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

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1655 by gezelter, Mon Oct 3 20:32:45 2011 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 -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	<	printf("      --density                   density plot (--sele1 must be specified)\n");
63	<	}
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	>	0
85	>	};
86
87	<	/* gengetopt_strdup() */
88	<	/* strdup.c replacement of strdup, which is not standard */
89	<	char *
90	<	gengetopt_strdup (const char *s)
91	<	{
73	<	char *result = (char*)malloc(strlen(s) + 1);
74	<	if (result == (char*)0)
75	<	return (char*)0;
76	<	strcpy(result, s);
77	<	return result;
78	<	}
87	>	typedef enum {ARG_NO
88	>	, ARG_STRING
89	>	, ARG_INT
90	>	, ARG_DOUBLE
91	>	} cmdline_parser_arg_type;
92
93	<	int
94	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
95	<	{
96	<	int c;        /* Character of the parsed option.  */
84	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
86	<
93	>	static
94	>	void clear_given (struct gengetopt_args_info *args_info);
95	>	static
96	>	void clear_args (struct gengetopt_args_info *args_info);
97
98	+	static int
99	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
100	+	struct cmdline_parser_params *params, const char *additional_error);
101	+
102	+	static int
103	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
104	+
105	+	static char *
106	+	gengetopt_strdup (const char *s);
107	+
108	+	static
109	+	void clear_given (struct gengetopt_args_info *args_info)
110	+	{
111		args_info->help_given = 0 ;
112		args_info->version_given = 0 ;
113		args_info->input_given = 0 ;
114		args_info->output_given = 0 ;
115		args_info->step_given = 0 ;
116	<	args_info->nrbins_given = 0 ;
116	>	args_info->nbins_given = 0 ;
117	>	args_info->nbins_x_given = 0 ;
118	>	args_info->nbins_y_given = 0 ;
119	>	args_info->nbins_z_given = 0 ;
120		args_info->nanglebins_given = 0 ;
121	+	args_info->rcut_given = 0 ;
122	+	args_info->dz_given = 0 ;
123		args_info->length_given = 0 ;
124	+	args_info->zlength_given = 0 ;
125	+	args_info->zoffset_given = 0 ;
126		args_info->sele1_given = 0 ;
127		args_info->sele2_given = 0 ;
128		args_info->sele3_given = 0 ;
129		args_info->refsele_given = 0 ;
130	+	args_info->comsele_given = 0 ;
131		args_info->molname_given = 0 ;
132		args_info->begin_given = 0 ;
133		args_info->end_given = 0 ;
134	+	args_info->radius_given = 0 ;
135	+	args_info->bo_given = 0 ;
136	+	args_info->bor_given = 0 ;
137	+	args_info->bad_given = 0 ;
138	+	args_info->count_given = 0 ;
139		args_info->gofr_given = 0 ;
140	+	args_info->gofz_given = 0 ;
141		args_info->r_theta_given = 0 ;
142		args_info->r_omega_given = 0 ;
143	+	args_info->r_z_given = 0 ;
144		args_info->theta_omega_given = 0 ;
145		args_info->gxyz_given = 0 ;
146	+	args_info->twodgofr_given = 0 ;
147		args_info->p2_given = 0 ;
148	+	args_info->rp2_given = 0 ;
149		args_info->scd_given = 0 ;
150		args_info->density_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; \
120	<	args_info->refsele_arg = NULL; \
121	<	args_info->molname_arg = NULL; \
151	>	args_info->slab_density_given = 0 ;
152	>	args_info->p_angle_given = 0 ;
153	>	args_info->hxy_given = 0 ;
154	>	args_info->rho_r_given = 0 ;
155	>	args_info->angle_r_given = 0 ;
156	>	args_info->hullvol_given = 0 ;
157	>	args_info->rodlength_given = 0 ;
158	>	args_info->tet_param_given = 0 ;
159	>	args_info->staticProps_group_counter = 0 ;
160		}
161
162	<	clear_args();
162	>	static
163	>	void clear_args (struct gengetopt_args_info *args_info)
164	>	{
165	>	FIX_UNUSED (args_info);
166	>	args_info->input_arg = NULL;
167	>	args_info->input_orig = NULL;
168	>	args_info->output_arg = NULL;
169	>	args_info->output_orig = NULL;
170	>	args_info->step_arg = 1;
171	>	args_info->step_orig = NULL;
172	>	args_info->nbins_arg = 100;
173	>	args_info->nbins_orig = NULL;
174	>	args_info->nbins_x_arg = 100;
175	>	args_info->nbins_x_orig = NULL;
176	>	args_info->nbins_y_arg = 100;
177	>	args_info->nbins_y_orig = NULL;
178	>	args_info->nbins_z_arg = 100;
179	>	args_info->nbins_z_orig = NULL;
180	>	args_info->nanglebins_arg = 50;
181	>	args_info->nanglebins_orig = NULL;
182	>	args_info->rcut_orig = NULL;
183	>	args_info->dz_orig = NULL;
184	>	args_info->length_orig = NULL;
185	>	args_info->zlength_orig = NULL;
186	>	args_info->zoffset_arg = 0;
187	>	args_info->zoffset_orig = NULL;
188	>	args_info->sele1_arg = NULL;
189	>	args_info->sele1_orig = NULL;
190	>	args_info->sele2_arg = NULL;
191	>	args_info->sele2_orig = NULL;
192	>	args_info->sele3_arg = NULL;
193	>	args_info->sele3_orig = NULL;
194	>	args_info->refsele_arg = NULL;
195	>	args_info->refsele_orig = NULL;
196	>	args_info->comsele_arg = NULL;
197	>	args_info->comsele_orig = NULL;
198	>	args_info->molname_arg = NULL;
199	>	args_info->molname_orig = NULL;
200	>	args_info->begin_orig = NULL;
201	>	args_info->end_orig = NULL;
202	>	args_info->radius_orig = NULL;
203	>
204	>	}
205
206	+	static
207	+	void init_args_info(struct gengetopt_args_info *args_info)
208	+	{
209	+
210	+
211	+	args_info->help_help = gengetopt_args_info_help[0] ;
212	+	args_info->version_help = gengetopt_args_info_help[1] ;
213	+	args_info->input_help = gengetopt_args_info_help[2] ;
214	+	args_info->output_help = gengetopt_args_info_help[3] ;
215	+	args_info->step_help = gengetopt_args_info_help[4] ;
216	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
217	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
218	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
219	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
220	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
221	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
222	+	args_info->dz_help = gengetopt_args_info_help[11] ;
223	+	args_info->length_help = gengetopt_args_info_help[12] ;
224	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
225	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
226	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
227	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
228	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
229	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
230	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
231	+	args_info->molname_help = gengetopt_args_info_help[20] ;
232	+	args_info->begin_help = gengetopt_args_info_help[21] ;
233	+	args_info->end_help = gengetopt_args_info_help[22] ;
234	+	args_info->radius_help = gengetopt_args_info_help[23] ;
235	+	args_info->bo_help = gengetopt_args_info_help[25] ;
236	+	args_info->bor_help = gengetopt_args_info_help[26] ;
237	+	args_info->bad_help = gengetopt_args_info_help[27] ;
238	+	args_info->count_help = gengetopt_args_info_help[28] ;
239	+	args_info->gofr_help = gengetopt_args_info_help[29] ;
240	+	args_info->gofz_help = gengetopt_args_info_help[30] ;
241	+	args_info->r_theta_help = gengetopt_args_info_help[31] ;
242	+	args_info->r_omega_help = gengetopt_args_info_help[32] ;
243	+	args_info->r_z_help = gengetopt_args_info_help[33] ;
244	+	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
245	+	args_info->gxyz_help = gengetopt_args_info_help[35] ;
246	+	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
247	+	args_info->p2_help = gengetopt_args_info_help[37] ;
248	+	args_info->rp2_help = gengetopt_args_info_help[38] ;
249	+	args_info->scd_help = gengetopt_args_info_help[39] ;
250	+	args_info->density_help = gengetopt_args_info_help[40] ;
251	+	args_info->slab_density_help = gengetopt_args_info_help[41] ;
252	+	args_info->p_angle_help = gengetopt_args_info_help[42] ;
253	+	args_info->hxy_help = gengetopt_args_info_help[43] ;
254	+	args_info->rho_r_help = gengetopt_args_info_help[44] ;
255	+	args_info->angle_r_help = gengetopt_args_info_help[45] ;
256	+	args_info->hullvol_help = gengetopt_args_info_help[46] ;
257	+	args_info->rodlength_help = gengetopt_args_info_help[47] ;
258	+	args_info->tet_param_help = gengetopt_args_info_help[48] ;
259	+
260	+	}
261	+
262	+	void
263	+	cmdline_parser_print_version (void)
264	+	{
265	+	printf ("%s %s\n",
266	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
267	+	CMDLINE_PARSER_VERSION);
268	+	}
269	+
270	+	static void print_help_common(void) {
271	+	cmdline_parser_print_version ();
272	+
273	+	if (strlen(gengetopt_args_info_purpose) > 0)
274	+	printf("\n%s\n", gengetopt_args_info_purpose);
275	+
276	+	if (strlen(gengetopt_args_info_usage) > 0)
277	+	printf("\n%s\n", gengetopt_args_info_usage);
278	+
279	+	printf("\n");
280	+
281	+	if (strlen(gengetopt_args_info_description) > 0)
282	+	printf("%s\n\n", gengetopt_args_info_description);
283	+	}
284	+
285	+	void
286	+	cmdline_parser_print_help (void)
287	+	{
288	+	int i = 0;
289	+	print_help_common();
290	+	while (gengetopt_args_info_help[i])
291	+	printf("%s\n", gengetopt_args_info_help[i++]);
292	+	}
293	+
294	+	void
295	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
296	+	{
297	+	clear_given (args_info);
298	+	clear_args (args_info);
299	+	init_args_info (args_info);
300	+
301	+	args_info->inputs = 0;
302	+	args_info->inputs_num = 0;
303	+	}
304	+
305	+	void
306	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
307	+	{
308	+	if (params)
309	+	{
310	+	params->override = 0;
311	+	params->initialize = 1;
312	+	params->check_required = 1;
313	+	params->check_ambiguity = 0;
314	+	params->print_errors = 1;
315	+	}
316	+	}
317	+
318	+	struct cmdline_parser_params *
319	+	cmdline_parser_params_create(void)
320	+	{
321	+	struct cmdline_parser_params *params =
322	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
323	+	cmdline_parser_params_init(params);
324	+	return params;
325	+	}
326	+
327	+	static void
328	+	free_string_field (char **s)
329	+	{
330	+	if (*s)
331	+	{
332	+	free (*s);
333	+	*s = 0;
334	+	}
335	+	}
336	+
337	+
338	+	static void
339	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
340	+	{
341	+	unsigned int i;
342	+	free_string_field (&(args_info->input_arg));
343	+	free_string_field (&(args_info->input_orig));
344	+	free_string_field (&(args_info->output_arg));
345	+	free_string_field (&(args_info->output_orig));
346	+	free_string_field (&(args_info->step_orig));
347	+	free_string_field (&(args_info->nbins_orig));
348	+	free_string_field (&(args_info->nbins_x_orig));
349	+	free_string_field (&(args_info->nbins_y_orig));
350	+	free_string_field (&(args_info->nbins_z_orig));
351	+	free_string_field (&(args_info->nanglebins_orig));
352	+	free_string_field (&(args_info->rcut_orig));
353	+	free_string_field (&(args_info->dz_orig));
354	+	free_string_field (&(args_info->length_orig));
355	+	free_string_field (&(args_info->zlength_orig));
356	+	free_string_field (&(args_info->zoffset_orig));
357	+	free_string_field (&(args_info->sele1_arg));
358	+	free_string_field (&(args_info->sele1_orig));
359	+	free_string_field (&(args_info->sele2_arg));
360	+	free_string_field (&(args_info->sele2_orig));
361	+	free_string_field (&(args_info->sele3_arg));
362	+	free_string_field (&(args_info->sele3_orig));
363	+	free_string_field (&(args_info->refsele_arg));
364	+	free_string_field (&(args_info->refsele_orig));
365	+	free_string_field (&(args_info->comsele_arg));
366	+	free_string_field (&(args_info->comsele_orig));
367	+	free_string_field (&(args_info->molname_arg));
368	+	free_string_field (&(args_info->molname_orig));
369	+	free_string_field (&(args_info->begin_orig));
370	+	free_string_field (&(args_info->end_orig));
371	+	free_string_field (&(args_info->radius_orig));
372	+
373	+
374	+	for (i = 0; i < args_info->inputs_num; ++i)
375	+	free (args_info->inputs [i]);
376	+
377	+	if (args_info->inputs_num)
378	+	free (args_info->inputs);
379	+
380	+	clear_given (args_info);
381	+	}
382	+
383	+
384	+	static void
385	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
386	+	{
387	+	FIX_UNUSED (values);
388	+	if (arg) {
389	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
390	+	} else {
391	+	fprintf(outfile, "%s\n", opt);
392	+	}
393	+	}
394	+
395	+
396	+	int
397	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
398	+	{
399	+	int i = 0;
400	+
401	+	if (!outfile)
402	+	{
403	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
404	+	return EXIT_FAILURE;
405	+	}
406	+
407	+	if (args_info->help_given)
408	+	write_into_file(outfile, "help", 0, 0 );
409	+	if (args_info->version_given)
410	+	write_into_file(outfile, "version", 0, 0 );
411	+	if (args_info->input_given)
412	+	write_into_file(outfile, "input", args_info->input_orig, 0);
413	+	if (args_info->output_given)
414	+	write_into_file(outfile, "output", args_info->output_orig, 0);
415	+	if (args_info->step_given)
416	+	write_into_file(outfile, "step", args_info->step_orig, 0);
417	+	if (args_info->nbins_given)
418	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
419	+	if (args_info->nbins_x_given)
420	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
421	+	if (args_info->nbins_y_given)
422	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
423	+	if (args_info->nbins_z_given)
424	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
425	+	if (args_info->nanglebins_given)
426	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
427	+	if (args_info->rcut_given)
428	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
429	+	if (args_info->dz_given)
430	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
431	+	if (args_info->length_given)
432	+	write_into_file(outfile, "length", args_info->length_orig, 0);
433	+	if (args_info->zlength_given)
434	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
435	+	if (args_info->zoffset_given)
436	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
437	+	if (args_info->sele1_given)
438	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
439	+	if (args_info->sele2_given)
440	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
441	+	if (args_info->sele3_given)
442	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
443	+	if (args_info->refsele_given)
444	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
445	+	if (args_info->comsele_given)
446	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
447	+	if (args_info->molname_given)
448	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
449	+	if (args_info->begin_given)
450	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
451	+	if (args_info->end_given)
452	+	write_into_file(outfile, "end", args_info->end_orig, 0);
453	+	if (args_info->radius_given)
454	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
455	+	if (args_info->bo_given)
456	+	write_into_file(outfile, "bo", 0, 0 );
457	+	if (args_info->bor_given)
458	+	write_into_file(outfile, "bor", 0, 0 );
459	+	if (args_info->bad_given)
460	+	write_into_file(outfile, "bad", 0, 0 );
461	+	if (args_info->count_given)
462	+	write_into_file(outfile, "count", 0, 0 );
463	+	if (args_info->gofr_given)
464	+	write_into_file(outfile, "gofr", 0, 0 );
465	+	if (args_info->gofz_given)
466	+	write_into_file(outfile, "gofz", 0, 0 );
467	+	if (args_info->r_theta_given)
468	+	write_into_file(outfile, "r_theta", 0, 0 );
469	+	if (args_info->r_omega_given)
470	+	write_into_file(outfile, "r_omega", 0, 0 );
471	+	if (args_info->r_z_given)
472	+	write_into_file(outfile, "r_z", 0, 0 );
473	+	if (args_info->theta_omega_given)
474	+	write_into_file(outfile, "theta_omega", 0, 0 );
475	+	if (args_info->gxyz_given)
476	+	write_into_file(outfile, "gxyz", 0, 0 );
477	+	if (args_info->twodgofr_given)
478	+	write_into_file(outfile, "twodgofr", 0, 0 );
479	+	if (args_info->p2_given)
480	+	write_into_file(outfile, "p2", 0, 0 );
481	+	if (args_info->rp2_given)
482	+	write_into_file(outfile, "rp2", 0, 0 );
483	+	if (args_info->scd_given)
484	+	write_into_file(outfile, "scd", 0, 0 );
485	+	if (args_info->density_given)
486	+	write_into_file(outfile, "density", 0, 0 );
487	+	if (args_info->slab_density_given)
488	+	write_into_file(outfile, "slab_density", 0, 0 );
489	+	if (args_info->p_angle_given)
490	+	write_into_file(outfile, "p_angle", 0, 0 );
491	+	if (args_info->hxy_given)
492	+	write_into_file(outfile, "hxy", 0, 0 );
493	+	if (args_info->rho_r_given)
494	+	write_into_file(outfile, "rho_r", 0, 0 );
495	+	if (args_info->angle_r_given)
496	+	write_into_file(outfile, "angle_r", 0, 0 );
497	+	if (args_info->hullvol_given)
498	+	write_into_file(outfile, "hullvol", 0, 0 );
499	+	if (args_info->rodlength_given)
500	+	write_into_file(outfile, "rodlength", 0, 0 );
501	+	if (args_info->tet_param_given)
502	+	write_into_file(outfile, "tet_param", 0, 0 );
503	+
504	+
505	+	i = EXIT_SUCCESS;
506	+	return i;
507	+	}
508	+
509	+	int
510	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
511	+	{
512	+	FILE *outfile;
513	+	int i = 0;
514	+
515	+	outfile = fopen(filename, "w");
516	+
517	+	if (!outfile)
518	+	{
519	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
520	+	return EXIT_FAILURE;
521	+	}
522	+
523	+	i = cmdline_parser_dump(outfile, args_info);
524	+	fclose (outfile);
525	+
526	+	return i;
527	+	}
528	+
529	+	void
530	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
531	+	{
532	+	cmdline_parser_release (args_info);
533	+	}
534	+
535	+	/** @brief replacement of strdup, which is not standard */
536	+	char *
537	+	gengetopt_strdup (const char *s)
538	+	{
539	+	char *result = 0;
540	+	if (!s)
541	+	return result;
542	+
543	+	result = (char*)malloc(strlen(s) + 1);
544	+	if (result == (char*)0)
545	+	return (char*)0;
546	+	strcpy(result, s);
547	+	return result;
548	+	}
549	+
550	+	static void
551	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
552	+	{
553	+	if (! args_info->staticProps_group_counter)
554	+	return;
555	+
556	+	args_info->bo_given = 0 ;
557	+	args_info->bor_given = 0 ;
558	+	args_info->bad_given = 0 ;
559	+	args_info->count_given = 0 ;
560	+	args_info->gofr_given = 0 ;
561	+	args_info->gofz_given = 0 ;
562	+	args_info->r_theta_given = 0 ;
563	+	args_info->r_omega_given = 0 ;
564	+	args_info->r_z_given = 0 ;
565	+	args_info->theta_omega_given = 0 ;
566	+	args_info->gxyz_given = 0 ;
567	+	args_info->twodgofr_given = 0 ;
568	+	args_info->p2_given = 0 ;
569	+	args_info->rp2_given = 0 ;
570	+	args_info->scd_given = 0 ;
571	+	args_info->density_given = 0 ;
572	+	args_info->slab_density_given = 0 ;
573	+	args_info->p_angle_given = 0 ;
574	+	args_info->hxy_given = 0 ;
575	+	args_info->rho_r_given = 0 ;
576	+	args_info->angle_r_given = 0 ;
577	+	args_info->hullvol_given = 0 ;
578	+	args_info->rodlength_given = 0 ;
579	+	args_info->tet_param_given = 0 ;
580	+
581	+	args_info->staticProps_group_counter = 0;
582	+	}
583	+
584	+	int
585	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
586	+	{
587	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
588	+	}
589	+
590	+	int
591	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
592	+	struct cmdline_parser_params *params)
593	+	{
594	+	int result;
595	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
596	+
597	+	if (result == EXIT_FAILURE)
598	+	{
599	+	cmdline_parser_free (args_info);
600	+	exit (EXIT_FAILURE);
601	+	}
602	+
603	+	return result;
604	+	}
605	+
606	+	int
607	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
608	+	{
609	+	int result;
610	+	struct cmdline_parser_params params;
611	+
612	+	params.override = override;
613	+	params.initialize = initialize;
614	+	params.check_required = check_required;
615	+	params.check_ambiguity = 0;
616	+	params.print_errors = 1;
617	+
618	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
619	+
620	+	if (result == EXIT_FAILURE)
621	+	{
622	+	cmdline_parser_free (args_info);
623	+	exit (EXIT_FAILURE);
624	+	}
625	+
626	+	return result;
627	+	}
628	+
629	+	int
630	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
631	+	{
632	+	int result = EXIT_SUCCESS;
633	+
634	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
635	+	result = EXIT_FAILURE;
636	+
637	+	if (result == EXIT_FAILURE)
638	+	{
639	+	cmdline_parser_free (args_info);
640	+	exit (EXIT_FAILURE);
641	+	}
642	+
643	+	return result;
644	+	}
645	+
646	+	int
647	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
648	+	{
649	+	int error = 0;
650	+	FIX_UNUSED (additional_error);
651	+
652	+	/* checks for required options */
653	+	if (! args_info->input_given)
654	+	{
655	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
656	+	error = 1;
657	+	}
658	+
659	+	if (args_info->staticProps_group_counter == 0)
660	+	{
661	+	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 : ""));
662	+	error = 1;
663	+	}
664	+
665	+
666	+	/* checks for dependences among options */
667	+
668	+	return error;
669	+	}
670	+
671	+
672	+	static char *package_name = 0;
673	+
674	+	/**
675	+	* @brief updates an option
676	+	* @param field the generic pointer to the field to update
677	+	* @param orig_field the pointer to the orig field
678	+	* @param field_given the pointer to the number of occurrence of this option
679	+	* @param prev_given the pointer to the number of occurrence already seen
680	+	* @param value the argument for this option (if null no arg was specified)
681	+	* @param possible_values the possible values for this option (if specified)
682	+	* @param default_value the default value (in case the option only accepts fixed values)
683	+	* @param arg_type the type of this option
684	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
685	+	* @param override @see cmdline_parser_params.override
686	+	* @param no_free whether to free a possible previous value
687	+	* @param multiple_option whether this is a multiple option
688	+	* @param long_opt the corresponding long option
689	+	* @param short_opt the corresponding short option (or '-' if none)
690	+	* @param additional_error possible further error specification
691	+	*/
692	+	static
693	+	int update_arg(void *field, char **orig_field,
694	+	unsigned int *field_given, unsigned int *prev_given,
695	+	char *value, const char *possible_values[],
696	+	const char *default_value,
697	+	cmdline_parser_arg_type arg_type,
698	+	int check_ambiguity, int override,
699	+	int no_free, int multiple_option,
700	+	const char *long_opt, char short_opt,
701	+	const char *additional_error)
702	+	{
703	+	char *stop_char = 0;
704	+	const char *val = value;
705	+	int found;
706	+	char **string_field;
707	+	FIX_UNUSED (field);
708	+
709	+	stop_char = 0;
710	+	found = 0;
711	+
712	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
713	+	{
714	+	if (short_opt != '-')
715	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
716	+	package_name, long_opt, short_opt,
717	+	(additional_error ? additional_error : ""));
718	+	else
719	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
720	+	package_name, long_opt,
721	+	(additional_error ? additional_error : ""));
722	+	return 1; /* failure */
723	+	}
724	+
725	+	FIX_UNUSED (default_value);
726	+
727	+	if (field_given && *field_given && ! override)
728	+	return 0;
729	+	if (prev_given)
730	+	(*prev_given)++;
731	+	if (field_given)
732	+	(*field_given)++;
733	+	if (possible_values)
734	+	val = possible_values[found];
735	+
736	+	switch(arg_type) {
737	+	case ARG_INT:
738	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
739	+	break;
740	+	case ARG_DOUBLE:
741	+	if (val) *((double *)field) = strtod (val, &stop_char);
742	+	break;
743	+	case ARG_STRING:
744	+	if (val) {
745	+	string_field = (char **)field;
746	+	if (!no_free && *string_field)
747	+	free (*string_field); /* free previous string */
748	+	*string_field = gengetopt_strdup (val);
749	+	}
750	+	break;
751	+	default:
752	+	break;
753	+	};
754	+
755	+	/* check numeric conversion */
756	+	switch(arg_type) {
757	+	case ARG_INT:
758	+	case ARG_DOUBLE:
759	+	if (val && !(stop_char && *stop_char == '\0')) {
760	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
761	+	return 1; /* failure */
762	+	}
763	+	break;
764	+	default:
765	+	;
766	+	};
767	+
768	+	/* store the original value */
769	+	switch(arg_type) {
770	+	case ARG_NO:
771	+	break;
772	+	default:
773	+	if (value && orig_field) {
774	+	if (no_free) {
775	+	*orig_field = value;
776	+	} else {
777	+	if (*orig_field)
778	+	free (*orig_field); /* free previous string */
779	+	*orig_field = gengetopt_strdup (value);
780	+	}
781	+	}
782	+	};
783	+
784	+	return 0; /* OK */
785	+	}
786	+
787	+
788	+	int
789	+	cmdline_parser_internal (
790	+	int argc, char **argv, struct gengetopt_args_info *args_info,
791	+	struct cmdline_parser_params *params, const char *additional_error)
792	+	{
793	+	int c;        /* Character of the parsed option.  */
794	+
795	+	int error = 0;
796	+	struct gengetopt_args_info local_args_info;
797	+
798	+	int override;
799	+	int initialize;
800	+	int check_required;
801	+	int check_ambiguity;
802	+
803	+	package_name = argv[0];
804	+
805	+	override = params->override;
806	+	initialize = params->initialize;
807	+	check_required = params->check_required;
808	+	check_ambiguity = params->check_ambiguity;
809	+
810	+	if (initialize)
811	+	cmdline_parser_init (args_info);
812	+
813	+	cmdline_parser_init (&local_args_info);
814	+
815		optarg = 0;
816	<	optind = 1;
817	<	opterr = 1;
816	>	optind = 0;
817	>	opterr = params->print_errors;
818		optopt = '?';
819
820		while (1)
821		{
822		int option_index = 0;
134	–	char *stop_char;
823
824		static struct option long_options[] = {
825		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 827 | cmdline_parser (int argc, char * const *argv, struct g
827		{ "input",      1, NULL, 'i' },
828		{ "output",     1, NULL, 'o' },
829		{ "step",       1, NULL, 'n' },
830	<	{ "nrbins",     1, NULL, 'r' },
830	>	{ "nbins",      1, NULL, 'b' },
831	>	{ "nbins_x",    1, NULL, 'x' },
832	>	{ "nbins_y",    1, NULL, 'y' },
833	>	{ "nbins_z",    1, NULL, 0 },
834		{ "nanglebins", 1, NULL, 'a' },
835	<	{ "length",     1, NULL, 'l' },
835	>	{ "rcut",       1, NULL, 'c' },
836	>	{ "dz", 1, NULL, 0 },
837	>	{ "length",     1, NULL, 0 },
838	>	{ "zlength",    1, NULL, 0 },
839	>	{ "zoffset",    1, NULL, 'z' },
840		{ "sele1",      1, NULL, 0 },
841		{ "sele2",      1, NULL, 0 },
842		{ "sele3",      1, NULL, 0 },
843		{ "refsele",    1, NULL, 0 },
844	+	{ "comsele",    1, NULL, 0 },
845		{ "molname",    1, NULL, 0 },
846		{ "begin",      1, NULL, 0 },
847		{ "end",        1, NULL, 0 },
848	<	{ "gofr",       0, NULL, 0 },
848	>	{ "radius",     1, NULL, 0 },
849	>	{ "bo", 0, NULL, 0 },
850	>	{ "bor",        0, NULL, 0 },
851	>	{ "bad",        0, NULL, 0 },
852	>	{ "count",      0, NULL, 0 },
853	>	{ "gofr",       0, NULL, 'g' },
854	>	{ "gofz",       0, NULL, 0 },
855		{ "r_theta",    0, NULL, 0 },
856		{ "r_omega",    0, NULL, 0 },
857	+	{ "r_z",        0, NULL, 0 },
858		{ "theta_omega",        0, NULL, 0 },
859		{ "gxyz",       0, NULL, 0 },
860	<	{ "p2", 0, NULL, 0 },
861	<	{ "scd",        0, NULL, 0 },
862	<	{ "density",    0, NULL, 0 },
863	<	{ NULL, 0, NULL, 0 }
860	>	{ "twodgofr",   0, NULL, 0 },
861	>	{ "p2", 0, NULL, 'p' },
862	>	{ "rp2",        0, NULL, 0 },
863	>	{ "scd",        0, NULL, 's' },
864	>	{ "density",    0, NULL, 'd' },
865	>	{ "slab_density",       0, NULL, 0 },
866	>	{ "p_angle",    0, NULL, 0 },
867	>	{ "hxy",        0, NULL, 0 },
868	>	{ "rho_r",      0, NULL, 0 },
869	>	{ "angle_r",    0, NULL, 0 },
870	>	{ "hullvol",    0, NULL, 0 },
871	>	{ "rodlength",  0, NULL, 0 },
872	>	{ "tet_param",  0, NULL, 'Q' },
873	>	{ 0,  0, 0, 0 }
874		};
875
876	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
876	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
877
878		if (c == -1) break;       /* Exit from `while (1)' loop.  */
879
880		switch (c)
881		{
882		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
883		cmdline_parser_print_help ();
884	+	cmdline_parser_free (&local_args_info);
885		exit (EXIT_SUCCESS);
886
887		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
888		cmdline_parser_print_version ();
889	+	cmdline_parser_free (&local_args_info);
890		exit (EXIT_SUCCESS);
891
892		case 'i':       /* input dump file.  */
893	<	if (args_info->input_given)
894	<	{
895	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
896	<	clear_args ();
897	<	exit (EXIT_FAILURE);
898	<	}
899	<	args_info->input_given = 1;
900	<	args_info->input_arg = gengetopt_strdup (optarg);
901	<	break;
902	<
893	>
894	>
895	>	if (update_arg( (void *)&(args_info->input_arg),
896	>	&(args_info->input_orig), &(args_info->input_given),
897	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
898	>	check_ambiguity, override, 0, 0,
899	>	"input", 'i',
900	>	additional_error))
901	>	goto failure;
902	>
903	>	break;
904		case 'o':       /* output file name.  */
905	<	if (args_info->output_given)
906	<	{
907	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
908	<	clear_args ();
909	<	exit (EXIT_FAILURE);
910	<	}
911	<	args_info->output_given = 1;
912	<	args_info->output_arg = gengetopt_strdup (optarg);
905	>
906	>
907	>	if (update_arg( (void *)&(args_info->output_arg),
908	>	&(args_info->output_orig), &(args_info->output_given),
909	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
910	>	check_ambiguity, override, 0, 0,
911	>	"output", 'o',
912	>	additional_error))
913	>	goto failure;
914	>
915		break;
201	–
916		case 'n':       /* process every n frame.  */
917	<	if (args_info->step_given)
918	<	{
919	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
920	<	clear_args ();
921	<	exit (EXIT_FAILURE);
922	<	}
923	<	args_info->step_given = 1;
924	<	args_info->step_arg = strtol (optarg,&stop_char,0);
917	>
918	>
919	>	if (update_arg( (void *)&(args_info->step_arg),
920	>	&(args_info->step_orig), &(args_info->step_given),
921	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
922	>	check_ambiguity, override, 0, 0,
923	>	"step", 'n',
924	>	additional_error))
925	>	goto failure;
926	>
927		break;
928	<
929	<	case 'r':       /* number of bins for distance.  */
930	<	if (args_info->nrbins_given)
931	<	{
932	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
933	<	clear_args ();
934	<	exit (EXIT_FAILURE);
935	<	}
936	<	args_info->nrbins_given = 1;
937	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
928	>	case 'b':       /* number of bins (general purpose).  */
929	>
930	>
931	>	if (update_arg( (void *)&(args_info->nbins_arg),
932	>	&(args_info->nbins_orig), &(args_info->nbins_given),
933	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
934	>	check_ambiguity, override, 0, 0,
935	>	"nbins", 'b',
936	>	additional_error))
937	>	goto failure;
938	>
939		break;
940	<
940	>	case 'x':       /* number of bins in x axis.  */
941	>
942	>
943	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
944	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
945	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
946	>	check_ambiguity, override, 0, 0,
947	>	"nbins_x", 'x',
948	>	additional_error))
949	>	goto failure;
950	>
951	>	break;
952	>	case 'y':       /* number of bins in y axis.  */
953	>
954	>
955	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
956	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
957	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
958	>	check_ambiguity, override, 0, 0,
959	>	"nbins_y", 'y',
960	>	additional_error))
961	>	goto failure;
962	>
963	>	break;
964		case 'a':       /* number of bins for cos(angle).  */
965	<	if (args_info->nanglebins_given)
966	<	{
967	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
968	<	clear_args ();
969	<	exit (EXIT_FAILURE);
970	<	}
971	<	args_info->nanglebins_given = 1;
972	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
965	>
966	>
967	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
968	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
969	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
970	>	check_ambiguity, override, 0, 0,
971	>	"nanglebins", 'a',
972	>	additional_error))
973	>	goto failure;
974	>
975		break;
976	<
977	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
978	<	if (args_info->length_given)
979	<	{
980	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
981	<	clear_args ();
982	<	exit (EXIT_FAILURE);
983	<	}
984	<	args_info->length_given = 1;
985	<	args_info->length_arg = strtod (optarg, NULL);
976	>	case 'c':       /* cutoff radius (rcut).  */
977	>
978	>
979	>	if (update_arg( (void *)&(args_info->rcut_arg),
980	>	&(args_info->rcut_orig), &(args_info->rcut_given),
981	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
982	>	check_ambiguity, override, 0, 0,
983	>	"rcut", 'c',
984	>	additional_error))
985	>	goto failure;
986	>
987		break;
988	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
989	+
990	+
991	+	if (update_arg( (void *)&(args_info->zoffset_arg),
992	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
993	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
994	+	check_ambiguity, override, 0, 0,
995	+	"zoffset", 'z',
996	+	additional_error))
997	+	goto failure;
998	+
999	+	break;
1000	+	case 'g':       /* g(r).  */
1001	+
1002	+	if (args_info->staticProps_group_counter && override)
1003	+	reset_group_staticProps (args_info);
1004	+	args_info->staticProps_group_counter += 1;
1005	+
1006	+	if (update_arg( 0 ,
1007	+	0 , &(args_info->gofr_given),
1008	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1009	+	check_ambiguity, override, 0, 0,
1010	+	"gofr", 'g',
1011	+	additional_error))
1012	+	goto failure;
1013	+
1014	+	break;
1015	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1016	+
1017	+	if (args_info->staticProps_group_counter && override)
1018	+	reset_group_staticProps (args_info);
1019	+	args_info->staticProps_group_counter += 1;
1020	+
1021	+	if (update_arg( 0 ,
1022	+	0 , &(args_info->p2_given),
1023	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1024	+	check_ambiguity, override, 0, 0,
1025	+	"p2", 'p',
1026	+	additional_error))
1027	+	goto failure;
1028	+
1029	+	break;
1030	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1031	+
1032	+	if (args_info->staticProps_group_counter && override)
1033	+	reset_group_staticProps (args_info);
1034	+	args_info->staticProps_group_counter += 1;
1035	+
1036	+	if (update_arg( 0 ,
1037	+	0 , &(args_info->scd_given),
1038	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1039	+	check_ambiguity, override, 0, 0,
1040	+	"scd", 's',
1041	+	additional_error))
1042	+	goto failure;
1043	+
1044	+	break;
1045	+	case 'd':       /* density plot.  */
1046	+
1047	+	if (args_info->staticProps_group_counter && override)
1048	+	reset_group_staticProps (args_info);
1049	+	args_info->staticProps_group_counter += 1;
1050	+
1051	+	if (update_arg( 0 ,
1052	+	0 , &(args_info->density_given),
1053	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1054	+	check_ambiguity, override, 0, 0,
1055	+	"density", 'd',
1056	+	additional_error))
1057	+	goto failure;
1058	+
1059	+	break;
1060	+	case 'Q':       /* tetrahedrality order parameter.  */
1061	+
1062	+	if (args_info->staticProps_group_counter && override)
1063	+	reset_group_staticProps (args_info);
1064	+	args_info->staticProps_group_counter += 1;
1065	+
1066	+	if (update_arg( 0 ,
1067	+	0 , &(args_info->tet_param_given),
1068	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1069	+	check_ambiguity, override, 0, 0,
1070	+	"tet_param", 'Q',
1071	+	additional_error))
1072	+	goto failure;
1073	+
1074	+	break;
1075
246	–
1076		case 0: /* Long option with no short option */
1077	<	/* select the first stuntdouble set.  */
1078	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1077	>	/* number of bins in z axis.  */
1078	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1079		{
1080	<	if (args_info->sele1_given)
1081	<	{
1082	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1083	<	clear_args ();
1084	<	exit (EXIT_FAILURE);
1085	<	}
1086	<	args_info->sele1_given = 1;
1087	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1088	<	break;
1080	>
1081	>
1082	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1083	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1084	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1085	>	check_ambiguity, override, 0, 0,
1086	>	"nbins_z", '-',
1087	>	additional_error))
1088	>	goto failure;
1089	>
1090		}
1091	+	/* slab width (dz).  */
1092	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1093	+	{
1094
1095	+
1096	+	if (update_arg( (void *)&(args_info->dz_arg),
1097	+	&(args_info->dz_orig), &(args_info->dz_given),
1098	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1099	+	check_ambiguity, override, 0, 0,
1100	+	"dz", '-',
1101	+	additional_error))
1102	+	goto failure;
1103	+
1104	+	}
1105	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1106	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1107	+	{
1108	+
1109	+
1110	+	if (update_arg( (void *)&(args_info->length_arg),
1111	+	&(args_info->length_orig), &(args_info->length_given),
1112	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1113	+	check_ambiguity, override, 0, 0,
1114	+	"length", '-',
1115	+	additional_error))
1116	+	goto failure;
1117	+
1118	+	}
1119	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1120	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1121	+	{
1122	+
1123	+
1124	+	if (update_arg( (void *)&(args_info->zlength_arg),
1125	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1126	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1127	+	check_ambiguity, override, 0, 0,
1128	+	"zlength", '-',
1129	+	additional_error))
1130	+	goto failure;
1131	+
1132	+	}
1133	+	/* select the first stuntdouble set.  */
1134	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1135	+	{
1136	+
1137	+
1138	+	if (update_arg( (void *)&(args_info->sele1_arg),
1139	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1140	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1141	+	check_ambiguity, override, 0, 0,
1142	+	"sele1", '-',
1143	+	additional_error))
1144	+	goto failure;
1145	+
1146	+	}
1147		/* select the second stuntdouble set.  */
1148		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1149		{
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	–	}
1150
1151	+
1152	+	if (update_arg( (void *)&(args_info->sele2_arg),
1153	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1154	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1155	+	check_ambiguity, override, 0, 0,
1156	+	"sele2", '-',
1157	+	additional_error))
1158	+	goto failure;
1159	+
1160	+	}
1161		/* select the third stuntdouble set.  */
1162		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1163		{
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	–	}
1164
1165	+
1166	+	if (update_arg( (void *)&(args_info->sele3_arg),
1167	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1168	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1169	+	check_ambiguity, override, 0, 0,
1170	+	"sele3", '-',
1171	+	additional_error))
1172	+	goto failure;
1173	+
1174	+	}
1175		/* select reference (use and only use with --gxyz).  */
1176		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1177		{
1178	<	if (args_info->refsele_given)
1179	<	{
1180	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1181	<	clear_args ();
1182	<	exit (EXIT_FAILURE);
1183	<	}
1184	<	args_info->refsele_given = 1;
1185	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1186	<	break;
1178	>
1179	>
1180	>	if (update_arg( (void *)&(args_info->refsele_arg),
1181	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1182	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1183	>	check_ambiguity, override, 0, 0,
1184	>	"refsele", '-',
1185	>	additional_error))
1186	>	goto failure;
1187	>
1188		}
1189	+	/* select stunt doubles for center-of-mass reference point.  */
1190	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1191	+	{
1192
1193	+
1194	+	if (update_arg( (void *)&(args_info->comsele_arg),
1195	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1196	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1197	+	check_ambiguity, override, 0, 0,
1198	+	"comsele", '-',
1199	+	additional_error))
1200	+	goto failure;
1201	+
1202	+	}
1203		/* molecule name.  */
1204		else if (strcmp (long_options[option_index].name, "molname") == 0)
1205		{
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	–	}
1206
1207	<	/* begin interanl index.  */
1207	>
1208	>	if (update_arg( (void *)&(args_info->molname_arg),
1209	>	&(args_info->molname_orig), &(args_info->molname_given),
1210	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1211	>	check_ambiguity, override, 0, 0,
1212	>	"molname", '-',
1213	>	additional_error))
1214	>	goto failure;
1215	>
1216	>	}
1217	>	/* begin internal index.  */
1218		else if (strcmp (long_options[option_index].name, "begin") == 0)
1219		{
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	–	}
1220
1221	+
1222	+	if (update_arg( (void *)&(args_info->begin_arg),
1223	+	&(args_info->begin_orig), &(args_info->begin_given),
1224	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1225	+	check_ambiguity, override, 0, 0,
1226	+	"begin", '-',
1227	+	additional_error))
1228	+	goto failure;
1229	+
1230	+	}
1231		/* end internal index.  */
1232		else if (strcmp (long_options[option_index].name, "end") == 0)
1233		{
1234	<	if (args_info->end_given)
1235	<	{
1236	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1237	<	clear_args ();
1238	<	exit (EXIT_FAILURE);
1239	<	}
1240	<	args_info->end_given = 1;
1241	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1242	<	break;
1234	>
1235	>
1236	>	if (update_arg( (void *)&(args_info->end_arg),
1237	>	&(args_info->end_orig), &(args_info->end_given),
1238	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1239	>	check_ambiguity, override, 0, 0,
1240	>	"end", '-',
1241	>	additional_error))
1242	>	goto failure;
1243	>
1244		}
1245	+	/* nanoparticle radius.  */
1246	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1247	+	{
1248
1249	<	/* g(r).  */
1250	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1249	>
1250	>	if (update_arg( (void *)&(args_info->radius_arg),
1251	>	&(args_info->radius_orig), &(args_info->radius_given),
1252	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1253	>	check_ambiguity, override, 0, 0,
1254	>	"radius", '-',
1255	>	additional_error))
1256	>	goto failure;
1257	>
1258	>	}
1259	>	/* bond order parameter (--rcut must be specified).  */
1260	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1261		{
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;
1262
1263	<	break;
1263	>	if (args_info->staticProps_group_counter && override)
1264	>	reset_group_staticProps (args_info);
1265	>	args_info->staticProps_group_counter += 1;
1266	>
1267	>	if (update_arg( 0 ,
1268	>	0 , &(args_info->bo_given),
1269	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1270	>	check_ambiguity, override, 0, 0,
1271	>	"bo", '-',
1272	>	additional_error))
1273	>	goto failure;
1274	>
1275		}
1276	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1277	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1278	+	{
1279
1280	+	if (args_info->staticProps_group_counter && override)
1281	+	reset_group_staticProps (args_info);
1282	+	args_info->staticProps_group_counter += 1;
1283	+
1284	+	if (update_arg( 0 ,
1285	+	0 , &(args_info->bor_given),
1286	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1287	+	check_ambiguity, override, 0, 0,
1288	+	"bor", '-',
1289	+	additional_error))
1290	+	goto failure;
1291	+
1292	+	}
1293	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1294	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1295	+	{
1296	+
1297	+	if (args_info->staticProps_group_counter && override)
1298	+	reset_group_staticProps (args_info);
1299	+	args_info->staticProps_group_counter += 1;
1300	+
1301	+	if (update_arg( 0 ,
1302	+	0 , &(args_info->bad_given),
1303	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1304	+	check_ambiguity, override, 0, 0,
1305	+	"bad", '-',
1306	+	additional_error))
1307	+	goto failure;
1308	+
1309	+	}
1310	+	/* count of molecules matching selection criteria (and associated statistics).  */
1311	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1312	+	{
1313	+
1314	+	if (args_info->staticProps_group_counter && override)
1315	+	reset_group_staticProps (args_info);
1316	+	args_info->staticProps_group_counter += 1;
1317	+
1318	+	if (update_arg( 0 ,
1319	+	0 , &(args_info->count_given),
1320	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1321	+	check_ambiguity, override, 0, 0,
1322	+	"count", '-',
1323	+	additional_error))
1324	+	goto failure;
1325	+
1326	+	}
1327	+	/* g(z).  */
1328	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1329	+	{
1330	+
1331	+	if (args_info->staticProps_group_counter && override)
1332	+	reset_group_staticProps (args_info);
1333	+	args_info->staticProps_group_counter += 1;
1334	+
1335	+	if (update_arg( 0 ,
1336	+	0 , &(args_info->gofz_given),
1337	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1338	+	check_ambiguity, override, 0, 0,
1339	+	"gofz", '-',
1340	+	additional_error))
1341	+	goto failure;
1342	+
1343	+	}
1344		/* g(r, cos(theta)).  */
1345		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1346		{
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;
1347
1348	<	break;
1349	<	}
1348	>	if (args_info->staticProps_group_counter && override)
1349	>	reset_group_staticProps (args_info);
1350	>	args_info->staticProps_group_counter += 1;
1351
1352	+	if (update_arg( 0 ,
1353	+	0 , &(args_info->r_theta_given),
1354	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1355	+	check_ambiguity, override, 0, 0,
1356	+	"r_theta", '-',
1357	+	additional_error))
1358	+	goto failure;
1359	+
1360	+	}
1361		/* g(r, cos(omega)).  */
1362		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1363		{
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;
1364
1365	<	break;
1365	>	if (args_info->staticProps_group_counter && override)
1366	>	reset_group_staticProps (args_info);
1367	>	args_info->staticProps_group_counter += 1;
1368	>
1369	>	if (update_arg( 0 ,
1370	>	0 , &(args_info->r_omega_given),
1371	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1372	>	check_ambiguity, override, 0, 0,
1373	>	"r_omega", '-',
1374	>	additional_error))
1375	>	goto failure;
1376	>
1377		}
1378	+	/* g(r, z).  */
1379	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1380	+	{
1381
1382	+	if (args_info->staticProps_group_counter && override)
1383	+	reset_group_staticProps (args_info);
1384	+	args_info->staticProps_group_counter += 1;
1385	+
1386	+	if (update_arg( 0 ,
1387	+	0 , &(args_info->r_z_given),
1388	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1389	+	check_ambiguity, override, 0, 0,
1390	+	"r_z", '-',
1391	+	additional_error))
1392	+	goto failure;
1393	+
1394	+	}
1395		/* g(cos(theta), cos(omega)).  */
1396		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1397		{
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;
1398
1399	<	break;
1400	<	}
1399	>	if (args_info->staticProps_group_counter && override)
1400	>	reset_group_staticProps (args_info);
1401	>	args_info->staticProps_group_counter += 1;
1402
1403	+	if (update_arg( 0 ,
1404	+	0 , &(args_info->theta_omega_given),
1405	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1406	+	check_ambiguity, override, 0, 0,
1407	+	"theta_omega", '-',
1408	+	additional_error))
1409	+	goto failure;
1410	+
1411	+	}
1412		/* g(x, y, z).  */
1413		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1414		{
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;
1415
1416	<	break;
1416	>	if (args_info->staticProps_group_counter && override)
1417	>	reset_group_staticProps (args_info);
1418	>	args_info->staticProps_group_counter += 1;
1419	>
1420	>	if (update_arg( 0 ,
1421	>	0 , &(args_info->gxyz_given),
1422	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1423	>	check_ambiguity, override, 0, 0,
1424	>	"gxyz", '-',
1425	>	additional_error))
1426	>	goto failure;
1427	>
1428		}
1429	+	/* 2D g(r) (Slab width --dz must be specified).  */
1430	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1431	+	{
1432
1433	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1434	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1433	>	if (args_info->staticProps_group_counter && override)
1434	>	reset_group_staticProps (args_info);
1435	>	args_info->staticProps_group_counter += 1;
1436	>
1437	>	if (update_arg( 0 ,
1438	>	0 , &(args_info->twodgofr_given),
1439	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1440	>	check_ambiguity, override, 0, 0,
1441	>	"twodgofr", '-',
1442	>	additional_error))
1443	>	goto failure;
1444	>
1445	>	}
1446	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1447	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1448		{
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;
1449
1450	<	break;
1450	>	if (args_info->staticProps_group_counter && override)
1451	>	reset_group_staticProps (args_info);
1452	>	args_info->staticProps_group_counter += 1;
1453	>
1454	>	if (update_arg( 0 ,
1455	>	0 , &(args_info->rp2_given),
1456	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1457	>	check_ambiguity, override, 0, 0,
1458	>	"rp2", '-',
1459	>	additional_error))
1460	>	goto failure;
1461	>
1462		}
1463	+	/* slab density.  */
1464	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1465	+	{
1466
1467	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1468	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1467	>	if (args_info->staticProps_group_counter && override)
1468	>	reset_group_staticProps (args_info);
1469	>	args_info->staticProps_group_counter += 1;
1470	>
1471	>	if (update_arg( 0 ,
1472	>	0 , &(args_info->slab_density_given),
1473	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1474	>	check_ambiguity, override, 0, 0,
1475	>	"slab_density", '-',
1476	>	additional_error))
1477	>	goto failure;
1478	>
1479	>	}
1480	>	/* p(cos(theta)).  */
1481	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1482		{
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;
1483
1484	<	break;
1484	>	if (args_info->staticProps_group_counter && override)
1485	>	reset_group_staticProps (args_info);
1486	>	args_info->staticProps_group_counter += 1;
1487	>
1488	>	if (update_arg( 0 ,
1489	>	0 , &(args_info->p_angle_given),
1490	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1491	>	check_ambiguity, override, 0, 0,
1492	>	"p_angle", '-',
1493	>	additional_error))
1494	>	goto failure;
1495	>
1496		}
1497	+	/* hxy.  */
1498	+	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1499	+	{
1500
1501	<	/* density plot (--sele1 must be specified).  */
1502	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1501	>	if (args_info->staticProps_group_counter && override)
1502	>	reset_group_staticProps (args_info);
1503	>	args_info->staticProps_group_counter += 1;
1504	>
1505	>	if (update_arg( 0 ,
1506	>	0 , &(args_info->hxy_given),
1507	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1508	>	check_ambiguity, override, 0, 0,
1509	>	"hxy", '-',
1510	>	additional_error))
1511	>	goto failure;
1512	>
1513	>	}
1514	>	/* rho of R.  */
1515	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1516		{
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;
1517
1518	<	break;
1518	>	if (args_info->staticProps_group_counter && override)
1519	>	reset_group_staticProps (args_info);
1520	>	args_info->staticProps_group_counter += 1;
1521	>
1522	>	if (update_arg( 0 ,
1523	>	0 , &(args_info->rho_r_given),
1524	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1525	>	check_ambiguity, override, 0, 0,
1526	>	"rho_r", '-',
1527	>	additional_error))
1528	>	goto failure;
1529	>
1530		}
1531	+	/* angle of R.  */
1532	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1533	+	{
1534
1535	<
1535	>	if (args_info->staticProps_group_counter && override)
1536	>	reset_group_staticProps (args_info);
1537	>	args_info->staticProps_group_counter += 1;
1538	>
1539	>	if (update_arg( 0 ,
1540	>	0 , &(args_info->angle_r_given),
1541	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1542	>	check_ambiguity, override, 0, 0,
1543	>	"angle_r", '-',
1544	>	additional_error))
1545	>	goto failure;
1546	>
1547	>	}
1548	>	/* hull volume of nanoparticle.  */
1549	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1550	>	{
1551	>
1552	>	if (args_info->staticProps_group_counter && override)
1553	>	reset_group_staticProps (args_info);
1554	>	args_info->staticProps_group_counter += 1;
1555	>
1556	>	if (update_arg( 0 ,
1557	>	0 , &(args_info->hullvol_given),
1558	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1559	>	check_ambiguity, override, 0, 0,
1560	>	"hullvol", '-',
1561	>	additional_error))
1562	>	goto failure;
1563	>
1564	>	}
1565	>	/* length of nanorod.  */
1566	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1567	>	{
1568	>
1569	>	if (args_info->staticProps_group_counter && override)
1570	>	reset_group_staticProps (args_info);
1571	>	args_info->staticProps_group_counter += 1;
1572	>
1573	>	if (update_arg( 0 ,
1574	>	0 , &(args_info->rodlength_given),
1575	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1576	>	check_ambiguity, override, 0, 0,
1577	>	"rodlength", '-',
1578	>	additional_error))
1579	>	goto failure;
1580	>
1581	>	}
1582	>
1583	>	break;
1584		case '?':       /* Invalid option.  */
1585		/* `getopt_long' already printed an error message.  */
1586	<	exit (EXIT_FAILURE);
1586	>	goto failure;
1587
1588		default:        /* bug: option not considered.  */
1589	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1589	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1590		abort ();
1591		} /* switch */
1592		} /* while */
1593
1594	<	if ( staticProps_group_counter != 1)
1594	>	if (args_info->staticProps_group_counter > 1)
1595		{
1596	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1597	<	missing_required_options = 1;
1596	>	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 : ""));
1597	>	error = 1;
1598		}
1599
1600
1601	<	if (! args_info->input_given)
1601	>
1602	>	if (check_required)
1603		{
1604	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1604	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1605		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1606
1607	+	cmdline_parser_release (&local_args_info);
1608	+
1609	+	if ( error )
1610	+	return (EXIT_FAILURE);
1611	+
1612	+	if (optind < argc)
1613	+	{
1614	+	int i = 0 ;
1615	+	int found_prog_name = 0;
1616	+	/* whether program name, i.e., argv[0], is in the remaining args
1617	+	(this may happen with some implementations of getopt,
1618	+	but surely not with the one included by gengetopt) */
1619	+
1620	+	i = optind;
1621	+	while (i < argc)
1622	+	if (argv[i++] == argv[0]) {
1623	+	found_prog_name = 1;
1624	+	break;
1625	+	}
1626	+	i = 0;
1627	+
1628	+	args_info->inputs_num = argc - optind - found_prog_name;
1629	+	args_info->inputs =
1630	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1631	+	while (optind < argc)
1632	+	if (argv[optind++] != argv[0])
1633	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1634	+	}
1635	+
1636		return 0;
1637	+
1638	+	failure:
1639	+
1640	+	cmdline_parser_release (&local_args_info);
1641	+	return (EXIT_FAILURE);
1642		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1655 by gezelter, Mon Oct 3 20:32:45 2011 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
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