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root/OpenMD/branches/development/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.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1865 by gezelter, Wed Apr 17 18:24:08 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	+	#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 (Qk)",
85	+	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
86	+	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
87	+	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
88		0
89		};
90
91	+	typedef enum {ARG_NO
92	+	, ARG_STRING
93	+	, ARG_INT
94	+	, ARG_DOUBLE
95	+	} cmdline_parser_arg_type;
96	+
97		static
98		void clear_given (struct gengetopt_args_info *args_info);
99		static
100		void clear_args (struct gengetopt_args_info *args_info);
101
102		static int
103	<	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);
103	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
104	>	struct cmdline_parser_params *params, const char *additional_error);
105
106		static int
107		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 94 | Line 120 | void clear_given (struct gengetopt_args_info *args_inf
120		args_info->nbins_given = 0 ;
121		args_info->nbins_x_given = 0 ;
122		args_info->nbins_y_given = 0 ;
123	+	args_info->nbins_z_given = 0 ;
124		args_info->nanglebins_given = 0 ;
98	–	args_info->length_given = 0 ;
125		args_info->rcut_given = 0 ;
126	+	args_info->dz_given = 0 ;
127	+	args_info->length_given = 0 ;
128	+	args_info->zlength_given = 0 ;
129		args_info->zoffset_given = 0 ;
130		args_info->sele1_given = 0 ;
131		args_info->sele2_given = 0 ;
132		args_info->sele3_given = 0 ;
133		args_info->refsele_given = 0 ;
134	+	args_info->comsele_given = 0 ;
135	+	args_info->seleoffset_given = 0 ;
136		args_info->molname_given = 0 ;
137		args_info->begin_given = 0 ;
138		args_info->end_given = 0 ;
#	Line 109 | Line 140 | void clear_given (struct gengetopt_args_info *args_inf
140		args_info->bo_given = 0 ;
141		args_info->bor_given = 0 ;
142		args_info->bad_given = 0 ;
143	+	args_info->count_given = 0 ;
144		args_info->gofr_given = 0 ;
145		args_info->gofz_given = 0 ;
146		args_info->r_theta_given = 0 ;
147		args_info->r_omega_given = 0 ;
148	+	args_info->r_z_given = 0 ;
149		args_info->theta_omega_given = 0 ;
150		args_info->gxyz_given = 0 ;
151	+	args_info->twodgofr_given = 0 ;
152		args_info->p2_given = 0 ;
153		args_info->rp2_given = 0 ;
154		args_info->scd_given = 0 ;
155		args_info->density_given = 0 ;
156		args_info->slab_density_given = 0 ;
157	+	args_info->p_angle_given = 0 ;
158		args_info->hxy_given = 0 ;
159		args_info->rho_r_given = 0 ;
160	+	args_info->angle_r_given = 0 ;
161		args_info->hullvol_given = 0 ;
162	+	args_info->rodlength_given = 0 ;
163	+	args_info->tet_param_given = 0 ;
164	+	args_info->tet_param_z_given = 0 ;
165	+	args_info->rnemdz_given = 0 ;
166	+	args_info->rnemdr_given = 0 ;
167		args_info->staticProps_group_counter = 0 ;
168		}
169
170		static
171		void clear_args (struct gengetopt_args_info *args_info)
172		{
173	+	FIX_UNUSED (args_info);
174		args_info->input_arg = NULL;
175		args_info->input_orig = NULL;
176		args_info->output_arg = NULL;
#	Line 141 | Line 183 | void clear_args (struct gengetopt_args_info *args_info
183		args_info->nbins_x_orig = NULL;
184		args_info->nbins_y_arg = 100;
185		args_info->nbins_y_orig = NULL;
186	+	args_info->nbins_z_arg = 100;
187	+	args_info->nbins_z_orig = NULL;
188		args_info->nanglebins_arg = 50;
189		args_info->nanglebins_orig = NULL;
146	–	args_info->length_orig = NULL;
190		args_info->rcut_orig = NULL;
191	+	args_info->dz_orig = NULL;
192	+	args_info->length_orig = NULL;
193	+	args_info->zlength_orig = NULL;
194		args_info->zoffset_arg = 0;
195		args_info->zoffset_orig = NULL;
196		args_info->sele1_arg = NULL;
#	Line 155 | Line 201 | void clear_args (struct gengetopt_args_info *args_info
201		args_info->sele3_orig = NULL;
202		args_info->refsele_arg = NULL;
203		args_info->refsele_orig = NULL;
204	+	args_info->comsele_arg = NULL;
205	+	args_info->comsele_orig = NULL;
206	+	args_info->seleoffset_orig = NULL;
207		args_info->molname_arg = NULL;
208		args_info->molname_orig = NULL;
209		args_info->begin_orig = NULL;
#	Line 166 | Line 215 | void init_args_info(struct gengetopt_args_info *args_i
215		static
216		void init_args_info(struct gengetopt_args_info *args_info)
217		{
218	+
219	+
220		args_info->help_help = gengetopt_args_info_help[0] ;
221		args_info->version_help = gengetopt_args_info_help[1] ;
222		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 174 | Line 225 | void init_args_info(struct gengetopt_args_info *args_i
225		args_info->nbins_help = gengetopt_args_info_help[5] ;
226		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
227		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
228	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
229	<	args_info->length_help = gengetopt_args_info_help[9] ;
228	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
229	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
230		args_info->rcut_help = gengetopt_args_info_help[10] ;
231	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
232	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
233	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
234	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
235	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
236	<	args_info->molname_help = gengetopt_args_info_help[16] ;
237	<	args_info->begin_help = gengetopt_args_info_help[17] ;
238	<	args_info->end_help = gengetopt_args_info_help[18] ;
239	<	args_info->radius_help = gengetopt_args_info_help[19] ;
240	<	args_info->bo_help = gengetopt_args_info_help[20] ;
241	<	args_info->bor_help = gengetopt_args_info_help[21] ;
242	<	args_info->bad_help = gengetopt_args_info_help[22] ;
243	<	args_info->gofr_help = gengetopt_args_info_help[23] ;
244	<	args_info->gofz_help = gengetopt_args_info_help[24] ;
245	<	args_info->r_theta_help = gengetopt_args_info_help[25] ;
246	<	args_info->r_omega_help = gengetopt_args_info_help[26] ;
247	<	args_info->theta_omega_help = gengetopt_args_info_help[27] ;
248	<	args_info->gxyz_help = gengetopt_args_info_help[28] ;
249	<	args_info->p2_help = gengetopt_args_info_help[29] ;
250	<	args_info->rp2_help = gengetopt_args_info_help[30] ;
251	<	args_info->scd_help = gengetopt_args_info_help[31] ;
252	<	args_info->density_help = gengetopt_args_info_help[32] ;
253	<	args_info->slab_density_help = gengetopt_args_info_help[33] ;
254	<	args_info->hxy_help = gengetopt_args_info_help[34] ;
255	<	args_info->rho_r_help = gengetopt_args_info_help[35] ;
256	<	args_info->hullvol_help = gengetopt_args_info_help[36] ;
231	>	args_info->dz_help = gengetopt_args_info_help[11] ;
232	>	args_info->length_help = gengetopt_args_info_help[12] ;
233	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
234	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
235	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
236	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
237	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
238	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
239	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
240	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
241	>	args_info->molname_help = gengetopt_args_info_help[21] ;
242	>	args_info->begin_help = gengetopt_args_info_help[22] ;
243	>	args_info->end_help = gengetopt_args_info_help[23] ;
244	>	args_info->radius_help = gengetopt_args_info_help[24] ;
245	>	args_info->bo_help = gengetopt_args_info_help[26] ;
246	>	args_info->bor_help = gengetopt_args_info_help[27] ;
247	>	args_info->bad_help = gengetopt_args_info_help[28] ;
248	>	args_info->count_help = gengetopt_args_info_help[29] ;
249	>	args_info->gofr_help = gengetopt_args_info_help[30] ;
250	>	args_info->gofz_help = gengetopt_args_info_help[31] ;
251	>	args_info->r_theta_help = gengetopt_args_info_help[32] ;
252	>	args_info->r_omega_help = gengetopt_args_info_help[33] ;
253	>	args_info->r_z_help = gengetopt_args_info_help[34] ;
254	>	args_info->theta_omega_help = gengetopt_args_info_help[35] ;
255	>	args_info->gxyz_help = gengetopt_args_info_help[36] ;
256	>	args_info->twodgofr_help = gengetopt_args_info_help[37] ;
257	>	args_info->p2_help = gengetopt_args_info_help[38] ;
258	>	args_info->rp2_help = gengetopt_args_info_help[39] ;
259	>	args_info->scd_help = gengetopt_args_info_help[40] ;
260	>	args_info->density_help = gengetopt_args_info_help[41] ;
261	>	args_info->slab_density_help = gengetopt_args_info_help[42] ;
262	>	args_info->p_angle_help = gengetopt_args_info_help[43] ;
263	>	args_info->hxy_help = gengetopt_args_info_help[44] ;
264	>	args_info->rho_r_help = gengetopt_args_info_help[45] ;
265	>	args_info->angle_r_help = gengetopt_args_info_help[46] ;
266	>	args_info->hullvol_help = gengetopt_args_info_help[47] ;
267	>	args_info->rodlength_help = gengetopt_args_info_help[48] ;
268	>	args_info->tet_param_help = gengetopt_args_info_help[49] ;
269	>	args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
270	>	args_info->rnemdz_help = gengetopt_args_info_help[51] ;
271	>	args_info->rnemdr_help = gengetopt_args_info_help[52] ;
272
273		}
274
275		void
276		cmdline_parser_print_version (void)
277		{
278	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
278	>	printf ("%s %s\n",
279	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
280	>	CMDLINE_PARSER_VERSION);
281		}
282
283	<	void
216	<	cmdline_parser_print_help (void)
217	<	{
218	<	int i = 0;
283	>	static void print_help_common(void) {
284		cmdline_parser_print_version ();
285
286		if (strlen(gengetopt_args_info_purpose) > 0)
287		printf("\n%s\n", gengetopt_args_info_purpose);
288
289	<	printf("\n%s\n\n", gengetopt_args_info_usage);
289	>	if (strlen(gengetopt_args_info_usage) > 0)
290	>	printf("\n%s\n", gengetopt_args_info_usage);
291
292	+	printf("\n");
293	+
294		if (strlen(gengetopt_args_info_description) > 0)
295	<	printf("%s\n", gengetopt_args_info_description);
295	>	printf("%s\n\n", gengetopt_args_info_description);
296	>	}
297
298	+	void
299	+	cmdline_parser_print_help (void)
300	+	{
301	+	int i = 0;
302	+	print_help_common();
303		while (gengetopt_args_info_help[i])
304		printf("%s\n", gengetopt_args_info_help[i++]);
305		}
#	Line 237 | Line 311 | cmdline_parser_init (struct gengetopt_args_info *args_
311		clear_args (args_info);
312		init_args_info (args_info);
313
314	<	args_info->inputs = NULL;
314	>	args_info->inputs = 0;
315		args_info->inputs_num = 0;
316		}
317
318	+	void
319	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
320	+	{
321	+	if (params)
322	+	{
323	+	params->override = 0;
324	+	params->initialize = 1;
325	+	params->check_required = 1;
326	+	params->check_ambiguity = 0;
327	+	params->print_errors = 1;
328	+	}
329	+	}
330	+
331	+	struct cmdline_parser_params *
332	+	cmdline_parser_params_create(void)
333	+	{
334	+	struct cmdline_parser_params *params =
335	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
336	+	cmdline_parser_params_init(params);
337	+	return params;
338	+	}
339	+
340		static void
341	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
341	>	free_string_field (char **s)
342		{
343	<
248	<	unsigned int i;
249	<	if (args_info->input_arg)
343	>	if (*s)
344		{
345	<	free (args_info->input_arg); /* free previous argument */
346	<	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;
345	>	free (*s);
346	>	*s = 0;
347		}
348	<	if (args_info->sele1_orig)
349	<	{
350	<	free (args_info->sele1_orig); /* free previous argument */
351	<	args_info->sele1_orig = 0;
352	<	}
353	<	if (args_info->sele2_arg)
354	<	{
355	<	free (args_info->sele2_arg); /* free previous argument */
356	<	args_info->sele2_arg = 0;
357	<	}
358	<	if (args_info->sele2_orig)
359	<	{
360	<	free (args_info->sele2_orig); /* free previous argument */
361	<	args_info->sele2_orig = 0;
362	<	}
363	<	if (args_info->sele3_arg)
364	<	{
365	<	free (args_info->sele3_arg); /* free previous argument */
366	<	args_info->sele3_arg = 0;
367	<	}
368	<	if (args_info->sele3_orig)
369	<	{
370	<	free (args_info->sele3_orig); /* free previous argument */
371	<	args_info->sele3_orig = 0;
372	<	}
373	<	if (args_info->refsele_arg)
374	<	{
375	<	free (args_info->refsele_arg); /* free previous argument */
376	<	args_info->refsele_arg = 0;
377	<	}
378	<	if (args_info->refsele_orig)
379	<	{
380	<	free (args_info->refsele_orig); /* free previous argument */
381	<	args_info->refsele_orig = 0;
382	<	}
383	<	if (args_info->molname_arg)
384	<	{
385	<	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	<	}
348	>	}
349	>
350	>
351	>	static void
352	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
353	>	{
354	>	unsigned int i;
355	>	free_string_field (&(args_info->input_arg));
356	>	free_string_field (&(args_info->input_orig));
357	>	free_string_field (&(args_info->output_arg));
358	>	free_string_field (&(args_info->output_orig));
359	>	free_string_field (&(args_info->step_orig));
360	>	free_string_field (&(args_info->nbins_orig));
361	>	free_string_field (&(args_info->nbins_x_orig));
362	>	free_string_field (&(args_info->nbins_y_orig));
363	>	free_string_field (&(args_info->nbins_z_orig));
364	>	free_string_field (&(args_info->nanglebins_orig));
365	>	free_string_field (&(args_info->rcut_orig));
366	>	free_string_field (&(args_info->dz_orig));
367	>	free_string_field (&(args_info->length_orig));
368	>	free_string_field (&(args_info->zlength_orig));
369	>	free_string_field (&(args_info->zoffset_orig));
370	>	free_string_field (&(args_info->sele1_arg));
371	>	free_string_field (&(args_info->sele1_orig));
372	>	free_string_field (&(args_info->sele2_arg));
373	>	free_string_field (&(args_info->sele2_orig));
374	>	free_string_field (&(args_info->sele3_arg));
375	>	free_string_field (&(args_info->sele3_orig));
376	>	free_string_field (&(args_info->refsele_arg));
377	>	free_string_field (&(args_info->refsele_orig));
378	>	free_string_field (&(args_info->comsele_arg));
379	>	free_string_field (&(args_info->comsele_orig));
380	>	free_string_field (&(args_info->seleoffset_orig));
381	>	free_string_field (&(args_info->molname_arg));
382	>	free_string_field (&(args_info->molname_orig));
383	>	free_string_field (&(args_info->begin_orig));
384	>	free_string_field (&(args_info->end_orig));
385	>	free_string_field (&(args_info->radius_orig));
386
387	+
388		for (i = 0; i < args_info->inputs_num; ++i)
389		free (args_info->inputs [i]);
390	<
390	>
391		if (args_info->inputs_num)
392		free (args_info->inputs);
393	<
393	>
394		clear_given (args_info);
395		}
396
397	+
398	+	static void
399	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
400	+	{
401	+	FIX_UNUSED (values);
402	+	if (arg) {
403	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
404	+	} else {
405	+	fprintf(outfile, "%s\n", opt);
406	+	}
407	+	}
408	+
409	+
410		int
411	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
412	+	{
413	+	int i = 0;
414	+
415	+	if (!outfile)
416	+	{
417	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
418	+	return EXIT_FAILURE;
419	+	}
420	+
421	+	if (args_info->help_given)
422	+	write_into_file(outfile, "help", 0, 0 );
423	+	if (args_info->version_given)
424	+	write_into_file(outfile, "version", 0, 0 );
425	+	if (args_info->input_given)
426	+	write_into_file(outfile, "input", args_info->input_orig, 0);
427	+	if (args_info->output_given)
428	+	write_into_file(outfile, "output", args_info->output_orig, 0);
429	+	if (args_info->step_given)
430	+	write_into_file(outfile, "step", args_info->step_orig, 0);
431	+	if (args_info->nbins_given)
432	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
433	+	if (args_info->nbins_x_given)
434	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
435	+	if (args_info->nbins_y_given)
436	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
437	+	if (args_info->nbins_z_given)
438	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
439	+	if (args_info->nanglebins_given)
440	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
441	+	if (args_info->rcut_given)
442	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
443	+	if (args_info->dz_given)
444	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
445	+	if (args_info->length_given)
446	+	write_into_file(outfile, "length", args_info->length_orig, 0);
447	+	if (args_info->zlength_given)
448	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
449	+	if (args_info->zoffset_given)
450	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
451	+	if (args_info->sele1_given)
452	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
453	+	if (args_info->sele2_given)
454	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
455	+	if (args_info->sele3_given)
456	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
457	+	if (args_info->refsele_given)
458	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
459	+	if (args_info->comsele_given)
460	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
461	+	if (args_info->seleoffset_given)
462	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
463	+	if (args_info->molname_given)
464	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
465	+	if (args_info->begin_given)
466	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
467	+	if (args_info->end_given)
468	+	write_into_file(outfile, "end", args_info->end_orig, 0);
469	+	if (args_info->radius_given)
470	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
471	+	if (args_info->bo_given)
472	+	write_into_file(outfile, "bo", 0, 0 );
473	+	if (args_info->bor_given)
474	+	write_into_file(outfile, "bor", 0, 0 );
475	+	if (args_info->bad_given)
476	+	write_into_file(outfile, "bad", 0, 0 );
477	+	if (args_info->count_given)
478	+	write_into_file(outfile, "count", 0, 0 );
479	+	if (args_info->gofr_given)
480	+	write_into_file(outfile, "gofr", 0, 0 );
481	+	if (args_info->gofz_given)
482	+	write_into_file(outfile, "gofz", 0, 0 );
483	+	if (args_info->r_theta_given)
484	+	write_into_file(outfile, "r_theta", 0, 0 );
485	+	if (args_info->r_omega_given)
486	+	write_into_file(outfile, "r_omega", 0, 0 );
487	+	if (args_info->r_z_given)
488	+	write_into_file(outfile, "r_z", 0, 0 );
489	+	if (args_info->theta_omega_given)
490	+	write_into_file(outfile, "theta_omega", 0, 0 );
491	+	if (args_info->gxyz_given)
492	+	write_into_file(outfile, "gxyz", 0, 0 );
493	+	if (args_info->twodgofr_given)
494	+	write_into_file(outfile, "twodgofr", 0, 0 );
495	+	if (args_info->p2_given)
496	+	write_into_file(outfile, "p2", 0, 0 );
497	+	if (args_info->rp2_given)
498	+	write_into_file(outfile, "rp2", 0, 0 );
499	+	if (args_info->scd_given)
500	+	write_into_file(outfile, "scd", 0, 0 );
501	+	if (args_info->density_given)
502	+	write_into_file(outfile, "density", 0, 0 );
503	+	if (args_info->slab_density_given)
504	+	write_into_file(outfile, "slab_density", 0, 0 );
505	+	if (args_info->p_angle_given)
506	+	write_into_file(outfile, "p_angle", 0, 0 );
507	+	if (args_info->hxy_given)
508	+	write_into_file(outfile, "hxy", 0, 0 );
509	+	if (args_info->rho_r_given)
510	+	write_into_file(outfile, "rho_r", 0, 0 );
511	+	if (args_info->angle_r_given)
512	+	write_into_file(outfile, "angle_r", 0, 0 );
513	+	if (args_info->hullvol_given)
514	+	write_into_file(outfile, "hullvol", 0, 0 );
515	+	if (args_info->rodlength_given)
516	+	write_into_file(outfile, "rodlength", 0, 0 );
517	+	if (args_info->tet_param_given)
518	+	write_into_file(outfile, "tet_param", 0, 0 );
519	+	if (args_info->tet_param_z_given)
520	+	write_into_file(outfile, "tet_param_z", 0, 0 );
521	+	if (args_info->rnemdz_given)
522	+	write_into_file(outfile, "rnemdz", 0, 0 );
523	+	if (args_info->rnemdr_given)
524	+	write_into_file(outfile, "rnemdr", 0, 0 );
525	+
526	+
527	+	i = EXIT_SUCCESS;
528	+	return i;
529	+	}
530	+
531	+	int
532		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
533		{
534		FILE *outfile;
#	Line 395 | Line 542 | cmdline_parser_file_save(const char *filename, struct
542		return EXIT_FAILURE;
543		}
544
545	<	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	<
545	>	i = cmdline_parser_dump(outfile, args_info);
546		fclose (outfile);
547
584	–	i = EXIT_SUCCESS;
548		return i;
549		}
550
#	Line 591 | Line 554 | cmdline_parser_free (struct gengetopt_args_info *args_
554		cmdline_parser_release (args_info);
555		}
556
557	<
595	<	/* gengetopt_strdup() */
596	<	/* strdup.c replacement of strdup, which is not standard */
557	>	/** @brief replacement of strdup, which is not standard */
558		char *
559		gengetopt_strdup (const char *s)
560		{
561	<	char *result = NULL;
561	>	char *result = 0;
562		if (!s)
563		return result;
564
#	Line 609 | Line 570 | static void
570		}
571
572		static void
612	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
613	–
614	–	static void
573		reset_group_staticProps(struct gengetopt_args_info *args_info)
574		{
575		if (! args_info->staticProps_group_counter)
#	Line 620 | Line 578 | reset_group_staticProps(struct gengetopt_args_info *ar
578		args_info->bo_given = 0 ;
579		args_info->bor_given = 0 ;
580		args_info->bad_given = 0 ;
581	+	args_info->count_given = 0 ;
582		args_info->gofr_given = 0 ;
583		args_info->gofz_given = 0 ;
584		args_info->r_theta_given = 0 ;
585		args_info->r_omega_given = 0 ;
586	+	args_info->r_z_given = 0 ;
587		args_info->theta_omega_given = 0 ;
588		args_info->gxyz_given = 0 ;
589	+	args_info->twodgofr_given = 0 ;
590		args_info->p2_given = 0 ;
591		args_info->rp2_given = 0 ;
592		args_info->scd_given = 0 ;
593		args_info->density_given = 0 ;
594		args_info->slab_density_given = 0 ;
595	+	args_info->p_angle_given = 0 ;
596		args_info->hxy_given = 0 ;
597		args_info->rho_r_given = 0 ;
598	+	args_info->angle_r_given = 0 ;
599		args_info->hullvol_given = 0 ;
600	+	args_info->rodlength_given = 0 ;
601	+	args_info->tet_param_given = 0 ;
602	+	args_info->tet_param_z_given = 0 ;
603	+	args_info->rnemdz_given = 0 ;
604	+	args_info->rnemdr_given = 0 ;
605
606		args_info->staticProps_group_counter = 0;
607		}
608
609		int
610	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
610	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
611		{
612		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
613		}
614
615		int
616	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
616	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
617	>	struct cmdline_parser_params *params)
618		{
619		int result;
620	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
621
622	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
622	>	if (result == EXIT_FAILURE)
623	>	{
624	>	cmdline_parser_free (args_info);
625	>	exit (EXIT_FAILURE);
626	>	}
627	>
628	>	return result;
629	>	}
630
631	+	int
632	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
633	+	{
634	+	int result;
635	+	struct cmdline_parser_params params;
636	+
637	+	params.override = override;
638	+	params.initialize = initialize;
639	+	params.check_required = check_required;
640	+	params.check_ambiguity = 0;
641	+	params.print_errors = 1;
642	+
643	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
644	+
645		if (result == EXIT_FAILURE)
646		{
647		cmdline_parser_free (args_info);
#	Line 665 | Line 656 | cmdline_parser_required (struct gengetopt_args_info *a
656		{
657		int result = EXIT_SUCCESS;
658
659	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
659	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
660		result = EXIT_FAILURE;
661
662		if (result == EXIT_FAILURE)
#	Line 681 | Line 672 | cmdline_parser_required2 (struct gengetopt_args_info *
672		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
673		{
674		int error = 0;
675	+	FIX_UNUSED (additional_error);
676
677		/* checks for required options */
678		if (! args_info->input_given)
#	Line 691 | Line 683 | cmdline_parser_required2 (struct gengetopt_args_info *
683
684		if (args_info->staticProps_group_counter == 0)
685		{
686	<	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 : ""));
686	>	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 : ""));
687		error = 1;
688		}
689
#	Line 701 | Line 693 | cmdline_parser_required2 (struct gengetopt_args_info *
693		return error;
694		}
695
696	+
697	+	static char *package_name = 0;
698	+
699	+	/**
700	+	* @brief updates an option
701	+	* @param field the generic pointer to the field to update
702	+	* @param orig_field the pointer to the orig field
703	+	* @param field_given the pointer to the number of occurrence of this option
704	+	* @param prev_given the pointer to the number of occurrence already seen
705	+	* @param value the argument for this option (if null no arg was specified)
706	+	* @param possible_values the possible values for this option (if specified)
707	+	* @param default_value the default value (in case the option only accepts fixed values)
708	+	* @param arg_type the type of this option
709	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
710	+	* @param override @see cmdline_parser_params.override
711	+	* @param no_free whether to free a possible previous value
712	+	* @param multiple_option whether this is a multiple option
713	+	* @param long_opt the corresponding long option
714	+	* @param short_opt the corresponding short option (or '-' if none)
715	+	* @param additional_error possible further error specification
716	+	*/
717	+	static
718	+	int update_arg(void *field, char **orig_field,
719	+	unsigned int *field_given, unsigned int *prev_given,
720	+	char *value, const char *possible_values[],
721	+	const char *default_value,
722	+	cmdline_parser_arg_type arg_type,
723	+	int check_ambiguity, int override,
724	+	int no_free, int multiple_option,
725	+	const char *long_opt, char short_opt,
726	+	const char *additional_error)
727	+	{
728	+	char *stop_char = 0;
729	+	const char *val = value;
730	+	int found;
731	+	char **string_field;
732	+	FIX_UNUSED (field);
733	+
734	+	stop_char = 0;
735	+	found = 0;
736	+
737	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
738	+	{
739	+	if (short_opt != '-')
740	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
741	+	package_name, long_opt, short_opt,
742	+	(additional_error ? additional_error : ""));
743	+	else
744	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
745	+	package_name, long_opt,
746	+	(additional_error ? additional_error : ""));
747	+	return 1; /* failure */
748	+	}
749	+
750	+	FIX_UNUSED (default_value);
751	+
752	+	if (field_given && *field_given && ! override)
753	+	return 0;
754	+	if (prev_given)
755	+	(*prev_given)++;
756	+	if (field_given)
757	+	(*field_given)++;
758	+	if (possible_values)
759	+	val = possible_values[found];
760	+
761	+	switch(arg_type) {
762	+	case ARG_INT:
763	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
764	+	break;
765	+	case ARG_DOUBLE:
766	+	if (val) *((double *)field) = strtod (val, &stop_char);
767	+	break;
768	+	case ARG_STRING:
769	+	if (val) {
770	+	string_field = (char **)field;
771	+	if (!no_free && *string_field)
772	+	free (*string_field); /* free previous string */
773	+	*string_field = gengetopt_strdup (val);
774	+	}
775	+	break;
776	+	default:
777	+	break;
778	+	};
779	+
780	+	/* check numeric conversion */
781	+	switch(arg_type) {
782	+	case ARG_INT:
783	+	case ARG_DOUBLE:
784	+	if (val && !(stop_char && *stop_char == '\0')) {
785	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
786	+	return 1; /* failure */
787	+	}
788	+	break;
789	+	default:
790	+	;
791	+	};
792	+
793	+	/* store the original value */
794	+	switch(arg_type) {
795	+	case ARG_NO:
796	+	break;
797	+	default:
798	+	if (value && orig_field) {
799	+	if (no_free) {
800	+	*orig_field = value;
801	+	} else {
802	+	if (*orig_field)
803	+	free (*orig_field); /* free previous string */
804	+	*orig_field = gengetopt_strdup (value);
805	+	}
806	+	}
807	+	};
808	+
809	+	return 0; /* OK */
810	+	}
811	+
812	+
813		int
814	<	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)
814	>	cmdline_parser_internal (
815	>	int argc, char **argv, struct gengetopt_args_info *args_info,
816	>	struct cmdline_parser_params *params, const char *additional_error)
817		{
818		int c;        /* Character of the parsed option.  */
819
820		int error = 0;
821		struct gengetopt_args_info local_args_info;
822	+
823	+	int override;
824	+	int initialize;
825	+	int check_required;
826	+	int check_ambiguity;
827	+
828	+	package_name = argv[0];
829	+
830	+	override = params->override;
831	+	initialize = params->initialize;
832	+	check_required = params->check_required;
833	+	check_ambiguity = params->check_ambiguity;
834
835		if (initialize)
836		cmdline_parser_init (args_info);
#	Line 716 | Line 839 | cmdline_parser_internal (int argc, char * const *argv,
839
840		optarg = 0;
841		optind = 0;
842	<	opterr = 1;
842	>	opterr = params->print_errors;
843		optopt = '?';
844
845		while (1)
846		{
847		int option_index = 0;
725	–	char *stop_char;
848
849		static struct option long_options[] = {
850		{ "help",       0, NULL, 'h' },
#	Line 733 | Line 855 | cmdline_parser_internal (int argc, char * const *argv,
855		{ "nbins",      1, NULL, 'b' },
856		{ "nbins_x",    1, NULL, 'x' },
857		{ "nbins_y",    1, NULL, 'y' },
858	+	{ "nbins_z",    1, NULL, 0 },
859		{ "nanglebins", 1, NULL, 'a' },
737	–	{ "length",     1, NULL, 0 },
860		{ "rcut",       1, NULL, 'c' },
861	+	{ "dz", 1, NULL, 0 },
862	+	{ "length",     1, NULL, 0 },
863	+	{ "zlength",    1, NULL, 0 },
864		{ "zoffset",    1, NULL, 'z' },
865		{ "sele1",      1, NULL, 0 },
866		{ "sele2",      1, NULL, 0 },
867		{ "sele3",      1, NULL, 0 },
868		{ "refsele",    1, NULL, 0 },
869	+	{ "comsele",    1, NULL, 0 },
870	+	{ "seleoffset", 1, NULL, 0 },
871		{ "molname",    1, NULL, 0 },
872		{ "begin",      1, NULL, 0 },
873		{ "end",        1, NULL, 0 },
#	Line 748 | Line 875 | cmdline_parser_internal (int argc, char * const *argv,
875		{ "bo", 0, NULL, 0 },
876		{ "bor",        0, NULL, 0 },
877		{ "bad",        0, NULL, 0 },
878	+	{ "count",      0, NULL, 0 },
879		{ "gofr",       0, NULL, 'g' },
880		{ "gofz",       0, NULL, 0 },
881		{ "r_theta",    0, NULL, 0 },
882		{ "r_omega",    0, NULL, 0 },
883	+	{ "r_z",        0, NULL, 0 },
884		{ "theta_omega",        0, NULL, 0 },
885		{ "gxyz",       0, NULL, 0 },
886	+	{ "twodgofr",   0, NULL, 0 },
887		{ "p2", 0, NULL, 'p' },
888		{ "rp2",        0, NULL, 0 },
889		{ "scd",        0, NULL, 's' },
890		{ "density",    0, NULL, 'd' },
891		{ "slab_density",       0, NULL, 0 },
892	+	{ "p_angle",    0, NULL, 0 },
893		{ "hxy",        0, NULL, 0 },
894		{ "rho_r",      0, NULL, 0 },
895	+	{ "angle_r",    0, NULL, 0 },
896		{ "hullvol",    0, NULL, 0 },
897	<	{ NULL, 0, NULL, 0 }
897	>	{ "rodlength",  0, NULL, 0 },
898	>	{ "tet_param",  0, NULL, 'Q' },
899	>	{ "tet_param_z",        0, NULL, 0 },
900	>	{ "rnemdz",     0, NULL, 0 },
901	>	{ "rnemdr",     0, NULL, 0 },
902	>	{ 0,  0, 0, 0 }
903		};
904
905	<	stop_char = 0;
769	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
905	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
906
907		if (c == -1) break;       /* Exit from `while (1)' loop.  */
908
#	Line 783 | Line 919 | cmdline_parser_internal (int argc, char * const *argv,
919		exit (EXIT_SUCCESS);
920
921		case 'i':       /* input dump file.  */
922	<	if (local_args_info.input_given)
923	<	{
924	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
925	<	goto failure;
926	<	}
927	<	if (args_info->input_given && ! override)
928	<	continue;
929	<	local_args_info.input_given = 1;
930	<	args_info->input_given = 1;
931	<	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);
922	>
923	>
924	>	if (update_arg( (void *)&(args_info->input_arg),
925	>	&(args_info->input_orig), &(args_info->input_given),
926	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
927	>	check_ambiguity, override, 0, 0,
928	>	"input", 'i',
929	>	additional_error))
930	>	goto failure;
931	>
932		break;
802	–
933		case 'o':       /* output file name.  */
934	<	if (local_args_info.output_given)
935	<	{
936	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
937	<	goto failure;
938	<	}
939	<	if (args_info->output_given && ! override)
940	<	continue;
941	<	local_args_info.output_given = 1;
942	<	args_info->output_given = 1;
943	<	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);
934	>
935	>
936	>	if (update_arg( (void *)&(args_info->output_arg),
937	>	&(args_info->output_orig), &(args_info->output_given),
938	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
939	>	check_ambiguity, override, 0, 0,
940	>	"output", 'o',
941	>	additional_error))
942	>	goto failure;
943	>
944		break;
820	–
945		case 'n':       /* process every n frame.  */
946	<	if (local_args_info.step_given)
947	<	{
948	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
949	<	goto failure;
950	<	}
951	<	if (args_info->step_given && ! override)
952	<	continue;
953	<	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);
946	>
947	>
948	>	if (update_arg( (void *)&(args_info->step_arg),
949	>	&(args_info->step_orig), &(args_info->step_given),
950	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
951	>	check_ambiguity, override, 0, 0,
952	>	"step", 'n',
953	>	additional_error))
954		goto failure;
955	<	}
836	<	if (args_info->step_orig)
837	<	free (args_info->step_orig); /* free previous string */
838	<	args_info->step_orig = gengetopt_strdup (optarg);
955	>
956		break;
840	–
957		case 'b':       /* number of bins (general purpose).  */
958	<	if (local_args_info.nbins_given)
959	<	{
960	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
961	<	goto failure;
962	<	}
963	<	if (args_info->nbins_given && ! override)
964	<	continue;
965	<	local_args_info.nbins_given = 1;
966	<	args_info->nbins_given = 1;
967	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
968	<	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	<
958	>
959	>
960	>	if (update_arg( (void *)&(args_info->nbins_arg),
961	>	&(args_info->nbins_orig), &(args_info->nbins_given),
962	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
963	>	check_ambiguity, override, 0, 0,
964	>	"nbins", 'b',
965	>	additional_error))
966	>	goto failure;
967	>
968	>	break;
969		case 'x':       /* number of bins in x axis.  */
970	<	if (local_args_info.nbins_x_given)
971	<	{
972	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
973	<	goto failure;
974	<	}
975	<	if (args_info->nbins_x_given && ! override)
976	<	continue;
977	<	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);
970	>
971	>
972	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
973	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
974	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
975	>	check_ambiguity, override, 0, 0,
976	>	"nbins_x", 'x',
977	>	additional_error))
978		goto failure;
979	<	}
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);
979	>
980		break;
880	–
981		case 'y':       /* number of bins in y axis.  */
982	<	if (local_args_info.nbins_y_given)
983	<	{
984	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
985	<	goto failure;
986	<	}
987	<	if (args_info->nbins_y_given && ! override)
988	<	continue;
989	<	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);
982	>
983	>
984	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
985	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
986	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
987	>	check_ambiguity, override, 0, 0,
988	>	"nbins_y", 'y',
989	>	additional_error))
990		goto failure;
991	<	}
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);
991	>
992		break;
900	–
993		case 'a':       /* number of bins for cos(angle).  */
994	<	if (local_args_info.nanglebins_given)
995	<	{
996	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
997	<	goto failure;
998	<	}
999	<	if (args_info->nanglebins_given && ! override)
1000	<	continue;
1001	<	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);
994	>
995	>
996	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
997	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
998	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
999	>	check_ambiguity, override, 0, 0,
1000	>	"nanglebins", 'a',
1001	>	additional_error))
1002		goto failure;
1003	<	}
916	<	if (args_info->nanglebins_orig)
917	<	free (args_info->nanglebins_orig); /* free previous string */
918	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
1003	>
1004		break;
920	–
1005		case 'c':       /* cutoff radius (rcut).  */
1006	<	if (local_args_info.rcut_given)
1007	<	{
1008	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1009	<	goto failure;
1010	<	}
1011	<	if (args_info->rcut_given && ! override)
1012	<	continue;
1013	<	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);
1006	>
1007	>
1008	>	if (update_arg( (void *)&(args_info->rcut_arg),
1009	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1010	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1011	>	check_ambiguity, override, 0, 0,
1012	>	"rcut", 'c',
1013	>	additional_error))
1014		goto failure;
1015	<	}
936	<	if (args_info->rcut_orig)
937	<	free (args_info->rcut_orig); /* free previous string */
938	<	args_info->rcut_orig = gengetopt_strdup (optarg);
1015	>
1016		break;
940	–
1017		case 'z':       /* Where to set the zero for the slab_density calculation.  */
1018	<	if (local_args_info.zoffset_given)
1019	<	{
1020	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1021	<	goto failure;
1022	<	}
1023	<	if (args_info->zoffset_given && ! override)
1024	<	continue;
1025	<	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);
1018	>
1019	>
1020	>	if (update_arg( (void *)&(args_info->zoffset_arg),
1021	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1022	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1023	>	check_ambiguity, override, 0, 0,
1024	>	"zoffset", 'z',
1025	>	additional_error))
1026		goto failure;
1027	<	}
956	<	if (args_info->zoffset_orig)
957	<	free (args_info->zoffset_orig); /* free previous string */
958	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
1027	>
1028		break;
960	–
1029		case 'g':       /* g(r).  */
1030	<	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;
1030	>
1031		if (args_info->staticProps_group_counter && override)
1032		reset_group_staticProps (args_info);
1033		args_info->staticProps_group_counter += 1;
1034	+
1035	+	if (update_arg( 0 ,
1036	+	0 , &(args_info->gofr_given),
1037	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1038	+	check_ambiguity, override, 0, 0,
1039	+	"gofr", 'g',
1040	+	additional_error))
1041	+	goto failure;
1042	+
1043		break;
1044	<
1045	<	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;
1044	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1045	>
1046		if (args_info->staticProps_group_counter && override)
1047		reset_group_staticProps (args_info);
1048		args_info->staticProps_group_counter += 1;
1049	+
1050	+	if (update_arg( 0 ,
1051	+	0 , &(args_info->p2_given),
1052	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1053	+	check_ambiguity, override, 0, 0,
1054	+	"p2", 'p',
1055	+	additional_error))
1056	+	goto failure;
1057	+
1058		break;
990	–
1059		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1060	<	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;
1060	>
1061		if (args_info->staticProps_group_counter && override)
1062		reset_group_staticProps (args_info);
1063		args_info->staticProps_group_counter += 1;
1064	+
1065	+	if (update_arg( 0 ,
1066	+	0 , &(args_info->scd_given),
1067	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1068	+	check_ambiguity, override, 0, 0,
1069	+	"scd", 's',
1070	+	additional_error))
1071	+	goto failure;
1072	+
1073		break;
1005	–
1074		case 'd':       /* density plot.  */
1075	<	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;
1075	>
1076		if (args_info->staticProps_group_counter && override)
1077		reset_group_staticProps (args_info);
1078		args_info->staticProps_group_counter += 1;
1079	+
1080	+	if (update_arg( 0 ,
1081	+	0 , &(args_info->density_given),
1082	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1083	+	check_ambiguity, override, 0, 0,
1084	+	"density", 'd',
1085	+	additional_error))
1086	+	goto failure;
1087	+
1088		break;
1089	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1090	+
1091	+	if (args_info->staticProps_group_counter && override)
1092	+	reset_group_staticProps (args_info);
1093	+	args_info->staticProps_group_counter += 1;
1094	+
1095	+	if (update_arg( 0 ,
1096	+	0 , &(args_info->tet_param_given),
1097	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1098	+	check_ambiguity, override, 0, 0,
1099	+	"tet_param", 'Q',
1100	+	additional_error))
1101	+	goto failure;
1102	+
1103	+	break;
1104
1021	–
1105		case 0: /* Long option with no short option */
1106	<	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1107	<	if (strcmp (long_options[option_index].name, "length") == 0)
1106	>	/* number of bins in z axis.  */
1107	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1108		{
1109	<	if (local_args_info.length_given)
1110	<	{
1111	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1112	<	goto failure;
1113	<	}
1114	<	if (args_info->length_given && ! override)
1115	<	continue;
1116	<	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);
1109	>
1110	>
1111	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1112	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1113	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1114	>	check_ambiguity, override, 0, 0,
1115	>	"nbins_z", '-',
1116	>	additional_error))
1117		goto failure;
1118	<	}
1040	<	if (args_info->length_orig)
1041	<	free (args_info->length_orig); /* free previous string */
1042	<	args_info->length_orig = gengetopt_strdup (optarg);
1118	>
1119		}
1120	+	/* slab width (dz).  */
1121	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1122	+	{
1123	+
1124	+
1125	+	if (update_arg( (void *)&(args_info->dz_arg),
1126	+	&(args_info->dz_orig), &(args_info->dz_given),
1127	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1128	+	check_ambiguity, override, 0, 0,
1129	+	"dz", '-',
1130	+	additional_error))
1131	+	goto failure;
1132	+
1133	+	}
1134	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1135	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1136	+	{
1137	+
1138	+
1139	+	if (update_arg( (void *)&(args_info->length_arg),
1140	+	&(args_info->length_orig), &(args_info->length_given),
1141	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1142	+	check_ambiguity, override, 0, 0,
1143	+	"length", '-',
1144	+	additional_error))
1145	+	goto failure;
1146	+
1147	+	}
1148	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1149	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1150	+	{
1151	+
1152	+
1153	+	if (update_arg( (void *)&(args_info->zlength_arg),
1154	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1155	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1156	+	check_ambiguity, override, 0, 0,
1157	+	"zlength", '-',
1158	+	additional_error))
1159	+	goto failure;
1160	+
1161	+	}
1162		/* select the first stuntdouble set.  */
1163		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1164		{
1165	<	if (local_args_info.sele1_given)
1166	<	{
1167	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1168	<	goto failure;
1169	<	}
1170	<	if (args_info->sele1_given && ! override)
1171	<	continue;
1172	<	local_args_info.sele1_given = 1;
1173	<	args_info->sele1_given = 1;
1174	<	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);
1165	>
1166	>
1167	>	if (update_arg( (void *)&(args_info->sele1_arg),
1168	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1169	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1170	>	check_ambiguity, override, 0, 0,
1171	>	"sele1", '-',
1172	>	additional_error))
1173	>	goto failure;
1174	>
1175		}
1176		/* select the second stuntdouble set.  */
1177		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1178		{
1179	<	if (local_args_info.sele2_given)
1180	<	{
1181	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1182	<	goto failure;
1183	<	}
1184	<	if (args_info->sele2_given && ! override)
1185	<	continue;
1186	<	local_args_info.sele2_given = 1;
1187	<	args_info->sele2_given = 1;
1188	<	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);
1179	>
1180	>
1181	>	if (update_arg( (void *)&(args_info->sele2_arg),
1182	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1183	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1184	>	check_ambiguity, override, 0, 0,
1185	>	"sele2", '-',
1186	>	additional_error))
1187	>	goto failure;
1188	>
1189		}
1190		/* select the third stuntdouble set.  */
1191		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1192		{
1193	<	if (local_args_info.sele3_given)
1194	<	{
1195	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1196	<	goto failure;
1197	<	}
1198	<	if (args_info->sele3_given && ! override)
1199	<	continue;
1200	<	local_args_info.sele3_given = 1;
1201	<	args_info->sele3_given = 1;
1202	<	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);
1193	>
1194	>
1195	>	if (update_arg( (void *)&(args_info->sele3_arg),
1196	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1197	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1198	>	check_ambiguity, override, 0, 0,
1199	>	"sele3", '-',
1200	>	additional_error))
1201	>	goto failure;
1202	>
1203		}
1204		/* select reference (use and only use with --gxyz).  */
1205		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1206		{
1207	<	if (local_args_info.refsele_given)
1208	<	{
1209	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1210	<	goto failure;
1211	<	}
1212	<	if (args_info->refsele_given && ! override)
1213	<	continue;
1214	<	local_args_info.refsele_given = 1;
1215	<	args_info->refsele_given = 1;
1216	<	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);
1207	>
1208	>
1209	>	if (update_arg( (void *)&(args_info->refsele_arg),
1210	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1211	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1212	>	check_ambiguity, override, 0, 0,
1213	>	"refsele", '-',
1214	>	additional_error))
1215	>	goto failure;
1216	>
1217		}
1218	+	/* select stunt doubles for center-of-mass reference point.  */
1219	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1220	+	{
1221	+
1222	+
1223	+	if (update_arg( (void *)&(args_info->comsele_arg),
1224	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1225	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1226	+	check_ambiguity, override, 0, 0,
1227	+	"comsele", '-',
1228	+	additional_error))
1229	+	goto failure;
1230	+
1231	+	}
1232	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1233	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1234	+	{
1235	+
1236	+
1237	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1238	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1239	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1240	+	check_ambiguity, override, 0, 0,
1241	+	"seleoffset", '-',
1242	+	additional_error))
1243	+	goto failure;
1244	+
1245	+	}
1246		/* molecule name.  */
1247		else if (strcmp (long_options[option_index].name, "molname") == 0)
1248		{
1249	<	if (local_args_info.molname_given)
1250	<	{
1251	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	<	goto failure;
1253	<	}
1254	<	if (args_info->molname_given && ! override)
1255	<	continue;
1256	<	local_args_info.molname_given = 1;
1257	<	args_info->molname_given = 1;
1258	<	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);
1249	>
1250	>
1251	>	if (update_arg( (void *)&(args_info->molname_arg),
1252	>	&(args_info->molname_orig), &(args_info->molname_given),
1253	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1254	>	check_ambiguity, override, 0, 0,
1255	>	"molname", '-',
1256	>	additional_error))
1257	>	goto failure;
1258	>
1259		}
1260		/* begin internal index.  */
1261		else if (strcmp (long_options[option_index].name, "begin") == 0)
1262		{
1263	<	if (local_args_info.begin_given)
1264	<	{
1265	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1266	<	goto failure;
1267	<	}
1268	<	if (args_info->begin_given && ! override)
1269	<	continue;
1270	<	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);
1263	>
1264	>
1265	>	if (update_arg( (void *)&(args_info->begin_arg),
1266	>	&(args_info->begin_orig), &(args_info->begin_given),
1267	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1268	>	check_ambiguity, override, 0, 0,
1269	>	"begin", '-',
1270	>	additional_error))
1271		goto failure;
1272	<	}
1156	<	if (args_info->begin_orig)
1157	<	free (args_info->begin_orig); /* free previous string */
1158	<	args_info->begin_orig = gengetopt_strdup (optarg);
1272	>
1273		}
1274		/* end internal index.  */
1275		else if (strcmp (long_options[option_index].name, "end") == 0)
1276		{
1277	<	if (local_args_info.end_given)
1278	<	{
1279	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1280	<	goto failure;
1281	<	}
1282	<	if (args_info->end_given && ! override)
1283	<	continue;
1284	<	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);
1277	>
1278	>
1279	>	if (update_arg( (void *)&(args_info->end_arg),
1280	>	&(args_info->end_orig), &(args_info->end_given),
1281	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1282	>	check_ambiguity, override, 0, 0,
1283	>	"end", '-',
1284	>	additional_error))
1285		goto failure;
1286	<	}
1177	<	if (args_info->end_orig)
1178	<	free (args_info->end_orig); /* free previous string */
1179	<	args_info->end_orig = gengetopt_strdup (optarg);
1286	>
1287		}
1288		/* nanoparticle radius.  */
1289		else if (strcmp (long_options[option_index].name, "radius") == 0)
1290		{
1291	<	if (local_args_info.radius_given)
1292	<	{
1293	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1294	<	goto failure;
1295	<	}
1296	<	if (args_info->radius_given && ! override)
1297	<	continue;
1298	<	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);
1291	>
1292	>
1293	>	if (update_arg( (void *)&(args_info->radius_arg),
1294	>	&(args_info->radius_orig), &(args_info->radius_given),
1295	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1296	>	check_ambiguity, override, 0, 0,
1297	>	"radius", '-',
1298	>	additional_error))
1299		goto failure;
1300	<	}
1198	<	if (args_info->radius_orig)
1199	<	free (args_info->radius_orig); /* free previous string */
1200	<	args_info->radius_orig = gengetopt_strdup (optarg);
1300	>
1301		}
1302		/* bond order parameter (--rcut must be specified).  */
1303		else if (strcmp (long_options[option_index].name, "bo") == 0)
1304		{
1305	<	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;
1305	>
1306		if (args_info->staticProps_group_counter && override)
1307		reset_group_staticProps (args_info);
1308		args_info->staticProps_group_counter += 1;
1309	<	break;
1309	>
1310	>	if (update_arg( 0 ,
1311	>	0 , &(args_info->bo_given),
1312	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1313	>	check_ambiguity, override, 0, 0,
1314	>	"bo", '-',
1315	>	additional_error))
1316	>	goto failure;
1317	>
1318		}
1319		/* bond order parameter as a function of radius (--rcut must be specified).  */
1320		else if (strcmp (long_options[option_index].name, "bor") == 0)
1321		{
1322	<	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;
1322	>
1323		if (args_info->staticProps_group_counter && override)
1324		reset_group_staticProps (args_info);
1325		args_info->staticProps_group_counter += 1;
1326	<	break;
1326	>
1327	>	if (update_arg( 0 ,
1328	>	0 , &(args_info->bor_given),
1329	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1330	>	check_ambiguity, override, 0, 0,
1331	>	"bor", '-',
1332	>	additional_error))
1333	>	goto failure;
1334	>
1335		}
1336		/* N(theta) bond angle density within (--rcut must be specified).  */
1337		else if (strcmp (long_options[option_index].name, "bad") == 0)
1338		{
1339	<	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;
1339	>
1340		if (args_info->staticProps_group_counter && override)
1341		reset_group_staticProps (args_info);
1342		args_info->staticProps_group_counter += 1;
1343	<	break;
1343	>
1344	>	if (update_arg( 0 ,
1345	>	0 , &(args_info->bad_given),
1346	>	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1347	>	check_ambiguity, override, 0, 0,
1348	>	"bad", '-',
1349	>	additional_error))
1350	>	goto failure;
1351	>
1352		}
1353	+	/* count of molecules matching selection criteria (and associated statistics).  */
1354	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1355	+	{
1356	+
1357	+	if (args_info->staticProps_group_counter && override)
1358	+	reset_group_staticProps (args_info);
1359	+	args_info->staticProps_group_counter += 1;
1360	+
1361	+	if (update_arg( 0 ,
1362	+	0 , &(args_info->count_given),
1363	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1364	+	check_ambiguity, override, 0, 0,
1365	+	"count", '-',
1366	+	additional_error))
1367	+	goto failure;
1368	+
1369	+	}
1370		/* g(z).  */
1371		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1372		{
1373	<	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;
1373	>
1374		if (args_info->staticProps_group_counter && override)
1375		reset_group_staticProps (args_info);
1376		args_info->staticProps_group_counter += 1;
1377	<	break;
1377	>
1378	>	if (update_arg( 0 ,
1379	>	0 , &(args_info->gofz_given),
1380	>	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1381	>	check_ambiguity, override, 0, 0,
1382	>	"gofz", '-',
1383	>	additional_error))
1384	>	goto failure;
1385	>
1386		}
1387		/* g(r, cos(theta)).  */
1388		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1389		{
1390	<	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;
1390	>
1391		if (args_info->staticProps_group_counter && override)
1392		reset_group_staticProps (args_info);
1393		args_info->staticProps_group_counter += 1;
1394	<	break;
1394	>
1395	>	if (update_arg( 0 ,
1396	>	0 , &(args_info->r_theta_given),
1397	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1398	>	check_ambiguity, override, 0, 0,
1399	>	"r_theta", '-',
1400	>	additional_error))
1401	>	goto failure;
1402	>
1403		}
1404		/* g(r, cos(omega)).  */
1405		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1406		{
1407	<	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;
1407	>
1408		if (args_info->staticProps_group_counter && override)
1409		reset_group_staticProps (args_info);
1410		args_info->staticProps_group_counter += 1;
1411	<	break;
1411	>
1412	>	if (update_arg( 0 ,
1413	>	0 , &(args_info->r_omega_given),
1414	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1415	>	check_ambiguity, override, 0, 0,
1416	>	"r_omega", '-',
1417	>	additional_error))
1418	>	goto failure;
1419	>
1420		}
1421	+	/* g(r, z).  */
1422	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1423	+	{
1424	+
1425	+	if (args_info->staticProps_group_counter && override)
1426	+	reset_group_staticProps (args_info);
1427	+	args_info->staticProps_group_counter += 1;
1428	+
1429	+	if (update_arg( 0 ,
1430	+	0 , &(args_info->r_z_given),
1431	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1432	+	check_ambiguity, override, 0, 0,
1433	+	"r_z", '-',
1434	+	additional_error))
1435	+	goto failure;
1436	+
1437	+	}
1438		/* g(cos(theta), cos(omega)).  */
1439		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1440		{
1441	<	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;
1441	>
1442		if (args_info->staticProps_group_counter && override)
1443		reset_group_staticProps (args_info);
1444		args_info->staticProps_group_counter += 1;
1445	<	break;
1445	>
1446	>	if (update_arg( 0 ,
1447	>	0 , &(args_info->theta_omega_given),
1448	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1449	>	check_ambiguity, override, 0, 0,
1450	>	"theta_omega", '-',
1451	>	additional_error))
1452	>	goto failure;
1453	>
1454		}
1455		/* g(x, y, z).  */
1456		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1457		{
1458	<	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;
1458	>
1459		if (args_info->staticProps_group_counter && override)
1460		reset_group_staticProps (args_info);
1461		args_info->staticProps_group_counter += 1;
1462	<	break;
1462	>
1463	>	if (update_arg( 0 ,
1464	>	0 , &(args_info->gxyz_given),
1465	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1466	>	check_ambiguity, override, 0, 0,
1467	>	"gxyz", '-',
1468	>	additional_error))
1469	>	goto failure;
1470	>
1471		}
1472	+	/* 2D g(r) (Slab width --dz must be specified).  */
1473	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1474	+	{
1475	+
1476	+	if (args_info->staticProps_group_counter && override)
1477	+	reset_group_staticProps (args_info);
1478	+	args_info->staticProps_group_counter += 1;
1479	+
1480	+	if (update_arg( 0 ,
1481	+	0 , &(args_info->twodgofr_given),
1482	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1483	+	check_ambiguity, override, 0, 0,
1484	+	"twodgofr", '-',
1485	+	additional_error))
1486	+	goto failure;
1487	+
1488	+	}
1489		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1490		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1491		{
1492	<	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;
1492	>
1493		if (args_info->staticProps_group_counter && override)
1494		reset_group_staticProps (args_info);
1495		args_info->staticProps_group_counter += 1;
1496	<	break;
1496	>
1497	>	if (update_arg( 0 ,
1498	>	0 , &(args_info->rp2_given),
1499	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1500	>	check_ambiguity, override, 0, 0,
1501	>	"rp2", '-',
1502	>	additional_error))
1503	>	goto failure;
1504	>
1505		}
1506		/* slab density.  */
1507		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1508		{
1509	<	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;
1509	>
1510		if (args_info->staticProps_group_counter && override)
1511		reset_group_staticProps (args_info);
1512		args_info->staticProps_group_counter += 1;
1513	<	break;
1513	>
1514	>	if (update_arg( 0 ,
1515	>	0 , &(args_info->slab_density_given),
1516	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1517	>	check_ambiguity, override, 0, 0,
1518	>	"slab_density", '-',
1519	>	additional_error))
1520	>	goto failure;
1521	>
1522		}
1523	+	/* p(cos(theta)).  */
1524	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1525	+	{
1526	+
1527	+	if (args_info->staticProps_group_counter && override)
1528	+	reset_group_staticProps (args_info);
1529	+	args_info->staticProps_group_counter += 1;
1530	+
1531	+	if (update_arg( 0 ,
1532	+	0 , &(args_info->p_angle_given),
1533	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1534	+	check_ambiguity, override, 0, 0,
1535	+	"p_angle", '-',
1536	+	additional_error))
1537	+	goto failure;
1538	+
1539	+	}
1540		/* hxy.  */
1541		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1542		{
1543	<	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;
1543	>
1544		if (args_info->staticProps_group_counter && override)
1545		reset_group_staticProps (args_info);
1546		args_info->staticProps_group_counter += 1;
1547	<	break;
1547	>
1548	>	if (update_arg( 0 ,
1549	>	0 , &(args_info->hxy_given),
1550	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1551	>	check_ambiguity, override, 0, 0,
1552	>	"hxy", '-',
1553	>	additional_error))
1554	>	goto failure;
1555	>
1556		}
1557		/* rho of R.  */
1558		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1559		{
1560	<	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;
1560	>
1561		if (args_info->staticProps_group_counter && override)
1562		reset_group_staticProps (args_info);
1563		args_info->staticProps_group_counter += 1;
1564	<	break;
1564	>
1565	>	if (update_arg( 0 ,
1566	>	0 , &(args_info->rho_r_given),
1567	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1568	>	check_ambiguity, override, 0, 0,
1569	>	"rho_r", '-',
1570	>	additional_error))
1571	>	goto failure;
1572	>
1573		}
1574	+	/* angle of R.  */
1575	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1576	+	{
1577	+
1578	+	if (args_info->staticProps_group_counter && override)
1579	+	reset_group_staticProps (args_info);
1580	+	args_info->staticProps_group_counter += 1;
1581	+
1582	+	if (update_arg( 0 ,
1583	+	0 , &(args_info->angle_r_given),
1584	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1585	+	check_ambiguity, override, 0, 0,
1586	+	"angle_r", '-',
1587	+	additional_error))
1588	+	goto failure;
1589	+
1590	+	}
1591		/* hull volume of nanoparticle.  */
1592		else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1593		{
1594	<	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;
1594	>
1595		if (args_info->staticProps_group_counter && override)
1596		reset_group_staticProps (args_info);
1597		args_info->staticProps_group_counter += 1;
1598	<	break;
1598	>
1599	>	if (update_arg( 0 ,
1600	>	0 , &(args_info->hullvol_given),
1601	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1602	>	check_ambiguity, override, 0, 0,
1603	>	"hullvol", '-',
1604	>	additional_error))
1605	>	goto failure;
1606	>
1607		}
1608	+	/* length of nanorod.  */
1609	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1610	+	{
1611
1612	+	if (args_info->staticProps_group_counter && override)
1613	+	reset_group_staticProps (args_info);
1614	+	args_info->staticProps_group_counter += 1;
1615	+
1616	+	if (update_arg( 0 ,
1617	+	0 , &(args_info->rodlength_given),
1618	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1619	+	check_ambiguity, override, 0, 0,
1620	+	"rodlength", '-',
1621	+	additional_error))
1622	+	goto failure;
1623	+
1624	+	}
1625	+	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1626	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1627	+	{
1628	+
1629	+	if (args_info->staticProps_group_counter && override)
1630	+	reset_group_staticProps (args_info);
1631	+	args_info->staticProps_group_counter += 1;
1632	+
1633	+	if (update_arg( 0 ,
1634	+	0 , &(args_info->tet_param_z_given),
1635	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1636	+	check_ambiguity, override, 0, 0,
1637	+	"tet_param_z", '-',
1638	+	additional_error))
1639	+	goto failure;
1640	+
1641	+	}
1642	+	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1643	+	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1644	+	{
1645	+
1646	+	if (args_info->staticProps_group_counter && override)
1647	+	reset_group_staticProps (args_info);
1648	+	args_info->staticProps_group_counter += 1;
1649	+
1650	+	if (update_arg( 0 ,
1651	+	0 , &(args_info->rnemdz_given),
1652	+	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1653	+	check_ambiguity, override, 0, 0,
1654	+	"rnemdz", '-',
1655	+	additional_error))
1656	+	goto failure;
1657	+
1658	+	}
1659	+	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1660	+	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1661	+	{
1662	+
1663	+	if (args_info->staticProps_group_counter && override)
1664	+	reset_group_staticProps (args_info);
1665	+	args_info->staticProps_group_counter += 1;
1666	+
1667	+	if (update_arg( 0 ,
1668	+	0 , &(args_info->rnemdr_given),
1669	+	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1670	+	check_ambiguity, override, 0, 0,
1671	+	"rnemdr", '-',
1672	+	additional_error))
1673	+	goto failure;
1674	+
1675	+	}
1676	+
1677		break;
1678		case '?':       /* Invalid option.  */
1679		/* `getopt_long' already printed an error message.  */
#	Line 1434 | Line 1687 | cmdline_parser_internal (int argc, char * const *argv,
1687
1688		if (args_info->staticProps_group_counter > 1)
1689		{
1690	<	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 : ""));
1690	>	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 : ""));
1691		error = 1;
1692		}
1693

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
branches/development/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1865 by gezelter, Wed Apr 17 18:24:08 2013 UTC

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

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