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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 1998 by gezelter, Fri May 30 19:48:35 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	>	"      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96	>	"  -m, --multipole               average multipole moment contained within a \n                                  cutoff sphere",
97	>	0
98	>	};
99
100	<	/* gengetopt_strdup() */
101	<	/* strdup.c replacement of strdup, which is not standard */
102	<	char *
103	<	gengetopt_strdup (const char *s)
104	<	{
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	<	}
100	>	typedef enum {ARG_NO
101	>	, ARG_STRING
102	>	, ARG_INT
103	>	, ARG_DOUBLE
104	>	} cmdline_parser_arg_type;
105
106	<	int
107	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
108	<	{
109	<	int c;        /* Character of the parsed option.  */
84	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
86	<
106	>	static
107	>	void clear_given (struct gengetopt_args_info *args_info);
108	>	static
109	>	void clear_args (struct gengetopt_args_info *args_info);
110
111	+	static int
112	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
113	+	struct cmdline_parser_params *params, const char *additional_error);
114	+
115	+	static int
116	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
117	+
118	+	static char *
119	+	gengetopt_strdup (const char *s);
120	+
121	+	static
122	+	void clear_given (struct gengetopt_args_info *args_info)
123	+	{
124		args_info->help_given = 0 ;
125		args_info->version_given = 0 ;
126		args_info->input_given = 0 ;
127		args_info->output_given = 0 ;
128		args_info->step_given = 0 ;
129	<	args_info->nrbins_given = 0 ;
129	>	args_info->nbins_given = 0 ;
130	>	args_info->nbins_x_given = 0 ;
131	>	args_info->nbins_y_given = 0 ;
132	>	args_info->nbins_z_given = 0 ;
133		args_info->nanglebins_given = 0 ;
134	+	args_info->rcut_given = 0 ;
135	+	args_info->dz_given = 0 ;
136		args_info->length_given = 0 ;
137	+	args_info->zlength_given = 0 ;
138	+	args_info->zoffset_given = 0 ;
139		args_info->sele1_given = 0 ;
140		args_info->sele2_given = 0 ;
141		args_info->sele3_given = 0 ;
142		args_info->refsele_given = 0 ;
143	+	args_info->comsele_given = 0 ;
144	+	args_info->seleoffset_given = 0 ;
145	+	args_info->seleoffset2_given = 0 ;
146		args_info->molname_given = 0 ;
147		args_info->begin_given = 0 ;
148		args_info->end_given = 0 ;
149	+	args_info->radius_given = 0 ;
150	+	args_info->bo_given = 0 ;
151	+	args_info->ior_given = 0 ;
152	+	args_info->for_given = 0 ;
153	+	args_info->bad_given = 0 ;
154	+	args_info->count_given = 0 ;
155		args_info->gofr_given = 0 ;
156	+	args_info->gofz_given = 0 ;
157		args_info->r_theta_given = 0 ;
158		args_info->r_omega_given = 0 ;
159	+	args_info->r_z_given = 0 ;
160		args_info->theta_omega_given = 0 ;
161		args_info->gxyz_given = 0 ;
162	+	args_info->twodgofr_given = 0 ;
163		args_info->p2_given = 0 ;
164	+	args_info->rp2_given = 0 ;
165		args_info->scd_given = 0 ;
166		args_info->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->slab_density_given = 0 ;
168	>	args_info->p_angle_given = 0 ;
169	>	args_info->hxy_given = 0 ;
170	>	args_info->rho_r_given = 0 ;
171	>	args_info->angle_r_given = 0 ;
172	>	args_info->hullvol_given = 0 ;
173	>	args_info->rodlength_given = 0 ;
174	>	args_info->tet_param_given = 0 ;
175	>	args_info->tet_param_z_given = 0 ;
176	>	args_info->rnemdz_given = 0 ;
177	>	args_info->rnemdr_given = 0 ;
178	>	args_info->rnemdrt_given = 0 ;
179	>	args_info->nitrile_given = 0 ;
180	>	args_info->multipole_given = 0 ;
181	>	args_info->staticProps_group_counter = 0 ;
182		}
183
184	<	clear_args();
184	>	static
185	>	void clear_args (struct gengetopt_args_info *args_info)
186	>	{
187	>	FIX_UNUSED (args_info);
188	>	args_info->input_arg = NULL;
189	>	args_info->input_orig = NULL;
190	>	args_info->output_arg = NULL;
191	>	args_info->output_orig = NULL;
192	>	args_info->step_arg = 1;
193	>	args_info->step_orig = NULL;
194	>	args_info->nbins_arg = 100;
195	>	args_info->nbins_orig = NULL;
196	>	args_info->nbins_x_arg = 100;
197	>	args_info->nbins_x_orig = NULL;
198	>	args_info->nbins_y_arg = 100;
199	>	args_info->nbins_y_orig = NULL;
200	>	args_info->nbins_z_arg = 100;
201	>	args_info->nbins_z_orig = NULL;
202	>	args_info->nanglebins_arg = 50;
203	>	args_info->nanglebins_orig = NULL;
204	>	args_info->rcut_orig = NULL;
205	>	args_info->dz_orig = NULL;
206	>	args_info->length_orig = NULL;
207	>	args_info->zlength_orig = NULL;
208	>	args_info->zoffset_arg = 0;
209	>	args_info->zoffset_orig = NULL;
210	>	args_info->sele1_arg = NULL;
211	>	args_info->sele1_orig = NULL;
212	>	args_info->sele2_arg = NULL;
213	>	args_info->sele2_orig = NULL;
214	>	args_info->sele3_arg = NULL;
215	>	args_info->sele3_orig = NULL;
216	>	args_info->refsele_arg = NULL;
217	>	args_info->refsele_orig = NULL;
218	>	args_info->comsele_arg = NULL;
219	>	args_info->comsele_orig = NULL;
220	>	args_info->seleoffset_orig = NULL;
221	>	args_info->seleoffset2_orig = NULL;
222	>	args_info->molname_arg = NULL;
223	>	args_info->molname_orig = NULL;
224	>	args_info->begin_orig = NULL;
225	>	args_info->end_orig = NULL;
226	>	args_info->radius_orig = NULL;
227	>
228	>	}
229	>
230	>	static
231	>	void init_args_info(struct gengetopt_args_info *args_info)
232	>	{
233	>
234	>
235	>	args_info->help_help = gengetopt_args_info_help[0] ;
236	>	args_info->version_help = gengetopt_args_info_help[1] ;
237	>	args_info->input_help = gengetopt_args_info_help[2] ;
238	>	args_info->output_help = gengetopt_args_info_help[3] ;
239	>	args_info->step_help = gengetopt_args_info_help[4] ;
240	>	args_info->nbins_help = gengetopt_args_info_help[5] ;
241	>	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
242	>	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
243	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
244	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
245	>	args_info->rcut_help = gengetopt_args_info_help[10] ;
246	>	args_info->dz_help = gengetopt_args_info_help[11] ;
247	>	args_info->length_help = gengetopt_args_info_help[12] ;
248	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
249	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
250	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
251	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
252	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
253	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
254	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
255	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
256	>	args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
257	>	args_info->molname_help = gengetopt_args_info_help[22] ;
258	>	args_info->begin_help = gengetopt_args_info_help[23] ;
259	>	args_info->end_help = gengetopt_args_info_help[24] ;
260	>	args_info->radius_help = gengetopt_args_info_help[25] ;
261	>	args_info->bo_help = gengetopt_args_info_help[27] ;
262	>	args_info->ior_help = gengetopt_args_info_help[28] ;
263	>	args_info->for_help = gengetopt_args_info_help[29] ;
264	>	args_info->bad_help = gengetopt_args_info_help[30] ;
265	>	args_info->count_help = gengetopt_args_info_help[31] ;
266	>	args_info->gofr_help = gengetopt_args_info_help[32] ;
267	>	args_info->gofz_help = gengetopt_args_info_help[33] ;
268	>	args_info->r_theta_help = gengetopt_args_info_help[34] ;
269	>	args_info->r_omega_help = gengetopt_args_info_help[35] ;
270	>	args_info->r_z_help = gengetopt_args_info_help[36] ;
271	>	args_info->theta_omega_help = gengetopt_args_info_help[37] ;
272	>	args_info->gxyz_help = gengetopt_args_info_help[38] ;
273	>	args_info->twodgofr_help = gengetopt_args_info_help[39] ;
274	>	args_info->p2_help = gengetopt_args_info_help[40] ;
275	>	args_info->rp2_help = gengetopt_args_info_help[41] ;
276	>	args_info->scd_help = gengetopt_args_info_help[42] ;
277	>	args_info->density_help = gengetopt_args_info_help[43] ;
278	>	args_info->slab_density_help = gengetopt_args_info_help[44] ;
279	>	args_info->p_angle_help = gengetopt_args_info_help[45] ;
280	>	args_info->hxy_help = gengetopt_args_info_help[46] ;
281	>	args_info->rho_r_help = gengetopt_args_info_help[47] ;
282	>	args_info->angle_r_help = gengetopt_args_info_help[48] ;
283	>	args_info->hullvol_help = gengetopt_args_info_help[49] ;
284	>	args_info->rodlength_help = gengetopt_args_info_help[50] ;
285	>	args_info->tet_param_help = gengetopt_args_info_help[51] ;
286	>	args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
287	>	args_info->rnemdz_help = gengetopt_args_info_help[53] ;
288	>	args_info->rnemdr_help = gengetopt_args_info_help[54] ;
289	>	args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
290	>	args_info->nitrile_help = gengetopt_args_info_help[56] ;
291	>	args_info->multipole_help = gengetopt_args_info_help[57] ;
292	>
293	>	}
294	>
295	>	void
296	>	cmdline_parser_print_version (void)
297	>	{
298	>	printf ("%s %s\n",
299	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
300	>	CMDLINE_PARSER_VERSION);
301	>	}
302	>
303	>	static void print_help_common(void) {
304	>	cmdline_parser_print_version ();
305	>
306	>	if (strlen(gengetopt_args_info_purpose) > 0)
307	>	printf("\n%s\n", gengetopt_args_info_purpose);
308	>
309	>	if (strlen(gengetopt_args_info_usage) > 0)
310	>	printf("\n%s\n", gengetopt_args_info_usage);
311	>
312	>	printf("\n");
313	>
314	>	if (strlen(gengetopt_args_info_description) > 0)
315	>	printf("%s\n\n", gengetopt_args_info_description);
316	>	}
317	>
318	>	void
319	>	cmdline_parser_print_help (void)
320	>	{
321	>	int i = 0;
322	>	print_help_common();
323	>	while (gengetopt_args_info_help[i])
324	>	printf("%s\n", gengetopt_args_info_help[i++]);
325	>	}
326	>
327	>	void
328	>	cmdline_parser_init (struct gengetopt_args_info *args_info)
329	>	{
330	>	clear_given (args_info);
331	>	clear_args (args_info);
332	>	init_args_info (args_info);
333	>
334	>	args_info->inputs = 0;
335	>	args_info->inputs_num = 0;
336	>	}
337	>
338	>	void
339	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
340	>	{
341	>	if (params)
342	>	{
343	>	params->override = 0;
344	>	params->initialize = 1;
345	>	params->check_required = 1;
346	>	params->check_ambiguity = 0;
347	>	params->print_errors = 1;
348	>	}
349	>	}
350	>
351	>	struct cmdline_parser_params *
352	>	cmdline_parser_params_create(void)
353	>	{
354	>	struct cmdline_parser_params *params =
355	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
356	>	cmdline_parser_params_init(params);
357	>	return params;
358	>	}
359	>
360	>	static void
361	>	free_string_field (char **s)
362	>	{
363	>	if (*s)
364	>	{
365	>	free (*s);
366	>	*s = 0;
367	>	}
368	>	}
369	>
370	>
371	>	static void
372	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
373	>	{
374	>	unsigned int i;
375	>	free_string_field (&(args_info->input_arg));
376	>	free_string_field (&(args_info->input_orig));
377	>	free_string_field (&(args_info->output_arg));
378	>	free_string_field (&(args_info->output_orig));
379	>	free_string_field (&(args_info->step_orig));
380	>	free_string_field (&(args_info->nbins_orig));
381	>	free_string_field (&(args_info->nbins_x_orig));
382	>	free_string_field (&(args_info->nbins_y_orig));
383	>	free_string_field (&(args_info->nbins_z_orig));
384	>	free_string_field (&(args_info->nanglebins_orig));
385	>	free_string_field (&(args_info->rcut_orig));
386	>	free_string_field (&(args_info->dz_orig));
387	>	free_string_field (&(args_info->length_orig));
388	>	free_string_field (&(args_info->zlength_orig));
389	>	free_string_field (&(args_info->zoffset_orig));
390	>	free_string_field (&(args_info->sele1_arg));
391	>	free_string_field (&(args_info->sele1_orig));
392	>	free_string_field (&(args_info->sele2_arg));
393	>	free_string_field (&(args_info->sele2_orig));
394	>	free_string_field (&(args_info->sele3_arg));
395	>	free_string_field (&(args_info->sele3_orig));
396	>	free_string_field (&(args_info->refsele_arg));
397	>	free_string_field (&(args_info->refsele_orig));
398	>	free_string_field (&(args_info->comsele_arg));
399	>	free_string_field (&(args_info->comsele_orig));
400	>	free_string_field (&(args_info->seleoffset_orig));
401	>	free_string_field (&(args_info->seleoffset2_orig));
402	>	free_string_field (&(args_info->molname_arg));
403	>	free_string_field (&(args_info->molname_orig));
404	>	free_string_field (&(args_info->begin_orig));
405	>	free_string_field (&(args_info->end_orig));
406	>	free_string_field (&(args_info->radius_orig));
407	>
408	>
409	>	for (i = 0; i < args_info->inputs_num; ++i)
410	>	free (args_info->inputs [i]);
411	>
412	>	if (args_info->inputs_num)
413	>	free (args_info->inputs);
414	>
415	>	clear_given (args_info);
416	>	}
417	>
418	>
419	>	static void
420	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
421	>	{
422	>	FIX_UNUSED (values);
423	>	if (arg) {
424	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
425	>	} else {
426	>	fprintf(outfile, "%s\n", opt);
427	>	}
428	>	}
429	>
430	>
431	>	int
432	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
433	>	{
434	>	int i = 0;
435	>
436	>	if (!outfile)
437	>	{
438	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
439	>	return EXIT_FAILURE;
440	>	}
441	>
442	>	if (args_info->help_given)
443	>	write_into_file(outfile, "help", 0, 0 );
444	>	if (args_info->version_given)
445	>	write_into_file(outfile, "version", 0, 0 );
446	>	if (args_info->input_given)
447	>	write_into_file(outfile, "input", args_info->input_orig, 0);
448	>	if (args_info->output_given)
449	>	write_into_file(outfile, "output", args_info->output_orig, 0);
450	>	if (args_info->step_given)
451	>	write_into_file(outfile, "step", args_info->step_orig, 0);
452	>	if (args_info->nbins_given)
453	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
454	>	if (args_info->nbins_x_given)
455	>	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
456	>	if (args_info->nbins_y_given)
457	>	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
458	>	if (args_info->nbins_z_given)
459	>	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
460	>	if (args_info->nanglebins_given)
461	>	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
462	>	if (args_info->rcut_given)
463	>	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
464	>	if (args_info->dz_given)
465	>	write_into_file(outfile, "dz", args_info->dz_orig, 0);
466	>	if (args_info->length_given)
467	>	write_into_file(outfile, "length", args_info->length_orig, 0);
468	>	if (args_info->zlength_given)
469	>	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
470	>	if (args_info->zoffset_given)
471	>	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
472	>	if (args_info->sele1_given)
473	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
474	>	if (args_info->sele2_given)
475	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
476	>	if (args_info->sele3_given)
477	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
478	>	if (args_info->refsele_given)
479	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
480	>	if (args_info->comsele_given)
481	>	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
482	>	if (args_info->seleoffset_given)
483	>	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
484	>	if (args_info->seleoffset2_given)
485	>	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
486	>	if (args_info->molname_given)
487	>	write_into_file(outfile, "molname", args_info->molname_orig, 0);
488	>	if (args_info->begin_given)
489	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
490	>	if (args_info->end_given)
491	>	write_into_file(outfile, "end", args_info->end_orig, 0);
492	>	if (args_info->radius_given)
493	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
494	>	if (args_info->bo_given)
495	>	write_into_file(outfile, "bo", 0, 0 );
496	>	if (args_info->ior_given)
497	>	write_into_file(outfile, "ior", 0, 0 );
498	>	if (args_info->for_given)
499	>	write_into_file(outfile, "for", 0, 0 );
500	>	if (args_info->bad_given)
501	>	write_into_file(outfile, "bad", 0, 0 );
502	>	if (args_info->count_given)
503	>	write_into_file(outfile, "count", 0, 0 );
504	>	if (args_info->gofr_given)
505	>	write_into_file(outfile, "gofr", 0, 0 );
506	>	if (args_info->gofz_given)
507	>	write_into_file(outfile, "gofz", 0, 0 );
508	>	if (args_info->r_theta_given)
509	>	write_into_file(outfile, "r_theta", 0, 0 );
510	>	if (args_info->r_omega_given)
511	>	write_into_file(outfile, "r_omega", 0, 0 );
512	>	if (args_info->r_z_given)
513	>	write_into_file(outfile, "r_z", 0, 0 );
514	>	if (args_info->theta_omega_given)
515	>	write_into_file(outfile, "theta_omega", 0, 0 );
516	>	if (args_info->gxyz_given)
517	>	write_into_file(outfile, "gxyz", 0, 0 );
518	>	if (args_info->twodgofr_given)
519	>	write_into_file(outfile, "twodgofr", 0, 0 );
520	>	if (args_info->p2_given)
521	>	write_into_file(outfile, "p2", 0, 0 );
522	>	if (args_info->rp2_given)
523	>	write_into_file(outfile, "rp2", 0, 0 );
524	>	if (args_info->scd_given)
525	>	write_into_file(outfile, "scd", 0, 0 );
526	>	if (args_info->density_given)
527	>	write_into_file(outfile, "density", 0, 0 );
528	>	if (args_info->slab_density_given)
529	>	write_into_file(outfile, "slab_density", 0, 0 );
530	>	if (args_info->p_angle_given)
531	>	write_into_file(outfile, "p_angle", 0, 0 );
532	>	if (args_info->hxy_given)
533	>	write_into_file(outfile, "hxy", 0, 0 );
534	>	if (args_info->rho_r_given)
535	>	write_into_file(outfile, "rho_r", 0, 0 );
536	>	if (args_info->angle_r_given)
537	>	write_into_file(outfile, "angle_r", 0, 0 );
538	>	if (args_info->hullvol_given)
539	>	write_into_file(outfile, "hullvol", 0, 0 );
540	>	if (args_info->rodlength_given)
541	>	write_into_file(outfile, "rodlength", 0, 0 );
542	>	if (args_info->tet_param_given)
543	>	write_into_file(outfile, "tet_param", 0, 0 );
544	>	if (args_info->tet_param_z_given)
545	>	write_into_file(outfile, "tet_param_z", 0, 0 );
546	>	if (args_info->rnemdz_given)
547	>	write_into_file(outfile, "rnemdz", 0, 0 );
548	>	if (args_info->rnemdr_given)
549	>	write_into_file(outfile, "rnemdr", 0, 0 );
550	>	if (args_info->rnemdrt_given)
551	>	write_into_file(outfile, "rnemdrt", 0, 0 );
552	>	if (args_info->nitrile_given)
553	>	write_into_file(outfile, "nitrile", 0, 0 );
554	>	if (args_info->multipole_given)
555	>	write_into_file(outfile, "multipole", 0, 0 );
556	>
557
558	+	i = EXIT_SUCCESS;
559	+	return i;
560	+	}
561	+
562	+	int
563	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
564	+	{
565	+	FILE *outfile;
566	+	int i = 0;
567	+
568	+	outfile = fopen(filename, "w");
569	+
570	+	if (!outfile)
571	+	{
572	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
573	+	return EXIT_FAILURE;
574	+	}
575	+
576	+	i = cmdline_parser_dump(outfile, args_info);
577	+	fclose (outfile);
578	+
579	+	return i;
580	+	}
581	+
582	+	void
583	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
584	+	{
585	+	cmdline_parser_release (args_info);
586	+	}
587	+
588	+	/** @brief replacement of strdup, which is not standard */
589	+	char *
590	+	gengetopt_strdup (const char *s)
591	+	{
592	+	char *result = 0;
593	+	if (!s)
594	+	return result;
595	+
596	+	result = (char*)malloc(strlen(s) + 1);
597	+	if (result == (char*)0)
598	+	return (char*)0;
599	+	strcpy(result, s);
600	+	return result;
601	+	}
602	+
603	+	static void
604	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
605	+	{
606	+	if (! args_info->staticProps_group_counter)
607	+	return;
608	+
609	+	args_info->bo_given = 0 ;
610	+	args_info->ior_given = 0 ;
611	+	args_info->for_given = 0 ;
612	+	args_info->bad_given = 0 ;
613	+	args_info->count_given = 0 ;
614	+	args_info->gofr_given = 0 ;
615	+	args_info->gofz_given = 0 ;
616	+	args_info->r_theta_given = 0 ;
617	+	args_info->r_omega_given = 0 ;
618	+	args_info->r_z_given = 0 ;
619	+	args_info->theta_omega_given = 0 ;
620	+	args_info->gxyz_given = 0 ;
621	+	args_info->twodgofr_given = 0 ;
622	+	args_info->p2_given = 0 ;
623	+	args_info->rp2_given = 0 ;
624	+	args_info->scd_given = 0 ;
625	+	args_info->density_given = 0 ;
626	+	args_info->slab_density_given = 0 ;
627	+	args_info->p_angle_given = 0 ;
628	+	args_info->hxy_given = 0 ;
629	+	args_info->rho_r_given = 0 ;
630	+	args_info->angle_r_given = 0 ;
631	+	args_info->hullvol_given = 0 ;
632	+	args_info->rodlength_given = 0 ;
633	+	args_info->tet_param_given = 0 ;
634	+	args_info->tet_param_z_given = 0 ;
635	+	args_info->rnemdz_given = 0 ;
636	+	args_info->rnemdr_given = 0 ;
637	+	args_info->rnemdrt_given = 0 ;
638	+	args_info->nitrile_given = 0 ;
639	+	args_info->multipole_given = 0 ;
640	+
641	+	args_info->staticProps_group_counter = 0;
642	+	}
643	+
644	+	int
645	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
646	+	{
647	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
648	+	}
649	+
650	+	int
651	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
652	+	struct cmdline_parser_params *params)
653	+	{
654	+	int result;
655	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
656	+
657	+	if (result == EXIT_FAILURE)
658	+	{
659	+	cmdline_parser_free (args_info);
660	+	exit (EXIT_FAILURE);
661	+	}
662	+
663	+	return result;
664	+	}
665	+
666	+	int
667	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
668	+	{
669	+	int result;
670	+	struct cmdline_parser_params params;
671	+
672	+	params.override = override;
673	+	params.initialize = initialize;
674	+	params.check_required = check_required;
675	+	params.check_ambiguity = 0;
676	+	params.print_errors = 1;
677	+
678	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
679	+
680	+	if (result == EXIT_FAILURE)
681	+	{
682	+	cmdline_parser_free (args_info);
683	+	exit (EXIT_FAILURE);
684	+	}
685	+
686	+	return result;
687	+	}
688	+
689	+	int
690	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
691	+	{
692	+	int result = EXIT_SUCCESS;
693	+
694	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
695	+	result = EXIT_FAILURE;
696	+
697	+	if (result == EXIT_FAILURE)
698	+	{
699	+	cmdline_parser_free (args_info);
700	+	exit (EXIT_FAILURE);
701	+	}
702	+
703	+	return result;
704	+	}
705	+
706	+	int
707	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
708	+	{
709	+	int error = 0;
710	+	FIX_UNUSED (additional_error);
711	+
712	+	/* checks for required options */
713	+	if (! args_info->input_given)
714	+	{
715	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
716	+	error = 1;
717	+	}
718	+
719	+	if (args_info->staticProps_group_counter == 0)
720	+	{
721	+	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 : ""));
722	+	error = 1;
723	+	}
724	+
725	+
726	+	/* checks for dependences among options */
727	+
728	+	return error;
729	+	}
730	+
731	+
732	+	static char *package_name = 0;
733	+
734	+	/**
735	+	* @brief updates an option
736	+	* @param field the generic pointer to the field to update
737	+	* @param orig_field the pointer to the orig field
738	+	* @param field_given the pointer to the number of occurrence of this option
739	+	* @param prev_given the pointer to the number of occurrence already seen
740	+	* @param value the argument for this option (if null no arg was specified)
741	+	* @param possible_values the possible values for this option (if specified)
742	+	* @param default_value the default value (in case the option only accepts fixed values)
743	+	* @param arg_type the type of this option
744	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
745	+	* @param override @see cmdline_parser_params.override
746	+	* @param no_free whether to free a possible previous value
747	+	* @param multiple_option whether this is a multiple option
748	+	* @param long_opt the corresponding long option
749	+	* @param short_opt the corresponding short option (or '-' if none)
750	+	* @param additional_error possible further error specification
751	+	*/
752	+	static
753	+	int update_arg(void *field, char **orig_field,
754	+	unsigned int *field_given, unsigned int *prev_given,
755	+	char *value, const char *possible_values[],
756	+	const char *default_value,
757	+	cmdline_parser_arg_type arg_type,
758	+	int check_ambiguity, int override,
759	+	int no_free, int multiple_option,
760	+	const char *long_opt, char short_opt,
761	+	const char *additional_error)
762	+	{
763	+	char *stop_char = 0;
764	+	const char *val = value;
765	+	int found;
766	+	char **string_field;
767	+	FIX_UNUSED (field);
768	+
769	+	stop_char = 0;
770	+	found = 0;
771	+
772	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
773	+	{
774	+	if (short_opt != '-')
775	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
776	+	package_name, long_opt, short_opt,
777	+	(additional_error ? additional_error : ""));
778	+	else
779	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
780	+	package_name, long_opt,
781	+	(additional_error ? additional_error : ""));
782	+	return 1; /* failure */
783	+	}
784	+
785	+	FIX_UNUSED (default_value);
786	+
787	+	if (field_given && *field_given && ! override)
788	+	return 0;
789	+	if (prev_given)
790	+	(*prev_given)++;
791	+	if (field_given)
792	+	(*field_given)++;
793	+	if (possible_values)
794	+	val = possible_values[found];
795	+
796	+	switch(arg_type) {
797	+	case ARG_INT:
798	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
799	+	break;
800	+	case ARG_DOUBLE:
801	+	if (val) *((double *)field) = strtod (val, &stop_char);
802	+	break;
803	+	case ARG_STRING:
804	+	if (val) {
805	+	string_field = (char **)field;
806	+	if (!no_free && *string_field)
807	+	free (*string_field); /* free previous string */
808	+	*string_field = gengetopt_strdup (val);
809	+	}
810	+	break;
811	+	default:
812	+	break;
813	+	};
814	+
815	+	/* check numeric conversion */
816	+	switch(arg_type) {
817	+	case ARG_INT:
818	+	case ARG_DOUBLE:
819	+	if (val && !(stop_char && *stop_char == '\0')) {
820	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
821	+	return 1; /* failure */
822	+	}
823	+	break;
824	+	default:
825	+	;
826	+	};
827	+
828	+	/* store the original value */
829	+	switch(arg_type) {
830	+	case ARG_NO:
831	+	break;
832	+	default:
833	+	if (value && orig_field) {
834	+	if (no_free) {
835	+	*orig_field = value;
836	+	} else {
837	+	if (*orig_field)
838	+	free (*orig_field); /* free previous string */
839	+	*orig_field = gengetopt_strdup (value);
840	+	}
841	+	}
842	+	};
843	+
844	+	return 0; /* OK */
845	+	}
846	+
847	+
848	+	int
849	+	cmdline_parser_internal (
850	+	int argc, char **argv, struct gengetopt_args_info *args_info,
851	+	struct cmdline_parser_params *params, const char *additional_error)
852	+	{
853	+	int c;        /* Character of the parsed option.  */
854	+
855	+	int error = 0;
856	+	struct gengetopt_args_info local_args_info;
857	+
858	+	int override;
859	+	int initialize;
860	+	int check_required;
861	+	int check_ambiguity;
862	+
863	+	package_name = argv[0];
864	+
865	+	override = params->override;
866	+	initialize = params->initialize;
867	+	check_required = params->check_required;
868	+	check_ambiguity = params->check_ambiguity;
869	+
870	+	if (initialize)
871	+	cmdline_parser_init (args_info);
872	+
873	+	cmdline_parser_init (&local_args_info);
874	+
875		optarg = 0;
876	<	optind = 1;
877	<	opterr = 1;
876	>	optind = 0;
877	>	opterr = params->print_errors;
878		optopt = '?';
879
880		while (1)
881		{
882		int option_index = 0;
134	–	char *stop_char;
883
884		static struct option long_options[] = {
885		{ "help",       0, NULL, 'h' },
#	Line 139 | Line 887 | cmdline_parser (int argc, char * const *argv, struct g
887		{ "input",      1, NULL, 'i' },
888		{ "output",     1, NULL, 'o' },
889		{ "step",       1, NULL, 'n' },
890	<	{ "nrbins",     1, NULL, 'r' },
890	>	{ "nbins",      1, NULL, 'b' },
891	>	{ "nbins_x",    1, NULL, 'x' },
892	>	{ "nbins_y",    1, NULL, 'y' },
893	>	{ "nbins_z",    1, NULL, 0 },
894		{ "nanglebins", 1, NULL, 'a' },
895	<	{ "length",     1, NULL, 'l' },
895	>	{ "rcut",       1, NULL, 'c' },
896	>	{ "dz", 1, NULL, 0 },
897	>	{ "length",     1, NULL, 0 },
898	>	{ "zlength",    1, NULL, 0 },
899	>	{ "zoffset",    1, NULL, 'z' },
900		{ "sele1",      1, NULL, 0 },
901		{ "sele2",      1, NULL, 0 },
902		{ "sele3",      1, NULL, 0 },
903		{ "refsele",    1, NULL, 0 },
904	+	{ "comsele",    1, NULL, 0 },
905	+	{ "seleoffset", 1, NULL, 0 },
906	+	{ "seleoffset2",        1, NULL, 0 },
907		{ "molname",    1, NULL, 0 },
908		{ "begin",      1, NULL, 0 },
909		{ "end",        1, NULL, 0 },
910	<	{ "gofr",       0, NULL, 0 },
910	>	{ "radius",     1, NULL, 0 },
911	>	{ "bo", 0, NULL, 0 },
912	>	{ "ior",        0, NULL, 0 },
913	>	{ "for",        0, NULL, 0 },
914	>	{ "bad",        0, NULL, 0 },
915	>	{ "count",      0, NULL, 0 },
916	>	{ "gofr",       0, NULL, 'g' },
917	>	{ "gofz",       0, NULL, 0 },
918		{ "r_theta",    0, NULL, 0 },
919		{ "r_omega",    0, NULL, 0 },
920	+	{ "r_z",        0, NULL, 0 },
921		{ "theta_omega",        0, NULL, 0 },
922		{ "gxyz",       0, NULL, 0 },
923	<	{ "p2", 0, NULL, 0 },
924	<	{ "scd",        0, NULL, 0 },
925	<	{ "density",    0, NULL, 0 },
926	<	{ NULL, 0, NULL, 0 }
923	>	{ "twodgofr",   0, NULL, 0 },
924	>	{ "p2", 0, NULL, 'p' },
925	>	{ "rp2",        0, NULL, 0 },
926	>	{ "scd",        0, NULL, 's' },
927	>	{ "density",    0, NULL, 'd' },
928	>	{ "slab_density",       0, NULL, 0 },
929	>	{ "p_angle",    0, NULL, 0 },
930	>	{ "hxy",        0, NULL, 0 },
931	>	{ "rho_r",      0, NULL, 0 },
932	>	{ "angle_r",    0, NULL, 0 },
933	>	{ "hullvol",    0, NULL, 0 },
934	>	{ "rodlength",  0, NULL, 0 },
935	>	{ "tet_param",  0, NULL, 'Q' },
936	>	{ "tet_param_z",        0, NULL, 0 },
937	>	{ "rnemdz",     0, NULL, 0 },
938	>	{ "rnemdr",     0, NULL, 0 },
939	>	{ "rnemdrt",    0, NULL, 0 },
940	>	{ "nitrile",    0, NULL, 0 },
941	>	{ "multipole",  0, NULL, 'm' },
942	>	{ 0,  0, 0, 0 }
943		};
944
945	<	stop_char = 0;
164	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
945	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQm", long_options, &option_index);
946
947		if (c == -1) break;       /* Exit from `while (1)' loop.  */
948
949		switch (c)
950		{
951		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
952		cmdline_parser_print_help ();
953	+	cmdline_parser_free (&local_args_info);
954		exit (EXIT_SUCCESS);
955
956		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
957		cmdline_parser_print_version ();
958	+	cmdline_parser_free (&local_args_info);
959		exit (EXIT_SUCCESS);
960
961		case 'i':       /* input dump file.  */
962	<	if (args_info->input_given)
963	<	{
964	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
965	<	clear_args ();
966	<	exit (EXIT_FAILURE);
967	<	}
968	<	args_info->input_given = 1;
969	<	args_info->input_arg = gengetopt_strdup (optarg);
962	>
963	>
964	>	if (update_arg( (void *)&(args_info->input_arg),
965	>	&(args_info->input_orig), &(args_info->input_given),
966	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
967	>	check_ambiguity, override, 0, 0,
968	>	"input", 'i',
969	>	additional_error))
970	>	goto failure;
971	>
972		break;
190	–
973		case 'o':       /* output file name.  */
974	<	if (args_info->output_given)
975	<	{
976	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
977	<	clear_args ();
978	<	exit (EXIT_FAILURE);
979	<	}
980	<	args_info->output_given = 1;
981	<	args_info->output_arg = gengetopt_strdup (optarg);
974	>
975	>
976	>	if (update_arg( (void *)&(args_info->output_arg),
977	>	&(args_info->output_orig), &(args_info->output_given),
978	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
979	>	check_ambiguity, override, 0, 0,
980	>	"output", 'o',
981	>	additional_error))
982	>	goto failure;
983	>
984		break;
201	–
985		case 'n':       /* process every n frame.  */
986	<	if (args_info->step_given)
987	<	{
988	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
989	<	clear_args ();
990	<	exit (EXIT_FAILURE);
991	<	}
992	<	args_info->step_given = 1;
993	<	args_info->step_arg = strtol (optarg,&stop_char,0);
986	>
987	>
988	>	if (update_arg( (void *)&(args_info->step_arg),
989	>	&(args_info->step_orig), &(args_info->step_given),
990	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
991	>	check_ambiguity, override, 0, 0,
992	>	"step", 'n',
993	>	additional_error))
994	>	goto failure;
995	>
996		break;
997	<
998	<	case 'r':       /* number of bins for distance.  */
999	<	if (args_info->nrbins_given)
1000	<	{
1001	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1002	<	clear_args ();
1003	<	exit (EXIT_FAILURE);
1004	<	}
1005	<	args_info->nrbins_given = 1;
1006	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
997	>	case 'b':       /* number of bins (general purpose).  */
998	>
999	>
1000	>	if (update_arg( (void *)&(args_info->nbins_arg),
1001	>	&(args_info->nbins_orig), &(args_info->nbins_given),
1002	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
1003	>	check_ambiguity, override, 0, 0,
1004	>	"nbins", 'b',
1005	>	additional_error))
1006	>	goto failure;
1007	>
1008		break;
1009	<
1009	>	case 'x':       /* number of bins in x axis.  */
1010	>
1011	>
1012	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
1013	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1014	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1015	>	check_ambiguity, override, 0, 0,
1016	>	"nbins_x", 'x',
1017	>	additional_error))
1018	>	goto failure;
1019	>
1020	>	break;
1021	>	case 'y':       /* number of bins in y axis.  */
1022	>
1023	>
1024	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
1025	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1026	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1027	>	check_ambiguity, override, 0, 0,
1028	>	"nbins_y", 'y',
1029	>	additional_error))
1030	>	goto failure;
1031	>
1032	>	break;
1033		case 'a':       /* number of bins for cos(angle).  */
1034	<	if (args_info->nanglebins_given)
1035	<	{
1036	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1037	<	clear_args ();
1038	<	exit (EXIT_FAILURE);
1039	<	}
1040	<	args_info->nanglebins_given = 1;
1041	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
1034	>
1035	>
1036	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1037	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1038	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1039	>	check_ambiguity, override, 0, 0,
1040	>	"nanglebins", 'a',
1041	>	additional_error))
1042	>	goto failure;
1043	>
1044		break;
1045	<
1046	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1047	<	if (args_info->length_given)
1048	<	{
1049	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1050	<	clear_args ();
1051	<	exit (EXIT_FAILURE);
1052	<	}
1053	<	args_info->length_given = 1;
1054	<	args_info->length_arg = strtod (optarg, NULL);
1045	>	case 'c':       /* cutoff radius (rcut).  */
1046	>
1047	>
1048	>	if (update_arg( (void *)&(args_info->rcut_arg),
1049	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1050	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1051	>	check_ambiguity, override, 0, 0,
1052	>	"rcut", 'c',
1053	>	additional_error))
1054	>	goto failure;
1055	>
1056		break;
1057	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1058	+
1059	+
1060	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1061	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1062	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1063	+	check_ambiguity, override, 0, 0,
1064	+	"zoffset", 'z',
1065	+	additional_error))
1066	+	goto failure;
1067	+
1068	+	break;
1069	+	case 'g':       /* g(r).  */
1070	+
1071	+	if (args_info->staticProps_group_counter && override)
1072	+	reset_group_staticProps (args_info);
1073	+	args_info->staticProps_group_counter += 1;
1074	+
1075	+	if (update_arg( 0 ,
1076	+	0 , &(args_info->gofr_given),
1077	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1078	+	check_ambiguity, override, 0, 0,
1079	+	"gofr", 'g',
1080	+	additional_error))
1081	+	goto failure;
1082	+
1083	+	break;
1084	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1085	+
1086	+	if (args_info->staticProps_group_counter && override)
1087	+	reset_group_staticProps (args_info);
1088	+	args_info->staticProps_group_counter += 1;
1089	+
1090	+	if (update_arg( 0 ,
1091	+	0 , &(args_info->p2_given),
1092	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1093	+	check_ambiguity, override, 0, 0,
1094	+	"p2", 'p',
1095	+	additional_error))
1096	+	goto failure;
1097	+
1098	+	break;
1099	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1100	+
1101	+	if (args_info->staticProps_group_counter && override)
1102	+	reset_group_staticProps (args_info);
1103	+	args_info->staticProps_group_counter += 1;
1104	+
1105	+	if (update_arg( 0 ,
1106	+	0 , &(args_info->scd_given),
1107	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1108	+	check_ambiguity, override, 0, 0,
1109	+	"scd", 's',
1110	+	additional_error))
1111	+	goto failure;
1112	+
1113	+	break;
1114	+	case 'd':       /* density plot.  */
1115	+
1116	+	if (args_info->staticProps_group_counter && override)
1117	+	reset_group_staticProps (args_info);
1118	+	args_info->staticProps_group_counter += 1;
1119	+
1120	+	if (update_arg( 0 ,
1121	+	0 , &(args_info->density_given),
1122	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1123	+	check_ambiguity, override, 0, 0,
1124	+	"density", 'd',
1125	+	additional_error))
1126	+	goto failure;
1127	+
1128	+	break;
1129	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1130	+
1131	+	if (args_info->staticProps_group_counter && override)
1132	+	reset_group_staticProps (args_info);
1133	+	args_info->staticProps_group_counter += 1;
1134	+
1135	+	if (update_arg( 0 ,
1136	+	0 , &(args_info->tet_param_given),
1137	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1138	+	check_ambiguity, override, 0, 0,
1139	+	"tet_param", 'Q',
1140	+	additional_error))
1141	+	goto failure;
1142	+
1143	+	break;
1144	+	case 'm':       /* average multipole moment contained within a cutoff sphere.  */
1145	+
1146	+	if (args_info->staticProps_group_counter && override)
1147	+	reset_group_staticProps (args_info);
1148	+	args_info->staticProps_group_counter += 1;
1149	+
1150	+	if (update_arg( 0 ,
1151	+	0 , &(args_info->multipole_given),
1152	+	&(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1153	+	check_ambiguity, override, 0, 0,
1154	+	"multipole", 'm',
1155	+	additional_error))
1156	+	goto failure;
1157	+
1158	+	break;
1159
246	–
1160		case 0: /* Long option with no short option */
1161	<	/* select the first stuntdouble set.  */
1162	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1161	>	/* number of bins in z axis.  */
1162	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1163		{
1164	<	if (args_info->sele1_given)
1165	<	{
1166	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1167	<	clear_args ();
1168	<	exit (EXIT_FAILURE);
1169	<	}
1170	<	args_info->sele1_given = 1;
1171	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1172	<	break;
1164	>
1165	>
1166	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1167	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1168	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1169	>	check_ambiguity, override, 0, 0,
1170	>	"nbins_z", '-',
1171	>	additional_error))
1172	>	goto failure;
1173	>
1174		}
1175	+	/* slab width (dz).  */
1176	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1177	+	{
1178
1179	+
1180	+	if (update_arg( (void *)&(args_info->dz_arg),
1181	+	&(args_info->dz_orig), &(args_info->dz_given),
1182	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1183	+	check_ambiguity, override, 0, 0,
1184	+	"dz", '-',
1185	+	additional_error))
1186	+	goto failure;
1187	+
1188	+	}
1189	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1190	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1191	+	{
1192	+
1193	+
1194	+	if (update_arg( (void *)&(args_info->length_arg),
1195	+	&(args_info->length_orig), &(args_info->length_given),
1196	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1197	+	check_ambiguity, override, 0, 0,
1198	+	"length", '-',
1199	+	additional_error))
1200	+	goto failure;
1201	+
1202	+	}
1203	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1204	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1205	+	{
1206	+
1207	+
1208	+	if (update_arg( (void *)&(args_info->zlength_arg),
1209	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1210	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1211	+	check_ambiguity, override, 0, 0,
1212	+	"zlength", '-',
1213	+	additional_error))
1214	+	goto failure;
1215	+
1216	+	}
1217	+	/* select the first stuntdouble set.  */
1218	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1219	+	{
1220	+
1221	+
1222	+	if (update_arg( (void *)&(args_info->sele1_arg),
1223	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1224	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1225	+	check_ambiguity, override, 0, 0,
1226	+	"sele1", '-',
1227	+	additional_error))
1228	+	goto failure;
1229	+
1230	+	}
1231		/* select the second stuntdouble set.  */
1232		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1233		{
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	–	}
1234
1235	+
1236	+	if (update_arg( (void *)&(args_info->sele2_arg),
1237	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1238	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1239	+	check_ambiguity, override, 0, 0,
1240	+	"sele2", '-',
1241	+	additional_error))
1242	+	goto failure;
1243	+
1244	+	}
1245		/* select the third stuntdouble set.  */
1246		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1247		{
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	–	}
1248
1249	+
1250	+	if (update_arg( (void *)&(args_info->sele3_arg),
1251	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1252	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1253	+	check_ambiguity, override, 0, 0,
1254	+	"sele3", '-',
1255	+	additional_error))
1256	+	goto failure;
1257	+
1258	+	}
1259		/* select reference (use and only use with --gxyz).  */
1260		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1261		{
1262	<	if (args_info->refsele_given)
1263	<	{
1264	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1265	<	clear_args ();
1266	<	exit (EXIT_FAILURE);
1267	<	}
1268	<	args_info->refsele_given = 1;
1269	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1270	<	break;
1262	>
1263	>
1264	>	if (update_arg( (void *)&(args_info->refsele_arg),
1265	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1266	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1267	>	check_ambiguity, override, 0, 0,
1268	>	"refsele", '-',
1269	>	additional_error))
1270	>	goto failure;
1271	>
1272		}
1273	+	/* select stunt doubles for center-of-mass reference point.  */
1274	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1275	+	{
1276
1277	+
1278	+	if (update_arg( (void *)&(args_info->comsele_arg),
1279	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1280	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1281	+	check_ambiguity, override, 0, 0,
1282	+	"comsele", '-',
1283	+	additional_error))
1284	+	goto failure;
1285	+
1286	+	}
1287	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1288	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1289	+	{
1290	+
1291	+
1292	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1293	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1294	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1295	+	check_ambiguity, override, 0, 0,
1296	+	"seleoffset", '-',
1297	+	additional_error))
1298	+	goto failure;
1299	+
1300	+	}
1301	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1302	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1303	+	{
1304	+
1305	+
1306	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1307	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1308	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1309	+	check_ambiguity, override, 0, 0,
1310	+	"seleoffset2", '-',
1311	+	additional_error))
1312	+	goto failure;
1313	+
1314	+	}
1315		/* molecule name.  */
1316		else if (strcmp (long_options[option_index].name, "molname") == 0)
1317		{
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	–	}
1318
1319	<	/* begin interanl index.  */
1319	>
1320	>	if (update_arg( (void *)&(args_info->molname_arg),
1321	>	&(args_info->molname_orig), &(args_info->molname_given),
1322	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1323	>	check_ambiguity, override, 0, 0,
1324	>	"molname", '-',
1325	>	additional_error))
1326	>	goto failure;
1327	>
1328	>	}
1329	>	/* begin internal index.  */
1330		else if (strcmp (long_options[option_index].name, "begin") == 0)
1331		{
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	–	}
1332
1333	+
1334	+	if (update_arg( (void *)&(args_info->begin_arg),
1335	+	&(args_info->begin_orig), &(args_info->begin_given),
1336	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1337	+	check_ambiguity, override, 0, 0,
1338	+	"begin", '-',
1339	+	additional_error))
1340	+	goto failure;
1341	+
1342	+	}
1343		/* end internal index.  */
1344		else if (strcmp (long_options[option_index].name, "end") == 0)
1345		{
1346	<	if (args_info->end_given)
1347	<	{
1348	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1349	<	clear_args ();
1350	<	exit (EXIT_FAILURE);
1351	<	}
1352	<	args_info->end_given = 1;
1353	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1354	<	break;
1346	>
1347	>
1348	>	if (update_arg( (void *)&(args_info->end_arg),
1349	>	&(args_info->end_orig), &(args_info->end_given),
1350	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1351	>	check_ambiguity, override, 0, 0,
1352	>	"end", '-',
1353	>	additional_error))
1354	>	goto failure;
1355	>
1356		}
1357	+	/* nanoparticle radius.  */
1358	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1359	+	{
1360
1361	<	/* g(r).  */
1362	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1361	>
1362	>	if (update_arg( (void *)&(args_info->radius_arg),
1363	>	&(args_info->radius_orig), &(args_info->radius_given),
1364	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1365	>	check_ambiguity, override, 0, 0,
1366	>	"radius", '-',
1367	>	additional_error))
1368	>	goto failure;
1369	>
1370	>	}
1371	>	/* bond order parameter (--rcut must be specified).  */
1372	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1373		{
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;
1374
1375	<	break;
1375	>	if (args_info->staticProps_group_counter && override)
1376	>	reset_group_staticProps (args_info);
1377	>	args_info->staticProps_group_counter += 1;
1378	>
1379	>	if (update_arg( 0 ,
1380	>	0 , &(args_info->bo_given),
1381	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1382	>	check_ambiguity, override, 0, 0,
1383	>	"bo", '-',
1384	>	additional_error))
1385	>	goto failure;
1386	>
1387	>	}
1388	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1389	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1390	>	{
1391	>
1392	>	if (args_info->staticProps_group_counter && override)
1393	>	reset_group_staticProps (args_info);
1394	>	args_info->staticProps_group_counter += 1;
1395	>
1396	>	if (update_arg( 0 ,
1397	>	0 , &(args_info->ior_given),
1398	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1399	>	check_ambiguity, override, 0, 0,
1400	>	"ior", '-',
1401	>	additional_error))
1402	>	goto failure;
1403	>
1404	>	}
1405	>	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1406	>	else if (strcmp (long_options[option_index].name, "for") == 0)
1407	>	{
1408	>
1409	>	if (args_info->staticProps_group_counter && override)
1410	>	reset_group_staticProps (args_info);
1411	>	args_info->staticProps_group_counter += 1;
1412	>
1413	>	if (update_arg( 0 ,
1414	>	0 , &(args_info->for_given),
1415	>	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1416	>	check_ambiguity, override, 0, 0,
1417	>	"for", '-',
1418	>	additional_error))
1419	>	goto failure;
1420	>
1421		}
1422	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1423	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1424	+	{
1425
1426	+	if (args_info->staticProps_group_counter && override)
1427	+	reset_group_staticProps (args_info);
1428	+	args_info->staticProps_group_counter += 1;
1429	+
1430	+	if (update_arg( 0 ,
1431	+	0 , &(args_info->bad_given),
1432	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1433	+	check_ambiguity, override, 0, 0,
1434	+	"bad", '-',
1435	+	additional_error))
1436	+	goto failure;
1437	+
1438	+	}
1439	+	/* count of molecules matching selection criteria (and associated statistics).  */
1440	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1441	+	{
1442	+
1443	+	if (args_info->staticProps_group_counter && override)
1444	+	reset_group_staticProps (args_info);
1445	+	args_info->staticProps_group_counter += 1;
1446	+
1447	+	if (update_arg( 0 ,
1448	+	0 , &(args_info->count_given),
1449	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1450	+	check_ambiguity, override, 0, 0,
1451	+	"count", '-',
1452	+	additional_error))
1453	+	goto failure;
1454	+
1455	+	}
1456	+	/* g(z).  */
1457	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1458	+	{
1459	+
1460	+	if (args_info->staticProps_group_counter && override)
1461	+	reset_group_staticProps (args_info);
1462	+	args_info->staticProps_group_counter += 1;
1463	+
1464	+	if (update_arg( 0 ,
1465	+	0 , &(args_info->gofz_given),
1466	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1467	+	check_ambiguity, override, 0, 0,
1468	+	"gofz", '-',
1469	+	additional_error))
1470	+	goto failure;
1471	+
1472	+	}
1473		/* g(r, cos(theta)).  */
1474		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1475		{
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;
1476
1477	<	break;
1478	<	}
1477	>	if (args_info->staticProps_group_counter && override)
1478	>	reset_group_staticProps (args_info);
1479	>	args_info->staticProps_group_counter += 1;
1480
1481	+	if (update_arg( 0 ,
1482	+	0 , &(args_info->r_theta_given),
1483	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1484	+	check_ambiguity, override, 0, 0,
1485	+	"r_theta", '-',
1486	+	additional_error))
1487	+	goto failure;
1488	+
1489	+	}
1490		/* g(r, cos(omega)).  */
1491		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1492		{
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;
1493
1494	<	break;
1494	>	if (args_info->staticProps_group_counter && override)
1495	>	reset_group_staticProps (args_info);
1496	>	args_info->staticProps_group_counter += 1;
1497	>
1498	>	if (update_arg( 0 ,
1499	>	0 , &(args_info->r_omega_given),
1500	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1501	>	check_ambiguity, override, 0, 0,
1502	>	"r_omega", '-',
1503	>	additional_error))
1504	>	goto failure;
1505	>
1506		}
1507	+	/* g(r, z).  */
1508	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1509	+	{
1510
1511	+	if (args_info->staticProps_group_counter && override)
1512	+	reset_group_staticProps (args_info);
1513	+	args_info->staticProps_group_counter += 1;
1514	+
1515	+	if (update_arg( 0 ,
1516	+	0 , &(args_info->r_z_given),
1517	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1518	+	check_ambiguity, override, 0, 0,
1519	+	"r_z", '-',
1520	+	additional_error))
1521	+	goto failure;
1522	+
1523	+	}
1524		/* g(cos(theta), cos(omega)).  */
1525		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1526		{
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;
1527
1528	<	break;
1529	<	}
1528	>	if (args_info->staticProps_group_counter && override)
1529	>	reset_group_staticProps (args_info);
1530	>	args_info->staticProps_group_counter += 1;
1531
1532	+	if (update_arg( 0 ,
1533	+	0 , &(args_info->theta_omega_given),
1534	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1535	+	check_ambiguity, override, 0, 0,
1536	+	"theta_omega", '-',
1537	+	additional_error))
1538	+	goto failure;
1539	+
1540	+	}
1541		/* g(x, y, z).  */
1542		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1543		{
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;
1544
1545	<	break;
1546	<	}
1545	>	if (args_info->staticProps_group_counter && override)
1546	>	reset_group_staticProps (args_info);
1547	>	args_info->staticProps_group_counter += 1;
1548
1549	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1550	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1549	>	if (update_arg( 0 ,
1550	>	0 , &(args_info->gxyz_given),
1551	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1552	>	check_ambiguity, override, 0, 0,
1553	>	"gxyz", '-',
1554	>	additional_error))
1555	>	goto failure;
1556	>
1557	>	}
1558	>	/* 2D g(r) (Slab width --dz must be specified).  */
1559	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1560		{
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;
1561
1562	<	break;
1562	>	if (args_info->staticProps_group_counter && override)
1563	>	reset_group_staticProps (args_info);
1564	>	args_info->staticProps_group_counter += 1;
1565	>
1566	>	if (update_arg( 0 ,
1567	>	0 , &(args_info->twodgofr_given),
1568	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1569	>	check_ambiguity, override, 0, 0,
1570	>	"twodgofr", '-',
1571	>	additional_error))
1572	>	goto failure;
1573	>
1574		}
1575	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1576	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1577	+	{
1578
1579	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1580	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1579	>	if (args_info->staticProps_group_counter && override)
1580	>	reset_group_staticProps (args_info);
1581	>	args_info->staticProps_group_counter += 1;
1582	>
1583	>	if (update_arg( 0 ,
1584	>	0 , &(args_info->rp2_given),
1585	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1586	>	check_ambiguity, override, 0, 0,
1587	>	"rp2", '-',
1588	>	additional_error))
1589	>	goto failure;
1590	>
1591	>	}
1592	>	/* slab density.  */
1593	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1594		{
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;
1595
1596	<	break;
1596	>	if (args_info->staticProps_group_counter && override)
1597	>	reset_group_staticProps (args_info);
1598	>	args_info->staticProps_group_counter += 1;
1599	>
1600	>	if (update_arg( 0 ,
1601	>	0 , &(args_info->slab_density_given),
1602	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1603	>	check_ambiguity, override, 0, 0,
1604	>	"slab_density", '-',
1605	>	additional_error))
1606	>	goto failure;
1607	>
1608		}
1609	+	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1610	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1611	+	{
1612
1613	<	/* density plot (--sele1 must be specified).  */
1614	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1613	>	if (args_info->staticProps_group_counter && override)
1614	>	reset_group_staticProps (args_info);
1615	>	args_info->staticProps_group_counter += 1;
1616	>
1617	>	if (update_arg( 0 ,
1618	>	0 , &(args_info->p_angle_given),
1619	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1620	>	check_ambiguity, override, 0, 0,
1621	>	"p_angle", '-',
1622	>	additional_error))
1623	>	goto failure;
1624	>
1625	>	}
1626	>	/* hxy.  */
1627	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1628		{
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;
1629
1630	<	break;
1630	>	if (args_info->staticProps_group_counter && override)
1631	>	reset_group_staticProps (args_info);
1632	>	args_info->staticProps_group_counter += 1;
1633	>
1634	>	if (update_arg( 0 ,
1635	>	0 , &(args_info->hxy_given),
1636	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1637	>	check_ambiguity, override, 0, 0,
1638	>	"hxy", '-',
1639	>	additional_error))
1640	>	goto failure;
1641	>
1642		}
1643	+	/* rho of R.  */
1644	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1645	+	{
1646
1647	<
1647	>	if (args_info->staticProps_group_counter && override)
1648	>	reset_group_staticProps (args_info);
1649	>	args_info->staticProps_group_counter += 1;
1650	>
1651	>	if (update_arg( 0 ,
1652	>	0 , &(args_info->rho_r_given),
1653	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1654	>	check_ambiguity, override, 0, 0,
1655	>	"rho_r", '-',
1656	>	additional_error))
1657	>	goto failure;
1658	>
1659	>	}
1660	>	/* angle of R.  */
1661	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1662	>	{
1663	>
1664	>	if (args_info->staticProps_group_counter && override)
1665	>	reset_group_staticProps (args_info);
1666	>	args_info->staticProps_group_counter += 1;
1667	>
1668	>	if (update_arg( 0 ,
1669	>	0 , &(args_info->angle_r_given),
1670	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1671	>	check_ambiguity, override, 0, 0,
1672	>	"angle_r", '-',
1673	>	additional_error))
1674	>	goto failure;
1675	>
1676	>	}
1677	>	/* hull volume of nanoparticle.  */
1678	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1679	>	{
1680	>
1681	>	if (args_info->staticProps_group_counter && override)
1682	>	reset_group_staticProps (args_info);
1683	>	args_info->staticProps_group_counter += 1;
1684	>
1685	>	if (update_arg( 0 ,
1686	>	0 , &(args_info->hullvol_given),
1687	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1688	>	check_ambiguity, override, 0, 0,
1689	>	"hullvol", '-',
1690	>	additional_error))
1691	>	goto failure;
1692	>
1693	>	}
1694	>	/* length of nanorod.  */
1695	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1696	>	{
1697	>
1698	>	if (args_info->staticProps_group_counter && override)
1699	>	reset_group_staticProps (args_info);
1700	>	args_info->staticProps_group_counter += 1;
1701	>
1702	>	if (update_arg( 0 ,
1703	>	0 , &(args_info->rodlength_given),
1704	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1705	>	check_ambiguity, override, 0, 0,
1706	>	"rodlength", '-',
1707	>	additional_error))
1708	>	goto failure;
1709	>
1710	>	}
1711	>	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1712	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1713	>	{
1714	>
1715	>	if (args_info->staticProps_group_counter && override)
1716	>	reset_group_staticProps (args_info);
1717	>	args_info->staticProps_group_counter += 1;
1718	>
1719	>	if (update_arg( 0 ,
1720	>	0 , &(args_info->tet_param_z_given),
1721	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1722	>	check_ambiguity, override, 0, 0,
1723	>	"tet_param_z", '-',
1724	>	additional_error))
1725	>	goto failure;
1726	>
1727	>	}
1728	>	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1729	>	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1730	>	{
1731	>
1732	>	if (args_info->staticProps_group_counter && override)
1733	>	reset_group_staticProps (args_info);
1734	>	args_info->staticProps_group_counter += 1;
1735	>
1736	>	if (update_arg( 0 ,
1737	>	0 , &(args_info->rnemdz_given),
1738	>	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1739	>	check_ambiguity, override, 0, 0,
1740	>	"rnemdz", '-',
1741	>	additional_error))
1742	>	goto failure;
1743	>
1744	>	}
1745	>	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1746	>	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1747	>	{
1748	>
1749	>	if (args_info->staticProps_group_counter && override)
1750	>	reset_group_staticProps (args_info);
1751	>	args_info->staticProps_group_counter += 1;
1752	>
1753	>	if (update_arg( 0 ,
1754	>	0 , &(args_info->rnemdr_given),
1755	>	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1756	>	check_ambiguity, override, 0, 0,
1757	>	"rnemdr", '-',
1758	>	additional_error))
1759	>	goto failure;
1760	>
1761	>	}
1762	>	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1763	>	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1764	>	{
1765	>
1766	>	if (args_info->staticProps_group_counter && override)
1767	>	reset_group_staticProps (args_info);
1768	>	args_info->staticProps_group_counter += 1;
1769	>
1770	>	if (update_arg( 0 ,
1771	>	0 , &(args_info->rnemdrt_given),
1772	>	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1773	>	check_ambiguity, override, 0, 0,
1774	>	"rnemdrt", '-',
1775	>	additional_error))
1776	>	goto failure;
1777	>
1778	>	}
1779	>	/* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1780	>	else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1781	>	{
1782	>
1783	>	if (args_info->staticProps_group_counter && override)
1784	>	reset_group_staticProps (args_info);
1785	>	args_info->staticProps_group_counter += 1;
1786	>
1787	>	if (update_arg( 0 ,
1788	>	0 , &(args_info->nitrile_given),
1789	>	&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1790	>	check_ambiguity, override, 0, 0,
1791	>	"nitrile", '-',
1792	>	additional_error))
1793	>	goto failure;
1794	>
1795	>	}
1796	>
1797	>	break;
1798		case '?':       /* Invalid option.  */
1799		/* `getopt_long' already printed an error message.  */
1800	<	exit (EXIT_FAILURE);
1800	>	goto failure;
1801
1802		default:        /* bug: option not considered.  */
1803	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1803	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1804		abort ();
1805		} /* switch */
1806		} /* while */
1807
1808	<	if ( staticProps_group_counter != 1)
1808	>	if (args_info->staticProps_group_counter > 1)
1809		{
1810	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1811	<	missing_required_options = 1;
1810	>	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 : ""));
1811	>	error = 1;
1812		}
1813
1814
1815	<	if (! args_info->input_given)
1815	>
1816	>	if (check_required)
1817		{
1818	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1818	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1819		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1820
1821	+	cmdline_parser_release (&local_args_info);
1822	+
1823	+	if ( error )
1824	+	return (EXIT_FAILURE);
1825	+
1826	+	if (optind < argc)
1827	+	{
1828	+	int i = 0 ;
1829	+	int found_prog_name = 0;
1830	+	/* whether program name, i.e., argv[0], is in the remaining args
1831	+	(this may happen with some implementations of getopt,
1832	+	but surely not with the one included by gengetopt) */
1833	+
1834	+	i = optind;
1835	+	while (i < argc)
1836	+	if (argv[i++] == argv[0]) {
1837	+	found_prog_name = 1;
1838	+	break;
1839	+	}
1840	+	i = 0;
1841	+
1842	+	args_info->inputs_num = argc - optind - found_prog_name;
1843	+	args_info->inputs =
1844	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1845	+	while (optind < argc)
1846	+	if (argv[optind++] != argv[0])
1847	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1848	+	}
1849	+
1850		return 0;
1851	+
1852	+	failure:
1853	+
1854	+	cmdline_parser_release (&local_args_info);
1855	+	return (EXIT_FAILURE);
1856		}

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 1998 by gezelter, Fri May 30 19:48:35 2014 UTC

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