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root/OpenMD/branches/development/src/applications/staticProps/StaticPropsCmd.cpp

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 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/program/gengetopt-2.11/src/gengetopt -F StaticPropsCmd
4	>	gengetopt --file-name=StaticPropsCmd --unamed-opts
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	>	#ifdef WIN32
25	>	#include "utils/wingetopt.h"
26	>	#else
27	>	#include <getopt.h>
28	>	#endif
29
30		#include "StaticPropsCmd.h"
31
32	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
32	>	const char *gengetopt_args_info_purpose = "";
33
34	<	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	<	printf("      --slab_density              slab density (--sele1 must be specified)\n");
64	<	}
34	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35
36	+	const char *gengetopt_args_info_description = "";
37
38	<	static char *gengetopt_strdup (const char *s);
38	>	const char *gengetopt_args_info_help[] = {
39	>	"  -h, --help                    Print help and exit",
40	>	"  -V, --version                 Print version and exit",
41	>	"  -i, --input=filename          input dump file",
42	>	"  -o, --output=filename         output file name",
43	>	"  -n, --step=INT                process every n frame  (default=`1')",
44	>	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
45	>	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
46	>	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
47	>	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
48	>	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
49	>	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50	>	"      --dz=DOUBLE               slab width (dz)",
51	>	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
52	>	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53	>	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
54	>	"      --sele1=selection script  select the first stuntdouble set",
55	>	"      --sele2=selection script  select the second stuntdouble set",
56	>	"      --sele3=selection script  select the third stuntdouble set",
57	>	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58	>	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59	>	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60	>	"      --molname=STRING          molecule name",
61	>	"      --begin=INT               begin internal index",
62	>	"      --end=INT                 end internal index",
63	>	"      --radius=DOUBLE           nanoparticle radius",
64	>	"\n Group: staticProps\n   an option of this group is required",
65	>	"      --bo                      bond order parameter (--rcut must be specified)",
66	>	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67	>	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
68	>	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
69	>	"  -g, --gofr                    g(r)",
70	>	"      --gofz                    g(z)",
71	>	"      --r_theta                 g(r, cos(theta))",
72	>	"      --r_omega                 g(r, cos(omega))",
73	>	"      --r_z                     g(r, z)",
74	>	"      --theta_omega             g(cos(theta), cos(omega))",
75	>	"      --gxyz                    g(x, y, z)",
76	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
77	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
78	>	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
79	>	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
80	>	"  -d, --density                 density plot",
81	>	"      --slab_density            slab density",
82	>	"      --p_angle                 p(cos(theta))",
83	>	"      --hxy                     hxy",
84	>	"      --rho_r                   rho of R",
85	>	"      --angle_r                 angle of R",
86	>	"      --hullvol                 hull volume of nanoparticle",
87	>	"      --rodlength               length of nanorod",
88	>	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
89	>	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
90	>	0
91	>	};
92
93	<	/* gengetopt_strdup() */
94	<	/* strdup.c replacement of strdup, which is not standard */
95	<	char *
96	<	gengetopt_strdup (const char *s)
97	<	{
74	<	char *result = (char*)malloc(strlen(s) + 1);
75	<	if (result == (char*)0)
76	<	return (char*)0;
77	<	strcpy(result, s);
78	<	return result;
79	<	}
93	>	typedef enum {ARG_NO
94	>	, ARG_STRING
95	>	, ARG_INT
96	>	, ARG_DOUBLE
97	>	} cmdline_parser_arg_type;
98
99	<	int
100	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
101	<	{
102	<	int c;        /* Character of the parsed option.  */
85	<	int missing_required_options = 0;
86	<	int staticProps_group_counter = 0;
87	<
99	>	static
100	>	void clear_given (struct gengetopt_args_info *args_info);
101	>	static
102	>	void clear_args (struct gengetopt_args_info *args_info);
103
104	+	static int
105	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
106	+	struct cmdline_parser_params *params, const char *additional_error);
107	+
108	+	static int
109	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
110	+
111	+	static char *
112	+	gengetopt_strdup (const char *s);
113	+
114	+	static
115	+	void clear_given (struct gengetopt_args_info *args_info)
116	+	{
117		args_info->help_given = 0 ;
118		args_info->version_given = 0 ;
119		args_info->input_given = 0 ;
120		args_info->output_given = 0 ;
121		args_info->step_given = 0 ;
122	<	args_info->nrbins_given = 0 ;
122	>	args_info->nbins_given = 0 ;
123	>	args_info->nbins_x_given = 0 ;
124	>	args_info->nbins_y_given = 0 ;
125	>	args_info->nbins_z_given = 0 ;
126		args_info->nanglebins_given = 0 ;
127	+	args_info->rcut_given = 0 ;
128	+	args_info->dz_given = 0 ;
129		args_info->length_given = 0 ;
130	+	args_info->zlength_given = 0 ;
131	+	args_info->zoffset_given = 0 ;
132		args_info->sele1_given = 0 ;
133		args_info->sele2_given = 0 ;
134		args_info->sele3_given = 0 ;
135		args_info->refsele_given = 0 ;
136	+	args_info->comsele_given = 0 ;
137	+	args_info->seleoffset_given = 0 ;
138		args_info->molname_given = 0 ;
139		args_info->begin_given = 0 ;
140		args_info->end_given = 0 ;
141	+	args_info->radius_given = 0 ;
142	+	args_info->bo_given = 0 ;
143	+	args_info->bor_given = 0 ;
144	+	args_info->bad_given = 0 ;
145	+	args_info->count_given = 0 ;
146		args_info->gofr_given = 0 ;
147	+	args_info->gofz_given = 0 ;
148		args_info->r_theta_given = 0 ;
149		args_info->r_omega_given = 0 ;
150	+	args_info->r_z_given = 0 ;
151		args_info->theta_omega_given = 0 ;
152		args_info->gxyz_given = 0 ;
153	+	args_info->twodgofr_given = 0 ;
154		args_info->p2_given = 0 ;
155	+	args_info->rp2_given = 0 ;
156		args_info->scd_given = 0 ;
157		args_info->density_given = 0 ;
158		args_info->slab_density_given = 0 ;
159	<	#define clear_args() { \
160	<	args_info->input_arg = NULL; \
161	<	args_info->output_arg = NULL; \
162	<	args_info->step_arg = 1 ;\
163	<	args_info->nrbins_arg = 100 ;\
164	<	args_info->nanglebins_arg = 50 ;\
165	<	args_info->sele1_arg = NULL; \
166	<	args_info->sele2_arg = NULL; \
167	<	args_info->sele3_arg = NULL; \
122	<	args_info->refsele_arg = NULL; \
123	<	args_info->molname_arg = NULL; \
159	>	args_info->p_angle_given = 0 ;
160	>	args_info->hxy_given = 0 ;
161	>	args_info->rho_r_given = 0 ;
162	>	args_info->angle_r_given = 0 ;
163	>	args_info->hullvol_given = 0 ;
164	>	args_info->rodlength_given = 0 ;
165	>	args_info->tet_param_given = 0 ;
166	>	args_info->tet_param_z_given = 0 ;
167	>	args_info->staticProps_group_counter = 0 ;
168		}
169
170	<	clear_args();
170	>	static
171	>	void clear_args (struct gengetopt_args_info *args_info)
172	>	{
173	>	FIX_UNUSED (args_info);
174	>	args_info->input_arg = NULL;
175	>	args_info->input_orig = NULL;
176	>	args_info->output_arg = NULL;
177	>	args_info->output_orig = NULL;
178	>	args_info->step_arg = 1;
179	>	args_info->step_orig = NULL;
180	>	args_info->nbins_arg = 100;
181	>	args_info->nbins_orig = NULL;
182	>	args_info->nbins_x_arg = 100;
183	>	args_info->nbins_x_orig = NULL;
184	>	args_info->nbins_y_arg = 100;
185	>	args_info->nbins_y_orig = NULL;
186	>	args_info->nbins_z_arg = 100;
187	>	args_info->nbins_z_orig = NULL;
188	>	args_info->nanglebins_arg = 50;
189	>	args_info->nanglebins_orig = NULL;
190	>	args_info->rcut_orig = NULL;
191	>	args_info->dz_orig = NULL;
192	>	args_info->length_orig = NULL;
193	>	args_info->zlength_orig = NULL;
194	>	args_info->zoffset_arg = 0;
195	>	args_info->zoffset_orig = NULL;
196	>	args_info->sele1_arg = NULL;
197	>	args_info->sele1_orig = NULL;
198	>	args_info->sele2_arg = NULL;
199	>	args_info->sele2_orig = NULL;
200	>	args_info->sele3_arg = NULL;
201	>	args_info->sele3_orig = NULL;
202	>	args_info->refsele_arg = NULL;
203	>	args_info->refsele_orig = NULL;
204	>	args_info->comsele_arg = NULL;
205	>	args_info->comsele_orig = NULL;
206	>	args_info->seleoffset_orig = NULL;
207	>	args_info->molname_arg = NULL;
208	>	args_info->molname_orig = NULL;
209	>	args_info->begin_orig = NULL;
210	>	args_info->end_orig = NULL;
211	>	args_info->radius_orig = NULL;
212	>
213	>	}
214
215	+	static
216	+	void init_args_info(struct gengetopt_args_info *args_info)
217	+	{
218	+
219	+
220	+	args_info->help_help = gengetopt_args_info_help[0] ;
221	+	args_info->version_help = gengetopt_args_info_help[1] ;
222	+	args_info->input_help = gengetopt_args_info_help[2] ;
223	+	args_info->output_help = gengetopt_args_info_help[3] ;
224	+	args_info->step_help = gengetopt_args_info_help[4] ;
225	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
226	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
227	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
228	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
229	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
230	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
231	+	args_info->dz_help = gengetopt_args_info_help[11] ;
232	+	args_info->length_help = gengetopt_args_info_help[12] ;
233	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
234	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
235	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
236	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
237	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
238	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
239	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
240	+	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
241	+	args_info->molname_help = gengetopt_args_info_help[21] ;
242	+	args_info->begin_help = gengetopt_args_info_help[22] ;
243	+	args_info->end_help = gengetopt_args_info_help[23] ;
244	+	args_info->radius_help = gengetopt_args_info_help[24] ;
245	+	args_info->bo_help = gengetopt_args_info_help[26] ;
246	+	args_info->bor_help = gengetopt_args_info_help[27] ;
247	+	args_info->bad_help = gengetopt_args_info_help[28] ;
248	+	args_info->count_help = gengetopt_args_info_help[29] ;
249	+	args_info->gofr_help = gengetopt_args_info_help[30] ;
250	+	args_info->gofz_help = gengetopt_args_info_help[31] ;
251	+	args_info->r_theta_help = gengetopt_args_info_help[32] ;
252	+	args_info->r_omega_help = gengetopt_args_info_help[33] ;
253	+	args_info->r_z_help = gengetopt_args_info_help[34] ;
254	+	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
255	+	args_info->gxyz_help = gengetopt_args_info_help[36] ;
256	+	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
257	+	args_info->p2_help = gengetopt_args_info_help[38] ;
258	+	args_info->rp2_help = gengetopt_args_info_help[39] ;
259	+	args_info->scd_help = gengetopt_args_info_help[40] ;
260	+	args_info->density_help = gengetopt_args_info_help[41] ;
261	+	args_info->slab_density_help = gengetopt_args_info_help[42] ;
262	+	args_info->p_angle_help = gengetopt_args_info_help[43] ;
263	+	args_info->hxy_help = gengetopt_args_info_help[44] ;
264	+	args_info->rho_r_help = gengetopt_args_info_help[45] ;
265	+	args_info->angle_r_help = gengetopt_args_info_help[46] ;
266	+	args_info->hullvol_help = gengetopt_args_info_help[47] ;
267	+	args_info->rodlength_help = gengetopt_args_info_help[48] ;
268	+	args_info->tet_param_help = gengetopt_args_info_help[49] ;
269	+	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
270	+
271	+	}
272	+
273	+	void
274	+	cmdline_parser_print_version (void)
275	+	{
276	+	printf ("%s %s\n",
277	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
278	+	CMDLINE_PARSER_VERSION);
279	+	}
280	+
281	+	static void print_help_common(void) {
282	+	cmdline_parser_print_version ();
283	+
284	+	if (strlen(gengetopt_args_info_purpose) > 0)
285	+	printf("\n%s\n", gengetopt_args_info_purpose);
286	+
287	+	if (strlen(gengetopt_args_info_usage) > 0)
288	+	printf("\n%s\n", gengetopt_args_info_usage);
289	+
290	+	printf("\n");
291	+
292	+	if (strlen(gengetopt_args_info_description) > 0)
293	+	printf("%s\n\n", gengetopt_args_info_description);
294	+	}
295	+
296	+	void
297	+	cmdline_parser_print_help (void)
298	+	{
299	+	int i = 0;
300	+	print_help_common();
301	+	while (gengetopt_args_info_help[i])
302	+	printf("%s\n", gengetopt_args_info_help[i++]);
303	+	}
304	+
305	+	void
306	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
307	+	{
308	+	clear_given (args_info);
309	+	clear_args (args_info);
310	+	init_args_info (args_info);
311	+
312	+	args_info->inputs = 0;
313	+	args_info->inputs_num = 0;
314	+	}
315	+
316	+	void
317	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
318	+	{
319	+	if (params)
320	+	{
321	+	params->override = 0;
322	+	params->initialize = 1;
323	+	params->check_required = 1;
324	+	params->check_ambiguity = 0;
325	+	params->print_errors = 1;
326	+	}
327	+	}
328	+
329	+	struct cmdline_parser_params *
330	+	cmdline_parser_params_create(void)
331	+	{
332	+	struct cmdline_parser_params *params =
333	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
334	+	cmdline_parser_params_init(params);
335	+	return params;
336	+	}
337	+
338	+	static void
339	+	free_string_field (char **s)
340	+	{
341	+	if (*s)
342	+	{
343	+	free (*s);
344	+	*s = 0;
345	+	}
346	+	}
347	+
348	+
349	+	static void
350	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
351	+	{
352	+	unsigned int i;
353	+	free_string_field (&(args_info->input_arg));
354	+	free_string_field (&(args_info->input_orig));
355	+	free_string_field (&(args_info->output_arg));
356	+	free_string_field (&(args_info->output_orig));
357	+	free_string_field (&(args_info->step_orig));
358	+	free_string_field (&(args_info->nbins_orig));
359	+	free_string_field (&(args_info->nbins_x_orig));
360	+	free_string_field (&(args_info->nbins_y_orig));
361	+	free_string_field (&(args_info->nbins_z_orig));
362	+	free_string_field (&(args_info->nanglebins_orig));
363	+	free_string_field (&(args_info->rcut_orig));
364	+	free_string_field (&(args_info->dz_orig));
365	+	free_string_field (&(args_info->length_orig));
366	+	free_string_field (&(args_info->zlength_orig));
367	+	free_string_field (&(args_info->zoffset_orig));
368	+	free_string_field (&(args_info->sele1_arg));
369	+	free_string_field (&(args_info->sele1_orig));
370	+	free_string_field (&(args_info->sele2_arg));
371	+	free_string_field (&(args_info->sele2_orig));
372	+	free_string_field (&(args_info->sele3_arg));
373	+	free_string_field (&(args_info->sele3_orig));
374	+	free_string_field (&(args_info->refsele_arg));
375	+	free_string_field (&(args_info->refsele_orig));
376	+	free_string_field (&(args_info->comsele_arg));
377	+	free_string_field (&(args_info->comsele_orig));
378	+	free_string_field (&(args_info->seleoffset_orig));
379	+	free_string_field (&(args_info->molname_arg));
380	+	free_string_field (&(args_info->molname_orig));
381	+	free_string_field (&(args_info->begin_orig));
382	+	free_string_field (&(args_info->end_orig));
383	+	free_string_field (&(args_info->radius_orig));
384	+
385	+
386	+	for (i = 0; i < args_info->inputs_num; ++i)
387	+	free (args_info->inputs [i]);
388	+
389	+	if (args_info->inputs_num)
390	+	free (args_info->inputs);
391	+
392	+	clear_given (args_info);
393	+	}
394	+
395	+
396	+	static void
397	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
398	+	{
399	+	FIX_UNUSED (values);
400	+	if (arg) {
401	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
402	+	} else {
403	+	fprintf(outfile, "%s\n", opt);
404	+	}
405	+	}
406	+
407	+
408	+	int
409	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
410	+	{
411	+	int i = 0;
412	+
413	+	if (!outfile)
414	+	{
415	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
416	+	return EXIT_FAILURE;
417	+	}
418	+
419	+	if (args_info->help_given)
420	+	write_into_file(outfile, "help", 0, 0 );
421	+	if (args_info->version_given)
422	+	write_into_file(outfile, "version", 0, 0 );
423	+	if (args_info->input_given)
424	+	write_into_file(outfile, "input", args_info->input_orig, 0);
425	+	if (args_info->output_given)
426	+	write_into_file(outfile, "output", args_info->output_orig, 0);
427	+	if (args_info->step_given)
428	+	write_into_file(outfile, "step", args_info->step_orig, 0);
429	+	if (args_info->nbins_given)
430	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
431	+	if (args_info->nbins_x_given)
432	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
433	+	if (args_info->nbins_y_given)
434	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
435	+	if (args_info->nbins_z_given)
436	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
437	+	if (args_info->nanglebins_given)
438	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
439	+	if (args_info->rcut_given)
440	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
441	+	if (args_info->dz_given)
442	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
443	+	if (args_info->length_given)
444	+	write_into_file(outfile, "length", args_info->length_orig, 0);
445	+	if (args_info->zlength_given)
446	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
447	+	if (args_info->zoffset_given)
448	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
449	+	if (args_info->sele1_given)
450	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
451	+	if (args_info->sele2_given)
452	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
453	+	if (args_info->sele3_given)
454	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
455	+	if (args_info->refsele_given)
456	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
457	+	if (args_info->comsele_given)
458	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
459	+	if (args_info->seleoffset_given)
460	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
461	+	if (args_info->molname_given)
462	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
463	+	if (args_info->begin_given)
464	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
465	+	if (args_info->end_given)
466	+	write_into_file(outfile, "end", args_info->end_orig, 0);
467	+	if (args_info->radius_given)
468	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
469	+	if (args_info->bo_given)
470	+	write_into_file(outfile, "bo", 0, 0 );
471	+	if (args_info->bor_given)
472	+	write_into_file(outfile, "bor", 0, 0 );
473	+	if (args_info->bad_given)
474	+	write_into_file(outfile, "bad", 0, 0 );
475	+	if (args_info->count_given)
476	+	write_into_file(outfile, "count", 0, 0 );
477	+	if (args_info->gofr_given)
478	+	write_into_file(outfile, "gofr", 0, 0 );
479	+	if (args_info->gofz_given)
480	+	write_into_file(outfile, "gofz", 0, 0 );
481	+	if (args_info->r_theta_given)
482	+	write_into_file(outfile, "r_theta", 0, 0 );
483	+	if (args_info->r_omega_given)
484	+	write_into_file(outfile, "r_omega", 0, 0 );
485	+	if (args_info->r_z_given)
486	+	write_into_file(outfile, "r_z", 0, 0 );
487	+	if (args_info->theta_omega_given)
488	+	write_into_file(outfile, "theta_omega", 0, 0 );
489	+	if (args_info->gxyz_given)
490	+	write_into_file(outfile, "gxyz", 0, 0 );
491	+	if (args_info->twodgofr_given)
492	+	write_into_file(outfile, "twodgofr", 0, 0 );
493	+	if (args_info->p2_given)
494	+	write_into_file(outfile, "p2", 0, 0 );
495	+	if (args_info->rp2_given)
496	+	write_into_file(outfile, "rp2", 0, 0 );
497	+	if (args_info->scd_given)
498	+	write_into_file(outfile, "scd", 0, 0 );
499	+	if (args_info->density_given)
500	+	write_into_file(outfile, "density", 0, 0 );
501	+	if (args_info->slab_density_given)
502	+	write_into_file(outfile, "slab_density", 0, 0 );
503	+	if (args_info->p_angle_given)
504	+	write_into_file(outfile, "p_angle", 0, 0 );
505	+	if (args_info->hxy_given)
506	+	write_into_file(outfile, "hxy", 0, 0 );
507	+	if (args_info->rho_r_given)
508	+	write_into_file(outfile, "rho_r", 0, 0 );
509	+	if (args_info->angle_r_given)
510	+	write_into_file(outfile, "angle_r", 0, 0 );
511	+	if (args_info->hullvol_given)
512	+	write_into_file(outfile, "hullvol", 0, 0 );
513	+	if (args_info->rodlength_given)
514	+	write_into_file(outfile, "rodlength", 0, 0 );
515	+	if (args_info->tet_param_given)
516	+	write_into_file(outfile, "tet_param", 0, 0 );
517	+	if (args_info->tet_param_z_given)
518	+	write_into_file(outfile, "tet_param_z", 0, 0 );
519	+
520	+
521	+	i = EXIT_SUCCESS;
522	+	return i;
523	+	}
524	+
525	+	int
526	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
527	+	{
528	+	FILE *outfile;
529	+	int i = 0;
530	+
531	+	outfile = fopen(filename, "w");
532	+
533	+	if (!outfile)
534	+	{
535	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
536	+	return EXIT_FAILURE;
537	+	}
538	+
539	+	i = cmdline_parser_dump(outfile, args_info);
540	+	fclose (outfile);
541	+
542	+	return i;
543	+	}
544	+
545	+	void
546	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
547	+	{
548	+	cmdline_parser_release (args_info);
549	+	}
550	+
551	+	/** @brief replacement of strdup, which is not standard */
552	+	char *
553	+	gengetopt_strdup (const char *s)
554	+	{
555	+	char *result = 0;
556	+	if (!s)
557	+	return result;
558	+
559	+	result = (char*)malloc(strlen(s) + 1);
560	+	if (result == (char*)0)
561	+	return (char*)0;
562	+	strcpy(result, s);
563	+	return result;
564	+	}
565	+
566	+	static void
567	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
568	+	{
569	+	if (! args_info->staticProps_group_counter)
570	+	return;
571	+
572	+	args_info->bo_given = 0 ;
573	+	args_info->bor_given = 0 ;
574	+	args_info->bad_given = 0 ;
575	+	args_info->count_given = 0 ;
576	+	args_info->gofr_given = 0 ;
577	+	args_info->gofz_given = 0 ;
578	+	args_info->r_theta_given = 0 ;
579	+	args_info->r_omega_given = 0 ;
580	+	args_info->r_z_given = 0 ;
581	+	args_info->theta_omega_given = 0 ;
582	+	args_info->gxyz_given = 0 ;
583	+	args_info->twodgofr_given = 0 ;
584	+	args_info->p2_given = 0 ;
585	+	args_info->rp2_given = 0 ;
586	+	args_info->scd_given = 0 ;
587	+	args_info->density_given = 0 ;
588	+	args_info->slab_density_given = 0 ;
589	+	args_info->p_angle_given = 0 ;
590	+	args_info->hxy_given = 0 ;
591	+	args_info->rho_r_given = 0 ;
592	+	args_info->angle_r_given = 0 ;
593	+	args_info->hullvol_given = 0 ;
594	+	args_info->rodlength_given = 0 ;
595	+	args_info->tet_param_given = 0 ;
596	+	args_info->tet_param_z_given = 0 ;
597	+
598	+	args_info->staticProps_group_counter = 0;
599	+	}
600	+
601	+	int
602	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
603	+	{
604	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
605	+	}
606	+
607	+	int
608	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
609	+	struct cmdline_parser_params *params)
610	+	{
611	+	int result;
612	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
613	+
614	+	if (result == EXIT_FAILURE)
615	+	{
616	+	cmdline_parser_free (args_info);
617	+	exit (EXIT_FAILURE);
618	+	}
619	+
620	+	return result;
621	+	}
622	+
623	+	int
624	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
625	+	{
626	+	int result;
627	+	struct cmdline_parser_params params;
628	+
629	+	params.override = override;
630	+	params.initialize = initialize;
631	+	params.check_required = check_required;
632	+	params.check_ambiguity = 0;
633	+	params.print_errors = 1;
634	+
635	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
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_required (struct gengetopt_args_info *args_info, const char *prog_name)
648	+	{
649	+	int result = EXIT_SUCCESS;
650	+
651	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
652	+	result = EXIT_FAILURE;
653	+
654	+	if (result == EXIT_FAILURE)
655	+	{
656	+	cmdline_parser_free (args_info);
657	+	exit (EXIT_FAILURE);
658	+	}
659	+
660	+	return result;
661	+	}
662	+
663	+	int
664	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
665	+	{
666	+	int error = 0;
667	+	FIX_UNUSED (additional_error);
668	+
669	+	/* checks for required options */
670	+	if (! args_info->input_given)
671	+	{
672	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
673	+	error = 1;
674	+	}
675	+
676	+	if (args_info->staticProps_group_counter == 0)
677	+	{
678	+	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 : ""));
679	+	error = 1;
680	+	}
681	+
682	+
683	+	/* checks for dependences among options */
684	+
685	+	return error;
686	+	}
687	+
688	+
689	+	static char *package_name = 0;
690	+
691	+	/**
692	+	* @brief updates an option
693	+	* @param field the generic pointer to the field to update
694	+	* @param orig_field the pointer to the orig field
695	+	* @param field_given the pointer to the number of occurrence of this option
696	+	* @param prev_given the pointer to the number of occurrence already seen
697	+	* @param value the argument for this option (if null no arg was specified)
698	+	* @param possible_values the possible values for this option (if specified)
699	+	* @param default_value the default value (in case the option only accepts fixed values)
700	+	* @param arg_type the type of this option
701	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
702	+	* @param override @see cmdline_parser_params.override
703	+	* @param no_free whether to free a possible previous value
704	+	* @param multiple_option whether this is a multiple option
705	+	* @param long_opt the corresponding long option
706	+	* @param short_opt the corresponding short option (or '-' if none)
707	+	* @param additional_error possible further error specification
708	+	*/
709	+	static
710	+	int update_arg(void *field, char **orig_field,
711	+	unsigned int *field_given, unsigned int *prev_given,
712	+	char *value, const char *possible_values[],
713	+	const char *default_value,
714	+	cmdline_parser_arg_type arg_type,
715	+	int check_ambiguity, int override,
716	+	int no_free, int multiple_option,
717	+	const char *long_opt, char short_opt,
718	+	const char *additional_error)
719	+	{
720	+	char *stop_char = 0;
721	+	const char *val = value;
722	+	int found;
723	+	char **string_field;
724	+	FIX_UNUSED (field);
725	+
726	+	stop_char = 0;
727	+	found = 0;
728	+
729	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
730	+	{
731	+	if (short_opt != '-')
732	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
733	+	package_name, long_opt, short_opt,
734	+	(additional_error ? additional_error : ""));
735	+	else
736	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
737	+	package_name, long_opt,
738	+	(additional_error ? additional_error : ""));
739	+	return 1; /* failure */
740	+	}
741	+
742	+	FIX_UNUSED (default_value);
743	+
744	+	if (field_given && *field_given && ! override)
745	+	return 0;
746	+	if (prev_given)
747	+	(*prev_given)++;
748	+	if (field_given)
749	+	(*field_given)++;
750	+	if (possible_values)
751	+	val = possible_values[found];
752	+
753	+	switch(arg_type) {
754	+	case ARG_INT:
755	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
756	+	break;
757	+	case ARG_DOUBLE:
758	+	if (val) *((double *)field) = strtod (val, &stop_char);
759	+	break;
760	+	case ARG_STRING:
761	+	if (val) {
762	+	string_field = (char **)field;
763	+	if (!no_free && *string_field)
764	+	free (*string_field); /* free previous string */
765	+	*string_field = gengetopt_strdup (val);
766	+	}
767	+	break;
768	+	default:
769	+	break;
770	+	};
771	+
772	+	/* check numeric conversion */
773	+	switch(arg_type) {
774	+	case ARG_INT:
775	+	case ARG_DOUBLE:
776	+	if (val && !(stop_char && *stop_char == '\0')) {
777	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
778	+	return 1; /* failure */
779	+	}
780	+	break;
781	+	default:
782	+	;
783	+	};
784	+
785	+	/* store the original value */
786	+	switch(arg_type) {
787	+	case ARG_NO:
788	+	break;
789	+	default:
790	+	if (value && orig_field) {
791	+	if (no_free) {
792	+	*orig_field = value;
793	+	} else {
794	+	if (*orig_field)
795	+	free (*orig_field); /* free previous string */
796	+	*orig_field = gengetopt_strdup (value);
797	+	}
798	+	}
799	+	};
800	+
801	+	return 0; /* OK */
802	+	}
803	+
804	+
805	+	int
806	+	cmdline_parser_internal (
807	+	int argc, char **argv, struct gengetopt_args_info *args_info,
808	+	struct cmdline_parser_params *params, const char *additional_error)
809	+	{
810	+	int c;        /* Character of the parsed option.  */
811	+
812	+	int error = 0;
813	+	struct gengetopt_args_info local_args_info;
814	+
815	+	int override;
816	+	int initialize;
817	+	int check_required;
818	+	int check_ambiguity;
819	+
820	+	package_name = argv[0];
821	+
822	+	override = params->override;
823	+	initialize = params->initialize;
824	+	check_required = params->check_required;
825	+	check_ambiguity = params->check_ambiguity;
826	+
827	+	if (initialize)
828	+	cmdline_parser_init (args_info);
829	+
830	+	cmdline_parser_init (&local_args_info);
831	+
832		optarg = 0;
833	<	optind = 1;
834	<	opterr = 1;
833	>	optind = 0;
834	>	opterr = params->print_errors;
835		optopt = '?';
836
837		while (1)
838		{
839		int option_index = 0;
136	–	char *stop_char;
840
841		static struct option long_options[] = {
842		{ "help",       0, NULL, 'h' },
#	Line 141 | Line 844 | cmdline_parser (int argc, char * const *argv, struct g
844		{ "input",      1, NULL, 'i' },
845		{ "output",     1, NULL, 'o' },
846		{ "step",       1, NULL, 'n' },
847	<	{ "nrbins",     1, NULL, 'r' },
847	>	{ "nbins",      1, NULL, 'b' },
848	>	{ "nbins_x",    1, NULL, 'x' },
849	>	{ "nbins_y",    1, NULL, 'y' },
850	>	{ "nbins_z",    1, NULL, 0 },
851		{ "nanglebins", 1, NULL, 'a' },
852	<	{ "length",     1, NULL, 'l' },
852	>	{ "rcut",       1, NULL, 'c' },
853	>	{ "dz", 1, NULL, 0 },
854	>	{ "length",     1, NULL, 0 },
855	>	{ "zlength",    1, NULL, 0 },
856	>	{ "zoffset",    1, NULL, 'z' },
857		{ "sele1",      1, NULL, 0 },
858		{ "sele2",      1, NULL, 0 },
859		{ "sele3",      1, NULL, 0 },
860		{ "refsele",    1, NULL, 0 },
861	+	{ "comsele",    1, NULL, 0 },
862	+	{ "seleoffset", 1, NULL, 0 },
863		{ "molname",    1, NULL, 0 },
864		{ "begin",      1, NULL, 0 },
865		{ "end",        1, NULL, 0 },
866	<	{ "gofr",       0, NULL, 0 },
866	>	{ "radius",     1, NULL, 0 },
867	>	{ "bo", 0, NULL, 0 },
868	>	{ "bor",        0, NULL, 0 },
869	>	{ "bad",        0, NULL, 0 },
870	>	{ "count",      0, NULL, 0 },
871	>	{ "gofr",       0, NULL, 'g' },
872	>	{ "gofz",       0, NULL, 0 },
873		{ "r_theta",    0, NULL, 0 },
874		{ "r_omega",    0, NULL, 0 },
875	+	{ "r_z",        0, NULL, 0 },
876		{ "theta_omega",        0, NULL, 0 },
877		{ "gxyz",       0, NULL, 0 },
878	<	{ "p2", 0, NULL, 0 },
879	<	{ "scd",        0, NULL, 0 },
880	<	{ "density",    0, NULL, 0 },
878	>	{ "twodgofr",   0, NULL, 0 },
879	>	{ "p2", 0, NULL, 'p' },
880	>	{ "rp2",        0, NULL, 0 },
881	>	{ "scd",        0, NULL, 's' },
882	>	{ "density",    0, NULL, 'd' },
883		{ "slab_density",       0, NULL, 0 },
884	<	{ NULL, 0, NULL, 0 }
884	>	{ "p_angle",    0, NULL, 0 },
885	>	{ "hxy",        0, NULL, 0 },
886	>	{ "rho_r",      0, NULL, 0 },
887	>	{ "angle_r",    0, NULL, 0 },
888	>	{ "hullvol",    0, NULL, 0 },
889	>	{ "rodlength",  0, NULL, 0 },
890	>	{ "tet_param",  0, NULL, 'Q' },
891	>	{ "tet_param_z",        0, NULL, 0 },
892	>	{ 0,  0, 0, 0 }
893		};
894
895	<	stop_char = 0;
167	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
895	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
896
897		if (c == -1) break;       /* Exit from `while (1)' loop.  */
898
899		switch (c)
900		{
901		case 'h':       /* Print help and exit.  */
174	–	clear_args ();
902		cmdline_parser_print_help ();
903	+	cmdline_parser_free (&local_args_info);
904		exit (EXIT_SUCCESS);
905
906		case 'V':       /* Print version and exit.  */
179	–	clear_args ();
907		cmdline_parser_print_version ();
908	+	cmdline_parser_free (&local_args_info);
909		exit (EXIT_SUCCESS);
910
911		case 'i':       /* input dump file.  */
912	<	if (args_info->input_given)
913	<	{
914	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
915	<	clear_args ();
916	<	exit (EXIT_FAILURE);
917	<	}
918	<	args_info->input_given = 1;
919	<	args_info->input_arg = gengetopt_strdup (optarg);
912	>
913	>
914	>	if (update_arg( (void *)&(args_info->input_arg),
915	>	&(args_info->input_orig), &(args_info->input_given),
916	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
917	>	check_ambiguity, override, 0, 0,
918	>	"input", 'i',
919	>	additional_error))
920	>	goto failure;
921	>
922		break;
193	–
923		case 'o':       /* output file name.  */
924	<	if (args_info->output_given)
925	<	{
926	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
927	<	clear_args ();
928	<	exit (EXIT_FAILURE);
929	<	}
930	<	args_info->output_given = 1;
931	<	args_info->output_arg = gengetopt_strdup (optarg);
924	>
925	>
926	>	if (update_arg( (void *)&(args_info->output_arg),
927	>	&(args_info->output_orig), &(args_info->output_given),
928	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
929	>	check_ambiguity, override, 0, 0,
930	>	"output", 'o',
931	>	additional_error))
932	>	goto failure;
933	>
934		break;
204	–
935		case 'n':       /* process every n frame.  */
936	<	if (args_info->step_given)
937	<	{
938	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
939	<	clear_args ();
940	<	exit (EXIT_FAILURE);
941	<	}
942	<	args_info->step_given = 1;
943	<	args_info->step_arg = strtol (optarg,&stop_char,0);
936	>
937	>
938	>	if (update_arg( (void *)&(args_info->step_arg),
939	>	&(args_info->step_orig), &(args_info->step_given),
940	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
941	>	check_ambiguity, override, 0, 0,
942	>	"step", 'n',
943	>	additional_error))
944	>	goto failure;
945	>
946		break;
947	<
948	<	case 'r':       /* number of bins for distance.  */
949	<	if (args_info->nrbins_given)
950	<	{
951	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
952	<	clear_args ();
953	<	exit (EXIT_FAILURE);
954	<	}
955	<	args_info->nrbins_given = 1;
956	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
947	>	case 'b':       /* number of bins (general purpose).  */
948	>
949	>
950	>	if (update_arg( (void *)&(args_info->nbins_arg),
951	>	&(args_info->nbins_orig), &(args_info->nbins_given),
952	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
953	>	check_ambiguity, override, 0, 0,
954	>	"nbins", 'b',
955	>	additional_error))
956	>	goto failure;
957	>
958		break;
959	<
959	>	case 'x':       /* number of bins in x axis.  */
960	>
961	>
962	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
963	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
964	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
965	>	check_ambiguity, override, 0, 0,
966	>	"nbins_x", 'x',
967	>	additional_error))
968	>	goto failure;
969	>
970	>	break;
971	>	case 'y':       /* number of bins in y axis.  */
972	>
973	>
974	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
975	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
976	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
977	>	check_ambiguity, override, 0, 0,
978	>	"nbins_y", 'y',
979	>	additional_error))
980	>	goto failure;
981	>
982	>	break;
983		case 'a':       /* number of bins for cos(angle).  */
984	<	if (args_info->nanglebins_given)
985	<	{
986	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
987	<	clear_args ();
988	<	exit (EXIT_FAILURE);
989	<	}
990	<	args_info->nanglebins_given = 1;
991	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
984	>
985	>
986	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
987	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
988	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
989	>	check_ambiguity, override, 0, 0,
990	>	"nanglebins", 'a',
991	>	additional_error))
992	>	goto failure;
993	>
994		break;
995	<
996	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
997	<	if (args_info->length_given)
998	<	{
999	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1000	<	clear_args ();
1001	<	exit (EXIT_FAILURE);
1002	<	}
1003	<	args_info->length_given = 1;
1004	<	args_info->length_arg = strtod (optarg, NULL);
995	>	case 'c':       /* cutoff radius (rcut).  */
996	>
997	>
998	>	if (update_arg( (void *)&(args_info->rcut_arg),
999	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1000	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1001	>	check_ambiguity, override, 0, 0,
1002	>	"rcut", 'c',
1003	>	additional_error))
1004	>	goto failure;
1005	>
1006		break;
1007	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1008	+
1009	+
1010	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1011	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1012	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1013	+	check_ambiguity, override, 0, 0,
1014	+	"zoffset", 'z',
1015	+	additional_error))
1016	+	goto failure;
1017	+
1018	+	break;
1019	+	case 'g':       /* g(r).  */
1020	+
1021	+	if (args_info->staticProps_group_counter && override)
1022	+	reset_group_staticProps (args_info);
1023	+	args_info->staticProps_group_counter += 1;
1024	+
1025	+	if (update_arg( 0 ,
1026	+	0 , &(args_info->gofr_given),
1027	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1028	+	check_ambiguity, override, 0, 0,
1029	+	"gofr", 'g',
1030	+	additional_error))
1031	+	goto failure;
1032	+
1033	+	break;
1034	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1035	+
1036	+	if (args_info->staticProps_group_counter && override)
1037	+	reset_group_staticProps (args_info);
1038	+	args_info->staticProps_group_counter += 1;
1039	+
1040	+	if (update_arg( 0 ,
1041	+	0 , &(args_info->p2_given),
1042	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1043	+	check_ambiguity, override, 0, 0,
1044	+	"p2", 'p',
1045	+	additional_error))
1046	+	goto failure;
1047	+
1048	+	break;
1049	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1050	+
1051	+	if (args_info->staticProps_group_counter && override)
1052	+	reset_group_staticProps (args_info);
1053	+	args_info->staticProps_group_counter += 1;
1054	+
1055	+	if (update_arg( 0 ,
1056	+	0 , &(args_info->scd_given),
1057	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1058	+	check_ambiguity, override, 0, 0,
1059	+	"scd", 's',
1060	+	additional_error))
1061	+	goto failure;
1062	+
1063	+	break;
1064	+	case 'd':       /* density plot.  */
1065	+
1066	+	if (args_info->staticProps_group_counter && override)
1067	+	reset_group_staticProps (args_info);
1068	+	args_info->staticProps_group_counter += 1;
1069	+
1070	+	if (update_arg( 0 ,
1071	+	0 , &(args_info->density_given),
1072	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1073	+	check_ambiguity, override, 0, 0,
1074	+	"density", 'd',
1075	+	additional_error))
1076	+	goto failure;
1077	+
1078	+	break;
1079	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1080	+
1081	+	if (args_info->staticProps_group_counter && override)
1082	+	reset_group_staticProps (args_info);
1083	+	args_info->staticProps_group_counter += 1;
1084	+
1085	+	if (update_arg( 0 ,
1086	+	0 , &(args_info->tet_param_given),
1087	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1088	+	check_ambiguity, override, 0, 0,
1089	+	"tet_param", 'Q',
1090	+	additional_error))
1091	+	goto failure;
1092	+
1093	+	break;
1094
249	–
1095		case 0: /* Long option with no short option */
1096	<	/* select the first stuntdouble set.  */
1097	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1096	>	/* number of bins in z axis.  */
1097	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1098		{
1099	<	if (args_info->sele1_given)
1100	<	{
1101	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1102	<	clear_args ();
1103	<	exit (EXIT_FAILURE);
1104	<	}
1105	<	args_info->sele1_given = 1;
1106	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1107	<	break;
1099	>
1100	>
1101	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1102	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1103	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1104	>	check_ambiguity, override, 0, 0,
1105	>	"nbins_z", '-',
1106	>	additional_error))
1107	>	goto failure;
1108	>
1109		}
1110	+	/* slab width (dz).  */
1111	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1112	+	{
1113
1114	+
1115	+	if (update_arg( (void *)&(args_info->dz_arg),
1116	+	&(args_info->dz_orig), &(args_info->dz_given),
1117	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1118	+	check_ambiguity, override, 0, 0,
1119	+	"dz", '-',
1120	+	additional_error))
1121	+	goto failure;
1122	+
1123	+	}
1124	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1125	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1126	+	{
1127	+
1128	+
1129	+	if (update_arg( (void *)&(args_info->length_arg),
1130	+	&(args_info->length_orig), &(args_info->length_given),
1131	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1132	+	check_ambiguity, override, 0, 0,
1133	+	"length", '-',
1134	+	additional_error))
1135	+	goto failure;
1136	+
1137	+	}
1138	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1139	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1140	+	{
1141	+
1142	+
1143	+	if (update_arg( (void *)&(args_info->zlength_arg),
1144	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1145	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1146	+	check_ambiguity, override, 0, 0,
1147	+	"zlength", '-',
1148	+	additional_error))
1149	+	goto failure;
1150	+
1151	+	}
1152	+	/* select the first stuntdouble set.  */
1153	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1154	+	{
1155	+
1156	+
1157	+	if (update_arg( (void *)&(args_info->sele1_arg),
1158	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1159	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1160	+	check_ambiguity, override, 0, 0,
1161	+	"sele1", '-',
1162	+	additional_error))
1163	+	goto failure;
1164	+
1165	+	}
1166		/* select the second stuntdouble set.  */
1167		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1168		{
268	–	if (args_info->sele2_given)
269	–	{
270	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
271	–	clear_args ();
272	–	exit (EXIT_FAILURE);
273	–	}
274	–	args_info->sele2_given = 1;
275	–	args_info->sele2_arg = gengetopt_strdup (optarg);
276	–	break;
277	–	}
1169
1170	+
1171	+	if (update_arg( (void *)&(args_info->sele2_arg),
1172	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1173	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1174	+	check_ambiguity, override, 0, 0,
1175	+	"sele2", '-',
1176	+	additional_error))
1177	+	goto failure;
1178	+
1179	+	}
1180		/* select the third stuntdouble set.  */
1181		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1182		{
282	–	if (args_info->sele3_given)
283	–	{
284	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
285	–	clear_args ();
286	–	exit (EXIT_FAILURE);
287	–	}
288	–	args_info->sele3_given = 1;
289	–	args_info->sele3_arg = gengetopt_strdup (optarg);
290	–	break;
291	–	}
1183
1184	+
1185	+	if (update_arg( (void *)&(args_info->sele3_arg),
1186	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1187	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1188	+	check_ambiguity, override, 0, 0,
1189	+	"sele3", '-',
1190	+	additional_error))
1191	+	goto failure;
1192	+
1193	+	}
1194		/* select reference (use and only use with --gxyz).  */
1195		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1196		{
1197	<	if (args_info->refsele_given)
1198	<	{
1199	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1200	<	clear_args ();
1201	<	exit (EXIT_FAILURE);
1202	<	}
1203	<	args_info->refsele_given = 1;
1204	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1205	<	break;
1197	>
1198	>
1199	>	if (update_arg( (void *)&(args_info->refsele_arg),
1200	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1201	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1202	>	check_ambiguity, override, 0, 0,
1203	>	"refsele", '-',
1204	>	additional_error))
1205	>	goto failure;
1206	>
1207		}
1208	+	/* select stunt doubles for center-of-mass reference point.  */
1209	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1210	+	{
1211
1212	+
1213	+	if (update_arg( (void *)&(args_info->comsele_arg),
1214	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1215	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1216	+	check_ambiguity, override, 0, 0,
1217	+	"comsele", '-',
1218	+	additional_error))
1219	+	goto failure;
1220	+
1221	+	}
1222	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1223	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1224	+	{
1225	+
1226	+
1227	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1228	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1229	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1230	+	check_ambiguity, override, 0, 0,
1231	+	"seleoffset", '-',
1232	+	additional_error))
1233	+	goto failure;
1234	+
1235	+	}
1236		/* molecule name.  */
1237		else if (strcmp (long_options[option_index].name, "molname") == 0)
1238		{
310	–	if (args_info->molname_given)
311	–	{
312	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
313	–	clear_args ();
314	–	exit (EXIT_FAILURE);
315	–	}
316	–	args_info->molname_given = 1;
317	–	args_info->molname_arg = gengetopt_strdup (optarg);
318	–	break;
319	–	}
1239
1240	<	/* begin interanl index.  */
1240	>
1241	>	if (update_arg( (void *)&(args_info->molname_arg),
1242	>	&(args_info->molname_orig), &(args_info->molname_given),
1243	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1244	>	check_ambiguity, override, 0, 0,
1245	>	"molname", '-',
1246	>	additional_error))
1247	>	goto failure;
1248	>
1249	>	}
1250	>	/* begin internal index.  */
1251		else if (strcmp (long_options[option_index].name, "begin") == 0)
1252		{
324	–	if (args_info->begin_given)
325	–	{
326	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
327	–	clear_args ();
328	–	exit (EXIT_FAILURE);
329	–	}
330	–	args_info->begin_given = 1;
331	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
332	–	break;
333	–	}
1253
1254	+
1255	+	if (update_arg( (void *)&(args_info->begin_arg),
1256	+	&(args_info->begin_orig), &(args_info->begin_given),
1257	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1258	+	check_ambiguity, override, 0, 0,
1259	+	"begin", '-',
1260	+	additional_error))
1261	+	goto failure;
1262	+
1263	+	}
1264		/* end internal index.  */
1265		else if (strcmp (long_options[option_index].name, "end") == 0)
1266		{
338	–	if (args_info->end_given)
339	–	{
340	–	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
341	–	clear_args ();
342	–	exit (EXIT_FAILURE);
343	–	}
344	–	args_info->end_given = 1;
345	–	args_info->end_arg = strtol (optarg,&stop_char,0);
346	–	break;
347	–	}
1267
1268	<	/* g(r).  */
1269	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1268	>
1269	>	if (update_arg( (void *)&(args_info->end_arg),
1270	>	&(args_info->end_orig), &(args_info->end_given),
1271	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1272	>	check_ambiguity, override, 0, 0,
1273	>	"end", '-',
1274	>	additional_error))
1275	>	goto failure;
1276	>
1277	>	}
1278	>	/* nanoparticle radius.  */
1279	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1280		{
352	–	if (args_info->gofr_given)
353	–	{
354	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
355	–	clear_args ();
356	–	exit (EXIT_FAILURE);
357	–	}
358	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1281
1282	<	break;
1282	>
1283	>	if (update_arg( (void *)&(args_info->radius_arg),
1284	>	&(args_info->radius_orig), &(args_info->radius_given),
1285	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1286	>	check_ambiguity, override, 0, 0,
1287	>	"radius", '-',
1288	>	additional_error))
1289	>	goto failure;
1290	>
1291		}
1292	+	/* bond order parameter (--rcut must be specified).  */
1293	+	else if (strcmp (long_options[option_index].name, "bo") == 0)
1294	+	{
1295
1296	+	if (args_info->staticProps_group_counter && override)
1297	+	reset_group_staticProps (args_info);
1298	+	args_info->staticProps_group_counter += 1;
1299	+
1300	+	if (update_arg( 0 ,
1301	+	0 , &(args_info->bo_given),
1302	+	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1303	+	check_ambiguity, override, 0, 0,
1304	+	"bo", '-',
1305	+	additional_error))
1306	+	goto failure;
1307	+
1308	+	}
1309	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1310	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1311	+	{
1312	+
1313	+	if (args_info->staticProps_group_counter && override)
1314	+	reset_group_staticProps (args_info);
1315	+	args_info->staticProps_group_counter += 1;
1316	+
1317	+	if (update_arg( 0 ,
1318	+	0 , &(args_info->bor_given),
1319	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1320	+	check_ambiguity, override, 0, 0,
1321	+	"bor", '-',
1322	+	additional_error))
1323	+	goto failure;
1324	+
1325	+	}
1326	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1327	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1328	+	{
1329	+
1330	+	if (args_info->staticProps_group_counter && override)
1331	+	reset_group_staticProps (args_info);
1332	+	args_info->staticProps_group_counter += 1;
1333	+
1334	+	if (update_arg( 0 ,
1335	+	0 , &(args_info->bad_given),
1336	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1337	+	check_ambiguity, override, 0, 0,
1338	+	"bad", '-',
1339	+	additional_error))
1340	+	goto failure;
1341	+
1342	+	}
1343	+	/* count of molecules matching selection criteria (and associated statistics).  */
1344	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1345	+	{
1346	+
1347	+	if (args_info->staticProps_group_counter && override)
1348	+	reset_group_staticProps (args_info);
1349	+	args_info->staticProps_group_counter += 1;
1350	+
1351	+	if (update_arg( 0 ,
1352	+	0 , &(args_info->count_given),
1353	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1354	+	check_ambiguity, override, 0, 0,
1355	+	"count", '-',
1356	+	additional_error))
1357	+	goto failure;
1358	+
1359	+	}
1360	+	/* g(z).  */
1361	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1362	+	{
1363	+
1364	+	if (args_info->staticProps_group_counter && override)
1365	+	reset_group_staticProps (args_info);
1366	+	args_info->staticProps_group_counter += 1;
1367	+
1368	+	if (update_arg( 0 ,
1369	+	0 , &(args_info->gofz_given),
1370	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1371	+	check_ambiguity, override, 0, 0,
1372	+	"gofz", '-',
1373	+	additional_error))
1374	+	goto failure;
1375	+
1376	+	}
1377		/* g(r, cos(theta)).  */
1378		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1379		{
366	–	if (args_info->r_theta_given)
367	–	{
368	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
369	–	clear_args ();
370	–	exit (EXIT_FAILURE);
371	–	}
372	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1380
1381	<	break;
1382	<	}
1381	>	if (args_info->staticProps_group_counter && override)
1382	>	reset_group_staticProps (args_info);
1383	>	args_info->staticProps_group_counter += 1;
1384
1385	+	if (update_arg( 0 ,
1386	+	0 , &(args_info->r_theta_given),
1387	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1388	+	check_ambiguity, override, 0, 0,
1389	+	"r_theta", '-',
1390	+	additional_error))
1391	+	goto failure;
1392	+
1393	+	}
1394		/* g(r, cos(omega)).  */
1395		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1396		{
380	–	if (args_info->r_omega_given)
381	–	{
382	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
383	–	clear_args ();
384	–	exit (EXIT_FAILURE);
385	–	}
386	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1397
1398	<	break;
1398	>	if (args_info->staticProps_group_counter && override)
1399	>	reset_group_staticProps (args_info);
1400	>	args_info->staticProps_group_counter += 1;
1401	>
1402	>	if (update_arg( 0 ,
1403	>	0 , &(args_info->r_omega_given),
1404	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1405	>	check_ambiguity, override, 0, 0,
1406	>	"r_omega", '-',
1407	>	additional_error))
1408	>	goto failure;
1409	>
1410		}
1411	+	/* g(r, z).  */
1412	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1413	+	{
1414
1415	+	if (args_info->staticProps_group_counter && override)
1416	+	reset_group_staticProps (args_info);
1417	+	args_info->staticProps_group_counter += 1;
1418	+
1419	+	if (update_arg( 0 ,
1420	+	0 , &(args_info->r_z_given),
1421	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1422	+	check_ambiguity, override, 0, 0,
1423	+	"r_z", '-',
1424	+	additional_error))
1425	+	goto failure;
1426	+
1427	+	}
1428		/* g(cos(theta), cos(omega)).  */
1429		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1430		{
394	–	if (args_info->theta_omega_given)
395	–	{
396	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
397	–	clear_args ();
398	–	exit (EXIT_FAILURE);
399	–	}
400	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1431
1432	<	break;
1433	<	}
1432	>	if (args_info->staticProps_group_counter && override)
1433	>	reset_group_staticProps (args_info);
1434	>	args_info->staticProps_group_counter += 1;
1435
1436	+	if (update_arg( 0 ,
1437	+	0 , &(args_info->theta_omega_given),
1438	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1439	+	check_ambiguity, override, 0, 0,
1440	+	"theta_omega", '-',
1441	+	additional_error))
1442	+	goto failure;
1443	+
1444	+	}
1445		/* g(x, y, z).  */
1446		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1447		{
408	–	if (args_info->gxyz_given)
409	–	{
410	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
411	–	clear_args ();
412	–	exit (EXIT_FAILURE);
413	–	}
414	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1448
1449	<	break;
1450	<	}
1449	>	if (args_info->staticProps_group_counter && override)
1450	>	reset_group_staticProps (args_info);
1451	>	args_info->staticProps_group_counter += 1;
1452
1453	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1454	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1453	>	if (update_arg( 0 ,
1454	>	0 , &(args_info->gxyz_given),
1455	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1456	>	check_ambiguity, override, 0, 0,
1457	>	"gxyz", '-',
1458	>	additional_error))
1459	>	goto failure;
1460	>
1461	>	}
1462	>	/* 2D g(r) (Slab width --dz must be specified).  */
1463	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1464		{
422	–	if (args_info->p2_given)
423	–	{
424	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
425	–	clear_args ();
426	–	exit (EXIT_FAILURE);
427	–	}
428	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1465
1466	<	break;
1466	>	if (args_info->staticProps_group_counter && override)
1467	>	reset_group_staticProps (args_info);
1468	>	args_info->staticProps_group_counter += 1;
1469	>
1470	>	if (update_arg( 0 ,
1471	>	0 , &(args_info->twodgofr_given),
1472	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1473	>	check_ambiguity, override, 0, 0,
1474	>	"twodgofr", '-',
1475	>	additional_error))
1476	>	goto failure;
1477	>
1478		}
1479	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1480	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1481	+	{
1482
1483	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1484	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1483	>	if (args_info->staticProps_group_counter && override)
1484	>	reset_group_staticProps (args_info);
1485	>	args_info->staticProps_group_counter += 1;
1486	>
1487	>	if (update_arg( 0 ,
1488	>	0 , &(args_info->rp2_given),
1489	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1490	>	check_ambiguity, override, 0, 0,
1491	>	"rp2", '-',
1492	>	additional_error))
1493	>	goto failure;
1494	>
1495	>	}
1496	>	/* slab density.  */
1497	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1498		{
436	–	if (args_info->scd_given)
437	–	{
438	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
439	–	clear_args ();
440	–	exit (EXIT_FAILURE);
441	–	}
442	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1499
1500	<	break;
1500	>	if (args_info->staticProps_group_counter && override)
1501	>	reset_group_staticProps (args_info);
1502	>	args_info->staticProps_group_counter += 1;
1503	>
1504	>	if (update_arg( 0 ,
1505	>	0 , &(args_info->slab_density_given),
1506	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1507	>	check_ambiguity, override, 0, 0,
1508	>	"slab_density", '-',
1509	>	additional_error))
1510	>	goto failure;
1511	>
1512		}
1513	+	/* p(cos(theta)).  */
1514	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1515	+	{
1516
1517	<	/* density plot (--sele1 must be specified).  */
1518	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1517	>	if (args_info->staticProps_group_counter && override)
1518	>	reset_group_staticProps (args_info);
1519	>	args_info->staticProps_group_counter += 1;
1520	>
1521	>	if (update_arg( 0 ,
1522	>	0 , &(args_info->p_angle_given),
1523	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1524	>	check_ambiguity, override, 0, 0,
1525	>	"p_angle", '-',
1526	>	additional_error))
1527	>	goto failure;
1528	>
1529	>	}
1530	>	/* hxy.  */
1531	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1532		{
450	–	if (args_info->density_given)
451	–	{
452	–	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
453	–	clear_args ();
454	–	exit (EXIT_FAILURE);
455	–	}
456	–	args_info->density_given = 1; staticProps_group_counter += 1;
1533
1534	<	break;
1534	>	if (args_info->staticProps_group_counter && override)
1535	>	reset_group_staticProps (args_info);
1536	>	args_info->staticProps_group_counter += 1;
1537	>
1538	>	if (update_arg( 0 ,
1539	>	0 , &(args_info->hxy_given),
1540	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1541	>	check_ambiguity, override, 0, 0,
1542	>	"hxy", '-',
1543	>	additional_error))
1544	>	goto failure;
1545	>
1546		}
1547	+	/* rho of R.  */
1548	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1549	+	{
1550
1551	<	/* slab density (--sele1 must be specified).  */
1552	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1551	>	if (args_info->staticProps_group_counter && override)
1552	>	reset_group_staticProps (args_info);
1553	>	args_info->staticProps_group_counter += 1;
1554	>
1555	>	if (update_arg( 0 ,
1556	>	0 , &(args_info->rho_r_given),
1557	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1558	>	check_ambiguity, override, 0, 0,
1559	>	"rho_r", '-',
1560	>	additional_error))
1561	>	goto failure;
1562	>
1563	>	}
1564	>	/* angle of R.  */
1565	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1566		{
464	–	if (args_info->slab_density_given)
465	–	{
466	–	fprintf (stderr, "%s: `--slab_density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
467	–	clear_args ();
468	–	exit (EXIT_FAILURE);
469	–	}
470	–	args_info->slab_density_given = 1; staticProps_group_counter += 1;
1567
1568	<	break;
1568	>	if (args_info->staticProps_group_counter && override)
1569	>	reset_group_staticProps (args_info);
1570	>	args_info->staticProps_group_counter += 1;
1571	>
1572	>	if (update_arg( 0 ,
1573	>	0 , &(args_info->angle_r_given),
1574	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1575	>	check_ambiguity, override, 0, 0,
1576	>	"angle_r", '-',
1577	>	additional_error))
1578	>	goto failure;
1579	>
1580		}
1581	+	/* hull volume of nanoparticle.  */
1582	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1583	+	{
1584
1585	<
1585	>	if (args_info->staticProps_group_counter && override)
1586	>	reset_group_staticProps (args_info);
1587	>	args_info->staticProps_group_counter += 1;
1588	>
1589	>	if (update_arg( 0 ,
1590	>	0 , &(args_info->hullvol_given),
1591	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1592	>	check_ambiguity, override, 0, 0,
1593	>	"hullvol", '-',
1594	>	additional_error))
1595	>	goto failure;
1596	>
1597	>	}
1598	>	/* length of nanorod.  */
1599	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1600	>	{
1601	>
1602	>	if (args_info->staticProps_group_counter && override)
1603	>	reset_group_staticProps (args_info);
1604	>	args_info->staticProps_group_counter += 1;
1605	>
1606	>	if (update_arg( 0 ,
1607	>	0 , &(args_info->rodlength_given),
1608	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1609	>	check_ambiguity, override, 0, 0,
1610	>	"rodlength", '-',
1611	>	additional_error))
1612	>	goto failure;
1613	>
1614	>	}
1615	>	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1616	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1617	>	{
1618	>
1619	>	if (args_info->staticProps_group_counter && override)
1620	>	reset_group_staticProps (args_info);
1621	>	args_info->staticProps_group_counter += 1;
1622	>
1623	>	if (update_arg( 0 ,
1624	>	0 , &(args_info->tet_param_z_given),
1625	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1626	>	check_ambiguity, override, 0, 0,
1627	>	"tet_param_z", '-',
1628	>	additional_error))
1629	>	goto failure;
1630	>
1631	>	}
1632	>
1633	>	break;
1634		case '?':       /* Invalid option.  */
1635		/* `getopt_long' already printed an error message.  */
1636	<	exit (EXIT_FAILURE);
1636	>	goto failure;
1637
1638		default:        /* bug: option not considered.  */
1639	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1639	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1640		abort ();
1641		} /* switch */
1642		} /* while */
1643
1644	<	if ( staticProps_group_counter != 1)
1644	>	if (args_info->staticProps_group_counter > 1)
1645		{
1646	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1647	<	missing_required_options = 1;
1646	>	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 : ""));
1647	>	error = 1;
1648		}
1649
1650
1651	<	if (! args_info->input_given)
1651	>
1652	>	if (check_required)
1653		{
1654	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
496	<	missing_required_options = 1;
1654	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1655		}
498	–	if ( missing_required_options )
499	–	exit (EXIT_FAILURE);
1656
1657	+	cmdline_parser_release (&local_args_info);
1658	+
1659	+	if ( error )
1660	+	return (EXIT_FAILURE);
1661	+
1662	+	if (optind < argc)
1663	+	{
1664	+	int i = 0 ;
1665	+	int found_prog_name = 0;
1666	+	/* whether program name, i.e., argv[0], is in the remaining args
1667	+	(this may happen with some implementations of getopt,
1668	+	but surely not with the one included by gengetopt) */
1669	+
1670	+	i = optind;
1671	+	while (i < argc)
1672	+	if (argv[i++] == argv[0]) {
1673	+	found_prog_name = 1;
1674	+	break;
1675	+	}
1676	+	i = 0;
1677	+
1678	+	args_info->inputs_num = argc - optind - found_prog_name;
1679	+	args_info->inputs =
1680	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1681	+	while (optind < argc)
1682	+	if (argv[optind++] != argv[0])
1683	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1684	+	}
1685	+
1686		return 0;
1687	+
1688	+	failure:
1689	+
1690	+	cmdline_parser_release (&local_args_info);
1691	+	return (EXIT_FAILURE);
1692		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 UTC

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