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

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 544 by tim, Fri May 27 04:41:34 2005 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 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -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:
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	>	#include <getopt.h>
25
26		#include "StaticPropsCmd.h"
27
28	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
28	>	const char *gengetopt_args_info_purpose = "";
29
30	<	void
32	<	cmdline_parser_print_help (void)
33	<	{
34	<	cmdline_parser_print_version ();
35	<	printf("\n"
36	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	<	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, --step=INT                  process every n frame  (default=`1')\n");
43	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
44	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
45	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
46	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
47	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
48	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
49	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
50	<	printf("      --molname=STRING            molecule name\n");
51	<	printf("      --begin=INT                 begin interanl index\n");
52	<	printf("      --end=INT                   end internal index\n");
53	<	printf("\n");
54	<	printf(" Group: staticProps  an option of this group is required\n");
55	<	printf("      --gofr                      g(r)\n");
56	<	printf("      --r_theta                   g(r, cos(theta))\n");
57	<	printf("      --r_omega                   g(r, cos(omega))\n");
58	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
59	<	printf("      --gxyz                      g(x, y, z)\n");
60	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
61	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
62	<	}
30	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
31
32	+	const char *gengetopt_args_info_description = "";
33
34	<	static char *gengetopt_strdup (const char *s);
34	>	const char *gengetopt_args_info_help[] = {
35	>	"  -h, --help                    Print help and exit",
36	>	"  -V, --version                 Print version and exit",
37	>	"  -i, --input=filename          input dump file",
38	>	"  -o, --output=filename         output file name",
39	>	"  -n, --step=INT                process every n frame  (default=`1')",
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')",
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	>	"      --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	>	"      --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
100	<	/* gengetopt_strdup() */
101	<	/* strdup.c replacement of strdup, which is not standard */
102	<	char *
103	<	gengetopt_strdup (const char *s)
104	<	{
72	<	char *result = (char*)malloc(strlen(s) + 1);
73	<	if (result == (char*)0)
74	<	return (char*)0;
75	<	strcpy(result, s);
76	<	return result;
77	<	}
100	>	typedef enum {ARG_NO
101	>	, ARG_STRING
102	>	, ARG_INT
103	>	, ARG_DOUBLE
104	>	} cmdline_parser_arg_type;
105
106	<	int
107	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
108	<	{
109	<	int c;        /* Character of the parsed option.  */
83	<	int missing_required_options = 0;
84	<	int staticProps_group_counter = 0;
85	<
106	>	static
107	>	void clear_given (struct gengetopt_args_info *args_info);
108	>	static
109	>	void clear_args (struct gengetopt_args_info *args_info);
110
111	+	static int
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
116	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
117	+
118	+	static char *
119	+	gengetopt_strdup (const char *s);
120	+
121	+	static
122	+	void clear_given (struct gengetopt_args_info *args_info)
123	+	{
124		args_info->help_given = 0 ;
125		args_info->version_given = 0 ;
126		args_info->input_given = 0 ;
127		args_info->output_given = 0 ;
128		args_info->step_given = 0 ;
129	<	args_info->nrbins_given = 0 ;
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 ;
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->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	<	#define clear_args() { \
169	<	args_info->input_arg = NULL; \
170	<	args_info->output_arg = NULL; \
171	<	args_info->step_arg = 1 ;\
172	<	args_info->nrbins_arg = 100 ;\
173	<	args_info->nanglebins_arg = 50 ;\
174	<	args_info->sele1_arg = NULL; \
175	<	args_info->sele2_arg = NULL; \
176	<	args_info->sele3_arg = NULL; \
177	<	args_info->refsele_arg = NULL; \
178	<	args_info->molname_arg = NULL; \
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	<	clear_args();
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;
195	>	args_info->output_orig = NULL;
196	>	args_info->step_arg = 1;
197	>	args_info->step_orig = NULL;
198	>	args_info->nbins_arg = 100;
199	>	args_info->nbins_orig = NULL;
200	>	args_info->nbins_x_arg = 100;
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;
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;
215	>	args_info->sele1_orig = NULL;
216	>	args_info->sele2_arg = NULL;
217	>	args_info->sele2_orig = NULL;
218	>	args_info->sele3_arg = NULL;
219	>	args_info->sele3_orig = NULL;
220	>	args_info->refsele_arg = NULL;
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
236	+	static
237	+	void init_args_info(struct gengetopt_args_info *args_info)
238	+	{
239	+
240	+
241	+	args_info->help_help = gengetopt_args_info_help[0] ;
242	+	args_info->version_help = gengetopt_args_info_help[1] ;
243	+	args_info->input_help = gengetopt_args_info_help[2] ;
244	+	args_info->output_help = gengetopt_args_info_help[3] ;
245	+	args_info->step_help = gengetopt_args_info_help[4] ;
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->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->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",
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) {
314	+	cmdline_parser_print_version ();
315	+
316	+	if (strlen(gengetopt_args_info_purpose) > 0)
317	+	printf("\n%s\n", gengetopt_args_info_purpose);
318	+
319	+	if (strlen(gengetopt_args_info_usage) > 0)
320	+	printf("\n%s\n", gengetopt_args_info_usage);
321	+
322	+	printf("\n");
323	+
324	+	if (strlen(gengetopt_args_info_description) > 0)
325	+	printf("%s\n\n", gengetopt_args_info_description);
326	+	}
327	+
328	+	void
329	+	cmdline_parser_print_help (void)
330	+	{
331	+	int i = 0;
332	+	print_help_common();
333	+	while (gengetopt_args_info_help[i])
334	+	printf("%s\n", gengetopt_args_info_help[i++]);
335	+	}
336	+
337	+	void
338	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
339	+	{
340	+	clear_given (args_info);
341	+	clear_args (args_info);
342	+	init_args_info (args_info);
343	+	}
344	+
345	+	void
346	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
347	+	{
348	+	if (params)
349	+	{
350	+	params->override = 0;
351	+	params->initialize = 1;
352	+	params->check_required = 1;
353	+	params->check_ambiguity = 0;
354	+	params->print_errors = 1;
355	+	}
356	+	}
357	+
358	+	struct cmdline_parser_params *
359	+	cmdline_parser_params_create(void)
360	+	{
361	+	struct cmdline_parser_params *params =
362	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
363	+	cmdline_parser_params_init(params);
364	+	return params;
365	+	}
366	+
367	+	static void
368	+	free_string_field (char **s)
369	+	{
370	+	if (*s)
371	+	{
372	+	free (*s);
373	+	*s = 0;
374	+	}
375	+	}
376	+
377	+
378	+	static void
379	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
380	+	{
381	+
382	+	free_string_field (&(args_info->input_arg));
383	+	free_string_field (&(args_info->input_orig));
384	+	free_string_field (&(args_info->output_arg));
385	+	free_string_field (&(args_info->output_orig));
386	+	free_string_field (&(args_info->step_orig));
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));
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));
399	+	free_string_field (&(args_info->sele2_arg));
400	+	free_string_field (&(args_info->sele2_orig));
401	+	free_string_field (&(args_info->sele3_arg));
402	+	free_string_field (&(args_info->sele3_orig));
403	+	free_string_field (&(args_info->refsele_arg));
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	+
419	+	clear_given (args_info);
420	+	}
421	+
422	+
423	+	static void
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 {
430	+	fprintf(outfile, "%s\n", opt);
431	+	}
432	+	}
433	+
434	+
435	+	int
436	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
437	+	{
438	+	int i = 0;
439	+
440	+	if (!outfile)
441	+	{
442	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
443	+	return EXIT_FAILURE;
444	+	}
445	+
446	+	if (args_info->help_given)
447	+	write_into_file(outfile, "help", 0, 0 );
448	+	if (args_info->version_given)
449	+	write_into_file(outfile, "version", 0, 0 );
450	+	if (args_info->input_given)
451	+	write_into_file(outfile, "input", args_info->input_orig, 0);
452	+	if (args_info->output_given)
453	+	write_into_file(outfile, "output", args_info->output_orig, 0);
454	+	if (args_info->step_given)
455	+	write_into_file(outfile, "step", args_info->step_orig, 0);
456	+	if (args_info->nbins_given)
457	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
458	+	if (args_info->nbins_x_given)
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);
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)
477	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
478	+	if (args_info->sele2_given)
479	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
480	+	if (args_info->sele3_given)
481	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
482	+	if (args_info->refsele_given)
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)
493	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
494	+	if (args_info->end_given)
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->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)
515	+	write_into_file(outfile, "gofz", 0, 0 );
516	+	if (args_info->r_theta_given)
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)
531	+	write_into_file(outfile, "rp2", 0, 0 );
532	+	if (args_info->scd_given)
533	+	write_into_file(outfile, "scd", 0, 0 );
534	+	if (args_info->density_given)
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;
571	+	return i;
572	+	}
573	+
574	+	int
575	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
576	+	{
577	+	FILE *outfile;
578	+	int i = 0;
579	+
580	+	outfile = fopen(filename, "w");
581	+
582	+	if (!outfile)
583	+	{
584	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
585	+	return EXIT_FAILURE;
586	+	}
587	+
588	+	i = cmdline_parser_dump(outfile, args_info);
589	+	fclose (outfile);
590	+
591	+	return i;
592	+	}
593	+
594	+	void
595	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
596	+	{
597	+	cmdline_parser_release (args_info);
598	+	}
599	+
600	+	/** @brief replacement of strdup, which is not standard */
601	+	char *
602	+	gengetopt_strdup (const char *s)
603	+	{
604	+	char *result = 0;
605	+	if (!s)
606	+	return result;
607	+
608	+	result = (char*)malloc(strlen(s) + 1);
609	+	if (result == (char*)0)
610	+	return (char*)0;
611	+	strcpy(result, s);
612	+	return result;
613	+	}
614	+
615	+	static void
616	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
617	+	{
618	+	if (! args_info->staticProps_group_counter)
619	+	return;
620	+
621	+	args_info->bo_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 **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 **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, 0);
670	+
671	+	if (result == EXIT_FAILURE)
672	+	{
673	+	cmdline_parser_free (args_info);
674	+	exit (EXIT_FAILURE);
675	+	}
676	+
677	+	return result;
678	+	}
679	+
680	+	int
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;
685	+
686	+	params.override = override;
687	+	params.initialize = initialize;
688	+	params.check_required = check_required;
689	+	params.check_ambiguity = 0;
690	+	params.print_errors = 1;
691	+
692	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
693	+
694	+	if (result == EXIT_FAILURE)
695	+	{
696	+	cmdline_parser_free (args_info);
697	+	exit (EXIT_FAILURE);
698	+	}
699	+
700	+	return result;
701	+	}
702	+
703	+	int
704	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
705	+	{
706	+	int result = EXIT_SUCCESS;
707	+
708	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
709	+	result = EXIT_FAILURE;
710	+
711	+	if (result == EXIT_FAILURE)
712	+	{
713	+	cmdline_parser_free (args_info);
714	+	exit (EXIT_FAILURE);
715	+	}
716	+
717	+	return result;
718	+	}
719	+
720	+	int
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)
728	+	{
729	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
730	+	error = 1;
731	+	}
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 : ""));
736	+	error = 1;
737	+	}
738	+
739	+
740	+	/* checks for dependences among options */
741	+
742	+	return error;
743	+	}
744	+
745	+
746	+	static char *package_name = 0;
747	+
748	+	/**
749	+	* @brief updates an option
750	+	* @param field the generic pointer to the field to update
751	+	* @param orig_field the pointer to the orig field
752	+	* @param field_given the pointer to the number of occurrence of this option
753	+	* @param prev_given the pointer to the number of occurrence already seen
754	+	* @param value the argument for this option (if null no arg was specified)
755	+	* @param possible_values the possible values for this option (if specified)
756	+	* @param default_value the default value (in case the option only accepts fixed values)
757	+	* @param arg_type the type of this option
758	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
759	+	* @param override @see cmdline_parser_params.override
760	+	* @param no_free whether to free a possible previous value
761	+	* @param multiple_option whether this is a multiple option
762	+	* @param long_opt the corresponding long option
763	+	* @param short_opt the corresponding short option (or '-' if none)
764	+	* @param additional_error possible further error specification
765	+	*/
766	+	static
767	+	int update_arg(void *field, char **orig_field,
768	+	unsigned int *field_given, unsigned int *prev_given,
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,
774	+	const char *long_opt, char short_opt,
775	+	const char *additional_error)
776	+	{
777	+	char *stop_char = 0;
778	+	const char *val = value;
779	+	int found;
780	+	char **string_field;
781	+	FIX_UNUSED (field);
782	+
783	+	stop_char = 0;
784	+	found = 0;
785	+
786	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
787	+	{
788	+	if (short_opt != '-')
789	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
790	+	package_name, long_opt, short_opt,
791	+	(additional_error ? additional_error : ""));
792	+	else
793	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
794	+	package_name, long_opt,
795	+	(additional_error ? additional_error : ""));
796	+	return 1; /* failure */
797	+	}
798	+
799	+	FIX_UNUSED (default_value);
800	+
801	+	if (field_given && *field_given && ! override)
802	+	return 0;
803	+	if (prev_given)
804	+	(*prev_given)++;
805	+	if (field_given)
806	+	(*field_given)++;
807	+	if (possible_values)
808	+	val = possible_values[found];
809	+
810	+	switch(arg_type) {
811	+	case ARG_INT:
812	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
813	+	break;
814	+	case ARG_DOUBLE:
815	+	if (val) *((double *)field) = strtod (val, &stop_char);
816	+	break;
817	+	case ARG_STRING:
818	+	if (val) {
819	+	string_field = (char **)field;
820	+	if (!no_free && *string_field)
821	+	free (*string_field); /* free previous string */
822	+	*string_field = gengetopt_strdup (val);
823	+	}
824	+	break;
825	+	default:
826	+	break;
827	+	};
828	+
829	+	/* check numeric conversion */
830	+	switch(arg_type) {
831	+	case ARG_INT:
832	+	case ARG_DOUBLE:
833	+	if (val && !(stop_char && *stop_char == '\0')) {
834	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
835	+	return 1; /* failure */
836	+	}
837	+	break;
838	+	default:
839	+	;
840	+	};
841	+
842	+	/* store the original value */
843	+	switch(arg_type) {
844	+	case ARG_NO:
845	+	break;
846	+	default:
847	+	if (value && orig_field) {
848	+	if (no_free) {
849	+	*orig_field = value;
850	+	} else {
851	+	if (*orig_field)
852	+	free (*orig_field); /* free previous string */
853	+	*orig_field = gengetopt_strdup (value);
854	+	}
855	+	}
856	+	};
857	+
858	+	return 0; /* OK */
859	+	}
860	+
861	+
862	+	int
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.  */
868	+
869	+	int error = 0;
870	+	struct gengetopt_args_info local_args_info;
871	+
872	+	int override;
873	+	int initialize;
874	+	int check_required;
875	+	int check_ambiguity;
876	+
877	+	package_name = argv[0];
878	+
879	+	override = params->override;
880	+	initialize = params->initialize;
881	+	check_required = params->check_required;
882	+	check_ambiguity = params->check_ambiguity;
883	+
884	+	if (initialize)
885	+	cmdline_parser_init (args_info);
886	+
887	+	cmdline_parser_init (&local_args_info);
888	+
889		optarg = 0;
890	<	optind = 1;
891	<	opterr = 1;
890	>	optind = 0;
891	>	opterr = params->print_errors;
892		optopt = '?';
893
894		while (1)
895		{
896		int option_index = 0;
132	–	char *stop_char;
897
898		static struct option long_options[] = {
899		{ "help",       0, NULL, 'h' },
#	Line 137 | Line 901 | cmdline_parser (int argc, char * const *argv, struct g
901		{ "input",      1, NULL, 'i' },
902		{ "output",     1, NULL, 'o' },
903		{ "step",       1, NULL, 'n' },
904	<	{ "nrbins",     1, NULL, 'r' },
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' },
909	<	{ "length",     1, NULL, 'l' },
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	<	{ "gofr",       0, NULL, 0 },
924	>	{ "radius",     1, NULL, 0 },
925	>	{ "voxelSize",  1, NULL, 'v' },
926	>	{ "gaussWidth", 1, NULL, 0 },
927	>	{ "bo", 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	<	{ "p2", 0, NULL, 0 },
940	<	{ "scd",        0, NULL, 0 },
941	<	{ NULL, 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	>	{ "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	<	stop_char = 0;
161	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", 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
967		switch (c)
968		{
969		case 'h':       /* Print help and exit.  */
168	–	clear_args ();
970		cmdline_parser_print_help ();
971	+	cmdline_parser_free (&local_args_info);
972		exit (EXIT_SUCCESS);
973
974		case 'V':       /* Print version and exit.  */
173	–	clear_args ();
975		cmdline_parser_print_version ();
976	+	cmdline_parser_free (&local_args_info);
977		exit (EXIT_SUCCESS);
978
979		case 'i':       /* input dump file.  */
980	<	if (args_info->input_given)
981	<	{
982	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
983	<	clear_args ();
984	<	exit (EXIT_FAILURE);
985	<	}
986	<	args_info->input_given = 1;
987	<	args_info->input_arg = gengetopt_strdup (optarg);
980	>
981	>
982	>	if (update_arg( (void *)&(args_info->input_arg),
983	>	&(args_info->input_orig), &(args_info->input_given),
984	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
985	>	check_ambiguity, override, 0, 0,
986	>	"input", 'i',
987	>	additional_error))
988	>	goto failure;
989	>
990		break;
187	–
991		case 'o':       /* output file name.  */
992	<	if (args_info->output_given)
993	<	{
994	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
995	<	clear_args ();
996	<	exit (EXIT_FAILURE);
997	<	}
998	<	args_info->output_given = 1;
999	<	args_info->output_arg = gengetopt_strdup (optarg);
992	>
993	>
994	>	if (update_arg( (void *)&(args_info->output_arg),
995	>	&(args_info->output_orig), &(args_info->output_given),
996	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
997	>	check_ambiguity, override, 0, 0,
998	>	"output", 'o',
999	>	additional_error))
1000	>	goto failure;
1001	>
1002		break;
198	–
1003		case 'n':       /* process every n frame.  */
1004	<	if (args_info->step_given)
1005	<	{
1006	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1007	<	clear_args ();
1008	<	exit (EXIT_FAILURE);
1009	<	}
1010	<	args_info->step_given = 1;
1011	<	args_info->step_arg = strtol (optarg,&stop_char,0);
1004	>
1005	>
1006	>	if (update_arg( (void *)&(args_info->step_arg),
1007	>	&(args_info->step_orig), &(args_info->step_given),
1008	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
1009	>	check_ambiguity, override, 0, 0,
1010	>	"step", 'n',
1011	>	additional_error))
1012	>	goto failure;
1013	>
1014		break;
1015	<
1016	<	case 'r':       /* number of bins for distance.  */
1017	<	if (args_info->nrbins_given)
1018	<	{
1019	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1020	<	clear_args ();
1021	<	exit (EXIT_FAILURE);
1022	<	}
1023	<	args_info->nrbins_given = 1;
1024	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
1015	>	case 'b':       /* number of bins (general purpose).  */
1016	>
1017	>
1018	>	if (update_arg( (void *)&(args_info->nbins_arg),
1019	>	&(args_info->nbins_orig), &(args_info->nbins_given),
1020	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
1021	>	check_ambiguity, override, 0, 0,
1022	>	"nbins", 'b',
1023	>	additional_error))
1024	>	goto failure;
1025	>
1026		break;
1027	<
1027	>	case 'x':       /* number of bins in x axis.  */
1028	>
1029	>
1030	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
1031	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
1032	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
1033	>	check_ambiguity, override, 0, 0,
1034	>	"nbins_x", 'x',
1035	>	additional_error))
1036	>	goto failure;
1037	>
1038	>	break;
1039	>	case 'y':       /* number of bins in y axis.  */
1040	>
1041	>
1042	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
1043	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
1044	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
1045	>	check_ambiguity, override, 0, 0,
1046	>	"nbins_y", 'y',
1047	>	additional_error))
1048	>	goto failure;
1049	>
1050	>	break;
1051		case 'a':       /* number of bins for cos(angle).  */
1052	<	if (args_info->nanglebins_given)
1053	<	{
1054	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1055	<	clear_args ();
1056	<	exit (EXIT_FAILURE);
1057	<	}
1058	<	args_info->nanglebins_given = 1;
1059	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
1052	>
1053	>
1054	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
1055	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
1056	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
1057	>	check_ambiguity, override, 0, 0,
1058	>	"nanglebins", 'a',
1059	>	additional_error))
1060	>	goto failure;
1061	>
1062		break;
1063	<
1064	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1065	<	if (args_info->length_given)
1066	<	{
1067	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
1068	<	clear_args ();
1069	<	exit (EXIT_FAILURE);
1070	<	}
1071	<	args_info->length_given = 1;
1072	<	args_info->length_arg = strtod (optarg, NULL);
1063	>	case 'c':       /* cutoff radius (rcut).  */
1064	>
1065	>
1066	>	if (update_arg( (void *)&(args_info->rcut_arg),
1067	>	&(args_info->rcut_orig), &(args_info->rcut_given),
1068	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
1069	>	check_ambiguity, override, 0, 0,
1070	>	"rcut", 'c',
1071	>	additional_error))
1072	>	goto failure;
1073	>
1074		break;
1075	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1076	+
1077	+
1078	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1079	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1080	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1081	+	check_ambiguity, override, 0, 0,
1082	+	"zoffset", 'z',
1083	+	additional_error))
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)
1102	+	reset_group_staticProps (args_info);
1103	+	args_info->staticProps_group_counter += 1;
1104	+
1105	+	if (update_arg( 0 ,
1106	+	0 , &(args_info->gofr_given),
1107	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1108	+	check_ambiguity, override, 0, 0,
1109	+	"gofr", 'g',
1110	+	additional_error))
1111	+	goto failure;
1112	+
1113	+	break;
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);
1118	+	args_info->staticProps_group_counter += 1;
1119	+
1120	+	if (update_arg( 0 ,
1121	+	0 , &(args_info->p2_given),
1122	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1123	+	check_ambiguity, override, 0, 0,
1124	+	"p2", 'p',
1125	+	additional_error))
1126	+	goto failure;
1127	+
1128	+	break;
1129	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1130	+
1131	+	if (args_info->staticProps_group_counter && override)
1132	+	reset_group_staticProps (args_info);
1133	+	args_info->staticProps_group_counter += 1;
1134	+
1135	+	if (update_arg( 0 ,
1136	+	0 , &(args_info->scd_given),
1137	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1138	+	check_ambiguity, override, 0, 0,
1139	+	"scd", 's',
1140	+	additional_error))
1141	+	goto failure;
1142	+
1143	+	break;
1144	+	case 'd':       /* density plot.  */
1145	+
1146	+	if (args_info->staticProps_group_counter && override)
1147	+	reset_group_staticProps (args_info);
1148	+	args_info->staticProps_group_counter += 1;
1149	+
1150	+	if (update_arg( 0 ,
1151	+	0 , &(args_info->density_given),
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
243	–
1190		case 0: /* Long option with no short option */
1191	<	/* select the first stuntdouble set.  */
1192	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1191	>	/* number of bins in z axis.  */
1192	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1193		{
1194	<	if (args_info->sele1_given)
1195	<	{
1196	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1197	<	clear_args ();
1198	<	exit (EXIT_FAILURE);
1199	<	}
1200	<	args_info->sele1_given = 1;
1201	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1202	<	break;
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	>	else if (strcmp (long_options[option_index].name, "length") == 0)
1221	>	{
1222	>
1223	>
1224	>	if (update_arg( (void *)&(args_info->length_arg),
1225	>	&(args_info->length_orig), &(args_info->length_given),
1226	>	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1227	>	check_ambiguity, override, 0, 0,
1228	>	"length", '-',
1229	>	additional_error))
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	+	{
1250
1251	+
1252	+	if (update_arg( (void *)&(args_info->sele1_arg),
1253	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1254	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1255	+	check_ambiguity, override, 0, 0,
1256	+	"sele1", '-',
1257	+	additional_error))
1258	+	goto failure;
1259	+
1260	+	}
1261		/* select the second stuntdouble set.  */
1262		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1263		{
262	–	if (args_info->sele2_given)
263	–	{
264	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
265	–	clear_args ();
266	–	exit (EXIT_FAILURE);
267	–	}
268	–	args_info->sele2_given = 1;
269	–	args_info->sele2_arg = gengetopt_strdup (optarg);
270	–	break;
271	–	}
1264
1265	+
1266	+	if (update_arg( (void *)&(args_info->sele2_arg),
1267	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1268	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1269	+	check_ambiguity, override, 0, 0,
1270	+	"sele2", '-',
1271	+	additional_error))
1272	+	goto failure;
1273	+
1274	+	}
1275		/* select the third stuntdouble set.  */
1276		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1277		{
276	–	if (args_info->sele3_given)
277	–	{
278	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
279	–	clear_args ();
280	–	exit (EXIT_FAILURE);
281	–	}
282	–	args_info->sele3_given = 1;
283	–	args_info->sele3_arg = gengetopt_strdup (optarg);
284	–	break;
285	–	}
1278
1279	+
1280	+	if (update_arg( (void *)&(args_info->sele3_arg),
1281	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1282	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1283	+	check_ambiguity, override, 0, 0,
1284	+	"sele3", '-',
1285	+	additional_error))
1286	+	goto failure;
1287	+
1288	+	}
1289		/* select reference (use and only use with --gxyz).  */
1290		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1291		{
1292	<	if (args_info->refsele_given)
1293	<	{
1294	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1295	<	clear_args ();
1296	<	exit (EXIT_FAILURE);
1297	<	}
1298	<	args_info->refsele_given = 1;
1299	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1300	<	break;
1292	>
1293	>
1294	>	if (update_arg( (void *)&(args_info->refsele_arg),
1295	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1296	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1297	>	check_ambiguity, override, 0, 0,
1298	>	"refsele", '-',
1299	>	additional_error))
1300	>	goto failure;
1301	>
1302		}
1303	+	/* select stunt doubles for center-of-mass reference point.  */
1304	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1305	+	{
1306
1307	+
1308	+	if (update_arg( (void *)&(args_info->comsele_arg),
1309	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1310	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1311	+	check_ambiguity, override, 0, 0,
1312	+	"comsele", '-',
1313	+	additional_error))
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		{
304	–	if (args_info->molname_given)
305	–	{
306	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
307	–	clear_args ();
308	–	exit (EXIT_FAILURE);
309	–	}
310	–	args_info->molname_given = 1;
311	–	args_info->molname_arg = gengetopt_strdup (optarg);
312	–	break;
313	–	}
1348
1349	<	/* begin interanl index.  */
1349	>
1350	>	if (update_arg( (void *)&(args_info->molname_arg),
1351	>	&(args_info->molname_orig), &(args_info->molname_given),
1352	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1353	>	check_ambiguity, override, 0, 0,
1354	>	"molname", '-',
1355	>	additional_error))
1356	>	goto failure;
1357	>
1358	>	}
1359	>	/* begin internal index.  */
1360		else if (strcmp (long_options[option_index].name, "begin") == 0)
1361		{
318	–	if (args_info->begin_given)
319	–	{
320	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
321	–	clear_args ();
322	–	exit (EXIT_FAILURE);
323	–	}
324	–	args_info->begin_given = 1;
325	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
326	–	break;
327	–	}
1362
1363	+
1364	+	if (update_arg( (void *)&(args_info->begin_arg),
1365	+	&(args_info->begin_orig), &(args_info->begin_given),
1366	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1367	+	check_ambiguity, override, 0, 0,
1368	+	"begin", '-',
1369	+	additional_error))
1370	+	goto failure;
1371	+
1372	+	}
1373		/* end internal index.  */
1374		else if (strcmp (long_options[option_index].name, "end") == 0)
1375		{
1376	<	if (args_info->end_given)
1377	<	{
1378	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1379	<	clear_args ();
1380	<	exit (EXIT_FAILURE);
1381	<	}
1382	<	args_info->end_given = 1;
1383	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1384	<	break;
1376	>
1377	>
1378	>	if (update_arg( (void *)&(args_info->end_arg),
1379	>	&(args_info->end_orig), &(args_info->end_given),
1380	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1381	>	check_ambiguity, override, 0, 0,
1382	>	"end", '-',
1383	>	additional_error))
1384	>	goto failure;
1385	>
1386		}
1387	+	/* nanoparticle radius.  */
1388	+	else if (strcmp (long_options[option_index].name, "radius") == 0)
1389	+	{
1390
1391	<	/* g(r).  */
1392	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1391	>
1392	>	if (update_arg( (void *)&(args_info->radius_arg),
1393	>	&(args_info->radius_orig), &(args_info->radius_given),
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		{
346	–	if (args_info->gofr_given)
347	–	{
348	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
349	–	clear_args ();
350	–	exit (EXIT_FAILURE);
351	–	}
352	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1404
1405	<	break;
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	>
1414	>	}
1415	>	/* bond order parameter (--rcut must be specified).  */
1416	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1417	>	{
1418	>
1419	>	if (args_info->staticProps_group_counter && override)
1420	>	reset_group_staticProps (args_info);
1421	>	args_info->staticProps_group_counter += 1;
1422	>
1423	>	if (update_arg( 0 ,
1424	>	0 , &(args_info->bo_given),
1425	>	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1426	>	check_ambiguity, override, 0, 0,
1427	>	"bo", '-',
1428	>	additional_error))
1429	>	goto failure;
1430	>
1431	>	}
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)
1437	>	reset_group_staticProps (args_info);
1438	>	args_info->staticProps_group_counter += 1;
1439	>
1440	>	if (update_arg( 0 ,
1441	>	0 , &(args_info->ior_given),
1442	>	&(local_args_info.ior_given), optarg, 0, 0, ARG_NO,
1443	>	check_ambiguity, override, 0, 0,
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	+	{
1469	+
1470	+	if (args_info->staticProps_group_counter && override)
1471	+	reset_group_staticProps (args_info);
1472	+	args_info->staticProps_group_counter += 1;
1473	+
1474	+	if (update_arg( 0 ,
1475	+	0 , &(args_info->bad_given),
1476	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1477	+	check_ambiguity, override, 0, 0,
1478	+	"bad", '-',
1479	+	additional_error))
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	+	{
1503	+
1504	+	if (args_info->staticProps_group_counter && override)
1505	+	reset_group_staticProps (args_info);
1506	+	args_info->staticProps_group_counter += 1;
1507	+
1508	+	if (update_arg( 0 ,
1509	+	0 , &(args_info->gofz_given),
1510	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1511	+	check_ambiguity, override, 0, 0,
1512	+	"gofz", '-',
1513	+	additional_error))
1514	+	goto failure;
1515	+
1516	+	}
1517		/* g(r, cos(theta)).  */
1518		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1519		{
360	–	if (args_info->r_theta_given)
361	–	{
362	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
363	–	clear_args ();
364	–	exit (EXIT_FAILURE);
365	–	}
366	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1520
1521	<	break;
1522	<	}
1521	>	if (args_info->staticProps_group_counter && override)
1522	>	reset_group_staticProps (args_info);
1523	>	args_info->staticProps_group_counter += 1;
1524
1525	+	if (update_arg( 0 ,
1526	+	0 , &(args_info->r_theta_given),
1527	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1528	+	check_ambiguity, override, 0, 0,
1529	+	"r_theta", '-',
1530	+	additional_error))
1531	+	goto failure;
1532	+
1533	+	}
1534		/* g(r, cos(omega)).  */
1535		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1536		{
374	–	if (args_info->r_omega_given)
375	–	{
376	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
377	–	clear_args ();
378	–	exit (EXIT_FAILURE);
379	–	}
380	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1537
1538	<	break;
1538	>	if (args_info->staticProps_group_counter && override)
1539	>	reset_group_staticProps (args_info);
1540	>	args_info->staticProps_group_counter += 1;
1541	>
1542	>	if (update_arg( 0 ,
1543	>	0 , &(args_info->r_omega_given),
1544	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1545	>	check_ambiguity, override, 0, 0,
1546	>	"r_omega", '-',
1547	>	additional_error))
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		{
388	–	if (args_info->theta_omega_given)
389	–	{
390	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
391	–	clear_args ();
392	–	exit (EXIT_FAILURE);
393	–	}
394	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1571
1572	<	break;
1573	<	}
1572	>	if (args_info->staticProps_group_counter && override)
1573	>	reset_group_staticProps (args_info);
1574	>	args_info->staticProps_group_counter += 1;
1575
1576	+	if (update_arg( 0 ,
1577	+	0 , &(args_info->theta_omega_given),
1578	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1579	+	check_ambiguity, override, 0, 0,
1580	+	"theta_omega", '-',
1581	+	additional_error))
1582	+	goto failure;
1583	+
1584	+	}
1585		/* g(x, y, z).  */
1586		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1587		{
402	–	if (args_info->gxyz_given)
403	–	{
404	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
405	–	clear_args ();
406	–	exit (EXIT_FAILURE);
407	–	}
408	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1588
1589	<	break;
1589	>	if (args_info->staticProps_group_counter && override)
1590	>	reset_group_staticProps (args_info);
1591	>	args_info->staticProps_group_counter += 1;
1592	>
1593	>	if (update_arg( 0 ,
1594	>	0 , &(args_info->gxyz_given),
1595	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1596	>	check_ambiguity, override, 0, 0,
1597	>	"gxyz", '-',
1598	>	additional_error))
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	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1607	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
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		{
416	–	if (args_info->p2_given)
417	–	{
418	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
419	–	clear_args ();
420	–	exit (EXIT_FAILURE);
421	–	}
422	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1622
1623	<	break;
1623	>	if (args_info->staticProps_group_counter && override)
1624	>	reset_group_staticProps (args_info);
1625	>	args_info->staticProps_group_counter += 1;
1626	>
1627	>	if (update_arg( 0 ,
1628	>	0 , &(args_info->rp2_given),
1629	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1630	>	check_ambiguity, override, 0, 0,
1631	>	"rp2", '-',
1632	>	additional_error))
1633	>	goto failure;
1634	>
1635		}
1636	+	/* slab density.  */
1637	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1638	+	{
1639
1640	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1641	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1640	>	if (args_info->staticProps_group_counter && override)
1641	>	reset_group_staticProps (args_info);
1642	>	args_info->staticProps_group_counter += 1;
1643	>
1644	>	if (update_arg( 0 ,
1645	>	0 , &(args_info->slab_density_given),
1646	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1647	>	check_ambiguity, override, 0, 0,
1648	>	"slab_density", '-',
1649	>	additional_error))
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		{
430	–	if (args_info->scd_given)
431	–	{
432	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
433	–	clear_args ();
434	–	exit (EXIT_FAILURE);
435	–	}
436	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1656
1657	<	break;
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	+	{
1673
1674	<
1674	>	if (args_info->staticProps_group_counter && override)
1675	>	reset_group_staticProps (args_info);
1676	>	args_info->staticProps_group_counter += 1;
1677	>
1678	>	if (update_arg( 0 ,
1679	>	0 , &(args_info->hxy_given),
1680	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1681	>	check_ambiguity, override, 0, 0,
1682	>	"hxy", '-',
1683	>	additional_error))
1684	>	goto failure;
1685	>
1686	>	}
1687	>	/* rho of R.  */
1688	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1689	>	{
1690	>
1691	>	if (args_info->staticProps_group_counter && override)
1692	>	reset_group_staticProps (args_info);
1693	>	args_info->staticProps_group_counter += 1;
1694	>
1695	>	if (update_arg( 0 ,
1696	>	0 , &(args_info->rho_r_given),
1697	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1698	>	check_ambiguity, override, 0, 0,
1699	>	"rho_r", '-',
1700	>	additional_error))
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	>	{
1724	>
1725	>	if (args_info->staticProps_group_counter && override)
1726	>	reset_group_staticProps (args_info);
1727	>	args_info->staticProps_group_counter += 1;
1728	>
1729	>	if (update_arg( 0 ,
1730	>	0 , &(args_info->hullvol_given),
1731	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1732	>	check_ambiguity, override, 0, 0,
1733	>	"hullvol", '-',
1734	>	additional_error))
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.  */
1878	<	exit (EXIT_FAILURE);
1878	>	goto failure;
1879
1880		default:        /* bug: option not considered.  */
1881	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1881	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1882		abort ();
1883		} /* switch */
1884		} /* while */
1885
1886	<	if ( staticProps_group_counter != 1)
1886	>	if (args_info->staticProps_group_counter > 1)
1887		{
1888	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1889	<	missing_required_options = 1;
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
1892
1893	<	if (! args_info->input_given)
1893	>
1894	>	if (check_required)
1895		{
1896	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
462	<	missing_required_options = 1;
1896	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1897		}
464	–	if ( missing_required_options )
465	–	exit (EXIT_FAILURE);
1898
1899	+	cmdline_parser_release (&local_args_info);
1900	+
1901	+	if ( error )
1902	+	return (EXIT_FAILURE);
1903	+
1904		return 0;
1905	+
1906	+	failure:
1907	+
1908	+	cmdline_parser_release (&local_args_info);
1909	+	return (EXIT_FAILURE);
1910		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 544 by tim, Fri May 27 04:41:34 2005 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

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