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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.16
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4		gengetopt -F StaticPropsCmd
5
#	Line 21 | Line 21
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"      --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	+	"      --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	+	"  -g, --gofr                    g(r)",
59	+	"      --gofz                    g(z)",
60	+	"      --r_theta                 g(r, cos(theta))",
61	+	"      --r_omega                 g(r, cos(omega))",
62	+	"      --r_z                     g(r, z)",
63	+	"      --theta_omega             g(cos(theta), cos(omega))",
64	+	"      --gxyz                    g(x, y, z)",
65	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
66	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
67	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
68	+	"  -d, --density                 density plot",
69	+	"      --slab_density            slab density",
70	+	"      --p_angle                 p(cos(theta))",
71	+	"      --hxy                     hxy",
72	+	"      --rho_r                   rho of R",
73	+	"      --hullvol                 hull volume of nanoparticle",
74	+	0
75	+	};
76	+
77	+	typedef enum {ARG_NO
78	+	, ARG_STRING
79	+	, ARG_INT
80	+	, ARG_DOUBLE
81	+	} cmdline_parser_arg_type;
82	+
83		static
84		void clear_given (struct gengetopt_args_info *args_info);
85		static
86		void clear_args (struct gengetopt_args_info *args_info);
87
88		static int
89	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
89	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
90	>	struct cmdline_parser_params *params, const char *additional_error);
91
92		static int
93		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 43 | Line 103 | void clear_given (struct gengetopt_args_info *args_inf
103		args_info->input_given = 0 ;
104		args_info->output_given = 0 ;
105		args_info->step_given = 0 ;
106	<	args_info->nrbins_given = 0 ;
106	>	args_info->nbins_given = 0 ;
107		args_info->nbins_x_given = 0 ;
108		args_info->nbins_y_given = 0 ;
109	+	args_info->nbins_z_given = 0 ;
110		args_info->nanglebins_given = 0 ;
111	+	args_info->rcut_given = 0 ;
112		args_info->length_given = 0 ;
113	+	args_info->zlength_given = 0 ;
114		args_info->zoffset_given = 0 ;
115		args_info->sele1_given = 0 ;
116		args_info->sele2_given = 0 ;
117		args_info->sele3_given = 0 ;
118		args_info->refsele_given = 0 ;
119	+	args_info->comsele_given = 0 ;
120		args_info->molname_given = 0 ;
121		args_info->begin_given = 0 ;
122		args_info->end_given = 0 ;
123	+	args_info->radius_given = 0 ;
124	+	args_info->bo_given = 0 ;
125	+	args_info->bor_given = 0 ;
126	+	args_info->bad_given = 0 ;
127		args_info->gofr_given = 0 ;
128	+	args_info->gofz_given = 0 ;
129		args_info->r_theta_given = 0 ;
130		args_info->r_omega_given = 0 ;
131	+	args_info->r_z_given = 0 ;
132		args_info->theta_omega_given = 0 ;
133		args_info->gxyz_given = 0 ;
134		args_info->p2_given = 0 ;
#	Line 66 | Line 136 | void clear_given (struct gengetopt_args_info *args_inf
136		args_info->scd_given = 0 ;
137		args_info->density_given = 0 ;
138		args_info->slab_density_given = 0 ;
139	+	args_info->p_angle_given = 0 ;
140		args_info->hxy_given = 0 ;
141	+	args_info->rho_r_given = 0 ;
142	+	args_info->hullvol_given = 0 ;
143		args_info->staticProps_group_counter = 0 ;
144		}
145
#	Line 79 | Line 152 | void clear_args (struct gengetopt_args_info *args_info
152		args_info->output_orig = NULL;
153		args_info->step_arg = 1;
154		args_info->step_orig = NULL;
155	<	args_info->nrbins_arg = 100;
156	<	args_info->nrbins_orig = NULL;
155	>	args_info->nbins_arg = 100;
156	>	args_info->nbins_orig = NULL;
157		args_info->nbins_x_arg = 100;
158		args_info->nbins_x_orig = NULL;
159		args_info->nbins_y_arg = 100;
160		args_info->nbins_y_orig = NULL;
161	+	args_info->nbins_z_arg = 100;
162	+	args_info->nbins_z_orig = NULL;
163		args_info->nanglebins_arg = 50;
164		args_info->nanglebins_orig = NULL;
165	+	args_info->rcut_orig = NULL;
166		args_info->length_orig = NULL;
167	+	args_info->zlength_orig = NULL;
168		args_info->zoffset_arg = 0;
169		args_info->zoffset_orig = NULL;
170		args_info->sele1_arg = NULL;
#	Line 98 | Line 175 | void clear_args (struct gengetopt_args_info *args_info
175		args_info->sele3_orig = NULL;
176		args_info->refsele_arg = NULL;
177		args_info->refsele_orig = NULL;
178	+	args_info->comsele_arg = NULL;
179	+	args_info->comsele_orig = NULL;
180		args_info->molname_arg = NULL;
181		args_info->molname_orig = NULL;
182		args_info->begin_orig = NULL;
183		args_info->end_orig = NULL;
184	+	args_info->radius_orig = NULL;
185
186		}
187
188	+	static
189	+	void init_args_info(struct gengetopt_args_info *args_info)
190	+	{
191	+
192	+
193	+	args_info->help_help = gengetopt_args_info_help[0] ;
194	+	args_info->version_help = gengetopt_args_info_help[1] ;
195	+	args_info->input_help = gengetopt_args_info_help[2] ;
196	+	args_info->output_help = gengetopt_args_info_help[3] ;
197	+	args_info->step_help = gengetopt_args_info_help[4] ;
198	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
199	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
200	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
201	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
202	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
203	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
204	+	args_info->length_help = gengetopt_args_info_help[11] ;
205	+	args_info->zlength_help = gengetopt_args_info_help[12] ;
206	+	args_info->zoffset_help = gengetopt_args_info_help[13] ;
207	+	args_info->sele1_help = gengetopt_args_info_help[14] ;
208	+	args_info->sele2_help = gengetopt_args_info_help[15] ;
209	+	args_info->sele3_help = gengetopt_args_info_help[16] ;
210	+	args_info->refsele_help = gengetopt_args_info_help[17] ;
211	+	args_info->comsele_help = gengetopt_args_info_help[18] ;
212	+	args_info->molname_help = gengetopt_args_info_help[19] ;
213	+	args_info->begin_help = gengetopt_args_info_help[20] ;
214	+	args_info->end_help = gengetopt_args_info_help[21] ;
215	+	args_info->radius_help = gengetopt_args_info_help[22] ;
216	+	args_info->bo_help = gengetopt_args_info_help[24] ;
217	+	args_info->bor_help = gengetopt_args_info_help[25] ;
218	+	args_info->bad_help = gengetopt_args_info_help[26] ;
219	+	args_info->gofr_help = gengetopt_args_info_help[27] ;
220	+	args_info->gofz_help = gengetopt_args_info_help[28] ;
221	+	args_info->r_theta_help = gengetopt_args_info_help[29] ;
222	+	args_info->r_omega_help = gengetopt_args_info_help[30] ;
223	+	args_info->r_z_help = gengetopt_args_info_help[31] ;
224	+	args_info->theta_omega_help = gengetopt_args_info_help[32] ;
225	+	args_info->gxyz_help = gengetopt_args_info_help[33] ;
226	+	args_info->p2_help = gengetopt_args_info_help[34] ;
227	+	args_info->rp2_help = gengetopt_args_info_help[35] ;
228	+	args_info->scd_help = gengetopt_args_info_help[36] ;
229	+	args_info->density_help = gengetopt_args_info_help[37] ;
230	+	args_info->slab_density_help = gengetopt_args_info_help[38] ;
231	+	args_info->p_angle_help = gengetopt_args_info_help[39] ;
232	+	args_info->hxy_help = gengetopt_args_info_help[40] ;
233	+	args_info->rho_r_help = gengetopt_args_info_help[41] ;
234	+	args_info->hullvol_help = gengetopt_args_info_help[42] ;
235	+
236	+	}
237	+
238		void
239		cmdline_parser_print_version (void)
240		{
241		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
242		}
243
244	+	static void print_help_common(void) {
245	+	cmdline_parser_print_version ();
246	+
247	+	if (strlen(gengetopt_args_info_purpose) > 0)
248	+	printf("\n%s\n", gengetopt_args_info_purpose);
249	+
250	+	if (strlen(gengetopt_args_info_usage) > 0)
251	+	printf("\n%s\n", gengetopt_args_info_usage);
252	+
253	+	printf("\n");
254	+
255	+	if (strlen(gengetopt_args_info_description) > 0)
256	+	printf("%s\n", gengetopt_args_info_description);
257	+	}
258	+
259		void
260		cmdline_parser_print_help (void)
261		{
262	<	cmdline_parser_print_version ();
263	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
264	<	printf("%s\n","  -h, --help                    Print help and exit");
265	<	printf("%s\n","  -V, --version                 Print version and exit");
121	<	printf("%s\n","  -i, --input=filename          input dump file");
122	<	printf("%s\n","  -o, --output=filename         output file name");
123	<	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
124	<	printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
125	<	printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
126	<	printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
127	<	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
128	<	printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
129	<	printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
130	<	printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
131	<	printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
132	<	printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
133	<	printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
134	<	printf("%s\n","      --molname=STRING          molecule name");
135	<	printf("%s\n","      --begin=INT               begin interanl index");
136	<	printf("%s\n","      --end=INT                 end internal index");
137	<	printf("%s\n","\n Group: staticProps\n   an option of this group is required");
138	<	printf("%s\n","      --gofr                    g(r)");
139	<	printf("%s\n","      --r_theta                 g(r, cos(theta))");
140	<	printf("%s\n","      --r_omega                 g(r, cos(omega))");
141	<	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
142	<	printf("%s\n","      --gxyz                    g(x, y, z)");
143	<	printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
144	<	printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
145	<	printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
146	<	printf("%s\n","      --density                 density plot (--sele1 must be specified)");
147	<	printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
148	<	printf("%s\n","      --hxy                     hxy (--sele1 must be specified)");
149	<
262	>	int i = 0;
263	>	print_help_common();
264	>	while (gengetopt_args_info_help[i])
265	>	printf("%s\n", gengetopt_args_info_help[i++]);
266		}
267
268		void
#	Line 154 | Line 270 | cmdline_parser_init (struct gengetopt_args_info *args_
270		{
271		clear_given (args_info);
272		clear_args (args_info);
273	+	init_args_info (args_info);
274		}
275
276	+	void
277	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
278	+	{
279	+	if (params)
280	+	{
281	+	params->override = 0;
282	+	params->initialize = 1;
283	+	params->check_required = 1;
284	+	params->check_ambiguity = 0;
285	+	params->print_errors = 1;
286	+	}
287	+	}
288	+
289	+	struct cmdline_parser_params *
290	+	cmdline_parser_params_create(void)
291	+	{
292	+	struct cmdline_parser_params *params =
293	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
294	+	cmdline_parser_params_init(params);
295	+	return params;
296	+	}
297	+
298		static void
299	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
299	>	free_string_field (char **s)
300		{
301	<
163	<	if (args_info->input_arg)
301	>	if (*s)
302		{
303	<	free (args_info->input_arg); /* free previous argument */
304	<	args_info->input_arg = 0;
167	<	}
168	<	if (args_info->input_orig)
169	<	{
170	<	free (args_info->input_orig); /* free previous argument */
171	<	args_info->input_orig = 0;
303	>	free (*s);
304	>	*s = 0;
305		}
306	<	if (args_info->output_arg)
306	>	}
307	>
308	>
309	>	static void
310	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
311	>	{
312	>
313	>	free_string_field (&(args_info->input_arg));
314	>	free_string_field (&(args_info->input_orig));
315	>	free_string_field (&(args_info->output_arg));
316	>	free_string_field (&(args_info->output_orig));
317	>	free_string_field (&(args_info->step_orig));
318	>	free_string_field (&(args_info->nbins_orig));
319	>	free_string_field (&(args_info->nbins_x_orig));
320	>	free_string_field (&(args_info->nbins_y_orig));
321	>	free_string_field (&(args_info->nbins_z_orig));
322	>	free_string_field (&(args_info->nanglebins_orig));
323	>	free_string_field (&(args_info->rcut_orig));
324	>	free_string_field (&(args_info->length_orig));
325	>	free_string_field (&(args_info->zlength_orig));
326	>	free_string_field (&(args_info->zoffset_orig));
327	>	free_string_field (&(args_info->sele1_arg));
328	>	free_string_field (&(args_info->sele1_orig));
329	>	free_string_field (&(args_info->sele2_arg));
330	>	free_string_field (&(args_info->sele2_orig));
331	>	free_string_field (&(args_info->sele3_arg));
332	>	free_string_field (&(args_info->sele3_orig));
333	>	free_string_field (&(args_info->refsele_arg));
334	>	free_string_field (&(args_info->refsele_orig));
335	>	free_string_field (&(args_info->comsele_arg));
336	>	free_string_field (&(args_info->comsele_orig));
337	>	free_string_field (&(args_info->molname_arg));
338	>	free_string_field (&(args_info->molname_orig));
339	>	free_string_field (&(args_info->begin_orig));
340	>	free_string_field (&(args_info->end_orig));
341	>	free_string_field (&(args_info->radius_orig));
342	>
343	>
344	>
345	>	clear_given (args_info);
346	>	}
347	>
348	>
349	>	static void
350	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
351	>	{
352	>	if (arg) {
353	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
354	>	} else {
355	>	fprintf(outfile, "%s\n", opt);
356	>	}
357	>	}
358	>
359	>
360	>	int
361	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
362	>	{
363	>	int i = 0;
364	>
365	>	if (!outfile)
366		{
367	<	free (args_info->output_arg); /* free previous argument */
368	<	args_info->output_arg = 0;
367	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
368	>	return EXIT_FAILURE;
369		}
370	<	if (args_info->output_orig)
371	<	{
372	<	free (args_info->output_orig); /* free previous argument */
373	<	args_info->output_orig = 0;
374	<	}
375	<	if (args_info->step_orig)
376	<	{
377	<	free (args_info->step_orig); /* free previous argument */
378	<	args_info->step_orig = 0;
379	<	}
380	<	if (args_info->nrbins_orig)
381	<	{
382	<	free (args_info->nrbins_orig); /* free previous argument */
383	<	args_info->nrbins_orig = 0;
384	<	}
385	<	if (args_info->nbins_x_orig)
386	<	{
387	<	free (args_info->nbins_x_orig); /* free previous argument */
388	<	args_info->nbins_x_orig = 0;
389	<	}
390	<	if (args_info->nbins_y_orig)
391	<	{
392	<	free (args_info->nbins_y_orig); /* free previous argument */
393	<	args_info->nbins_y_orig = 0;
394	<	}
395	<	if (args_info->nanglebins_orig)
396	<	{
397	<	free (args_info->nanglebins_orig); /* free previous argument */
398	<	args_info->nanglebins_orig = 0;
399	<	}
400	<	if (args_info->length_orig)
401	<	{
402	<	free (args_info->length_orig); /* free previous argument */
403	<	args_info->length_orig = 0;
404	<	}
405	<	if (args_info->zoffset_orig)
406	<	{
407	<	free (args_info->zoffset_orig); /* free previous argument */
408	<	args_info->zoffset_orig = 0;
409	<	}
410	<	if (args_info->sele1_arg)
411	<	{
412	<	free (args_info->sele1_arg); /* free previous argument */
413	<	args_info->sele1_arg = 0;
414	<	}
415	<	if (args_info->sele1_orig)
416	<	{
417	<	free (args_info->sele1_orig); /* free previous argument */
418	<	args_info->sele1_orig = 0;
419	<	}
420	<	if (args_info->sele2_arg)
421	<	{
422	<	free (args_info->sele2_arg); /* free previous argument */
423	<	args_info->sele2_arg = 0;
424	<	}
425	<	if (args_info->sele2_orig)
426	<	{
427	<	free (args_info->sele2_orig); /* free previous argument */
428	<	args_info->sele2_orig = 0;
429	<	}
430	<	if (args_info->sele3_arg)
431	<	{
432	<	free (args_info->sele3_arg); /* free previous argument */
433	<	args_info->sele3_arg = 0;
434	<	}
435	<	if (args_info->sele3_orig)
436	<	{
437	<	free (args_info->sele3_orig); /* free previous argument */
438	<	args_info->sele3_orig = 0;
439	<	}
440	<	if (args_info->refsele_arg)
441	<	{
442	<	free (args_info->refsele_arg); /* free previous argument */
443	<	args_info->refsele_arg = 0;
444	<	}
445	<	if (args_info->refsele_orig)
446	<	{
447	<	free (args_info->refsele_orig); /* free previous argument */
448	<	args_info->refsele_orig = 0;
449	<	}
450	<	if (args_info->molname_arg)
451	<	{
452	<	free (args_info->molname_arg); /* free previous argument */
453	<	args_info->molname_arg = 0;
454	<	}
263	<	if (args_info->molname_orig)
264	<	{
265	<	free (args_info->molname_orig); /* free previous argument */
266	<	args_info->molname_orig = 0;
267	<	}
268	<	if (args_info->begin_orig)
269	<	{
270	<	free (args_info->begin_orig); /* free previous argument */
271	<	args_info->begin_orig = 0;
272	<	}
273	<	if (args_info->end_orig)
274	<	{
275	<	free (args_info->end_orig); /* free previous argument */
276	<	args_info->end_orig = 0;
277	<	}
370	>
371	>	if (args_info->help_given)
372	>	write_into_file(outfile, "help", 0, 0 );
373	>	if (args_info->version_given)
374	>	write_into_file(outfile, "version", 0, 0 );
375	>	if (args_info->input_given)
376	>	write_into_file(outfile, "input", args_info->input_orig, 0);
377	>	if (args_info->output_given)
378	>	write_into_file(outfile, "output", args_info->output_orig, 0);
379	>	if (args_info->step_given)
380	>	write_into_file(outfile, "step", args_info->step_orig, 0);
381	>	if (args_info->nbins_given)
382	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
383	>	if (args_info->nbins_x_given)
384	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
385	>	if (args_info->nbins_y_given)
386	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
387	>	if (args_info->nbins_z_given)
388	>	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
389	>	if (args_info->nanglebins_given)
390	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
391	>	if (args_info->rcut_given)
392	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
393	>	if (args_info->length_given)
394	>	write_into_file(outfile, "length", args_info->length_orig, 0);
395	>	if (args_info->zlength_given)
396	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
397	>	if (args_info->zoffset_given)
398	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
399	>	if (args_info->sele1_given)
400	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
401	>	if (args_info->sele2_given)
402	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
403	>	if (args_info->sele3_given)
404	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
405	>	if (args_info->refsele_given)
406	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
407	>	if (args_info->comsele_given)
408	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
409	>	if (args_info->molname_given)
410	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
411	>	if (args_info->begin_given)
412	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
413	>	if (args_info->end_given)
414	>	write_into_file(outfile, "end", args_info->end_orig, 0);
415	>	if (args_info->radius_given)
416	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
417	>	if (args_info->bo_given)
418	>	write_into_file(outfile, "bo", 0, 0 );
419	>	if (args_info->bor_given)
420	>	write_into_file(outfile, "bor", 0, 0 );
421	>	if (args_info->bad_given)
422	>	write_into_file(outfile, "bad", 0, 0 );
423	>	if (args_info->gofr_given)
424	>	write_into_file(outfile, "gofr", 0, 0 );
425	>	if (args_info->gofz_given)
426	>	write_into_file(outfile, "gofz", 0, 0 );
427	>	if (args_info->r_theta_given)
428	>	write_into_file(outfile, "r_theta", 0, 0 );
429	>	if (args_info->r_omega_given)
430	>	write_into_file(outfile, "r_omega", 0, 0 );
431	>	if (args_info->r_z_given)
432	>	write_into_file(outfile, "r_z", 0, 0 );
433	>	if (args_info->theta_omega_given)
434	>	write_into_file(outfile, "theta_omega", 0, 0 );
435	>	if (args_info->gxyz_given)
436	>	write_into_file(outfile, "gxyz", 0, 0 );
437	>	if (args_info->p2_given)
438	>	write_into_file(outfile, "p2", 0, 0 );
439	>	if (args_info->rp2_given)
440	>	write_into_file(outfile, "rp2", 0, 0 );
441	>	if (args_info->scd_given)
442	>	write_into_file(outfile, "scd", 0, 0 );
443	>	if (args_info->density_given)
444	>	write_into_file(outfile, "density", 0, 0 );
445	>	if (args_info->slab_density_given)
446	>	write_into_file(outfile, "slab_density", 0, 0 );
447	>	if (args_info->p_angle_given)
448	>	write_into_file(outfile, "p_angle", 0, 0 );
449	>	if (args_info->hxy_given)
450	>	write_into_file(outfile, "hxy", 0, 0 );
451	>	if (args_info->rho_r_given)
452	>	write_into_file(outfile, "rho_r", 0, 0 );
453	>	if (args_info->hullvol_given)
454	>	write_into_file(outfile, "hullvol", 0, 0 );
455
456	<	clear_given (args_info);
456	>
457	>	i = EXIT_SUCCESS;
458	>	return i;
459		}
460
461		int
#	Line 293 | Line 472 | cmdline_parser_file_save(const char *filename, struct
472		return EXIT_FAILURE;
473		}
474
475	<	if (args_info->help_given) {
297	<	fprintf(outfile, "%s\n", "help");
298	<	}
299	<	if (args_info->version_given) {
300	<	fprintf(outfile, "%s\n", "version");
301	<	}
302	<	if (args_info->input_given) {
303	<	if (args_info->input_orig) {
304	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
305	<	} else {
306	<	fprintf(outfile, "%s\n", "input");
307	<	}
308	<	}
309	<	if (args_info->output_given) {
310	<	if (args_info->output_orig) {
311	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
312	<	} else {
313	<	fprintf(outfile, "%s\n", "output");
314	<	}
315	<	}
316	<	if (args_info->step_given) {
317	<	if (args_info->step_orig) {
318	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
319	<	} else {
320	<	fprintf(outfile, "%s\n", "step");
321	<	}
322	<	}
323	<	if (args_info->nrbins_given) {
324	<	if (args_info->nrbins_orig) {
325	<	fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
326	<	} else {
327	<	fprintf(outfile, "%s\n", "nrbins");
328	<	}
329	<	}
330	<	if (args_info->nbins_x_given) {
331	<	if (args_info->nbins_x_orig) {
332	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
333	<	} else {
334	<	fprintf(outfile, "%s\n", "nbins_x");
335	<	}
336	<	}
337	<	if (args_info->nbins_y_given) {
338	<	if (args_info->nbins_y_orig) {
339	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
340	<	} else {
341	<	fprintf(outfile, "%s\n", "nbins_y");
342	<	}
343	<	}
344	<	if (args_info->nanglebins_given) {
345	<	if (args_info->nanglebins_orig) {
346	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
347	<	} else {
348	<	fprintf(outfile, "%s\n", "nanglebins");
349	<	}
350	<	}
351	<	if (args_info->length_given) {
352	<	if (args_info->length_orig) {
353	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
354	<	} else {
355	<	fprintf(outfile, "%s\n", "length");
356	<	}
357	<	}
358	<	if (args_info->zoffset_given) {
359	<	if (args_info->zoffset_orig) {
360	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
361	<	} else {
362	<	fprintf(outfile, "%s\n", "zoffset");
363	<	}
364	<	}
365	<	if (args_info->sele1_given) {
366	<	if (args_info->sele1_orig) {
367	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
368	<	} else {
369	<	fprintf(outfile, "%s\n", "sele1");
370	<	}
371	<	}
372	<	if (args_info->sele2_given) {
373	<	if (args_info->sele2_orig) {
374	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
375	<	} else {
376	<	fprintf(outfile, "%s\n", "sele2");
377	<	}
378	<	}
379	<	if (args_info->sele3_given) {
380	<	if (args_info->sele3_orig) {
381	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
382	<	} else {
383	<	fprintf(outfile, "%s\n", "sele3");
384	<	}
385	<	}
386	<	if (args_info->refsele_given) {
387	<	if (args_info->refsele_orig) {
388	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
389	<	} else {
390	<	fprintf(outfile, "%s\n", "refsele");
391	<	}
392	<	}
393	<	if (args_info->molname_given) {
394	<	if (args_info->molname_orig) {
395	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
396	<	} else {
397	<	fprintf(outfile, "%s\n", "molname");
398	<	}
399	<	}
400	<	if (args_info->begin_given) {
401	<	if (args_info->begin_orig) {
402	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
403	<	} else {
404	<	fprintf(outfile, "%s\n", "begin");
405	<	}
406	<	}
407	<	if (args_info->end_given) {
408	<	if (args_info->end_orig) {
409	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
410	<	} else {
411	<	fprintf(outfile, "%s\n", "end");
412	<	}
413	<	}
414	<	if (args_info->gofr_given) {
415	<	fprintf(outfile, "%s\n", "gofr");
416	<	}
417	<	if (args_info->r_theta_given) {
418	<	fprintf(outfile, "%s\n", "r_theta");
419	<	}
420	<	if (args_info->r_omega_given) {
421	<	fprintf(outfile, "%s\n", "r_omega");
422	<	}
423	<	if (args_info->theta_omega_given) {
424	<	fprintf(outfile, "%s\n", "theta_omega");
425	<	}
426	<	if (args_info->gxyz_given) {
427	<	fprintf(outfile, "%s\n", "gxyz");
428	<	}
429	<	if (args_info->p2_given) {
430	<	fprintf(outfile, "%s\n", "p2");
431	<	}
432	<	if (args_info->rp2_given) {
433	<	fprintf(outfile, "%s\n", "rp2");
434	<	}
435	<	if (args_info->scd_given) {
436	<	fprintf(outfile, "%s\n", "scd");
437	<	}
438	<	if (args_info->density_given) {
439	<	fprintf(outfile, "%s\n", "density");
440	<	}
441	<	if (args_info->slab_density_given) {
442	<	fprintf(outfile, "%s\n", "slab_density");
443	<	}
444	<	if (args_info->hxy_given) {
445	<	fprintf(outfile, "%s\n", "hxy");
446	<	}
447	<
475	>	i = cmdline_parser_dump(outfile, args_info);
476		fclose (outfile);
477
450	–	i = EXIT_SUCCESS;
478		return i;
479		}
480
#	Line 457 | Line 484 | cmdline_parser_free (struct gengetopt_args_info *args_
484		cmdline_parser_release (args_info);
485		}
486
487	<
461	<	/* gengetopt_strdup() */
462	<	/* strdup.c replacement of strdup, which is not standard */
487	>	/** @brief replacement of strdup, which is not standard */
488		char *
489		gengetopt_strdup (const char *s)
490		{
#	Line 475 | Line 500 | static void
500		}
501
502		static void
478	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
479	–
480	–	static void
503		reset_group_staticProps(struct gengetopt_args_info *args_info)
504		{
505		if (! args_info->staticProps_group_counter)
506		return;
507
508	+	args_info->bo_given = 0 ;
509	+	args_info->bor_given = 0 ;
510	+	args_info->bad_given = 0 ;
511		args_info->gofr_given = 0 ;
512	+	args_info->gofz_given = 0 ;
513		args_info->r_theta_given = 0 ;
514		args_info->r_omega_given = 0 ;
515	+	args_info->r_z_given = 0 ;
516		args_info->theta_omega_given = 0 ;
517		args_info->gxyz_given = 0 ;
518		args_info->p2_given = 0 ;
#	Line 493 | Line 520 | reset_group_staticProps(struct gengetopt_args_info *ar
520		args_info->scd_given = 0 ;
521		args_info->density_given = 0 ;
522		args_info->slab_density_given = 0 ;
523	+	args_info->p_angle_given = 0 ;
524		args_info->hxy_given = 0 ;
525	+	args_info->rho_r_given = 0 ;
526	+	args_info->hullvol_given = 0 ;
527
528		args_info->staticProps_group_counter = 0;
529		}
#	Line 505 | Line 535 | int
535		}
536
537		int
538	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
539	+	struct cmdline_parser_params *params)
540	+	{
541	+	int result;
542	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
543	+
544	+	if (result == EXIT_FAILURE)
545	+	{
546	+	cmdline_parser_free (args_info);
547	+	exit (EXIT_FAILURE);
548	+	}
549	+
550	+	return result;
551	+	}
552	+
553	+	int
554		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
555		{
556		int result;
557	+	struct cmdline_parser_params params;
558	+
559	+	params.override = override;
560	+	params.initialize = initialize;
561	+	params.check_required = check_required;
562	+	params.check_ambiguity = 0;
563	+	params.print_errors = 1;
564
565	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
565	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
566
567		if (result == EXIT_FAILURE)
568		{
#	Line 542 | Line 595 | cmdline_parser_required2 (struct gengetopt_args_info *
595		{
596		int error = 0;
597
598	+	/* checks for required options */
599		if (! args_info->input_given)
600		{
601		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
602		error = 1;
603		}
604	+
605		if (args_info->staticProps_group_counter == 0)
606		{
607		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 554 | Line 609 | cmdline_parser_required2 (struct gengetopt_args_info *
609		}
610
611
612	+	/* checks for dependences among options */
613	+
614		return error;
615		}
616
617	+
618	+	static char *package_name = 0;
619	+
620	+	/**
621	+	* @brief updates an option
622	+	* @param field the generic pointer to the field to update
623	+	* @param orig_field the pointer to the orig field
624	+	* @param field_given the pointer to the number of occurrence of this option
625	+	* @param prev_given the pointer to the number of occurrence already seen
626	+	* @param value the argument for this option (if null no arg was specified)
627	+	* @param possible_values the possible values for this option (if specified)
628	+	* @param default_value the default value (in case the option only accepts fixed values)
629	+	* @param arg_type the type of this option
630	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
631	+	* @param override @see cmdline_parser_params.override
632	+	* @param no_free whether to free a possible previous value
633	+	* @param multiple_option whether this is a multiple option
634	+	* @param long_opt the corresponding long option
635	+	* @param short_opt the corresponding short option (or '-' if none)
636	+	* @param additional_error possible further error specification
637	+	*/
638	+	static
639	+	int update_arg(void *field, char **orig_field,
640	+	unsigned int *field_given, unsigned int *prev_given,
641	+	char *value, char *possible_values[], const char *default_value,
642	+	cmdline_parser_arg_type arg_type,
643	+	int check_ambiguity, int override,
644	+	int no_free, int multiple_option,
645	+	const char *long_opt, char short_opt,
646	+	const char *additional_error)
647	+	{
648	+	char *stop_char = 0;
649	+	const char *val = value;
650	+	int found;
651	+	char **string_field;
652	+
653	+	stop_char = 0;
654	+	found = 0;
655	+
656	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
657	+	{
658	+	if (short_opt != '-')
659	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
660	+	package_name, long_opt, short_opt,
661	+	(additional_error ? additional_error : ""));
662	+	else
663	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
664	+	package_name, long_opt,
665	+	(additional_error ? additional_error : ""));
666	+	return 1; /* failure */
667	+	}
668	+
669	+
670	+	if (field_given && *field_given && ! override)
671	+	return 0;
672	+	if (prev_given)
673	+	(*prev_given)++;
674	+	if (field_given)
675	+	(*field_given)++;
676	+	if (possible_values)
677	+	val = possible_values[found];
678	+
679	+	switch(arg_type) {
680	+	case ARG_INT:
681	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
682	+	break;
683	+	case ARG_DOUBLE:
684	+	if (val) *((double *)field) = strtod (val, &stop_char);
685	+	break;
686	+	case ARG_STRING:
687	+	if (val) {
688	+	string_field = (char **)field;
689	+	if (!no_free && *string_field)
690	+	free (*string_field); /* free previous string */
691	+	*string_field = gengetopt_strdup (val);
692	+	}
693	+	break;
694	+	default:
695	+	break;
696	+	};
697	+
698	+	/* check numeric conversion */
699	+	switch(arg_type) {
700	+	case ARG_INT:
701	+	case ARG_DOUBLE:
702	+	if (val && !(stop_char && *stop_char == '\0')) {
703	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
704	+	return 1; /* failure */
705	+	}
706	+	break;
707	+	default:
708	+	;
709	+	};
710	+
711	+	/* store the original value */
712	+	switch(arg_type) {
713	+	case ARG_NO:
714	+	break;
715	+	default:
716	+	if (value && orig_field) {
717	+	if (no_free) {
718	+	*orig_field = value;
719	+	} else {
720	+	if (*orig_field)
721	+	free (*orig_field); /* free previous string */
722	+	*orig_field = gengetopt_strdup (value);
723	+	}
724	+	}
725	+	};
726	+
727	+	return 0; /* OK */
728	+	}
729	+
730	+
731		int
732	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
732	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
733	>	struct cmdline_parser_params *params, const char *additional_error)
734		{
735		int c;        /* Character of the parsed option.  */
736
737		int error = 0;
738		struct gengetopt_args_info local_args_info;
739	+
740	+	int override;
741	+	int initialize;
742	+	int check_required;
743	+	int check_ambiguity;
744	+
745	+	package_name = argv[0];
746	+
747	+	override = params->override;
748	+	initialize = params->initialize;
749	+	check_required = params->check_required;
750	+	check_ambiguity = params->check_ambiguity;
751
752		if (initialize)
753		cmdline_parser_init (args_info);
#	Line 572 | Line 756 | cmdline_parser_internal (int argc, char * const *argv,
756
757		optarg = 0;
758		optind = 0;
759	<	opterr = 1;
759	>	opterr = params->print_errors;
760		optopt = '?';
761
762		while (1)
763		{
764		int option_index = 0;
581	–	char *stop_char;
765
766		static struct option long_options[] = {
767		{ "help",       0, NULL, 'h' },
#	Line 586 | Line 769 | cmdline_parser_internal (int argc, char * const *argv,
769		{ "input",      1, NULL, 'i' },
770		{ "output",     1, NULL, 'o' },
771		{ "step",       1, NULL, 'n' },
772	<	{ "nrbins",     1, NULL, 'r' },
772	>	{ "nbins",      1, NULL, 'b' },
773		{ "nbins_x",    1, NULL, 'x' },
774		{ "nbins_y",    1, NULL, 'y' },
775	+	{ "nbins_z",    1, NULL, 0 },
776		{ "nanglebins", 1, NULL, 'a' },
777	<	{ "length",     1, NULL, 'l' },
777	>	{ "rcut",       1, NULL, 'c' },
778	>	{ "length",     1, NULL, 0 },
779	>	{ "zlength",    1, NULL, 0 },
780		{ "zoffset",    1, NULL, 'z' },
781		{ "sele1",      1, NULL, 0 },
782		{ "sele2",      1, NULL, 0 },
783		{ "sele3",      1, NULL, 0 },
784		{ "refsele",    1, NULL, 0 },
785	+	{ "comsele",    1, NULL, 0 },
786		{ "molname",    1, NULL, 0 },
787		{ "begin",      1, NULL, 0 },
788		{ "end",        1, NULL, 0 },
789	<	{ "gofr",       0, NULL, 0 },
789	>	{ "radius",     1, NULL, 0 },
790	>	{ "bo", 0, NULL, 0 },
791	>	{ "bor",        0, NULL, 0 },
792	>	{ "bad",        0, NULL, 0 },
793	>	{ "gofr",       0, NULL, 'g' },
794	>	{ "gofz",       0, NULL, 0 },
795		{ "r_theta",    0, NULL, 0 },
796		{ "r_omega",    0, NULL, 0 },
797	+	{ "r_z",        0, NULL, 0 },
798		{ "theta_omega",        0, NULL, 0 },
799		{ "gxyz",       0, NULL, 0 },
800	<	{ "p2", 0, NULL, 0 },
800	>	{ "p2", 0, NULL, 'p' },
801		{ "rp2",        0, NULL, 0 },
802	<	{ "scd",        0, NULL, 0 },
803	<	{ "density",    0, NULL, 0 },
802	>	{ "scd",        0, NULL, 's' },
803	>	{ "density",    0, NULL, 'd' },
804		{ "slab_density",       0, NULL, 0 },
805	+	{ "p_angle",    0, NULL, 0 },
806		{ "hxy",        0, NULL, 0 },
807	+	{ "rho_r",      0, NULL, 0 },
808	+	{ "hullvol",    0, NULL, 0 },
809		{ NULL, 0, NULL, 0 }
810		};
811
812	<	stop_char = 0;
617	<	c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index);
812	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
813
814		if (c == -1) break;       /* Exit from `while (1)' loop.  */
815
#	Line 631 | Line 826 | cmdline_parser_internal (int argc, char * const *argv,
826		exit (EXIT_SUCCESS);
827
828		case 'i':       /* input dump file.  */
829	<	if (local_args_info.input_given)
830	<	{
831	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
832	<	goto failure;
833	<	}
834	<	if (args_info->input_given && ! override)
835	<	continue;
836	<	local_args_info.input_given = 1;
837	<	args_info->input_given = 1;
838	<	if (args_info->input_arg)
644	<	free (args_info->input_arg); /* free previous string */
645	<	args_info->input_arg = gengetopt_strdup (optarg);
646	<	if (args_info->input_orig)
647	<	free (args_info->input_orig); /* free previous string */
648	<	args_info->input_orig = gengetopt_strdup (optarg);
829	>
830	>
831	>	if (update_arg( (void *)&(args_info->input_arg),
832	>	&(args_info->input_orig), &(args_info->input_given),
833	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
834	>	check_ambiguity, override, 0, 0,
835	>	"input", 'i',
836	>	additional_error))
837	>	goto failure;
838	>
839		break;
650	–
840		case 'o':       /* output file name.  */
841	<	if (local_args_info.output_given)
842	<	{
843	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
844	<	goto failure;
845	<	}
846	<	if (args_info->output_given && ! override)
847	<	continue;
848	<	local_args_info.output_given = 1;
849	<	args_info->output_given = 1;
850	<	if (args_info->output_arg)
851	<	free (args_info->output_arg); /* free previous string */
663	<	args_info->output_arg = gengetopt_strdup (optarg);
664	<	if (args_info->output_orig)
665	<	free (args_info->output_orig); /* free previous string */
666	<	args_info->output_orig = gengetopt_strdup (optarg);
667	<	break;
668	<
841	>
842	>
843	>	if (update_arg( (void *)&(args_info->output_arg),
844	>	&(args_info->output_orig), &(args_info->output_given),
845	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
846	>	check_ambiguity, override, 0, 0,
847	>	"output", 'o',
848	>	additional_error))
849	>	goto failure;
850	>
851	>	break;
852		case 'n':       /* process every n frame.  */
853	<	if (local_args_info.step_given)
854	<	{
855	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
856	<	goto failure;
857	<	}
858	<	if (args_info->step_given && ! override)
859	<	continue;
860	<	local_args_info.step_given = 1;
678	<	args_info->step_given = 1;
679	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
680	<	if (!(stop_char && *stop_char == '\0')) {
681	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
853	>
854	>
855	>	if (update_arg( (void *)&(args_info->step_arg),
856	>	&(args_info->step_orig), &(args_info->step_given),
857	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
858	>	check_ambiguity, override, 0, 0,
859	>	"step", 'n',
860	>	additional_error))
861		goto failure;
862	<	}
684	<	if (args_info->step_orig)
685	<	free (args_info->step_orig); /* free previous string */
686	<	args_info->step_orig = gengetopt_strdup (optarg);
862	>
863		break;
864	<
865	<	case 'r':       /* number of bins for distance.  */
866	<	if (local_args_info.nrbins_given)
867	<	{
868	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
869	<	goto failure;
870	<	}
871	<	if (args_info->nrbins_given && ! override)
872	<	continue;
697	<	local_args_info.nrbins_given = 1;
698	<	args_info->nrbins_given = 1;
699	<	args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
700	<	if (!(stop_char && *stop_char == '\0')) {
701	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
864	>	case 'b':       /* number of bins (general purpose).  */
865	>
866	>
867	>	if (update_arg( (void *)&(args_info->nbins_arg),
868	>	&(args_info->nbins_orig), &(args_info->nbins_given),
869	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
870	>	check_ambiguity, override, 0, 0,
871	>	"nbins", 'b',
872	>	additional_error))
873		goto failure;
874	<	}
704	<	if (args_info->nrbins_orig)
705	<	free (args_info->nrbins_orig); /* free previous string */
706	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
874	>
875		break;
708	–
876		case 'x':       /* number of bins in x axis.  */
877	<	if (local_args_info.nbins_x_given)
878	<	{
879	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
880	<	goto failure;
881	<	}
882	<	if (args_info->nbins_x_given && ! override)
883	<	continue;
884	<	local_args_info.nbins_x_given = 1;
718	<	args_info->nbins_x_given = 1;
719	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
720	<	if (!(stop_char && *stop_char == '\0')) {
721	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
877	>
878	>
879	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
880	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
881	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
882	>	check_ambiguity, override, 0, 0,
883	>	"nbins_x", 'x',
884	>	additional_error))
885		goto failure;
886	<	}
724	<	if (args_info->nbins_x_orig)
725	<	free (args_info->nbins_x_orig); /* free previous string */
726	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
886	>
887		break;
728	–
888		case 'y':       /* number of bins in y axis.  */
889	<	if (local_args_info.nbins_y_given)
890	<	{
891	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
892	<	goto failure;
893	<	}
894	<	if (args_info->nbins_y_given && ! override)
895	<	continue;
896	<	local_args_info.nbins_y_given = 1;
738	<	args_info->nbins_y_given = 1;
739	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
740	<	if (!(stop_char && *stop_char == '\0')) {
741	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
889	>
890	>
891	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
892	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
893	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
894	>	check_ambiguity, override, 0, 0,
895	>	"nbins_y", 'y',
896	>	additional_error))
897		goto failure;
898	<	}
744	<	if (args_info->nbins_y_orig)
745	<	free (args_info->nbins_y_orig); /* free previous string */
746	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
898	>
899		break;
748	–
900		case 'a':       /* number of bins for cos(angle).  */
901	<	if (local_args_info.nanglebins_given)
902	<	{
903	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
904	<	goto failure;
905	<	}
906	<	if (args_info->nanglebins_given && ! override)
907	<	continue;
908	<	local_args_info.nanglebins_given = 1;
758	<	args_info->nanglebins_given = 1;
759	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
760	<	if (!(stop_char && *stop_char == '\0')) {
761	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
901	>
902	>
903	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
904	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
905	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
906	>	check_ambiguity, override, 0, 0,
907	>	"nanglebins", 'a',
908	>	additional_error))
909		goto failure;
910	<	}
764	<	if (args_info->nanglebins_orig)
765	<	free (args_info->nanglebins_orig); /* free previous string */
766	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
910	>
911		break;
912	<
913	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
914	<	if (local_args_info.length_given)
915	<	{
916	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	<	goto failure;
918	<	}
919	<	if (args_info->length_given && ! override)
920	<	continue;
777	<	local_args_info.length_given = 1;
778	<	args_info->length_given = 1;
779	<	args_info->length_arg = strtod (optarg, &stop_char);
780	<	if (!(stop_char && *stop_char == '\0')) {
781	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
912	>	case 'c':       /* cutoff radius (rcut).  */
913	>
914	>
915	>	if (update_arg( (void *)&(args_info->rcut_arg),
916	>	&(args_info->rcut_orig), &(args_info->rcut_given),
917	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
918	>	check_ambiguity, override, 0, 0,
919	>	"rcut", 'c',
920	>	additional_error))
921		goto failure;
922	<	}
784	<	if (args_info->length_orig)
785	<	free (args_info->length_orig); /* free previous string */
786	<	args_info->length_orig = gengetopt_strdup (optarg);
922	>
923		break;
788	–
924		case 'z':       /* Where to set the zero for the slab_density calculation.  */
925	<	if (local_args_info.zoffset_given)
926	<	{
927	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
928	<	goto failure;
929	<	}
930	<	if (args_info->zoffset_given && ! override)
931	<	continue;
932	<	local_args_info.zoffset_given = 1;
798	<	args_info->zoffset_given = 1;
799	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
800	<	if (!(stop_char && *stop_char == '\0')) {
801	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
925	>
926	>
927	>	if (update_arg( (void *)&(args_info->zoffset_arg),
928	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
929	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
930	>	check_ambiguity, override, 0, 0,
931	>	"zoffset", 'z',
932	>	additional_error))
933		goto failure;
934	<	}
804	<	if (args_info->zoffset_orig)
805	<	free (args_info->zoffset_orig); /* free previous string */
806	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
934	>
935		break;
936	+	case 'g':       /* g(r).  */
937	+
938	+	if (args_info->staticProps_group_counter && override)
939	+	reset_group_staticProps (args_info);
940	+	args_info->staticProps_group_counter += 1;
941	+
942	+	if (update_arg( 0 ,
943	+	0 , &(args_info->gofr_given),
944	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
945	+	check_ambiguity, override, 0, 0,
946	+	"gofr", 'g',
947	+	additional_error))
948	+	goto failure;
949	+
950	+	break;
951	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
952	+
953	+	if (args_info->staticProps_group_counter && override)
954	+	reset_group_staticProps (args_info);
955	+	args_info->staticProps_group_counter += 1;
956	+
957	+	if (update_arg( 0 ,
958	+	0 , &(args_info->p2_given),
959	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
960	+	check_ambiguity, override, 0, 0,
961	+	"p2", 'p',
962	+	additional_error))
963	+	goto failure;
964	+
965	+	break;
966	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
967	+
968	+	if (args_info->staticProps_group_counter && override)
969	+	reset_group_staticProps (args_info);
970	+	args_info->staticProps_group_counter += 1;
971	+
972	+	if (update_arg( 0 ,
973	+	0 , &(args_info->scd_given),
974	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
975	+	check_ambiguity, override, 0, 0,
976	+	"scd", 's',
977	+	additional_error))
978	+	goto failure;
979	+
980	+	break;
981	+	case 'd':       /* density plot.  */
982	+
983	+	if (args_info->staticProps_group_counter && override)
984	+	reset_group_staticProps (args_info);
985	+	args_info->staticProps_group_counter += 1;
986	+
987	+	if (update_arg( 0 ,
988	+	0 , &(args_info->density_given),
989	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
990	+	check_ambiguity, override, 0, 0,
991	+	"density", 'd',
992	+	additional_error))
993	+	goto failure;
994	+
995	+	break;
996
809	–
997		case 0: /* Long option with no short option */
998	+	/* number of bins in z axis.  */
999	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1000	+	{
1001	+
1002	+
1003	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1004	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1005	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1006	+	check_ambiguity, override, 0, 0,
1007	+	"nbins_z", '-',
1008	+	additional_error))
1009	+	goto failure;
1010	+
1011	+	}
1012	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1013	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1014	+	{
1015	+
1016	+
1017	+	if (update_arg( (void *)&(args_info->length_arg),
1018	+	&(args_info->length_orig), &(args_info->length_given),
1019	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1020	+	check_ambiguity, override, 0, 0,
1021	+	"length", '-',
1022	+	additional_error))
1023	+	goto failure;
1024	+
1025	+	}
1026	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1027	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1028	+	{
1029	+
1030	+
1031	+	if (update_arg( (void *)&(args_info->zlength_arg),
1032	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1033	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1034	+	check_ambiguity, override, 0, 0,
1035	+	"zlength", '-',
1036	+	additional_error))
1037	+	goto failure;
1038	+
1039	+	}
1040		/* select the first stuntdouble set.  */
1041	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1041	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1042		{
1043	<	if (local_args_info.sele1_given)
1044	<	{
1045	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1046	<	goto failure;
1047	<	}
1048	<	if (args_info->sele1_given && ! override)
1049	<	continue;
1050	<	local_args_info.sele1_given = 1;
1051	<	args_info->sele1_given = 1;
1052	<	if (args_info->sele1_arg)
824	<	free (args_info->sele1_arg); /* free previous string */
825	<	args_info->sele1_arg = gengetopt_strdup (optarg);
826	<	if (args_info->sele1_orig)
827	<	free (args_info->sele1_orig); /* free previous string */
828	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1043	>
1044	>
1045	>	if (update_arg( (void *)&(args_info->sele1_arg),
1046	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1047	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1048	>	check_ambiguity, override, 0, 0,
1049	>	"sele1", '-',
1050	>	additional_error))
1051	>	goto failure;
1052	>
1053		}
1054		/* select the second stuntdouble set.  */
1055		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1056		{
1057	<	if (local_args_info.sele2_given)
1058	<	{
1059	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1060	<	goto failure;
1061	<	}
1062	<	if (args_info->sele2_given && ! override)
1063	<	continue;
1064	<	local_args_info.sele2_given = 1;
1065	<	args_info->sele2_given = 1;
1066	<	if (args_info->sele2_arg)
843	<	free (args_info->sele2_arg); /* free previous string */
844	<	args_info->sele2_arg = gengetopt_strdup (optarg);
845	<	if (args_info->sele2_orig)
846	<	free (args_info->sele2_orig); /* free previous string */
847	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1057	>
1058	>
1059	>	if (update_arg( (void *)&(args_info->sele2_arg),
1060	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1061	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1062	>	check_ambiguity, override, 0, 0,
1063	>	"sele2", '-',
1064	>	additional_error))
1065	>	goto failure;
1066	>
1067		}
1068		/* select the third stuntdouble set.  */
1069		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1070		{
1071	<	if (local_args_info.sele3_given)
1072	<	{
1073	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1074	<	goto failure;
1075	<	}
1076	<	if (args_info->sele3_given && ! override)
1077	<	continue;
1078	<	local_args_info.sele3_given = 1;
1079	<	args_info->sele3_given = 1;
1080	<	if (args_info->sele3_arg)
862	<	free (args_info->sele3_arg); /* free previous string */
863	<	args_info->sele3_arg = gengetopt_strdup (optarg);
864	<	if (args_info->sele3_orig)
865	<	free (args_info->sele3_orig); /* free previous string */
866	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1071	>
1072	>
1073	>	if (update_arg( (void *)&(args_info->sele3_arg),
1074	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1075	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1076	>	check_ambiguity, override, 0, 0,
1077	>	"sele3", '-',
1078	>	additional_error))
1079	>	goto failure;
1080	>
1081		}
1082		/* select reference (use and only use with --gxyz).  */
1083		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1084		{
1085	<	if (local_args_info.refsele_given)
1086	<	{
1087	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1088	<	goto failure;
1089	<	}
1090	<	if (args_info->refsele_given && ! override)
1091	<	continue;
1092	<	local_args_info.refsele_given = 1;
1093	<	args_info->refsele_given = 1;
1094	<	if (args_info->refsele_arg)
881	<	free (args_info->refsele_arg); /* free previous string */
882	<	args_info->refsele_arg = gengetopt_strdup (optarg);
883	<	if (args_info->refsele_orig)
884	<	free (args_info->refsele_orig); /* free previous string */
885	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1085	>
1086	>
1087	>	if (update_arg( (void *)&(args_info->refsele_arg),
1088	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1089	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1090	>	check_ambiguity, override, 0, 0,
1091	>	"refsele", '-',
1092	>	additional_error))
1093	>	goto failure;
1094	>
1095		}
1096	+	/* select stunt doubles for center-of-mass reference point.  */
1097	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1098	+	{
1099	+
1100	+
1101	+	if (update_arg( (void *)&(args_info->comsele_arg),
1102	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1103	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1104	+	check_ambiguity, override, 0, 0,
1105	+	"comsele", '-',
1106	+	additional_error))
1107	+	goto failure;
1108	+
1109	+	}
1110		/* molecule name.  */
1111		else if (strcmp (long_options[option_index].name, "molname") == 0)
1112		{
1113	<	if (local_args_info.molname_given)
1114	<	{
1115	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1116	<	goto failure;
1117	<	}
1118	<	if (args_info->molname_given && ! override)
1119	<	continue;
1120	<	local_args_info.molname_given = 1;
1121	<	args_info->molname_given = 1;
1122	<	if (args_info->molname_arg)
900	<	free (args_info->molname_arg); /* free previous string */
901	<	args_info->molname_arg = gengetopt_strdup (optarg);
902	<	if (args_info->molname_orig)
903	<	free (args_info->molname_orig); /* free previous string */
904	<	args_info->molname_orig = gengetopt_strdup (optarg);
1113	>
1114	>
1115	>	if (update_arg( (void *)&(args_info->molname_arg),
1116	>	&(args_info->molname_orig), &(args_info->molname_given),
1117	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"molname", '-',
1120	>	additional_error))
1121	>	goto failure;
1122	>
1123		}
1124	<	/* begin interanl index.  */
1124	>	/* begin internal index.  */
1125		else if (strcmp (long_options[option_index].name, "begin") == 0)
1126		{
1127	<	if (local_args_info.begin_given)
1128	<	{
1129	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1130	<	goto failure;
1131	<	}
1132	<	if (args_info->begin_given && ! override)
1133	<	continue;
1134	<	local_args_info.begin_given = 1;
917	<	args_info->begin_given = 1;
918	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
919	<	if (!(stop_char && *stop_char == '\0')) {
920	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1127	>
1128	>
1129	>	if (update_arg( (void *)&(args_info->begin_arg),
1130	>	&(args_info->begin_orig), &(args_info->begin_given),
1131	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1132	>	check_ambiguity, override, 0, 0,
1133	>	"begin", '-',
1134	>	additional_error))
1135		goto failure;
1136	<	}
923	<	if (args_info->begin_orig)
924	<	free (args_info->begin_orig); /* free previous string */
925	<	args_info->begin_orig = gengetopt_strdup (optarg);
1136	>
1137		}
1138		/* end internal index.  */
1139		else if (strcmp (long_options[option_index].name, "end") == 0)
1140		{
1141	<	if (local_args_info.end_given)
1142	<	{
1143	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1144	<	goto failure;
1145	<	}
1146	<	if (args_info->end_given && ! override)
1147	<	continue;
1148	<	local_args_info.end_given = 1;
938	<	args_info->end_given = 1;
939	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
940	<	if (!(stop_char && *stop_char == '\0')) {
941	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1141	>
1142	>
1143	>	if (update_arg( (void *)&(args_info->end_arg),
1144	>	&(args_info->end_orig), &(args_info->end_given),
1145	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1146	>	check_ambiguity, override, 0, 0,
1147	>	"end", '-',
1148	>	additional_error))
1149		goto failure;
1150	<	}
944	<	if (args_info->end_orig)
945	<	free (args_info->end_orig); /* free previous string */
946	<	args_info->end_orig = gengetopt_strdup (optarg);
1150	>
1151		}
1152	<	/* g(r).  */
1153	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1152	>	/* nanoparticle radius.  */
1153	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1154		{
1155	<	if (local_args_info.gofr_given)
1156	<	{
1157	<	fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1158	<	goto failure;
1159	<	}
1160	<	if (args_info->gofr_given && ! override)
1161	<	continue;
1162	<	local_args_info.gofr_given = 1;
1163	<	args_info->gofr_given = 1;
1155	>
1156	>
1157	>	if (update_arg( (void *)&(args_info->radius_arg),
1158	>	&(args_info->radius_orig), &(args_info->radius_given),
1159	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1160	>	check_ambiguity, override, 0, 0,
1161	>	"radius", '-',
1162	>	additional_error))
1163	>	goto failure;
1164	>
1165	>	}
1166	>	/* bond order parameter (--rcut must be specified).  */
1167	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1168	>	{
1169	>
1170		if (args_info->staticProps_group_counter && override)
1171		reset_group_staticProps (args_info);
1172		args_info->staticProps_group_counter += 1;
1173	<	break;
1173	>
1174	>	if (update_arg( 0 ,
1175	>	0 , &(args_info->bo_given),
1176	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1177	>	check_ambiguity, override, 0, 0,
1178	>	"bo", '-',
1179	>	additional_error))
1180	>	goto failure;
1181	>
1182		}
1183	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1184	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1185	+	{
1186	+
1187	+	if (args_info->staticProps_group_counter && override)
1188	+	reset_group_staticProps (args_info);
1189	+	args_info->staticProps_group_counter += 1;
1190	+
1191	+	if (update_arg( 0 ,
1192	+	0 , &(args_info->bor_given),
1193	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1194	+	check_ambiguity, override, 0, 0,
1195	+	"bor", '-',
1196	+	additional_error))
1197	+	goto failure;
1198	+
1199	+	}
1200	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1201	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1202	+	{
1203	+
1204	+	if (args_info->staticProps_group_counter && override)
1205	+	reset_group_staticProps (args_info);
1206	+	args_info->staticProps_group_counter += 1;
1207	+
1208	+	if (update_arg( 0 ,
1209	+	0 , &(args_info->bad_given),
1210	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1211	+	check_ambiguity, override, 0, 0,
1212	+	"bad", '-',
1213	+	additional_error))
1214	+	goto failure;
1215	+
1216	+	}
1217	+	/* g(z).  */
1218	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1219	+	{
1220	+
1221	+	if (args_info->staticProps_group_counter && override)
1222	+	reset_group_staticProps (args_info);
1223	+	args_info->staticProps_group_counter += 1;
1224	+
1225	+	if (update_arg( 0 ,
1226	+	0 , &(args_info->gofz_given),
1227	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1228	+	check_ambiguity, override, 0, 0,
1229	+	"gofz", '-',
1230	+	additional_error))
1231	+	goto failure;
1232	+
1233	+	}
1234		/* g(r, cos(theta)).  */
1235		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1236		{
1237	<	if (local_args_info.r_theta_given)
969	<	{
970	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	<	goto failure;
972	<	}
973	<	if (args_info->r_theta_given && ! override)
974	<	continue;
975	<	local_args_info.r_theta_given = 1;
976	<	args_info->r_theta_given = 1;
1237	>
1238		if (args_info->staticProps_group_counter && override)
1239		reset_group_staticProps (args_info);
1240		args_info->staticProps_group_counter += 1;
1241	<	break;
1241	>
1242	>	if (update_arg( 0 ,
1243	>	0 , &(args_info->r_theta_given),
1244	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1245	>	check_ambiguity, override, 0, 0,
1246	>	"r_theta", '-',
1247	>	additional_error))
1248	>	goto failure;
1249	>
1250		}
1251		/* g(r, cos(omega)).  */
1252		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1253		{
1254	<	if (local_args_info.r_omega_given)
986	<	{
987	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
988	<	goto failure;
989	<	}
990	<	if (args_info->r_omega_given && ! override)
991	<	continue;
992	<	local_args_info.r_omega_given = 1;
993	<	args_info->r_omega_given = 1;
1254	>
1255		if (args_info->staticProps_group_counter && override)
1256		reset_group_staticProps (args_info);
1257		args_info->staticProps_group_counter += 1;
1258	<	break;
1258	>
1259	>	if (update_arg( 0 ,
1260	>	0 , &(args_info->r_omega_given),
1261	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1262	>	check_ambiguity, override, 0, 0,
1263	>	"r_omega", '-',
1264	>	additional_error))
1265	>	goto failure;
1266	>
1267	>	}
1268	>	/* g(r, z).  */
1269	>	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1270	>	{
1271	>
1272	>	if (args_info->staticProps_group_counter && override)
1273	>	reset_group_staticProps (args_info);
1274	>	args_info->staticProps_group_counter += 1;
1275	>
1276	>	if (update_arg( 0 ,
1277	>	0 , &(args_info->r_z_given),
1278	>	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1279	>	check_ambiguity, override, 0, 0,
1280	>	"r_z", '-',
1281	>	additional_error))
1282	>	goto failure;
1283	>
1284		}
1285		/* g(cos(theta), cos(omega)).  */
1286		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1287		{
1288	<	if (local_args_info.theta_omega_given)
1003	<	{
1004	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1005	<	goto failure;
1006	<	}
1007	<	if (args_info->theta_omega_given && ! override)
1008	<	continue;
1009	<	local_args_info.theta_omega_given = 1;
1010	<	args_info->theta_omega_given = 1;
1288	>
1289		if (args_info->staticProps_group_counter && override)
1290		reset_group_staticProps (args_info);
1291		args_info->staticProps_group_counter += 1;
1292	<	break;
1292	>
1293	>	if (update_arg( 0 ,
1294	>	0 , &(args_info->theta_omega_given),
1295	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1296	>	check_ambiguity, override, 0, 0,
1297	>	"theta_omega", '-',
1298	>	additional_error))
1299	>	goto failure;
1300	>
1301		}
1302		/* g(x, y, z).  */
1303		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1304		{
1305	<	if (local_args_info.gxyz_given)
1020	<	{
1021	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1022	<	goto failure;
1023	<	}
1024	<	if (args_info->gxyz_given && ! override)
1025	<	continue;
1026	<	local_args_info.gxyz_given = 1;
1027	<	args_info->gxyz_given = 1;
1305	>
1306		if (args_info->staticProps_group_counter && override)
1307		reset_group_staticProps (args_info);
1308		args_info->staticProps_group_counter += 1;
1309	<	break;
1309	>
1310	>	if (update_arg( 0 ,
1311	>	0 , &(args_info->gxyz_given),
1312	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1313	>	check_ambiguity, override, 0, 0,
1314	>	"gxyz", '-',
1315	>	additional_error))
1316	>	goto failure;
1317	>
1318		}
1319	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1320	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1319	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1320	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1321		{
1322	<	if (local_args_info.p2_given)
1037	<	{
1038	<	fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1039	<	goto failure;
1040	<	}
1041	<	if (args_info->p2_given && ! override)
1042	<	continue;
1043	<	local_args_info.p2_given = 1;
1044	<	args_info->p2_given = 1;
1322	>
1323		if (args_info->staticProps_group_counter && override)
1324		reset_group_staticProps (args_info);
1325		args_info->staticProps_group_counter += 1;
1326	<	break;
1326	>
1327	>	if (update_arg( 0 ,
1328	>	0 , &(args_info->rp2_given),
1329	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1330	>	check_ambiguity, override, 0, 0,
1331	>	"rp2", '-',
1332	>	additional_error))
1333	>	goto failure;
1334	>
1335		}
1336	<	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1337	<	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1336	>	/* slab density.  */
1337	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1338		{
1339	<	if (local_args_info.rp2_given)
1054	<	{
1055	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1056	<	goto failure;
1057	<	}
1058	<	if (args_info->rp2_given && ! override)
1059	<	continue;
1060	<	local_args_info.rp2_given = 1;
1061	<	args_info->rp2_given = 1;
1339	>
1340		if (args_info->staticProps_group_counter && override)
1341		reset_group_staticProps (args_info);
1342		args_info->staticProps_group_counter += 1;
1343	<	break;
1343	>
1344	>	if (update_arg( 0 ,
1345	>	0 , &(args_info->slab_density_given),
1346	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1347	>	check_ambiguity, override, 0, 0,
1348	>	"slab_density", '-',
1349	>	additional_error))
1350	>	goto failure;
1351	>
1352		}
1353	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1354	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1353	>	/* p(cos(theta)).  */
1354	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1355		{
1356	<	if (local_args_info.scd_given)
1071	<	{
1072	<	fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1073	<	goto failure;
1074	<	}
1075	<	if (args_info->scd_given && ! override)
1076	<	continue;
1077	<	local_args_info.scd_given = 1;
1078	<	args_info->scd_given = 1;
1356	>
1357		if (args_info->staticProps_group_counter && override)
1358		reset_group_staticProps (args_info);
1359		args_info->staticProps_group_counter += 1;
1360	<	break;
1360	>
1361	>	if (update_arg( 0 ,
1362	>	0 , &(args_info->p_angle_given),
1363	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1364	>	check_ambiguity, override, 0, 0,
1365	>	"p_angle", '-',
1366	>	additional_error))
1367	>	goto failure;
1368	>
1369		}
1370	<	/* density plot (--sele1 must be specified).  */
1371	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1370	>	/* hxy.  */
1371	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1372		{
1373	<	if (local_args_info.density_given)
1088	<	{
1089	<	fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1090	<	goto failure;
1091	<	}
1092	<	if (args_info->density_given && ! override)
1093	<	continue;
1094	<	local_args_info.density_given = 1;
1095	<	args_info->density_given = 1;
1373	>
1374		if (args_info->staticProps_group_counter && override)
1375		reset_group_staticProps (args_info);
1376		args_info->staticProps_group_counter += 1;
1377	<	break;
1377	>
1378	>	if (update_arg( 0 ,
1379	>	0 , &(args_info->hxy_given),
1380	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1381	>	check_ambiguity, override, 0, 0,
1382	>	"hxy", '-',
1383	>	additional_error))
1384	>	goto failure;
1385	>
1386		}
1387	<	/* slab density (--sele1 must be specified).  */
1388	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1387	>	/* rho of R.  */
1388	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1389		{
1390	<	if (local_args_info.slab_density_given)
1105	<	{
1106	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1107	<	goto failure;
1108	<	}
1109	<	if (args_info->slab_density_given && ! override)
1110	<	continue;
1111	<	local_args_info.slab_density_given = 1;
1112	<	args_info->slab_density_given = 1;
1390	>
1391		if (args_info->staticProps_group_counter && override)
1392		reset_group_staticProps (args_info);
1393		args_info->staticProps_group_counter += 1;
1394	<	break;
1394	>
1395	>	if (update_arg( 0 ,
1396	>	0 , &(args_info->rho_r_given),
1397	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1398	>	check_ambiguity, override, 0, 0,
1399	>	"rho_r", '-',
1400	>	additional_error))
1401	>	goto failure;
1402	>
1403		}
1404	<	/* hxy (--sele1 must be specified).  */
1405	<	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1404	>	/* hull volume of nanoparticle.  */
1405	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1406		{
1407	<	if (local_args_info.hxy_given)
1122	<	{
1123	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1124	<	goto failure;
1125	<	}
1126	<	if (args_info->hxy_given && ! override)
1127	<	continue;
1128	<	local_args_info.hxy_given = 1;
1129	<	args_info->hxy_given = 1;
1407	>
1408		if (args_info->staticProps_group_counter && override)
1409		reset_group_staticProps (args_info);
1410		args_info->staticProps_group_counter += 1;
1411	<	break;
1411	>
1412	>	if (update_arg( 0 ,
1413	>	0 , &(args_info->hullvol_given),
1414	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1415	>	check_ambiguity, override, 0, 0,
1416	>	"hullvol", '-',
1417	>	additional_error))
1418	>	goto failure;
1419	>
1420		}
1421
1422		break;

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords):
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

#	Line 0 | Line 1
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