ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
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 2049 by gezelter, Tue Jan 6 21:44:10 2015 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	+	"      --thetacut=DOUBLE         cutoff angle (thetacut)",
51	+	"      --dz=DOUBLE               slab width (dz)",
52	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
54		"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
55		"      --sele1=selection script  select the first stuntdouble set",
56		"      --sele2=selection script  select the second stuntdouble set",
57		"      --sele3=selection script  select the third stuntdouble set",
58		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
59		"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
60	+	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
61	+	"      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
62		"      --molname=STRING          molecule name",
63		"      --begin=INT               begin internal index",
64		"      --end=INT                 end internal index",
65		"      --radius=DOUBLE           nanoparticle radius",
66	+	"  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
67	+	"      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
68		"\n Group: staticProps\n   an option of this group is required",
69		"      --bo                      bond order parameter (--rcut must be specified)",
70	<	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
70	>	"      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
71	>	"      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
72		"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
73	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
74		"  -g, --gofr                    g(r)",
75		"      --gofz                    g(z)",
76		"      --r_theta                 g(r, cos(theta))",
77		"      --r_omega                 g(r, cos(omega))",
78	+	"      --r_z                     g(r, z)",
79		"      --theta_omega             g(cos(theta), cos(omega))",
80		"      --gxyz                    g(x, y, z)",
81	<	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
81	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
82	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
83		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
84		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
85		"  -d, --density                 density plot",
86		"      --slab_density            slab density",
87	+	"      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
88		"      --hxy                     hxy",
89		"      --rho_r                   rho of R",
90	+	"      --angle_r                 angle of R",
91		"      --hullvol                 hull volume of nanoparticle",
92	+	"      --rodlength               length of nanorod",
93	+	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
94	+	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
95	+	"      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
96	+	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
97	+	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
98	+	"      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
99	+	"      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
100	+	"  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
101	+	"      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
102	+	"      --hbond                   Hydrogen Bonding statistics using geometric \n                                  criteria (rcut and thetacut must be \n                                  specified)",
103		0
104		};
105
#	Line 82 | Line 115 | static int
115		void clear_args (struct gengetopt_args_info *args_info);
116
117		static int
118	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
118	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
119		struct cmdline_parser_params *params, const char *additional_error);
120
121		static int
#	Line 102 | Line 135 | void clear_given (struct gengetopt_args_info *args_inf
135		args_info->nbins_given = 0 ;
136		args_info->nbins_x_given = 0 ;
137		args_info->nbins_y_given = 0 ;
138	+	args_info->nbins_z_given = 0 ;
139		args_info->nanglebins_given = 0 ;
106	–	args_info->length_given = 0 ;
140		args_info->rcut_given = 0 ;
141	+	args_info->thetacut_given = 0 ;
142	+	args_info->dz_given = 0 ;
143	+	args_info->length_given = 0 ;
144	+	args_info->zlength_given = 0 ;
145		args_info->zoffset_given = 0 ;
146		args_info->sele1_given = 0 ;
147		args_info->sele2_given = 0 ;
148		args_info->sele3_given = 0 ;
149		args_info->refsele_given = 0 ;
150		args_info->comsele_given = 0 ;
151	+	args_info->seleoffset_given = 0 ;
152	+	args_info->seleoffset2_given = 0 ;
153		args_info->molname_given = 0 ;
154		args_info->begin_given = 0 ;
155		args_info->end_given = 0 ;
156		args_info->radius_given = 0 ;
157	+	args_info->voxelSize_given = 0 ;
158	+	args_info->gaussWidth_given = 0 ;
159		args_info->bo_given = 0 ;
160	<	args_info->bor_given = 0 ;
160	>	args_info->ior_given = 0 ;
161	>	args_info->for_given = 0 ;
162		args_info->bad_given = 0 ;
163	+	args_info->count_given = 0 ;
164		args_info->gofr_given = 0 ;
165		args_info->gofz_given = 0 ;
166		args_info->r_theta_given = 0 ;
167		args_info->r_omega_given = 0 ;
168	+	args_info->r_z_given = 0 ;
169		args_info->theta_omega_given = 0 ;
170		args_info->gxyz_given = 0 ;
171	+	args_info->twodgofr_given = 0 ;
172		args_info->p2_given = 0 ;
173		args_info->rp2_given = 0 ;
174		args_info->scd_given = 0 ;
175		args_info->density_given = 0 ;
176		args_info->slab_density_given = 0 ;
177	+	args_info->p_angle_given = 0 ;
178		args_info->hxy_given = 0 ;
179		args_info->rho_r_given = 0 ;
180	+	args_info->angle_r_given = 0 ;
181		args_info->hullvol_given = 0 ;
182	+	args_info->rodlength_given = 0 ;
183	+	args_info->tet_param_given = 0 ;
184	+	args_info->tet_param_z_given = 0 ;
185	+	args_info->tet_param_xyz_given = 0 ;
186	+	args_info->rnemdz_given = 0 ;
187	+	args_info->rnemdr_given = 0 ;
188	+	args_info->rnemdrt_given = 0 ;
189	+	args_info->nitrile_given = 0 ;
190	+	args_info->multipole_given = 0 ;
191	+	args_info->surfDiffusion_given = 0 ;
192	+	args_info->hbond_given = 0 ;
193		args_info->staticProps_group_counter = 0 ;
194		}
195
196		static
197		void clear_args (struct gengetopt_args_info *args_info)
198		{
199	+	FIX_UNUSED (args_info);
200		args_info->input_arg = NULL;
201		args_info->input_orig = NULL;
202		args_info->output_arg = NULL;
#	Line 150 | Line 209 | void clear_args (struct gengetopt_args_info *args_info
209		args_info->nbins_x_orig = NULL;
210		args_info->nbins_y_arg = 100;
211		args_info->nbins_y_orig = NULL;
212	+	args_info->nbins_z_arg = 100;
213	+	args_info->nbins_z_orig = NULL;
214		args_info->nanglebins_arg = 50;
215		args_info->nanglebins_orig = NULL;
155	–	args_info->length_orig = NULL;
216		args_info->rcut_orig = NULL;
217	+	args_info->thetacut_orig = NULL;
218	+	args_info->dz_orig = NULL;
219	+	args_info->length_orig = NULL;
220	+	args_info->zlength_orig = NULL;
221		args_info->zoffset_arg = 0;
222		args_info->zoffset_orig = NULL;
223		args_info->sele1_arg = NULL;
#	Line 166 | Line 230 | void clear_args (struct gengetopt_args_info *args_info
230		args_info->refsele_orig = NULL;
231		args_info->comsele_arg = NULL;
232		args_info->comsele_orig = NULL;
233	+	args_info->seleoffset_orig = NULL;
234	+	args_info->seleoffset2_orig = NULL;
235		args_info->molname_arg = NULL;
236		args_info->molname_orig = NULL;
237		args_info->begin_orig = NULL;
238		args_info->end_orig = NULL;
239		args_info->radius_orig = NULL;
240	+	args_info->voxelSize_orig = NULL;
241	+	args_info->gaussWidth_orig = NULL;
242
243		}
244
#	Line 187 | Line 255 | void init_args_info(struct gengetopt_args_info *args_i
255		args_info->nbins_help = gengetopt_args_info_help[5] ;
256		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
257		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
258	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
259	<	args_info->length_help = gengetopt_args_info_help[9] ;
258	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
259	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
260		args_info->rcut_help = gengetopt_args_info_help[10] ;
261	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
262	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
263	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
264	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
265	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
266	<	args_info->comsele_help = gengetopt_args_info_help[16] ;
267	<	args_info->molname_help = gengetopt_args_info_help[17] ;
268	<	args_info->begin_help = gengetopt_args_info_help[18] ;
269	<	args_info->end_help = gengetopt_args_info_help[19] ;
270	<	args_info->radius_help = gengetopt_args_info_help[20] ;
271	<	args_info->bo_help = gengetopt_args_info_help[22] ;
272	<	args_info->bor_help = gengetopt_args_info_help[23] ;
273	<	args_info->bad_help = gengetopt_args_info_help[24] ;
274	<	args_info->gofr_help = gengetopt_args_info_help[25] ;
275	<	args_info->gofz_help = gengetopt_args_info_help[26] ;
276	<	args_info->r_theta_help = gengetopt_args_info_help[27] ;
277	<	args_info->r_omega_help = gengetopt_args_info_help[28] ;
278	<	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
279	<	args_info->gxyz_help = gengetopt_args_info_help[30] ;
280	<	args_info->p2_help = gengetopt_args_info_help[31] ;
281	<	args_info->rp2_help = gengetopt_args_info_help[32] ;
282	<	args_info->scd_help = gengetopt_args_info_help[33] ;
283	<	args_info->density_help = gengetopt_args_info_help[34] ;
284	<	args_info->slab_density_help = gengetopt_args_info_help[35] ;
285	<	args_info->hxy_help = gengetopt_args_info_help[36] ;
286	<	args_info->rho_r_help = gengetopt_args_info_help[37] ;
287	<	args_info->hullvol_help = gengetopt_args_info_help[38] ;
261	>	args_info->thetacut_help = gengetopt_args_info_help[11] ;
262	>	args_info->dz_help = gengetopt_args_info_help[12] ;
263	>	args_info->length_help = gengetopt_args_info_help[13] ;
264	>	args_info->zlength_help = gengetopt_args_info_help[14] ;
265	>	args_info->zoffset_help = gengetopt_args_info_help[15] ;
266	>	args_info->sele1_help = gengetopt_args_info_help[16] ;
267	>	args_info->sele2_help = gengetopt_args_info_help[17] ;
268	>	args_info->sele3_help = gengetopt_args_info_help[18] ;
269	>	args_info->refsele_help = gengetopt_args_info_help[19] ;
270	>	args_info->comsele_help = gengetopt_args_info_help[20] ;
271	>	args_info->seleoffset_help = gengetopt_args_info_help[21] ;
272	>	args_info->seleoffset2_help = gengetopt_args_info_help[22] ;
273	>	args_info->molname_help = gengetopt_args_info_help[23] ;
274	>	args_info->begin_help = gengetopt_args_info_help[24] ;
275	>	args_info->end_help = gengetopt_args_info_help[25] ;
276	>	args_info->radius_help = gengetopt_args_info_help[26] ;
277	>	args_info->voxelSize_help = gengetopt_args_info_help[27] ;
278	>	args_info->gaussWidth_help = gengetopt_args_info_help[28] ;
279	>	args_info->bo_help = gengetopt_args_info_help[30] ;
280	>	args_info->ior_help = gengetopt_args_info_help[31] ;
281	>	args_info->for_help = gengetopt_args_info_help[32] ;
282	>	args_info->bad_help = gengetopt_args_info_help[33] ;
283	>	args_info->count_help = gengetopt_args_info_help[34] ;
284	>	args_info->gofr_help = gengetopt_args_info_help[35] ;
285	>	args_info->gofz_help = gengetopt_args_info_help[36] ;
286	>	args_info->r_theta_help = gengetopt_args_info_help[37] ;
287	>	args_info->r_omega_help = gengetopt_args_info_help[38] ;
288	>	args_info->r_z_help = gengetopt_args_info_help[39] ;
289	>	args_info->theta_omega_help = gengetopt_args_info_help[40] ;
290	>	args_info->gxyz_help = gengetopt_args_info_help[41] ;
291	>	args_info->twodgofr_help = gengetopt_args_info_help[42] ;
292	>	args_info->p2_help = gengetopt_args_info_help[43] ;
293	>	args_info->rp2_help = gengetopt_args_info_help[44] ;
294	>	args_info->scd_help = gengetopt_args_info_help[45] ;
295	>	args_info->density_help = gengetopt_args_info_help[46] ;
296	>	args_info->slab_density_help = gengetopt_args_info_help[47] ;
297	>	args_info->p_angle_help = gengetopt_args_info_help[48] ;
298	>	args_info->hxy_help = gengetopt_args_info_help[49] ;
299	>	args_info->rho_r_help = gengetopt_args_info_help[50] ;
300	>	args_info->angle_r_help = gengetopt_args_info_help[51] ;
301	>	args_info->hullvol_help = gengetopt_args_info_help[52] ;
302	>	args_info->rodlength_help = gengetopt_args_info_help[53] ;
303	>	args_info->tet_param_help = gengetopt_args_info_help[54] ;
304	>	args_info->tet_param_z_help = gengetopt_args_info_help[55] ;
305	>	args_info->tet_param_xyz_help = gengetopt_args_info_help[56] ;
306	>	args_info->rnemdz_help = gengetopt_args_info_help[57] ;
307	>	args_info->rnemdr_help = gengetopt_args_info_help[58] ;
308	>	args_info->rnemdrt_help = gengetopt_args_info_help[59] ;
309	>	args_info->nitrile_help = gengetopt_args_info_help[60] ;
310	>	args_info->multipole_help = gengetopt_args_info_help[61] ;
311	>	args_info->surfDiffusion_help = gengetopt_args_info_help[62] ;
312	>	args_info->hbond_help = gengetopt_args_info_help[63] ;
313
314		}
315
316		void
317		cmdline_parser_print_version (void)
318		{
319	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
319	>	printf ("%s %s\n",
320	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
321	>	CMDLINE_PARSER_VERSION);
322		}
323
324		static void print_help_common(void) {
#	Line 238 | Line 333 | static void print_help_common(void) {
333		printf("\n");
334
335		if (strlen(gengetopt_args_info_description) > 0)
336	<	printf("%s\n", gengetopt_args_info_description);
336	>	printf("%s\n\n", gengetopt_args_info_description);
337		}
338
339		void
#	Line 256 | Line 351 | cmdline_parser_init (struct gengetopt_args_info *args_
351		clear_given (args_info);
352		clear_args (args_info);
353		init_args_info (args_info);
354	+
355	+	args_info->inputs = 0;
356	+	args_info->inputs_num = 0;
357		}
358
359		void
#	Line 294 | Line 392 | cmdline_parser_release (struct gengetopt_args_info *ar
392		static void
393		cmdline_parser_release (struct gengetopt_args_info *args_info)
394		{
395	<
395	>	unsigned int i;
396		free_string_field (&(args_info->input_arg));
397		free_string_field (&(args_info->input_orig));
398		free_string_field (&(args_info->output_arg));
#	Line 303 | Line 401 | cmdline_parser_release (struct gengetopt_args_info *ar
401		free_string_field (&(args_info->nbins_orig));
402		free_string_field (&(args_info->nbins_x_orig));
403		free_string_field (&(args_info->nbins_y_orig));
404	+	free_string_field (&(args_info->nbins_z_orig));
405		free_string_field (&(args_info->nanglebins_orig));
307	–	free_string_field (&(args_info->length_orig));
406		free_string_field (&(args_info->rcut_orig));
407	+	free_string_field (&(args_info->thetacut_orig));
408	+	free_string_field (&(args_info->dz_orig));
409	+	free_string_field (&(args_info->length_orig));
410	+	free_string_field (&(args_info->zlength_orig));
411		free_string_field (&(args_info->zoffset_orig));
412		free_string_field (&(args_info->sele1_arg));
413		free_string_field (&(args_info->sele1_orig));
#	Line 317 | Line 419 | cmdline_parser_release (struct gengetopt_args_info *ar
419		free_string_field (&(args_info->refsele_orig));
420		free_string_field (&(args_info->comsele_arg));
421		free_string_field (&(args_info->comsele_orig));
422	+	free_string_field (&(args_info->seleoffset_orig));
423	+	free_string_field (&(args_info->seleoffset2_orig));
424		free_string_field (&(args_info->molname_arg));
425		free_string_field (&(args_info->molname_orig));
426		free_string_field (&(args_info->begin_orig));
427		free_string_field (&(args_info->end_orig));
428		free_string_field (&(args_info->radius_orig));
429	+	free_string_field (&(args_info->voxelSize_orig));
430	+	free_string_field (&(args_info->gaussWidth_orig));
431
432
433	+	for (i = 0; i < args_info->inputs_num; ++i)
434	+	free (args_info->inputs [i]);
435
436	+	if (args_info->inputs_num)
437	+	free (args_info->inputs);
438	+
439		clear_given (args_info);
440		}
441
442
443		static void
444	<	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
444	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
445		{
446	+	FIX_UNUSED (values);
447		if (arg) {
448		fprintf(outfile, "%s=\"%s\"\n", opt, arg);
449		} else {
#	Line 367 | Line 479 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
479		write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
480		if (args_info->nbins_y_given)
481		write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
482	+	if (args_info->nbins_z_given)
483	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
484		if (args_info->nanglebins_given)
485		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);
486		if (args_info->rcut_given)
487		write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
488	+	if (args_info->thetacut_given)
489	+	write_into_file(outfile, "thetacut", args_info->thetacut_orig, 0);
490	+	if (args_info->dz_given)
491	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
492	+	if (args_info->length_given)
493	+	write_into_file(outfile, "length", args_info->length_orig, 0);
494	+	if (args_info->zlength_given)
495	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
496		if (args_info->zoffset_given)
497		write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
498		if (args_info->sele1_given)
#	Line 385 | Line 505 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
505		write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
506		if (args_info->comsele_given)
507		write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
508	+	if (args_info->seleoffset_given)
509	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
510	+	if (args_info->seleoffset2_given)
511	+	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
512		if (args_info->molname_given)
513		write_into_file(outfile, "molname", args_info->molname_orig, 0);
514		if (args_info->begin_given)
#	Line 393 | Line 517 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
517		write_into_file(outfile, "end", args_info->end_orig, 0);
518		if (args_info->radius_given)
519		write_into_file(outfile, "radius", args_info->radius_orig, 0);
520	+	if (args_info->voxelSize_given)
521	+	write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
522	+	if (args_info->gaussWidth_given)
523	+	write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
524		if (args_info->bo_given)
525		write_into_file(outfile, "bo", 0, 0 );
526	<	if (args_info->bor_given)
527	<	write_into_file(outfile, "bor", 0, 0 );
526	>	if (args_info->ior_given)
527	>	write_into_file(outfile, "ior", 0, 0 );
528	>	if (args_info->for_given)
529	>	write_into_file(outfile, "for", 0, 0 );
530		if (args_info->bad_given)
531		write_into_file(outfile, "bad", 0, 0 );
532	+	if (args_info->count_given)
533	+	write_into_file(outfile, "count", 0, 0 );
534		if (args_info->gofr_given)
535		write_into_file(outfile, "gofr", 0, 0 );
536		if (args_info->gofz_given)
#	Line 407 | Line 539 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
539		write_into_file(outfile, "r_theta", 0, 0 );
540		if (args_info->r_omega_given)
541		write_into_file(outfile, "r_omega", 0, 0 );
542	+	if (args_info->r_z_given)
543	+	write_into_file(outfile, "r_z", 0, 0 );
544		if (args_info->theta_omega_given)
545		write_into_file(outfile, "theta_omega", 0, 0 );
546		if (args_info->gxyz_given)
547		write_into_file(outfile, "gxyz", 0, 0 );
548	+	if (args_info->twodgofr_given)
549	+	write_into_file(outfile, "twodgofr", 0, 0 );
550		if (args_info->p2_given)
551		write_into_file(outfile, "p2", 0, 0 );
552		if (args_info->rp2_given)
#	Line 421 | Line 557 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
557		write_into_file(outfile, "density", 0, 0 );
558		if (args_info->slab_density_given)
559		write_into_file(outfile, "slab_density", 0, 0 );
560	+	if (args_info->p_angle_given)
561	+	write_into_file(outfile, "p_angle", 0, 0 );
562		if (args_info->hxy_given)
563		write_into_file(outfile, "hxy", 0, 0 );
564		if (args_info->rho_r_given)
565		write_into_file(outfile, "rho_r", 0, 0 );
566	+	if (args_info->angle_r_given)
567	+	write_into_file(outfile, "angle_r", 0, 0 );
568		if (args_info->hullvol_given)
569		write_into_file(outfile, "hullvol", 0, 0 );
570	+	if (args_info->rodlength_given)
571	+	write_into_file(outfile, "rodlength", 0, 0 );
572	+	if (args_info->tet_param_given)
573	+	write_into_file(outfile, "tet_param", 0, 0 );
574	+	if (args_info->tet_param_z_given)
575	+	write_into_file(outfile, "tet_param_z", 0, 0 );
576	+	if (args_info->tet_param_xyz_given)
577	+	write_into_file(outfile, "tet_param_xyz", 0, 0 );
578	+	if (args_info->rnemdz_given)
579	+	write_into_file(outfile, "rnemdz", 0, 0 );
580	+	if (args_info->rnemdr_given)
581	+	write_into_file(outfile, "rnemdr", 0, 0 );
582	+	if (args_info->rnemdrt_given)
583	+	write_into_file(outfile, "rnemdrt", 0, 0 );
584	+	if (args_info->nitrile_given)
585	+	write_into_file(outfile, "nitrile", 0, 0 );
586	+	if (args_info->multipole_given)
587	+	write_into_file(outfile, "multipole", 0, 0 );
588	+	if (args_info->surfDiffusion_given)
589	+	write_into_file(outfile, "surfDiffusion", 0, 0 );
590	+	if (args_info->hbond_given)
591	+	write_into_file(outfile, "hbond", 0, 0 );
592
593
594		i = EXIT_SUCCESS;
#	Line 463 | Line 625 | gengetopt_strdup (const char *s)
625		char *
626		gengetopt_strdup (const char *s)
627		{
628	<	char *result = NULL;
628	>	char *result = 0;
629		if (!s)
630		return result;
631
#	Line 481 | Line 643 | reset_group_staticProps(struct gengetopt_args_info *ar
643		return;
644
645		args_info->bo_given = 0 ;
646	<	args_info->bor_given = 0 ;
646	>	args_info->ior_given = 0 ;
647	>	args_info->for_given = 0 ;
648		args_info->bad_given = 0 ;
649	+	args_info->count_given = 0 ;
650		args_info->gofr_given = 0 ;
651		args_info->gofz_given = 0 ;
652		args_info->r_theta_given = 0 ;
653		args_info->r_omega_given = 0 ;
654	+	args_info->r_z_given = 0 ;
655		args_info->theta_omega_given = 0 ;
656		args_info->gxyz_given = 0 ;
657	+	args_info->twodgofr_given = 0 ;
658		args_info->p2_given = 0 ;
659		args_info->rp2_given = 0 ;
660		args_info->scd_given = 0 ;
661		args_info->density_given = 0 ;
662		args_info->slab_density_given = 0 ;
663	+	args_info->p_angle_given = 0 ;
664		args_info->hxy_given = 0 ;
665		args_info->rho_r_given = 0 ;
666	+	args_info->angle_r_given = 0 ;
667		args_info->hullvol_given = 0 ;
668	+	args_info->rodlength_given = 0 ;
669	+	args_info->tet_param_given = 0 ;
670	+	args_info->tet_param_z_given = 0 ;
671	+	args_info->tet_param_xyz_given = 0 ;
672	+	args_info->rnemdz_given = 0 ;
673	+	args_info->rnemdr_given = 0 ;
674	+	args_info->rnemdrt_given = 0 ;
675	+	args_info->nitrile_given = 0 ;
676	+	args_info->multipole_given = 0 ;
677	+	args_info->surfDiffusion_given = 0 ;
678	+	args_info->hbond_given = 0 ;
679
680		args_info->staticProps_group_counter = 0;
681		}
682
683		int
684	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
684	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
685		{
686		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
687		}
688
689		int
690	<	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
690	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
691		struct cmdline_parser_params *params)
692		{
693		int result;
694	<	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
694	>	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
695
696		if (result == EXIT_FAILURE)
697		{
#	Line 524 | Line 703 | int
703		}
704
705		int
706	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
706	>	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
707		{
708		int result;
709		struct cmdline_parser_params params;
#	Line 535 | Line 714 | cmdline_parser2 (int argc, char * const *argv, struct
714		params.check_ambiguity = 0;
715		params.print_errors = 1;
716
717	<	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
717	>	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
718
719		if (result == EXIT_FAILURE)
720		{
#	Line 551 | Line 730 | cmdline_parser_required (struct gengetopt_args_info *a
730		{
731		int result = EXIT_SUCCESS;
732
733	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
733	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
734		result = EXIT_FAILURE;
735
736		if (result == EXIT_FAILURE)
#	Line 567 | Line 746 | cmdline_parser_required2 (struct gengetopt_args_info *
746		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
747		{
748		int error = 0;
749	+	FIX_UNUSED (additional_error);
750
751		/* checks for required options */
752		if (! args_info->input_given)
#	Line 577 | Line 757 | cmdline_parser_required2 (struct gengetopt_args_info *
757
758		if (args_info->staticProps_group_counter == 0)
759		{
760	<	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 : ""));
760	>	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 : ""));
761		error = 1;
762		}
763
#	Line 611 | Line 791 | int update_arg(void *field, char **orig_field,
791		static
792		int update_arg(void *field, char **orig_field,
793		unsigned int *field_given, unsigned int *prev_given,
794	<	char *value, char *possible_values[], const char *default_value,
794	>	char *value, const char *possible_values[],
795	>	const char *default_value,
796		cmdline_parser_arg_type arg_type,
797		int check_ambiguity, int override,
798		int no_free, int multiple_option,
#	Line 622 | Line 803 | int update_arg(void *field, char **orig_field,
803		const char *val = value;
804		int found;
805		char **string_field;
806	+	FIX_UNUSED (field);
807
808		stop_char = 0;
809		found = 0;
#	Line 639 | Line 821 | int update_arg(void *field, char **orig_field,
821		return 1; /* failure */
822		}
823
824	+	FIX_UNUSED (default_value);
825
826		if (field_given && *field_given && ! override)
827		return 0;
#	Line 702 | Line 885 | int
885
886
887		int
888	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
888	>	cmdline_parser_internal (
889	>	int argc, char **argv, struct gengetopt_args_info *args_info,
890		struct cmdline_parser_params *params, const char *additional_error)
891		{
892		int c;        /* Character of the parsed option.  */
#	Line 745 | Line 929 | cmdline_parser_internal (int argc, char * const *argv,
929		{ "nbins",      1, NULL, 'b' },
930		{ "nbins_x",    1, NULL, 'x' },
931		{ "nbins_y",    1, NULL, 'y' },
932	+	{ "nbins_z",    1, NULL, 0 },
933		{ "nanglebins", 1, NULL, 'a' },
749	–	{ "length",     1, NULL, 0 },
934		{ "rcut",       1, NULL, 'c' },
935	+	{ "thetacut",   1, NULL, 0 },
936	+	{ "dz", 1, NULL, 0 },
937	+	{ "length",     1, NULL, 0 },
938	+	{ "zlength",    1, NULL, 0 },
939		{ "zoffset",    1, NULL, 'z' },
940		{ "sele1",      1, NULL, 0 },
941		{ "sele2",      1, NULL, 0 },
942		{ "sele3",      1, NULL, 0 },
943		{ "refsele",    1, NULL, 0 },
944		{ "comsele",    1, NULL, 0 },
945	+	{ "seleoffset", 1, NULL, 0 },
946	+	{ "seleoffset2",        1, NULL, 0 },
947		{ "molname",    1, NULL, 0 },
948		{ "begin",      1, NULL, 0 },
949		{ "end",        1, NULL, 0 },
950		{ "radius",     1, NULL, 0 },
951	+	{ "voxelSize",  1, NULL, 'v' },
952	+	{ "gaussWidth", 1, NULL, 0 },
953		{ "bo", 0, NULL, 0 },
954	<	{ "bor",        0, NULL, 0 },
954	>	{ "ior",        0, NULL, 0 },
955	>	{ "for",        0, NULL, 0 },
956		{ "bad",        0, NULL, 0 },
957	+	{ "count",      0, NULL, 0 },
958		{ "gofr",       0, NULL, 'g' },
959		{ "gofz",       0, NULL, 0 },
960		{ "r_theta",    0, NULL, 0 },
961		{ "r_omega",    0, NULL, 0 },
962	+	{ "r_z",        0, NULL, 0 },
963		{ "theta_omega",        0, NULL, 0 },
964		{ "gxyz",       0, NULL, 0 },
965	+	{ "twodgofr",   0, NULL, 0 },
966		{ "p2", 0, NULL, 'p' },
967		{ "rp2",        0, NULL, 0 },
968		{ "scd",        0, NULL, 's' },
969		{ "density",    0, NULL, 'd' },
970		{ "slab_density",       0, NULL, 0 },
971	+	{ "p_angle",    0, NULL, 0 },
972		{ "hxy",        0, NULL, 0 },
973		{ "rho_r",      0, NULL, 0 },
974	+	{ "angle_r",    0, NULL, 0 },
975		{ "hullvol",    0, NULL, 0 },
976	<	{ NULL, 0, NULL, 0 }
976	>	{ "rodlength",  0, NULL, 0 },
977	>	{ "tet_param",  0, NULL, 'Q' },
978	>	{ "tet_param_z",        0, NULL, 0 },
979	>	{ "tet_param_xyz",      0, NULL, 0 },
980	>	{ "rnemdz",     0, NULL, 0 },
981	>	{ "rnemdr",     0, NULL, 0 },
982	>	{ "rnemdrt",    0, NULL, 0 },
983	>	{ "nitrile",    0, NULL, 0 },
984	>	{ "multipole",  0, NULL, 'm' },
985	>	{ "surfDiffusion",      0, NULL, 0 },
986	>	{ "hbond",      0, NULL, 0 },
987	>	{ 0,  0, 0, 0 }
988		};
989
990	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
990	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);
991
992		if (c == -1) break;       /* Exit from `while (1)' loop.  */
993
#	Line 898 | Line 1107 | cmdline_parser_internal (int argc, char * const *argv,
1107		&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1108		check_ambiguity, override, 0, 0,
1109		"zoffset", 'z',
1110	+	additional_error))
1111	+	goto failure;
1112	+
1113	+	break;
1114	+	case 'v':       /* voxel size (angstroms).  */
1115	+
1116	+
1117	+	if (update_arg( (void *)&(args_info->voxelSize_arg),
1118	+	&(args_info->voxelSize_orig), &(args_info->voxelSize_given),
1119	+	&(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
1120	+	check_ambiguity, override, 0, 0,
1121	+	"voxelSize", 'v',
1122		additional_error))
1123		goto failure;
1124
#	Line 917 | Line 1138 | cmdline_parser_internal (int argc, char * const *argv,
1138		goto failure;
1139
1140		break;
1141	<	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1141	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1142
1143		if (args_info->staticProps_group_counter && override)
1144		reset_group_staticProps (args_info);
#	Line 962 | Line 1183 | cmdline_parser_internal (int argc, char * const *argv,
1183		goto failure;
1184
1185		break;
1186	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1187	+
1188	+	if (args_info->staticProps_group_counter && override)
1189	+	reset_group_staticProps (args_info);
1190	+	args_info->staticProps_group_counter += 1;
1191	+
1192	+	if (update_arg( 0 ,
1193	+	0 , &(args_info->tet_param_given),
1194	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1195	+	check_ambiguity, override, 0, 0,
1196	+	"tet_param", 'Q',
1197	+	additional_error))
1198	+	goto failure;
1199	+
1200	+	break;
1201	+	case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1202	+
1203	+	if (args_info->staticProps_group_counter && override)
1204	+	reset_group_staticProps (args_info);
1205	+	args_info->staticProps_group_counter += 1;
1206	+
1207	+	if (update_arg( 0 ,
1208	+	0 , &(args_info->multipole_given),
1209	+	&(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1210	+	check_ambiguity, override, 0, 0,
1211	+	"multipole", 'm',
1212	+	additional_error))
1213	+	goto failure;
1214	+
1215	+	break;
1216
1217		case 0: /* Long option with no short option */
1218	+	/* number of bins in z axis.  */
1219	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1220	+	{
1221	+
1222	+
1223	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1224	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1225	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1226	+	check_ambiguity, override, 0, 0,
1227	+	"nbins_z", '-',
1228	+	additional_error))
1229	+	goto failure;
1230	+
1231	+	}
1232	+	/* cutoff angle (thetacut).  */
1233	+	else if (strcmp (long_options[option_index].name, "thetacut") == 0)
1234	+	{
1235	+
1236	+
1237	+	if (update_arg( (void *)&(args_info->thetacut_arg),
1238	+	&(args_info->thetacut_orig), &(args_info->thetacut_given),
1239	+	&(local_args_info.thetacut_given), optarg, 0, 0, ARG_DOUBLE,
1240	+	check_ambiguity, override, 0, 0,
1241	+	"thetacut", '-',
1242	+	additional_error))
1243	+	goto failure;
1244	+
1245	+	}
1246	+	/* slab width (dz).  */
1247	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1248	+	{
1249	+
1250	+
1251	+	if (update_arg( (void *)&(args_info->dz_arg),
1252	+	&(args_info->dz_orig), &(args_info->dz_given),
1253	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1254	+	check_ambiguity, override, 0, 0,
1255	+	"dz", '-',
1256	+	additional_error))
1257	+	goto failure;
1258	+
1259	+	}
1260		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1261	<	if (strcmp (long_options[option_index].name, "length") == 0)
1261	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1262		{
1263
1264
#	Line 978 | Line 1271 | cmdline_parser_internal (int argc, char * const *argv,
1271		goto failure;
1272
1273		}
1274	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1275	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1276	+	{
1277	+
1278	+
1279	+	if (update_arg( (void *)&(args_info->zlength_arg),
1280	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1281	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1282	+	check_ambiguity, override, 0, 0,
1283	+	"zlength", '-',
1284	+	additional_error))
1285	+	goto failure;
1286	+
1287	+	}
1288		/* select the first stuntdouble set.  */
1289		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1290		{
#	Line 1048 | Line 1355 | cmdline_parser_internal (int argc, char * const *argv,
1355		goto failure;
1356
1357		}
1358	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1359	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1360	+	{
1361	+
1362	+
1363	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1364	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1365	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1366	+	check_ambiguity, override, 0, 0,
1367	+	"seleoffset", '-',
1368	+	additional_error))
1369	+	goto failure;
1370	+
1371	+	}
1372	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1373	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1374	+	{
1375	+
1376	+
1377	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1378	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1379	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1380	+	check_ambiguity, override, 0, 0,
1381	+	"seleoffset2", '-',
1382	+	additional_error))
1383	+	goto failure;
1384	+
1385	+	}
1386		/* molecule name.  */
1387		else if (strcmp (long_options[option_index].name, "molname") == 0)
1388		{
#	Line 1104 | Line 1439 | cmdline_parser_internal (int argc, char * const *argv,
1439		goto failure;
1440
1441		}
1442	+	/* Gaussian width (angstroms).  */
1443	+	else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
1444	+	{
1445	+
1446	+
1447	+	if (update_arg( (void *)&(args_info->gaussWidth_arg),
1448	+	&(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
1449	+	&(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
1450	+	check_ambiguity, override, 0, 0,
1451	+	"gaussWidth", '-',
1452	+	additional_error))
1453	+	goto failure;
1454	+
1455	+	}
1456		/* bond order parameter (--rcut must be specified).  */
1457		else if (strcmp (long_options[option_index].name, "bo") == 0)
1458		{
#	Line 1121 | Line 1470 | cmdline_parser_internal (int argc, char * const *argv,
1470		goto failure;
1471
1472		}
1473	<	/* bond order parameter as a function of radius (--rcut must be specified).  */
1474	<	else if (strcmp (long_options[option_index].name, "bor") == 0)
1473	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1474	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1475	>	{
1476	>
1477	>	if (args_info->staticProps_group_counter && override)
1478	>	reset_group_staticProps (args_info);
1479	>	args_info->staticProps_group_counter += 1;
1480	>
1481	>	if (update_arg( 0 ,
1482	>	0 , &(args_info->ior_given),
1483	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1484	>	check_ambiguity, override, 0, 0,
1485	>	"ior", '-',
1486	>	additional_error))
1487	>	goto failure;
1488	>
1489	>	}
1490	>	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1491	>	else if (strcmp (long_options[option_index].name, "for") == 0)
1492		{
1493
1494		if (args_info->staticProps_group_counter && override)
#	Line 1130 | Line 1496 | cmdline_parser_internal (int argc, char * const *argv,
1496		args_info->staticProps_group_counter += 1;
1497
1498		if (update_arg( 0 ,
1499	<	0 , &(args_info->bor_given),
1500	<	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1499	>	0 , &(args_info->for_given),
1500	>	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1501		check_ambiguity, override, 0, 0,
1502	<	"bor", '-',
1502	>	"for", '-',
1503		additional_error))
1504		goto failure;
1505
#	Line 1155 | Line 1521 | cmdline_parser_internal (int argc, char * const *argv,
1521		goto failure;
1522
1523		}
1524	+	/* count of molecules matching selection criteria (and associated statistics).  */
1525	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1526	+	{
1527	+
1528	+	if (args_info->staticProps_group_counter && override)
1529	+	reset_group_staticProps (args_info);
1530	+	args_info->staticProps_group_counter += 1;
1531	+
1532	+	if (update_arg( 0 ,
1533	+	0 , &(args_info->count_given),
1534	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1535	+	check_ambiguity, override, 0, 0,
1536	+	"count", '-',
1537	+	additional_error))
1538	+	goto failure;
1539	+
1540	+	}
1541		/* g(z).  */
1542		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1543		{
#	Line 1206 | Line 1589 | cmdline_parser_internal (int argc, char * const *argv,
1589		goto failure;
1590
1591		}
1592	+	/* g(r, z).  */
1593	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1594	+	{
1595	+
1596	+	if (args_info->staticProps_group_counter && override)
1597	+	reset_group_staticProps (args_info);
1598	+	args_info->staticProps_group_counter += 1;
1599	+
1600	+	if (update_arg( 0 ,
1601	+	0 , &(args_info->r_z_given),
1602	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1603	+	check_ambiguity, override, 0, 0,
1604	+	"r_z", '-',
1605	+	additional_error))
1606	+	goto failure;
1607	+
1608	+	}
1609		/* g(cos(theta), cos(omega)).  */
1610		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1611		{
#	Line 1240 | Line 1640 | cmdline_parser_internal (int argc, char * const *argv,
1640		goto failure;
1641
1642		}
1643	+	/* 2D g(r) (Slab width --dz must be specified).  */
1644	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1645	+	{
1646	+
1647	+	if (args_info->staticProps_group_counter && override)
1648	+	reset_group_staticProps (args_info);
1649	+	args_info->staticProps_group_counter += 1;
1650	+
1651	+	if (update_arg( 0 ,
1652	+	0 , &(args_info->twodgofr_given),
1653	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1654	+	check_ambiguity, override, 0, 0,
1655	+	"twodgofr", '-',
1656	+	additional_error))
1657	+	goto failure;
1658	+
1659	+	}
1660		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1661		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1662		{
#	Line 1274 | Line 1691 | cmdline_parser_internal (int argc, char * const *argv,
1691		goto failure;
1692
1693		}
1694	+	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1695	+	else if (strcmp (long_options[option_index].name, "p_angle") == 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->p_angle_given),
1704	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1705	+	check_ambiguity, override, 0, 0,
1706	+	"p_angle", '-',
1707	+	additional_error))
1708	+	goto failure;
1709	+
1710	+	}
1711		/* hxy.  */
1712		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1713		{
#	Line 1304 | Line 1738 | cmdline_parser_internal (int argc, char * const *argv,
1738		&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1739		check_ambiguity, override, 0, 0,
1740		"rho_r", '-',
1741	+	additional_error))
1742	+	goto failure;
1743	+
1744	+	}
1745	+	/* angle of R.  */
1746	+	else if (strcmp (long_options[option_index].name, "angle_r") == 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->angle_r_given),
1755	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1756	+	check_ambiguity, override, 0, 0,
1757	+	"angle_r", '-',
1758		additional_error))
1759		goto failure;
1760
#	Line 1325 | Line 1776 | cmdline_parser_internal (int argc, char * const *argv,
1776		goto failure;
1777
1778		}
1779	+	/* length of nanorod.  */
1780	+	else if (strcmp (long_options[option_index].name, "rodlength") == 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->rodlength_given),
1789	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1790	+	check_ambiguity, override, 0, 0,
1791	+	"rodlength", '-',
1792	+	additional_error))
1793	+	goto failure;
1794	+
1795	+	}
1796	+	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1797	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1798	+	{
1799	+
1800	+	if (args_info->staticProps_group_counter && override)
1801	+	reset_group_staticProps (args_info);
1802	+	args_info->staticProps_group_counter += 1;
1803	+
1804	+	if (update_arg( 0 ,
1805	+	0 , &(args_info->tet_param_z_given),
1806	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1807	+	check_ambiguity, override, 0, 0,
1808	+	"tet_param_z", '-',
1809	+	additional_error))
1810	+	goto failure;
1811	+
1812	+	}
1813	+	/* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
1814	+	else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
1815	+	{
1816	+
1817	+	if (args_info->staticProps_group_counter && override)
1818	+	reset_group_staticProps (args_info);
1819	+	args_info->staticProps_group_counter += 1;
1820	+
1821	+	if (update_arg( 0 ,
1822	+	0 , &(args_info->tet_param_xyz_given),
1823	+	&(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
1824	+	check_ambiguity, override, 0, 0,
1825	+	"tet_param_xyz", '-',
1826	+	additional_error))
1827	+	goto failure;
1828	+
1829	+	}
1830	+	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1831	+	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1832	+	{
1833	+
1834	+	if (args_info->staticProps_group_counter && override)
1835	+	reset_group_staticProps (args_info);
1836	+	args_info->staticProps_group_counter += 1;
1837	+
1838	+	if (update_arg( 0 ,
1839	+	0 , &(args_info->rnemdz_given),
1840	+	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1841	+	check_ambiguity, override, 0, 0,
1842	+	"rnemdz", '-',
1843	+	additional_error))
1844	+	goto failure;
1845	+
1846	+	}
1847	+	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1848	+	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1849	+	{
1850	+
1851	+	if (args_info->staticProps_group_counter && override)
1852	+	reset_group_staticProps (args_info);
1853	+	args_info->staticProps_group_counter += 1;
1854	+
1855	+	if (update_arg( 0 ,
1856	+	0 , &(args_info->rnemdr_given),
1857	+	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1858	+	check_ambiguity, override, 0, 0,
1859	+	"rnemdr", '-',
1860	+	additional_error))
1861	+	goto failure;
1862	+
1863	+	}
1864	+	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1865	+	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1866	+	{
1867	+
1868	+	if (args_info->staticProps_group_counter && override)
1869	+	reset_group_staticProps (args_info);
1870	+	args_info->staticProps_group_counter += 1;
1871	+
1872	+	if (update_arg( 0 ,
1873	+	0 , &(args_info->rnemdrt_given),
1874	+	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1875	+	check_ambiguity, override, 0, 0,
1876	+	"rnemdrt", '-',
1877	+	additional_error))
1878	+	goto failure;
1879	+
1880	+	}
1881	+	/* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1882	+	else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1883	+	{
1884	+
1885	+	if (args_info->staticProps_group_counter && override)
1886	+	reset_group_staticProps (args_info);
1887	+	args_info->staticProps_group_counter += 1;
1888	+
1889	+	if (update_arg( 0 ,
1890	+	0 , &(args_info->nitrile_given),
1891	+	&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1892	+	check_ambiguity, override, 0, 0,
1893	+	"nitrile", '-',
1894	+	additional_error))
1895	+	goto failure;
1896	+
1897	+	}
1898	+	/* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
1899	+	else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0)
1900	+	{
1901	+
1902	+	if (args_info->staticProps_group_counter && override)
1903	+	reset_group_staticProps (args_info);
1904	+	args_info->staticProps_group_counter += 1;
1905	+
1906	+	if (update_arg( 0 ,
1907	+	0 , &(args_info->surfDiffusion_given),
1908	+	&(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
1909	+	check_ambiguity, override, 0, 0,
1910	+	"surfDiffusion", '-',
1911	+	additional_error))
1912	+	goto failure;
1913	+
1914	+	}
1915	+	/* Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified).  */
1916	+	else if (strcmp (long_options[option_index].name, "hbond") == 0)
1917	+	{
1918	+
1919	+	if (args_info->staticProps_group_counter && override)
1920	+	reset_group_staticProps (args_info);
1921	+	args_info->staticProps_group_counter += 1;
1922	+
1923	+	if (update_arg( 0 ,
1924	+	0 , &(args_info->hbond_given),
1925	+	&(local_args_info.hbond_given), optarg, 0, 0, ARG_NO,
1926	+	check_ambiguity, override, 0, 0,
1927	+	"hbond", '-',
1928	+	additional_error))
1929	+	goto failure;
1930	+
1931	+	}
1932	+
1933		break;
1934		case '?':       /* Invalid option.  */
1935		/* `getopt_long' already printed an error message.  */
#	Line 1339 | Line 1943 | cmdline_parser_internal (int argc, char * const *argv,
1943
1944		if (args_info->staticProps_group_counter > 1)
1945		{
1946	<	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 : ""));
1946	>	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 : ""));
1947		error = 1;
1948		}
1949
#	Line 1355 | Line 1959 | cmdline_parser_internal (int argc, char * const *argv,
1959		if ( error )
1960		return (EXIT_FAILURE);
1961
1962	+	if (optind < argc)
1963	+	{
1964	+	int i = 0 ;
1965	+	int found_prog_name = 0;
1966	+	/* whether program name, i.e., argv[0], is in the remaining args
1967	+	(this may happen with some implementations of getopt,
1968	+	but surely not with the one included by gengetopt) */
1969	+
1970	+	i = optind;
1971	+	while (i < argc)
1972	+	if (argv[i++] == argv[0]) {
1973	+	found_prog_name = 1;
1974	+	break;
1975	+	}
1976	+	i = 0;
1977	+
1978	+	args_info->inputs_num = argc - optind - found_prog_name;
1979	+	args_info->inputs =
1980	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1981	+	while (optind < argc)
1982	+	if (argv[optind++] != argv[0])
1983	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1984	+	}
1985	+
1986		return 0;
1987
1988		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 2049 by gezelter, Tue Jan 6 21:44:10 2015 UTC

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

Diff Legend

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