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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.19.1
2	>	File autogenerated by gengetopt version 2.22
3		generated with the following command:
4	<	gengetopt -i StaticProps.ggo -F StaticPropsCmd -u
4	>	gengetopt -F StaticPropsCmd -u
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
#	Line 37 | Line 37 | const char *gengetopt_args_info_help[] = {
37		"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38		"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39		"  -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)",
40		"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
41	+	"      --dz=DOUBLE               slab width (dz)",
42	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
43	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
44		"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
45		"      --sele1=selection script  select the first stuntdouble set",
46		"      --sele2=selection script  select the second stuntdouble set",
47		"      --sele3=selection script  select the third stuntdouble set",
48		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
49	+	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
50		"      --molname=STRING          molecule name",
51		"      --begin=INT               begin internal index",
52		"      --end=INT                 end internal index",
#	Line 51 | Line 54 | const char *gengetopt_args_info_help[] = {
54		"\n Group: staticProps\n   an option of this group is required",
55		"      --bo                      bond order parameter (--rcut must be specified)",
56		"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
57	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
58	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
59		"  -g, --gofr                    g(r)",
60	+	"      --gofz                    g(z)",
61		"      --r_theta                 g(r, cos(theta))",
62		"      --r_omega                 g(r, cos(omega))",
63		"      --theta_omega             g(cos(theta), cos(omega))",
64		"      --gxyz                    g(x, y, z)",
65	+	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
66		"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
67		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
68		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
69		"  -d, --density                 density plot",
70		"      --slab_density            slab density",
71	+	"      --p_angle                 p(cos(theta))",
72		"      --hxy                     hxy",
73		"      --rho_r                   rho of R",
74	+	"      --angle_r                 angle of R",
75	+	"      --hullvol                 hull volume of nanoparticle",
76		0
77		};
78
79	+	typedef enum {ARG_NO
80	+	, ARG_STRING
81	+	, ARG_INT
82	+	, ARG_DOUBLE
83	+	} cmdline_parser_arg_type;
84	+
85		static
86		void clear_given (struct gengetopt_args_info *args_info);
87		static
88		void clear_args (struct gengetopt_args_info *args_info);
89
90		static int
91	<	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);
91	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
92	>	struct cmdline_parser_params *params, const char *additional_error);
93
94		static int
95		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 92 | Line 109 | void clear_given (struct gengetopt_args_info *args_inf
109		args_info->nbins_x_given = 0 ;
110		args_info->nbins_y_given = 0 ;
111		args_info->nanglebins_given = 0 ;
95	–	args_info->length_given = 0 ;
112		args_info->rcut_given = 0 ;
113	+	args_info->dz_given = 0 ;
114	+	args_info->length_given = 0 ;
115	+	args_info->zlength_given = 0 ;
116		args_info->zoffset_given = 0 ;
117		args_info->sele1_given = 0 ;
118		args_info->sele2_given = 0 ;
119		args_info->sele3_given = 0 ;
120		args_info->refsele_given = 0 ;
121	+	args_info->comsele_given = 0 ;
122		args_info->molname_given = 0 ;
123		args_info->begin_given = 0 ;
124		args_info->end_given = 0 ;
125		args_info->radius_given = 0 ;
126		args_info->bo_given = 0 ;
127		args_info->bor_given = 0 ;
128	+	args_info->bad_given = 0 ;
129	+	args_info->count_given = 0 ;
130		args_info->gofr_given = 0 ;
131	+	args_info->gofz_given = 0 ;
132		args_info->r_theta_given = 0 ;
133		args_info->r_omega_given = 0 ;
134		args_info->theta_omega_given = 0 ;
135		args_info->gxyz_given = 0 ;
136	+	args_info->twodgofr_given = 0 ;
137		args_info->p2_given = 0 ;
138		args_info->rp2_given = 0 ;
139		args_info->scd_given = 0 ;
140		args_info->density_given = 0 ;
141		args_info->slab_density_given = 0 ;
142	+	args_info->p_angle_given = 0 ;
143		args_info->hxy_given = 0 ;
144		args_info->rho_r_given = 0 ;
145	+	args_info->angle_r_given = 0 ;
146	+	args_info->hullvol_given = 0 ;
147		args_info->staticProps_group_counter = 0 ;
148		}
149
#	Line 137 | Line 164 | void clear_args (struct gengetopt_args_info *args_info
164		args_info->nbins_y_orig = NULL;
165		args_info->nanglebins_arg = 50;
166		args_info->nanglebins_orig = NULL;
140	–	args_info->length_orig = NULL;
167		args_info->rcut_orig = NULL;
168	+	args_info->dz_orig = NULL;
169	+	args_info->length_orig = NULL;
170	+	args_info->zlength_orig = NULL;
171		args_info->zoffset_arg = 0;
172		args_info->zoffset_orig = NULL;
173		args_info->sele1_arg = NULL;
#	Line 149 | Line 178 | void clear_args (struct gengetopt_args_info *args_info
178		args_info->sele3_orig = NULL;
179		args_info->refsele_arg = NULL;
180		args_info->refsele_orig = NULL;
181	+	args_info->comsele_arg = NULL;
182	+	args_info->comsele_orig = NULL;
183		args_info->molname_arg = NULL;
184		args_info->molname_orig = NULL;
185		args_info->begin_orig = NULL;
#	Line 160 | Line 191 | void init_args_info(struct gengetopt_args_info *args_i
191		static
192		void init_args_info(struct gengetopt_args_info *args_info)
193		{
194	+
195	+
196		args_info->help_help = gengetopt_args_info_help[0] ;
197		args_info->version_help = gengetopt_args_info_help[1] ;
198		args_info->input_help = gengetopt_args_info_help[2] ;
#	Line 168 | Line 201 | void init_args_info(struct gengetopt_args_info *args_i
201		args_info->nbins_help = gengetopt_args_info_help[5] ;
202		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
203		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
204	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
205	<	args_info->length_help = gengetopt_args_info_help[9] ;
204	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
205	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
206		args_info->rcut_help = gengetopt_args_info_help[10] ;
207	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
208	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
209	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
210	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
211	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
212	<	args_info->molname_help = gengetopt_args_info_help[16] ;
213	<	args_info->begin_help = gengetopt_args_info_help[17] ;
214	<	args_info->end_help = gengetopt_args_info_help[18] ;
215	<	args_info->radius_help = gengetopt_args_info_help[19] ;
216	<	args_info->bo_help = gengetopt_args_info_help[20] ;
217	<	args_info->bor_help = gengetopt_args_info_help[21] ;
218	<	args_info->gofr_help = gengetopt_args_info_help[22] ;
219	<	args_info->r_theta_help = gengetopt_args_info_help[23] ;
220	<	args_info->r_omega_help = gengetopt_args_info_help[24] ;
221	<	args_info->theta_omega_help = gengetopt_args_info_help[25] ;
222	<	args_info->gxyz_help = gengetopt_args_info_help[26] ;
223	<	args_info->p2_help = gengetopt_args_info_help[27] ;
224	<	args_info->rp2_help = gengetopt_args_info_help[28] ;
225	<	args_info->scd_help = gengetopt_args_info_help[29] ;
226	<	args_info->density_help = gengetopt_args_info_help[30] ;
227	<	args_info->slab_density_help = gengetopt_args_info_help[31] ;
228	<	args_info->hxy_help = gengetopt_args_info_help[32] ;
229	<	args_info->rho_r_help = gengetopt_args_info_help[33] ;
207	>	args_info->dz_help = gengetopt_args_info_help[11] ;
208	>	args_info->length_help = gengetopt_args_info_help[12] ;
209	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
210	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
211	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
212	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
213	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
214	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
215	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
216	>	args_info->molname_help = gengetopt_args_info_help[20] ;
217	>	args_info->begin_help = gengetopt_args_info_help[21] ;
218	>	args_info->end_help = gengetopt_args_info_help[22] ;
219	>	args_info->radius_help = gengetopt_args_info_help[23] ;
220	>	args_info->bo_help = gengetopt_args_info_help[25] ;
221	>	args_info->bor_help = gengetopt_args_info_help[26] ;
222	>	args_info->bad_help = gengetopt_args_info_help[27] ;
223	>	args_info->count_help = gengetopt_args_info_help[28] ;
224	>	args_info->gofr_help = gengetopt_args_info_help[29] ;
225	>	args_info->gofz_help = gengetopt_args_info_help[30] ;
226	>	args_info->r_theta_help = gengetopt_args_info_help[31] ;
227	>	args_info->r_omega_help = gengetopt_args_info_help[32] ;
228	>	args_info->r_z_help = gengetopt_args_info_help[33] ;
229	>	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
230	>	args_info->gxyz_help = gengetopt_args_info_help[35] ;
231	>	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
232	>	args_info->p2_help = gengetopt_args_info_help[37] ;
233	>	args_info->rp2_help = gengetopt_args_info_help[38] ;
234	>	args_info->scd_help = gengetopt_args_info_help[39] ;
235	>	args_info->density_help = gengetopt_args_info_help[40] ;
236	>	args_info->slab_density_help = gengetopt_args_info_help[41] ;
237	>	args_info->p_angle_help = gengetopt_args_info_help[42] ;
238	>	args_info->hxy_help = gengetopt_args_info_help[43] ;
239	>	args_info->rho_r_help = gengetopt_args_info_help[44] ;
240	>	args_info->hullvol_help = gengetopt_args_info_help[45] ;
241
242		}
243
#	Line 203 | Line 247 | cmdline_parser_print_version (void)
247		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
248		}
249
250	<	void
207	<	cmdline_parser_print_help (void)
208	<	{
209	<	int i = 0;
250	>	static void print_help_common(void) {
251		cmdline_parser_print_version ();
252
253		if (strlen(gengetopt_args_info_purpose) > 0)
254		printf("\n%s\n", gengetopt_args_info_purpose);
255
256	<	printf("\n%s\n\n", gengetopt_args_info_usage);
256	>	if (strlen(gengetopt_args_info_usage) > 0)
257	>	printf("\n%s\n", gengetopt_args_info_usage);
258
259	+	printf("\n");
260	+
261		if (strlen(gengetopt_args_info_description) > 0)
262		printf("%s\n", gengetopt_args_info_description);
263	+	}
264
265	+	void
266	+	cmdline_parser_print_help (void)
267	+	{
268	+	int i = 0;
269	+	print_help_common();
270		while (gengetopt_args_info_help[i])
271		printf("%s\n", gengetopt_args_info_help[i++]);
272		}
#	Line 232 | Line 282 | cmdline_parser_init (struct gengetopt_args_info *args_
282		args_info->inputs_num = 0;
283		}
284
285	+	void
286	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
287	+	{
288	+	if (params)
289	+	{
290	+	params->override = 0;
291	+	params->initialize = 1;
292	+	params->check_required = 1;
293	+	params->check_ambiguity = 0;
294	+	params->print_errors = 1;
295	+	}
296	+	}
297	+
298	+	struct cmdline_parser_params *
299	+	cmdline_parser_params_create(void)
300	+	{
301	+	struct cmdline_parser_params *params =
302	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
303	+	cmdline_parser_params_init(params);
304	+	return params;
305	+	}
306	+
307		static void
308	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
308	>	free_string_field (char **s)
309		{
310	<
239	<	unsigned int i;
240	<	if (args_info->input_arg)
310	>	if (*s)
311		{
312	<	free (args_info->input_arg); /* free previous argument */
313	<	args_info->input_arg = 0;
312	>	free (*s);
313	>	*s = 0;
314		}
315	<	if (args_info->input_orig)
316	<	{
317	<	free (args_info->input_orig); /* free previous argument */
318	<	args_info->input_orig = 0;
319	<	}
320	<	if (args_info->output_arg)
321	<	{
322	<	free (args_info->output_arg); /* free previous argument */
323	<	args_info->output_arg = 0;
324	<	}
325	<	if (args_info->output_orig)
326	<	{
327	<	free (args_info->output_orig); /* free previous argument */
328	<	args_info->output_orig = 0;
329	<	}
330	<	if (args_info->step_orig)
331	<	{
332	<	free (args_info->step_orig); /* free previous argument */
333	<	args_info->step_orig = 0;
334	<	}
335	<	if (args_info->nbins_orig)
336	<	{
337	<	free (args_info->nbins_orig); /* free previous argument */
338	<	args_info->nbins_orig = 0;
339	<	}
340	<	if (args_info->nbins_x_orig)
341	<	{
342	<	free (args_info->nbins_x_orig); /* free previous argument */
343	<	args_info->nbins_x_orig = 0;
344	<	}
345	<	if (args_info->nbins_y_orig)
346	<	{
347	<	free (args_info->nbins_y_orig); /* free previous argument */
348	<	args_info->nbins_y_orig = 0;
349	<	}
350	<	if (args_info->nanglebins_orig)
281	<	{
282	<	free (args_info->nanglebins_orig); /* free previous argument */
283	<	args_info->nanglebins_orig = 0;
284	<	}
285	<	if (args_info->length_orig)
286	<	{
287	<	free (args_info->length_orig); /* free previous argument */
288	<	args_info->length_orig = 0;
289	<	}
290	<	if (args_info->rcut_orig)
291	<	{
292	<	free (args_info->rcut_orig); /* free previous argument */
293	<	args_info->rcut_orig = 0;
294	<	}
295	<	if (args_info->zoffset_orig)
296	<	{
297	<	free (args_info->zoffset_orig); /* free previous argument */
298	<	args_info->zoffset_orig = 0;
299	<	}
300	<	if (args_info->sele1_arg)
301	<	{
302	<	free (args_info->sele1_arg); /* free previous argument */
303	<	args_info->sele1_arg = 0;
304	<	}
305	<	if (args_info->sele1_orig)
306	<	{
307	<	free (args_info->sele1_orig); /* free previous argument */
308	<	args_info->sele1_orig = 0;
309	<	}
310	<	if (args_info->sele2_arg)
311	<	{
312	<	free (args_info->sele2_arg); /* free previous argument */
313	<	args_info->sele2_arg = 0;
314	<	}
315	<	if (args_info->sele2_orig)
316	<	{
317	<	free (args_info->sele2_orig); /* free previous argument */
318	<	args_info->sele2_orig = 0;
319	<	}
320	<	if (args_info->sele3_arg)
321	<	{
322	<	free (args_info->sele3_arg); /* free previous argument */
323	<	args_info->sele3_arg = 0;
324	<	}
325	<	if (args_info->sele3_orig)
326	<	{
327	<	free (args_info->sele3_orig); /* free previous argument */
328	<	args_info->sele3_orig = 0;
329	<	}
330	<	if (args_info->refsele_arg)
331	<	{
332	<	free (args_info->refsele_arg); /* free previous argument */
333	<	args_info->refsele_arg = 0;
334	<	}
335	<	if (args_info->refsele_orig)
336	<	{
337	<	free (args_info->refsele_orig); /* free previous argument */
338	<	args_info->refsele_orig = 0;
339	<	}
340	<	if (args_info->molname_arg)
341	<	{
342	<	free (args_info->molname_arg); /* free previous argument */
343	<	args_info->molname_arg = 0;
344	<	}
345	<	if (args_info->molname_orig)
346	<	{
347	<	free (args_info->molname_orig); /* free previous argument */
348	<	args_info->molname_orig = 0;
349	<	}
350	<	if (args_info->begin_orig)
351	<	{
352	<	free (args_info->begin_orig); /* free previous argument */
353	<	args_info->begin_orig = 0;
354	<	}
355	<	if (args_info->end_orig)
356	<	{
357	<	free (args_info->end_orig); /* free previous argument */
358	<	args_info->end_orig = 0;
359	<	}
360	<	if (args_info->radius_orig)
361	<	{
362	<	free (args_info->radius_orig); /* free previous argument */
363	<	args_info->radius_orig = 0;
364	<	}
315	>	}
316	>
317	>
318	>	static void
319	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
320	>	{
321	>	unsigned int i;
322	>	free_string_field (&(args_info->input_arg));
323	>	free_string_field (&(args_info->input_orig));
324	>	free_string_field (&(args_info->output_arg));
325	>	free_string_field (&(args_info->output_orig));
326	>	free_string_field (&(args_info->step_orig));
327	>	free_string_field (&(args_info->nbins_orig));
328	>	free_string_field (&(args_info->nbins_x_orig));
329	>	free_string_field (&(args_info->nbins_y_orig));
330	>	free_string_field (&(args_info->nanglebins_orig));
331	>	free_string_field (&(args_info->rcut_orig));
332	>	free_string_field (&(args_info->dz_orig));
333	>	free_string_field (&(args_info->length_orig));
334	>	free_string_field (&(args_info->zlength_orig));
335	>	free_string_field (&(args_info->zoffset_orig));
336	>	free_string_field (&(args_info->sele1_arg));
337	>	free_string_field (&(args_info->sele1_orig));
338	>	free_string_field (&(args_info->sele2_arg));
339	>	free_string_field (&(args_info->sele2_orig));
340	>	free_string_field (&(args_info->sele3_arg));
341	>	free_string_field (&(args_info->sele3_orig));
342	>	free_string_field (&(args_info->refsele_arg));
343	>	free_string_field (&(args_info->refsele_orig));
344	>	free_string_field (&(args_info->comsele_arg));
345	>	free_string_field (&(args_info->comsele_orig));
346	>	free_string_field (&(args_info->molname_arg));
347	>	free_string_field (&(args_info->molname_orig));
348	>	free_string_field (&(args_info->begin_orig));
349	>	free_string_field (&(args_info->end_orig));
350	>	free_string_field (&(args_info->radius_orig));
351
352	+
353		for (i = 0; i < args_info->inputs_num; ++i)
354		free (args_info->inputs [i]);
355	<
355	>
356		if (args_info->inputs_num)
357		free (args_info->inputs);
358	<
358	>
359		clear_given (args_info);
360		}
361
362	+
363	+	static void
364	+	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
365	+	{
366	+	if (arg) {
367	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
368	+	} else {
369	+	fprintf(outfile, "%s\n", opt);
370	+	}
371	+	}
372	+
373	+
374		int
375	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
376	+	{
377	+	int i = 0;
378	+
379	+	if (!outfile)
380	+	{
381	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
382	+	return EXIT_FAILURE;
383	+	}
384	+
385	+	if (args_info->help_given)
386	+	write_into_file(outfile, "help", 0, 0 );
387	+	if (args_info->version_given)
388	+	write_into_file(outfile, "version", 0, 0 );
389	+	if (args_info->input_given)
390	+	write_into_file(outfile, "input", args_info->input_orig, 0);
391	+	if (args_info->output_given)
392	+	write_into_file(outfile, "output", args_info->output_orig, 0);
393	+	if (args_info->step_given)
394	+	write_into_file(outfile, "step", args_info->step_orig, 0);
395	+	if (args_info->nbins_given)
396	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
397	+	if (args_info->nbins_x_given)
398	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
399	+	if (args_info->nbins_y_given)
400	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
401	+	if (args_info->nanglebins_given)
402	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
403	+	if (args_info->rcut_given)
404	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
405	+	if (args_info->dz_given)
406	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
407	+	if (args_info->length_given)
408	+	write_into_file(outfile, "length", args_info->length_orig, 0);
409	+	if (args_info->zlength_given)
410	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
411	+	if (args_info->zoffset_given)
412	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
413	+	if (args_info->sele1_given)
414	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
415	+	if (args_info->sele2_given)
416	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
417	+	if (args_info->sele3_given)
418	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
419	+	if (args_info->refsele_given)
420	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
421	+	if (args_info->comsele_given)
422	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
423	+	if (args_info->molname_given)
424	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
425	+	if (args_info->begin_given)
426	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
427	+	if (args_info->end_given)
428	+	write_into_file(outfile, "end", args_info->end_orig, 0);
429	+	if (args_info->radius_given)
430	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
431	+	if (args_info->bo_given)
432	+	write_into_file(outfile, "bo", 0, 0 );
433	+	if (args_info->bor_given)
434	+	write_into_file(outfile, "bor", 0, 0 );
435	+	if (args_info->bad_given)
436	+	write_into_file(outfile, "bad", 0, 0 );
437	+	if (args_info->count_given)
438	+	write_into_file(outfile, "count", 0, 0 );
439	+	if (args_info->gofr_given)
440	+	write_into_file(outfile, "gofr", 0, 0 );
441	+	if (args_info->gofz_given)
442	+	write_into_file(outfile, "gofz", 0, 0 );
443	+	if (args_info->r_theta_given)
444	+	write_into_file(outfile, "r_theta", 0, 0 );
445	+	if (args_info->r_omega_given)
446	+	write_into_file(outfile, "r_omega", 0, 0 );
447	+	if (args_info->theta_omega_given)
448	+	write_into_file(outfile, "theta_omega", 0, 0 );
449	+	if (args_info->gxyz_given)
450	+	write_into_file(outfile, "gxyz", 0, 0 );
451	+	if (args_info->twodgofr_given)
452	+	write_into_file(outfile, "twodgofr", 0, 0 );
453	+	if (args_info->p2_given)
454	+	write_into_file(outfile, "p2", 0, 0 );
455	+	if (args_info->rp2_given)
456	+	write_into_file(outfile, "rp2", 0, 0 );
457	+	if (args_info->scd_given)
458	+	write_into_file(outfile, "scd", 0, 0 );
459	+	if (args_info->density_given)
460	+	write_into_file(outfile, "density", 0, 0 );
461	+	if (args_info->slab_density_given)
462	+	write_into_file(outfile, "slab_density", 0, 0 );
463	+	if (args_info->p_angle_given)
464	+	write_into_file(outfile, "p_angle", 0, 0 );
465	+	if (args_info->hxy_given)
466	+	write_into_file(outfile, "hxy", 0, 0 );
467	+	if (args_info->rho_r_given)
468	+	write_into_file(outfile, "rho_r", 0, 0 );
469	+	if (args_info->angle_r_given)
470	+	write_into_file(outfile, "angle_r", 0, 0 );
471	+	if (args_info->hullvol_given)
472	+	write_into_file(outfile, "hullvol", 0, 0 );
473	+
474	+
475	+	i = EXIT_SUCCESS;
476	+	return i;
477	+	}
478	+
479	+	int
480		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
481		{
482		FILE *outfile;
#	Line 386 | Line 490 | cmdline_parser_file_save(const char *filename, struct
490		return EXIT_FAILURE;
491		}
492
493	<	if (args_info->help_given) {
390	<	fprintf(outfile, "%s\n", "help");
391	<	}
392	<	if (args_info->version_given) {
393	<	fprintf(outfile, "%s\n", "version");
394	<	}
395	<	if (args_info->input_given) {
396	<	if (args_info->input_orig) {
397	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
398	<	} else {
399	<	fprintf(outfile, "%s\n", "input");
400	<	}
401	<	}
402	<	if (args_info->output_given) {
403	<	if (args_info->output_orig) {
404	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
405	<	} else {
406	<	fprintf(outfile, "%s\n", "output");
407	<	}
408	<	}
409	<	if (args_info->step_given) {
410	<	if (args_info->step_orig) {
411	<	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
412	<	} else {
413	<	fprintf(outfile, "%s\n", "step");
414	<	}
415	<	}
416	<	if (args_info->nbins_given) {
417	<	if (args_info->nbins_orig) {
418	<	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
419	<	} else {
420	<	fprintf(outfile, "%s\n", "nbins");
421	<	}
422	<	}
423	<	if (args_info->nbins_x_given) {
424	<	if (args_info->nbins_x_orig) {
425	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
426	<	} else {
427	<	fprintf(outfile, "%s\n", "nbins_x");
428	<	}
429	<	}
430	<	if (args_info->nbins_y_given) {
431	<	if (args_info->nbins_y_orig) {
432	<	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
433	<	} else {
434	<	fprintf(outfile, "%s\n", "nbins_y");
435	<	}
436	<	}
437	<	if (args_info->nanglebins_given) {
438	<	if (args_info->nanglebins_orig) {
439	<	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
440	<	} else {
441	<	fprintf(outfile, "%s\n", "nanglebins");
442	<	}
443	<	}
444	<	if (args_info->length_given) {
445	<	if (args_info->length_orig) {
446	<	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
447	<	} else {
448	<	fprintf(outfile, "%s\n", "length");
449	<	}
450	<	}
451	<	if (args_info->rcut_given) {
452	<	if (args_info->rcut_orig) {
453	<	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
454	<	} else {
455	<	fprintf(outfile, "%s\n", "rcut");
456	<	}
457	<	}
458	<	if (args_info->zoffset_given) {
459	<	if (args_info->zoffset_orig) {
460	<	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
461	<	} else {
462	<	fprintf(outfile, "%s\n", "zoffset");
463	<	}
464	<	}
465	<	if (args_info->sele1_given) {
466	<	if (args_info->sele1_orig) {
467	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
468	<	} else {
469	<	fprintf(outfile, "%s\n", "sele1");
470	<	}
471	<	}
472	<	if (args_info->sele2_given) {
473	<	if (args_info->sele2_orig) {
474	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
475	<	} else {
476	<	fprintf(outfile, "%s\n", "sele2");
477	<	}
478	<	}
479	<	if (args_info->sele3_given) {
480	<	if (args_info->sele3_orig) {
481	<	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
482	<	} else {
483	<	fprintf(outfile, "%s\n", "sele3");
484	<	}
485	<	}
486	<	if (args_info->refsele_given) {
487	<	if (args_info->refsele_orig) {
488	<	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
489	<	} else {
490	<	fprintf(outfile, "%s\n", "refsele");
491	<	}
492	<	}
493	<	if (args_info->molname_given) {
494	<	if (args_info->molname_orig) {
495	<	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
496	<	} else {
497	<	fprintf(outfile, "%s\n", "molname");
498	<	}
499	<	}
500	<	if (args_info->begin_given) {
501	<	if (args_info->begin_orig) {
502	<	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
503	<	} else {
504	<	fprintf(outfile, "%s\n", "begin");
505	<	}
506	<	}
507	<	if (args_info->end_given) {
508	<	if (args_info->end_orig) {
509	<	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
510	<	} else {
511	<	fprintf(outfile, "%s\n", "end");
512	<	}
513	<	}
514	<	if (args_info->radius_given) {
515	<	if (args_info->radius_orig) {
516	<	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
517	<	} else {
518	<	fprintf(outfile, "%s\n", "radius");
519	<	}
520	<	}
521	<	if (args_info->bo_given) {
522	<	fprintf(outfile, "%s\n", "bo");
523	<	}
524	<	if (args_info->bor_given) {
525	<	fprintf(outfile, "%s\n", "bor");
526	<	}
527	<	if (args_info->gofr_given) {
528	<	fprintf(outfile, "%s\n", "gofr");
529	<	}
530	<	if (args_info->r_theta_given) {
531	<	fprintf(outfile, "%s\n", "r_theta");
532	<	}
533	<	if (args_info->r_omega_given) {
534	<	fprintf(outfile, "%s\n", "r_omega");
535	<	}
536	<	if (args_info->theta_omega_given) {
537	<	fprintf(outfile, "%s\n", "theta_omega");
538	<	}
539	<	if (args_info->gxyz_given) {
540	<	fprintf(outfile, "%s\n", "gxyz");
541	<	}
542	<	if (args_info->p2_given) {
543	<	fprintf(outfile, "%s\n", "p2");
544	<	}
545	<	if (args_info->rp2_given) {
546	<	fprintf(outfile, "%s\n", "rp2");
547	<	}
548	<	if (args_info->scd_given) {
549	<	fprintf(outfile, "%s\n", "scd");
550	<	}
551	<	if (args_info->density_given) {
552	<	fprintf(outfile, "%s\n", "density");
553	<	}
554	<	if (args_info->slab_density_given) {
555	<	fprintf(outfile, "%s\n", "slab_density");
556	<	}
557	<	if (args_info->hxy_given) {
558	<	fprintf(outfile, "%s\n", "hxy");
559	<	}
560	<	if (args_info->rho_r_given) {
561	<	fprintf(outfile, "%s\n", "rho_r");
562	<	}
563	<
493	>	i = cmdline_parser_dump(outfile, args_info);
494		fclose (outfile);
495
566	–	i = EXIT_SUCCESS;
496		return i;
497		}
498
#	Line 573 | Line 502 | cmdline_parser_free (struct gengetopt_args_info *args_
502		cmdline_parser_release (args_info);
503		}
504
505	<
577	<	/* gengetopt_strdup() */
578	<	/* strdup.c replacement of strdup, which is not standard */
505	>	/** @brief replacement of strdup, which is not standard */
506		char *
507		gengetopt_strdup (const char *s)
508		{
#	Line 591 | Line 518 | static void
518		}
519
520		static void
594	–	reset_group_staticProps(struct gengetopt_args_info *args_info);
595	–
596	–	static void
521		reset_group_staticProps(struct gengetopt_args_info *args_info)
522		{
523		if (! args_info->staticProps_group_counter)
#	Line 601 | Line 525 | reset_group_staticProps(struct gengetopt_args_info *ar
525
526		args_info->bo_given = 0 ;
527		args_info->bor_given = 0 ;
528	+	args_info->bad_given = 0 ;
529	+	args_info->count_given = 0 ;
530		args_info->gofr_given = 0 ;
531	+	args_info->gofz_given = 0 ;
532		args_info->r_theta_given = 0 ;
533		args_info->r_omega_given = 0 ;
534		args_info->theta_omega_given = 0 ;
535		args_info->gxyz_given = 0 ;
536	+	args_info->twodgofr_given = 0 ;
537		args_info->p2_given = 0 ;
538		args_info->rp2_given = 0 ;
539		args_info->scd_given = 0 ;
540		args_info->density_given = 0 ;
541		args_info->slab_density_given = 0 ;
542	+	args_info->p_angle_given = 0 ;
543		args_info->hxy_given = 0 ;
544		args_info->rho_r_given = 0 ;
545	+	args_info->angle_r_given = 0 ;
546	+	args_info->hullvol_given = 0 ;
547
548		args_info->staticProps_group_counter = 0;
549		}
#	Line 624 | Line 555 | int
555		}
556
557		int
558	+	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
559	+	struct cmdline_parser_params *params)
560	+	{
561	+	int result;
562	+	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
563	+
564	+	if (result == EXIT_FAILURE)
565	+	{
566	+	cmdline_parser_free (args_info);
567	+	exit (EXIT_FAILURE);
568	+	}
569	+
570	+	return result;
571	+	}
572	+
573	+	int
574		cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
575		{
576		int result;
577	+	struct cmdline_parser_params params;
578	+
579	+	params.override = override;
580	+	params.initialize = initialize;
581	+	params.check_required = check_required;
582	+	params.check_ambiguity = 0;
583	+	params.print_errors = 1;
584
585	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
585	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
586
587		if (result == EXIT_FAILURE)
588		{
#	Line 678 | Line 632 | cmdline_parser_required2 (struct gengetopt_args_info *
632		/* checks for dependences among options */
633
634		return error;
635	+	}
636	+
637	+
638	+	static char *package_name = 0;
639	+
640	+	/**
641	+	* @brief updates an option
642	+	* @param field the generic pointer to the field to update
643	+	* @param orig_field the pointer to the orig field
644	+	* @param field_given the pointer to the number of occurrence of this option
645	+	* @param prev_given the pointer to the number of occurrence already seen
646	+	* @param value the argument for this option (if null no arg was specified)
647	+	* @param possible_values the possible values for this option (if specified)
648	+	* @param default_value the default value (in case the option only accepts fixed values)
649	+	* @param arg_type the type of this option
650	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
651	+	* @param override @see cmdline_parser_params.override
652	+	* @param no_free whether to free a possible previous value
653	+	* @param multiple_option whether this is a multiple option
654	+	* @param long_opt the corresponding long option
655	+	* @param short_opt the corresponding short option (or '-' if none)
656	+	* @param additional_error possible further error specification
657	+	*/
658	+	static
659	+	int update_arg(void *field, char **orig_field,
660	+	unsigned int *field_given, unsigned int *prev_given,
661	+	char *value, char *possible_values[], const char *default_value,
662	+	cmdline_parser_arg_type arg_type,
663	+	int check_ambiguity, int override,
664	+	int no_free, int multiple_option,
665	+	const char *long_opt, char short_opt,
666	+	const char *additional_error)
667	+	{
668	+	char *stop_char = 0;
669	+	const char *val = value;
670	+	int found;
671	+	char **string_field;
672	+
673	+	stop_char = 0;
674	+	found = 0;
675	+
676	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
677	+	{
678	+	if (short_opt != '-')
679	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
680	+	package_name, long_opt, short_opt,
681	+	(additional_error ? additional_error : ""));
682	+	else
683	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
684	+	package_name, long_opt,
685	+	(additional_error ? additional_error : ""));
686	+	return 1; /* failure */
687	+	}
688	+
689	+
690	+	if (field_given && *field_given && ! override)
691	+	return 0;
692	+	if (prev_given)
693	+	(*prev_given)++;
694	+	if (field_given)
695	+	(*field_given)++;
696	+	if (possible_values)
697	+	val = possible_values[found];
698	+
699	+	switch(arg_type) {
700	+	case ARG_INT:
701	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
702	+	break;
703	+	case ARG_DOUBLE:
704	+	if (val) *((double *)field) = strtod (val, &stop_char);
705	+	break;
706	+	case ARG_STRING:
707	+	if (val) {
708	+	string_field = (char **)field;
709	+	if (!no_free && *string_field)
710	+	free (*string_field); /* free previous string */
711	+	*string_field = gengetopt_strdup (val);
712	+	}
713	+	break;
714	+	default:
715	+	break;
716	+	};
717	+
718	+	/* check numeric conversion */
719	+	switch(arg_type) {
720	+	case ARG_INT:
721	+	case ARG_DOUBLE:
722	+	if (val && !(stop_char && *stop_char == '\0')) {
723	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
724	+	return 1; /* failure */
725	+	}
726	+	break;
727	+	default:
728	+	;
729	+	};
730	+
731	+	/* store the original value */
732	+	switch(arg_type) {
733	+	case ARG_NO:
734	+	break;
735	+	default:
736	+	if (value && orig_field) {
737	+	if (no_free) {
738	+	*orig_field = value;
739	+	} else {
740	+	if (*orig_field)
741	+	free (*orig_field); /* free previous string */
742	+	*orig_field = gengetopt_strdup (value);
743	+	}
744	+	}
745	+	};
746	+
747	+	return 0; /* OK */
748		}
749
750	+
751		int
752	<	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)
752	>	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
753	>	struct cmdline_parser_params *params, const char *additional_error)
754		{
755		int c;        /* Character of the parsed option.  */
756
757		int error = 0;
758		struct gengetopt_args_info local_args_info;
759	+
760	+	int override;
761	+	int initialize;
762	+	int check_required;
763	+	int check_ambiguity;
764	+
765	+	package_name = argv[0];
766	+
767	+	override = params->override;
768	+	initialize = params->initialize;
769	+	check_required = params->check_required;
770	+	check_ambiguity = params->check_ambiguity;
771
772		if (initialize)
773		cmdline_parser_init (args_info);
#	Line 695 | Line 776 | cmdline_parser_internal (int argc, char * const *argv,
776
777		optarg = 0;
778		optind = 0;
779	<	opterr = 1;
779	>	opterr = params->print_errors;
780		optopt = '?';
781
782		while (1)
783		{
784		int option_index = 0;
704	–	char *stop_char;
785
786		static struct option long_options[] = {
787		{ "help",       0, NULL, 'h' },
#	Line 713 | Line 793 | cmdline_parser_internal (int argc, char * const *argv,
793		{ "nbins_x",    1, NULL, 'x' },
794		{ "nbins_y",    1, NULL, 'y' },
795		{ "nanglebins", 1, NULL, 'a' },
716	–	{ "length",     1, NULL, 0 },
796		{ "rcut",       1, NULL, 'c' },
797	+	{ "dz", 1, NULL, 0 },
798	+	{ "length",     1, NULL, 0 },
799	+	{ "zlength",    1, NULL, 0 },
800		{ "zoffset",    1, NULL, 'z' },
801		{ "sele1",      1, NULL, 0 },
802		{ "sele2",      1, NULL, 0 },
803		{ "sele3",      1, NULL, 0 },
804		{ "refsele",    1, NULL, 0 },
805	+	{ "comsele",    1, NULL, 0 },
806		{ "molname",    1, NULL, 0 },
807		{ "begin",      1, NULL, 0 },
808		{ "end",        1, NULL, 0 },
809		{ "radius",     1, NULL, 0 },
810		{ "bo", 0, NULL, 0 },
811		{ "bor",        0, NULL, 0 },
812	+	{ "bad",        0, NULL, 0 },
813	+	{ "count",      0, NULL, 0 },
814		{ "gofr",       0, NULL, 'g' },
815	+	{ "gofz",       0, NULL, 0 },
816		{ "r_theta",    0, NULL, 0 },
817		{ "r_omega",    0, NULL, 0 },
818		{ "theta_omega",        0, NULL, 0 },
819		{ "gxyz",       0, NULL, 0 },
820	+	{ "twodgofr",   0, NULL, 0 },
821		{ "p2", 0, NULL, 'p' },
822		{ "rp2",        0, NULL, 0 },
823		{ "scd",        0, NULL, 's' },
824		{ "density",    0, NULL, 'd' },
825		{ "slab_density",       0, NULL, 0 },
826	+	{ "p_angle",    0, NULL, 0 },
827		{ "hxy",        0, NULL, 0 },
828		{ "rho_r",      0, NULL, 0 },
829	+	{ "angle_r",    0, NULL, 0 },
830	+	{ "hullvol",    0, NULL, 0 },
831		{ NULL, 0, NULL, 0 }
832		};
833
744	–	stop_char = 0;
834		c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
835
836		if (c == -1) break;       /* Exit from `while (1)' loop.  */
#	Line 759 | Line 848 | cmdline_parser_internal (int argc, char * const *argv,
848		exit (EXIT_SUCCESS);
849
850		case 'i':       /* input dump file.  */
851	<	if (local_args_info.input_given)
852	<	{
853	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
854	<	goto failure;
855	<	}
856	<	if (args_info->input_given && ! override)
857	<	continue;
858	<	local_args_info.input_given = 1;
859	<	args_info->input_given = 1;
860	<	if (args_info->input_arg)
772	<	free (args_info->input_arg); /* free previous string */
773	<	args_info->input_arg = gengetopt_strdup (optarg);
774	<	if (args_info->input_orig)
775	<	free (args_info->input_orig); /* free previous string */
776	<	args_info->input_orig = gengetopt_strdup (optarg);
851	>
852	>
853	>	if (update_arg( (void *)&(args_info->input_arg),
854	>	&(args_info->input_orig), &(args_info->input_given),
855	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
856	>	check_ambiguity, override, 0, 0,
857	>	"input", 'i',
858	>	additional_error))
859	>	goto failure;
860	>
861		break;
778	–
862		case 'o':       /* output file name.  */
863	<	if (local_args_info.output_given)
864	<	{
865	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
866	<	goto failure;
867	<	}
868	<	if (args_info->output_given && ! override)
869	<	continue;
870	<	local_args_info.output_given = 1;
871	<	args_info->output_given = 1;
872	<	if (args_info->output_arg)
790	<	free (args_info->output_arg); /* free previous string */
791	<	args_info->output_arg = gengetopt_strdup (optarg);
792	<	if (args_info->output_orig)
793	<	free (args_info->output_orig); /* free previous string */
794	<	args_info->output_orig = gengetopt_strdup (optarg);
863	>
864	>
865	>	if (update_arg( (void *)&(args_info->output_arg),
866	>	&(args_info->output_orig), &(args_info->output_given),
867	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
868	>	check_ambiguity, override, 0, 0,
869	>	"output", 'o',
870	>	additional_error))
871	>	goto failure;
872	>
873		break;
796	–
874		case 'n':       /* process every n frame.  */
875	<	if (local_args_info.step_given)
876	<	{
877	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
878	<	goto failure;
879	<	}
880	<	if (args_info->step_given && ! override)
881	<	continue;
882	<	local_args_info.step_given = 1;
806	<	args_info->step_given = 1;
807	<	args_info->step_arg = strtol (optarg, &stop_char, 0);
808	<	if (!(stop_char && *stop_char == '\0')) {
809	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
875	>
876	>
877	>	if (update_arg( (void *)&(args_info->step_arg),
878	>	&(args_info->step_orig), &(args_info->step_given),
879	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
880	>	check_ambiguity, override, 0, 0,
881	>	"step", 'n',
882	>	additional_error))
883		goto failure;
884	<	}
812	<	if (args_info->step_orig)
813	<	free (args_info->step_orig); /* free previous string */
814	<	args_info->step_orig = gengetopt_strdup (optarg);
884	>
885		break;
816	–
886		case 'b':       /* number of bins (general purpose).  */
887	<	if (local_args_info.nbins_given)
888	<	{
889	<	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
890	<	goto failure;
891	<	}
892	<	if (args_info->nbins_given && ! override)
893	<	continue;
894	<	local_args_info.nbins_given = 1;
826	<	args_info->nbins_given = 1;
827	<	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
828	<	if (!(stop_char && *stop_char == '\0')) {
829	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
887	>
888	>
889	>	if (update_arg( (void *)&(args_info->nbins_arg),
890	>	&(args_info->nbins_orig), &(args_info->nbins_given),
891	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
892	>	check_ambiguity, override, 0, 0,
893	>	"nbins", 'b',
894	>	additional_error))
895		goto failure;
896	<	}
832	<	if (args_info->nbins_orig)
833	<	free (args_info->nbins_orig); /* free previous string */
834	<	args_info->nbins_orig = gengetopt_strdup (optarg);
896	>
897		break;
836	–
898		case 'x':       /* number of bins in x axis.  */
899	<	if (local_args_info.nbins_x_given)
900	<	{
901	<	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
902	<	goto failure;
903	<	}
904	<	if (args_info->nbins_x_given && ! override)
905	<	continue;
906	<	local_args_info.nbins_x_given = 1;
846	<	args_info->nbins_x_given = 1;
847	<	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
848	<	if (!(stop_char && *stop_char == '\0')) {
849	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
899	>
900	>
901	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
902	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
903	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
904	>	check_ambiguity, override, 0, 0,
905	>	"nbins_x", 'x',
906	>	additional_error))
907		goto failure;
908	<	}
852	<	if (args_info->nbins_x_orig)
853	<	free (args_info->nbins_x_orig); /* free previous string */
854	<	args_info->nbins_x_orig = gengetopt_strdup (optarg);
908	>
909		break;
856	–
910		case 'y':       /* number of bins in y axis.  */
911	<	if (local_args_info.nbins_y_given)
912	<	{
913	<	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
914	<	goto failure;
915	<	}
916	<	if (args_info->nbins_y_given && ! override)
917	<	continue;
918	<	local_args_info.nbins_y_given = 1;
866	<	args_info->nbins_y_given = 1;
867	<	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
868	<	if (!(stop_char && *stop_char == '\0')) {
869	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
911	>
912	>
913	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
914	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
915	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
916	>	check_ambiguity, override, 0, 0,
917	>	"nbins_y", 'y',
918	>	additional_error))
919		goto failure;
920	<	}
872	<	if (args_info->nbins_y_orig)
873	<	free (args_info->nbins_y_orig); /* free previous string */
874	<	args_info->nbins_y_orig = gengetopt_strdup (optarg);
920	>
921		break;
876	–
922		case 'a':       /* number of bins for cos(angle).  */
923	<	if (local_args_info.nanglebins_given)
924	<	{
925	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
926	<	goto failure;
927	<	}
928	<	if (args_info->nanglebins_given && ! override)
929	<	continue;
930	<	local_args_info.nanglebins_given = 1;
886	<	args_info->nanglebins_given = 1;
887	<	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
888	<	if (!(stop_char && *stop_char == '\0')) {
889	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
923	>
924	>
925	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
926	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
927	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
928	>	check_ambiguity, override, 0, 0,
929	>	"nanglebins", 'a',
930	>	additional_error))
931		goto failure;
932	<	}
892	<	if (args_info->nanglebins_orig)
893	<	free (args_info->nanglebins_orig); /* free previous string */
894	<	args_info->nanglebins_orig = gengetopt_strdup (optarg);
932	>
933		break;
896	–
934		case 'c':       /* cutoff radius (rcut).  */
935	<	if (local_args_info.rcut_given)
936	<	{
937	<	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
938	<	goto failure;
939	<	}
940	<	if (args_info->rcut_given && ! override)
941	<	continue;
942	<	local_args_info.rcut_given = 1;
906	<	args_info->rcut_given = 1;
907	<	args_info->rcut_arg = strtod (optarg, &stop_char);
908	<	if (!(stop_char && *stop_char == '\0')) {
909	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
935	>
936	>
937	>	if (update_arg( (void *)&(args_info->rcut_arg),
938	>	&(args_info->rcut_orig), &(args_info->rcut_given),
939	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
940	>	check_ambiguity, override, 0, 0,
941	>	"rcut", 'c',
942	>	additional_error))
943		goto failure;
944	<	}
912	<	if (args_info->rcut_orig)
913	<	free (args_info->rcut_orig); /* free previous string */
914	<	args_info->rcut_orig = gengetopt_strdup (optarg);
944	>
945		break;
916	–
946		case 'z':       /* Where to set the zero for the slab_density calculation.  */
947	<	if (local_args_info.zoffset_given)
948	<	{
949	<	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
950	<	goto failure;
951	<	}
952	<	if (args_info->zoffset_given && ! override)
953	<	continue;
954	<	local_args_info.zoffset_given = 1;
926	<	args_info->zoffset_given = 1;
927	<	args_info->zoffset_arg = strtod (optarg, &stop_char);
928	<	if (!(stop_char && *stop_char == '\0')) {
929	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
947	>
948	>
949	>	if (update_arg( (void *)&(args_info->zoffset_arg),
950	>	&(args_info->zoffset_orig), &(args_info->zoffset_given),
951	>	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
952	>	check_ambiguity, override, 0, 0,
953	>	"zoffset", 'z',
954	>	additional_error))
955		goto failure;
956	<	}
932	<	if (args_info->zoffset_orig)
933	<	free (args_info->zoffset_orig); /* free previous string */
934	<	args_info->zoffset_orig = gengetopt_strdup (optarg);
956	>
957		break;
936	–
958		case 'g':       /* g(r).  */
959	<	if (local_args_info.gofr_given)
939	<	{
940	<	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
941	<	goto failure;
942	<	}
943	<	if (args_info->gofr_given && ! override)
944	<	continue;
945	<	local_args_info.gofr_given = 1;
946	<	args_info->gofr_given = 1;
959	>
960		if (args_info->staticProps_group_counter && override)
961		reset_group_staticProps (args_info);
962		args_info->staticProps_group_counter += 1;
963	+
964	+	if (update_arg( 0 ,
965	+	0 , &(args_info->gofr_given),
966	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
967	+	check_ambiguity, override, 0, 0,
968	+	"gofr", 'g',
969	+	additional_error))
970	+	goto failure;
971	+
972		break;
951	–
973		case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
974	<	if (local_args_info.p2_given)
954	<	{
955	<	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
956	<	goto failure;
957	<	}
958	<	if (args_info->p2_given && ! override)
959	<	continue;
960	<	local_args_info.p2_given = 1;
961	<	args_info->p2_given = 1;
974	>
975		if (args_info->staticProps_group_counter && override)
976		reset_group_staticProps (args_info);
977		args_info->staticProps_group_counter += 1;
978	+
979	+	if (update_arg( 0 ,
980	+	0 , &(args_info->p2_given),
981	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
982	+	check_ambiguity, override, 0, 0,
983	+	"p2", 'p',
984	+	additional_error))
985	+	goto failure;
986	+
987		break;
966	–
988		case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
989	<	if (local_args_info.scd_given)
969	<	{
970	<	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	<	goto failure;
972	<	}
973	<	if (args_info->scd_given && ! override)
974	<	continue;
975	<	local_args_info.scd_given = 1;
976	<	args_info->scd_given = 1;
989	>
990		if (args_info->staticProps_group_counter && override)
991		reset_group_staticProps (args_info);
992		args_info->staticProps_group_counter += 1;
993	<	break;
994	<
993	>
994	>	if (update_arg( 0 ,
995	>	0 , &(args_info->scd_given),
996	>	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
997	>	check_ambiguity, override, 0, 0,
998	>	"scd", 's',
999	>	additional_error))
1000	>	goto failure;
1001	>
1002	>	break;
1003		case 'd':       /* density plot.  */
1004	<	if (local_args_info.density_given)
984	<	{
985	<	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
986	<	goto failure;
987	<	}
988	<	if (args_info->density_given && ! override)
989	<	continue;
990	<	local_args_info.density_given = 1;
991	<	args_info->density_given = 1;
1004	>
1005		if (args_info->staticProps_group_counter && override)
1006		reset_group_staticProps (args_info);
1007		args_info->staticProps_group_counter += 1;
1008	+
1009	+	if (update_arg( 0 ,
1010	+	0 , &(args_info->density_given),
1011	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1012	+	check_ambiguity, override, 0, 0,
1013	+	"density", 'd',
1014	+	additional_error))
1015	+	goto failure;
1016	+
1017		break;
1018
997	–
1019		case 0: /* Long option with no short option */
1020	+	/* slab width (dz).  */
1021	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1022	+	{
1023	+
1024	+
1025	+	if (update_arg( (void *)&(args_info->dz_arg),
1026	+	&(args_info->dz_orig), &(args_info->dz_given),
1027	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1028	+	check_ambiguity, override, 0, 0,
1029	+	"dz", '-',
1030	+	additional_error))
1031	+	goto failure;
1032	+
1033	+	}
1034		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1035		if (strcmp (long_options[option_index].name, "length") == 0)
1036		{
1037	<	if (local_args_info.length_given)
1038	<	{
1039	<	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1040	<	goto failure;
1041	<	}
1042	<	if (args_info->length_given && ! override)
1043	<	continue;
1044	<	local_args_info.length_given = 1;
1010	<	args_info->length_given = 1;
1011	<	args_info->length_arg = strtod (optarg, &stop_char);
1012	<	if (!(stop_char && *stop_char == '\0')) {
1013	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1037	>
1038	>
1039	>	if (update_arg( (void *)&(args_info->length_arg),
1040	>	&(args_info->length_orig), &(args_info->length_given),
1041	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1042	>	check_ambiguity, override, 0, 0,
1043	>	"length", '-',
1044	>	additional_error))
1045		goto failure;
1046	<	}
1016	<	if (args_info->length_orig)
1017	<	free (args_info->length_orig); /* free previous string */
1018	<	args_info->length_orig = gengetopt_strdup (optarg);
1046	>
1047		}
1048	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1049	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1050	+	{
1051	+
1052	+
1053	+	if (update_arg( (void *)&(args_info->zlength_arg),
1054	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1055	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1056	+	check_ambiguity, override, 0, 0,
1057	+	"zlength", '-',
1058	+	additional_error))
1059	+	goto failure;
1060	+
1061	+	}
1062		/* select the first stuntdouble set.  */
1063		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1064		{
1065	<	if (local_args_info.sele1_given)
1066	<	{
1067	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1068	<	goto failure;
1069	<	}
1070	<	if (args_info->sele1_given && ! override)
1071	<	continue;
1072	<	local_args_info.sele1_given = 1;
1073	<	args_info->sele1_given = 1;
1074	<	if (args_info->sele1_arg)
1033	<	free (args_info->sele1_arg); /* free previous string */
1034	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1035	<	if (args_info->sele1_orig)
1036	<	free (args_info->sele1_orig); /* free previous string */
1037	<	args_info->sele1_orig = gengetopt_strdup (optarg);
1065	>
1066	>
1067	>	if (update_arg( (void *)&(args_info->sele1_arg),
1068	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1069	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1070	>	check_ambiguity, override, 0, 0,
1071	>	"sele1", '-',
1072	>	additional_error))
1073	>	goto failure;
1074	>
1075		}
1076		/* select the second stuntdouble set.  */
1077		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1078		{
1079	<	if (local_args_info.sele2_given)
1080	<	{
1081	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1082	<	goto failure;
1083	<	}
1084	<	if (args_info->sele2_given && ! override)
1085	<	continue;
1086	<	local_args_info.sele2_given = 1;
1087	<	args_info->sele2_given = 1;
1088	<	if (args_info->sele2_arg)
1052	<	free (args_info->sele2_arg); /* free previous string */
1053	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1054	<	if (args_info->sele2_orig)
1055	<	free (args_info->sele2_orig); /* free previous string */
1056	<	args_info->sele2_orig = gengetopt_strdup (optarg);
1079	>
1080	>
1081	>	if (update_arg( (void *)&(args_info->sele2_arg),
1082	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1083	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1084	>	check_ambiguity, override, 0, 0,
1085	>	"sele2", '-',
1086	>	additional_error))
1087	>	goto failure;
1088	>
1089		}
1090		/* select the third stuntdouble set.  */
1091		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1092		{
1093	<	if (local_args_info.sele3_given)
1094	<	{
1095	<	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1096	<	goto failure;
1097	<	}
1098	<	if (args_info->sele3_given && ! override)
1099	<	continue;
1100	<	local_args_info.sele3_given = 1;
1101	<	args_info->sele3_given = 1;
1102	<	if (args_info->sele3_arg)
1071	<	free (args_info->sele3_arg); /* free previous string */
1072	<	args_info->sele3_arg = gengetopt_strdup (optarg);
1073	<	if (args_info->sele3_orig)
1074	<	free (args_info->sele3_orig); /* free previous string */
1075	<	args_info->sele3_orig = gengetopt_strdup (optarg);
1093	>
1094	>
1095	>	if (update_arg( (void *)&(args_info->sele3_arg),
1096	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1097	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1098	>	check_ambiguity, override, 0, 0,
1099	>	"sele3", '-',
1100	>	additional_error))
1101	>	goto failure;
1102	>
1103		}
1104		/* select reference (use and only use with --gxyz).  */
1105		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1106		{
1107	<	if (local_args_info.refsele_given)
1108	<	{
1109	<	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1110	<	goto failure;
1111	<	}
1112	<	if (args_info->refsele_given && ! override)
1113	<	continue;
1114	<	local_args_info.refsele_given = 1;
1115	<	args_info->refsele_given = 1;
1116	<	if (args_info->refsele_arg)
1090	<	free (args_info->refsele_arg); /* free previous string */
1091	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1092	<	if (args_info->refsele_orig)
1093	<	free (args_info->refsele_orig); /* free previous string */
1094	<	args_info->refsele_orig = gengetopt_strdup (optarg);
1107	>
1108	>
1109	>	if (update_arg( (void *)&(args_info->refsele_arg),
1110	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1111	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1112	>	check_ambiguity, override, 0, 0,
1113	>	"refsele", '-',
1114	>	additional_error))
1115	>	goto failure;
1116	>
1117		}
1118	+	/* select stunt doubles for center-of-mass reference point.  */
1119	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1120	+	{
1121	+
1122	+
1123	+	if (update_arg( (void *)&(args_info->comsele_arg),
1124	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1125	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1126	+	check_ambiguity, override, 0, 0,
1127	+	"comsele", '-',
1128	+	additional_error))
1129	+	goto failure;
1130	+
1131	+	}
1132		/* molecule name.  */
1133		else if (strcmp (long_options[option_index].name, "molname") == 0)
1134		{
1135	<	if (local_args_info.molname_given)
1136	<	{
1137	<	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1138	<	goto failure;
1139	<	}
1140	<	if (args_info->molname_given && ! override)
1141	<	continue;
1142	<	local_args_info.molname_given = 1;
1143	<	args_info->molname_given = 1;
1144	<	if (args_info->molname_arg)
1109	<	free (args_info->molname_arg); /* free previous string */
1110	<	args_info->molname_arg = gengetopt_strdup (optarg);
1111	<	if (args_info->molname_orig)
1112	<	free (args_info->molname_orig); /* free previous string */
1113	<	args_info->molname_orig = gengetopt_strdup (optarg);
1135	>
1136	>
1137	>	if (update_arg( (void *)&(args_info->molname_arg),
1138	>	&(args_info->molname_orig), &(args_info->molname_given),
1139	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1140	>	check_ambiguity, override, 0, 0,
1141	>	"molname", '-',
1142	>	additional_error))
1143	>	goto failure;
1144	>
1145		}
1146		/* begin internal index.  */
1147		else if (strcmp (long_options[option_index].name, "begin") == 0)
1148		{
1149	<	if (local_args_info.begin_given)
1150	<	{
1151	<	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1152	<	goto failure;
1153	<	}
1154	<	if (args_info->begin_given && ! override)
1155	<	continue;
1156	<	local_args_info.begin_given = 1;
1126	<	args_info->begin_given = 1;
1127	<	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1128	<	if (!(stop_char && *stop_char == '\0')) {
1129	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1149	>
1150	>
1151	>	if (update_arg( (void *)&(args_info->begin_arg),
1152	>	&(args_info->begin_orig), &(args_info->begin_given),
1153	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1154	>	check_ambiguity, override, 0, 0,
1155	>	"begin", '-',
1156	>	additional_error))
1157		goto failure;
1158	<	}
1132	<	if (args_info->begin_orig)
1133	<	free (args_info->begin_orig); /* free previous string */
1134	<	args_info->begin_orig = gengetopt_strdup (optarg);
1158	>
1159		}
1160		/* end internal index.  */
1161		else if (strcmp (long_options[option_index].name, "end") == 0)
1162		{
1163	<	if (local_args_info.end_given)
1164	<	{
1165	<	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1166	<	goto failure;
1167	<	}
1168	<	if (args_info->end_given && ! override)
1169	<	continue;
1170	<	local_args_info.end_given = 1;
1147	<	args_info->end_given = 1;
1148	<	args_info->end_arg = strtol (optarg, &stop_char, 0);
1149	<	if (!(stop_char && *stop_char == '\0')) {
1150	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1163	>
1164	>
1165	>	if (update_arg( (void *)&(args_info->end_arg),
1166	>	&(args_info->end_orig), &(args_info->end_given),
1167	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1168	>	check_ambiguity, override, 0, 0,
1169	>	"end", '-',
1170	>	additional_error))
1171		goto failure;
1172	<	}
1153	<	if (args_info->end_orig)
1154	<	free (args_info->end_orig); /* free previous string */
1155	<	args_info->end_orig = gengetopt_strdup (optarg);
1172	>
1173		}
1174		/* nanoparticle radius.  */
1175		else if (strcmp (long_options[option_index].name, "radius") == 0)
1176		{
1177	<	if (local_args_info.radius_given)
1178	<	{
1179	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1180	<	goto failure;
1181	<	}
1182	<	if (args_info->radius_given && ! override)
1183	<	continue;
1184	<	local_args_info.radius_given = 1;
1168	<	args_info->radius_given = 1;
1169	<	args_info->radius_arg = strtod (optarg, &stop_char);
1170	<	if (!(stop_char && *stop_char == '\0')) {
1171	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1177	>
1178	>
1179	>	if (update_arg( (void *)&(args_info->radius_arg),
1180	>	&(args_info->radius_orig), &(args_info->radius_given),
1181	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1182	>	check_ambiguity, override, 0, 0,
1183	>	"radius", '-',
1184	>	additional_error))
1185		goto failure;
1186	<	}
1174	<	if (args_info->radius_orig)
1175	<	free (args_info->radius_orig); /* free previous string */
1176	<	args_info->radius_orig = gengetopt_strdup (optarg);
1186	>
1187		}
1188		/* bond order parameter (--rcut must be specified).  */
1189		else if (strcmp (long_options[option_index].name, "bo") == 0)
1190		{
1191	<	if (local_args_info.bo_given)
1182	<	{
1183	<	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1184	<	goto failure;
1185	<	}
1186	<	if (args_info->bo_given && ! override)
1187	<	continue;
1188	<	local_args_info.bo_given = 1;
1189	<	args_info->bo_given = 1;
1191	>
1192		if (args_info->staticProps_group_counter && override)
1193		reset_group_staticProps (args_info);
1194		args_info->staticProps_group_counter += 1;
1195	<	break;
1195	>
1196	>	if (update_arg( 0 ,
1197	>	0 , &(args_info->bo_given),
1198	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1199	>	check_ambiguity, override, 0, 0,
1200	>	"bo", '-',
1201	>	additional_error))
1202	>	goto failure;
1203	>
1204		}
1205		/* bond order parameter as a function of radius (--rcut must be specified).  */
1206		else if (strcmp (long_options[option_index].name, "bor") == 0)
1207		{
1208	<	if (local_args_info.bor_given)
1199	<	{
1200	<	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1201	<	goto failure;
1202	<	}
1203	<	if (args_info->bor_given && ! override)
1204	<	continue;
1205	<	local_args_info.bor_given = 1;
1206	<	args_info->bor_given = 1;
1208	>
1209		if (args_info->staticProps_group_counter && override)
1210		reset_group_staticProps (args_info);
1211		args_info->staticProps_group_counter += 1;
1212	<	break;
1212	>
1213	>	if (update_arg( 0 ,
1214	>	0 , &(args_info->bor_given),
1215	>	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1216	>	check_ambiguity, override, 0, 0,
1217	>	"bor", '-',
1218	>	additional_error))
1219	>	goto failure;
1220	>
1221		}
1222	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1223	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1224	+	{
1225	+
1226	+	if (args_info->staticProps_group_counter && override)
1227	+	reset_group_staticProps (args_info);
1228	+	args_info->staticProps_group_counter += 1;
1229	+
1230	+	if (update_arg( 0 ,
1231	+	0 , &(args_info->bad_given),
1232	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1233	+	check_ambiguity, override, 0, 0,
1234	+	"bad", '-',
1235	+	additional_error))
1236	+	goto failure;
1237	+
1238	+	}
1239	+	/* count of molecules matching selection criteria (and associated statistics).  */
1240	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1241	+	{
1242	+
1243	+	if (args_info->staticProps_group_counter && override)
1244	+	reset_group_staticProps (args_info);
1245	+	args_info->staticProps_group_counter += 1;
1246	+
1247	+	if (update_arg( 0 ,
1248	+	0 , &(args_info->count_given),
1249	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1250	+	check_ambiguity, override, 0, 0,
1251	+	"count", '-',
1252	+	additional_error))
1253	+	goto failure;
1254	+
1255	+	}
1256	+	/* g(z).  */
1257	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1258	+	{
1259	+
1260	+	if (args_info->staticProps_group_counter && override)
1261	+	reset_group_staticProps (args_info);
1262	+	args_info->staticProps_group_counter += 1;
1263	+
1264	+	if (update_arg( 0 ,
1265	+	0 , &(args_info->gofz_given),
1266	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1267	+	check_ambiguity, override, 0, 0,
1268	+	"gofz", '-',
1269	+	additional_error))
1270	+	goto failure;
1271	+
1272	+	}
1273		/* g(r, cos(theta)).  */
1274		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1275		{
1276	<	if (local_args_info.r_theta_given)
1216	<	{
1217	<	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1218	<	goto failure;
1219	<	}
1220	<	if (args_info->r_theta_given && ! override)
1221	<	continue;
1222	<	local_args_info.r_theta_given = 1;
1223	<	args_info->r_theta_given = 1;
1276	>
1277		if (args_info->staticProps_group_counter && override)
1278		reset_group_staticProps (args_info);
1279		args_info->staticProps_group_counter += 1;
1280	<	break;
1280	>
1281	>	if (update_arg( 0 ,
1282	>	0 , &(args_info->r_theta_given),
1283	>	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1284	>	check_ambiguity, override, 0, 0,
1285	>	"r_theta", '-',
1286	>	additional_error))
1287	>	goto failure;
1288	>
1289		}
1290		/* g(r, cos(omega)).  */
1291		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1292		{
1293	<	if (local_args_info.r_omega_given)
1233	<	{
1234	<	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1235	<	goto failure;
1236	<	}
1237	<	if (args_info->r_omega_given && ! override)
1238	<	continue;
1239	<	local_args_info.r_omega_given = 1;
1240	<	args_info->r_omega_given = 1;
1293	>
1294		if (args_info->staticProps_group_counter && override)
1295		reset_group_staticProps (args_info);
1296		args_info->staticProps_group_counter += 1;
1297	<	break;
1297	>
1298	>	if (update_arg( 0 ,
1299	>	0 , &(args_info->r_omega_given),
1300	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1301	>	check_ambiguity, override, 0, 0,
1302	>	"r_omega", '-',
1303	>	additional_error))
1304	>	goto failure;
1305	>
1306		}
1307		/* g(cos(theta), cos(omega)).  */
1308		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1309		{
1310	<	if (local_args_info.theta_omega_given)
1250	<	{
1251	<	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	<	goto failure;
1253	<	}
1254	<	if (args_info->theta_omega_given && ! override)
1255	<	continue;
1256	<	local_args_info.theta_omega_given = 1;
1257	<	args_info->theta_omega_given = 1;
1310	>
1311		if (args_info->staticProps_group_counter && override)
1312		reset_group_staticProps (args_info);
1313		args_info->staticProps_group_counter += 1;
1314	<	break;
1314	>
1315	>	if (update_arg( 0 ,
1316	>	0 , &(args_info->theta_omega_given),
1317	>	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1318	>	check_ambiguity, override, 0, 0,
1319	>	"theta_omega", '-',
1320	>	additional_error))
1321	>	goto failure;
1322	>
1323		}
1324		/* g(x, y, z).  */
1325		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1326		{
1327	<	if (local_args_info.gxyz_given)
1267	<	{
1268	<	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1269	<	goto failure;
1270	<	}
1271	<	if (args_info->gxyz_given && ! override)
1272	<	continue;
1273	<	local_args_info.gxyz_given = 1;
1274	<	args_info->gxyz_given = 1;
1327	>
1328		if (args_info->staticProps_group_counter && override)
1329		reset_group_staticProps (args_info);
1330		args_info->staticProps_group_counter += 1;
1331	<	break;
1331	>
1332	>	if (update_arg( 0 ,
1333	>	0 , &(args_info->gxyz_given),
1334	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1335	>	check_ambiguity, override, 0, 0,
1336	>	"gxyz", '-',
1337	>	additional_error))
1338	>	goto failure;
1339	>
1340		}
1341	+	/* 2D g(r) (Slab width --dz must be specified).  */
1342	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1343	+	{
1344	+
1345	+	if (args_info->staticProps_group_counter && override)
1346	+	reset_group_staticProps (args_info);
1347	+	args_info->staticProps_group_counter += 1;
1348	+
1349	+	if (update_arg( 0 ,
1350	+	0 , &(args_info->twodgofr_given),
1351	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1352	+	check_ambiguity, override, 0, 0,
1353	+	"twodgofr", '-',
1354	+	additional_error))
1355	+	goto failure;
1356	+
1357	+	}
1358		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1359		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1360		{
1361	<	if (local_args_info.rp2_given)
1284	<	{
1285	<	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1286	<	goto failure;
1287	<	}
1288	<	if (args_info->rp2_given && ! override)
1289	<	continue;
1290	<	local_args_info.rp2_given = 1;
1291	<	args_info->rp2_given = 1;
1361	>
1362		if (args_info->staticProps_group_counter && override)
1363		reset_group_staticProps (args_info);
1364		args_info->staticProps_group_counter += 1;
1365	<	break;
1365	>
1366	>	if (update_arg( 0 ,
1367	>	0 , &(args_info->rp2_given),
1368	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1369	>	check_ambiguity, override, 0, 0,
1370	>	"rp2", '-',
1371	>	additional_error))
1372	>	goto failure;
1373	>
1374		}
1375		/* slab density.  */
1376		else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1377		{
1378	<	if (local_args_info.slab_density_given)
1301	<	{
1302	<	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1303	<	goto failure;
1304	<	}
1305	<	if (args_info->slab_density_given && ! override)
1306	<	continue;
1307	<	local_args_info.slab_density_given = 1;
1308	<	args_info->slab_density_given = 1;
1378	>
1379		if (args_info->staticProps_group_counter && override)
1380		reset_group_staticProps (args_info);
1381		args_info->staticProps_group_counter += 1;
1382	<	break;
1382	>
1383	>	if (update_arg( 0 ,
1384	>	0 , &(args_info->slab_density_given),
1385	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1386	>	check_ambiguity, override, 0, 0,
1387	>	"slab_density", '-',
1388	>	additional_error))
1389	>	goto failure;
1390	>
1391		}
1392	+	/* p(cos(theta)).  */
1393	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1394	+	{
1395	+
1396	+	if (args_info->staticProps_group_counter && override)
1397	+	reset_group_staticProps (args_info);
1398	+	args_info->staticProps_group_counter += 1;
1399	+
1400	+	if (update_arg( 0 ,
1401	+	0 , &(args_info->p_angle_given),
1402	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1403	+	check_ambiguity, override, 0, 0,
1404	+	"p_angle", '-',
1405	+	additional_error))
1406	+	goto failure;
1407	+
1408	+	}
1409		/* hxy.  */
1410		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1411		{
1412	<	if (local_args_info.hxy_given)
1318	<	{
1319	<	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1320	<	goto failure;
1321	<	}
1322	<	if (args_info->hxy_given && ! override)
1323	<	continue;
1324	<	local_args_info.hxy_given = 1;
1325	<	args_info->hxy_given = 1;
1412	>
1413		if (args_info->staticProps_group_counter && override)
1414		reset_group_staticProps (args_info);
1415		args_info->staticProps_group_counter += 1;
1416	<	break;
1416	>
1417	>	if (update_arg( 0 ,
1418	>	0 , &(args_info->hxy_given),
1419	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1420	>	check_ambiguity, override, 0, 0,
1421	>	"hxy", '-',
1422	>	additional_error))
1423	>	goto failure;
1424	>
1425		}
1426		/* rho of R.  */
1427		else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1428		{
1429	<	if (local_args_info.rho_r_given)
1335	<	{
1336	<	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1337	<	goto failure;
1338	<	}
1339	<	if (args_info->rho_r_given && ! override)
1340	<	continue;
1341	<	local_args_info.rho_r_given = 1;
1342	<	args_info->rho_r_given = 1;
1429	>
1430		if (args_info->staticProps_group_counter && override)
1431		reset_group_staticProps (args_info);
1432		args_info->staticProps_group_counter += 1;
1433	<	break;
1433	>
1434	>	if (update_arg( 0 ,
1435	>	0 , &(args_info->rho_r_given),
1436	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1437	>	check_ambiguity, override, 0, 0,
1438	>	"rho_r", '-',
1439	>	additional_error))
1440	>	goto failure;
1441	>
1442		}
1443	+	/* angle of R.  */
1444	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1445	+	{
1446
1447	+	if (args_info->staticProps_group_counter && override)
1448	+	reset_group_staticProps (args_info);
1449	+	args_info->staticProps_group_counter += 1;
1450	+
1451	+	if (update_arg( 0 ,
1452	+	0 , &(args_info->angle_r_given),
1453	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1454	+	check_ambiguity, override, 0, 0,
1455	+	"angle_r", '-',
1456	+	additional_error))
1457	+	goto failure;
1458	+
1459	+	}
1460	+	/* hull volume of nanoparticle.  */
1461	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1462	+	{
1463	+
1464	+	if (args_info->staticProps_group_counter && override)
1465	+	reset_group_staticProps (args_info);
1466	+	args_info->staticProps_group_counter += 1;
1467	+
1468	+	if (update_arg( 0 ,
1469	+	0 , &(args_info->hullvol_given),
1470	+	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1471	+	check_ambiguity, override, 0, 0,
1472	+	"hullvol", '-',
1473	+	additional_error))
1474	+	goto failure;
1475	+
1476	+	}
1477	+
1478		break;
1479		case '?':       /* Invalid option.  */
1480		/* `getopt_long' already printed an error message.  */

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords):
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC vs.
Revision 1522 by kstocke1, Fri Nov 19 20:26:36 2010 UTC

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

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