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

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 544 by tim, Fri May 27 04:41:34 2005 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1762 by plouden, Thu Jun 28 20:17:33 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd
4	>	gengetopt -i StaticProps.ggo -c cpp -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	+	/* 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	<	/* If we use autoconf.  */
21	<	#ifdef HAVE_CONFIG_H
18	<	#include "config.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22		#endif
23
24	<	#include "getopt.h"
24	>	#include <getopt.h>
25
26		#include "StaticPropsCmd.h"
27
28	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
28	>	const char *gengetopt_args_info_purpose = "";
29
30	<	void
32	<	cmdline_parser_print_help (void)
33	<	{
34	<	cmdline_parser_print_version ();
35	<	printf("\n"
36	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	<	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	<	}
30	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
31
32	+	const char *gengetopt_args_info_description = "";
33
34	<	static char *gengetopt_strdup (const char *s);
34	>	const char *gengetopt_args_info_help[] = {
35	>	"  -h, --help                    Print help and exit",
36	>	"  -V, --version                 Print version and exit",
37	>	"  -i, --input=filename          input dump file",
38	>	"  -o, --output=filename         output file name",
39	>	"  -n, --step=INT                process every n frame  (default=`1')",
40	>	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
41	>	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
42	>	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
43	>	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
44	>	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
45	>	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
46	>	"      --dz=DOUBLE               slab width (dz)",
47	>	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
48	>	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
49	>	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
50	>	"      --sele1=selection script  select the first stuntdouble set",
51	>	"      --sele2=selection script  select the second stuntdouble set",
52	>	"      --sele3=selection script  select the third stuntdouble set",
53	>	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
54	>	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
55	>	"      --molname=STRING          molecule name",
56	>	"      --begin=INT               begin internal index",
57	>	"      --end=INT                 end internal index",
58	>	"      --radius=DOUBLE           nanoparticle radius",
59	>	"\n Group: staticProps\n   an option of this group is required",
60	>	"      --bo                      bond order parameter (--rcut must be specified)",
61	>	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
62	>	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
63	>	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
64	>	"  -g, --gofr                    g(r)",
65	>	"      --gofz                    g(z)",
66	>	"      --r_theta                 g(r, cos(theta))",
67	>	"      --r_omega                 g(r, cos(omega))",
68	>	"      --r_z                     g(r, z)",
69	>	"      --theta_omega             g(cos(theta), cos(omega))",
70	>	"      --gxyz                    g(x, y, z)",
71	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
72	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
73	>	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
74	>	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
75	>	"  -d, --density                 density plot",
76	>	"      --slab_density            slab density",
77	>	"      --p_angle                 p(cos(theta))",
78	>	"      --hxy                     hxy",
79	>	"      --rho_r                   rho of R",
80	>	"      --angle_r                 angle of R",
81	>	"      --hullvol                 hull volume of nanoparticle",
82	>	"      --rodlength               length of nanorod",
83	>	"  -Q, --tet_param               tetrahedrality order parameter",
84	>	"      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
85	>	0
86	>	};
87
88	<	/* gengetopt_strdup() */
89	<	/* strdup.c replacement of strdup, which is not standard */
90	<	char *
91	<	gengetopt_strdup (const char *s)
92	<	{
72	<	char *result = (char*)malloc(strlen(s) + 1);
73	<	if (result == (char*)0)
74	<	return (char*)0;
75	<	strcpy(result, s);
76	<	return result;
77	<	}
88	>	typedef enum {ARG_NO
89	>	, ARG_STRING
90	>	, ARG_INT
91	>	, ARG_DOUBLE
92	>	} cmdline_parser_arg_type;
93
94	<	int
95	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
96	<	{
97	<	int c;        /* Character of the parsed option.  */
83	<	int missing_required_options = 0;
84	<	int staticProps_group_counter = 0;
85	<
94	>	static
95	>	void clear_given (struct gengetopt_args_info *args_info);
96	>	static
97	>	void clear_args (struct gengetopt_args_info *args_info);
98
99	+	static int
100	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
101	+	struct cmdline_parser_params *params, const char *additional_error);
102	+
103	+	static int
104	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
105	+
106	+	static char *
107	+	gengetopt_strdup (const char *s);
108	+
109	+	static
110	+	void clear_given (struct gengetopt_args_info *args_info)
111	+	{
112		args_info->help_given = 0 ;
113		args_info->version_given = 0 ;
114		args_info->input_given = 0 ;
115		args_info->output_given = 0 ;
116		args_info->step_given = 0 ;
117	<	args_info->nrbins_given = 0 ;
117	>	args_info->nbins_given = 0 ;
118	>	args_info->nbins_x_given = 0 ;
119	>	args_info->nbins_y_given = 0 ;
120	>	args_info->nbins_z_given = 0 ;
121		args_info->nanglebins_given = 0 ;
122	+	args_info->rcut_given = 0 ;
123	+	args_info->dz_given = 0 ;
124		args_info->length_given = 0 ;
125	+	args_info->zlength_given = 0 ;
126	+	args_info->zoffset_given = 0 ;
127		args_info->sele1_given = 0 ;
128		args_info->sele2_given = 0 ;
129		args_info->sele3_given = 0 ;
130		args_info->refsele_given = 0 ;
131	+	args_info->comsele_given = 0 ;
132		args_info->molname_given = 0 ;
133		args_info->begin_given = 0 ;
134		args_info->end_given = 0 ;
135	+	args_info->radius_given = 0 ;
136	+	args_info->bo_given = 0 ;
137	+	args_info->bor_given = 0 ;
138	+	args_info->bad_given = 0 ;
139	+	args_info->count_given = 0 ;
140		args_info->gofr_given = 0 ;
141	+	args_info->gofz_given = 0 ;
142		args_info->r_theta_given = 0 ;
143		args_info->r_omega_given = 0 ;
144	+	args_info->r_z_given = 0 ;
145		args_info->theta_omega_given = 0 ;
146		args_info->gxyz_given = 0 ;
147	+	args_info->twodgofr_given = 0 ;
148		args_info->p2_given = 0 ;
149	+	args_info->rp2_given = 0 ;
150		args_info->scd_given = 0 ;
151	<	#define clear_args() { \
152	<	args_info->input_arg = NULL; \
153	<	args_info->output_arg = NULL; \
154	<	args_info->step_arg = 1 ;\
155	<	args_info->nrbins_arg = 100 ;\
156	<	args_info->nanglebins_arg = 50 ;\
157	<	args_info->sele1_arg = NULL; \
158	<	args_info->sele2_arg = NULL; \
159	<	args_info->sele3_arg = NULL; \
160	<	args_info->refsele_arg = NULL; \
161	<	args_info->molname_arg = NULL; \
151	>	args_info->density_given = 0 ;
152	>	args_info->slab_density_given = 0 ;
153	>	args_info->p_angle_given = 0 ;
154	>	args_info->hxy_given = 0 ;
155	>	args_info->rho_r_given = 0 ;
156	>	args_info->angle_r_given = 0 ;
157	>	args_info->hullvol_given = 0 ;
158	>	args_info->rodlength_given = 0 ;
159	>	args_info->tet_param_given = 0 ;
160	>	args_info->tet_param_z_given = 0 ;
161	>	args_info->staticProps_group_counter = 0 ;
162		}
163
164	<	clear_args();
164	>	static
165	>	void clear_args (struct gengetopt_args_info *args_info)
166	>	{
167	>	FIX_UNUSED (args_info);
168	>	args_info->input_arg = NULL;
169	>	args_info->input_orig = NULL;
170	>	args_info->output_arg = NULL;
171	>	args_info->output_orig = NULL;
172	>	args_info->step_arg = 1;
173	>	args_info->step_orig = NULL;
174	>	args_info->nbins_arg = 100;
175	>	args_info->nbins_orig = NULL;
176	>	args_info->nbins_x_arg = 100;
177	>	args_info->nbins_x_orig = NULL;
178	>	args_info->nbins_y_arg = 100;
179	>	args_info->nbins_y_orig = NULL;
180	>	args_info->nbins_z_arg = 100;
181	>	args_info->nbins_z_orig = NULL;
182	>	args_info->nanglebins_arg = 50;
183	>	args_info->nanglebins_orig = NULL;
184	>	args_info->rcut_orig = NULL;
185	>	args_info->dz_orig = NULL;
186	>	args_info->length_orig = NULL;
187	>	args_info->zlength_orig = NULL;
188	>	args_info->zoffset_arg = 0;
189	>	args_info->zoffset_orig = NULL;
190	>	args_info->sele1_arg = NULL;
191	>	args_info->sele1_orig = NULL;
192	>	args_info->sele2_arg = NULL;
193	>	args_info->sele2_orig = NULL;
194	>	args_info->sele3_arg = NULL;
195	>	args_info->sele3_orig = NULL;
196	>	args_info->refsele_arg = NULL;
197	>	args_info->refsele_orig = NULL;
198	>	args_info->comsele_arg = NULL;
199	>	args_info->comsele_orig = NULL;
200	>	args_info->molname_arg = NULL;
201	>	args_info->molname_orig = NULL;
202	>	args_info->begin_orig = NULL;
203	>	args_info->end_orig = NULL;
204	>	args_info->radius_orig = NULL;
205	>
206	>	}
207
208	+	static
209	+	void init_args_info(struct gengetopt_args_info *args_info)
210	+	{
211	+
212	+
213	+	args_info->help_help = gengetopt_args_info_help[0] ;
214	+	args_info->version_help = gengetopt_args_info_help[1] ;
215	+	args_info->input_help = gengetopt_args_info_help[2] ;
216	+	args_info->output_help = gengetopt_args_info_help[3] ;
217	+	args_info->step_help = gengetopt_args_info_help[4] ;
218	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
219	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
220	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
221	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
222	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
223	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
224	+	args_info->dz_help = gengetopt_args_info_help[11] ;
225	+	args_info->length_help = gengetopt_args_info_help[12] ;
226	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
227	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
228	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
229	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
230	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
231	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
232	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
233	+	args_info->molname_help = gengetopt_args_info_help[20] ;
234	+	args_info->begin_help = gengetopt_args_info_help[21] ;
235	+	args_info->end_help = gengetopt_args_info_help[22] ;
236	+	args_info->radius_help = gengetopt_args_info_help[23] ;
237	+	args_info->bo_help = gengetopt_args_info_help[25] ;
238	+	args_info->bor_help = gengetopt_args_info_help[26] ;
239	+	args_info->bad_help = gengetopt_args_info_help[27] ;
240	+	args_info->count_help = gengetopt_args_info_help[28] ;
241	+	args_info->gofr_help = gengetopt_args_info_help[29] ;
242	+	args_info->gofz_help = gengetopt_args_info_help[30] ;
243	+	args_info->r_theta_help = gengetopt_args_info_help[31] ;
244	+	args_info->r_omega_help = gengetopt_args_info_help[32] ;
245	+	args_info->r_z_help = gengetopt_args_info_help[33] ;
246	+	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
247	+	args_info->gxyz_help = gengetopt_args_info_help[35] ;
248	+	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
249	+	args_info->p2_help = gengetopt_args_info_help[37] ;
250	+	args_info->rp2_help = gengetopt_args_info_help[38] ;
251	+	args_info->scd_help = gengetopt_args_info_help[39] ;
252	+	args_info->density_help = gengetopt_args_info_help[40] ;
253	+	args_info->slab_density_help = gengetopt_args_info_help[41] ;
254	+	args_info->p_angle_help = gengetopt_args_info_help[42] ;
255	+	args_info->hxy_help = gengetopt_args_info_help[43] ;
256	+	args_info->rho_r_help = gengetopt_args_info_help[44] ;
257	+	args_info->angle_r_help = gengetopt_args_info_help[45] ;
258	+	args_info->hullvol_help = gengetopt_args_info_help[46] ;
259	+	args_info->rodlength_help = gengetopt_args_info_help[47] ;
260	+	args_info->tet_param_help = gengetopt_args_info_help[48] ;
261	+	args_info->tet_param_z_help = gengetopt_args_info_help[49] ;
262	+
263	+	}
264	+
265	+	void
266	+	cmdline_parser_print_version (void)
267	+	{
268	+	printf ("%s %s\n",
269	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
270	+	CMDLINE_PARSER_VERSION);
271	+	}
272	+
273	+	static void print_help_common(void) {
274	+	cmdline_parser_print_version ();
275	+
276	+	if (strlen(gengetopt_args_info_purpose) > 0)
277	+	printf("\n%s\n", gengetopt_args_info_purpose);
278	+
279	+	if (strlen(gengetopt_args_info_usage) > 0)
280	+	printf("\n%s\n", gengetopt_args_info_usage);
281	+
282	+	printf("\n");
283	+
284	+	if (strlen(gengetopt_args_info_description) > 0)
285	+	printf("%s\n\n", gengetopt_args_info_description);
286	+	}
287	+
288	+	void
289	+	cmdline_parser_print_help (void)
290	+	{
291	+	int i = 0;
292	+	print_help_common();
293	+	while (gengetopt_args_info_help[i])
294	+	printf("%s\n", gengetopt_args_info_help[i++]);
295	+	}
296	+
297	+	void
298	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
299	+	{
300	+	clear_given (args_info);
301	+	clear_args (args_info);
302	+	init_args_info (args_info);
303	+
304	+	args_info->inputs = 0;
305	+	args_info->inputs_num = 0;
306	+	}
307	+
308	+	void
309	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
310	+	{
311	+	if (params)
312	+	{
313	+	params->override = 0;
314	+	params->initialize = 1;
315	+	params->check_required = 1;
316	+	params->check_ambiguity = 0;
317	+	params->print_errors = 1;
318	+	}
319	+	}
320	+
321	+	struct cmdline_parser_params *
322	+	cmdline_parser_params_create(void)
323	+	{
324	+	struct cmdline_parser_params *params =
325	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
326	+	cmdline_parser_params_init(params);
327	+	return params;
328	+	}
329	+
330	+	static void
331	+	free_string_field (char **s)
332	+	{
333	+	if (*s)
334	+	{
335	+	free (*s);
336	+	*s = 0;
337	+	}
338	+	}
339	+
340	+
341	+	static void
342	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
343	+	{
344	+	unsigned int i;
345	+	free_string_field (&(args_info->input_arg));
346	+	free_string_field (&(args_info->input_orig));
347	+	free_string_field (&(args_info->output_arg));
348	+	free_string_field (&(args_info->output_orig));
349	+	free_string_field (&(args_info->step_orig));
350	+	free_string_field (&(args_info->nbins_orig));
351	+	free_string_field (&(args_info->nbins_x_orig));
352	+	free_string_field (&(args_info->nbins_y_orig));
353	+	free_string_field (&(args_info->nbins_z_orig));
354	+	free_string_field (&(args_info->nanglebins_orig));
355	+	free_string_field (&(args_info->rcut_orig));
356	+	free_string_field (&(args_info->dz_orig));
357	+	free_string_field (&(args_info->length_orig));
358	+	free_string_field (&(args_info->zlength_orig));
359	+	free_string_field (&(args_info->zoffset_orig));
360	+	free_string_field (&(args_info->sele1_arg));
361	+	free_string_field (&(args_info->sele1_orig));
362	+	free_string_field (&(args_info->sele2_arg));
363	+	free_string_field (&(args_info->sele2_orig));
364	+	free_string_field (&(args_info->sele3_arg));
365	+	free_string_field (&(args_info->sele3_orig));
366	+	free_string_field (&(args_info->refsele_arg));
367	+	free_string_field (&(args_info->refsele_orig));
368	+	free_string_field (&(args_info->comsele_arg));
369	+	free_string_field (&(args_info->comsele_orig));
370	+	free_string_field (&(args_info->molname_arg));
371	+	free_string_field (&(args_info->molname_orig));
372	+	free_string_field (&(args_info->begin_orig));
373	+	free_string_field (&(args_info->end_orig));
374	+	free_string_field (&(args_info->radius_orig));
375	+
376	+
377	+	for (i = 0; i < args_info->inputs_num; ++i)
378	+	free (args_info->inputs [i]);
379	+
380	+	if (args_info->inputs_num)
381	+	free (args_info->inputs);
382	+
383	+	clear_given (args_info);
384	+	}
385	+
386	+
387	+	static void
388	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
389	+	{
390	+	FIX_UNUSED (values);
391	+	if (arg) {
392	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
393	+	} else {
394	+	fprintf(outfile, "%s\n", opt);
395	+	}
396	+	}
397	+
398	+
399	+	int
400	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
401	+	{
402	+	int i = 0;
403	+
404	+	if (!outfile)
405	+	{
406	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
407	+	return EXIT_FAILURE;
408	+	}
409	+
410	+	if (args_info->help_given)
411	+	write_into_file(outfile, "help", 0, 0 );
412	+	if (args_info->version_given)
413	+	write_into_file(outfile, "version", 0, 0 );
414	+	if (args_info->input_given)
415	+	write_into_file(outfile, "input", args_info->input_orig, 0);
416	+	if (args_info->output_given)
417	+	write_into_file(outfile, "output", args_info->output_orig, 0);
418	+	if (args_info->step_given)
419	+	write_into_file(outfile, "step", args_info->step_orig, 0);
420	+	if (args_info->nbins_given)
421	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
422	+	if (args_info->nbins_x_given)
423	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
424	+	if (args_info->nbins_y_given)
425	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
426	+	if (args_info->nbins_z_given)
427	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
428	+	if (args_info->nanglebins_given)
429	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
430	+	if (args_info->rcut_given)
431	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
432	+	if (args_info->dz_given)
433	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
434	+	if (args_info->length_given)
435	+	write_into_file(outfile, "length", args_info->length_orig, 0);
436	+	if (args_info->zlength_given)
437	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
438	+	if (args_info->zoffset_given)
439	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
440	+	if (args_info->sele1_given)
441	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
442	+	if (args_info->sele2_given)
443	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
444	+	if (args_info->sele3_given)
445	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
446	+	if (args_info->refsele_given)
447	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
448	+	if (args_info->comsele_given)
449	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
450	+	if (args_info->molname_given)
451	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
452	+	if (args_info->begin_given)
453	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
454	+	if (args_info->end_given)
455	+	write_into_file(outfile, "end", args_info->end_orig, 0);
456	+	if (args_info->radius_given)
457	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
458	+	if (args_info->bo_given)
459	+	write_into_file(outfile, "bo", 0, 0 );
460	+	if (args_info->bor_given)
461	+	write_into_file(outfile, "bor", 0, 0 );
462	+	if (args_info->bad_given)
463	+	write_into_file(outfile, "bad", 0, 0 );
464	+	if (args_info->count_given)
465	+	write_into_file(outfile, "count", 0, 0 );
466	+	if (args_info->gofr_given)
467	+	write_into_file(outfile, "gofr", 0, 0 );
468	+	if (args_info->gofz_given)
469	+	write_into_file(outfile, "gofz", 0, 0 );
470	+	if (args_info->r_theta_given)
471	+	write_into_file(outfile, "r_theta", 0, 0 );
472	+	if (args_info->r_omega_given)
473	+	write_into_file(outfile, "r_omega", 0, 0 );
474	+	if (args_info->r_z_given)
475	+	write_into_file(outfile, "r_z", 0, 0 );
476	+	if (args_info->theta_omega_given)
477	+	write_into_file(outfile, "theta_omega", 0, 0 );
478	+	if (args_info->gxyz_given)
479	+	write_into_file(outfile, "gxyz", 0, 0 );
480	+	if (args_info->twodgofr_given)
481	+	write_into_file(outfile, "twodgofr", 0, 0 );
482	+	if (args_info->p2_given)
483	+	write_into_file(outfile, "p2", 0, 0 );
484	+	if (args_info->rp2_given)
485	+	write_into_file(outfile, "rp2", 0, 0 );
486	+	if (args_info->scd_given)
487	+	write_into_file(outfile, "scd", 0, 0 );
488	+	if (args_info->density_given)
489	+	write_into_file(outfile, "density", 0, 0 );
490	+	if (args_info->slab_density_given)
491	+	write_into_file(outfile, "slab_density", 0, 0 );
492	+	if (args_info->p_angle_given)
493	+	write_into_file(outfile, "p_angle", 0, 0 );
494	+	if (args_info->hxy_given)
495	+	write_into_file(outfile, "hxy", 0, 0 );
496	+	if (args_info->rho_r_given)
497	+	write_into_file(outfile, "rho_r", 0, 0 );
498	+	if (args_info->angle_r_given)
499	+	write_into_file(outfile, "angle_r", 0, 0 );
500	+	if (args_info->hullvol_given)
501	+	write_into_file(outfile, "hullvol", 0, 0 );
502	+	if (args_info->rodlength_given)
503	+	write_into_file(outfile, "rodlength", 0, 0 );
504	+	if (args_info->tet_param_given)
505	+	write_into_file(outfile, "tet_param", 0, 0 );
506	+	if (args_info->tet_param_z_given)
507	+	write_into_file(outfile, "tet_param_z", 0, 0 );
508	+
509	+
510	+	i = EXIT_SUCCESS;
511	+	return i;
512	+	}
513	+
514	+	int
515	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
516	+	{
517	+	FILE *outfile;
518	+	int i = 0;
519	+
520	+	outfile = fopen(filename, "w");
521	+
522	+	if (!outfile)
523	+	{
524	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
525	+	return EXIT_FAILURE;
526	+	}
527	+
528	+	i = cmdline_parser_dump(outfile, args_info);
529	+	fclose (outfile);
530	+
531	+	return i;
532	+	}
533	+
534	+	void
535	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
536	+	{
537	+	cmdline_parser_release (args_info);
538	+	}
539	+
540	+	/** @brief replacement of strdup, which is not standard */
541	+	char *
542	+	gengetopt_strdup (const char *s)
543	+	{
544	+	char *result = 0;
545	+	if (!s)
546	+	return result;
547	+
548	+	result = (char*)malloc(strlen(s) + 1);
549	+	if (result == (char*)0)
550	+	return (char*)0;
551	+	strcpy(result, s);
552	+	return result;
553	+	}
554	+
555	+	static void
556	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
557	+	{
558	+	if (! args_info->staticProps_group_counter)
559	+	return;
560	+
561	+	args_info->bo_given = 0 ;
562	+	args_info->bor_given = 0 ;
563	+	args_info->bad_given = 0 ;
564	+	args_info->count_given = 0 ;
565	+	args_info->gofr_given = 0 ;
566	+	args_info->gofz_given = 0 ;
567	+	args_info->r_theta_given = 0 ;
568	+	args_info->r_omega_given = 0 ;
569	+	args_info->r_z_given = 0 ;
570	+	args_info->theta_omega_given = 0 ;
571	+	args_info->gxyz_given = 0 ;
572	+	args_info->twodgofr_given = 0 ;
573	+	args_info->p2_given = 0 ;
574	+	args_info->rp2_given = 0 ;
575	+	args_info->scd_given = 0 ;
576	+	args_info->density_given = 0 ;
577	+	args_info->slab_density_given = 0 ;
578	+	args_info->p_angle_given = 0 ;
579	+	args_info->hxy_given = 0 ;
580	+	args_info->rho_r_given = 0 ;
581	+	args_info->angle_r_given = 0 ;
582	+	args_info->hullvol_given = 0 ;
583	+	args_info->rodlength_given = 0 ;
584	+	args_info->tet_param_given = 0 ;
585	+	args_info->tet_param_z_given = 0 ;
586	+
587	+	args_info->staticProps_group_counter = 0;
588	+	}
589	+
590	+	int
591	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
592	+	{
593	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
594	+	}
595	+
596	+	int
597	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
598	+	struct cmdline_parser_params *params)
599	+	{
600	+	int result;
601	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
602	+
603	+	if (result == EXIT_FAILURE)
604	+	{
605	+	cmdline_parser_free (args_info);
606	+	exit (EXIT_FAILURE);
607	+	}
608	+
609	+	return result;
610	+	}
611	+
612	+	int
613	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
614	+	{
615	+	int result;
616	+	struct cmdline_parser_params params;
617	+
618	+	params.override = override;
619	+	params.initialize = initialize;
620	+	params.check_required = check_required;
621	+	params.check_ambiguity = 0;
622	+	params.print_errors = 1;
623	+
624	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
625	+
626	+	if (result == EXIT_FAILURE)
627	+	{
628	+	cmdline_parser_free (args_info);
629	+	exit (EXIT_FAILURE);
630	+	}
631	+
632	+	return result;
633	+	}
634	+
635	+	int
636	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
637	+	{
638	+	int result = EXIT_SUCCESS;
639	+
640	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
641	+	result = EXIT_FAILURE;
642	+
643	+	if (result == EXIT_FAILURE)
644	+	{
645	+	cmdline_parser_free (args_info);
646	+	exit (EXIT_FAILURE);
647	+	}
648	+
649	+	return result;
650	+	}
651	+
652	+	int
653	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
654	+	{
655	+	int error = 0;
656	+	FIX_UNUSED (additional_error);
657	+
658	+	/* checks for required options */
659	+	if (! args_info->input_given)
660	+	{
661	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
662	+	error = 1;
663	+	}
664	+
665	+	if (args_info->staticProps_group_counter == 0)
666	+	{
667	+	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 : ""));
668	+	error = 1;
669	+	}
670	+
671	+
672	+	/* checks for dependences among options */
673	+
674	+	return error;
675	+	}
676	+
677	+
678	+	static char *package_name = 0;
679	+
680	+	/**
681	+	* @brief updates an option
682	+	* @param field the generic pointer to the field to update
683	+	* @param orig_field the pointer to the orig field
684	+	* @param field_given the pointer to the number of occurrence of this option
685	+	* @param prev_given the pointer to the number of occurrence already seen
686	+	* @param value the argument for this option (if null no arg was specified)
687	+	* @param possible_values the possible values for this option (if specified)
688	+	* @param default_value the default value (in case the option only accepts fixed values)
689	+	* @param arg_type the type of this option
690	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
691	+	* @param override @see cmdline_parser_params.override
692	+	* @param no_free whether to free a possible previous value
693	+	* @param multiple_option whether this is a multiple option
694	+	* @param long_opt the corresponding long option
695	+	* @param short_opt the corresponding short option (or '-' if none)
696	+	* @param additional_error possible further error specification
697	+	*/
698	+	static
699	+	int update_arg(void *field, char **orig_field,
700	+	unsigned int *field_given, unsigned int *prev_given,
701	+	char *value, const char *possible_values[],
702	+	const char *default_value,
703	+	cmdline_parser_arg_type arg_type,
704	+	int check_ambiguity, int override,
705	+	int no_free, int multiple_option,
706	+	const char *long_opt, char short_opt,
707	+	const char *additional_error)
708	+	{
709	+	char *stop_char = 0;
710	+	const char *val = value;
711	+	int found;
712	+	char **string_field;
713	+	FIX_UNUSED (field);
714	+
715	+	stop_char = 0;
716	+	found = 0;
717	+
718	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
719	+	{
720	+	if (short_opt != '-')
721	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
722	+	package_name, long_opt, short_opt,
723	+	(additional_error ? additional_error : ""));
724	+	else
725	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
726	+	package_name, long_opt,
727	+	(additional_error ? additional_error : ""));
728	+	return 1; /* failure */
729	+	}
730	+
731	+	FIX_UNUSED (default_value);
732	+
733	+	if (field_given && *field_given && ! override)
734	+	return 0;
735	+	if (prev_given)
736	+	(*prev_given)++;
737	+	if (field_given)
738	+	(*field_given)++;
739	+	if (possible_values)
740	+	val = possible_values[found];
741	+
742	+	switch(arg_type) {
743	+	case ARG_INT:
744	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
745	+	break;
746	+	case ARG_DOUBLE:
747	+	if (val) *((double *)field) = strtod (val, &stop_char);
748	+	break;
749	+	case ARG_STRING:
750	+	if (val) {
751	+	string_field = (char **)field;
752	+	if (!no_free && *string_field)
753	+	free (*string_field); /* free previous string */
754	+	*string_field = gengetopt_strdup (val);
755	+	}
756	+	break;
757	+	default:
758	+	break;
759	+	};
760	+
761	+	/* check numeric conversion */
762	+	switch(arg_type) {
763	+	case ARG_INT:
764	+	case ARG_DOUBLE:
765	+	if (val && !(stop_char && *stop_char == '\0')) {
766	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
767	+	return 1; /* failure */
768	+	}
769	+	break;
770	+	default:
771	+	;
772	+	};
773	+
774	+	/* store the original value */
775	+	switch(arg_type) {
776	+	case ARG_NO:
777	+	break;
778	+	default:
779	+	if (value && orig_field) {
780	+	if (no_free) {
781	+	*orig_field = value;
782	+	} else {
783	+	if (*orig_field)
784	+	free (*orig_field); /* free previous string */
785	+	*orig_field = gengetopt_strdup (value);
786	+	}
787	+	}
788	+	};
789	+
790	+	return 0; /* OK */
791	+	}
792	+
793	+
794	+	int
795	+	cmdline_parser_internal (
796	+	int argc, char **argv, struct gengetopt_args_info *args_info,
797	+	struct cmdline_parser_params *params, const char *additional_error)
798	+	{
799	+	int c;        /* Character of the parsed option.  */
800	+
801	+	int error = 0;
802	+	struct gengetopt_args_info local_args_info;
803	+
804	+	int override;
805	+	int initialize;
806	+	int check_required;
807	+	int check_ambiguity;
808	+
809	+	package_name = argv[0];
810	+
811	+	override = params->override;
812	+	initialize = params->initialize;
813	+	check_required = params->check_required;
814	+	check_ambiguity = params->check_ambiguity;
815	+
816	+	if (initialize)
817	+	cmdline_parser_init (args_info);
818	+
819	+	cmdline_parser_init (&local_args_info);
820	+
821		optarg = 0;
822	<	optind = 1;
823	<	opterr = 1;
822	>	optind = 0;
823	>	opterr = params->print_errors;
824		optopt = '?';
825
826		while (1)
827		{
828		int option_index = 0;
132	–	char *stop_char;
829
830		static struct option long_options[] = {
831		{ "help",       0, NULL, 'h' },
#	Line 137 | Line 833 | cmdline_parser (int argc, char * const *argv, struct g
833		{ "input",      1, NULL, 'i' },
834		{ "output",     1, NULL, 'o' },
835		{ "step",       1, NULL, 'n' },
836	<	{ "nrbins",     1, NULL, 'r' },
836	>	{ "nbins",      1, NULL, 'b' },
837	>	{ "nbins_x",    1, NULL, 'x' },
838	>	{ "nbins_y",    1, NULL, 'y' },
839	>	{ "nbins_z",    1, NULL, 0 },
840		{ "nanglebins", 1, NULL, 'a' },
841	<	{ "length",     1, NULL, 'l' },
841	>	{ "rcut",       1, NULL, 'c' },
842	>	{ "dz", 1, NULL, 0 },
843	>	{ "length",     1, NULL, 0 },
844	>	{ "zlength",    1, NULL, 0 },
845	>	{ "zoffset",    1, NULL, 'z' },
846		{ "sele1",      1, NULL, 0 },
847		{ "sele2",      1, NULL, 0 },
848		{ "sele3",      1, NULL, 0 },
849		{ "refsele",    1, NULL, 0 },
850	+	{ "comsele",    1, NULL, 0 },
851		{ "molname",    1, NULL, 0 },
852		{ "begin",      1, NULL, 0 },
853		{ "end",        1, NULL, 0 },
854	<	{ "gofr",       0, NULL, 0 },
854	>	{ "radius",     1, NULL, 0 },
855	>	{ "bo", 0, NULL, 0 },
856	>	{ "bor",        0, NULL, 0 },
857	>	{ "bad",        0, NULL, 0 },
858	>	{ "count",      0, NULL, 0 },
859	>	{ "gofr",       0, NULL, 'g' },
860	>	{ "gofz",       0, NULL, 0 },
861		{ "r_theta",    0, NULL, 0 },
862		{ "r_omega",    0, NULL, 0 },
863	+	{ "r_z",        0, NULL, 0 },
864		{ "theta_omega",        0, NULL, 0 },
865		{ "gxyz",       0, NULL, 0 },
866	<	{ "p2", 0, NULL, 0 },
867	<	{ "scd",        0, NULL, 0 },
868	<	{ NULL, 0, NULL, 0 }
866	>	{ "twodgofr",   0, NULL, 0 },
867	>	{ "p2", 0, NULL, 'p' },
868	>	{ "rp2",        0, NULL, 0 },
869	>	{ "scd",        0, NULL, 's' },
870	>	{ "density",    0, NULL, 'd' },
871	>	{ "slab_density",       0, NULL, 0 },
872	>	{ "p_angle",    0, NULL, 0 },
873	>	{ "hxy",        0, NULL, 0 },
874	>	{ "rho_r",      0, NULL, 0 },
875	>	{ "angle_r",    0, NULL, 0 },
876	>	{ "hullvol",    0, NULL, 0 },
877	>	{ "rodlength",  0, NULL, 0 },
878	>	{ "tet_param",  0, NULL, 'Q' },
879	>	{ "tet_param_z",        0, NULL, 0 },
880	>	{ 0,  0, 0, 0 }
881		};
882
883	<	stop_char = 0;
161	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
883	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
884
885		if (c == -1) break;       /* Exit from `while (1)' loop.  */
886
887		switch (c)
888		{
889		case 'h':       /* Print help and exit.  */
168	–	clear_args ();
890		cmdline_parser_print_help ();
891	+	cmdline_parser_free (&local_args_info);
892		exit (EXIT_SUCCESS);
893
894		case 'V':       /* Print version and exit.  */
173	–	clear_args ();
895		cmdline_parser_print_version ();
896	+	cmdline_parser_free (&local_args_info);
897		exit (EXIT_SUCCESS);
898
899		case 'i':       /* input dump file.  */
900	<	if (args_info->input_given)
901	<	{
902	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
903	<	clear_args ();
904	<	exit (EXIT_FAILURE);
905	<	}
906	<	args_info->input_given = 1;
907	<	args_info->input_arg = gengetopt_strdup (optarg);
908	<	break;
909	<
900	>
901	>
902	>	if (update_arg( (void *)&(args_info->input_arg),
903	>	&(args_info->input_orig), &(args_info->input_given),
904	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
905	>	check_ambiguity, override, 0, 0,
906	>	"input", 'i',
907	>	additional_error))
908	>	goto failure;
909	>
910	>	break;
911		case 'o':       /* output file name.  */
912	<	if (args_info->output_given)
913	<	{
914	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
915	<	clear_args ();
916	<	exit (EXIT_FAILURE);
917	<	}
918	<	args_info->output_given = 1;
919	<	args_info->output_arg = gengetopt_strdup (optarg);
912	>
913	>
914	>	if (update_arg( (void *)&(args_info->output_arg),
915	>	&(args_info->output_orig), &(args_info->output_given),
916	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
917	>	check_ambiguity, override, 0, 0,
918	>	"output", 'o',
919	>	additional_error))
920	>	goto failure;
921	>
922		break;
198	–
923		case 'n':       /* process every n frame.  */
924	<	if (args_info->step_given)
925	<	{
926	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
927	<	clear_args ();
928	<	exit (EXIT_FAILURE);
929	<	}
930	<	args_info->step_given = 1;
931	<	args_info->step_arg = strtol (optarg,&stop_char,0);
924	>
925	>
926	>	if (update_arg( (void *)&(args_info->step_arg),
927	>	&(args_info->step_orig), &(args_info->step_given),
928	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
929	>	check_ambiguity, override, 0, 0,
930	>	"step", 'n',
931	>	additional_error))
932	>	goto failure;
933	>
934		break;
935	<
936	<	case 'r':       /* number of bins for distance.  */
937	<	if (args_info->nrbins_given)
938	<	{
939	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
940	<	clear_args ();
941	<	exit (EXIT_FAILURE);
942	<	}
943	<	args_info->nrbins_given = 1;
944	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
935	>	case 'b':       /* number of bins (general purpose).  */
936	>
937	>
938	>	if (update_arg( (void *)&(args_info->nbins_arg),
939	>	&(args_info->nbins_orig), &(args_info->nbins_given),
940	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
941	>	check_ambiguity, override, 0, 0,
942	>	"nbins", 'b',
943	>	additional_error))
944	>	goto failure;
945	>
946		break;
947	<
947	>	case 'x':       /* number of bins in x axis.  */
948	>
949	>
950	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
951	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
952	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
953	>	check_ambiguity, override, 0, 0,
954	>	"nbins_x", 'x',
955	>	additional_error))
956	>	goto failure;
957	>
958	>	break;
959	>	case 'y':       /* number of bins in y axis.  */
960	>
961	>
962	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
963	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
964	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
965	>	check_ambiguity, override, 0, 0,
966	>	"nbins_y", 'y',
967	>	additional_error))
968	>	goto failure;
969	>
970	>	break;
971		case 'a':       /* number of bins for cos(angle).  */
972	<	if (args_info->nanglebins_given)
973	<	{
974	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
975	<	clear_args ();
976	<	exit (EXIT_FAILURE);
977	<	}
978	<	args_info->nanglebins_given = 1;
979	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
972	>
973	>
974	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
975	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
976	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
977	>	check_ambiguity, override, 0, 0,
978	>	"nanglebins", 'a',
979	>	additional_error))
980	>	goto failure;
981	>
982		break;
983	<
984	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
985	<	if (args_info->length_given)
986	<	{
987	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
988	<	clear_args ();
989	<	exit (EXIT_FAILURE);
990	<	}
991	<	args_info->length_given = 1;
992	<	args_info->length_arg = strtod (optarg, NULL);
983	>	case 'c':       /* cutoff radius (rcut).  */
984	>
985	>
986	>	if (update_arg( (void *)&(args_info->rcut_arg),
987	>	&(args_info->rcut_orig), &(args_info->rcut_given),
988	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
989	>	check_ambiguity, override, 0, 0,
990	>	"rcut", 'c',
991	>	additional_error))
992	>	goto failure;
993	>
994		break;
995	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
996	+
997	+
998	+	if (update_arg( (void *)&(args_info->zoffset_arg),
999	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1000	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1001	+	check_ambiguity, override, 0, 0,
1002	+	"zoffset", 'z',
1003	+	additional_error))
1004	+	goto failure;
1005	+
1006	+	break;
1007	+	case 'g':       /* g(r).  */
1008	+
1009	+	if (args_info->staticProps_group_counter && override)
1010	+	reset_group_staticProps (args_info);
1011	+	args_info->staticProps_group_counter += 1;
1012	+
1013	+	if (update_arg( 0 ,
1014	+	0 , &(args_info->gofr_given),
1015	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1016	+	check_ambiguity, override, 0, 0,
1017	+	"gofr", 'g',
1018	+	additional_error))
1019	+	goto failure;
1020	+
1021	+	break;
1022	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1023	+
1024	+	if (args_info->staticProps_group_counter && override)
1025	+	reset_group_staticProps (args_info);
1026	+	args_info->staticProps_group_counter += 1;
1027	+
1028	+	if (update_arg( 0 ,
1029	+	0 , &(args_info->p2_given),
1030	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1031	+	check_ambiguity, override, 0, 0,
1032	+	"p2", 'p',
1033	+	additional_error))
1034	+	goto failure;
1035	+
1036	+	break;
1037	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1038	+
1039	+	if (args_info->staticProps_group_counter && override)
1040	+	reset_group_staticProps (args_info);
1041	+	args_info->staticProps_group_counter += 1;
1042	+
1043	+	if (update_arg( 0 ,
1044	+	0 , &(args_info->scd_given),
1045	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1046	+	check_ambiguity, override, 0, 0,
1047	+	"scd", 's',
1048	+	additional_error))
1049	+	goto failure;
1050	+
1051	+	break;
1052	+	case 'd':       /* density plot.  */
1053	+
1054	+	if (args_info->staticProps_group_counter && override)
1055	+	reset_group_staticProps (args_info);
1056	+	args_info->staticProps_group_counter += 1;
1057	+
1058	+	if (update_arg( 0 ,
1059	+	0 , &(args_info->density_given),
1060	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1061	+	check_ambiguity, override, 0, 0,
1062	+	"density", 'd',
1063	+	additional_error))
1064	+	goto failure;
1065	+
1066	+	break;
1067	+	case 'Q':       /* tetrahedrality order parameter.  */
1068	+
1069	+	if (args_info->staticProps_group_counter && override)
1070	+	reset_group_staticProps (args_info);
1071	+	args_info->staticProps_group_counter += 1;
1072	+
1073	+	if (update_arg( 0 ,
1074	+	0 , &(args_info->tet_param_given),
1075	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1076	+	check_ambiguity, override, 0, 0,
1077	+	"tet_param", 'Q',
1078	+	additional_error))
1079	+	goto failure;
1080	+
1081	+	break;
1082
243	–
1083		case 0: /* Long option with no short option */
1084	<	/* select the first stuntdouble set.  */
1085	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1084	>	/* number of bins in z axis.  */
1085	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1086		{
1087	<	if (args_info->sele1_given)
1088	<	{
1089	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1090	<	clear_args ();
1091	<	exit (EXIT_FAILURE);
1092	<	}
1093	<	args_info->sele1_given = 1;
1094	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1095	<	break;
1087	>
1088	>
1089	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1090	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1091	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1092	>	check_ambiguity, override, 0, 0,
1093	>	"nbins_z", '-',
1094	>	additional_error))
1095	>	goto failure;
1096	>
1097		}
1098	+	/* slab width (dz).  */
1099	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1100	+	{
1101
1102	+
1103	+	if (update_arg( (void *)&(args_info->dz_arg),
1104	+	&(args_info->dz_orig), &(args_info->dz_given),
1105	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1106	+	check_ambiguity, override, 0, 0,
1107	+	"dz", '-',
1108	+	additional_error))
1109	+	goto failure;
1110	+
1111	+	}
1112	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1113	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1114	+	{
1115	+
1116	+
1117	+	if (update_arg( (void *)&(args_info->length_arg),
1118	+	&(args_info->length_orig), &(args_info->length_given),
1119	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1120	+	check_ambiguity, override, 0, 0,
1121	+	"length", '-',
1122	+	additional_error))
1123	+	goto failure;
1124	+
1125	+	}
1126	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1127	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1128	+	{
1129	+
1130	+
1131	+	if (update_arg( (void *)&(args_info->zlength_arg),
1132	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1133	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1134	+	check_ambiguity, override, 0, 0,
1135	+	"zlength", '-',
1136	+	additional_error))
1137	+	goto failure;
1138	+
1139	+	}
1140	+	/* select the first stuntdouble set.  */
1141	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1142	+	{
1143	+
1144	+
1145	+	if (update_arg( (void *)&(args_info->sele1_arg),
1146	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1147	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1148	+	check_ambiguity, override, 0, 0,
1149	+	"sele1", '-',
1150	+	additional_error))
1151	+	goto failure;
1152	+
1153	+	}
1154		/* select the second stuntdouble set.  */
1155		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1156		{
262	–	if (args_info->sele2_given)
263	–	{
264	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
265	–	clear_args ();
266	–	exit (EXIT_FAILURE);
267	–	}
268	–	args_info->sele2_given = 1;
269	–	args_info->sele2_arg = gengetopt_strdup (optarg);
270	–	break;
271	–	}
1157
1158	+
1159	+	if (update_arg( (void *)&(args_info->sele2_arg),
1160	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1161	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1162	+	check_ambiguity, override, 0, 0,
1163	+	"sele2", '-',
1164	+	additional_error))
1165	+	goto failure;
1166	+
1167	+	}
1168		/* select the third stuntdouble set.  */
1169		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1170		{
276	–	if (args_info->sele3_given)
277	–	{
278	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
279	–	clear_args ();
280	–	exit (EXIT_FAILURE);
281	–	}
282	–	args_info->sele3_given = 1;
283	–	args_info->sele3_arg = gengetopt_strdup (optarg);
284	–	break;
285	–	}
1171
1172	+
1173	+	if (update_arg( (void *)&(args_info->sele3_arg),
1174	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1175	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1176	+	check_ambiguity, override, 0, 0,
1177	+	"sele3", '-',
1178	+	additional_error))
1179	+	goto failure;
1180	+
1181	+	}
1182		/* select reference (use and only use with --gxyz).  */
1183		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1184		{
1185	<	if (args_info->refsele_given)
1186	<	{
1187	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1188	<	clear_args ();
1189	<	exit (EXIT_FAILURE);
1190	<	}
1191	<	args_info->refsele_given = 1;
1192	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1193	<	break;
1185	>
1186	>
1187	>	if (update_arg( (void *)&(args_info->refsele_arg),
1188	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1189	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1190	>	check_ambiguity, override, 0, 0,
1191	>	"refsele", '-',
1192	>	additional_error))
1193	>	goto failure;
1194	>
1195		}
1196	+	/* select stunt doubles for center-of-mass reference point.  */
1197	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1198	+	{
1199
1200	+
1201	+	if (update_arg( (void *)&(args_info->comsele_arg),
1202	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1203	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1204	+	check_ambiguity, override, 0, 0,
1205	+	"comsele", '-',
1206	+	additional_error))
1207	+	goto failure;
1208	+
1209	+	}
1210		/* molecule name.  */
1211		else if (strcmp (long_options[option_index].name, "molname") == 0)
1212		{
304	–	if (args_info->molname_given)
305	–	{
306	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
307	–	clear_args ();
308	–	exit (EXIT_FAILURE);
309	–	}
310	–	args_info->molname_given = 1;
311	–	args_info->molname_arg = gengetopt_strdup (optarg);
312	–	break;
313	–	}
1213
1214	<	/* begin interanl index.  */
1214	>
1215	>	if (update_arg( (void *)&(args_info->molname_arg),
1216	>	&(args_info->molname_orig), &(args_info->molname_given),
1217	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1218	>	check_ambiguity, override, 0, 0,
1219	>	"molname", '-',
1220	>	additional_error))
1221	>	goto failure;
1222	>
1223	>	}
1224	>	/* begin internal index.  */
1225		else if (strcmp (long_options[option_index].name, "begin") == 0)
1226		{
318	–	if (args_info->begin_given)
319	–	{
320	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
321	–	clear_args ();
322	–	exit (EXIT_FAILURE);
323	–	}
324	–	args_info->begin_given = 1;
325	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
326	–	break;
327	–	}
1227
1228	+
1229	+	if (update_arg( (void *)&(args_info->begin_arg),
1230	+	&(args_info->begin_orig), &(args_info->begin_given),
1231	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1232	+	check_ambiguity, override, 0, 0,
1233	+	"begin", '-',
1234	+	additional_error))
1235	+	goto failure;
1236	+
1237	+	}
1238		/* end internal index.  */
1239		else if (strcmp (long_options[option_index].name, "end") == 0)
1240		{
332	–	if (args_info->end_given)
333	–	{
334	–	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
335	–	clear_args ();
336	–	exit (EXIT_FAILURE);
337	–	}
338	–	args_info->end_given = 1;
339	–	args_info->end_arg = strtol (optarg,&stop_char,0);
340	–	break;
341	–	}
1241
1242	<	/* g(r).  */
1243	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1242	>
1243	>	if (update_arg( (void *)&(args_info->end_arg),
1244	>	&(args_info->end_orig), &(args_info->end_given),
1245	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1246	>	check_ambiguity, override, 0, 0,
1247	>	"end", '-',
1248	>	additional_error))
1249	>	goto failure;
1250	>
1251	>	}
1252	>	/* nanoparticle radius.  */
1253	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1254		{
346	–	if (args_info->gofr_given)
347	–	{
348	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
349	–	clear_args ();
350	–	exit (EXIT_FAILURE);
351	–	}
352	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1255
1256	<	break;
1256	>
1257	>	if (update_arg( (void *)&(args_info->radius_arg),
1258	>	&(args_info->radius_orig), &(args_info->radius_given),
1259	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1260	>	check_ambiguity, override, 0, 0,
1261	>	"radius", '-',
1262	>	additional_error))
1263	>	goto failure;
1264	>
1265		}
1266	+	/* bond order parameter (--rcut must be specified).  */
1267	+	else if (strcmp (long_options[option_index].name, "bo") == 0)
1268	+	{
1269
1270	+	if (args_info->staticProps_group_counter && override)
1271	+	reset_group_staticProps (args_info);
1272	+	args_info->staticProps_group_counter += 1;
1273	+
1274	+	if (update_arg( 0 ,
1275	+	0 , &(args_info->bo_given),
1276	+	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1277	+	check_ambiguity, override, 0, 0,
1278	+	"bo", '-',
1279	+	additional_error))
1280	+	goto failure;
1281	+
1282	+	}
1283	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1284	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1285	+	{
1286	+
1287	+	if (args_info->staticProps_group_counter && override)
1288	+	reset_group_staticProps (args_info);
1289	+	args_info->staticProps_group_counter += 1;
1290	+
1291	+	if (update_arg( 0 ,
1292	+	0 , &(args_info->bor_given),
1293	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1294	+	check_ambiguity, override, 0, 0,
1295	+	"bor", '-',
1296	+	additional_error))
1297	+	goto failure;
1298	+
1299	+	}
1300	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1301	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1302	+	{
1303	+
1304	+	if (args_info->staticProps_group_counter && override)
1305	+	reset_group_staticProps (args_info);
1306	+	args_info->staticProps_group_counter += 1;
1307	+
1308	+	if (update_arg( 0 ,
1309	+	0 , &(args_info->bad_given),
1310	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1311	+	check_ambiguity, override, 0, 0,
1312	+	"bad", '-',
1313	+	additional_error))
1314	+	goto failure;
1315	+
1316	+	}
1317	+	/* count of molecules matching selection criteria (and associated statistics).  */
1318	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1319	+	{
1320	+
1321	+	if (args_info->staticProps_group_counter && override)
1322	+	reset_group_staticProps (args_info);
1323	+	args_info->staticProps_group_counter += 1;
1324	+
1325	+	if (update_arg( 0 ,
1326	+	0 , &(args_info->count_given),
1327	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1328	+	check_ambiguity, override, 0, 0,
1329	+	"count", '-',
1330	+	additional_error))
1331	+	goto failure;
1332	+
1333	+	}
1334	+	/* g(z).  */
1335	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1336	+	{
1337	+
1338	+	if (args_info->staticProps_group_counter && override)
1339	+	reset_group_staticProps (args_info);
1340	+	args_info->staticProps_group_counter += 1;
1341	+
1342	+	if (update_arg( 0 ,
1343	+	0 , &(args_info->gofz_given),
1344	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1345	+	check_ambiguity, override, 0, 0,
1346	+	"gofz", '-',
1347	+	additional_error))
1348	+	goto failure;
1349	+
1350	+	}
1351		/* g(r, cos(theta)).  */
1352		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1353		{
360	–	if (args_info->r_theta_given)
361	–	{
362	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
363	–	clear_args ();
364	–	exit (EXIT_FAILURE);
365	–	}
366	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1354
1355	<	break;
1356	<	}
1355	>	if (args_info->staticProps_group_counter && override)
1356	>	reset_group_staticProps (args_info);
1357	>	args_info->staticProps_group_counter += 1;
1358
1359	+	if (update_arg( 0 ,
1360	+	0 , &(args_info->r_theta_given),
1361	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1362	+	check_ambiguity, override, 0, 0,
1363	+	"r_theta", '-',
1364	+	additional_error))
1365	+	goto failure;
1366	+
1367	+	}
1368		/* g(r, cos(omega)).  */
1369		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1370		{
374	–	if (args_info->r_omega_given)
375	–	{
376	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
377	–	clear_args ();
378	–	exit (EXIT_FAILURE);
379	–	}
380	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1371
1372	<	break;
1372	>	if (args_info->staticProps_group_counter && override)
1373	>	reset_group_staticProps (args_info);
1374	>	args_info->staticProps_group_counter += 1;
1375	>
1376	>	if (update_arg( 0 ,
1377	>	0 , &(args_info->r_omega_given),
1378	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1379	>	check_ambiguity, override, 0, 0,
1380	>	"r_omega", '-',
1381	>	additional_error))
1382	>	goto failure;
1383	>
1384		}
1385	+	/* g(r, z).  */
1386	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1387	+	{
1388
1389	+	if (args_info->staticProps_group_counter && override)
1390	+	reset_group_staticProps (args_info);
1391	+	args_info->staticProps_group_counter += 1;
1392	+
1393	+	if (update_arg( 0 ,
1394	+	0 , &(args_info->r_z_given),
1395	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1396	+	check_ambiguity, override, 0, 0,
1397	+	"r_z", '-',
1398	+	additional_error))
1399	+	goto failure;
1400	+
1401	+	}
1402		/* g(cos(theta), cos(omega)).  */
1403		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1404		{
388	–	if (args_info->theta_omega_given)
389	–	{
390	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
391	–	clear_args ();
392	–	exit (EXIT_FAILURE);
393	–	}
394	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1405
1406	<	break;
1407	<	}
1406	>	if (args_info->staticProps_group_counter && override)
1407	>	reset_group_staticProps (args_info);
1408	>	args_info->staticProps_group_counter += 1;
1409
1410	+	if (update_arg( 0 ,
1411	+	0 , &(args_info->theta_omega_given),
1412	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1413	+	check_ambiguity, override, 0, 0,
1414	+	"theta_omega", '-',
1415	+	additional_error))
1416	+	goto failure;
1417	+
1418	+	}
1419		/* g(x, y, z).  */
1420		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1421		{
402	–	if (args_info->gxyz_given)
403	–	{
404	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
405	–	clear_args ();
406	–	exit (EXIT_FAILURE);
407	–	}
408	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1422
1423	<	break;
1424	<	}
1423	>	if (args_info->staticProps_group_counter && override)
1424	>	reset_group_staticProps (args_info);
1425	>	args_info->staticProps_group_counter += 1;
1426
1427	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1428	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1427	>	if (update_arg( 0 ,
1428	>	0 , &(args_info->gxyz_given),
1429	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1430	>	check_ambiguity, override, 0, 0,
1431	>	"gxyz", '-',
1432	>	additional_error))
1433	>	goto failure;
1434	>
1435	>	}
1436	>	/* 2D g(r) (Slab width --dz must be specified).  */
1437	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1438		{
416	–	if (args_info->p2_given)
417	–	{
418	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
419	–	clear_args ();
420	–	exit (EXIT_FAILURE);
421	–	}
422	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1439
1440	<	break;
1440	>	if (args_info->staticProps_group_counter && override)
1441	>	reset_group_staticProps (args_info);
1442	>	args_info->staticProps_group_counter += 1;
1443	>
1444	>	if (update_arg( 0 ,
1445	>	0 , &(args_info->twodgofr_given),
1446	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1447	>	check_ambiguity, override, 0, 0,
1448	>	"twodgofr", '-',
1449	>	additional_error))
1450	>	goto failure;
1451	>
1452		}
1453	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1454	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1455	+	{
1456
1457	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1458	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1457	>	if (args_info->staticProps_group_counter && override)
1458	>	reset_group_staticProps (args_info);
1459	>	args_info->staticProps_group_counter += 1;
1460	>
1461	>	if (update_arg( 0 ,
1462	>	0 , &(args_info->rp2_given),
1463	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1464	>	check_ambiguity, override, 0, 0,
1465	>	"rp2", '-',
1466	>	additional_error))
1467	>	goto failure;
1468	>
1469	>	}
1470	>	/* slab density.  */
1471	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1472		{
430	–	if (args_info->scd_given)
431	–	{
432	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
433	–	clear_args ();
434	–	exit (EXIT_FAILURE);
435	–	}
436	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1473
1474	<	break;
1474	>	if (args_info->staticProps_group_counter && override)
1475	>	reset_group_staticProps (args_info);
1476	>	args_info->staticProps_group_counter += 1;
1477	>
1478	>	if (update_arg( 0 ,
1479	>	0 , &(args_info->slab_density_given),
1480	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1481	>	check_ambiguity, override, 0, 0,
1482	>	"slab_density", '-',
1483	>	additional_error))
1484	>	goto failure;
1485	>
1486		}
1487	+	/* p(cos(theta)).  */
1488	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1489	+	{
1490
1491	<
1491	>	if (args_info->staticProps_group_counter && override)
1492	>	reset_group_staticProps (args_info);
1493	>	args_info->staticProps_group_counter += 1;
1494	>
1495	>	if (update_arg( 0 ,
1496	>	0 , &(args_info->p_angle_given),
1497	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1498	>	check_ambiguity, override, 0, 0,
1499	>	"p_angle", '-',
1500	>	additional_error))
1501	>	goto failure;
1502	>
1503	>	}
1504	>	/* hxy.  */
1505	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1506	>	{
1507	>
1508	>	if (args_info->staticProps_group_counter && override)
1509	>	reset_group_staticProps (args_info);
1510	>	args_info->staticProps_group_counter += 1;
1511	>
1512	>	if (update_arg( 0 ,
1513	>	0 , &(args_info->hxy_given),
1514	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1515	>	check_ambiguity, override, 0, 0,
1516	>	"hxy", '-',
1517	>	additional_error))
1518	>	goto failure;
1519	>
1520	>	}
1521	>	/* rho of R.  */
1522	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1523	>	{
1524	>
1525	>	if (args_info->staticProps_group_counter && override)
1526	>	reset_group_staticProps (args_info);
1527	>	args_info->staticProps_group_counter += 1;
1528	>
1529	>	if (update_arg( 0 ,
1530	>	0 , &(args_info->rho_r_given),
1531	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1532	>	check_ambiguity, override, 0, 0,
1533	>	"rho_r", '-',
1534	>	additional_error))
1535	>	goto failure;
1536	>
1537	>	}
1538	>	/* angle of R.  */
1539	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1540	>	{
1541	>
1542	>	if (args_info->staticProps_group_counter && override)
1543	>	reset_group_staticProps (args_info);
1544	>	args_info->staticProps_group_counter += 1;
1545	>
1546	>	if (update_arg( 0 ,
1547	>	0 , &(args_info->angle_r_given),
1548	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1549	>	check_ambiguity, override, 0, 0,
1550	>	"angle_r", '-',
1551	>	additional_error))
1552	>	goto failure;
1553	>
1554	>	}
1555	>	/* hull volume of nanoparticle.  */
1556	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1557	>	{
1558	>
1559	>	if (args_info->staticProps_group_counter && override)
1560	>	reset_group_staticProps (args_info);
1561	>	args_info->staticProps_group_counter += 1;
1562	>
1563	>	if (update_arg( 0 ,
1564	>	0 , &(args_info->hullvol_given),
1565	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1566	>	check_ambiguity, override, 0, 0,
1567	>	"hullvol", '-',
1568	>	additional_error))
1569	>	goto failure;
1570	>
1571	>	}
1572	>	/* length of nanorod.  */
1573	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1574	>	{
1575	>
1576	>	if (args_info->staticProps_group_counter && override)
1577	>	reset_group_staticProps (args_info);
1578	>	args_info->staticProps_group_counter += 1;
1579	>
1580	>	if (update_arg( 0 ,
1581	>	0 , &(args_info->rodlength_given),
1582	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1583	>	check_ambiguity, override, 0, 0,
1584	>	"rodlength", '-',
1585	>	additional_error))
1586	>	goto failure;
1587	>
1588	>	}
1589	>	/* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1590	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1591	>	{
1592	>
1593	>	if (args_info->staticProps_group_counter && override)
1594	>	reset_group_staticProps (args_info);
1595	>	args_info->staticProps_group_counter += 1;
1596	>
1597	>	if (update_arg( 0 ,
1598	>	0 , &(args_info->tet_param_z_given),
1599	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1600	>	check_ambiguity, override, 0, 0,
1601	>	"tet_param_z", '-',
1602	>	additional_error))
1603	>	goto failure;
1604	>
1605	>	}
1606	>
1607	>	break;
1608		case '?':       /* Invalid option.  */
1609		/* `getopt_long' already printed an error message.  */
1610	<	exit (EXIT_FAILURE);
1610	>	goto failure;
1611
1612		default:        /* bug: option not considered.  */
1613	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1613	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1614		abort ();
1615		} /* switch */
1616		} /* while */
1617
1618	<	if ( staticProps_group_counter != 1)
1618	>	if (args_info->staticProps_group_counter > 1)
1619		{
1620	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1621	<	missing_required_options = 1;
1620	>	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 : ""));
1621	>	error = 1;
1622		}
1623
1624
1625	<	if (! args_info->input_given)
1625	>
1626	>	if (check_required)
1627		{
1628	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
462	<	missing_required_options = 1;
1628	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1629		}
464	–	if ( missing_required_options )
465	–	exit (EXIT_FAILURE);
1630
1631	+	cmdline_parser_release (&local_args_info);
1632	+
1633	+	if ( error )
1634	+	return (EXIT_FAILURE);
1635	+
1636	+	if (optind < argc)
1637	+	{
1638	+	int i = 0 ;
1639	+	int found_prog_name = 0;
1640	+	/* whether program name, i.e., argv[0], is in the remaining args
1641	+	(this may happen with some implementations of getopt,
1642	+	but surely not with the one included by gengetopt) */
1643	+
1644	+	i = optind;
1645	+	while (i < argc)
1646	+	if (argv[i++] == argv[0]) {
1647	+	found_prog_name = 1;
1648	+	break;
1649	+	}
1650	+	i = 0;
1651	+
1652	+	args_info->inputs_num = argc - optind - found_prog_name;
1653	+	args_info->inputs =
1654	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1655	+	while (optind < argc)
1656	+	if (argv[optind++] != argv[0])
1657	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1658	+	}
1659	+
1660		return 0;
1661	+
1662	+	failure:
1663	+
1664	+	cmdline_parser_release (&local_args_info);
1665	+	return (EXIT_FAILURE);
1666		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 544 by tim, Fri May 27 04:41:34 2005 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1762 by plouden, Thu Jun 28 20:17:33 2012 UTC

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