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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 1413 by gezelter, Mon Mar 22 19:21:22 2010 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 -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:
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]... [FILES]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	+	"      --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	+	"      --p_angle                 p(cos(theta))",
68	+	"      --hxy                     hxy",
69	+	"      --rho_r                   rho of R",
70	+	"      --hullvol                 hull volume of nanoparticle",
71	+	0
72	+	};
73	+
74	+	typedef enum {ARG_NO
75	+	, ARG_STRING
76	+	, ARG_INT
77	+	, ARG_DOUBLE
78	+	} cmdline_parser_arg_type;
79	+
80	+	static
81	+	void clear_given (struct gengetopt_args_info *args_info);
82	+	static
83	+	void clear_args (struct gengetopt_args_info *args_info);
84	+
85	+	static int
86	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
87	+	struct cmdline_parser_params *params, const char *additional_error);
88	+
89	+	static int
90	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
91	+
92	+	static char *
93	+	gengetopt_strdup (const char *s);
94	+
95	+	static
96	+	void clear_given (struct gengetopt_args_info *args_info)
97	+	{
98	+	args_info->help_given = 0 ;
99	+	args_info->version_given = 0 ;
100	+	args_info->input_given = 0 ;
101	+	args_info->output_given = 0 ;
102	+	args_info->step_given = 0 ;
103	+	args_info->nbins_given = 0 ;
104	+	args_info->nbins_x_given = 0 ;
105	+	args_info->nbins_y_given = 0 ;
106	+	args_info->nanglebins_given = 0 ;
107	+	args_info->length_given = 0 ;
108	+	args_info->rcut_given = 0 ;
109	+	args_info->zoffset_given = 0 ;
110	+	args_info->sele1_given = 0 ;
111	+	args_info->sele2_given = 0 ;
112	+	args_info->sele3_given = 0 ;
113	+	args_info->refsele_given = 0 ;
114	+	args_info->comsele_given = 0 ;
115	+	args_info->molname_given = 0 ;
116	+	args_info->begin_given = 0 ;
117	+	args_info->end_given = 0 ;
118	+	args_info->radius_given = 0 ;
119	+	args_info->bo_given = 0 ;
120	+	args_info->bor_given = 0 ;
121	+	args_info->bad_given = 0 ;
122	+	args_info->gofr_given = 0 ;
123	+	args_info->gofz_given = 0 ;
124	+	args_info->r_theta_given = 0 ;
125	+	args_info->r_omega_given = 0 ;
126	+	args_info->theta_omega_given = 0 ;
127	+	args_info->gxyz_given = 0 ;
128	+	args_info->p2_given = 0 ;
129	+	args_info->rp2_given = 0 ;
130	+	args_info->scd_given = 0 ;
131	+	args_info->density_given = 0 ;
132	+	args_info->slab_density_given = 0 ;
133	+	args_info->p_angle_given = 0 ;
134	+	args_info->hxy_given = 0 ;
135	+	args_info->rho_r_given = 0 ;
136	+	args_info->hullvol_given = 0 ;
137	+	args_info->staticProps_group_counter = 0 ;
138	+	}
139	+
140	+	static
141	+	void clear_args (struct gengetopt_args_info *args_info)
142	+	{
143	+	args_info->input_arg = NULL;
144	+	args_info->input_orig = NULL;
145	+	args_info->output_arg = NULL;
146	+	args_info->output_orig = NULL;
147	+	args_info->step_arg = 1;
148	+	args_info->step_orig = NULL;
149	+	args_info->nbins_arg = 100;
150	+	args_info->nbins_orig = NULL;
151	+	args_info->nbins_x_arg = 100;
152	+	args_info->nbins_x_orig = NULL;
153	+	args_info->nbins_y_arg = 100;
154	+	args_info->nbins_y_orig = NULL;
155	+	args_info->nanglebins_arg = 50;
156	+	args_info->nanglebins_orig = NULL;
157	+	args_info->length_orig = NULL;
158	+	args_info->rcut_orig = NULL;
159	+	args_info->zoffset_arg = 0;
160	+	args_info->zoffset_orig = NULL;
161	+	args_info->sele1_arg = NULL;
162	+	args_info->sele1_orig = NULL;
163	+	args_info->sele2_arg = NULL;
164	+	args_info->sele2_orig = NULL;
165	+	args_info->sele3_arg = NULL;
166	+	args_info->sele3_orig = NULL;
167	+	args_info->refsele_arg = NULL;
168	+	args_info->refsele_orig = NULL;
169	+	args_info->comsele_arg = NULL;
170	+	args_info->comsele_orig = NULL;
171	+	args_info->molname_arg = NULL;
172	+	args_info->molname_orig = NULL;
173	+	args_info->begin_orig = NULL;
174	+	args_info->end_orig = NULL;
175	+	args_info->radius_orig = NULL;
176	+
177	+	}
178	+
179	+	static
180	+	void init_args_info(struct gengetopt_args_info *args_info)
181	+	{
182	+
183	+
184	+	args_info->help_help = gengetopt_args_info_help[0] ;
185	+	args_info->version_help = gengetopt_args_info_help[1] ;
186	+	args_info->input_help = gengetopt_args_info_help[2] ;
187	+	args_info->output_help = gengetopt_args_info_help[3] ;
188	+	args_info->step_help = gengetopt_args_info_help[4] ;
189	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
190	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
191	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
192	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
193	+	args_info->length_help = gengetopt_args_info_help[9] ;
194	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
195	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
196	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
197	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
198	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
199	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
200	+	args_info->comsele_help = gengetopt_args_info_help[16] ;
201	+	args_info->molname_help = gengetopt_args_info_help[17] ;
202	+	args_info->begin_help = gengetopt_args_info_help[18] ;
203	+	args_info->end_help = gengetopt_args_info_help[19] ;
204	+	args_info->radius_help = gengetopt_args_info_help[20] ;
205	+	args_info->bo_help = gengetopt_args_info_help[22] ;
206	+	args_info->bor_help = gengetopt_args_info_help[23] ;
207	+	args_info->bad_help = gengetopt_args_info_help[24] ;
208	+	args_info->gofr_help = gengetopt_args_info_help[25] ;
209	+	args_info->gofz_help = gengetopt_args_info_help[26] ;
210	+	args_info->r_theta_help = gengetopt_args_info_help[27] ;
211	+	args_info->r_omega_help = gengetopt_args_info_help[28] ;
212	+	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
213	+	args_info->gxyz_help = gengetopt_args_info_help[30] ;
214	+	args_info->p2_help = gengetopt_args_info_help[31] ;
215	+	args_info->rp2_help = gengetopt_args_info_help[32] ;
216	+	args_info->scd_help = gengetopt_args_info_help[33] ;
217	+	args_info->density_help = gengetopt_args_info_help[34] ;
218	+	args_info->slab_density_help = gengetopt_args_info_help[35] ;
219	+	args_info->p_angle_help = gengetopt_args_info_help[36] ;
220	+	args_info->hxy_help = gengetopt_args_info_help[37] ;
221	+	args_info->rho_r_help = gengetopt_args_info_help[38] ;
222	+	args_info->hullvol_help = gengetopt_args_info_help[39] ;
223	+
224	+	}
225	+
226		void
227		cmdline_parser_print_version (void)
228		{
229		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
230		}
231
232	+	static void print_help_common(void) {
233	+	cmdline_parser_print_version ();
234	+
235	+	if (strlen(gengetopt_args_info_purpose) > 0)
236	+	printf("\n%s\n", gengetopt_args_info_purpose);
237	+
238	+	if (strlen(gengetopt_args_info_usage) > 0)
239	+	printf("\n%s\n", gengetopt_args_info_usage);
240	+
241	+	printf("\n");
242	+
243	+	if (strlen(gengetopt_args_info_description) > 0)
244	+	printf("%s\n", gengetopt_args_info_description);
245	+	}
246	+
247		void
248		cmdline_parser_print_help (void)
249		{
250	<	cmdline_parser_print_version ();
251	<	printf("\n"
252	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
253	<	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");
250	>	int i = 0;
251	>	print_help_common();
252	>	while (gengetopt_args_info_help[i])
253	>	printf("%s\n", gengetopt_args_info_help[i++]);
254		}
255
256	+	void
257	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
258	+	{
259	+	clear_given (args_info);
260	+	clear_args (args_info);
261	+	init_args_info (args_info);
262
263	<	static char *gengetopt_strdup (const char *s);
263	>	args_info->inputs = NULL;
264	>	args_info->inputs_num = 0;
265	>	}
266
267	<	/* gengetopt_strdup() */
268	<	/* strdup.c replacement of strdup, which is not standard */
267	>	void
268	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
269	>	{
270	>	if (params)
271	>	{
272	>	params->override = 0;
273	>	params->initialize = 1;
274	>	params->check_required = 1;
275	>	params->check_ambiguity = 0;
276	>	params->print_errors = 1;
277	>	}
278	>	}
279	>
280	>	struct cmdline_parser_params *
281	>	cmdline_parser_params_create(void)
282	>	{
283	>	struct cmdline_parser_params *params =
284	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
285	>	cmdline_parser_params_init(params);
286	>	return params;
287	>	}
288	>
289	>	static void
290	>	free_string_field (char **s)
291	>	{
292	>	if (*s)
293	>	{
294	>	free (*s);
295	>	*s = 0;
296	>	}
297	>	}
298	>
299	>
300	>	static void
301	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
302	>	{
303	>	unsigned int i;
304	>	free_string_field (&(args_info->input_arg));
305	>	free_string_field (&(args_info->input_orig));
306	>	free_string_field (&(args_info->output_arg));
307	>	free_string_field (&(args_info->output_orig));
308	>	free_string_field (&(args_info->step_orig));
309	>	free_string_field (&(args_info->nbins_orig));
310	>	free_string_field (&(args_info->nbins_x_orig));
311	>	free_string_field (&(args_info->nbins_y_orig));
312	>	free_string_field (&(args_info->nanglebins_orig));
313	>	free_string_field (&(args_info->length_orig));
314	>	free_string_field (&(args_info->rcut_orig));
315	>	free_string_field (&(args_info->zoffset_orig));
316	>	free_string_field (&(args_info->sele1_arg));
317	>	free_string_field (&(args_info->sele1_orig));
318	>	free_string_field (&(args_info->sele2_arg));
319	>	free_string_field (&(args_info->sele2_orig));
320	>	free_string_field (&(args_info->sele3_arg));
321	>	free_string_field (&(args_info->sele3_orig));
322	>	free_string_field (&(args_info->refsele_arg));
323	>	free_string_field (&(args_info->refsele_orig));
324	>	free_string_field (&(args_info->comsele_arg));
325	>	free_string_field (&(args_info->comsele_orig));
326	>	free_string_field (&(args_info->molname_arg));
327	>	free_string_field (&(args_info->molname_orig));
328	>	free_string_field (&(args_info->begin_orig));
329	>	free_string_field (&(args_info->end_orig));
330	>	free_string_field (&(args_info->radius_orig));
331	>
332	>
333	>	for (i = 0; i < args_info->inputs_num; ++i)
334	>	free (args_info->inputs [i]);
335	>
336	>	if (args_info->inputs_num)
337	>	free (args_info->inputs);
338	>
339	>	clear_given (args_info);
340	>	}
341	>
342	>
343	>	static void
344	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
345	>	{
346	>	if (arg) {
347	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
348	>	} else {
349	>	fprintf(outfile, "%s\n", opt);
350	>	}
351	>	}
352	>
353	>
354	>	int
355	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
356	>	{
357	>	int i = 0;
358	>
359	>	if (!outfile)
360	>	{
361	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
362	>	return EXIT_FAILURE;
363	>	}
364	>
365	>	if (args_info->help_given)
366	>	write_into_file(outfile, "help", 0, 0 );
367	>	if (args_info->version_given)
368	>	write_into_file(outfile, "version", 0, 0 );
369	>	if (args_info->input_given)
370	>	write_into_file(outfile, "input", args_info->input_orig, 0);
371	>	if (args_info->output_given)
372	>	write_into_file(outfile, "output", args_info->output_orig, 0);
373	>	if (args_info->step_given)
374	>	write_into_file(outfile, "step", args_info->step_orig, 0);
375	>	if (args_info->nbins_given)
376	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
377	>	if (args_info->nbins_x_given)
378	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
379	>	if (args_info->nbins_y_given)
380	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
381	>	if (args_info->nanglebins_given)
382	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
383	>	if (args_info->length_given)
384	>	write_into_file(outfile, "length", args_info->length_orig, 0);
385	>	if (args_info->rcut_given)
386	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
387	>	if (args_info->zoffset_given)
388	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
389	>	if (args_info->sele1_given)
390	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
391	>	if (args_info->sele2_given)
392	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
393	>	if (args_info->sele3_given)
394	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
395	>	if (args_info->refsele_given)
396	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
397	>	if (args_info->comsele_given)
398	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
399	>	if (args_info->molname_given)
400	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
401	>	if (args_info->begin_given)
402	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
403	>	if (args_info->end_given)
404	>	write_into_file(outfile, "end", args_info->end_orig, 0);
405	>	if (args_info->radius_given)
406	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
407	>	if (args_info->bo_given)
408	>	write_into_file(outfile, "bo", 0, 0 );
409	>	if (args_info->bor_given)
410	>	write_into_file(outfile, "bor", 0, 0 );
411	>	if (args_info->bad_given)
412	>	write_into_file(outfile, "bad", 0, 0 );
413	>	if (args_info->gofr_given)
414	>	write_into_file(outfile, "gofr", 0, 0 );
415	>	if (args_info->gofz_given)
416	>	write_into_file(outfile, "gofz", 0, 0 );
417	>	if (args_info->r_theta_given)
418	>	write_into_file(outfile, "r_theta", 0, 0 );
419	>	if (args_info->r_omega_given)
420	>	write_into_file(outfile, "r_omega", 0, 0 );
421	>	if (args_info->theta_omega_given)
422	>	write_into_file(outfile, "theta_omega", 0, 0 );
423	>	if (args_info->gxyz_given)
424	>	write_into_file(outfile, "gxyz", 0, 0 );
425	>	if (args_info->p2_given)
426	>	write_into_file(outfile, "p2", 0, 0 );
427	>	if (args_info->rp2_given)
428	>	write_into_file(outfile, "rp2", 0, 0 );
429	>	if (args_info->scd_given)
430	>	write_into_file(outfile, "scd", 0, 0 );
431	>	if (args_info->density_given)
432	>	write_into_file(outfile, "density", 0, 0 );
433	>	if (args_info->slab_density_given)
434	>	write_into_file(outfile, "slab_density", 0, 0 );
435	>	if (args_info->p_angle_given)
436	>	write_into_file(outfile, "p_angle", 0, 0 );
437	>	if (args_info->hxy_given)
438	>	write_into_file(outfile, "hxy", 0, 0 );
439	>	if (args_info->rho_r_given)
440	>	write_into_file(outfile, "rho_r", 0, 0 );
441	>	if (args_info->hullvol_given)
442	>	write_into_file(outfile, "hullvol", 0, 0 );
443	>
444	>
445	>	i = EXIT_SUCCESS;
446	>	return i;
447	>	}
448	>
449	>	int
450	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
451	>	{
452	>	FILE *outfile;
453	>	int i = 0;
454	>
455	>	outfile = fopen(filename, "w");
456	>
457	>	if (!outfile)
458	>	{
459	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
460	>	return EXIT_FAILURE;
461	>	}
462	>
463	>	i = cmdline_parser_dump(outfile, args_info);
464	>	fclose (outfile);
465	>
466	>	return i;
467	>	}
468	>
469	>	void
470	>	cmdline_parser_free (struct gengetopt_args_info *args_info)
471	>	{
472	>	cmdline_parser_release (args_info);
473	>	}
474	>
475	>	/** @brief replacement of strdup, which is not standard */
476		char *
477		gengetopt_strdup (const char *s)
478		{
479	<	char *result = (char*)malloc(strlen(s) + 1);
479	>	char *result = NULL;
480	>	if (!s)
481	>	return result;
482	>
483	>	result = (char*)malloc(strlen(s) + 1);
484		if (result == (char*)0)
485		return (char*)0;
486		strcpy(result, s);
487		return result;
488		}
489
490	<	int
491	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
490	>	static void
491	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
492		{
493	<	int c;        /* Character of the parsed option.  */
494	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
493	>	if (! args_info->staticProps_group_counter)
494	>	return;
495
496	<
497	<	args_info->help_given = 0 ;
498	<	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 ;
496	>	args_info->bo_given = 0 ;
497	>	args_info->bor_given = 0 ;
498	>	args_info->bad_given = 0 ;
499		args_info->gofr_given = 0 ;
500	+	args_info->gofz_given = 0 ;
501		args_info->r_theta_given = 0 ;
502		args_info->r_omega_given = 0 ;
503		args_info->theta_omega_given = 0 ;
504		args_info->gxyz_given = 0 ;
505		args_info->p2_given = 0 ;
506	+	args_info->rp2_given = 0 ;
507		args_info->scd_given = 0 ;
508		args_info->density_given = 0 ;
509	<	#define clear_args() { \
510	<	args_info->input_arg = NULL; \
511	<	args_info->output_arg = NULL; \
512	<	args_info->step_arg = 1 ;\
513	<	args_info->nrbins_arg = 100 ;\
514	<	args_info->nanglebins_arg = 50 ;\
515	<	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; \
509	>	args_info->slab_density_given = 0 ;
510	>	args_info->p_angle_given = 0 ;
511	>	args_info->hxy_given = 0 ;
512	>	args_info->rho_r_given = 0 ;
513	>	args_info->hullvol_given = 0 ;
514	>
515	>	args_info->staticProps_group_counter = 0;
516		}
517
518	<	clear_args();
518	>	int
519	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
520	>	{
521	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
522	>	}
523
524	+	int
525	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
526	+	struct cmdline_parser_params *params)
527	+	{
528	+	int result;
529	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
530	+
531	+	if (result == EXIT_FAILURE)
532	+	{
533	+	cmdline_parser_free (args_info);
534	+	exit (EXIT_FAILURE);
535	+	}
536	+
537	+	return result;
538	+	}
539	+
540	+	int
541	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
542	+	{
543	+	int result;
544	+	struct cmdline_parser_params params;
545	+
546	+	params.override = override;
547	+	params.initialize = initialize;
548	+	params.check_required = check_required;
549	+	params.check_ambiguity = 0;
550	+	params.print_errors = 1;
551	+
552	+	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
553	+
554	+	if (result == EXIT_FAILURE)
555	+	{
556	+	cmdline_parser_free (args_info);
557	+	exit (EXIT_FAILURE);
558	+	}
559	+
560	+	return result;
561	+	}
562	+
563	+	int
564	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
565	+	{
566	+	int result = EXIT_SUCCESS;
567	+
568	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
569	+	result = EXIT_FAILURE;
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_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
582	+	{
583	+	int error = 0;
584	+
585	+	/* checks for required options */
586	+	if (! args_info->input_given)
587	+	{
588	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
589	+	error = 1;
590	+	}
591	+
592	+	if (args_info->staticProps_group_counter == 0)
593	+	{
594	+	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 : ""));
595	+	error = 1;
596	+	}
597	+
598	+
599	+	/* checks for dependences among options */
600	+
601	+	return error;
602	+	}
603	+
604	+
605	+	static char *package_name = 0;
606	+
607	+	/**
608	+	* @brief updates an option
609	+	* @param field the generic pointer to the field to update
610	+	* @param orig_field the pointer to the orig field
611	+	* @param field_given the pointer to the number of occurrence of this option
612	+	* @param prev_given the pointer to the number of occurrence already seen
613	+	* @param value the argument for this option (if null no arg was specified)
614	+	* @param possible_values the possible values for this option (if specified)
615	+	* @param default_value the default value (in case the option only accepts fixed values)
616	+	* @param arg_type the type of this option
617	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
618	+	* @param override @see cmdline_parser_params.override
619	+	* @param no_free whether to free a possible previous value
620	+	* @param multiple_option whether this is a multiple option
621	+	* @param long_opt the corresponding long option
622	+	* @param short_opt the corresponding short option (or '-' if none)
623	+	* @param additional_error possible further error specification
624	+	*/
625	+	static
626	+	int update_arg(void *field, char **orig_field,
627	+	unsigned int *field_given, unsigned int *prev_given,
628	+	char *value, char *possible_values[], const char *default_value,
629	+	cmdline_parser_arg_type arg_type,
630	+	int check_ambiguity, int override,
631	+	int no_free, int multiple_option,
632	+	const char *long_opt, char short_opt,
633	+	const char *additional_error)
634	+	{
635	+	char *stop_char = 0;
636	+	const char *val = value;
637	+	int found;
638	+	char **string_field;
639	+
640	+	stop_char = 0;
641	+	found = 0;
642	+
643	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
644	+	{
645	+	if (short_opt != '-')
646	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
647	+	package_name, long_opt, short_opt,
648	+	(additional_error ? additional_error : ""));
649	+	else
650	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
651	+	package_name, long_opt,
652	+	(additional_error ? additional_error : ""));
653	+	return 1; /* failure */
654	+	}
655	+
656	+
657	+	if (field_given && *field_given && ! override)
658	+	return 0;
659	+	if (prev_given)
660	+	(*prev_given)++;
661	+	if (field_given)
662	+	(*field_given)++;
663	+	if (possible_values)
664	+	val = possible_values[found];
665	+
666	+	switch(arg_type) {
667	+	case ARG_INT:
668	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
669	+	break;
670	+	case ARG_DOUBLE:
671	+	if (val) *((double *)field) = strtod (val, &stop_char);
672	+	break;
673	+	case ARG_STRING:
674	+	if (val) {
675	+	string_field = (char **)field;
676	+	if (!no_free && *string_field)
677	+	free (*string_field); /* free previous string */
678	+	*string_field = gengetopt_strdup (val);
679	+	}
680	+	break;
681	+	default:
682	+	break;
683	+	};
684	+
685	+	/* check numeric conversion */
686	+	switch(arg_type) {
687	+	case ARG_INT:
688	+	case ARG_DOUBLE:
689	+	if (val && !(stop_char && *stop_char == '\0')) {
690	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
691	+	return 1; /* failure */
692	+	}
693	+	break;
694	+	default:
695	+	;
696	+	};
697	+
698	+	/* store the original value */
699	+	switch(arg_type) {
700	+	case ARG_NO:
701	+	break;
702	+	default:
703	+	if (value && orig_field) {
704	+	if (no_free) {
705	+	*orig_field = value;
706	+	} else {
707	+	if (*orig_field)
708	+	free (*orig_field); /* free previous string */
709	+	*orig_field = gengetopt_strdup (value);
710	+	}
711	+	}
712	+	};
713	+
714	+	return 0; /* OK */
715	+	}
716	+
717	+
718	+	int
719	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
720	+	struct cmdline_parser_params *params, const char *additional_error)
721	+	{
722	+	int c;        /* Character of the parsed option.  */
723	+
724	+	int error = 0;
725	+	struct gengetopt_args_info local_args_info;
726	+
727	+	int override;
728	+	int initialize;
729	+	int check_required;
730	+	int check_ambiguity;
731	+
732	+	package_name = argv[0];
733	+
734	+	override = params->override;
735	+	initialize = params->initialize;
736	+	check_required = params->check_required;
737	+	check_ambiguity = params->check_ambiguity;
738	+
739	+	if (initialize)
740	+	cmdline_parser_init (args_info);
741	+
742	+	cmdline_parser_init (&local_args_info);
743	+
744		optarg = 0;
745	<	optind = 1;
746	<	opterr = 1;
745	>	optind = 0;
746	>	opterr = params->print_errors;
747		optopt = '?';
748
749		while (1)
750		{
751		int option_index = 0;
134	–	char *stop_char;
752
753		static struct option long_options[] = {
754		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 756 | cmdline_parser (int argc, char * const *argv, struct g
756		{ "input",      1, NULL, 'i' },
757		{ "output",     1, NULL, 'o' },
758		{ "step",       1, NULL, 'n' },
759	<	{ "nrbins",     1, NULL, 'r' },
759	>	{ "nbins",      1, NULL, 'b' },
760	>	{ "nbins_x",    1, NULL, 'x' },
761	>	{ "nbins_y",    1, NULL, 'y' },
762		{ "nanglebins", 1, NULL, 'a' },
763	<	{ "length",     1, NULL, 'l' },
763	>	{ "length",     1, NULL, 0 },
764	>	{ "rcut",       1, NULL, 'c' },
765	>	{ "zoffset",    1, NULL, 'z' },
766		{ "sele1",      1, NULL, 0 },
767		{ "sele2",      1, NULL, 0 },
768		{ "sele3",      1, NULL, 0 },
769		{ "refsele",    1, NULL, 0 },
770	+	{ "comsele",    1, NULL, 0 },
771		{ "molname",    1, NULL, 0 },
772		{ "begin",      1, NULL, 0 },
773		{ "end",        1, NULL, 0 },
774	<	{ "gofr",       0, NULL, 0 },
774	>	{ "radius",     1, NULL, 0 },
775	>	{ "bo", 0, NULL, 0 },
776	>	{ "bor",        0, NULL, 0 },
777	>	{ "bad",        0, NULL, 0 },
778	>	{ "gofr",       0, NULL, 'g' },
779	>	{ "gofz",       0, NULL, 0 },
780		{ "r_theta",    0, NULL, 0 },
781		{ "r_omega",    0, NULL, 0 },
782		{ "theta_omega",        0, NULL, 0 },
783		{ "gxyz",       0, NULL, 0 },
784	<	{ "p2", 0, NULL, 0 },
785	<	{ "scd",        0, NULL, 0 },
786	<	{ "density",    0, NULL, 0 },
784	>	{ "p2", 0, NULL, 'p' },
785	>	{ "rp2",        0, NULL, 0 },
786	>	{ "scd",        0, NULL, 's' },
787	>	{ "density",    0, NULL, 'd' },
788	>	{ "slab_density",       0, NULL, 0 },
789	>	{ "p_angle",    0, NULL, 0 },
790	>	{ "hxy",        0, NULL, 0 },
791	>	{ "rho_r",      0, NULL, 0 },
792	>	{ "hullvol",    0, NULL, 0 },
793		{ NULL, 0, NULL, 0 }
794		};
795
796	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
796	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
797
798		if (c == -1) break;       /* Exit from `while (1)' loop.  */
799
800		switch (c)
801		{
802		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
803		cmdline_parser_print_help ();
804	+	cmdline_parser_free (&local_args_info);
805		exit (EXIT_SUCCESS);
806
807		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
808		cmdline_parser_print_version ();
809	+	cmdline_parser_free (&local_args_info);
810		exit (EXIT_SUCCESS);
811
812		case 'i':       /* input dump file.  */
813	<	if (args_info->input_given)
814	<	{
815	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
816	<	clear_args ();
817	<	exit (EXIT_FAILURE);
818	<	}
819	<	args_info->input_given = 1;
820	<	args_info->input_arg = gengetopt_strdup (optarg);
813	>
814	>
815	>	if (update_arg( (void *)&(args_info->input_arg),
816	>	&(args_info->input_orig), &(args_info->input_given),
817	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
818	>	check_ambiguity, override, 0, 0,
819	>	"input", 'i',
820	>	additional_error))
821	>	goto failure;
822	>
823		break;
190	–
824		case 'o':       /* output file name.  */
825	<	if (args_info->output_given)
826	<	{
827	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
828	<	clear_args ();
829	<	exit (EXIT_FAILURE);
830	<	}
831	<	args_info->output_given = 1;
832	<	args_info->output_arg = gengetopt_strdup (optarg);
825	>
826	>
827	>	if (update_arg( (void *)&(args_info->output_arg),
828	>	&(args_info->output_orig), &(args_info->output_given),
829	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
830	>	check_ambiguity, override, 0, 0,
831	>	"output", 'o',
832	>	additional_error))
833	>	goto failure;
834	>
835		break;
201	–
836		case 'n':       /* process every n frame.  */
837	<	if (args_info->step_given)
838	<	{
839	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
840	<	clear_args ();
841	<	exit (EXIT_FAILURE);
842	<	}
843	<	args_info->step_given = 1;
844	<	args_info->step_arg = strtol (optarg,&stop_char,0);
837	>
838	>
839	>	if (update_arg( (void *)&(args_info->step_arg),
840	>	&(args_info->step_orig), &(args_info->step_given),
841	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
842	>	check_ambiguity, override, 0, 0,
843	>	"step", 'n',
844	>	additional_error))
845	>	goto failure;
846	>
847		break;
848	<
849	<	case 'r':       /* number of bins for distance.  */
850	<	if (args_info->nrbins_given)
851	<	{
852	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
853	<	clear_args ();
854	<	exit (EXIT_FAILURE);
855	<	}
856	<	args_info->nrbins_given = 1;
857	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
848	>	case 'b':       /* number of bins (general purpose).  */
849	>
850	>
851	>	if (update_arg( (void *)&(args_info->nbins_arg),
852	>	&(args_info->nbins_orig), &(args_info->nbins_given),
853	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
854	>	check_ambiguity, override, 0, 0,
855	>	"nbins", 'b',
856	>	additional_error))
857	>	goto failure;
858	>
859		break;
860	<
860	>	case 'x':       /* number of bins in x axis.  */
861	>
862	>
863	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
864	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
865	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
866	>	check_ambiguity, override, 0, 0,
867	>	"nbins_x", 'x',
868	>	additional_error))
869	>	goto failure;
870	>
871	>	break;
872	>	case 'y':       /* number of bins in y axis.  */
873	>
874	>
875	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
876	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
877	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
878	>	check_ambiguity, override, 0, 0,
879	>	"nbins_y", 'y',
880	>	additional_error))
881	>	goto failure;
882	>
883	>	break;
884		case 'a':       /* number of bins for cos(angle).  */
885	<	if (args_info->nanglebins_given)
886	<	{
887	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
888	<	clear_args ();
889	<	exit (EXIT_FAILURE);
890	<	}
891	<	args_info->nanglebins_given = 1;
892	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
885	>
886	>
887	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
888	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
889	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
890	>	check_ambiguity, override, 0, 0,
891	>	"nanglebins", 'a',
892	>	additional_error))
893	>	goto failure;
894	>
895		break;
896	<
897	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
898	<	if (args_info->length_given)
899	<	{
900	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
901	<	clear_args ();
902	<	exit (EXIT_FAILURE);
903	<	}
904	<	args_info->length_given = 1;
905	<	args_info->length_arg = strtod (optarg, NULL);
896	>	case 'c':       /* cutoff radius (rcut).  */
897	>
898	>
899	>	if (update_arg( (void *)&(args_info->rcut_arg),
900	>	&(args_info->rcut_orig), &(args_info->rcut_given),
901	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
902	>	check_ambiguity, override, 0, 0,
903	>	"rcut", 'c',
904	>	additional_error))
905	>	goto failure;
906	>
907		break;
908	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
909	+
910	+
911	+	if (update_arg( (void *)&(args_info->zoffset_arg),
912	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
913	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
914	+	check_ambiguity, override, 0, 0,
915	+	"zoffset", 'z',
916	+	additional_error))
917	+	goto failure;
918	+
919	+	break;
920	+	case 'g':       /* g(r).  */
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->gofr_given),
928	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
929	+	check_ambiguity, override, 0, 0,
930	+	"gofr", 'g',
931	+	additional_error))
932	+	goto failure;
933	+
934	+	break;
935	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be 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->p2_given),
943	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
944	+	check_ambiguity, override, 0, 0,
945	+	"p2", 'p',
946	+	additional_error))
947	+	goto failure;
948	+
949	+	break;
950	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
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->scd_given),
958	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
959	+	check_ambiguity, override, 0, 0,
960	+	"scd", 's',
961	+	additional_error))
962	+	goto failure;
963	+
964	+	break;
965	+	case 'd':       /* density plot.  */
966	+
967	+	if (args_info->staticProps_group_counter && override)
968	+	reset_group_staticProps (args_info);
969	+	args_info->staticProps_group_counter += 1;
970	+
971	+	if (update_arg( 0 ,
972	+	0 , &(args_info->density_given),
973	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
974	+	check_ambiguity, override, 0, 0,
975	+	"density", 'd',
976	+	additional_error))
977	+	goto failure;
978	+
979	+	break;
980
246	–
981		case 0: /* Long option with no short option */
982	<	/* select the first stuntdouble set.  */
983	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
982	>	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
983	>	if (strcmp (long_options[option_index].name, "length") == 0)
984		{
985	<	if (args_info->sele1_given)
986	<	{
987	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
988	<	clear_args ();
989	<	exit (EXIT_FAILURE);
990	<	}
991	<	args_info->sele1_given = 1;
992	<	args_info->sele1_arg = gengetopt_strdup (optarg);
993	<	break;
985	>
986	>
987	>	if (update_arg( (void *)&(args_info->length_arg),
988	>	&(args_info->length_orig), &(args_info->length_given),
989	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
990	>	check_ambiguity, override, 0, 0,
991	>	"length", '-',
992	>	additional_error))
993	>	goto failure;
994	>
995		}
996	+	/* select the first stuntdouble set.  */
997	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
998	+	{
999
1000	+
1001	+	if (update_arg( (void *)&(args_info->sele1_arg),
1002	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1003	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1004	+	check_ambiguity, override, 0, 0,
1005	+	"sele1", '-',
1006	+	additional_error))
1007	+	goto failure;
1008	+
1009	+	}
1010		/* select the second stuntdouble set.  */
1011		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1012		{
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	–	}
1013
1014	+
1015	+	if (update_arg( (void *)&(args_info->sele2_arg),
1016	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1017	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1018	+	check_ambiguity, override, 0, 0,
1019	+	"sele2", '-',
1020	+	additional_error))
1021	+	goto failure;
1022	+
1023	+	}
1024		/* select the third stuntdouble set.  */
1025		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1026		{
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	–	}
1027
1028	+
1029	+	if (update_arg( (void *)&(args_info->sele3_arg),
1030	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1031	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1032	+	check_ambiguity, override, 0, 0,
1033	+	"sele3", '-',
1034	+	additional_error))
1035	+	goto failure;
1036	+
1037	+	}
1038		/* select reference (use and only use with --gxyz).  */
1039		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1040		{
1041	<	if (args_info->refsele_given)
1042	<	{
1043	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1044	<	clear_args ();
1045	<	exit (EXIT_FAILURE);
1046	<	}
1047	<	args_info->refsele_given = 1;
1048	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1049	<	break;
1041	>
1042	>
1043	>	if (update_arg( (void *)&(args_info->refsele_arg),
1044	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1045	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1046	>	check_ambiguity, override, 0, 0,
1047	>	"refsele", '-',
1048	>	additional_error))
1049	>	goto failure;
1050	>
1051		}
1052	+	/* select stunt doubles for center-of-mass reference point.  */
1053	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1054	+	{
1055
1056	+
1057	+	if (update_arg( (void *)&(args_info->comsele_arg),
1058	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1059	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1060	+	check_ambiguity, override, 0, 0,
1061	+	"comsele", '-',
1062	+	additional_error))
1063	+	goto failure;
1064	+
1065	+	}
1066		/* molecule name.  */
1067		else if (strcmp (long_options[option_index].name, "molname") == 0)
1068		{
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	–	}
1069
1070	<	/* begin interanl index.  */
1070	>
1071	>	if (update_arg( (void *)&(args_info->molname_arg),
1072	>	&(args_info->molname_orig), &(args_info->molname_given),
1073	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1074	>	check_ambiguity, override, 0, 0,
1075	>	"molname", '-',
1076	>	additional_error))
1077	>	goto failure;
1078	>
1079	>	}
1080	>	/* begin internal index.  */
1081		else if (strcmp (long_options[option_index].name, "begin") == 0)
1082		{
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	–	}
1083
1084	+
1085	+	if (update_arg( (void *)&(args_info->begin_arg),
1086	+	&(args_info->begin_orig), &(args_info->begin_given),
1087	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1088	+	check_ambiguity, override, 0, 0,
1089	+	"begin", '-',
1090	+	additional_error))
1091	+	goto failure;
1092	+
1093	+	}
1094		/* end internal index.  */
1095		else if (strcmp (long_options[option_index].name, "end") == 0)
1096		{
1097	<	if (args_info->end_given)
1098	<	{
1099	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1100	<	clear_args ();
1101	<	exit (EXIT_FAILURE);
1102	<	}
1103	<	args_info->end_given = 1;
1104	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1105	<	break;
1097	>
1098	>
1099	>	if (update_arg( (void *)&(args_info->end_arg),
1100	>	&(args_info->end_orig), &(args_info->end_given),
1101	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1102	>	check_ambiguity, override, 0, 0,
1103	>	"end", '-',
1104	>	additional_error))
1105	>	goto failure;
1106	>
1107		}
1108	+	/* nanoparticle radius.  */
1109	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1110	+	{
1111
1112	<	/* g(r).  */
1113	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1112	>
1113	>	if (update_arg( (void *)&(args_info->radius_arg),
1114	>	&(args_info->radius_orig), &(args_info->radius_given),
1115	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1116	>	check_ambiguity, override, 0, 0,
1117	>	"radius", '-',
1118	>	additional_error))
1119	>	goto failure;
1120	>
1121	>	}
1122	>	/* bond order parameter (--rcut must be specified).  */
1123	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1124		{
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;
1125
1126	<	break;
1126	>	if (args_info->staticProps_group_counter && override)
1127	>	reset_group_staticProps (args_info);
1128	>	args_info->staticProps_group_counter += 1;
1129	>
1130	>	if (update_arg( 0 ,
1131	>	0 , &(args_info->bo_given),
1132	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1133	>	check_ambiguity, override, 0, 0,
1134	>	"bo", '-',
1135	>	additional_error))
1136	>	goto failure;
1137	>
1138		}
1139	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1140	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1141	+	{
1142
1143	+	if (args_info->staticProps_group_counter && override)
1144	+	reset_group_staticProps (args_info);
1145	+	args_info->staticProps_group_counter += 1;
1146	+
1147	+	if (update_arg( 0 ,
1148	+	0 , &(args_info->bor_given),
1149	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1150	+	check_ambiguity, override, 0, 0,
1151	+	"bor", '-',
1152	+	additional_error))
1153	+	goto failure;
1154	+
1155	+	}
1156	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1157	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1158	+	{
1159	+
1160	+	if (args_info->staticProps_group_counter && override)
1161	+	reset_group_staticProps (args_info);
1162	+	args_info->staticProps_group_counter += 1;
1163	+
1164	+	if (update_arg( 0 ,
1165	+	0 , &(args_info->bad_given),
1166	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1167	+	check_ambiguity, override, 0, 0,
1168	+	"bad", '-',
1169	+	additional_error))
1170	+	goto failure;
1171	+
1172	+	}
1173	+	/* g(z).  */
1174	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1175	+	{
1176	+
1177	+	if (args_info->staticProps_group_counter && override)
1178	+	reset_group_staticProps (args_info);
1179	+	args_info->staticProps_group_counter += 1;
1180	+
1181	+	if (update_arg( 0 ,
1182	+	0 , &(args_info->gofz_given),
1183	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1184	+	check_ambiguity, override, 0, 0,
1185	+	"gofz", '-',
1186	+	additional_error))
1187	+	goto failure;
1188	+
1189	+	}
1190		/* g(r, cos(theta)).  */
1191		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1192		{
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;
1193
1194	<	break;
1195	<	}
1194	>	if (args_info->staticProps_group_counter && override)
1195	>	reset_group_staticProps (args_info);
1196	>	args_info->staticProps_group_counter += 1;
1197
1198	+	if (update_arg( 0 ,
1199	+	0 , &(args_info->r_theta_given),
1200	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1201	+	check_ambiguity, override, 0, 0,
1202	+	"r_theta", '-',
1203	+	additional_error))
1204	+	goto failure;
1205	+
1206	+	}
1207		/* g(r, cos(omega)).  */
1208		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1209		{
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;
1210
1211	<	break;
1212	<	}
1211	>	if (args_info->staticProps_group_counter && override)
1212	>	reset_group_staticProps (args_info);
1213	>	args_info->staticProps_group_counter += 1;
1214
1215	+	if (update_arg( 0 ,
1216	+	0 , &(args_info->r_omega_given),
1217	+	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1218	+	check_ambiguity, override, 0, 0,
1219	+	"r_omega", '-',
1220	+	additional_error))
1221	+	goto failure;
1222	+
1223	+	}
1224		/* g(cos(theta), cos(omega)).  */
1225		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1226		{
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;
1227
1228	<	break;
1229	<	}
1228	>	if (args_info->staticProps_group_counter && override)
1229	>	reset_group_staticProps (args_info);
1230	>	args_info->staticProps_group_counter += 1;
1231
1232	+	if (update_arg( 0 ,
1233	+	0 , &(args_info->theta_omega_given),
1234	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1235	+	check_ambiguity, override, 0, 0,
1236	+	"theta_omega", '-',
1237	+	additional_error))
1238	+	goto failure;
1239	+
1240	+	}
1241		/* g(x, y, z).  */
1242		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1243		{
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;
1244
1245	<	break;
1245	>	if (args_info->staticProps_group_counter && override)
1246	>	reset_group_staticProps (args_info);
1247	>	args_info->staticProps_group_counter += 1;
1248	>
1249	>	if (update_arg( 0 ,
1250	>	0 , &(args_info->gxyz_given),
1251	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1252	>	check_ambiguity, override, 0, 0,
1253	>	"gxyz", '-',
1254	>	additional_error))
1255	>	goto failure;
1256	>
1257		}
1258	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1259	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1260	+	{
1261
1262	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1263	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1262	>	if (args_info->staticProps_group_counter && override)
1263	>	reset_group_staticProps (args_info);
1264	>	args_info->staticProps_group_counter += 1;
1265	>
1266	>	if (update_arg( 0 ,
1267	>	0 , &(args_info->rp2_given),
1268	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1269	>	check_ambiguity, override, 0, 0,
1270	>	"rp2", '-',
1271	>	additional_error))
1272	>	goto failure;
1273	>
1274	>	}
1275	>	/* slab density.  */
1276	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1277		{
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;
1278
1279	<	break;
1279	>	if (args_info->staticProps_group_counter && override)
1280	>	reset_group_staticProps (args_info);
1281	>	args_info->staticProps_group_counter += 1;
1282	>
1283	>	if (update_arg( 0 ,
1284	>	0 , &(args_info->slab_density_given),
1285	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1286	>	check_ambiguity, override, 0, 0,
1287	>	"slab_density", '-',
1288	>	additional_error))
1289	>	goto failure;
1290	>
1291		}
1292	+	/* p(cos(theta)).  */
1293	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1294	+	{
1295
1296	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1297	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1296	>	if (args_info->staticProps_group_counter && override)
1297	>	reset_group_staticProps (args_info);
1298	>	args_info->staticProps_group_counter += 1;
1299	>
1300	>	if (update_arg( 0 ,
1301	>	0 , &(args_info->p_angle_given),
1302	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1303	>	check_ambiguity, override, 0, 0,
1304	>	"p_angle", '-',
1305	>	additional_error))
1306	>	goto failure;
1307	>
1308	>	}
1309	>	/* hxy.  */
1310	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1311		{
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;
1312
1313	<	break;
1313	>	if (args_info->staticProps_group_counter && override)
1314	>	reset_group_staticProps (args_info);
1315	>	args_info->staticProps_group_counter += 1;
1316	>
1317	>	if (update_arg( 0 ,
1318	>	0 , &(args_info->hxy_given),
1319	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1320	>	check_ambiguity, override, 0, 0,
1321	>	"hxy", '-',
1322	>	additional_error))
1323	>	goto failure;
1324	>
1325		}
1326	+	/* rho of R.  */
1327	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1328	+	{
1329
1330	<	/* density plot (--sele1 must be specified).  */
1331	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1330	>	if (args_info->staticProps_group_counter && override)
1331	>	reset_group_staticProps (args_info);
1332	>	args_info->staticProps_group_counter += 1;
1333	>
1334	>	if (update_arg( 0 ,
1335	>	0 , &(args_info->rho_r_given),
1336	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1337	>	check_ambiguity, override, 0, 0,
1338	>	"rho_r", '-',
1339	>	additional_error))
1340	>	goto failure;
1341	>
1342	>	}
1343	>	/* hull volume of nanoparticle.  */
1344	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1345		{
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;
1346
1347	<	break;
1347	>	if (args_info->staticProps_group_counter && override)
1348	>	reset_group_staticProps (args_info);
1349	>	args_info->staticProps_group_counter += 1;
1350	>
1351	>	if (update_arg( 0 ,
1352	>	0 , &(args_info->hullvol_given),
1353	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1354	>	check_ambiguity, override, 0, 0,
1355	>	"hullvol", '-',
1356	>	additional_error))
1357	>	goto failure;
1358	>
1359		}
1360
1361	<
1361	>	break;
1362		case '?':       /* Invalid option.  */
1363		/* `getopt_long' already printed an error message.  */
1364	<	exit (EXIT_FAILURE);
1364	>	goto failure;
1365
1366		default:        /* bug: option not considered.  */
1367	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1367	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1368		abort ();
1369		} /* switch */
1370		} /* while */
1371
1372	<	if ( staticProps_group_counter != 1)
1372	>	if (args_info->staticProps_group_counter > 1)
1373		{
1374	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1375	<	missing_required_options = 1;
1374	>	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 : ""));
1375	>	error = 1;
1376		}
1377
1378
1379	<	if (! args_info->input_given)
1379	>
1380	>	if (check_required)
1381		{
1382	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1382	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1383		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1384
1385	+	cmdline_parser_release (&local_args_info);
1386	+
1387	+	if ( error )
1388	+	return (EXIT_FAILURE);
1389	+
1390	+	if (optind < argc)
1391	+	{
1392	+	int i = 0 ;
1393	+	int found_prog_name = 0;
1394	+	/* whether program name, i.e., argv[0], is in the remaining args
1395	+	(this may happen with some implementations of getopt,
1396	+	but surely not with the one included by gengetopt) */
1397	+
1398	+	i = optind;
1399	+	while (i < argc)
1400	+	if (argv[i++] == argv[0]) {
1401	+	found_prog_name = 1;
1402	+	break;
1403	+	}
1404	+	i = 0;
1405	+
1406	+	args_info->inputs_num = argc - optind - found_prog_name;
1407	+	args_info->inputs =
1408	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1409	+	while (optind < argc)
1410	+	if (argv[optind++] != argv[0])
1411	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1412	+	}
1413	+
1414		return 0;
1415	+
1416	+	failure:
1417	+
1418	+	cmdline_parser_release (&local_args_info);
1419	+	return (EXIT_FAILURE);
1420		}

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