[ViewVC] Diff of: OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1819 by gezelter, Thu Dec 13 16:57:39 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 --file-name=StaticPropsCmd -u
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:
#	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	+	#include <getopt.h>
25	+
26		#include "StaticPropsCmd.h"
27
28		const char *gengetopt_args_info_purpose = "";
#	Line 36 \| Line 40 \| *const char gengetopt_args_info_help[] = {**
40		" -b, --nbins=INT number of bins (general purpose) \n (default=`100')",
41		" -x, --nbins_x=INT number of bins in x axis (default=`100')",
42		" -y, --nbins_y=INT number of bins in y axis (default=`100')",
43	+	" --nbins_z=INT number of bins in z axis (default=`100')",
44		" -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)",
45		" -c, --rcut=DOUBLE cutoff radius (rcut)",
46	+	" --dz=DOUBLE slab width (dz)",
47	+	" --length=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
48	+	" --zlength=DOUBLE maximum length (Defaults to 1/2 smallest length \n of first frame)",
49		" -z, --zoffset=DOUBLE Where to set the zero for the slab_density \n calculation (default=`0')",
50		" --sele1=selection script select the first stuntdouble set",
51		" --sele2=selection script select the second stuntdouble set",
52		" --sele3=selection script select the third stuntdouble set",
53		" --refsele=selection script\n select reference (use and only use with --gxyz)",
54	+	" --comsele=selection script\n select stunt doubles for center-of-mass \n reference point",
55	+	" --seleoffset=INT global index offset for a second object (used \n to define a vector between sites in molecule)",
56		" --molname=STRING molecule name",
57		" --begin=INT begin internal index",
58		" --end=INT end internal index",
#	Line 52 \| Line 61 \| *const char gengetopt_args_info_help[] = {**
61		" --bo bond order parameter (--rcut must be specified)",
62		" --bor bond order parameter as a function of radius \n (--rcut must be specified)",
63		" --bad N(theta) bond angle density within (--rcut must \n be specified)",
64	+	" --count count of molecules matching selection criteria \n (and associated statistics)",
65		" -g, --gofr g(r)",
66		" --gofz g(z)",
67		" --r_theta g(r, cos(theta))",
68		" --r_omega g(r, cos(omega))",
69	+	" --r_z g(r, z)",
70		" --theta_omega g(cos(theta), cos(omega))",
71		" --gxyz g(x, y, z)",
72	<	" -p, --p2 p2 order parameter (--sele1 and --sele2 must be \n specified)",
72	>	" --twodgofr 2D g(r) (Slab width --dz must be specified)",
73	>	" -p, --p2 p2 order parameter (--sele1 must be specified, \n --sele2 is optional)",
74		" --rp2 rp2 order parameter (--sele1 and --sele2 must \n be specified)",
75		" -s, --scd scd order parameter (either --sele1, --sele2, \n --sele3 are specified or --molname, --begin, \n --end are specified)",
76		" -d, --density density plot",
77		" --slab_density slab density",
78	+	" --p_angle p(cos(theta))",
79		" --hxy hxy",
80		" --rho_r rho of R",
81	+	" --angle_r angle of R",
82		" --hullvol hull volume of nanoparticle",
83	+	" --rodlength length of nanorod",
84	+	" -Q, --tet_param tetrahedrality order parameter",
85	+	" --tet_param_z tetrahedrality order parameter by zbin(--sele1 \n must be specified)",
86		0
87		};
88
89	+	typedef enum {ARG_NO
90	+	, ARG_STRING
91	+	, ARG_INT
92	+	, ARG_DOUBLE
93	+	} cmdline_parser_arg_type;
94	+
95		static
96		void clear_given (struct gengetopt_args_info *args_info);
97		static
98		void clear_args (struct gengetopt_args_info *args_info);
99
100		static int
101	<	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);
101	>	cmdline_parser_internal (int argc, char *argv, struct gengetopt_args_info args_info,
102	>	struct cmdline_parser_params params, const char additional_error);
103
104		static int
105		cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error);
#	Line 94 \| Line 118 \| *void clear_given (struct gengetopt_args_info args_inf**
118		args_info->nbins_given = 0 ;
119		args_info->nbins_x_given = 0 ;
120		args_info->nbins_y_given = 0 ;
121	+	args_info->nbins_z_given = 0 ;
122		args_info->nanglebins_given = 0 ;
98	–	args_info->length_given = 0 ;
123		args_info->rcut_given = 0 ;
124	+	args_info->dz_given = 0 ;
125	+	args_info->length_given = 0 ;
126	+	args_info->zlength_given = 0 ;
127		args_info->zoffset_given = 0 ;
128		args_info->sele1_given = 0 ;
129		args_info->sele2_given = 0 ;
130		args_info->sele3_given = 0 ;
131		args_info->refsele_given = 0 ;
132	+	args_info->comsele_given = 0 ;
133	+	args_info->seleoffset_given = 0 ;
134		args_info->molname_given = 0 ;
135		args_info->begin_given = 0 ;
136		args_info->end_given = 0 ;
#	Line 109 \| Line 138 \| *void clear_given (struct gengetopt_args_info args_inf**
138		args_info->bo_given = 0 ;
139		args_info->bor_given = 0 ;
140		args_info->bad_given = 0 ;
141	+	args_info->count_given = 0 ;
142		args_info->gofr_given = 0 ;
143		args_info->gofz_given = 0 ;
144		args_info->r_theta_given = 0 ;
145		args_info->r_omega_given = 0 ;
146	+	args_info->r_z_given = 0 ;
147		args_info->theta_omega_given = 0 ;
148		args_info->gxyz_given = 0 ;
149	+	args_info->twodgofr_given = 0 ;
150		args_info->p2_given = 0 ;
151		args_info->rp2_given = 0 ;
152		args_info->scd_given = 0 ;
153		args_info->density_given = 0 ;
154		args_info->slab_density_given = 0 ;
155	+	args_info->p_angle_given = 0 ;
156		args_info->hxy_given = 0 ;
157		args_info->rho_r_given = 0 ;
158	+	args_info->angle_r_given = 0 ;
159		args_info->hullvol_given = 0 ;
160	+	args_info->rodlength_given = 0 ;
161	+	args_info->tet_param_given = 0 ;
162	+	args_info->tet_param_z_given = 0 ;
163		args_info->staticProps_group_counter = 0 ;
164		}
165
166		static
167		void clear_args (struct gengetopt_args_info *args_info)
168		{
169	+	FIX_UNUSED (args_info);
170		args_info->input_arg = NULL;
171		args_info->input_orig = NULL;
172		args_info->output_arg = NULL;
#	Line 141 \| Line 179 \| *void clear_args (struct gengetopt_args_info args_info**
179		args_info->nbins_x_orig = NULL;
180		args_info->nbins_y_arg = 100;
181		args_info->nbins_y_orig = NULL;
182	+	args_info->nbins_z_arg = 100;
183	+	args_info->nbins_z_orig = NULL;
184		args_info->nanglebins_arg = 50;
185		args_info->nanglebins_orig = NULL;
146	–	args_info->length_orig = NULL;
186		args_info->rcut_orig = NULL;
187	+	args_info->dz_orig = NULL;
188	+	args_info->length_orig = NULL;
189	+	args_info->zlength_orig = NULL;
190		args_info->zoffset_arg = 0;
191		args_info->zoffset_orig = NULL;
192		args_info->sele1_arg = NULL;
#	Line 155 \| Line 197 \| *void clear_args (struct gengetopt_args_info args_info**
197		args_info->sele3_orig = NULL;
198		args_info->refsele_arg = NULL;
199		args_info->refsele_orig = NULL;
200	+	args_info->comsele_arg = NULL;
201	+	args_info->comsele_orig = NULL;
202	+	args_info->seleoffset_orig = NULL;
203		args_info->molname_arg = NULL;
204		args_info->molname_orig = NULL;
205		args_info->begin_orig = NULL;
#	Line 166 \| Line 211 \| *void init_args_info(struct gengetopt_args_info args_i**
211		static
212		void init_args_info(struct gengetopt_args_info *args_info)
213		{
214	+
215	+
216		args_info->help_help = gengetopt_args_info_help[0] ;
217		args_info->version_help = gengetopt_args_info_help[1] ;
218		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 174 \| Line 221 \| *void init_args_info(struct gengetopt_args_info args_i**
221		args_info->nbins_help = gengetopt_args_info_help[5] ;
222		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
223		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
224	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
225	<	args_info->length_help = gengetopt_args_info_help[9] ;
224	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
225	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
226		args_info->rcut_help = gengetopt_args_info_help[10] ;
227	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
228	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
229	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
230	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
231	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
232	<	args_info->molname_help = gengetopt_args_info_help[16] ;
233	<	args_info->begin_help = gengetopt_args_info_help[17] ;
234	<	args_info->end_help = gengetopt_args_info_help[18] ;
235	<	args_info->radius_help = gengetopt_args_info_help[19] ;
236	<	args_info->bo_help = gengetopt_args_info_help[20] ;
237	<	args_info->bor_help = gengetopt_args_info_help[21] ;
238	<	args_info->bad_help = gengetopt_args_info_help[22] ;
239	<	args_info->gofr_help = gengetopt_args_info_help[23] ;
240	<	args_info->gofz_help = gengetopt_args_info_help[24] ;
241	<	args_info->r_theta_help = gengetopt_args_info_help[25] ;
242	<	args_info->r_omega_help = gengetopt_args_info_help[26] ;
243	<	args_info->theta_omega_help = gengetopt_args_info_help[27] ;
244	<	args_info->gxyz_help = gengetopt_args_info_help[28] ;
245	<	args_info->p2_help = gengetopt_args_info_help[29] ;
246	<	args_info->rp2_help = gengetopt_args_info_help[30] ;
247	<	args_info->scd_help = gengetopt_args_info_help[31] ;
248	<	args_info->density_help = gengetopt_args_info_help[32] ;
249	<	args_info->slab_density_help = gengetopt_args_info_help[33] ;
250	<	args_info->hxy_help = gengetopt_args_info_help[34] ;
251	<	args_info->rho_r_help = gengetopt_args_info_help[35] ;
252	<	args_info->hullvol_help = gengetopt_args_info_help[36] ;
227	>	args_info->dz_help = gengetopt_args_info_help[11] ;
228	>	args_info->length_help = gengetopt_args_info_help[12] ;
229	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
230	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
231	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
232	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
233	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
234	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
235	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
236	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
237	>	args_info->molname_help = gengetopt_args_info_help[21] ;
238	>	args_info->begin_help = gengetopt_args_info_help[22] ;
239	>	args_info->end_help = gengetopt_args_info_help[23] ;
240	>	args_info->radius_help = gengetopt_args_info_help[24] ;
241	>	args_info->bo_help = gengetopt_args_info_help[26] ;
242	>	args_info->bor_help = gengetopt_args_info_help[27] ;
243	>	args_info->bad_help = gengetopt_args_info_help[28] ;
244	>	args_info->count_help = gengetopt_args_info_help[29] ;
245	>	args_info->gofr_help = gengetopt_args_info_help[30] ;
246	>	args_info->gofz_help = gengetopt_args_info_help[31] ;
247	>	args_info->r_theta_help = gengetopt_args_info_help[32] ;
248	>	args_info->r_omega_help = gengetopt_args_info_help[33] ;
249	>	args_info->r_z_help = gengetopt_args_info_help[34] ;
250	>	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
251	>	args_info->gxyz_help = gengetopt_args_info_help[36] ;
252	>	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
253	>	args_info->p2_help = gengetopt_args_info_help[38] ;
254	>	args_info->rp2_help = gengetopt_args_info_help[39] ;
255	>	args_info->scd_help = gengetopt_args_info_help[40] ;
256	>	args_info->density_help = gengetopt_args_info_help[41] ;
257	>	args_info->slab_density_help = gengetopt_args_info_help[42] ;
258	>	args_info->p_angle_help = gengetopt_args_info_help[43] ;
259	>	args_info->hxy_help = gengetopt_args_info_help[44] ;
260	>	args_info->rho_r_help = gengetopt_args_info_help[45] ;
261	>	args_info->angle_r_help = gengetopt_args_info_help[46] ;
262	>	args_info->hullvol_help = gengetopt_args_info_help[47] ;
263	>	args_info->rodlength_help = gengetopt_args_info_help[48] ;
264	>	args_info->tet_param_help = gengetopt_args_info_help[49] ;
265	>	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
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
216	<	cmdline_parser_print_help (void)
217	<	{
218	<	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 237 \| 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	<
248	<	unsigned int i;
249	<	if (args_info->input_arg)
337	>	if (*s)
338		{
339	<	free (args_info->input_arg); /* free previous argument */
340	<	args_info->input_arg = 0;
253	<	}
254	<	if (args_info->input_orig)
255	<	{
256	<	free (args_info->input_orig); /* free previous argument */
257	<	args_info->input_orig = 0;
258	<	}
259	<	if (args_info->output_arg)
260	<	{
261	<	free (args_info->output_arg); /* free previous argument */
262	<	args_info->output_arg = 0;
263	<	}
264	<	if (args_info->output_orig)
265	<	{
266	<	free (args_info->output_orig); /* free previous argument */
267	<	args_info->output_orig = 0;
268	<	}
269	<	if (args_info->step_orig)
270	<	{
271	<	free (args_info->step_orig); /* free previous argument */
272	<	args_info->step_orig = 0;
273	<	}
274	<	if (args_info->nbins_orig)
275	<	{
276	<	free (args_info->nbins_orig); /* free previous argument */
277	<	args_info->nbins_orig = 0;
278	<	}
279	<	if (args_info->nbins_x_orig)
280	<	{
281	<	free (args_info->nbins_x_orig); /* free previous argument */
282	<	args_info->nbins_x_orig = 0;
283	<	}
284	<	if (args_info->nbins_y_orig)
285	<	{
286	<	free (args_info->nbins_y_orig); /* free previous argument */
287	<	args_info->nbins_y_orig = 0;
288	<	}
289	<	if (args_info->nanglebins_orig)
290	<	{
291	<	free (args_info->nanglebins_orig); /* free previous argument */
292	<	args_info->nanglebins_orig = 0;
293	<	}
294	<	if (args_info->length_orig)
295	<	{
296	<	free (args_info->length_orig); /* free previous argument */
297	<	args_info->length_orig = 0;
298	<	}
299	<	if (args_info->rcut_orig)
300	<	{
301	<	free (args_info->rcut_orig); /* free previous argument */
302	<	args_info->rcut_orig = 0;
303	<	}
304	<	if (args_info->zoffset_orig)
305	<	{
306	<	free (args_info->zoffset_orig); /* free previous argument */
307	<	args_info->zoffset_orig = 0;
308	<	}
309	<	if (args_info->sele1_arg)
310	<	{
311	<	free (args_info->sele1_arg); /* free previous argument */
312	<	args_info->sele1_arg = 0;
339	>	free (*s);
340	>	*s = 0;
341		}
342	<	if (args_info->sele1_orig)
343	<	{
344	<	free (args_info->sele1_orig); /* free previous argument */
345	<	args_info->sele1_orig = 0;
346	<	}
347	<	if (args_info->sele2_arg)
348	<	{
349	<	free (args_info->sele2_arg); /* free previous argument */
350	<	args_info->sele2_arg = 0;
351	<	}
352	<	if (args_info->sele2_orig)
353	<	{
354	<	free (args_info->sele2_orig); /* free previous argument */
355	<	args_info->sele2_orig = 0;
356	<	}
357	<	if (args_info->sele3_arg)
358	<	{
359	<	free (args_info->sele3_arg); /* free previous argument */
360	<	args_info->sele3_arg = 0;
361	<	}
362	<	if (args_info->sele3_orig)
363	<	{
364	<	free (args_info->sele3_orig); /* free previous argument */
365	<	args_info->sele3_orig = 0;
366	<	}
367	<	if (args_info->refsele_arg)
368	<	{
369	<	free (args_info->refsele_arg); /* free previous argument */
370	<	args_info->refsele_arg = 0;
371	<	}
372	<	if (args_info->refsele_orig)
373	<	{
374	<	free (args_info->refsele_orig); /* free previous argument */
375	<	args_info->refsele_orig = 0;
376	<	}
377	<	if (args_info->molname_arg)
378	<	{
379	<	free (args_info->molname_arg); /* free previous argument */
352	<	args_info->molname_arg = 0;
353	<	}
354	<	if (args_info->molname_orig)
355	<	{
356	<	free (args_info->molname_orig); /* free previous argument */
357	<	args_info->molname_orig = 0;
358	<	}
359	<	if (args_info->begin_orig)
360	<	{
361	<	free (args_info->begin_orig); /* free previous argument */
362	<	args_info->begin_orig = 0;
363	<	}
364	<	if (args_info->end_orig)
365	<	{
366	<	free (args_info->end_orig); /* free previous argument */
367	<	args_info->end_orig = 0;
368	<	}
369	<	if (args_info->radius_orig)
370	<	{
371	<	free (args_info->radius_orig); /* free previous argument */
372	<	args_info->radius_orig = 0;
373	<	}
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->seleoffset_orig));
375	>	free_string_field (&(args_info->molname_arg));
376	>	free_string_field (&(args_info->molname_orig));
377	>	free_string_field (&(args_info->begin_orig));
378	>	free_string_field (&(args_info->end_orig));
379	>	free_string_field (&(args_info->radius_orig));
380
381	+
382		for (i = 0; i < args_info->inputs_num; ++i)
383		free (args_info->inputs [i]);
384	<
384	>
385		if (args_info->inputs_num)
386		free (args_info->inputs);
387	<
387	>
388		clear_given (args_info);
389		}
390
391	+
392	+	static void
393	+	write_into_file(FILE outfile, const char opt, const char arg, const char values[])
394	+	{
395	+	FIX_UNUSED (values);
396	+	if (arg) {
397	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
398	+	} else {
399	+	fprintf(outfile, "%s\n", opt);
400	+	}
401	+	}
402	+
403	+
404		int
405	+	cmdline_parser_dump(FILE outfile, struct gengetopt_args_info args_info)
406	+	{
407	+	int i = 0;
408	+
409	+	if (!outfile)
410	+	{
411	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
412	+	return EXIT_FAILURE;
413	+	}
414	+
415	+	if (args_info->help_given)
416	+	write_into_file(outfile, "help", 0, 0 );
417	+	if (args_info->version_given)
418	+	write_into_file(outfile, "version", 0, 0 );
419	+	if (args_info->input_given)
420	+	write_into_file(outfile, "input", args_info->input_orig, 0);
421	+	if (args_info->output_given)
422	+	write_into_file(outfile, "output", args_info->output_orig, 0);
423	+	if (args_info->step_given)
424	+	write_into_file(outfile, "step", args_info->step_orig, 0);
425	+	if (args_info->nbins_given)
426	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
427	+	if (args_info->nbins_x_given)
428	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
429	+	if (args_info->nbins_y_given)
430	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
431	+	if (args_info->nbins_z_given)
432	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
433	+	if (args_info->nanglebins_given)
434	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
435	+	if (args_info->rcut_given)
436	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
437	+	if (args_info->dz_given)
438	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
439	+	if (args_info->length_given)
440	+	write_into_file(outfile, "length", args_info->length_orig, 0);
441	+	if (args_info->zlength_given)
442	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
443	+	if (args_info->zoffset_given)
444	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
445	+	if (args_info->sele1_given)
446	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
447	+	if (args_info->sele2_given)
448	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
449	+	if (args_info->sele3_given)
450	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
451	+	if (args_info->refsele_given)
452	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
453	+	if (args_info->comsele_given)
454	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
455	+	if (args_info->seleoffset_given)
456	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
457	+	if (args_info->molname_given)
458	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
459	+	if (args_info->begin_given)
460	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
461	+	if (args_info->end_given)
462	+	write_into_file(outfile, "end", args_info->end_orig, 0);
463	+	if (args_info->radius_given)
464	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
465	+	if (args_info->bo_given)
466	+	write_into_file(outfile, "bo", 0, 0 );
467	+	if (args_info->bor_given)
468	+	write_into_file(outfile, "bor", 0, 0 );
469	+	if (args_info->bad_given)
470	+	write_into_file(outfile, "bad", 0, 0 );
471	+	if (args_info->count_given)
472	+	write_into_file(outfile, "count", 0, 0 );
473	+	if (args_info->gofr_given)
474	+	write_into_file(outfile, "gofr", 0, 0 );
475	+	if (args_info->gofz_given)
476	+	write_into_file(outfile, "gofz", 0, 0 );
477	+	if (args_info->r_theta_given)
478	+	write_into_file(outfile, "r_theta", 0, 0 );
479	+	if (args_info->r_omega_given)
480	+	write_into_file(outfile, "r_omega", 0, 0 );
481	+	if (args_info->r_z_given)
482	+	write_into_file(outfile, "r_z", 0, 0 );
483	+	if (args_info->theta_omega_given)
484	+	write_into_file(outfile, "theta_omega", 0, 0 );
485	+	if (args_info->gxyz_given)
486	+	write_into_file(outfile, "gxyz", 0, 0 );
487	+	if (args_info->twodgofr_given)
488	+	write_into_file(outfile, "twodgofr", 0, 0 );
489	+	if (args_info->p2_given)
490	+	write_into_file(outfile, "p2", 0, 0 );
491	+	if (args_info->rp2_given)
492	+	write_into_file(outfile, "rp2", 0, 0 );
493	+	if (args_info->scd_given)
494	+	write_into_file(outfile, "scd", 0, 0 );
495	+	if (args_info->density_given)
496	+	write_into_file(outfile, "density", 0, 0 );
497	+	if (args_info->slab_density_given)
498	+	write_into_file(outfile, "slab_density", 0, 0 );
499	+	if (args_info->p_angle_given)
500	+	write_into_file(outfile, "p_angle", 0, 0 );
501	+	if (args_info->hxy_given)
502	+	write_into_file(outfile, "hxy", 0, 0 );
503	+	if (args_info->rho_r_given)
504	+	write_into_file(outfile, "rho_r", 0, 0 );
505	+	if (args_info->angle_r_given)
506	+	write_into_file(outfile, "angle_r", 0, 0 );
507	+	if (args_info->hullvol_given)
508	+	write_into_file(outfile, "hullvol", 0, 0 );
509	+	if (args_info->rodlength_given)
510	+	write_into_file(outfile, "rodlength", 0, 0 );
511	+	if (args_info->tet_param_given)
512	+	write_into_file(outfile, "tet_param", 0, 0 );
513	+	if (args_info->tet_param_z_given)
514	+	write_into_file(outfile, "tet_param_z", 0, 0 );
515	+
516	+
517	+	i = EXIT_SUCCESS;
518	+	return i;
519	+	}
520	+
521	+	int
522		cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
523		{
524		FILE *outfile;
#	Line 395 \| Line 532 \| *cmdline_parser_file_save(const char filename, struct**
532		return EXIT_FAILURE;
533		}
534
535	<	if (args_info->help_given) {
399	<	fprintf(outfile, "%s\n", "help");
400	<	}
401	<	if (args_info->version_given) {
402	<	fprintf(outfile, "%s\n", "version");
403	<	}
404	<	if (args_info->input_given) {
405	<	if (args_info->input_orig) {
406	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
407	<	} else {
408	<	fprintf(outfile, "%s\n", "input");
409	<	}
410	<	}
411	<	if (args_info->output_given) {
412	<	if (args_info->output_orig) {
413	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
414	<	} else {
415	<	fprintf(outfile, "%s\n", "output");
416	<	}
417	<	}
418	<	if (args_info->step_given) {
419	<	if (args_info->step_orig) {
420	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
421	<	} else {
422	<	fprintf(outfile, "%s\n", "step");
423	<	}
424	<	}
425	<	if (args_info->nbins_given) {
426	<	if (args_info->nbins_orig) {
427	<	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
428	<	} else {
429	<	fprintf(outfile, "%s\n", "nbins");
430	<	}
431	<	}
432	<	if (args_info->nbins_x_given) {
433	<	if (args_info->nbins_x_orig) {
434	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
435	<	} else {
436	<	fprintf(outfile, "%s\n", "nbins_x");
437	<	}
438	<	}
439	<	if (args_info->nbins_y_given) {
440	<	if (args_info->nbins_y_orig) {
441	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
442	<	} else {
443	<	fprintf(outfile, "%s\n", "nbins_y");
444	<	}
445	<	}
446	<	if (args_info->nanglebins_given) {
447	<	if (args_info->nanglebins_orig) {
448	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
449	<	} else {
450	<	fprintf(outfile, "%s\n", "nanglebins");
451	<	}
452	<	}
453	<	if (args_info->length_given) {
454	<	if (args_info->length_orig) {
455	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
456	<	} else {
457	<	fprintf(outfile, "%s\n", "length");
458	<	}
459	<	}
460	<	if (args_info->rcut_given) {
461	<	if (args_info->rcut_orig) {
462	<	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
463	<	} else {
464	<	fprintf(outfile, "%s\n", "rcut");
465	<	}
466	<	}
467	<	if (args_info->zoffset_given) {
468	<	if (args_info->zoffset_orig) {
469	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
470	<	} else {
471	<	fprintf(outfile, "%s\n", "zoffset");
472	<	}
473	<	}
474	<	if (args_info->sele1_given) {
475	<	if (args_info->sele1_orig) {
476	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
477	<	} else {
478	<	fprintf(outfile, "%s\n", "sele1");
479	<	}
480	<	}
481	<	if (args_info->sele2_given) {
482	<	if (args_info->sele2_orig) {
483	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
484	<	} else {
485	<	fprintf(outfile, "%s\n", "sele2");
486	<	}
487	<	}
488	<	if (args_info->sele3_given) {
489	<	if (args_info->sele3_orig) {
490	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
491	<	} else {
492	<	fprintf(outfile, "%s\n", "sele3");
493	<	}
494	<	}
495	<	if (args_info->refsele_given) {
496	<	if (args_info->refsele_orig) {
497	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
498	<	} else {
499	<	fprintf(outfile, "%s\n", "refsele");
500	<	}
501	<	}
502	<	if (args_info->molname_given) {
503	<	if (args_info->molname_orig) {
504	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
505	<	} else {
506	<	fprintf(outfile, "%s\n", "molname");
507	<	}
508	<	}
509	<	if (args_info->begin_given) {
510	<	if (args_info->begin_orig) {
511	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
512	<	} else {
513	<	fprintf(outfile, "%s\n", "begin");
514	<	}
515	<	}
516	<	if (args_info->end_given) {
517	<	if (args_info->end_orig) {
518	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
519	<	} else {
520	<	fprintf(outfile, "%s\n", "end");
521	<	}
522	<	}
523	<	if (args_info->radius_given) {
524	<	if (args_info->radius_orig) {
525	<	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
526	<	} else {
527	<	fprintf(outfile, "%s\n", "radius");
528	<	}
529	<	}
530	<	if (args_info->bo_given) {
531	<	fprintf(outfile, "%s\n", "bo");
532	<	}
533	<	if (args_info->bor_given) {
534	<	fprintf(outfile, "%s\n", "bor");
535	<	}
536	<	if (args_info->bad_given) {
537	<	fprintf(outfile, "%s\n", "bad");
538	<	}
539	<	if (args_info->gofr_given) {
540	<	fprintf(outfile, "%s\n", "gofr");
541	<	}
542	<	if (args_info->gofz_given) {
543	<	fprintf(outfile, "%s\n", "gofz");
544	<	}
545	<	if (args_info->r_theta_given) {
546	<	fprintf(outfile, "%s\n", "r_theta");
547	<	}
548	<	if (args_info->r_omega_given) {
549	<	fprintf(outfile, "%s\n", "r_omega");
550	<	}
551	<	if (args_info->theta_omega_given) {
552	<	fprintf(outfile, "%s\n", "theta_omega");
553	<	}
554	<	if (args_info->gxyz_given) {
555	<	fprintf(outfile, "%s\n", "gxyz");
556	<	}
557	<	if (args_info->p2_given) {
558	<	fprintf(outfile, "%s\n", "p2");
559	<	}
560	<	if (args_info->rp2_given) {
561	<	fprintf(outfile, "%s\n", "rp2");
562	<	}
563	<	if (args_info->scd_given) {
564	<	fprintf(outfile, "%s\n", "scd");
565	<	}
566	<	if (args_info->density_given) {
567	<	fprintf(outfile, "%s\n", "density");
568	<	}
569	<	if (args_info->slab_density_given) {
570	<	fprintf(outfile, "%s\n", "slab_density");
571	<	}
572	<	if (args_info->hxy_given) {
573	<	fprintf(outfile, "%s\n", "hxy");
574	<	}
575	<	if (args_info->rho_r_given) {
576	<	fprintf(outfile, "%s\n", "rho_r");
577	<	}
578	<	if (args_info->hullvol_given) {
579	<	fprintf(outfile, "%s\n", "hullvol");
580	<	}
581	<
535	>	i = cmdline_parser_dump(outfile, args_info);
536		fclose (outfile);
537
584	–	i = EXIT_SUCCESS;
538		return i;
539		}
540
#	Line 591 \| Line 544 \| *cmdline_parser_free (struct gengetopt_args_info args_**
544		cmdline_parser_release (args_info);
545		}
546
547	<
595	<	/* gengetopt_strdup() */
596	<	/* strdup.c replacement of strdup, which is not standard */
547	>	/** @brief replacement of strdup, which is not standard */
548		char *
549		gengetopt_strdup (const char *s)
550		{
551	<	char *result = NULL;
551	>	char *result = 0;
552		if (!s)
553		return result;
554
#	Line 609 \| Line 560 \| static void
560		}
561
562		static void
612	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
613	–
614	–	static void
563		reset_group_staticProps(struct gengetopt_args_info *args_info)
564		{
565		if (! args_info->staticProps_group_counter)
#	Line 620 \| Line 568 \| *reset_group_staticProps(struct gengetopt_args_info ar**
568		args_info->bo_given = 0 ;
569		args_info->bor_given = 0 ;
570		args_info->bad_given = 0 ;
571	+	args_info->count_given = 0 ;
572		args_info->gofr_given = 0 ;
573		args_info->gofz_given = 0 ;
574		args_info->r_theta_given = 0 ;
575		args_info->r_omega_given = 0 ;
576	+	args_info->r_z_given = 0 ;
577		args_info->theta_omega_given = 0 ;
578		args_info->gxyz_given = 0 ;
579	+	args_info->twodgofr_given = 0 ;
580		args_info->p2_given = 0 ;
581		args_info->rp2_given = 0 ;
582		args_info->scd_given = 0 ;
583		args_info->density_given = 0 ;
584		args_info->slab_density_given = 0 ;
585	+	args_info->p_angle_given = 0 ;
586		args_info->hxy_given = 0 ;
587		args_info->rho_r_given = 0 ;
588	+	args_info->angle_r_given = 0 ;
589		args_info->hullvol_given = 0 ;
590	+	args_info->rodlength_given = 0 ;
591	+	args_info->tet_param_given = 0 ;
592	+	args_info->tet_param_z_given = 0 ;
593
594		args_info->staticProps_group_counter = 0;
595		}
596
597		int
598	<	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
598	>	cmdline_parser (int argc, char *argv, struct gengetopt_args_info args_info)
599		{
600		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
601		}
602
603		int
604	<	cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
604	>	cmdline_parser_ext (int argc, char *argv, struct gengetopt_args_info args_info,
605	>	struct cmdline_parser_params *params)
606		{
607		int result;
608	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
609
610	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
610	>	if (result == EXIT_FAILURE)
611	>	{
612	>	cmdline_parser_free (args_info);
613	>	exit (EXIT_FAILURE);
614	>	}
615	>
616	>	return result;
617	>	}
618
619	+	int
620	+	cmdline_parser2 (int argc, char *argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
621	+	{
622	+	int result;
623	+	struct cmdline_parser_params params;
624	+
625	+	params.override = override;
626	+	params.initialize = initialize;
627	+	params.check_required = check_required;
628	+	params.check_ambiguity = 0;
629	+	params.print_errors = 1;
630	+
631	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
632	+
633		if (result == EXIT_FAILURE)
634		{
635		cmdline_parser_free (args_info);
#	Line 665 \| Line 644 \| *cmdline_parser_required (struct gengetopt_args_info a**
644		{
645		int result = EXIT_SUCCESS;
646
647	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
647	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
648		result = EXIT_FAILURE;
649
650		if (result == EXIT_FAILURE)
#	Line 681 \| Line 660 \| cmdline_parser_required2 (struct gengetopt_args_info *
660		cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
661		{
662		int error = 0;
663	+	FIX_UNUSED (additional_error);
664
665		/* checks for required options */
666		if (! args_info->input_given)
#	Line 691 \| Line 671 \| cmdline_parser_required2 (struct gengetopt_args_info *
671
672		if (args_info->staticProps_group_counter == 0)
673		{
674	<	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 : ""));
674	>	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 : ""));
675		error = 1;
676		}
677
#	Line 701 \| Line 681 \| cmdline_parser_required2 (struct gengetopt_args_info *
681		return error;
682		}
683
684	+
685	+	static char *package_name = 0;
686	+
687	+	/**
688	+	* @brief updates an option
689	+	* @param field the generic pointer to the field to update
690	+	* @param orig_field the pointer to the orig field
691	+	* @param field_given the pointer to the number of occurrence of this option
692	+	* @param prev_given the pointer to the number of occurrence already seen
693	+	* @param value the argument for this option (if null no arg was specified)
694	+	* @param possible_values the possible values for this option (if specified)
695	+	* @param default_value the default value (in case the option only accepts fixed values)
696	+	* @param arg_type the type of this option
697	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
698	+	* @param override @see cmdline_parser_params.override
699	+	* @param no_free whether to free a possible previous value
700	+	* @param multiple_option whether this is a multiple option
701	+	* @param long_opt the corresponding long option
702	+	* @param short_opt the corresponding short option (or '-' if none)
703	+	* @param additional_error possible further error specification
704	+	*/
705	+	static
706	+	int update_arg(void field, char *orig_field,
707	+	unsigned int field_given, unsigned int prev_given,
708	+	char value, const char possible_values[],
709	+	const char *default_value,
710	+	cmdline_parser_arg_type arg_type,
711	+	int check_ambiguity, int override,
712	+	int no_free, int multiple_option,
713	+	const char *long_opt, char short_opt,
714	+	const char *additional_error)
715	+	{
716	+	char *stop_char = 0;
717	+	const char *val = value;
718	+	int found;
719	+	char **string_field;
720	+	FIX_UNUSED (field);
721	+
722	+	stop_char = 0;
723	+	found = 0;
724	+
725	+	if (!multiple_option && prev_given && (prev_given \|\| (check_ambiguity && field_given)))
726	+	{
727	+	if (short_opt != '-')
728	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
729	+	package_name, long_opt, short_opt,
730	+	(additional_error ? additional_error : ""));
731	+	else
732	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
733	+	package_name, long_opt,
734	+	(additional_error ? additional_error : ""));
735	+	return 1; /* failure */
736	+	}
737	+
738	+	FIX_UNUSED (default_value);
739	+
740	+	if (field_given && *field_given && ! override)
741	+	return 0;
742	+	if (prev_given)
743	+	(*prev_given)++;
744	+	if (field_given)
745	+	(*field_given)++;
746	+	if (possible_values)
747	+	val = possible_values[found];
748	+
749	+	switch(arg_type) {
750	+	case ARG_INT:
751	+	if (val) ((int )field) = strtol (val, &stop_char, 0);
752	+	break;
753	+	case ARG_DOUBLE:
754	+	if (val) ((double )field) = strtod (val, &stop_char);
755	+	break;
756	+	case ARG_STRING:
757	+	if (val) {
758	+	string_field = (char **)field;
759	+	if (!no_free && *string_field)
760	+	free (string_field); / free previous string */
761	+	*string_field = gengetopt_strdup (val);
762	+	}
763	+	break;
764	+	default:
765	+	break;
766	+	};
767	+
768	+	/* check numeric conversion */
769	+	switch(arg_type) {
770	+	case ARG_INT:
771	+	case ARG_DOUBLE:
772	+	if (val && !(stop_char && *stop_char == '\0')) {
773	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
774	+	return 1; /* failure */
775	+	}
776	+	break;
777	+	default:
778	+	;
779	+	};
780	+
781	+	/* store the original value */
782	+	switch(arg_type) {
783	+	case ARG_NO:
784	+	break;
785	+	default:
786	+	if (value && orig_field) {
787	+	if (no_free) {
788	+	*orig_field = value;
789	+	} else {
790	+	if (*orig_field)
791	+	free (orig_field); / free previous string */
792	+	*orig_field = gengetopt_strdup (value);
793	+	}
794	+	}
795	+	};
796	+
797	+	return 0; /* OK */
798	+	}
799	+
800	+
801		int
802	<	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)
802	>	cmdline_parser_internal (
803	>	int argc, char *argv, struct gengetopt_args_info args_info,
804	>	struct cmdline_parser_params params, const char additional_error)
805		{
806		int c; /* Character of the parsed option. */
807
808		int error = 0;
809		struct gengetopt_args_info local_args_info;
810	+
811	+	int override;
812	+	int initialize;
813	+	int check_required;
814	+	int check_ambiguity;
815	+
816	+	package_name = argv[0];
817	+
818	+	override = params->override;
819	+	initialize = params->initialize;
820	+	check_required = params->check_required;
821	+	check_ambiguity = params->check_ambiguity;
822
823		if (initialize)
824		cmdline_parser_init (args_info);
#	Line 716 \| Line 827 \| *cmdline_parser_internal (int argc, char const argv,*
827
828		optarg = 0;
829		optind = 0;
830	<	opterr = 1;
830	>	opterr = params->print_errors;
831		optopt = '?';
832
833		while (1)
834		{
835		int option_index = 0;
725	–	char *stop_char;
836
837		static struct option long_options[] = {
838		{ "help", 0, NULL, 'h' },
#	Line 733 \| Line 843 \| *cmdline_parser_internal (int argc, char const argv,*
843		{ "nbins", 1, NULL, 'b' },
844		{ "nbins_x", 1, NULL, 'x' },
845		{ "nbins_y", 1, NULL, 'y' },
846	+	{ "nbins_z", 1, NULL, 0 },
847		{ "nanglebins", 1, NULL, 'a' },
737	–	{ "length", 1, NULL, 0 },
848		{ "rcut", 1, NULL, 'c' },
849	+	{ "dz", 1, NULL, 0 },
850	+	{ "length", 1, NULL, 0 },
851	+	{ "zlength", 1, NULL, 0 },
852		{ "zoffset", 1, NULL, 'z' },
853		{ "sele1", 1, NULL, 0 },
854		{ "sele2", 1, NULL, 0 },
855		{ "sele3", 1, NULL, 0 },
856		{ "refsele", 1, NULL, 0 },
857	+	{ "comsele", 1, NULL, 0 },
858	+	{ "seleoffset", 1, NULL, 0 },
859		{ "molname", 1, NULL, 0 },
860		{ "begin", 1, NULL, 0 },
861		{ "end", 1, NULL, 0 },
#	Line 748 \| Line 863 \| *cmdline_parser_internal (int argc, char const argv,*
863		{ "bo", 0, NULL, 0 },
864		{ "bor", 0, NULL, 0 },
865		{ "bad", 0, NULL, 0 },
866	+	{ "count", 0, NULL, 0 },
867		{ "gofr", 0, NULL, 'g' },
868		{ "gofz", 0, NULL, 0 },
869		{ "r_theta", 0, NULL, 0 },
870		{ "r_omega", 0, NULL, 0 },
871	+	{ "r_z", 0, NULL, 0 },
872		{ "theta_omega", 0, NULL, 0 },
873		{ "gxyz", 0, NULL, 0 },
874	+	{ "twodgofr", 0, NULL, 0 },
875		{ "p2", 0, NULL, 'p' },
876		{ "rp2", 0, NULL, 0 },
877		{ "scd", 0, NULL, 's' },
878		{ "density", 0, NULL, 'd' },
879		{ "slab_density", 0, NULL, 0 },
880	+	{ "p_angle", 0, NULL, 0 },
881		{ "hxy", 0, NULL, 0 },
882		{ "rho_r", 0, NULL, 0 },
883	+	{ "angle_r", 0, NULL, 0 },
884		{ "hullvol", 0, NULL, 0 },
885	<	{ NULL, 0, NULL, 0 }
885	>	{ "rodlength", 0, NULL, 0 },
886	>	{ "tet_param", 0, NULL, 'Q' },
887	>	{ "tet_param_z", 0, NULL, 0 },
888	>	{ 0, 0, 0, 0 }
889		};
890
891	<	stop_char = 0;
769	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
891	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
892
893		if (c == -1) break; /* Exit from `while (1)' loop. */
894
#	Line 783 \| Line 905 \| *cmdline_parser_internal (int argc, char const argv,*
905		exit (EXIT_SUCCESS);
906
907		case 'i': /* input dump file. */
908	<	if (local_args_info.input_given)
909	<	{
910	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
911	<	goto failure;
912	<	}
913	<	if (args_info->input_given && ! override)
914	<	continue;
915	<	local_args_info.input_given = 1;
916	<	args_info->input_given = 1;
917	<	if (args_info->input_arg)
796	<	free (args_info->input_arg); /* free previous string */
797	<	args_info->input_arg = gengetopt_strdup (optarg);
798	<	if (args_info->input_orig)
799	<	free (args_info->input_orig); /* free previous string */
800	<	args_info->input_orig = gengetopt_strdup (optarg);
908	>
909	>
910	>	if (update_arg( (void *)&(args_info->input_arg),
911	>	&(args_info->input_orig), &(args_info->input_given),
912	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
913	>	check_ambiguity, override, 0, 0,
914	>	"input", 'i',
915	>	additional_error))
916	>	goto failure;
917	>
918		break;
802	–
919		case 'o': /* output file name. */
920	<	if (local_args_info.output_given)
921	<	{
922	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
923	<	goto failure;
924	<	}
925	<	if (args_info->output_given && ! override)
926	<	continue;
927	<	local_args_info.output_given = 1;
928	<	args_info->output_given = 1;
929	<	if (args_info->output_arg)
814	<	free (args_info->output_arg); /* free previous string */
815	<	args_info->output_arg = gengetopt_strdup (optarg);
816	<	if (args_info->output_orig)
817	<	free (args_info->output_orig); /* free previous string */
818	<	args_info->output_orig = gengetopt_strdup (optarg);
920	>
921	>
922	>	if (update_arg( (void *)&(args_info->output_arg),
923	>	&(args_info->output_orig), &(args_info->output_given),
924	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
925	>	check_ambiguity, override, 0, 0,
926	>	"output", 'o',
927	>	additional_error))
928	>	goto failure;
929	>
930		break;
820	–
931		case 'n': /* process every n frame. */
932	<	if (local_args_info.step_given)
933	<	{
934	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
935	<	goto failure;
936	<	}
937	<	if (args_info->step_given && ! override)
938	<	continue;
939	<	local_args_info.step_given = 1;
830	<	args_info->step_given = 1;
831	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
832	<	if (!(stop_char && *stop_char == '\0')) {
833	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
932	>
933	>
934	>	if (update_arg( (void *)&(args_info->step_arg),
935	>	&(args_info->step_orig), &(args_info->step_given),
936	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
937	>	check_ambiguity, override, 0, 0,
938	>	"step", 'n',
939	>	additional_error))
940		goto failure;
941	<	}
836	<	if (args_info->step_orig)
837	<	free (args_info->step_orig); /* free previous string */
838	<	args_info->step_orig = gengetopt_strdup (optarg);
941	>
942		break;
840	–
943		case 'b': /* number of bins (general purpose). */
944	<	if (local_args_info.nbins_given)
945	<	{
946	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
947	<	goto failure;
948	<	}
949	<	if (args_info->nbins_given && ! override)
950	<	continue;
951	<	local_args_info.nbins_given = 1;
850	<	args_info->nbins_given = 1;
851	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
852	<	if (!(stop_char && *stop_char == '\0')) {
853	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
944	>
945	>
946	>	if (update_arg( (void *)&(args_info->nbins_arg),
947	>	&(args_info->nbins_orig), &(args_info->nbins_given),
948	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
949	>	check_ambiguity, override, 0, 0,
950	>	"nbins", 'b',
951	>	additional_error))
952		goto failure;
953	<	}
856	<	if (args_info->nbins_orig)
857	<	free (args_info->nbins_orig); /* free previous string */
858	<	args_info->nbins_orig = gengetopt_strdup (optarg);
953	>
954		break;
860	–
955		case 'x': /* number of bins in x axis. */
956	<	if (local_args_info.nbins_x_given)
957	<	{
958	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
959	<	goto failure;
960	<	}
961	<	if (args_info->nbins_x_given && ! override)
962	<	continue;
963	<	local_args_info.nbins_x_given = 1;
870	<	args_info->nbins_x_given = 1;
871	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
872	<	if (!(stop_char && *stop_char == '\0')) {
873	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
956	>
957	>
958	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
959	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
960	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
961	>	check_ambiguity, override, 0, 0,
962	>	"nbins_x", 'x',
963	>	additional_error))
964		goto failure;
965	<	}
876	<	if (args_info->nbins_x_orig)
877	<	free (args_info->nbins_x_orig); /* free previous string */
878	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
965	>
966		break;
880	–
967		case 'y': /* number of bins in y axis. */
968	<	if (local_args_info.nbins_y_given)
969	<	{
970	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	<	goto failure;
972	<	}
973	<	if (args_info->nbins_y_given && ! override)
974	<	continue;
975	<	local_args_info.nbins_y_given = 1;
890	<	args_info->nbins_y_given = 1;
891	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
892	<	if (!(stop_char && *stop_char == '\0')) {
893	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
968	>
969	>
970	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
971	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
972	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
973	>	check_ambiguity, override, 0, 0,
974	>	"nbins_y", 'y',
975	>	additional_error))
976		goto failure;
977	<	}
896	<	if (args_info->nbins_y_orig)
897	<	free (args_info->nbins_y_orig); /* free previous string */
898	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
977	>
978		break;
900	–
979		case 'a': /* number of bins for cos(angle). */
980	<	if (local_args_info.nanglebins_given)
981	<	{
982	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
983	<	goto failure;
984	<	}
985	<	if (args_info->nanglebins_given && ! override)
986	<	continue;
987	<	local_args_info.nanglebins_given = 1;
910	<	args_info->nanglebins_given = 1;
911	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
912	<	if (!(stop_char && *stop_char == '\0')) {
913	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
980	>
981	>
982	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
983	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
984	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
985	>	check_ambiguity, override, 0, 0,
986	>	"nanglebins", 'a',
987	>	additional_error))
988		goto failure;
989	<	}
916	<	if (args_info->nanglebins_orig)
917	<	free (args_info->nanglebins_orig); /* free previous string */
918	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
989	>
990		break;
920	–
991		case 'c': /* cutoff radius (rcut). */
992	<	if (local_args_info.rcut_given)
993	<	{
994	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
995	<	goto failure;
996	<	}
997	<	if (args_info->rcut_given && ! override)
998	<	continue;
999	<	local_args_info.rcut_given = 1;
930	<	args_info->rcut_given = 1;
931	<	args_info->rcut_arg = strtod (optarg, &stop_char);
932	<	if (!(stop_char && *stop_char == '\0')) {
933	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
992	>
993	>
994	>	if (update_arg( (void *)&(args_info->rcut_arg),
995	>	&(args_info->rcut_orig), &(args_info->rcut_given),
996	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
997	>	check_ambiguity, override, 0, 0,
998	>	"rcut", 'c',
999	>	additional_error))
1000		goto failure;
1001	<	}
936	<	if (args_info->rcut_orig)
937	<	free (args_info->rcut_orig); /* free previous string */
938	<	args_info->rcut_orig = gengetopt_strdup (optarg);
1001	>
1002		break;
940	–
1003		case 'z': /* Where to set the zero for the slab_density calculation. */
1004	<	if (local_args_info.zoffset_given)
1005	<	{
1006	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1007	<	goto failure;
1008	<	}
1009	<	if (args_info->zoffset_given && ! override)
1010	<	continue;
1011	<	local_args_info.zoffset_given = 1;
950	<	args_info->zoffset_given = 1;
951	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
952	<	if (!(stop_char && *stop_char == '\0')) {
953	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1004	>
1005	>
1006	>	if (update_arg( (void *)&(args_info->zoffset_arg),
1007	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1008	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1009	>	check_ambiguity, override, 0, 0,
1010	>	"zoffset", 'z',
1011	>	additional_error))
1012		goto failure;
1013	<	}
956	<	if (args_info->zoffset_orig)
957	<	free (args_info->zoffset_orig); /* free previous string */
958	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
1013	>
1014		break;
960	–
1015		case 'g': /* g(r). */
1016	<	if (local_args_info.gofr_given)
963	<	{
964	<	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
965	<	goto failure;
966	<	}
967	<	if (args_info->gofr_given && ! override)
968	<	continue;
969	<	local_args_info.gofr_given = 1;
970	<	args_info->gofr_given = 1;
1016	>
1017		if (args_info->staticProps_group_counter && override)
1018		reset_group_staticProps (args_info);
1019		args_info->staticProps_group_counter += 1;
1020	+
1021	+	if (update_arg( 0 ,
1022	+	0 , &(args_info->gofr_given),
1023	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1024	+	check_ambiguity, override, 0, 0,
1025	+	"gofr", 'g',
1026	+	additional_error))
1027	+	goto failure;
1028	+
1029		break;
1030	<
1031	<	case 'p': /* p2 order parameter (--sele1 and --sele2 must be specified). */
977	<	if (local_args_info.p2_given)
978	<	{
979	<	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
980	<	goto failure;
981	<	}
982	<	if (args_info->p2_given && ! override)
983	<	continue;
984	<	local_args_info.p2_given = 1;
985	<	args_info->p2_given = 1;
1030	>	case 'p': /* p2 order parameter (--sele1 must be specified, --sele2 is optional). */
1031	>
1032		if (args_info->staticProps_group_counter && override)
1033		reset_group_staticProps (args_info);
1034		args_info->staticProps_group_counter += 1;
1035	+
1036	+	if (update_arg( 0 ,
1037	+	0 , &(args_info->p2_given),
1038	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1039	+	check_ambiguity, override, 0, 0,
1040	+	"p2", 'p',
1041	+	additional_error))
1042	+	goto failure;
1043	+
1044		break;
990	–
1045		case 's': /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified). */
1046	<	if (local_args_info.scd_given)
993	<	{
994	<	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
995	<	goto failure;
996	<	}
997	<	if (args_info->scd_given && ! override)
998	<	continue;
999	<	local_args_info.scd_given = 1;
1000	<	args_info->scd_given = 1;
1046	>
1047		if (args_info->staticProps_group_counter && override)
1048		reset_group_staticProps (args_info);
1049		args_info->staticProps_group_counter += 1;
1050	+
1051	+	if (update_arg( 0 ,
1052	+	0 , &(args_info->scd_given),
1053	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1054	+	check_ambiguity, override, 0, 0,
1055	+	"scd", 's',
1056	+	additional_error))
1057	+	goto failure;
1058	+
1059		break;
1005	–
1060		case 'd': /* density plot. */
1061	<	if (local_args_info.density_given)
1008	<	{
1009	<	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1010	<	goto failure;
1011	<	}
1012	<	if (args_info->density_given && ! override)
1013	<	continue;
1014	<	local_args_info.density_given = 1;
1015	<	args_info->density_given = 1;
1061	>
1062		if (args_info->staticProps_group_counter && override)
1063		reset_group_staticProps (args_info);
1064		args_info->staticProps_group_counter += 1;
1065	+
1066	+	if (update_arg( 0 ,
1067	+	0 , &(args_info->density_given),
1068	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1069	+	check_ambiguity, override, 0, 0,
1070	+	"density", 'd',
1071	+	additional_error))
1072	+	goto failure;
1073	+
1074		break;
1075	<
1075	>	case 'Q': /* tetrahedrality order parameter. */
1076	>
1077	>	if (args_info->staticProps_group_counter && override)
1078	>	reset_group_staticProps (args_info);
1079	>	args_info->staticProps_group_counter += 1;
1080	>
1081	>	if (update_arg( 0 ,
1082	>	0 , &(args_info->tet_param_given),
1083	>	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1084	>	check_ambiguity, override, 0, 0,
1085	>	"tet_param", 'Q',
1086	>	additional_error))
1087	>	goto failure;
1088	>
1089	>	break;
1090
1091		case 0: /* Long option with no short option */
1092	+	/* number of bins in z axis. */
1093	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1094	+	{
1095	+
1096	+
1097	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1098	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1099	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1100	+	check_ambiguity, override, 0, 0,
1101	+	"nbins_z", '-',
1102	+	additional_error))
1103	+	goto failure;
1104	+
1105	+	}
1106	+	/* slab width (dz). */
1107	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1108	+	{
1109	+
1110	+
1111	+	if (update_arg( (void *)&(args_info->dz_arg),
1112	+	&(args_info->dz_orig), &(args_info->dz_given),
1113	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1114	+	check_ambiguity, override, 0, 0,
1115	+	"dz", '-',
1116	+	additional_error))
1117	+	goto failure;
1118	+
1119	+	}
1120		/* maximum length (Defaults to 1/2 smallest length of first frame). */
1121	<	if (strcmp (long_options[option_index].name, "length") == 0)
1121	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1122		{
1123	<	if (local_args_info.length_given)
1124	<	{
1125	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1126	<	goto failure;
1127	<	}
1128	<	if (args_info->length_given && ! override)
1129	<	continue;
1130	<	local_args_info.length_given = 1;
1034	<	args_info->length_given = 1;
1035	<	args_info->length_arg = strtod (optarg, &stop_char);
1036	<	if (!(stop_char && *stop_char == '\0')) {
1037	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1123	>
1124	>
1125	>	if (update_arg( (void *)&(args_info->length_arg),
1126	>	&(args_info->length_orig), &(args_info->length_given),
1127	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1128	>	check_ambiguity, override, 0, 0,
1129	>	"length", '-',
1130	>	additional_error))
1131		goto failure;
1132	<	}
1040	<	if (args_info->length_orig)
1041	<	free (args_info->length_orig); /* free previous string */
1042	<	args_info->length_orig = gengetopt_strdup (optarg);
1132	>
1133		}
1134	+	/* maximum length (Defaults to 1/2 smallest length of first frame). */
1135	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1136	+	{
1137	+
1138	+
1139	+	if (update_arg( (void *)&(args_info->zlength_arg),
1140	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1141	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1142	+	check_ambiguity, override, 0, 0,
1143	+	"zlength", '-',
1144	+	additional_error))
1145	+	goto failure;
1146	+
1147	+	}
1148		/* select the first stuntdouble set. */
1149		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1150		{
1151	<	if (local_args_info.sele1_given)
1152	<	{
1153	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1154	<	goto failure;
1155	<	}
1156	<	if (args_info->sele1_given && ! override)
1157	<	continue;
1158	<	local_args_info.sele1_given = 1;
1159	<	args_info->sele1_given = 1;
1160	<	if (args_info->sele1_arg)
1057	<	free (args_info->sele1_arg); /* free previous string */
1058	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1059	<	if (args_info->sele1_orig)
1060	<	free (args_info->sele1_orig); /* free previous string */
1061	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1151	>
1152	>
1153	>	if (update_arg( (void *)&(args_info->sele1_arg),
1154	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1155	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1156	>	check_ambiguity, override, 0, 0,
1157	>	"sele1", '-',
1158	>	additional_error))
1159	>	goto failure;
1160	>
1161		}
1162		/* select the second stuntdouble set. */
1163		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1164		{
1165	<	if (local_args_info.sele2_given)
1166	<	{
1167	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1168	<	goto failure;
1169	<	}
1170	<	if (args_info->sele2_given && ! override)
1171	<	continue;
1172	<	local_args_info.sele2_given = 1;
1173	<	args_info->sele2_given = 1;
1174	<	if (args_info->sele2_arg)
1076	<	free (args_info->sele2_arg); /* free previous string */
1077	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1078	<	if (args_info->sele2_orig)
1079	<	free (args_info->sele2_orig); /* free previous string */
1080	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1165	>
1166	>
1167	>	if (update_arg( (void *)&(args_info->sele2_arg),
1168	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1169	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1170	>	check_ambiguity, override, 0, 0,
1171	>	"sele2", '-',
1172	>	additional_error))
1173	>	goto failure;
1174	>
1175		}
1176		/* select the third stuntdouble set. */
1177		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1178		{
1179	<	if (local_args_info.sele3_given)
1180	<	{
1181	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1182	<	goto failure;
1183	<	}
1184	<	if (args_info->sele3_given && ! override)
1185	<	continue;
1186	<	local_args_info.sele3_given = 1;
1187	<	args_info->sele3_given = 1;
1188	<	if (args_info->sele3_arg)
1095	<	free (args_info->sele3_arg); /* free previous string */
1096	<	args_info->sele3_arg = gengetopt_strdup (optarg);
1097	<	if (args_info->sele3_orig)
1098	<	free (args_info->sele3_orig); /* free previous string */
1099	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1179	>
1180	>
1181	>	if (update_arg( (void *)&(args_info->sele3_arg),
1182	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1183	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1184	>	check_ambiguity, override, 0, 0,
1185	>	"sele3", '-',
1186	>	additional_error))
1187	>	goto failure;
1188	>
1189		}
1190		/* select reference (use and only use with --gxyz). */
1191		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1192		{
1193	<	if (local_args_info.refsele_given)
1194	<	{
1195	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1196	<	goto failure;
1197	<	}
1198	<	if (args_info->refsele_given && ! override)
1199	<	continue;
1200	<	local_args_info.refsele_given = 1;
1201	<	args_info->refsele_given = 1;
1202	<	if (args_info->refsele_arg)
1114	<	free (args_info->refsele_arg); /* free previous string */
1115	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1116	<	if (args_info->refsele_orig)
1117	<	free (args_info->refsele_orig); /* free previous string */
1118	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1193	>
1194	>
1195	>	if (update_arg( (void *)&(args_info->refsele_arg),
1196	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1197	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1198	>	check_ambiguity, override, 0, 0,
1199	>	"refsele", '-',
1200	>	additional_error))
1201	>	goto failure;
1202	>
1203		}
1204	+	/* select stunt doubles for center-of-mass reference point. */
1205	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1206	+	{
1207	+
1208	+
1209	+	if (update_arg( (void *)&(args_info->comsele_arg),
1210	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1211	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1212	+	check_ambiguity, override, 0, 0,
1213	+	"comsele", '-',
1214	+	additional_error))
1215	+	goto failure;
1216	+
1217	+	}
1218	+	/* global index offset for a second object (used to define a vector between sites in molecule). */
1219	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1220	+	{
1221	+
1222	+
1223	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1224	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1225	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1226	+	check_ambiguity, override, 0, 0,
1227	+	"seleoffset", '-',
1228	+	additional_error))
1229	+	goto failure;
1230	+
1231	+	}
1232		/* molecule name. */
1233		else if (strcmp (long_options[option_index].name, "molname") == 0)
1234		{
1235	<	if (local_args_info.molname_given)
1236	<	{
1237	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1238	<	goto failure;
1239	<	}
1240	<	if (args_info->molname_given && ! override)
1241	<	continue;
1242	<	local_args_info.molname_given = 1;
1243	<	args_info->molname_given = 1;
1244	<	if (args_info->molname_arg)
1133	<	free (args_info->molname_arg); /* free previous string */
1134	<	args_info->molname_arg = gengetopt_strdup (optarg);
1135	<	if (args_info->molname_orig)
1136	<	free (args_info->molname_orig); /* free previous string */
1137	<	args_info->molname_orig = gengetopt_strdup (optarg);
1235	>
1236	>
1237	>	if (update_arg( (void *)&(args_info->molname_arg),
1238	>	&(args_info->molname_orig), &(args_info->molname_given),
1239	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1240	>	check_ambiguity, override, 0, 0,
1241	>	"molname", '-',
1242	>	additional_error))
1243	>	goto failure;
1244	>
1245		}
1246		/* begin internal index. */
1247		else if (strcmp (long_options[option_index].name, "begin") == 0)
1248		{
1249	<	if (local_args_info.begin_given)
1250	<	{
1251	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	<	goto failure;
1253	<	}
1254	<	if (args_info->begin_given && ! override)
1255	<	continue;
1256	<	local_args_info.begin_given = 1;
1150	<	args_info->begin_given = 1;
1151	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1152	<	if (!(stop_char && *stop_char == '\0')) {
1153	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1249	>
1250	>
1251	>	if (update_arg( (void *)&(args_info->begin_arg),
1252	>	&(args_info->begin_orig), &(args_info->begin_given),
1253	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1254	>	check_ambiguity, override, 0, 0,
1255	>	"begin", '-',
1256	>	additional_error))
1257		goto failure;
1258	<	}
1156	<	if (args_info->begin_orig)
1157	<	free (args_info->begin_orig); /* free previous string */
1158	<	args_info->begin_orig = gengetopt_strdup (optarg);
1258	>
1259		}
1260		/* end internal index. */
1261		else if (strcmp (long_options[option_index].name, "end") == 0)
1262		{
1263	<	if (local_args_info.end_given)
1264	<	{
1265	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1266	<	goto failure;
1267	<	}
1268	<	if (args_info->end_given && ! override)
1269	<	continue;
1270	<	local_args_info.end_given = 1;
1171	<	args_info->end_given = 1;
1172	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
1173	<	if (!(stop_char && *stop_char == '\0')) {
1174	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1263	>
1264	>
1265	>	if (update_arg( (void *)&(args_info->end_arg),
1266	>	&(args_info->end_orig), &(args_info->end_given),
1267	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1268	>	check_ambiguity, override, 0, 0,
1269	>	"end", '-',
1270	>	additional_error))
1271		goto failure;
1272	<	}
1177	<	if (args_info->end_orig)
1178	<	free (args_info->end_orig); /* free previous string */
1179	<	args_info->end_orig = gengetopt_strdup (optarg);
1272	>
1273		}
1274		/* nanoparticle radius. */
1275		else if (strcmp (long_options[option_index].name, "radius") == 0)
1276		{
1277	<	if (local_args_info.radius_given)
1278	<	{
1279	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1280	<	goto failure;
1281	<	}
1282	<	if (args_info->radius_given && ! override)
1283	<	continue;
1284	<	local_args_info.radius_given = 1;
1192	<	args_info->radius_given = 1;
1193	<	args_info->radius_arg = strtod (optarg, &stop_char);
1194	<	if (!(stop_char && *stop_char == '\0')) {
1195	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1277	>
1278	>
1279	>	if (update_arg( (void *)&(args_info->radius_arg),
1280	>	&(args_info->radius_orig), &(args_info->radius_given),
1281	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1282	>	check_ambiguity, override, 0, 0,
1283	>	"radius", '-',
1284	>	additional_error))
1285		goto failure;
1286	<	}
1198	<	if (args_info->radius_orig)
1199	<	free (args_info->radius_orig); /* free previous string */
1200	<	args_info->radius_orig = gengetopt_strdup (optarg);
1286	>
1287		}
1288		/* bond order parameter (--rcut must be specified). */
1289		else if (strcmp (long_options[option_index].name, "bo") == 0)
1290		{
1291	<	if (local_args_info.bo_given)
1206	<	{
1207	<	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1208	<	goto failure;
1209	<	}
1210	<	if (args_info->bo_given && ! override)
1211	<	continue;
1212	<	local_args_info.bo_given = 1;
1213	<	args_info->bo_given = 1;
1291	>
1292		if (args_info->staticProps_group_counter && override)
1293		reset_group_staticProps (args_info);
1294		args_info->staticProps_group_counter += 1;
1295	<	break;
1295	>
1296	>	if (update_arg( 0 ,
1297	>	0 , &(args_info->bo_given),
1298	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1299	>	check_ambiguity, override, 0, 0,
1300	>	"bo", '-',
1301	>	additional_error))
1302	>	goto failure;
1303	>
1304		}
1305		/* bond order parameter as a function of radius (--rcut must be specified). */
1306		else if (strcmp (long_options[option_index].name, "bor") == 0)
1307		{
1308	<	if (local_args_info.bor_given)
1223	<	{
1224	<	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1225	<	goto failure;
1226	<	}
1227	<	if (args_info->bor_given && ! override)
1228	<	continue;
1229	<	local_args_info.bor_given = 1;
1230	<	args_info->bor_given = 1;
1308	>
1309		if (args_info->staticProps_group_counter && override)
1310		reset_group_staticProps (args_info);
1311		args_info->staticProps_group_counter += 1;
1312	<	break;
1312	>
1313	>	if (update_arg( 0 ,
1314	>	0 , &(args_info->bor_given),
1315	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1316	>	check_ambiguity, override, 0, 0,
1317	>	"bor", '-',
1318	>	additional_error))
1319	>	goto failure;
1320	>
1321		}
1322		/* N(theta) bond angle density within (--rcut must be specified). */
1323		else if (strcmp (long_options[option_index].name, "bad") == 0)
1324		{
1325	<	if (local_args_info.bad_given)
1240	<	{
1241	<	fprintf (stderr, "%s: `--bad' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1242	<	goto failure;
1243	<	}
1244	<	if (args_info->bad_given && ! override)
1245	<	continue;
1246	<	local_args_info.bad_given = 1;
1247	<	args_info->bad_given = 1;
1325	>
1326		if (args_info->staticProps_group_counter && override)
1327		reset_group_staticProps (args_info);
1328		args_info->staticProps_group_counter += 1;
1329	<	break;
1329	>
1330	>	if (update_arg( 0 ,
1331	>	0 , &(args_info->bad_given),
1332	>	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1333	>	check_ambiguity, override, 0, 0,
1334	>	"bad", '-',
1335	>	additional_error))
1336	>	goto failure;
1337	>
1338		}
1339	+	/* count of molecules matching selection criteria (and associated statistics). */
1340	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1341	+	{
1342	+
1343	+	if (args_info->staticProps_group_counter && override)
1344	+	reset_group_staticProps (args_info);
1345	+	args_info->staticProps_group_counter += 1;
1346	+
1347	+	if (update_arg( 0 ,
1348	+	0 , &(args_info->count_given),
1349	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1350	+	check_ambiguity, override, 0, 0,
1351	+	"count", '-',
1352	+	additional_error))
1353	+	goto failure;
1354	+
1355	+	}
1356		/* g(z). */
1357		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1358		{
1359	<	if (local_args_info.gofz_given)
1257	<	{
1258	<	fprintf (stderr, "%s: `--gofz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1259	<	goto failure;
1260	<	}
1261	<	if (args_info->gofz_given && ! override)
1262	<	continue;
1263	<	local_args_info.gofz_given = 1;
1264	<	args_info->gofz_given = 1;
1359	>
1360		if (args_info->staticProps_group_counter && override)
1361		reset_group_staticProps (args_info);
1362		args_info->staticProps_group_counter += 1;
1363	<	break;
1363	>
1364	>	if (update_arg( 0 ,
1365	>	0 , &(args_info->gofz_given),
1366	>	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1367	>	check_ambiguity, override, 0, 0,
1368	>	"gofz", '-',
1369	>	additional_error))
1370	>	goto failure;
1371	>
1372		}
1373		/* g(r, cos(theta)). */
1374		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1375		{
1376	<	if (local_args_info.r_theta_given)
1274	<	{
1275	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1276	<	goto failure;
1277	<	}
1278	<	if (args_info->r_theta_given && ! override)
1279	<	continue;
1280	<	local_args_info.r_theta_given = 1;
1281	<	args_info->r_theta_given = 1;
1376	>
1377		if (args_info->staticProps_group_counter && override)
1378		reset_group_staticProps (args_info);
1379		args_info->staticProps_group_counter += 1;
1380	<	break;
1380	>
1381	>	if (update_arg( 0 ,
1382	>	0 , &(args_info->r_theta_given),
1383	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1384	>	check_ambiguity, override, 0, 0,
1385	>	"r_theta", '-',
1386	>	additional_error))
1387	>	goto failure;
1388	>
1389		}
1390		/* g(r, cos(omega)). */
1391		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1392		{
1393	<	if (local_args_info.r_omega_given)
1291	<	{
1292	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1293	<	goto failure;
1294	<	}
1295	<	if (args_info->r_omega_given && ! override)
1296	<	continue;
1297	<	local_args_info.r_omega_given = 1;
1298	<	args_info->r_omega_given = 1;
1393	>
1394		if (args_info->staticProps_group_counter && override)
1395		reset_group_staticProps (args_info);
1396		args_info->staticProps_group_counter += 1;
1397	<	break;
1397	>
1398	>	if (update_arg( 0 ,
1399	>	0 , &(args_info->r_omega_given),
1400	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1401	>	check_ambiguity, override, 0, 0,
1402	>	"r_omega", '-',
1403	>	additional_error))
1404	>	goto failure;
1405	>
1406		}
1407	+	/* g(r, z). */
1408	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1409	+	{
1410	+
1411	+	if (args_info->staticProps_group_counter && override)
1412	+	reset_group_staticProps (args_info);
1413	+	args_info->staticProps_group_counter += 1;
1414	+
1415	+	if (update_arg( 0 ,
1416	+	0 , &(args_info->r_z_given),
1417	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1418	+	check_ambiguity, override, 0, 0,
1419	+	"r_z", '-',
1420	+	additional_error))
1421	+	goto failure;
1422	+
1423	+	}
1424		/* g(cos(theta), cos(omega)). */
1425		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1426		{
1427	<	if (local_args_info.theta_omega_given)
1308	<	{
1309	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1310	<	goto failure;
1311	<	}
1312	<	if (args_info->theta_omega_given && ! override)
1313	<	continue;
1314	<	local_args_info.theta_omega_given = 1;
1315	<	args_info->theta_omega_given = 1;
1427	>
1428		if (args_info->staticProps_group_counter && override)
1429		reset_group_staticProps (args_info);
1430		args_info->staticProps_group_counter += 1;
1431	<	break;
1431	>
1432	>	if (update_arg( 0 ,
1433	>	0 , &(args_info->theta_omega_given),
1434	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1435	>	check_ambiguity, override, 0, 0,
1436	>	"theta_omega", '-',
1437	>	additional_error))
1438	>	goto failure;
1439	>
1440		}
1441		/* g(x, y, z). */
1442		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1443		{
1444	<	if (local_args_info.gxyz_given)
1325	<	{
1326	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1327	<	goto failure;
1328	<	}
1329	<	if (args_info->gxyz_given && ! override)
1330	<	continue;
1331	<	local_args_info.gxyz_given = 1;
1332	<	args_info->gxyz_given = 1;
1444	>
1445		if (args_info->staticProps_group_counter && override)
1446		reset_group_staticProps (args_info);
1447		args_info->staticProps_group_counter += 1;
1448	<	break;
1448	>
1449	>	if (update_arg( 0 ,
1450	>	0 , &(args_info->gxyz_given),
1451	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1452	>	check_ambiguity, override, 0, 0,
1453	>	"gxyz", '-',
1454	>	additional_error))
1455	>	goto failure;
1456	>
1457		}
1458	+	/* 2D g(r) (Slab width --dz must be specified). */
1459	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1460	+	{
1461	+
1462	+	if (args_info->staticProps_group_counter && override)
1463	+	reset_group_staticProps (args_info);
1464	+	args_info->staticProps_group_counter += 1;
1465	+
1466	+	if (update_arg( 0 ,
1467	+	0 , &(args_info->twodgofr_given),
1468	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1469	+	check_ambiguity, override, 0, 0,
1470	+	"twodgofr", '-',
1471	+	additional_error))
1472	+	goto failure;
1473	+
1474	+	}
1475		/* rp2 order parameter (--sele1 and --sele2 must be specified). */
1476		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1477		{
1478	<	if (local_args_info.rp2_given)
1342	<	{
1343	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1344	<	goto failure;
1345	<	}
1346	<	if (args_info->rp2_given && ! override)
1347	<	continue;
1348	<	local_args_info.rp2_given = 1;
1349	<	args_info->rp2_given = 1;
1478	>
1479		if (args_info->staticProps_group_counter && override)
1480		reset_group_staticProps (args_info);
1481		args_info->staticProps_group_counter += 1;
1482	<	break;
1482	>
1483	>	if (update_arg( 0 ,
1484	>	0 , &(args_info->rp2_given),
1485	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1486	>	check_ambiguity, override, 0, 0,
1487	>	"rp2", '-',
1488	>	additional_error))
1489	>	goto failure;
1490	>
1491		}
1492		/* slab density. */
1493		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1494		{
1495	<	if (local_args_info.slab_density_given)
1359	<	{
1360	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1361	<	goto failure;
1362	<	}
1363	<	if (args_info->slab_density_given && ! override)
1364	<	continue;
1365	<	local_args_info.slab_density_given = 1;
1366	<	args_info->slab_density_given = 1;
1495	>
1496		if (args_info->staticProps_group_counter && override)
1497		reset_group_staticProps (args_info);
1498		args_info->staticProps_group_counter += 1;
1499	<	break;
1499	>
1500	>	if (update_arg( 0 ,
1501	>	0 , &(args_info->slab_density_given),
1502	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1503	>	check_ambiguity, override, 0, 0,
1504	>	"slab_density", '-',
1505	>	additional_error))
1506	>	goto failure;
1507	>
1508		}
1509	+	/* p(cos(theta)). */
1510	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1511	+	{
1512	+
1513	+	if (args_info->staticProps_group_counter && override)
1514	+	reset_group_staticProps (args_info);
1515	+	args_info->staticProps_group_counter += 1;
1516	+
1517	+	if (update_arg( 0 ,
1518	+	0 , &(args_info->p_angle_given),
1519	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1520	+	check_ambiguity, override, 0, 0,
1521	+	"p_angle", '-',
1522	+	additional_error))
1523	+	goto failure;
1524	+
1525	+	}
1526		/* hxy. */
1527		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1528		{
1529	<	if (local_args_info.hxy_given)
1376	<	{
1377	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1378	<	goto failure;
1379	<	}
1380	<	if (args_info->hxy_given && ! override)
1381	<	continue;
1382	<	local_args_info.hxy_given = 1;
1383	<	args_info->hxy_given = 1;
1529	>
1530		if (args_info->staticProps_group_counter && override)
1531		reset_group_staticProps (args_info);
1532		args_info->staticProps_group_counter += 1;
1533	<	break;
1533	>
1534	>	if (update_arg( 0 ,
1535	>	0 , &(args_info->hxy_given),
1536	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1537	>	check_ambiguity, override, 0, 0,
1538	>	"hxy", '-',
1539	>	additional_error))
1540	>	goto failure;
1541	>
1542		}
1543		/* rho of R. */
1544		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1545		{
1546	<	if (local_args_info.rho_r_given)
1393	<	{
1394	<	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1395	<	goto failure;
1396	<	}
1397	<	if (args_info->rho_r_given && ! override)
1398	<	continue;
1399	<	local_args_info.rho_r_given = 1;
1400	<	args_info->rho_r_given = 1;
1546	>
1547		if (args_info->staticProps_group_counter && override)
1548		reset_group_staticProps (args_info);
1549		args_info->staticProps_group_counter += 1;
1550	<	break;
1550	>
1551	>	if (update_arg( 0 ,
1552	>	0 , &(args_info->rho_r_given),
1553	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1554	>	check_ambiguity, override, 0, 0,
1555	>	"rho_r", '-',
1556	>	additional_error))
1557	>	goto failure;
1558	>
1559		}
1560	+	/* angle of R. */
1561	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1562	+	{
1563	+
1564	+	if (args_info->staticProps_group_counter && override)
1565	+	reset_group_staticProps (args_info);
1566	+	args_info->staticProps_group_counter += 1;
1567	+
1568	+	if (update_arg( 0 ,
1569	+	0 , &(args_info->angle_r_given),
1570	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1571	+	check_ambiguity, override, 0, 0,
1572	+	"angle_r", '-',
1573	+	additional_error))
1574	+	goto failure;
1575	+
1576	+	}
1577		/* hull volume of nanoparticle. */
1578		else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1579		{
1580	<	if (local_args_info.hullvol_given)
1410	<	{
1411	<	fprintf (stderr, "%s: `--hullvol' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1412	<	goto failure;
1413	<	}
1414	<	if (args_info->hullvol_given && ! override)
1415	<	continue;
1416	<	local_args_info.hullvol_given = 1;
1417	<	args_info->hullvol_given = 1;
1580	>
1581		if (args_info->staticProps_group_counter && override)
1582		reset_group_staticProps (args_info);
1583		args_info->staticProps_group_counter += 1;
1584	<	break;
1584	>
1585	>	if (update_arg( 0 ,
1586	>	0 , &(args_info->hullvol_given),
1587	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1588	>	check_ambiguity, override, 0, 0,
1589	>	"hullvol", '-',
1590	>	additional_error))
1591	>	goto failure;
1592	>
1593		}
1594	+	/* length of nanorod. */
1595	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1596	+	{
1597
1598	+	if (args_info->staticProps_group_counter && override)
1599	+	reset_group_staticProps (args_info);
1600	+	args_info->staticProps_group_counter += 1;
1601	+
1602	+	if (update_arg( 0 ,
1603	+	0 , &(args_info->rodlength_given),
1604	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1605	+	check_ambiguity, override, 0, 0,
1606	+	"rodlength", '-',
1607	+	additional_error))
1608	+	goto failure;
1609	+
1610	+	}
1611	+	/* tetrahedrality order parameter by zbin(--sele1 must be specified). */
1612	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1613	+	{
1614	+
1615	+	if (args_info->staticProps_group_counter && override)
1616	+	reset_group_staticProps (args_info);
1617	+	args_info->staticProps_group_counter += 1;
1618	+
1619	+	if (update_arg( 0 ,
1620	+	0 , &(args_info->tet_param_z_given),
1621	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1622	+	check_ambiguity, override, 0, 0,
1623	+	"tet_param_z", '-',
1624	+	additional_error))
1625	+	goto failure;
1626	+
1627	+	}
1628	+
1629		break;
1630		case '?': /* Invalid option. */
1631		/* `getopt_long' already printed an error message. */
#	Line 1434 \| Line 1639 \| *cmdline_parser_internal (int argc, char const argv,*
1639
1640		if (args_info->staticProps_group_counter > 1)
1641		{
1642	<	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 : ""));
1642	>	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 : ""));
1643		error = 1;
1644		}
1645

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

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

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing: trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs. trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

Comparing: trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs. trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

Diff Legend

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC