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

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1994 by gezelter, Wed Apr 30 18:50:45 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/program/gengetopt-2.11/src/gengetopt -F StaticPropsCmd
4	>	gengetopt --file-name=StaticPropsCmd --unamed-opts
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
8		we make no copyright claims on it.
9		*/
10
11	+	/* If we use autoconf.  */
12	+	#ifdef HAVE_CONFIG_H
13	+	#include "config.h"
14	+	#endif
15
16		#include <stdio.h>
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	/* If we use autoconf.  */
21	<	#ifdef HAVE_CONFIG_H
18	<	#include "config.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22		#endif
23
24	<	#include "getopt.h"
24	>	#ifdef WIN32
25	>	#include "utils/wingetopt.h"
26	>	#else
27	>	#include <getopt.h>
28	>	#endif
29
30		#include "StaticPropsCmd.h"
31
32	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
32	>	const char *gengetopt_args_info_purpose = "";
33
34	<	void
32	<	cmdline_parser_print_help (void)
33	<	{
34	<	cmdline_parser_print_version ();
35	<	printf("\n"
36	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	<	printf("\n");
38	<	printf("  -h, --help                      Print help and exit\n");
39	<	printf("  -V, --version                   Print version and exit\n");
40	<	printf("  -i, --input=filename            input dump file\n");
41	<	printf("  -o, --output=filename           output file name\n");
42	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
43	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
44	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
45	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
46	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
47	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
48	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
49	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
50	<	printf("      --molname=STRING            molecule name\n");
51	<	printf("      --begin=INT                 begin interanl index\n");
52	<	printf("      --end=INT                   end internal index\n");
53	<	printf("\n");
54	<	printf(" Group: staticProps  an option of this group is required\n");
55	<	printf("      --gofr                      g(r)\n");
56	<	printf("      --r_theta                   g(r, cos(theta))\n");
57	<	printf("      --r_omega                   g(r, cos(omega))\n");
58	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
59	<	printf("      --gxyz                      g(x, y, z)\n");
60	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
61	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
62	<	printf("      --density                   density plot (--sele1 must be specified)\n");
63	<	printf("      --slab_density              slab density (--sele1 must be specified)\n");
64	<	}
34	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35
36	+	const char *gengetopt_args_info_description = "";
37
38	<	static char *gengetopt_strdup (const char *s);
38	>	const char *gengetopt_args_info_help[] = {
39	>	"  -h, --help                    Print help and exit",
40	>	"  -V, --version                 Print version and exit",
41	>	"  -i, --input=filename          input dump file",
42	>	"  -o, --output=filename         output file name",
43	>	"  -n, --step=INT                process every n frame  (default=`1')",
44	>	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
45	>	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
46	>	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
47	>	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
48	>	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
49	>	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50	>	"      --dz=DOUBLE               slab width (dz)",
51	>	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
52	>	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53	>	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
54	>	"      --sele1=selection script  select the first stuntdouble set",
55	>	"      --sele2=selection script  select the second stuntdouble set",
56	>	"      --sele3=selection script  select the third stuntdouble set",
57	>	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58	>	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59	>	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60	>	"      --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	>	"      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96	>	0
97	>	};
98
99	<	/* gengetopt_strdup() */
100	<	/* strdup.c replacement of strdup, which is not standard */
101	<	char *
102	<	gengetopt_strdup (const char *s)
103	<	{
74	<	char *result = (char*)malloc(strlen(s) + 1);
75	<	if (result == (char*)0)
76	<	return (char*)0;
77	<	strcpy(result, s);
78	<	return result;
79	<	}
99	>	typedef enum {ARG_NO
100	>	, ARG_STRING
101	>	, ARG_INT
102	>	, ARG_DOUBLE
103	>	} cmdline_parser_arg_type;
104
105	<	int
106	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
107	<	{
108	<	int c;        /* Character of the parsed option.  */
85	<	int missing_required_options = 0;
86	<	int staticProps_group_counter = 0;
87	<
105	>	static
106	>	void clear_given (struct gengetopt_args_info *args_info);
107	>	static
108	>	void clear_args (struct gengetopt_args_info *args_info);
109
110	+	static int
111	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
112	+	struct cmdline_parser_params *params, const char *additional_error);
113	+
114	+	static int
115	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
116	+
117	+	static char *
118	+	gengetopt_strdup (const char *s);
119	+
120	+	static
121	+	void clear_given (struct gengetopt_args_info *args_info)
122	+	{
123		args_info->help_given = 0 ;
124		args_info->version_given = 0 ;
125		args_info->input_given = 0 ;
126		args_info->output_given = 0 ;
127		args_info->step_given = 0 ;
128	<	args_info->nrbins_given = 0 ;
128	>	args_info->nbins_given = 0 ;
129	>	args_info->nbins_x_given = 0 ;
130	>	args_info->nbins_y_given = 0 ;
131	>	args_info->nbins_z_given = 0 ;
132		args_info->nanglebins_given = 0 ;
133	+	args_info->rcut_given = 0 ;
134	+	args_info->dz_given = 0 ;
135		args_info->length_given = 0 ;
136	+	args_info->zlength_given = 0 ;
137	+	args_info->zoffset_given = 0 ;
138		args_info->sele1_given = 0 ;
139		args_info->sele2_given = 0 ;
140		args_info->sele3_given = 0 ;
141		args_info->refsele_given = 0 ;
142	+	args_info->comsele_given = 0 ;
143	+	args_info->seleoffset_given = 0 ;
144	+	args_info->seleoffset2_given = 0 ;
145		args_info->molname_given = 0 ;
146		args_info->begin_given = 0 ;
147		args_info->end_given = 0 ;
148	+	args_info->radius_given = 0 ;
149	+	args_info->bo_given = 0 ;
150	+	args_info->ior_given = 0 ;
151	+	args_info->for_given = 0 ;
152	+	args_info->bad_given = 0 ;
153	+	args_info->count_given = 0 ;
154		args_info->gofr_given = 0 ;
155	+	args_info->gofz_given = 0 ;
156		args_info->r_theta_given = 0 ;
157		args_info->r_omega_given = 0 ;
158	+	args_info->r_z_given = 0 ;
159		args_info->theta_omega_given = 0 ;
160		args_info->gxyz_given = 0 ;
161	+	args_info->twodgofr_given = 0 ;
162		args_info->p2_given = 0 ;
163	+	args_info->rp2_given = 0 ;
164		args_info->scd_given = 0 ;
165		args_info->density_given = 0 ;
166		args_info->slab_density_given = 0 ;
167	<	#define clear_args() { \
168	<	args_info->input_arg = NULL; \
169	<	args_info->output_arg = NULL; \
170	<	args_info->step_arg = 1 ;\
171	<	args_info->nrbins_arg = 100 ;\
172	<	args_info->nanglebins_arg = 50 ;\
173	<	args_info->sele1_arg = NULL; \
174	<	args_info->sele2_arg = NULL; \
175	<	args_info->sele3_arg = NULL; \
176	<	args_info->refsele_arg = NULL; \
177	<	args_info->molname_arg = NULL; \
167	>	args_info->p_angle_given = 0 ;
168	>	args_info->hxy_given = 0 ;
169	>	args_info->rho_r_given = 0 ;
170	>	args_info->angle_r_given = 0 ;
171	>	args_info->hullvol_given = 0 ;
172	>	args_info->rodlength_given = 0 ;
173	>	args_info->tet_param_given = 0 ;
174	>	args_info->tet_param_z_given = 0 ;
175	>	args_info->rnemdz_given = 0 ;
176	>	args_info->rnemdr_given = 0 ;
177	>	args_info->rnemdrt_given = 0 ;
178	>	args_info->nitrile_given = 0 ;
179	>	args_info->staticProps_group_counter = 0 ;
180		}
181
182	<	clear_args();
182	>	static
183	>	void clear_args (struct gengetopt_args_info *args_info)
184	>	{
185	>	FIX_UNUSED (args_info);
186	>	args_info->input_arg = NULL;
187	>	args_info->input_orig = NULL;
188	>	args_info->output_arg = NULL;
189	>	args_info->output_orig = NULL;
190	>	args_info->step_arg = 1;
191	>	args_info->step_orig = NULL;
192	>	args_info->nbins_arg = 100;
193	>	args_info->nbins_orig = NULL;
194	>	args_info->nbins_x_arg = 100;
195	>	args_info->nbins_x_orig = NULL;
196	>	args_info->nbins_y_arg = 100;
197	>	args_info->nbins_y_orig = NULL;
198	>	args_info->nbins_z_arg = 100;
199	>	args_info->nbins_z_orig = NULL;
200	>	args_info->nanglebins_arg = 50;
201	>	args_info->nanglebins_orig = NULL;
202	>	args_info->rcut_orig = NULL;
203	>	args_info->dz_orig = NULL;
204	>	args_info->length_orig = NULL;
205	>	args_info->zlength_orig = NULL;
206	>	args_info->zoffset_arg = 0;
207	>	args_info->zoffset_orig = NULL;
208	>	args_info->sele1_arg = NULL;
209	>	args_info->sele1_orig = NULL;
210	>	args_info->sele2_arg = NULL;
211	>	args_info->sele2_orig = NULL;
212	>	args_info->sele3_arg = NULL;
213	>	args_info->sele3_orig = NULL;
214	>	args_info->refsele_arg = NULL;
215	>	args_info->refsele_orig = NULL;
216	>	args_info->comsele_arg = NULL;
217	>	args_info->comsele_orig = NULL;
218	>	args_info->seleoffset_orig = NULL;
219	>	args_info->seleoffset2_orig = NULL;
220	>	args_info->molname_arg = NULL;
221	>	args_info->molname_orig = NULL;
222	>	args_info->begin_orig = NULL;
223	>	args_info->end_orig = NULL;
224	>	args_info->radius_orig = NULL;
225	>
226	>	}
227
228	+	static
229	+	void init_args_info(struct gengetopt_args_info *args_info)
230	+	{
231	+
232	+
233	+	args_info->help_help = gengetopt_args_info_help[0] ;
234	+	args_info->version_help = gengetopt_args_info_help[1] ;
235	+	args_info->input_help = gengetopt_args_info_help[2] ;
236	+	args_info->output_help = gengetopt_args_info_help[3] ;
237	+	args_info->step_help = gengetopt_args_info_help[4] ;
238	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
239	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
240	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
241	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
242	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
243	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
244	+	args_info->dz_help = gengetopt_args_info_help[11] ;
245	+	args_info->length_help = gengetopt_args_info_help[12] ;
246	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
247	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
248	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
249	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
250	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
251	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
252	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
253	+	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
254	+	args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
255	+	args_info->molname_help = gengetopt_args_info_help[22] ;
256	+	args_info->begin_help = gengetopt_args_info_help[23] ;
257	+	args_info->end_help = gengetopt_args_info_help[24] ;
258	+	args_info->radius_help = gengetopt_args_info_help[25] ;
259	+	args_info->bo_help = gengetopt_args_info_help[27] ;
260	+	args_info->ior_help = gengetopt_args_info_help[28] ;
261	+	args_info->for_help = gengetopt_args_info_help[29] ;
262	+	args_info->bad_help = gengetopt_args_info_help[30] ;
263	+	args_info->count_help = gengetopt_args_info_help[31] ;
264	+	args_info->gofr_help = gengetopt_args_info_help[32] ;
265	+	args_info->gofz_help = gengetopt_args_info_help[33] ;
266	+	args_info->r_theta_help = gengetopt_args_info_help[34] ;
267	+	args_info->r_omega_help = gengetopt_args_info_help[35] ;
268	+	args_info->r_z_help = gengetopt_args_info_help[36] ;
269	+	args_info->theta_omega_help = gengetopt_args_info_help[37] ;
270	+	args_info->gxyz_help = gengetopt_args_info_help[38] ;
271	+	args_info->twodgofr_help = gengetopt_args_info_help[39] ;
272	+	args_info->p2_help = gengetopt_args_info_help[40] ;
273	+	args_info->rp2_help = gengetopt_args_info_help[41] ;
274	+	args_info->scd_help = gengetopt_args_info_help[42] ;
275	+	args_info->density_help = gengetopt_args_info_help[43] ;
276	+	args_info->slab_density_help = gengetopt_args_info_help[44] ;
277	+	args_info->p_angle_help = gengetopt_args_info_help[45] ;
278	+	args_info->hxy_help = gengetopt_args_info_help[46] ;
279	+	args_info->rho_r_help = gengetopt_args_info_help[47] ;
280	+	args_info->angle_r_help = gengetopt_args_info_help[48] ;
281	+	args_info->hullvol_help = gengetopt_args_info_help[49] ;
282	+	args_info->rodlength_help = gengetopt_args_info_help[50] ;
283	+	args_info->tet_param_help = gengetopt_args_info_help[51] ;
284	+	args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
285	+	args_info->rnemdz_help = gengetopt_args_info_help[53] ;
286	+	args_info->rnemdr_help = gengetopt_args_info_help[54] ;
287	+	args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
288	+	args_info->nitrile_help = gengetopt_args_info_help[56] ;
289	+
290	+	}
291	+
292	+	void
293	+	cmdline_parser_print_version (void)
294	+	{
295	+	printf ("%s %s\n",
296	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
297	+	CMDLINE_PARSER_VERSION);
298	+	}
299	+
300	+	static void print_help_common(void) {
301	+	cmdline_parser_print_version ();
302	+
303	+	if (strlen(gengetopt_args_info_purpose) > 0)
304	+	printf("\n%s\n", gengetopt_args_info_purpose);
305	+
306	+	if (strlen(gengetopt_args_info_usage) > 0)
307	+	printf("\n%s\n", gengetopt_args_info_usage);
308	+
309	+	printf("\n");
310	+
311	+	if (strlen(gengetopt_args_info_description) > 0)
312	+	printf("%s\n\n", gengetopt_args_info_description);
313	+	}
314	+
315	+	void
316	+	cmdline_parser_print_help (void)
317	+	{
318	+	int i = 0;
319	+	print_help_common();
320	+	while (gengetopt_args_info_help[i])
321	+	printf("%s\n", gengetopt_args_info_help[i++]);
322	+	}
323	+
324	+	void
325	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
326	+	{
327	+	clear_given (args_info);
328	+	clear_args (args_info);
329	+	init_args_info (args_info);
330	+
331	+	args_info->inputs = 0;
332	+	args_info->inputs_num = 0;
333	+	}
334	+
335	+	void
336	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
337	+	{
338	+	if (params)
339	+	{
340	+	params->override = 0;
341	+	params->initialize = 1;
342	+	params->check_required = 1;
343	+	params->check_ambiguity = 0;
344	+	params->print_errors = 1;
345	+	}
346	+	}
347	+
348	+	struct cmdline_parser_params *
349	+	cmdline_parser_params_create(void)
350	+	{
351	+	struct cmdline_parser_params *params =
352	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
353	+	cmdline_parser_params_init(params);
354	+	return params;
355	+	}
356	+
357	+	static void
358	+	free_string_field (char **s)
359	+	{
360	+	if (*s)
361	+	{
362	+	free (*s);
363	+	*s = 0;
364	+	}
365	+	}
366	+
367	+
368	+	static void
369	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
370	+	{
371	+	unsigned int i;
372	+	free_string_field (&(args_info->input_arg));
373	+	free_string_field (&(args_info->input_orig));
374	+	free_string_field (&(args_info->output_arg));
375	+	free_string_field (&(args_info->output_orig));
376	+	free_string_field (&(args_info->step_orig));
377	+	free_string_field (&(args_info->nbins_orig));
378	+	free_string_field (&(args_info->nbins_x_orig));
379	+	free_string_field (&(args_info->nbins_y_orig));
380	+	free_string_field (&(args_info->nbins_z_orig));
381	+	free_string_field (&(args_info->nanglebins_orig));
382	+	free_string_field (&(args_info->rcut_orig));
383	+	free_string_field (&(args_info->dz_orig));
384	+	free_string_field (&(args_info->length_orig));
385	+	free_string_field (&(args_info->zlength_orig));
386	+	free_string_field (&(args_info->zoffset_orig));
387	+	free_string_field (&(args_info->sele1_arg));
388	+	free_string_field (&(args_info->sele1_orig));
389	+	free_string_field (&(args_info->sele2_arg));
390	+	free_string_field (&(args_info->sele2_orig));
391	+	free_string_field (&(args_info->sele3_arg));
392	+	free_string_field (&(args_info->sele3_orig));
393	+	free_string_field (&(args_info->refsele_arg));
394	+	free_string_field (&(args_info->refsele_orig));
395	+	free_string_field (&(args_info->comsele_arg));
396	+	free_string_field (&(args_info->comsele_orig));
397	+	free_string_field (&(args_info->seleoffset_orig));
398	+	free_string_field (&(args_info->seleoffset2_orig));
399	+	free_string_field (&(args_info->molname_arg));
400	+	free_string_field (&(args_info->molname_orig));
401	+	free_string_field (&(args_info->begin_orig));
402	+	free_string_field (&(args_info->end_orig));
403	+	free_string_field (&(args_info->radius_orig));
404	+
405	+
406	+	for (i = 0; i < args_info->inputs_num; ++i)
407	+	free (args_info->inputs [i]);
408	+
409	+	if (args_info->inputs_num)
410	+	free (args_info->inputs);
411	+
412	+	clear_given (args_info);
413	+	}
414	+
415	+
416	+	static void
417	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
418	+	{
419	+	FIX_UNUSED (values);
420	+	if (arg) {
421	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
422	+	} else {
423	+	fprintf(outfile, "%s\n", opt);
424	+	}
425	+	}
426	+
427	+
428	+	int
429	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
430	+	{
431	+	int i = 0;
432	+
433	+	if (!outfile)
434	+	{
435	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
436	+	return EXIT_FAILURE;
437	+	}
438	+
439	+	if (args_info->help_given)
440	+	write_into_file(outfile, "help", 0, 0 );
441	+	if (args_info->version_given)
442	+	write_into_file(outfile, "version", 0, 0 );
443	+	if (args_info->input_given)
444	+	write_into_file(outfile, "input", args_info->input_orig, 0);
445	+	if (args_info->output_given)
446	+	write_into_file(outfile, "output", args_info->output_orig, 0);
447	+	if (args_info->step_given)
448	+	write_into_file(outfile, "step", args_info->step_orig, 0);
449	+	if (args_info->nbins_given)
450	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
451	+	if (args_info->nbins_x_given)
452	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
453	+	if (args_info->nbins_y_given)
454	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
455	+	if (args_info->nbins_z_given)
456	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
457	+	if (args_info->nanglebins_given)
458	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
459	+	if (args_info->rcut_given)
460	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
461	+	if (args_info->dz_given)
462	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
463	+	if (args_info->length_given)
464	+	write_into_file(outfile, "length", args_info->length_orig, 0);
465	+	if (args_info->zlength_given)
466	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
467	+	if (args_info->zoffset_given)
468	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
469	+	if (args_info->sele1_given)
470	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
471	+	if (args_info->sele2_given)
472	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
473	+	if (args_info->sele3_given)
474	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
475	+	if (args_info->refsele_given)
476	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
477	+	if (args_info->comsele_given)
478	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
479	+	if (args_info->seleoffset_given)
480	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
481	+	if (args_info->seleoffset2_given)
482	+	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
483	+	if (args_info->molname_given)
484	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
485	+	if (args_info->begin_given)
486	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
487	+	if (args_info->end_given)
488	+	write_into_file(outfile, "end", args_info->end_orig, 0);
489	+	if (args_info->radius_given)
490	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
491	+	if (args_info->bo_given)
492	+	write_into_file(outfile, "bo", 0, 0 );
493	+	if (args_info->ior_given)
494	+	write_into_file(outfile, "ior", 0, 0 );
495	+	if (args_info->for_given)
496	+	write_into_file(outfile, "for", 0, 0 );
497	+	if (args_info->bad_given)
498	+	write_into_file(outfile, "bad", 0, 0 );
499	+	if (args_info->count_given)
500	+	write_into_file(outfile, "count", 0, 0 );
501	+	if (args_info->gofr_given)
502	+	write_into_file(outfile, "gofr", 0, 0 );
503	+	if (args_info->gofz_given)
504	+	write_into_file(outfile, "gofz", 0, 0 );
505	+	if (args_info->r_theta_given)
506	+	write_into_file(outfile, "r_theta", 0, 0 );
507	+	if (args_info->r_omega_given)
508	+	write_into_file(outfile, "r_omega", 0, 0 );
509	+	if (args_info->r_z_given)
510	+	write_into_file(outfile, "r_z", 0, 0 );
511	+	if (args_info->theta_omega_given)
512	+	write_into_file(outfile, "theta_omega", 0, 0 );
513	+	if (args_info->gxyz_given)
514	+	write_into_file(outfile, "gxyz", 0, 0 );
515	+	if (args_info->twodgofr_given)
516	+	write_into_file(outfile, "twodgofr", 0, 0 );
517	+	if (args_info->p2_given)
518	+	write_into_file(outfile, "p2", 0, 0 );
519	+	if (args_info->rp2_given)
520	+	write_into_file(outfile, "rp2", 0, 0 );
521	+	if (args_info->scd_given)
522	+	write_into_file(outfile, "scd", 0, 0 );
523	+	if (args_info->density_given)
524	+	write_into_file(outfile, "density", 0, 0 );
525	+	if (args_info->slab_density_given)
526	+	write_into_file(outfile, "slab_density", 0, 0 );
527	+	if (args_info->p_angle_given)
528	+	write_into_file(outfile, "p_angle", 0, 0 );
529	+	if (args_info->hxy_given)
530	+	write_into_file(outfile, "hxy", 0, 0 );
531	+	if (args_info->rho_r_given)
532	+	write_into_file(outfile, "rho_r", 0, 0 );
533	+	if (args_info->angle_r_given)
534	+	write_into_file(outfile, "angle_r", 0, 0 );
535	+	if (args_info->hullvol_given)
536	+	write_into_file(outfile, "hullvol", 0, 0 );
537	+	if (args_info->rodlength_given)
538	+	write_into_file(outfile, "rodlength", 0, 0 );
539	+	if (args_info->tet_param_given)
540	+	write_into_file(outfile, "tet_param", 0, 0 );
541	+	if (args_info->tet_param_z_given)
542	+	write_into_file(outfile, "tet_param_z", 0, 0 );
543	+	if (args_info->rnemdz_given)
544	+	write_into_file(outfile, "rnemdz", 0, 0 );
545	+	if (args_info->rnemdr_given)
546	+	write_into_file(outfile, "rnemdr", 0, 0 );
547	+	if (args_info->rnemdrt_given)
548	+	write_into_file(outfile, "rnemdrt", 0, 0 );
549	+	if (args_info->nitrile_given)
550	+	write_into_file(outfile, "nitrile", 0, 0 );
551	+
552	+
553	+	i = EXIT_SUCCESS;
554	+	return i;
555	+	}
556	+
557	+	int
558	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
559	+	{
560	+	FILE *outfile;
561	+	int i = 0;
562	+
563	+	outfile = fopen(filename, "w");
564	+
565	+	if (!outfile)
566	+	{
567	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
568	+	return EXIT_FAILURE;
569	+	}
570	+
571	+	i = cmdline_parser_dump(outfile, args_info);
572	+	fclose (outfile);
573	+
574	+	return i;
575	+	}
576	+
577	+	void
578	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
579	+	{
580	+	cmdline_parser_release (args_info);
581	+	}
582	+
583	+	/** @brief replacement of strdup, which is not standard */
584	+	char *
585	+	gengetopt_strdup (const char *s)
586	+	{
587	+	char *result = 0;
588	+	if (!s)
589	+	return result;
590	+
591	+	result = (char*)malloc(strlen(s) + 1);
592	+	if (result == (char*)0)
593	+	return (char*)0;
594	+	strcpy(result, s);
595	+	return result;
596	+	}
597	+
598	+	static void
599	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
600	+	{
601	+	if (! args_info->staticProps_group_counter)
602	+	return;
603	+
604	+	args_info->bo_given = 0 ;
605	+	args_info->ior_given = 0 ;
606	+	args_info->for_given = 0 ;
607	+	args_info->bad_given = 0 ;
608	+	args_info->count_given = 0 ;
609	+	args_info->gofr_given = 0 ;
610	+	args_info->gofz_given = 0 ;
611	+	args_info->r_theta_given = 0 ;
612	+	args_info->r_omega_given = 0 ;
613	+	args_info->r_z_given = 0 ;
614	+	args_info->theta_omega_given = 0 ;
615	+	args_info->gxyz_given = 0 ;
616	+	args_info->twodgofr_given = 0 ;
617	+	args_info->p2_given = 0 ;
618	+	args_info->rp2_given = 0 ;
619	+	args_info->scd_given = 0 ;
620	+	args_info->density_given = 0 ;
621	+	args_info->slab_density_given = 0 ;
622	+	args_info->p_angle_given = 0 ;
623	+	args_info->hxy_given = 0 ;
624	+	args_info->rho_r_given = 0 ;
625	+	args_info->angle_r_given = 0 ;
626	+	args_info->hullvol_given = 0 ;
627	+	args_info->rodlength_given = 0 ;
628	+	args_info->tet_param_given = 0 ;
629	+	args_info->tet_param_z_given = 0 ;
630	+	args_info->rnemdz_given = 0 ;
631	+	args_info->rnemdr_given = 0 ;
632	+	args_info->rnemdrt_given = 0 ;
633	+	args_info->nitrile_given = 0 ;
634	+
635	+	args_info->staticProps_group_counter = 0;
636	+	}
637	+
638	+	int
639	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
640	+	{
641	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
642	+	}
643	+
644	+	int
645	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
646	+	struct cmdline_parser_params *params)
647	+	{
648	+	int result;
649	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
650	+
651	+	if (result == EXIT_FAILURE)
652	+	{
653	+	cmdline_parser_free (args_info);
654	+	exit (EXIT_FAILURE);
655	+	}
656	+
657	+	return result;
658	+	}
659	+
660	+	int
661	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
662	+	{
663	+	int result;
664	+	struct cmdline_parser_params params;
665	+
666	+	params.override = override;
667	+	params.initialize = initialize;
668	+	params.check_required = check_required;
669	+	params.check_ambiguity = 0;
670	+	params.print_errors = 1;
671	+
672	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
673	+
674	+	if (result == EXIT_FAILURE)
675	+	{
676	+	cmdline_parser_free (args_info);
677	+	exit (EXIT_FAILURE);
678	+	}
679	+
680	+	return result;
681	+	}
682	+
683	+	int
684	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
685	+	{
686	+	int result = EXIT_SUCCESS;
687	+
688	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
689	+	result = EXIT_FAILURE;
690	+
691	+	if (result == EXIT_FAILURE)
692	+	{
693	+	cmdline_parser_free (args_info);
694	+	exit (EXIT_FAILURE);
695	+	}
696	+
697	+	return result;
698	+	}
699	+
700	+	int
701	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
702	+	{
703	+	int error = 0;
704	+	FIX_UNUSED (additional_error);
705	+
706	+	/* checks for required options */
707	+	if (! args_info->input_given)
708	+	{
709	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
710	+	error = 1;
711	+	}
712	+
713	+	if (args_info->staticProps_group_counter == 0)
714	+	{
715	+	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 : ""));
716	+	error = 1;
717	+	}
718	+
719	+
720	+	/* checks for dependences among options */
721	+
722	+	return error;
723	+	}
724	+
725	+
726	+	static char *package_name = 0;
727	+
728	+	/**
729	+	* @brief updates an option
730	+	* @param field the generic pointer to the field to update
731	+	* @param orig_field the pointer to the orig field
732	+	* @param field_given the pointer to the number of occurrence of this option
733	+	* @param prev_given the pointer to the number of occurrence already seen
734	+	* @param value the argument for this option (if null no arg was specified)
735	+	* @param possible_values the possible values for this option (if specified)
736	+	* @param default_value the default value (in case the option only accepts fixed values)
737	+	* @param arg_type the type of this option
738	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
739	+	* @param override @see cmdline_parser_params.override
740	+	* @param no_free whether to free a possible previous value
741	+	* @param multiple_option whether this is a multiple option
742	+	* @param long_opt the corresponding long option
743	+	* @param short_opt the corresponding short option (or '-' if none)
744	+	* @param additional_error possible further error specification
745	+	*/
746	+	static
747	+	int update_arg(void *field, char **orig_field,
748	+	unsigned int *field_given, unsigned int *prev_given,
749	+	char *value, const char *possible_values[],
750	+	const char *default_value,
751	+	cmdline_parser_arg_type arg_type,
752	+	int check_ambiguity, int override,
753	+	int no_free, int multiple_option,
754	+	const char *long_opt, char short_opt,
755	+	const char *additional_error)
756	+	{
757	+	char *stop_char = 0;
758	+	const char *val = value;
759	+	int found;
760	+	char **string_field;
761	+	FIX_UNUSED (field);
762	+
763	+	stop_char = 0;
764	+	found = 0;
765	+
766	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
767	+	{
768	+	if (short_opt != '-')
769	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
770	+	package_name, long_opt, short_opt,
771	+	(additional_error ? additional_error : ""));
772	+	else
773	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
774	+	package_name, long_opt,
775	+	(additional_error ? additional_error : ""));
776	+	return 1; /* failure */
777	+	}
778	+
779	+	FIX_UNUSED (default_value);
780	+
781	+	if (field_given && *field_given && ! override)
782	+	return 0;
783	+	if (prev_given)
784	+	(*prev_given)++;
785	+	if (field_given)
786	+	(*field_given)++;
787	+	if (possible_values)
788	+	val = possible_values[found];
789	+
790	+	switch(arg_type) {
791	+	case ARG_INT:
792	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
793	+	break;
794	+	case ARG_DOUBLE:
795	+	if (val) *((double *)field) = strtod (val, &stop_char);
796	+	break;
797	+	case ARG_STRING:
798	+	if (val) {
799	+	string_field = (char **)field;
800	+	if (!no_free && *string_field)
801	+	free (*string_field); /* free previous string */
802	+	*string_field = gengetopt_strdup (val);
803	+	}
804	+	break;
805	+	default:
806	+	break;
807	+	};
808	+
809	+	/* check numeric conversion */
810	+	switch(arg_type) {
811	+	case ARG_INT:
812	+	case ARG_DOUBLE:
813	+	if (val && !(stop_char && *stop_char == '\0')) {
814	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
815	+	return 1; /* failure */
816	+	}
817	+	break;
818	+	default:
819	+	;
820	+	};
821	+
822	+	/* store the original value */
823	+	switch(arg_type) {
824	+	case ARG_NO:
825	+	break;
826	+	default:
827	+	if (value && orig_field) {
828	+	if (no_free) {
829	+	*orig_field = value;
830	+	} else {
831	+	if (*orig_field)
832	+	free (*orig_field); /* free previous string */
833	+	*orig_field = gengetopt_strdup (value);
834	+	}
835	+	}
836	+	};
837	+
838	+	return 0; /* OK */
839	+	}
840	+
841	+
842	+	int
843	+	cmdline_parser_internal (
844	+	int argc, char **argv, struct gengetopt_args_info *args_info,
845	+	struct cmdline_parser_params *params, const char *additional_error)
846	+	{
847	+	int c;        /* Character of the parsed option.  */
848	+
849	+	int error = 0;
850	+	struct gengetopt_args_info local_args_info;
851	+
852	+	int override;
853	+	int initialize;
854	+	int check_required;
855	+	int check_ambiguity;
856	+
857	+	package_name = argv[0];
858	+
859	+	override = params->override;
860	+	initialize = params->initialize;
861	+	check_required = params->check_required;
862	+	check_ambiguity = params->check_ambiguity;
863	+
864	+	if (initialize)
865	+	cmdline_parser_init (args_info);
866	+
867	+	cmdline_parser_init (&local_args_info);
868	+
869		optarg = 0;
870	<	optind = 1;
871	<	opterr = 1;
870	>	optind = 0;
871	>	opterr = params->print_errors;
872		optopt = '?';
873
874		while (1)
875		{
876		int option_index = 0;
136	–	char *stop_char;
877
878		static struct option long_options[] = {
879		{ "help",       0, NULL, 'h' },
#	Line 141 | Line 881 | cmdline_parser (int argc, char * const *argv, struct g
881		{ "input",      1, NULL, 'i' },
882		{ "output",     1, NULL, 'o' },
883		{ "step",       1, NULL, 'n' },
884	<	{ "nrbins",     1, NULL, 'r' },
884	>	{ "nbins",      1, NULL, 'b' },
885	>	{ "nbins_x",    1, NULL, 'x' },
886	>	{ "nbins_y",    1, NULL, 'y' },
887	>	{ "nbins_z",    1, NULL, 0 },
888		{ "nanglebins", 1, NULL, 'a' },
889	<	{ "length",     1, NULL, 'l' },
889	>	{ "rcut",       1, NULL, 'c' },
890	>	{ "dz", 1, NULL, 0 },
891	>	{ "length",     1, NULL, 0 },
892	>	{ "zlength",    1, NULL, 0 },
893	>	{ "zoffset",    1, NULL, 'z' },
894		{ "sele1",      1, NULL, 0 },
895		{ "sele2",      1, NULL, 0 },
896		{ "sele3",      1, NULL, 0 },
897		{ "refsele",    1, NULL, 0 },
898	+	{ "comsele",    1, NULL, 0 },
899	+	{ "seleoffset", 1, NULL, 0 },
900	+	{ "seleoffset2",        1, NULL, 0 },
901		{ "molname",    1, NULL, 0 },
902		{ "begin",      1, NULL, 0 },
903		{ "end",        1, NULL, 0 },
904	<	{ "gofr",       0, NULL, 0 },
904	>	{ "radius",     1, NULL, 0 },
905	>	{ "bo", 0, NULL, 0 },
906	>	{ "ior",        0, NULL, 0 },
907	>	{ "for",        0, NULL, 0 },
908	>	{ "bad",        0, NULL, 0 },
909	>	{ "count",      0, NULL, 0 },
910	>	{ "gofr",       0, NULL, 'g' },
911	>	{ "gofz",       0, NULL, 0 },
912		{ "r_theta",    0, NULL, 0 },
913		{ "r_omega",    0, NULL, 0 },
914	+	{ "r_z",        0, NULL, 0 },
915		{ "theta_omega",        0, NULL, 0 },
916		{ "gxyz",       0, NULL, 0 },
917	<	{ "p2", 0, NULL, 0 },
918	<	{ "scd",        0, NULL, 0 },
919	<	{ "density",    0, NULL, 0 },
917	>	{ "twodgofr",   0, NULL, 0 },
918	>	{ "p2", 0, NULL, 'p' },
919	>	{ "rp2",        0, NULL, 0 },
920	>	{ "scd",        0, NULL, 's' },
921	>	{ "density",    0, NULL, 'd' },
922		{ "slab_density",       0, NULL, 0 },
923	<	{ NULL, 0, NULL, 0 }
923	>	{ "p_angle",    0, NULL, 0 },
924	>	{ "hxy",        0, NULL, 0 },
925	>	{ "rho_r",      0, NULL, 0 },
926	>	{ "angle_r",    0, NULL, 0 },
927	>	{ "hullvol",    0, NULL, 0 },
928	>	{ "rodlength",  0, NULL, 0 },
929	>	{ "tet_param",  0, NULL, 'Q' },
930	>	{ "tet_param_z",        0, NULL, 0 },
931	>	{ "rnemdz",     0, NULL, 0 },
932	>	{ "rnemdr",     0, NULL, 0 },
933	>	{ "rnemdrt",    0, NULL, 0 },
934	>	{ "nitrile",    0, NULL, 0 },
935	>	{ 0,  0, 0, 0 }
936		};
937
938	<	stop_char = 0;
167	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
938	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
939
940		if (c == -1) break;       /* Exit from `while (1)' loop.  */
941
942		switch (c)
943		{
944		case 'h':       /* Print help and exit.  */
174	–	clear_args ();
945		cmdline_parser_print_help ();
946	+	cmdline_parser_free (&local_args_info);
947		exit (EXIT_SUCCESS);
948
949		case 'V':       /* Print version and exit.  */
179	–	clear_args ();
950		cmdline_parser_print_version ();
951	+	cmdline_parser_free (&local_args_info);
952		exit (EXIT_SUCCESS);
953
954		case 'i':       /* input dump file.  */
955	<	if (args_info->input_given)
956	<	{
957	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
958	<	clear_args ();
959	<	exit (EXIT_FAILURE);
960	<	}
961	<	args_info->input_given = 1;
962	<	args_info->input_arg = gengetopt_strdup (optarg);
955	>
956	>
957	>	if (update_arg( (void *)&(args_info->input_arg),
958	>	&(args_info->input_orig), &(args_info->input_given),
959	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
960	>	check_ambiguity, override, 0, 0,
961	>	"input", 'i',
962	>	additional_error))
963	>	goto failure;
964	>
965		break;
193	–
966		case 'o':       /* output file name.  */
967	<	if (args_info->output_given)
968	<	{
969	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
970	<	clear_args ();
971	<	exit (EXIT_FAILURE);
972	<	}
973	<	args_info->output_given = 1;
974	<	args_info->output_arg = gengetopt_strdup (optarg);
967	>
968	>
969	>	if (update_arg( (void *)&(args_info->output_arg),
970	>	&(args_info->output_orig), &(args_info->output_given),
971	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
972	>	check_ambiguity, override, 0, 0,
973	>	"output", 'o',
974	>	additional_error))
975	>	goto failure;
976	>
977		break;
204	–
978		case 'n':       /* process every n frame.  */
979	<	if (args_info->step_given)
980	<	{
981	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
982	<	clear_args ();
983	<	exit (EXIT_FAILURE);
984	<	}
985	<	args_info->step_given = 1;
986	<	args_info->step_arg = strtol (optarg,&stop_char,0);
979	>
980	>
981	>	if (update_arg( (void *)&(args_info->step_arg),
982	>	&(args_info->step_orig), &(args_info->step_given),
983	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
984	>	check_ambiguity, override, 0, 0,
985	>	"step", 'n',
986	>	additional_error))
987	>	goto failure;
988	>
989		break;
990	<
991	<	case 'r':       /* number of bins for distance.  */
992	<	if (args_info->nrbins_given)
993	<	{
994	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
995	<	clear_args ();
996	<	exit (EXIT_FAILURE);
997	<	}
998	<	args_info->nrbins_given = 1;
999	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
990	>	case 'b':       /* number of bins (general purpose).  */
991	>
992	>
993	>	if (update_arg( (void *)&(args_info->nbins_arg),
994	>	&(args_info->nbins_orig), &(args_info->nbins_given),
995	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
996	>	check_ambiguity, override, 0, 0,
997	>	"nbins", 'b',
998	>	additional_error))
999	>	goto failure;
1000	>
1001		break;
1002	<
1002	>	case 'x':       /* number of bins in x axis.  */
1003	>
1004	>
1005	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
1006	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1007	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1008	>	check_ambiguity, override, 0, 0,
1009	>	"nbins_x", 'x',
1010	>	additional_error))
1011	>	goto failure;
1012	>
1013	>	break;
1014	>	case 'y':       /* number of bins in y axis.  */
1015	>
1016	>
1017	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
1018	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1019	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1020	>	check_ambiguity, override, 0, 0,
1021	>	"nbins_y", 'y',
1022	>	additional_error))
1023	>	goto failure;
1024	>
1025	>	break;
1026		case 'a':       /* number of bins for cos(angle).  */
1027	<	if (args_info->nanglebins_given)
1028	<	{
1029	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1030	<	clear_args ();
1031	<	exit (EXIT_FAILURE);
1032	<	}
1033	<	args_info->nanglebins_given = 1;
1034	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
1027	>
1028	>
1029	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1030	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1031	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1032	>	check_ambiguity, override, 0, 0,
1033	>	"nanglebins", 'a',
1034	>	additional_error))
1035	>	goto failure;
1036	>
1037		break;
1038	<
1039	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1040	<	if (args_info->length_given)
1041	<	{
1042	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1043	<	clear_args ();
1044	<	exit (EXIT_FAILURE);
1045	<	}
1046	<	args_info->length_given = 1;
1047	<	args_info->length_arg = strtod (optarg, NULL);
1038	>	case 'c':       /* cutoff radius (rcut).  */
1039	>
1040	>
1041	>	if (update_arg( (void *)&(args_info->rcut_arg),
1042	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1043	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1044	>	check_ambiguity, override, 0, 0,
1045	>	"rcut", 'c',
1046	>	additional_error))
1047	>	goto failure;
1048	>
1049		break;
1050	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1051	+
1052	+
1053	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1054	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1055	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1056	+	check_ambiguity, override, 0, 0,
1057	+	"zoffset", 'z',
1058	+	additional_error))
1059	+	goto failure;
1060	+
1061	+	break;
1062	+	case 'g':       /* g(r).  */
1063	+
1064	+	if (args_info->staticProps_group_counter && override)
1065	+	reset_group_staticProps (args_info);
1066	+	args_info->staticProps_group_counter += 1;
1067	+
1068	+	if (update_arg( 0 ,
1069	+	0 , &(args_info->gofr_given),
1070	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1071	+	check_ambiguity, override, 0, 0,
1072	+	"gofr", 'g',
1073	+	additional_error))
1074	+	goto failure;
1075	+
1076	+	break;
1077	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1078	+
1079	+	if (args_info->staticProps_group_counter && override)
1080	+	reset_group_staticProps (args_info);
1081	+	args_info->staticProps_group_counter += 1;
1082	+
1083	+	if (update_arg( 0 ,
1084	+	0 , &(args_info->p2_given),
1085	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1086	+	check_ambiguity, override, 0, 0,
1087	+	"p2", 'p',
1088	+	additional_error))
1089	+	goto failure;
1090	+
1091	+	break;
1092	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1093	+
1094	+	if (args_info->staticProps_group_counter && override)
1095	+	reset_group_staticProps (args_info);
1096	+	args_info->staticProps_group_counter += 1;
1097	+
1098	+	if (update_arg( 0 ,
1099	+	0 , &(args_info->scd_given),
1100	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1101	+	check_ambiguity, override, 0, 0,
1102	+	"scd", 's',
1103	+	additional_error))
1104	+	goto failure;
1105	+
1106	+	break;
1107	+	case 'd':       /* density plot.  */
1108	+
1109	+	if (args_info->staticProps_group_counter && override)
1110	+	reset_group_staticProps (args_info);
1111	+	args_info->staticProps_group_counter += 1;
1112	+
1113	+	if (update_arg( 0 ,
1114	+	0 , &(args_info->density_given),
1115	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1116	+	check_ambiguity, override, 0, 0,
1117	+	"density", 'd',
1118	+	additional_error))
1119	+	goto failure;
1120	+
1121	+	break;
1122	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1123	+
1124	+	if (args_info->staticProps_group_counter && override)
1125	+	reset_group_staticProps (args_info);
1126	+	args_info->staticProps_group_counter += 1;
1127	+
1128	+	if (update_arg( 0 ,
1129	+	0 , &(args_info->tet_param_given),
1130	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1131	+	check_ambiguity, override, 0, 0,
1132	+	"tet_param", 'Q',
1133	+	additional_error))
1134	+	goto failure;
1135	+
1136	+	break;
1137
249	–
1138		case 0: /* Long option with no short option */
1139	<	/* select the first stuntdouble set.  */
1140	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1139	>	/* number of bins in z axis.  */
1140	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1141		{
1142	<	if (args_info->sele1_given)
1143	<	{
1144	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1145	<	clear_args ();
1146	<	exit (EXIT_FAILURE);
1147	<	}
1148	<	args_info->sele1_given = 1;
1149	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1150	<	break;
1142	>
1143	>
1144	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1145	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1146	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1147	>	check_ambiguity, override, 0, 0,
1148	>	"nbins_z", '-',
1149	>	additional_error))
1150	>	goto failure;
1151	>
1152		}
1153	+	/* slab width (dz).  */
1154	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1155	+	{
1156
1157	+
1158	+	if (update_arg( (void *)&(args_info->dz_arg),
1159	+	&(args_info->dz_orig), &(args_info->dz_given),
1160	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1161	+	check_ambiguity, override, 0, 0,
1162	+	"dz", '-',
1163	+	additional_error))
1164	+	goto failure;
1165	+
1166	+	}
1167	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1168	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1169	+	{
1170	+
1171	+
1172	+	if (update_arg( (void *)&(args_info->length_arg),
1173	+	&(args_info->length_orig), &(args_info->length_given),
1174	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1175	+	check_ambiguity, override, 0, 0,
1176	+	"length", '-',
1177	+	additional_error))
1178	+	goto failure;
1179	+
1180	+	}
1181	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1182	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1183	+	{
1184	+
1185	+
1186	+	if (update_arg( (void *)&(args_info->zlength_arg),
1187	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1188	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1189	+	check_ambiguity, override, 0, 0,
1190	+	"zlength", '-',
1191	+	additional_error))
1192	+	goto failure;
1193	+
1194	+	}
1195	+	/* select the first stuntdouble set.  */
1196	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1197	+	{
1198	+
1199	+
1200	+	if (update_arg( (void *)&(args_info->sele1_arg),
1201	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1202	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1203	+	check_ambiguity, override, 0, 0,
1204	+	"sele1", '-',
1205	+	additional_error))
1206	+	goto failure;
1207	+
1208	+	}
1209		/* select the second stuntdouble set.  */
1210		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1211		{
268	–	if (args_info->sele2_given)
269	–	{
270	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
271	–	clear_args ();
272	–	exit (EXIT_FAILURE);
273	–	}
274	–	args_info->sele2_given = 1;
275	–	args_info->sele2_arg = gengetopt_strdup (optarg);
276	–	break;
277	–	}
1212
1213	+
1214	+	if (update_arg( (void *)&(args_info->sele2_arg),
1215	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1216	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1217	+	check_ambiguity, override, 0, 0,
1218	+	"sele2", '-',
1219	+	additional_error))
1220	+	goto failure;
1221	+
1222	+	}
1223		/* select the third stuntdouble set.  */
1224		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1225		{
282	–	if (args_info->sele3_given)
283	–	{
284	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
285	–	clear_args ();
286	–	exit (EXIT_FAILURE);
287	–	}
288	–	args_info->sele3_given = 1;
289	–	args_info->sele3_arg = gengetopt_strdup (optarg);
290	–	break;
291	–	}
1226
1227	+
1228	+	if (update_arg( (void *)&(args_info->sele3_arg),
1229	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1230	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1231	+	check_ambiguity, override, 0, 0,
1232	+	"sele3", '-',
1233	+	additional_error))
1234	+	goto failure;
1235	+
1236	+	}
1237		/* select reference (use and only use with --gxyz).  */
1238		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1239		{
1240	<	if (args_info->refsele_given)
1241	<	{
1242	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1243	<	clear_args ();
1244	<	exit (EXIT_FAILURE);
1245	<	}
1246	<	args_info->refsele_given = 1;
1247	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1248	<	break;
1240	>
1241	>
1242	>	if (update_arg( (void *)&(args_info->refsele_arg),
1243	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1244	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1245	>	check_ambiguity, override, 0, 0,
1246	>	"refsele", '-',
1247	>	additional_error))
1248	>	goto failure;
1249	>
1250		}
1251	+	/* select stunt doubles for center-of-mass reference point.  */
1252	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1253	+	{
1254
1255	+
1256	+	if (update_arg( (void *)&(args_info->comsele_arg),
1257	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1258	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1259	+	check_ambiguity, override, 0, 0,
1260	+	"comsele", '-',
1261	+	additional_error))
1262	+	goto failure;
1263	+
1264	+	}
1265	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1266	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1267	+	{
1268	+
1269	+
1270	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1271	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1272	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1273	+	check_ambiguity, override, 0, 0,
1274	+	"seleoffset", '-',
1275	+	additional_error))
1276	+	goto failure;
1277	+
1278	+	}
1279	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1280	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1281	+	{
1282	+
1283	+
1284	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1285	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1286	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1287	+	check_ambiguity, override, 0, 0,
1288	+	"seleoffset2", '-',
1289	+	additional_error))
1290	+	goto failure;
1291	+
1292	+	}
1293		/* molecule name.  */
1294		else if (strcmp (long_options[option_index].name, "molname") == 0)
1295		{
310	–	if (args_info->molname_given)
311	–	{
312	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
313	–	clear_args ();
314	–	exit (EXIT_FAILURE);
315	–	}
316	–	args_info->molname_given = 1;
317	–	args_info->molname_arg = gengetopt_strdup (optarg);
318	–	break;
319	–	}
1296
1297	<	/* begin interanl index.  */
1297	>
1298	>	if (update_arg( (void *)&(args_info->molname_arg),
1299	>	&(args_info->molname_orig), &(args_info->molname_given),
1300	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1301	>	check_ambiguity, override, 0, 0,
1302	>	"molname", '-',
1303	>	additional_error))
1304	>	goto failure;
1305	>
1306	>	}
1307	>	/* begin internal index.  */
1308		else if (strcmp (long_options[option_index].name, "begin") == 0)
1309		{
324	–	if (args_info->begin_given)
325	–	{
326	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
327	–	clear_args ();
328	–	exit (EXIT_FAILURE);
329	–	}
330	–	args_info->begin_given = 1;
331	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
332	–	break;
333	–	}
1310
1311	+
1312	+	if (update_arg( (void *)&(args_info->begin_arg),
1313	+	&(args_info->begin_orig), &(args_info->begin_given),
1314	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1315	+	check_ambiguity, override, 0, 0,
1316	+	"begin", '-',
1317	+	additional_error))
1318	+	goto failure;
1319	+
1320	+	}
1321		/* end internal index.  */
1322		else if (strcmp (long_options[option_index].name, "end") == 0)
1323		{
1324	<	if (args_info->end_given)
1325	<	{
1326	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1327	<	clear_args ();
1328	<	exit (EXIT_FAILURE);
1329	<	}
1330	<	args_info->end_given = 1;
1331	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1332	<	break;
1324	>
1325	>
1326	>	if (update_arg( (void *)&(args_info->end_arg),
1327	>	&(args_info->end_orig), &(args_info->end_given),
1328	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1329	>	check_ambiguity, override, 0, 0,
1330	>	"end", '-',
1331	>	additional_error))
1332	>	goto failure;
1333	>
1334		}
1335	+	/* nanoparticle radius.  */
1336	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1337	+	{
1338
1339	<	/* g(r).  */
1340	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1339	>
1340	>	if (update_arg( (void *)&(args_info->radius_arg),
1341	>	&(args_info->radius_orig), &(args_info->radius_given),
1342	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1343	>	check_ambiguity, override, 0, 0,
1344	>	"radius", '-',
1345	>	additional_error))
1346	>	goto failure;
1347	>
1348	>	}
1349	>	/* bond order parameter (--rcut must be specified).  */
1350	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1351		{
352	–	if (args_info->gofr_given)
353	–	{
354	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
355	–	clear_args ();
356	–	exit (EXIT_FAILURE);
357	–	}
358	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1352
1353	<	break;
1353	>	if (args_info->staticProps_group_counter && override)
1354	>	reset_group_staticProps (args_info);
1355	>	args_info->staticProps_group_counter += 1;
1356	>
1357	>	if (update_arg( 0 ,
1358	>	0 , &(args_info->bo_given),
1359	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1360	>	check_ambiguity, override, 0, 0,
1361	>	"bo", '-',
1362	>	additional_error))
1363	>	goto failure;
1364	>
1365	>	}
1366	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1367	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1368	>	{
1369	>
1370	>	if (args_info->staticProps_group_counter && override)
1371	>	reset_group_staticProps (args_info);
1372	>	args_info->staticProps_group_counter += 1;
1373	>
1374	>	if (update_arg( 0 ,
1375	>	0 , &(args_info->ior_given),
1376	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1377	>	check_ambiguity, override, 0, 0,
1378	>	"ior", '-',
1379	>	additional_error))
1380	>	goto failure;
1381	>
1382	>	}
1383	>	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1384	>	else if (strcmp (long_options[option_index].name, "for") == 0)
1385	>	{
1386	>
1387	>	if (args_info->staticProps_group_counter && override)
1388	>	reset_group_staticProps (args_info);
1389	>	args_info->staticProps_group_counter += 1;
1390	>
1391	>	if (update_arg( 0 ,
1392	>	0 , &(args_info->for_given),
1393	>	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1394	>	check_ambiguity, override, 0, 0,
1395	>	"for", '-',
1396	>	additional_error))
1397	>	goto failure;
1398	>
1399		}
1400	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1401	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1402	+	{
1403
1404	+	if (args_info->staticProps_group_counter && override)
1405	+	reset_group_staticProps (args_info);
1406	+	args_info->staticProps_group_counter += 1;
1407	+
1408	+	if (update_arg( 0 ,
1409	+	0 , &(args_info->bad_given),
1410	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1411	+	check_ambiguity, override, 0, 0,
1412	+	"bad", '-',
1413	+	additional_error))
1414	+	goto failure;
1415	+
1416	+	}
1417	+	/* count of molecules matching selection criteria (and associated statistics).  */
1418	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1419	+	{
1420	+
1421	+	if (args_info->staticProps_group_counter && override)
1422	+	reset_group_staticProps (args_info);
1423	+	args_info->staticProps_group_counter += 1;
1424	+
1425	+	if (update_arg( 0 ,
1426	+	0 , &(args_info->count_given),
1427	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1428	+	check_ambiguity, override, 0, 0,
1429	+	"count", '-',
1430	+	additional_error))
1431	+	goto failure;
1432	+
1433	+	}
1434	+	/* g(z).  */
1435	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1436	+	{
1437	+
1438	+	if (args_info->staticProps_group_counter && override)
1439	+	reset_group_staticProps (args_info);
1440	+	args_info->staticProps_group_counter += 1;
1441	+
1442	+	if (update_arg( 0 ,
1443	+	0 , &(args_info->gofz_given),
1444	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1445	+	check_ambiguity, override, 0, 0,
1446	+	"gofz", '-',
1447	+	additional_error))
1448	+	goto failure;
1449	+
1450	+	}
1451		/* g(r, cos(theta)).  */
1452		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1453		{
366	–	if (args_info->r_theta_given)
367	–	{
368	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
369	–	clear_args ();
370	–	exit (EXIT_FAILURE);
371	–	}
372	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1454
1455	<	break;
1456	<	}
1455	>	if (args_info->staticProps_group_counter && override)
1456	>	reset_group_staticProps (args_info);
1457	>	args_info->staticProps_group_counter += 1;
1458
1459	+	if (update_arg( 0 ,
1460	+	0 , &(args_info->r_theta_given),
1461	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1462	+	check_ambiguity, override, 0, 0,
1463	+	"r_theta", '-',
1464	+	additional_error))
1465	+	goto failure;
1466	+
1467	+	}
1468		/* g(r, cos(omega)).  */
1469		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1470		{
380	–	if (args_info->r_omega_given)
381	–	{
382	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
383	–	clear_args ();
384	–	exit (EXIT_FAILURE);
385	–	}
386	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1471
1472	<	break;
1472	>	if (args_info->staticProps_group_counter && override)
1473	>	reset_group_staticProps (args_info);
1474	>	args_info->staticProps_group_counter += 1;
1475	>
1476	>	if (update_arg( 0 ,
1477	>	0 , &(args_info->r_omega_given),
1478	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1479	>	check_ambiguity, override, 0, 0,
1480	>	"r_omega", '-',
1481	>	additional_error))
1482	>	goto failure;
1483	>
1484		}
1485	+	/* g(r, z).  */
1486	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1487	+	{
1488
1489	+	if (args_info->staticProps_group_counter && override)
1490	+	reset_group_staticProps (args_info);
1491	+	args_info->staticProps_group_counter += 1;
1492	+
1493	+	if (update_arg( 0 ,
1494	+	0 , &(args_info->r_z_given),
1495	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1496	+	check_ambiguity, override, 0, 0,
1497	+	"r_z", '-',
1498	+	additional_error))
1499	+	goto failure;
1500	+
1501	+	}
1502		/* g(cos(theta), cos(omega)).  */
1503		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1504		{
394	–	if (args_info->theta_omega_given)
395	–	{
396	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
397	–	clear_args ();
398	–	exit (EXIT_FAILURE);
399	–	}
400	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1505
1506	<	break;
1507	<	}
1506	>	if (args_info->staticProps_group_counter && override)
1507	>	reset_group_staticProps (args_info);
1508	>	args_info->staticProps_group_counter += 1;
1509
1510	+	if (update_arg( 0 ,
1511	+	0 , &(args_info->theta_omega_given),
1512	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1513	+	check_ambiguity, override, 0, 0,
1514	+	"theta_omega", '-',
1515	+	additional_error))
1516	+	goto failure;
1517	+
1518	+	}
1519		/* g(x, y, z).  */
1520		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1521		{
408	–	if (args_info->gxyz_given)
409	–	{
410	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
411	–	clear_args ();
412	–	exit (EXIT_FAILURE);
413	–	}
414	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1522
1523	<	break;
1523	>	if (args_info->staticProps_group_counter && override)
1524	>	reset_group_staticProps (args_info);
1525	>	args_info->staticProps_group_counter += 1;
1526	>
1527	>	if (update_arg( 0 ,
1528	>	0 , &(args_info->gxyz_given),
1529	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1530	>	check_ambiguity, override, 0, 0,
1531	>	"gxyz", '-',
1532	>	additional_error))
1533	>	goto failure;
1534	>
1535		}
1536	+	/* 2D g(r) (Slab width --dz must be specified).  */
1537	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1538	+	{
1539
1540	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1541	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1540	>	if (args_info->staticProps_group_counter && override)
1541	>	reset_group_staticProps (args_info);
1542	>	args_info->staticProps_group_counter += 1;
1543	>
1544	>	if (update_arg( 0 ,
1545	>	0 , &(args_info->twodgofr_given),
1546	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1547	>	check_ambiguity, override, 0, 0,
1548	>	"twodgofr", '-',
1549	>	additional_error))
1550	>	goto failure;
1551	>
1552	>	}
1553	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1554	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1555		{
422	–	if (args_info->p2_given)
423	–	{
424	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
425	–	clear_args ();
426	–	exit (EXIT_FAILURE);
427	–	}
428	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1556
1557	<	break;
1557	>	if (args_info->staticProps_group_counter && override)
1558	>	reset_group_staticProps (args_info);
1559	>	args_info->staticProps_group_counter += 1;
1560	>
1561	>	if (update_arg( 0 ,
1562	>	0 , &(args_info->rp2_given),
1563	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1564	>	check_ambiguity, override, 0, 0,
1565	>	"rp2", '-',
1566	>	additional_error))
1567	>	goto failure;
1568	>
1569		}
1570	+	/* slab density.  */
1571	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1572	+	{
1573
1574	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1575	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1574	>	if (args_info->staticProps_group_counter && override)
1575	>	reset_group_staticProps (args_info);
1576	>	args_info->staticProps_group_counter += 1;
1577	>
1578	>	if (update_arg( 0 ,
1579	>	0 , &(args_info->slab_density_given),
1580	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1581	>	check_ambiguity, override, 0, 0,
1582	>	"slab_density", '-',
1583	>	additional_error))
1584	>	goto failure;
1585	>
1586	>	}
1587	>	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1588	>	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1589		{
436	–	if (args_info->scd_given)
437	–	{
438	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
439	–	clear_args ();
440	–	exit (EXIT_FAILURE);
441	–	}
442	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1590
1591	<	break;
1591	>	if (args_info->staticProps_group_counter && override)
1592	>	reset_group_staticProps (args_info);
1593	>	args_info->staticProps_group_counter += 1;
1594	>
1595	>	if (update_arg( 0 ,
1596	>	0 , &(args_info->p_angle_given),
1597	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1598	>	check_ambiguity, override, 0, 0,
1599	>	"p_angle", '-',
1600	>	additional_error))
1601	>	goto failure;
1602	>
1603		}
1604	+	/* hxy.  */
1605	+	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1606	+	{
1607
1608	<	/* density plot (--sele1 must be specified).  */
1609	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1608	>	if (args_info->staticProps_group_counter && override)
1609	>	reset_group_staticProps (args_info);
1610	>	args_info->staticProps_group_counter += 1;
1611	>
1612	>	if (update_arg( 0 ,
1613	>	0 , &(args_info->hxy_given),
1614	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1615	>	check_ambiguity, override, 0, 0,
1616	>	"hxy", '-',
1617	>	additional_error))
1618	>	goto failure;
1619	>
1620	>	}
1621	>	/* rho of R.  */
1622	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1623		{
450	–	if (args_info->density_given)
451	–	{
452	–	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
453	–	clear_args ();
454	–	exit (EXIT_FAILURE);
455	–	}
456	–	args_info->density_given = 1; staticProps_group_counter += 1;
1624
1625	<	break;
1625	>	if (args_info->staticProps_group_counter && override)
1626	>	reset_group_staticProps (args_info);
1627	>	args_info->staticProps_group_counter += 1;
1628	>
1629	>	if (update_arg( 0 ,
1630	>	0 , &(args_info->rho_r_given),
1631	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1632	>	check_ambiguity, override, 0, 0,
1633	>	"rho_r", '-',
1634	>	additional_error))
1635	>	goto failure;
1636	>
1637		}
1638	+	/* angle of R.  */
1639	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1640	+	{
1641
1642	<	/* slab density (--sele1 must be specified).  */
1643	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1642	>	if (args_info->staticProps_group_counter && override)
1643	>	reset_group_staticProps (args_info);
1644	>	args_info->staticProps_group_counter += 1;
1645	>
1646	>	if (update_arg( 0 ,
1647	>	0 , &(args_info->angle_r_given),
1648	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1649	>	check_ambiguity, override, 0, 0,
1650	>	"angle_r", '-',
1651	>	additional_error))
1652	>	goto failure;
1653	>
1654	>	}
1655	>	/* hull volume of nanoparticle.  */
1656	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1657		{
464	–	if (args_info->slab_density_given)
465	–	{
466	–	fprintf (stderr, "%s: `--slab_density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
467	–	clear_args ();
468	–	exit (EXIT_FAILURE);
469	–	}
470	–	args_info->slab_density_given = 1; staticProps_group_counter += 1;
1658
1659	<	break;
1659	>	if (args_info->staticProps_group_counter && override)
1660	>	reset_group_staticProps (args_info);
1661	>	args_info->staticProps_group_counter += 1;
1662	>
1663	>	if (update_arg( 0 ,
1664	>	0 , &(args_info->hullvol_given),
1665	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1666	>	check_ambiguity, override, 0, 0,
1667	>	"hullvol", '-',
1668	>	additional_error))
1669	>	goto failure;
1670	>
1671		}
1672	+	/* length of nanorod.  */
1673	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1674	+	{
1675
1676	<
1676	>	if (args_info->staticProps_group_counter && override)
1677	>	reset_group_staticProps (args_info);
1678	>	args_info->staticProps_group_counter += 1;
1679	>
1680	>	if (update_arg( 0 ,
1681	>	0 , &(args_info->rodlength_given),
1682	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1683	>	check_ambiguity, override, 0, 0,
1684	>	"rodlength", '-',
1685	>	additional_error))
1686	>	goto failure;
1687	>
1688	>	}
1689	>	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1690	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1691	>	{
1692	>
1693	>	if (args_info->staticProps_group_counter && override)
1694	>	reset_group_staticProps (args_info);
1695	>	args_info->staticProps_group_counter += 1;
1696	>
1697	>	if (update_arg( 0 ,
1698	>	0 , &(args_info->tet_param_z_given),
1699	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1700	>	check_ambiguity, override, 0, 0,
1701	>	"tet_param_z", '-',
1702	>	additional_error))
1703	>	goto failure;
1704	>
1705	>	}
1706	>	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1707	>	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1708	>	{
1709	>
1710	>	if (args_info->staticProps_group_counter && override)
1711	>	reset_group_staticProps (args_info);
1712	>	args_info->staticProps_group_counter += 1;
1713	>
1714	>	if (update_arg( 0 ,
1715	>	0 , &(args_info->rnemdz_given),
1716	>	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1717	>	check_ambiguity, override, 0, 0,
1718	>	"rnemdz", '-',
1719	>	additional_error))
1720	>	goto failure;
1721	>
1722	>	}
1723	>	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1724	>	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1725	>	{
1726	>
1727	>	if (args_info->staticProps_group_counter && override)
1728	>	reset_group_staticProps (args_info);
1729	>	args_info->staticProps_group_counter += 1;
1730	>
1731	>	if (update_arg( 0 ,
1732	>	0 , &(args_info->rnemdr_given),
1733	>	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1734	>	check_ambiguity, override, 0, 0,
1735	>	"rnemdr", '-',
1736	>	additional_error))
1737	>	goto failure;
1738	>
1739	>	}
1740	>	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1741	>	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1742	>	{
1743	>
1744	>	if (args_info->staticProps_group_counter && override)
1745	>	reset_group_staticProps (args_info);
1746	>	args_info->staticProps_group_counter += 1;
1747	>
1748	>	if (update_arg( 0 ,
1749	>	0 , &(args_info->rnemdrt_given),
1750	>	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1751	>	check_ambiguity, override, 0, 0,
1752	>	"rnemdrt", '-',
1753	>	additional_error))
1754	>	goto failure;
1755	>
1756	>	}
1757	>	/* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1758	>	else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1759	>	{
1760	>
1761	>	if (args_info->staticProps_group_counter && override)
1762	>	reset_group_staticProps (args_info);
1763	>	args_info->staticProps_group_counter += 1;
1764	>
1765	>	if (update_arg( 0 ,
1766	>	0 , &(args_info->nitrile_given),
1767	>	&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1768	>	check_ambiguity, override, 0, 0,
1769	>	"nitrile", '-',
1770	>	additional_error))
1771	>	goto failure;
1772	>
1773	>	}
1774	>
1775	>	break;
1776		case '?':       /* Invalid option.  */
1777		/* `getopt_long' already printed an error message.  */
1778	<	exit (EXIT_FAILURE);
1778	>	goto failure;
1779
1780		default:        /* bug: option not considered.  */
1781	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1781	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1782		abort ();
1783		} /* switch */
1784		} /* while */
1785
1786	<	if ( staticProps_group_counter != 1)
1786	>	if (args_info->staticProps_group_counter > 1)
1787		{
1788	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1789	<	missing_required_options = 1;
1788	>	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 : ""));
1789	>	error = 1;
1790		}
1791
1792
1793	<	if (! args_info->input_given)
1793	>
1794	>	if (check_required)
1795		{
1796	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
496	<	missing_required_options = 1;
1796	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1797		}
498	–	if ( missing_required_options )
499	–	exit (EXIT_FAILURE);
1798
1799	+	cmdline_parser_release (&local_args_info);
1800	+
1801	+	if ( error )
1802	+	return (EXIT_FAILURE);
1803	+
1804	+	if (optind < argc)
1805	+	{
1806	+	int i = 0 ;
1807	+	int found_prog_name = 0;
1808	+	/* whether program name, i.e., argv[0], is in the remaining args
1809	+	(this may happen with some implementations of getopt,
1810	+	but surely not with the one included by gengetopt) */
1811	+
1812	+	i = optind;
1813	+	while (i < argc)
1814	+	if (argv[i++] == argv[0]) {
1815	+	found_prog_name = 1;
1816	+	break;
1817	+	}
1818	+	i = 0;
1819	+
1820	+	args_info->inputs_num = argc - optind - found_prog_name;
1821	+	args_info->inputs =
1822	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1823	+	while (optind < argc)
1824	+	if (argv[optind++] != argv[0])
1825	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1826	+	}
1827	+
1828		return 0;
1829	+
1830	+	failure:
1831	+
1832	+	cmdline_parser_release (&local_args_info);
1833	+	return (EXIT_FAILURE);
1834		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1994 by gezelter, Wed Apr 30 18:50:45 2014 UTC

#	Line 0 | Line 1
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