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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 840 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
Revision 1128 by chuckv, Wed Apr 11 23:27:20 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/program/gengetopt-2.11/src/gengetopt -F StaticPropsCmd
4	>	gengetopt -i StaticProps.ggo -F 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	+	"  -g, --gofr                    g(r)",
55	+	"      --r_theta                 g(r, cos(theta))",
56	+	"      --r_omega                 g(r, cos(omega))",
57	+	"      --theta_omega             g(cos(theta), cos(omega))",
58	+	"      --gxyz                    g(x, y, z)",
59	+	"  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
60	+	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
61	+	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
62	+	"  -d, --density                 density plot",
63	+	"      --slab_density            slab density",
64	+	"      --hxy                     hxy",
65	+	"      --rho_r                   rho of R",
66	+	0
67	+	};
68	+
69	+	static
70	+	void clear_given (struct gengetopt_args_info *args_info);
71	+	static
72	+	void clear_args (struct gengetopt_args_info *args_info);
73	+
74	+	static int
75	+	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);
76	+
77	+	static int
78	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
79	+
80	+	static char *
81	+	gengetopt_strdup (const char *s);
82	+
83	+	static
84	+	void clear_given (struct gengetopt_args_info *args_info)
85	+	{
86	+	args_info->help_given = 0 ;
87	+	args_info->version_given = 0 ;
88	+	args_info->input_given = 0 ;
89	+	args_info->output_given = 0 ;
90	+	args_info->step_given = 0 ;
91	+	args_info->nbins_given = 0 ;
92	+	args_info->nbins_x_given = 0 ;
93	+	args_info->nbins_y_given = 0 ;
94	+	args_info->nanglebins_given = 0 ;
95	+	args_info->length_given = 0 ;
96	+	args_info->rcut_given = 0 ;
97	+	args_info->zoffset_given = 0 ;
98	+	args_info->sele1_given = 0 ;
99	+	args_info->sele2_given = 0 ;
100	+	args_info->sele3_given = 0 ;
101	+	args_info->refsele_given = 0 ;
102	+	args_info->molname_given = 0 ;
103	+	args_info->begin_given = 0 ;
104	+	args_info->end_given = 0 ;
105	+	args_info->radius_given = 0 ;
106	+	args_info->bo_given = 0 ;
107	+	args_info->bor_given = 0 ;
108	+	args_info->gofr_given = 0 ;
109	+	args_info->r_theta_given = 0 ;
110	+	args_info->r_omega_given = 0 ;
111	+	args_info->theta_omega_given = 0 ;
112	+	args_info->gxyz_given = 0 ;
113	+	args_info->p2_given = 0 ;
114	+	args_info->rp2_given = 0 ;
115	+	args_info->scd_given = 0 ;
116	+	args_info->density_given = 0 ;
117	+	args_info->slab_density_given = 0 ;
118	+	args_info->hxy_given = 0 ;
119	+	args_info->rho_r_given = 0 ;
120	+	args_info->staticProps_group_counter = 0 ;
121	+	}
122	+
123	+	static
124	+	void clear_args (struct gengetopt_args_info *args_info)
125	+	{
126	+	args_info->input_arg = NULL;
127	+	args_info->input_orig = NULL;
128	+	args_info->output_arg = NULL;
129	+	args_info->output_orig = NULL;
130	+	args_info->step_arg = 1;
131	+	args_info->step_orig = NULL;
132	+	args_info->nbins_arg = 100;
133	+	args_info->nbins_orig = NULL;
134	+	args_info->nbins_x_arg = 100;
135	+	args_info->nbins_x_orig = NULL;
136	+	args_info->nbins_y_arg = 100;
137	+	args_info->nbins_y_orig = NULL;
138	+	args_info->nanglebins_arg = 50;
139	+	args_info->nanglebins_orig = NULL;
140	+	args_info->length_orig = NULL;
141	+	args_info->rcut_orig = NULL;
142	+	args_info->zoffset_arg = 0;
143	+	args_info->zoffset_orig = NULL;
144	+	args_info->sele1_arg = NULL;
145	+	args_info->sele1_orig = NULL;
146	+	args_info->sele2_arg = NULL;
147	+	args_info->sele2_orig = NULL;
148	+	args_info->sele3_arg = NULL;
149	+	args_info->sele3_orig = NULL;
150	+	args_info->refsele_arg = NULL;
151	+	args_info->refsele_orig = NULL;
152	+	args_info->molname_arg = NULL;
153	+	args_info->molname_orig = NULL;
154	+	args_info->begin_orig = NULL;
155	+	args_info->end_orig = NULL;
156	+	args_info->radius_orig = NULL;
157	+
158	+	}
159	+
160	+	static
161	+	void init_args_info(struct gengetopt_args_info *args_info)
162	+	{
163	+	args_info->help_help = gengetopt_args_info_help[0] ;
164	+	args_info->version_help = gengetopt_args_info_help[1] ;
165	+	args_info->input_help = gengetopt_args_info_help[2] ;
166	+	args_info->output_help = gengetopt_args_info_help[3] ;
167	+	args_info->step_help = gengetopt_args_info_help[4] ;
168	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
169	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
170	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
171	+	args_info->nanglebins_help = gengetopt_args_info_help[8] ;
172	+	args_info->length_help = gengetopt_args_info_help[9] ;
173	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
174	+	args_info->zoffset_help = gengetopt_args_info_help[11] ;
175	+	args_info->sele1_help = gengetopt_args_info_help[12] ;
176	+	args_info->sele2_help = gengetopt_args_info_help[13] ;
177	+	args_info->sele3_help = gengetopt_args_info_help[14] ;
178	+	args_info->refsele_help = gengetopt_args_info_help[15] ;
179	+	args_info->molname_help = gengetopt_args_info_help[16] ;
180	+	args_info->begin_help = gengetopt_args_info_help[17] ;
181	+	args_info->end_help = gengetopt_args_info_help[18] ;
182	+	args_info->radius_help = gengetopt_args_info_help[19] ;
183	+	args_info->bo_help = gengetopt_args_info_help[20] ;
184	+	args_info->bor_help = gengetopt_args_info_help[21] ;
185	+	args_info->gofr_help = gengetopt_args_info_help[22] ;
186	+	args_info->r_theta_help = gengetopt_args_info_help[23] ;
187	+	args_info->r_omega_help = gengetopt_args_info_help[24] ;
188	+	args_info->theta_omega_help = gengetopt_args_info_help[25] ;
189	+	args_info->gxyz_help = gengetopt_args_info_help[26] ;
190	+	args_info->p2_help = gengetopt_args_info_help[27] ;
191	+	args_info->rp2_help = gengetopt_args_info_help[28] ;
192	+	args_info->scd_help = gengetopt_args_info_help[29] ;
193	+	args_info->density_help = gengetopt_args_info_help[30] ;
194	+	args_info->slab_density_help = gengetopt_args_info_help[31] ;
195	+	args_info->hxy_help = gengetopt_args_info_help[32] ;
196	+	args_info->rho_r_help = gengetopt_args_info_help[33] ;
197	+
198	+	}
199	+
200		void
201		cmdline_parser_print_version (void)
202		{
#	Line 31 | Line 206 | cmdline_parser_print_help (void)
206		void
207		cmdline_parser_print_help (void)
208		{
209	+	int i = 0;
210		cmdline_parser_print_version ();
211	<	printf("\n"
212	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
213	<	printf("\n");
214	<	printf("  -h, --help                      Print help and exit\n");
215	<	printf("  -V, --version                   Print version and exit\n");
216	<	printf("  -i, --input=filename            input dump file\n");
217	<	printf("  -o, --output=filename           output file name\n");
218	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
219	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
220	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
221	<	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	<	printf("      --density                   density plot (--sele1 must be specified)\n");
63	<	printf("      --slab_density              slab density (--sele1 must be specified)\n");
211	>
212	>	if (strlen(gengetopt_args_info_purpose) > 0)
213	>	printf("\n%s\n", gengetopt_args_info_purpose);
214	>
215	>	printf("\n%s\n\n", gengetopt_args_info_usage);
216	>
217	>	if (strlen(gengetopt_args_info_description) > 0)
218	>	printf("%s\n", gengetopt_args_info_description);
219	>
220	>	while (gengetopt_args_info_help[i])
221	>	printf("%s\n", gengetopt_args_info_help[i++]);
222		}
223
224	+	void
225	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
226	+	{
227	+	clear_given (args_info);
228	+	clear_args (args_info);
229	+	init_args_info (args_info);
230
231	<	static char *gengetopt_strdup (const char *s);
231	>	args_info->inputs = NULL;
232	>	args_info->inputs_num = 0;
233	>	}
234	>
235	>	static void
236	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
237	>	{
238	>
239	>	unsigned int i;
240	>	if (args_info->input_arg)
241	>	{
242	>	free (args_info->input_arg); /* free previous argument */
243	>	args_info->input_arg = 0;
244	>	}
245	>	if (args_info->input_orig)
246	>	{
247	>	free (args_info->input_orig); /* free previous argument */
248	>	args_info->input_orig = 0;
249	>	}
250	>	if (args_info->output_arg)
251	>	{
252	>	free (args_info->output_arg); /* free previous argument */
253	>	args_info->output_arg = 0;
254	>	}
255	>	if (args_info->output_orig)
256	>	{
257	>	free (args_info->output_orig); /* free previous argument */
258	>	args_info->output_orig = 0;
259	>	}
260	>	if (args_info->step_orig)
261	>	{
262	>	free (args_info->step_orig); /* free previous argument */
263	>	args_info->step_orig = 0;
264	>	}
265	>	if (args_info->nbins_orig)
266	>	{
267	>	free (args_info->nbins_orig); /* free previous argument */
268	>	args_info->nbins_orig = 0;
269	>	}
270	>	if (args_info->nbins_x_orig)
271	>	{
272	>	free (args_info->nbins_x_orig); /* free previous argument */
273	>	args_info->nbins_x_orig = 0;
274	>	}
275	>	if (args_info->nbins_y_orig)
276	>	{
277	>	free (args_info->nbins_y_orig); /* free previous argument */
278	>	args_info->nbins_y_orig = 0;
279	>	}
280	>	if (args_info->nanglebins_orig)
281	>	{
282	>	free (args_info->nanglebins_orig); /* free previous argument */
283	>	args_info->nanglebins_orig = 0;
284	>	}
285	>	if (args_info->length_orig)
286	>	{
287	>	free (args_info->length_orig); /* free previous argument */
288	>	args_info->length_orig = 0;
289	>	}
290	>	if (args_info->rcut_orig)
291	>	{
292	>	free (args_info->rcut_orig); /* free previous argument */
293	>	args_info->rcut_orig = 0;
294	>	}
295	>	if (args_info->zoffset_orig)
296	>	{
297	>	free (args_info->zoffset_orig); /* free previous argument */
298	>	args_info->zoffset_orig = 0;
299	>	}
300	>	if (args_info->sele1_arg)
301	>	{
302	>	free (args_info->sele1_arg); /* free previous argument */
303	>	args_info->sele1_arg = 0;
304	>	}
305	>	if (args_info->sele1_orig)
306	>	{
307	>	free (args_info->sele1_orig); /* free previous argument */
308	>	args_info->sele1_orig = 0;
309	>	}
310	>	if (args_info->sele2_arg)
311	>	{
312	>	free (args_info->sele2_arg); /* free previous argument */
313	>	args_info->sele2_arg = 0;
314	>	}
315	>	if (args_info->sele2_orig)
316	>	{
317	>	free (args_info->sele2_orig); /* free previous argument */
318	>	args_info->sele2_orig = 0;
319	>	}
320	>	if (args_info->sele3_arg)
321	>	{
322	>	free (args_info->sele3_arg); /* free previous argument */
323	>	args_info->sele3_arg = 0;
324	>	}
325	>	if (args_info->sele3_orig)
326	>	{
327	>	free (args_info->sele3_orig); /* free previous argument */
328	>	args_info->sele3_orig = 0;
329	>	}
330	>	if (args_info->refsele_arg)
331	>	{
332	>	free (args_info->refsele_arg); /* free previous argument */
333	>	args_info->refsele_arg = 0;
334	>	}
335	>	if (args_info->refsele_orig)
336	>	{
337	>	free (args_info->refsele_orig); /* free previous argument */
338	>	args_info->refsele_orig = 0;
339	>	}
340	>	if (args_info->molname_arg)
341	>	{
342	>	free (args_info->molname_arg); /* free previous argument */
343	>	args_info->molname_arg = 0;
344	>	}
345	>	if (args_info->molname_orig)
346	>	{
347	>	free (args_info->molname_orig); /* free previous argument */
348	>	args_info->molname_orig = 0;
349	>	}
350	>	if (args_info->begin_orig)
351	>	{
352	>	free (args_info->begin_orig); /* free previous argument */
353	>	args_info->begin_orig = 0;
354	>	}
355	>	if (args_info->end_orig)
356	>	{
357	>	free (args_info->end_orig); /* free previous argument */
358	>	args_info->end_orig = 0;
359	>	}
360	>	if (args_info->radius_orig)
361	>	{
362	>	free (args_info->radius_orig); /* free previous argument */
363	>	args_info->radius_orig = 0;
364	>	}
365	>
366	>	for (i = 0; i < args_info->inputs_num; ++i)
367	>	free (args_info->inputs [i]);
368	>
369	>	if (args_info->inputs_num)
370	>	free (args_info->inputs);
371	>
372	>	clear_given (args_info);
373	>	}
374	>
375	>	int
376	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
377	>	{
378	>	FILE *outfile;
379	>	int i = 0;
380	>
381	>	outfile = fopen(filename, "w");
382	>
383	>	if (!outfile)
384	>	{
385	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
386	>	return EXIT_FAILURE;
387	>	}
388
389	+	if (args_info->help_given) {
390	+	fprintf(outfile, "%s\n", "help");
391	+	}
392	+	if (args_info->version_given) {
393	+	fprintf(outfile, "%s\n", "version");
394	+	}
395	+	if (args_info->input_given) {
396	+	if (args_info->input_orig) {
397	+	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
398	+	} else {
399	+	fprintf(outfile, "%s\n", "input");
400	+	}
401	+	}
402	+	if (args_info->output_given) {
403	+	if (args_info->output_orig) {
404	+	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
405	+	} else {
406	+	fprintf(outfile, "%s\n", "output");
407	+	}
408	+	}
409	+	if (args_info->step_given) {
410	+	if (args_info->step_orig) {
411	+	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
412	+	} else {
413	+	fprintf(outfile, "%s\n", "step");
414	+	}
415	+	}
416	+	if (args_info->nbins_given) {
417	+	if (args_info->nbins_orig) {
418	+	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
419	+	} else {
420	+	fprintf(outfile, "%s\n", "nbins");
421	+	}
422	+	}
423	+	if (args_info->nbins_x_given) {
424	+	if (args_info->nbins_x_orig) {
425	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
426	+	} else {
427	+	fprintf(outfile, "%s\n", "nbins_x");
428	+	}
429	+	}
430	+	if (args_info->nbins_y_given) {
431	+	if (args_info->nbins_y_orig) {
432	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
433	+	} else {
434	+	fprintf(outfile, "%s\n", "nbins_y");
435	+	}
436	+	}
437	+	if (args_info->nanglebins_given) {
438	+	if (args_info->nanglebins_orig) {
439	+	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
440	+	} else {
441	+	fprintf(outfile, "%s\n", "nanglebins");
442	+	}
443	+	}
444	+	if (args_info->length_given) {
445	+	if (args_info->length_orig) {
446	+	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
447	+	} else {
448	+	fprintf(outfile, "%s\n", "length");
449	+	}
450	+	}
451	+	if (args_info->rcut_given) {
452	+	if (args_info->rcut_orig) {
453	+	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
454	+	} else {
455	+	fprintf(outfile, "%s\n", "rcut");
456	+	}
457	+	}
458	+	if (args_info->zoffset_given) {
459	+	if (args_info->zoffset_orig) {
460	+	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
461	+	} else {
462	+	fprintf(outfile, "%s\n", "zoffset");
463	+	}
464	+	}
465	+	if (args_info->sele1_given) {
466	+	if (args_info->sele1_orig) {
467	+	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
468	+	} else {
469	+	fprintf(outfile, "%s\n", "sele1");
470	+	}
471	+	}
472	+	if (args_info->sele2_given) {
473	+	if (args_info->sele2_orig) {
474	+	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
475	+	} else {
476	+	fprintf(outfile, "%s\n", "sele2");
477	+	}
478	+	}
479	+	if (args_info->sele3_given) {
480	+	if (args_info->sele3_orig) {
481	+	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
482	+	} else {
483	+	fprintf(outfile, "%s\n", "sele3");
484	+	}
485	+	}
486	+	if (args_info->refsele_given) {
487	+	if (args_info->refsele_orig) {
488	+	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
489	+	} else {
490	+	fprintf(outfile, "%s\n", "refsele");
491	+	}
492	+	}
493	+	if (args_info->molname_given) {
494	+	if (args_info->molname_orig) {
495	+	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
496	+	} else {
497	+	fprintf(outfile, "%s\n", "molname");
498	+	}
499	+	}
500	+	if (args_info->begin_given) {
501	+	if (args_info->begin_orig) {
502	+	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
503	+	} else {
504	+	fprintf(outfile, "%s\n", "begin");
505	+	}
506	+	}
507	+	if (args_info->end_given) {
508	+	if (args_info->end_orig) {
509	+	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
510	+	} else {
511	+	fprintf(outfile, "%s\n", "end");
512	+	}
513	+	}
514	+	if (args_info->radius_given) {
515	+	if (args_info->radius_orig) {
516	+	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
517	+	} else {
518	+	fprintf(outfile, "%s\n", "radius");
519	+	}
520	+	}
521	+	if (args_info->bo_given) {
522	+	fprintf(outfile, "%s\n", "bo");
523	+	}
524	+	if (args_info->bor_given) {
525	+	fprintf(outfile, "%s\n", "bor");
526	+	}
527	+	if (args_info->gofr_given) {
528	+	fprintf(outfile, "%s\n", "gofr");
529	+	}
530	+	if (args_info->r_theta_given) {
531	+	fprintf(outfile, "%s\n", "r_theta");
532	+	}
533	+	if (args_info->r_omega_given) {
534	+	fprintf(outfile, "%s\n", "r_omega");
535	+	}
536	+	if (args_info->theta_omega_given) {
537	+	fprintf(outfile, "%s\n", "theta_omega");
538	+	}
539	+	if (args_info->gxyz_given) {
540	+	fprintf(outfile, "%s\n", "gxyz");
541	+	}
542	+	if (args_info->p2_given) {
543	+	fprintf(outfile, "%s\n", "p2");
544	+	}
545	+	if (args_info->rp2_given) {
546	+	fprintf(outfile, "%s\n", "rp2");
547	+	}
548	+	if (args_info->scd_given) {
549	+	fprintf(outfile, "%s\n", "scd");
550	+	}
551	+	if (args_info->density_given) {
552	+	fprintf(outfile, "%s\n", "density");
553	+	}
554	+	if (args_info->slab_density_given) {
555	+	fprintf(outfile, "%s\n", "slab_density");
556	+	}
557	+	if (args_info->hxy_given) {
558	+	fprintf(outfile, "%s\n", "hxy");
559	+	}
560	+	if (args_info->rho_r_given) {
561	+	fprintf(outfile, "%s\n", "rho_r");
562	+	}
563	+
564	+	fclose (outfile);
565	+
566	+	i = EXIT_SUCCESS;
567	+	return i;
568	+	}
569	+
570	+	void
571	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
572	+	{
573	+	cmdline_parser_release (args_info);
574	+	}
575	+
576	+
577		/* gengetopt_strdup() */
578		/* strdup.c replacement of strdup, which is not standard */
579		char *
580		gengetopt_strdup (const char *s)
581		{
582	<	char *result = (char*)malloc(strlen(s) + 1);
582	>	char *result = NULL;
583	>	if (!s)
584	>	return result;
585	>
586	>	result = (char*)malloc(strlen(s) + 1);
587		if (result == (char*)0)
588		return (char*)0;
589		strcpy(result, s);
590		return result;
591		}
592
593	<	int
594	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
593	>	static void
594	>	reset_group_staticProps(struct gengetopt_args_info *args_info);
595	>
596	>	static void
597	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
598		{
599	<	int c;        /* Character of the parsed option.  */
600	<	int missing_required_options = 0;
86	<	int staticProps_group_counter = 0;
599	>	if (! args_info->staticProps_group_counter)
600	>	return;
601
602	<
603	<	args_info->help_given = 0 ;
90	<	args_info->version_given = 0 ;
91	<	args_info->input_given = 0 ;
92	<	args_info->output_given = 0 ;
93	<	args_info->step_given = 0 ;
94	<	args_info->nrbins_given = 0 ;
95	<	args_info->nanglebins_given = 0 ;
96	<	args_info->length_given = 0 ;
97	<	args_info->sele1_given = 0 ;
98	<	args_info->sele2_given = 0 ;
99	<	args_info->sele3_given = 0 ;
100	<	args_info->refsele_given = 0 ;
101	<	args_info->molname_given = 0 ;
102	<	args_info->begin_given = 0 ;
103	<	args_info->end_given = 0 ;
602	>	args_info->bo_given = 0 ;
603	>	args_info->bor_given = 0 ;
604		args_info->gofr_given = 0 ;
605		args_info->r_theta_given = 0 ;
606		args_info->r_omega_given = 0 ;
607		args_info->theta_omega_given = 0 ;
608		args_info->gxyz_given = 0 ;
609		args_info->p2_given = 0 ;
610	+	args_info->rp2_given = 0 ;
611		args_info->scd_given = 0 ;
612		args_info->density_given = 0 ;
613		args_info->slab_density_given = 0 ;
614	<	#define clear_args() { \
615	<	args_info->input_arg = NULL; \
616	<	args_info->output_arg = NULL; \
617	<	args_info->step_arg = 1 ;\
117	<	args_info->nrbins_arg = 100 ;\
118	<	args_info->nanglebins_arg = 50 ;\
119	<	args_info->sele1_arg = NULL; \
120	<	args_info->sele2_arg = NULL; \
121	<	args_info->sele3_arg = NULL; \
122	<	args_info->refsele_arg = NULL; \
123	<	args_info->molname_arg = NULL; \
614	>	args_info->hxy_given = 0 ;
615	>	args_info->rho_r_given = 0 ;
616	>
617	>	args_info->staticProps_group_counter = 0;
618		}
619
620	<	clear_args();
620	>	int
621	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
622	>	{
623	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
624	>	}
625
626	+	int
627	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
628	+	{
629	+	int result;
630	+
631	+	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
632	+
633	+	if (result == EXIT_FAILURE)
634	+	{
635	+	cmdline_parser_free (args_info);
636	+	exit (EXIT_FAILURE);
637	+	}
638	+
639	+	return result;
640	+	}
641	+
642	+	int
643	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
644	+	{
645	+	int result = EXIT_SUCCESS;
646	+
647	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
648	+	result = EXIT_FAILURE;
649	+
650	+	if (result == EXIT_FAILURE)
651	+	{
652	+	cmdline_parser_free (args_info);
653	+	exit (EXIT_FAILURE);
654	+	}
655	+
656	+	return result;
657	+	}
658	+
659	+	int
660	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
661	+	{
662	+	int error = 0;
663	+
664	+	/* checks for required options */
665	+	if (! args_info->input_given)
666	+	{
667	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
668	+	error = 1;
669	+	}
670	+
671	+	if (args_info->staticProps_group_counter == 0)
672	+	{
673	+	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 : ""));
674	+	error = 1;
675	+	}
676	+
677	+
678	+	/* checks for dependences among options */
679	+
680	+	return error;
681	+	}
682	+
683	+	int
684	+	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)
685	+	{
686	+	int c;        /* Character of the parsed option.  */
687	+
688	+	int error = 0;
689	+	struct gengetopt_args_info local_args_info;
690	+
691	+	if (initialize)
692	+	cmdline_parser_init (args_info);
693	+
694	+	cmdline_parser_init (&local_args_info);
695	+
696		optarg = 0;
697	<	optind = 1;
697	>	optind = 0;
698		opterr = 1;
699		optopt = '?';
700
#	Line 141 | Line 709 | cmdline_parser (int argc, char * const *argv, struct g
709		{ "input",      1, NULL, 'i' },
710		{ "output",     1, NULL, 'o' },
711		{ "step",       1, NULL, 'n' },
712	<	{ "nrbins",     1, NULL, 'r' },
712	>	{ "nbins",      1, NULL, 'b' },
713	>	{ "nbins_x",    1, NULL, 'x' },
714	>	{ "nbins_y",    1, NULL, 'y' },
715		{ "nanglebins", 1, NULL, 'a' },
716	<	{ "length",     1, NULL, 'l' },
716	>	{ "length",     1, NULL, 0 },
717	>	{ "rcut",       1, NULL, 'c' },
718	>	{ "zoffset",    1, NULL, 'z' },
719		{ "sele1",      1, NULL, 0 },
720		{ "sele2",      1, NULL, 0 },
721		{ "sele3",      1, NULL, 0 },
#	Line 151 | Line 723 | cmdline_parser (int argc, char * const *argv, struct g
723		{ "molname",    1, NULL, 0 },
724		{ "begin",      1, NULL, 0 },
725		{ "end",        1, NULL, 0 },
726	<	{ "gofr",       0, NULL, 0 },
726	>	{ "radius",     1, NULL, 0 },
727	>	{ "bo", 0, NULL, 0 },
728	>	{ "bor",        0, NULL, 0 },
729	>	{ "gofr",       0, NULL, 'g' },
730		{ "r_theta",    0, NULL, 0 },
731		{ "r_omega",    0, NULL, 0 },
732		{ "theta_omega",        0, NULL, 0 },
733		{ "gxyz",       0, NULL, 0 },
734	<	{ "p2", 0, NULL, 0 },
735	<	{ "scd",        0, NULL, 0 },
736	<	{ "density",    0, NULL, 0 },
734	>	{ "p2", 0, NULL, 'p' },
735	>	{ "rp2",        0, NULL, 0 },
736	>	{ "scd",        0, NULL, 's' },
737	>	{ "density",    0, NULL, 'd' },
738		{ "slab_density",       0, NULL, 0 },
739	+	{ "hxy",        0, NULL, 0 },
740	+	{ "rho_r",      0, NULL, 0 },
741		{ NULL, 0, NULL, 0 }
742		};
743
744		stop_char = 0;
745	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
745	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
746
747		if (c == -1) break;       /* Exit from `while (1)' loop.  */
748
749		switch (c)
750		{
751		case 'h':       /* Print help and exit.  */
174	–	clear_args ();
752		cmdline_parser_print_help ();
753	+	cmdline_parser_free (&local_args_info);
754		exit (EXIT_SUCCESS);
755
756		case 'V':       /* Print version and exit.  */
179	–	clear_args ();
757		cmdline_parser_print_version ();
758	+	cmdline_parser_free (&local_args_info);
759		exit (EXIT_SUCCESS);
760
761		case 'i':       /* input dump file.  */
762	<	if (args_info->input_given)
762	>	if (local_args_info.input_given)
763		{
764	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
765	<	clear_args ();
188	<	exit (EXIT_FAILURE);
764	>	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
765	>	goto failure;
766		}
767	+	if (args_info->input_given && ! override)
768	+	continue;
769	+	local_args_info.input_given = 1;
770		args_info->input_given = 1;
771	+	if (args_info->input_arg)
772	+	free (args_info->input_arg); /* free previous string */
773		args_info->input_arg = gengetopt_strdup (optarg);
774	+	if (args_info->input_orig)
775	+	free (args_info->input_orig); /* free previous string */
776	+	args_info->input_orig = gengetopt_strdup (optarg);
777		break;
778
779		case 'o':       /* output file name.  */
780	<	if (args_info->output_given)
780	>	if (local_args_info.output_given)
781		{
782	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
783	<	clear_args ();
199	<	exit (EXIT_FAILURE);
782	>	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
783	>	goto failure;
784		}
785	+	if (args_info->output_given && ! override)
786	+	continue;
787	+	local_args_info.output_given = 1;
788		args_info->output_given = 1;
789	+	if (args_info->output_arg)
790	+	free (args_info->output_arg); /* free previous string */
791		args_info->output_arg = gengetopt_strdup (optarg);
792	+	if (args_info->output_orig)
793	+	free (args_info->output_orig); /* free previous string */
794	+	args_info->output_orig = gengetopt_strdup (optarg);
795		break;
796
797		case 'n':       /* process every n frame.  */
798	<	if (args_info->step_given)
798	>	if (local_args_info.step_given)
799		{
800	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
801	<	clear_args ();
210	<	exit (EXIT_FAILURE);
800	>	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
801	>	goto failure;
802		}
803	+	if (args_info->step_given && ! override)
804	+	continue;
805	+	local_args_info.step_given = 1;
806		args_info->step_given = 1;
807	<	args_info->step_arg = strtol (optarg,&stop_char,0);
807	>	args_info->step_arg = strtol (optarg, &stop_char, 0);
808	>	if (!(stop_char && *stop_char == '\0')) {
809	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
810	>	goto failure;
811	>	}
812	>	if (args_info->step_orig)
813	>	free (args_info->step_orig); /* free previous string */
814	>	args_info->step_orig = gengetopt_strdup (optarg);
815		break;
816
817	<	case 'r':       /* number of bins for distance.  */
818	<	if (args_info->nrbins_given)
817	>	case 'b':       /* number of bins (general purpose).  */
818	>	if (local_args_info.nbins_given)
819		{
820	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
821	<	clear_args ();
221	<	exit (EXIT_FAILURE);
820	>	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
821	>	goto failure;
822		}
823	<	args_info->nrbins_given = 1;
824	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
823	>	if (args_info->nbins_given && ! override)
824	>	continue;
825	>	local_args_info.nbins_given = 1;
826	>	args_info->nbins_given = 1;
827	>	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
828	>	if (!(stop_char && *stop_char == '\0')) {
829	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
830	>	goto failure;
831	>	}
832	>	if (args_info->nbins_orig)
833	>	free (args_info->nbins_orig); /* free previous string */
834	>	args_info->nbins_orig = gengetopt_strdup (optarg);
835		break;
836
837	+	case 'x':       /* number of bins in x axis.  */
838	+	if (local_args_info.nbins_x_given)
839	+	{
840	+	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
841	+	goto failure;
842	+	}
843	+	if (args_info->nbins_x_given && ! override)
844	+	continue;
845	+	local_args_info.nbins_x_given = 1;
846	+	args_info->nbins_x_given = 1;
847	+	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
848	+	if (!(stop_char && *stop_char == '\0')) {
849	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
850	+	goto failure;
851	+	}
852	+	if (args_info->nbins_x_orig)
853	+	free (args_info->nbins_x_orig); /* free previous string */
854	+	args_info->nbins_x_orig = gengetopt_strdup (optarg);
855	+	break;
856	+
857	+	case 'y':       /* number of bins in y axis.  */
858	+	if (local_args_info.nbins_y_given)
859	+	{
860	+	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
861	+	goto failure;
862	+	}
863	+	if (args_info->nbins_y_given && ! override)
864	+	continue;
865	+	local_args_info.nbins_y_given = 1;
866	+	args_info->nbins_y_given = 1;
867	+	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
868	+	if (!(stop_char && *stop_char == '\0')) {
869	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
870	+	goto failure;
871	+	}
872	+	if (args_info->nbins_y_orig)
873	+	free (args_info->nbins_y_orig); /* free previous string */
874	+	args_info->nbins_y_orig = gengetopt_strdup (optarg);
875	+	break;
876	+
877		case 'a':       /* number of bins for cos(angle).  */
878	<	if (args_info->nanglebins_given)
878	>	if (local_args_info.nanglebins_given)
879		{
880	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
881	<	clear_args ();
232	<	exit (EXIT_FAILURE);
880	>	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
881	>	goto failure;
882		}
883	+	if (args_info->nanglebins_given && ! override)
884	+	continue;
885	+	local_args_info.nanglebins_given = 1;
886		args_info->nanglebins_given = 1;
887	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
887	>	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
888	>	if (!(stop_char && *stop_char == '\0')) {
889	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
890	>	goto failure;
891	>	}
892	>	if (args_info->nanglebins_orig)
893	>	free (args_info->nanglebins_orig); /* free previous string */
894	>	args_info->nanglebins_orig = gengetopt_strdup (optarg);
895		break;
896
897	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
898	<	if (args_info->length_given)
897	>	case 'c':       /* cutoff radius (rcut).  */
898	>	if (local_args_info.rcut_given)
899		{
900	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
901	<	clear_args ();
243	<	exit (EXIT_FAILURE);
900	>	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
901	>	goto failure;
902		}
903	<	args_info->length_given = 1;
904	<	args_info->length_arg = strtod (optarg, NULL);
903	>	if (args_info->rcut_given && ! override)
904	>	continue;
905	>	local_args_info.rcut_given = 1;
906	>	args_info->rcut_given = 1;
907	>	args_info->rcut_arg = strtod (optarg, &stop_char);
908	>	if (!(stop_char && *stop_char == '\0')) {
909	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
910	>	goto failure;
911	>	}
912	>	if (args_info->rcut_orig)
913	>	free (args_info->rcut_orig); /* free previous string */
914	>	args_info->rcut_orig = gengetopt_strdup (optarg);
915		break;
916
917	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
918	+	if (local_args_info.zoffset_given)
919	+	{
920	+	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
921	+	goto failure;
922	+	}
923	+	if (args_info->zoffset_given && ! override)
924	+	continue;
925	+	local_args_info.zoffset_given = 1;
926	+	args_info->zoffset_given = 1;
927	+	args_info->zoffset_arg = strtod (optarg, &stop_char);
928	+	if (!(stop_char && *stop_char == '\0')) {
929	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
930	+	goto failure;
931	+	}
932	+	if (args_info->zoffset_orig)
933	+	free (args_info->zoffset_orig); /* free previous string */
934	+	args_info->zoffset_orig = gengetopt_strdup (optarg);
935	+	break;
936
937	+	case 'g':       /* g(r).  */
938	+	if (local_args_info.gofr_given)
939	+	{
940	+	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
941	+	goto failure;
942	+	}
943	+	if (args_info->gofr_given && ! override)
944	+	continue;
945	+	local_args_info.gofr_given = 1;
946	+	args_info->gofr_given = 1;
947	+	if (args_info->staticProps_group_counter && override)
948	+	reset_group_staticProps (args_info);
949	+	args_info->staticProps_group_counter += 1;
950	+	break;
951	+
952	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
953	+	if (local_args_info.p2_given)
954	+	{
955	+	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
956	+	goto failure;
957	+	}
958	+	if (args_info->p2_given && ! override)
959	+	continue;
960	+	local_args_info.p2_given = 1;
961	+	args_info->p2_given = 1;
962	+	if (args_info->staticProps_group_counter && override)
963	+	reset_group_staticProps (args_info);
964	+	args_info->staticProps_group_counter += 1;
965	+	break;
966	+
967	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
968	+	if (local_args_info.scd_given)
969	+	{
970	+	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971	+	goto failure;
972	+	}
973	+	if (args_info->scd_given && ! override)
974	+	continue;
975	+	local_args_info.scd_given = 1;
976	+	args_info->scd_given = 1;
977	+	if (args_info->staticProps_group_counter && override)
978	+	reset_group_staticProps (args_info);
979	+	args_info->staticProps_group_counter += 1;
980	+	break;
981	+
982	+	case 'd':       /* density plot.  */
983	+	if (local_args_info.density_given)
984	+	{
985	+	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
986	+	goto failure;
987	+	}
988	+	if (args_info->density_given && ! override)
989	+	continue;
990	+	local_args_info.density_given = 1;
991	+	args_info->density_given = 1;
992	+	if (args_info->staticProps_group_counter && override)
993	+	reset_group_staticProps (args_info);
994	+	args_info->staticProps_group_counter += 1;
995	+	break;
996	+
997	+
998		case 0: /* Long option with no short option */
999	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1000	+	if (strcmp (long_options[option_index].name, "length") == 0)
1001	+	{
1002	+	if (local_args_info.length_given)
1003	+	{
1004	+	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1005	+	goto failure;
1006	+	}
1007	+	if (args_info->length_given && ! override)
1008	+	continue;
1009	+	local_args_info.length_given = 1;
1010	+	args_info->length_given = 1;
1011	+	args_info->length_arg = strtod (optarg, &stop_char);
1012	+	if (!(stop_char && *stop_char == '\0')) {
1013	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1014	+	goto failure;
1015	+	}
1016	+	if (args_info->length_orig)
1017	+	free (args_info->length_orig); /* free previous string */
1018	+	args_info->length_orig = gengetopt_strdup (optarg);
1019	+	}
1020		/* select the first stuntdouble set.  */
1021	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1021	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1022		{
1023	<	if (args_info->sele1_given)
1023	>	if (local_args_info.sele1_given)
1024		{
1025	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1026	<	clear_args ();
258	<	exit (EXIT_FAILURE);
1025	>	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1026	>	goto failure;
1027		}
1028	+	if (args_info->sele1_given && ! override)
1029	+	continue;
1030	+	local_args_info.sele1_given = 1;
1031		args_info->sele1_given = 1;
1032	+	if (args_info->sele1_arg)
1033	+	free (args_info->sele1_arg); /* free previous string */
1034		args_info->sele1_arg = gengetopt_strdup (optarg);
1035	<	break;
1035	>	if (args_info->sele1_orig)
1036	>	free (args_info->sele1_orig); /* free previous string */
1037	>	args_info->sele1_orig = gengetopt_strdup (optarg);
1038		}
264	–
1039		/* select the second stuntdouble set.  */
1040		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1041		{
1042	<	if (args_info->sele2_given)
1042	>	if (local_args_info.sele2_given)
1043		{
1044	<	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1045	<	clear_args ();
272	<	exit (EXIT_FAILURE);
1044	>	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1045	>	goto failure;
1046		}
1047	+	if (args_info->sele2_given && ! override)
1048	+	continue;
1049	+	local_args_info.sele2_given = 1;
1050		args_info->sele2_given = 1;
1051	+	if (args_info->sele2_arg)
1052	+	free (args_info->sele2_arg); /* free previous string */
1053		args_info->sele2_arg = gengetopt_strdup (optarg);
1054	<	break;
1054	>	if (args_info->sele2_orig)
1055	>	free (args_info->sele2_orig); /* free previous string */
1056	>	args_info->sele2_orig = gengetopt_strdup (optarg);
1057		}
278	–
1058		/* select the third stuntdouble set.  */
1059		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1060		{
1061	<	if (args_info->sele3_given)
1061	>	if (local_args_info.sele3_given)
1062		{
1063	<	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1064	<	clear_args ();
286	<	exit (EXIT_FAILURE);
1063	>	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1064	>	goto failure;
1065		}
1066	+	if (args_info->sele3_given && ! override)
1067	+	continue;
1068	+	local_args_info.sele3_given = 1;
1069		args_info->sele3_given = 1;
1070	+	if (args_info->sele3_arg)
1071	+	free (args_info->sele3_arg); /* free previous string */
1072		args_info->sele3_arg = gengetopt_strdup (optarg);
1073	<	break;
1073	>	if (args_info->sele3_orig)
1074	>	free (args_info->sele3_orig); /* free previous string */
1075	>	args_info->sele3_orig = gengetopt_strdup (optarg);
1076		}
292	–
1077		/* select reference (use and only use with --gxyz).  */
1078		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1079		{
1080	<	if (args_info->refsele_given)
1080	>	if (local_args_info.refsele_given)
1081		{
1082	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1083	<	clear_args ();
300	<	exit (EXIT_FAILURE);
1082	>	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1083	>	goto failure;
1084		}
1085	+	if (args_info->refsele_given && ! override)
1086	+	continue;
1087	+	local_args_info.refsele_given = 1;
1088		args_info->refsele_given = 1;
1089	+	if (args_info->refsele_arg)
1090	+	free (args_info->refsele_arg); /* free previous string */
1091		args_info->refsele_arg = gengetopt_strdup (optarg);
1092	<	break;
1092	>	if (args_info->refsele_orig)
1093	>	free (args_info->refsele_orig); /* free previous string */
1094	>	args_info->refsele_orig = gengetopt_strdup (optarg);
1095		}
306	–
1096		/* molecule name.  */
1097		else if (strcmp (long_options[option_index].name, "molname") == 0)
1098		{
1099	<	if (args_info->molname_given)
1099	>	if (local_args_info.molname_given)
1100		{
1101	<	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1102	<	clear_args ();
314	<	exit (EXIT_FAILURE);
1101	>	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1102	>	goto failure;
1103		}
1104	+	if (args_info->molname_given && ! override)
1105	+	continue;
1106	+	local_args_info.molname_given = 1;
1107		args_info->molname_given = 1;
1108	+	if (args_info->molname_arg)
1109	+	free (args_info->molname_arg); /* free previous string */
1110		args_info->molname_arg = gengetopt_strdup (optarg);
1111	<	break;
1111	>	if (args_info->molname_orig)
1112	>	free (args_info->molname_orig); /* free previous string */
1113	>	args_info->molname_orig = gengetopt_strdup (optarg);
1114		}
1115	<
321	<	/* begin interanl index.  */
1115	>	/* begin internal index.  */
1116		else if (strcmp (long_options[option_index].name, "begin") == 0)
1117		{
1118	<	if (args_info->begin_given)
1118	>	if (local_args_info.begin_given)
1119		{
1120	<	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1121	<	clear_args ();
328	<	exit (EXIT_FAILURE);
1120	>	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1121	>	goto failure;
1122		}
1123	+	if (args_info->begin_given && ! override)
1124	+	continue;
1125	+	local_args_info.begin_given = 1;
1126		args_info->begin_given = 1;
1127	<	args_info->begin_arg = strtol (optarg,&stop_char,0);
1128	<	break;
1127	>	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1128	>	if (!(stop_char && *stop_char == '\0')) {
1129	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1130	>	goto failure;
1131	>	}
1132	>	if (args_info->begin_orig)
1133	>	free (args_info->begin_orig); /* free previous string */
1134	>	args_info->begin_orig = gengetopt_strdup (optarg);
1135		}
334	–
1136		/* end internal index.  */
1137		else if (strcmp (long_options[option_index].name, "end") == 0)
1138		{
1139	<	if (args_info->end_given)
1139	>	if (local_args_info.end_given)
1140		{
1141	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1142	<	clear_args ();
342	<	exit (EXIT_FAILURE);
1141	>	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1142	>	goto failure;
1143		}
1144	+	if (args_info->end_given && ! override)
1145	+	continue;
1146	+	local_args_info.end_given = 1;
1147		args_info->end_given = 1;
1148	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1148	>	args_info->end_arg = strtol (optarg, &stop_char, 0);
1149	>	if (!(stop_char && *stop_char == '\0')) {
1150	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1151	>	goto failure;
1152	>	}
1153	>	if (args_info->end_orig)
1154	>	free (args_info->end_orig); /* free previous string */
1155	>	args_info->end_orig = gengetopt_strdup (optarg);
1156	>	}
1157	>	/* nanoparticle radius.  */
1158	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1159	>	{
1160	>	if (local_args_info.radius_given)
1161	>	{
1162	>	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1163	>	goto failure;
1164	>	}
1165	>	if (args_info->radius_given && ! override)
1166	>	continue;
1167	>	local_args_info.radius_given = 1;
1168	>	args_info->radius_given = 1;
1169	>	args_info->radius_arg = strtod (optarg, &stop_char);
1170	>	if (!(stop_char && *stop_char == '\0')) {
1171	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1172	>	goto failure;
1173	>	}
1174	>	if (args_info->radius_orig)
1175	>	free (args_info->radius_orig); /* free previous string */
1176	>	args_info->radius_orig = gengetopt_strdup (optarg);
1177	>	}
1178	>	/* bond order parameter (--rcut must be specified).  */
1179	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1180	>	{
1181	>	if (local_args_info.bo_given)
1182	>	{
1183	>	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1184	>	goto failure;
1185	>	}
1186	>	if (args_info->bo_given && ! override)
1187	>	continue;
1188	>	local_args_info.bo_given = 1;
1189	>	args_info->bo_given = 1;
1190	>	if (args_info->staticProps_group_counter && override)
1191	>	reset_group_staticProps (args_info);
1192	>	args_info->staticProps_group_counter += 1;
1193		break;
1194		}
1195	<
1196	<	/* g(r).  */
350	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1195	>	/* bond order parameter as a function of radius (--rcut must be specified).  */
1196	>	else if (strcmp (long_options[option_index].name, "bor") == 0)
1197		{
1198	<	if (args_info->gofr_given)
1198	>	if (local_args_info.bor_given)
1199		{
1200	<	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1201	<	clear_args ();
356	<	exit (EXIT_FAILURE);
1200	>	fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1201	>	goto failure;
1202		}
1203	<	args_info->gofr_given = 1; staticProps_group_counter += 1;
1204	<
1203	>	if (args_info->bor_given && ! override)
1204	>	continue;
1205	>	local_args_info.bor_given = 1;
1206	>	args_info->bor_given = 1;
1207	>	if (args_info->staticProps_group_counter && override)
1208	>	reset_group_staticProps (args_info);
1209	>	args_info->staticProps_group_counter += 1;
1210		break;
1211		}
362	–
1212		/* g(r, cos(theta)).  */
1213		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1214		{
1215	<	if (args_info->r_theta_given)
1215	>	if (local_args_info.r_theta_given)
1216		{
1217	<	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1218	<	clear_args ();
370	<	exit (EXIT_FAILURE);
1217	>	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1218	>	goto failure;
1219		}
1220	<	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1221	<
1220	>	if (args_info->r_theta_given && ! override)
1221	>	continue;
1222	>	local_args_info.r_theta_given = 1;
1223	>	args_info->r_theta_given = 1;
1224	>	if (args_info->staticProps_group_counter && override)
1225	>	reset_group_staticProps (args_info);
1226	>	args_info->staticProps_group_counter += 1;
1227		break;
1228		}
376	–
1229		/* g(r, cos(omega)).  */
1230		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1231		{
1232	<	if (args_info->r_omega_given)
1232	>	if (local_args_info.r_omega_given)
1233		{
1234	<	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1235	<	clear_args ();
384	<	exit (EXIT_FAILURE);
1234	>	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1235	>	goto failure;
1236		}
1237	<	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1238	<
1237	>	if (args_info->r_omega_given && ! override)
1238	>	continue;
1239	>	local_args_info.r_omega_given = 1;
1240	>	args_info->r_omega_given = 1;
1241	>	if (args_info->staticProps_group_counter && override)
1242	>	reset_group_staticProps (args_info);
1243	>	args_info->staticProps_group_counter += 1;
1244		break;
1245		}
390	–
1246		/* g(cos(theta), cos(omega)).  */
1247		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1248		{
1249	<	if (args_info->theta_omega_given)
1249	>	if (local_args_info.theta_omega_given)
1250		{
1251	<	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1252	<	clear_args ();
398	<	exit (EXIT_FAILURE);
1251	>	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1252	>	goto failure;
1253		}
1254	<	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1255	<
1254	>	if (args_info->theta_omega_given && ! override)
1255	>	continue;
1256	>	local_args_info.theta_omega_given = 1;
1257	>	args_info->theta_omega_given = 1;
1258	>	if (args_info->staticProps_group_counter && override)
1259	>	reset_group_staticProps (args_info);
1260	>	args_info->staticProps_group_counter += 1;
1261		break;
1262		}
404	–
1263		/* g(x, y, z).  */
1264		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1265		{
1266	<	if (args_info->gxyz_given)
1266	>	if (local_args_info.gxyz_given)
1267		{
1268	<	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1269	<	clear_args ();
412	<	exit (EXIT_FAILURE);
1268	>	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1269	>	goto failure;
1270		}
1271	<	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1272	<
1271	>	if (args_info->gxyz_given && ! override)
1272	>	continue;
1273	>	local_args_info.gxyz_given = 1;
1274	>	args_info->gxyz_given = 1;
1275	>	if (args_info->staticProps_group_counter && override)
1276	>	reset_group_staticProps (args_info);
1277	>	args_info->staticProps_group_counter += 1;
1278		break;
1279		}
1280	<
1281	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
420	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1280	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1281	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1282		{
1283	<	if (args_info->p2_given)
1283	>	if (local_args_info.rp2_given)
1284		{
1285	<	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1286	<	clear_args ();
426	<	exit (EXIT_FAILURE);
1285	>	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1286	>	goto failure;
1287		}
1288	<	args_info->p2_given = 1; staticProps_group_counter += 1;
1289	<
1288	>	if (args_info->rp2_given && ! override)
1289	>	continue;
1290	>	local_args_info.rp2_given = 1;
1291	>	args_info->rp2_given = 1;
1292	>	if (args_info->staticProps_group_counter && override)
1293	>	reset_group_staticProps (args_info);
1294	>	args_info->staticProps_group_counter += 1;
1295		break;
1296		}
1297	<
1298	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
434	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1297	>	/* slab density.  */
1298	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1299		{
1300	<	if (args_info->scd_given)
1300	>	if (local_args_info.slab_density_given)
1301		{
1302	<	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1303	<	clear_args ();
440	<	exit (EXIT_FAILURE);
1302	>	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1303	>	goto failure;
1304		}
1305	<	args_info->scd_given = 1; staticProps_group_counter += 1;
1306	<
1305	>	if (args_info->slab_density_given && ! override)
1306	>	continue;
1307	>	local_args_info.slab_density_given = 1;
1308	>	args_info->slab_density_given = 1;
1309	>	if (args_info->staticProps_group_counter && override)
1310	>	reset_group_staticProps (args_info);
1311	>	args_info->staticProps_group_counter += 1;
1312		break;
1313		}
1314	<
1315	<	/* density plot (--sele1 must be specified).  */
448	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1314	>	/* hxy.  */
1315	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1316		{
1317	<	if (args_info->density_given)
1317	>	if (local_args_info.hxy_given)
1318		{
1319	<	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1320	<	clear_args ();
454	<	exit (EXIT_FAILURE);
1319	>	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1320	>	goto failure;
1321		}
1322	<	args_info->density_given = 1; staticProps_group_counter += 1;
1323	<
1322	>	if (args_info->hxy_given && ! override)
1323	>	continue;
1324	>	local_args_info.hxy_given = 1;
1325	>	args_info->hxy_given = 1;
1326	>	if (args_info->staticProps_group_counter && override)
1327	>	reset_group_staticProps (args_info);
1328	>	args_info->staticProps_group_counter += 1;
1329		break;
1330		}
1331	<
1332	<	/* slab density (--sele1 must be specified).  */
462	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1331	>	/* rho of R.  */
1332	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1333		{
1334	<	if (args_info->slab_density_given)
1334	>	if (local_args_info.rho_r_given)
1335		{
1336	<	fprintf (stderr, "%s: `--slab_density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1337	<	clear_args ();
468	<	exit (EXIT_FAILURE);
1336	>	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1337	>	goto failure;
1338		}
1339	<	args_info->slab_density_given = 1; staticProps_group_counter += 1;
1340	<
1339	>	if (args_info->rho_r_given && ! override)
1340	>	continue;
1341	>	local_args_info.rho_r_given = 1;
1342	>	args_info->rho_r_given = 1;
1343	>	if (args_info->staticProps_group_counter && override)
1344	>	reset_group_staticProps (args_info);
1345	>	args_info->staticProps_group_counter += 1;
1346		break;
1347		}
1348
1349	<
1349	>	break;
1350		case '?':       /* Invalid option.  */
1351		/* `getopt_long' already printed an error message.  */
1352	<	exit (EXIT_FAILURE);
1352	>	goto failure;
1353
1354		default:        /* bug: option not considered.  */
1355	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1355	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1356		abort ();
1357		} /* switch */
1358		} /* while */
1359
1360	<	if ( staticProps_group_counter != 1)
1360	>	if (args_info->staticProps_group_counter > 1)
1361		{
1362	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1363	<	missing_required_options = 1;
1362	>	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 : ""));
1363	>	error = 1;
1364		}
1365
1366
1367	<	if (! args_info->input_given)
1367	>
1368	>	if (check_required)
1369		{
1370	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
496	<	missing_required_options = 1;
1370	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1371		}
498	–	if ( missing_required_options )
499	–	exit (EXIT_FAILURE);
1372
1373	+	cmdline_parser_release (&local_args_info);
1374	+
1375	+	if ( error )
1376	+	return (EXIT_FAILURE);
1377	+
1378	+	if (optind < argc)
1379	+	{
1380	+	int i = 0 ;
1381	+	int found_prog_name = 0;
1382	+	/* whether program name, i.e., argv[0], is in the remaining args
1383	+	(this may happen with some implementations of getopt,
1384	+	but surely not with the one included by gengetopt) */
1385	+
1386	+	i = optind;
1387	+	while (i < argc)
1388	+	if (argv[i++] == argv[0]) {
1389	+	found_prog_name = 1;
1390	+	break;
1391	+	}
1392	+	i = 0;
1393	+
1394	+	args_info->inputs_num = argc - optind - found_prog_name;
1395	+	args_info->inputs =
1396	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1397	+	while (optind < argc)
1398	+	if (argv[optind++] != argv[0])
1399	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1400	+	}
1401	+
1402		return 0;
1403	+
1404	+	failure:
1405	+
1406	+	cmdline_parser_release (&local_args_info);
1407	+	return (EXIT_FAILURE);
1408		}

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