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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 967 by xsun, Mon May 22 15:30:42 2006 UTC vs.
Revision 1513 by gezelter, Tue Oct 19 18:40:54 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	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
60	+	"  -g, --gofr                    g(r)",
61	+	"      --gofz                    g(z)",
62	+	"      --r_theta                 g(r, cos(theta))",
63	+	"      --r_omega                 g(r, cos(omega))",
64	+	"      --r_z                     g(r, z)",
65	+	"      --theta_omega             g(cos(theta), cos(omega))",
66	+	"      --gxyz                    g(x, y, z)",
67	+	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
68	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
69	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
70	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
71	+	"  -d, --density                 density plot",
72	+	"      --slab_density            slab density",
73	+	"      --p_angle                 p(cos(theta))",
74	+	"      --hxy                     hxy",
75	+	"      --rho_r                   rho of R",
76	+	"      --hullvol                 hull volume of nanoparticle",
77	+	0
78	+	};
79	+
80	+	typedef enum {ARG_NO
81	+	, ARG_STRING
82	+	, ARG_INT
83	+	, ARG_DOUBLE
84	+	} cmdline_parser_arg_type;
85	+
86		static
87		void clear_given (struct gengetopt_args_info *args_info);
88		static
89		void clear_args (struct gengetopt_args_info *args_info);
90
91		static int
92	<	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);
92	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
93	>	struct cmdline_parser_params *params, const char *additional_error);
94
95		static int
96		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 43 | Line 106 | void clear_given (struct gengetopt_args_info *args_inf
106		args_info->input_given = 0 ;
107		args_info->output_given = 0 ;
108		args_info->step_given = 0 ;
109	<	args_info->nrbins_given = 0 ;
109	>	args_info->nbins_given = 0 ;
110		args_info->nbins_x_given = 0 ;
111		args_info->nbins_y_given = 0 ;
112	+	args_info->nbins_z_given = 0 ;
113		args_info->nanglebins_given = 0 ;
114	+	args_info->rcut_given = 0 ;
115	+	args_info->dz_given = 0 ;
116		args_info->length_given = 0 ;
117	+	args_info->zlength_given = 0 ;
118		args_info->zoffset_given = 0 ;
119		args_info->sele1_given = 0 ;
120		args_info->sele2_given = 0 ;
121		args_info->sele3_given = 0 ;
122		args_info->refsele_given = 0 ;
123	+	args_info->comsele_given = 0 ;
124		args_info->molname_given = 0 ;
125		args_info->begin_given = 0 ;
126		args_info->end_given = 0 ;
127	+	args_info->radius_given = 0 ;
128	+	args_info->bo_given = 0 ;
129	+	args_info->bor_given = 0 ;
130	+	args_info->bad_given = 0 ;
131	+	args_info->count_given = 0 ;
132		args_info->gofr_given = 0 ;
133	+	args_info->gofz_given = 0 ;
134		args_info->r_theta_given = 0 ;
135		args_info->r_omega_given = 0 ;
136	+	args_info->r_z_given = 0 ;
137		args_info->theta_omega_given = 0 ;
138		args_info->gxyz_given = 0 ;
139	+	args_info->twodgofr_given = 0 ;
140		args_info->p2_given = 0 ;
141	+	args_info->rp2_given = 0 ;
142		args_info->scd_given = 0 ;
143		args_info->density_given = 0 ;
144		args_info->slab_density_given = 0 ;
145	+	args_info->p_angle_given = 0 ;
146		args_info->hxy_given = 0 ;
147	+	args_info->rho_r_given = 0 ;
148	+	args_info->hullvol_given = 0 ;
149		args_info->staticProps_group_counter = 0 ;
150		}
151
#	Line 78 | Line 158 | void clear_args (struct gengetopt_args_info *args_info
158		args_info->output_orig = NULL;
159		args_info->step_arg = 1;
160		args_info->step_orig = NULL;
161	<	args_info->nrbins_arg = 100;
162	<	args_info->nrbins_orig = NULL;
161	>	args_info->nbins_arg = 100;
162	>	args_info->nbins_orig = NULL;
163		args_info->nbins_x_arg = 100;
164		args_info->nbins_x_orig = NULL;
165		args_info->nbins_y_arg = 100;
166		args_info->nbins_y_orig = NULL;
167	+	args_info->nbins_z_arg = 100;
168	+	args_info->nbins_z_orig = NULL;
169		args_info->nanglebins_arg = 50;
170		args_info->nanglebins_orig = NULL;
171	+	args_info->rcut_orig = NULL;
172	+	args_info->dz_orig = NULL;
173		args_info->length_orig = NULL;
174	+	args_info->zlength_orig = NULL;
175		args_info->zoffset_arg = 0;
176		args_info->zoffset_orig = NULL;
177		args_info->sele1_arg = NULL;
#	Line 97 | Line 182 | void clear_args (struct gengetopt_args_info *args_info
182		args_info->sele3_orig = NULL;
183		args_info->refsele_arg = NULL;
184		args_info->refsele_orig = NULL;
185	+	args_info->comsele_arg = NULL;
186	+	args_info->comsele_orig = NULL;
187		args_info->molname_arg = NULL;
188		args_info->molname_orig = NULL;
189		args_info->begin_orig = NULL;
190		args_info->end_orig = NULL;
191	+	args_info->radius_orig = NULL;
192
193		}
194
195	+	static
196	+	void init_args_info(struct gengetopt_args_info *args_info)
197	+	{
198	+
199	+
200	+	args_info->help_help = gengetopt_args_info_help[0] ;
201	+	args_info->version_help = gengetopt_args_info_help[1] ;
202	+	args_info->input_help = gengetopt_args_info_help[2] ;
203	+	args_info->output_help = gengetopt_args_info_help[3] ;
204	+	args_info->step_help = gengetopt_args_info_help[4] ;
205	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
206	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
207	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
208	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
209	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
210	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
211	+	args_info->dz_help = gengetopt_args_info_help[11] ;
212	+	args_info->length_help = gengetopt_args_info_help[12] ;
213	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
214	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
215	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
216	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
217	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
218	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
219	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
220	+	args_info->molname_help = gengetopt_args_info_help[20] ;
221	+	args_info->begin_help = gengetopt_args_info_help[21] ;
222	+	args_info->end_help = gengetopt_args_info_help[22] ;
223	+	args_info->radius_help = gengetopt_args_info_help[23] ;
224	+	args_info->bo_help = gengetopt_args_info_help[25] ;
225	+	args_info->bor_help = gengetopt_args_info_help[26] ;
226	+	args_info->bad_help = gengetopt_args_info_help[27] ;
227	+	args_info->count_help = gengetopt_args_info_help[28] ;
228	+	args_info->gofr_help = gengetopt_args_info_help[29] ;
229	+	args_info->gofz_help = gengetopt_args_info_help[30] ;
230	+	args_info->r_theta_help = gengetopt_args_info_help[31] ;
231	+	args_info->r_omega_help = gengetopt_args_info_help[32] ;
232	+	args_info->r_z_help = gengetopt_args_info_help[33] ;
233	+	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
234	+	args_info->gxyz_help = gengetopt_args_info_help[35] ;
235	+	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
236	+	args_info->p2_help = gengetopt_args_info_help[37] ;
237	+	args_info->rp2_help = gengetopt_args_info_help[38] ;
238	+	args_info->scd_help = gengetopt_args_info_help[39] ;
239	+	args_info->density_help = gengetopt_args_info_help[40] ;
240	+	args_info->slab_density_help = gengetopt_args_info_help[41] ;
241	+	args_info->p_angle_help = gengetopt_args_info_help[42] ;
242	+	args_info->hxy_help = gengetopt_args_info_help[43] ;
243	+	args_info->rho_r_help = gengetopt_args_info_help[44] ;
244	+	args_info->hullvol_help = gengetopt_args_info_help[45] ;
245	+
246	+	}
247	+
248		void
249		cmdline_parser_print_version (void)
250		{
251		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
252		}
253
254	+	static void print_help_common(void) {
255	+	cmdline_parser_print_version ();
256	+
257	+	if (strlen(gengetopt_args_info_purpose) > 0)
258	+	printf("\n%s\n", gengetopt_args_info_purpose);
259	+
260	+	if (strlen(gengetopt_args_info_usage) > 0)
261	+	printf("\n%s\n", gengetopt_args_info_usage);
262	+
263	+	printf("\n");
264	+
265	+	if (strlen(gengetopt_args_info_description) > 0)
266	+	printf("%s\n", gengetopt_args_info_description);
267	+	}
268	+
269		void
270		cmdline_parser_print_help (void)
271		{
272	<	cmdline_parser_print_version ();
273	<	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
274	<	printf("%s\n","  -h, --help                    Print help and exit");
275	<	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	<
272	>	int i = 0;
273	>	print_help_common();
274	>	while (gengetopt_args_info_help[i])
275	>	printf("%s\n", gengetopt_args_info_help[i++]);
276		}
277
278		void
#	Line 152 | Line 280 | cmdline_parser_init (struct gengetopt_args_info *args_
280		{
281		clear_given (args_info);
282		clear_args (args_info);
283	+	init_args_info (args_info);
284	+
285	+	args_info->inputs = NULL;
286	+	args_info->inputs_num = 0;
287	+	}
288	+
289	+	void
290	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
291	+	{
292	+	if (params)
293	+	{
294	+	params->override = 0;
295	+	params->initialize = 1;
296	+	params->check_required = 1;
297	+	params->check_ambiguity = 0;
298	+	params->print_errors = 1;
299	+	}
300	+	}
301	+
302	+	struct cmdline_parser_params *
303	+	cmdline_parser_params_create(void)
304	+	{
305	+	struct cmdline_parser_params *params =
306	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
307	+	cmdline_parser_params_init(params);
308	+	return params;
309	+	}
310	+
311	+	static void
312	+	free_string_field (char **s)
313	+	{
314	+	if (*s)
315	+	{
316	+	free (*s);
317	+	*s = 0;
318	+	}
319		}
320
321	+
322		static void
323		cmdline_parser_release (struct gengetopt_args_info *args_info)
324		{
325	+	unsigned int i;
326	+	free_string_field (&(args_info->input_arg));
327	+	free_string_field (&(args_info->input_orig));
328	+	free_string_field (&(args_info->output_arg));
329	+	free_string_field (&(args_info->output_orig));
330	+	free_string_field (&(args_info->step_orig));
331	+	free_string_field (&(args_info->nbins_orig));
332	+	free_string_field (&(args_info->nbins_x_orig));
333	+	free_string_field (&(args_info->nbins_y_orig));
334	+	free_string_field (&(args_info->nbins_z_orig));
335	+	free_string_field (&(args_info->nanglebins_orig));
336	+	free_string_field (&(args_info->rcut_orig));
337	+	free_string_field (&(args_info->dz_orig));
338	+	free_string_field (&(args_info->length_orig));
339	+	free_string_field (&(args_info->zlength_orig));
340	+	free_string_field (&(args_info->zoffset_orig));
341	+	free_string_field (&(args_info->sele1_arg));
342	+	free_string_field (&(args_info->sele1_orig));
343	+	free_string_field (&(args_info->sele2_arg));
344	+	free_string_field (&(args_info->sele2_orig));
345	+	free_string_field (&(args_info->sele3_arg));
346	+	free_string_field (&(args_info->sele3_orig));
347	+	free_string_field (&(args_info->refsele_arg));
348	+	free_string_field (&(args_info->refsele_orig));
349	+	free_string_field (&(args_info->comsele_arg));
350	+	free_string_field (&(args_info->comsele_orig));
351	+	free_string_field (&(args_info->molname_arg));
352	+	free_string_field (&(args_info->molname_orig));
353	+	free_string_field (&(args_info->begin_orig));
354	+	free_string_field (&(args_info->end_orig));
355	+	free_string_field (&(args_info->radius_orig));
356
357	<	if (args_info->input_arg)
357	>
358	>	for (i = 0; i < args_info->inputs_num; ++i)
359	>	free (args_info->inputs [i]);
360	>
361	>	if (args_info->inputs_num)
362	>	free (args_info->inputs);
363	>
364	>	clear_given (args_info);
365	>	}
366	>
367	>
368	>	static void
369	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
370	>	{
371	>	if (arg) {
372	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
373	>	} else {
374	>	fprintf(outfile, "%s\n", opt);
375	>	}
376	>	}
377	>
378	>
379	>	int
380	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
381	>	{
382	>	int i = 0;
383	>
384	>	if (!outfile)
385		{
386	<	free (args_info->input_arg); /* free previous argument */
387	<	args_info->input_arg = 0;
386	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
387	>	return EXIT_FAILURE;
388		}
389	<	if (args_info->input_orig)
390	<	{
391	<	free (args_info->input_orig); /* free previous argument */
392	<	args_info->input_orig = 0;
393	<	}
394	<	if (args_info->output_arg)
395	<	{
396	<	free (args_info->output_arg); /* free previous argument */
397	<	args_info->output_arg = 0;
398	<	}
399	<	if (args_info->output_orig)
400	<	{
401	<	free (args_info->output_orig); /* free previous argument */
402	<	args_info->output_orig = 0;
403	<	}
404	<	if (args_info->step_orig)
405	<	{
406	<	free (args_info->step_orig); /* free previous argument */
407	<	args_info->step_orig = 0;
408	<	}
409	<	if (args_info->nrbins_orig)
410	<	{
411	<	free (args_info->nrbins_orig); /* free previous argument */
412	<	args_info->nrbins_orig = 0;
413	<	}
414	<	if (args_info->nbins_x_orig)
415	<	{
416	<	free (args_info->nbins_x_orig); /* free previous argument */
417	<	args_info->nbins_x_orig = 0;
418	<	}
419	<	if (args_info->nbins_y_orig)
420	<	{
421	<	free (args_info->nbins_y_orig); /* free previous argument */
422	<	args_info->nbins_y_orig = 0;
423	<	}
424	<	if (args_info->nanglebins_orig)
425	<	{
426	<	free (args_info->nanglebins_orig); /* free previous argument */
427	<	args_info->nanglebins_orig = 0;
428	<	}
429	<	if (args_info->length_orig)
430	<	{
431	<	free (args_info->length_orig); /* free previous argument */
432	<	args_info->length_orig = 0;
433	<	}
434	<	if (args_info->zoffset_orig)
435	<	{
436	<	free (args_info->zoffset_orig); /* free previous argument */
437	<	args_info->zoffset_orig = 0;
438	<	}
439	<	if (args_info->sele1_arg)
440	<	{
441	<	free (args_info->sele1_arg); /* free previous argument */
442	<	args_info->sele1_arg = 0;
443	<	}
444	<	if (args_info->sele1_orig)
445	<	{
446	<	free (args_info->sele1_orig); /* free previous argument */
447	<	args_info->sele1_orig = 0;
448	<	}
449	<	if (args_info->sele2_arg)
450	<	{
451	<	free (args_info->sele2_arg); /* free previous argument */
452	<	args_info->sele2_arg = 0;
453	<	}
454	<	if (args_info->sele2_orig)
455	<	{
456	<	free (args_info->sele2_orig); /* free previous argument */
457	<	args_info->sele2_orig = 0;
458	<	}
459	<	if (args_info->sele3_arg)
460	<	{
461	<	free (args_info->sele3_arg); /* free previous argument */
462	<	args_info->sele3_arg = 0;
463	<	}
464	<	if (args_info->sele3_orig)
465	<	{
466	<	free (args_info->sele3_orig); /* free previous argument */
467	<	args_info->sele3_orig = 0;
468	<	}
469	<	if (args_info->refsele_arg)
470	<	{
471	<	free (args_info->refsele_arg); /* free previous argument */
472	<	args_info->refsele_arg = 0;
473	<	}
474	<	if (args_info->refsele_orig)
475	<	{
476	<	free (args_info->refsele_orig); /* free previous argument */
477	<	args_info->refsele_orig = 0;
478	<	}
479	<	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	<	}
389	>
390	>	if (args_info->help_given)
391	>	write_into_file(outfile, "help", 0, 0 );
392	>	if (args_info->version_given)
393	>	write_into_file(outfile, "version", 0, 0 );
394	>	if (args_info->input_given)
395	>	write_into_file(outfile, "input", args_info->input_orig, 0);
396	>	if (args_info->output_given)
397	>	write_into_file(outfile, "output", args_info->output_orig, 0);
398	>	if (args_info->step_given)
399	>	write_into_file(outfile, "step", args_info->step_orig, 0);
400	>	if (args_info->nbins_given)
401	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
402	>	if (args_info->nbins_x_given)
403	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
404	>	if (args_info->nbins_y_given)
405	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
406	>	if (args_info->nbins_z_given)
407	>	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
408	>	if (args_info->nanglebins_given)
409	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
410	>	if (args_info->rcut_given)
411	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
412	>	if (args_info->dz_given)
413	>	write_into_file(outfile, "dz", args_info->dz_orig, 0);
414	>	if (args_info->length_given)
415	>	write_into_file(outfile, "length", args_info->length_orig, 0);
416	>	if (args_info->zlength_given)
417	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
418	>	if (args_info->zoffset_given)
419	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
420	>	if (args_info->sele1_given)
421	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
422	>	if (args_info->sele2_given)
423	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
424	>	if (args_info->sele3_given)
425	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
426	>	if (args_info->refsele_given)
427	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
428	>	if (args_info->comsele_given)
429	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
430	>	if (args_info->molname_given)
431	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
432	>	if (args_info->begin_given)
433	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
434	>	if (args_info->end_given)
435	>	write_into_file(outfile, "end", args_info->end_orig, 0);
436	>	if (args_info->radius_given)
437	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
438	>	if (args_info->bo_given)
439	>	write_into_file(outfile, "bo", 0, 0 );
440	>	if (args_info->bor_given)
441	>	write_into_file(outfile, "bor", 0, 0 );
442	>	if (args_info->bad_given)
443	>	write_into_file(outfile, "bad", 0, 0 );
444	>	if (args_info->count_given)
445	>	write_into_file(outfile, "count", 0, 0 );
446	>	if (args_info->gofr_given)
447	>	write_into_file(outfile, "gofr", 0, 0 );
448	>	if (args_info->gofz_given)
449	>	write_into_file(outfile, "gofz", 0, 0 );
450	>	if (args_info->r_theta_given)
451	>	write_into_file(outfile, "r_theta", 0, 0 );
452	>	if (args_info->r_omega_given)
453	>	write_into_file(outfile, "r_omega", 0, 0 );
454	>	if (args_info->r_z_given)
455	>	write_into_file(outfile, "r_z", 0, 0 );
456	>	if (args_info->theta_omega_given)
457	>	write_into_file(outfile, "theta_omega", 0, 0 );
458	>	if (args_info->gxyz_given)
459	>	write_into_file(outfile, "gxyz", 0, 0 );
460	>	if (args_info->twodgofr_given)
461	>	write_into_file(outfile, "twodgofr", 0, 0 );
462	>	if (args_info->p2_given)
463	>	write_into_file(outfile, "p2", 0, 0 );
464	>	if (args_info->rp2_given)
465	>	write_into_file(outfile, "rp2", 0, 0 );
466	>	if (args_info->scd_given)
467	>	write_into_file(outfile, "scd", 0, 0 );
468	>	if (args_info->density_given)
469	>	write_into_file(outfile, "density", 0, 0 );
470	>	if (args_info->slab_density_given)
471	>	write_into_file(outfile, "slab_density", 0, 0 );
472	>	if (args_info->p_angle_given)
473	>	write_into_file(outfile, "p_angle", 0, 0 );
474	>	if (args_info->hxy_given)
475	>	write_into_file(outfile, "hxy", 0, 0 );
476	>	if (args_info->rho_r_given)
477	>	write_into_file(outfile, "rho_r", 0, 0 );
478	>	if (args_info->hullvol_given)
479	>	write_into_file(outfile, "hullvol", 0, 0 );
480
481	<	clear_given (args_info);
481	>
482	>	i = EXIT_SUCCESS;
483	>	return i;
484		}
485
486		int
#	Line 291 | Line 497 | cmdline_parser_file_save(const char *filename, struct
497		return EXIT_FAILURE;
498		}
499
500	<	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	<
500	>	i = cmdline_parser_dump(outfile, args_info);
501		fclose (outfile);
502
445	–	i = EXIT_SUCCESS;
503		return i;
504		}
505
#	Line 452 | Line 509 | cmdline_parser_free (struct gengetopt_args_info *args_
509		cmdline_parser_release (args_info);
510		}
511
512	<
456	<	/* gengetopt_strdup() */
457	<	/* strdup.c replacement of strdup, which is not standard */
512	>	/** @brief replacement of strdup, which is not standard */
513		char *
514		gengetopt_strdup (const char *s)
515		{
#	Line 470 | Line 525 | static void
525		}
526
527		static void
473	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
474	–
475	–	static void
528		reset_group_staticProps(struct gengetopt_args_info *args_info)
529		{
530		if (! args_info->staticProps_group_counter)
531		return;
532
533	+	args_info->bo_given = 0 ;
534	+	args_info->bor_given = 0 ;
535	+	args_info->bad_given = 0 ;
536	+	args_info->count_given = 0 ;
537		args_info->gofr_given = 0 ;
538	+	args_info->gofz_given = 0 ;
539		args_info->r_theta_given = 0 ;
540		args_info->r_omega_given = 0 ;
541	+	args_info->r_z_given = 0 ;
542		args_info->theta_omega_given = 0 ;
543		args_info->gxyz_given = 0 ;
544	+	args_info->twodgofr_given = 0 ;
545		args_info->p2_given = 0 ;
546	+	args_info->rp2_given = 0 ;
547		args_info->scd_given = 0 ;
548		args_info->density_given = 0 ;
549		args_info->slab_density_given = 0 ;
550	+	args_info->p_angle_given = 0 ;
551		args_info->hxy_given = 0 ;
552	+	args_info->rho_r_given = 0 ;
553	+	args_info->hullvol_given = 0 ;
554
555		args_info->staticProps_group_counter = 0;
556		}
#	Line 499 | Line 562 | int
562		}
563
564		int
565	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
566	+	struct cmdline_parser_params *params)
567	+	{
568	+	int result;
569	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
570	+
571	+	if (result == EXIT_FAILURE)
572	+	{
573	+	cmdline_parser_free (args_info);
574	+	exit (EXIT_FAILURE);
575	+	}
576	+
577	+	return result;
578	+	}
579	+
580	+	int
581		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
582		{
583		int result;
584	+	struct cmdline_parser_params params;
585	+
586	+	params.override = override;
587	+	params.initialize = initialize;
588	+	params.check_required = check_required;
589	+	params.check_ambiguity = 0;
590	+	params.print_errors = 1;
591
592	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
592	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
593
594		if (result == EXIT_FAILURE)
595		{
#	Line 536 | Line 622 | cmdline_parser_required2 (struct gengetopt_args_info *
622		{
623		int error = 0;
624
625	+	/* checks for required options */
626		if (! args_info->input_given)
627		{
628		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
629		error = 1;
630		}
631	+
632		if (args_info->staticProps_group_counter == 0)
633		{
634		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 636 | cmdline_parser_required2 (struct gengetopt_args_info *
636		}
637
638
639	+	/* checks for dependences among options */
640	+
641		return error;
642		}
643
644	+
645	+	static char *package_name = 0;
646	+
647	+	/**
648	+	* @brief updates an option
649	+	* @param field the generic pointer to the field to update
650	+	* @param orig_field the pointer to the orig field
651	+	* @param field_given the pointer to the number of occurrence of this option
652	+	* @param prev_given the pointer to the number of occurrence already seen
653	+	* @param value the argument for this option (if null no arg was specified)
654	+	* @param possible_values the possible values for this option (if specified)
655	+	* @param default_value the default value (in case the option only accepts fixed values)
656	+	* @param arg_type the type of this option
657	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
658	+	* @param override @see cmdline_parser_params.override
659	+	* @param no_free whether to free a possible previous value
660	+	* @param multiple_option whether this is a multiple option
661	+	* @param long_opt the corresponding long option
662	+	* @param short_opt the corresponding short option (or '-' if none)
663	+	* @param additional_error possible further error specification
664	+	*/
665	+	static
666	+	int update_arg(void *field, char **orig_field,
667	+	unsigned int *field_given, unsigned int *prev_given,
668	+	char *value, char *possible_values[], const char *default_value,
669	+	cmdline_parser_arg_type arg_type,
670	+	int check_ambiguity, int override,
671	+	int no_free, int multiple_option,
672	+	const char *long_opt, char short_opt,
673	+	const char *additional_error)
674	+	{
675	+	char *stop_char = 0;
676	+	const char *val = value;
677	+	int found;
678	+	char **string_field;
679	+
680	+	stop_char = 0;
681	+	found = 0;
682	+
683	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
684	+	{
685	+	if (short_opt != '-')
686	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
687	+	package_name, long_opt, short_opt,
688	+	(additional_error ? additional_error : ""));
689	+	else
690	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
691	+	package_name, long_opt,
692	+	(additional_error ? additional_error : ""));
693	+	return 1; /* failure */
694	+	}
695	+
696	+
697	+	if (field_given && *field_given && ! override)
698	+	return 0;
699	+	if (prev_given)
700	+	(*prev_given)++;
701	+	if (field_given)
702	+	(*field_given)++;
703	+	if (possible_values)
704	+	val = possible_values[found];
705	+
706	+	switch(arg_type) {
707	+	case ARG_INT:
708	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
709	+	break;
710	+	case ARG_DOUBLE:
711	+	if (val) *((double *)field) = strtod (val, &stop_char);
712	+	break;
713	+	case ARG_STRING:
714	+	if (val) {
715	+	string_field = (char **)field;
716	+	if (!no_free && *string_field)
717	+	free (*string_field); /* free previous string */
718	+	*string_field = gengetopt_strdup (val);
719	+	}
720	+	break;
721	+	default:
722	+	break;
723	+	};
724	+
725	+	/* check numeric conversion */
726	+	switch(arg_type) {
727	+	case ARG_INT:
728	+	case ARG_DOUBLE:
729	+	if (val && !(stop_char && *stop_char == '\0')) {
730	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
731	+	return 1; /* failure */
732	+	}
733	+	break;
734	+	default:
735	+	;
736	+	};
737	+
738	+	/* store the original value */
739	+	switch(arg_type) {
740	+	case ARG_NO:
741	+	break;
742	+	default:
743	+	if (value && orig_field) {
744	+	if (no_free) {
745	+	*orig_field = value;
746	+	} else {
747	+	if (*orig_field)
748	+	free (*orig_field); /* free previous string */
749	+	*orig_field = gengetopt_strdup (value);
750	+	}
751	+	}
752	+	};
753	+
754	+	return 0; /* OK */
755	+	}
756	+
757	+
758		int
759	<	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)
759	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
760	>	struct cmdline_parser_params *params, const char *additional_error)
761		{
762		int c;        /* Character of the parsed option.  */
763
764		int error = 0;
765		struct gengetopt_args_info local_args_info;
766	+
767	+	int override;
768	+	int initialize;
769	+	int check_required;
770	+	int check_ambiguity;
771	+
772	+	package_name = argv[0];
773	+
774	+	override = params->override;
775	+	initialize = params->initialize;
776	+	check_required = params->check_required;
777	+	check_ambiguity = params->check_ambiguity;
778
779		if (initialize)
780		cmdline_parser_init (args_info);
#	Line 566 | Line 783 | cmdline_parser_internal (int argc, char * const *argv,
783
784		optarg = 0;
785		optind = 0;
786	<	opterr = 1;
786	>	opterr = params->print_errors;
787		optopt = '?';
788
789		while (1)
790		{
791		int option_index = 0;
575	–	char *stop_char;
792
793		static struct option long_options[] = {
794		{ "help",       0, NULL, 'h' },
#	Line 580 | Line 796 | cmdline_parser_internal (int argc, char * const *argv,
796		{ "input",      1, NULL, 'i' },
797		{ "output",     1, NULL, 'o' },
798		{ "step",       1, NULL, 'n' },
799	<	{ "nrbins",     1, NULL, 'r' },
799	>	{ "nbins",      1, NULL, 'b' },
800		{ "nbins_x",    1, NULL, 'x' },
801		{ "nbins_y",    1, NULL, 'y' },
802	+	{ "nbins_z",    1, NULL, 0 },
803		{ "nanglebins", 1, NULL, 'a' },
804	<	{ "length",     1, NULL, 'l' },
804	>	{ "rcut",       1, NULL, 'c' },
805	>	{ "dz", 1, NULL, 0 },
806	>	{ "length",     1, NULL, 0 },
807	>	{ "zlength",    1, NULL, 0 },
808		{ "zoffset",    1, NULL, 'z' },
809		{ "sele1",      1, NULL, 0 },
810		{ "sele2",      1, NULL, 0 },
811		{ "sele3",      1, NULL, 0 },
812		{ "refsele",    1, NULL, 0 },
813	+	{ "comsele",    1, NULL, 0 },
814		{ "molname",    1, NULL, 0 },
815		{ "begin",      1, NULL, 0 },
816		{ "end",        1, NULL, 0 },
817	<	{ "gofr",       0, NULL, 0 },
817	>	{ "radius",     1, NULL, 0 },
818	>	{ "bo", 0, NULL, 0 },
819	>	{ "bor",        0, NULL, 0 },
820	>	{ "bad",        0, NULL, 0 },
821	>	{ "count",      0, NULL, 0 },
822	>	{ "gofr",       0, NULL, 'g' },
823	>	{ "gofz",       0, NULL, 0 },
824		{ "r_theta",    0, NULL, 0 },
825		{ "r_omega",    0, NULL, 0 },
826	+	{ "r_z",        0, NULL, 0 },
827		{ "theta_omega",        0, NULL, 0 },
828		{ "gxyz",       0, NULL, 0 },
829	<	{ "p2", 0, NULL, 0 },
830	<	{ "scd",        0, NULL, 0 },
831	<	{ "density",    0, NULL, 0 },
829	>	{ "twodgofr",   0, NULL, 0 },
830	>	{ "p2", 0, NULL, 'p' },
831	>	{ "rp2",        0, NULL, 0 },
832	>	{ "scd",        0, NULL, 's' },
833	>	{ "density",    0, NULL, 'd' },
834		{ "slab_density",       0, NULL, 0 },
835	+	{ "p_angle",    0, NULL, 0 },
836		{ "hxy",        0, NULL, 0 },
837	+	{ "rho_r",      0, NULL, 0 },
838	+	{ "hullvol",    0, NULL, 0 },
839		{ NULL, 0, NULL, 0 }
840		};
841
842	<	stop_char = 0;
610	<	c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index);
842	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
843
844		if (c == -1) break;       /* Exit from `while (1)' loop.  */
845
#	Line 624 | Line 856 | cmdline_parser_internal (int argc, char * const *argv,
856		exit (EXIT_SUCCESS);
857
858		case 'i':       /* input dump file.  */
859	<	if (local_args_info.input_given)
860	<	{
861	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
862	<	goto failure;
863	<	}
864	<	if (args_info->input_given && ! override)
865	<	continue;
866	<	local_args_info.input_given = 1;
867	<	args_info->input_given = 1;
868	<	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);
859	>
860	>
861	>	if (update_arg( (void *)&(args_info->input_arg),
862	>	&(args_info->input_orig), &(args_info->input_given),
863	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
864	>	check_ambiguity, override, 0, 0,
865	>	"input", 'i',
866	>	additional_error))
867	>	goto failure;
868	>
869		break;
643	–
870		case 'o':       /* output file name.  */
871	<	if (local_args_info.output_given)
872	<	{
873	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
874	<	goto failure;
875	<	}
876	<	if (args_info->output_given && ! override)
877	<	continue;
878	<	local_args_info.output_given = 1;
879	<	args_info->output_given = 1;
880	<	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);
871	>
872	>
873	>	if (update_arg( (void *)&(args_info->output_arg),
874	>	&(args_info->output_orig), &(args_info->output_given),
875	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
876	>	check_ambiguity, override, 0, 0,
877	>	"output", 'o',
878	>	additional_error))
879	>	goto failure;
880	>
881		break;
661	–
882		case 'n':       /* process every n frame.  */
883	<	if (local_args_info.step_given)
884	<	{
885	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
886	<	goto failure;
887	<	}
888	<	if (args_info->step_given && ! override)
889	<	continue;
890	<	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);
883	>
884	>
885	>	if (update_arg( (void *)&(args_info->step_arg),
886	>	&(args_info->step_orig), &(args_info->step_given),
887	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
888	>	check_ambiguity, override, 0, 0,
889	>	"step", 'n',
890	>	additional_error))
891		goto failure;
892	<	}
677	<	if (args_info->step_orig)
678	<	free (args_info->step_orig); /* free previous string */
679	<	args_info->step_orig = gengetopt_strdup (optarg);
892	>
893		break;
894	<
895	<	case 'r':       /* number of bins for distance.  */
896	<	if (local_args_info.nrbins_given)
897	<	{
898	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
899	<	goto failure;
900	<	}
901	<	if (args_info->nrbins_given && ! override)
902	<	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);
894	>	case 'b':       /* number of bins (general purpose).  */
895	>
896	>
897	>	if (update_arg( (void *)&(args_info->nbins_arg),
898	>	&(args_info->nbins_orig), &(args_info->nbins_given),
899	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
900	>	check_ambiguity, override, 0, 0,
901	>	"nbins", 'b',
902	>	additional_error))
903		goto failure;
904	<	}
697	<	if (args_info->nrbins_orig)
698	<	free (args_info->nrbins_orig); /* free previous string */
699	<	args_info->nrbins_orig = gengetopt_strdup (optarg);
904	>
905		break;
701	–
906		case 'x':       /* number of bins in x axis.  */
907	<	if (local_args_info.nbins_x_given)
908	<	{
909	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
910	<	goto failure;
911	<	}
912	<	if (args_info->nbins_x_given && ! override)
913	<	continue;
914	<	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);
907	>
908	>
909	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
910	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
911	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
912	>	check_ambiguity, override, 0, 0,
913	>	"nbins_x", 'x',
914	>	additional_error))
915		goto failure;
916	<	}
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);
916	>
917		break;
721	–
918		case 'y':       /* number of bins in y axis.  */
919	<	if (local_args_info.nbins_y_given)
920	<	{
921	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
922	<	goto failure;
923	<	}
924	<	if (args_info->nbins_y_given && ! override)
925	<	continue;
926	<	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);
919	>
920	>
921	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
922	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
923	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
924	>	check_ambiguity, override, 0, 0,
925	>	"nbins_y", 'y',
926	>	additional_error))
927		goto failure;
928	<	}
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);
928	>
929		break;
741	–
930		case 'a':       /* number of bins for cos(angle).  */
931	<	if (local_args_info.nanglebins_given)
932	<	{
933	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
934	<	goto failure;
935	<	}
936	<	if (args_info->nanglebins_given && ! override)
937	<	continue;
938	<	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);
931	>
932	>
933	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
934	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
935	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
936	>	check_ambiguity, override, 0, 0,
937	>	"nanglebins", 'a',
938	>	additional_error))
939		goto failure;
940	<	}
757	<	if (args_info->nanglebins_orig)
758	<	free (args_info->nanglebins_orig); /* free previous string */
759	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
940	>
941		break;
942	<
943	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
944	<	if (local_args_info.length_given)
945	<	{
946	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
947	<	goto failure;
948	<	}
949	<	if (args_info->length_given && ! override)
950	<	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);
942	>	case 'c':       /* cutoff radius (rcut).  */
943	>
944	>
945	>	if (update_arg( (void *)&(args_info->rcut_arg),
946	>	&(args_info->rcut_orig), &(args_info->rcut_given),
947	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
948	>	check_ambiguity, override, 0, 0,
949	>	"rcut", 'c',
950	>	additional_error))
951		goto failure;
952	<	}
777	<	if (args_info->length_orig)
778	<	free (args_info->length_orig); /* free previous string */
779	<	args_info->length_orig = gengetopt_strdup (optarg);
952	>
953		break;
781	–
954		case 'z':       /* Where to set the zero for the slab_density calculation.  */
955	<	if (local_args_info.zoffset_given)
956	<	{
957	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
958	<	goto failure;
959	<	}
960	<	if (args_info->zoffset_given && ! override)
961	<	continue;
962	<	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);
955	>
956	>
957	>	if (update_arg( (void *)&(args_info->zoffset_arg),
958	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
959	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
960	>	check_ambiguity, override, 0, 0,
961	>	"zoffset", 'z',
962	>	additional_error))
963		goto failure;
964	<	}
797	<	if (args_info->zoffset_orig)
798	<	free (args_info->zoffset_orig); /* free previous string */
799	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
964	>
965		break;
966	<
966	>	case 'g':       /* g(r).  */
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->gofr_given),
974	>	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
975	>	check_ambiguity, override, 0, 0,
976	>	"gofr", 'g',
977	>	additional_error))
978	>	goto failure;
979	>
980	>	break;
981	>	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
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->p2_given),
989	>	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
990	>	check_ambiguity, override, 0, 0,
991	>	"p2", 'p',
992	>	additional_error))
993	>	goto failure;
994	>
995	>	break;
996	>	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
997	>
998	>	if (args_info->staticProps_group_counter && override)
999	>	reset_group_staticProps (args_info);
1000	>	args_info->staticProps_group_counter += 1;
1001	>
1002	>	if (update_arg( 0 ,
1003	>	0 , &(args_info->scd_given),
1004	>	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1005	>	check_ambiguity, override, 0, 0,
1006	>	"scd", 's',
1007	>	additional_error))
1008	>	goto failure;
1009	>
1010	>	break;
1011	>	case 'd':       /* density plot.  */
1012	>
1013	>	if (args_info->staticProps_group_counter && override)
1014	>	reset_group_staticProps (args_info);
1015	>	args_info->staticProps_group_counter += 1;
1016	>
1017	>	if (update_arg( 0 ,
1018	>	0 , &(args_info->density_given),
1019	>	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1020	>	check_ambiguity, override, 0, 0,
1021	>	"density", 'd',
1022	>	additional_error))
1023	>	goto failure;
1024	>
1025	>	break;
1026
1027		case 0: /* Long option with no short option */
1028	+	/* number of bins in z axis.  */
1029	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1030	+	{
1031	+
1032	+
1033	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1034	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1035	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1036	+	check_ambiguity, override, 0, 0,
1037	+	"nbins_z", '-',
1038	+	additional_error))
1039	+	goto failure;
1040	+
1041	+	}
1042	+	/* slab width (dz).  */
1043	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1044	+	{
1045	+
1046	+
1047	+	if (update_arg( (void *)&(args_info->dz_arg),
1048	+	&(args_info->dz_orig), &(args_info->dz_given),
1049	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1050	+	check_ambiguity, override, 0, 0,
1051	+	"dz", '-',
1052	+	additional_error))
1053	+	goto failure;
1054	+
1055	+	}
1056	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1057	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1058	+	{
1059	+
1060	+
1061	+	if (update_arg( (void *)&(args_info->length_arg),
1062	+	&(args_info->length_orig), &(args_info->length_given),
1063	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1064	+	check_ambiguity, override, 0, 0,
1065	+	"length", '-',
1066	+	additional_error))
1067	+	goto failure;
1068	+
1069	+	}
1070	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1071	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1072	+	{
1073	+
1074	+
1075	+	if (update_arg( (void *)&(args_info->zlength_arg),
1076	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1077	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1078	+	check_ambiguity, override, 0, 0,
1079	+	"zlength", '-',
1080	+	additional_error))
1081	+	goto failure;
1082	+
1083	+	}
1084		/* select the first stuntdouble set.  */
1085	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1085	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1086		{
1087	<	if (local_args_info.sele1_given)
1088	<	{
1089	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1090	<	goto failure;
1091	<	}
1092	<	if (args_info->sele1_given && ! override)
1093	<	continue;
1094	<	local_args_info.sele1_given = 1;
1095	<	args_info->sele1_given = 1;
1096	<	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);
1087	>
1088	>
1089	>	if (update_arg( (void *)&(args_info->sele1_arg),
1090	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1091	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1092	>	check_ambiguity, override, 0, 0,
1093	>	"sele1", '-',
1094	>	additional_error))
1095	>	goto failure;
1096	>
1097		}
1098		/* select the second stuntdouble set.  */
1099		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1100		{
1101	<	if (local_args_info.sele2_given)
1102	<	{
1103	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1104	<	goto failure;
1105	<	}
1106	<	if (args_info->sele2_given && ! override)
1107	<	continue;
1108	<	local_args_info.sele2_given = 1;
1109	<	args_info->sele2_given = 1;
1110	<	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);
1101	>
1102	>
1103	>	if (update_arg( (void *)&(args_info->sele2_arg),
1104	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1105	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1106	>	check_ambiguity, override, 0, 0,
1107	>	"sele2", '-',
1108	>	additional_error))
1109	>	goto failure;
1110	>
1111		}
1112		/* select the third stuntdouble set.  */
1113		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1114		{
1115	<	if (local_args_info.sele3_given)
1116	<	{
1117	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1118	<	goto failure;
1119	<	}
1120	<	if (args_info->sele3_given && ! override)
1121	<	continue;
1122	<	local_args_info.sele3_given = 1;
1123	<	args_info->sele3_given = 1;
1124	<	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);
1115	>
1116	>
1117	>	if (update_arg( (void *)&(args_info->sele3_arg),
1118	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1119	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1120	>	check_ambiguity, override, 0, 0,
1121	>	"sele3", '-',
1122	>	additional_error))
1123	>	goto failure;
1124	>
1125		}
1126		/* select reference (use and only use with --gxyz).  */
1127		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1128		{
1129	<	if (local_args_info.refsele_given)
1130	<	{
1131	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1132	<	goto failure;
1133	<	}
1134	<	if (args_info->refsele_given && ! override)
1135	<	continue;
1136	<	local_args_info.refsele_given = 1;
1137	<	args_info->refsele_given = 1;
1138	<	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);
1129	>
1130	>
1131	>	if (update_arg( (void *)&(args_info->refsele_arg),
1132	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1133	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1134	>	check_ambiguity, override, 0, 0,
1135	>	"refsele", '-',
1136	>	additional_error))
1137	>	goto failure;
1138	>
1139		}
1140	+	/* select stunt doubles for center-of-mass reference point.  */
1141	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1142	+	{
1143	+
1144	+
1145	+	if (update_arg( (void *)&(args_info->comsele_arg),
1146	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1147	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1148	+	check_ambiguity, override, 0, 0,
1149	+	"comsele", '-',
1150	+	additional_error))
1151	+	goto failure;
1152	+
1153	+	}
1154		/* molecule name.  */
1155		else if (strcmp (long_options[option_index].name, "molname") == 0)
1156		{
1157	<	if (local_args_info.molname_given)
1158	<	{
1159	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1160	<	goto failure;
1161	<	}
1162	<	if (args_info->molname_given && ! override)
1163	<	continue;
1164	<	local_args_info.molname_given = 1;
1165	<	args_info->molname_given = 1;
1166	<	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);
1157	>
1158	>
1159	>	if (update_arg( (void *)&(args_info->molname_arg),
1160	>	&(args_info->molname_orig), &(args_info->molname_given),
1161	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1162	>	check_ambiguity, override, 0, 0,
1163	>	"molname", '-',
1164	>	additional_error))
1165	>	goto failure;
1166	>
1167		}
1168	<	/* begin interanl index.  */
1168	>	/* begin internal index.  */
1169		else if (strcmp (long_options[option_index].name, "begin") == 0)
1170		{
1171	<	if (local_args_info.begin_given)
1172	<	{
1173	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1174	<	goto failure;
1175	<	}
1176	<	if (args_info->begin_given && ! override)
1177	<	continue;
1178	<	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);
1171	>
1172	>
1173	>	if (update_arg( (void *)&(args_info->begin_arg),
1174	>	&(args_info->begin_orig), &(args_info->begin_given),
1175	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1176	>	check_ambiguity, override, 0, 0,
1177	>	"begin", '-',
1178	>	additional_error))
1179		goto failure;
1180	<	}
916	<	if (args_info->begin_orig)
917	<	free (args_info->begin_orig); /* free previous string */
918	<	args_info->begin_orig = gengetopt_strdup (optarg);
1180	>
1181		}
1182		/* end internal index.  */
1183		else if (strcmp (long_options[option_index].name, "end") == 0)
1184		{
1185	<	if (local_args_info.end_given)
1186	<	{
1187	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1188	<	goto failure;
1189	<	}
1190	<	if (args_info->end_given && ! override)
1191	<	continue;
1192	<	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);
1185	>
1186	>
1187	>	if (update_arg( (void *)&(args_info->end_arg),
1188	>	&(args_info->end_orig), &(args_info->end_given),
1189	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1190	>	check_ambiguity, override, 0, 0,
1191	>	"end", '-',
1192	>	additional_error))
1193		goto failure;
1194	<	}
937	<	if (args_info->end_orig)
938	<	free (args_info->end_orig); /* free previous string */
939	<	args_info->end_orig = gengetopt_strdup (optarg);
1194	>
1195		}
1196	<	/* g(r).  */
1197	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1196	>	/* nanoparticle radius.  */
1197	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1198		{
1199	<	if (local_args_info.gofr_given)
1200	<	{
1201	<	fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1202	<	goto failure;
1203	<	}
1204	<	if (args_info->gofr_given && ! override)
1205	<	continue;
1206	<	local_args_info.gofr_given = 1;
1207	<	args_info->gofr_given = 1;
1199	>
1200	>
1201	>	if (update_arg( (void *)&(args_info->radius_arg),
1202	>	&(args_info->radius_orig), &(args_info->radius_given),
1203	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1204	>	check_ambiguity, override, 0, 0,
1205	>	"radius", '-',
1206	>	additional_error))
1207	>	goto failure;
1208	>
1209	>	}
1210	>	/* bond order parameter (--rcut must be specified).  */
1211	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1212	>	{
1213	>
1214		if (args_info->staticProps_group_counter && override)
1215		reset_group_staticProps (args_info);
1216		args_info->staticProps_group_counter += 1;
1217	<	break;
1217	>
1218	>	if (update_arg( 0 ,
1219	>	0 , &(args_info->bo_given),
1220	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1221	>	check_ambiguity, override, 0, 0,
1222	>	"bo", '-',
1223	>	additional_error))
1224	>	goto failure;
1225	>
1226		}
1227	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1228	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1229	+	{
1230	+
1231	+	if (args_info->staticProps_group_counter && override)
1232	+	reset_group_staticProps (args_info);
1233	+	args_info->staticProps_group_counter += 1;
1234	+
1235	+	if (update_arg( 0 ,
1236	+	0 , &(args_info->bor_given),
1237	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1238	+	check_ambiguity, override, 0, 0,
1239	+	"bor", '-',
1240	+	additional_error))
1241	+	goto failure;
1242	+
1243	+	}
1244	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1245	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1246	+	{
1247	+
1248	+	if (args_info->staticProps_group_counter && override)
1249	+	reset_group_staticProps (args_info);
1250	+	args_info->staticProps_group_counter += 1;
1251	+
1252	+	if (update_arg( 0 ,
1253	+	0 , &(args_info->bad_given),
1254	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1255	+	check_ambiguity, override, 0, 0,
1256	+	"bad", '-',
1257	+	additional_error))
1258	+	goto failure;
1259	+
1260	+	}
1261	+	/* count of molecules matching selection criteria (and associated statistics).  */
1262	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1263	+	{
1264	+
1265	+	if (args_info->staticProps_group_counter && override)
1266	+	reset_group_staticProps (args_info);
1267	+	args_info->staticProps_group_counter += 1;
1268	+
1269	+	if (update_arg( 0 ,
1270	+	0 , &(args_info->count_given),
1271	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1272	+	check_ambiguity, override, 0, 0,
1273	+	"count", '-',
1274	+	additional_error))
1275	+	goto failure;
1276	+
1277	+	}
1278	+	/* g(z).  */
1279	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1280	+	{
1281	+
1282	+	if (args_info->staticProps_group_counter && override)
1283	+	reset_group_staticProps (args_info);
1284	+	args_info->staticProps_group_counter += 1;
1285	+
1286	+	if (update_arg( 0 ,
1287	+	0 , &(args_info->gofz_given),
1288	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1289	+	check_ambiguity, override, 0, 0,
1290	+	"gofz", '-',
1291	+	additional_error))
1292	+	goto failure;
1293	+
1294	+	}
1295		/* g(r, cos(theta)).  */
1296		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1297		{
1298	<	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;
1298	>
1299		if (args_info->staticProps_group_counter && override)
1300		reset_group_staticProps (args_info);
1301		args_info->staticProps_group_counter += 1;
1302	<	break;
1302	>
1303	>	if (update_arg( 0 ,
1304	>	0 , &(args_info->r_theta_given),
1305	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1306	>	check_ambiguity, override, 0, 0,
1307	>	"r_theta", '-',
1308	>	additional_error))
1309	>	goto failure;
1310	>
1311		}
1312		/* g(r, cos(omega)).  */
1313		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1314		{
1315	<	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;
1315	>
1316		if (args_info->staticProps_group_counter && override)
1317		reset_group_staticProps (args_info);
1318		args_info->staticProps_group_counter += 1;
1319	<	break;
1319	>
1320	>	if (update_arg( 0 ,
1321	>	0 , &(args_info->r_omega_given),
1322	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1323	>	check_ambiguity, override, 0, 0,
1324	>	"r_omega", '-',
1325	>	additional_error))
1326	>	goto failure;
1327	>
1328		}
1329	+	/* g(r, z).  */
1330	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1331	+	{
1332	+
1333	+	if (args_info->staticProps_group_counter && override)
1334	+	reset_group_staticProps (args_info);
1335	+	args_info->staticProps_group_counter += 1;
1336	+
1337	+	if (update_arg( 0 ,
1338	+	0 , &(args_info->r_z_given),
1339	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1340	+	check_ambiguity, override, 0, 0,
1341	+	"r_z", '-',
1342	+	additional_error))
1343	+	goto failure;
1344	+
1345	+	}
1346		/* g(cos(theta), cos(omega)).  */
1347		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1348		{
1349	<	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;
1349	>
1350		if (args_info->staticProps_group_counter && override)
1351		reset_group_staticProps (args_info);
1352		args_info->staticProps_group_counter += 1;
1353	<	break;
1353	>
1354	>	if (update_arg( 0 ,
1355	>	0 , &(args_info->theta_omega_given),
1356	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1357	>	check_ambiguity, override, 0, 0,
1358	>	"theta_omega", '-',
1359	>	additional_error))
1360	>	goto failure;
1361	>
1362		}
1363		/* g(x, y, z).  */
1364		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1365		{
1366	<	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;
1366	>
1367		if (args_info->staticProps_group_counter && override)
1368		reset_group_staticProps (args_info);
1369		args_info->staticProps_group_counter += 1;
1370	<	break;
1370	>
1371	>	if (update_arg( 0 ,
1372	>	0 , &(args_info->gxyz_given),
1373	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1374	>	check_ambiguity, override, 0, 0,
1375	>	"gxyz", '-',
1376	>	additional_error))
1377	>	goto failure;
1378	>
1379		}
1380	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1381	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1380	>	/* 2D g(r) (Slab width --dz must be specified).  */
1381	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1382		{
1383	<	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;
1383	>
1384		if (args_info->staticProps_group_counter && override)
1385		reset_group_staticProps (args_info);
1386		args_info->staticProps_group_counter += 1;
1387	<	break;
1387	>
1388	>	if (update_arg( 0 ,
1389	>	0 , &(args_info->twodgofr_given),
1390	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1391	>	check_ambiguity, override, 0, 0,
1392	>	"twodgofr", '-',
1393	>	additional_error))
1394	>	goto failure;
1395	>
1396		}
1397	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1398	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1397	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1398	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1399		{
1400	<	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;
1400	>
1401		if (args_info->staticProps_group_counter && override)
1402		reset_group_staticProps (args_info);
1403		args_info->staticProps_group_counter += 1;
1404	<	break;
1404	>
1405	>	if (update_arg( 0 ,
1406	>	0 , &(args_info->rp2_given),
1407	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1408	>	check_ambiguity, override, 0, 0,
1409	>	"rp2", '-',
1410	>	additional_error))
1411	>	goto failure;
1412	>
1413		}
1414	<	/* density plot (--sele1 must be specified).  */
1415	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1414	>	/* slab density.  */
1415	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1416		{
1417	<	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;
1417	>
1418		if (args_info->staticProps_group_counter && override)
1419		reset_group_staticProps (args_info);
1420		args_info->staticProps_group_counter += 1;
1421	<	break;
1421	>
1422	>	if (update_arg( 0 ,
1423	>	0 , &(args_info->slab_density_given),
1424	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1425	>	check_ambiguity, override, 0, 0,
1426	>	"slab_density", '-',
1427	>	additional_error))
1428	>	goto failure;
1429	>
1430		}
1431	<	/* slab density (--sele1 must be specified).  */
1432	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1431	>	/* p(cos(theta)).  */
1432	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1433		{
1434	<	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;
1434	>
1435		if (args_info->staticProps_group_counter && override)
1436		reset_group_staticProps (args_info);
1437		args_info->staticProps_group_counter += 1;
1438	<	break;
1438	>
1439	>	if (update_arg( 0 ,
1440	>	0 , &(args_info->p_angle_given),
1441	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1442	>	check_ambiguity, override, 0, 0,
1443	>	"p_angle", '-',
1444	>	additional_error))
1445	>	goto failure;
1446	>
1447		}
1448	<	/* hxy (--sele1 must be specified).  */
1448	>	/* hxy.  */
1449		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1450		{
1451	<	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;
1451	>
1452		if (args_info->staticProps_group_counter && override)
1453		reset_group_staticProps (args_info);
1454		args_info->staticProps_group_counter += 1;
1455	<	break;
1455	>
1456	>	if (update_arg( 0 ,
1457	>	0 , &(args_info->hxy_given),
1458	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1459	>	check_ambiguity, override, 0, 0,
1460	>	"hxy", '-',
1461	>	additional_error))
1462	>	goto failure;
1463	>
1464		}
1465	+	/* rho of R.  */
1466	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1467	+	{
1468
1469	+	if (args_info->staticProps_group_counter && override)
1470	+	reset_group_staticProps (args_info);
1471	+	args_info->staticProps_group_counter += 1;
1472	+
1473	+	if (update_arg( 0 ,
1474	+	0 , &(args_info->rho_r_given),
1475	+	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1476	+	check_ambiguity, override, 0, 0,
1477	+	"rho_r", '-',
1478	+	additional_error))
1479	+	goto failure;
1480	+
1481	+	}
1482	+	/* hull volume of nanoparticle.  */
1483	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1484	+	{
1485	+
1486	+	if (args_info->staticProps_group_counter && override)
1487	+	reset_group_staticProps (args_info);
1488	+	args_info->staticProps_group_counter += 1;
1489	+
1490	+	if (update_arg( 0 ,
1491	+	0 , &(args_info->hullvol_given),
1492	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1493	+	check_ambiguity, override, 0, 0,
1494	+	"hullvol", '-',
1495	+	additional_error))
1496	+	goto failure;
1497	+
1498	+	}
1499	+
1500		break;
1501		case '?':       /* Invalid option.  */
1502		/* `getopt_long' already printed an error message.  */
#	Line 1138 | Line 1526 | cmdline_parser_internal (int argc, char * const *argv,
1526		if ( error )
1527		return (EXIT_FAILURE);
1528
1529	+	if (optind < argc)
1530	+	{
1531	+	int i = 0 ;
1532	+	int found_prog_name = 0;
1533	+	/* whether program name, i.e., argv[0], is in the remaining args
1534	+	(this may happen with some implementations of getopt,
1535	+	but surely not with the one included by gengetopt) */
1536	+
1537	+	i = optind;
1538	+	while (i < argc)
1539	+	if (argv[i++] == argv[0]) {
1540	+	found_prog_name = 1;
1541	+	break;
1542	+	}
1543	+	i = 0;
1544	+
1545	+	args_info->inputs_num = argc - optind - found_prog_name;
1546	+	args_info->inputs =
1547	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1548	+	while (optind < argc)
1549	+	if (argv[optind++] != argv[0])
1550	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1551	+	}
1552	+
1553		return 0;
1554
1555		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 1513 by gezelter, Tue Oct 19 18:40:54 2010 UTC

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

Diff Legend

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+	Added lines
<	Changed lines
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