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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 2031 by jmichalk, Fri Oct 31 18:40:40 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 -i StaticProps.ggo -F StaticPropsCmd -c cpp
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
#	Line 17 | Line 17
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	#include "getopt.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22	>	#endif
23
24	+	#include <getopt.h>
25	+
26		#include "StaticPropsCmd.h"
27
28		const char *gengetopt_args_info_purpose = "";
#	Line 36 | Line 40 | const char *gengetopt_args_info_help[] = {
40		"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
41		"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
42		"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
43	+	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
44		"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	–	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
45		"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
46	+	"      --dz=DOUBLE               slab width (dz)",
47	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
48	+	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
49		"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
50		"      --sele1=selection script  select the first stuntdouble set",
51		"      --sele2=selection script  select the second stuntdouble set",
52		"      --sele3=selection script  select the third stuntdouble set",
53		"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
54		"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
55	+	"      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
56	+	"      --seleoffset2=INT         global index offset for a third object (used to \n                                  define a vector between sites in molecule)",
57		"      --molname=STRING          molecule name",
58		"      --begin=INT               begin internal index",
59		"      --end=INT                 end internal index",
60		"      --radius=DOUBLE           nanoparticle radius",
61	+	"  -v, --voxelSize=DOUBLE        voxel size (angstroms)",
62	+	"      --gaussWidth=DOUBLE       Gaussian width (angstroms)",
63		"\n Group: staticProps\n   an option of this group is required",
64		"      --bo                      bond order parameter (--rcut must be specified)",
65	<	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
65	>	"      --ior                     icosahedral bond order parameter as a function \n                                  of radius (--rcut must be specified)",
66	>	"      --for                     FCC bond order parameter as a function of \n                                  radius (--rcut must be specified)",
67		"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
68	+	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
69		"  -g, --gofr                    g(r)",
70		"      --gofz                    g(z)",
71		"      --r_theta                 g(r, cos(theta))",
72		"      --r_omega                 g(r, cos(omega))",
73	+	"      --r_z                     g(r, z)",
74		"      --theta_omega             g(cos(theta), cos(omega))",
75		"      --gxyz                    g(x, y, z)",
76	<	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
76	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
77	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
78		"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
79		"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
80		"  -d, --density                 density plot",
81		"      --slab_density            slab density",
82	+	"      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
83		"      --hxy                     hxy",
84		"      --rho_r                   rho of R",
85	+	"      --angle_r                 angle of R",
86		"      --hullvol                 hull volume of nanoparticle",
87	+	"      --rodlength               length of nanorod",
88	+	"  -Q, --tet_param               tetrahedrality order parameter (Qk)",
89	+	"      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
90	+	"      --tet_param_xyz           volume-resolved tetrahedrality order parameter \n                                  Qk(x,y,z).  (voxelSize, rcut, and gaussWidth \n                                  must be specified)",
91	+	"      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
92	+	"      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
93	+	"      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
94	+	"      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
95	+	"  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
96	+	"      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
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->voxelSize_given = 0 ;
151	+	args_info->gaussWidth_given = 0 ;
152		args_info->bo_given = 0 ;
153	<	args_info->bor_given = 0 ;
153	>	args_info->ior_given = 0 ;
154	>	args_info->for_given = 0 ;
155		args_info->bad_given = 0 ;
156	+	args_info->count_given = 0 ;
157		args_info->gofr_given = 0 ;
158		args_info->gofz_given = 0 ;
159		args_info->r_theta_given = 0 ;
160		args_info->r_omega_given = 0 ;
161	+	args_info->r_z_given = 0 ;
162		args_info->theta_omega_given = 0 ;
163		args_info->gxyz_given = 0 ;
164	+	args_info->twodgofr_given = 0 ;
165		args_info->p2_given = 0 ;
166		args_info->rp2_given = 0 ;
167		args_info->scd_given = 0 ;
168		args_info->density_given = 0 ;
169		args_info->slab_density_given = 0 ;
170	+	args_info->p_angle_given = 0 ;
171		args_info->hxy_given = 0 ;
172		args_info->rho_r_given = 0 ;
173	+	args_info->angle_r_given = 0 ;
174		args_info->hullvol_given = 0 ;
175	+	args_info->rodlength_given = 0 ;
176	+	args_info->tet_param_given = 0 ;
177	+	args_info->tet_param_z_given = 0 ;
178	+	args_info->tet_param_xyz_given = 0 ;
179	+	args_info->rnemdz_given = 0 ;
180	+	args_info->rnemdr_given = 0 ;
181	+	args_info->rnemdrt_given = 0 ;
182	+	args_info->nitrile_given = 0 ;
183	+	args_info->multipole_given = 0 ;
184	+	args_info->surfDiffusion_given = 0 ;
185		args_info->staticProps_group_counter = 0 ;
186		}
187
188		static
189		void clear_args (struct gengetopt_args_info *args_info)
190		{
191	+	FIX_UNUSED (args_info);
192		args_info->input_arg = NULL;
193		args_info->input_orig = NULL;
194		args_info->output_arg = NULL;
#	Line 150 | Line 201 | void clear_args (struct gengetopt_args_info *args_info
201		args_info->nbins_x_orig = NULL;
202		args_info->nbins_y_arg = 100;
203		args_info->nbins_y_orig = NULL;
204	+	args_info->nbins_z_arg = 100;
205	+	args_info->nbins_z_orig = NULL;
206		args_info->nanglebins_arg = 50;
207		args_info->nanglebins_orig = NULL;
155	–	args_info->length_orig = NULL;
208		args_info->rcut_orig = NULL;
209	+	args_info->dz_orig = NULL;
210	+	args_info->length_orig = NULL;
211	+	args_info->zlength_orig = NULL;
212		args_info->zoffset_arg = 0;
213		args_info->zoffset_orig = NULL;
214		args_info->sele1_arg = NULL;
#	Line 166 | Line 221 | void clear_args (struct gengetopt_args_info *args_info
221		args_info->refsele_orig = NULL;
222		args_info->comsele_arg = NULL;
223		args_info->comsele_orig = NULL;
224	+	args_info->seleoffset_orig = NULL;
225	+	args_info->seleoffset2_orig = NULL;
226		args_info->molname_arg = NULL;
227		args_info->molname_orig = NULL;
228		args_info->begin_orig = NULL;
229		args_info->end_orig = NULL;
230		args_info->radius_orig = NULL;
231	+	args_info->voxelSize_orig = NULL;
232	+	args_info->gaussWidth_orig = NULL;
233
234		}
235
#	Line 187 | Line 246 | void init_args_info(struct gengetopt_args_info *args_i
246		args_info->nbins_help = gengetopt_args_info_help[5] ;
247		args_info->nbins_x_help = gengetopt_args_info_help[6] ;
248		args_info->nbins_y_help = gengetopt_args_info_help[7] ;
249	<	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
250	<	args_info->length_help = gengetopt_args_info_help[9] ;
249	>	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
250	>	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
251		args_info->rcut_help = gengetopt_args_info_help[10] ;
252	<	args_info->zoffset_help = gengetopt_args_info_help[11] ;
253	<	args_info->sele1_help = gengetopt_args_info_help[12] ;
254	<	args_info->sele2_help = gengetopt_args_info_help[13] ;
255	<	args_info->sele3_help = gengetopt_args_info_help[14] ;
256	<	args_info->refsele_help = gengetopt_args_info_help[15] ;
257	<	args_info->comsele_help = gengetopt_args_info_help[16] ;
258	<	args_info->molname_help = gengetopt_args_info_help[17] ;
259	<	args_info->begin_help = gengetopt_args_info_help[18] ;
260	<	args_info->end_help = gengetopt_args_info_help[19] ;
261	<	args_info->radius_help = gengetopt_args_info_help[20] ;
262	<	args_info->bo_help = gengetopt_args_info_help[22] ;
263	<	args_info->bor_help = gengetopt_args_info_help[23] ;
264	<	args_info->bad_help = gengetopt_args_info_help[24] ;
265	<	args_info->gofr_help = gengetopt_args_info_help[25] ;
266	<	args_info->gofz_help = gengetopt_args_info_help[26] ;
267	<	args_info->r_theta_help = gengetopt_args_info_help[27] ;
268	<	args_info->r_omega_help = gengetopt_args_info_help[28] ;
269	<	args_info->theta_omega_help = gengetopt_args_info_help[29] ;
270	<	args_info->gxyz_help = gengetopt_args_info_help[30] ;
271	<	args_info->p2_help = gengetopt_args_info_help[31] ;
272	<	args_info->rp2_help = gengetopt_args_info_help[32] ;
273	<	args_info->scd_help = gengetopt_args_info_help[33] ;
274	<	args_info->density_help = gengetopt_args_info_help[34] ;
275	<	args_info->slab_density_help = gengetopt_args_info_help[35] ;
276	<	args_info->hxy_help = gengetopt_args_info_help[36] ;
277	<	args_info->rho_r_help = gengetopt_args_info_help[37] ;
278	<	args_info->hullvol_help = gengetopt_args_info_help[38] ;
252	>	args_info->dz_help = gengetopt_args_info_help[11] ;
253	>	args_info->length_help = gengetopt_args_info_help[12] ;
254	>	args_info->zlength_help = gengetopt_args_info_help[13] ;
255	>	args_info->zoffset_help = gengetopt_args_info_help[14] ;
256	>	args_info->sele1_help = gengetopt_args_info_help[15] ;
257	>	args_info->sele2_help = gengetopt_args_info_help[16] ;
258	>	args_info->sele3_help = gengetopt_args_info_help[17] ;
259	>	args_info->refsele_help = gengetopt_args_info_help[18] ;
260	>	args_info->comsele_help = gengetopt_args_info_help[19] ;
261	>	args_info->seleoffset_help = gengetopt_args_info_help[20] ;
262	>	args_info->seleoffset2_help = gengetopt_args_info_help[21] ;
263	>	args_info->molname_help = gengetopt_args_info_help[22] ;
264	>	args_info->begin_help = gengetopt_args_info_help[23] ;
265	>	args_info->end_help = gengetopt_args_info_help[24] ;
266	>	args_info->radius_help = gengetopt_args_info_help[25] ;
267	>	args_info->voxelSize_help = gengetopt_args_info_help[26] ;
268	>	args_info->gaussWidth_help = gengetopt_args_info_help[27] ;
269	>	args_info->bo_help = gengetopt_args_info_help[29] ;
270	>	args_info->ior_help = gengetopt_args_info_help[30] ;
271	>	args_info->for_help = gengetopt_args_info_help[31] ;
272	>	args_info->bad_help = gengetopt_args_info_help[32] ;
273	>	args_info->count_help = gengetopt_args_info_help[33] ;
274	>	args_info->gofr_help = gengetopt_args_info_help[34] ;
275	>	args_info->gofz_help = gengetopt_args_info_help[35] ;
276	>	args_info->r_theta_help = gengetopt_args_info_help[36] ;
277	>	args_info->r_omega_help = gengetopt_args_info_help[37] ;
278	>	args_info->r_z_help = gengetopt_args_info_help[38] ;
279	>	args_info->theta_omega_help = gengetopt_args_info_help[39] ;
280	>	args_info->gxyz_help = gengetopt_args_info_help[40] ;
281	>	args_info->twodgofr_help = gengetopt_args_info_help[41] ;
282	>	args_info->p2_help = gengetopt_args_info_help[42] ;
283	>	args_info->rp2_help = gengetopt_args_info_help[43] ;
284	>	args_info->scd_help = gengetopt_args_info_help[44] ;
285	>	args_info->density_help = gengetopt_args_info_help[45] ;
286	>	args_info->slab_density_help = gengetopt_args_info_help[46] ;
287	>	args_info->p_angle_help = gengetopt_args_info_help[47] ;
288	>	args_info->hxy_help = gengetopt_args_info_help[48] ;
289	>	args_info->rho_r_help = gengetopt_args_info_help[49] ;
290	>	args_info->angle_r_help = gengetopt_args_info_help[50] ;
291	>	args_info->hullvol_help = gengetopt_args_info_help[51] ;
292	>	args_info->rodlength_help = gengetopt_args_info_help[52] ;
293	>	args_info->tet_param_help = gengetopt_args_info_help[53] ;
294	>	args_info->tet_param_z_help = gengetopt_args_info_help[54] ;
295	>	args_info->tet_param_xyz_help = gengetopt_args_info_help[55] ;
296	>	args_info->rnemdz_help = gengetopt_args_info_help[56] ;
297	>	args_info->rnemdr_help = gengetopt_args_info_help[57] ;
298	>	args_info->rnemdrt_help = gengetopt_args_info_help[58] ;
299	>	args_info->nitrile_help = gengetopt_args_info_help[59] ;
300	>	args_info->multipole_help = gengetopt_args_info_help[60] ;
301	>	args_info->surfDiffusion_help = gengetopt_args_info_help[61] ;
302
303		}
304
305		void
306		cmdline_parser_print_version (void)
307		{
308	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
308	>	printf ("%s %s\n",
309	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
310	>	CMDLINE_PARSER_VERSION);
311		}
312
313		static void print_help_common(void) {
#	Line 238 | Line 322 | static void print_help_common(void) {
322		printf("\n");
323
324		if (strlen(gengetopt_args_info_description) > 0)
325	<	printf("%s\n", gengetopt_args_info_description);
325	>	printf("%s\n\n", gengetopt_args_info_description);
326		}
327
328		void
#	Line 303 | Line 387 | cmdline_parser_release (struct gengetopt_args_info *ar
387		free_string_field (&(args_info->nbins_orig));
388		free_string_field (&(args_info->nbins_x_orig));
389		free_string_field (&(args_info->nbins_y_orig));
390	+	free_string_field (&(args_info->nbins_z_orig));
391		free_string_field (&(args_info->nanglebins_orig));
307	–	free_string_field (&(args_info->length_orig));
392		free_string_field (&(args_info->rcut_orig));
393	+	free_string_field (&(args_info->dz_orig));
394	+	free_string_field (&(args_info->length_orig));
395	+	free_string_field (&(args_info->zlength_orig));
396		free_string_field (&(args_info->zoffset_orig));
397		free_string_field (&(args_info->sele1_arg));
398		free_string_field (&(args_info->sele1_orig));
#	Line 317 | Line 404 | cmdline_parser_release (struct gengetopt_args_info *ar
404		free_string_field (&(args_info->refsele_orig));
405		free_string_field (&(args_info->comsele_arg));
406		free_string_field (&(args_info->comsele_orig));
407	+	free_string_field (&(args_info->seleoffset_orig));
408	+	free_string_field (&(args_info->seleoffset2_orig));
409		free_string_field (&(args_info->molname_arg));
410		free_string_field (&(args_info->molname_orig));
411		free_string_field (&(args_info->begin_orig));
412		free_string_field (&(args_info->end_orig));
413		free_string_field (&(args_info->radius_orig));
414	+	free_string_field (&(args_info->voxelSize_orig));
415	+	free_string_field (&(args_info->gaussWidth_orig));
416
417
418
#	Line 330 | Line 421 | static void
421
422
423		static void
424	<	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
424	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
425		{
426	+	FIX_UNUSED (values);
427		if (arg) {
428		fprintf(outfile, "%s=\"%s\"\n", opt, arg);
429		} else {
#	Line 367 | Line 459 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
459		write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
460		if (args_info->nbins_y_given)
461		write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
462	+	if (args_info->nbins_z_given)
463	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
464		if (args_info->nanglebins_given)
465		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);
466		if (args_info->rcut_given)
467		write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
468	+	if (args_info->dz_given)
469	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
470	+	if (args_info->length_given)
471	+	write_into_file(outfile, "length", args_info->length_orig, 0);
472	+	if (args_info->zlength_given)
473	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
474		if (args_info->zoffset_given)
475		write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
476		if (args_info->sele1_given)
#	Line 385 | Line 483 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
483		write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
484		if (args_info->comsele_given)
485		write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
486	+	if (args_info->seleoffset_given)
487	+	write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
488	+	if (args_info->seleoffset2_given)
489	+	write_into_file(outfile, "seleoffset2", args_info->seleoffset2_orig, 0);
490		if (args_info->molname_given)
491		write_into_file(outfile, "molname", args_info->molname_orig, 0);
492		if (args_info->begin_given)
#	Line 393 | Line 495 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
495		write_into_file(outfile, "end", args_info->end_orig, 0);
496		if (args_info->radius_given)
497		write_into_file(outfile, "radius", args_info->radius_orig, 0);
498	+	if (args_info->voxelSize_given)
499	+	write_into_file(outfile, "voxelSize", args_info->voxelSize_orig, 0);
500	+	if (args_info->gaussWidth_given)
501	+	write_into_file(outfile, "gaussWidth", args_info->gaussWidth_orig, 0);
502		if (args_info->bo_given)
503		write_into_file(outfile, "bo", 0, 0 );
504	<	if (args_info->bor_given)
505	<	write_into_file(outfile, "bor", 0, 0 );
504	>	if (args_info->ior_given)
505	>	write_into_file(outfile, "ior", 0, 0 );
506	>	if (args_info->for_given)
507	>	write_into_file(outfile, "for", 0, 0 );
508		if (args_info->bad_given)
509		write_into_file(outfile, "bad", 0, 0 );
510	+	if (args_info->count_given)
511	+	write_into_file(outfile, "count", 0, 0 );
512		if (args_info->gofr_given)
513		write_into_file(outfile, "gofr", 0, 0 );
514		if (args_info->gofz_given)
#	Line 407 | Line 517 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
517		write_into_file(outfile, "r_theta", 0, 0 );
518		if (args_info->r_omega_given)
519		write_into_file(outfile, "r_omega", 0, 0 );
520	+	if (args_info->r_z_given)
521	+	write_into_file(outfile, "r_z", 0, 0 );
522		if (args_info->theta_omega_given)
523		write_into_file(outfile, "theta_omega", 0, 0 );
524		if (args_info->gxyz_given)
525		write_into_file(outfile, "gxyz", 0, 0 );
526	+	if (args_info->twodgofr_given)
527	+	write_into_file(outfile, "twodgofr", 0, 0 );
528		if (args_info->p2_given)
529		write_into_file(outfile, "p2", 0, 0 );
530		if (args_info->rp2_given)
#	Line 421 | Line 535 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
535		write_into_file(outfile, "density", 0, 0 );
536		if (args_info->slab_density_given)
537		write_into_file(outfile, "slab_density", 0, 0 );
538	+	if (args_info->p_angle_given)
539	+	write_into_file(outfile, "p_angle", 0, 0 );
540		if (args_info->hxy_given)
541		write_into_file(outfile, "hxy", 0, 0 );
542		if (args_info->rho_r_given)
543		write_into_file(outfile, "rho_r", 0, 0 );
544	+	if (args_info->angle_r_given)
545	+	write_into_file(outfile, "angle_r", 0, 0 );
546		if (args_info->hullvol_given)
547		write_into_file(outfile, "hullvol", 0, 0 );
548	+	if (args_info->rodlength_given)
549	+	write_into_file(outfile, "rodlength", 0, 0 );
550	+	if (args_info->tet_param_given)
551	+	write_into_file(outfile, "tet_param", 0, 0 );
552	+	if (args_info->tet_param_z_given)
553	+	write_into_file(outfile, "tet_param_z", 0, 0 );
554	+	if (args_info->tet_param_xyz_given)
555	+	write_into_file(outfile, "tet_param_xyz", 0, 0 );
556	+	if (args_info->rnemdz_given)
557	+	write_into_file(outfile, "rnemdz", 0, 0 );
558	+	if (args_info->rnemdr_given)
559	+	write_into_file(outfile, "rnemdr", 0, 0 );
560	+	if (args_info->rnemdrt_given)
561	+	write_into_file(outfile, "rnemdrt", 0, 0 );
562	+	if (args_info->nitrile_given)
563	+	write_into_file(outfile, "nitrile", 0, 0 );
564	+	if (args_info->multipole_given)
565	+	write_into_file(outfile, "multipole", 0, 0 );
566	+	if (args_info->surfDiffusion_given)
567	+	write_into_file(outfile, "surfDiffusion", 0, 0 );
568
569
570		i = EXIT_SUCCESS;
#	Line 463 | Line 601 | gengetopt_strdup (const char *s)
601		char *
602		gengetopt_strdup (const char *s)
603		{
604	<	char *result = NULL;
604	>	char *result = 0;
605		if (!s)
606		return result;
607
#	Line 481 | Line 619 | reset_group_staticProps(struct gengetopt_args_info *ar
619		return;
620
621		args_info->bo_given = 0 ;
622	<	args_info->bor_given = 0 ;
622	>	args_info->ior_given = 0 ;
623	>	args_info->for_given = 0 ;
624		args_info->bad_given = 0 ;
625	+	args_info->count_given = 0 ;
626		args_info->gofr_given = 0 ;
627		args_info->gofz_given = 0 ;
628		args_info->r_theta_given = 0 ;
629		args_info->r_omega_given = 0 ;
630	+	args_info->r_z_given = 0 ;
631		args_info->theta_omega_given = 0 ;
632		args_info->gxyz_given = 0 ;
633	+	args_info->twodgofr_given = 0 ;
634		args_info->p2_given = 0 ;
635		args_info->rp2_given = 0 ;
636		args_info->scd_given = 0 ;
637		args_info->density_given = 0 ;
638		args_info->slab_density_given = 0 ;
639	+	args_info->p_angle_given = 0 ;
640		args_info->hxy_given = 0 ;
641		args_info->rho_r_given = 0 ;
642	+	args_info->angle_r_given = 0 ;
643		args_info->hullvol_given = 0 ;
644	+	args_info->rodlength_given = 0 ;
645	+	args_info->tet_param_given = 0 ;
646	+	args_info->tet_param_z_given = 0 ;
647	+	args_info->tet_param_xyz_given = 0 ;
648	+	args_info->rnemdz_given = 0 ;
649	+	args_info->rnemdr_given = 0 ;
650	+	args_info->rnemdrt_given = 0 ;
651	+	args_info->nitrile_given = 0 ;
652	+	args_info->multipole_given = 0 ;
653	+	args_info->surfDiffusion_given = 0 ;
654
655		args_info->staticProps_group_counter = 0;
656		}
657
658		int
659	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
659	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
660		{
661		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
662		}
663
664		int
665	<	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
665	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
666		struct cmdline_parser_params *params)
667		{
668		int result;
669	<	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
669	>	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
670
671		if (result == EXIT_FAILURE)
672		{
#	Line 524 | Line 678 | int
678		}
679
680		int
681	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
681	>	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
682		{
683		int result;
684		struct cmdline_parser_params params;
#	Line 535 | Line 689 | cmdline_parser2 (int argc, char * const *argv, struct
689		params.check_ambiguity = 0;
690		params.print_errors = 1;
691
692	<	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
692	>	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
693
694		if (result == EXIT_FAILURE)
695		{
#	Line 551 | Line 705 | cmdline_parser_required (struct gengetopt_args_info *a
705		{
706		int result = EXIT_SUCCESS;
707
708	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
708	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
709		result = EXIT_FAILURE;
710
711		if (result == EXIT_FAILURE)
#	Line 567 | Line 721 | cmdline_parser_required2 (struct gengetopt_args_info *
721		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
722		{
723		int error = 0;
724	+	FIX_UNUSED (additional_error);
725
726		/* checks for required options */
727		if (! args_info->input_given)
#	Line 577 | Line 732 | cmdline_parser_required2 (struct gengetopt_args_info *
732
733		if (args_info->staticProps_group_counter == 0)
734		{
735	<	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 : ""));
735	>	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 : ""));
736		error = 1;
737		}
738
#	Line 611 | Line 766 | int update_arg(void *field, char **orig_field,
766		static
767		int update_arg(void *field, char **orig_field,
768		unsigned int *field_given, unsigned int *prev_given,
769	<	char *value, char *possible_values[], const char *default_value,
769	>	char *value, const char *possible_values[],
770	>	const char *default_value,
771		cmdline_parser_arg_type arg_type,
772		int check_ambiguity, int override,
773		int no_free, int multiple_option,
#	Line 622 | Line 778 | int update_arg(void *field, char **orig_field,
778		const char *val = value;
779		int found;
780		char **string_field;
781	+	FIX_UNUSED (field);
782
783		stop_char = 0;
784		found = 0;
#	Line 639 | Line 796 | int update_arg(void *field, char **orig_field,
796		return 1; /* failure */
797		}
798
799	+	FIX_UNUSED (default_value);
800
801		if (field_given && *field_given && ! override)
802		return 0;
#	Line 702 | Line 860 | int
860
861
862		int
863	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
863	>	cmdline_parser_internal (
864	>	int argc, char **argv, struct gengetopt_args_info *args_info,
865		struct cmdline_parser_params *params, const char *additional_error)
866		{
867		int c;        /* Character of the parsed option.  */
#	Line 745 | Line 904 | cmdline_parser_internal (int argc, char * const *argv,
904		{ "nbins",      1, NULL, 'b' },
905		{ "nbins_x",    1, NULL, 'x' },
906		{ "nbins_y",    1, NULL, 'y' },
907	+	{ "nbins_z",    1, NULL, 0 },
908		{ "nanglebins", 1, NULL, 'a' },
749	–	{ "length",     1, NULL, 0 },
909		{ "rcut",       1, NULL, 'c' },
910	+	{ "dz", 1, NULL, 0 },
911	+	{ "length",     1, NULL, 0 },
912	+	{ "zlength",    1, NULL, 0 },
913		{ "zoffset",    1, NULL, 'z' },
914		{ "sele1",      1, NULL, 0 },
915		{ "sele2",      1, NULL, 0 },
916		{ "sele3",      1, NULL, 0 },
917		{ "refsele",    1, NULL, 0 },
918		{ "comsele",    1, NULL, 0 },
919	+	{ "seleoffset", 1, NULL, 0 },
920	+	{ "seleoffset2",        1, NULL, 0 },
921		{ "molname",    1, NULL, 0 },
922		{ "begin",      1, NULL, 0 },
923		{ "end",        1, NULL, 0 },
924		{ "radius",     1, NULL, 0 },
925	+	{ "voxelSize",  1, NULL, 'v' },
926	+	{ "gaussWidth", 1, NULL, 0 },
927		{ "bo", 0, NULL, 0 },
928	<	{ "bor",        0, NULL, 0 },
928	>	{ "ior",        0, NULL, 0 },
929	>	{ "for",        0, NULL, 0 },
930		{ "bad",        0, NULL, 0 },
931	+	{ "count",      0, NULL, 0 },
932		{ "gofr",       0, NULL, 'g' },
933		{ "gofz",       0, NULL, 0 },
934		{ "r_theta",    0, NULL, 0 },
935		{ "r_omega",    0, NULL, 0 },
936	+	{ "r_z",        0, NULL, 0 },
937		{ "theta_omega",        0, NULL, 0 },
938		{ "gxyz",       0, NULL, 0 },
939	+	{ "twodgofr",   0, NULL, 0 },
940		{ "p2", 0, NULL, 'p' },
941		{ "rp2",        0, NULL, 0 },
942		{ "scd",        0, NULL, 's' },
943		{ "density",    0, NULL, 'd' },
944		{ "slab_density",       0, NULL, 0 },
945	+	{ "p_angle",    0, NULL, 0 },
946		{ "hxy",        0, NULL, 0 },
947		{ "rho_r",      0, NULL, 0 },
948	+	{ "angle_r",    0, NULL, 0 },
949		{ "hullvol",    0, NULL, 0 },
950	<	{ NULL, 0, NULL, 0 }
950	>	{ "rodlength",  0, NULL, 0 },
951	>	{ "tet_param",  0, NULL, 'Q' },
952	>	{ "tet_param_z",        0, NULL, 0 },
953	>	{ "tet_param_xyz",      0, NULL, 0 },
954	>	{ "rnemdz",     0, NULL, 0 },
955	>	{ "rnemdr",     0, NULL, 0 },
956	>	{ "rnemdrt",    0, NULL, 0 },
957	>	{ "nitrile",    0, NULL, 0 },
958	>	{ "multipole",  0, NULL, 'm' },
959	>	{ "surfDiffusion",      0, NULL, 0 },
960	>	{ 0,  0, 0, 0 }
961		};
962
963	<	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
963	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:v:gpsdQm", long_options, &option_index);
964
965		if (c == -1) break;       /* Exit from `while (1)' loop.  */
966
#	Line 902 | Line 1084 | cmdline_parser_internal (int argc, char * const *argv,
1084		goto failure;
1085
1086		break;
1087	+	case 'v':       /* voxel size (angstroms).  */
1088	+
1089	+
1090	+	if (update_arg( (void *)&(args_info->voxelSize_arg),
1091	+	&(args_info->voxelSize_orig), &(args_info->voxelSize_given),
1092	+	&(local_args_info.voxelSize_given), optarg, 0, 0, ARG_DOUBLE,
1093	+	check_ambiguity, override, 0, 0,
1094	+	"voxelSize", 'v',
1095	+	additional_error))
1096	+	goto failure;
1097	+
1098	+	break;
1099		case 'g':       /* g(r).  */
1100
1101		if (args_info->staticProps_group_counter && override)
#	Line 917 | Line 1111 | cmdline_parser_internal (int argc, char * const *argv,
1111		goto failure;
1112
1113		break;
1114	<	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1114	>	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1115
1116		if (args_info->staticProps_group_counter && override)
1117		reset_group_staticProps (args_info);
#	Line 958 | Line 1152 | cmdline_parser_internal (int argc, char * const *argv,
1152		&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1153		check_ambiguity, override, 0, 0,
1154		"density", 'd',
1155	+	additional_error))
1156	+	goto failure;
1157	+
1158	+	break;
1159	+	case 'Q':       /* tetrahedrality order parameter (Qk).  */
1160	+
1161	+	if (args_info->staticProps_group_counter && override)
1162	+	reset_group_staticProps (args_info);
1163	+	args_info->staticProps_group_counter += 1;
1164	+
1165	+	if (update_arg( 0 ,
1166	+	0 , &(args_info->tet_param_given),
1167	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1168	+	check_ambiguity, override, 0, 0,
1169	+	"tet_param", 'Q',
1170	+	additional_error))
1171	+	goto failure;
1172	+
1173	+	break;
1174	+	case 'm':       /* average multipole moments contained within cutoff spheres as a function of radius.  */
1175	+
1176	+	if (args_info->staticProps_group_counter && override)
1177	+	reset_group_staticProps (args_info);
1178	+	args_info->staticProps_group_counter += 1;
1179	+
1180	+	if (update_arg( 0 ,
1181	+	0 , &(args_info->multipole_given),
1182	+	&(local_args_info.multipole_given), optarg, 0, 0, ARG_NO,
1183	+	check_ambiguity, override, 0, 0,
1184	+	"multipole", 'm',
1185		additional_error))
1186		goto failure;
1187
1188		break;
1189
1190		case 0: /* Long option with no short option */
1191	+	/* number of bins in z axis.  */
1192	+	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1193	+	{
1194	+
1195	+
1196	+	if (update_arg( (void *)&(args_info->nbins_z_arg),
1197	+	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1198	+	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1199	+	check_ambiguity, override, 0, 0,
1200	+	"nbins_z", '-',
1201	+	additional_error))
1202	+	goto failure;
1203	+
1204	+	}
1205	+	/* slab width (dz).  */
1206	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1207	+	{
1208	+
1209	+
1210	+	if (update_arg( (void *)&(args_info->dz_arg),
1211	+	&(args_info->dz_orig), &(args_info->dz_given),
1212	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1213	+	check_ambiguity, override, 0, 0,
1214	+	"dz", '-',
1215	+	additional_error))
1216	+	goto failure;
1217	+
1218	+	}
1219		/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1220	<	if (strcmp (long_options[option_index].name, "length") == 0)
1220	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1221		{
1222
1223
#	Line 978 | Line 1230 | cmdline_parser_internal (int argc, char * const *argv,
1230		goto failure;
1231
1232		}
1233	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1234	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1235	+	{
1236	+
1237	+
1238	+	if (update_arg( (void *)&(args_info->zlength_arg),
1239	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1240	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1241	+	check_ambiguity, override, 0, 0,
1242	+	"zlength", '-',
1243	+	additional_error))
1244	+	goto failure;
1245	+
1246	+	}
1247		/* select the first stuntdouble set.  */
1248		else if (strcmp (long_options[option_index].name, "sele1") == 0)
1249		{
#	Line 1048 | Line 1314 | cmdline_parser_internal (int argc, char * const *argv,
1314		goto failure;
1315
1316		}
1317	+	/* global index offset for a second object (used to define a vector between sites in molecule).  */
1318	+	else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1319	+	{
1320	+
1321	+
1322	+	if (update_arg( (void *)&(args_info->seleoffset_arg),
1323	+	&(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1324	+	&(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1325	+	check_ambiguity, override, 0, 0,
1326	+	"seleoffset", '-',
1327	+	additional_error))
1328	+	goto failure;
1329	+
1330	+	}
1331	+	/* global index offset for a third object (used to define a vector between sites in molecule).  */
1332	+	else if (strcmp (long_options[option_index].name, "seleoffset2") == 0)
1333	+	{
1334	+
1335	+
1336	+	if (update_arg( (void *)&(args_info->seleoffset2_arg),
1337	+	&(args_info->seleoffset2_orig), &(args_info->seleoffset2_given),
1338	+	&(local_args_info.seleoffset2_given), optarg, 0, 0, ARG_INT,
1339	+	check_ambiguity, override, 0, 0,
1340	+	"seleoffset2", '-',
1341	+	additional_error))
1342	+	goto failure;
1343	+
1344	+	}
1345		/* molecule name.  */
1346		else if (strcmp (long_options[option_index].name, "molname") == 0)
1347		{
#	Line 1100 | Line 1394 | cmdline_parser_internal (int argc, char * const *argv,
1394		&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1395		check_ambiguity, override, 0, 0,
1396		"radius", '-',
1397	+	additional_error))
1398	+	goto failure;
1399	+
1400	+	}
1401	+	/* Gaussian width (angstroms).  */
1402	+	else if (strcmp (long_options[option_index].name, "gaussWidth") == 0)
1403	+	{
1404	+
1405	+
1406	+	if (update_arg( (void *)&(args_info->gaussWidth_arg),
1407	+	&(args_info->gaussWidth_orig), &(args_info->gaussWidth_given),
1408	+	&(local_args_info.gaussWidth_given), optarg, 0, 0, ARG_DOUBLE,
1409	+	check_ambiguity, override, 0, 0,
1410	+	"gaussWidth", '-',
1411		additional_error))
1412		goto failure;
1413
#	Line 1121 | Line 1429 | cmdline_parser_internal (int argc, char * const *argv,
1429		goto failure;
1430
1431		}
1432	<	/* bond order parameter as a function of radius (--rcut must be specified).  */
1433	<	else if (strcmp (long_options[option_index].name, "bor") == 0)
1432	>	/* icosahedral bond order parameter as a function of radius (--rcut must be specified).  */
1433	>	else if (strcmp (long_options[option_index].name, "ior") == 0)
1434		{
1435
1436		if (args_info->staticProps_group_counter && override)
#	Line 1130 | Line 1438 | cmdline_parser_internal (int argc, char * const *argv,
1438		args_info->staticProps_group_counter += 1;
1439
1440		if (update_arg( 0 ,
1441	<	0 , &(args_info->bor_given),
1442	<	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1441	>	0 , &(args_info->ior_given),
1442	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1443		check_ambiguity, override, 0, 0,
1444	<	"bor", '-',
1444	>	"ior", '-',
1445		additional_error))
1446		goto failure;
1447
1448		}
1449	+	/* FCC bond order parameter as a function of radius (--rcut must be specified).  */
1450	+	else if (strcmp (long_options[option_index].name, "for") == 0)
1451	+	{
1452	+
1453	+	if (args_info->staticProps_group_counter && override)
1454	+	reset_group_staticProps (args_info);
1455	+	args_info->staticProps_group_counter += 1;
1456	+
1457	+	if (update_arg( 0 ,
1458	+	0 , &(args_info->for_given),
1459	+	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1460	+	check_ambiguity, override, 0, 0,
1461	+	"for", '-',
1462	+	additional_error))
1463	+	goto failure;
1464	+
1465	+	}
1466		/* N(theta) bond angle density within (--rcut must be specified).  */
1467		else if (strcmp (long_options[option_index].name, "bad") == 0)
1468		{
#	Line 1155 | Line 1480 | cmdline_parser_internal (int argc, char * const *argv,
1480		goto failure;
1481
1482		}
1483	+	/* count of molecules matching selection criteria (and associated statistics).  */
1484	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1485	+	{
1486	+
1487	+	if (args_info->staticProps_group_counter && override)
1488	+	reset_group_staticProps (args_info);
1489	+	args_info->staticProps_group_counter += 1;
1490	+
1491	+	if (update_arg( 0 ,
1492	+	0 , &(args_info->count_given),
1493	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1494	+	check_ambiguity, override, 0, 0,
1495	+	"count", '-',
1496	+	additional_error))
1497	+	goto failure;
1498	+
1499	+	}
1500		/* g(z).  */
1501		else if (strcmp (long_options[option_index].name, "gofz") == 0)
1502		{
#	Line 1206 | Line 1548 | cmdline_parser_internal (int argc, char * const *argv,
1548		goto failure;
1549
1550		}
1551	+	/* g(r, z).  */
1552	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1553	+	{
1554	+
1555	+	if (args_info->staticProps_group_counter && override)
1556	+	reset_group_staticProps (args_info);
1557	+	args_info->staticProps_group_counter += 1;
1558	+
1559	+	if (update_arg( 0 ,
1560	+	0 , &(args_info->r_z_given),
1561	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1562	+	check_ambiguity, override, 0, 0,
1563	+	"r_z", '-',
1564	+	additional_error))
1565	+	goto failure;
1566	+
1567	+	}
1568		/* g(cos(theta), cos(omega)).  */
1569		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1570		{
#	Line 1240 | Line 1599 | cmdline_parser_internal (int argc, char * const *argv,
1599		goto failure;
1600
1601		}
1602	+	/* 2D g(r) (Slab width --dz must be specified).  */
1603	+	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1604	+	{
1605	+
1606	+	if (args_info->staticProps_group_counter && override)
1607	+	reset_group_staticProps (args_info);
1608	+	args_info->staticProps_group_counter += 1;
1609	+
1610	+	if (update_arg( 0 ,
1611	+	0 , &(args_info->twodgofr_given),
1612	+	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1613	+	check_ambiguity, override, 0, 0,
1614	+	"twodgofr", '-',
1615	+	additional_error))
1616	+	goto failure;
1617	+
1618	+	}
1619		/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1620		else if (strcmp (long_options[option_index].name, "rp2") == 0)
1621		{
#	Line 1274 | Line 1650 | cmdline_parser_internal (int argc, char * const *argv,
1650		goto failure;
1651
1652		}
1653	+	/* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1654	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1655	+	{
1656	+
1657	+	if (args_info->staticProps_group_counter && override)
1658	+	reset_group_staticProps (args_info);
1659	+	args_info->staticProps_group_counter += 1;
1660	+
1661	+	if (update_arg( 0 ,
1662	+	0 , &(args_info->p_angle_given),
1663	+	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1664	+	check_ambiguity, override, 0, 0,
1665	+	"p_angle", '-',
1666	+	additional_error))
1667	+	goto failure;
1668	+
1669	+	}
1670		/* hxy.  */
1671		else if (strcmp (long_options[option_index].name, "hxy") == 0)
1672		{
#	Line 1308 | Line 1701 | cmdline_parser_internal (int argc, char * const *argv,
1701		goto failure;
1702
1703		}
1704	+	/* angle of R.  */
1705	+	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1706	+	{
1707	+
1708	+	if (args_info->staticProps_group_counter && override)
1709	+	reset_group_staticProps (args_info);
1710	+	args_info->staticProps_group_counter += 1;
1711	+
1712	+	if (update_arg( 0 ,
1713	+	0 , &(args_info->angle_r_given),
1714	+	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1715	+	check_ambiguity, override, 0, 0,
1716	+	"angle_r", '-',
1717	+	additional_error))
1718	+	goto failure;
1719	+
1720	+	}
1721		/* hull volume of nanoparticle.  */
1722		else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1723		{
#	Line 1325 | Line 1735 | cmdline_parser_internal (int argc, char * const *argv,
1735		goto failure;
1736
1737		}
1738	+	/* length of nanorod.  */
1739	+	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1740	+	{
1741
1742	+	if (args_info->staticProps_group_counter && override)
1743	+	reset_group_staticProps (args_info);
1744	+	args_info->staticProps_group_counter += 1;
1745	+
1746	+	if (update_arg( 0 ,
1747	+	0 , &(args_info->rodlength_given),
1748	+	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1749	+	check_ambiguity, override, 0, 0,
1750	+	"rodlength", '-',
1751	+	additional_error))
1752	+	goto failure;
1753	+
1754	+	}
1755	+	/* spatially-resolved tetrahedrality order parameter Qk(z).  */
1756	+	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1757	+	{
1758	+
1759	+	if (args_info->staticProps_group_counter && override)
1760	+	reset_group_staticProps (args_info);
1761	+	args_info->staticProps_group_counter += 1;
1762	+
1763	+	if (update_arg( 0 ,
1764	+	0 , &(args_info->tet_param_z_given),
1765	+	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1766	+	check_ambiguity, override, 0, 0,
1767	+	"tet_param_z", '-',
1768	+	additional_error))
1769	+	goto failure;
1770	+
1771	+	}
1772	+	/* volume-resolved tetrahedrality order parameter Qk(x,y,z).  (voxelSize, rcut, and gaussWidth must be specified).  */
1773	+	else if (strcmp (long_options[option_index].name, "tet_param_xyz") == 0)
1774	+	{
1775	+
1776	+	if (args_info->staticProps_group_counter && override)
1777	+	reset_group_staticProps (args_info);
1778	+	args_info->staticProps_group_counter += 1;
1779	+
1780	+	if (update_arg( 0 ,
1781	+	0 , &(args_info->tet_param_xyz_given),
1782	+	&(local_args_info.tet_param_xyz_given), optarg, 0, 0, ARG_NO,
1783	+	check_ambiguity, override, 0, 0,
1784	+	"tet_param_xyz", '-',
1785	+	additional_error))
1786	+	goto failure;
1787	+
1788	+	}
1789	+	/* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1790	+	else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1791	+	{
1792	+
1793	+	if (args_info->staticProps_group_counter && override)
1794	+	reset_group_staticProps (args_info);
1795	+	args_info->staticProps_group_counter += 1;
1796	+
1797	+	if (update_arg( 0 ,
1798	+	0 , &(args_info->rnemdz_given),
1799	+	&(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1800	+	check_ambiguity, override, 0, 0,
1801	+	"rnemdz", '-',
1802	+	additional_error))
1803	+	goto failure;
1804	+
1805	+	}
1806	+	/* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1807	+	else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1808	+	{
1809	+
1810	+	if (args_info->staticProps_group_counter && override)
1811	+	reset_group_staticProps (args_info);
1812	+	args_info->staticProps_group_counter += 1;
1813	+
1814	+	if (update_arg( 0 ,
1815	+	0 , &(args_info->rnemdr_given),
1816	+	&(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1817	+	check_ambiguity, override, 0, 0,
1818	+	"rnemdr", '-',
1819	+	additional_error))
1820	+	goto failure;
1821	+
1822	+	}
1823	+	/* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1824	+	else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1825	+	{
1826	+
1827	+	if (args_info->staticProps_group_counter && override)
1828	+	reset_group_staticProps (args_info);
1829	+	args_info->staticProps_group_counter += 1;
1830	+
1831	+	if (update_arg( 0 ,
1832	+	0 , &(args_info->rnemdrt_given),
1833	+	&(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1834	+	check_ambiguity, override, 0, 0,
1835	+	"rnemdrt", '-',
1836	+	additional_error))
1837	+	goto failure;
1838	+
1839	+	}
1840	+	/* electrostatic potential to frequency map based on the Cho nitrile fits.  */
1841	+	else if (strcmp (long_options[option_index].name, "nitrile") == 0)
1842	+	{
1843	+
1844	+	if (args_info->staticProps_group_counter && override)
1845	+	reset_group_staticProps (args_info);
1846	+	args_info->staticProps_group_counter += 1;
1847	+
1848	+	if (update_arg( 0 ,
1849	+	0 , &(args_info->nitrile_given),
1850	+	&(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
1851	+	check_ambiguity, override, 0, 0,
1852	+	"nitrile", '-',
1853	+	additional_error))
1854	+	goto failure;
1855	+
1856	+	}
1857	+	/* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
1858	+	else if (strcmp (long_options[option_index].name, "surfDiffusion") == 0)
1859	+	{
1860	+
1861	+	if (args_info->staticProps_group_counter && override)
1862	+	reset_group_staticProps (args_info);
1863	+	args_info->staticProps_group_counter += 1;
1864	+
1865	+	if (update_arg( 0 ,
1866	+	0 , &(args_info->surfDiffusion_given),
1867	+	&(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
1868	+	check_ambiguity, override, 0, 0,
1869	+	"surfDiffusion", '-',
1870	+	additional_error))
1871	+	goto failure;
1872	+
1873	+	}
1874	+
1875		break;
1876		case '?':       /* Invalid option.  */
1877		/* `getopt_long' already printed an error message.  */
#	Line 1339 | Line 1885 | cmdline_parser_internal (int argc, char * const *argv,
1885
1886		if (args_info->staticProps_group_counter > 1)
1887		{
1888	<	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 : ""));
1888	>	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 : ""));
1889		error = 1;
1890		}
1891

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 2031 by jmichalk, Fri Oct 31 18:40:40 2014 UTC

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

Diff Legend

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+	Added lines
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