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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd
4	>	gengetopt -F StaticPropsCmd
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
8		we make no copyright claims on it.
9		*/
10
11	–
12	–	#include <stdio.h>
13	–	#include <stdlib.h>
14	–	#include <string.h>
15	–
11		/* If we use autoconf.  */
12		#ifdef HAVE_CONFIG_H
13		#include "config.h"
14		#endif
15
16	+	#include <stdio.h>
17	+	#include <stdlib.h>
18	+	#include <string.h>
19	+
20		#include "getopt.h"
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
41	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
43	+	"      --sele1=selection script  select the first stuntdouble set",
44	+	"      --sele2=selection script  select the second stuntdouble set",
45	+	"      --sele3=selection script  select the third stuntdouble set",
46	+	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
47	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
48	+	"      --molname=STRING          molecule name",
49	+	"      --begin=INT               begin internal index",
50	+	"      --end=INT                 end internal index",
51	+	"      --radius=DOUBLE           nanoparticle radius",
52	+	"\n Group: staticProps\n   an option of this group is required",
53	+	"      --bo                      bond order parameter (--rcut must be specified)",
54	+	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
55	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
56	+	"  -g, --gofr                    g(r)",
57	+	"      --gofz                    g(z)",
58	+	"      --r_theta                 g(r, cos(theta))",
59	+	"      --r_omega                 g(r, cos(omega))",
60	+	"      --theta_omega             g(cos(theta), cos(omega))",
61	+	"      --gxyz                    g(x, y, z)",
62	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
63	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
64	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
65	+	"  -d, --density                 density plot",
66	+	"      --slab_density            slab density",
67	+	"      --hxy                     hxy",
68	+	"      --rho_r                   rho of R",
69	+	"      --hullvol                 hull volume of nanoparticle",
70	+	0
71	+	};
72	+
73	+	typedef enum {ARG_NO
74	+	, ARG_STRING
75	+	, ARG_INT
76	+	, ARG_DOUBLE
77	+	} cmdline_parser_arg_type;
78	+
79	+	static
80	+	void clear_given (struct gengetopt_args_info *args_info);
81	+	static
82	+	void clear_args (struct gengetopt_args_info *args_info);
83	+
84	+	static int
85	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
86	+	struct cmdline_parser_params *params, const char *additional_error);
87	+
88	+	static int
89	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
90	+
91	+	static char *
92	+	gengetopt_strdup (const char *s);
93	+
94	+	static
95	+	void clear_given (struct gengetopt_args_info *args_info)
96	+	{
97	+	args_info->help_given = 0 ;
98	+	args_info->version_given = 0 ;
99	+	args_info->input_given = 0 ;
100	+	args_info->output_given = 0 ;
101	+	args_info->step_given = 0 ;
102	+	args_info->nbins_given = 0 ;
103	+	args_info->nbins_x_given = 0 ;
104	+	args_info->nbins_y_given = 0 ;
105	+	args_info->nanglebins_given = 0 ;
106	+	args_info->length_given = 0 ;
107	+	args_info->rcut_given = 0 ;
108	+	args_info->zoffset_given = 0 ;
109	+	args_info->sele1_given = 0 ;
110	+	args_info->sele2_given = 0 ;
111	+	args_info->sele3_given = 0 ;
112	+	args_info->refsele_given = 0 ;
113	+	args_info->comsele_given = 0 ;
114	+	args_info->molname_given = 0 ;
115	+	args_info->begin_given = 0 ;
116	+	args_info->end_given = 0 ;
117	+	args_info->radius_given = 0 ;
118	+	args_info->bo_given = 0 ;
119	+	args_info->bor_given = 0 ;
120	+	args_info->bad_given = 0 ;
121	+	args_info->gofr_given = 0 ;
122	+	args_info->gofz_given = 0 ;
123	+	args_info->r_theta_given = 0 ;
124	+	args_info->r_omega_given = 0 ;
125	+	args_info->theta_omega_given = 0 ;
126	+	args_info->gxyz_given = 0 ;
127	+	args_info->p2_given = 0 ;
128	+	args_info->rp2_given = 0 ;
129	+	args_info->scd_given = 0 ;
130	+	args_info->density_given = 0 ;
131	+	args_info->slab_density_given = 0 ;
132	+	args_info->hxy_given = 0 ;
133	+	args_info->rho_r_given = 0 ;
134	+	args_info->hullvol_given = 0 ;
135	+	args_info->staticProps_group_counter = 0 ;
136	+	}
137	+
138	+	static
139	+	void clear_args (struct gengetopt_args_info *args_info)
140	+	{
141	+	args_info->input_arg = NULL;
142	+	args_info->input_orig = NULL;
143	+	args_info->output_arg = NULL;
144	+	args_info->output_orig = NULL;
145	+	args_info->step_arg = 1;
146	+	args_info->step_orig = NULL;
147	+	args_info->nbins_arg = 100;
148	+	args_info->nbins_orig = NULL;
149	+	args_info->nbins_x_arg = 100;
150	+	args_info->nbins_x_orig = NULL;
151	+	args_info->nbins_y_arg = 100;
152	+	args_info->nbins_y_orig = NULL;
153	+	args_info->nanglebins_arg = 50;
154	+	args_info->nanglebins_orig = NULL;
155	+	args_info->length_orig = NULL;
156	+	args_info->rcut_orig = NULL;
157	+	args_info->zoffset_arg = 0;
158	+	args_info->zoffset_orig = NULL;
159	+	args_info->sele1_arg = NULL;
160	+	args_info->sele1_orig = NULL;
161	+	args_info->sele2_arg = NULL;
162	+	args_info->sele2_orig = NULL;
163	+	args_info->sele3_arg = NULL;
164	+	args_info->sele3_orig = NULL;
165	+	args_info->refsele_arg = NULL;
166	+	args_info->refsele_orig = NULL;
167	+	args_info->comsele_arg = NULL;
168	+	args_info->comsele_orig = NULL;
169	+	args_info->molname_arg = NULL;
170	+	args_info->molname_orig = NULL;
171	+	args_info->begin_orig = NULL;
172	+	args_info->end_orig = NULL;
173	+	args_info->radius_orig = NULL;
174	+
175	+	}
176	+
177	+	static
178	+	void init_args_info(struct gengetopt_args_info *args_info)
179	+	{
180	+
181	+
182	+	args_info->help_help = gengetopt_args_info_help[0] ;
183	+	args_info->version_help = gengetopt_args_info_help[1] ;
184	+	args_info->input_help = gengetopt_args_info_help[2] ;
185	+	args_info->output_help = gengetopt_args_info_help[3] ;
186	+	args_info->step_help = gengetopt_args_info_help[4] ;
187	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
188	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
189	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
190	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
191	+	args_info->length_help = gengetopt_args_info_help[9] ;
192	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
193	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
194	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
195	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
196	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
197	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
198	+	args_info->comsele_help = gengetopt_args_info_help[16] ;
199	+	args_info->molname_help = gengetopt_args_info_help[17] ;
200	+	args_info->begin_help = gengetopt_args_info_help[18] ;
201	+	args_info->end_help = gengetopt_args_info_help[19] ;
202	+	args_info->radius_help = gengetopt_args_info_help[20] ;
203	+	args_info->bo_help = gengetopt_args_info_help[22] ;
204	+	args_info->bor_help = gengetopt_args_info_help[23] ;
205	+	args_info->bad_help = gengetopt_args_info_help[24] ;
206	+	args_info->gofr_help = gengetopt_args_info_help[25] ;
207	+	args_info->gofz_help = gengetopt_args_info_help[26] ;
208	+	args_info->r_theta_help = gengetopt_args_info_help[27] ;
209	+	args_info->r_omega_help = gengetopt_args_info_help[28] ;
210	+	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
211	+	args_info->gxyz_help = gengetopt_args_info_help[30] ;
212	+	args_info->p2_help = gengetopt_args_info_help[31] ;
213	+	args_info->rp2_help = gengetopt_args_info_help[32] ;
214	+	args_info->scd_help = gengetopt_args_info_help[33] ;
215	+	args_info->density_help = gengetopt_args_info_help[34] ;
216	+	args_info->slab_density_help = gengetopt_args_info_help[35] ;
217	+	args_info->hxy_help = gengetopt_args_info_help[36] ;
218	+	args_info->rho_r_help = gengetopt_args_info_help[37] ;
219	+	args_info->hullvol_help = gengetopt_args_info_help[38] ;
220	+
221	+	}
222	+
223		void
224		cmdline_parser_print_version (void)
225		{
226		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
227		}
228
229	+	static void print_help_common(void) {
230	+	cmdline_parser_print_version ();
231	+
232	+	if (strlen(gengetopt_args_info_purpose) > 0)
233	+	printf("\n%s\n", gengetopt_args_info_purpose);
234	+
235	+	if (strlen(gengetopt_args_info_usage) > 0)
236	+	printf("\n%s\n", gengetopt_args_info_usage);
237	+
238	+	printf("\n");
239	+
240	+	if (strlen(gengetopt_args_info_description) > 0)
241	+	printf("%s\n", gengetopt_args_info_description);
242	+	}
243	+
244		void
245		cmdline_parser_print_help (void)
246		{
247	<	cmdline_parser_print_version ();
248	<	printf("\n"
249	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
250	<	printf("\n");
38	<	printf("  -h, --help                      Print help and exit\n");
39	<	printf("  -V, --version                   Print version and exit\n");
40	<	printf("  -i, --input=filename            input dump file\n");
41	<	printf("  -o, --output=filename           output file name\n");
42	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
43	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
44	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
45	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
46	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
47	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
48	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
49	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
50	<	printf("      --molname=STRING            molecule name\n");
51	<	printf("      --begin=INT                 begin interanl index\n");
52	<	printf("      --end=INT                   end internal index\n");
53	<	printf("\n");
54	<	printf(" Group: staticProps  an option of this group is required\n");
55	<	printf("      --gofr                      g(r)\n");
56	<	printf("      --r_theta                   g(r, cos(theta))\n");
57	<	printf("      --r_omega                   g(r, cos(omega))\n");
58	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
59	<	printf("      --gxyz                      g(x, y, z)\n");
60	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
61	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
62	<	printf("      --density                   density plot (--sele1 must be specified)\n");
247	>	int i = 0;
248	>	print_help_common();
249	>	while (gengetopt_args_info_help[i])
250	>	printf("%s\n", gengetopt_args_info_help[i++]);
251		}
252
253	+	void
254	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
255	+	{
256	+	clear_given (args_info);
257	+	clear_args (args_info);
258	+	init_args_info (args_info);
259	+	}
260
261	<	static char *gengetopt_strdup (const char *s);
261	>	void
262	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
263	>	{
264	>	if (params)
265	>	{
266	>	params->override = 0;
267	>	params->initialize = 1;
268	>	params->check_required = 1;
269	>	params->check_ambiguity = 0;
270	>	params->print_errors = 1;
271	>	}
272	>	}
273
274	<	/* gengetopt_strdup() */
275	<	/* strdup.c replacement of strdup, which is not standard */
274	>	struct cmdline_parser_params *
275	>	cmdline_parser_params_create(void)
276	>	{
277	>	struct cmdline_parser_params *params =
278	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
279	>	cmdline_parser_params_init(params);
280	>	return params;
281	>	}
282	>
283	>	static void
284	>	free_string_field (char **s)
285	>	{
286	>	if (*s)
287	>	{
288	>	free (*s);
289	>	*s = 0;
290	>	}
291	>	}
292	>
293	>
294	>	static void
295	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
296	>	{
297	>
298	>	free_string_field (&(args_info->input_arg));
299	>	free_string_field (&(args_info->input_orig));
300	>	free_string_field (&(args_info->output_arg));
301	>	free_string_field (&(args_info->output_orig));
302	>	free_string_field (&(args_info->step_orig));
303	>	free_string_field (&(args_info->nbins_orig));
304	>	free_string_field (&(args_info->nbins_x_orig));
305	>	free_string_field (&(args_info->nbins_y_orig));
306	>	free_string_field (&(args_info->nanglebins_orig));
307	>	free_string_field (&(args_info->length_orig));
308	>	free_string_field (&(args_info->rcut_orig));
309	>	free_string_field (&(args_info->zoffset_orig));
310	>	free_string_field (&(args_info->sele1_arg));
311	>	free_string_field (&(args_info->sele1_orig));
312	>	free_string_field (&(args_info->sele2_arg));
313	>	free_string_field (&(args_info->sele2_orig));
314	>	free_string_field (&(args_info->sele3_arg));
315	>	free_string_field (&(args_info->sele3_orig));
316	>	free_string_field (&(args_info->refsele_arg));
317	>	free_string_field (&(args_info->refsele_orig));
318	>	free_string_field (&(args_info->comsele_arg));
319	>	free_string_field (&(args_info->comsele_orig));
320	>	free_string_field (&(args_info->molname_arg));
321	>	free_string_field (&(args_info->molname_orig));
322	>	free_string_field (&(args_info->begin_orig));
323	>	free_string_field (&(args_info->end_orig));
324	>	free_string_field (&(args_info->radius_orig));
325	>
326	>
327	>
328	>	clear_given (args_info);
329	>	}
330	>
331	>
332	>	static void
333	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
334	>	{
335	>	if (arg) {
336	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
337	>	} else {
338	>	fprintf(outfile, "%s\n", opt);
339	>	}
340	>	}
341	>
342	>
343	>	int
344	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
345	>	{
346	>	int i = 0;
347	>
348	>	if (!outfile)
349	>	{
350	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
351	>	return EXIT_FAILURE;
352	>	}
353	>
354	>	if (args_info->help_given)
355	>	write_into_file(outfile, "help", 0, 0 );
356	>	if (args_info->version_given)
357	>	write_into_file(outfile, "version", 0, 0 );
358	>	if (args_info->input_given)
359	>	write_into_file(outfile, "input", args_info->input_orig, 0);
360	>	if (args_info->output_given)
361	>	write_into_file(outfile, "output", args_info->output_orig, 0);
362	>	if (args_info->step_given)
363	>	write_into_file(outfile, "step", args_info->step_orig, 0);
364	>	if (args_info->nbins_given)
365	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
366	>	if (args_info->nbins_x_given)
367	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
368	>	if (args_info->nbins_y_given)
369	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
370	>	if (args_info->nanglebins_given)
371	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
372	>	if (args_info->length_given)
373	>	write_into_file(outfile, "length", args_info->length_orig, 0);
374	>	if (args_info->rcut_given)
375	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
376	>	if (args_info->zoffset_given)
377	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
378	>	if (args_info->sele1_given)
379	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
380	>	if (args_info->sele2_given)
381	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
382	>	if (args_info->sele3_given)
383	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
384	>	if (args_info->refsele_given)
385	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
386	>	if (args_info->comsele_given)
387	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
388	>	if (args_info->molname_given)
389	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
390	>	if (args_info->begin_given)
391	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
392	>	if (args_info->end_given)
393	>	write_into_file(outfile, "end", args_info->end_orig, 0);
394	>	if (args_info->radius_given)
395	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
396	>	if (args_info->bo_given)
397	>	write_into_file(outfile, "bo", 0, 0 );
398	>	if (args_info->bor_given)
399	>	write_into_file(outfile, "bor", 0, 0 );
400	>	if (args_info->bad_given)
401	>	write_into_file(outfile, "bad", 0, 0 );
402	>	if (args_info->gofr_given)
403	>	write_into_file(outfile, "gofr", 0, 0 );
404	>	if (args_info->gofz_given)
405	>	write_into_file(outfile, "gofz", 0, 0 );
406	>	if (args_info->r_theta_given)
407	>	write_into_file(outfile, "r_theta", 0, 0 );
408	>	if (args_info->r_omega_given)
409	>	write_into_file(outfile, "r_omega", 0, 0 );
410	>	if (args_info->theta_omega_given)
411	>	write_into_file(outfile, "theta_omega", 0, 0 );
412	>	if (args_info->gxyz_given)
413	>	write_into_file(outfile, "gxyz", 0, 0 );
414	>	if (args_info->p2_given)
415	>	write_into_file(outfile, "p2", 0, 0 );
416	>	if (args_info->rp2_given)
417	>	write_into_file(outfile, "rp2", 0, 0 );
418	>	if (args_info->scd_given)
419	>	write_into_file(outfile, "scd", 0, 0 );
420	>	if (args_info->density_given)
421	>	write_into_file(outfile, "density", 0, 0 );
422	>	if (args_info->slab_density_given)
423	>	write_into_file(outfile, "slab_density", 0, 0 );
424	>	if (args_info->hxy_given)
425	>	write_into_file(outfile, "hxy", 0, 0 );
426	>	if (args_info->rho_r_given)
427	>	write_into_file(outfile, "rho_r", 0, 0 );
428	>	if (args_info->hullvol_given)
429	>	write_into_file(outfile, "hullvol", 0, 0 );
430	>
431	>
432	>	i = EXIT_SUCCESS;
433	>	return i;
434	>	}
435	>
436	>	int
437	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
438	>	{
439	>	FILE *outfile;
440	>	int i = 0;
441	>
442	>	outfile = fopen(filename, "w");
443	>
444	>	if (!outfile)
445	>	{
446	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
447	>	return EXIT_FAILURE;
448	>	}
449	>
450	>	i = cmdline_parser_dump(outfile, args_info);
451	>	fclose (outfile);
452	>
453	>	return i;
454	>	}
455	>
456	>	void
457	>	cmdline_parser_free (struct gengetopt_args_info *args_info)
458	>	{
459	>	cmdline_parser_release (args_info);
460	>	}
461	>
462	>	/** @brief replacement of strdup, which is not standard */
463		char *
464		gengetopt_strdup (const char *s)
465		{
466	<	char *result = (char*)malloc(strlen(s) + 1);
466	>	char *result = NULL;
467	>	if (!s)
468	>	return result;
469	>
470	>	result = (char*)malloc(strlen(s) + 1);
471		if (result == (char*)0)
472		return (char*)0;
473		strcpy(result, s);
474		return result;
475		}
476
477	<	int
478	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
477	>	static void
478	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
479		{
480	<	int c;        /* Character of the parsed option.  */
481	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
480	>	if (! args_info->staticProps_group_counter)
481	>	return;
482
483	<
484	<	args_info->help_given = 0 ;
485	<	args_info->version_given = 0 ;
90	<	args_info->input_given = 0 ;
91	<	args_info->output_given = 0 ;
92	<	args_info->step_given = 0 ;
93	<	args_info->nrbins_given = 0 ;
94	<	args_info->nanglebins_given = 0 ;
95	<	args_info->length_given = 0 ;
96	<	args_info->sele1_given = 0 ;
97	<	args_info->sele2_given = 0 ;
98	<	args_info->sele3_given = 0 ;
99	<	args_info->refsele_given = 0 ;
100	<	args_info->molname_given = 0 ;
101	<	args_info->begin_given = 0 ;
102	<	args_info->end_given = 0 ;
483	>	args_info->bo_given = 0 ;
484	>	args_info->bor_given = 0 ;
485	>	args_info->bad_given = 0 ;
486		args_info->gofr_given = 0 ;
487	+	args_info->gofz_given = 0 ;
488		args_info->r_theta_given = 0 ;
489		args_info->r_omega_given = 0 ;
490		args_info->theta_omega_given = 0 ;
491		args_info->gxyz_given = 0 ;
492		args_info->p2_given = 0 ;
493	+	args_info->rp2_given = 0 ;
494		args_info->scd_given = 0 ;
495		args_info->density_given = 0 ;
496	<	#define clear_args() { \
497	<	args_info->input_arg = NULL; \
498	<	args_info->output_arg = NULL; \
499	<	args_info->step_arg = 1 ;\
500	<	args_info->nrbins_arg = 100 ;\
501	<	args_info->nanglebins_arg = 50 ;\
117	<	args_info->sele1_arg = NULL; \
118	<	args_info->sele2_arg = NULL; \
119	<	args_info->sele3_arg = NULL; \
120	<	args_info->refsele_arg = NULL; \
121	<	args_info->molname_arg = NULL; \
496	>	args_info->slab_density_given = 0 ;
497	>	args_info->hxy_given = 0 ;
498	>	args_info->rho_r_given = 0 ;
499	>	args_info->hullvol_given = 0 ;
500	>
501	>	args_info->staticProps_group_counter = 0;
502		}
503
504	<	clear_args();
504	>	int
505	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
506	>	{
507	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
508	>	}
509
510	+	int
511	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
512	+	struct cmdline_parser_params *params)
513	+	{
514	+	int result;
515	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
516	+
517	+	if (result == EXIT_FAILURE)
518	+	{
519	+	cmdline_parser_free (args_info);
520	+	exit (EXIT_FAILURE);
521	+	}
522	+
523	+	return result;
524	+	}
525	+
526	+	int
527	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
528	+	{
529	+	int result;
530	+	struct cmdline_parser_params params;
531	+
532	+	params.override = override;
533	+	params.initialize = initialize;
534	+	params.check_required = check_required;
535	+	params.check_ambiguity = 0;
536	+	params.print_errors = 1;
537	+
538	+	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
539	+
540	+	if (result == EXIT_FAILURE)
541	+	{
542	+	cmdline_parser_free (args_info);
543	+	exit (EXIT_FAILURE);
544	+	}
545	+
546	+	return result;
547	+	}
548	+
549	+	int
550	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
551	+	{
552	+	int result = EXIT_SUCCESS;
553	+
554	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
555	+	result = EXIT_FAILURE;
556	+
557	+	if (result == EXIT_FAILURE)
558	+	{
559	+	cmdline_parser_free (args_info);
560	+	exit (EXIT_FAILURE);
561	+	}
562	+
563	+	return result;
564	+	}
565	+
566	+	int
567	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
568	+	{
569	+	int error = 0;
570	+
571	+	/* checks for required options */
572	+	if (! args_info->input_given)
573	+	{
574	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
575	+	error = 1;
576	+	}
577	+
578	+	if (args_info->staticProps_group_counter == 0)
579	+	{
580	+	fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
581	+	error = 1;
582	+	}
583	+
584	+
585	+	/* checks for dependences among options */
586	+
587	+	return error;
588	+	}
589	+
590	+
591	+	static char *package_name = 0;
592	+
593	+	/**
594	+	* @brief updates an option
595	+	* @param field the generic pointer to the field to update
596	+	* @param orig_field the pointer to the orig field
597	+	* @param field_given the pointer to the number of occurrence of this option
598	+	* @param prev_given the pointer to the number of occurrence already seen
599	+	* @param value the argument for this option (if null no arg was specified)
600	+	* @param possible_values the possible values for this option (if specified)
601	+	* @param default_value the default value (in case the option only accepts fixed values)
602	+	* @param arg_type the type of this option
603	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
604	+	* @param override @see cmdline_parser_params.override
605	+	* @param no_free whether to free a possible previous value
606	+	* @param multiple_option whether this is a multiple option
607	+	* @param long_opt the corresponding long option
608	+	* @param short_opt the corresponding short option (or '-' if none)
609	+	* @param additional_error possible further error specification
610	+	*/
611	+	static
612	+	int update_arg(void *field, char **orig_field,
613	+	unsigned int *field_given, unsigned int *prev_given,
614	+	char *value, char *possible_values[], const char *default_value,
615	+	cmdline_parser_arg_type arg_type,
616	+	int check_ambiguity, int override,
617	+	int no_free, int multiple_option,
618	+	const char *long_opt, char short_opt,
619	+	const char *additional_error)
620	+	{
621	+	char *stop_char = 0;
622	+	const char *val = value;
623	+	int found;
624	+	char **string_field;
625	+
626	+	stop_char = 0;
627	+	found = 0;
628	+
629	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
630	+	{
631	+	if (short_opt != '-')
632	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
633	+	package_name, long_opt, short_opt,
634	+	(additional_error ? additional_error : ""));
635	+	else
636	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
637	+	package_name, long_opt,
638	+	(additional_error ? additional_error : ""));
639	+	return 1; /* failure */
640	+	}
641	+
642	+
643	+	if (field_given && *field_given && ! override)
644	+	return 0;
645	+	if (prev_given)
646	+	(*prev_given)++;
647	+	if (field_given)
648	+	(*field_given)++;
649	+	if (possible_values)
650	+	val = possible_values[found];
651	+
652	+	switch(arg_type) {
653	+	case ARG_INT:
654	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
655	+	break;
656	+	case ARG_DOUBLE:
657	+	if (val) *((double *)field) = strtod (val, &stop_char);
658	+	break;
659	+	case ARG_STRING:
660	+	if (val) {
661	+	string_field = (char **)field;
662	+	if (!no_free && *string_field)
663	+	free (*string_field); /* free previous string */
664	+	*string_field = gengetopt_strdup (val);
665	+	}
666	+	break;
667	+	default:
668	+	break;
669	+	};
670	+
671	+	/* check numeric conversion */
672	+	switch(arg_type) {
673	+	case ARG_INT:
674	+	case ARG_DOUBLE:
675	+	if (val && !(stop_char && *stop_char == '\0')) {
676	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
677	+	return 1; /* failure */
678	+	}
679	+	break;
680	+	default:
681	+	;
682	+	};
683	+
684	+	/* store the original value */
685	+	switch(arg_type) {
686	+	case ARG_NO:
687	+	break;
688	+	default:
689	+	if (value && orig_field) {
690	+	if (no_free) {
691	+	*orig_field = value;
692	+	} else {
693	+	if (*orig_field)
694	+	free (*orig_field); /* free previous string */
695	+	*orig_field = gengetopt_strdup (value);
696	+	}
697	+	}
698	+	};
699	+
700	+	return 0; /* OK */
701	+	}
702	+
703	+
704	+	int
705	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
706	+	struct cmdline_parser_params *params, const char *additional_error)
707	+	{
708	+	int c;        /* Character of the parsed option.  */
709	+
710	+	int error = 0;
711	+	struct gengetopt_args_info local_args_info;
712	+
713	+	int override;
714	+	int initialize;
715	+	int check_required;
716	+	int check_ambiguity;
717	+
718	+	package_name = argv[0];
719	+
720	+	override = params->override;
721	+	initialize = params->initialize;
722	+	check_required = params->check_required;
723	+	check_ambiguity = params->check_ambiguity;
724	+
725	+	if (initialize)
726	+	cmdline_parser_init (args_info);
727	+
728	+	cmdline_parser_init (&local_args_info);
729	+
730		optarg = 0;
731	<	optind = 1;
732	<	opterr = 1;
731	>	optind = 0;
732	>	opterr = params->print_errors;
733		optopt = '?';
734
735		while (1)
736		{
737		int option_index = 0;
134	–	char *stop_char;
738
739		static struct option long_options[] = {
740		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 742 | cmdline_parser (int argc, char * const *argv, struct g
742		{ "input",      1, NULL, 'i' },
743		{ "output",     1, NULL, 'o' },
744		{ "step",       1, NULL, 'n' },
745	<	{ "nrbins",     1, NULL, 'r' },
745	>	{ "nbins",      1, NULL, 'b' },
746	>	{ "nbins_x",    1, NULL, 'x' },
747	>	{ "nbins_y",    1, NULL, 'y' },
748		{ "nanglebins", 1, NULL, 'a' },
749	<	{ "length",     1, NULL, 'l' },
749	>	{ "length",     1, NULL, 0 },
750	>	{ "rcut",       1, NULL, 'c' },
751	>	{ "zoffset",    1, NULL, 'z' },
752		{ "sele1",      1, NULL, 0 },
753		{ "sele2",      1, NULL, 0 },
754		{ "sele3",      1, NULL, 0 },
755		{ "refsele",    1, NULL, 0 },
756	+	{ "comsele",    1, NULL, 0 },
757		{ "molname",    1, NULL, 0 },
758		{ "begin",      1, NULL, 0 },
759		{ "end",        1, NULL, 0 },
760	<	{ "gofr",       0, NULL, 0 },
760	>	{ "radius",     1, NULL, 0 },
761	>	{ "bo", 0, NULL, 0 },
762	>	{ "bor",        0, NULL, 0 },
763	>	{ "bad",        0, NULL, 0 },
764	>	{ "gofr",       0, NULL, 'g' },
765	>	{ "gofz",       0, NULL, 0 },
766		{ "r_theta",    0, NULL, 0 },
767		{ "r_omega",    0, NULL, 0 },
768		{ "theta_omega",        0, NULL, 0 },
769		{ "gxyz",       0, NULL, 0 },
770	<	{ "p2", 0, NULL, 0 },
771	<	{ "scd",        0, NULL, 0 },
772	<	{ "density",    0, NULL, 0 },
770	>	{ "p2", 0, NULL, 'p' },
771	>	{ "rp2",        0, NULL, 0 },
772	>	{ "scd",        0, NULL, 's' },
773	>	{ "density",    0, NULL, 'd' },
774	>	{ "slab_density",       0, NULL, 0 },
775	>	{ "hxy",        0, NULL, 0 },
776	>	{ "rho_r",      0, NULL, 0 },
777	>	{ "hullvol",    0, NULL, 0 },
778		{ NULL, 0, NULL, 0 }
779		};
780
781	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
781	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
782
783		if (c == -1) break;       /* Exit from `while (1)' loop.  */
784
785		switch (c)
786		{
787		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
788		cmdline_parser_print_help ();
789	+	cmdline_parser_free (&local_args_info);
790		exit (EXIT_SUCCESS);
791
792		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
793		cmdline_parser_print_version ();
794	+	cmdline_parser_free (&local_args_info);
795		exit (EXIT_SUCCESS);
796
797		case 'i':       /* input dump file.  */
798	<	if (args_info->input_given)
799	<	{
800	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
801	<	clear_args ();
802	<	exit (EXIT_FAILURE);
803	<	}
804	<	args_info->input_given = 1;
805	<	args_info->input_arg = gengetopt_strdup (optarg);
798	>
799	>
800	>	if (update_arg( (void *)&(args_info->input_arg),
801	>	&(args_info->input_orig), &(args_info->input_given),
802	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
803	>	check_ambiguity, override, 0, 0,
804	>	"input", 'i',
805	>	additional_error))
806	>	goto failure;
807	>
808		break;
190	–
809		case 'o':       /* output file name.  */
810	<	if (args_info->output_given)
811	<	{
812	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
813	<	clear_args ();
814	<	exit (EXIT_FAILURE);
815	<	}
816	<	args_info->output_given = 1;
817	<	args_info->output_arg = gengetopt_strdup (optarg);
810	>
811	>
812	>	if (update_arg( (void *)&(args_info->output_arg),
813	>	&(args_info->output_orig), &(args_info->output_given),
814	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
815	>	check_ambiguity, override, 0, 0,
816	>	"output", 'o',
817	>	additional_error))
818	>	goto failure;
819	>
820		break;
201	–
821		case 'n':       /* process every n frame.  */
822	<	if (args_info->step_given)
823	<	{
824	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
825	<	clear_args ();
826	<	exit (EXIT_FAILURE);
827	<	}
828	<	args_info->step_given = 1;
829	<	args_info->step_arg = strtol (optarg,&stop_char,0);
822	>
823	>
824	>	if (update_arg( (void *)&(args_info->step_arg),
825	>	&(args_info->step_orig), &(args_info->step_given),
826	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
827	>	check_ambiguity, override, 0, 0,
828	>	"step", 'n',
829	>	additional_error))
830	>	goto failure;
831	>
832		break;
833	<
834	<	case 'r':       /* number of bins for distance.  */
835	<	if (args_info->nrbins_given)
836	<	{
837	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
838	<	clear_args ();
839	<	exit (EXIT_FAILURE);
840	<	}
841	<	args_info->nrbins_given = 1;
842	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
833	>	case 'b':       /* number of bins (general purpose).  */
834	>
835	>
836	>	if (update_arg( (void *)&(args_info->nbins_arg),
837	>	&(args_info->nbins_orig), &(args_info->nbins_given),
838	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
839	>	check_ambiguity, override, 0, 0,
840	>	"nbins", 'b',
841	>	additional_error))
842	>	goto failure;
843	>
844		break;
845	<
845	>	case 'x':       /* number of bins in x axis.  */
846	>
847	>
848	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
849	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
850	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
851	>	check_ambiguity, override, 0, 0,
852	>	"nbins_x", 'x',
853	>	additional_error))
854	>	goto failure;
855	>
856	>	break;
857	>	case 'y':       /* number of bins in y axis.  */
858	>
859	>
860	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
861	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
862	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
863	>	check_ambiguity, override, 0, 0,
864	>	"nbins_y", 'y',
865	>	additional_error))
866	>	goto failure;
867	>
868	>	break;
869		case 'a':       /* number of bins for cos(angle).  */
870	<	if (args_info->nanglebins_given)
871	<	{
872	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
873	<	clear_args ();
874	<	exit (EXIT_FAILURE);
875	<	}
876	<	args_info->nanglebins_given = 1;
877	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
870	>
871	>
872	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
873	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
874	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
875	>	check_ambiguity, override, 0, 0,
876	>	"nanglebins", 'a',
877	>	additional_error))
878	>	goto failure;
879	>
880		break;
881	<
882	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
883	<	if (args_info->length_given)
884	<	{
885	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
886	<	clear_args ();
887	<	exit (EXIT_FAILURE);
888	<	}
889	<	args_info->length_given = 1;
890	<	args_info->length_arg = strtod (optarg, NULL);
881	>	case 'c':       /* cutoff radius (rcut).  */
882	>
883	>
884	>	if (update_arg( (void *)&(args_info->rcut_arg),
885	>	&(args_info->rcut_orig), &(args_info->rcut_given),
886	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
887	>	check_ambiguity, override, 0, 0,
888	>	"rcut", 'c',
889	>	additional_error))
890	>	goto failure;
891	>
892		break;
893	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
894	+
895	+
896	+	if (update_arg( (void *)&(args_info->zoffset_arg),
897	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
898	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
899	+	check_ambiguity, override, 0, 0,
900	+	"zoffset", 'z',
901	+	additional_error))
902	+	goto failure;
903	+
904	+	break;
905	+	case 'g':       /* g(r).  */
906	+
907	+	if (args_info->staticProps_group_counter && override)
908	+	reset_group_staticProps (args_info);
909	+	args_info->staticProps_group_counter += 1;
910	+
911	+	if (update_arg( 0 ,
912	+	0 , &(args_info->gofr_given),
913	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
914	+	check_ambiguity, override, 0, 0,
915	+	"gofr", 'g',
916	+	additional_error))
917	+	goto failure;
918	+
919	+	break;
920	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
921	+
922	+	if (args_info->staticProps_group_counter && override)
923	+	reset_group_staticProps (args_info);
924	+	args_info->staticProps_group_counter += 1;
925	+
926	+	if (update_arg( 0 ,
927	+	0 , &(args_info->p2_given),
928	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
929	+	check_ambiguity, override, 0, 0,
930	+	"p2", 'p',
931	+	additional_error))
932	+	goto failure;
933	+
934	+	break;
935	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
936	+
937	+	if (args_info->staticProps_group_counter && override)
938	+	reset_group_staticProps (args_info);
939	+	args_info->staticProps_group_counter += 1;
940	+
941	+	if (update_arg( 0 ,
942	+	0 , &(args_info->scd_given),
943	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
944	+	check_ambiguity, override, 0, 0,
945	+	"scd", 's',
946	+	additional_error))
947	+	goto failure;
948	+
949	+	break;
950	+	case 'd':       /* density plot.  */
951	+
952	+	if (args_info->staticProps_group_counter && override)
953	+	reset_group_staticProps (args_info);
954	+	args_info->staticProps_group_counter += 1;
955	+
956	+	if (update_arg( 0 ,
957	+	0 , &(args_info->density_given),
958	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
959	+	check_ambiguity, override, 0, 0,
960	+	"density", 'd',
961	+	additional_error))
962	+	goto failure;
963	+
964	+	break;
965
246	–
966		case 0: /* Long option with no short option */
967	<	/* select the first stuntdouble set.  */
968	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
967	>	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
968	>	if (strcmp (long_options[option_index].name, "length") == 0)
969		{
970	<	if (args_info->sele1_given)
971	<	{
972	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
973	<	clear_args ();
974	<	exit (EXIT_FAILURE);
975	<	}
976	<	args_info->sele1_given = 1;
977	<	args_info->sele1_arg = gengetopt_strdup (optarg);
978	<	break;
970	>
971	>
972	>	if (update_arg( (void *)&(args_info->length_arg),
973	>	&(args_info->length_orig), &(args_info->length_given),
974	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
975	>	check_ambiguity, override, 0, 0,
976	>	"length", '-',
977	>	additional_error))
978	>	goto failure;
979	>
980		}
981	+	/* select the first stuntdouble set.  */
982	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
983	+	{
984
985	+
986	+	if (update_arg( (void *)&(args_info->sele1_arg),
987	+	&(args_info->sele1_orig), &(args_info->sele1_given),
988	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
989	+	check_ambiguity, override, 0, 0,
990	+	"sele1", '-',
991	+	additional_error))
992	+	goto failure;
993	+
994	+	}
995		/* select the second stuntdouble set.  */
996		else if (strcmp (long_options[option_index].name, "sele2") == 0)
997		{
265	–	if (args_info->sele2_given)
266	–	{
267	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
268	–	clear_args ();
269	–	exit (EXIT_FAILURE);
270	–	}
271	–	args_info->sele2_given = 1;
272	–	args_info->sele2_arg = gengetopt_strdup (optarg);
273	–	break;
274	–	}
998
999	+
1000	+	if (update_arg( (void *)&(args_info->sele2_arg),
1001	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1002	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1003	+	check_ambiguity, override, 0, 0,
1004	+	"sele2", '-',
1005	+	additional_error))
1006	+	goto failure;
1007	+
1008	+	}
1009		/* select the third stuntdouble set.  */
1010		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1011		{
279	–	if (args_info->sele3_given)
280	–	{
281	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
282	–	clear_args ();
283	–	exit (EXIT_FAILURE);
284	–	}
285	–	args_info->sele3_given = 1;
286	–	args_info->sele3_arg = gengetopt_strdup (optarg);
287	–	break;
288	–	}
1012
1013	+
1014	+	if (update_arg( (void *)&(args_info->sele3_arg),
1015	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1016	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1017	+	check_ambiguity, override, 0, 0,
1018	+	"sele3", '-',
1019	+	additional_error))
1020	+	goto failure;
1021	+
1022	+	}
1023		/* select reference (use and only use with --gxyz).  */
1024		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1025		{
1026	<	if (args_info->refsele_given)
1027	<	{
1028	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1029	<	clear_args ();
1030	<	exit (EXIT_FAILURE);
1031	<	}
1032	<	args_info->refsele_given = 1;
1033	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1034	<	break;
1026	>
1027	>
1028	>	if (update_arg( (void *)&(args_info->refsele_arg),
1029	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1030	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1031	>	check_ambiguity, override, 0, 0,
1032	>	"refsele", '-',
1033	>	additional_error))
1034	>	goto failure;
1035	>
1036		}
1037	+	/* select stunt doubles for center-of-mass reference point.  */
1038	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1039	+	{
1040
1041	+
1042	+	if (update_arg( (void *)&(args_info->comsele_arg),
1043	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1044	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1045	+	check_ambiguity, override, 0, 0,
1046	+	"comsele", '-',
1047	+	additional_error))
1048	+	goto failure;
1049	+
1050	+	}
1051		/* molecule name.  */
1052		else if (strcmp (long_options[option_index].name, "molname") == 0)
1053		{
307	–	if (args_info->molname_given)
308	–	{
309	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
310	–	clear_args ();
311	–	exit (EXIT_FAILURE);
312	–	}
313	–	args_info->molname_given = 1;
314	–	args_info->molname_arg = gengetopt_strdup (optarg);
315	–	break;
316	–	}
1054
1055	<	/* begin interanl index.  */
1055	>
1056	>	if (update_arg( (void *)&(args_info->molname_arg),
1057	>	&(args_info->molname_orig), &(args_info->molname_given),
1058	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1059	>	check_ambiguity, override, 0, 0,
1060	>	"molname", '-',
1061	>	additional_error))
1062	>	goto failure;
1063	>
1064	>	}
1065	>	/* begin internal index.  */
1066		else if (strcmp (long_options[option_index].name, "begin") == 0)
1067		{
321	–	if (args_info->begin_given)
322	–	{
323	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
324	–	clear_args ();
325	–	exit (EXIT_FAILURE);
326	–	}
327	–	args_info->begin_given = 1;
328	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
329	–	break;
330	–	}
1068
1069	+
1070	+	if (update_arg( (void *)&(args_info->begin_arg),
1071	+	&(args_info->begin_orig), &(args_info->begin_given),
1072	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1073	+	check_ambiguity, override, 0, 0,
1074	+	"begin", '-',
1075	+	additional_error))
1076	+	goto failure;
1077	+
1078	+	}
1079		/* end internal index.  */
1080		else if (strcmp (long_options[option_index].name, "end") == 0)
1081		{
1082	<	if (args_info->end_given)
1083	<	{
1084	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1085	<	clear_args ();
1086	<	exit (EXIT_FAILURE);
1087	<	}
1088	<	args_info->end_given = 1;
1089	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1090	<	break;
1082	>
1083	>
1084	>	if (update_arg( (void *)&(args_info->end_arg),
1085	>	&(args_info->end_orig), &(args_info->end_given),
1086	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1087	>	check_ambiguity, override, 0, 0,
1088	>	"end", '-',
1089	>	additional_error))
1090	>	goto failure;
1091	>
1092		}
1093	+	/* nanoparticle radius.  */
1094	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1095	+	{
1096
1097	<	/* g(r).  */
1098	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1097	>
1098	>	if (update_arg( (void *)&(args_info->radius_arg),
1099	>	&(args_info->radius_orig), &(args_info->radius_given),
1100	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1101	>	check_ambiguity, override, 0, 0,
1102	>	"radius", '-',
1103	>	additional_error))
1104	>	goto failure;
1105	>
1106	>	}
1107	>	/* bond order parameter (--rcut must be specified).  */
1108	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1109		{
349	–	if (args_info->gofr_given)
350	–	{
351	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
352	–	clear_args ();
353	–	exit (EXIT_FAILURE);
354	–	}
355	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1110
1111	<	break;
1111	>	if (args_info->staticProps_group_counter && override)
1112	>	reset_group_staticProps (args_info);
1113	>	args_info->staticProps_group_counter += 1;
1114	>
1115	>	if (update_arg( 0 ,
1116	>	0 , &(args_info->bo_given),
1117	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"bo", '-',
1120	>	additional_error))
1121	>	goto failure;
1122	>
1123		}
1124	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1125	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1126	+	{
1127
1128	+	if (args_info->staticProps_group_counter && override)
1129	+	reset_group_staticProps (args_info);
1130	+	args_info->staticProps_group_counter += 1;
1131	+
1132	+	if (update_arg( 0 ,
1133	+	0 , &(args_info->bor_given),
1134	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1135	+	check_ambiguity, override, 0, 0,
1136	+	"bor", '-',
1137	+	additional_error))
1138	+	goto failure;
1139	+
1140	+	}
1141	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1142	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1143	+	{
1144	+
1145	+	if (args_info->staticProps_group_counter && override)
1146	+	reset_group_staticProps (args_info);
1147	+	args_info->staticProps_group_counter += 1;
1148	+
1149	+	if (update_arg( 0 ,
1150	+	0 , &(args_info->bad_given),
1151	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1152	+	check_ambiguity, override, 0, 0,
1153	+	"bad", '-',
1154	+	additional_error))
1155	+	goto failure;
1156	+
1157	+	}
1158	+	/* g(z).  */
1159	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1160	+	{
1161	+
1162	+	if (args_info->staticProps_group_counter && override)
1163	+	reset_group_staticProps (args_info);
1164	+	args_info->staticProps_group_counter += 1;
1165	+
1166	+	if (update_arg( 0 ,
1167	+	0 , &(args_info->gofz_given),
1168	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1169	+	check_ambiguity, override, 0, 0,
1170	+	"gofz", '-',
1171	+	additional_error))
1172	+	goto failure;
1173	+
1174	+	}
1175		/* g(r, cos(theta)).  */
1176		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1177		{
363	–	if (args_info->r_theta_given)
364	–	{
365	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
366	–	clear_args ();
367	–	exit (EXIT_FAILURE);
368	–	}
369	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1178
1179	<	break;
1180	<	}
1179	>	if (args_info->staticProps_group_counter && override)
1180	>	reset_group_staticProps (args_info);
1181	>	args_info->staticProps_group_counter += 1;
1182
1183	+	if (update_arg( 0 ,
1184	+	0 , &(args_info->r_theta_given),
1185	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1186	+	check_ambiguity, override, 0, 0,
1187	+	"r_theta", '-',
1188	+	additional_error))
1189	+	goto failure;
1190	+
1191	+	}
1192		/* g(r, cos(omega)).  */
1193		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1194		{
377	–	if (args_info->r_omega_given)
378	–	{
379	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
380	–	clear_args ();
381	–	exit (EXIT_FAILURE);
382	–	}
383	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1195
1196	<	break;
1197	<	}
1196	>	if (args_info->staticProps_group_counter && override)
1197	>	reset_group_staticProps (args_info);
1198	>	args_info->staticProps_group_counter += 1;
1199
1200	+	if (update_arg( 0 ,
1201	+	0 , &(args_info->r_omega_given),
1202	+	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1203	+	check_ambiguity, override, 0, 0,
1204	+	"r_omega", '-',
1205	+	additional_error))
1206	+	goto failure;
1207	+
1208	+	}
1209		/* g(cos(theta), cos(omega)).  */
1210		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1211		{
391	–	if (args_info->theta_omega_given)
392	–	{
393	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
394	–	clear_args ();
395	–	exit (EXIT_FAILURE);
396	–	}
397	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1212
1213	<	break;
1214	<	}
1213	>	if (args_info->staticProps_group_counter && override)
1214	>	reset_group_staticProps (args_info);
1215	>	args_info->staticProps_group_counter += 1;
1216
1217	+	if (update_arg( 0 ,
1218	+	0 , &(args_info->theta_omega_given),
1219	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1220	+	check_ambiguity, override, 0, 0,
1221	+	"theta_omega", '-',
1222	+	additional_error))
1223	+	goto failure;
1224	+
1225	+	}
1226		/* g(x, y, z).  */
1227		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1228		{
405	–	if (args_info->gxyz_given)
406	–	{
407	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
408	–	clear_args ();
409	–	exit (EXIT_FAILURE);
410	–	}
411	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1229
1230	<	break;
1231	<	}
1230	>	if (args_info->staticProps_group_counter && override)
1231	>	reset_group_staticProps (args_info);
1232	>	args_info->staticProps_group_counter += 1;
1233
1234	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1235	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1234	>	if (update_arg( 0 ,
1235	>	0 , &(args_info->gxyz_given),
1236	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1237	>	check_ambiguity, override, 0, 0,
1238	>	"gxyz", '-',
1239	>	additional_error))
1240	>	goto failure;
1241	>
1242	>	}
1243	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1244	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1245		{
419	–	if (args_info->p2_given)
420	–	{
421	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
422	–	clear_args ();
423	–	exit (EXIT_FAILURE);
424	–	}
425	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1246
1247	<	break;
1247	>	if (args_info->staticProps_group_counter && override)
1248	>	reset_group_staticProps (args_info);
1249	>	args_info->staticProps_group_counter += 1;
1250	>
1251	>	if (update_arg( 0 ,
1252	>	0 , &(args_info->rp2_given),
1253	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1254	>	check_ambiguity, override, 0, 0,
1255	>	"rp2", '-',
1256	>	additional_error))
1257	>	goto failure;
1258	>
1259		}
1260	+	/* slab density.  */
1261	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1262	+	{
1263
1264	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1265	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1264	>	if (args_info->staticProps_group_counter && override)
1265	>	reset_group_staticProps (args_info);
1266	>	args_info->staticProps_group_counter += 1;
1267	>
1268	>	if (update_arg( 0 ,
1269	>	0 , &(args_info->slab_density_given),
1270	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1271	>	check_ambiguity, override, 0, 0,
1272	>	"slab_density", '-',
1273	>	additional_error))
1274	>	goto failure;
1275	>
1276	>	}
1277	>	/* hxy.  */
1278	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1279		{
433	–	if (args_info->scd_given)
434	–	{
435	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
436	–	clear_args ();
437	–	exit (EXIT_FAILURE);
438	–	}
439	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1280
1281	<	break;
1281	>	if (args_info->staticProps_group_counter && override)
1282	>	reset_group_staticProps (args_info);
1283	>	args_info->staticProps_group_counter += 1;
1284	>
1285	>	if (update_arg( 0 ,
1286	>	0 , &(args_info->hxy_given),
1287	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1288	>	check_ambiguity, override, 0, 0,
1289	>	"hxy", '-',
1290	>	additional_error))
1291	>	goto failure;
1292	>
1293		}
1294	+	/* rho of R.  */
1295	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1296	+	{
1297
1298	<	/* density plot (--sele1 must be specified).  */
1299	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1298	>	if (args_info->staticProps_group_counter && override)
1299	>	reset_group_staticProps (args_info);
1300	>	args_info->staticProps_group_counter += 1;
1301	>
1302	>	if (update_arg( 0 ,
1303	>	0 , &(args_info->rho_r_given),
1304	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1305	>	check_ambiguity, override, 0, 0,
1306	>	"rho_r", '-',
1307	>	additional_error))
1308	>	goto failure;
1309	>
1310	>	}
1311	>	/* hull volume of nanoparticle.  */
1312	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1313		{
447	–	if (args_info->density_given)
448	–	{
449	–	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
450	–	clear_args ();
451	–	exit (EXIT_FAILURE);
452	–	}
453	–	args_info->density_given = 1; staticProps_group_counter += 1;
1314
1315	<	break;
1315	>	if (args_info->staticProps_group_counter && override)
1316	>	reset_group_staticProps (args_info);
1317	>	args_info->staticProps_group_counter += 1;
1318	>
1319	>	if (update_arg( 0 ,
1320	>	0 , &(args_info->hullvol_given),
1321	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1322	>	check_ambiguity, override, 0, 0,
1323	>	"hullvol", '-',
1324	>	additional_error))
1325	>	goto failure;
1326	>
1327		}
1328
1329	<
1329	>	break;
1330		case '?':       /* Invalid option.  */
1331		/* `getopt_long' already printed an error message.  */
1332	<	exit (EXIT_FAILURE);
1332	>	goto failure;
1333
1334		default:        /* bug: option not considered.  */
1335	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1335	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1336		abort ();
1337		} /* switch */
1338		} /* while */
1339
1340	<	if ( staticProps_group_counter != 1)
1340	>	if (args_info->staticProps_group_counter > 1)
1341		{
1342	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1343	<	missing_required_options = 1;
1342	>	fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
1343	>	error = 1;
1344		}
1345
1346
1347	<	if (! args_info->input_given)
1347	>
1348	>	if (check_required)
1349		{
1350	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1350	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1351		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1352
1353	+	cmdline_parser_release (&local_args_info);
1354	+
1355	+	if ( error )
1356	+	return (EXIT_FAILURE);
1357	+
1358		return 0;
1359	+
1360	+	failure:
1361	+
1362	+	cmdline_parser_release (&local_args_info);
1363	+	return (EXIT_FAILURE);
1364		}

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