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

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trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.19.1
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	gengetopt -i StaticProps.ggo -F StaticPropsCmd -u
4	>	gengetopt -i StaticProps.ggo -c cpp -F StaticPropsCmd -u
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
#	Line 17 | Line 17
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	#include "getopt.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22	>	#endif
23
24	+	#ifdef WIN32
25	+	#include "utils/wingetopt.h"
26	+	#else
27	+	#include <getopt.h>
28	+	#endif
29	+
30		#include "StaticPropsCmd.h"
31
32		const char *gengetopt_args_info_purpose = "";
#	Line 36 | Line 44 | const char *gengetopt_args_info_help[] = {
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')",
40	–	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
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		"      --molname=STRING          molecule name",
60		"      --begin=INT               begin internal index",
61		"      --end=INT                 end internal index",
#	Line 51 | Line 63 | const char *gengetopt_args_info_help[] = {
63		"\n Group: staticProps\n   an option of this group is required",
64		"      --bo                      bond order parameter (--rcut must be specified)",
65		"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
66	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
67	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
68		"  -g, --gofr                    g(r)",
69	+	"      --gofz                    g(z)",
70		"      --r_theta                 g(r, cos(theta))",
71		"      --r_omega                 g(r, cos(omega))",
72	+	"      --r_z                     g(r, z)",
73		"      --theta_omega             g(cos(theta), cos(omega))",
74		"      --gxyz                    g(x, y, z)",
75	<	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
75	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
76	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
77		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
78		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
79		"  -d, --density                 density plot",
80		"      --slab_density            slab density",
81	+	"      --p_angle                 p(cos(theta))",
82		"      --hxy                     hxy",
83		"      --rho_r                   rho of R",
84	+	"      --angle_r                 angle of R",
85	+	"      --hullvol                 hull volume of nanoparticle",
86	+	"      --rodlength               length of nanorod",
87	+	"  -Q, --tet_param               tetrahedrality order parameter",
88	+	"      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
89		0
90		};
91
92	+	typedef enum {ARG_NO
93	+	, ARG_STRING
94	+	, ARG_INT
95	+	, ARG_DOUBLE
96	+	} cmdline_parser_arg_type;
97	+
98		static
99		void clear_given (struct gengetopt_args_info *args_info);
100		static
101		void clear_args (struct gengetopt_args_info *args_info);
102
103		static int
104	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
104	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
105	>	struct cmdline_parser_params *params, const char *additional_error);
106
107		static int
108		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 91 | Line 121 | void clear_given (struct gengetopt_args_info *args_inf
121		args_info->nbins_given = 0 ;
122		args_info->nbins_x_given = 0 ;
123		args_info->nbins_y_given = 0 ;
124	+	args_info->nbins_z_given = 0 ;
125		args_info->nanglebins_given = 0 ;
95	–	args_info->length_given = 0 ;
126		args_info->rcut_given = 0 ;
127	+	args_info->dz_given = 0 ;
128	+	args_info->length_given = 0 ;
129	+	args_info->zlength_given = 0 ;
130		args_info->zoffset_given = 0 ;
131		args_info->sele1_given = 0 ;
132		args_info->sele2_given = 0 ;
133		args_info->sele3_given = 0 ;
134		args_info->refsele_given = 0 ;
135	+	args_info->comsele_given = 0 ;
136		args_info->molname_given = 0 ;
137		args_info->begin_given = 0 ;
138		args_info->end_given = 0 ;
139		args_info->radius_given = 0 ;
140		args_info->bo_given = 0 ;
141		args_info->bor_given = 0 ;
142	+	args_info->bad_given = 0 ;
143	+	args_info->count_given = 0 ;
144		args_info->gofr_given = 0 ;
145	+	args_info->gofz_given = 0 ;
146		args_info->r_theta_given = 0 ;
147		args_info->r_omega_given = 0 ;
148	+	args_info->r_z_given = 0 ;
149		args_info->theta_omega_given = 0 ;
150		args_info->gxyz_given = 0 ;
151	+	args_info->twodgofr_given = 0 ;
152		args_info->p2_given = 0 ;
153		args_info->rp2_given = 0 ;
154		args_info->scd_given = 0 ;
155		args_info->density_given = 0 ;
156		args_info->slab_density_given = 0 ;
157	+	args_info->p_angle_given = 0 ;
158		args_info->hxy_given = 0 ;
159		args_info->rho_r_given = 0 ;
160	+	args_info->angle_r_given = 0 ;
161	+	args_info->hullvol_given = 0 ;
162	+	args_info->rodlength_given = 0 ;
163	+	args_info->tet_param_given = 0 ;
164	+	args_info->tet_param_z_given = 0 ;
165		args_info->staticProps_group_counter = 0 ;
166		}
167
168		static
169		void clear_args (struct gengetopt_args_info *args_info)
170		{
171	+	FIX_UNUSED (args_info);
172		args_info->input_arg = NULL;
173		args_info->input_orig = NULL;
174		args_info->output_arg = NULL;
#	Line 135 | Line 181 | void clear_args (struct gengetopt_args_info *args_info
181		args_info->nbins_x_orig = NULL;
182		args_info->nbins_y_arg = 100;
183		args_info->nbins_y_orig = NULL;
184	+	args_info->nbins_z_arg = 100;
185	+	args_info->nbins_z_orig = NULL;
186		args_info->nanglebins_arg = 50;
187		args_info->nanglebins_orig = NULL;
140	–	args_info->length_orig = NULL;
188		args_info->rcut_orig = NULL;
189	+	args_info->dz_orig = NULL;
190	+	args_info->length_orig = NULL;
191	+	args_info->zlength_orig = NULL;
192		args_info->zoffset_arg = 0;
193		args_info->zoffset_orig = NULL;
194		args_info->sele1_arg = NULL;
#	Line 149 | Line 199 | void clear_args (struct gengetopt_args_info *args_info
199		args_info->sele3_orig = NULL;
200		args_info->refsele_arg = NULL;
201		args_info->refsele_orig = NULL;
202	+	args_info->comsele_arg = NULL;
203	+	args_info->comsele_orig = NULL;
204		args_info->molname_arg = NULL;
205		args_info->molname_orig = NULL;
206		args_info->begin_orig = NULL;
#	Line 160 | Line 212 | void init_args_info(struct gengetopt_args_info *args_i
212		static
213		void init_args_info(struct gengetopt_args_info *args_info)
214		{
215	+
216	+
217		args_info->help_help = gengetopt_args_info_help[0] ;
218		args_info->version_help = gengetopt_args_info_help[1] ;
219		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 168 | Line 222 | void init_args_info(struct gengetopt_args_info *args_i
222		args_info->nbins_help = gengetopt_args_info_help[5] ;
223		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
224		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
225	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
226	<	args_info->length_help = gengetopt_args_info_help[9] ;
225	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
226	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
227		args_info->rcut_help = gengetopt_args_info_help[10] ;
228	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
229	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
230	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
231	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
232	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
233	<	args_info->molname_help = gengetopt_args_info_help[16] ;
234	<	args_info->begin_help = gengetopt_args_info_help[17] ;
235	<	args_info->end_help = gengetopt_args_info_help[18] ;
236	<	args_info->radius_help = gengetopt_args_info_help[19] ;
237	<	args_info->bo_help = gengetopt_args_info_help[20] ;
238	<	args_info->bor_help = gengetopt_args_info_help[21] ;
239	<	args_info->gofr_help = gengetopt_args_info_help[22] ;
240	<	args_info->r_theta_help = gengetopt_args_info_help[23] ;
241	<	args_info->r_omega_help = gengetopt_args_info_help[24] ;
242	<	args_info->theta_omega_help = gengetopt_args_info_help[25] ;
243	<	args_info->gxyz_help = gengetopt_args_info_help[26] ;
244	<	args_info->p2_help = gengetopt_args_info_help[27] ;
245	<	args_info->rp2_help = gengetopt_args_info_help[28] ;
246	<	args_info->scd_help = gengetopt_args_info_help[29] ;
247	<	args_info->density_help = gengetopt_args_info_help[30] ;
248	<	args_info->slab_density_help = gengetopt_args_info_help[31] ;
249	<	args_info->hxy_help = gengetopt_args_info_help[32] ;
250	<	args_info->rho_r_help = gengetopt_args_info_help[33] ;
228	>	args_info->dz_help = gengetopt_args_info_help[11] ;
229	>	args_info->length_help = gengetopt_args_info_help[12] ;
230	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
231	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
232	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
233	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
234	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
235	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
236	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
237	>	args_info->molname_help = gengetopt_args_info_help[20] ;
238	>	args_info->begin_help = gengetopt_args_info_help[21] ;
239	>	args_info->end_help = gengetopt_args_info_help[22] ;
240	>	args_info->radius_help = gengetopt_args_info_help[23] ;
241	>	args_info->bo_help = gengetopt_args_info_help[25] ;
242	>	args_info->bor_help = gengetopt_args_info_help[26] ;
243	>	args_info->bad_help = gengetopt_args_info_help[27] ;
244	>	args_info->count_help = gengetopt_args_info_help[28] ;
245	>	args_info->gofr_help = gengetopt_args_info_help[29] ;
246	>	args_info->gofz_help = gengetopt_args_info_help[30] ;
247	>	args_info->r_theta_help = gengetopt_args_info_help[31] ;
248	>	args_info->r_omega_help = gengetopt_args_info_help[32] ;
249	>	args_info->r_z_help = gengetopt_args_info_help[33] ;
250	>	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
251	>	args_info->gxyz_help = gengetopt_args_info_help[35] ;
252	>	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
253	>	args_info->p2_help = gengetopt_args_info_help[37] ;
254	>	args_info->rp2_help = gengetopt_args_info_help[38] ;
255	>	args_info->scd_help = gengetopt_args_info_help[39] ;
256	>	args_info->density_help = gengetopt_args_info_help[40] ;
257	>	args_info->slab_density_help = gengetopt_args_info_help[41] ;
258	>	args_info->p_angle_help = gengetopt_args_info_help[42] ;
259	>	args_info->hxy_help = gengetopt_args_info_help[43] ;
260	>	args_info->rho_r_help = gengetopt_args_info_help[44] ;
261	>	args_info->angle_r_help = gengetopt_args_info_help[45] ;
262	>	args_info->hullvol_help = gengetopt_args_info_help[46] ;
263	>	args_info->rodlength_help = gengetopt_args_info_help[47] ;
264	>	args_info->tet_param_help = gengetopt_args_info_help[48] ;
265	>	args_info->tet_param_z_help = gengetopt_args_info_help[49] ;
266
267		}
268
269		void
270		cmdline_parser_print_version (void)
271		{
272	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
272	>	printf ("%s %s\n",
273	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
274	>	CMDLINE_PARSER_VERSION);
275		}
276
277	<	void
207	<	cmdline_parser_print_help (void)
208	<	{
209	<	int i = 0;
277	>	static void print_help_common(void) {
278		cmdline_parser_print_version ();
279
280		if (strlen(gengetopt_args_info_purpose) > 0)
281		printf("\n%s\n", gengetopt_args_info_purpose);
282
283	<	printf("\n%s\n\n", gengetopt_args_info_usage);
283	>	if (strlen(gengetopt_args_info_usage) > 0)
284	>	printf("\n%s\n", gengetopt_args_info_usage);
285
286	+	printf("\n");
287	+
288		if (strlen(gengetopt_args_info_description) > 0)
289	<	printf("%s\n", gengetopt_args_info_description);
289	>	printf("%s\n\n", gengetopt_args_info_description);
290	>	}
291
292	+	void
293	+	cmdline_parser_print_help (void)
294	+	{
295	+	int i = 0;
296	+	print_help_common();
297		while (gengetopt_args_info_help[i])
298		printf("%s\n", gengetopt_args_info_help[i++]);
299		}
#	Line 228 | Line 305 | cmdline_parser_init (struct gengetopt_args_info *args_
305		clear_args (args_info);
306		init_args_info (args_info);
307
308	<	args_info->inputs = NULL;
308	>	args_info->inputs = 0;
309		args_info->inputs_num = 0;
310		}
311
312	+	void
313	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
314	+	{
315	+	if (params)
316	+	{
317	+	params->override = 0;
318	+	params->initialize = 1;
319	+	params->check_required = 1;
320	+	params->check_ambiguity = 0;
321	+	params->print_errors = 1;
322	+	}
323	+	}
324	+
325	+	struct cmdline_parser_params *
326	+	cmdline_parser_params_create(void)
327	+	{
328	+	struct cmdline_parser_params *params =
329	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
330	+	cmdline_parser_params_init(params);
331	+	return params;
332	+	}
333	+
334		static void
335	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
335	>	free_string_field (char **s)
336		{
337	<
239	<	unsigned int i;
240	<	if (args_info->input_arg)
337	>	if (*s)
338		{
339	<	free (args_info->input_arg); /* free previous argument */
340	<	args_info->input_arg = 0;
339	>	free (*s);
340	>	*s = 0;
341		}
342	<	if (args_info->input_orig)
343	<	{
344	<	free (args_info->input_orig); /* free previous argument */
345	<	args_info->input_orig = 0;
346	<	}
347	<	if (args_info->output_arg)
348	<	{
349	<	free (args_info->output_arg); /* free previous argument */
350	<	args_info->output_arg = 0;
351	<	}
352	<	if (args_info->output_orig)
353	<	{
354	<	free (args_info->output_orig); /* free previous argument */
355	<	args_info->output_orig = 0;
356	<	}
357	<	if (args_info->step_orig)
358	<	{
359	<	free (args_info->step_orig); /* free previous argument */
360	<	args_info->step_orig = 0;
361	<	}
362	<	if (args_info->nbins_orig)
363	<	{
364	<	free (args_info->nbins_orig); /* free previous argument */
365	<	args_info->nbins_orig = 0;
366	<	}
367	<	if (args_info->nbins_x_orig)
368	<	{
369	<	free (args_info->nbins_x_orig); /* free previous argument */
370	<	args_info->nbins_x_orig = 0;
371	<	}
372	<	if (args_info->nbins_y_orig)
373	<	{
374	<	free (args_info->nbins_y_orig); /* free previous argument */
375	<	args_info->nbins_y_orig = 0;
376	<	}
377	<	if (args_info->nanglebins_orig)
378	<	{
282	<	free (args_info->nanglebins_orig); /* free previous argument */
283	<	args_info->nanglebins_orig = 0;
284	<	}
285	<	if (args_info->length_orig)
286	<	{
287	<	free (args_info->length_orig); /* free previous argument */
288	<	args_info->length_orig = 0;
289	<	}
290	<	if (args_info->rcut_orig)
291	<	{
292	<	free (args_info->rcut_orig); /* free previous argument */
293	<	args_info->rcut_orig = 0;
294	<	}
295	<	if (args_info->zoffset_orig)
296	<	{
297	<	free (args_info->zoffset_orig); /* free previous argument */
298	<	args_info->zoffset_orig = 0;
299	<	}
300	<	if (args_info->sele1_arg)
301	<	{
302	<	free (args_info->sele1_arg); /* free previous argument */
303	<	args_info->sele1_arg = 0;
304	<	}
305	<	if (args_info->sele1_orig)
306	<	{
307	<	free (args_info->sele1_orig); /* free previous argument */
308	<	args_info->sele1_orig = 0;
309	<	}
310	<	if (args_info->sele2_arg)
311	<	{
312	<	free (args_info->sele2_arg); /* free previous argument */
313	<	args_info->sele2_arg = 0;
314	<	}
315	<	if (args_info->sele2_orig)
316	<	{
317	<	free (args_info->sele2_orig); /* free previous argument */
318	<	args_info->sele2_orig = 0;
319	<	}
320	<	if (args_info->sele3_arg)
321	<	{
322	<	free (args_info->sele3_arg); /* free previous argument */
323	<	args_info->sele3_arg = 0;
324	<	}
325	<	if (args_info->sele3_orig)
326	<	{
327	<	free (args_info->sele3_orig); /* free previous argument */
328	<	args_info->sele3_orig = 0;
329	<	}
330	<	if (args_info->refsele_arg)
331	<	{
332	<	free (args_info->refsele_arg); /* free previous argument */
333	<	args_info->refsele_arg = 0;
334	<	}
335	<	if (args_info->refsele_orig)
336	<	{
337	<	free (args_info->refsele_orig); /* free previous argument */
338	<	args_info->refsele_orig = 0;
339	<	}
340	<	if (args_info->molname_arg)
341	<	{
342	<	free (args_info->molname_arg); /* free previous argument */
343	<	args_info->molname_arg = 0;
344	<	}
345	<	if (args_info->molname_orig)
346	<	{
347	<	free (args_info->molname_orig); /* free previous argument */
348	<	args_info->molname_orig = 0;
349	<	}
350	<	if (args_info->begin_orig)
351	<	{
352	<	free (args_info->begin_orig); /* free previous argument */
353	<	args_info->begin_orig = 0;
354	<	}
355	<	if (args_info->end_orig)
356	<	{
357	<	free (args_info->end_orig); /* free previous argument */
358	<	args_info->end_orig = 0;
359	<	}
360	<	if (args_info->radius_orig)
361	<	{
362	<	free (args_info->radius_orig); /* free previous argument */
363	<	args_info->radius_orig = 0;
364	<	}
342	>	}
343	>
344	>
345	>	static void
346	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
347	>	{
348	>	unsigned int i;
349	>	free_string_field (&(args_info->input_arg));
350	>	free_string_field (&(args_info->input_orig));
351	>	free_string_field (&(args_info->output_arg));
352	>	free_string_field (&(args_info->output_orig));
353	>	free_string_field (&(args_info->step_orig));
354	>	free_string_field (&(args_info->nbins_orig));
355	>	free_string_field (&(args_info->nbins_x_orig));
356	>	free_string_field (&(args_info->nbins_y_orig));
357	>	free_string_field (&(args_info->nbins_z_orig));
358	>	free_string_field (&(args_info->nanglebins_orig));
359	>	free_string_field (&(args_info->rcut_orig));
360	>	free_string_field (&(args_info->dz_orig));
361	>	free_string_field (&(args_info->length_orig));
362	>	free_string_field (&(args_info->zlength_orig));
363	>	free_string_field (&(args_info->zoffset_orig));
364	>	free_string_field (&(args_info->sele1_arg));
365	>	free_string_field (&(args_info->sele1_orig));
366	>	free_string_field (&(args_info->sele2_arg));
367	>	free_string_field (&(args_info->sele2_orig));
368	>	free_string_field (&(args_info->sele3_arg));
369	>	free_string_field (&(args_info->sele3_orig));
370	>	free_string_field (&(args_info->refsele_arg));
371	>	free_string_field (&(args_info->refsele_orig));
372	>	free_string_field (&(args_info->comsele_arg));
373	>	free_string_field (&(args_info->comsele_orig));
374	>	free_string_field (&(args_info->molname_arg));
375	>	free_string_field (&(args_info->molname_orig));
376	>	free_string_field (&(args_info->begin_orig));
377	>	free_string_field (&(args_info->end_orig));
378	>	free_string_field (&(args_info->radius_orig));
379
380	+
381		for (i = 0; i < args_info->inputs_num; ++i)
382		free (args_info->inputs [i]);
383	<
383	>
384		if (args_info->inputs_num)
385		free (args_info->inputs);
386	<
386	>
387		clear_given (args_info);
388		}
389
390	+
391	+	static void
392	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
393	+	{
394	+	FIX_UNUSED (values);
395	+	if (arg) {
396	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
397	+	} else {
398	+	fprintf(outfile, "%s\n", opt);
399	+	}
400	+	}
401	+
402	+
403		int
404	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
405	+	{
406	+	int i = 0;
407	+
408	+	if (!outfile)
409	+	{
410	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
411	+	return EXIT_FAILURE;
412	+	}
413	+
414	+	if (args_info->help_given)
415	+	write_into_file(outfile, "help", 0, 0 );
416	+	if (args_info->version_given)
417	+	write_into_file(outfile, "version", 0, 0 );
418	+	if (args_info->input_given)
419	+	write_into_file(outfile, "input", args_info->input_orig, 0);
420	+	if (args_info->output_given)
421	+	write_into_file(outfile, "output", args_info->output_orig, 0);
422	+	if (args_info->step_given)
423	+	write_into_file(outfile, "step", args_info->step_orig, 0);
424	+	if (args_info->nbins_given)
425	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
426	+	if (args_info->nbins_x_given)
427	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
428	+	if (args_info->nbins_y_given)
429	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
430	+	if (args_info->nbins_z_given)
431	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
432	+	if (args_info->nanglebins_given)
433	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
434	+	if (args_info->rcut_given)
435	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
436	+	if (args_info->dz_given)
437	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
438	+	if (args_info->length_given)
439	+	write_into_file(outfile, "length", args_info->length_orig, 0);
440	+	if (args_info->zlength_given)
441	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
442	+	if (args_info->zoffset_given)
443	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
444	+	if (args_info->sele1_given)
445	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
446	+	if (args_info->sele2_given)
447	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
448	+	if (args_info->sele3_given)
449	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
450	+	if (args_info->refsele_given)
451	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
452	+	if (args_info->comsele_given)
453	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
454	+	if (args_info->molname_given)
455	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
456	+	if (args_info->begin_given)
457	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
458	+	if (args_info->end_given)
459	+	write_into_file(outfile, "end", args_info->end_orig, 0);
460	+	if (args_info->radius_given)
461	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
462	+	if (args_info->bo_given)
463	+	write_into_file(outfile, "bo", 0, 0 );
464	+	if (args_info->bor_given)
465	+	write_into_file(outfile, "bor", 0, 0 );
466	+	if (args_info->bad_given)
467	+	write_into_file(outfile, "bad", 0, 0 );
468	+	if (args_info->count_given)
469	+	write_into_file(outfile, "count", 0, 0 );
470	+	if (args_info->gofr_given)
471	+	write_into_file(outfile, "gofr", 0, 0 );
472	+	if (args_info->gofz_given)
473	+	write_into_file(outfile, "gofz", 0, 0 );
474	+	if (args_info->r_theta_given)
475	+	write_into_file(outfile, "r_theta", 0, 0 );
476	+	if (args_info->r_omega_given)
477	+	write_into_file(outfile, "r_omega", 0, 0 );
478	+	if (args_info->r_z_given)
479	+	write_into_file(outfile, "r_z", 0, 0 );
480	+	if (args_info->theta_omega_given)
481	+	write_into_file(outfile, "theta_omega", 0, 0 );
482	+	if (args_info->gxyz_given)
483	+	write_into_file(outfile, "gxyz", 0, 0 );
484	+	if (args_info->twodgofr_given)
485	+	write_into_file(outfile, "twodgofr", 0, 0 );
486	+	if (args_info->p2_given)
487	+	write_into_file(outfile, "p2", 0, 0 );
488	+	if (args_info->rp2_given)
489	+	write_into_file(outfile, "rp2", 0, 0 );
490	+	if (args_info->scd_given)
491	+	write_into_file(outfile, "scd", 0, 0 );
492	+	if (args_info->density_given)
493	+	write_into_file(outfile, "density", 0, 0 );
494	+	if (args_info->slab_density_given)
495	+	write_into_file(outfile, "slab_density", 0, 0 );
496	+	if (args_info->p_angle_given)
497	+	write_into_file(outfile, "p_angle", 0, 0 );
498	+	if (args_info->hxy_given)
499	+	write_into_file(outfile, "hxy", 0, 0 );
500	+	if (args_info->rho_r_given)
501	+	write_into_file(outfile, "rho_r", 0, 0 );
502	+	if (args_info->angle_r_given)
503	+	write_into_file(outfile, "angle_r", 0, 0 );
504	+	if (args_info->hullvol_given)
505	+	write_into_file(outfile, "hullvol", 0, 0 );
506	+	if (args_info->rodlength_given)
507	+	write_into_file(outfile, "rodlength", 0, 0 );
508	+	if (args_info->tet_param_given)
509	+	write_into_file(outfile, "tet_param", 0, 0 );
510	+	if (args_info->tet_param_z_given)
511	+	write_into_file(outfile, "tet_param_z", 0, 0 );
512	+
513	+
514	+	i = EXIT_SUCCESS;
515	+	return i;
516	+	}
517	+
518	+	int
519		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
520		{
521		FILE *outfile;
#	Line 386 | Line 529 | cmdline_parser_file_save(const char *filename, struct
529		return EXIT_FAILURE;
530		}
531
532	<	if (args_info->help_given) {
390	<	fprintf(outfile, "%s\n", "help");
391	<	}
392	<	if (args_info->version_given) {
393	<	fprintf(outfile, "%s\n", "version");
394	<	}
395	<	if (args_info->input_given) {
396	<	if (args_info->input_orig) {
397	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
398	<	} else {
399	<	fprintf(outfile, "%s\n", "input");
400	<	}
401	<	}
402	<	if (args_info->output_given) {
403	<	if (args_info->output_orig) {
404	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
405	<	} else {
406	<	fprintf(outfile, "%s\n", "output");
407	<	}
408	<	}
409	<	if (args_info->step_given) {
410	<	if (args_info->step_orig) {
411	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
412	<	} else {
413	<	fprintf(outfile, "%s\n", "step");
414	<	}
415	<	}
416	<	if (args_info->nbins_given) {
417	<	if (args_info->nbins_orig) {
418	<	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
419	<	} else {
420	<	fprintf(outfile, "%s\n", "nbins");
421	<	}
422	<	}
423	<	if (args_info->nbins_x_given) {
424	<	if (args_info->nbins_x_orig) {
425	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
426	<	} else {
427	<	fprintf(outfile, "%s\n", "nbins_x");
428	<	}
429	<	}
430	<	if (args_info->nbins_y_given) {
431	<	if (args_info->nbins_y_orig) {
432	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
433	<	} else {
434	<	fprintf(outfile, "%s\n", "nbins_y");
435	<	}
436	<	}
437	<	if (args_info->nanglebins_given) {
438	<	if (args_info->nanglebins_orig) {
439	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
440	<	} else {
441	<	fprintf(outfile, "%s\n", "nanglebins");
442	<	}
443	<	}
444	<	if (args_info->length_given) {
445	<	if (args_info->length_orig) {
446	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
447	<	} else {
448	<	fprintf(outfile, "%s\n", "length");
449	<	}
450	<	}
451	<	if (args_info->rcut_given) {
452	<	if (args_info->rcut_orig) {
453	<	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
454	<	} else {
455	<	fprintf(outfile, "%s\n", "rcut");
456	<	}
457	<	}
458	<	if (args_info->zoffset_given) {
459	<	if (args_info->zoffset_orig) {
460	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
461	<	} else {
462	<	fprintf(outfile, "%s\n", "zoffset");
463	<	}
464	<	}
465	<	if (args_info->sele1_given) {
466	<	if (args_info->sele1_orig) {
467	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
468	<	} else {
469	<	fprintf(outfile, "%s\n", "sele1");
470	<	}
471	<	}
472	<	if (args_info->sele2_given) {
473	<	if (args_info->sele2_orig) {
474	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
475	<	} else {
476	<	fprintf(outfile, "%s\n", "sele2");
477	<	}
478	<	}
479	<	if (args_info->sele3_given) {
480	<	if (args_info->sele3_orig) {
481	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
482	<	} else {
483	<	fprintf(outfile, "%s\n", "sele3");
484	<	}
485	<	}
486	<	if (args_info->refsele_given) {
487	<	if (args_info->refsele_orig) {
488	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
489	<	} else {
490	<	fprintf(outfile, "%s\n", "refsele");
491	<	}
492	<	}
493	<	if (args_info->molname_given) {
494	<	if (args_info->molname_orig) {
495	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
496	<	} else {
497	<	fprintf(outfile, "%s\n", "molname");
498	<	}
499	<	}
500	<	if (args_info->begin_given) {
501	<	if (args_info->begin_orig) {
502	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
503	<	} else {
504	<	fprintf(outfile, "%s\n", "begin");
505	<	}
506	<	}
507	<	if (args_info->end_given) {
508	<	if (args_info->end_orig) {
509	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
510	<	} else {
511	<	fprintf(outfile, "%s\n", "end");
512	<	}
513	<	}
514	<	if (args_info->radius_given) {
515	<	if (args_info->radius_orig) {
516	<	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
517	<	} else {
518	<	fprintf(outfile, "%s\n", "radius");
519	<	}
520	<	}
521	<	if (args_info->bo_given) {
522	<	fprintf(outfile, "%s\n", "bo");
523	<	}
524	<	if (args_info->bor_given) {
525	<	fprintf(outfile, "%s\n", "bor");
526	<	}
527	<	if (args_info->gofr_given) {
528	<	fprintf(outfile, "%s\n", "gofr");
529	<	}
530	<	if (args_info->r_theta_given) {
531	<	fprintf(outfile, "%s\n", "r_theta");
532	<	}
533	<	if (args_info->r_omega_given) {
534	<	fprintf(outfile, "%s\n", "r_omega");
535	<	}
536	<	if (args_info->theta_omega_given) {
537	<	fprintf(outfile, "%s\n", "theta_omega");
538	<	}
539	<	if (args_info->gxyz_given) {
540	<	fprintf(outfile, "%s\n", "gxyz");
541	<	}
542	<	if (args_info->p2_given) {
543	<	fprintf(outfile, "%s\n", "p2");
544	<	}
545	<	if (args_info->rp2_given) {
546	<	fprintf(outfile, "%s\n", "rp2");
547	<	}
548	<	if (args_info->scd_given) {
549	<	fprintf(outfile, "%s\n", "scd");
550	<	}
551	<	if (args_info->density_given) {
552	<	fprintf(outfile, "%s\n", "density");
553	<	}
554	<	if (args_info->slab_density_given) {
555	<	fprintf(outfile, "%s\n", "slab_density");
556	<	}
557	<	if (args_info->hxy_given) {
558	<	fprintf(outfile, "%s\n", "hxy");
559	<	}
560	<	if (args_info->rho_r_given) {
561	<	fprintf(outfile, "%s\n", "rho_r");
562	<	}
563	<
532	>	i = cmdline_parser_dump(outfile, args_info);
533		fclose (outfile);
534
566	–	i = EXIT_SUCCESS;
535		return i;
536		}
537
#	Line 573 | Line 541 | cmdline_parser_free (struct gengetopt_args_info *args_
541		cmdline_parser_release (args_info);
542		}
543
544	<
577	<	/* gengetopt_strdup() */
578	<	/* strdup.c replacement of strdup, which is not standard */
544	>	/** @brief replacement of strdup, which is not standard */
545		char *
546		gengetopt_strdup (const char *s)
547		{
548	<	char *result = NULL;
548	>	char *result = 0;
549		if (!s)
550		return result;
551
#	Line 591 | Line 557 | static void
557		}
558
559		static void
594	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
595	–
596	–	static void
560		reset_group_staticProps(struct gengetopt_args_info *args_info)
561		{
562		if (! args_info->staticProps_group_counter)
#	Line 601 | Line 564 | reset_group_staticProps(struct gengetopt_args_info *ar
564
565		args_info->bo_given = 0 ;
566		args_info->bor_given = 0 ;
567	+	args_info->bad_given = 0 ;
568	+	args_info->count_given = 0 ;
569		args_info->gofr_given = 0 ;
570	+	args_info->gofz_given = 0 ;
571		args_info->r_theta_given = 0 ;
572		args_info->r_omega_given = 0 ;
573	+	args_info->r_z_given = 0 ;
574		args_info->theta_omega_given = 0 ;
575		args_info->gxyz_given = 0 ;
576	+	args_info->twodgofr_given = 0 ;
577		args_info->p2_given = 0 ;
578		args_info->rp2_given = 0 ;
579		args_info->scd_given = 0 ;
580		args_info->density_given = 0 ;
581		args_info->slab_density_given = 0 ;
582	+	args_info->p_angle_given = 0 ;
583		args_info->hxy_given = 0 ;
584		args_info->rho_r_given = 0 ;
585	+	args_info->angle_r_given = 0 ;
586	+	args_info->hullvol_given = 0 ;
587	+	args_info->rodlength_given = 0 ;
588	+	args_info->tet_param_given = 0 ;
589	+	args_info->tet_param_z_given = 0 ;
590
591		args_info->staticProps_group_counter = 0;
592		}
593
594		int
595	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
595	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
596		{
597		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
598		}
599
600		int
601	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
601	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
602	>	struct cmdline_parser_params *params)
603		{
604		int result;
605	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
606
607	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
607	>	if (result == EXIT_FAILURE)
608	>	{
609	>	cmdline_parser_free (args_info);
610	>	exit (EXIT_FAILURE);
611	>	}
612	>
613	>	return result;
614	>	}
615
616	+	int
617	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
618	+	{
619	+	int result;
620	+	struct cmdline_parser_params params;
621	+
622	+	params.override = override;
623	+	params.initialize = initialize;
624	+	params.check_required = check_required;
625	+	params.check_ambiguity = 0;
626	+	params.print_errors = 1;
627	+
628	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
629	+
630		if (result == EXIT_FAILURE)
631		{
632		cmdline_parser_free (args_info);
#	Line 644 | Line 641 | cmdline_parser_required (struct gengetopt_args_info *a
641		{
642		int result = EXIT_SUCCESS;
643
644	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
644	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
645		result = EXIT_FAILURE;
646
647		if (result == EXIT_FAILURE)
#	Line 660 | Line 657 | cmdline_parser_required2 (struct gengetopt_args_info *
657		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
658		{
659		int error = 0;
660	+	FIX_UNUSED (additional_error);
661
662		/* checks for required options */
663		if (! args_info->input_given)
#	Line 670 | Line 668 | cmdline_parser_required2 (struct gengetopt_args_info *
668
669		if (args_info->staticProps_group_counter == 0)
670		{
671	<	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 : ""));
671	>	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 : ""));
672		error = 1;
673		}
674
#	Line 680 | Line 678 | cmdline_parser_required2 (struct gengetopt_args_info *
678		return error;
679		}
680
681	+
682	+	static char *package_name = 0;
683	+
684	+	/**
685	+	* @brief updates an option
686	+	* @param field the generic pointer to the field to update
687	+	* @param orig_field the pointer to the orig field
688	+	* @param field_given the pointer to the number of occurrence of this option
689	+	* @param prev_given the pointer to the number of occurrence already seen
690	+	* @param value the argument for this option (if null no arg was specified)
691	+	* @param possible_values the possible values for this option (if specified)
692	+	* @param default_value the default value (in case the option only accepts fixed values)
693	+	* @param arg_type the type of this option
694	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
695	+	* @param override @see cmdline_parser_params.override
696	+	* @param no_free whether to free a possible previous value
697	+	* @param multiple_option whether this is a multiple option
698	+	* @param long_opt the corresponding long option
699	+	* @param short_opt the corresponding short option (or '-' if none)
700	+	* @param additional_error possible further error specification
701	+	*/
702	+	static
703	+	int update_arg(void *field, char **orig_field,
704	+	unsigned int *field_given, unsigned int *prev_given,
705	+	char *value, const char *possible_values[],
706	+	const char *default_value,
707	+	cmdline_parser_arg_type arg_type,
708	+	int check_ambiguity, int override,
709	+	int no_free, int multiple_option,
710	+	const char *long_opt, char short_opt,
711	+	const char *additional_error)
712	+	{
713	+	char *stop_char = 0;
714	+	const char *val = value;
715	+	int found;
716	+	char **string_field;
717	+	FIX_UNUSED (field);
718	+
719	+	stop_char = 0;
720	+	found = 0;
721	+
722	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
723	+	{
724	+	if (short_opt != '-')
725	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
726	+	package_name, long_opt, short_opt,
727	+	(additional_error ? additional_error : ""));
728	+	else
729	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
730	+	package_name, long_opt,
731	+	(additional_error ? additional_error : ""));
732	+	return 1; /* failure */
733	+	}
734	+
735	+	FIX_UNUSED (default_value);
736	+
737	+	if (field_given && *field_given && ! override)
738	+	return 0;
739	+	if (prev_given)
740	+	(*prev_given)++;
741	+	if (field_given)
742	+	(*field_given)++;
743	+	if (possible_values)
744	+	val = possible_values[found];
745	+
746	+	switch(arg_type) {
747	+	case ARG_INT:
748	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
749	+	break;
750	+	case ARG_DOUBLE:
751	+	if (val) *((double *)field) = strtod (val, &stop_char);
752	+	break;
753	+	case ARG_STRING:
754	+	if (val) {
755	+	string_field = (char **)field;
756	+	if (!no_free && *string_field)
757	+	free (*string_field); /* free previous string */
758	+	*string_field = gengetopt_strdup (val);
759	+	}
760	+	break;
761	+	default:
762	+	break;
763	+	};
764	+
765	+	/* check numeric conversion */
766	+	switch(arg_type) {
767	+	case ARG_INT:
768	+	case ARG_DOUBLE:
769	+	if (val && !(stop_char && *stop_char == '\0')) {
770	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
771	+	return 1; /* failure */
772	+	}
773	+	break;
774	+	default:
775	+	;
776	+	};
777	+
778	+	/* store the original value */
779	+	switch(arg_type) {
780	+	case ARG_NO:
781	+	break;
782	+	default:
783	+	if (value && orig_field) {
784	+	if (no_free) {
785	+	*orig_field = value;
786	+	} else {
787	+	if (*orig_field)
788	+	free (*orig_field); /* free previous string */
789	+	*orig_field = gengetopt_strdup (value);
790	+	}
791	+	}
792	+	};
793	+
794	+	return 0; /* OK */
795	+	}
796	+
797	+
798		int
799	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
799	>	cmdline_parser_internal (
800	>	int argc, char **argv, struct gengetopt_args_info *args_info,
801	>	struct cmdline_parser_params *params, const char *additional_error)
802		{
803		int c;        /* Character of the parsed option.  */
804
805		int error = 0;
806		struct gengetopt_args_info local_args_info;
807	+
808	+	int override;
809	+	int initialize;
810	+	int check_required;
811	+	int check_ambiguity;
812	+
813	+	package_name = argv[0];
814	+
815	+	override = params->override;
816	+	initialize = params->initialize;
817	+	check_required = params->check_required;
818	+	check_ambiguity = params->check_ambiguity;
819
820		if (initialize)
821		cmdline_parser_init (args_info);
#	Line 695 | Line 824 | cmdline_parser_internal (int argc, char * const *argv,
824
825		optarg = 0;
826		optind = 0;
827	<	opterr = 1;
827	>	opterr = params->print_errors;
828		optopt = '?';
829
830		while (1)
831		{
832		int option_index = 0;
704	–	char *stop_char;
833
834		static struct option long_options[] = {
835		{ "help",       0, NULL, 'h' },
#	Line 712 | Line 840 | cmdline_parser_internal (int argc, char * const *argv,
840		{ "nbins",      1, NULL, 'b' },
841		{ "nbins_x",    1, NULL, 'x' },
842		{ "nbins_y",    1, NULL, 'y' },
843	+	{ "nbins_z",    1, NULL, 0 },
844		{ "nanglebins", 1, NULL, 'a' },
716	–	{ "length",     1, NULL, 0 },
845		{ "rcut",       1, NULL, 'c' },
846	+	{ "dz", 1, NULL, 0 },
847	+	{ "length",     1, NULL, 0 },
848	+	{ "zlength",    1, NULL, 0 },
849		{ "zoffset",    1, NULL, 'z' },
850		{ "sele1",      1, NULL, 0 },
851		{ "sele2",      1, NULL, 0 },
852		{ "sele3",      1, NULL, 0 },
853		{ "refsele",    1, NULL, 0 },
854	+	{ "comsele",    1, NULL, 0 },
855		{ "molname",    1, NULL, 0 },
856		{ "begin",      1, NULL, 0 },
857		{ "end",        1, NULL, 0 },
858		{ "radius",     1, NULL, 0 },
859		{ "bo", 0, NULL, 0 },
860		{ "bor",        0, NULL, 0 },
861	+	{ "bad",        0, NULL, 0 },
862	+	{ "count",      0, NULL, 0 },
863		{ "gofr",       0, NULL, 'g' },
864	+	{ "gofz",       0, NULL, 0 },
865		{ "r_theta",    0, NULL, 0 },
866		{ "r_omega",    0, NULL, 0 },
867	+	{ "r_z",        0, NULL, 0 },
868		{ "theta_omega",        0, NULL, 0 },
869		{ "gxyz",       0, NULL, 0 },
870	+	{ "twodgofr",   0, NULL, 0 },
871		{ "p2", 0, NULL, 'p' },
872		{ "rp2",        0, NULL, 0 },
873		{ "scd",        0, NULL, 's' },
874		{ "density",    0, NULL, 'd' },
875		{ "slab_density",       0, NULL, 0 },
876	+	{ "p_angle",    0, NULL, 0 },
877		{ "hxy",        0, NULL, 0 },
878		{ "rho_r",      0, NULL, 0 },
879	<	{ NULL, 0, NULL, 0 }
879	>	{ "angle_r",    0, NULL, 0 },
880	>	{ "hullvol",    0, NULL, 0 },
881	>	{ "rodlength",  0, NULL, 0 },
882	>	{ "tet_param",  0, NULL, 'Q' },
883	>	{ "tet_param_z",        0, NULL, 0 },
884	>	{ 0,  0, 0, 0 }
885		};
886
887	<	stop_char = 0;
745	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
887	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
888
889		if (c == -1) break;       /* Exit from `while (1)' loop.  */
890
#	Line 759 | Line 901 | cmdline_parser_internal (int argc, char * const *argv,
901		exit (EXIT_SUCCESS);
902
903		case 'i':       /* input dump file.  */
904	<	if (local_args_info.input_given)
905	<	{
906	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
907	<	goto failure;
908	<	}
909	<	if (args_info->input_given && ! override)
910	<	continue;
911	<	local_args_info.input_given = 1;
912	<	args_info->input_given = 1;
913	<	if (args_info->input_arg)
772	<	free (args_info->input_arg); /* free previous string */
773	<	args_info->input_arg = gengetopt_strdup (optarg);
774	<	if (args_info->input_orig)
775	<	free (args_info->input_orig); /* free previous string */
776	<	args_info->input_orig = gengetopt_strdup (optarg);
904	>
905	>
906	>	if (update_arg( (void *)&(args_info->input_arg),
907	>	&(args_info->input_orig), &(args_info->input_given),
908	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
909	>	check_ambiguity, override, 0, 0,
910	>	"input", 'i',
911	>	additional_error))
912	>	goto failure;
913	>
914		break;
778	–
915		case 'o':       /* output file name.  */
916	<	if (local_args_info.output_given)
917	<	{
918	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
919	<	goto failure;
920	<	}
921	<	if (args_info->output_given && ! override)
922	<	continue;
923	<	local_args_info.output_given = 1;
924	<	args_info->output_given = 1;
925	<	if (args_info->output_arg)
790	<	free (args_info->output_arg); /* free previous string */
791	<	args_info->output_arg = gengetopt_strdup (optarg);
792	<	if (args_info->output_orig)
793	<	free (args_info->output_orig); /* free previous string */
794	<	args_info->output_orig = gengetopt_strdup (optarg);
916	>
917	>
918	>	if (update_arg( (void *)&(args_info->output_arg),
919	>	&(args_info->output_orig), &(args_info->output_given),
920	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
921	>	check_ambiguity, override, 0, 0,
922	>	"output", 'o',
923	>	additional_error))
924	>	goto failure;
925	>
926		break;
796	–
927		case 'n':       /* process every n frame.  */
928	<	if (local_args_info.step_given)
929	<	{
930	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
931	<	goto failure;
932	<	}
933	<	if (args_info->step_given && ! override)
934	<	continue;
935	<	local_args_info.step_given = 1;
806	<	args_info->step_given = 1;
807	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
808	<	if (!(stop_char && *stop_char == '\0')) {
809	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
928	>
929	>
930	>	if (update_arg( (void *)&(args_info->step_arg),
931	>	&(args_info->step_orig), &(args_info->step_given),
932	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
933	>	check_ambiguity, override, 0, 0,
934	>	"step", 'n',
935	>	additional_error))
936		goto failure;
937	<	}
812	<	if (args_info->step_orig)
813	<	free (args_info->step_orig); /* free previous string */
814	<	args_info->step_orig = gengetopt_strdup (optarg);
937	>
938		break;
816	–
939		case 'b':       /* number of bins (general purpose).  */
940	<	if (local_args_info.nbins_given)
941	<	{
942	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
943	<	goto failure;
944	<	}
945	<	if (args_info->nbins_given && ! override)
946	<	continue;
947	<	local_args_info.nbins_given = 1;
826	<	args_info->nbins_given = 1;
827	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
828	<	if (!(stop_char && *stop_char == '\0')) {
829	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
940	>
941	>
942	>	if (update_arg( (void *)&(args_info->nbins_arg),
943	>	&(args_info->nbins_orig), &(args_info->nbins_given),
944	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
945	>	check_ambiguity, override, 0, 0,
946	>	"nbins", 'b',
947	>	additional_error))
948		goto failure;
949	<	}
832	<	if (args_info->nbins_orig)
833	<	free (args_info->nbins_orig); /* free previous string */
834	<	args_info->nbins_orig = gengetopt_strdup (optarg);
949	>
950		break;
836	–
951		case 'x':       /* number of bins in x axis.  */
952	<	if (local_args_info.nbins_x_given)
953	<	{
954	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
955	<	goto failure;
956	<	}
957	<	if (args_info->nbins_x_given && ! override)
958	<	continue;
959	<	local_args_info.nbins_x_given = 1;
846	<	args_info->nbins_x_given = 1;
847	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
848	<	if (!(stop_char && *stop_char == '\0')) {
849	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
952	>
953	>
954	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
955	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
956	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
957	>	check_ambiguity, override, 0, 0,
958	>	"nbins_x", 'x',
959	>	additional_error))
960		goto failure;
961	<	}
852	<	if (args_info->nbins_x_orig)
853	<	free (args_info->nbins_x_orig); /* free previous string */
854	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
961	>
962		break;
856	–
963		case 'y':       /* number of bins in y axis.  */
964	<	if (local_args_info.nbins_y_given)
965	<	{
966	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
967	<	goto failure;
968	<	}
969	<	if (args_info->nbins_y_given && ! override)
970	<	continue;
971	<	local_args_info.nbins_y_given = 1;
866	<	args_info->nbins_y_given = 1;
867	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
868	<	if (!(stop_char && *stop_char == '\0')) {
869	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
964	>
965	>
966	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
967	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
968	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
969	>	check_ambiguity, override, 0, 0,
970	>	"nbins_y", 'y',
971	>	additional_error))
972		goto failure;
973	<	}
872	<	if (args_info->nbins_y_orig)
873	<	free (args_info->nbins_y_orig); /* free previous string */
874	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
973	>
974		break;
876	–
975		case 'a':       /* number of bins for cos(angle).  */
976	<	if (local_args_info.nanglebins_given)
977	<	{
978	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
979	<	goto failure;
980	<	}
981	<	if (args_info->nanglebins_given && ! override)
982	<	continue;
983	<	local_args_info.nanglebins_given = 1;
886	<	args_info->nanglebins_given = 1;
887	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
888	<	if (!(stop_char && *stop_char == '\0')) {
889	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
976	>
977	>
978	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
979	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
980	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
981	>	check_ambiguity, override, 0, 0,
982	>	"nanglebins", 'a',
983	>	additional_error))
984		goto failure;
985	<	}
892	<	if (args_info->nanglebins_orig)
893	<	free (args_info->nanglebins_orig); /* free previous string */
894	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
985	>
986		break;
896	–
987		case 'c':       /* cutoff radius (rcut).  */
988	<	if (local_args_info.rcut_given)
989	<	{
990	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
991	<	goto failure;
992	<	}
993	<	if (args_info->rcut_given && ! override)
994	<	continue;
995	<	local_args_info.rcut_given = 1;
906	<	args_info->rcut_given = 1;
907	<	args_info->rcut_arg = strtod (optarg, &stop_char);
908	<	if (!(stop_char && *stop_char == '\0')) {
909	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
988	>
989	>
990	>	if (update_arg( (void *)&(args_info->rcut_arg),
991	>	&(args_info->rcut_orig), &(args_info->rcut_given),
992	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
993	>	check_ambiguity, override, 0, 0,
994	>	"rcut", 'c',
995	>	additional_error))
996		goto failure;
997	<	}
912	<	if (args_info->rcut_orig)
913	<	free (args_info->rcut_orig); /* free previous string */
914	<	args_info->rcut_orig = gengetopt_strdup (optarg);
997	>
998		break;
916	–
999		case 'z':       /* Where to set the zero for the slab_density calculation.  */
1000	<	if (local_args_info.zoffset_given)
1001	<	{
1002	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1003	<	goto failure;
1004	<	}
1005	<	if (args_info->zoffset_given && ! override)
1006	<	continue;
1007	<	local_args_info.zoffset_given = 1;
926	<	args_info->zoffset_given = 1;
927	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
928	<	if (!(stop_char && *stop_char == '\0')) {
929	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1000	>
1001	>
1002	>	if (update_arg( (void *)&(args_info->zoffset_arg),
1003	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1004	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1005	>	check_ambiguity, override, 0, 0,
1006	>	"zoffset", 'z',
1007	>	additional_error))
1008		goto failure;
1009	<	}
932	<	if (args_info->zoffset_orig)
933	<	free (args_info->zoffset_orig); /* free previous string */
934	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
1009	>
1010		break;
936	–
1011		case 'g':       /* g(r).  */
1012	<	if (local_args_info.gofr_given)
939	<	{
940	<	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
941	<	goto failure;
942	<	}
943	<	if (args_info->gofr_given && ! override)
944	<	continue;
945	<	local_args_info.gofr_given = 1;
946	<	args_info->gofr_given = 1;
1012	>
1013		if (args_info->staticProps_group_counter && override)
1014		reset_group_staticProps (args_info);
1015		args_info->staticProps_group_counter += 1;
1016	+
1017	+	if (update_arg( 0 ,
1018	+	0 , &(args_info->gofr_given),
1019	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1020	+	check_ambiguity, override, 0, 0,
1021	+	"gofr", 'g',
1022	+	additional_error))
1023	+	goto failure;
1024	+
1025		break;
1026	<
1027	<	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
953	<	if (local_args_info.p2_given)
954	<	{
955	<	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
956	<	goto failure;
957	<	}
958	<	if (args_info->p2_given && ! override)
959	<	continue;
960	<	local_args_info.p2_given = 1;
961	<	args_info->p2_given = 1;
1026	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1027	>
1028		if (args_info->staticProps_group_counter && override)
1029		reset_group_staticProps (args_info);
1030		args_info->staticProps_group_counter += 1;
1031	+
1032	+	if (update_arg( 0 ,
1033	+	0 , &(args_info->p2_given),
1034	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1035	+	check_ambiguity, override, 0, 0,
1036	+	"p2", 'p',
1037	+	additional_error))
1038	+	goto failure;
1039	+
1040		break;
966	–
1041		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1042	<	if (local_args_info.scd_given)
969	<	{
970	<	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	<	goto failure;
972	<	}
973	<	if (args_info->scd_given && ! override)
974	<	continue;
975	<	local_args_info.scd_given = 1;
976	<	args_info->scd_given = 1;
1042	>
1043		if (args_info->staticProps_group_counter && override)
1044		reset_group_staticProps (args_info);
1045		args_info->staticProps_group_counter += 1;
1046	+
1047	+	if (update_arg( 0 ,
1048	+	0 , &(args_info->scd_given),
1049	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1050	+	check_ambiguity, override, 0, 0,
1051	+	"scd", 's',
1052	+	additional_error))
1053	+	goto failure;
1054	+
1055		break;
981	–
1056		case 'd':       /* density plot.  */
1057	<	if (local_args_info.density_given)
1058	<	{
1059	<	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1060	<	goto failure;
1061	<	}
1062	<	if (args_info->density_given && ! override)
1063	<	continue;
1064	<	local_args_info.density_given = 1;
1065	<	args_info->density_given = 1;
1057	>
1058	>	if (args_info->staticProps_group_counter && override)
1059	>	reset_group_staticProps (args_info);
1060	>	args_info->staticProps_group_counter += 1;
1061	>
1062	>	if (update_arg( 0 ,
1063	>	0 , &(args_info->density_given),
1064	>	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1065	>	check_ambiguity, override, 0, 0,
1066	>	"density", 'd',
1067	>	additional_error))
1068	>	goto failure;
1069	>
1070	>	break;
1071	>	case 'Q':       /* tetrahedrality order parameter.  */
1072	>
1073		if (args_info->staticProps_group_counter && override)
1074		reset_group_staticProps (args_info);
1075		args_info->staticProps_group_counter += 1;
1076	+
1077	+	if (update_arg( 0 ,
1078	+	0 , &(args_info->tet_param_given),
1079	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1080	+	check_ambiguity, override, 0, 0,
1081	+	"tet_param", 'Q',
1082	+	additional_error))
1083	+	goto failure;
1084	+
1085		break;
1086
997	–
1087		case 0: /* Long option with no short option */
1088	+	/* number of bins in z axis.  */
1089	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1090	+	{
1091	+
1092	+
1093	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1094	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1095	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1096	+	check_ambiguity, override, 0, 0,
1097	+	"nbins_z", '-',
1098	+	additional_error))
1099	+	goto failure;
1100	+
1101	+	}
1102	+	/* slab width (dz).  */
1103	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1104	+	{
1105	+
1106	+
1107	+	if (update_arg( (void *)&(args_info->dz_arg),
1108	+	&(args_info->dz_orig), &(args_info->dz_given),
1109	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1110	+	check_ambiguity, override, 0, 0,
1111	+	"dz", '-',
1112	+	additional_error))
1113	+	goto failure;
1114	+
1115	+	}
1116		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1117	<	if (strcmp (long_options[option_index].name, "length") == 0)
1117	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1118		{
1119	<	if (local_args_info.length_given)
1120	<	{
1121	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1122	<	goto failure;
1123	<	}
1124	<	if (args_info->length_given && ! override)
1125	<	continue;
1126	<	local_args_info.length_given = 1;
1010	<	args_info->length_given = 1;
1011	<	args_info->length_arg = strtod (optarg, &stop_char);
1012	<	if (!(stop_char && *stop_char == '\0')) {
1013	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1119	>
1120	>
1121	>	if (update_arg( (void *)&(args_info->length_arg),
1122	>	&(args_info->length_orig), &(args_info->length_given),
1123	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1124	>	check_ambiguity, override, 0, 0,
1125	>	"length", '-',
1126	>	additional_error))
1127		goto failure;
1128	<	}
1016	<	if (args_info->length_orig)
1017	<	free (args_info->length_orig); /* free previous string */
1018	<	args_info->length_orig = gengetopt_strdup (optarg);
1128	>
1129		}
1130	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1131	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1132	+	{
1133	+
1134	+
1135	+	if (update_arg( (void *)&(args_info->zlength_arg),
1136	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1137	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1138	+	check_ambiguity, override, 0, 0,
1139	+	"zlength", '-',
1140	+	additional_error))
1141	+	goto failure;
1142	+
1143	+	}
1144		/* select the first stuntdouble set.  */
1145		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1146		{
1147	<	if (local_args_info.sele1_given)
1148	<	{
1149	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1150	<	goto failure;
1151	<	}
1152	<	if (args_info->sele1_given && ! override)
1153	<	continue;
1154	<	local_args_info.sele1_given = 1;
1155	<	args_info->sele1_given = 1;
1156	<	if (args_info->sele1_arg)
1033	<	free (args_info->sele1_arg); /* free previous string */
1034	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1035	<	if (args_info->sele1_orig)
1036	<	free (args_info->sele1_orig); /* free previous string */
1037	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1147	>
1148	>
1149	>	if (update_arg( (void *)&(args_info->sele1_arg),
1150	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1151	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1152	>	check_ambiguity, override, 0, 0,
1153	>	"sele1", '-',
1154	>	additional_error))
1155	>	goto failure;
1156	>
1157		}
1158		/* select the second stuntdouble set.  */
1159		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1160		{
1161	<	if (local_args_info.sele2_given)
1162	<	{
1163	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1164	<	goto failure;
1165	<	}
1166	<	if (args_info->sele2_given && ! override)
1167	<	continue;
1168	<	local_args_info.sele2_given = 1;
1169	<	args_info->sele2_given = 1;
1170	<	if (args_info->sele2_arg)
1052	<	free (args_info->sele2_arg); /* free previous string */
1053	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1054	<	if (args_info->sele2_orig)
1055	<	free (args_info->sele2_orig); /* free previous string */
1056	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1161	>
1162	>
1163	>	if (update_arg( (void *)&(args_info->sele2_arg),
1164	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1165	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1166	>	check_ambiguity, override, 0, 0,
1167	>	"sele2", '-',
1168	>	additional_error))
1169	>	goto failure;
1170	>
1171		}
1172		/* select the third stuntdouble set.  */
1173		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1174		{
1175	<	if (local_args_info.sele3_given)
1176	<	{
1177	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1178	<	goto failure;
1179	<	}
1180	<	if (args_info->sele3_given && ! override)
1181	<	continue;
1182	<	local_args_info.sele3_given = 1;
1183	<	args_info->sele3_given = 1;
1184	<	if (args_info->sele3_arg)
1071	<	free (args_info->sele3_arg); /* free previous string */
1072	<	args_info->sele3_arg = gengetopt_strdup (optarg);
1073	<	if (args_info->sele3_orig)
1074	<	free (args_info->sele3_orig); /* free previous string */
1075	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1175	>
1176	>
1177	>	if (update_arg( (void *)&(args_info->sele3_arg),
1178	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1179	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1180	>	check_ambiguity, override, 0, 0,
1181	>	"sele3", '-',
1182	>	additional_error))
1183	>	goto failure;
1184	>
1185		}
1186		/* select reference (use and only use with --gxyz).  */
1187		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1188		{
1189	<	if (local_args_info.refsele_given)
1190	<	{
1191	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1192	<	goto failure;
1193	<	}
1194	<	if (args_info->refsele_given && ! override)
1195	<	continue;
1196	<	local_args_info.refsele_given = 1;
1197	<	args_info->refsele_given = 1;
1198	<	if (args_info->refsele_arg)
1090	<	free (args_info->refsele_arg); /* free previous string */
1091	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1092	<	if (args_info->refsele_orig)
1093	<	free (args_info->refsele_orig); /* free previous string */
1094	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1189	>
1190	>
1191	>	if (update_arg( (void *)&(args_info->refsele_arg),
1192	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1193	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1194	>	check_ambiguity, override, 0, 0,
1195	>	"refsele", '-',
1196	>	additional_error))
1197	>	goto failure;
1198	>
1199		}
1200	+	/* select stunt doubles for center-of-mass reference point.  */
1201	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1202	+	{
1203	+
1204	+
1205	+	if (update_arg( (void *)&(args_info->comsele_arg),
1206	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1207	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1208	+	check_ambiguity, override, 0, 0,
1209	+	"comsele", '-',
1210	+	additional_error))
1211	+	goto failure;
1212	+
1213	+	}
1214		/* molecule name.  */
1215		else if (strcmp (long_options[option_index].name, "molname") == 0)
1216		{
1217	<	if (local_args_info.molname_given)
1218	<	{
1219	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1220	<	goto failure;
1221	<	}
1222	<	if (args_info->molname_given && ! override)
1223	<	continue;
1224	<	local_args_info.molname_given = 1;
1225	<	args_info->molname_given = 1;
1226	<	if (args_info->molname_arg)
1109	<	free (args_info->molname_arg); /* free previous string */
1110	<	args_info->molname_arg = gengetopt_strdup (optarg);
1111	<	if (args_info->molname_orig)
1112	<	free (args_info->molname_orig); /* free previous string */
1113	<	args_info->molname_orig = gengetopt_strdup (optarg);
1217	>
1218	>
1219	>	if (update_arg( (void *)&(args_info->molname_arg),
1220	>	&(args_info->molname_orig), &(args_info->molname_given),
1221	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1222	>	check_ambiguity, override, 0, 0,
1223	>	"molname", '-',
1224	>	additional_error))
1225	>	goto failure;
1226	>
1227		}
1228		/* begin internal index.  */
1229		else if (strcmp (long_options[option_index].name, "begin") == 0)
1230		{
1231	<	if (local_args_info.begin_given)
1232	<	{
1233	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1234	<	goto failure;
1235	<	}
1236	<	if (args_info->begin_given && ! override)
1237	<	continue;
1238	<	local_args_info.begin_given = 1;
1126	<	args_info->begin_given = 1;
1127	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1128	<	if (!(stop_char && *stop_char == '\0')) {
1129	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1231	>
1232	>
1233	>	if (update_arg( (void *)&(args_info->begin_arg),
1234	>	&(args_info->begin_orig), &(args_info->begin_given),
1235	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1236	>	check_ambiguity, override, 0, 0,
1237	>	"begin", '-',
1238	>	additional_error))
1239		goto failure;
1240	<	}
1132	<	if (args_info->begin_orig)
1133	<	free (args_info->begin_orig); /* free previous string */
1134	<	args_info->begin_orig = gengetopt_strdup (optarg);
1240	>
1241		}
1242		/* end internal index.  */
1243		else if (strcmp (long_options[option_index].name, "end") == 0)
1244		{
1245	<	if (local_args_info.end_given)
1246	<	{
1247	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1248	<	goto failure;
1249	<	}
1250	<	if (args_info->end_given && ! override)
1251	<	continue;
1252	<	local_args_info.end_given = 1;
1147	<	args_info->end_given = 1;
1148	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
1149	<	if (!(stop_char && *stop_char == '\0')) {
1150	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1245	>
1246	>
1247	>	if (update_arg( (void *)&(args_info->end_arg),
1248	>	&(args_info->end_orig), &(args_info->end_given),
1249	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1250	>	check_ambiguity, override, 0, 0,
1251	>	"end", '-',
1252	>	additional_error))
1253		goto failure;
1254	<	}
1153	<	if (args_info->end_orig)
1154	<	free (args_info->end_orig); /* free previous string */
1155	<	args_info->end_orig = gengetopt_strdup (optarg);
1254	>
1255		}
1256		/* nanoparticle radius.  */
1257		else if (strcmp (long_options[option_index].name, "radius") == 0)
1258		{
1259	<	if (local_args_info.radius_given)
1260	<	{
1261	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1262	<	goto failure;
1263	<	}
1264	<	if (args_info->radius_given && ! override)
1265	<	continue;
1266	<	local_args_info.radius_given = 1;
1168	<	args_info->radius_given = 1;
1169	<	args_info->radius_arg = strtod (optarg, &stop_char);
1170	<	if (!(stop_char && *stop_char == '\0')) {
1171	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1259	>
1260	>
1261	>	if (update_arg( (void *)&(args_info->radius_arg),
1262	>	&(args_info->radius_orig), &(args_info->radius_given),
1263	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1264	>	check_ambiguity, override, 0, 0,
1265	>	"radius", '-',
1266	>	additional_error))
1267		goto failure;
1268	<	}
1174	<	if (args_info->radius_orig)
1175	<	free (args_info->radius_orig); /* free previous string */
1176	<	args_info->radius_orig = gengetopt_strdup (optarg);
1268	>
1269		}
1270		/* bond order parameter (--rcut must be specified).  */
1271		else if (strcmp (long_options[option_index].name, "bo") == 0)
1272		{
1273	<	if (local_args_info.bo_given)
1182	<	{
1183	<	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1184	<	goto failure;
1185	<	}
1186	<	if (args_info->bo_given && ! override)
1187	<	continue;
1188	<	local_args_info.bo_given = 1;
1189	<	args_info->bo_given = 1;
1273	>
1274		if (args_info->staticProps_group_counter && override)
1275		reset_group_staticProps (args_info);
1276		args_info->staticProps_group_counter += 1;
1277	<	break;
1277	>
1278	>	if (update_arg( 0 ,
1279	>	0 , &(args_info->bo_given),
1280	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1281	>	check_ambiguity, override, 0, 0,
1282	>	"bo", '-',
1283	>	additional_error))
1284	>	goto failure;
1285	>
1286		}
1287		/* bond order parameter as a function of radius (--rcut must be specified).  */
1288		else if (strcmp (long_options[option_index].name, "bor") == 0)
1289		{
1290	<	if (local_args_info.bor_given)
1199	<	{
1200	<	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1201	<	goto failure;
1202	<	}
1203	<	if (args_info->bor_given && ! override)
1204	<	continue;
1205	<	local_args_info.bor_given = 1;
1206	<	args_info->bor_given = 1;
1290	>
1291		if (args_info->staticProps_group_counter && override)
1292		reset_group_staticProps (args_info);
1293		args_info->staticProps_group_counter += 1;
1294	<	break;
1294	>
1295	>	if (update_arg( 0 ,
1296	>	0 , &(args_info->bor_given),
1297	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1298	>	check_ambiguity, override, 0, 0,
1299	>	"bor", '-',
1300	>	additional_error))
1301	>	goto failure;
1302	>
1303		}
1304	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1305	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1306	+	{
1307	+
1308	+	if (args_info->staticProps_group_counter && override)
1309	+	reset_group_staticProps (args_info);
1310	+	args_info->staticProps_group_counter += 1;
1311	+
1312	+	if (update_arg( 0 ,
1313	+	0 , &(args_info->bad_given),
1314	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1315	+	check_ambiguity, override, 0, 0,
1316	+	"bad", '-',
1317	+	additional_error))
1318	+	goto failure;
1319	+
1320	+	}
1321	+	/* count of molecules matching selection criteria (and associated statistics).  */
1322	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1323	+	{
1324	+
1325	+	if (args_info->staticProps_group_counter && override)
1326	+	reset_group_staticProps (args_info);
1327	+	args_info->staticProps_group_counter += 1;
1328	+
1329	+	if (update_arg( 0 ,
1330	+	0 , &(args_info->count_given),
1331	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1332	+	check_ambiguity, override, 0, 0,
1333	+	"count", '-',
1334	+	additional_error))
1335	+	goto failure;
1336	+
1337	+	}
1338	+	/* g(z).  */
1339	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1340	+	{
1341	+
1342	+	if (args_info->staticProps_group_counter && override)
1343	+	reset_group_staticProps (args_info);
1344	+	args_info->staticProps_group_counter += 1;
1345	+
1346	+	if (update_arg( 0 ,
1347	+	0 , &(args_info->gofz_given),
1348	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1349	+	check_ambiguity, override, 0, 0,
1350	+	"gofz", '-',
1351	+	additional_error))
1352	+	goto failure;
1353	+
1354	+	}
1355		/* g(r, cos(theta)).  */
1356		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1357		{
1358	<	if (local_args_info.r_theta_given)
1216	<	{
1217	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1218	<	goto failure;
1219	<	}
1220	<	if (args_info->r_theta_given && ! override)
1221	<	continue;
1222	<	local_args_info.r_theta_given = 1;
1223	<	args_info->r_theta_given = 1;
1358	>
1359		if (args_info->staticProps_group_counter && override)
1360		reset_group_staticProps (args_info);
1361		args_info->staticProps_group_counter += 1;
1362	<	break;
1362	>
1363	>	if (update_arg( 0 ,
1364	>	0 , &(args_info->r_theta_given),
1365	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1366	>	check_ambiguity, override, 0, 0,
1367	>	"r_theta", '-',
1368	>	additional_error))
1369	>	goto failure;
1370	>
1371		}
1372		/* g(r, cos(omega)).  */
1373		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1374		{
1375	<	if (local_args_info.r_omega_given)
1233	<	{
1234	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1235	<	goto failure;
1236	<	}
1237	<	if (args_info->r_omega_given && ! override)
1238	<	continue;
1239	<	local_args_info.r_omega_given = 1;
1240	<	args_info->r_omega_given = 1;
1375	>
1376		if (args_info->staticProps_group_counter && override)
1377		reset_group_staticProps (args_info);
1378		args_info->staticProps_group_counter += 1;
1379	<	break;
1379	>
1380	>	if (update_arg( 0 ,
1381	>	0 , &(args_info->r_omega_given),
1382	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1383	>	check_ambiguity, override, 0, 0,
1384	>	"r_omega", '-',
1385	>	additional_error))
1386	>	goto failure;
1387	>
1388		}
1389	+	/* g(r, z).  */
1390	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1391	+	{
1392	+
1393	+	if (args_info->staticProps_group_counter && override)
1394	+	reset_group_staticProps (args_info);
1395	+	args_info->staticProps_group_counter += 1;
1396	+
1397	+	if (update_arg( 0 ,
1398	+	0 , &(args_info->r_z_given),
1399	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1400	+	check_ambiguity, override, 0, 0,
1401	+	"r_z", '-',
1402	+	additional_error))
1403	+	goto failure;
1404	+
1405	+	}
1406		/* g(cos(theta), cos(omega)).  */
1407		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1408		{
1409	<	if (local_args_info.theta_omega_given)
1250	<	{
1251	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	<	goto failure;
1253	<	}
1254	<	if (args_info->theta_omega_given && ! override)
1255	<	continue;
1256	<	local_args_info.theta_omega_given = 1;
1257	<	args_info->theta_omega_given = 1;
1409	>
1410		if (args_info->staticProps_group_counter && override)
1411		reset_group_staticProps (args_info);
1412		args_info->staticProps_group_counter += 1;
1413	<	break;
1413	>
1414	>	if (update_arg( 0 ,
1415	>	0 , &(args_info->theta_omega_given),
1416	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1417	>	check_ambiguity, override, 0, 0,
1418	>	"theta_omega", '-',
1419	>	additional_error))
1420	>	goto failure;
1421	>
1422		}
1423		/* g(x, y, z).  */
1424		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1425		{
1426	<	if (local_args_info.gxyz_given)
1267	<	{
1268	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1269	<	goto failure;
1270	<	}
1271	<	if (args_info->gxyz_given && ! override)
1272	<	continue;
1273	<	local_args_info.gxyz_given = 1;
1274	<	args_info->gxyz_given = 1;
1426	>
1427		if (args_info->staticProps_group_counter && override)
1428		reset_group_staticProps (args_info);
1429		args_info->staticProps_group_counter += 1;
1430	<	break;
1430	>
1431	>	if (update_arg( 0 ,
1432	>	0 , &(args_info->gxyz_given),
1433	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1434	>	check_ambiguity, override, 0, 0,
1435	>	"gxyz", '-',
1436	>	additional_error))
1437	>	goto failure;
1438	>
1439		}
1440	+	/* 2D g(r) (Slab width --dz must be specified).  */
1441	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1442	+	{
1443	+
1444	+	if (args_info->staticProps_group_counter && override)
1445	+	reset_group_staticProps (args_info);
1446	+	args_info->staticProps_group_counter += 1;
1447	+
1448	+	if (update_arg( 0 ,
1449	+	0 , &(args_info->twodgofr_given),
1450	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1451	+	check_ambiguity, override, 0, 0,
1452	+	"twodgofr", '-',
1453	+	additional_error))
1454	+	goto failure;
1455	+
1456	+	}
1457		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1458		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1459		{
1460	<	if (local_args_info.rp2_given)
1284	<	{
1285	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1286	<	goto failure;
1287	<	}
1288	<	if (args_info->rp2_given && ! override)
1289	<	continue;
1290	<	local_args_info.rp2_given = 1;
1291	<	args_info->rp2_given = 1;
1460	>
1461		if (args_info->staticProps_group_counter && override)
1462		reset_group_staticProps (args_info);
1463		args_info->staticProps_group_counter += 1;
1464	<	break;
1464	>
1465	>	if (update_arg( 0 ,
1466	>	0 , &(args_info->rp2_given),
1467	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1468	>	check_ambiguity, override, 0, 0,
1469	>	"rp2", '-',
1470	>	additional_error))
1471	>	goto failure;
1472	>
1473		}
1474		/* slab density.  */
1475		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1476		{
1477	<	if (local_args_info.slab_density_given)
1301	<	{
1302	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1303	<	goto failure;
1304	<	}
1305	<	if (args_info->slab_density_given && ! override)
1306	<	continue;
1307	<	local_args_info.slab_density_given = 1;
1308	<	args_info->slab_density_given = 1;
1477	>
1478		if (args_info->staticProps_group_counter && override)
1479		reset_group_staticProps (args_info);
1480		args_info->staticProps_group_counter += 1;
1481	<	break;
1481	>
1482	>	if (update_arg( 0 ,
1483	>	0 , &(args_info->slab_density_given),
1484	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1485	>	check_ambiguity, override, 0, 0,
1486	>	"slab_density", '-',
1487	>	additional_error))
1488	>	goto failure;
1489	>
1490		}
1491	+	/* p(cos(theta)).  */
1492	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1493	+	{
1494	+
1495	+	if (args_info->staticProps_group_counter && override)
1496	+	reset_group_staticProps (args_info);
1497	+	args_info->staticProps_group_counter += 1;
1498	+
1499	+	if (update_arg( 0 ,
1500	+	0 , &(args_info->p_angle_given),
1501	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1502	+	check_ambiguity, override, 0, 0,
1503	+	"p_angle", '-',
1504	+	additional_error))
1505	+	goto failure;
1506	+
1507	+	}
1508		/* hxy.  */
1509		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1510		{
1511	<	if (local_args_info.hxy_given)
1318	<	{
1319	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1320	<	goto failure;
1321	<	}
1322	<	if (args_info->hxy_given && ! override)
1323	<	continue;
1324	<	local_args_info.hxy_given = 1;
1325	<	args_info->hxy_given = 1;
1511	>
1512		if (args_info->staticProps_group_counter && override)
1513		reset_group_staticProps (args_info);
1514		args_info->staticProps_group_counter += 1;
1515	<	break;
1515	>
1516	>	if (update_arg( 0 ,
1517	>	0 , &(args_info->hxy_given),
1518	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1519	>	check_ambiguity, override, 0, 0,
1520	>	"hxy", '-',
1521	>	additional_error))
1522	>	goto failure;
1523	>
1524		}
1525		/* rho of R.  */
1526		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1527		{
1528	<	if (local_args_info.rho_r_given)
1335	<	{
1336	<	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1337	<	goto failure;
1338	<	}
1339	<	if (args_info->rho_r_given && ! override)
1340	<	continue;
1341	<	local_args_info.rho_r_given = 1;
1342	<	args_info->rho_r_given = 1;
1528	>
1529		if (args_info->staticProps_group_counter && override)
1530		reset_group_staticProps (args_info);
1531		args_info->staticProps_group_counter += 1;
1532	<	break;
1532	>
1533	>	if (update_arg( 0 ,
1534	>	0 , &(args_info->rho_r_given),
1535	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1536	>	check_ambiguity, override, 0, 0,
1537	>	"rho_r", '-',
1538	>	additional_error))
1539	>	goto failure;
1540	>
1541		}
1542	+	/* angle of R.  */
1543	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1544	+	{
1545
1546	+	if (args_info->staticProps_group_counter && override)
1547	+	reset_group_staticProps (args_info);
1548	+	args_info->staticProps_group_counter += 1;
1549	+
1550	+	if (update_arg( 0 ,
1551	+	0 , &(args_info->angle_r_given),
1552	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1553	+	check_ambiguity, override, 0, 0,
1554	+	"angle_r", '-',
1555	+	additional_error))
1556	+	goto failure;
1557	+
1558	+	}
1559	+	/* hull volume of nanoparticle.  */
1560	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1561	+	{
1562	+
1563	+	if (args_info->staticProps_group_counter && override)
1564	+	reset_group_staticProps (args_info);
1565	+	args_info->staticProps_group_counter += 1;
1566	+
1567	+	if (update_arg( 0 ,
1568	+	0 , &(args_info->hullvol_given),
1569	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1570	+	check_ambiguity, override, 0, 0,
1571	+	"hullvol", '-',
1572	+	additional_error))
1573	+	goto failure;
1574	+
1575	+	}
1576	+	/* length of nanorod.  */
1577	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1578	+	{
1579	+
1580	+	if (args_info->staticProps_group_counter && override)
1581	+	reset_group_staticProps (args_info);
1582	+	args_info->staticProps_group_counter += 1;
1583	+
1584	+	if (update_arg( 0 ,
1585	+	0 , &(args_info->rodlength_given),
1586	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1587	+	check_ambiguity, override, 0, 0,
1588	+	"rodlength", '-',
1589	+	additional_error))
1590	+	goto failure;
1591	+
1592	+	}
1593	+	/* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1594	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1595	+	{
1596	+
1597	+	if (args_info->staticProps_group_counter && override)
1598	+	reset_group_staticProps (args_info);
1599	+	args_info->staticProps_group_counter += 1;
1600	+
1601	+	if (update_arg( 0 ,
1602	+	0 , &(args_info->tet_param_z_given),
1603	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1604	+	check_ambiguity, override, 0, 0,
1605	+	"tet_param_z", '-',
1606	+	additional_error))
1607	+	goto failure;
1608	+
1609	+	}
1610	+
1611		break;
1612		case '?':       /* Invalid option.  */
1613		/* `getopt_long' already printed an error message.  */
#	Line 1359 | Line 1621 | cmdline_parser_internal (int argc, char * const *argv,
1621
1622		if (args_info->staticProps_group_counter > 1)
1623		{
1624	<	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 : ""));
1624	>	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 : ""));
1625		error = 1;
1626		}
1627

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
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