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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1180 by chuckv, Mon Sep 17 20:05:51 2007 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.19.1
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -F StaticPropsCmd
4	>	gengetopt --file-name=StaticPropsCmd -u
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	–
12	–	#include <stdio.h>
13	–	#include <stdlib.h>
14	–	#include <string.h>
15	–
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		#include "getopt.h"
21
22		#include "StaticPropsCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --step=INT                process every n frame  (default=`1')",
36	+	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37	+	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38	+	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39	+	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40	+	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
41	+	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42	+	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
43	+	"      --sele1=selection script  select the first stuntdouble set",
44	+	"      --sele2=selection script  select the second stuntdouble set",
45	+	"      --sele3=selection script  select the third stuntdouble set",
46	+	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
47	+	"      --molname=STRING          molecule name",
48	+	"      --begin=INT               begin internal index",
49	+	"      --end=INT                 end internal index",
50	+	"      --radius=DOUBLE           nanoparticle radius",
51	+	"\n Group: staticProps\n   an option of this group is required",
52	+	"      --bo                      bond order parameter (--rcut must be specified)",
53	+	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
54	+	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
55	+	"  -g, --gofr                    g(r)",
56	+	"      --r_theta                 g(r, cos(theta))",
57	+	"      --r_omega                 g(r, cos(omega))",
58	+	"      --theta_omega             g(cos(theta), cos(omega))",
59	+	"      --gxyz                    g(x, y, z)",
60	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
61	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
62	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
63	+	"  -d, --density                 density plot",
64	+	"      --slab_density            slab density",
65	+	"      --hxy                     hxy",
66	+	"      --rho_r                   rho of R",
67	+	"      --hullvol                 hull volume of nanoparticle",
68	+	0
69	+	};
70	+
71	+	static
72	+	void clear_given (struct gengetopt_args_info *args_info);
73	+	static
74	+	void clear_args (struct gengetopt_args_info *args_info);
75	+
76	+	static int
77	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
78	+
79	+	static int
80	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
81	+
82	+	static char *
83	+	gengetopt_strdup (const char *s);
84	+
85	+	static
86	+	void clear_given (struct gengetopt_args_info *args_info)
87	+	{
88	+	args_info->help_given = 0 ;
89	+	args_info->version_given = 0 ;
90	+	args_info->input_given = 0 ;
91	+	args_info->output_given = 0 ;
92	+	args_info->step_given = 0 ;
93	+	args_info->nbins_given = 0 ;
94	+	args_info->nbins_x_given = 0 ;
95	+	args_info->nbins_y_given = 0 ;
96	+	args_info->nanglebins_given = 0 ;
97	+	args_info->length_given = 0 ;
98	+	args_info->rcut_given = 0 ;
99	+	args_info->zoffset_given = 0 ;
100	+	args_info->sele1_given = 0 ;
101	+	args_info->sele2_given = 0 ;
102	+	args_info->sele3_given = 0 ;
103	+	args_info->refsele_given = 0 ;
104	+	args_info->molname_given = 0 ;
105	+	args_info->begin_given = 0 ;
106	+	args_info->end_given = 0 ;
107	+	args_info->radius_given = 0 ;
108	+	args_info->bo_given = 0 ;
109	+	args_info->bor_given = 0 ;
110	+	args_info->bad_given = 0 ;
111	+	args_info->gofr_given = 0 ;
112	+	args_info->r_theta_given = 0 ;
113	+	args_info->r_omega_given = 0 ;
114	+	args_info->theta_omega_given = 0 ;
115	+	args_info->gxyz_given = 0 ;
116	+	args_info->p2_given = 0 ;
117	+	args_info->rp2_given = 0 ;
118	+	args_info->scd_given = 0 ;
119	+	args_info->density_given = 0 ;
120	+	args_info->slab_density_given = 0 ;
121	+	args_info->hxy_given = 0 ;
122	+	args_info->rho_r_given = 0 ;
123	+	args_info->hullvol_given = 0 ;
124	+	args_info->staticProps_group_counter = 0 ;
125	+	}
126	+
127	+	static
128	+	void clear_args (struct gengetopt_args_info *args_info)
129	+	{
130	+	args_info->input_arg = NULL;
131	+	args_info->input_orig = NULL;
132	+	args_info->output_arg = NULL;
133	+	args_info->output_orig = NULL;
134	+	args_info->step_arg = 1;
135	+	args_info->step_orig = NULL;
136	+	args_info->nbins_arg = 100;
137	+	args_info->nbins_orig = NULL;
138	+	args_info->nbins_x_arg = 100;
139	+	args_info->nbins_x_orig = NULL;
140	+	args_info->nbins_y_arg = 100;
141	+	args_info->nbins_y_orig = NULL;
142	+	args_info->nanglebins_arg = 50;
143	+	args_info->nanglebins_orig = NULL;
144	+	args_info->length_orig = NULL;
145	+	args_info->rcut_orig = NULL;
146	+	args_info->zoffset_arg = 0;
147	+	args_info->zoffset_orig = NULL;
148	+	args_info->sele1_arg = NULL;
149	+	args_info->sele1_orig = NULL;
150	+	args_info->sele2_arg = NULL;
151	+	args_info->sele2_orig = NULL;
152	+	args_info->sele3_arg = NULL;
153	+	args_info->sele3_orig = NULL;
154	+	args_info->refsele_arg = NULL;
155	+	args_info->refsele_orig = NULL;
156	+	args_info->molname_arg = NULL;
157	+	args_info->molname_orig = NULL;
158	+	args_info->begin_orig = NULL;
159	+	args_info->end_orig = NULL;
160	+	args_info->radius_orig = NULL;
161	+
162	+	}
163	+
164	+	static
165	+	void init_args_info(struct gengetopt_args_info *args_info)
166	+	{
167	+	args_info->help_help = gengetopt_args_info_help[0] ;
168	+	args_info->version_help = gengetopt_args_info_help[1] ;
169	+	args_info->input_help = gengetopt_args_info_help[2] ;
170	+	args_info->output_help = gengetopt_args_info_help[3] ;
171	+	args_info->step_help = gengetopt_args_info_help[4] ;
172	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
173	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
174	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
175	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
176	+	args_info->length_help = gengetopt_args_info_help[9] ;
177	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
178	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
179	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
180	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
181	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
182	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
183	+	args_info->molname_help = gengetopt_args_info_help[16] ;
184	+	args_info->begin_help = gengetopt_args_info_help[17] ;
185	+	args_info->end_help = gengetopt_args_info_help[18] ;
186	+	args_info->radius_help = gengetopt_args_info_help[19] ;
187	+	args_info->bo_help = gengetopt_args_info_help[20] ;
188	+	args_info->bor_help = gengetopt_args_info_help[21] ;
189	+	args_info->bad_help = gengetopt_args_info_help[22] ;
190	+	args_info->gofr_help = gengetopt_args_info_help[23] ;
191	+	args_info->r_theta_help = gengetopt_args_info_help[24] ;
192	+	args_info->r_omega_help = gengetopt_args_info_help[25] ;
193	+	args_info->theta_omega_help = gengetopt_args_info_help[26] ;
194	+	args_info->gxyz_help = gengetopt_args_info_help[27] ;
195	+	args_info->p2_help = gengetopt_args_info_help[28] ;
196	+	args_info->rp2_help = gengetopt_args_info_help[29] ;
197	+	args_info->scd_help = gengetopt_args_info_help[30] ;
198	+	args_info->density_help = gengetopt_args_info_help[31] ;
199	+	args_info->slab_density_help = gengetopt_args_info_help[32] ;
200	+	args_info->hxy_help = gengetopt_args_info_help[33] ;
201	+	args_info->rho_r_help = gengetopt_args_info_help[34] ;
202	+	args_info->hullvol_help = gengetopt_args_info_help[35] ;
203	+
204	+	}
205	+
206		void
207		cmdline_parser_print_version (void)
208		{
#	Line 31 | Line 212 | cmdline_parser_print_help (void)
212		void
213		cmdline_parser_print_help (void)
214		{
215	+	int i = 0;
216		cmdline_parser_print_version ();
217	<	printf("\n"
218	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
219	<	printf("\n");
220	<	printf("  -h, --help                      Print help and exit\n");
221	<	printf("  -V, --version                   Print version and exit\n");
222	<	printf("  -i, --input=filename            input dump file\n");
223	<	printf("  -o, --output=filename           output file name\n");
224	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
225	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
226	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
227	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
46	<	printf("      --sele1=selection script    select first stuntdouble set\n");
47	<	printf("      --sele2=selection script    select second stuntdouble set\n");
48	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
49	<	printf("\n");
50	<	printf(" Group: staticProps  an option of this group is required\n");
51	<	printf("      --gofr                      g(r)\n");
52	<	printf("      --r_theta                   g(r, cos(theta))\n");
53	<	printf("      --r_omega                   g(r, cos(omega))\n");
54	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
55	<	printf("      --gxyz                      g(x, y, z)\n");
217	>
218	>	if (strlen(gengetopt_args_info_purpose) > 0)
219	>	printf("\n%s\n", gengetopt_args_info_purpose);
220	>
221	>	printf("\n%s\n\n", gengetopt_args_info_usage);
222	>
223	>	if (strlen(gengetopt_args_info_description) > 0)
224	>	printf("%s\n", gengetopt_args_info_description);
225	>
226	>	while (gengetopt_args_info_help[i])
227	>	printf("%s\n", gengetopt_args_info_help[i++]);
228		}
229
230	+	void
231	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
232	+	{
233	+	clear_given (args_info);
234	+	clear_args (args_info);
235	+	init_args_info (args_info);
236
237	<	static char *gengetopt_strdup (const char *s);
237	>	args_info->inputs = NULL;
238	>	args_info->inputs_num = 0;
239	>	}
240	>
241	>	static void
242	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
243	>	{
244	>
245	>	unsigned int i;
246	>	if (args_info->input_arg)
247	>	{
248	>	free (args_info->input_arg); /* free previous argument */
249	>	args_info->input_arg = 0;
250	>	}
251	>	if (args_info->input_orig)
252	>	{
253	>	free (args_info->input_orig); /* free previous argument */
254	>	args_info->input_orig = 0;
255	>	}
256	>	if (args_info->output_arg)
257	>	{
258	>	free (args_info->output_arg); /* free previous argument */
259	>	args_info->output_arg = 0;
260	>	}
261	>	if (args_info->output_orig)
262	>	{
263	>	free (args_info->output_orig); /* free previous argument */
264	>	args_info->output_orig = 0;
265	>	}
266	>	if (args_info->step_orig)
267	>	{
268	>	free (args_info->step_orig); /* free previous argument */
269	>	args_info->step_orig = 0;
270	>	}
271	>	if (args_info->nbins_orig)
272	>	{
273	>	free (args_info->nbins_orig); /* free previous argument */
274	>	args_info->nbins_orig = 0;
275	>	}
276	>	if (args_info->nbins_x_orig)
277	>	{
278	>	free (args_info->nbins_x_orig); /* free previous argument */
279	>	args_info->nbins_x_orig = 0;
280	>	}
281	>	if (args_info->nbins_y_orig)
282	>	{
283	>	free (args_info->nbins_y_orig); /* free previous argument */
284	>	args_info->nbins_y_orig = 0;
285	>	}
286	>	if (args_info->nanglebins_orig)
287	>	{
288	>	free (args_info->nanglebins_orig); /* free previous argument */
289	>	args_info->nanglebins_orig = 0;
290	>	}
291	>	if (args_info->length_orig)
292	>	{
293	>	free (args_info->length_orig); /* free previous argument */
294	>	args_info->length_orig = 0;
295	>	}
296	>	if (args_info->rcut_orig)
297	>	{
298	>	free (args_info->rcut_orig); /* free previous argument */
299	>	args_info->rcut_orig = 0;
300	>	}
301	>	if (args_info->zoffset_orig)
302	>	{
303	>	free (args_info->zoffset_orig); /* free previous argument */
304	>	args_info->zoffset_orig = 0;
305	>	}
306	>	if (args_info->sele1_arg)
307	>	{
308	>	free (args_info->sele1_arg); /* free previous argument */
309	>	args_info->sele1_arg = 0;
310	>	}
311	>	if (args_info->sele1_orig)
312	>	{
313	>	free (args_info->sele1_orig); /* free previous argument */
314	>	args_info->sele1_orig = 0;
315	>	}
316	>	if (args_info->sele2_arg)
317	>	{
318	>	free (args_info->sele2_arg); /* free previous argument */
319	>	args_info->sele2_arg = 0;
320	>	}
321	>	if (args_info->sele2_orig)
322	>	{
323	>	free (args_info->sele2_orig); /* free previous argument */
324	>	args_info->sele2_orig = 0;
325	>	}
326	>	if (args_info->sele3_arg)
327	>	{
328	>	free (args_info->sele3_arg); /* free previous argument */
329	>	args_info->sele3_arg = 0;
330	>	}
331	>	if (args_info->sele3_orig)
332	>	{
333	>	free (args_info->sele3_orig); /* free previous argument */
334	>	args_info->sele3_orig = 0;
335	>	}
336	>	if (args_info->refsele_arg)
337	>	{
338	>	free (args_info->refsele_arg); /* free previous argument */
339	>	args_info->refsele_arg = 0;
340	>	}
341	>	if (args_info->refsele_orig)
342	>	{
343	>	free (args_info->refsele_orig); /* free previous argument */
344	>	args_info->refsele_orig = 0;
345	>	}
346	>	if (args_info->molname_arg)
347	>	{
348	>	free (args_info->molname_arg); /* free previous argument */
349	>	args_info->molname_arg = 0;
350	>	}
351	>	if (args_info->molname_orig)
352	>	{
353	>	free (args_info->molname_orig); /* free previous argument */
354	>	args_info->molname_orig = 0;
355	>	}
356	>	if (args_info->begin_orig)
357	>	{
358	>	free (args_info->begin_orig); /* free previous argument */
359	>	args_info->begin_orig = 0;
360	>	}
361	>	if (args_info->end_orig)
362	>	{
363	>	free (args_info->end_orig); /* free previous argument */
364	>	args_info->end_orig = 0;
365	>	}
366	>	if (args_info->radius_orig)
367	>	{
368	>	free (args_info->radius_orig); /* free previous argument */
369	>	args_info->radius_orig = 0;
370	>	}
371	>
372	>	for (i = 0; i < args_info->inputs_num; ++i)
373	>	free (args_info->inputs [i]);
374	>
375	>	if (args_info->inputs_num)
376	>	free (args_info->inputs);
377	>
378	>	clear_given (args_info);
379	>	}
380	>
381	>	int
382	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
383	>	{
384	>	FILE *outfile;
385	>	int i = 0;
386	>
387	>	outfile = fopen(filename, "w");
388	>
389	>	if (!outfile)
390	>	{
391	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
392	>	return EXIT_FAILURE;
393	>	}
394
395	+	if (args_info->help_given) {
396	+	fprintf(outfile, "%s\n", "help");
397	+	}
398	+	if (args_info->version_given) {
399	+	fprintf(outfile, "%s\n", "version");
400	+	}
401	+	if (args_info->input_given) {
402	+	if (args_info->input_orig) {
403	+	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
404	+	} else {
405	+	fprintf(outfile, "%s\n", "input");
406	+	}
407	+	}
408	+	if (args_info->output_given) {
409	+	if (args_info->output_orig) {
410	+	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
411	+	} else {
412	+	fprintf(outfile, "%s\n", "output");
413	+	}
414	+	}
415	+	if (args_info->step_given) {
416	+	if (args_info->step_orig) {
417	+	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
418	+	} else {
419	+	fprintf(outfile, "%s\n", "step");
420	+	}
421	+	}
422	+	if (args_info->nbins_given) {
423	+	if (args_info->nbins_orig) {
424	+	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
425	+	} else {
426	+	fprintf(outfile, "%s\n", "nbins");
427	+	}
428	+	}
429	+	if (args_info->nbins_x_given) {
430	+	if (args_info->nbins_x_orig) {
431	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
432	+	} else {
433	+	fprintf(outfile, "%s\n", "nbins_x");
434	+	}
435	+	}
436	+	if (args_info->nbins_y_given) {
437	+	if (args_info->nbins_y_orig) {
438	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
439	+	} else {
440	+	fprintf(outfile, "%s\n", "nbins_y");
441	+	}
442	+	}
443	+	if (args_info->nanglebins_given) {
444	+	if (args_info->nanglebins_orig) {
445	+	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
446	+	} else {
447	+	fprintf(outfile, "%s\n", "nanglebins");
448	+	}
449	+	}
450	+	if (args_info->length_given) {
451	+	if (args_info->length_orig) {
452	+	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
453	+	} else {
454	+	fprintf(outfile, "%s\n", "length");
455	+	}
456	+	}
457	+	if (args_info->rcut_given) {
458	+	if (args_info->rcut_orig) {
459	+	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
460	+	} else {
461	+	fprintf(outfile, "%s\n", "rcut");
462	+	}
463	+	}
464	+	if (args_info->zoffset_given) {
465	+	if (args_info->zoffset_orig) {
466	+	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
467	+	} else {
468	+	fprintf(outfile, "%s\n", "zoffset");
469	+	}
470	+	}
471	+	if (args_info->sele1_given) {
472	+	if (args_info->sele1_orig) {
473	+	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
474	+	} else {
475	+	fprintf(outfile, "%s\n", "sele1");
476	+	}
477	+	}
478	+	if (args_info->sele2_given) {
479	+	if (args_info->sele2_orig) {
480	+	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
481	+	} else {
482	+	fprintf(outfile, "%s\n", "sele2");
483	+	}
484	+	}
485	+	if (args_info->sele3_given) {
486	+	if (args_info->sele3_orig) {
487	+	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
488	+	} else {
489	+	fprintf(outfile, "%s\n", "sele3");
490	+	}
491	+	}
492	+	if (args_info->refsele_given) {
493	+	if (args_info->refsele_orig) {
494	+	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
495	+	} else {
496	+	fprintf(outfile, "%s\n", "refsele");
497	+	}
498	+	}
499	+	if (args_info->molname_given) {
500	+	if (args_info->molname_orig) {
501	+	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
502	+	} else {
503	+	fprintf(outfile, "%s\n", "molname");
504	+	}
505	+	}
506	+	if (args_info->begin_given) {
507	+	if (args_info->begin_orig) {
508	+	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
509	+	} else {
510	+	fprintf(outfile, "%s\n", "begin");
511	+	}
512	+	}
513	+	if (args_info->end_given) {
514	+	if (args_info->end_orig) {
515	+	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
516	+	} else {
517	+	fprintf(outfile, "%s\n", "end");
518	+	}
519	+	}
520	+	if (args_info->radius_given) {
521	+	if (args_info->radius_orig) {
522	+	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
523	+	} else {
524	+	fprintf(outfile, "%s\n", "radius");
525	+	}
526	+	}
527	+	if (args_info->bo_given) {
528	+	fprintf(outfile, "%s\n", "bo");
529	+	}
530	+	if (args_info->bor_given) {
531	+	fprintf(outfile, "%s\n", "bor");
532	+	}
533	+	if (args_info->bad_given) {
534	+	fprintf(outfile, "%s\n", "bad");
535	+	}
536	+	if (args_info->gofr_given) {
537	+	fprintf(outfile, "%s\n", "gofr");
538	+	}
539	+	if (args_info->r_theta_given) {
540	+	fprintf(outfile, "%s\n", "r_theta");
541	+	}
542	+	if (args_info->r_omega_given) {
543	+	fprintf(outfile, "%s\n", "r_omega");
544	+	}
545	+	if (args_info->theta_omega_given) {
546	+	fprintf(outfile, "%s\n", "theta_omega");
547	+	}
548	+	if (args_info->gxyz_given) {
549	+	fprintf(outfile, "%s\n", "gxyz");
550	+	}
551	+	if (args_info->p2_given) {
552	+	fprintf(outfile, "%s\n", "p2");
553	+	}
554	+	if (args_info->rp2_given) {
555	+	fprintf(outfile, "%s\n", "rp2");
556	+	}
557	+	if (args_info->scd_given) {
558	+	fprintf(outfile, "%s\n", "scd");
559	+	}
560	+	if (args_info->density_given) {
561	+	fprintf(outfile, "%s\n", "density");
562	+	}
563	+	if (args_info->slab_density_given) {
564	+	fprintf(outfile, "%s\n", "slab_density");
565	+	}
566	+	if (args_info->hxy_given) {
567	+	fprintf(outfile, "%s\n", "hxy");
568	+	}
569	+	if (args_info->rho_r_given) {
570	+	fprintf(outfile, "%s\n", "rho_r");
571	+	}
572	+	if (args_info->hullvol_given) {
573	+	fprintf(outfile, "%s\n", "hullvol");
574	+	}
575	+
576	+	fclose (outfile);
577	+
578	+	i = EXIT_SUCCESS;
579	+	return i;
580	+	}
581	+
582	+	void
583	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
584	+	{
585	+	cmdline_parser_release (args_info);
586	+	}
587	+
588	+
589		/* gengetopt_strdup() */
590		/* strdup.c replacement of strdup, which is not standard */
591		char *
592		gengetopt_strdup (const char *s)
593		{
594	<	char *result = (char*)malloc(strlen(s) + 1);
594	>	char *result = NULL;
595	>	if (!s)
596	>	return result;
597	>
598	>	result = (char*)malloc(strlen(s) + 1);
599		if (result == (char*)0)
600		return (char*)0;
601		strcpy(result, s);
602		return result;
603		}
604
605	<	int
606	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
605	>	static void
606	>	reset_group_staticProps(struct gengetopt_args_info *args_info);
607	>
608	>	static void
609	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
610		{
611	<	int c;        /* Character of the parsed option.  */
612	<	int missing_required_options = 0;
78	<	int staticProps_group_counter = 0;
611	>	if (! args_info->staticProps_group_counter)
612	>	return;
613
614	<
615	<	args_info->help_given = 0 ;
616	<	args_info->version_given = 0 ;
83	<	args_info->input_given = 0 ;
84	<	args_info->output_given = 0 ;
85	<	args_info->step_given = 0 ;
86	<	args_info->nrbins_given = 0 ;
87	<	args_info->nanglebins_given = 0 ;
88	<	args_info->length_given = 0 ;
89	<	args_info->sele1_given = 0 ;
90	<	args_info->sele2_given = 0 ;
91	<	args_info->refsele_given = 0 ;
614	>	args_info->bo_given = 0 ;
615	>	args_info->bor_given = 0 ;
616	>	args_info->bad_given = 0 ;
617		args_info->gofr_given = 0 ;
618		args_info->r_theta_given = 0 ;
619		args_info->r_omega_given = 0 ;
620		args_info->theta_omega_given = 0 ;
621		args_info->gxyz_given = 0 ;
622	<	#define clear_args() { \
623	<	args_info->input_arg = NULL; \
624	<	args_info->output_arg = NULL; \
625	<	args_info->step_arg = 1 ;\
626	<	args_info->nrbins_arg = 100 ;\
627	<	args_info->nanglebins_arg = 50 ;\
628	<	args_info->sele1_arg = NULL; \
629	<	args_info->sele2_arg = NULL; \
630	<	args_info->refsele_arg = NULL; \
622	>	args_info->p2_given = 0 ;
623	>	args_info->rp2_given = 0 ;
624	>	args_info->scd_given = 0 ;
625	>	args_info->density_given = 0 ;
626	>	args_info->slab_density_given = 0 ;
627	>	args_info->hxy_given = 0 ;
628	>	args_info->rho_r_given = 0 ;
629	>	args_info->hullvol_given = 0 ;
630	>
631	>	args_info->staticProps_group_counter = 0;
632		}
633
634	<	clear_args();
634	>	int
635	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
636	>	{
637	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
638	>	}
639
640	+	int
641	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
642	+	{
643	+	int result;
644	+
645	+	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
646	+
647	+	if (result == EXIT_FAILURE)
648	+	{
649	+	cmdline_parser_free (args_info);
650	+	exit (EXIT_FAILURE);
651	+	}
652	+
653	+	return result;
654	+	}
655	+
656	+	int
657	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
658	+	{
659	+	int result = EXIT_SUCCESS;
660	+
661	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
662	+	result = EXIT_FAILURE;
663	+
664	+	if (result == EXIT_FAILURE)
665	+	{
666	+	cmdline_parser_free (args_info);
667	+	exit (EXIT_FAILURE);
668	+	}
669	+
670	+	return result;
671	+	}
672	+
673	+	int
674	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
675	+	{
676	+	int error = 0;
677	+
678	+	/* checks for required options */
679	+	if (! args_info->input_given)
680	+	{
681	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
682	+	error = 1;
683	+	}
684	+
685	+	if (args_info->staticProps_group_counter == 0)
686	+	{
687	+	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 : ""));
688	+	error = 1;
689	+	}
690	+
691	+
692	+	/* checks for dependences among options */
693	+
694	+	return error;
695	+	}
696	+
697	+	int
698	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
699	+	{
700	+	int c;        /* Character of the parsed option.  */
701	+
702	+	int error = 0;
703	+	struct gengetopt_args_info local_args_info;
704	+
705	+	if (initialize)
706	+	cmdline_parser_init (args_info);
707	+
708	+	cmdline_parser_init (&local_args_info);
709	+
710		optarg = 0;
711	<	optind = 1;
711	>	optind = 0;
712		opterr = 1;
713		optopt = '?';
714
#	Line 123 | Line 723 | cmdline_parser (int argc, char * const *argv, struct g
723		{ "input",      1, NULL, 'i' },
724		{ "output",     1, NULL, 'o' },
725		{ "step",       1, NULL, 'n' },
726	<	{ "nrbins",     1, NULL, 'r' },
726	>	{ "nbins",      1, NULL, 'b' },
727	>	{ "nbins_x",    1, NULL, 'x' },
728	>	{ "nbins_y",    1, NULL, 'y' },
729		{ "nanglebins", 1, NULL, 'a' },
730	<	{ "length",     1, NULL, 'l' },
730	>	{ "length",     1, NULL, 0 },
731	>	{ "rcut",       1, NULL, 'c' },
732	>	{ "zoffset",    1, NULL, 'z' },
733		{ "sele1",      1, NULL, 0 },
734		{ "sele2",      1, NULL, 0 },
735	+	{ "sele3",      1, NULL, 0 },
736		{ "refsele",    1, NULL, 0 },
737	<	{ "gofr",       0, NULL, 0 },
737	>	{ "molname",    1, NULL, 0 },
738	>	{ "begin",      1, NULL, 0 },
739	>	{ "end",        1, NULL, 0 },
740	>	{ "radius",     1, NULL, 0 },
741	>	{ "bo", 0, NULL, 0 },
742	>	{ "bor",        0, NULL, 0 },
743	>	{ "bad",        0, NULL, 0 },
744	>	{ "gofr",       0, NULL, 'g' },
745		{ "r_theta",    0, NULL, 0 },
746		{ "r_omega",    0, NULL, 0 },
747		{ "theta_omega",        0, NULL, 0 },
748		{ "gxyz",       0, NULL, 0 },
749	+	{ "p2", 0, NULL, 'p' },
750	+	{ "rp2",        0, NULL, 0 },
751	+	{ "scd",        0, NULL, 's' },
752	+	{ "density",    0, NULL, 'd' },
753	+	{ "slab_density",       0, NULL, 0 },
754	+	{ "hxy",        0, NULL, 0 },
755	+	{ "rho_r",      0, NULL, 0 },
756	+	{ "hullvol",    0, NULL, 0 },
757		{ NULL, 0, NULL, 0 }
758		};
759
760		stop_char = 0;
761	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
761	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
762
763		if (c == -1) break;       /* Exit from `while (1)' loop.  */
764
765		switch (c)
766		{
767		case 'h':       /* Print help and exit.  */
148	–	clear_args ();
768		cmdline_parser_print_help ();
769	+	cmdline_parser_free (&local_args_info);
770		exit (EXIT_SUCCESS);
771
772		case 'V':       /* Print version and exit.  */
153	–	clear_args ();
773		cmdline_parser_print_version ();
774	+	cmdline_parser_free (&local_args_info);
775		exit (EXIT_SUCCESS);
776
777		case 'i':       /* input dump file.  */
778	<	if (args_info->input_given)
778	>	if (local_args_info.input_given)
779		{
780	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
781	<	clear_args ();
162	<	exit (EXIT_FAILURE);
780	>	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
781	>	goto failure;
782		}
783	+	if (args_info->input_given && ! override)
784	+	continue;
785	+	local_args_info.input_given = 1;
786		args_info->input_given = 1;
787	+	if (args_info->input_arg)
788	+	free (args_info->input_arg); /* free previous string */
789		args_info->input_arg = gengetopt_strdup (optarg);
790	+	if (args_info->input_orig)
791	+	free (args_info->input_orig); /* free previous string */
792	+	args_info->input_orig = gengetopt_strdup (optarg);
793		break;
794
795		case 'o':       /* output file name.  */
796	<	if (args_info->output_given)
796	>	if (local_args_info.output_given)
797		{
798	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
799	<	clear_args ();
173	<	exit (EXIT_FAILURE);
798	>	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
799	>	goto failure;
800		}
801	+	if (args_info->output_given && ! override)
802	+	continue;
803	+	local_args_info.output_given = 1;
804		args_info->output_given = 1;
805	+	if (args_info->output_arg)
806	+	free (args_info->output_arg); /* free previous string */
807		args_info->output_arg = gengetopt_strdup (optarg);
808	+	if (args_info->output_orig)
809	+	free (args_info->output_orig); /* free previous string */
810	+	args_info->output_orig = gengetopt_strdup (optarg);
811		break;
812
813		case 'n':       /* process every n frame.  */
814	<	if (args_info->step_given)
814	>	if (local_args_info.step_given)
815		{
816	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
817	<	clear_args ();
184	<	exit (EXIT_FAILURE);
816	>	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
817	>	goto failure;
818		}
819	+	if (args_info->step_given && ! override)
820	+	continue;
821	+	local_args_info.step_given = 1;
822		args_info->step_given = 1;
823	<	args_info->step_arg = strtol (optarg,&stop_char,0);
823	>	args_info->step_arg = strtol (optarg, &stop_char, 0);
824	>	if (!(stop_char && *stop_char == '\0')) {
825	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
826	>	goto failure;
827	>	}
828	>	if (args_info->step_orig)
829	>	free (args_info->step_orig); /* free previous string */
830	>	args_info->step_orig = gengetopt_strdup (optarg);
831		break;
832
833	<	case 'r':       /* number of bins for distance.  */
834	<	if (args_info->nrbins_given)
833	>	case 'b':       /* number of bins (general purpose).  */
834	>	if (local_args_info.nbins_given)
835		{
836	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
837	<	clear_args ();
195	<	exit (EXIT_FAILURE);
836	>	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
837	>	goto failure;
838		}
839	<	args_info->nrbins_given = 1;
840	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
839	>	if (args_info->nbins_given && ! override)
840	>	continue;
841	>	local_args_info.nbins_given = 1;
842	>	args_info->nbins_given = 1;
843	>	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
844	>	if (!(stop_char && *stop_char == '\0')) {
845	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
846	>	goto failure;
847	>	}
848	>	if (args_info->nbins_orig)
849	>	free (args_info->nbins_orig); /* free previous string */
850	>	args_info->nbins_orig = gengetopt_strdup (optarg);
851		break;
852
853	+	case 'x':       /* number of bins in x axis.  */
854	+	if (local_args_info.nbins_x_given)
855	+	{
856	+	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
857	+	goto failure;
858	+	}
859	+	if (args_info->nbins_x_given && ! override)
860	+	continue;
861	+	local_args_info.nbins_x_given = 1;
862	+	args_info->nbins_x_given = 1;
863	+	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
864	+	if (!(stop_char && *stop_char == '\0')) {
865	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
866	+	goto failure;
867	+	}
868	+	if (args_info->nbins_x_orig)
869	+	free (args_info->nbins_x_orig); /* free previous string */
870	+	args_info->nbins_x_orig = gengetopt_strdup (optarg);
871	+	break;
872	+
873	+	case 'y':       /* number of bins in y axis.  */
874	+	if (local_args_info.nbins_y_given)
875	+	{
876	+	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
877	+	goto failure;
878	+	}
879	+	if (args_info->nbins_y_given && ! override)
880	+	continue;
881	+	local_args_info.nbins_y_given = 1;
882	+	args_info->nbins_y_given = 1;
883	+	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
884	+	if (!(stop_char && *stop_char == '\0')) {
885	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
886	+	goto failure;
887	+	}
888	+	if (args_info->nbins_y_orig)
889	+	free (args_info->nbins_y_orig); /* free previous string */
890	+	args_info->nbins_y_orig = gengetopt_strdup (optarg);
891	+	break;
892	+
893		case 'a':       /* number of bins for cos(angle).  */
894	<	if (args_info->nanglebins_given)
894	>	if (local_args_info.nanglebins_given)
895		{
896	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
897	<	clear_args ();
206	<	exit (EXIT_FAILURE);
896	>	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
897	>	goto failure;
898		}
899	+	if (args_info->nanglebins_given && ! override)
900	+	continue;
901	+	local_args_info.nanglebins_given = 1;
902		args_info->nanglebins_given = 1;
903	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
903	>	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
904	>	if (!(stop_char && *stop_char == '\0')) {
905	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
906	>	goto failure;
907	>	}
908	>	if (args_info->nanglebins_orig)
909	>	free (args_info->nanglebins_orig); /* free previous string */
910	>	args_info->nanglebins_orig = gengetopt_strdup (optarg);
911		break;
912
913	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
914	<	if (args_info->length_given)
913	>	case 'c':       /* cutoff radius (rcut).  */
914	>	if (local_args_info.rcut_given)
915		{
916	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
917	<	clear_args ();
217	<	exit (EXIT_FAILURE);
916	>	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	>	goto failure;
918		}
919	<	args_info->length_given = 1;
920	<	args_info->length_arg = strtod (optarg, NULL);
919	>	if (args_info->rcut_given && ! override)
920	>	continue;
921	>	local_args_info.rcut_given = 1;
922	>	args_info->rcut_given = 1;
923	>	args_info->rcut_arg = strtod (optarg, &stop_char);
924	>	if (!(stop_char && *stop_char == '\0')) {
925	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
926	>	goto failure;
927	>	}
928	>	if (args_info->rcut_orig)
929	>	free (args_info->rcut_orig); /* free previous string */
930	>	args_info->rcut_orig = gengetopt_strdup (optarg);
931		break;
932
933	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
934	+	if (local_args_info.zoffset_given)
935	+	{
936	+	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
937	+	goto failure;
938	+	}
939	+	if (args_info->zoffset_given && ! override)
940	+	continue;
941	+	local_args_info.zoffset_given = 1;
942	+	args_info->zoffset_given = 1;
943	+	args_info->zoffset_arg = strtod (optarg, &stop_char);
944	+	if (!(stop_char && *stop_char == '\0')) {
945	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
946	+	goto failure;
947	+	}
948	+	if (args_info->zoffset_orig)
949	+	free (args_info->zoffset_orig); /* free previous string */
950	+	args_info->zoffset_orig = gengetopt_strdup (optarg);
951	+	break;
952
953	+	case 'g':       /* g(r).  */
954	+	if (local_args_info.gofr_given)
955	+	{
956	+	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
957	+	goto failure;
958	+	}
959	+	if (args_info->gofr_given && ! override)
960	+	continue;
961	+	local_args_info.gofr_given = 1;
962	+	args_info->gofr_given = 1;
963	+	if (args_info->staticProps_group_counter && override)
964	+	reset_group_staticProps (args_info);
965	+	args_info->staticProps_group_counter += 1;
966	+	break;
967	+
968	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
969	+	if (local_args_info.p2_given)
970	+	{
971	+	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
972	+	goto failure;
973	+	}
974	+	if (args_info->p2_given && ! override)
975	+	continue;
976	+	local_args_info.p2_given = 1;
977	+	args_info->p2_given = 1;
978	+	if (args_info->staticProps_group_counter && override)
979	+	reset_group_staticProps (args_info);
980	+	args_info->staticProps_group_counter += 1;
981	+	break;
982	+
983	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
984	+	if (local_args_info.scd_given)
985	+	{
986	+	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
987	+	goto failure;
988	+	}
989	+	if (args_info->scd_given && ! override)
990	+	continue;
991	+	local_args_info.scd_given = 1;
992	+	args_info->scd_given = 1;
993	+	if (args_info->staticProps_group_counter && override)
994	+	reset_group_staticProps (args_info);
995	+	args_info->staticProps_group_counter += 1;
996	+	break;
997	+
998	+	case 'd':       /* density plot.  */
999	+	if (local_args_info.density_given)
1000	+	{
1001	+	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1002	+	goto failure;
1003	+	}
1004	+	if (args_info->density_given && ! override)
1005	+	continue;
1006	+	local_args_info.density_given = 1;
1007	+	args_info->density_given = 1;
1008	+	if (args_info->staticProps_group_counter && override)
1009	+	reset_group_staticProps (args_info);
1010	+	args_info->staticProps_group_counter += 1;
1011	+	break;
1012	+
1013	+
1014		case 0: /* Long option with no short option */
1015	<	/* select first stuntdouble set.  */
1016	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1015	>	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1016	>	if (strcmp (long_options[option_index].name, "length") == 0)
1017		{
1018	<	if (args_info->sele1_given)
1018	>	if (local_args_info.length_given)
1019		{
1020	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1021	<	clear_args ();
232	<	exit (EXIT_FAILURE);
1020	>	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1021	>	goto failure;
1022		}
1023	+	if (args_info->length_given && ! override)
1024	+	continue;
1025	+	local_args_info.length_given = 1;
1026	+	args_info->length_given = 1;
1027	+	args_info->length_arg = strtod (optarg, &stop_char);
1028	+	if (!(stop_char && *stop_char == '\0')) {
1029	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1030	+	goto failure;
1031	+	}
1032	+	if (args_info->length_orig)
1033	+	free (args_info->length_orig); /* free previous string */
1034	+	args_info->length_orig = gengetopt_strdup (optarg);
1035	+	}
1036	+	/* select the first stuntdouble set.  */
1037	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1038	+	{
1039	+	if (local_args_info.sele1_given)
1040	+	{
1041	+	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1042	+	goto failure;
1043	+	}
1044	+	if (args_info->sele1_given && ! override)
1045	+	continue;
1046	+	local_args_info.sele1_given = 1;
1047		args_info->sele1_given = 1;
1048	+	if (args_info->sele1_arg)
1049	+	free (args_info->sele1_arg); /* free previous string */
1050		args_info->sele1_arg = gengetopt_strdup (optarg);
1051	<	break;
1051	>	if (args_info->sele1_orig)
1052	>	free (args_info->sele1_orig); /* free previous string */
1053	>	args_info->sele1_orig = gengetopt_strdup (optarg);
1054		}
1055	<
239	<	/* select second stuntdouble set.  */
1055	>	/* select the second stuntdouble set.  */
1056		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1057		{
1058	<	if (args_info->sele2_given)
1058	>	if (local_args_info.sele2_given)
1059		{
1060	<	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1061	<	clear_args ();
246	<	exit (EXIT_FAILURE);
1060	>	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1061	>	goto failure;
1062		}
1063	+	if (args_info->sele2_given && ! override)
1064	+	continue;
1065	+	local_args_info.sele2_given = 1;
1066		args_info->sele2_given = 1;
1067	+	if (args_info->sele2_arg)
1068	+	free (args_info->sele2_arg); /* free previous string */
1069		args_info->sele2_arg = gengetopt_strdup (optarg);
1070	<	break;
1070	>	if (args_info->sele2_orig)
1071	>	free (args_info->sele2_orig); /* free previous string */
1072	>	args_info->sele2_orig = gengetopt_strdup (optarg);
1073		}
1074	<
1074	>	/* select the third stuntdouble set.  */
1075	>	else if (strcmp (long_options[option_index].name, "sele3") == 0)
1076	>	{
1077	>	if (local_args_info.sele3_given)
1078	>	{
1079	>	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1080	>	goto failure;
1081	>	}
1082	>	if (args_info->sele3_given && ! override)
1083	>	continue;
1084	>	local_args_info.sele3_given = 1;
1085	>	args_info->sele3_given = 1;
1086	>	if (args_info->sele3_arg)
1087	>	free (args_info->sele3_arg); /* free previous string */
1088	>	args_info->sele3_arg = gengetopt_strdup (optarg);
1089	>	if (args_info->sele3_orig)
1090	>	free (args_info->sele3_orig); /* free previous string */
1091	>	args_info->sele3_orig = gengetopt_strdup (optarg);
1092	>	}
1093		/* select reference (use and only use with --gxyz).  */
1094		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1095		{
1096	<	if (args_info->refsele_given)
1096	>	if (local_args_info.refsele_given)
1097		{
1098	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1099	<	clear_args ();
260	<	exit (EXIT_FAILURE);
1098	>	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1099	>	goto failure;
1100		}
1101	+	if (args_info->refsele_given && ! override)
1102	+	continue;
1103	+	local_args_info.refsele_given = 1;
1104		args_info->refsele_given = 1;
1105	+	if (args_info->refsele_arg)
1106	+	free (args_info->refsele_arg); /* free previous string */
1107		args_info->refsele_arg = gengetopt_strdup (optarg);
1108	<	break;
1108	>	if (args_info->refsele_orig)
1109	>	free (args_info->refsele_orig); /* free previous string */
1110	>	args_info->refsele_orig = gengetopt_strdup (optarg);
1111		}
1112	<
1113	<	/* g(r).  */
268	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1112	>	/* molecule name.  */
1113	>	else if (strcmp (long_options[option_index].name, "molname") == 0)
1114		{
1115	<	if (args_info->gofr_given)
1115	>	if (local_args_info.molname_given)
1116		{
1117	<	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1118	<	clear_args ();
274	<	exit (EXIT_FAILURE);
1117	>	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1118	>	goto failure;
1119		}
1120	<	args_info->gofr_given = 1; staticProps_group_counter += 1;
1121	<
1120	>	if (args_info->molname_given && ! override)
1121	>	continue;
1122	>	local_args_info.molname_given = 1;
1123	>	args_info->molname_given = 1;
1124	>	if (args_info->molname_arg)
1125	>	free (args_info->molname_arg); /* free previous string */
1126	>	args_info->molname_arg = gengetopt_strdup (optarg);
1127	>	if (args_info->molname_orig)
1128	>	free (args_info->molname_orig); /* free previous string */
1129	>	args_info->molname_orig = gengetopt_strdup (optarg);
1130	>	}
1131	>	/* begin internal index.  */
1132	>	else if (strcmp (long_options[option_index].name, "begin") == 0)
1133	>	{
1134	>	if (local_args_info.begin_given)
1135	>	{
1136	>	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1137	>	goto failure;
1138	>	}
1139	>	if (args_info->begin_given && ! override)
1140	>	continue;
1141	>	local_args_info.begin_given = 1;
1142	>	args_info->begin_given = 1;
1143	>	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1144	>	if (!(stop_char && *stop_char == '\0')) {
1145	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1146	>	goto failure;
1147	>	}
1148	>	if (args_info->begin_orig)
1149	>	free (args_info->begin_orig); /* free previous string */
1150	>	args_info->begin_orig = gengetopt_strdup (optarg);
1151	>	}
1152	>	/* end internal index.  */
1153	>	else if (strcmp (long_options[option_index].name, "end") == 0)
1154	>	{
1155	>	if (local_args_info.end_given)
1156	>	{
1157	>	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1158	>	goto failure;
1159	>	}
1160	>	if (args_info->end_given && ! override)
1161	>	continue;
1162	>	local_args_info.end_given = 1;
1163	>	args_info->end_given = 1;
1164	>	args_info->end_arg = strtol (optarg, &stop_char, 0);
1165	>	if (!(stop_char && *stop_char == '\0')) {
1166	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1167	>	goto failure;
1168	>	}
1169	>	if (args_info->end_orig)
1170	>	free (args_info->end_orig); /* free previous string */
1171	>	args_info->end_orig = gengetopt_strdup (optarg);
1172	>	}
1173	>	/* nanoparticle radius.  */
1174	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1175	>	{
1176	>	if (local_args_info.radius_given)
1177	>	{
1178	>	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1179	>	goto failure;
1180	>	}
1181	>	if (args_info->radius_given && ! override)
1182	>	continue;
1183	>	local_args_info.radius_given = 1;
1184	>	args_info->radius_given = 1;
1185	>	args_info->radius_arg = strtod (optarg, &stop_char);
1186	>	if (!(stop_char && *stop_char == '\0')) {
1187	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1188	>	goto failure;
1189	>	}
1190	>	if (args_info->radius_orig)
1191	>	free (args_info->radius_orig); /* free previous string */
1192	>	args_info->radius_orig = gengetopt_strdup (optarg);
1193	>	}
1194	>	/* bond order parameter (--rcut must be specified).  */
1195	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1196	>	{
1197	>	if (local_args_info.bo_given)
1198	>	{
1199	>	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1200	>	goto failure;
1201	>	}
1202	>	if (args_info->bo_given && ! override)
1203	>	continue;
1204	>	local_args_info.bo_given = 1;
1205	>	args_info->bo_given = 1;
1206	>	if (args_info->staticProps_group_counter && override)
1207	>	reset_group_staticProps (args_info);
1208	>	args_info->staticProps_group_counter += 1;
1209		break;
1210		}
1211	<
1211	>	/* bond order parameter as a function of radius (--rcut must be specified).  */
1212	>	else if (strcmp (long_options[option_index].name, "bor") == 0)
1213	>	{
1214	>	if (local_args_info.bor_given)
1215	>	{
1216	>	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1217	>	goto failure;
1218	>	}
1219	>	if (args_info->bor_given && ! override)
1220	>	continue;
1221	>	local_args_info.bor_given = 1;
1222	>	args_info->bor_given = 1;
1223	>	if (args_info->staticProps_group_counter && override)
1224	>	reset_group_staticProps (args_info);
1225	>	args_info->staticProps_group_counter += 1;
1226	>	break;
1227	>	}
1228	>	/* N(theta) bond angle density within (--rcut must be specified).  */
1229	>	else if (strcmp (long_options[option_index].name, "bad") == 0)
1230	>	{
1231	>	if (local_args_info.bad_given)
1232	>	{
1233	>	fprintf (stderr, "%s: `--bad' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1234	>	goto failure;
1235	>	}
1236	>	if (args_info->bad_given && ! override)
1237	>	continue;
1238	>	local_args_info.bad_given = 1;
1239	>	args_info->bad_given = 1;
1240	>	if (args_info->staticProps_group_counter && override)
1241	>	reset_group_staticProps (args_info);
1242	>	args_info->staticProps_group_counter += 1;
1243	>	break;
1244	>	}
1245		/* g(r, cos(theta)).  */
1246		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1247		{
1248	<	if (args_info->r_theta_given)
1248	>	if (local_args_info.r_theta_given)
1249		{
1250	<	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1251	<	clear_args ();
288	<	exit (EXIT_FAILURE);
1250	>	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1251	>	goto failure;
1252		}
1253	<	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1254	<
1253	>	if (args_info->r_theta_given && ! override)
1254	>	continue;
1255	>	local_args_info.r_theta_given = 1;
1256	>	args_info->r_theta_given = 1;
1257	>	if (args_info->staticProps_group_counter && override)
1258	>	reset_group_staticProps (args_info);
1259	>	args_info->staticProps_group_counter += 1;
1260		break;
1261		}
294	–
1262		/* g(r, cos(omega)).  */
1263		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1264		{
1265	<	if (args_info->r_omega_given)
1265	>	if (local_args_info.r_omega_given)
1266		{
1267	<	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1268	<	clear_args ();
302	<	exit (EXIT_FAILURE);
1267	>	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1268	>	goto failure;
1269		}
1270	<	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1271	<
1270	>	if (args_info->r_omega_given && ! override)
1271	>	continue;
1272	>	local_args_info.r_omega_given = 1;
1273	>	args_info->r_omega_given = 1;
1274	>	if (args_info->staticProps_group_counter && override)
1275	>	reset_group_staticProps (args_info);
1276	>	args_info->staticProps_group_counter += 1;
1277		break;
1278		}
308	–
1279		/* g(cos(theta), cos(omega)).  */
1280		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1281		{
1282	<	if (args_info->theta_omega_given)
1282	>	if (local_args_info.theta_omega_given)
1283		{
1284	<	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1285	<	clear_args ();
316	<	exit (EXIT_FAILURE);
1284	>	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1285	>	goto failure;
1286		}
1287	<	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1288	<
1287	>	if (args_info->theta_omega_given && ! override)
1288	>	continue;
1289	>	local_args_info.theta_omega_given = 1;
1290	>	args_info->theta_omega_given = 1;
1291	>	if (args_info->staticProps_group_counter && override)
1292	>	reset_group_staticProps (args_info);
1293	>	args_info->staticProps_group_counter += 1;
1294		break;
1295		}
322	–
1296		/* g(x, y, z).  */
1297		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1298		{
1299	<	if (args_info->gxyz_given)
1299	>	if (local_args_info.gxyz_given)
1300		{
1301	<	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1302	<	clear_args ();
330	<	exit (EXIT_FAILURE);
1301	>	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1302	>	goto failure;
1303		}
1304	<	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1305	<
1304	>	if (args_info->gxyz_given && ! override)
1305	>	continue;
1306	>	local_args_info.gxyz_given = 1;
1307	>	args_info->gxyz_given = 1;
1308	>	if (args_info->staticProps_group_counter && override)
1309	>	reset_group_staticProps (args_info);
1310	>	args_info->staticProps_group_counter += 1;
1311		break;
1312		}
1313	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1314	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1315	+	{
1316	+	if (local_args_info.rp2_given)
1317	+	{
1318	+	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1319	+	goto failure;
1320	+	}
1321	+	if (args_info->rp2_given && ! override)
1322	+	continue;
1323	+	local_args_info.rp2_given = 1;
1324	+	args_info->rp2_given = 1;
1325	+	if (args_info->staticProps_group_counter && override)
1326	+	reset_group_staticProps (args_info);
1327	+	args_info->staticProps_group_counter += 1;
1328	+	break;
1329	+	}
1330	+	/* slab density.  */
1331	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1332	+	{
1333	+	if (local_args_info.slab_density_given)
1334	+	{
1335	+	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1336	+	goto failure;
1337	+	}
1338	+	if (args_info->slab_density_given && ! override)
1339	+	continue;
1340	+	local_args_info.slab_density_given = 1;
1341	+	args_info->slab_density_given = 1;
1342	+	if (args_info->staticProps_group_counter && override)
1343	+	reset_group_staticProps (args_info);
1344	+	args_info->staticProps_group_counter += 1;
1345	+	break;
1346	+	}
1347	+	/* hxy.  */
1348	+	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1349	+	{
1350	+	if (local_args_info.hxy_given)
1351	+	{
1352	+	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1353	+	goto failure;
1354	+	}
1355	+	if (args_info->hxy_given && ! override)
1356	+	continue;
1357	+	local_args_info.hxy_given = 1;
1358	+	args_info->hxy_given = 1;
1359	+	if (args_info->staticProps_group_counter && override)
1360	+	reset_group_staticProps (args_info);
1361	+	args_info->staticProps_group_counter += 1;
1362	+	break;
1363	+	}
1364	+	/* rho of R.  */
1365	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1366	+	{
1367	+	if (local_args_info.rho_r_given)
1368	+	{
1369	+	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1370	+	goto failure;
1371	+	}
1372	+	if (args_info->rho_r_given && ! override)
1373	+	continue;
1374	+	local_args_info.rho_r_given = 1;
1375	+	args_info->rho_r_given = 1;
1376	+	if (args_info->staticProps_group_counter && override)
1377	+	reset_group_staticProps (args_info);
1378	+	args_info->staticProps_group_counter += 1;
1379	+	break;
1380	+	}
1381	+	/* hull volume of nanoparticle.  */
1382	+	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1383	+	{
1384	+	if (local_args_info.hullvol_given)
1385	+	{
1386	+	fprintf (stderr, "%s: `--hullvol' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1387	+	goto failure;
1388	+	}
1389	+	if (args_info->hullvol_given && ! override)
1390	+	continue;
1391	+	local_args_info.hullvol_given = 1;
1392	+	args_info->hullvol_given = 1;
1393	+	if (args_info->staticProps_group_counter && override)
1394	+	reset_group_staticProps (args_info);
1395	+	args_info->staticProps_group_counter += 1;
1396	+	break;
1397	+	}
1398
1399	<
1399	>	break;
1400		case '?':       /* Invalid option.  */
1401		/* `getopt_long' already printed an error message.  */
1402	<	exit (EXIT_FAILURE);
1402	>	goto failure;
1403
1404		default:        /* bug: option not considered.  */
1405	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1405	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1406		abort ();
1407		} /* switch */
1408		} /* while */
1409
1410	<	if ( staticProps_group_counter != 1)
1410	>	if (args_info->staticProps_group_counter > 1)
1411		{
1412	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1413	<	missing_required_options = 1;
1412	>	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 : ""));
1413	>	error = 1;
1414		}
1415
1416
1417	<	if (! args_info->input_given)
1417	>
1418	>	if (check_required)
1419		{
1420	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
358	<	missing_required_options = 1;
1420	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1421		}
360	–	if ( missing_required_options )
361	–	exit (EXIT_FAILURE);
1422
1423	+	cmdline_parser_release (&local_args_info);
1424	+
1425	+	if ( error )
1426	+	return (EXIT_FAILURE);
1427	+
1428	+	if (optind < argc)
1429	+	{
1430	+	int i = 0 ;
1431	+	int found_prog_name = 0;
1432	+	/* whether program name, i.e., argv[0], is in the remaining args
1433	+	(this may happen with some implementations of getopt,
1434	+	but surely not with the one included by gengetopt) */
1435	+
1436	+	i = optind;
1437	+	while (i < argc)
1438	+	if (argv[i++] == argv[0]) {
1439	+	found_prog_name = 1;
1440	+	break;
1441	+	}
1442	+	i = 0;
1443	+
1444	+	args_info->inputs_num = argc - optind - found_prog_name;
1445	+	args_info->inputs =
1446	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1447	+	while (optind < argc)
1448	+	if (argv[optind++] != argv[0])
1449	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1450	+	}
1451	+
1452		return 0;
1453	+
1454	+	failure:
1455	+
1456	+	cmdline_parser_release (&local_args_info);
1457	+	return (EXIT_FAILURE);
1458		}

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