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

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 310 by tim, Thu Feb 10 18:14:03 2005 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 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/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:
8		we make no copyright claims on it.
9		*/
10
11	+	/* If we use autoconf.  */
12	+	#ifdef HAVE_CONFIG_H
13	+	#include "config.h"
14	+	#endif
15
16		#include <stdio.h>
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	/* If we use autoconf.  */
21	<	#ifdef HAVE_CONFIG_H
18	<	#include "config.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22		#endif
23
24	<	#include "getopt.h"
24	>	#ifdef WIN32
25	>	#include "utils/wingetopt.h"
26	>	#else
27	>	#include <getopt.h>
28	>	#endif
29
30	<	#include "staticPropsCmd.h"
30	>	#include "StaticPropsCmd.h"
31	>
32	>	const char *gengetopt_args_info_purpose = "";
33	>
34	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35	>
36	>	const char *gengetopt_args_info_description = "";
37	>
38	>	const char *gengetopt_args_info_help[] = {
39	>	"  -h, --help                    Print help and exit",
40	>	"  -V, --version                 Print version and exit",
41	>	"  -i, --input=filename          input dump file",
42	>	"  -o, --output=filename         output file name",
43	>	"  -n, --step=INT                process every n frame  (default=`1')",
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')",
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	>	"      --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	>	"      --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	>
106	>	typedef enum {ARG_NO
107	>	, ARG_STRING
108	>	, ARG_INT
109	>	, ARG_DOUBLE
110	>	} cmdline_parser_arg_type;
111	>
112	>	static
113	>	void clear_given (struct gengetopt_args_info *args_info);
114	>	static
115	>	void clear_args (struct gengetopt_args_info *args_info);
116	>
117	>	static int
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
122	>	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
123	>
124	>	static char *
125	>	gengetopt_strdup (const char *s);
126	>
127	>	static
128	>	void clear_given (struct gengetopt_args_info *args_info)
129	>	{
130	>	args_info->help_given = 0 ;
131	>	args_info->version_given = 0 ;
132	>	args_info->input_given = 0 ;
133	>	args_info->output_given = 0 ;
134	>	args_info->step_given = 0 ;
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 ;
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->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;
203	>	args_info->output_orig = NULL;
204	>	args_info->step_arg = 1;
205	>	args_info->step_orig = NULL;
206	>	args_info->nbins_arg = 100;
207	>	args_info->nbins_orig = NULL;
208	>	args_info->nbins_x_arg = 100;
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;
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;
224	>	args_info->sele1_orig = NULL;
225	>	args_info->sele2_arg = NULL;
226	>	args_info->sele2_orig = NULL;
227	>	args_info->sele3_arg = NULL;
228	>	args_info->sele3_orig = NULL;
229	>	args_info->refsele_arg = NULL;
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	>
245	>	static
246	>	void init_args_info(struct gengetopt_args_info *args_info)
247	>	{
248	>
249	>
250	>	args_info->help_help = gengetopt_args_info_help[0] ;
251	>	args_info->version_help = gengetopt_args_info_help[1] ;
252	>	args_info->input_help = gengetopt_args_info_help[2] ;
253	>	args_info->output_help = gengetopt_args_info_help[3] ;
254	>	args_info->step_help = gengetopt_args_info_help[4] ;
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->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->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) {
325	+	cmdline_parser_print_version ();
326	+
327	+	if (strlen(gengetopt_args_info_purpose) > 0)
328	+	printf("\n%s\n", gengetopt_args_info_purpose);
329	+
330	+	if (strlen(gengetopt_args_info_usage) > 0)
331	+	printf("\n%s\n", gengetopt_args_info_usage);
332	+
333	+	printf("\n");
334	+
335	+	if (strlen(gengetopt_args_info_description) > 0)
336	+	printf("%s\n\n", gengetopt_args_info_description);
337	+	}
338	+
339		void
340		cmdline_parser_print_help (void)
341		{
342	<	cmdline_parser_print_version ();
343	<	printf("\n"
344	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
345	<	printf("\n");
38	<	printf("  -h, --help                    Print help and exit\n");
39	<	printf("  -V, --version                 Print version and exit\n");
40	<	printf("  -i, --input=filename          input dump file\n");
41	<	printf("  -o, --output=filename         output file name\n");
42	<	printf("  -n, --frame=INT               print every n frame  (default=`1')\n");
43	<	printf("  -d, --ndistebins=INT          number of bins for distance  (default=`50')\n");
44	<	printf("  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')\n");
45	<	printf("  -l, --length=DOUBLE           maximum length\n");
46	<	printf("      --sele1=selection script  select first stuntdouble set\n");
47	<	printf("      --sele2=selection script  select second stuntdouble set\n");
48	<	printf("\n");
49	<	printf(" Group: staticProps  an option of this group is required\n");
50	<	printf("      --gofr                    g(r)\n");
51	<	printf("      --r_theta                 g(r, cos(theta))\n");
52	<	printf("      --r_omega                 g(r, cos(omega))\n");
53	<	printf("      --theta_omega             g(cos(theta), cos(omega))\n");
54	<	printf("      --xyz                     g(x, y, z)\n");
342	>	int i = 0;
343	>	print_help_common();
344	>	while (gengetopt_args_info_help[i])
345	>	printf("%s\n", gengetopt_args_info_help[i++]);
346		}
347
348	+	void
349	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
350	+	{
351	+	clear_given (args_info);
352	+	clear_args (args_info);
353	+	init_args_info (args_info);
354
355	<	static char *gengetopt_strdup (const char *s);
355	>	args_info->inputs = 0;
356	>	args_info->inputs_num = 0;
357	>	}
358
359	<	/* gengetopt_strdup() */
360	<	/* strdup.c replacement of strdup, which is not standard */
359	>	void
360	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
361	>	{
362	>	if (params)
363	>	{
364	>	params->override = 0;
365	>	params->initialize = 1;
366	>	params->check_required = 1;
367	>	params->check_ambiguity = 0;
368	>	params->print_errors = 1;
369	>	}
370	>	}
371	>
372	>	struct cmdline_parser_params *
373	>	cmdline_parser_params_create(void)
374	>	{
375	>	struct cmdline_parser_params *params =
376	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
377	>	cmdline_parser_params_init(params);
378	>	return params;
379	>	}
380	>
381	>	static void
382	>	free_string_field (char **s)
383	>	{
384	>	if (*s)
385	>	{
386	>	free (*s);
387	>	*s = 0;
388	>	}
389	>	}
390	>
391	>
392	>	static void
393	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
394	>	{
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));
399	>	free_string_field (&(args_info->output_orig));
400	>	free_string_field (&(args_info->step_orig));
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));
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));
414	>	free_string_field (&(args_info->sele2_arg));
415	>	free_string_field (&(args_info->sele2_orig));
416	>	free_string_field (&(args_info->sele3_arg));
417	>	free_string_field (&(args_info->sele3_orig));
418	>	free_string_field (&(args_info->refsele_arg));
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, const char *values[])
445	>	{
446	>	FIX_UNUSED (values);
447	>	if (arg) {
448	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
449	>	} else {
450	>	fprintf(outfile, "%s\n", opt);
451	>	}
452	>	}
453	>
454	>
455	>	int
456	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
457	>	{
458	>	int i = 0;
459	>
460	>	if (!outfile)
461	>	{
462	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
463	>	return EXIT_FAILURE;
464	>	}
465	>
466	>	if (args_info->help_given)
467	>	write_into_file(outfile, "help", 0, 0 );
468	>	if (args_info->version_given)
469	>	write_into_file(outfile, "version", 0, 0 );
470	>	if (args_info->input_given)
471	>	write_into_file(outfile, "input", args_info->input_orig, 0);
472	>	if (args_info->output_given)
473	>	write_into_file(outfile, "output", args_info->output_orig, 0);
474	>	if (args_info->step_given)
475	>	write_into_file(outfile, "step", args_info->step_orig, 0);
476	>	if (args_info->nbins_given)
477	>	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
478	>	if (args_info->nbins_x_given)
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);
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)
499	>	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
500	>	if (args_info->sele2_given)
501	>	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
502	>	if (args_info->sele3_given)
503	>	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
504	>	if (args_info->refsele_given)
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)
515	>	write_into_file(outfile, "begin", args_info->begin_orig, 0);
516	>	if (args_info->end_given)
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->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)
537	>	write_into_file(outfile, "gofz", 0, 0 );
538	>	if (args_info->r_theta_given)
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)
553	>	write_into_file(outfile, "rp2", 0, 0 );
554	>	if (args_info->scd_given)
555	>	write_into_file(outfile, "scd", 0, 0 );
556	>	if (args_info->density_given)
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;
595	>	return i;
596	>	}
597	>
598	>	int
599	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
600	>	{
601	>	FILE *outfile;
602	>	int i = 0;
603	>
604	>	outfile = fopen(filename, "w");
605	>
606	>	if (!outfile)
607	>	{
608	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
609	>	return EXIT_FAILURE;
610	>	}
611	>
612	>	i = cmdline_parser_dump(outfile, args_info);
613	>	fclose (outfile);
614	>
615	>	return i;
616	>	}
617	>
618	>	void
619	>	cmdline_parser_free (struct gengetopt_args_info *args_info)
620	>	{
621	>	cmdline_parser_release (args_info);
622	>	}
623	>
624	>	/** @brief replacement of strdup, which is not standard */
625		char *
626		gengetopt_strdup (const char *s)
627		{
628	<	char *result = (char*)malloc(strlen(s) + 1);
628	>	char *result = 0;
629	>	if (!s)
630	>	return result;
631	>
632	>	result = (char*)malloc(strlen(s) + 1);
633		if (result == (char*)0)
634		return (char*)0;
635		strcpy(result, s);
636		return result;
637		}
638
639	<	int
640	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
639	>	static void
640	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
641		{
642	<	int c;        /* Character of the parsed option.  */
643	<	int missing_required_options = 0;
77	<	int staticProps_group_counter = 0;
642	>	if (! args_info->staticProps_group_counter)
643	>	return;
644
645	<
646	<	args_info->help_given = 0 ;
647	<	args_info->version_given = 0 ;
648	<	args_info->input_given = 0 ;
649	<	args_info->output_given = 0 ;
84	<	args_info->frame_given = 0 ;
85	<	args_info->ndistebins_given = 0 ;
86	<	args_info->nanglebins_given = 0 ;
87	<	args_info->length_given = 0 ;
88	<	args_info->sele1_given = 0 ;
89	<	args_info->sele2_given = 0 ;
645	>	args_info->bo_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->xyz_given = 0 ;
657	<	#define clear_args() { \
658	<	args_info->input_arg = NULL; \
659	<	args_info->output_arg = NULL; \
660	<	args_info->frame_arg = 1 ;\
661	<	args_info->ndistebins_arg = 50 ;\
662	<	args_info->nanglebins_arg = 50 ;\
663	<	args_info->sele1_arg = NULL; \
664	<	args_info->sele2_arg = NULL; \
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	<	clear_args();
683	>	int
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 **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, 0);
695	>
696	>	if (result == EXIT_FAILURE)
697	>	{
698	>	cmdline_parser_free (args_info);
699	>	exit (EXIT_FAILURE);
700	>	}
701	>
702	>	return result;
703	>	}
704	>
705	>	int
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;
710	>
711	>	params.override = override;
712	>	params.initialize = initialize;
713	>	params.check_required = check_required;
714	>	params.check_ambiguity = 0;
715	>	params.print_errors = 1;
716	>
717	>	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
718	>
719	>	if (result == EXIT_FAILURE)
720	>	{
721	>	cmdline_parser_free (args_info);
722	>	exit (EXIT_FAILURE);
723	>	}
724	>
725	>	return result;
726	>	}
727	>
728	>	int
729	>	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
730	>	{
731	>	int result = EXIT_SUCCESS;
732	>
733	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
734	>	result = EXIT_FAILURE;
735	>
736	>	if (result == EXIT_FAILURE)
737	>	{
738	>	cmdline_parser_free (args_info);
739	>	exit (EXIT_FAILURE);
740	>	}
741	>
742	>	return result;
743	>	}
744	>
745	>	int
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)
753	>	{
754	>	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
755	>	error = 1;
756	>	}
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 : ""));
761	>	error = 1;
762	>	}
763	>
764
765	+	/* checks for dependences among options */
766	+
767	+	return error;
768	+	}
769	+
770	+
771	+	static char *package_name = 0;
772	+
773	+	/**
774	+	* @brief updates an option
775	+	* @param field the generic pointer to the field to update
776	+	* @param orig_field the pointer to the orig field
777	+	* @param field_given the pointer to the number of occurrence of this option
778	+	* @param prev_given the pointer to the number of occurrence already seen
779	+	* @param value the argument for this option (if null no arg was specified)
780	+	* @param possible_values the possible values for this option (if specified)
781	+	* @param default_value the default value (in case the option only accepts fixed values)
782	+	* @param arg_type the type of this option
783	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
784	+	* @param override @see cmdline_parser_params.override
785	+	* @param no_free whether to free a possible previous value
786	+	* @param multiple_option whether this is a multiple option
787	+	* @param long_opt the corresponding long option
788	+	* @param short_opt the corresponding short option (or '-' if none)
789	+	* @param additional_error possible further error specification
790	+	*/
791	+	static
792	+	int update_arg(void *field, char **orig_field,
793	+	unsigned int *field_given, unsigned int *prev_given,
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,
799	+	const char *long_opt, char short_opt,
800	+	const char *additional_error)
801	+	{
802	+	char *stop_char = 0;
803	+	const char *val = value;
804	+	int found;
805	+	char **string_field;
806	+	FIX_UNUSED (field);
807	+
808	+	stop_char = 0;
809	+	found = 0;
810	+
811	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
812	+	{
813	+	if (short_opt != '-')
814	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
815	+	package_name, long_opt, short_opt,
816	+	(additional_error ? additional_error : ""));
817	+	else
818	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
819	+	package_name, long_opt,
820	+	(additional_error ? additional_error : ""));
821	+	return 1; /* failure */
822	+	}
823	+
824	+	FIX_UNUSED (default_value);
825	+
826	+	if (field_given && *field_given && ! override)
827	+	return 0;
828	+	if (prev_given)
829	+	(*prev_given)++;
830	+	if (field_given)
831	+	(*field_given)++;
832	+	if (possible_values)
833	+	val = possible_values[found];
834	+
835	+	switch(arg_type) {
836	+	case ARG_INT:
837	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
838	+	break;
839	+	case ARG_DOUBLE:
840	+	if (val) *((double *)field) = strtod (val, &stop_char);
841	+	break;
842	+	case ARG_STRING:
843	+	if (val) {
844	+	string_field = (char **)field;
845	+	if (!no_free && *string_field)
846	+	free (*string_field); /* free previous string */
847	+	*string_field = gengetopt_strdup (val);
848	+	}
849	+	break;
850	+	default:
851	+	break;
852	+	};
853	+
854	+	/* check numeric conversion */
855	+	switch(arg_type) {
856	+	case ARG_INT:
857	+	case ARG_DOUBLE:
858	+	if (val && !(stop_char && *stop_char == '\0')) {
859	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
860	+	return 1; /* failure */
861	+	}
862	+	break;
863	+	default:
864	+	;
865	+	};
866	+
867	+	/* store the original value */
868	+	switch(arg_type) {
869	+	case ARG_NO:
870	+	break;
871	+	default:
872	+	if (value && orig_field) {
873	+	if (no_free) {
874	+	*orig_field = value;
875	+	} else {
876	+	if (*orig_field)
877	+	free (*orig_field); /* free previous string */
878	+	*orig_field = gengetopt_strdup (value);
879	+	}
880	+	}
881	+	};
882	+
883	+	return 0; /* OK */
884	+	}
885	+
886	+
887	+	int
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.  */
893	+
894	+	int error = 0;
895	+	struct gengetopt_args_info local_args_info;
896	+
897	+	int override;
898	+	int initialize;
899	+	int check_required;
900	+	int check_ambiguity;
901	+
902	+	package_name = argv[0];
903	+
904	+	override = params->override;
905	+	initialize = params->initialize;
906	+	check_required = params->check_required;
907	+	check_ambiguity = params->check_ambiguity;
908	+
909	+	if (initialize)
910	+	cmdline_parser_init (args_info);
911	+
912	+	cmdline_parser_init (&local_args_info);
913	+
914		optarg = 0;
915	<	optind = 1;
916	<	opterr = 1;
915	>	optind = 0;
916	>	opterr = params->print_errors;
917		optopt = '?';
918
919		while (1)
920		{
921		int option_index = 0;
115	–	char *stop_char;
922
923		static struct option long_options[] = {
924		{ "help",       0, NULL, 'h' },
925		{ "version",    0, NULL, 'V' },
926		{ "input",      1, NULL, 'i' },
927		{ "output",     1, NULL, 'o' },
928	<	{ "frame",      1, NULL, 'n' },
929	<	{ "ndistebins", 1, NULL, 'd' },
928	>	{ "step",       1, NULL, 'n' },
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' },
934	<	{ "length",     1, NULL, 'l' },
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	<	{ "gofr",       0, 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	>	{ "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	<	{ "xyz",        0, NULL, 0 },
965	<	{ NULL, 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	>	{ "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	<	stop_char = 0;
137	<	c = getopt_long (argc, argv, "hVi:o:n:d:a:l:", 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
994		switch (c)
995		{
996		case 'h':       /* Print help and exit.  */
144	–	clear_args ();
997		cmdline_parser_print_help ();
998	+	cmdline_parser_free (&local_args_info);
999		exit (EXIT_SUCCESS);
1000
1001		case 'V':       /* Print version and exit.  */
149	–	clear_args ();
1002		cmdline_parser_print_version ();
1003	+	cmdline_parser_free (&local_args_info);
1004		exit (EXIT_SUCCESS);
1005
1006		case 'i':       /* input dump file.  */
1007	<	if (args_info->input_given)
1008	<	{
1009	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1010	<	clear_args ();
1011	<	exit (EXIT_FAILURE);
1012	<	}
1013	<	args_info->input_given = 1;
1014	<	args_info->input_arg = gengetopt_strdup (optarg);
1007	>
1008	>
1009	>	if (update_arg( (void *)&(args_info->input_arg),
1010	>	&(args_info->input_orig), &(args_info->input_given),
1011	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
1012	>	check_ambiguity, override, 0, 0,
1013	>	"input", 'i',
1014	>	additional_error))
1015	>	goto failure;
1016	>
1017		break;
163	–
1018		case 'o':       /* output file name.  */
1019	<	if (args_info->output_given)
1020	<	{
1021	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1022	<	clear_args ();
1023	<	exit (EXIT_FAILURE);
1024	<	}
1025	<	args_info->output_given = 1;
1026	<	args_info->output_arg = gengetopt_strdup (optarg);
1027	<	break;
1028	<
175	<	case 'n':       /* print every n frame.  */
176	<	if (args_info->frame_given)
177	<	{
178	<	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
179	<	clear_args ();
180	<	exit (EXIT_FAILURE);
181	<	}
182	<	args_info->frame_given = 1;
183	<	args_info->frame_arg = strtol (optarg,&stop_char,0);
1019	>
1020	>
1021	>	if (update_arg( (void *)&(args_info->output_arg),
1022	>	&(args_info->output_orig), &(args_info->output_given),
1023	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
1024	>	check_ambiguity, override, 0, 0,
1025	>	"output", 'o',
1026	>	additional_error))
1027	>	goto failure;
1028	>
1029		break;
1030	<
1031	<	case 'd':       /* number of bins for distance.  */
1032	<	if (args_info->ndistebins_given)
1033	<	{
1034	<	fprintf (stderr, "%s: `--ndistebins' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1035	<	clear_args ();
1036	<	exit (EXIT_FAILURE);
1037	<	}
1038	<	args_info->ndistebins_given = 1;
1039	<	args_info->ndistebins_arg = strtol (optarg,&stop_char,0);
1030	>	case 'n':       /* process every n frame.  */
1031	>
1032	>
1033	>	if (update_arg( (void *)&(args_info->step_arg),
1034	>	&(args_info->step_orig), &(args_info->step_given),
1035	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
1036	>	check_ambiguity, override, 0, 0,
1037	>	"step", 'n',
1038	>	additional_error))
1039	>	goto failure;
1040	>
1041		break;
1042	<
1042	>	case 'b':       /* number of bins (general purpose).  */
1043	>
1044	>
1045	>	if (update_arg( (void *)&(args_info->nbins_arg),
1046	>	&(args_info->nbins_orig), &(args_info->nbins_given),
1047	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
1048	>	check_ambiguity, override, 0, 0,
1049	>	"nbins", 'b',
1050	>	additional_error))
1051	>	goto failure;
1052	>
1053	>	break;
1054	>	case 'x':       /* number of bins in x axis.  */
1055	>
1056	>
1057	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
1058	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1059	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1060	>	check_ambiguity, override, 0, 0,
1061	>	"nbins_x", 'x',
1062	>	additional_error))
1063	>	goto failure;
1064	>
1065	>	break;
1066	>	case 'y':       /* number of bins in y axis.  */
1067	>
1068	>
1069	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
1070	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1071	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1072	>	check_ambiguity, override, 0, 0,
1073	>	"nbins_y", 'y',
1074	>	additional_error))
1075	>	goto failure;
1076	>
1077	>	break;
1078		case 'a':       /* number of bins for cos(angle).  */
1079	<	if (args_info->nanglebins_given)
1080	<	{
1081	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1082	<	clear_args ();
1083	<	exit (EXIT_FAILURE);
1084	<	}
1085	<	args_info->nanglebins_given = 1;
1086	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
1079	>
1080	>
1081	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1082	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1083	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1084	>	check_ambiguity, override, 0, 0,
1085	>	"nanglebins", 'a',
1086	>	additional_error))
1087	>	goto failure;
1088	>
1089		break;
1090	<
1091	<	case 'l':       /* maximum length.  */
1092	<	if (args_info->length_given)
1093	<	{
1094	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1095	<	clear_args ();
1096	<	exit (EXIT_FAILURE);
1097	<	}
1098	<	args_info->length_given = 1;
1099	<	args_info->length_arg = strtod (optarg, NULL);
1090	>	case 'c':       /* cutoff radius (rcut).  */
1091	>
1092	>
1093	>	if (update_arg( (void *)&(args_info->rcut_arg),
1094	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1095	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1096	>	check_ambiguity, override, 0, 0,
1097	>	"rcut", 'c',
1098	>	additional_error))
1099	>	goto failure;
1100	>
1101		break;
1102	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1103	+
1104	+
1105	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1106	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
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	+
1125	+	break;
1126	+	case 'g':       /* g(r).  */
1127	+
1128	+	if (args_info->staticProps_group_counter && override)
1129	+	reset_group_staticProps (args_info);
1130	+	args_info->staticProps_group_counter += 1;
1131	+
1132	+	if (update_arg( 0 ,
1133	+	0 , &(args_info->gofr_given),
1134	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1135	+	check_ambiguity, override, 0, 0,
1136	+	"gofr", 'g',
1137	+	additional_error))
1138	+	goto failure;
1139	+
1140	+	break;
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);
1145	+	args_info->staticProps_group_counter += 1;
1146	+
1147	+	if (update_arg( 0 ,
1148	+	0 , &(args_info->p2_given),
1149	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1150	+	check_ambiguity, override, 0, 0,
1151	+	"p2", 'p',
1152	+	additional_error))
1153	+	goto failure;
1154	+
1155	+	break;
1156	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1157	+
1158	+	if (args_info->staticProps_group_counter && override)
1159	+	reset_group_staticProps (args_info);
1160	+	args_info->staticProps_group_counter += 1;
1161	+
1162	+	if (update_arg( 0 ,
1163	+	0 , &(args_info->scd_given),
1164	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1165	+	check_ambiguity, override, 0, 0,
1166	+	"scd", 's',
1167	+	additional_error))
1168	+	goto failure;
1169	+
1170	+	break;
1171	+	case 'd':       /* density plot.  */
1172	+
1173	+	if (args_info->staticProps_group_counter && override)
1174	+	reset_group_staticProps (args_info);
1175	+	args_info->staticProps_group_counter += 1;
1176	+
1177	+	if (update_arg( 0 ,
1178	+	0 , &(args_info->density_given),
1179	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1180	+	check_ambiguity, override, 0, 0,
1181	+	"density", 'd',
1182	+	additional_error))
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
219	–
1217		case 0: /* Long option with no short option */
1218	<	/* select first stuntdouble set.  */
1219	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1218	>	/* number of bins in z axis.  */
1219	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1220		{
1221	<	if (args_info->sele1_given)
1222	<	{
1223	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1224	<	clear_args ();
1225	<	exit (EXIT_FAILURE);
1226	<	}
1227	<	args_info->sele1_given = 1;
1228	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1229	<	break;
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	<	/* select second stuntdouble set.  */
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	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1262	>	{
1263	>
1264	>
1265	>	if (update_arg( (void *)&(args_info->length_arg),
1266	>	&(args_info->length_orig), &(args_info->length_given),
1267	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1268	>	check_ambiguity, override, 0, 0,
1269	>	"length", '-',
1270	>	additional_error))
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	>	{
1291	>
1292	>
1293	>	if (update_arg( (void *)&(args_info->sele1_arg),
1294	>	&(args_info->sele1_orig), &(args_info->sele1_given),
1295	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1296	>	check_ambiguity, override, 0, 0,
1297	>	"sele1", '-',
1298	>	additional_error))
1299	>	goto failure;
1300	>
1301	>	}
1302	>	/* select the second stuntdouble set.  */
1303		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1304		{
1305	<	if (args_info->sele2_given)
1306	<	{
1307	<	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1308	<	clear_args ();
1309	<	exit (EXIT_FAILURE);
1310	<	}
1311	<	args_info->sele2_given = 1;
1312	<	args_info->sele2_arg = gengetopt_strdup (optarg);
1313	<	break;
1305	>
1306	>
1307	>	if (update_arg( (void *)&(args_info->sele2_arg),
1308	>	&(args_info->sele2_orig), &(args_info->sele2_given),
1309	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1310	>	check_ambiguity, override, 0, 0,
1311	>	"sele2", '-',
1312	>	additional_error))
1313	>	goto failure;
1314	>
1315		}
1316	+	/* select the third stuntdouble set.  */
1317	+	else if (strcmp (long_options[option_index].name, "sele3") == 0)
1318	+	{
1319
1320	<	/* g(r).  */
1321	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1320	>
1321	>	if (update_arg( (void *)&(args_info->sele3_arg),
1322	>	&(args_info->sele3_orig), &(args_info->sele3_given),
1323	>	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1324	>	check_ambiguity, override, 0, 0,
1325	>	"sele3", '-',
1326	>	additional_error))
1327	>	goto failure;
1328	>
1329	>	}
1330	>	/* select reference (use and only use with --gxyz).  */
1331	>	else if (strcmp (long_options[option_index].name, "refsele") == 0)
1332		{
252	–	if (args_info->gofr_given)
253	–	{
254	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
255	–	clear_args ();
256	–	exit (EXIT_FAILURE);
257	–	}
258	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1333
1334	<	break;
1334	>
1335	>	if (update_arg( (void *)&(args_info->refsele_arg),
1336	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1337	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1338	>	check_ambiguity, override, 0, 0,
1339	>	"refsele", '-',
1340	>	additional_error))
1341	>	goto failure;
1342	>
1343	>	}
1344	>	/* select stunt doubles for center-of-mass reference point.  */
1345	>	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1346	>	{
1347	>
1348	>
1349	>	if (update_arg( (void *)&(args_info->comsele_arg),
1350	>	&(args_info->comsele_orig), &(args_info->comsele_given),
1351	>	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1352	>	check_ambiguity, override, 0, 0,
1353	>	"comsele", '-',
1354	>	additional_error))
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	>	{
1389	>
1390	>
1391	>	if (update_arg( (void *)&(args_info->molname_arg),
1392	>	&(args_info->molname_orig), &(args_info->molname_given),
1393	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1394	>	check_ambiguity, override, 0, 0,
1395	>	"molname", '-',
1396	>	additional_error))
1397	>	goto failure;
1398	>
1399	>	}
1400	>	/* begin internal index.  */
1401	>	else if (strcmp (long_options[option_index].name, "begin") == 0)
1402	>	{
1403	>
1404	>
1405	>	if (update_arg( (void *)&(args_info->begin_arg),
1406	>	&(args_info->begin_orig), &(args_info->begin_given),
1407	>	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1408	>	check_ambiguity, override, 0, 0,
1409	>	"begin", '-',
1410	>	additional_error))
1411	>	goto failure;
1412	>
1413	>	}
1414	>	/* end internal index.  */
1415	>	else if (strcmp (long_options[option_index].name, "end") == 0)
1416	>	{
1417	>
1418	>
1419	>	if (update_arg( (void *)&(args_info->end_arg),
1420	>	&(args_info->end_orig), &(args_info->end_given),
1421	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1422	>	check_ambiguity, override, 0, 0,
1423	>	"end", '-',
1424	>	additional_error))
1425	>	goto failure;
1426	>
1427	>	}
1428	>	/* nanoparticle radius.  */
1429	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1430	>	{
1431	>
1432	>
1433	>	if (update_arg( (void *)&(args_info->radius_arg),
1434	>	&(args_info->radius_orig), &(args_info->radius_given),
1435	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1436	>	check_ambiguity, override, 0, 0,
1437	>	"radius", '-',
1438	>	additional_error))
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	>	{
1459	>
1460	>	if (args_info->staticProps_group_counter && override)
1461	>	reset_group_staticProps (args_info);
1462	>	args_info->staticProps_group_counter += 1;
1463	>
1464	>	if (update_arg( 0 ,
1465	>	0 , &(args_info->bo_given),
1466	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1467	>	check_ambiguity, override, 0, 0,
1468	>	"bo", '-',
1469	>	additional_error))
1470	>	goto failure;
1471	>
1472	>	}
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)
1495	>	reset_group_staticProps (args_info);
1496	>	args_info->staticProps_group_counter += 1;
1497	>
1498	>	if (update_arg( 0 ,
1499	>	0 , &(args_info->for_given),
1500	>	&(local_args_info.for_given), optarg, 0, 0, ARG_NO,
1501	>	check_ambiguity, override, 0, 0,
1502	>	"for", '-',
1503	>	additional_error))
1504	>	goto failure;
1505	>
1506		}
1507	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1508	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1509	+	{
1510
1511	+	if (args_info->staticProps_group_counter && override)
1512	+	reset_group_staticProps (args_info);
1513	+	args_info->staticProps_group_counter += 1;
1514	+
1515	+	if (update_arg( 0 ,
1516	+	0 , &(args_info->bad_given),
1517	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1518	+	check_ambiguity, override, 0, 0,
1519	+	"bad", '-',
1520	+	additional_error))
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	+	{
1544	+
1545	+	if (args_info->staticProps_group_counter && override)
1546	+	reset_group_staticProps (args_info);
1547	+	args_info->staticProps_group_counter += 1;
1548	+
1549	+	if (update_arg( 0 ,
1550	+	0 , &(args_info->gofz_given),
1551	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1552	+	check_ambiguity, override, 0, 0,
1553	+	"gofz", '-',
1554	+	additional_error))
1555	+	goto failure;
1556	+
1557	+	}
1558		/* g(r, cos(theta)).  */
1559		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1560		{
266	–	if (args_info->r_theta_given)
267	–	{
268	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
269	–	clear_args ();
270	–	exit (EXIT_FAILURE);
271	–	}
272	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1561
1562	<	break;
1563	<	}
1562	>	if (args_info->staticProps_group_counter && override)
1563	>	reset_group_staticProps (args_info);
1564	>	args_info->staticProps_group_counter += 1;
1565
1566	+	if (update_arg( 0 ,
1567	+	0 , &(args_info->r_theta_given),
1568	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1569	+	check_ambiguity, override, 0, 0,
1570	+	"r_theta", '-',
1571	+	additional_error))
1572	+	goto failure;
1573	+
1574	+	}
1575		/* g(r, cos(omega)).  */
1576		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1577		{
280	–	if (args_info->r_omega_given)
281	–	{
282	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
283	–	clear_args ();
284	–	exit (EXIT_FAILURE);
285	–	}
286	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1578
1579	<	break;
1579	>	if (args_info->staticProps_group_counter && override)
1580	>	reset_group_staticProps (args_info);
1581	>	args_info->staticProps_group_counter += 1;
1582	>
1583	>	if (update_arg( 0 ,
1584	>	0 , &(args_info->r_omega_given),
1585	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1586	>	check_ambiguity, override, 0, 0,
1587	>	"r_omega", '-',
1588	>	additional_error))
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		{
294	–	if (args_info->theta_omega_given)
295	–	{
296	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
297	–	clear_args ();
298	–	exit (EXIT_FAILURE);
299	–	}
300	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1612
1613	<	break;
1614	<	}
1613	>	if (args_info->staticProps_group_counter && override)
1614	>	reset_group_staticProps (args_info);
1615	>	args_info->staticProps_group_counter += 1;
1616
1617	+	if (update_arg( 0 ,
1618	+	0 , &(args_info->theta_omega_given),
1619	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1620	+	check_ambiguity, override, 0, 0,
1621	+	"theta_omega", '-',
1622	+	additional_error))
1623	+	goto failure;
1624	+
1625	+	}
1626		/* g(x, y, z).  */
1627	<	else if (strcmp (long_options[option_index].name, "xyz") == 0)
1627	>	else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1628		{
308	–	if (args_info->xyz_given)
309	–	{
310	–	fprintf (stderr, "%s: `--xyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
311	–	clear_args ();
312	–	exit (EXIT_FAILURE);
313	–	}
314	–	args_info->xyz_given = 1; staticProps_group_counter += 1;
1629
1630	<	break;
1630	>	if (args_info->staticProps_group_counter && override)
1631	>	reset_group_staticProps (args_info);
1632	>	args_info->staticProps_group_counter += 1;
1633	>
1634	>	if (update_arg( 0 ,
1635	>	0 , &(args_info->gxyz_given),
1636	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1637	>	check_ambiguity, override, 0, 0,
1638	>	"gxyz", '-',
1639	>	additional_error))
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	<
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	>	{
1663	>
1664	>	if (args_info->staticProps_group_counter && override)
1665	>	reset_group_staticProps (args_info);
1666	>	args_info->staticProps_group_counter += 1;
1667	>
1668	>	if (update_arg( 0 ,
1669	>	0 , &(args_info->rp2_given),
1670	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1671	>	check_ambiguity, override, 0, 0,
1672	>	"rp2", '-',
1673	>	additional_error))
1674	>	goto failure;
1675	>
1676	>	}
1677	>	/* slab density.  */
1678	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1679	>	{
1680	>
1681	>	if (args_info->staticProps_group_counter && override)
1682	>	reset_group_staticProps (args_info);
1683	>	args_info->staticProps_group_counter += 1;
1684	>
1685	>	if (update_arg( 0 ,
1686	>	0 , &(args_info->slab_density_given),
1687	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1688	>	check_ambiguity, override, 0, 0,
1689	>	"slab_density", '-',
1690	>	additional_error))
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	>	{
1714	>
1715	>	if (args_info->staticProps_group_counter && override)
1716	>	reset_group_staticProps (args_info);
1717	>	args_info->staticProps_group_counter += 1;
1718	>
1719	>	if (update_arg( 0 ,
1720	>	0 , &(args_info->hxy_given),
1721	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1722	>	check_ambiguity, override, 0, 0,
1723	>	"hxy", '-',
1724	>	additional_error))
1725	>	goto failure;
1726	>
1727	>	}
1728	>	/* rho of R.  */
1729	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1730	>	{
1731	>
1732	>	if (args_info->staticProps_group_counter && override)
1733	>	reset_group_staticProps (args_info);
1734	>	args_info->staticProps_group_counter += 1;
1735	>
1736	>	if (update_arg( 0 ,
1737	>	0 , &(args_info->rho_r_given),
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	>
1761	>	}
1762	>	/* hull volume of nanoparticle.  */
1763	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1764	>	{
1765	>
1766	>	if (args_info->staticProps_group_counter && override)
1767	>	reset_group_staticProps (args_info);
1768	>	args_info->staticProps_group_counter += 1;
1769	>
1770	>	if (update_arg( 0 ,
1771	>	0 , &(args_info->hullvol_given),
1772	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1773	>	check_ambiguity, override, 0, 0,
1774	>	"hullvol", '-',
1775	>	additional_error))
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.  */
1936	<	exit (EXIT_FAILURE);
1936	>	goto failure;
1937
1938		default:        /* bug: option not considered.  */
1939	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1939	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1940		abort ();
1941		} /* switch */
1942		} /* while */
1943
1944	<	if ( staticProps_group_counter != 1)
1944	>	if (args_info->staticProps_group_counter > 1)
1945		{
1946	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1947	<	missing_required_options = 1;
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
1950
1951	<	if (! args_info->input_given)
1951	>
1952	>	if (check_required)
1953		{
1954	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
340	<	missing_required_options = 1;
1954	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1955		}
1956	<	if (! args_info->length_given)
1956	>
1957	>	cmdline_parser_release (&local_args_info);
1958	>
1959	>	if ( error )
1960	>	return (EXIT_FAILURE);
1961	>
1962	>	if (optind < argc)
1963		{
1964	<	fprintf (stderr, "%s: '--length' ('-l') option required\n", CMDLINE_PARSER_PACKAGE);
1965	<	missing_required_options = 1;
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		}
347	–	if ( missing_required_options )
348	–	exit (EXIT_FAILURE);
1985
1986		return 0;
1987	+
1988	+	failure:
1989	+
1990	+	cmdline_parser_release (&local_args_info);
1991	+	return (EXIT_FAILURE);
1992		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 310 by tim, Thu Feb 10 18:14:03 2005 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

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