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

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trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1999 by gezelter, Sat May 31 21:00:46 2014 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.22
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	gengetopt -F StaticPropsCmd
4	>	gengetopt --file-name=StaticPropsCmd --unamed-opts
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
#	Line 17 | Line 17
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	#include "getopt.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22	>	#endif
23
24	+	#ifdef WIN32
25	+	#include "utils/wingetopt.h"
26	+	#else
27	+	#include <getopt.h>
28	+	#endif
29	+
30		#include "StaticPropsCmd.h"
31
32		const char *gengetopt_args_info_purpose = "";
33
34	<	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
34	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35
36		const char *gengetopt_args_info_description = "";
37
#	Line 36 | Line 44 | const char *gengetopt_args_info_help[] = {
44		"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
45		"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
46		"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
47	+	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
48		"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	–	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
49		"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50	+	"      --dz=DOUBLE               slab width (dz)",
51	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
52	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53		"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
54		"      --sele1=selection script  select the first stuntdouble set",
55		"      --sele2=selection script  select the second stuntdouble set",
56		"      --sele3=selection script  select the third stuntdouble set",
57		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58		"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59	+	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60	+	"      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
61		"      --molname=STRING          molecule name",
62		"      --begin=INT               begin internal index",
63		"      --end=INT                 end internal index",
64		"      --radius=DOUBLE           nanoparticle radius",
65		"\n Group: staticProps\n   an option of this group is required",
66		"      --bo                      bond order parameter (--rcut must be specified)",
67	<	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67	>	"      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
68	>	"      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
69		"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
70	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
71		"  -g, --gofr                    g(r)",
72		"      --gofz                    g(z)",
73		"      --r_theta                 g(r, cos(theta))",
74		"      --r_omega                 g(r, cos(omega))",
75	+	"      --r_z                     g(r, z)",
76		"      --theta_omega             g(cos(theta), cos(omega))",
77		"      --gxyz                    g(x, y, z)",
78	<	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
78	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
79	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
80		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
81		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
82		"  -d, --density                 density plot",
83		"      --slab_density            slab density",
84	+	"      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
85		"      --hxy                     hxy",
86		"      --rho_r                   rho of R",
87	+	"      --angle_r                 angle of R",
88		"      --hullvol                 hull volume of nanoparticle",
89	+	"      --rodlength               length of nanorod",
90	+	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
91	+	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
92	+	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
93	+	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
94	+	"      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
95	+	"      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
96	+	"  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
97		0
98		};
99
#	Line 82 | Line 109 | static int
109		void clear_args (struct gengetopt_args_info *args_info);
110
111		static int
112	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
112	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
113		struct cmdline_parser_params *params, const char *additional_error);
114
115		static int
#	Line 102 | Line 129 | void clear_given (struct gengetopt_args_info *args_inf
129		args_info->nbins_given = 0 ;
130		args_info->nbins_x_given = 0 ;
131		args_info->nbins_y_given = 0 ;
132	+	args_info->nbins_z_given = 0 ;
133		args_info->nanglebins_given = 0 ;
106	–	args_info->length_given = 0 ;
134		args_info->rcut_given = 0 ;
135	+	args_info->dz_given = 0 ;
136	+	args_info->length_given = 0 ;
137	+	args_info->zlength_given = 0 ;
138		args_info->zoffset_given = 0 ;
139		args_info->sele1_given = 0 ;
140		args_info->sele2_given = 0 ;
141		args_info->sele3_given = 0 ;
142		args_info->refsele_given = 0 ;
143		args_info->comsele_given = 0 ;
144	+	args_info->seleoffset_given = 0 ;
145	+	args_info->seleoffset2_given = 0 ;
146		args_info->molname_given = 0 ;
147		args_info->begin_given = 0 ;
148		args_info->end_given = 0 ;
149		args_info->radius_given = 0 ;
150		args_info->bo_given = 0 ;
151	<	args_info->bor_given = 0 ;
151	>	args_info->ior_given = 0 ;
152	>	args_info->for_given = 0 ;
153		args_info->bad_given = 0 ;
154	+	args_info->count_given = 0 ;
155		args_info->gofr_given = 0 ;
156		args_info->gofz_given = 0 ;
157		args_info->r_theta_given = 0 ;
158		args_info->r_omega_given = 0 ;
159	+	args_info->r_z_given = 0 ;
160		args_info->theta_omega_given = 0 ;
161		args_info->gxyz_given = 0 ;
162	+	args_info->twodgofr_given = 0 ;
163		args_info->p2_given = 0 ;
164		args_info->rp2_given = 0 ;
165		args_info->scd_given = 0 ;
166		args_info->density_given = 0 ;
167		args_info->slab_density_given = 0 ;
168	+	args_info->p_angle_given = 0 ;
169		args_info->hxy_given = 0 ;
170		args_info->rho_r_given = 0 ;
171	+	args_info->angle_r_given = 0 ;
172		args_info->hullvol_given = 0 ;
173	+	args_info->rodlength_given = 0 ;
174	+	args_info->tet_param_given = 0 ;
175	+	args_info->tet_param_z_given = 0 ;
176	+	args_info->rnemdz_given = 0 ;
177	+	args_info->rnemdr_given = 0 ;
178	+	args_info->rnemdrt_given = 0 ;
179	+	args_info->nitrile_given = 0 ;
180	+	args_info->multipole_given = 0 ;
181		args_info->staticProps_group_counter = 0 ;
182		}
183
184		static
185		void clear_args (struct gengetopt_args_info *args_info)
186		{
187	+	FIX_UNUSED (args_info);
188		args_info->input_arg = NULL;
189		args_info->input_orig = NULL;
190		args_info->output_arg = NULL;
#	Line 150 | Line 197 | void clear_args (struct gengetopt_args_info *args_info
197		args_info->nbins_x_orig = NULL;
198		args_info->nbins_y_arg = 100;
199		args_info->nbins_y_orig = NULL;
200	+	args_info->nbins_z_arg = 100;
201	+	args_info->nbins_z_orig = NULL;
202		args_info->nanglebins_arg = 50;
203		args_info->nanglebins_orig = NULL;
155	–	args_info->length_orig = NULL;
204		args_info->rcut_orig = NULL;
205	+	args_info->dz_orig = NULL;
206	+	args_info->length_orig = NULL;
207	+	args_info->zlength_orig = NULL;
208		args_info->zoffset_arg = 0;
209		args_info->zoffset_orig = NULL;
210		args_info->sele1_arg = NULL;
#	Line 166 | Line 217 | void clear_args (struct gengetopt_args_info *args_info
217		args_info->refsele_orig = NULL;
218		args_info->comsele_arg = NULL;
219		args_info->comsele_orig = NULL;
220	+	args_info->seleoffset_orig = NULL;
221	+	args_info->seleoffset2_orig = NULL;
222		args_info->molname_arg = NULL;
223		args_info->molname_orig = NULL;
224		args_info->begin_orig = NULL;
#	Line 187 | Line 240 | void init_args_info(struct gengetopt_args_info *args_i
240		args_info->nbins_help = gengetopt_args_info_help[5] ;
241		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
242		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
243	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
244	<	args_info->length_help = gengetopt_args_info_help[9] ;
243	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
244	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
245		args_info->rcut_help = gengetopt_args_info_help[10] ;
246	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
247	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
248	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
249	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
250	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
251	<	args_info->comsele_help = gengetopt_args_info_help[16] ;
252	<	args_info->molname_help = gengetopt_args_info_help[17] ;
253	<	args_info->begin_help = gengetopt_args_info_help[18] ;
254	<	args_info->end_help = gengetopt_args_info_help[19] ;
255	<	args_info->radius_help = gengetopt_args_info_help[20] ;
256	<	args_info->bo_help = gengetopt_args_info_help[22] ;
257	<	args_info->bor_help = gengetopt_args_info_help[23] ;
258	<	args_info->bad_help = gengetopt_args_info_help[24] ;
259	<	args_info->gofr_help = gengetopt_args_info_help[25] ;
260	<	args_info->gofz_help = gengetopt_args_info_help[26] ;
261	<	args_info->r_theta_help = gengetopt_args_info_help[27] ;
262	<	args_info->r_omega_help = gengetopt_args_info_help[28] ;
263	<	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
264	<	args_info->gxyz_help = gengetopt_args_info_help[30] ;
265	<	args_info->p2_help = gengetopt_args_info_help[31] ;
266	<	args_info->rp2_help = gengetopt_args_info_help[32] ;
267	<	args_info->scd_help = gengetopt_args_info_help[33] ;
268	<	args_info->density_help = gengetopt_args_info_help[34] ;
269	<	args_info->slab_density_help = gengetopt_args_info_help[35] ;
270	<	args_info->hxy_help = gengetopt_args_info_help[36] ;
271	<	args_info->rho_r_help = gengetopt_args_info_help[37] ;
272	<	args_info->hullvol_help = gengetopt_args_info_help[38] ;
246	>	args_info->dz_help = gengetopt_args_info_help[11] ;
247	>	args_info->length_help = gengetopt_args_info_help[12] ;
248	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
249	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
250	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
251	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
252	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
253	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
254	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
255	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
256	>	args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
257	>	args_info->molname_help = gengetopt_args_info_help[22] ;
258	>	args_info->begin_help = gengetopt_args_info_help[23] ;
259	>	args_info->end_help = gengetopt_args_info_help[24] ;
260	>	args_info->radius_help = gengetopt_args_info_help[25] ;
261	>	args_info->bo_help = gengetopt_args_info_help[27] ;
262	>	args_info->ior_help = gengetopt_args_info_help[28] ;
263	>	args_info->for_help = gengetopt_args_info_help[29] ;
264	>	args_info->bad_help = gengetopt_args_info_help[30] ;
265	>	args_info->count_help = gengetopt_args_info_help[31] ;
266	>	args_info->gofr_help = gengetopt_args_info_help[32] ;
267	>	args_info->gofz_help = gengetopt_args_info_help[33] ;
268	>	args_info->r_theta_help = gengetopt_args_info_help[34] ;
269	>	args_info->r_omega_help = gengetopt_args_info_help[35] ;
270	>	args_info->r_z_help = gengetopt_args_info_help[36] ;
271	>	args_info->theta_omega_help = gengetopt_args_info_help[37] ;
272	>	args_info->gxyz_help = gengetopt_args_info_help[38] ;
273	>	args_info->twodgofr_help = gengetopt_args_info_help[39] ;
274	>	args_info->p2_help = gengetopt_args_info_help[40] ;
275	>	args_info->rp2_help = gengetopt_args_info_help[41] ;
276	>	args_info->scd_help = gengetopt_args_info_help[42] ;
277	>	args_info->density_help = gengetopt_args_info_help[43] ;
278	>	args_info->slab_density_help = gengetopt_args_info_help[44] ;
279	>	args_info->p_angle_help = gengetopt_args_info_help[45] ;
280	>	args_info->hxy_help = gengetopt_args_info_help[46] ;
281	>	args_info->rho_r_help = gengetopt_args_info_help[47] ;
282	>	args_info->angle_r_help = gengetopt_args_info_help[48] ;
283	>	args_info->hullvol_help = gengetopt_args_info_help[49] ;
284	>	args_info->rodlength_help = gengetopt_args_info_help[50] ;
285	>	args_info->tet_param_help = gengetopt_args_info_help[51] ;
286	>	args_info->tet_param_z_help = gengetopt_args_info_help[52] ;
287	>	args_info->rnemdz_help = gengetopt_args_info_help[53] ;
288	>	args_info->rnemdr_help = gengetopt_args_info_help[54] ;
289	>	args_info->rnemdrt_help = gengetopt_args_info_help[55] ;
290	>	args_info->nitrile_help = gengetopt_args_info_help[56] ;
291	>	args_info->multipole_help = gengetopt_args_info_help[57] ;
292
293		}
294
295		void
296		cmdline_parser_print_version (void)
297		{
298	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
298	>	printf ("%s %s\n",
299	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
300	>	CMDLINE_PARSER_VERSION);
301		}
302
303		static void print_help_common(void) {
#	Line 238 | Line 312 | static void print_help_common(void) {
312		printf("\n");
313
314		if (strlen(gengetopt_args_info_description) > 0)
315	<	printf("%s\n", gengetopt_args_info_description);
315	>	printf("%s\n\n", gengetopt_args_info_description);
316		}
317
318		void
#	Line 256 | Line 330 | cmdline_parser_init (struct gengetopt_args_info *args_
330		clear_given (args_info);
331		clear_args (args_info);
332		init_args_info (args_info);
333	+
334	+	args_info->inputs = 0;
335	+	args_info->inputs_num = 0;
336		}
337
338		void
#	Line 294 | Line 371 | cmdline_parser_release (struct gengetopt_args_info *ar
371		static void
372		cmdline_parser_release (struct gengetopt_args_info *args_info)
373		{
374	<
374	>	unsigned int i;
375		free_string_field (&(args_info->input_arg));
376		free_string_field (&(args_info->input_orig));
377		free_string_field (&(args_info->output_arg));
#	Line 303 | Line 380 | cmdline_parser_release (struct gengetopt_args_info *ar
380		free_string_field (&(args_info->nbins_orig));
381		free_string_field (&(args_info->nbins_x_orig));
382		free_string_field (&(args_info->nbins_y_orig));
383	+	free_string_field (&(args_info->nbins_z_orig));
384		free_string_field (&(args_info->nanglebins_orig));
307	–	free_string_field (&(args_info->length_orig));
385		free_string_field (&(args_info->rcut_orig));
386	+	free_string_field (&(args_info->dz_orig));
387	+	free_string_field (&(args_info->length_orig));
388	+	free_string_field (&(args_info->zlength_orig));
389		free_string_field (&(args_info->zoffset_orig));
390		free_string_field (&(args_info->sele1_arg));
391		free_string_field (&(args_info->sele1_orig));
#	Line 317 | Line 397 | cmdline_parser_release (struct gengetopt_args_info *ar
397		free_string_field (&(args_info->refsele_orig));
398		free_string_field (&(args_info->comsele_arg));
399		free_string_field (&(args_info->comsele_orig));
400	+	free_string_field (&(args_info->seleoffset_orig));
401	+	free_string_field (&(args_info->seleoffset2_orig));
402		free_string_field (&(args_info->molname_arg));
403		free_string_field (&(args_info->molname_orig));
404		free_string_field (&(args_info->begin_orig));
#	Line 324 | Line 406 | cmdline_parser_release (struct gengetopt_args_info *ar
406		free_string_field (&(args_info->radius_orig));
407
408
409	+	for (i = 0; i < args_info->inputs_num; ++i)
410	+	free (args_info->inputs [i]);
411
412	+	if (args_info->inputs_num)
413	+	free (args_info->inputs);
414	+
415		clear_given (args_info);
416		}
417
418
419		static void
420	<	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
420	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
421		{
422	+	FIX_UNUSED (values);
423		if (arg) {
424		fprintf(outfile, "%s=\"%s\"\n", opt, arg);
425		} else {
#	Line 367 | Line 455 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
455		write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
456		if (args_info->nbins_y_given)
457		write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
458	+	if (args_info->nbins_z_given)
459	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
460		if (args_info->nanglebins_given)
461		write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
372	–	if (args_info->length_given)
373	–	write_into_file(outfile, "length", args_info->length_orig, 0);
462		if (args_info->rcut_given)
463		write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
464	+	if (args_info->dz_given)
465	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
466	+	if (args_info->length_given)
467	+	write_into_file(outfile, "length", args_info->length_orig, 0);
468	+	if (args_info->zlength_given)
469	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
470		if (args_info->zoffset_given)
471		write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
472		if (args_info->sele1_given)
#	Line 385 | Line 479 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
479		write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
480		if (args_info->comsele_given)
481		write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
482	+	if (args_info->seleoffset_given)
483	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
484	+	if (args_info->seleoffset2_given)
485	+	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
486		if (args_info->molname_given)
487		write_into_file(outfile, "molname", args_info->molname_orig, 0);
488		if (args_info->begin_given)
#	Line 395 | Line 493 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
493		write_into_file(outfile, "radius", args_info->radius_orig, 0);
494		if (args_info->bo_given)
495		write_into_file(outfile, "bo", 0, 0 );
496	<	if (args_info->bor_given)
497	<	write_into_file(outfile, "bor", 0, 0 );
496	>	if (args_info->ior_given)
497	>	write_into_file(outfile, "ior", 0, 0 );
498	>	if (args_info->for_given)
499	>	write_into_file(outfile, "for", 0, 0 );
500		if (args_info->bad_given)
501		write_into_file(outfile, "bad", 0, 0 );
502	+	if (args_info->count_given)
503	+	write_into_file(outfile, "count", 0, 0 );
504		if (args_info->gofr_given)
505		write_into_file(outfile, "gofr", 0, 0 );
506		if (args_info->gofz_given)
#	Line 407 | Line 509 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
509		write_into_file(outfile, "r_theta", 0, 0 );
510		if (args_info->r_omega_given)
511		write_into_file(outfile, "r_omega", 0, 0 );
512	+	if (args_info->r_z_given)
513	+	write_into_file(outfile, "r_z", 0, 0 );
514		if (args_info->theta_omega_given)
515		write_into_file(outfile, "theta_omega", 0, 0 );
516		if (args_info->gxyz_given)
517		write_into_file(outfile, "gxyz", 0, 0 );
518	+	if (args_info->twodgofr_given)
519	+	write_into_file(outfile, "twodgofr", 0, 0 );
520		if (args_info->p2_given)
521		write_into_file(outfile, "p2", 0, 0 );
522		if (args_info->rp2_given)
#	Line 421 | Line 527 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
527		write_into_file(outfile, "density", 0, 0 );
528		if (args_info->slab_density_given)
529		write_into_file(outfile, "slab_density", 0, 0 );
530	+	if (args_info->p_angle_given)
531	+	write_into_file(outfile, "p_angle", 0, 0 );
532		if (args_info->hxy_given)
533		write_into_file(outfile, "hxy", 0, 0 );
534		if (args_info->rho_r_given)
535		write_into_file(outfile, "rho_r", 0, 0 );
536	+	if (args_info->angle_r_given)
537	+	write_into_file(outfile, "angle_r", 0, 0 );
538		if (args_info->hullvol_given)
539		write_into_file(outfile, "hullvol", 0, 0 );
540	+	if (args_info->rodlength_given)
541	+	write_into_file(outfile, "rodlength", 0, 0 );
542	+	if (args_info->tet_param_given)
543	+	write_into_file(outfile, "tet_param", 0, 0 );
544	+	if (args_info->tet_param_z_given)
545	+	write_into_file(outfile, "tet_param_z", 0, 0 );
546	+	if (args_info->rnemdz_given)
547	+	write_into_file(outfile, "rnemdz", 0, 0 );
548	+	if (args_info->rnemdr_given)
549	+	write_into_file(outfile, "rnemdr", 0, 0 );
550	+	if (args_info->rnemdrt_given)
551	+	write_into_file(outfile, "rnemdrt", 0, 0 );
552	+	if (args_info->nitrile_given)
553	+	write_into_file(outfile, "nitrile", 0, 0 );
554	+	if (args_info->multipole_given)
555	+	write_into_file(outfile, "multipole", 0, 0 );
556
557
558		i = EXIT_SUCCESS;
#	Line 463 | Line 589 | gengetopt_strdup (const char *s)
589		char *
590		gengetopt_strdup (const char *s)
591		{
592	<	char *result = NULL;
592	>	char *result = 0;
593		if (!s)
594		return result;
595
#	Line 481 | Line 607 | reset_group_staticProps(struct gengetopt_args_info *ar
607		return;
608
609		args_info->bo_given = 0 ;
610	<	args_info->bor_given = 0 ;
610	>	args_info->ior_given = 0 ;
611	>	args_info->for_given = 0 ;
612		args_info->bad_given = 0 ;
613	+	args_info->count_given = 0 ;
614		args_info->gofr_given = 0 ;
615		args_info->gofz_given = 0 ;
616		args_info->r_theta_given = 0 ;
617		args_info->r_omega_given = 0 ;
618	+	args_info->r_z_given = 0 ;
619		args_info->theta_omega_given = 0 ;
620		args_info->gxyz_given = 0 ;
621	+	args_info->twodgofr_given = 0 ;
622		args_info->p2_given = 0 ;
623		args_info->rp2_given = 0 ;
624		args_info->scd_given = 0 ;
625		args_info->density_given = 0 ;
626		args_info->slab_density_given = 0 ;
627	+	args_info->p_angle_given = 0 ;
628		args_info->hxy_given = 0 ;
629		args_info->rho_r_given = 0 ;
630	+	args_info->angle_r_given = 0 ;
631		args_info->hullvol_given = 0 ;
632	+	args_info->rodlength_given = 0 ;
633	+	args_info->tet_param_given = 0 ;
634	+	args_info->tet_param_z_given = 0 ;
635	+	args_info->rnemdz_given = 0 ;
636	+	args_info->rnemdr_given = 0 ;
637	+	args_info->rnemdrt_given = 0 ;
638	+	args_info->nitrile_given = 0 ;
639	+	args_info->multipole_given = 0 ;
640
641		args_info->staticProps_group_counter = 0;
642		}
643
644		int
645	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
645	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
646		{
647		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
648		}
649
650		int
651	<	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
651	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
652		struct cmdline_parser_params *params)
653		{
654		int result;
655	<	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
655	>	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
656
657		if (result == EXIT_FAILURE)
658		{
#	Line 524 | Line 664 | int
664		}
665
666		int
667	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
667	>	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
668		{
669		int result;
670		struct cmdline_parser_params params;
#	Line 535 | Line 675 | cmdline_parser2 (int argc, char * const *argv, struct
675		params.check_ambiguity = 0;
676		params.print_errors = 1;
677
678	<	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
678	>	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
679
680		if (result == EXIT_FAILURE)
681		{
#	Line 551 | Line 691 | cmdline_parser_required (struct gengetopt_args_info *a
691		{
692		int result = EXIT_SUCCESS;
693
694	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
694	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
695		result = EXIT_FAILURE;
696
697		if (result == EXIT_FAILURE)
#	Line 567 | Line 707 | cmdline_parser_required2 (struct gengetopt_args_info *
707		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
708		{
709		int error = 0;
710	+	FIX_UNUSED (additional_error);
711
712		/* checks for required options */
713		if (! args_info->input_given)
#	Line 577 | Line 718 | cmdline_parser_required2 (struct gengetopt_args_info *
718
719		if (args_info->staticProps_group_counter == 0)
720		{
721	<	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 : ""));
721	>	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 : ""));
722		error = 1;
723		}
724
#	Line 611 | Line 752 | int update_arg(void *field, char **orig_field,
752		static
753		int update_arg(void *field, char **orig_field,
754		unsigned int *field_given, unsigned int *prev_given,
755	<	char *value, char *possible_values[], const char *default_value,
755	>	char *value, const char *possible_values[],
756	>	const char *default_value,
757		cmdline_parser_arg_type arg_type,
758		int check_ambiguity, int override,
759		int no_free, int multiple_option,
#	Line 622 | Line 764 | int update_arg(void *field, char **orig_field,
764		const char *val = value;
765		int found;
766		char **string_field;
767	+	FIX_UNUSED (field);
768
769		stop_char = 0;
770		found = 0;
#	Line 639 | Line 782 | int update_arg(void *field, char **orig_field,
782		return 1; /* failure */
783		}
784
785	+	FIX_UNUSED (default_value);
786
787		if (field_given && *field_given && ! override)
788		return 0;
#	Line 702 | Line 846 | int
846
847
848		int
849	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
849	>	cmdline_parser_internal (
850	>	int argc, char **argv, struct gengetopt_args_info *args_info,
851		struct cmdline_parser_params *params, const char *additional_error)
852		{
853		int c;        /* Character of the parsed option.  */
#	Line 745 | Line 890 | cmdline_parser_internal (int argc, char * const *argv,
890		{ "nbins",      1, NULL, 'b' },
891		{ "nbins_x",    1, NULL, 'x' },
892		{ "nbins_y",    1, NULL, 'y' },
893	+	{ "nbins_z",    1, NULL, 0 },
894		{ "nanglebins", 1, NULL, 'a' },
749	–	{ "length",     1, NULL, 0 },
895		{ "rcut",       1, NULL, 'c' },
896	+	{ "dz", 1, NULL, 0 },
897	+	{ "length",     1, NULL, 0 },
898	+	{ "zlength",    1, NULL, 0 },
899		{ "zoffset",    1, NULL, 'z' },
900		{ "sele1",      1, NULL, 0 },
901		{ "sele2",      1, NULL, 0 },
902		{ "sele3",      1, NULL, 0 },
903		{ "refsele",    1, NULL, 0 },
904		{ "comsele",    1, NULL, 0 },
905	+	{ "seleoffset", 1, NULL, 0 },
906	+	{ "seleoffset2",        1, NULL, 0 },
907		{ "molname",    1, NULL, 0 },
908		{ "begin",      1, NULL, 0 },
909		{ "end",        1, NULL, 0 },
910		{ "radius",     1, NULL, 0 },
911		{ "bo", 0, NULL, 0 },
912	<	{ "bor",        0, NULL, 0 },
912	>	{ "ior",        0, NULL, 0 },
913	>	{ "for",        0, NULL, 0 },
914		{ "bad",        0, NULL, 0 },
915	+	{ "count",      0, NULL, 0 },
916		{ "gofr",       0, NULL, 'g' },
917		{ "gofz",       0, NULL, 0 },
918		{ "r_theta",    0, NULL, 0 },
919		{ "r_omega",    0, NULL, 0 },
920	+	{ "r_z",        0, NULL, 0 },
921		{ "theta_omega",        0, NULL, 0 },
922		{ "gxyz",       0, NULL, 0 },
923	+	{ "twodgofr",   0, NULL, 0 },
924		{ "p2", 0, NULL, 'p' },
925		{ "rp2",        0, NULL, 0 },
926		{ "scd",        0, NULL, 's' },
927		{ "density",    0, NULL, 'd' },
928		{ "slab_density",       0, NULL, 0 },
929	+	{ "p_angle",    0, NULL, 0 },
930		{ "hxy",        0, NULL, 0 },
931		{ "rho_r",      0, NULL, 0 },
932	+	{ "angle_r",    0, NULL, 0 },
933		{ "hullvol",    0, NULL, 0 },
934	<	{ NULL, 0, NULL, 0 }
934	>	{ "rodlength",  0, NULL, 0 },
935	>	{ "tet_param",  0, NULL, 'Q' },
936	>	{ "tet_param_z",        0, NULL, 0 },
937	>	{ "rnemdz",     0, NULL, 0 },
938	>	{ "rnemdr",     0, NULL, 0 },
939	>	{ "rnemdrt",    0, NULL, 0 },
940	>	{ "nitrile",    0, NULL, 0 },
941	>	{ "multipole",  0, NULL, 'm' },
942	>	{ 0,  0, 0, 0 }
943		};
944
945	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
945	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQm", long_options, &option_index);
946
947		if (c == -1) break;       /* Exit from `while (1)' loop.  */
948
#	Line 917 | Line 1081 | cmdline_parser_internal (int argc, char * const *argv,
1081		goto failure;
1082
1083		break;
1084	<	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1084	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1085
1086		if (args_info->staticProps_group_counter && override)
1087		reset_group_staticProps (args_info);
#	Line 958 | Line 1122 | cmdline_parser_internal (int argc, char * const *argv,
1122		&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1123		check_ambiguity, override, 0, 0,
1124		"density", 'd',
1125	+	additional_error))
1126	+	goto failure;
1127	+
1128	+	break;
1129	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1130	+
1131	+	if (args_info->staticProps_group_counter && override)
1132	+	reset_group_staticProps (args_info);
1133	+	args_info->staticProps_group_counter += 1;
1134	+
1135	+	if (update_arg( 0 ,
1136	+	0 , &(args_info->tet_param_given),
1137	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1138	+	check_ambiguity, override, 0, 0,
1139	+	"tet_param", 'Q',
1140	+	additional_error))
1141	+	goto failure;
1142	+
1143	+	break;
1144	+	case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1145	+
1146	+	if (args_info->staticProps_group_counter && override)
1147	+	reset_group_staticProps (args_info);
1148	+	args_info->staticProps_group_counter += 1;
1149	+
1150	+	if (update_arg( 0 ,
1151	+	0 , &(args_info->multipole_given),
1152	+	&(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1153	+	check_ambiguity, override, 0, 0,
1154	+	"multipole", 'm',
1155		additional_error))
1156		goto failure;
1157
1158		break;
1159
1160		case 0: /* Long option with no short option */
1161	+	/* number of bins in z axis.  */
1162	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1163	+	{
1164	+
1165	+
1166	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1167	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1168	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1169	+	check_ambiguity, override, 0, 0,
1170	+	"nbins_z", '-',
1171	+	additional_error))
1172	+	goto failure;
1173	+
1174	+	}
1175	+	/* slab width (dz).  */
1176	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1177	+	{
1178	+
1179	+
1180	+	if (update_arg( (void *)&(args_info->dz_arg),
1181	+	&(args_info->dz_orig), &(args_info->dz_given),
1182	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1183	+	check_ambiguity, override, 0, 0,
1184	+	"dz", '-',
1185	+	additional_error))
1186	+	goto failure;
1187	+
1188	+	}
1189		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1190	<	if (strcmp (long_options[option_index].name, "length") == 0)
1190	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1191		{
1192
1193
#	Line 978 | Line 1200 | cmdline_parser_internal (int argc, char * const *argv,
1200		goto failure;
1201
1202		}
1203	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1204	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1205	+	{
1206	+
1207	+
1208	+	if (update_arg( (void *)&(args_info->zlength_arg),
1209	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1210	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1211	+	check_ambiguity, override, 0, 0,
1212	+	"zlength", '-',
1213	+	additional_error))
1214	+	goto failure;
1215	+
1216	+	}
1217		/* select the first stuntdouble set.  */
1218		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1219		{
#	Line 1048 | Line 1284 | cmdline_parser_internal (int argc, char * const *argv,
1284		goto failure;
1285
1286		}
1287	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1288	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1289	+	{
1290	+
1291	+
1292	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1293	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1294	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1295	+	check_ambiguity, override, 0, 0,
1296	+	"seleoffset", '-',
1297	+	additional_error))
1298	+	goto failure;
1299	+
1300	+	}
1301	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1302	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1303	+	{
1304	+
1305	+
1306	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1307	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1308	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1309	+	check_ambiguity, override, 0, 0,
1310	+	"seleoffset2", '-',
1311	+	additional_error))
1312	+	goto failure;
1313	+
1314	+	}
1315		/* molecule name.  */
1316		else if (strcmp (long_options[option_index].name, "molname") == 0)
1317		{
#	Line 1121 | Line 1385 | cmdline_parser_internal (int argc, char * const *argv,
1385		goto failure;
1386
1387		}
1388	<	/* bond order parameter as a function of radius (--rcut must be specified).  */
1389	<	else if (strcmp (long_options[option_index].name, "bor") == 0)
1388	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1389	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1390	>	{
1391	>
1392	>	if (args_info->staticProps_group_counter && override)
1393	>	reset_group_staticProps (args_info);
1394	>	args_info->staticProps_group_counter += 1;
1395	>
1396	>	if (update_arg( 0 ,
1397	>	0 , &(args_info->ior_given),
1398	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1399	>	check_ambiguity, override, 0, 0,
1400	>	"ior", '-',
1401	>	additional_error))
1402	>	goto failure;
1403	>
1404	>	}
1405	>	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1406	>	else if (strcmp (long_options[option_index].name, "for") == 0)
1407		{
1408
1409		if (args_info->staticProps_group_counter && override)
#	Line 1130 | Line 1411 | cmdline_parser_internal (int argc, char * const *argv,
1411		args_info->staticProps_group_counter += 1;
1412
1413		if (update_arg( 0 ,
1414	<	0 , &(args_info->bor_given),
1415	<	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1414	>	0 , &(args_info->for_given),
1415	>	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1416		check_ambiguity, override, 0, 0,
1417	<	"bor", '-',
1417	>	"for", '-',
1418		additional_error))
1419		goto failure;
1420
#	Line 1155 | Line 1436 | cmdline_parser_internal (int argc, char * const *argv,
1436		goto failure;
1437
1438		}
1439	+	/* count of molecules matching selection criteria (and associated statistics).  */
1440	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1441	+	{
1442	+
1443	+	if (args_info->staticProps_group_counter && override)
1444	+	reset_group_staticProps (args_info);
1445	+	args_info->staticProps_group_counter += 1;
1446	+
1447	+	if (update_arg( 0 ,
1448	+	0 , &(args_info->count_given),
1449	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1450	+	check_ambiguity, override, 0, 0,
1451	+	"count", '-',
1452	+	additional_error))
1453	+	goto failure;
1454	+
1455	+	}
1456		/* g(z).  */
1457		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1458		{
#	Line 1206 | Line 1504 | cmdline_parser_internal (int argc, char * const *argv,
1504		goto failure;
1505
1506		}
1507	+	/* g(r, z).  */
1508	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1509	+	{
1510	+
1511	+	if (args_info->staticProps_group_counter && override)
1512	+	reset_group_staticProps (args_info);
1513	+	args_info->staticProps_group_counter += 1;
1514	+
1515	+	if (update_arg( 0 ,
1516	+	0 , &(args_info->r_z_given),
1517	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1518	+	check_ambiguity, override, 0, 0,
1519	+	"r_z", '-',
1520	+	additional_error))
1521	+	goto failure;
1522	+
1523	+	}
1524		/* g(cos(theta), cos(omega)).  */
1525		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1526		{
#	Line 1240 | Line 1555 | cmdline_parser_internal (int argc, char * const *argv,
1555		goto failure;
1556
1557		}
1558	+	/* 2D g(r) (Slab width --dz must be specified).  */
1559	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1560	+	{
1561	+
1562	+	if (args_info->staticProps_group_counter && override)
1563	+	reset_group_staticProps (args_info);
1564	+	args_info->staticProps_group_counter += 1;
1565	+
1566	+	if (update_arg( 0 ,
1567	+	0 , &(args_info->twodgofr_given),
1568	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1569	+	check_ambiguity, override, 0, 0,
1570	+	"twodgofr", '-',
1571	+	additional_error))
1572	+	goto failure;
1573	+
1574	+	}
1575		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1576		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1577		{
#	Line 1270 | Line 1602 | cmdline_parser_internal (int argc, char * const *argv,
1602		&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1603		check_ambiguity, override, 0, 0,
1604		"slab_density", '-',
1605	+	additional_error))
1606	+	goto failure;
1607	+
1608	+	}
1609	+	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1610	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1611	+	{
1612	+
1613	+	if (args_info->staticProps_group_counter && override)
1614	+	reset_group_staticProps (args_info);
1615	+	args_info->staticProps_group_counter += 1;
1616	+
1617	+	if (update_arg( 0 ,
1618	+	0 , &(args_info->p_angle_given),
1619	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1620	+	check_ambiguity, override, 0, 0,
1621	+	"p_angle", '-',
1622		additional_error))
1623		goto failure;
1624
#	Line 1308 | Line 1657 | cmdline_parser_internal (int argc, char * const *argv,
1657		goto failure;
1658
1659		}
1660	+	/* angle of R.  */
1661	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1662	+	{
1663	+
1664	+	if (args_info->staticProps_group_counter && override)
1665	+	reset_group_staticProps (args_info);
1666	+	args_info->staticProps_group_counter += 1;
1667	+
1668	+	if (update_arg( 0 ,
1669	+	0 , &(args_info->angle_r_given),
1670	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1671	+	check_ambiguity, override, 0, 0,
1672	+	"angle_r", '-',
1673	+	additional_error))
1674	+	goto failure;
1675	+
1676	+	}
1677		/* hull volume of nanoparticle.  */
1678		else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1679		{
#	Line 1325 | Line 1691 | cmdline_parser_internal (int argc, char * const *argv,
1691		goto failure;
1692
1693		}
1694	+	/* length of nanorod.  */
1695	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1696	+	{
1697
1698	+	if (args_info->staticProps_group_counter && override)
1699	+	reset_group_staticProps (args_info);
1700	+	args_info->staticProps_group_counter += 1;
1701	+
1702	+	if (update_arg( 0 ,
1703	+	0 , &(args_info->rodlength_given),
1704	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1705	+	check_ambiguity, override, 0, 0,
1706	+	"rodlength", '-',
1707	+	additional_error))
1708	+	goto failure;
1709	+
1710	+	}
1711	+	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1712	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1713	+	{
1714	+
1715	+	if (args_info->staticProps_group_counter && override)
1716	+	reset_group_staticProps (args_info);
1717	+	args_info->staticProps_group_counter += 1;
1718	+
1719	+	if (update_arg( 0 ,
1720	+	0 , &(args_info->tet_param_z_given),
1721	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1722	+	check_ambiguity, override, 0, 0,
1723	+	"tet_param_z", '-',
1724	+	additional_error))
1725	+	goto failure;
1726	+
1727	+	}
1728	+	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1729	+	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1730	+	{
1731	+
1732	+	if (args_info->staticProps_group_counter && override)
1733	+	reset_group_staticProps (args_info);
1734	+	args_info->staticProps_group_counter += 1;
1735	+
1736	+	if (update_arg( 0 ,
1737	+	0 , &(args_info->rnemdz_given),
1738	+	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1739	+	check_ambiguity, override, 0, 0,
1740	+	"rnemdz", '-',
1741	+	additional_error))
1742	+	goto failure;
1743	+
1744	+	}
1745	+	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1746	+	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1747	+	{
1748	+
1749	+	if (args_info->staticProps_group_counter && override)
1750	+	reset_group_staticProps (args_info);
1751	+	args_info->staticProps_group_counter += 1;
1752	+
1753	+	if (update_arg( 0 ,
1754	+	0 , &(args_info->rnemdr_given),
1755	+	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1756	+	check_ambiguity, override, 0, 0,
1757	+	"rnemdr", '-',
1758	+	additional_error))
1759	+	goto failure;
1760	+
1761	+	}
1762	+	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1763	+	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1764	+	{
1765	+
1766	+	if (args_info->staticProps_group_counter && override)
1767	+	reset_group_staticProps (args_info);
1768	+	args_info->staticProps_group_counter += 1;
1769	+
1770	+	if (update_arg( 0 ,
1771	+	0 , &(args_info->rnemdrt_given),
1772	+	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1773	+	check_ambiguity, override, 0, 0,
1774	+	"rnemdrt", '-',
1775	+	additional_error))
1776	+	goto failure;
1777	+
1778	+	}
1779	+	/* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1780	+	else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1781	+	{
1782	+
1783	+	if (args_info->staticProps_group_counter && override)
1784	+	reset_group_staticProps (args_info);
1785	+	args_info->staticProps_group_counter += 1;
1786	+
1787	+	if (update_arg( 0 ,
1788	+	0 , &(args_info->nitrile_given),
1789	+	&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1790	+	check_ambiguity, override, 0, 0,
1791	+	"nitrile", '-',
1792	+	additional_error))
1793	+	goto failure;
1794	+
1795	+	}
1796	+
1797		break;
1798		case '?':       /* Invalid option.  */
1799		/* `getopt_long' already printed an error message.  */
#	Line 1339 | Line 1807 | cmdline_parser_internal (int argc, char * const *argv,
1807
1808		if (args_info->staticProps_group_counter > 1)
1809		{
1810	<	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 : ""));
1810	>	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 : ""));
1811		error = 1;
1812		}
1813
#	Line 1355 | Line 1823 | cmdline_parser_internal (int argc, char * const *argv,
1823		if ( error )
1824		return (EXIT_FAILURE);
1825
1826	+	if (optind < argc)
1827	+	{
1828	+	int i = 0 ;
1829	+	int found_prog_name = 0;
1830	+	/* whether program name, i.e., argv[0], is in the remaining args
1831	+	(this may happen with some implementations of getopt,
1832	+	but surely not with the one included by gengetopt) */
1833	+
1834	+	i = optind;
1835	+	while (i < argc)
1836	+	if (argv[i++] == argv[0]) {
1837	+	found_prog_name = 1;
1838	+	break;
1839	+	}
1840	+	i = 0;
1841	+
1842	+	args_info->inputs_num = argc - optind - found_prog_name;
1843	+	args_info->inputs =
1844	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1845	+	while (optind < argc)
1846	+	if (argv[optind++] != argv[0])
1847	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1848	+	}
1849	+
1850		return 0;
1851
1852		failure:

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1999 by gezelter, Sat May 31 21:00:46 2014 UTC

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

Diff Legend

–	Removed lines
+	Added lines
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