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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 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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	+	#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	+	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60		"      --molname=STRING          molecule name",
61		"      --begin=INT               begin internal index",
62		"      --end=INT                 end internal index",
#	Line 52 | Line 65 | const char *gengetopt_args_info_help[] = {
65		"      --bo                      bond order parameter (--rcut must be specified)",
66		"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67		"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
68	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
69		"  -g, --gofr                    g(r)",
70		"      --gofz                    g(z)",
71		"      --r_theta                 g(r, cos(theta))",
72		"      --r_omega                 g(r, cos(omega))",
73	+	"      --r_z                     g(r, z)",
74		"      --theta_omega             g(cos(theta), cos(omega))",
75		"      --gxyz                    g(x, y, z)",
76	<	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
76	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
77	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
78		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
79		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
80		"  -d, --density                 density plot",
81		"      --slab_density            slab density",
82	+	"      --p_angle                 p(cos(theta))",
83		"      --hxy                     hxy",
84		"      --rho_r                   rho of R",
85	+	"      --angle_r                 angle of R",
86		"      --hullvol                 hull volume of nanoparticle",
87	+	"      --rodlength               length of nanorod",
88	+	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
89	+	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
90	+	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
91	+	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
92		0
93		};
94
95	+	typedef enum {ARG_NO
96	+	, ARG_STRING
97	+	, ARG_INT
98	+	, ARG_DOUBLE
99	+	} cmdline_parser_arg_type;
100	+
101		static
102		void clear_given (struct gengetopt_args_info *args_info);
103		static
104		void clear_args (struct gengetopt_args_info *args_info);
105
106		static int
107	<	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);
107	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
108	>	struct cmdline_parser_params *params, const char *additional_error);
109
110		static int
111		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 94 | Line 124 | void clear_given (struct gengetopt_args_info *args_inf
124		args_info->nbins_given = 0 ;
125		args_info->nbins_x_given = 0 ;
126		args_info->nbins_y_given = 0 ;
127	+	args_info->nbins_z_given = 0 ;
128		args_info->nanglebins_given = 0 ;
98	–	args_info->length_given = 0 ;
129		args_info->rcut_given = 0 ;
130	+	args_info->dz_given = 0 ;
131	+	args_info->length_given = 0 ;
132	+	args_info->zlength_given = 0 ;
133		args_info->zoffset_given = 0 ;
134		args_info->sele1_given = 0 ;
135		args_info->sele2_given = 0 ;
136		args_info->sele3_given = 0 ;
137		args_info->refsele_given = 0 ;
138	+	args_info->comsele_given = 0 ;
139	+	args_info->seleoffset_given = 0 ;
140		args_info->molname_given = 0 ;
141		args_info->begin_given = 0 ;
142		args_info->end_given = 0 ;
#	Line 109 | Line 144 | void clear_given (struct gengetopt_args_info *args_inf
144		args_info->bo_given = 0 ;
145		args_info->bor_given = 0 ;
146		args_info->bad_given = 0 ;
147	+	args_info->count_given = 0 ;
148		args_info->gofr_given = 0 ;
149		args_info->gofz_given = 0 ;
150		args_info->r_theta_given = 0 ;
151		args_info->r_omega_given = 0 ;
152	+	args_info->r_z_given = 0 ;
153		args_info->theta_omega_given = 0 ;
154		args_info->gxyz_given = 0 ;
155	+	args_info->twodgofr_given = 0 ;
156		args_info->p2_given = 0 ;
157		args_info->rp2_given = 0 ;
158		args_info->scd_given = 0 ;
159		args_info->density_given = 0 ;
160		args_info->slab_density_given = 0 ;
161	+	args_info->p_angle_given = 0 ;
162		args_info->hxy_given = 0 ;
163		args_info->rho_r_given = 0 ;
164	+	args_info->angle_r_given = 0 ;
165		args_info->hullvol_given = 0 ;
166	+	args_info->rodlength_given = 0 ;
167	+	args_info->tet_param_given = 0 ;
168	+	args_info->tet_param_z_given = 0 ;
169	+	args_info->rnemdz_given = 0 ;
170	+	args_info->rnemdr_given = 0 ;
171		args_info->staticProps_group_counter = 0 ;
172		}
173
174		static
175		void clear_args (struct gengetopt_args_info *args_info)
176		{
177	+	FIX_UNUSED (args_info);
178		args_info->input_arg = NULL;
179		args_info->input_orig = NULL;
180		args_info->output_arg = NULL;
#	Line 141 | Line 187 | void clear_args (struct gengetopt_args_info *args_info
187		args_info->nbins_x_orig = NULL;
188		args_info->nbins_y_arg = 100;
189		args_info->nbins_y_orig = NULL;
190	+	args_info->nbins_z_arg = 100;
191	+	args_info->nbins_z_orig = NULL;
192		args_info->nanglebins_arg = 50;
193		args_info->nanglebins_orig = NULL;
146	–	args_info->length_orig = NULL;
194		args_info->rcut_orig = NULL;
195	+	args_info->dz_orig = NULL;
196	+	args_info->length_orig = NULL;
197	+	args_info->zlength_orig = NULL;
198		args_info->zoffset_arg = 0;
199		args_info->zoffset_orig = NULL;
200		args_info->sele1_arg = NULL;
#	Line 155 | Line 205 | void clear_args (struct gengetopt_args_info *args_info
205		args_info->sele3_orig = NULL;
206		args_info->refsele_arg = NULL;
207		args_info->refsele_orig = NULL;
208	+	args_info->comsele_arg = NULL;
209	+	args_info->comsele_orig = NULL;
210	+	args_info->seleoffset_orig = NULL;
211		args_info->molname_arg = NULL;
212		args_info->molname_orig = NULL;
213		args_info->begin_orig = NULL;
#	Line 166 | Line 219 | void init_args_info(struct gengetopt_args_info *args_i
219		static
220		void init_args_info(struct gengetopt_args_info *args_info)
221		{
222	+
223	+
224		args_info->help_help = gengetopt_args_info_help[0] ;
225		args_info->version_help = gengetopt_args_info_help[1] ;
226		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 174 | Line 229 | void init_args_info(struct gengetopt_args_info *args_i
229		args_info->nbins_help = gengetopt_args_info_help[5] ;
230		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
231		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
232	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
233	<	args_info->length_help = gengetopt_args_info_help[9] ;
232	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
233	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
234		args_info->rcut_help = gengetopt_args_info_help[10] ;
235	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
236	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
237	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
238	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
239	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
240	<	args_info->molname_help = gengetopt_args_info_help[16] ;
241	<	args_info->begin_help = gengetopt_args_info_help[17] ;
242	<	args_info->end_help = gengetopt_args_info_help[18] ;
243	<	args_info->radius_help = gengetopt_args_info_help[19] ;
244	<	args_info->bo_help = gengetopt_args_info_help[20] ;
245	<	args_info->bor_help = gengetopt_args_info_help[21] ;
246	<	args_info->bad_help = gengetopt_args_info_help[22] ;
247	<	args_info->gofr_help = gengetopt_args_info_help[23] ;
248	<	args_info->gofz_help = gengetopt_args_info_help[24] ;
249	<	args_info->r_theta_help = gengetopt_args_info_help[25] ;
250	<	args_info->r_omega_help = gengetopt_args_info_help[26] ;
251	<	args_info->theta_omega_help = gengetopt_args_info_help[27] ;
252	<	args_info->gxyz_help = gengetopt_args_info_help[28] ;
253	<	args_info->p2_help = gengetopt_args_info_help[29] ;
254	<	args_info->rp2_help = gengetopt_args_info_help[30] ;
255	<	args_info->scd_help = gengetopt_args_info_help[31] ;
256	<	args_info->density_help = gengetopt_args_info_help[32] ;
257	<	args_info->slab_density_help = gengetopt_args_info_help[33] ;
258	<	args_info->hxy_help = gengetopt_args_info_help[34] ;
259	<	args_info->rho_r_help = gengetopt_args_info_help[35] ;
260	<	args_info->hullvol_help = gengetopt_args_info_help[36] ;
235	>	args_info->dz_help = gengetopt_args_info_help[11] ;
236	>	args_info->length_help = gengetopt_args_info_help[12] ;
237	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
238	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
239	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
240	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
241	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
242	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
243	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
244	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
245	>	args_info->molname_help = gengetopt_args_info_help[21] ;
246	>	args_info->begin_help = gengetopt_args_info_help[22] ;
247	>	args_info->end_help = gengetopt_args_info_help[23] ;
248	>	args_info->radius_help = gengetopt_args_info_help[24] ;
249	>	args_info->bo_help = gengetopt_args_info_help[26] ;
250	>	args_info->bor_help = gengetopt_args_info_help[27] ;
251	>	args_info->bad_help = gengetopt_args_info_help[28] ;
252	>	args_info->count_help = gengetopt_args_info_help[29] ;
253	>	args_info->gofr_help = gengetopt_args_info_help[30] ;
254	>	args_info->gofz_help = gengetopt_args_info_help[31] ;
255	>	args_info->r_theta_help = gengetopt_args_info_help[32] ;
256	>	args_info->r_omega_help = gengetopt_args_info_help[33] ;
257	>	args_info->r_z_help = gengetopt_args_info_help[34] ;
258	>	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
259	>	args_info->gxyz_help = gengetopt_args_info_help[36] ;
260	>	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
261	>	args_info->p2_help = gengetopt_args_info_help[38] ;
262	>	args_info->rp2_help = gengetopt_args_info_help[39] ;
263	>	args_info->scd_help = gengetopt_args_info_help[40] ;
264	>	args_info->density_help = gengetopt_args_info_help[41] ;
265	>	args_info->slab_density_help = gengetopt_args_info_help[42] ;
266	>	args_info->p_angle_help = gengetopt_args_info_help[43] ;
267	>	args_info->hxy_help = gengetopt_args_info_help[44] ;
268	>	args_info->rho_r_help = gengetopt_args_info_help[45] ;
269	>	args_info->angle_r_help = gengetopt_args_info_help[46] ;
270	>	args_info->hullvol_help = gengetopt_args_info_help[47] ;
271	>	args_info->rodlength_help = gengetopt_args_info_help[48] ;
272	>	args_info->tet_param_help = gengetopt_args_info_help[49] ;
273	>	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
274	>	args_info->rnemdz_help = gengetopt_args_info_help[51] ;
275	>	args_info->rnemdr_help = gengetopt_args_info_help[52] ;
276
277		}
278
279		void
280		cmdline_parser_print_version (void)
281		{
282	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
282	>	printf ("%s %s\n",
283	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
284	>	CMDLINE_PARSER_VERSION);
285		}
286
287	<	void
216	<	cmdline_parser_print_help (void)
217	<	{
218	<	int i = 0;
287	>	static void print_help_common(void) {
288		cmdline_parser_print_version ();
289
290		if (strlen(gengetopt_args_info_purpose) > 0)
291		printf("\n%s\n", gengetopt_args_info_purpose);
292
293	<	printf("\n%s\n\n", gengetopt_args_info_usage);
293	>	if (strlen(gengetopt_args_info_usage) > 0)
294	>	printf("\n%s\n", gengetopt_args_info_usage);
295
296	+	printf("\n");
297	+
298		if (strlen(gengetopt_args_info_description) > 0)
299	<	printf("%s\n", gengetopt_args_info_description);
299	>	printf("%s\n\n", gengetopt_args_info_description);
300	>	}
301
302	+	void
303	+	cmdline_parser_print_help (void)
304	+	{
305	+	int i = 0;
306	+	print_help_common();
307		while (gengetopt_args_info_help[i])
308		printf("%s\n", gengetopt_args_info_help[i++]);
309		}
#	Line 237 | Line 315 | cmdline_parser_init (struct gengetopt_args_info *args_
315		clear_args (args_info);
316		init_args_info (args_info);
317
318	<	args_info->inputs = NULL;
318	>	args_info->inputs = 0;
319		args_info->inputs_num = 0;
320		}
321
322	+	void
323	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
324	+	{
325	+	if (params)
326	+	{
327	+	params->override = 0;
328	+	params->initialize = 1;
329	+	params->check_required = 1;
330	+	params->check_ambiguity = 0;
331	+	params->print_errors = 1;
332	+	}
333	+	}
334	+
335	+	struct cmdline_parser_params *
336	+	cmdline_parser_params_create(void)
337	+	{
338	+	struct cmdline_parser_params *params =
339	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
340	+	cmdline_parser_params_init(params);
341	+	return params;
342	+	}
343	+
344		static void
345	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
345	>	free_string_field (char **s)
346		{
347	<
248	<	unsigned int i;
249	<	if (args_info->input_arg)
347	>	if (*s)
348		{
349	<	free (args_info->input_arg); /* free previous argument */
350	<	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;
349	>	free (*s);
350	>	*s = 0;
351		}
352	<	if (args_info->sele1_arg)
353	<	{
354	<	free (args_info->sele1_arg); /* free previous argument */
355	<	args_info->sele1_arg = 0;
356	<	}
357	<	if (args_info->sele1_orig)
358	<	{
359	<	free (args_info->sele1_orig); /* free previous argument */
360	<	args_info->sele1_orig = 0;
361	<	}
362	<	if (args_info->sele2_arg)
363	<	{
364	<	free (args_info->sele2_arg); /* free previous argument */
365	<	args_info->sele2_arg = 0;
366	<	}
367	<	if (args_info->sele2_orig)
368	<	{
369	<	free (args_info->sele2_orig); /* free previous argument */
370	<	args_info->sele2_orig = 0;
371	<	}
372	<	if (args_info->sele3_arg)
373	<	{
374	<	free (args_info->sele3_arg); /* free previous argument */
375	<	args_info->sele3_arg = 0;
376	<	}
377	<	if (args_info->sele3_orig)
378	<	{
379	<	free (args_info->sele3_orig); /* free previous argument */
380	<	args_info->sele3_orig = 0;
381	<	}
382	<	if (args_info->refsele_arg)
383	<	{
384	<	free (args_info->refsele_arg); /* free previous argument */
385	<	args_info->refsele_arg = 0;
386	<	}
387	<	if (args_info->refsele_orig)
388	<	{
389	<	free (args_info->refsele_orig); /* free previous argument */
347	<	args_info->refsele_orig = 0;
348	<	}
349	<	if (args_info->molname_arg)
350	<	{
351	<	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	<	}
352	>	}
353	>
354	>
355	>	static void
356	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
357	>	{
358	>	unsigned int i;
359	>	free_string_field (&(args_info->input_arg));
360	>	free_string_field (&(args_info->input_orig));
361	>	free_string_field (&(args_info->output_arg));
362	>	free_string_field (&(args_info->output_orig));
363	>	free_string_field (&(args_info->step_orig));
364	>	free_string_field (&(args_info->nbins_orig));
365	>	free_string_field (&(args_info->nbins_x_orig));
366	>	free_string_field (&(args_info->nbins_y_orig));
367	>	free_string_field (&(args_info->nbins_z_orig));
368	>	free_string_field (&(args_info->nanglebins_orig));
369	>	free_string_field (&(args_info->rcut_orig));
370	>	free_string_field (&(args_info->dz_orig));
371	>	free_string_field (&(args_info->length_orig));
372	>	free_string_field (&(args_info->zlength_orig));
373	>	free_string_field (&(args_info->zoffset_orig));
374	>	free_string_field (&(args_info->sele1_arg));
375	>	free_string_field (&(args_info->sele1_orig));
376	>	free_string_field (&(args_info->sele2_arg));
377	>	free_string_field (&(args_info->sele2_orig));
378	>	free_string_field (&(args_info->sele3_arg));
379	>	free_string_field (&(args_info->sele3_orig));
380	>	free_string_field (&(args_info->refsele_arg));
381	>	free_string_field (&(args_info->refsele_orig));
382	>	free_string_field (&(args_info->comsele_arg));
383	>	free_string_field (&(args_info->comsele_orig));
384	>	free_string_field (&(args_info->seleoffset_orig));
385	>	free_string_field (&(args_info->molname_arg));
386	>	free_string_field (&(args_info->molname_orig));
387	>	free_string_field (&(args_info->begin_orig));
388	>	free_string_field (&(args_info->end_orig));
389	>	free_string_field (&(args_info->radius_orig));
390
391	+
392		for (i = 0; i < args_info->inputs_num; ++i)
393		free (args_info->inputs [i]);
394	<
394	>
395		if (args_info->inputs_num)
396		free (args_info->inputs);
397	<
397	>
398		clear_given (args_info);
399		}
400
401	+
402	+	static void
403	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
404	+	{
405	+	FIX_UNUSED (values);
406	+	if (arg) {
407	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
408	+	} else {
409	+	fprintf(outfile, "%s\n", opt);
410	+	}
411	+	}
412	+
413	+
414		int
415	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
416	+	{
417	+	int i = 0;
418	+
419	+	if (!outfile)
420	+	{
421	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
422	+	return EXIT_FAILURE;
423	+	}
424	+
425	+	if (args_info->help_given)
426	+	write_into_file(outfile, "help", 0, 0 );
427	+	if (args_info->version_given)
428	+	write_into_file(outfile, "version", 0, 0 );
429	+	if (args_info->input_given)
430	+	write_into_file(outfile, "input", args_info->input_orig, 0);
431	+	if (args_info->output_given)
432	+	write_into_file(outfile, "output", args_info->output_orig, 0);
433	+	if (args_info->step_given)
434	+	write_into_file(outfile, "step", args_info->step_orig, 0);
435	+	if (args_info->nbins_given)
436	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
437	+	if (args_info->nbins_x_given)
438	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
439	+	if (args_info->nbins_y_given)
440	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
441	+	if (args_info->nbins_z_given)
442	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
443	+	if (args_info->nanglebins_given)
444	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
445	+	if (args_info->rcut_given)
446	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
447	+	if (args_info->dz_given)
448	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
449	+	if (args_info->length_given)
450	+	write_into_file(outfile, "length", args_info->length_orig, 0);
451	+	if (args_info->zlength_given)
452	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
453	+	if (args_info->zoffset_given)
454	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
455	+	if (args_info->sele1_given)
456	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
457	+	if (args_info->sele2_given)
458	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
459	+	if (args_info->sele3_given)
460	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
461	+	if (args_info->refsele_given)
462	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
463	+	if (args_info->comsele_given)
464	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
465	+	if (args_info->seleoffset_given)
466	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
467	+	if (args_info->molname_given)
468	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
469	+	if (args_info->begin_given)
470	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
471	+	if (args_info->end_given)
472	+	write_into_file(outfile, "end", args_info->end_orig, 0);
473	+	if (args_info->radius_given)
474	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
475	+	if (args_info->bo_given)
476	+	write_into_file(outfile, "bo", 0, 0 );
477	+	if (args_info->bor_given)
478	+	write_into_file(outfile, "bor", 0, 0 );
479	+	if (args_info->bad_given)
480	+	write_into_file(outfile, "bad", 0, 0 );
481	+	if (args_info->count_given)
482	+	write_into_file(outfile, "count", 0, 0 );
483	+	if (args_info->gofr_given)
484	+	write_into_file(outfile, "gofr", 0, 0 );
485	+	if (args_info->gofz_given)
486	+	write_into_file(outfile, "gofz", 0, 0 );
487	+	if (args_info->r_theta_given)
488	+	write_into_file(outfile, "r_theta", 0, 0 );
489	+	if (args_info->r_omega_given)
490	+	write_into_file(outfile, "r_omega", 0, 0 );
491	+	if (args_info->r_z_given)
492	+	write_into_file(outfile, "r_z", 0, 0 );
493	+	if (args_info->theta_omega_given)
494	+	write_into_file(outfile, "theta_omega", 0, 0 );
495	+	if (args_info->gxyz_given)
496	+	write_into_file(outfile, "gxyz", 0, 0 );
497	+	if (args_info->twodgofr_given)
498	+	write_into_file(outfile, "twodgofr", 0, 0 );
499	+	if (args_info->p2_given)
500	+	write_into_file(outfile, "p2", 0, 0 );
501	+	if (args_info->rp2_given)
502	+	write_into_file(outfile, "rp2", 0, 0 );
503	+	if (args_info->scd_given)
504	+	write_into_file(outfile, "scd", 0, 0 );
505	+	if (args_info->density_given)
506	+	write_into_file(outfile, "density", 0, 0 );
507	+	if (args_info->slab_density_given)
508	+	write_into_file(outfile, "slab_density", 0, 0 );
509	+	if (args_info->p_angle_given)
510	+	write_into_file(outfile, "p_angle", 0, 0 );
511	+	if (args_info->hxy_given)
512	+	write_into_file(outfile, "hxy", 0, 0 );
513	+	if (args_info->rho_r_given)
514	+	write_into_file(outfile, "rho_r", 0, 0 );
515	+	if (args_info->angle_r_given)
516	+	write_into_file(outfile, "angle_r", 0, 0 );
517	+	if (args_info->hullvol_given)
518	+	write_into_file(outfile, "hullvol", 0, 0 );
519	+	if (args_info->rodlength_given)
520	+	write_into_file(outfile, "rodlength", 0, 0 );
521	+	if (args_info->tet_param_given)
522	+	write_into_file(outfile, "tet_param", 0, 0 );
523	+	if (args_info->tet_param_z_given)
524	+	write_into_file(outfile, "tet_param_z", 0, 0 );
525	+	if (args_info->rnemdz_given)
526	+	write_into_file(outfile, "rnemdz", 0, 0 );
527	+	if (args_info->rnemdr_given)
528	+	write_into_file(outfile, "rnemdr", 0, 0 );
529	+
530	+
531	+	i = EXIT_SUCCESS;
532	+	return i;
533	+	}
534	+
535	+	int
536		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
537		{
538		FILE *outfile;
#	Line 395 | Line 546 | cmdline_parser_file_save(const char *filename, struct
546		return EXIT_FAILURE;
547		}
548
549	<	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	<
549	>	i = cmdline_parser_dump(outfile, args_info);
550		fclose (outfile);
551
584	–	i = EXIT_SUCCESS;
552		return i;
553		}
554
#	Line 591 | Line 558 | cmdline_parser_free (struct gengetopt_args_info *args_
558		cmdline_parser_release (args_info);
559		}
560
561	<
595	<	/* gengetopt_strdup() */
596	<	/* strdup.c replacement of strdup, which is not standard */
561	>	/** @brief replacement of strdup, which is not standard */
562		char *
563		gengetopt_strdup (const char *s)
564		{
565	<	char *result = NULL;
565	>	char *result = 0;
566		if (!s)
567		return result;
568
#	Line 609 | Line 574 | static void
574		}
575
576		static void
612	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
613	–
614	–	static void
577		reset_group_staticProps(struct gengetopt_args_info *args_info)
578		{
579		if (! args_info->staticProps_group_counter)
#	Line 620 | Line 582 | reset_group_staticProps(struct gengetopt_args_info *ar
582		args_info->bo_given = 0 ;
583		args_info->bor_given = 0 ;
584		args_info->bad_given = 0 ;
585	+	args_info->count_given = 0 ;
586		args_info->gofr_given = 0 ;
587		args_info->gofz_given = 0 ;
588		args_info->r_theta_given = 0 ;
589		args_info->r_omega_given = 0 ;
590	+	args_info->r_z_given = 0 ;
591		args_info->theta_omega_given = 0 ;
592		args_info->gxyz_given = 0 ;
593	+	args_info->twodgofr_given = 0 ;
594		args_info->p2_given = 0 ;
595		args_info->rp2_given = 0 ;
596		args_info->scd_given = 0 ;
597		args_info->density_given = 0 ;
598		args_info->slab_density_given = 0 ;
599	+	args_info->p_angle_given = 0 ;
600		args_info->hxy_given = 0 ;
601		args_info->rho_r_given = 0 ;
602	+	args_info->angle_r_given = 0 ;
603		args_info->hullvol_given = 0 ;
604	+	args_info->rodlength_given = 0 ;
605	+	args_info->tet_param_given = 0 ;
606	+	args_info->tet_param_z_given = 0 ;
607	+	args_info->rnemdz_given = 0 ;
608	+	args_info->rnemdr_given = 0 ;
609
610		args_info->staticProps_group_counter = 0;
611		}
612
613		int
614	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
614	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
615		{
616		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
617		}
618
619		int
620	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
620	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
621	>	struct cmdline_parser_params *params)
622		{
623		int result;
624	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
625
626	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
626	>	if (result == EXIT_FAILURE)
627	>	{
628	>	cmdline_parser_free (args_info);
629	>	exit (EXIT_FAILURE);
630	>	}
631	>
632	>	return result;
633	>	}
634
635	+	int
636	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
637	+	{
638	+	int result;
639	+	struct cmdline_parser_params params;
640	+
641	+	params.override = override;
642	+	params.initialize = initialize;
643	+	params.check_required = check_required;
644	+	params.check_ambiguity = 0;
645	+	params.print_errors = 1;
646	+
647	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
648	+
649		if (result == EXIT_FAILURE)
650		{
651		cmdline_parser_free (args_info);
#	Line 665 | Line 660 | cmdline_parser_required (struct gengetopt_args_info *a
660		{
661		int result = EXIT_SUCCESS;
662
663	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
663	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
664		result = EXIT_FAILURE;
665
666		if (result == EXIT_FAILURE)
#	Line 681 | Line 676 | cmdline_parser_required2 (struct gengetopt_args_info *
676		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
677		{
678		int error = 0;
679	+	FIX_UNUSED (additional_error);
680
681		/* checks for required options */
682		if (! args_info->input_given)
#	Line 691 | Line 687 | cmdline_parser_required2 (struct gengetopt_args_info *
687
688		if (args_info->staticProps_group_counter == 0)
689		{
690	<	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 : ""));
690	>	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 : ""));
691		error = 1;
692		}
693
#	Line 699 | Line 695 | cmdline_parser_required2 (struct gengetopt_args_info *
695		/* checks for dependences among options */
696
697		return error;
698	+	}
699	+
700	+
701	+	static char *package_name = 0;
702	+
703	+	/**
704	+	* @brief updates an option
705	+	* @param field the generic pointer to the field to update
706	+	* @param orig_field the pointer to the orig field
707	+	* @param field_given the pointer to the number of occurrence of this option
708	+	* @param prev_given the pointer to the number of occurrence already seen
709	+	* @param value the argument for this option (if null no arg was specified)
710	+	* @param possible_values the possible values for this option (if specified)
711	+	* @param default_value the default value (in case the option only accepts fixed values)
712	+	* @param arg_type the type of this option
713	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
714	+	* @param override @see cmdline_parser_params.override
715	+	* @param no_free whether to free a possible previous value
716	+	* @param multiple_option whether this is a multiple option
717	+	* @param long_opt the corresponding long option
718	+	* @param short_opt the corresponding short option (or '-' if none)
719	+	* @param additional_error possible further error specification
720	+	*/
721	+	static
722	+	int update_arg(void *field, char **orig_field,
723	+	unsigned int *field_given, unsigned int *prev_given,
724	+	char *value, const char *possible_values[],
725	+	const char *default_value,
726	+	cmdline_parser_arg_type arg_type,
727	+	int check_ambiguity, int override,
728	+	int no_free, int multiple_option,
729	+	const char *long_opt, char short_opt,
730	+	const char *additional_error)
731	+	{
732	+	char *stop_char = 0;
733	+	const char *val = value;
734	+	int found;
735	+	char **string_field;
736	+	FIX_UNUSED (field);
737	+
738	+	stop_char = 0;
739	+	found = 0;
740	+
741	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
742	+	{
743	+	if (short_opt != '-')
744	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
745	+	package_name, long_opt, short_opt,
746	+	(additional_error ? additional_error : ""));
747	+	else
748	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
749	+	package_name, long_opt,
750	+	(additional_error ? additional_error : ""));
751	+	return 1; /* failure */
752	+	}
753	+
754	+	FIX_UNUSED (default_value);
755	+
756	+	if (field_given && *field_given && ! override)
757	+	return 0;
758	+	if (prev_given)
759	+	(*prev_given)++;
760	+	if (field_given)
761	+	(*field_given)++;
762	+	if (possible_values)
763	+	val = possible_values[found];
764	+
765	+	switch(arg_type) {
766	+	case ARG_INT:
767	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
768	+	break;
769	+	case ARG_DOUBLE:
770	+	if (val) *((double *)field) = strtod (val, &stop_char);
771	+	break;
772	+	case ARG_STRING:
773	+	if (val) {
774	+	string_field = (char **)field;
775	+	if (!no_free && *string_field)
776	+	free (*string_field); /* free previous string */
777	+	*string_field = gengetopt_strdup (val);
778	+	}
779	+	break;
780	+	default:
781	+	break;
782	+	};
783	+
784	+	/* check numeric conversion */
785	+	switch(arg_type) {
786	+	case ARG_INT:
787	+	case ARG_DOUBLE:
788	+	if (val && !(stop_char && *stop_char == '\0')) {
789	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
790	+	return 1; /* failure */
791	+	}
792	+	break;
793	+	default:
794	+	;
795	+	};
796	+
797	+	/* store the original value */
798	+	switch(arg_type) {
799	+	case ARG_NO:
800	+	break;
801	+	default:
802	+	if (value && orig_field) {
803	+	if (no_free) {
804	+	*orig_field = value;
805	+	} else {
806	+	if (*orig_field)
807	+	free (*orig_field); /* free previous string */
808	+	*orig_field = gengetopt_strdup (value);
809	+	}
810	+	}
811	+	};
812	+
813	+	return 0; /* OK */
814		}
815
816	+
817		int
818	<	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)
818	>	cmdline_parser_internal (
819	>	int argc, char **argv, struct gengetopt_args_info *args_info,
820	>	struct cmdline_parser_params *params, const char *additional_error)
821		{
822		int c;        /* Character of the parsed option.  */
823
824		int error = 0;
825		struct gengetopt_args_info local_args_info;
826	+
827	+	int override;
828	+	int initialize;
829	+	int check_required;
830	+	int check_ambiguity;
831	+
832	+	package_name = argv[0];
833	+
834	+	override = params->override;
835	+	initialize = params->initialize;
836	+	check_required = params->check_required;
837	+	check_ambiguity = params->check_ambiguity;
838
839		if (initialize)
840		cmdline_parser_init (args_info);
#	Line 716 | Line 843 | cmdline_parser_internal (int argc, char * const *argv,
843
844		optarg = 0;
845		optind = 0;
846	<	opterr = 1;
846	>	opterr = params->print_errors;
847		optopt = '?';
848
849		while (1)
850		{
851		int option_index = 0;
725	–	char *stop_char;
852
853		static struct option long_options[] = {
854		{ "help",       0, NULL, 'h' },
#	Line 733 | Line 859 | cmdline_parser_internal (int argc, char * const *argv,
859		{ "nbins",      1, NULL, 'b' },
860		{ "nbins_x",    1, NULL, 'x' },
861		{ "nbins_y",    1, NULL, 'y' },
862	+	{ "nbins_z",    1, NULL, 0 },
863		{ "nanglebins", 1, NULL, 'a' },
737	–	{ "length",     1, NULL, 0 },
864		{ "rcut",       1, NULL, 'c' },
865	+	{ "dz", 1, NULL, 0 },
866	+	{ "length",     1, NULL, 0 },
867	+	{ "zlength",    1, NULL, 0 },
868		{ "zoffset",    1, NULL, 'z' },
869		{ "sele1",      1, NULL, 0 },
870		{ "sele2",      1, NULL, 0 },
871		{ "sele3",      1, NULL, 0 },
872		{ "refsele",    1, NULL, 0 },
873	+	{ "comsele",    1, NULL, 0 },
874	+	{ "seleoffset", 1, NULL, 0 },
875		{ "molname",    1, NULL, 0 },
876		{ "begin",      1, NULL, 0 },
877		{ "end",        1, NULL, 0 },
#	Line 748 | Line 879 | cmdline_parser_internal (int argc, char * const *argv,
879		{ "bo", 0, NULL, 0 },
880		{ "bor",        0, NULL, 0 },
881		{ "bad",        0, NULL, 0 },
882	+	{ "count",      0, NULL, 0 },
883		{ "gofr",       0, NULL, 'g' },
884		{ "gofz",       0, NULL, 0 },
885		{ "r_theta",    0, NULL, 0 },
886		{ "r_omega",    0, NULL, 0 },
887	+	{ "r_z",        0, NULL, 0 },
888		{ "theta_omega",        0, NULL, 0 },
889		{ "gxyz",       0, NULL, 0 },
890	+	{ "twodgofr",   0, NULL, 0 },
891		{ "p2", 0, NULL, 'p' },
892		{ "rp2",        0, NULL, 0 },
893		{ "scd",        0, NULL, 's' },
894		{ "density",    0, NULL, 'd' },
895		{ "slab_density",       0, NULL, 0 },
896	+	{ "p_angle",    0, NULL, 0 },
897		{ "hxy",        0, NULL, 0 },
898		{ "rho_r",      0, NULL, 0 },
899	+	{ "angle_r",    0, NULL, 0 },
900		{ "hullvol",    0, NULL, 0 },
901	<	{ NULL, 0, NULL, 0 }
901	>	{ "rodlength",  0, NULL, 0 },
902	>	{ "tet_param",  0, NULL, 'Q' },
903	>	{ "tet_param_z",        0, NULL, 0 },
904	>	{ "rnemdz",     0, NULL, 0 },
905	>	{ "rnemdr",     0, NULL, 0 },
906	>	{ 0,  0, 0, 0 }
907		};
908
909	<	stop_char = 0;
769	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
909	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
910
911		if (c == -1) break;       /* Exit from `while (1)' loop.  */
912
#	Line 783 | Line 923 | cmdline_parser_internal (int argc, char * const *argv,
923		exit (EXIT_SUCCESS);
924
925		case 'i':       /* input dump file.  */
926	<	if (local_args_info.input_given)
927	<	{
928	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
929	<	goto failure;
930	<	}
931	<	if (args_info->input_given && ! override)
932	<	continue;
933	<	local_args_info.input_given = 1;
934	<	args_info->input_given = 1;
935	<	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);
926	>
927	>
928	>	if (update_arg( (void *)&(args_info->input_arg),
929	>	&(args_info->input_orig), &(args_info->input_given),
930	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
931	>	check_ambiguity, override, 0, 0,
932	>	"input", 'i',
933	>	additional_error))
934	>	goto failure;
935	>
936		break;
802	–
937		case 'o':       /* output file name.  */
938	<	if (local_args_info.output_given)
939	<	{
940	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
941	<	goto failure;
942	<	}
943	<	if (args_info->output_given && ! override)
944	<	continue;
945	<	local_args_info.output_given = 1;
946	<	args_info->output_given = 1;
947	<	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);
938	>
939	>
940	>	if (update_arg( (void *)&(args_info->output_arg),
941	>	&(args_info->output_orig), &(args_info->output_given),
942	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
943	>	check_ambiguity, override, 0, 0,
944	>	"output", 'o',
945	>	additional_error))
946	>	goto failure;
947	>
948		break;
820	–
949		case 'n':       /* process every n frame.  */
950	<	if (local_args_info.step_given)
951	<	{
952	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
953	<	goto failure;
954	<	}
955	<	if (args_info->step_given && ! override)
956	<	continue;
957	<	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);
950	>
951	>
952	>	if (update_arg( (void *)&(args_info->step_arg),
953	>	&(args_info->step_orig), &(args_info->step_given),
954	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
955	>	check_ambiguity, override, 0, 0,
956	>	"step", 'n',
957	>	additional_error))
958		goto failure;
959	<	}
836	<	if (args_info->step_orig)
837	<	free (args_info->step_orig); /* free previous string */
838	<	args_info->step_orig = gengetopt_strdup (optarg);
959	>
960		break;
840	–
961		case 'b':       /* number of bins (general purpose).  */
962	<	if (local_args_info.nbins_given)
963	<	{
964	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
965	<	goto failure;
966	<	}
967	<	if (args_info->nbins_given && ! override)
968	<	continue;
969	<	local_args_info.nbins_given = 1;
970	<	args_info->nbins_given = 1;
971	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
972	<	if (!(stop_char && *stop_char == '\0')) {
853	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
854	<	goto failure;
855	<	}
856	<	if (args_info->nbins_orig)
857	<	free (args_info->nbins_orig); /* free previous string */
858	<	args_info->nbins_orig = gengetopt_strdup (optarg);
859	<	break;
860	<
962	>
963	>
964	>	if (update_arg( (void *)&(args_info->nbins_arg),
965	>	&(args_info->nbins_orig), &(args_info->nbins_given),
966	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
967	>	check_ambiguity, override, 0, 0,
968	>	"nbins", 'b',
969	>	additional_error))
970	>	goto failure;
971	>
972	>	break;
973		case 'x':       /* number of bins in x axis.  */
974	<	if (local_args_info.nbins_x_given)
975	<	{
976	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
977	<	goto failure;
978	<	}
979	<	if (args_info->nbins_x_given && ! override)
980	<	continue;
981	<	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);
974	>
975	>
976	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
977	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
978	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
979	>	check_ambiguity, override, 0, 0,
980	>	"nbins_x", 'x',
981	>	additional_error))
982		goto failure;
983	<	}
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);
983	>
984		break;
880	–
985		case 'y':       /* number of bins in y axis.  */
986	<	if (local_args_info.nbins_y_given)
987	<	{
988	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
989	<	goto failure;
990	<	}
991	<	if (args_info->nbins_y_given && ! override)
992	<	continue;
993	<	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);
986	>
987	>
988	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
989	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
990	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
991	>	check_ambiguity, override, 0, 0,
992	>	"nbins_y", 'y',
993	>	additional_error))
994		goto failure;
995	<	}
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);
995	>
996		break;
900	–
997		case 'a':       /* number of bins for cos(angle).  */
998	<	if (local_args_info.nanglebins_given)
999	<	{
1000	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001	<	goto failure;
1002	<	}
1003	<	if (args_info->nanglebins_given && ! override)
1004	<	continue;
1005	<	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);
998	>
999	>
1000	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1001	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1002	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1003	>	check_ambiguity, override, 0, 0,
1004	>	"nanglebins", 'a',
1005	>	additional_error))
1006		goto failure;
1007	<	}
916	<	if (args_info->nanglebins_orig)
917	<	free (args_info->nanglebins_orig); /* free previous string */
918	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
1007	>
1008		break;
920	–
1009		case 'c':       /* cutoff radius (rcut).  */
1010	<	if (local_args_info.rcut_given)
1011	<	{
1012	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1013	<	goto failure;
1014	<	}
1015	<	if (args_info->rcut_given && ! override)
1016	<	continue;
1017	<	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);
1010	>
1011	>
1012	>	if (update_arg( (void *)&(args_info->rcut_arg),
1013	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1014	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1015	>	check_ambiguity, override, 0, 0,
1016	>	"rcut", 'c',
1017	>	additional_error))
1018		goto failure;
1019	<	}
936	<	if (args_info->rcut_orig)
937	<	free (args_info->rcut_orig); /* free previous string */
938	<	args_info->rcut_orig = gengetopt_strdup (optarg);
1019	>
1020		break;
940	–
1021		case 'z':       /* Where to set the zero for the slab_density calculation.  */
1022	<	if (local_args_info.zoffset_given)
1023	<	{
1024	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1025	<	goto failure;
1026	<	}
1027	<	if (args_info->zoffset_given && ! override)
1028	<	continue;
1029	<	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);
1022	>
1023	>
1024	>	if (update_arg( (void *)&(args_info->zoffset_arg),
1025	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1026	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1027	>	check_ambiguity, override, 0, 0,
1028	>	"zoffset", 'z',
1029	>	additional_error))
1030		goto failure;
1031	<	}
956	<	if (args_info->zoffset_orig)
957	<	free (args_info->zoffset_orig); /* free previous string */
958	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
1031	>
1032		break;
960	–
1033		case 'g':       /* g(r).  */
1034	<	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;
1034	>
1035		if (args_info->staticProps_group_counter && override)
1036		reset_group_staticProps (args_info);
1037		args_info->staticProps_group_counter += 1;
1038	+
1039	+	if (update_arg( 0 ,
1040	+	0 , &(args_info->gofr_given),
1041	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1042	+	check_ambiguity, override, 0, 0,
1043	+	"gofr", 'g',
1044	+	additional_error))
1045	+	goto failure;
1046	+
1047		break;
1048	<
1049	<	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;
1048	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1049	>
1050		if (args_info->staticProps_group_counter && override)
1051		reset_group_staticProps (args_info);
1052		args_info->staticProps_group_counter += 1;
1053	+
1054	+	if (update_arg( 0 ,
1055	+	0 , &(args_info->p2_given),
1056	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1057	+	check_ambiguity, override, 0, 0,
1058	+	"p2", 'p',
1059	+	additional_error))
1060	+	goto failure;
1061	+
1062		break;
990	–
1063		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1064	<	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;
1064	>
1065		if (args_info->staticProps_group_counter && override)
1066		reset_group_staticProps (args_info);
1067		args_info->staticProps_group_counter += 1;
1068	+
1069	+	if (update_arg( 0 ,
1070	+	0 , &(args_info->scd_given),
1071	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1072	+	check_ambiguity, override, 0, 0,
1073	+	"scd", 's',
1074	+	additional_error))
1075	+	goto failure;
1076	+
1077		break;
1005	–
1078		case 'd':       /* density plot.  */
1079	<	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;
1079	>
1080		if (args_info->staticProps_group_counter && override)
1081		reset_group_staticProps (args_info);
1082		args_info->staticProps_group_counter += 1;
1083	+
1084	+	if (update_arg( 0 ,
1085	+	0 , &(args_info->density_given),
1086	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1087	+	check_ambiguity, override, 0, 0,
1088	+	"density", 'd',
1089	+	additional_error))
1090	+	goto failure;
1091	+
1092		break;
1093	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1094	+
1095	+	if (args_info->staticProps_group_counter && override)
1096	+	reset_group_staticProps (args_info);
1097	+	args_info->staticProps_group_counter += 1;
1098	+
1099	+	if (update_arg( 0 ,
1100	+	0 , &(args_info->tet_param_given),
1101	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1102	+	check_ambiguity, override, 0, 0,
1103	+	"tet_param", 'Q',
1104	+	additional_error))
1105	+	goto failure;
1106	+
1107	+	break;
1108
1021	–
1109		case 0: /* Long option with no short option */
1110	<	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1111	<	if (strcmp (long_options[option_index].name, "length") == 0)
1110	>	/* number of bins in z axis.  */
1111	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1112		{
1113	<	if (local_args_info.length_given)
1114	<	{
1115	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1116	<	goto failure;
1117	<	}
1118	<	if (args_info->length_given && ! override)
1119	<	continue;
1120	<	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);
1113	>
1114	>
1115	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1116	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1117	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1118	>	check_ambiguity, override, 0, 0,
1119	>	"nbins_z", '-',
1120	>	additional_error))
1121		goto failure;
1122	<	}
1040	<	if (args_info->length_orig)
1041	<	free (args_info->length_orig); /* free previous string */
1042	<	args_info->length_orig = gengetopt_strdup (optarg);
1122	>
1123		}
1124	+	/* slab width (dz).  */
1125	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1126	+	{
1127	+
1128	+
1129	+	if (update_arg( (void *)&(args_info->dz_arg),
1130	+	&(args_info->dz_orig), &(args_info->dz_given),
1131	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1132	+	check_ambiguity, override, 0, 0,
1133	+	"dz", '-',
1134	+	additional_error))
1135	+	goto failure;
1136	+
1137	+	}
1138	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1139	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1140	+	{
1141	+
1142	+
1143	+	if (update_arg( (void *)&(args_info->length_arg),
1144	+	&(args_info->length_orig), &(args_info->length_given),
1145	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1146	+	check_ambiguity, override, 0, 0,
1147	+	"length", '-',
1148	+	additional_error))
1149	+	goto failure;
1150	+
1151	+	}
1152	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1153	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1154	+	{
1155	+
1156	+
1157	+	if (update_arg( (void *)&(args_info->zlength_arg),
1158	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1159	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1160	+	check_ambiguity, override, 0, 0,
1161	+	"zlength", '-',
1162	+	additional_error))
1163	+	goto failure;
1164	+
1165	+	}
1166		/* select the first stuntdouble set.  */
1167		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1168		{
1169	<	if (local_args_info.sele1_given)
1170	<	{
1171	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1172	<	goto failure;
1173	<	}
1174	<	if (args_info->sele1_given && ! override)
1175	<	continue;
1176	<	local_args_info.sele1_given = 1;
1177	<	args_info->sele1_given = 1;
1178	<	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);
1169	>
1170	>
1171	>	if (update_arg( (void *)&(args_info->sele1_arg),
1172	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1173	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1174	>	check_ambiguity, override, 0, 0,
1175	>	"sele1", '-',
1176	>	additional_error))
1177	>	goto failure;
1178	>
1179		}
1180		/* select the second stuntdouble set.  */
1181		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1182		{
1183	<	if (local_args_info.sele2_given)
1184	<	{
1185	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1186	<	goto failure;
1187	<	}
1188	<	if (args_info->sele2_given && ! override)
1189	<	continue;
1190	<	local_args_info.sele2_given = 1;
1191	<	args_info->sele2_given = 1;
1192	<	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);
1183	>
1184	>
1185	>	if (update_arg( (void *)&(args_info->sele2_arg),
1186	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1187	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1188	>	check_ambiguity, override, 0, 0,
1189	>	"sele2", '-',
1190	>	additional_error))
1191	>	goto failure;
1192	>
1193		}
1194		/* select the third stuntdouble set.  */
1195		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1196		{
1197	<	if (local_args_info.sele3_given)
1198	<	{
1199	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1200	<	goto failure;
1201	<	}
1202	<	if (args_info->sele3_given && ! override)
1203	<	continue;
1204	<	local_args_info.sele3_given = 1;
1205	<	args_info->sele3_given = 1;
1206	<	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);
1197	>
1198	>
1199	>	if (update_arg( (void *)&(args_info->sele3_arg),
1200	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1201	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1202	>	check_ambiguity, override, 0, 0,
1203	>	"sele3", '-',
1204	>	additional_error))
1205	>	goto failure;
1206	>
1207		}
1208		/* select reference (use and only use with --gxyz).  */
1209		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1210		{
1211	<	if (local_args_info.refsele_given)
1212	<	{
1213	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1214	<	goto failure;
1215	<	}
1216	<	if (args_info->refsele_given && ! override)
1217	<	continue;
1218	<	local_args_info.refsele_given = 1;
1219	<	args_info->refsele_given = 1;
1220	<	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);
1211	>
1212	>
1213	>	if (update_arg( (void *)&(args_info->refsele_arg),
1214	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1215	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1216	>	check_ambiguity, override, 0, 0,
1217	>	"refsele", '-',
1218	>	additional_error))
1219	>	goto failure;
1220	>
1221		}
1222	+	/* select stunt doubles for center-of-mass reference point.  */
1223	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1224	+	{
1225	+
1226	+
1227	+	if (update_arg( (void *)&(args_info->comsele_arg),
1228	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1229	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1230	+	check_ambiguity, override, 0, 0,
1231	+	"comsele", '-',
1232	+	additional_error))
1233	+	goto failure;
1234	+
1235	+	}
1236	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1237	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1238	+	{
1239	+
1240	+
1241	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1242	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1243	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1244	+	check_ambiguity, override, 0, 0,
1245	+	"seleoffset", '-',
1246	+	additional_error))
1247	+	goto failure;
1248	+
1249	+	}
1250		/* molecule name.  */
1251		else if (strcmp (long_options[option_index].name, "molname") == 0)
1252		{
1253	<	if (local_args_info.molname_given)
1254	<	{
1255	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1256	<	goto failure;
1257	<	}
1258	<	if (args_info->molname_given && ! override)
1259	<	continue;
1260	<	local_args_info.molname_given = 1;
1261	<	args_info->molname_given = 1;
1262	<	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);
1253	>
1254	>
1255	>	if (update_arg( (void *)&(args_info->molname_arg),
1256	>	&(args_info->molname_orig), &(args_info->molname_given),
1257	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1258	>	check_ambiguity, override, 0, 0,
1259	>	"molname", '-',
1260	>	additional_error))
1261	>	goto failure;
1262	>
1263		}
1264		/* begin internal index.  */
1265		else if (strcmp (long_options[option_index].name, "begin") == 0)
1266		{
1267	<	if (local_args_info.begin_given)
1268	<	{
1269	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1270	<	goto failure;
1271	<	}
1272	<	if (args_info->begin_given && ! override)
1273	<	continue;
1274	<	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);
1267	>
1268	>
1269	>	if (update_arg( (void *)&(args_info->begin_arg),
1270	>	&(args_info->begin_orig), &(args_info->begin_given),
1271	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1272	>	check_ambiguity, override, 0, 0,
1273	>	"begin", '-',
1274	>	additional_error))
1275		goto failure;
1276	<	}
1156	<	if (args_info->begin_orig)
1157	<	free (args_info->begin_orig); /* free previous string */
1158	<	args_info->begin_orig = gengetopt_strdup (optarg);
1276	>
1277		}
1278		/* end internal index.  */
1279		else if (strcmp (long_options[option_index].name, "end") == 0)
1280		{
1281	<	if (local_args_info.end_given)
1282	<	{
1283	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1284	<	goto failure;
1285	<	}
1286	<	if (args_info->end_given && ! override)
1287	<	continue;
1288	<	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);
1281	>
1282	>
1283	>	if (update_arg( (void *)&(args_info->end_arg),
1284	>	&(args_info->end_orig), &(args_info->end_given),
1285	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1286	>	check_ambiguity, override, 0, 0,
1287	>	"end", '-',
1288	>	additional_error))
1289		goto failure;
1290	<	}
1177	<	if (args_info->end_orig)
1178	<	free (args_info->end_orig); /* free previous string */
1179	<	args_info->end_orig = gengetopt_strdup (optarg);
1290	>
1291		}
1292		/* nanoparticle radius.  */
1293		else if (strcmp (long_options[option_index].name, "radius") == 0)
1294		{
1295	<	if (local_args_info.radius_given)
1296	<	{
1297	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1298	<	goto failure;
1299	<	}
1300	<	if (args_info->radius_given && ! override)
1301	<	continue;
1302	<	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);
1295	>
1296	>
1297	>	if (update_arg( (void *)&(args_info->radius_arg),
1298	>	&(args_info->radius_orig), &(args_info->radius_given),
1299	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1300	>	check_ambiguity, override, 0, 0,
1301	>	"radius", '-',
1302	>	additional_error))
1303		goto failure;
1304	<	}
1198	<	if (args_info->radius_orig)
1199	<	free (args_info->radius_orig); /* free previous string */
1200	<	args_info->radius_orig = gengetopt_strdup (optarg);
1304	>
1305		}
1306		/* bond order parameter (--rcut must be specified).  */
1307		else if (strcmp (long_options[option_index].name, "bo") == 0)
1308		{
1309	<	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;
1309	>
1310		if (args_info->staticProps_group_counter && override)
1311		reset_group_staticProps (args_info);
1312		args_info->staticProps_group_counter += 1;
1313	<	break;
1313	>
1314	>	if (update_arg( 0 ,
1315	>	0 , &(args_info->bo_given),
1316	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1317	>	check_ambiguity, override, 0, 0,
1318	>	"bo", '-',
1319	>	additional_error))
1320	>	goto failure;
1321	>
1322		}
1323		/* bond order parameter as a function of radius (--rcut must be specified).  */
1324		else if (strcmp (long_options[option_index].name, "bor") == 0)
1325		{
1326	<	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;
1326	>
1327		if (args_info->staticProps_group_counter && override)
1328		reset_group_staticProps (args_info);
1329		args_info->staticProps_group_counter += 1;
1330	<	break;
1330	>
1331	>	if (update_arg( 0 ,
1332	>	0 , &(args_info->bor_given),
1333	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1334	>	check_ambiguity, override, 0, 0,
1335	>	"bor", '-',
1336	>	additional_error))
1337	>	goto failure;
1338	>
1339		}
1340		/* N(theta) bond angle density within (--rcut must be specified).  */
1341		else if (strcmp (long_options[option_index].name, "bad") == 0)
1342		{
1343	<	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;
1343	>
1344		if (args_info->staticProps_group_counter && override)
1345		reset_group_staticProps (args_info);
1346		args_info->staticProps_group_counter += 1;
1347	<	break;
1347	>
1348	>	if (update_arg( 0 ,
1349	>	0 , &(args_info->bad_given),
1350	>	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1351	>	check_ambiguity, override, 0, 0,
1352	>	"bad", '-',
1353	>	additional_error))
1354	>	goto failure;
1355	>
1356		}
1357	+	/* count of molecules matching selection criteria (and associated statistics).  */
1358	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1359	+	{
1360	+
1361	+	if (args_info->staticProps_group_counter && override)
1362	+	reset_group_staticProps (args_info);
1363	+	args_info->staticProps_group_counter += 1;
1364	+
1365	+	if (update_arg( 0 ,
1366	+	0 , &(args_info->count_given),
1367	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1368	+	check_ambiguity, override, 0, 0,
1369	+	"count", '-',
1370	+	additional_error))
1371	+	goto failure;
1372	+
1373	+	}
1374		/* g(z).  */
1375		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1376		{
1377	<	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;
1377	>
1378		if (args_info->staticProps_group_counter && override)
1379		reset_group_staticProps (args_info);
1380		args_info->staticProps_group_counter += 1;
1381	<	break;
1381	>
1382	>	if (update_arg( 0 ,
1383	>	0 , &(args_info->gofz_given),
1384	>	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1385	>	check_ambiguity, override, 0, 0,
1386	>	"gofz", '-',
1387	>	additional_error))
1388	>	goto failure;
1389	>
1390		}
1391		/* g(r, cos(theta)).  */
1392		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1393		{
1394	<	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;
1394	>
1395		if (args_info->staticProps_group_counter && override)
1396		reset_group_staticProps (args_info);
1397		args_info->staticProps_group_counter += 1;
1398	<	break;
1398	>
1399	>	if (update_arg( 0 ,
1400	>	0 , &(args_info->r_theta_given),
1401	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1402	>	check_ambiguity, override, 0, 0,
1403	>	"r_theta", '-',
1404	>	additional_error))
1405	>	goto failure;
1406	>
1407		}
1408		/* g(r, cos(omega)).  */
1409		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1410		{
1411	<	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;
1411	>
1412		if (args_info->staticProps_group_counter && override)
1413		reset_group_staticProps (args_info);
1414		args_info->staticProps_group_counter += 1;
1415	<	break;
1415	>
1416	>	if (update_arg( 0 ,
1417	>	0 , &(args_info->r_omega_given),
1418	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1419	>	check_ambiguity, override, 0, 0,
1420	>	"r_omega", '-',
1421	>	additional_error))
1422	>	goto failure;
1423	>
1424		}
1425	+	/* g(r, z).  */
1426	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1427	+	{
1428	+
1429	+	if (args_info->staticProps_group_counter && override)
1430	+	reset_group_staticProps (args_info);
1431	+	args_info->staticProps_group_counter += 1;
1432	+
1433	+	if (update_arg( 0 ,
1434	+	0 , &(args_info->r_z_given),
1435	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1436	+	check_ambiguity, override, 0, 0,
1437	+	"r_z", '-',
1438	+	additional_error))
1439	+	goto failure;
1440	+
1441	+	}
1442		/* g(cos(theta), cos(omega)).  */
1443		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1444		{
1445	<	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;
1445	>
1446		if (args_info->staticProps_group_counter && override)
1447		reset_group_staticProps (args_info);
1448		args_info->staticProps_group_counter += 1;
1449	<	break;
1449	>
1450	>	if (update_arg( 0 ,
1451	>	0 , &(args_info->theta_omega_given),
1452	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1453	>	check_ambiguity, override, 0, 0,
1454	>	"theta_omega", '-',
1455	>	additional_error))
1456	>	goto failure;
1457	>
1458		}
1459		/* g(x, y, z).  */
1460		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1461		{
1462	<	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;
1462	>
1463		if (args_info->staticProps_group_counter && override)
1464		reset_group_staticProps (args_info);
1465		args_info->staticProps_group_counter += 1;
1466	<	break;
1466	>
1467	>	if (update_arg( 0 ,
1468	>	0 , &(args_info->gxyz_given),
1469	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1470	>	check_ambiguity, override, 0, 0,
1471	>	"gxyz", '-',
1472	>	additional_error))
1473	>	goto failure;
1474	>
1475		}
1476	+	/* 2D g(r) (Slab width --dz must be specified).  */
1477	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1478	+	{
1479	+
1480	+	if (args_info->staticProps_group_counter && override)
1481	+	reset_group_staticProps (args_info);
1482	+	args_info->staticProps_group_counter += 1;
1483	+
1484	+	if (update_arg( 0 ,
1485	+	0 , &(args_info->twodgofr_given),
1486	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1487	+	check_ambiguity, override, 0, 0,
1488	+	"twodgofr", '-',
1489	+	additional_error))
1490	+	goto failure;
1491	+
1492	+	}
1493		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1494		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1495		{
1496	<	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;
1496	>
1497		if (args_info->staticProps_group_counter && override)
1498		reset_group_staticProps (args_info);
1499		args_info->staticProps_group_counter += 1;
1500	<	break;
1500	>
1501	>	if (update_arg( 0 ,
1502	>	0 , &(args_info->rp2_given),
1503	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1504	>	check_ambiguity, override, 0, 0,
1505	>	"rp2", '-',
1506	>	additional_error))
1507	>	goto failure;
1508	>
1509		}
1510		/* slab density.  */
1511		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1512		{
1513	<	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;
1513	>
1514		if (args_info->staticProps_group_counter && override)
1515		reset_group_staticProps (args_info);
1516		args_info->staticProps_group_counter += 1;
1517	<	break;
1517	>
1518	>	if (update_arg( 0 ,
1519	>	0 , &(args_info->slab_density_given),
1520	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1521	>	check_ambiguity, override, 0, 0,
1522	>	"slab_density", '-',
1523	>	additional_error))
1524	>	goto failure;
1525	>
1526		}
1527	+	/* p(cos(theta)).  */
1528	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1529	+	{
1530	+
1531	+	if (args_info->staticProps_group_counter && override)
1532	+	reset_group_staticProps (args_info);
1533	+	args_info->staticProps_group_counter += 1;
1534	+
1535	+	if (update_arg( 0 ,
1536	+	0 , &(args_info->p_angle_given),
1537	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1538	+	check_ambiguity, override, 0, 0,
1539	+	"p_angle", '-',
1540	+	additional_error))
1541	+	goto failure;
1542	+
1543	+	}
1544		/* hxy.  */
1545		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1546		{
1547	<	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;
1547	>
1548		if (args_info->staticProps_group_counter && override)
1549		reset_group_staticProps (args_info);
1550		args_info->staticProps_group_counter += 1;
1551	<	break;
1551	>
1552	>	if (update_arg( 0 ,
1553	>	0 , &(args_info->hxy_given),
1554	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1555	>	check_ambiguity, override, 0, 0,
1556	>	"hxy", '-',
1557	>	additional_error))
1558	>	goto failure;
1559	>
1560		}
1561		/* rho of R.  */
1562		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1563		{
1564	<	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;
1564	>
1565		if (args_info->staticProps_group_counter && override)
1566		reset_group_staticProps (args_info);
1567		args_info->staticProps_group_counter += 1;
1568	<	break;
1568	>
1569	>	if (update_arg( 0 ,
1570	>	0 , &(args_info->rho_r_given),
1571	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1572	>	check_ambiguity, override, 0, 0,
1573	>	"rho_r", '-',
1574	>	additional_error))
1575	>	goto failure;
1576	>
1577		}
1578	+	/* angle of R.  */
1579	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1580	+	{
1581	+
1582	+	if (args_info->staticProps_group_counter && override)
1583	+	reset_group_staticProps (args_info);
1584	+	args_info->staticProps_group_counter += 1;
1585	+
1586	+	if (update_arg( 0 ,
1587	+	0 , &(args_info->angle_r_given),
1588	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1589	+	check_ambiguity, override, 0, 0,
1590	+	"angle_r", '-',
1591	+	additional_error))
1592	+	goto failure;
1593	+
1594	+	}
1595		/* hull volume of nanoparticle.  */
1596		else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1597		{
1598	<	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;
1598	>
1599		if (args_info->staticProps_group_counter && override)
1600		reset_group_staticProps (args_info);
1601		args_info->staticProps_group_counter += 1;
1602	<	break;
1602	>
1603	>	if (update_arg( 0 ,
1604	>	0 , &(args_info->hullvol_given),
1605	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1606	>	check_ambiguity, override, 0, 0,
1607	>	"hullvol", '-',
1608	>	additional_error))
1609	>	goto failure;
1610	>
1611		}
1612	+	/* length of nanorod.  */
1613	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1614	+	{
1615
1616	+	if (args_info->staticProps_group_counter && override)
1617	+	reset_group_staticProps (args_info);
1618	+	args_info->staticProps_group_counter += 1;
1619	+
1620	+	if (update_arg( 0 ,
1621	+	0 , &(args_info->rodlength_given),
1622	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1623	+	check_ambiguity, override, 0, 0,
1624	+	"rodlength", '-',
1625	+	additional_error))
1626	+	goto failure;
1627	+
1628	+	}
1629	+	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1630	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1631	+	{
1632	+
1633	+	if (args_info->staticProps_group_counter && override)
1634	+	reset_group_staticProps (args_info);
1635	+	args_info->staticProps_group_counter += 1;
1636	+
1637	+	if (update_arg( 0 ,
1638	+	0 , &(args_info->tet_param_z_given),
1639	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1640	+	check_ambiguity, override, 0, 0,
1641	+	"tet_param_z", '-',
1642	+	additional_error))
1643	+	goto failure;
1644	+
1645	+	}
1646	+	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1647	+	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1648	+	{
1649	+
1650	+	if (args_info->staticProps_group_counter && override)
1651	+	reset_group_staticProps (args_info);
1652	+	args_info->staticProps_group_counter += 1;
1653	+
1654	+	if (update_arg( 0 ,
1655	+	0 , &(args_info->rnemdz_given),
1656	+	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1657	+	check_ambiguity, override, 0, 0,
1658	+	"rnemdz", '-',
1659	+	additional_error))
1660	+	goto failure;
1661	+
1662	+	}
1663	+	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1664	+	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1665	+	{
1666	+
1667	+	if (args_info->staticProps_group_counter && override)
1668	+	reset_group_staticProps (args_info);
1669	+	args_info->staticProps_group_counter += 1;
1670	+
1671	+	if (update_arg( 0 ,
1672	+	0 , &(args_info->rnemdr_given),
1673	+	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1674	+	check_ambiguity, override, 0, 0,
1675	+	"rnemdr", '-',
1676	+	additional_error))
1677	+	goto failure;
1678	+
1679	+	}
1680	+
1681		break;
1682		case '?':       /* Invalid option.  */
1683		/* `getopt_long' already printed an error message.  */
#	Line 1434 | Line 1691 | cmdline_parser_internal (int argc, char * const *argv,
1691
1692		if (args_info->staticProps_group_counter > 1)
1693		{
1694	<	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 : ""));
1694	>	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 : ""));
1695		error = 1;
1696		}
1697

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 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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

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