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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.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd
4	>	gengetopt --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	>	#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	>	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
56	>	"      --molname=STRING          molecule name",
57	>	"      --begin=INT               begin internal index",
58	>	"      --end=INT                 end internal index",
59	>	"      --radius=DOUBLE           nanoparticle radius",
60	>	"\n Group: staticProps\n   an option of this group is required",
61	>	"      --bo                      bond order parameter (--rcut must be specified)",
62	>	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
63	>	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
64	>	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
65	>	"  -g, --gofr                    g(r)",
66	>	"      --gofz                    g(z)",
67	>	"      --r_theta                 g(r, cos(theta))",
68	>	"      --r_omega                 g(r, cos(omega))",
69	>	"      --r_z                     g(r, z)",
70	>	"      --theta_omega             g(cos(theta), cos(omega))",
71	>	"      --gxyz                    g(x, y, z)",
72	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
73	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
74	>	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
75	>	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
76	>	"  -d, --density                 density plot",
77	>	"      --slab_density            slab density",
78	>	"      --p_angle                 p(cos(theta))",
79	>	"      --hxy                     hxy",
80	>	"      --rho_r                   rho of R",
81	>	"      --angle_r                 angle of R",
82	>	"      --hullvol                 hull volume of nanoparticle",
83	>	"      --rodlength               length of nanorod",
84	>	"  -Q, --tet_param               tetrahedrality order parameter",
85	>	"      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
86	>	0
87	>	};
88
89	<	/* gengetopt_strdup() */
90	<	/* strdup.c replacement of strdup, which is not standard */
91	<	char *
92	<	gengetopt_strdup (const char *s)
93	<	{
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	<	}
89	>	typedef enum {ARG_NO
90	>	, ARG_STRING
91	>	, ARG_INT
92	>	, ARG_DOUBLE
93	>	} cmdline_parser_arg_type;
94
95	<	int
96	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
97	<	{
98	<	int c;        /* Character of the parsed option.  */
84	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
86	<
95	>	static
96	>	void clear_given (struct gengetopt_args_info *args_info);
97	>	static
98	>	void clear_args (struct gengetopt_args_info *args_info);
99
100	+	static int
101	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
102	+	struct cmdline_parser_params *params, const char *additional_error);
103	+
104	+	static int
105	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
106	+
107	+	static char *
108	+	gengetopt_strdup (const char *s);
109	+
110	+	static
111	+	void clear_given (struct gengetopt_args_info *args_info)
112	+	{
113		args_info->help_given = 0 ;
114		args_info->version_given = 0 ;
115		args_info->input_given = 0 ;
116		args_info->output_given = 0 ;
117		args_info->step_given = 0 ;
118	<	args_info->nrbins_given = 0 ;
118	>	args_info->nbins_given = 0 ;
119	>	args_info->nbins_x_given = 0 ;
120	>	args_info->nbins_y_given = 0 ;
121	>	args_info->nbins_z_given = 0 ;
122		args_info->nanglebins_given = 0 ;
123	+	args_info->rcut_given = 0 ;
124	+	args_info->dz_given = 0 ;
125		args_info->length_given = 0 ;
126	+	args_info->zlength_given = 0 ;
127	+	args_info->zoffset_given = 0 ;
128		args_info->sele1_given = 0 ;
129		args_info->sele2_given = 0 ;
130		args_info->sele3_given = 0 ;
131		args_info->refsele_given = 0 ;
132	+	args_info->comsele_given = 0 ;
133	+	args_info->seleoffset_given = 0 ;
134		args_info->molname_given = 0 ;
135		args_info->begin_given = 0 ;
136		args_info->end_given = 0 ;
137	+	args_info->radius_given = 0 ;
138	+	args_info->bo_given = 0 ;
139	+	args_info->bor_given = 0 ;
140	+	args_info->bad_given = 0 ;
141	+	args_info->count_given = 0 ;
142		args_info->gofr_given = 0 ;
143	+	args_info->gofz_given = 0 ;
144		args_info->r_theta_given = 0 ;
145		args_info->r_omega_given = 0 ;
146	+	args_info->r_z_given = 0 ;
147		args_info->theta_omega_given = 0 ;
148		args_info->gxyz_given = 0 ;
149	+	args_info->twodgofr_given = 0 ;
150		args_info->p2_given = 0 ;
151	+	args_info->rp2_given = 0 ;
152		args_info->scd_given = 0 ;
153		args_info->density_given = 0 ;
154	<	#define clear_args() { \
155	<	args_info->input_arg = NULL; \
156	<	args_info->output_arg = NULL; \
157	<	args_info->step_arg = 1 ;\
158	<	args_info->nrbins_arg = 100 ;\
159	<	args_info->nanglebins_arg = 50 ;\
160	<	args_info->sele1_arg = NULL; \
161	<	args_info->sele2_arg = NULL; \
162	<	args_info->sele3_arg = NULL; \
163	<	args_info->refsele_arg = NULL; \
121	<	args_info->molname_arg = NULL; \
154	>	args_info->slab_density_given = 0 ;
155	>	args_info->p_angle_given = 0 ;
156	>	args_info->hxy_given = 0 ;
157	>	args_info->rho_r_given = 0 ;
158	>	args_info->angle_r_given = 0 ;
159	>	args_info->hullvol_given = 0 ;
160	>	args_info->rodlength_given = 0 ;
161	>	args_info->tet_param_given = 0 ;
162	>	args_info->tet_param_z_given = 0 ;
163	>	args_info->staticProps_group_counter = 0 ;
164		}
165
166	<	clear_args();
166	>	static
167	>	void clear_args (struct gengetopt_args_info *args_info)
168	>	{
169	>	FIX_UNUSED (args_info);
170	>	args_info->input_arg = NULL;
171	>	args_info->input_orig = NULL;
172	>	args_info->output_arg = NULL;
173	>	args_info->output_orig = NULL;
174	>	args_info->step_arg = 1;
175	>	args_info->step_orig = NULL;
176	>	args_info->nbins_arg = 100;
177	>	args_info->nbins_orig = NULL;
178	>	args_info->nbins_x_arg = 100;
179	>	args_info->nbins_x_orig = NULL;
180	>	args_info->nbins_y_arg = 100;
181	>	args_info->nbins_y_orig = NULL;
182	>	args_info->nbins_z_arg = 100;
183	>	args_info->nbins_z_orig = NULL;
184	>	args_info->nanglebins_arg = 50;
185	>	args_info->nanglebins_orig = NULL;
186	>	args_info->rcut_orig = NULL;
187	>	args_info->dz_orig = NULL;
188	>	args_info->length_orig = NULL;
189	>	args_info->zlength_orig = NULL;
190	>	args_info->zoffset_arg = 0;
191	>	args_info->zoffset_orig = NULL;
192	>	args_info->sele1_arg = NULL;
193	>	args_info->sele1_orig = NULL;
194	>	args_info->sele2_arg = NULL;
195	>	args_info->sele2_orig = NULL;
196	>	args_info->sele3_arg = NULL;
197	>	args_info->sele3_orig = NULL;
198	>	args_info->refsele_arg = NULL;
199	>	args_info->refsele_orig = NULL;
200	>	args_info->comsele_arg = NULL;
201	>	args_info->comsele_orig = NULL;
202	>	args_info->seleoffset_orig = NULL;
203	>	args_info->molname_arg = NULL;
204	>	args_info->molname_orig = NULL;
205	>	args_info->begin_orig = NULL;
206	>	args_info->end_orig = NULL;
207	>	args_info->radius_orig = NULL;
208	>
209	>	}
210	>
211	>	static
212	>	void init_args_info(struct gengetopt_args_info *args_info)
213	>	{
214	>
215	>
216	>	args_info->help_help = gengetopt_args_info_help[0] ;
217	>	args_info->version_help = gengetopt_args_info_help[1] ;
218	>	args_info->input_help = gengetopt_args_info_help[2] ;
219	>	args_info->output_help = gengetopt_args_info_help[3] ;
220	>	args_info->step_help = gengetopt_args_info_help[4] ;
221	>	args_info->nbins_help = gengetopt_args_info_help[5] ;
222	>	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
223	>	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
224	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
225	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
226	>	args_info->rcut_help = gengetopt_args_info_help[10] ;
227	>	args_info->dz_help = gengetopt_args_info_help[11] ;
228	>	args_info->length_help = gengetopt_args_info_help[12] ;
229	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
230	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
231	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
232	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
233	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
234	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
235	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
236	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
237	>	args_info->molname_help = gengetopt_args_info_help[21] ;
238	>	args_info->begin_help = gengetopt_args_info_help[22] ;
239	>	args_info->end_help = gengetopt_args_info_help[23] ;
240	>	args_info->radius_help = gengetopt_args_info_help[24] ;
241	>	args_info->bo_help = gengetopt_args_info_help[26] ;
242	>	args_info->bor_help = gengetopt_args_info_help[27] ;
243	>	args_info->bad_help = gengetopt_args_info_help[28] ;
244	>	args_info->count_help = gengetopt_args_info_help[29] ;
245	>	args_info->gofr_help = gengetopt_args_info_help[30] ;
246	>	args_info->gofz_help = gengetopt_args_info_help[31] ;
247	>	args_info->r_theta_help = gengetopt_args_info_help[32] ;
248	>	args_info->r_omega_help = gengetopt_args_info_help[33] ;
249	>	args_info->r_z_help = gengetopt_args_info_help[34] ;
250	>	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
251	>	args_info->gxyz_help = gengetopt_args_info_help[36] ;
252	>	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
253	>	args_info->p2_help = gengetopt_args_info_help[38] ;
254	>	args_info->rp2_help = gengetopt_args_info_help[39] ;
255	>	args_info->scd_help = gengetopt_args_info_help[40] ;
256	>	args_info->density_help = gengetopt_args_info_help[41] ;
257	>	args_info->slab_density_help = gengetopt_args_info_help[42] ;
258	>	args_info->p_angle_help = gengetopt_args_info_help[43] ;
259	>	args_info->hxy_help = gengetopt_args_info_help[44] ;
260	>	args_info->rho_r_help = gengetopt_args_info_help[45] ;
261	>	args_info->angle_r_help = gengetopt_args_info_help[46] ;
262	>	args_info->hullvol_help = gengetopt_args_info_help[47] ;
263	>	args_info->rodlength_help = gengetopt_args_info_help[48] ;
264	>	args_info->tet_param_help = gengetopt_args_info_help[49] ;
265	>	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
266	>
267	>	}
268	>
269	>	void
270	>	cmdline_parser_print_version (void)
271	>	{
272	>	printf ("%s %s\n",
273	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
274	>	CMDLINE_PARSER_VERSION);
275	>	}
276	>
277	>	static void print_help_common(void) {
278	>	cmdline_parser_print_version ();
279	>
280	>	if (strlen(gengetopt_args_info_purpose) > 0)
281	>	printf("\n%s\n", gengetopt_args_info_purpose);
282	>
283	>	if (strlen(gengetopt_args_info_usage) > 0)
284	>	printf("\n%s\n", gengetopt_args_info_usage);
285	>
286	>	printf("\n");
287	>
288	>	if (strlen(gengetopt_args_info_description) > 0)
289	>	printf("%s\n\n", gengetopt_args_info_description);
290	>	}
291	>
292	>	void
293	>	cmdline_parser_print_help (void)
294	>	{
295	>	int i = 0;
296	>	print_help_common();
297	>	while (gengetopt_args_info_help[i])
298	>	printf("%s\n", gengetopt_args_info_help[i++]);
299	>	}
300	>
301	>	void
302	>	cmdline_parser_init (struct gengetopt_args_info *args_info)
303	>	{
304	>	clear_given (args_info);
305	>	clear_args (args_info);
306	>	init_args_info (args_info);
307	>
308	>	args_info->inputs = 0;
309	>	args_info->inputs_num = 0;
310	>	}
311	>
312	>	void
313	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
314	>	{
315	>	if (params)
316	>	{
317	>	params->override = 0;
318	>	params->initialize = 1;
319	>	params->check_required = 1;
320	>	params->check_ambiguity = 0;
321	>	params->print_errors = 1;
322	>	}
323	>	}
324	>
325	>	struct cmdline_parser_params *
326	>	cmdline_parser_params_create(void)
327	>	{
328	>	struct cmdline_parser_params *params =
329	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
330	>	cmdline_parser_params_init(params);
331	>	return params;
332	>	}
333	>
334	>	static void
335	>	free_string_field (char **s)
336	>	{
337	>	if (*s)
338	>	{
339	>	free (*s);
340	>	*s = 0;
341	>	}
342	>	}
343	>
344	>
345	>	static void
346	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
347	>	{
348	>	unsigned int i;
349	>	free_string_field (&(args_info->input_arg));
350	>	free_string_field (&(args_info->input_orig));
351	>	free_string_field (&(args_info->output_arg));
352	>	free_string_field (&(args_info->output_orig));
353	>	free_string_field (&(args_info->step_orig));
354	>	free_string_field (&(args_info->nbins_orig));
355	>	free_string_field (&(args_info->nbins_x_orig));
356	>	free_string_field (&(args_info->nbins_y_orig));
357	>	free_string_field (&(args_info->nbins_z_orig));
358	>	free_string_field (&(args_info->nanglebins_orig));
359	>	free_string_field (&(args_info->rcut_orig));
360	>	free_string_field (&(args_info->dz_orig));
361	>	free_string_field (&(args_info->length_orig));
362	>	free_string_field (&(args_info->zlength_orig));
363	>	free_string_field (&(args_info->zoffset_orig));
364	>	free_string_field (&(args_info->sele1_arg));
365	>	free_string_field (&(args_info->sele1_orig));
366	>	free_string_field (&(args_info->sele2_arg));
367	>	free_string_field (&(args_info->sele2_orig));
368	>	free_string_field (&(args_info->sele3_arg));
369	>	free_string_field (&(args_info->sele3_orig));
370	>	free_string_field (&(args_info->refsele_arg));
371	>	free_string_field (&(args_info->refsele_orig));
372	>	free_string_field (&(args_info->comsele_arg));
373	>	free_string_field (&(args_info->comsele_orig));
374	>	free_string_field (&(args_info->seleoffset_orig));
375	>	free_string_field (&(args_info->molname_arg));
376	>	free_string_field (&(args_info->molname_orig));
377	>	free_string_field (&(args_info->begin_orig));
378	>	free_string_field (&(args_info->end_orig));
379	>	free_string_field (&(args_info->radius_orig));
380	>
381	>
382	>	for (i = 0; i < args_info->inputs_num; ++i)
383	>	free (args_info->inputs [i]);
384	>
385	>	if (args_info->inputs_num)
386	>	free (args_info->inputs);
387	>
388	>	clear_given (args_info);
389	>	}
390	>
391	>
392	>	static void
393	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
394	>	{
395	>	FIX_UNUSED (values);
396	>	if (arg) {
397	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
398	>	} else {
399	>	fprintf(outfile, "%s\n", opt);
400	>	}
401	>	}
402	>
403	>
404	>	int
405	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
406	>	{
407	>	int i = 0;
408	>
409	>	if (!outfile)
410	>	{
411	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
412	>	return EXIT_FAILURE;
413	>	}
414	>
415	>	if (args_info->help_given)
416	>	write_into_file(outfile, "help", 0, 0 );
417	>	if (args_info->version_given)
418	>	write_into_file(outfile, "version", 0, 0 );
419	>	if (args_info->input_given)
420	>	write_into_file(outfile, "input", args_info->input_orig, 0);
421	>	if (args_info->output_given)
422	>	write_into_file(outfile, "output", args_info->output_orig, 0);
423	>	if (args_info->step_given)
424	>	write_into_file(outfile, "step", args_info->step_orig, 0);
425	>	if (args_info->nbins_given)
426	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
427	>	if (args_info->nbins_x_given)
428	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
429	>	if (args_info->nbins_y_given)
430	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
431	>	if (args_info->nbins_z_given)
432	>	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
433	>	if (args_info->nanglebins_given)
434	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
435	>	if (args_info->rcut_given)
436	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
437	>	if (args_info->dz_given)
438	>	write_into_file(outfile, "dz", args_info->dz_orig, 0);
439	>	if (args_info->length_given)
440	>	write_into_file(outfile, "length", args_info->length_orig, 0);
441	>	if (args_info->zlength_given)
442	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
443	>	if (args_info->zoffset_given)
444	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
445	>	if (args_info->sele1_given)
446	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
447	>	if (args_info->sele2_given)
448	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
449	>	if (args_info->sele3_given)
450	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
451	>	if (args_info->refsele_given)
452	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
453	>	if (args_info->comsele_given)
454	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
455	>	if (args_info->seleoffset_given)
456	>	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
457	>	if (args_info->molname_given)
458	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
459	>	if (args_info->begin_given)
460	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
461	>	if (args_info->end_given)
462	>	write_into_file(outfile, "end", args_info->end_orig, 0);
463	>	if (args_info->radius_given)
464	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
465	>	if (args_info->bo_given)
466	>	write_into_file(outfile, "bo", 0, 0 );
467	>	if (args_info->bor_given)
468	>	write_into_file(outfile, "bor", 0, 0 );
469	>	if (args_info->bad_given)
470	>	write_into_file(outfile, "bad", 0, 0 );
471	>	if (args_info->count_given)
472	>	write_into_file(outfile, "count", 0, 0 );
473	>	if (args_info->gofr_given)
474	>	write_into_file(outfile, "gofr", 0, 0 );
475	>	if (args_info->gofz_given)
476	>	write_into_file(outfile, "gofz", 0, 0 );
477	>	if (args_info->r_theta_given)
478	>	write_into_file(outfile, "r_theta", 0, 0 );
479	>	if (args_info->r_omega_given)
480	>	write_into_file(outfile, "r_omega", 0, 0 );
481	>	if (args_info->r_z_given)
482	>	write_into_file(outfile, "r_z", 0, 0 );
483	>	if (args_info->theta_omega_given)
484	>	write_into_file(outfile, "theta_omega", 0, 0 );
485	>	if (args_info->gxyz_given)
486	>	write_into_file(outfile, "gxyz", 0, 0 );
487	>	if (args_info->twodgofr_given)
488	>	write_into_file(outfile, "twodgofr", 0, 0 );
489	>	if (args_info->p2_given)
490	>	write_into_file(outfile, "p2", 0, 0 );
491	>	if (args_info->rp2_given)
492	>	write_into_file(outfile, "rp2", 0, 0 );
493	>	if (args_info->scd_given)
494	>	write_into_file(outfile, "scd", 0, 0 );
495	>	if (args_info->density_given)
496	>	write_into_file(outfile, "density", 0, 0 );
497	>	if (args_info->slab_density_given)
498	>	write_into_file(outfile, "slab_density", 0, 0 );
499	>	if (args_info->p_angle_given)
500	>	write_into_file(outfile, "p_angle", 0, 0 );
501	>	if (args_info->hxy_given)
502	>	write_into_file(outfile, "hxy", 0, 0 );
503	>	if (args_info->rho_r_given)
504	>	write_into_file(outfile, "rho_r", 0, 0 );
505	>	if (args_info->angle_r_given)
506	>	write_into_file(outfile, "angle_r", 0, 0 );
507	>	if (args_info->hullvol_given)
508	>	write_into_file(outfile, "hullvol", 0, 0 );
509	>	if (args_info->rodlength_given)
510	>	write_into_file(outfile, "rodlength", 0, 0 );
511	>	if (args_info->tet_param_given)
512	>	write_into_file(outfile, "tet_param", 0, 0 );
513	>	if (args_info->tet_param_z_given)
514	>	write_into_file(outfile, "tet_param_z", 0, 0 );
515	>
516
517	+	i = EXIT_SUCCESS;
518	+	return i;
519	+	}
520	+
521	+	int
522	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
523	+	{
524	+	FILE *outfile;
525	+	int i = 0;
526	+
527	+	outfile = fopen(filename, "w");
528	+
529	+	if (!outfile)
530	+	{
531	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
532	+	return EXIT_FAILURE;
533	+	}
534	+
535	+	i = cmdline_parser_dump(outfile, args_info);
536	+	fclose (outfile);
537	+
538	+	return i;
539	+	}
540	+
541	+	void
542	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
543	+	{
544	+	cmdline_parser_release (args_info);
545	+	}
546	+
547	+	/** @brief replacement of strdup, which is not standard */
548	+	char *
549	+	gengetopt_strdup (const char *s)
550	+	{
551	+	char *result = 0;
552	+	if (!s)
553	+	return result;
554	+
555	+	result = (char*)malloc(strlen(s) + 1);
556	+	if (result == (char*)0)
557	+	return (char*)0;
558	+	strcpy(result, s);
559	+	return result;
560	+	}
561	+
562	+	static void
563	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
564	+	{
565	+	if (! args_info->staticProps_group_counter)
566	+	return;
567	+
568	+	args_info->bo_given = 0 ;
569	+	args_info->bor_given = 0 ;
570	+	args_info->bad_given = 0 ;
571	+	args_info->count_given = 0 ;
572	+	args_info->gofr_given = 0 ;
573	+	args_info->gofz_given = 0 ;
574	+	args_info->r_theta_given = 0 ;
575	+	args_info->r_omega_given = 0 ;
576	+	args_info->r_z_given = 0 ;
577	+	args_info->theta_omega_given = 0 ;
578	+	args_info->gxyz_given = 0 ;
579	+	args_info->twodgofr_given = 0 ;
580	+	args_info->p2_given = 0 ;
581	+	args_info->rp2_given = 0 ;
582	+	args_info->scd_given = 0 ;
583	+	args_info->density_given = 0 ;
584	+	args_info->slab_density_given = 0 ;
585	+	args_info->p_angle_given = 0 ;
586	+	args_info->hxy_given = 0 ;
587	+	args_info->rho_r_given = 0 ;
588	+	args_info->angle_r_given = 0 ;
589	+	args_info->hullvol_given = 0 ;
590	+	args_info->rodlength_given = 0 ;
591	+	args_info->tet_param_given = 0 ;
592	+	args_info->tet_param_z_given = 0 ;
593	+
594	+	args_info->staticProps_group_counter = 0;
595	+	}
596	+
597	+	int
598	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
599	+	{
600	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
601	+	}
602	+
603	+	int
604	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
605	+	struct cmdline_parser_params *params)
606	+	{
607	+	int result;
608	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
609	+
610	+	if (result == EXIT_FAILURE)
611	+	{
612	+	cmdline_parser_free (args_info);
613	+	exit (EXIT_FAILURE);
614	+	}
615	+
616	+	return result;
617	+	}
618	+
619	+	int
620	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
621	+	{
622	+	int result;
623	+	struct cmdline_parser_params params;
624	+
625	+	params.override = override;
626	+	params.initialize = initialize;
627	+	params.check_required = check_required;
628	+	params.check_ambiguity = 0;
629	+	params.print_errors = 1;
630	+
631	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
632	+
633	+	if (result == EXIT_FAILURE)
634	+	{
635	+	cmdline_parser_free (args_info);
636	+	exit (EXIT_FAILURE);
637	+	}
638	+
639	+	return result;
640	+	}
641	+
642	+	int
643	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
644	+	{
645	+	int result = EXIT_SUCCESS;
646	+
647	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
648	+	result = EXIT_FAILURE;
649	+
650	+	if (result == EXIT_FAILURE)
651	+	{
652	+	cmdline_parser_free (args_info);
653	+	exit (EXIT_FAILURE);
654	+	}
655	+
656	+	return result;
657	+	}
658	+
659	+	int
660	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
661	+	{
662	+	int error = 0;
663	+	FIX_UNUSED (additional_error);
664	+
665	+	/* checks for required options */
666	+	if (! args_info->input_given)
667	+	{
668	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
669	+	error = 1;
670	+	}
671	+
672	+	if (args_info->staticProps_group_counter == 0)
673	+	{
674	+	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 : ""));
675	+	error = 1;
676	+	}
677	+
678	+
679	+	/* checks for dependences among options */
680	+
681	+	return error;
682	+	}
683	+
684	+
685	+	static char *package_name = 0;
686	+
687	+	/**
688	+	* @brief updates an option
689	+	* @param field the generic pointer to the field to update
690	+	* @param orig_field the pointer to the orig field
691	+	* @param field_given the pointer to the number of occurrence of this option
692	+	* @param prev_given the pointer to the number of occurrence already seen
693	+	* @param value the argument for this option (if null no arg was specified)
694	+	* @param possible_values the possible values for this option (if specified)
695	+	* @param default_value the default value (in case the option only accepts fixed values)
696	+	* @param arg_type the type of this option
697	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
698	+	* @param override @see cmdline_parser_params.override
699	+	* @param no_free whether to free a possible previous value
700	+	* @param multiple_option whether this is a multiple option
701	+	* @param long_opt the corresponding long option
702	+	* @param short_opt the corresponding short option (or '-' if none)
703	+	* @param additional_error possible further error specification
704	+	*/
705	+	static
706	+	int update_arg(void *field, char **orig_field,
707	+	unsigned int *field_given, unsigned int *prev_given,
708	+	char *value, const char *possible_values[],
709	+	const char *default_value,
710	+	cmdline_parser_arg_type arg_type,
711	+	int check_ambiguity, int override,
712	+	int no_free, int multiple_option,
713	+	const char *long_opt, char short_opt,
714	+	const char *additional_error)
715	+	{
716	+	char *stop_char = 0;
717	+	const char *val = value;
718	+	int found;
719	+	char **string_field;
720	+	FIX_UNUSED (field);
721	+
722	+	stop_char = 0;
723	+	found = 0;
724	+
725	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
726	+	{
727	+	if (short_opt != '-')
728	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
729	+	package_name, long_opt, short_opt,
730	+	(additional_error ? additional_error : ""));
731	+	else
732	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
733	+	package_name, long_opt,
734	+	(additional_error ? additional_error : ""));
735	+	return 1; /* failure */
736	+	}
737	+
738	+	FIX_UNUSED (default_value);
739	+
740	+	if (field_given && *field_given && ! override)
741	+	return 0;
742	+	if (prev_given)
743	+	(*prev_given)++;
744	+	if (field_given)
745	+	(*field_given)++;
746	+	if (possible_values)
747	+	val = possible_values[found];
748	+
749	+	switch(arg_type) {
750	+	case ARG_INT:
751	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
752	+	break;
753	+	case ARG_DOUBLE:
754	+	if (val) *((double *)field) = strtod (val, &stop_char);
755	+	break;
756	+	case ARG_STRING:
757	+	if (val) {
758	+	string_field = (char **)field;
759	+	if (!no_free && *string_field)
760	+	free (*string_field); /* free previous string */
761	+	*string_field = gengetopt_strdup (val);
762	+	}
763	+	break;
764	+	default:
765	+	break;
766	+	};
767	+
768	+	/* check numeric conversion */
769	+	switch(arg_type) {
770	+	case ARG_INT:
771	+	case ARG_DOUBLE:
772	+	if (val && !(stop_char && *stop_char == '\0')) {
773	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
774	+	return 1; /* failure */
775	+	}
776	+	break;
777	+	default:
778	+	;
779	+	};
780	+
781	+	/* store the original value */
782	+	switch(arg_type) {
783	+	case ARG_NO:
784	+	break;
785	+	default:
786	+	if (value && orig_field) {
787	+	if (no_free) {
788	+	*orig_field = value;
789	+	} else {
790	+	if (*orig_field)
791	+	free (*orig_field); /* free previous string */
792	+	*orig_field = gengetopt_strdup (value);
793	+	}
794	+	}
795	+	};
796	+
797	+	return 0; /* OK */
798	+	}
799	+
800	+
801	+	int
802	+	cmdline_parser_internal (
803	+	int argc, char **argv, struct gengetopt_args_info *args_info,
804	+	struct cmdline_parser_params *params, const char *additional_error)
805	+	{
806	+	int c;        /* Character of the parsed option.  */
807	+
808	+	int error = 0;
809	+	struct gengetopt_args_info local_args_info;
810	+
811	+	int override;
812	+	int initialize;
813	+	int check_required;
814	+	int check_ambiguity;
815	+
816	+	package_name = argv[0];
817	+
818	+	override = params->override;
819	+	initialize = params->initialize;
820	+	check_required = params->check_required;
821	+	check_ambiguity = params->check_ambiguity;
822	+
823	+	if (initialize)
824	+	cmdline_parser_init (args_info);
825	+
826	+	cmdline_parser_init (&local_args_info);
827	+
828		optarg = 0;
829	<	optind = 1;
830	<	opterr = 1;
829	>	optind = 0;
830	>	opterr = params->print_errors;
831		optopt = '?';
832
833		while (1)
834		{
835		int option_index = 0;
134	–	char *stop_char;
836
837		static struct option long_options[] = {
838		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 840 | cmdline_parser (int argc, char * const *argv, struct g
840		{ "input",      1, NULL, 'i' },
841		{ "output",     1, NULL, 'o' },
842		{ "step",       1, NULL, 'n' },
843	<	{ "nrbins",     1, NULL, 'r' },
843	>	{ "nbins",      1, NULL, 'b' },
844	>	{ "nbins_x",    1, NULL, 'x' },
845	>	{ "nbins_y",    1, NULL, 'y' },
846	>	{ "nbins_z",    1, NULL, 0 },
847		{ "nanglebins", 1, NULL, 'a' },
848	<	{ "length",     1, NULL, 'l' },
848	>	{ "rcut",       1, NULL, 'c' },
849	>	{ "dz", 1, NULL, 0 },
850	>	{ "length",     1, NULL, 0 },
851	>	{ "zlength",    1, NULL, 0 },
852	>	{ "zoffset",    1, NULL, 'z' },
853		{ "sele1",      1, NULL, 0 },
854		{ "sele2",      1, NULL, 0 },
855		{ "sele3",      1, NULL, 0 },
856		{ "refsele",    1, NULL, 0 },
857	+	{ "comsele",    1, NULL, 0 },
858	+	{ "seleoffset", 1, NULL, 0 },
859		{ "molname",    1, NULL, 0 },
860		{ "begin",      1, NULL, 0 },
861		{ "end",        1, NULL, 0 },
862	<	{ "gofr",       0, NULL, 0 },
862	>	{ "radius",     1, NULL, 0 },
863	>	{ "bo", 0, NULL, 0 },
864	>	{ "bor",        0, NULL, 0 },
865	>	{ "bad",        0, NULL, 0 },
866	>	{ "count",      0, NULL, 0 },
867	>	{ "gofr",       0, NULL, 'g' },
868	>	{ "gofz",       0, NULL, 0 },
869		{ "r_theta",    0, NULL, 0 },
870		{ "r_omega",    0, NULL, 0 },
871	+	{ "r_z",        0, NULL, 0 },
872		{ "theta_omega",        0, NULL, 0 },
873		{ "gxyz",       0, NULL, 0 },
874	<	{ "p2", 0, NULL, 0 },
875	<	{ "scd",        0, NULL, 0 },
876	<	{ "density",    0, NULL, 0 },
877	<	{ NULL, 0, NULL, 0 }
874	>	{ "twodgofr",   0, NULL, 0 },
875	>	{ "p2", 0, NULL, 'p' },
876	>	{ "rp2",        0, NULL, 0 },
877	>	{ "scd",        0, NULL, 's' },
878	>	{ "density",    0, NULL, 'd' },
879	>	{ "slab_density",       0, NULL, 0 },
880	>	{ "p_angle",    0, NULL, 0 },
881	>	{ "hxy",        0, NULL, 0 },
882	>	{ "rho_r",      0, NULL, 0 },
883	>	{ "angle_r",    0, NULL, 0 },
884	>	{ "hullvol",    0, NULL, 0 },
885	>	{ "rodlength",  0, NULL, 0 },
886	>	{ "tet_param",  0, NULL, 'Q' },
887	>	{ "tet_param_z",        0, NULL, 0 },
888	>	{ 0,  0, 0, 0 }
889		};
890
891	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
891	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
892
893		if (c == -1) break;       /* Exit from `while (1)' loop.  */
894
895		switch (c)
896		{
897		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
898		cmdline_parser_print_help ();
899	+	cmdline_parser_free (&local_args_info);
900		exit (EXIT_SUCCESS);
901
902		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
903		cmdline_parser_print_version ();
904	+	cmdline_parser_free (&local_args_info);
905		exit (EXIT_SUCCESS);
906
907		case 'i':       /* input dump file.  */
908	<	if (args_info->input_given)
909	<	{
910	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
911	<	clear_args ();
912	<	exit (EXIT_FAILURE);
913	<	}
914	<	args_info->input_given = 1;
915	<	args_info->input_arg = gengetopt_strdup (optarg);
908	>
909	>
910	>	if (update_arg( (void *)&(args_info->input_arg),
911	>	&(args_info->input_orig), &(args_info->input_given),
912	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
913	>	check_ambiguity, override, 0, 0,
914	>	"input", 'i',
915	>	additional_error))
916	>	goto failure;
917	>
918		break;
190	–
919		case 'o':       /* output file name.  */
920	<	if (args_info->output_given)
921	<	{
922	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
923	<	clear_args ();
924	<	exit (EXIT_FAILURE);
925	<	}
926	<	args_info->output_given = 1;
927	<	args_info->output_arg = gengetopt_strdup (optarg);
920	>
921	>
922	>	if (update_arg( (void *)&(args_info->output_arg),
923	>	&(args_info->output_orig), &(args_info->output_given),
924	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
925	>	check_ambiguity, override, 0, 0,
926	>	"output", 'o',
927	>	additional_error))
928	>	goto failure;
929	>
930		break;
201	–
931		case 'n':       /* process every n frame.  */
932	<	if (args_info->step_given)
933	<	{
934	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
935	<	clear_args ();
936	<	exit (EXIT_FAILURE);
937	<	}
938	<	args_info->step_given = 1;
939	<	args_info->step_arg = strtol (optarg,&stop_char,0);
932	>
933	>
934	>	if (update_arg( (void *)&(args_info->step_arg),
935	>	&(args_info->step_orig), &(args_info->step_given),
936	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
937	>	check_ambiguity, override, 0, 0,
938	>	"step", 'n',
939	>	additional_error))
940	>	goto failure;
941	>
942		break;
943	<
944	<	case 'r':       /* number of bins for distance.  */
945	<	if (args_info->nrbins_given)
946	<	{
947	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
948	<	clear_args ();
949	<	exit (EXIT_FAILURE);
950	<	}
951	<	args_info->nrbins_given = 1;
952	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
943	>	case 'b':       /* number of bins (general purpose).  */
944	>
945	>
946	>	if (update_arg( (void *)&(args_info->nbins_arg),
947	>	&(args_info->nbins_orig), &(args_info->nbins_given),
948	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
949	>	check_ambiguity, override, 0, 0,
950	>	"nbins", 'b',
951	>	additional_error))
952	>	goto failure;
953	>
954		break;
955	<
955	>	case 'x':       /* number of bins in x axis.  */
956	>
957	>
958	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
959	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
960	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
961	>	check_ambiguity, override, 0, 0,
962	>	"nbins_x", 'x',
963	>	additional_error))
964	>	goto failure;
965	>
966	>	break;
967	>	case 'y':       /* number of bins in y axis.  */
968	>
969	>
970	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
971	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
972	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
973	>	check_ambiguity, override, 0, 0,
974	>	"nbins_y", 'y',
975	>	additional_error))
976	>	goto failure;
977	>
978	>	break;
979		case 'a':       /* number of bins for cos(angle).  */
980	<	if (args_info->nanglebins_given)
981	<	{
982	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
983	<	clear_args ();
984	<	exit (EXIT_FAILURE);
985	<	}
986	<	args_info->nanglebins_given = 1;
987	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
980	>
981	>
982	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
983	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
984	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
985	>	check_ambiguity, override, 0, 0,
986	>	"nanglebins", 'a',
987	>	additional_error))
988	>	goto failure;
989	>
990		break;
991	<
992	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
993	<	if (args_info->length_given)
994	<	{
995	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
996	<	clear_args ();
997	<	exit (EXIT_FAILURE);
998	<	}
999	<	args_info->length_given = 1;
1000	<	args_info->length_arg = strtod (optarg, NULL);
991	>	case 'c':       /* cutoff radius (rcut).  */
992	>
993	>
994	>	if (update_arg( (void *)&(args_info->rcut_arg),
995	>	&(args_info->rcut_orig), &(args_info->rcut_given),
996	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
997	>	check_ambiguity, override, 0, 0,
998	>	"rcut", 'c',
999	>	additional_error))
1000	>	goto failure;
1001	>
1002		break;
1003	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1004	+
1005	+
1006	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1007	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1008	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1009	+	check_ambiguity, override, 0, 0,
1010	+	"zoffset", 'z',
1011	+	additional_error))
1012	+	goto failure;
1013	+
1014	+	break;
1015	+	case 'g':       /* g(r).  */
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->gofr_given),
1023	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1024	+	check_ambiguity, override, 0, 0,
1025	+	"gofr", 'g',
1026	+	additional_error))
1027	+	goto failure;
1028	+
1029	+	break;
1030	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
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->p2_given),
1038	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1039	+	check_ambiguity, override, 0, 0,
1040	+	"p2", 'p',
1041	+	additional_error))
1042	+	goto failure;
1043	+
1044	+	break;
1045	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
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->scd_given),
1053	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1054	+	check_ambiguity, override, 0, 0,
1055	+	"scd", 's',
1056	+	additional_error))
1057	+	goto failure;
1058	+
1059	+	break;
1060	+	case 'd':       /* density plot.  */
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->density_given),
1068	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1069	+	check_ambiguity, override, 0, 0,
1070	+	"density", 'd',
1071	+	additional_error))
1072	+	goto failure;
1073	+
1074	+	break;
1075	+	case 'Q':       /* tetrahedrality order parameter.  */
1076	+
1077	+	if (args_info->staticProps_group_counter && override)
1078	+	reset_group_staticProps (args_info);
1079	+	args_info->staticProps_group_counter += 1;
1080	+
1081	+	if (update_arg( 0 ,
1082	+	0 , &(args_info->tet_param_given),
1083	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1084	+	check_ambiguity, override, 0, 0,
1085	+	"tet_param", 'Q',
1086	+	additional_error))
1087	+	goto failure;
1088	+
1089	+	break;
1090
246	–
1091		case 0: /* Long option with no short option */
1092	<	/* select the first stuntdouble set.  */
1093	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1092	>	/* number of bins in z axis.  */
1093	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1094		{
1095	<	if (args_info->sele1_given)
1096	<	{
1097	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1098	<	clear_args ();
1099	<	exit (EXIT_FAILURE);
1100	<	}
1101	<	args_info->sele1_given = 1;
1102	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1103	<	break;
1095	>
1096	>
1097	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1098	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1099	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1100	>	check_ambiguity, override, 0, 0,
1101	>	"nbins_z", '-',
1102	>	additional_error))
1103	>	goto failure;
1104	>
1105		}
1106	+	/* slab width (dz).  */
1107	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1108	+	{
1109
1110	+
1111	+	if (update_arg( (void *)&(args_info->dz_arg),
1112	+	&(args_info->dz_orig), &(args_info->dz_given),
1113	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1114	+	check_ambiguity, override, 0, 0,
1115	+	"dz", '-',
1116	+	additional_error))
1117	+	goto failure;
1118	+
1119	+	}
1120	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1121	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1122	+	{
1123	+
1124	+
1125	+	if (update_arg( (void *)&(args_info->length_arg),
1126	+	&(args_info->length_orig), &(args_info->length_given),
1127	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1128	+	check_ambiguity, override, 0, 0,
1129	+	"length", '-',
1130	+	additional_error))
1131	+	goto failure;
1132	+
1133	+	}
1134	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1135	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1136	+	{
1137	+
1138	+
1139	+	if (update_arg( (void *)&(args_info->zlength_arg),
1140	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1141	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1142	+	check_ambiguity, override, 0, 0,
1143	+	"zlength", '-',
1144	+	additional_error))
1145	+	goto failure;
1146	+
1147	+	}
1148	+	/* select the first stuntdouble set.  */
1149	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1150	+	{
1151	+
1152	+
1153	+	if (update_arg( (void *)&(args_info->sele1_arg),
1154	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1155	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1156	+	check_ambiguity, override, 0, 0,
1157	+	"sele1", '-',
1158	+	additional_error))
1159	+	goto failure;
1160	+
1161	+	}
1162		/* select the second stuntdouble set.  */
1163		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1164		{
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	–	}
1165
1166	+
1167	+	if (update_arg( (void *)&(args_info->sele2_arg),
1168	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1169	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1170	+	check_ambiguity, override, 0, 0,
1171	+	"sele2", '-',
1172	+	additional_error))
1173	+	goto failure;
1174	+
1175	+	}
1176		/* select the third stuntdouble set.  */
1177		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1178		{
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	–	}
1179
1180	+
1181	+	if (update_arg( (void *)&(args_info->sele3_arg),
1182	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1183	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1184	+	check_ambiguity, override, 0, 0,
1185	+	"sele3", '-',
1186	+	additional_error))
1187	+	goto failure;
1188	+
1189	+	}
1190		/* select reference (use and only use with --gxyz).  */
1191		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1192		{
1193	<	if (args_info->refsele_given)
1194	<	{
1195	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1196	<	clear_args ();
1197	<	exit (EXIT_FAILURE);
1198	<	}
1199	<	args_info->refsele_given = 1;
1200	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1201	<	break;
1193	>
1194	>
1195	>	if (update_arg( (void *)&(args_info->refsele_arg),
1196	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1197	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1198	>	check_ambiguity, override, 0, 0,
1199	>	"refsele", '-',
1200	>	additional_error))
1201	>	goto failure;
1202	>
1203		}
1204	+	/* select stunt doubles for center-of-mass reference point.  */
1205	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1206	+	{
1207
1208	+
1209	+	if (update_arg( (void *)&(args_info->comsele_arg),
1210	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1211	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1212	+	check_ambiguity, override, 0, 0,
1213	+	"comsele", '-',
1214	+	additional_error))
1215	+	goto failure;
1216	+
1217	+	}
1218	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1219	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1220	+	{
1221	+
1222	+
1223	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1224	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1225	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1226	+	check_ambiguity, override, 0, 0,
1227	+	"seleoffset", '-',
1228	+	additional_error))
1229	+	goto failure;
1230	+
1231	+	}
1232		/* molecule name.  */
1233		else if (strcmp (long_options[option_index].name, "molname") == 0)
1234		{
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	–	}
1235
1236	<	/* begin interanl index.  */
1236	>
1237	>	if (update_arg( (void *)&(args_info->molname_arg),
1238	>	&(args_info->molname_orig), &(args_info->molname_given),
1239	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1240	>	check_ambiguity, override, 0, 0,
1241	>	"molname", '-',
1242	>	additional_error))
1243	>	goto failure;
1244	>
1245	>	}
1246	>	/* begin internal index.  */
1247		else if (strcmp (long_options[option_index].name, "begin") == 0)
1248		{
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	–	}
1249
1250	+
1251	+	if (update_arg( (void *)&(args_info->begin_arg),
1252	+	&(args_info->begin_orig), &(args_info->begin_given),
1253	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1254	+	check_ambiguity, override, 0, 0,
1255	+	"begin", '-',
1256	+	additional_error))
1257	+	goto failure;
1258	+
1259	+	}
1260		/* end internal index.  */
1261		else if (strcmp (long_options[option_index].name, "end") == 0)
1262		{
335	–	if (args_info->end_given)
336	–	{
337	–	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
338	–	clear_args ();
339	–	exit (EXIT_FAILURE);
340	–	}
341	–	args_info->end_given = 1;
342	–	args_info->end_arg = strtol (optarg,&stop_char,0);
343	–	break;
344	–	}
1263
1264	<	/* g(r).  */
1265	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1264	>
1265	>	if (update_arg( (void *)&(args_info->end_arg),
1266	>	&(args_info->end_orig), &(args_info->end_given),
1267	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1268	>	check_ambiguity, override, 0, 0,
1269	>	"end", '-',
1270	>	additional_error))
1271	>	goto failure;
1272	>
1273	>	}
1274	>	/* nanoparticle radius.  */
1275	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1276		{
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;
1277
1278	<	break;
1278	>
1279	>	if (update_arg( (void *)&(args_info->radius_arg),
1280	>	&(args_info->radius_orig), &(args_info->radius_given),
1281	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1282	>	check_ambiguity, override, 0, 0,
1283	>	"radius", '-',
1284	>	additional_error))
1285	>	goto failure;
1286	>
1287		}
1288	+	/* bond order parameter (--rcut must be specified).  */
1289	+	else if (strcmp (long_options[option_index].name, "bo") == 0)
1290	+	{
1291
1292	+	if (args_info->staticProps_group_counter && override)
1293	+	reset_group_staticProps (args_info);
1294	+	args_info->staticProps_group_counter += 1;
1295	+
1296	+	if (update_arg( 0 ,
1297	+	0 , &(args_info->bo_given),
1298	+	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1299	+	check_ambiguity, override, 0, 0,
1300	+	"bo", '-',
1301	+	additional_error))
1302	+	goto failure;
1303	+
1304	+	}
1305	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1306	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1307	+	{
1308	+
1309	+	if (args_info->staticProps_group_counter && override)
1310	+	reset_group_staticProps (args_info);
1311	+	args_info->staticProps_group_counter += 1;
1312	+
1313	+	if (update_arg( 0 ,
1314	+	0 , &(args_info->bor_given),
1315	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1316	+	check_ambiguity, override, 0, 0,
1317	+	"bor", '-',
1318	+	additional_error))
1319	+	goto failure;
1320	+
1321	+	}
1322	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1323	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1324	+	{
1325	+
1326	+	if (args_info->staticProps_group_counter && override)
1327	+	reset_group_staticProps (args_info);
1328	+	args_info->staticProps_group_counter += 1;
1329	+
1330	+	if (update_arg( 0 ,
1331	+	0 , &(args_info->bad_given),
1332	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1333	+	check_ambiguity, override, 0, 0,
1334	+	"bad", '-',
1335	+	additional_error))
1336	+	goto failure;
1337	+
1338	+	}
1339	+	/* count of molecules matching selection criteria (and associated statistics).  */
1340	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1341	+	{
1342	+
1343	+	if (args_info->staticProps_group_counter && override)
1344	+	reset_group_staticProps (args_info);
1345	+	args_info->staticProps_group_counter += 1;
1346	+
1347	+	if (update_arg( 0 ,
1348	+	0 , &(args_info->count_given),
1349	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1350	+	check_ambiguity, override, 0, 0,
1351	+	"count", '-',
1352	+	additional_error))
1353	+	goto failure;
1354	+
1355	+	}
1356	+	/* g(z).  */
1357	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1358	+	{
1359	+
1360	+	if (args_info->staticProps_group_counter && override)
1361	+	reset_group_staticProps (args_info);
1362	+	args_info->staticProps_group_counter += 1;
1363	+
1364	+	if (update_arg( 0 ,
1365	+	0 , &(args_info->gofz_given),
1366	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1367	+	check_ambiguity, override, 0, 0,
1368	+	"gofz", '-',
1369	+	additional_error))
1370	+	goto failure;
1371	+
1372	+	}
1373		/* g(r, cos(theta)).  */
1374		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1375		{
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;
1376
1377	<	break;
1378	<	}
1377	>	if (args_info->staticProps_group_counter && override)
1378	>	reset_group_staticProps (args_info);
1379	>	args_info->staticProps_group_counter += 1;
1380
1381	+	if (update_arg( 0 ,
1382	+	0 , &(args_info->r_theta_given),
1383	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1384	+	check_ambiguity, override, 0, 0,
1385	+	"r_theta", '-',
1386	+	additional_error))
1387	+	goto failure;
1388	+
1389	+	}
1390		/* g(r, cos(omega)).  */
1391		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1392		{
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;
1393
1394	<	break;
1394	>	if (args_info->staticProps_group_counter && override)
1395	>	reset_group_staticProps (args_info);
1396	>	args_info->staticProps_group_counter += 1;
1397	>
1398	>	if (update_arg( 0 ,
1399	>	0 , &(args_info->r_omega_given),
1400	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1401	>	check_ambiguity, override, 0, 0,
1402	>	"r_omega", '-',
1403	>	additional_error))
1404	>	goto failure;
1405	>
1406		}
1407	+	/* g(r, z).  */
1408	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1409	+	{
1410
1411	+	if (args_info->staticProps_group_counter && override)
1412	+	reset_group_staticProps (args_info);
1413	+	args_info->staticProps_group_counter += 1;
1414	+
1415	+	if (update_arg( 0 ,
1416	+	0 , &(args_info->r_z_given),
1417	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1418	+	check_ambiguity, override, 0, 0,
1419	+	"r_z", '-',
1420	+	additional_error))
1421	+	goto failure;
1422	+
1423	+	}
1424		/* g(cos(theta), cos(omega)).  */
1425		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1426		{
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;
1427
1428	<	break;
1429	<	}
1428	>	if (args_info->staticProps_group_counter && override)
1429	>	reset_group_staticProps (args_info);
1430	>	args_info->staticProps_group_counter += 1;
1431
1432	+	if (update_arg( 0 ,
1433	+	0 , &(args_info->theta_omega_given),
1434	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1435	+	check_ambiguity, override, 0, 0,
1436	+	"theta_omega", '-',
1437	+	additional_error))
1438	+	goto failure;
1439	+
1440	+	}
1441		/* g(x, y, z).  */
1442		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1443		{
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;
1444
1445	<	break;
1446	<	}
1445	>	if (args_info->staticProps_group_counter && override)
1446	>	reset_group_staticProps (args_info);
1447	>	args_info->staticProps_group_counter += 1;
1448
1449	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1450	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1449	>	if (update_arg( 0 ,
1450	>	0 , &(args_info->gxyz_given),
1451	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1452	>	check_ambiguity, override, 0, 0,
1453	>	"gxyz", '-',
1454	>	additional_error))
1455	>	goto failure;
1456	>
1457	>	}
1458	>	/* 2D g(r) (Slab width --dz must be specified).  */
1459	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1460		{
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;
1461
1462	<	break;
1462	>	if (args_info->staticProps_group_counter && override)
1463	>	reset_group_staticProps (args_info);
1464	>	args_info->staticProps_group_counter += 1;
1465	>
1466	>	if (update_arg( 0 ,
1467	>	0 , &(args_info->twodgofr_given),
1468	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1469	>	check_ambiguity, override, 0, 0,
1470	>	"twodgofr", '-',
1471	>	additional_error))
1472	>	goto failure;
1473	>
1474		}
1475	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1476	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1477	+	{
1478
1479	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1480	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1479	>	if (args_info->staticProps_group_counter && override)
1480	>	reset_group_staticProps (args_info);
1481	>	args_info->staticProps_group_counter += 1;
1482	>
1483	>	if (update_arg( 0 ,
1484	>	0 , &(args_info->rp2_given),
1485	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1486	>	check_ambiguity, override, 0, 0,
1487	>	"rp2", '-',
1488	>	additional_error))
1489	>	goto failure;
1490	>
1491	>	}
1492	>	/* slab density.  */
1493	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1494		{
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;
1495
1496	<	break;
1496	>	if (args_info->staticProps_group_counter && override)
1497	>	reset_group_staticProps (args_info);
1498	>	args_info->staticProps_group_counter += 1;
1499	>
1500	>	if (update_arg( 0 ,
1501	>	0 , &(args_info->slab_density_given),
1502	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1503	>	check_ambiguity, override, 0, 0,
1504	>	"slab_density", '-',
1505	>	additional_error))
1506	>	goto failure;
1507	>
1508		}
1509	+	/* p(cos(theta)).  */
1510	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1511	+	{
1512
1513	<	/* density plot (--sele1 must be specified).  */
1514	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1513	>	if (args_info->staticProps_group_counter && override)
1514	>	reset_group_staticProps (args_info);
1515	>	args_info->staticProps_group_counter += 1;
1516	>
1517	>	if (update_arg( 0 ,
1518	>	0 , &(args_info->p_angle_given),
1519	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1520	>	check_ambiguity, override, 0, 0,
1521	>	"p_angle", '-',
1522	>	additional_error))
1523	>	goto failure;
1524	>
1525	>	}
1526	>	/* hxy.  */
1527	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1528		{
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;
1529
1530	<	break;
1530	>	if (args_info->staticProps_group_counter && override)
1531	>	reset_group_staticProps (args_info);
1532	>	args_info->staticProps_group_counter += 1;
1533	>
1534	>	if (update_arg( 0 ,
1535	>	0 , &(args_info->hxy_given),
1536	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1537	>	check_ambiguity, override, 0, 0,
1538	>	"hxy", '-',
1539	>	additional_error))
1540	>	goto failure;
1541	>
1542		}
1543	+	/* rho of R.  */
1544	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1545	+	{
1546
1547	<
1547	>	if (args_info->staticProps_group_counter && override)
1548	>	reset_group_staticProps (args_info);
1549	>	args_info->staticProps_group_counter += 1;
1550	>
1551	>	if (update_arg( 0 ,
1552	>	0 , &(args_info->rho_r_given),
1553	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1554	>	check_ambiguity, override, 0, 0,
1555	>	"rho_r", '-',
1556	>	additional_error))
1557	>	goto failure;
1558	>
1559	>	}
1560	>	/* angle of R.  */
1561	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1562	>	{
1563	>
1564	>	if (args_info->staticProps_group_counter && override)
1565	>	reset_group_staticProps (args_info);
1566	>	args_info->staticProps_group_counter += 1;
1567	>
1568	>	if (update_arg( 0 ,
1569	>	0 , &(args_info->angle_r_given),
1570	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1571	>	check_ambiguity, override, 0, 0,
1572	>	"angle_r", '-',
1573	>	additional_error))
1574	>	goto failure;
1575	>
1576	>	}
1577	>	/* hull volume of nanoparticle.  */
1578	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1579	>	{
1580	>
1581	>	if (args_info->staticProps_group_counter && override)
1582	>	reset_group_staticProps (args_info);
1583	>	args_info->staticProps_group_counter += 1;
1584	>
1585	>	if (update_arg( 0 ,
1586	>	0 , &(args_info->hullvol_given),
1587	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1588	>	check_ambiguity, override, 0, 0,
1589	>	"hullvol", '-',
1590	>	additional_error))
1591	>	goto failure;
1592	>
1593	>	}
1594	>	/* length of nanorod.  */
1595	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1596	>	{
1597	>
1598	>	if (args_info->staticProps_group_counter && override)
1599	>	reset_group_staticProps (args_info);
1600	>	args_info->staticProps_group_counter += 1;
1601	>
1602	>	if (update_arg( 0 ,
1603	>	0 , &(args_info->rodlength_given),
1604	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1605	>	check_ambiguity, override, 0, 0,
1606	>	"rodlength", '-',
1607	>	additional_error))
1608	>	goto failure;
1609	>
1610	>	}
1611	>	/* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1612	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1613	>	{
1614	>
1615	>	if (args_info->staticProps_group_counter && override)
1616	>	reset_group_staticProps (args_info);
1617	>	args_info->staticProps_group_counter += 1;
1618	>
1619	>	if (update_arg( 0 ,
1620	>	0 , &(args_info->tet_param_z_given),
1621	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1622	>	check_ambiguity, override, 0, 0,
1623	>	"tet_param_z", '-',
1624	>	additional_error))
1625	>	goto failure;
1626	>
1627	>	}
1628	>
1629	>	break;
1630		case '?':       /* Invalid option.  */
1631		/* `getopt_long' already printed an error message.  */
1632	<	exit (EXIT_FAILURE);
1632	>	goto failure;
1633
1634		default:        /* bug: option not considered.  */
1635	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1635	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1636		abort ();
1637		} /* switch */
1638		} /* while */
1639
1640	<	if ( staticProps_group_counter != 1)
1640	>	if (args_info->staticProps_group_counter > 1)
1641		{
1642	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1643	<	missing_required_options = 1;
1642	>	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 : ""));
1643	>	error = 1;
1644		}
1645
1646
1647	<	if (! args_info->input_given)
1647	>
1648	>	if (check_required)
1649		{
1650	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1650	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1651		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1652
1653	+	cmdline_parser_release (&local_args_info);
1654	+
1655	+	if ( error )
1656	+	return (EXIT_FAILURE);
1657	+
1658	+	if (optind < argc)
1659	+	{
1660	+	int i = 0 ;
1661	+	int found_prog_name = 0;
1662	+	/* whether program name, i.e., argv[0], is in the remaining args
1663	+	(this may happen with some implementations of getopt,
1664	+	but surely not with the one included by gengetopt) */
1665	+
1666	+	i = optind;
1667	+	while (i < argc)
1668	+	if (argv[i++] == argv[0]) {
1669	+	found_prog_name = 1;
1670	+	break;
1671	+	}
1672	+	i = 0;
1673	+
1674	+	args_info->inputs_num = argc - optind - found_prog_name;
1675	+	args_info->inputs =
1676	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1677	+	while (optind < argc)
1678	+	if (argv[optind++] != argv[0])
1679	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1680	+	}
1681	+
1682		return 0;
1683	+
1684	+	failure:
1685	+
1686	+	cmdline_parser_release (&local_args_info);
1687	+	return (EXIT_FAILURE);
1688		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 545 by tim, Fri May 27 21:11:24 2005 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

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