (field_given && *field_given && ! override)
692	+	return 0;
693	+	if (prev_given)
694	+	(*prev_given)++;
695	+	if (field_given)
696	+	(*field_given)++;
697	+	if (possible_values)
698	+	val = possible_values[found];
699	+
700	+	switch(arg_type) {
701	+	case ARG_INT:
702	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
703	+	break;
704	+	case ARG_DOUBLE:
705	+	if (val) *((double *)field) = strtod (val, &stop_char);
706	+	break;
707	+	case ARG_STRING:
708	+	if (val) {
709	+	string_field = (char **)field;
710	+	if (!no_free && *string_field)
711	+	free (*string_field); /* free previous string */
712	+	*string_field = gengetopt_strdup (val);
713	+	}
714	+	break;
715	+	default:
716	+	break;
717	+	};
718	+
719	+	/* check numeric conversion */
720	+	switch(arg_type) {
721	+	case ARG_INT:
722	+	case ARG_DOUBLE:
723	+	if (val && !(stop_char && *stop_char == '\0')) {
724	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
725	+	return 1; /* failure */
726	+	}
727	+	break;
728	+	default:
729	+	;
730	+	};
731	+
732	+	/* store the original value */
733	+	switch(arg_type) {
734	+	case ARG_NO:
735	+	break;
736	+	default:
737	+	if (value && orig_field) {
738	+	if (no_free) {
739	+	*orig_field = value;
740	+	} else {
741	+	if (*orig_field)
742	+	free (*orig_field); /* free previous string */
743	+	*orig_field = gengetopt_strdup (value);
744	+	}
745	+	}
746	+	};
747	+
748	+	return 0; /* OK */
749	+	}
750	+
751	+
752		int
753	<	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)
753	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
754	>	struct cmdline_parser_params *params, const char *additional_error)
755		{
756		int c;        /* Character of the parsed option.  */
757
758		int error = 0;
759		struct gengetopt_args_info local_args_info;
760	+
761	+	int override;
762	+	int initialize;
763	+	int check_required;
764	+	int check_ambiguity;
765	+
766	+	package_name = argv[0];
767	+
768	+	override = params->override;
769	+	initialize = params->initialize;
770	+	check_required = params->check_required;
771	+	check_ambiguity = params->check_ambiguity;
772
773		if (initialize)
774		cmdline_parser_init (args_info);
#	Line 566 | Line 777 | cmdline_parser_internal (int argc, char * const *argv,
777
778		optarg = 0;
779		optind = 0;
780	<	opterr = 1;
780	>	opterr = params->print_errors;
781		optopt = '?';
782
783		while (1)
784		{
785		int option_index = 0;
575	–	char *stop_char;
786
787		static struct option long_options[] = {
788		{ "help",       0, NULL, 'h' },
#	Line 580 | Line 790 | cmdline_parser_internal (int argc, char * const *argv,
790		{ "input",      1, NULL, 'i' },
791		{ "output",     1, NULL, 'o' },
792		{ "step",       1, NULL, 'n' },
793	<	{ "nrbins",     1, NULL, 'r' },
793	>	{ "nbins",      1, NULL, 'b' },
794		{ "nbins_x",    1, NULL, 'x' },
795		{ "nbins_y",    1, NULL, 'y' },
796	+	{ "nbins_z",    1, NULL, 0 },
797		{ "nanglebins", 1, NULL, 'a' },
798	<	{ "length",     1, NULL, 'l' },
798	>	{ "rcut",       1, NULL, 'c' },
799	>	{ "dz", 1, NULL, 0 },
800	>	{ "length",     1, NULL, 0 },
801	>	{ "zlength",    1, NULL, 0 },
802		{ "zoffset",    1, NULL, 'z' },
803		{ "sele1",      1, NULL, 0 },
804		{ "sele2",      1, NULL, 0 },
805		{ "sele3",      1, NULL, 0 },
806		{ "refsele",    1, NULL, 0 },
807	+	{ "comsele",    1, NULL, 0 },
808		{ "molname",    1, NULL, 0 },
809		{ "begin",      1, NULL, 0 },
810		{ "end",        1, NULL, 0 },
811	<	{ "gofr",       0, NULL, 0 },
811	>	{ "radius",     1, NULL, 0 },
812	>	{ "bo", 0, NULL, 0 },
813	>	{ "bor",        0, NULL, 0 },
814	>	{ "bad",        0, NULL, 0 },
815	>	{ "gofr",       0, NULL, 'g' },
816	>	{ "gofz",       0, NULL, 0 },
817		{ "r_theta",    0, NULL, 0 },
818		{ "r_omega",    0, NULL, 0 },
819	+	{ "r_z",        0, NULL, 0 },
820		{ "theta_omega",        0, NULL, 0 },
821		{ "gxyz",       0, NULL, 0 },
822	<	{ "p2", 0, NULL, 0 },
823	<	{ "scd",        0, NULL, 0 },
824	<	{ "density",    0, NULL, 0 },
822	>	{ "twodgofr",   0, NULL, 0 },
823	>	{ "p2", 0, NULL, 'p' },
824	>	{ "rp2",        0, NULL, 0 },
825	>	{ "scd",        0, NULL, 's' },
826	>	{ "density",    0, NULL, 'd' },
827		{ "slab_density",       0, NULL, 0 },
828	+	{ "p_angle",    0, NULL, 0 },
829		{ "hxy",        0, NULL, 0 },
830	+	{ "rho_r",      0, NULL, 0 },
831	+	{ "hullvol",    0, NULL, 0 },
832		{ NULL, 0, NULL, 0 }
833		};
834
835	<	stop_char = 0;
610	<	c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index);
835	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
836
837		if (c == -1) break;       /* Exit from `while (1)' loop.  */
838
#	Line 624 | Line 849 | cmdline_parser_internal (int argc, char * const *argv,
849		exit (EXIT_SUCCESS);
850
851		case 'i':       /* input dump file.  */
852	<	if (local_args_info.input_given)
853	<	{
854	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
855	<	goto failure;
856	<	}
857	<	if (args_info->input_given && ! override)
858	<	continue;
859	<	local_args_info.input_given = 1;
860	<	args_info->input_given = 1;
861	<	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);
852	>
853	>
854	>	if (update_arg( (void *)&(args_info->input_arg),
855	>	&(args_info->input_orig), &(args_info->input_given),
856	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
857	>	check_ambiguity, override, 0, 0,
858	>	"input", 'i',
859	>	additional_error))
860	>	goto failure;
861	>
862		break;
643	–
863		case 'o':       /* output file name.  */
864	<	if (local_args_info.output_given)
865	<	{
866	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
867	<	goto failure;
868	<	}
869	<	if (args_info->output_given && ! override)
870	<	continue;
871	<	local_args_info.output_given = 1;
872	<	args_info->output_given = 1;
873	<	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);
864	>
865	>
866	>	if (update_arg( (void *)&(args_info->output_arg),
867	>	&(args_info->output_orig), &(args_info->output_given),
868	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
869	>	check_ambiguity, override, 0, 0,
870	>	"output", 'o',
871	>	additional_error))
872	>	goto failure;
873	>
874		break;
661	–
875		case 'n':       /* process every n frame.  */
876	<	if (local_args_info.step_given)
877	<	{
878	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
879	<	goto failure;
880	<	}
881	<	if (args_info->step_given && ! override)
882	<	continue;
883	<	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);
876	>
877	>
878	>	if (update_arg( (void *)&(args_info->step_arg),
879	>	&(args_info->step_orig), &(args_info->step_given),
880	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
881	>	check_ambiguity, override, 0, 0,
882	>	"step", 'n',
883	>	additional_error))
884		goto failure;
885	<	}
677	<	if (args_info->step_orig)
678	<	free (args_info->step_orig); /* free previous string */
679	<	args_info->step_orig = gengetopt_strdup (optarg);
885	>
886		break;
887	<
888	<	case 'r':       /* number of bins for distance.  */
889	<	if (local_args_info.nrbins_given)
890	<	{
891	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
892	<	goto failure;
893	<	}
894	<	if (args_info->nrbins_given && ! override)
895	<	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);
887	>	case 'b':       /* number of bins (general purpose).  */
888	>
889	>
890	>	if (update_arg( (void *)&(args_info->nbins_arg),
891	>	&(args_info->nbins_orig), &(args_info->nbins_given),
892	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
893	>	check_ambiguity, override, 0, 0,
894	>	"nbins", 'b',
895	>	additional_error))
896		goto failure;
897	<	}
697	<	if (args_info->nrbins_orig)
698	<	free (args_info->nrbins_orig); /* free previous string */
699	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
897	>
898		break;
701	–
899		case 'x':       /* number of bins in x axis.  */
900	<	if (local_args_info.nbins_x_given)
901	<	{
902	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
903	<	goto failure;
904	<	}
905	<	if (args_info->nbins_x_given && ! override)
906	<	continue;
907	<	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);
900	>
901	>
902	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
903	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
904	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
905	>	check_ambiguity, override, 0, 0,
906	>	"nbins_x", 'x',
907	>	additional_error))
908		goto failure;
909	<	}
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);
909	>
910		break;
721	–
911		case 'y':       /* number of bins in y axis.  */
912	<	if (local_args_info.nbins_y_given)
913	<	{
914	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
915	<	goto failure;
916	<	}
917	<	if (args_info->nbins_y_given && ! override)
918	<	continue;
919	<	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);
912	>
913	>
914	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
915	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
916	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
917	>	check_ambiguity, override, 0, 0,
918	>	"nbins_y", 'y',
919	>	additional_error))
920		goto failure;
921	<	}
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);
921	>
922		break;
741	–
923		case 'a':       /* number of bins for cos(angle).  */
924	<	if (local_args_info.nanglebins_given)
925	<	{
926	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
927	<	goto failure;
928	<	}
929	<	if (args_info->nanglebins_given && ! override)
930	<	continue;
931	<	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);
924	>
925	>
926	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
927	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
928	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
929	>	check_ambiguity, override, 0, 0,
930	>	"nanglebins", 'a',
931	>	additional_error))
932		goto failure;
933	<	}
757	<	if (args_info->nanglebins_orig)
758	<	free (args_info->nanglebins_orig); /* free previous string */
759	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
933	>
934		break;
935	<
936	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
937	<	if (local_args_info.length_given)
938	<	{
939	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
940	<	goto failure;
941	<	}
942	<	if (args_info->length_given && ! override)
943	<	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);
935	>	case 'c':       /* cutoff radius (rcut).  */
936	>
937	>
938	>	if (update_arg( (void *)&(args_info->rcut_arg),
939	>	&(args_info->rcut_orig), &(args_info->rcut_given),
940	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
941	>	check_ambiguity, override, 0, 0,
942	>	"rcut", 'c',
943	>	additional_error))
944		goto failure;
945	<	}
777	<	if (args_info->length_orig)
778	<	free (args_info->length_orig); /* free previous string */
779	<	args_info->length_orig = gengetopt_strdup (optarg);
945	>
946		break;
781	–
947		case 'z':       /* Where to set the zero for the slab_density calculation.  */
948	<	if (local_args_info.zoffset_given)
949	<	{
950	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
951	<	goto failure;
952	<	}
953	<	if (args_info->zoffset_given && ! override)
954	<	continue;
955	<	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);
948	>
949	>
950	>	if (update_arg( (void *)&(args_info->zoffset_arg),
951	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
952	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
953	>	check_ambiguity, override, 0, 0,
954	>	"zoffset", 'z',
955	>	additional_error))
956		goto failure;
957	<	}
797	<	if (args_info->zoffset_orig)
798	<	free (args_info->zoffset_orig); /* free previous string */
799	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
957	>
958		break;
959	<
959	>	case 'g':       /* g(r).  */
960	>
961	>	if (args_info->staticProps_group_counter && override)
962	>	reset_group_staticProps (args_info);
963	>	args_info->staticProps_group_counter += 1;
964	>
965	>	if (update_arg( 0 ,
966	>	0 , &(args_info->gofr_given),
967	>	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
968	>	check_ambiguity, override, 0, 0,
969	>	"gofr", 'g',
970	>	additional_error))
971	>	goto failure;
972	>
973	>	break;
974	>	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
975	>
976	>	if (args_info->staticProps_group_counter && override)
977	>	reset_group_staticProps (args_info);
978	>	args_info->staticProps_group_counter += 1;
979	>
980	>	if (update_arg( 0 ,
981	>	0 , &(args_info->p2_given),
982	>	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
983	>	check_ambiguity, override, 0, 0,
984	>	"p2", 'p',
985	>	additional_error))
986	>	goto failure;
987	>
988	>	break;
989	>	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
990	>
991	>	if (args_info->staticProps_group_counter && override)
992	>	reset_group_staticProps (args_info);
993	>	args_info->staticProps_group_counter += 1;
994	>
995	>	if (update_arg( 0 ,
996	>	0 , &(args_info->scd_given),
997	>	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
998	>	check_ambiguity, override, 0, 0,
999	>	"scd", 's',
1000	>	additional_error))
1001	>	goto failure;
1002	>
1003	>	break;
1004	>	case 'd':       /* density plot.  */
1005	>
1006	>	if (args_info->staticProps_group_counter && override)
1007	>	reset_group_staticProps (args_info);
1008	>	args_info->staticProps_group_counter += 1;
1009	>
1010	>	if (update_arg( 0 ,
1011	>	0 , &(args_info->density_given),
1012	>	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1013	>	check_ambiguity, override, 0, 0,
1014	>	"density", 'd',
1015	>	additional_error))
1016	>	goto failure;
1017	>
1018	>	break;
1019
1020		case 0: /* Long option with no short option */
1021	+	/* number of bins in z axis.  */
1022	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1023	+	{
1024	+
1025	+
1026	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1027	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1028	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1029	+	check_ambiguity, override, 0, 0,
1030	+	"nbins_z", '-',
1031	+	additional_error))
1032	+	goto failure;
1033	+
1034	+	}
1035	+	/* slab width (dz).  */
1036	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1037	+	{
1038	+
1039	+
1040	+	if (update_arg( (void *)&(args_info->dz_arg),
1041	+	&(args_info->dz_orig), &(args_info->dz_given),
1042	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1043	+	check_ambiguity, override, 0, 0,
1044	+	"dz", '-',
1045	+	additional_error))
1046	+	goto failure;
1047	+
1048	+	}
1049	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1050	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1051	+	{
1052	+
1053	+
1054	+	if (update_arg( (void *)&(args_info->length_arg),
1055	+	&(args_info->length_orig), &(args_info->length_given),
1056	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1057	+	check_ambiguity, override, 0, 0,
1058	+	"length", '-',
1059	+	additional_error))
1060	+	goto failure;
1061	+
1062	+	}
1063	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1064	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1065	+	{
1066	+
1067	+
1068	+	if (update_arg( (void *)&(args_info->zlength_arg),
1069	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1070	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1071	+	check_ambiguity, override, 0, 0,
1072	+	"zlength", '-',
1073	+	additional_error))
1074	+	goto failure;
1075	+
1076	+	}
1077		/* select the first stuntdouble set.  */
1078	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1078	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1079		{
1080	<	if (local_args_info.sele1_given)
1081	<	{
1082	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1083	<	goto failure;
1084	<	}
1085	<	if (args_info->sele1_given && ! override)
1086	<	continue;
1087	<	local_args_info.sele1_given = 1;
1088	<	args_info->sele1_given = 1;
1089	<	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);
1080	>
1081	>
1082	>	if (update_arg( (void *)&(args_info->sele1_arg),
1083	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1084	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1085	>	check_ambiguity, override, 0, 0,
1086	>	"sele1", '-',
1087	>	additional_error))
1088	>	goto failure;
1089	>
1090		}
1091		/* select the second stuntdouble set.  */
1092		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1093		{
1094	<	if (local_args_info.sele2_given)
1095	<	{
1096	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1097	<	goto failure;
1098	<	}
1099	<	if (args_info->sele2_given && ! override)
1100	<	continue;
1101	<	local_args_info.sele2_given = 1;
1102	<	args_info->sele2_given = 1;
1103	<	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);
1094	>
1095	>
1096	>	if (update_arg( (void *)&(args_info->sele2_arg),
1097	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1098	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1099	>	check_ambiguity, override, 0, 0,
1100	>	"sele2", '-',
1101	>	additional_error))
1102	>	goto failure;
1103	>
1104		}
1105		/* select the third stuntdouble set.  */
1106		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1107		{
1108	<	if (local_args_info.sele3_given)
1109	<	{
1110	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1111	<	goto failure;
1112	<	}
1113	<	if (args_info->sele3_given && ! override)
1114	<	continue;
1115	<	local_args_info.sele3_given = 1;
1116	<	args_info->sele3_given = 1;
1117	<	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);
1108	>
1109	>
1110	>	if (update_arg( (void *)&(args_info->sele3_arg),
1111	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1112	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1113	>	check_ambiguity, override, 0, 0,
1114	>	"sele3", '-',
1115	>	additional_error))
1116	>	goto failure;
1117	>
1118		}
1119		/* select reference (use and only use with --gxyz).  */
1120		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1121		{
1122	<	if (local_args_info.refsele_given)
1123	<	{
1124	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1125	<	goto failure;
1126	<	}
1127	<	if (args_info->refsele_given && ! override)
1128	<	continue;
1129	<	local_args_info.refsele_given = 1;
1130	<	args_info->refsele_given = 1;
1131	<	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);
1122	>
1123	>
1124	>	if (update_arg( (void *)&(args_info->refsele_arg),
1125	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1126	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1127	>	check_ambiguity, override, 0, 0,
1128	>	"refsele", '-',
1129	>	additional_error))
1130	>	goto failure;
1131	>
1132		}
1133	+	/* select stunt doubles for center-of-mass reference point.  */
1134	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1135	+	{
1136	+
1137	+
1138	+	if (update_arg( (void *)&(args_info->comsele_arg),
1139	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1140	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1141	+	check_ambiguity, override, 0, 0,
1142	+	"comsele", '-',
1143	+	additional_error))
1144	+	goto failure;
1145	+
1146	+	}
1147		/* molecule name.  */
1148		else if (strcmp (long_options[option_index].name, "molname") == 0)
1149		{
1150	<	if (local_args_info.molname_given)
1151	<	{
1152	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1153	<	goto failure;
1154	<	}
1155	<	if (args_info->molname_given && ! override)
1156	<	continue;
1157	<	local_args_info.molname_given = 1;
1158	<	args_info->molname_given = 1;
1159	<	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);
1150	>
1151	>
1152	>	if (update_arg( (void *)&(args_info->molname_arg),
1153	>	&(args_info->molname_orig), &(args_info->molname_given),
1154	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1155	>	check_ambiguity, override, 0, 0,
1156	>	"molname", '-',
1157	>	additional_error))
1158	>	goto failure;
1159	>
1160		}
1161	<	/* begin interanl index.  */
1161	>	/* begin internal index.  */
1162		else if (strcmp (long_options[option_index].name, "begin") == 0)
1163		{
1164	<	if (local_args_info.begin_given)
1165	<	{
1166	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1167	<	goto failure;
1168	<	}
1169	<	if (args_info->begin_given && ! override)
1170	<	continue;
1171	<	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);
1164	>
1165	>
1166	>	if (update_arg( (void *)&(args_info->begin_arg),
1167	>	&(args_info->begin_orig), &(args_info->begin_given),
1168	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1169	>	check_ambiguity, override, 0, 0,
1170	>	"begin", '-',
1171	>	additional_error))
1172		goto failure;
1173	<	}
916	<	if (args_info->begin_orig)
917	<	free (args_info->begin_orig); /* free previous string */
918	<	args_info->begin_orig = gengetopt_strdup (optarg);
1173	>
1174		}
1175		/* end internal index.  */
1176		else if (strcmp (long_options[option_index].name, "end") == 0)
1177		{
1178	<	if (local_args_info.end_given)
1179	<	{
1180	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1181	<	goto failure;
1182	<	}
1183	<	if (args_info->end_given && ! override)
1184	<	continue;
1185	<	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);
1178	>
1179	>
1180	>	if (update_arg( (void *)&(args_info->end_arg),
1181	>	&(args_info->end_orig), &(args_info->end_given),
1182	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1183	>	check_ambiguity, override, 0, 0,
1184	>	"end", '-',
1185	>	additional_error))
1186		goto failure;
1187	<	}
937	<	if (args_info->end_orig)
938	<	free (args_info->end_orig); /* free previous string */
939	<	args_info->end_orig = gengetopt_strdup (optarg);
1187	>
1188		}
1189	<	/* g(r).  */
1190	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1189	>	/* nanoparticle radius.  */
1190	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1191		{
1192	<	if (local_args_info.gofr_given)
1193	<	{
1194	<	fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1195	<	goto failure;
1196	<	}
1197	<	if (args_info->gofr_given && ! override)
1198	<	continue;
1199	<	local_args_info.gofr_given = 1;
1200	<	args_info->gofr_given = 1;
1192	>
1193	>
1194	>	if (update_arg( (void *)&(args_info->radius_arg),
1195	>	&(args_info->radius_orig), &(args_info->radius_given),
1196	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1197	>	check_ambiguity, override, 0, 0,
1198	>	"radius", '-',
1199	>	additional_error))
1200	>	goto failure;
1201	>
1202	>	}
1203	>	/* bond order parameter (--rcut must be specified).  */
1204	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1205	>	{
1206	>
1207		if (args_info->staticProps_group_counter && override)
1208		reset_group_staticProps (args_info);
1209		args_info->staticProps_group_counter += 1;
1210	<	break;
1210	>
1211	>	if (update_arg( 0 ,
1212	>	0 , &(args_info->bo_given),
1213	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1214	>	check_ambiguity, override, 0, 0,
1215	>	"bo", '-',
1216	>	additional_error))
1217	>	goto failure;
1218	>
1219		}
1220	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1221	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1222	+	{
1223	+
1224	+	if (args_info->staticProps_group_counter && override)
1225	+	reset_group_staticProps (args_info);
1226	+	args_info->staticProps_group_counter += 1;
1227	+
1228	+	if (update_arg( 0 ,
1229	+	0 , &(args_info->bor_given),
1230	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1231	+	check_ambiguity, override, 0, 0,
1232	+	"bor", '-',
1233	+	additional_error))
1234	+	goto failure;
1235	+
1236	+	}
1237	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1238	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1239	+	{
1240	+
1241	+	if (args_info->staticProps_group_counter && override)
1242	+	reset_group_staticProps (args_info);
1243	+	args_info->staticProps_group_counter += 1;
1244	+
1245	+	if (update_arg( 0 ,
1246	+	0 , &(args_info->bad_given),
1247	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1248	+	check_ambiguity, override, 0, 0,
1249	+	"bad", '-',
1250	+	additional_error))
1251	+	goto failure;
1252	+
1253	+	}
1254	+	/* g(z).  */
1255	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1256	+	{
1257	+
1258	+	if (args_info->staticProps_group_counter && override)
1259	+	reset_group_staticProps (args_info);
1260	+	args_info->staticProps_group_counter += 1;
1261	+
1262	+	if (update_arg( 0 ,
1263	+	0 , &(args_info->gofz_given),
1264	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1265	+	check_ambiguity, override, 0, 0,
1266	+	"gofz", '-',
1267	+	additional_error))
1268	+	goto failure;
1269	+
1270	+	}
1271		/* g(r, cos(theta)).  */
1272		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1273		{
1274	<	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;
1274	>
1275		if (args_info->staticProps_group_counter && override)
1276		reset_group_staticProps (args_info);
1277		args_info->staticProps_group_counter += 1;
1278	<	break;
1278	>
1279	>	if (update_arg( 0 ,
1280	>	0 , &(args_info->r_theta_given),
1281	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1282	>	check_ambiguity, override, 0, 0,
1283	>	"r_theta", '-',
1284	>	additional_error))
1285	>	goto failure;
1286	>
1287		}
1288		/* g(r, cos(omega)).  */
1289		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1290		{
1291	<	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;
1291	>
1292		if (args_info->staticProps_group_counter && override)
1293		reset_group_staticProps (args_info);
1294		args_info->staticProps_group_counter += 1;
1295	<	break;
1295	>
1296	>	if (update_arg( 0 ,
1297	>	0 , &(args_info->r_omega_given),
1298	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1299	>	check_ambiguity, override, 0, 0,
1300	>	"r_omega", '-',
1301	>	additional_error))
1302	>	goto failure;
1303	>
1304		}
1305	+	/* g(r, z).  */
1306	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1307	+	{
1308	+
1309	+	if (args_info->staticProps_group_counter && override)
1310	+	reset_group_staticProps (args_info);
1311	+	args_info->staticProps_group_counter += 1;
1312	+
1313	+	if (update_arg( 0 ,
1314	+	0 , &(args_info->r_z_given),
1315	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1316	+	check_ambiguity, override, 0, 0,
1317	+	"r_z", '-',
1318	+	additional_error))
1319	+	goto failure;
1320	+
1321	+	}
1322		/* g(cos(theta), cos(omega)).  */
1323		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1324		{
1325	<	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;
1325	>
1326		if (args_info->staticProps_group_counter && override)
1327		reset_group_staticProps (args_info);
1328		args_info->staticProps_group_counter += 1;
1329	<	break;
1329	>
1330	>	if (update_arg( 0 ,
1331	>	0 , &(args_info->theta_omega_given),
1332	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1333	>	check_ambiguity, override, 0, 0,
1334	>	"theta_omega", '-',
1335	>	additional_error))
1336	>	goto failure;
1337	>
1338		}
1339		/* g(x, y, z).  */
1340		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1341		{
1342	<	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;
1342	>
1343		if (args_info->staticProps_group_counter && override)
1344		reset_group_staticProps (args_info);
1345		args_info->staticProps_group_counter += 1;
1346	<	break;
1346	>
1347	>	if (update_arg( 0 ,
1348	>	0 , &(args_info->gxyz_given),
1349	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1350	>	check_ambiguity, override, 0, 0,
1351	>	"gxyz", '-',
1352	>	additional_error))
1353	>	goto failure;
1354	>
1355		}
1356	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1357	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1356	>	/* 2D g(r) (Slab width --dz must be specified).  */
1357	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1358		{
1359	<	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;
1359	>
1360		if (args_info->staticProps_group_counter && override)
1361		reset_group_staticProps (args_info);
1362		args_info->staticProps_group_counter += 1;
1363	<	break;
1363	>
1364	>	if (update_arg( 0 ,
1365	>	0 , &(args_info->twodgofr_given),
1366	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1367	>	check_ambiguity, override, 0, 0,
1368	>	"twodgofr", '-',
1369	>	additional_error))
1370	>	goto failure;
1371	>
1372		}
1373	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1374	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1373	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1374	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1375		{
1376	<	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;
1376	>
1377		if (args_info->staticProps_group_counter && override)
1378		reset_group_staticProps (args_info);
1379		args_info->staticProps_group_counter += 1;
1380	<	break;
1380	>
1381	>	if (update_arg( 0 ,
1382	>	0 , &(args_info->rp2_given),
1383	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1384	>	check_ambiguity, override, 0, 0,
1385	>	"rp2", '-',
1386	>	additional_error))
1387	>	goto failure;
1388	>
1389		}
1390	<	/* density plot (--sele1 must be specified).  */
1391	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1390	>	/* slab density.  */
1391	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1392		{
1393	<	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;
1393	>
1394		if (args_info->staticProps_group_counter && override)
1395		reset_group_staticProps (args_info);
1396		args_info->staticProps_group_counter += 1;
1397	<	break;
1397	>
1398	>	if (update_arg( 0 ,
1399	>	0 , &(args_info->slab_density_given),
1400	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1401	>	check_ambiguity, override, 0, 0,
1402	>	"slab_density", '-',
1403	>	additional_error))
1404	>	goto failure;
1405	>
1406		}
1407	<	/* slab density (--sele1 must be specified).  */
1408	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1407	>	/* p(cos(theta)).  */
1408	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1409		{
1410	<	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;
1410	>
1411		if (args_info->staticProps_group_counter && override)
1412		reset_group_staticProps (args_info);
1413		args_info->staticProps_group_counter += 1;
1414	<	break;
1414	>
1415	>	if (update_arg( 0 ,
1416	>	0 , &(args_info->p_angle_given),
1417	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1418	>	check_ambiguity, override, 0, 0,
1419	>	"p_angle", '-',
1420	>	additional_error))
1421	>	goto failure;
1422	>
1423		}
1424	<	/* hxy (--sele1 must be specified).  */
1424	>	/* hxy.  */
1425		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1426		{
1427	<	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;
1427	>
1428		if (args_info->staticProps_group_counter && override)
1429		reset_group_staticProps (args_info);
1430		args_info->staticProps_group_counter += 1;
1431	<	break;
1431	>
1432	>	if (update_arg( 0 ,
1433	>	0 , &(args_info->hxy_given),
1434	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1435	>	check_ambiguity, override, 0, 0,
1436	>	"hxy", '-',
1437	>	additional_error))
1438	>	goto failure;
1439	>
1440		}
1441	+	/* rho of R.  */
1442	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1443	+	{
1444
1445	+	if (args_info->staticProps_group_counter && override)
1446	+	reset_group_staticProps (args_info);
1447	+	args_info->staticProps_group_counter += 1;
1448	+
1449	+	if (update_arg( 0 ,
1450	+	0 , &(args_info->rho_r_given),
1451	+	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1452	+	check_ambiguity, override, 0, 0,
1453	+	"rho_r", '-',
1454	+	additional_error))
1455	+	goto failure;
1456	+
1457	+	}
1458	+	/* hull volume of nanoparticle.  */
1459	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1460	+	{
1461	+
1462	+	if (args_info->staticProps_group_counter && override)
1463	+	reset_group_staticProps (args_info);
1464	+	args_info->staticProps_group_counter += 1;
1465	+
1466	+	if (update_arg( 0 ,
1467	+	0 , &(args_info->hullvol_given),
1468	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1469	+	check_ambiguity, override, 0, 0,
1470	+	"hullvol", '-',
1471	+	additional_error))
1472	+	goto failure;
1473	+
1474	+	}
1475	+
1476		break;
1477		case '?':       /* Invalid option.  */
1478		/* `getopt_long' already printed an error message.  */
#	Line 1138 | Line 1502 | cmdline_parser_internal (int argc, char * const *argv,
1502		if ( error )
1503		return (EXIT_FAILURE);
1504
1505	+	if (optind < argc)
1506	+	{
1507	+	int i = 0 ;
1508	+	int found_prog_name = 0;
1509	+	/* whether program name, i.e., argv[0], is in the remaining args
1510	+	(this may happen with some implementations of getopt,
1511	+	but surely not with the one included by gengetopt) */
1512	+
1513	+	i = optind;
1514	+	while (i < argc)
1515	+	if (argv[i++] == argv[0]) {
1516	+	found_prog_name = 1;
1517	+	break;
1518	+	}
1519	+	i = 0;
1520	+
1521	+	args_info->inputs_num = argc - optind - found_prog_name;
1522	+	args_info->inputs =
1523	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1524	+	while (optind < argc)
1525	+	if (argv[optind++] != argv[0])
1526	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1527	+	}
1528	+
1529		return 0;
1530
1531		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 1454 by gezelter, Wed Jun 23 19:25:02 2010 UTC

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

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+	Added lines
<	Changed lines
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