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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 1992 by gezelter, Thu Apr 24 17:30:00 2014 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	>	"      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
61	>	"      --molname=STRING          molecule name",
62	>	"      --begin=INT               begin internal index",
63	>	"      --end=INT                 end internal index",
64	>	"      --radius=DOUBLE           nanoparticle radius",
65	>	"\n Group: staticProps\n   an option of this group is required",
66	>	"      --bo                      bond order parameter (--rcut must be specified)",
67	>	"      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
68	>	"      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
69	>	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
70	>	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
71	>	"  -g, --gofr                    g(r)",
72	>	"      --gofz                    g(z)",
73	>	"      --r_theta                 g(r, cos(theta))",
74	>	"      --r_omega                 g(r, cos(omega))",
75	>	"      --r_z                     g(r, z)",
76	>	"      --theta_omega             g(cos(theta), cos(omega))",
77	>	"      --gxyz                    g(x, y, z)",
78	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
79	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
80	>	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
81	>	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
82	>	"  -d, --density                 density plot",
83	>	"      --slab_density            slab density",
84	>	"      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
85	>	"      --hxy                     hxy",
86	>	"      --rho_r                   rho of R",
87	>	"      --angle_r                 angle of R",
88	>	"      --hullvol                 hull volume of nanoparticle",
89	>	"      --rodlength               length of nanorod",
90	>	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
91	>	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
92	>	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
93	>	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
94	>	"      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
95	>	0
96	>	};
97
98	<	/* gengetopt_strdup() */
99	<	/* strdup.c replacement of strdup, which is not standard */
100	<	char *
101	<	gengetopt_strdup (const char *s)
102	<	{
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	<	}
98	>	typedef enum {ARG_NO
99	>	, ARG_STRING
100	>	, ARG_INT
101	>	, ARG_DOUBLE
102	>	} cmdline_parser_arg_type;
103
104	<	int
105	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
106	<	{
107	<	int c;        /* Character of the parsed option.  */
84	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
86	<
104	>	static
105	>	void clear_given (struct gengetopt_args_info *args_info);
106	>	static
107	>	void clear_args (struct gengetopt_args_info *args_info);
108
109	+	static int
110	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
111	+	struct cmdline_parser_params *params, const char *additional_error);
112	+
113	+	static int
114	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
115	+
116	+	static char *
117	+	gengetopt_strdup (const char *s);
118	+
119	+	static
120	+	void clear_given (struct gengetopt_args_info *args_info)
121	+	{
122		args_info->help_given = 0 ;
123		args_info->version_given = 0 ;
124		args_info->input_given = 0 ;
125		args_info->output_given = 0 ;
126		args_info->step_given = 0 ;
127	<	args_info->nrbins_given = 0 ;
127	>	args_info->nbins_given = 0 ;
128	>	args_info->nbins_x_given = 0 ;
129	>	args_info->nbins_y_given = 0 ;
130	>	args_info->nbins_z_given = 0 ;
131		args_info->nanglebins_given = 0 ;
132	+	args_info->rcut_given = 0 ;
133	+	args_info->dz_given = 0 ;
134		args_info->length_given = 0 ;
135	+	args_info->zlength_given = 0 ;
136	+	args_info->zoffset_given = 0 ;
137		args_info->sele1_given = 0 ;
138		args_info->sele2_given = 0 ;
139		args_info->sele3_given = 0 ;
140		args_info->refsele_given = 0 ;
141	+	args_info->comsele_given = 0 ;
142	+	args_info->seleoffset_given = 0 ;
143	+	args_info->seleoffset2_given = 0 ;
144		args_info->molname_given = 0 ;
145		args_info->begin_given = 0 ;
146		args_info->end_given = 0 ;
147	+	args_info->radius_given = 0 ;
148	+	args_info->bo_given = 0 ;
149	+	args_info->ior_given = 0 ;
150	+	args_info->for_given = 0 ;
151	+	args_info->bad_given = 0 ;
152	+	args_info->count_given = 0 ;
153		args_info->gofr_given = 0 ;
154	+	args_info->gofz_given = 0 ;
155		args_info->r_theta_given = 0 ;
156		args_info->r_omega_given = 0 ;
157	+	args_info->r_z_given = 0 ;
158		args_info->theta_omega_given = 0 ;
159		args_info->gxyz_given = 0 ;
160	+	args_info->twodgofr_given = 0 ;
161		args_info->p2_given = 0 ;
162	+	args_info->rp2_given = 0 ;
163		args_info->scd_given = 0 ;
164		args_info->density_given = 0 ;
165	<	#define clear_args() { \
166	<	args_info->input_arg = NULL; \
167	<	args_info->output_arg = NULL; \
168	<	args_info->step_arg = 1 ;\
169	<	args_info->nrbins_arg = 100 ;\
170	<	args_info->nanglebins_arg = 50 ;\
171	<	args_info->sele1_arg = NULL; \
172	<	args_info->sele2_arg = NULL; \
173	<	args_info->sele3_arg = NULL; \
174	<	args_info->refsele_arg = NULL; \
175	<	args_info->molname_arg = NULL; \
165	>	args_info->slab_density_given = 0 ;
166	>	args_info->p_angle_given = 0 ;
167	>	args_info->hxy_given = 0 ;
168	>	args_info->rho_r_given = 0 ;
169	>	args_info->angle_r_given = 0 ;
170	>	args_info->hullvol_given = 0 ;
171	>	args_info->rodlength_given = 0 ;
172	>	args_info->tet_param_given = 0 ;
173	>	args_info->tet_param_z_given = 0 ;
174	>	args_info->rnemdz_given = 0 ;
175	>	args_info->rnemdr_given = 0 ;
176	>	args_info->rnemdrt_given = 0 ;
177	>	args_info->staticProps_group_counter = 0 ;
178		}
179
180	<	clear_args();
180	>	static
181	>	void clear_args (struct gengetopt_args_info *args_info)
182	>	{
183	>	FIX_UNUSED (args_info);
184	>	args_info->input_arg = NULL;
185	>	args_info->input_orig = NULL;
186	>	args_info->output_arg = NULL;
187	>	args_info->output_orig = NULL;
188	>	args_info->step_arg = 1;
189	>	args_info->step_orig = NULL;
190	>	args_info->nbins_arg = 100;
191	>	args_info->nbins_orig = NULL;
192	>	args_info->nbins_x_arg = 100;
193	>	args_info->nbins_x_orig = NULL;
194	>	args_info->nbins_y_arg = 100;
195	>	args_info->nbins_y_orig = NULL;
196	>	args_info->nbins_z_arg = 100;
197	>	args_info->nbins_z_orig = NULL;
198	>	args_info->nanglebins_arg = 50;
199	>	args_info->nanglebins_orig = NULL;
200	>	args_info->rcut_orig = NULL;
201	>	args_info->dz_orig = NULL;
202	>	args_info->length_orig = NULL;
203	>	args_info->zlength_orig = NULL;
204	>	args_info->zoffset_arg = 0;
205	>	args_info->zoffset_orig = NULL;
206	>	args_info->sele1_arg = NULL;
207	>	args_info->sele1_orig = NULL;
208	>	args_info->sele2_arg = NULL;
209	>	args_info->sele2_orig = NULL;
210	>	args_info->sele3_arg = NULL;
211	>	args_info->sele3_orig = NULL;
212	>	args_info->refsele_arg = NULL;
213	>	args_info->refsele_orig = NULL;
214	>	args_info->comsele_arg = NULL;
215	>	args_info->comsele_orig = NULL;
216	>	args_info->seleoffset_orig = NULL;
217	>	args_info->seleoffset2_orig = NULL;
218	>	args_info->molname_arg = NULL;
219	>	args_info->molname_orig = NULL;
220	>	args_info->begin_orig = NULL;
221	>	args_info->end_orig = NULL;
222	>	args_info->radius_orig = NULL;
223	>
224	>	}
225
226	+	static
227	+	void init_args_info(struct gengetopt_args_info *args_info)
228	+	{
229	+
230	+
231	+	args_info->help_help = gengetopt_args_info_help[0] ;
232	+	args_info->version_help = gengetopt_args_info_help[1] ;
233	+	args_info->input_help = gengetopt_args_info_help[2] ;
234	+	args_info->output_help = gengetopt_args_info_help[3] ;
235	+	args_info->step_help = gengetopt_args_info_help[4] ;
236	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
237	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
238	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
239	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
240	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
241	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
242	+	args_info->dz_help = gengetopt_args_info_help[11] ;
243	+	args_info->length_help = gengetopt_args_info_help[12] ;
244	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
245	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
246	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
247	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
248	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
249	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
250	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
251	+	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
252	+	args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
253	+	args_info->molname_help = gengetopt_args_info_help[22] ;
254	+	args_info->begin_help = gengetopt_args_info_help[23] ;
255	+	args_info->end_help = gengetopt_args_info_help[24] ;
256	+	args_info->radius_help = gengetopt_args_info_help[25] ;
257	+	args_info->bo_help = gengetopt_args_info_help[27] ;
258	+	args_info->ior_help = gengetopt_args_info_help[28] ;
259	+	args_info->for_help = gengetopt_args_info_help[29] ;
260	+	args_info->bad_help = gengetopt_args_info_help[30] ;
261	+	args_info->count_help = gengetopt_args_info_help[31] ;
262	+	args_info->gofr_help = gengetopt_args_info_help[32] ;
263	+	args_info->gofz_help = gengetopt_args_info_help[33] ;
264	+	args_info->r_theta_help = gengetopt_args_info_help[34] ;
265	+	args_info->r_omega_help = gengetopt_args_info_help[35] ;
266	+	args_info->r_z_help = gengetopt_args_info_help[36] ;
267	+	args_info->theta_omega_help = gengetopt_args_info_help[37] ;
268	+	args_info->gxyz_help = gengetopt_args_info_help[38] ;
269	+	args_info->twodgofr_help = gengetopt_args_info_help[39] ;
270	+	args_info->p2_help = gengetopt_args_info_help[40] ;
271	+	args_info->rp2_help = gengetopt_args_info_help[41] ;
272	+	args_info->scd_help = gengetopt_args_info_help[42] ;
273	+	args_info->density_help = gengetopt_args_info_help[43] ;
274	+	args_info->slab_density_help = gengetopt_args_info_help[44] ;
275	+	args_info->p_angle_help = gengetopt_args_info_help[45] ;
276	+	args_info->hxy_help = gengetopt_args_info_help[46] ;
277	+	args_info->rho_r_help = gengetopt_args_info_help[47] ;
278	+	args_info->angle_r_help = gengetopt_args_info_help[48] ;
279	+	args_info->hullvol_help = gengetopt_args_info_help[49] ;
280	+	args_info->rodlength_help = gengetopt_args_info_help[50] ;
281	+	args_info->tet_param_help = gengetopt_args_info_help[51] ;
282	+	args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
283	+	args_info->rnemdz_help = gengetopt_args_info_help[53] ;
284	+	args_info->rnemdr_help = gengetopt_args_info_help[54] ;
285	+	args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
286	+
287	+	}
288	+
289	+	void
290	+	cmdline_parser_print_version (void)
291	+	{
292	+	printf ("%s %s\n",
293	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
294	+	CMDLINE_PARSER_VERSION);
295	+	}
296	+
297	+	static void print_help_common(void) {
298	+	cmdline_parser_print_version ();
299	+
300	+	if (strlen(gengetopt_args_info_purpose) > 0)
301	+	printf("\n%s\n", gengetopt_args_info_purpose);
302	+
303	+	if (strlen(gengetopt_args_info_usage) > 0)
304	+	printf("\n%s\n", gengetopt_args_info_usage);
305	+
306	+	printf("\n");
307	+
308	+	if (strlen(gengetopt_args_info_description) > 0)
309	+	printf("%s\n\n", gengetopt_args_info_description);
310	+	}
311	+
312	+	void
313	+	cmdline_parser_print_help (void)
314	+	{
315	+	int i = 0;
316	+	print_help_common();
317	+	while (gengetopt_args_info_help[i])
318	+	printf("%s\n", gengetopt_args_info_help[i++]);
319	+	}
320	+
321	+	void
322	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
323	+	{
324	+	clear_given (args_info);
325	+	clear_args (args_info);
326	+	init_args_info (args_info);
327	+
328	+	args_info->inputs = 0;
329	+	args_info->inputs_num = 0;
330	+	}
331	+
332	+	void
333	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
334	+	{
335	+	if (params)
336	+	{
337	+	params->override = 0;
338	+	params->initialize = 1;
339	+	params->check_required = 1;
340	+	params->check_ambiguity = 0;
341	+	params->print_errors = 1;
342	+	}
343	+	}
344	+
345	+	struct cmdline_parser_params *
346	+	cmdline_parser_params_create(void)
347	+	{
348	+	struct cmdline_parser_params *params =
349	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
350	+	cmdline_parser_params_init(params);
351	+	return params;
352	+	}
353	+
354	+	static void
355	+	free_string_field (char **s)
356	+	{
357	+	if (*s)
358	+	{
359	+	free (*s);
360	+	*s = 0;
361	+	}
362	+	}
363	+
364	+
365	+	static void
366	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
367	+	{
368	+	unsigned int i;
369	+	free_string_field (&(args_info->input_arg));
370	+	free_string_field (&(args_info->input_orig));
371	+	free_string_field (&(args_info->output_arg));
372	+	free_string_field (&(args_info->output_orig));
373	+	free_string_field (&(args_info->step_orig));
374	+	free_string_field (&(args_info->nbins_orig));
375	+	free_string_field (&(args_info->nbins_x_orig));
376	+	free_string_field (&(args_info->nbins_y_orig));
377	+	free_string_field (&(args_info->nbins_z_orig));
378	+	free_string_field (&(args_info->nanglebins_orig));
379	+	free_string_field (&(args_info->rcut_orig));
380	+	free_string_field (&(args_info->dz_orig));
381	+	free_string_field (&(args_info->length_orig));
382	+	free_string_field (&(args_info->zlength_orig));
383	+	free_string_field (&(args_info->zoffset_orig));
384	+	free_string_field (&(args_info->sele1_arg));
385	+	free_string_field (&(args_info->sele1_orig));
386	+	free_string_field (&(args_info->sele2_arg));
387	+	free_string_field (&(args_info->sele2_orig));
388	+	free_string_field (&(args_info->sele3_arg));
389	+	free_string_field (&(args_info->sele3_orig));
390	+	free_string_field (&(args_info->refsele_arg));
391	+	free_string_field (&(args_info->refsele_orig));
392	+	free_string_field (&(args_info->comsele_arg));
393	+	free_string_field (&(args_info->comsele_orig));
394	+	free_string_field (&(args_info->seleoffset_orig));
395	+	free_string_field (&(args_info->seleoffset2_orig));
396	+	free_string_field (&(args_info->molname_arg));
397	+	free_string_field (&(args_info->molname_orig));
398	+	free_string_field (&(args_info->begin_orig));
399	+	free_string_field (&(args_info->end_orig));
400	+	free_string_field (&(args_info->radius_orig));
401	+
402	+
403	+	for (i = 0; i < args_info->inputs_num; ++i)
404	+	free (args_info->inputs [i]);
405	+
406	+	if (args_info->inputs_num)
407	+	free (args_info->inputs);
408	+
409	+	clear_given (args_info);
410	+	}
411	+
412	+
413	+	static void
414	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
415	+	{
416	+	FIX_UNUSED (values);
417	+	if (arg) {
418	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
419	+	} else {
420	+	fprintf(outfile, "%s\n", opt);
421	+	}
422	+	}
423	+
424	+
425	+	int
426	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
427	+	{
428	+	int i = 0;
429	+
430	+	if (!outfile)
431	+	{
432	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
433	+	return EXIT_FAILURE;
434	+	}
435	+
436	+	if (args_info->help_given)
437	+	write_into_file(outfile, "help", 0, 0 );
438	+	if (args_info->version_given)
439	+	write_into_file(outfile, "version", 0, 0 );
440	+	if (args_info->input_given)
441	+	write_into_file(outfile, "input", args_info->input_orig, 0);
442	+	if (args_info->output_given)
443	+	write_into_file(outfile, "output", args_info->output_orig, 0);
444	+	if (args_info->step_given)
445	+	write_into_file(outfile, "step", args_info->step_orig, 0);
446	+	if (args_info->nbins_given)
447	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
448	+	if (args_info->nbins_x_given)
449	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
450	+	if (args_info->nbins_y_given)
451	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
452	+	if (args_info->nbins_z_given)
453	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
454	+	if (args_info->nanglebins_given)
455	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
456	+	if (args_info->rcut_given)
457	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
458	+	if (args_info->dz_given)
459	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
460	+	if (args_info->length_given)
461	+	write_into_file(outfile, "length", args_info->length_orig, 0);
462	+	if (args_info->zlength_given)
463	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
464	+	if (args_info->zoffset_given)
465	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
466	+	if (args_info->sele1_given)
467	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
468	+	if (args_info->sele2_given)
469	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
470	+	if (args_info->sele3_given)
471	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
472	+	if (args_info->refsele_given)
473	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
474	+	if (args_info->comsele_given)
475	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
476	+	if (args_info->seleoffset_given)
477	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
478	+	if (args_info->seleoffset2_given)
479	+	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
480	+	if (args_info->molname_given)
481	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
482	+	if (args_info->begin_given)
483	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
484	+	if (args_info->end_given)
485	+	write_into_file(outfile, "end", args_info->end_orig, 0);
486	+	if (args_info->radius_given)
487	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
488	+	if (args_info->bo_given)
489	+	write_into_file(outfile, "bo", 0, 0 );
490	+	if (args_info->ior_given)
491	+	write_into_file(outfile, "ior", 0, 0 );
492	+	if (args_info->for_given)
493	+	write_into_file(outfile, "for", 0, 0 );
494	+	if (args_info->bad_given)
495	+	write_into_file(outfile, "bad", 0, 0 );
496	+	if (args_info->count_given)
497	+	write_into_file(outfile, "count", 0, 0 );
498	+	if (args_info->gofr_given)
499	+	write_into_file(outfile, "gofr", 0, 0 );
500	+	if (args_info->gofz_given)
501	+	write_into_file(outfile, "gofz", 0, 0 );
502	+	if (args_info->r_theta_given)
503	+	write_into_file(outfile, "r_theta", 0, 0 );
504	+	if (args_info->r_omega_given)
505	+	write_into_file(outfile, "r_omega", 0, 0 );
506	+	if (args_info->r_z_given)
507	+	write_into_file(outfile, "r_z", 0, 0 );
508	+	if (args_info->theta_omega_given)
509	+	write_into_file(outfile, "theta_omega", 0, 0 );
510	+	if (args_info->gxyz_given)
511	+	write_into_file(outfile, "gxyz", 0, 0 );
512	+	if (args_info->twodgofr_given)
513	+	write_into_file(outfile, "twodgofr", 0, 0 );
514	+	if (args_info->p2_given)
515	+	write_into_file(outfile, "p2", 0, 0 );
516	+	if (args_info->rp2_given)
517	+	write_into_file(outfile, "rp2", 0, 0 );
518	+	if (args_info->scd_given)
519	+	write_into_file(outfile, "scd", 0, 0 );
520	+	if (args_info->density_given)
521	+	write_into_file(outfile, "density", 0, 0 );
522	+	if (args_info->slab_density_given)
523	+	write_into_file(outfile, "slab_density", 0, 0 );
524	+	if (args_info->p_angle_given)
525	+	write_into_file(outfile, "p_angle", 0, 0 );
526	+	if (args_info->hxy_given)
527	+	write_into_file(outfile, "hxy", 0, 0 );
528	+	if (args_info->rho_r_given)
529	+	write_into_file(outfile, "rho_r", 0, 0 );
530	+	if (args_info->angle_r_given)
531	+	write_into_file(outfile, "angle_r", 0, 0 );
532	+	if (args_info->hullvol_given)
533	+	write_into_file(outfile, "hullvol", 0, 0 );
534	+	if (args_info->rodlength_given)
535	+	write_into_file(outfile, "rodlength", 0, 0 );
536	+	if (args_info->tet_param_given)
537	+	write_into_file(outfile, "tet_param", 0, 0 );
538	+	if (args_info->tet_param_z_given)
539	+	write_into_file(outfile, "tet_param_z", 0, 0 );
540	+	if (args_info->rnemdz_given)
541	+	write_into_file(outfile, "rnemdz", 0, 0 );
542	+	if (args_info->rnemdr_given)
543	+	write_into_file(outfile, "rnemdr", 0, 0 );
544	+	if (args_info->rnemdrt_given)
545	+	write_into_file(outfile, "rnemdrt", 0, 0 );
546	+
547	+
548	+	i = EXIT_SUCCESS;
549	+	return i;
550	+	}
551	+
552	+	int
553	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
554	+	{
555	+	FILE *outfile;
556	+	int i = 0;
557	+
558	+	outfile = fopen(filename, "w");
559	+
560	+	if (!outfile)
561	+	{
562	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
563	+	return EXIT_FAILURE;
564	+	}
565	+
566	+	i = cmdline_parser_dump(outfile, args_info);
567	+	fclose (outfile);
568	+
569	+	return i;
570	+	}
571	+
572	+	void
573	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
574	+	{
575	+	cmdline_parser_release (args_info);
576	+	}
577	+
578	+	/** @brief replacement of strdup, which is not standard */
579	+	char *
580	+	gengetopt_strdup (const char *s)
581	+	{
582	+	char *result = 0;
583	+	if (!s)
584	+	return result;
585	+
586	+	result = (char*)malloc(strlen(s) + 1);
587	+	if (result == (char*)0)
588	+	return (char*)0;
589	+	strcpy(result, s);
590	+	return result;
591	+	}
592	+
593	+	static void
594	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
595	+	{
596	+	if (! args_info->staticProps_group_counter)
597	+	return;
598	+
599	+	args_info->bo_given = 0 ;
600	+	args_info->ior_given = 0 ;
601	+	args_info->for_given = 0 ;
602	+	args_info->bad_given = 0 ;
603	+	args_info->count_given = 0 ;
604	+	args_info->gofr_given = 0 ;
605	+	args_info->gofz_given = 0 ;
606	+	args_info->r_theta_given = 0 ;
607	+	args_info->r_omega_given = 0 ;
608	+	args_info->r_z_given = 0 ;
609	+	args_info->theta_omega_given = 0 ;
610	+	args_info->gxyz_given = 0 ;
611	+	args_info->twodgofr_given = 0 ;
612	+	args_info->p2_given = 0 ;
613	+	args_info->rp2_given = 0 ;
614	+	args_info->scd_given = 0 ;
615	+	args_info->density_given = 0 ;
616	+	args_info->slab_density_given = 0 ;
617	+	args_info->p_angle_given = 0 ;
618	+	args_info->hxy_given = 0 ;
619	+	args_info->rho_r_given = 0 ;
620	+	args_info->angle_r_given = 0 ;
621	+	args_info->hullvol_given = 0 ;
622	+	args_info->rodlength_given = 0 ;
623	+	args_info->tet_param_given = 0 ;
624	+	args_info->tet_param_z_given = 0 ;
625	+	args_info->rnemdz_given = 0 ;
626	+	args_info->rnemdr_given = 0 ;
627	+	args_info->rnemdrt_given = 0 ;
628	+
629	+	args_info->staticProps_group_counter = 0;
630	+	}
631	+
632	+	int
633	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
634	+	{
635	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
636	+	}
637	+
638	+	int
639	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
640	+	struct cmdline_parser_params *params)
641	+	{
642	+	int result;
643	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
644	+
645	+	if (result == EXIT_FAILURE)
646	+	{
647	+	cmdline_parser_free (args_info);
648	+	exit (EXIT_FAILURE);
649	+	}
650	+
651	+	return result;
652	+	}
653	+
654	+	int
655	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
656	+	{
657	+	int result;
658	+	struct cmdline_parser_params params;
659	+
660	+	params.override = override;
661	+	params.initialize = initialize;
662	+	params.check_required = check_required;
663	+	params.check_ambiguity = 0;
664	+	params.print_errors = 1;
665	+
666	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
667	+
668	+	if (result == EXIT_FAILURE)
669	+	{
670	+	cmdline_parser_free (args_info);
671	+	exit (EXIT_FAILURE);
672	+	}
673	+
674	+	return result;
675	+	}
676	+
677	+	int
678	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
679	+	{
680	+	int result = EXIT_SUCCESS;
681	+
682	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
683	+	result = EXIT_FAILURE;
684	+
685	+	if (result == EXIT_FAILURE)
686	+	{
687	+	cmdline_parser_free (args_info);
688	+	exit (EXIT_FAILURE);
689	+	}
690	+
691	+	return result;
692	+	}
693	+
694	+	int
695	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
696	+	{
697	+	int error = 0;
698	+	FIX_UNUSED (additional_error);
699	+
700	+	/* checks for required options */
701	+	if (! args_info->input_given)
702	+	{
703	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
704	+	error = 1;
705	+	}
706	+
707	+	if (args_info->staticProps_group_counter == 0)
708	+	{
709	+	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 : ""));
710	+	error = 1;
711	+	}
712	+
713	+
714	+	/* checks for dependences among options */
715	+
716	+	return error;
717	+	}
718	+
719	+
720	+	static char *package_name = 0;
721	+
722	+	/**
723	+	* @brief updates an option
724	+	* @param field the generic pointer to the field to update
725	+	* @param orig_field the pointer to the orig field
726	+	* @param field_given the pointer to the number of occurrence of this option
727	+	* @param prev_given the pointer to the number of occurrence already seen
728	+	* @param value the argument for this option (if null no arg was specified)
729	+	* @param possible_values the possible values for this option (if specified)
730	+	* @param default_value the default value (in case the option only accepts fixed values)
731	+	* @param arg_type the type of this option
732	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
733	+	* @param override @see cmdline_parser_params.override
734	+	* @param no_free whether to free a possible previous value
735	+	* @param multiple_option whether this is a multiple option
736	+	* @param long_opt the corresponding long option
737	+	* @param short_opt the corresponding short option (or '-' if none)
738	+	* @param additional_error possible further error specification
739	+	*/
740	+	static
741	+	int update_arg(void *field, char **orig_field,
742	+	unsigned int *field_given, unsigned int *prev_given,
743	+	char *value, const char *possible_values[],
744	+	const char *default_value,
745	+	cmdline_parser_arg_type arg_type,
746	+	int check_ambiguity, int override,
747	+	int no_free, int multiple_option,
748	+	const char *long_opt, char short_opt,
749	+	const char *additional_error)
750	+	{
751	+	char *stop_char = 0;
752	+	const char *val = value;
753	+	int found;
754	+	char **string_field;
755	+	FIX_UNUSED (field);
756	+
757	+	stop_char = 0;
758	+	found = 0;
759	+
760	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
761	+	{
762	+	if (short_opt != '-')
763	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
764	+	package_name, long_opt, short_opt,
765	+	(additional_error ? additional_error : ""));
766	+	else
767	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
768	+	package_name, long_opt,
769	+	(additional_error ? additional_error : ""));
770	+	return 1; /* failure */
771	+	}
772	+
773	+	FIX_UNUSED (default_value);
774	+
775	+	if (field_given && *field_given && ! override)
776	+	return 0;
777	+	if (prev_given)
778	+	(*prev_given)++;
779	+	if (field_given)
780	+	(*field_given)++;
781	+	if (possible_values)
782	+	val = possible_values[found];
783	+
784	+	switch(arg_type) {
785	+	case ARG_INT:
786	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
787	+	break;
788	+	case ARG_DOUBLE:
789	+	if (val) *((double *)field) = strtod (val, &stop_char);
790	+	break;
791	+	case ARG_STRING:
792	+	if (val) {
793	+	string_field = (char **)field;
794	+	if (!no_free && *string_field)
795	+	free (*string_field); /* free previous string */
796	+	*string_field = gengetopt_strdup (val);
797	+	}
798	+	break;
799	+	default:
800	+	break;
801	+	};
802	+
803	+	/* check numeric conversion */
804	+	switch(arg_type) {
805	+	case ARG_INT:
806	+	case ARG_DOUBLE:
807	+	if (val && !(stop_char && *stop_char == '\0')) {
808	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
809	+	return 1; /* failure */
810	+	}
811	+	break;
812	+	default:
813	+	;
814	+	};
815	+
816	+	/* store the original value */
817	+	switch(arg_type) {
818	+	case ARG_NO:
819	+	break;
820	+	default:
821	+	if (value && orig_field) {
822	+	if (no_free) {
823	+	*orig_field = value;
824	+	} else {
825	+	if (*orig_field)
826	+	free (*orig_field); /* free previous string */
827	+	*orig_field = gengetopt_strdup (value);
828	+	}
829	+	}
830	+	};
831	+
832	+	return 0; /* OK */
833	+	}
834	+
835	+
836	+	int
837	+	cmdline_parser_internal (
838	+	int argc, char **argv, struct gengetopt_args_info *args_info,
839	+	struct cmdline_parser_params *params, const char *additional_error)
840	+	{
841	+	int c;        /* Character of the parsed option.  */
842	+
843	+	int error = 0;
844	+	struct gengetopt_args_info local_args_info;
845	+
846	+	int override;
847	+	int initialize;
848	+	int check_required;
849	+	int check_ambiguity;
850	+
851	+	package_name = argv[0];
852	+
853	+	override = params->override;
854	+	initialize = params->initialize;
855	+	check_required = params->check_required;
856	+	check_ambiguity = params->check_ambiguity;
857	+
858	+	if (initialize)
859	+	cmdline_parser_init (args_info);
860	+
861	+	cmdline_parser_init (&local_args_info);
862	+
863		optarg = 0;
864	<	optind = 1;
865	<	opterr = 1;
864	>	optind = 0;
865	>	opterr = params->print_errors;
866		optopt = '?';
867
868		while (1)
869		{
870		int option_index = 0;
134	–	char *stop_char;
871
872		static struct option long_options[] = {
873		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 875 | cmdline_parser (int argc, char * const *argv, struct g
875		{ "input",      1, NULL, 'i' },
876		{ "output",     1, NULL, 'o' },
877		{ "step",       1, NULL, 'n' },
878	<	{ "nrbins",     1, NULL, 'r' },
878	>	{ "nbins",      1, NULL, 'b' },
879	>	{ "nbins_x",    1, NULL, 'x' },
880	>	{ "nbins_y",    1, NULL, 'y' },
881	>	{ "nbins_z",    1, NULL, 0 },
882		{ "nanglebins", 1, NULL, 'a' },
883	<	{ "length",     1, NULL, 'l' },
883	>	{ "rcut",       1, NULL, 'c' },
884	>	{ "dz", 1, NULL, 0 },
885	>	{ "length",     1, NULL, 0 },
886	>	{ "zlength",    1, NULL, 0 },
887	>	{ "zoffset",    1, NULL, 'z' },
888		{ "sele1",      1, NULL, 0 },
889		{ "sele2",      1, NULL, 0 },
890		{ "sele3",      1, NULL, 0 },
891		{ "refsele",    1, NULL, 0 },
892	+	{ "comsele",    1, NULL, 0 },
893	+	{ "seleoffset", 1, NULL, 0 },
894	+	{ "seleoffset2",        1, NULL, 0 },
895		{ "molname",    1, NULL, 0 },
896		{ "begin",      1, NULL, 0 },
897		{ "end",        1, NULL, 0 },
898	<	{ "gofr",       0, NULL, 0 },
898	>	{ "radius",     1, NULL, 0 },
899	>	{ "bo", 0, NULL, 0 },
900	>	{ "ior",        0, NULL, 0 },
901	>	{ "for",        0, NULL, 0 },
902	>	{ "bad",        0, NULL, 0 },
903	>	{ "count",      0, NULL, 0 },
904	>	{ "gofr",       0, NULL, 'g' },
905	>	{ "gofz",       0, NULL, 0 },
906		{ "r_theta",    0, NULL, 0 },
907		{ "r_omega",    0, NULL, 0 },
908	+	{ "r_z",        0, NULL, 0 },
909		{ "theta_omega",        0, NULL, 0 },
910		{ "gxyz",       0, NULL, 0 },
911	<	{ "p2", 0, NULL, 0 },
912	<	{ "scd",        0, NULL, 0 },
913	<	{ "density",    0, NULL, 0 },
914	<	{ NULL, 0, NULL, 0 }
911	>	{ "twodgofr",   0, NULL, 0 },
912	>	{ "p2", 0, NULL, 'p' },
913	>	{ "rp2",        0, NULL, 0 },
914	>	{ "scd",        0, NULL, 's' },
915	>	{ "density",    0, NULL, 'd' },
916	>	{ "slab_density",       0, NULL, 0 },
917	>	{ "p_angle",    0, NULL, 0 },
918	>	{ "hxy",        0, NULL, 0 },
919	>	{ "rho_r",      0, NULL, 0 },
920	>	{ "angle_r",    0, NULL, 0 },
921	>	{ "hullvol",    0, NULL, 0 },
922	>	{ "rodlength",  0, NULL, 0 },
923	>	{ "tet_param",  0, NULL, 'Q' },
924	>	{ "tet_param_z",        0, NULL, 0 },
925	>	{ "rnemdz",     0, NULL, 0 },
926	>	{ "rnemdr",     0, NULL, 0 },
927	>	{ "rnemdrt",    0, NULL, 0 },
928	>	{ 0,  0, 0, 0 }
929		};
930
931	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
931	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
932
933		if (c == -1) break;       /* Exit from `while (1)' loop.  */
934
935		switch (c)
936		{
937		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
938		cmdline_parser_print_help ();
939	+	cmdline_parser_free (&local_args_info);
940		exit (EXIT_SUCCESS);
941
942		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
943		cmdline_parser_print_version ();
944	+	cmdline_parser_free (&local_args_info);
945		exit (EXIT_SUCCESS);
946
947		case 'i':       /* input dump file.  */
948	<	if (args_info->input_given)
949	<	{
950	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
951	<	clear_args ();
952	<	exit (EXIT_FAILURE);
953	<	}
954	<	args_info->input_given = 1;
955	<	args_info->input_arg = gengetopt_strdup (optarg);
948	>
949	>
950	>	if (update_arg( (void *)&(args_info->input_arg),
951	>	&(args_info->input_orig), &(args_info->input_given),
952	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
953	>	check_ambiguity, override, 0, 0,
954	>	"input", 'i',
955	>	additional_error))
956	>	goto failure;
957	>
958		break;
190	–
959		case 'o':       /* output file name.  */
960	<	if (args_info->output_given)
961	<	{
962	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
963	<	clear_args ();
964	<	exit (EXIT_FAILURE);
965	<	}
966	<	args_info->output_given = 1;
967	<	args_info->output_arg = gengetopt_strdup (optarg);
960	>
961	>
962	>	if (update_arg( (void *)&(args_info->output_arg),
963	>	&(args_info->output_orig), &(args_info->output_given),
964	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
965	>	check_ambiguity, override, 0, 0,
966	>	"output", 'o',
967	>	additional_error))
968	>	goto failure;
969	>
970		break;
201	–
971		case 'n':       /* process every n frame.  */
972	<	if (args_info->step_given)
973	<	{
974	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
975	<	clear_args ();
976	<	exit (EXIT_FAILURE);
977	<	}
978	<	args_info->step_given = 1;
979	<	args_info->step_arg = strtol (optarg,&stop_char,0);
972	>
973	>
974	>	if (update_arg( (void *)&(args_info->step_arg),
975	>	&(args_info->step_orig), &(args_info->step_given),
976	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
977	>	check_ambiguity, override, 0, 0,
978	>	"step", 'n',
979	>	additional_error))
980	>	goto failure;
981	>
982		break;
983	<
984	<	case 'r':       /* number of bins for distance.  */
985	<	if (args_info->nrbins_given)
986	<	{
987	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
988	<	clear_args ();
989	<	exit (EXIT_FAILURE);
990	<	}
991	<	args_info->nrbins_given = 1;
992	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
983	>	case 'b':       /* number of bins (general purpose).  */
984	>
985	>
986	>	if (update_arg( (void *)&(args_info->nbins_arg),
987	>	&(args_info->nbins_orig), &(args_info->nbins_given),
988	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
989	>	check_ambiguity, override, 0, 0,
990	>	"nbins", 'b',
991	>	additional_error))
992	>	goto failure;
993	>
994		break;
995	<
995	>	case 'x':       /* number of bins in x axis.  */
996	>
997	>
998	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
999	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1000	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1001	>	check_ambiguity, override, 0, 0,
1002	>	"nbins_x", 'x',
1003	>	additional_error))
1004	>	goto failure;
1005	>
1006	>	break;
1007	>	case 'y':       /* number of bins in y axis.  */
1008	>
1009	>
1010	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
1011	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1012	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1013	>	check_ambiguity, override, 0, 0,
1014	>	"nbins_y", 'y',
1015	>	additional_error))
1016	>	goto failure;
1017	>
1018	>	break;
1019		case 'a':       /* number of bins for cos(angle).  */
1020	<	if (args_info->nanglebins_given)
1021	<	{
1022	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1023	<	clear_args ();
1024	<	exit (EXIT_FAILURE);
1025	<	}
1026	<	args_info->nanglebins_given = 1;
1027	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
1020	>
1021	>
1022	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1023	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1024	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1025	>	check_ambiguity, override, 0, 0,
1026	>	"nanglebins", 'a',
1027	>	additional_error))
1028	>	goto failure;
1029	>
1030		break;
1031	<
1032	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1033	<	if (args_info->length_given)
1034	<	{
1035	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1036	<	clear_args ();
1037	<	exit (EXIT_FAILURE);
1038	<	}
1039	<	args_info->length_given = 1;
1040	<	args_info->length_arg = strtod (optarg, NULL);
1031	>	case 'c':       /* cutoff radius (rcut).  */
1032	>
1033	>
1034	>	if (update_arg( (void *)&(args_info->rcut_arg),
1035	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1036	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1037	>	check_ambiguity, override, 0, 0,
1038	>	"rcut", 'c',
1039	>	additional_error))
1040	>	goto failure;
1041	>
1042		break;
1043	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1044	+
1045	+
1046	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1047	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1048	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1049	+	check_ambiguity, override, 0, 0,
1050	+	"zoffset", 'z',
1051	+	additional_error))
1052	+	goto failure;
1053	+
1054	+	break;
1055	+	case 'g':       /* g(r).  */
1056	+
1057	+	if (args_info->staticProps_group_counter && override)
1058	+	reset_group_staticProps (args_info);
1059	+	args_info->staticProps_group_counter += 1;
1060	+
1061	+	if (update_arg( 0 ,
1062	+	0 , &(args_info->gofr_given),
1063	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1064	+	check_ambiguity, override, 0, 0,
1065	+	"gofr", 'g',
1066	+	additional_error))
1067	+	goto failure;
1068	+
1069	+	break;
1070	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1071	+
1072	+	if (args_info->staticProps_group_counter && override)
1073	+	reset_group_staticProps (args_info);
1074	+	args_info->staticProps_group_counter += 1;
1075	+
1076	+	if (update_arg( 0 ,
1077	+	0 , &(args_info->p2_given),
1078	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1079	+	check_ambiguity, override, 0, 0,
1080	+	"p2", 'p',
1081	+	additional_error))
1082	+	goto failure;
1083	+
1084	+	break;
1085	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1086	+
1087	+	if (args_info->staticProps_group_counter && override)
1088	+	reset_group_staticProps (args_info);
1089	+	args_info->staticProps_group_counter += 1;
1090	+
1091	+	if (update_arg( 0 ,
1092	+	0 , &(args_info->scd_given),
1093	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1094	+	check_ambiguity, override, 0, 0,
1095	+	"scd", 's',
1096	+	additional_error))
1097	+	goto failure;
1098	+
1099	+	break;
1100	+	case 'd':       /* density plot.  */
1101	+
1102	+	if (args_info->staticProps_group_counter && override)
1103	+	reset_group_staticProps (args_info);
1104	+	args_info->staticProps_group_counter += 1;
1105	+
1106	+	if (update_arg( 0 ,
1107	+	0 , &(args_info->density_given),
1108	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1109	+	check_ambiguity, override, 0, 0,
1110	+	"density", 'd',
1111	+	additional_error))
1112	+	goto failure;
1113	+
1114	+	break;
1115	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1116	+
1117	+	if (args_info->staticProps_group_counter && override)
1118	+	reset_group_staticProps (args_info);
1119	+	args_info->staticProps_group_counter += 1;
1120	+
1121	+	if (update_arg( 0 ,
1122	+	0 , &(args_info->tet_param_given),
1123	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1124	+	check_ambiguity, override, 0, 0,
1125	+	"tet_param", 'Q',
1126	+	additional_error))
1127	+	goto failure;
1128	+
1129	+	break;
1130
246	–
1131		case 0: /* Long option with no short option */
1132	<	/* select the first stuntdouble set.  */
1133	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1132	>	/* number of bins in z axis.  */
1133	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1134		{
1135	<	if (args_info->sele1_given)
1136	<	{
1137	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1138	<	clear_args ();
1139	<	exit (EXIT_FAILURE);
1140	<	}
1141	<	args_info->sele1_given = 1;
1142	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1143	<	break;
1135	>
1136	>
1137	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1138	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1139	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1140	>	check_ambiguity, override, 0, 0,
1141	>	"nbins_z", '-',
1142	>	additional_error))
1143	>	goto failure;
1144	>
1145		}
1146	+	/* slab width (dz).  */
1147	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1148	+	{
1149
1150	+
1151	+	if (update_arg( (void *)&(args_info->dz_arg),
1152	+	&(args_info->dz_orig), &(args_info->dz_given),
1153	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1154	+	check_ambiguity, override, 0, 0,
1155	+	"dz", '-',
1156	+	additional_error))
1157	+	goto failure;
1158	+
1159	+	}
1160	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1161	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1162	+	{
1163	+
1164	+
1165	+	if (update_arg( (void *)&(args_info->length_arg),
1166	+	&(args_info->length_orig), &(args_info->length_given),
1167	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1168	+	check_ambiguity, override, 0, 0,
1169	+	"length", '-',
1170	+	additional_error))
1171	+	goto failure;
1172	+
1173	+	}
1174	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1175	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1176	+	{
1177	+
1178	+
1179	+	if (update_arg( (void *)&(args_info->zlength_arg),
1180	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1181	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1182	+	check_ambiguity, override, 0, 0,
1183	+	"zlength", '-',
1184	+	additional_error))
1185	+	goto failure;
1186	+
1187	+	}
1188	+	/* select the first stuntdouble set.  */
1189	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1190	+	{
1191	+
1192	+
1193	+	if (update_arg( (void *)&(args_info->sele1_arg),
1194	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1195	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1196	+	check_ambiguity, override, 0, 0,
1197	+	"sele1", '-',
1198	+	additional_error))
1199	+	goto failure;
1200	+
1201	+	}
1202		/* select the second stuntdouble set.  */
1203		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1204		{
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	–	}
1205
1206	+
1207	+	if (update_arg( (void *)&(args_info->sele2_arg),
1208	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1209	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1210	+	check_ambiguity, override, 0, 0,
1211	+	"sele2", '-',
1212	+	additional_error))
1213	+	goto failure;
1214	+
1215	+	}
1216		/* select the third stuntdouble set.  */
1217		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1218		{
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	–	}
1219
1220	+
1221	+	if (update_arg( (void *)&(args_info->sele3_arg),
1222	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1223	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1224	+	check_ambiguity, override, 0, 0,
1225	+	"sele3", '-',
1226	+	additional_error))
1227	+	goto failure;
1228	+
1229	+	}
1230		/* select reference (use and only use with --gxyz).  */
1231		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1232		{
1233	<	if (args_info->refsele_given)
1234	<	{
1235	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1236	<	clear_args ();
1237	<	exit (EXIT_FAILURE);
1238	<	}
1239	<	args_info->refsele_given = 1;
1240	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1241	<	break;
1233	>
1234	>
1235	>	if (update_arg( (void *)&(args_info->refsele_arg),
1236	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1237	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1238	>	check_ambiguity, override, 0, 0,
1239	>	"refsele", '-',
1240	>	additional_error))
1241	>	goto failure;
1242	>
1243		}
1244	+	/* select stunt doubles for center-of-mass reference point.  */
1245	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1246	+	{
1247
1248	+
1249	+	if (update_arg( (void *)&(args_info->comsele_arg),
1250	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1251	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1252	+	check_ambiguity, override, 0, 0,
1253	+	"comsele", '-',
1254	+	additional_error))
1255	+	goto failure;
1256	+
1257	+	}
1258	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1259	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1260	+	{
1261	+
1262	+
1263	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1264	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1265	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1266	+	check_ambiguity, override, 0, 0,
1267	+	"seleoffset", '-',
1268	+	additional_error))
1269	+	goto failure;
1270	+
1271	+	}
1272	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1273	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1274	+	{
1275	+
1276	+
1277	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1278	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1279	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1280	+	check_ambiguity, override, 0, 0,
1281	+	"seleoffset2", '-',
1282	+	additional_error))
1283	+	goto failure;
1284	+
1285	+	}
1286		/* molecule name.  */
1287		else if (strcmp (long_options[option_index].name, "molname") == 0)
1288		{
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	–	}
1289
1290	<	/* begin interanl index.  */
1290	>
1291	>	if (update_arg( (void *)&(args_info->molname_arg),
1292	>	&(args_info->molname_orig), &(args_info->molname_given),
1293	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1294	>	check_ambiguity, override, 0, 0,
1295	>	"molname", '-',
1296	>	additional_error))
1297	>	goto failure;
1298	>
1299	>	}
1300	>	/* begin internal index.  */
1301		else if (strcmp (long_options[option_index].name, "begin") == 0)
1302		{
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	–	}
1303
1304	+
1305	+	if (update_arg( (void *)&(args_info->begin_arg),
1306	+	&(args_info->begin_orig), &(args_info->begin_given),
1307	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1308	+	check_ambiguity, override, 0, 0,
1309	+	"begin", '-',
1310	+	additional_error))
1311	+	goto failure;
1312	+
1313	+	}
1314		/* end internal index.  */
1315		else if (strcmp (long_options[option_index].name, "end") == 0)
1316		{
1317	<	if (args_info->end_given)
1318	<	{
1319	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1320	<	clear_args ();
1321	<	exit (EXIT_FAILURE);
1322	<	}
1323	<	args_info->end_given = 1;
1324	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1325	<	break;
1317	>
1318	>
1319	>	if (update_arg( (void *)&(args_info->end_arg),
1320	>	&(args_info->end_orig), &(args_info->end_given),
1321	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1322	>	check_ambiguity, override, 0, 0,
1323	>	"end", '-',
1324	>	additional_error))
1325	>	goto failure;
1326	>
1327		}
1328	+	/* nanoparticle radius.  */
1329	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1330	+	{
1331
1332	<	/* g(r).  */
1333	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1332	>
1333	>	if (update_arg( (void *)&(args_info->radius_arg),
1334	>	&(args_info->radius_orig), &(args_info->radius_given),
1335	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1336	>	check_ambiguity, override, 0, 0,
1337	>	"radius", '-',
1338	>	additional_error))
1339	>	goto failure;
1340	>
1341	>	}
1342	>	/* bond order parameter (--rcut must be specified).  */
1343	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1344		{
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;
1345
1346	<	break;
1346	>	if (args_info->staticProps_group_counter && override)
1347	>	reset_group_staticProps (args_info);
1348	>	args_info->staticProps_group_counter += 1;
1349	>
1350	>	if (update_arg( 0 ,
1351	>	0 , &(args_info->bo_given),
1352	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1353	>	check_ambiguity, override, 0, 0,
1354	>	"bo", '-',
1355	>	additional_error))
1356	>	goto failure;
1357	>
1358	>	}
1359	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1360	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1361	>	{
1362	>
1363	>	if (args_info->staticProps_group_counter && override)
1364	>	reset_group_staticProps (args_info);
1365	>	args_info->staticProps_group_counter += 1;
1366	>
1367	>	if (update_arg( 0 ,
1368	>	0 , &(args_info->ior_given),
1369	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1370	>	check_ambiguity, override, 0, 0,
1371	>	"ior", '-',
1372	>	additional_error))
1373	>	goto failure;
1374	>
1375		}
1376	+	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1377	+	else if (strcmp (long_options[option_index].name, "for") == 0)
1378	+	{
1379
1380	+	if (args_info->staticProps_group_counter && override)
1381	+	reset_group_staticProps (args_info);
1382	+	args_info->staticProps_group_counter += 1;
1383	+
1384	+	if (update_arg( 0 ,
1385	+	0 , &(args_info->for_given),
1386	+	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1387	+	check_ambiguity, override, 0, 0,
1388	+	"for", '-',
1389	+	additional_error))
1390	+	goto failure;
1391	+
1392	+	}
1393	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1394	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1395	+	{
1396	+
1397	+	if (args_info->staticProps_group_counter && override)
1398	+	reset_group_staticProps (args_info);
1399	+	args_info->staticProps_group_counter += 1;
1400	+
1401	+	if (update_arg( 0 ,
1402	+	0 , &(args_info->bad_given),
1403	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1404	+	check_ambiguity, override, 0, 0,
1405	+	"bad", '-',
1406	+	additional_error))
1407	+	goto failure;
1408	+
1409	+	}
1410	+	/* count of molecules matching selection criteria (and associated statistics).  */
1411	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1412	+	{
1413	+
1414	+	if (args_info->staticProps_group_counter && override)
1415	+	reset_group_staticProps (args_info);
1416	+	args_info->staticProps_group_counter += 1;
1417	+
1418	+	if (update_arg( 0 ,
1419	+	0 , &(args_info->count_given),
1420	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1421	+	check_ambiguity, override, 0, 0,
1422	+	"count", '-',
1423	+	additional_error))
1424	+	goto failure;
1425	+
1426	+	}
1427	+	/* g(z).  */
1428	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1429	+	{
1430	+
1431	+	if (args_info->staticProps_group_counter && override)
1432	+	reset_group_staticProps (args_info);
1433	+	args_info->staticProps_group_counter += 1;
1434	+
1435	+	if (update_arg( 0 ,
1436	+	0 , &(args_info->gofz_given),
1437	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1438	+	check_ambiguity, override, 0, 0,
1439	+	"gofz", '-',
1440	+	additional_error))
1441	+	goto failure;
1442	+
1443	+	}
1444		/* g(r, cos(theta)).  */
1445		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1446		{
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;
1447
1448	<	break;
1449	<	}
1448	>	if (args_info->staticProps_group_counter && override)
1449	>	reset_group_staticProps (args_info);
1450	>	args_info->staticProps_group_counter += 1;
1451
1452	+	if (update_arg( 0 ,
1453	+	0 , &(args_info->r_theta_given),
1454	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1455	+	check_ambiguity, override, 0, 0,
1456	+	"r_theta", '-',
1457	+	additional_error))
1458	+	goto failure;
1459	+
1460	+	}
1461		/* g(r, cos(omega)).  */
1462		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1463		{
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;
1464
1465	<	break;
1465	>	if (args_info->staticProps_group_counter && override)
1466	>	reset_group_staticProps (args_info);
1467	>	args_info->staticProps_group_counter += 1;
1468	>
1469	>	if (update_arg( 0 ,
1470	>	0 , &(args_info->r_omega_given),
1471	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1472	>	check_ambiguity, override, 0, 0,
1473	>	"r_omega", '-',
1474	>	additional_error))
1475	>	goto failure;
1476	>
1477		}
1478	+	/* g(r, z).  */
1479	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1480	+	{
1481
1482	+	if (args_info->staticProps_group_counter && override)
1483	+	reset_group_staticProps (args_info);
1484	+	args_info->staticProps_group_counter += 1;
1485	+
1486	+	if (update_arg( 0 ,
1487	+	0 , &(args_info->r_z_given),
1488	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1489	+	check_ambiguity, override, 0, 0,
1490	+	"r_z", '-',
1491	+	additional_error))
1492	+	goto failure;
1493	+
1494	+	}
1495		/* g(cos(theta), cos(omega)).  */
1496		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1497		{
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;
1498
1499	<	break;
1500	<	}
1499	>	if (args_info->staticProps_group_counter && override)
1500	>	reset_group_staticProps (args_info);
1501	>	args_info->staticProps_group_counter += 1;
1502
1503	+	if (update_arg( 0 ,
1504	+	0 , &(args_info->theta_omega_given),
1505	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1506	+	check_ambiguity, override, 0, 0,
1507	+	"theta_omega", '-',
1508	+	additional_error))
1509	+	goto failure;
1510	+
1511	+	}
1512		/* g(x, y, z).  */
1513		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1514		{
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;
1515
1516	<	break;
1517	<	}
1516	>	if (args_info->staticProps_group_counter && override)
1517	>	reset_group_staticProps (args_info);
1518	>	args_info->staticProps_group_counter += 1;
1519
1520	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1521	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1520	>	if (update_arg( 0 ,
1521	>	0 , &(args_info->gxyz_given),
1522	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1523	>	check_ambiguity, override, 0, 0,
1524	>	"gxyz", '-',
1525	>	additional_error))
1526	>	goto failure;
1527	>
1528	>	}
1529	>	/* 2D g(r) (Slab width --dz must be specified).  */
1530	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1531		{
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;
1532
1533	<	break;
1533	>	if (args_info->staticProps_group_counter && override)
1534	>	reset_group_staticProps (args_info);
1535	>	args_info->staticProps_group_counter += 1;
1536	>
1537	>	if (update_arg( 0 ,
1538	>	0 , &(args_info->twodgofr_given),
1539	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1540	>	check_ambiguity, override, 0, 0,
1541	>	"twodgofr", '-',
1542	>	additional_error))
1543	>	goto failure;
1544	>
1545		}
1546	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1547	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1548	+	{
1549
1550	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1551	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1550	>	if (args_info->staticProps_group_counter && override)
1551	>	reset_group_staticProps (args_info);
1552	>	args_info->staticProps_group_counter += 1;
1553	>
1554	>	if (update_arg( 0 ,
1555	>	0 , &(args_info->rp2_given),
1556	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1557	>	check_ambiguity, override, 0, 0,
1558	>	"rp2", '-',
1559	>	additional_error))
1560	>	goto failure;
1561	>
1562	>	}
1563	>	/* slab density.  */
1564	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1565		{
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;
1566
1567	<	break;
1567	>	if (args_info->staticProps_group_counter && override)
1568	>	reset_group_staticProps (args_info);
1569	>	args_info->staticProps_group_counter += 1;
1570	>
1571	>	if (update_arg( 0 ,
1572	>	0 , &(args_info->slab_density_given),
1573	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1574	>	check_ambiguity, override, 0, 0,
1575	>	"slab_density", '-',
1576	>	additional_error))
1577	>	goto failure;
1578	>
1579		}
1580	+	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1581	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1582	+	{
1583
1584	<	/* density plot (--sele1 must be specified).  */
1585	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1584	>	if (args_info->staticProps_group_counter && override)
1585	>	reset_group_staticProps (args_info);
1586	>	args_info->staticProps_group_counter += 1;
1587	>
1588	>	if (update_arg( 0 ,
1589	>	0 , &(args_info->p_angle_given),
1590	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1591	>	check_ambiguity, override, 0, 0,
1592	>	"p_angle", '-',
1593	>	additional_error))
1594	>	goto failure;
1595	>
1596	>	}
1597	>	/* hxy.  */
1598	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1599		{
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;
1600
1601	<	break;
1601	>	if (args_info->staticProps_group_counter && override)
1602	>	reset_group_staticProps (args_info);
1603	>	args_info->staticProps_group_counter += 1;
1604	>
1605	>	if (update_arg( 0 ,
1606	>	0 , &(args_info->hxy_given),
1607	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1608	>	check_ambiguity, override, 0, 0,
1609	>	"hxy", '-',
1610	>	additional_error))
1611	>	goto failure;
1612	>
1613		}
1614	+	/* rho of R.  */
1615	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1616	+	{
1617
1618	<
1618	>	if (args_info->staticProps_group_counter && override)
1619	>	reset_group_staticProps (args_info);
1620	>	args_info->staticProps_group_counter += 1;
1621	>
1622	>	if (update_arg( 0 ,
1623	>	0 , &(args_info->rho_r_given),
1624	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1625	>	check_ambiguity, override, 0, 0,
1626	>	"rho_r", '-',
1627	>	additional_error))
1628	>	goto failure;
1629	>
1630	>	}
1631	>	/* angle of R.  */
1632	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1633	>	{
1634	>
1635	>	if (args_info->staticProps_group_counter && override)
1636	>	reset_group_staticProps (args_info);
1637	>	args_info->staticProps_group_counter += 1;
1638	>
1639	>	if (update_arg( 0 ,
1640	>	0 , &(args_info->angle_r_given),
1641	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1642	>	check_ambiguity, override, 0, 0,
1643	>	"angle_r", '-',
1644	>	additional_error))
1645	>	goto failure;
1646	>
1647	>	}
1648	>	/* hull volume of nanoparticle.  */
1649	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1650	>	{
1651	>
1652	>	if (args_info->staticProps_group_counter && override)
1653	>	reset_group_staticProps (args_info);
1654	>	args_info->staticProps_group_counter += 1;
1655	>
1656	>	if (update_arg( 0 ,
1657	>	0 , &(args_info->hullvol_given),
1658	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1659	>	check_ambiguity, override, 0, 0,
1660	>	"hullvol", '-',
1661	>	additional_error))
1662	>	goto failure;
1663	>
1664	>	}
1665	>	/* length of nanorod.  */
1666	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1667	>	{
1668	>
1669	>	if (args_info->staticProps_group_counter && override)
1670	>	reset_group_staticProps (args_info);
1671	>	args_info->staticProps_group_counter += 1;
1672	>
1673	>	if (update_arg( 0 ,
1674	>	0 , &(args_info->rodlength_given),
1675	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1676	>	check_ambiguity, override, 0, 0,
1677	>	"rodlength", '-',
1678	>	additional_error))
1679	>	goto failure;
1680	>
1681	>	}
1682	>	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1683	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1684	>	{
1685	>
1686	>	if (args_info->staticProps_group_counter && override)
1687	>	reset_group_staticProps (args_info);
1688	>	args_info->staticProps_group_counter += 1;
1689	>
1690	>	if (update_arg( 0 ,
1691	>	0 , &(args_info->tet_param_z_given),
1692	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1693	>	check_ambiguity, override, 0, 0,
1694	>	"tet_param_z", '-',
1695	>	additional_error))
1696	>	goto failure;
1697	>
1698	>	}
1699	>	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1700	>	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1701	>	{
1702	>
1703	>	if (args_info->staticProps_group_counter && override)
1704	>	reset_group_staticProps (args_info);
1705	>	args_info->staticProps_group_counter += 1;
1706	>
1707	>	if (update_arg( 0 ,
1708	>	0 , &(args_info->rnemdz_given),
1709	>	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1710	>	check_ambiguity, override, 0, 0,
1711	>	"rnemdz", '-',
1712	>	additional_error))
1713	>	goto failure;
1714	>
1715	>	}
1716	>	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1717	>	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1718	>	{
1719	>
1720	>	if (args_info->staticProps_group_counter && override)
1721	>	reset_group_staticProps (args_info);
1722	>	args_info->staticProps_group_counter += 1;
1723	>
1724	>	if (update_arg( 0 ,
1725	>	0 , &(args_info->rnemdr_given),
1726	>	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1727	>	check_ambiguity, override, 0, 0,
1728	>	"rnemdr", '-',
1729	>	additional_error))
1730	>	goto failure;
1731	>
1732	>	}
1733	>	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1734	>	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1735	>	{
1736	>
1737	>	if (args_info->staticProps_group_counter && override)
1738	>	reset_group_staticProps (args_info);
1739	>	args_info->staticProps_group_counter += 1;
1740	>
1741	>	if (update_arg( 0 ,
1742	>	0 , &(args_info->rnemdrt_given),
1743	>	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1744	>	check_ambiguity, override, 0, 0,
1745	>	"rnemdrt", '-',
1746	>	additional_error))
1747	>	goto failure;
1748	>
1749	>	}
1750	>
1751	>	break;
1752		case '?':       /* Invalid option.  */
1753		/* `getopt_long' already printed an error message.  */
1754	<	exit (EXIT_FAILURE);
1754	>	goto failure;
1755
1756		default:        /* bug: option not considered.  */
1757	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1757	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1758		abort ();
1759		} /* switch */
1760		} /* while */
1761
1762	<	if ( staticProps_group_counter != 1)
1762	>	if (args_info->staticProps_group_counter > 1)
1763		{
1764	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1765	<	missing_required_options = 1;
1764	>	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 : ""));
1765	>	error = 1;
1766		}
1767
1768
1769	<	if (! args_info->input_given)
1769	>
1770	>	if (check_required)
1771		{
1772	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1772	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1773		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1774
1775	+	cmdline_parser_release (&local_args_info);
1776	+
1777	+	if ( error )
1778	+	return (EXIT_FAILURE);
1779	+
1780	+	if (optind < argc)
1781	+	{
1782	+	int i = 0 ;
1783	+	int found_prog_name = 0;
1784	+	/* whether program name, i.e., argv[0], is in the remaining args
1785	+	(this may happen with some implementations of getopt,
1786	+	but surely not with the one included by gengetopt) */
1787	+
1788	+	i = optind;
1789	+	while (i < argc)
1790	+	if (argv[i++] == argv[0]) {
1791	+	found_prog_name = 1;
1792	+	break;
1793	+	}
1794	+	i = 0;
1795	+
1796	+	args_info->inputs_num = argc - optind - found_prog_name;
1797	+	args_info->inputs =
1798	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1799	+	while (optind < argc)
1800	+	if (argv[optind++] != argv[0])
1801	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1802	+	}
1803	+
1804		return 0;
1805	+
1806	+	failure:
1807	+
1808	+	cmdline_parser_release (&local_args_info);
1809	+	return (EXIT_FAILURE);
1810		}

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 1992 by gezelter, Thu Apr 24 17:30:00 2014 UTC

#	Line 0 | Line 1
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