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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 1879 by gezelter, Sun Jun 16 15:15:42 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/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	>	#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	<	}
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	>	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
91	>	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
92	>	0
93	>	};
94
95	<	/* gengetopt_strdup() */
96	<	/* strdup.c replacement of strdup, which is not standard */
97	<	char *
98	<	gengetopt_strdup (const char *s)
99	<	{
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	<	}
95	>	typedef enum {ARG_NO
96	>	, ARG_STRING
97	>	, ARG_INT
98	>	, ARG_DOUBLE
99	>	} cmdline_parser_arg_type;
100
101	<	int
102	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
103	<	{
104	<	int c;        /* Character of the parsed option.  */
84	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
86	<
101	>	static
102	>	void clear_given (struct gengetopt_args_info *args_info);
103	>	static
104	>	void clear_args (struct gengetopt_args_info *args_info);
105
106	+	static int
107	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
108	+	struct cmdline_parser_params *params, const char *additional_error);
109	+
110	+	static int
111	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
112	+
113	+	static char *
114	+	gengetopt_strdup (const char *s);
115	+
116	+	static
117	+	void clear_given (struct gengetopt_args_info *args_info)
118	+	{
119		args_info->help_given = 0 ;
120		args_info->version_given = 0 ;
121		args_info->input_given = 0 ;
122		args_info->output_given = 0 ;
123		args_info->step_given = 0 ;
124	<	args_info->nrbins_given = 0 ;
124	>	args_info->nbins_given = 0 ;
125	>	args_info->nbins_x_given = 0 ;
126	>	args_info->nbins_y_given = 0 ;
127	>	args_info->nbins_z_given = 0 ;
128		args_info->nanglebins_given = 0 ;
129	+	args_info->rcut_given = 0 ;
130	+	args_info->dz_given = 0 ;
131		args_info->length_given = 0 ;
132	+	args_info->zlength_given = 0 ;
133	+	args_info->zoffset_given = 0 ;
134		args_info->sele1_given = 0 ;
135		args_info->sele2_given = 0 ;
136		args_info->sele3_given = 0 ;
137		args_info->refsele_given = 0 ;
138	+	args_info->comsele_given = 0 ;
139	+	args_info->seleoffset_given = 0 ;
140		args_info->molname_given = 0 ;
141		args_info->begin_given = 0 ;
142		args_info->end_given = 0 ;
143	+	args_info->radius_given = 0 ;
144	+	args_info->bo_given = 0 ;
145	+	args_info->bor_given = 0 ;
146	+	args_info->bad_given = 0 ;
147	+	args_info->count_given = 0 ;
148		args_info->gofr_given = 0 ;
149	+	args_info->gofz_given = 0 ;
150		args_info->r_theta_given = 0 ;
151		args_info->r_omega_given = 0 ;
152	+	args_info->r_z_given = 0 ;
153		args_info->theta_omega_given = 0 ;
154		args_info->gxyz_given = 0 ;
155	+	args_info->twodgofr_given = 0 ;
156		args_info->p2_given = 0 ;
157	+	args_info->rp2_given = 0 ;
158		args_info->scd_given = 0 ;
159		args_info->density_given = 0 ;
160	<	#define clear_args() { \
161	<	args_info->input_arg = NULL; \
162	<	args_info->output_arg = NULL; \
163	<	args_info->step_arg = 1 ;\
164	<	args_info->nrbins_arg = 100 ;\
165	<	args_info->nanglebins_arg = 50 ;\
166	<	args_info->sele1_arg = NULL; \
167	<	args_info->sele2_arg = NULL; \
168	<	args_info->sele3_arg = NULL; \
169	<	args_info->refsele_arg = NULL; \
170	<	args_info->molname_arg = NULL; \
160	>	args_info->slab_density_given = 0 ;
161	>	args_info->p_angle_given = 0 ;
162	>	args_info->hxy_given = 0 ;
163	>	args_info->rho_r_given = 0 ;
164	>	args_info->angle_r_given = 0 ;
165	>	args_info->hullvol_given = 0 ;
166	>	args_info->rodlength_given = 0 ;
167	>	args_info->tet_param_given = 0 ;
168	>	args_info->tet_param_z_given = 0 ;
169	>	args_info->rnemdz_given = 0 ;
170	>	args_info->rnemdr_given = 0 ;
171	>	args_info->staticProps_group_counter = 0 ;
172		}
173
174	<	clear_args();
174	>	static
175	>	void clear_args (struct gengetopt_args_info *args_info)
176	>	{
177	>	FIX_UNUSED (args_info);
178	>	args_info->input_arg = NULL;
179	>	args_info->input_orig = NULL;
180	>	args_info->output_arg = NULL;
181	>	args_info->output_orig = NULL;
182	>	args_info->step_arg = 1;
183	>	args_info->step_orig = NULL;
184	>	args_info->nbins_arg = 100;
185	>	args_info->nbins_orig = NULL;
186	>	args_info->nbins_x_arg = 100;
187	>	args_info->nbins_x_orig = NULL;
188	>	args_info->nbins_y_arg = 100;
189	>	args_info->nbins_y_orig = NULL;
190	>	args_info->nbins_z_arg = 100;
191	>	args_info->nbins_z_orig = NULL;
192	>	args_info->nanglebins_arg = 50;
193	>	args_info->nanglebins_orig = NULL;
194	>	args_info->rcut_orig = NULL;
195	>	args_info->dz_orig = NULL;
196	>	args_info->length_orig = NULL;
197	>	args_info->zlength_orig = NULL;
198	>	args_info->zoffset_arg = 0;
199	>	args_info->zoffset_orig = NULL;
200	>	args_info->sele1_arg = NULL;
201	>	args_info->sele1_orig = NULL;
202	>	args_info->sele2_arg = NULL;
203	>	args_info->sele2_orig = NULL;
204	>	args_info->sele3_arg = NULL;
205	>	args_info->sele3_orig = NULL;
206	>	args_info->refsele_arg = NULL;
207	>	args_info->refsele_orig = NULL;
208	>	args_info->comsele_arg = NULL;
209	>	args_info->comsele_orig = NULL;
210	>	args_info->seleoffset_orig = NULL;
211	>	args_info->molname_arg = NULL;
212	>	args_info->molname_orig = NULL;
213	>	args_info->begin_orig = NULL;
214	>	args_info->end_orig = NULL;
215	>	args_info->radius_orig = NULL;
216	>
217	>	}
218
219	+	static
220	+	void init_args_info(struct gengetopt_args_info *args_info)
221	+	{
222	+
223	+
224	+	args_info->help_help = gengetopt_args_info_help[0] ;
225	+	args_info->version_help = gengetopt_args_info_help[1] ;
226	+	args_info->input_help = gengetopt_args_info_help[2] ;
227	+	args_info->output_help = gengetopt_args_info_help[3] ;
228	+	args_info->step_help = gengetopt_args_info_help[4] ;
229	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
230	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
231	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
232	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
233	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
234	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
235	+	args_info->dz_help = gengetopt_args_info_help[11] ;
236	+	args_info->length_help = gengetopt_args_info_help[12] ;
237	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
238	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
239	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
240	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
241	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
242	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
243	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
244	+	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
245	+	args_info->molname_help = gengetopt_args_info_help[21] ;
246	+	args_info->begin_help = gengetopt_args_info_help[22] ;
247	+	args_info->end_help = gengetopt_args_info_help[23] ;
248	+	args_info->radius_help = gengetopt_args_info_help[24] ;
249	+	args_info->bo_help = gengetopt_args_info_help[26] ;
250	+	args_info->bor_help = gengetopt_args_info_help[27] ;
251	+	args_info->bad_help = gengetopt_args_info_help[28] ;
252	+	args_info->count_help = gengetopt_args_info_help[29] ;
253	+	args_info->gofr_help = gengetopt_args_info_help[30] ;
254	+	args_info->gofz_help = gengetopt_args_info_help[31] ;
255	+	args_info->r_theta_help = gengetopt_args_info_help[32] ;
256	+	args_info->r_omega_help = gengetopt_args_info_help[33] ;
257	+	args_info->r_z_help = gengetopt_args_info_help[34] ;
258	+	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
259	+	args_info->gxyz_help = gengetopt_args_info_help[36] ;
260	+	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
261	+	args_info->p2_help = gengetopt_args_info_help[38] ;
262	+	args_info->rp2_help = gengetopt_args_info_help[39] ;
263	+	args_info->scd_help = gengetopt_args_info_help[40] ;
264	+	args_info->density_help = gengetopt_args_info_help[41] ;
265	+	args_info->slab_density_help = gengetopt_args_info_help[42] ;
266	+	args_info->p_angle_help = gengetopt_args_info_help[43] ;
267	+	args_info->hxy_help = gengetopt_args_info_help[44] ;
268	+	args_info->rho_r_help = gengetopt_args_info_help[45] ;
269	+	args_info->angle_r_help = gengetopt_args_info_help[46] ;
270	+	args_info->hullvol_help = gengetopt_args_info_help[47] ;
271	+	args_info->rodlength_help = gengetopt_args_info_help[48] ;
272	+	args_info->tet_param_help = gengetopt_args_info_help[49] ;
273	+	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
274	+	args_info->rnemdz_help = gengetopt_args_info_help[51] ;
275	+	args_info->rnemdr_help = gengetopt_args_info_help[52] ;
276	+
277	+	}
278	+
279	+	void
280	+	cmdline_parser_print_version (void)
281	+	{
282	+	printf ("%s %s\n",
283	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
284	+	CMDLINE_PARSER_VERSION);
285	+	}
286	+
287	+	static void print_help_common(void) {
288	+	cmdline_parser_print_version ();
289	+
290	+	if (strlen(gengetopt_args_info_purpose) > 0)
291	+	printf("\n%s\n", gengetopt_args_info_purpose);
292	+
293	+	if (strlen(gengetopt_args_info_usage) > 0)
294	+	printf("\n%s\n", gengetopt_args_info_usage);
295	+
296	+	printf("\n");
297	+
298	+	if (strlen(gengetopt_args_info_description) > 0)
299	+	printf("%s\n\n", gengetopt_args_info_description);
300	+	}
301	+
302	+	void
303	+	cmdline_parser_print_help (void)
304	+	{
305	+	int i = 0;
306	+	print_help_common();
307	+	while (gengetopt_args_info_help[i])
308	+	printf("%s\n", gengetopt_args_info_help[i++]);
309	+	}
310	+
311	+	void
312	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
313	+	{
314	+	clear_given (args_info);
315	+	clear_args (args_info);
316	+	init_args_info (args_info);
317	+
318	+	args_info->inputs = 0;
319	+	args_info->inputs_num = 0;
320	+	}
321	+
322	+	void
323	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
324	+	{
325	+	if (params)
326	+	{
327	+	params->override = 0;
328	+	params->initialize = 1;
329	+	params->check_required = 1;
330	+	params->check_ambiguity = 0;
331	+	params->print_errors = 1;
332	+	}
333	+	}
334	+
335	+	struct cmdline_parser_params *
336	+	cmdline_parser_params_create(void)
337	+	{
338	+	struct cmdline_parser_params *params =
339	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
340	+	cmdline_parser_params_init(params);
341	+	return params;
342	+	}
343	+
344	+	static void
345	+	free_string_field (char **s)
346	+	{
347	+	if (*s)
348	+	{
349	+	free (*s);
350	+	*s = 0;
351	+	}
352	+	}
353	+
354	+
355	+	static void
356	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
357	+	{
358	+	unsigned int i;
359	+	free_string_field (&(args_info->input_arg));
360	+	free_string_field (&(args_info->input_orig));
361	+	free_string_field (&(args_info->output_arg));
362	+	free_string_field (&(args_info->output_orig));
363	+	free_string_field (&(args_info->step_orig));
364	+	free_string_field (&(args_info->nbins_orig));
365	+	free_string_field (&(args_info->nbins_x_orig));
366	+	free_string_field (&(args_info->nbins_y_orig));
367	+	free_string_field (&(args_info->nbins_z_orig));
368	+	free_string_field (&(args_info->nanglebins_orig));
369	+	free_string_field (&(args_info->rcut_orig));
370	+	free_string_field (&(args_info->dz_orig));
371	+	free_string_field (&(args_info->length_orig));
372	+	free_string_field (&(args_info->zlength_orig));
373	+	free_string_field (&(args_info->zoffset_orig));
374	+	free_string_field (&(args_info->sele1_arg));
375	+	free_string_field (&(args_info->sele1_orig));
376	+	free_string_field (&(args_info->sele2_arg));
377	+	free_string_field (&(args_info->sele2_orig));
378	+	free_string_field (&(args_info->sele3_arg));
379	+	free_string_field (&(args_info->sele3_orig));
380	+	free_string_field (&(args_info->refsele_arg));
381	+	free_string_field (&(args_info->refsele_orig));
382	+	free_string_field (&(args_info->comsele_arg));
383	+	free_string_field (&(args_info->comsele_orig));
384	+	free_string_field (&(args_info->seleoffset_orig));
385	+	free_string_field (&(args_info->molname_arg));
386	+	free_string_field (&(args_info->molname_orig));
387	+	free_string_field (&(args_info->begin_orig));
388	+	free_string_field (&(args_info->end_orig));
389	+	free_string_field (&(args_info->radius_orig));
390	+
391	+
392	+	for (i = 0; i < args_info->inputs_num; ++i)
393	+	free (args_info->inputs [i]);
394	+
395	+	if (args_info->inputs_num)
396	+	free (args_info->inputs);
397	+
398	+	clear_given (args_info);
399	+	}
400	+
401	+
402	+	static void
403	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
404	+	{
405	+	FIX_UNUSED (values);
406	+	if (arg) {
407	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
408	+	} else {
409	+	fprintf(outfile, "%s\n", opt);
410	+	}
411	+	}
412	+
413	+
414	+	int
415	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
416	+	{
417	+	int i = 0;
418	+
419	+	if (!outfile)
420	+	{
421	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
422	+	return EXIT_FAILURE;
423	+	}
424	+
425	+	if (args_info->help_given)
426	+	write_into_file(outfile, "help", 0, 0 );
427	+	if (args_info->version_given)
428	+	write_into_file(outfile, "version", 0, 0 );
429	+	if (args_info->input_given)
430	+	write_into_file(outfile, "input", args_info->input_orig, 0);
431	+	if (args_info->output_given)
432	+	write_into_file(outfile, "output", args_info->output_orig, 0);
433	+	if (args_info->step_given)
434	+	write_into_file(outfile, "step", args_info->step_orig, 0);
435	+	if (args_info->nbins_given)
436	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
437	+	if (args_info->nbins_x_given)
438	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
439	+	if (args_info->nbins_y_given)
440	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
441	+	if (args_info->nbins_z_given)
442	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
443	+	if (args_info->nanglebins_given)
444	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
445	+	if (args_info->rcut_given)
446	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
447	+	if (args_info->dz_given)
448	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
449	+	if (args_info->length_given)
450	+	write_into_file(outfile, "length", args_info->length_orig, 0);
451	+	if (args_info->zlength_given)
452	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
453	+	if (args_info->zoffset_given)
454	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
455	+	if (args_info->sele1_given)
456	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
457	+	if (args_info->sele2_given)
458	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
459	+	if (args_info->sele3_given)
460	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
461	+	if (args_info->refsele_given)
462	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
463	+	if (args_info->comsele_given)
464	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
465	+	if (args_info->seleoffset_given)
466	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
467	+	if (args_info->molname_given)
468	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
469	+	if (args_info->begin_given)
470	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
471	+	if (args_info->end_given)
472	+	write_into_file(outfile, "end", args_info->end_orig, 0);
473	+	if (args_info->radius_given)
474	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
475	+	if (args_info->bo_given)
476	+	write_into_file(outfile, "bo", 0, 0 );
477	+	if (args_info->bor_given)
478	+	write_into_file(outfile, "bor", 0, 0 );
479	+	if (args_info->bad_given)
480	+	write_into_file(outfile, "bad", 0, 0 );
481	+	if (args_info->count_given)
482	+	write_into_file(outfile, "count", 0, 0 );
483	+	if (args_info->gofr_given)
484	+	write_into_file(outfile, "gofr", 0, 0 );
485	+	if (args_info->gofz_given)
486	+	write_into_file(outfile, "gofz", 0, 0 );
487	+	if (args_info->r_theta_given)
488	+	write_into_file(outfile, "r_theta", 0, 0 );
489	+	if (args_info->r_omega_given)
490	+	write_into_file(outfile, "r_omega", 0, 0 );
491	+	if (args_info->r_z_given)
492	+	write_into_file(outfile, "r_z", 0, 0 );
493	+	if (args_info->theta_omega_given)
494	+	write_into_file(outfile, "theta_omega", 0, 0 );
495	+	if (args_info->gxyz_given)
496	+	write_into_file(outfile, "gxyz", 0, 0 );
497	+	if (args_info->twodgofr_given)
498	+	write_into_file(outfile, "twodgofr", 0, 0 );
499	+	if (args_info->p2_given)
500	+	write_into_file(outfile, "p2", 0, 0 );
501	+	if (args_info->rp2_given)
502	+	write_into_file(outfile, "rp2", 0, 0 );
503	+	if (args_info->scd_given)
504	+	write_into_file(outfile, "scd", 0, 0 );
505	+	if (args_info->density_given)
506	+	write_into_file(outfile, "density", 0, 0 );
507	+	if (args_info->slab_density_given)
508	+	write_into_file(outfile, "slab_density", 0, 0 );
509	+	if (args_info->p_angle_given)
510	+	write_into_file(outfile, "p_angle", 0, 0 );
511	+	if (args_info->hxy_given)
512	+	write_into_file(outfile, "hxy", 0, 0 );
513	+	if (args_info->rho_r_given)
514	+	write_into_file(outfile, "rho_r", 0, 0 );
515	+	if (args_info->angle_r_given)
516	+	write_into_file(outfile, "angle_r", 0, 0 );
517	+	if (args_info->hullvol_given)
518	+	write_into_file(outfile, "hullvol", 0, 0 );
519	+	if (args_info->rodlength_given)
520	+	write_into_file(outfile, "rodlength", 0, 0 );
521	+	if (args_info->tet_param_given)
522	+	write_into_file(outfile, "tet_param", 0, 0 );
523	+	if (args_info->tet_param_z_given)
524	+	write_into_file(outfile, "tet_param_z", 0, 0 );
525	+	if (args_info->rnemdz_given)
526	+	write_into_file(outfile, "rnemdz", 0, 0 );
527	+	if (args_info->rnemdr_given)
528	+	write_into_file(outfile, "rnemdr", 0, 0 );
529	+
530	+
531	+	i = EXIT_SUCCESS;
532	+	return i;
533	+	}
534	+
535	+	int
536	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
537	+	{
538	+	FILE *outfile;
539	+	int i = 0;
540	+
541	+	outfile = fopen(filename, "w");
542	+
543	+	if (!outfile)
544	+	{
545	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
546	+	return EXIT_FAILURE;
547	+	}
548	+
549	+	i = cmdline_parser_dump(outfile, args_info);
550	+	fclose (outfile);
551	+
552	+	return i;
553	+	}
554	+
555	+	void
556	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
557	+	{
558	+	cmdline_parser_release (args_info);
559	+	}
560	+
561	+	/** @brief replacement of strdup, which is not standard */
562	+	char *
563	+	gengetopt_strdup (const char *s)
564	+	{
565	+	char *result = 0;
566	+	if (!s)
567	+	return result;
568	+
569	+	result = (char*)malloc(strlen(s) + 1);
570	+	if (result == (char*)0)
571	+	return (char*)0;
572	+	strcpy(result, s);
573	+	return result;
574	+	}
575	+
576	+	static void
577	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
578	+	{
579	+	if (! args_info->staticProps_group_counter)
580	+	return;
581	+
582	+	args_info->bo_given = 0 ;
583	+	args_info->bor_given = 0 ;
584	+	args_info->bad_given = 0 ;
585	+	args_info->count_given = 0 ;
586	+	args_info->gofr_given = 0 ;
587	+	args_info->gofz_given = 0 ;
588	+	args_info->r_theta_given = 0 ;
589	+	args_info->r_omega_given = 0 ;
590	+	args_info->r_z_given = 0 ;
591	+	args_info->theta_omega_given = 0 ;
592	+	args_info->gxyz_given = 0 ;
593	+	args_info->twodgofr_given = 0 ;
594	+	args_info->p2_given = 0 ;
595	+	args_info->rp2_given = 0 ;
596	+	args_info->scd_given = 0 ;
597	+	args_info->density_given = 0 ;
598	+	args_info->slab_density_given = 0 ;
599	+	args_info->p_angle_given = 0 ;
600	+	args_info->hxy_given = 0 ;
601	+	args_info->rho_r_given = 0 ;
602	+	args_info->angle_r_given = 0 ;
603	+	args_info->hullvol_given = 0 ;
604	+	args_info->rodlength_given = 0 ;
605	+	args_info->tet_param_given = 0 ;
606	+	args_info->tet_param_z_given = 0 ;
607	+	args_info->rnemdz_given = 0 ;
608	+	args_info->rnemdr_given = 0 ;
609	+
610	+	args_info->staticProps_group_counter = 0;
611	+	}
612	+
613	+	int
614	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
615	+	{
616	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
617	+	}
618	+
619	+	int
620	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
621	+	struct cmdline_parser_params *params)
622	+	{
623	+	int result;
624	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
625	+
626	+	if (result == EXIT_FAILURE)
627	+	{
628	+	cmdline_parser_free (args_info);
629	+	exit (EXIT_FAILURE);
630	+	}
631	+
632	+	return result;
633	+	}
634	+
635	+	int
636	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
637	+	{
638	+	int result;
639	+	struct cmdline_parser_params params;
640	+
641	+	params.override = override;
642	+	params.initialize = initialize;
643	+	params.check_required = check_required;
644	+	params.check_ambiguity = 0;
645	+	params.print_errors = 1;
646	+
647	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
648	+
649	+	if (result == EXIT_FAILURE)
650	+	{
651	+	cmdline_parser_free (args_info);
652	+	exit (EXIT_FAILURE);
653	+	}
654	+
655	+	return result;
656	+	}
657	+
658	+	int
659	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
660	+	{
661	+	int result = EXIT_SUCCESS;
662	+
663	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
664	+	result = EXIT_FAILURE;
665	+
666	+	if (result == EXIT_FAILURE)
667	+	{
668	+	cmdline_parser_free (args_info);
669	+	exit (EXIT_FAILURE);
670	+	}
671	+
672	+	return result;
673	+	}
674	+
675	+	int
676	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
677	+	{
678	+	int error = 0;
679	+	FIX_UNUSED (additional_error);
680	+
681	+	/* checks for required options */
682	+	if (! args_info->input_given)
683	+	{
684	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
685	+	error = 1;
686	+	}
687	+
688	+	if (args_info->staticProps_group_counter == 0)
689	+	{
690	+	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 : ""));
691	+	error = 1;
692	+	}
693	+
694	+
695	+	/* checks for dependences among options */
696	+
697	+	return error;
698	+	}
699	+
700	+
701	+	static char *package_name = 0;
702	+
703	+	/**
704	+	* @brief updates an option
705	+	* @param field the generic pointer to the field to update
706	+	* @param orig_field the pointer to the orig field
707	+	* @param field_given the pointer to the number of occurrence of this option
708	+	* @param prev_given the pointer to the number of occurrence already seen
709	+	* @param value the argument for this option (if null no arg was specified)
710	+	* @param possible_values the possible values for this option (if specified)
711	+	* @param default_value the default value (in case the option only accepts fixed values)
712	+	* @param arg_type the type of this option
713	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
714	+	* @param override @see cmdline_parser_params.override
715	+	* @param no_free whether to free a possible previous value
716	+	* @param multiple_option whether this is a multiple option
717	+	* @param long_opt the corresponding long option
718	+	* @param short_opt the corresponding short option (or '-' if none)
719	+	* @param additional_error possible further error specification
720	+	*/
721	+	static
722	+	int update_arg(void *field, char **orig_field,
723	+	unsigned int *field_given, unsigned int *prev_given,
724	+	char *value, const char *possible_values[],
725	+	const char *default_value,
726	+	cmdline_parser_arg_type arg_type,
727	+	int check_ambiguity, int override,
728	+	int no_free, int multiple_option,
729	+	const char *long_opt, char short_opt,
730	+	const char *additional_error)
731	+	{
732	+	char *stop_char = 0;
733	+	const char *val = value;
734	+	int found;
735	+	char **string_field;
736	+	FIX_UNUSED (field);
737	+
738	+	stop_char = 0;
739	+	found = 0;
740	+
741	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
742	+	{
743	+	if (short_opt != '-')
744	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
745	+	package_name, long_opt, short_opt,
746	+	(additional_error ? additional_error : ""));
747	+	else
748	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
749	+	package_name, long_opt,
750	+	(additional_error ? additional_error : ""));
751	+	return 1; /* failure */
752	+	}
753	+
754	+	FIX_UNUSED (default_value);
755	+
756	+	if (field_given && *field_given && ! override)
757	+	return 0;
758	+	if (prev_given)
759	+	(*prev_given)++;
760	+	if (field_given)
761	+	(*field_given)++;
762	+	if (possible_values)
763	+	val = possible_values[found];
764	+
765	+	switch(arg_type) {
766	+	case ARG_INT:
767	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
768	+	break;
769	+	case ARG_DOUBLE:
770	+	if (val) *((double *)field) = strtod (val, &stop_char);
771	+	break;
772	+	case ARG_STRING:
773	+	if (val) {
774	+	string_field = (char **)field;
775	+	if (!no_free && *string_field)
776	+	free (*string_field); /* free previous string */
777	+	*string_field = gengetopt_strdup (val);
778	+	}
779	+	break;
780	+	default:
781	+	break;
782	+	};
783	+
784	+	/* check numeric conversion */
785	+	switch(arg_type) {
786	+	case ARG_INT:
787	+	case ARG_DOUBLE:
788	+	if (val && !(stop_char && *stop_char == '\0')) {
789	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
790	+	return 1; /* failure */
791	+	}
792	+	break;
793	+	default:
794	+	;
795	+	};
796	+
797	+	/* store the original value */
798	+	switch(arg_type) {
799	+	case ARG_NO:
800	+	break;
801	+	default:
802	+	if (value && orig_field) {
803	+	if (no_free) {
804	+	*orig_field = value;
805	+	} else {
806	+	if (*orig_field)
807	+	free (*orig_field); /* free previous string */
808	+	*orig_field = gengetopt_strdup (value);
809	+	}
810	+	}
811	+	};
812	+
813	+	return 0; /* OK */
814	+	}
815	+
816	+
817	+	int
818	+	cmdline_parser_internal (
819	+	int argc, char **argv, struct gengetopt_args_info *args_info,
820	+	struct cmdline_parser_params *params, const char *additional_error)
821	+	{
822	+	int c;        /* Character of the parsed option.  */
823	+
824	+	int error = 0;
825	+	struct gengetopt_args_info local_args_info;
826	+
827	+	int override;
828	+	int initialize;
829	+	int check_required;
830	+	int check_ambiguity;
831	+
832	+	package_name = argv[0];
833	+
834	+	override = params->override;
835	+	initialize = params->initialize;
836	+	check_required = params->check_required;
837	+	check_ambiguity = params->check_ambiguity;
838	+
839	+	if (initialize)
840	+	cmdline_parser_init (args_info);
841	+
842	+	cmdline_parser_init (&local_args_info);
843	+
844		optarg = 0;
845	<	optind = 1;
846	<	opterr = 1;
845	>	optind = 0;
846	>	opterr = params->print_errors;
847		optopt = '?';
848
849		while (1)
850		{
851		int option_index = 0;
134	–	char *stop_char;
852
853		static struct option long_options[] = {
854		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 856 | cmdline_parser (int argc, char * const *argv, struct g
856		{ "input",      1, NULL, 'i' },
857		{ "output",     1, NULL, 'o' },
858		{ "step",       1, NULL, 'n' },
859	<	{ "nrbins",     1, NULL, 'r' },
859	>	{ "nbins",      1, NULL, 'b' },
860	>	{ "nbins_x",    1, NULL, 'x' },
861	>	{ "nbins_y",    1, NULL, 'y' },
862	>	{ "nbins_z",    1, NULL, 0 },
863		{ "nanglebins", 1, NULL, 'a' },
864	<	{ "length",     1, NULL, 'l' },
864	>	{ "rcut",       1, NULL, 'c' },
865	>	{ "dz", 1, NULL, 0 },
866	>	{ "length",     1, NULL, 0 },
867	>	{ "zlength",    1, NULL, 0 },
868	>	{ "zoffset",    1, NULL, 'z' },
869		{ "sele1",      1, NULL, 0 },
870		{ "sele2",      1, NULL, 0 },
871		{ "sele3",      1, NULL, 0 },
872		{ "refsele",    1, NULL, 0 },
873	+	{ "comsele",    1, NULL, 0 },
874	+	{ "seleoffset", 1, NULL, 0 },
875		{ "molname",    1, NULL, 0 },
876		{ "begin",      1, NULL, 0 },
877		{ "end",        1, NULL, 0 },
878	<	{ "gofr",       0, NULL, 0 },
878	>	{ "radius",     1, NULL, 0 },
879	>	{ "bo", 0, NULL, 0 },
880	>	{ "bor",        0, NULL, 0 },
881	>	{ "bad",        0, NULL, 0 },
882	>	{ "count",      0, NULL, 0 },
883	>	{ "gofr",       0, NULL, 'g' },
884	>	{ "gofz",       0, NULL, 0 },
885		{ "r_theta",    0, NULL, 0 },
886		{ "r_omega",    0, NULL, 0 },
887	+	{ "r_z",        0, NULL, 0 },
888		{ "theta_omega",        0, NULL, 0 },
889		{ "gxyz",       0, NULL, 0 },
890	<	{ "p2", 0, NULL, 0 },
891	<	{ "scd",        0, NULL, 0 },
892	<	{ "density",    0, NULL, 0 },
893	<	{ NULL, 0, NULL, 0 }
890	>	{ "twodgofr",   0, NULL, 0 },
891	>	{ "p2", 0, NULL, 'p' },
892	>	{ "rp2",        0, NULL, 0 },
893	>	{ "scd",        0, NULL, 's' },
894	>	{ "density",    0, NULL, 'd' },
895	>	{ "slab_density",       0, NULL, 0 },
896	>	{ "p_angle",    0, NULL, 0 },
897	>	{ "hxy",        0, NULL, 0 },
898	>	{ "rho_r",      0, NULL, 0 },
899	>	{ "angle_r",    0, NULL, 0 },
900	>	{ "hullvol",    0, NULL, 0 },
901	>	{ "rodlength",  0, NULL, 0 },
902	>	{ "tet_param",  0, NULL, 'Q' },
903	>	{ "tet_param_z",        0, NULL, 0 },
904	>	{ "rnemdz",     0, NULL, 0 },
905	>	{ "rnemdr",     0, NULL, 0 },
906	>	{ 0,  0, 0, 0 }
907		};
908
909	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
909	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
910
911		if (c == -1) break;       /* Exit from `while (1)' loop.  */
912
913		switch (c)
914		{
915		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
916		cmdline_parser_print_help ();
917	+	cmdline_parser_free (&local_args_info);
918		exit (EXIT_SUCCESS);
919
920		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
921		cmdline_parser_print_version ();
922	+	cmdline_parser_free (&local_args_info);
923		exit (EXIT_SUCCESS);
924
925		case 'i':       /* input dump file.  */
926	<	if (args_info->input_given)
927	<	{
928	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
929	<	clear_args ();
930	<	exit (EXIT_FAILURE);
931	<	}
932	<	args_info->input_given = 1;
933	<	args_info->input_arg = gengetopt_strdup (optarg);
926	>
927	>
928	>	if (update_arg( (void *)&(args_info->input_arg),
929	>	&(args_info->input_orig), &(args_info->input_given),
930	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
931	>	check_ambiguity, override, 0, 0,
932	>	"input", 'i',
933	>	additional_error))
934	>	goto failure;
935	>
936		break;
190	–
937		case 'o':       /* output file name.  */
938	<	if (args_info->output_given)
939	<	{
940	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
941	<	clear_args ();
942	<	exit (EXIT_FAILURE);
943	<	}
944	<	args_info->output_given = 1;
945	<	args_info->output_arg = gengetopt_strdup (optarg);
938	>
939	>
940	>	if (update_arg( (void *)&(args_info->output_arg),
941	>	&(args_info->output_orig), &(args_info->output_given),
942	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
943	>	check_ambiguity, override, 0, 0,
944	>	"output", 'o',
945	>	additional_error))
946	>	goto failure;
947	>
948		break;
201	–
949		case 'n':       /* process every n frame.  */
950	<	if (args_info->step_given)
951	<	{
952	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
953	<	clear_args ();
954	<	exit (EXIT_FAILURE);
955	<	}
956	<	args_info->step_given = 1;
957	<	args_info->step_arg = strtol (optarg,&stop_char,0);
950	>
951	>
952	>	if (update_arg( (void *)&(args_info->step_arg),
953	>	&(args_info->step_orig), &(args_info->step_given),
954	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
955	>	check_ambiguity, override, 0, 0,
956	>	"step", 'n',
957	>	additional_error))
958	>	goto failure;
959	>
960		break;
961	<
962	<	case 'r':       /* number of bins for distance.  */
963	<	if (args_info->nrbins_given)
964	<	{
965	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
966	<	clear_args ();
967	<	exit (EXIT_FAILURE);
968	<	}
969	<	args_info->nrbins_given = 1;
970	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
961	>	case 'b':       /* number of bins (general purpose).  */
962	>
963	>
964	>	if (update_arg( (void *)&(args_info->nbins_arg),
965	>	&(args_info->nbins_orig), &(args_info->nbins_given),
966	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
967	>	check_ambiguity, override, 0, 0,
968	>	"nbins", 'b',
969	>	additional_error))
970	>	goto failure;
971	>
972		break;
973	<
973	>	case 'x':       /* number of bins in x axis.  */
974	>
975	>
976	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
977	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
978	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
979	>	check_ambiguity, override, 0, 0,
980	>	"nbins_x", 'x',
981	>	additional_error))
982	>	goto failure;
983	>
984	>	break;
985	>	case 'y':       /* number of bins in y axis.  */
986	>
987	>
988	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
989	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
990	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
991	>	check_ambiguity, override, 0, 0,
992	>	"nbins_y", 'y',
993	>	additional_error))
994	>	goto failure;
995	>
996	>	break;
997		case 'a':       /* number of bins for cos(angle).  */
998	<	if (args_info->nanglebins_given)
999	<	{
1000	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1001	<	clear_args ();
1002	<	exit (EXIT_FAILURE);
1003	<	}
1004	<	args_info->nanglebins_given = 1;
1005	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
998	>
999	>
1000	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1001	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1002	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1003	>	check_ambiguity, override, 0, 0,
1004	>	"nanglebins", 'a',
1005	>	additional_error))
1006	>	goto failure;
1007	>
1008		break;
1009	<
1010	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1011	<	if (args_info->length_given)
1012	<	{
1013	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1014	<	clear_args ();
1015	<	exit (EXIT_FAILURE);
1016	<	}
1017	<	args_info->length_given = 1;
1018	<	args_info->length_arg = strtod (optarg, NULL);
1009	>	case 'c':       /* cutoff radius (rcut).  */
1010	>
1011	>
1012	>	if (update_arg( (void *)&(args_info->rcut_arg),
1013	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1014	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1015	>	check_ambiguity, override, 0, 0,
1016	>	"rcut", 'c',
1017	>	additional_error))
1018	>	goto failure;
1019	>
1020		break;
1021	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1022	+
1023	+
1024	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1025	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1026	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1027	+	check_ambiguity, override, 0, 0,
1028	+	"zoffset", 'z',
1029	+	additional_error))
1030	+	goto failure;
1031	+
1032	+	break;
1033	+	case 'g':       /* g(r).  */
1034	+
1035	+	if (args_info->staticProps_group_counter && override)
1036	+	reset_group_staticProps (args_info);
1037	+	args_info->staticProps_group_counter += 1;
1038	+
1039	+	if (update_arg( 0 ,
1040	+	0 , &(args_info->gofr_given),
1041	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1042	+	check_ambiguity, override, 0, 0,
1043	+	"gofr", 'g',
1044	+	additional_error))
1045	+	goto failure;
1046	+
1047	+	break;
1048	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1049	+
1050	+	if (args_info->staticProps_group_counter && override)
1051	+	reset_group_staticProps (args_info);
1052	+	args_info->staticProps_group_counter += 1;
1053	+
1054	+	if (update_arg( 0 ,
1055	+	0 , &(args_info->p2_given),
1056	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1057	+	check_ambiguity, override, 0, 0,
1058	+	"p2", 'p',
1059	+	additional_error))
1060	+	goto failure;
1061	+
1062	+	break;
1063	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1064	+
1065	+	if (args_info->staticProps_group_counter && override)
1066	+	reset_group_staticProps (args_info);
1067	+	args_info->staticProps_group_counter += 1;
1068	+
1069	+	if (update_arg( 0 ,
1070	+	0 , &(args_info->scd_given),
1071	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1072	+	check_ambiguity, override, 0, 0,
1073	+	"scd", 's',
1074	+	additional_error))
1075	+	goto failure;
1076	+
1077	+	break;
1078	+	case 'd':       /* density plot.  */
1079	+
1080	+	if (args_info->staticProps_group_counter && override)
1081	+	reset_group_staticProps (args_info);
1082	+	args_info->staticProps_group_counter += 1;
1083	+
1084	+	if (update_arg( 0 ,
1085	+	0 , &(args_info->density_given),
1086	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1087	+	check_ambiguity, override, 0, 0,
1088	+	"density", 'd',
1089	+	additional_error))
1090	+	goto failure;
1091	+
1092	+	break;
1093	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1094	+
1095	+	if (args_info->staticProps_group_counter && override)
1096	+	reset_group_staticProps (args_info);
1097	+	args_info->staticProps_group_counter += 1;
1098	+
1099	+	if (update_arg( 0 ,
1100	+	0 , &(args_info->tet_param_given),
1101	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1102	+	check_ambiguity, override, 0, 0,
1103	+	"tet_param", 'Q',
1104	+	additional_error))
1105	+	goto failure;
1106	+
1107	+	break;
1108
246	–
1109		case 0: /* Long option with no short option */
1110	<	/* select the first stuntdouble set.  */
1111	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1110	>	/* number of bins in z axis.  */
1111	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1112		{
1113	<	if (args_info->sele1_given)
1114	<	{
1115	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1116	<	clear_args ();
1117	<	exit (EXIT_FAILURE);
1118	<	}
1119	<	args_info->sele1_given = 1;
1120	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1121	<	break;
1113	>
1114	>
1115	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1116	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1117	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"nbins_z", '-',
1120	>	additional_error))
1121	>	goto failure;
1122	>
1123	>	}
1124	>	/* slab width (dz).  */
1125	>	else if (strcmp (long_options[option_index].name, "dz") == 0)
1126	>	{
1127	>
1128	>
1129	>	if (update_arg( (void *)&(args_info->dz_arg),
1130	>	&(args_info->dz_orig), &(args_info->dz_given),
1131	>	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1132	>	check_ambiguity, override, 0, 0,
1133	>	"dz", '-',
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, "length") == 0)
1140	+	{
1141
1142	+
1143	+	if (update_arg( (void *)&(args_info->length_arg),
1144	+	&(args_info->length_orig), &(args_info->length_given),
1145	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1146	+	check_ambiguity, override, 0, 0,
1147	+	"length", '-',
1148	+	additional_error))
1149	+	goto failure;
1150	+
1151	+	}
1152	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1153	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1154	+	{
1155	+
1156	+
1157	+	if (update_arg( (void *)&(args_info->zlength_arg),
1158	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1159	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1160	+	check_ambiguity, override, 0, 0,
1161	+	"zlength", '-',
1162	+	additional_error))
1163	+	goto failure;
1164	+
1165	+	}
1166	+	/* select the first stuntdouble set.  */
1167	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1168	+	{
1169	+
1170	+
1171	+	if (update_arg( (void *)&(args_info->sele1_arg),
1172	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1173	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1174	+	check_ambiguity, override, 0, 0,
1175	+	"sele1", '-',
1176	+	additional_error))
1177	+	goto failure;
1178	+
1179	+	}
1180		/* select the second stuntdouble set.  */
1181		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1182		{
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	–	}
1183
1184	+
1185	+	if (update_arg( (void *)&(args_info->sele2_arg),
1186	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1187	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1188	+	check_ambiguity, override, 0, 0,
1189	+	"sele2", '-',
1190	+	additional_error))
1191	+	goto failure;
1192	+
1193	+	}
1194		/* select the third stuntdouble set.  */
1195		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1196		{
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	–	}
1197
1198	+
1199	+	if (update_arg( (void *)&(args_info->sele3_arg),
1200	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1201	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1202	+	check_ambiguity, override, 0, 0,
1203	+	"sele3", '-',
1204	+	additional_error))
1205	+	goto failure;
1206	+
1207	+	}
1208		/* select reference (use and only use with --gxyz).  */
1209		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1210		{
1211	<	if (args_info->refsele_given)
1212	<	{
1213	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1214	<	clear_args ();
1215	<	exit (EXIT_FAILURE);
1216	<	}
1217	<	args_info->refsele_given = 1;
1218	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1219	<	break;
1211	>
1212	>
1213	>	if (update_arg( (void *)&(args_info->refsele_arg),
1214	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1215	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1216	>	check_ambiguity, override, 0, 0,
1217	>	"refsele", '-',
1218	>	additional_error))
1219	>	goto failure;
1220	>
1221		}
1222	+	/* select stunt doubles for center-of-mass reference point.  */
1223	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1224	+	{
1225
1226	+
1227	+	if (update_arg( (void *)&(args_info->comsele_arg),
1228	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1229	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1230	+	check_ambiguity, override, 0, 0,
1231	+	"comsele", '-',
1232	+	additional_error))
1233	+	goto failure;
1234	+
1235	+	}
1236	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1237	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1238	+	{
1239	+
1240	+
1241	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1242	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1243	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1244	+	check_ambiguity, override, 0, 0,
1245	+	"seleoffset", '-',
1246	+	additional_error))
1247	+	goto failure;
1248	+
1249	+	}
1250		/* molecule name.  */
1251		else if (strcmp (long_options[option_index].name, "molname") == 0)
1252		{
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	–	}
1253
1254	<	/* begin interanl index.  */
1254	>
1255	>	if (update_arg( (void *)&(args_info->molname_arg),
1256	>	&(args_info->molname_orig), &(args_info->molname_given),
1257	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1258	>	check_ambiguity, override, 0, 0,
1259	>	"molname", '-',
1260	>	additional_error))
1261	>	goto failure;
1262	>
1263	>	}
1264	>	/* begin internal index.  */
1265		else if (strcmp (long_options[option_index].name, "begin") == 0)
1266		{
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	–	}
1267
1268	+
1269	+	if (update_arg( (void *)&(args_info->begin_arg),
1270	+	&(args_info->begin_orig), &(args_info->begin_given),
1271	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1272	+	check_ambiguity, override, 0, 0,
1273	+	"begin", '-',
1274	+	additional_error))
1275	+	goto failure;
1276	+
1277	+	}
1278		/* end internal index.  */
1279		else if (strcmp (long_options[option_index].name, "end") == 0)
1280		{
1281	<	if (args_info->end_given)
1282	<	{
1283	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1284	<	clear_args ();
1285	<	exit (EXIT_FAILURE);
1286	<	}
1287	<	args_info->end_given = 1;
1288	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1289	<	break;
1281	>
1282	>
1283	>	if (update_arg( (void *)&(args_info->end_arg),
1284	>	&(args_info->end_orig), &(args_info->end_given),
1285	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1286	>	check_ambiguity, override, 0, 0,
1287	>	"end", '-',
1288	>	additional_error))
1289	>	goto failure;
1290	>
1291		}
1292	+	/* nanoparticle radius.  */
1293	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1294	+	{
1295
1296	<	/* g(r).  */
1297	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1296	>
1297	>	if (update_arg( (void *)&(args_info->radius_arg),
1298	>	&(args_info->radius_orig), &(args_info->radius_given),
1299	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1300	>	check_ambiguity, override, 0, 0,
1301	>	"radius", '-',
1302	>	additional_error))
1303	>	goto failure;
1304	>
1305	>	}
1306	>	/* bond order parameter (--rcut must be specified).  */
1307	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1308		{
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;
1309
1310	<	break;
1310	>	if (args_info->staticProps_group_counter && override)
1311	>	reset_group_staticProps (args_info);
1312	>	args_info->staticProps_group_counter += 1;
1313	>
1314	>	if (update_arg( 0 ,
1315	>	0 , &(args_info->bo_given),
1316	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1317	>	check_ambiguity, override, 0, 0,
1318	>	"bo", '-',
1319	>	additional_error))
1320	>	goto failure;
1321	>
1322		}
1323	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1324	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1325	+	{
1326
1327	+	if (args_info->staticProps_group_counter && override)
1328	+	reset_group_staticProps (args_info);
1329	+	args_info->staticProps_group_counter += 1;
1330	+
1331	+	if (update_arg( 0 ,
1332	+	0 , &(args_info->bor_given),
1333	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1334	+	check_ambiguity, override, 0, 0,
1335	+	"bor", '-',
1336	+	additional_error))
1337	+	goto failure;
1338	+
1339	+	}
1340	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1341	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1342	+	{
1343	+
1344	+	if (args_info->staticProps_group_counter && override)
1345	+	reset_group_staticProps (args_info);
1346	+	args_info->staticProps_group_counter += 1;
1347	+
1348	+	if (update_arg( 0 ,
1349	+	0 , &(args_info->bad_given),
1350	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1351	+	check_ambiguity, override, 0, 0,
1352	+	"bad", '-',
1353	+	additional_error))
1354	+	goto failure;
1355	+
1356	+	}
1357	+	/* count of molecules matching selection criteria (and associated statistics).  */
1358	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1359	+	{
1360	+
1361	+	if (args_info->staticProps_group_counter && override)
1362	+	reset_group_staticProps (args_info);
1363	+	args_info->staticProps_group_counter += 1;
1364	+
1365	+	if (update_arg( 0 ,
1366	+	0 , &(args_info->count_given),
1367	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1368	+	check_ambiguity, override, 0, 0,
1369	+	"count", '-',
1370	+	additional_error))
1371	+	goto failure;
1372	+
1373	+	}
1374	+	/* g(z).  */
1375	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1376	+	{
1377	+
1378	+	if (args_info->staticProps_group_counter && override)
1379	+	reset_group_staticProps (args_info);
1380	+	args_info->staticProps_group_counter += 1;
1381	+
1382	+	if (update_arg( 0 ,
1383	+	0 , &(args_info->gofz_given),
1384	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1385	+	check_ambiguity, override, 0, 0,
1386	+	"gofz", '-',
1387	+	additional_error))
1388	+	goto failure;
1389	+
1390	+	}
1391		/* g(r, cos(theta)).  */
1392		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1393		{
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;
1394
1395	<	break;
1396	<	}
1395	>	if (args_info->staticProps_group_counter && override)
1396	>	reset_group_staticProps (args_info);
1397	>	args_info->staticProps_group_counter += 1;
1398
1399	+	if (update_arg( 0 ,
1400	+	0 , &(args_info->r_theta_given),
1401	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1402	+	check_ambiguity, override, 0, 0,
1403	+	"r_theta", '-',
1404	+	additional_error))
1405	+	goto failure;
1406	+
1407	+	}
1408		/* g(r, cos(omega)).  */
1409		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1410		{
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;
1411
1412	<	break;
1412	>	if (args_info->staticProps_group_counter && override)
1413	>	reset_group_staticProps (args_info);
1414	>	args_info->staticProps_group_counter += 1;
1415	>
1416	>	if (update_arg( 0 ,
1417	>	0 , &(args_info->r_omega_given),
1418	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1419	>	check_ambiguity, override, 0, 0,
1420	>	"r_omega", '-',
1421	>	additional_error))
1422	>	goto failure;
1423	>
1424		}
1425	+	/* g(r, z).  */
1426	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1427	+	{
1428
1429	+	if (args_info->staticProps_group_counter && override)
1430	+	reset_group_staticProps (args_info);
1431	+	args_info->staticProps_group_counter += 1;
1432	+
1433	+	if (update_arg( 0 ,
1434	+	0 , &(args_info->r_z_given),
1435	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1436	+	check_ambiguity, override, 0, 0,
1437	+	"r_z", '-',
1438	+	additional_error))
1439	+	goto failure;
1440	+
1441	+	}
1442		/* g(cos(theta), cos(omega)).  */
1443		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1444		{
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;
1445
1446	<	break;
1447	<	}
1446	>	if (args_info->staticProps_group_counter && override)
1447	>	reset_group_staticProps (args_info);
1448	>	args_info->staticProps_group_counter += 1;
1449
1450	+	if (update_arg( 0 ,
1451	+	0 , &(args_info->theta_omega_given),
1452	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1453	+	check_ambiguity, override, 0, 0,
1454	+	"theta_omega", '-',
1455	+	additional_error))
1456	+	goto failure;
1457	+
1458	+	}
1459		/* g(x, y, z).  */
1460		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1461		{
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;
1462
1463	<	break;
1463	>	if (args_info->staticProps_group_counter && override)
1464	>	reset_group_staticProps (args_info);
1465	>	args_info->staticProps_group_counter += 1;
1466	>
1467	>	if (update_arg( 0 ,
1468	>	0 , &(args_info->gxyz_given),
1469	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1470	>	check_ambiguity, override, 0, 0,
1471	>	"gxyz", '-',
1472	>	additional_error))
1473	>	goto failure;
1474	>
1475		}
1476	+	/* 2D g(r) (Slab width --dz must be specified).  */
1477	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1478	+	{
1479
1480	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1481	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1480	>	if (args_info->staticProps_group_counter && override)
1481	>	reset_group_staticProps (args_info);
1482	>	args_info->staticProps_group_counter += 1;
1483	>
1484	>	if (update_arg( 0 ,
1485	>	0 , &(args_info->twodgofr_given),
1486	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1487	>	check_ambiguity, override, 0, 0,
1488	>	"twodgofr", '-',
1489	>	additional_error))
1490	>	goto failure;
1491	>
1492	>	}
1493	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1494	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1495		{
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;
1496
1497	<	break;
1497	>	if (args_info->staticProps_group_counter && override)
1498	>	reset_group_staticProps (args_info);
1499	>	args_info->staticProps_group_counter += 1;
1500	>
1501	>	if (update_arg( 0 ,
1502	>	0 , &(args_info->rp2_given),
1503	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1504	>	check_ambiguity, override, 0, 0,
1505	>	"rp2", '-',
1506	>	additional_error))
1507	>	goto failure;
1508	>
1509		}
1510	+	/* slab density.  */
1511	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1512	+	{
1513
1514	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1515	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1514	>	if (args_info->staticProps_group_counter && override)
1515	>	reset_group_staticProps (args_info);
1516	>	args_info->staticProps_group_counter += 1;
1517	>
1518	>	if (update_arg( 0 ,
1519	>	0 , &(args_info->slab_density_given),
1520	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1521	>	check_ambiguity, override, 0, 0,
1522	>	"slab_density", '-',
1523	>	additional_error))
1524	>	goto failure;
1525	>
1526	>	}
1527	>	/* p(cos(theta)).  */
1528	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1529		{
1530	<	if (args_info->scd_given)
1531	<	{
1532	<	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1533	<	clear_args ();
437	<	exit (EXIT_FAILURE);
438	<	}
439	<	args_info->scd_given = 1; staticProps_group_counter += 1;
1530	>
1531	>	if (args_info->staticProps_group_counter && override)
1532	>	reset_group_staticProps (args_info);
1533	>	args_info->staticProps_group_counter += 1;
1534
1535	<	break;
1535	>	if (update_arg( 0 ,
1536	>	0 , &(args_info->p_angle_given),
1537	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1538	>	check_ambiguity, override, 0, 0,
1539	>	"p_angle", '-',
1540	>	additional_error))
1541	>	goto failure;
1542	>
1543		}
1544	+	/* hxy.  */
1545	+	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1546	+	{
1547
1548	<	/* density plot (--sele1 must be specified).  */
1549	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1548	>	if (args_info->staticProps_group_counter && override)
1549	>	reset_group_staticProps (args_info);
1550	>	args_info->staticProps_group_counter += 1;
1551	>
1552	>	if (update_arg( 0 ,
1553	>	0 , &(args_info->hxy_given),
1554	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1555	>	check_ambiguity, override, 0, 0,
1556	>	"hxy", '-',
1557	>	additional_error))
1558	>	goto failure;
1559	>
1560	>	}
1561	>	/* rho of R.  */
1562	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1563		{
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;
1564
1565	<	break;
1565	>	if (args_info->staticProps_group_counter && override)
1566	>	reset_group_staticProps (args_info);
1567	>	args_info->staticProps_group_counter += 1;
1568	>
1569	>	if (update_arg( 0 ,
1570	>	0 , &(args_info->rho_r_given),
1571	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1572	>	check_ambiguity, override, 0, 0,
1573	>	"rho_r", '-',
1574	>	additional_error))
1575	>	goto failure;
1576	>
1577		}
1578	+	/* angle of R.  */
1579	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1580	+	{
1581
1582	<
1582	>	if (args_info->staticProps_group_counter && override)
1583	>	reset_group_staticProps (args_info);
1584	>	args_info->staticProps_group_counter += 1;
1585	>
1586	>	if (update_arg( 0 ,
1587	>	0 , &(args_info->angle_r_given),
1588	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1589	>	check_ambiguity, override, 0, 0,
1590	>	"angle_r", '-',
1591	>	additional_error))
1592	>	goto failure;
1593	>
1594	>	}
1595	>	/* hull volume of nanoparticle.  */
1596	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1597	>	{
1598	>
1599	>	if (args_info->staticProps_group_counter && override)
1600	>	reset_group_staticProps (args_info);
1601	>	args_info->staticProps_group_counter += 1;
1602	>
1603	>	if (update_arg( 0 ,
1604	>	0 , &(args_info->hullvol_given),
1605	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1606	>	check_ambiguity, override, 0, 0,
1607	>	"hullvol", '-',
1608	>	additional_error))
1609	>	goto failure;
1610	>
1611	>	}
1612	>	/* length of nanorod.  */
1613	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1614	>	{
1615	>
1616	>	if (args_info->staticProps_group_counter && override)
1617	>	reset_group_staticProps (args_info);
1618	>	args_info->staticProps_group_counter += 1;
1619	>
1620	>	if (update_arg( 0 ,
1621	>	0 , &(args_info->rodlength_given),
1622	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1623	>	check_ambiguity, override, 0, 0,
1624	>	"rodlength", '-',
1625	>	additional_error))
1626	>	goto failure;
1627	>
1628	>	}
1629	>	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1630	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1631	>	{
1632	>
1633	>	if (args_info->staticProps_group_counter && override)
1634	>	reset_group_staticProps (args_info);
1635	>	args_info->staticProps_group_counter += 1;
1636	>
1637	>	if (update_arg( 0 ,
1638	>	0 , &(args_info->tet_param_z_given),
1639	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1640	>	check_ambiguity, override, 0, 0,
1641	>	"tet_param_z", '-',
1642	>	additional_error))
1643	>	goto failure;
1644	>
1645	>	}
1646	>	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1647	>	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1648	>	{
1649	>
1650	>	if (args_info->staticProps_group_counter && override)
1651	>	reset_group_staticProps (args_info);
1652	>	args_info->staticProps_group_counter += 1;
1653	>
1654	>	if (update_arg( 0 ,
1655	>	0 , &(args_info->rnemdz_given),
1656	>	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1657	>	check_ambiguity, override, 0, 0,
1658	>	"rnemdz", '-',
1659	>	additional_error))
1660	>	goto failure;
1661	>
1662	>	}
1663	>	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1664	>	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1665	>	{
1666	>
1667	>	if (args_info->staticProps_group_counter && override)
1668	>	reset_group_staticProps (args_info);
1669	>	args_info->staticProps_group_counter += 1;
1670	>
1671	>	if (update_arg( 0 ,
1672	>	0 , &(args_info->rnemdr_given),
1673	>	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1674	>	check_ambiguity, override, 0, 0,
1675	>	"rnemdr", '-',
1676	>	additional_error))
1677	>	goto failure;
1678	>
1679	>	}
1680	>
1681	>	break;
1682		case '?':       /* Invalid option.  */
1683		/* `getopt_long' already printed an error message.  */
1684	<	exit (EXIT_FAILURE);
1684	>	goto failure;
1685
1686		default:        /* bug: option not considered.  */
1687	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1687	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1688		abort ();
1689		} /* switch */
1690		} /* while */
1691
1692	<	if ( staticProps_group_counter != 1)
1692	>	if (args_info->staticProps_group_counter > 1)
1693		{
1694	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1695	<	missing_required_options = 1;
1694	>	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 : ""));
1695	>	error = 1;
1696		}
1697
1698
1699	<	if (! args_info->input_given)
1699	>
1700	>	if (check_required)
1701		{
1702	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1702	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1703		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1704
1705	+	cmdline_parser_release (&local_args_info);
1706	+
1707	+	if ( error )
1708	+	return (EXIT_FAILURE);
1709	+
1710	+	if (optind < argc)
1711	+	{
1712	+	int i = 0 ;
1713	+	int found_prog_name = 0;
1714	+	/* whether program name, i.e., argv[0], is in the remaining args
1715	+	(this may happen with some implementations of getopt,
1716	+	but surely not with the one included by gengetopt) */
1717	+
1718	+	i = optind;
1719	+	while (i < argc)
1720	+	if (argv[i++] == argv[0]) {
1721	+	found_prog_name = 1;
1722	+	break;
1723	+	}
1724	+	i = 0;
1725	+
1726	+	args_info->inputs_num = argc - optind - found_prog_name;
1727	+	args_info->inputs =
1728	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1729	+	while (optind < argc)
1730	+	if (argv[optind++] != argv[0])
1731	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1732	+	}
1733	+
1734		return 0;
1735	+
1736	+	failure:
1737	+
1738	+	cmdline_parser_release (&local_args_info);
1739	+	return (EXIT_FAILURE);
1740		}

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 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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