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

Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1091 by chuckv, Fri Nov 10 18:45:29 2006 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.15
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -F staticPropsCmd
4	>	gengetopt -i StaticProps.ggo -F StaticPropsCmd
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"
22	>	#include "StaticPropsCmd.h"
23
24	+	static
25	+	void clear_given (struct gengetopt_args_info *args_info);
26	+	static
27	+	void clear_args (struct gengetopt_args_info *args_info);
28	+
29	+	static int
30	+	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);
31	+
32	+	static int
33	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
34	+
35	+	static char *
36	+	gengetopt_strdup (const char *s);
37	+
38	+	static
39	+	void clear_given (struct gengetopt_args_info *args_info)
40	+	{
41	+	args_info->help_given = 0 ;
42	+	args_info->version_given = 0 ;
43	+	args_info->input_given = 0 ;
44	+	args_info->output_given = 0 ;
45	+	args_info->step_given = 0 ;
46	+	args_info->nbins_given = 0 ;
47	+	args_info->nbins_x_given = 0 ;
48	+	args_info->nbins_y_given = 0 ;
49	+	args_info->nanglebins_given = 0 ;
50	+	args_info->length_given = 0 ;
51	+	args_info->rcut_given = 0 ;
52	+	args_info->zoffset_given = 0 ;
53	+	args_info->sele1_given = 0 ;
54	+	args_info->sele2_given = 0 ;
55	+	args_info->sele3_given = 0 ;
56	+	args_info->refsele_given = 0 ;
57	+	args_info->molname_given = 0 ;
58	+	args_info->begin_given = 0 ;
59	+	args_info->end_given = 0 ;
60	+	args_info->radius_given = 0 ;
61	+	args_info->bo_given = 0 ;
62	+	args_info->gofr_given = 0 ;
63	+	args_info->r_theta_given = 0 ;
64	+	args_info->r_omega_given = 0 ;
65	+	args_info->theta_omega_given = 0 ;
66	+	args_info->gxyz_given = 0 ;
67	+	args_info->p2_given = 0 ;
68	+	args_info->rp2_given = 0 ;
69	+	args_info->scd_given = 0 ;
70	+	args_info->density_given = 0 ;
71	+	args_info->slab_density_given = 0 ;
72	+	args_info->hxy_given = 0 ;
73	+	args_info->rho_r_given = 0 ;
74	+	args_info->staticProps_group_counter = 0 ;
75	+	}
76	+
77	+	static
78	+	void clear_args (struct gengetopt_args_info *args_info)
79	+	{
80	+	args_info->input_arg = NULL;
81	+	args_info->input_orig = NULL;
82	+	args_info->output_arg = NULL;
83	+	args_info->output_orig = NULL;
84	+	args_info->step_arg = 1;
85	+	args_info->step_orig = NULL;
86	+	args_info->nbins_arg = 100;
87	+	args_info->nbins_orig = NULL;
88	+	args_info->nbins_x_arg = 100;
89	+	args_info->nbins_x_orig = NULL;
90	+	args_info->nbins_y_arg = 100;
91	+	args_info->nbins_y_orig = NULL;
92	+	args_info->nanglebins_arg = 50;
93	+	args_info->nanglebins_orig = NULL;
94	+	args_info->length_orig = NULL;
95	+	args_info->rcut_orig = NULL;
96	+	args_info->zoffset_arg = 0;
97	+	args_info->zoffset_orig = NULL;
98	+	args_info->sele1_arg = NULL;
99	+	args_info->sele1_orig = NULL;
100	+	args_info->sele2_arg = NULL;
101	+	args_info->sele2_orig = NULL;
102	+	args_info->sele3_arg = NULL;
103	+	args_info->sele3_orig = NULL;
104	+	args_info->refsele_arg = NULL;
105	+	args_info->refsele_orig = NULL;
106	+	args_info->molname_arg = NULL;
107	+	args_info->molname_orig = NULL;
108	+	args_info->begin_orig = NULL;
109	+	args_info->end_orig = NULL;
110	+	args_info->radius_orig = NULL;
111	+
112	+	}
113	+
114		void
115		cmdline_parser_print_version (void)
116		{
#	Line 32 | Line 121 | cmdline_parser_print_help (void)
121		cmdline_parser_print_help (void)
122		{
123		cmdline_parser_print_version ();
124	<	printf("\n"
125	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
126	<	printf("\n");
127	<	printf("  -h, --help                    Print help and exit\n");
128	<	printf("  -V, --version                 Print version and exit\n");
129	<	printf("  -i, --input=filename          input dump file\n");
130	<	printf("  -o, --output=filename         output file name\n");
131	<	printf("  -n, --frame=INT               print every n frame  (default=`1')\n");
132	<	printf("  -d, --ndistebins=INT          number of bins for distance  (default=`50')\n");
133	<	printf("  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')\n");
134	<	printf("  -l, --length=DOUBLE           maximum length\n");
135	<	printf("      --sele1=selection script  select first stuntdouble set\n");
136	<	printf("      --sele2=selection script  select second stuntdouble set\n");
137	<	printf("\n");
138	<	printf(" Group: staticProps  an option of this group is required\n");
139	<	printf("      --gofr                    g(r)\n");
140	<	printf("      --r_theta                 g(r, cos(theta))\n");
141	<	printf("      --r_omega                 g(r, cos(omega))\n");
142	<	printf("      --theta_omega             g(cos(theta), cos(omega))\n");
143	<	printf("      --xyz                     g(x, y, z)\n");
124	>	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
125	>	printf("%s\n","  -h, --help                    Print help and exit");
126	>	printf("%s\n","  -V, --version                 Print version and exit");
127	>	printf("%s\n","  -i, --input=filename          input dump file");
128	>	printf("%s\n","  -o, --output=filename         output file name");
129	>	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
130	>	printf("%s\n","  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')");
131	>	printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
132	>	printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
133	>	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
134	>	printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
135	>	printf("%s\n","  -c, --rcut=DOUBLE             cutoff radius (rcut)");
136	>	printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
137	>	printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
138	>	printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
139	>	printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
140	>	printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
141	>	printf("%s\n","      --molname=STRING          molecule name");
142	>	printf("%s\n","      --begin=INT               begin internal index");
143	>	printf("%s\n","      --end=INT                 end internal index");
144	>	printf("%s\n","      --radius=DOUBLE           nanoparticle radius");
145	>	printf("%s\n","\n Group: staticProps\n   an option of this group is required");
146	>	printf("%s\n","      --bo                      bond order parameter (--rcut must be specified");
147	>	printf("%s\n","  -g, --gofr                    g(r)");
148	>	printf("%s\n","      --r_theta                 g(r, cos(theta))");
149	>	printf("%s\n","      --r_omega                 g(r, cos(omega))");
150	>	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
151	>	printf("%s\n","      --gxyz                    g(x, y, z)");
152	>	printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
153	>	printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
154	>	printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
155	>	printf("%s\n","  -d, --density                 density plot");
156	>	printf("%s\n","      --slab_density            slab density");
157	>	printf("%s\n","      --hxy                     hxy");
158	>	printf("%s\n","      --rho_r                   rho of R");
159	>
160		}
161
162	+	void
163	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
164	+	{
165	+	clear_given (args_info);
166	+	clear_args (args_info);
167	+	}
168
169	<	static char *gengetopt_strdup (const char *s);
169	>	static void
170	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
171	>	{
172	>
173	>	if (args_info->input_arg)
174	>	{
175	>	free (args_info->input_arg); /* free previous argument */
176	>	args_info->input_arg = 0;
177	>	}
178	>	if (args_info->input_orig)
179	>	{
180	>	free (args_info->input_orig); /* free previous argument */
181	>	args_info->input_orig = 0;
182	>	}
183	>	if (args_info->output_arg)
184	>	{
185	>	free (args_info->output_arg); /* free previous argument */
186	>	args_info->output_arg = 0;
187	>	}
188	>	if (args_info->output_orig)
189	>	{
190	>	free (args_info->output_orig); /* free previous argument */
191	>	args_info->output_orig = 0;
192	>	}
193	>	if (args_info->step_orig)
194	>	{
195	>	free (args_info->step_orig); /* free previous argument */
196	>	args_info->step_orig = 0;
197	>	}
198	>	if (args_info->nbins_orig)
199	>	{
200	>	free (args_info->nbins_orig); /* free previous argument */
201	>	args_info->nbins_orig = 0;
202	>	}
203	>	if (args_info->nbins_x_orig)
204	>	{
205	>	free (args_info->nbins_x_orig); /* free previous argument */
206	>	args_info->nbins_x_orig = 0;
207	>	}
208	>	if (args_info->nbins_y_orig)
209	>	{
210	>	free (args_info->nbins_y_orig); /* free previous argument */
211	>	args_info->nbins_y_orig = 0;
212	>	}
213	>	if (args_info->nanglebins_orig)
214	>	{
215	>	free (args_info->nanglebins_orig); /* free previous argument */
216	>	args_info->nanglebins_orig = 0;
217	>	}
218	>	if (args_info->length_orig)
219	>	{
220	>	free (args_info->length_orig); /* free previous argument */
221	>	args_info->length_orig = 0;
222	>	}
223	>	if (args_info->rcut_orig)
224	>	{
225	>	free (args_info->rcut_orig); /* free previous argument */
226	>	args_info->rcut_orig = 0;
227	>	}
228	>	if (args_info->zoffset_orig)
229	>	{
230	>	free (args_info->zoffset_orig); /* free previous argument */
231	>	args_info->zoffset_orig = 0;
232	>	}
233	>	if (args_info->sele1_arg)
234	>	{
235	>	free (args_info->sele1_arg); /* free previous argument */
236	>	args_info->sele1_arg = 0;
237	>	}
238	>	if (args_info->sele1_orig)
239	>	{
240	>	free (args_info->sele1_orig); /* free previous argument */
241	>	args_info->sele1_orig = 0;
242	>	}
243	>	if (args_info->sele2_arg)
244	>	{
245	>	free (args_info->sele2_arg); /* free previous argument */
246	>	args_info->sele2_arg = 0;
247	>	}
248	>	if (args_info->sele2_orig)
249	>	{
250	>	free (args_info->sele2_orig); /* free previous argument */
251	>	args_info->sele2_orig = 0;
252	>	}
253	>	if (args_info->sele3_arg)
254	>	{
255	>	free (args_info->sele3_arg); /* free previous argument */
256	>	args_info->sele3_arg = 0;
257	>	}
258	>	if (args_info->sele3_orig)
259	>	{
260	>	free (args_info->sele3_orig); /* free previous argument */
261	>	args_info->sele3_orig = 0;
262	>	}
263	>	if (args_info->refsele_arg)
264	>	{
265	>	free (args_info->refsele_arg); /* free previous argument */
266	>	args_info->refsele_arg = 0;
267	>	}
268	>	if (args_info->refsele_orig)
269	>	{
270	>	free (args_info->refsele_orig); /* free previous argument */
271	>	args_info->refsele_orig = 0;
272	>	}
273	>	if (args_info->molname_arg)
274	>	{
275	>	free (args_info->molname_arg); /* free previous argument */
276	>	args_info->molname_arg = 0;
277	>	}
278	>	if (args_info->molname_orig)
279	>	{
280	>	free (args_info->molname_orig); /* free previous argument */
281	>	args_info->molname_orig = 0;
282	>	}
283	>	if (args_info->begin_orig)
284	>	{
285	>	free (args_info->begin_orig); /* free previous argument */
286	>	args_info->begin_orig = 0;
287	>	}
288	>	if (args_info->end_orig)
289	>	{
290	>	free (args_info->end_orig); /* free previous argument */
291	>	args_info->end_orig = 0;
292	>	}
293	>	if (args_info->radius_orig)
294	>	{
295	>	free (args_info->radius_orig); /* free previous argument */
296	>	args_info->radius_orig = 0;
297	>	}
298	>
299	>	clear_given (args_info);
300	>	}
301
302	+	int
303	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
304	+	{
305	+	FILE *outfile;
306	+	int i = 0;
307	+
308	+	outfile = fopen(filename, "w");
309	+
310	+	if (!outfile)
311	+	{
312	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
313	+	return EXIT_FAILURE;
314	+	}
315	+
316	+	if (args_info->help_given) {
317	+	fprintf(outfile, "%s\n", "help");
318	+	}
319	+	if (args_info->version_given) {
320	+	fprintf(outfile, "%s\n", "version");
321	+	}
322	+	if (args_info->input_given) {
323	+	if (args_info->input_orig) {
324	+	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
325	+	} else {
326	+	fprintf(outfile, "%s\n", "input");
327	+	}
328	+	}
329	+	if (args_info->output_given) {
330	+	if (args_info->output_orig) {
331	+	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
332	+	} else {
333	+	fprintf(outfile, "%s\n", "output");
334	+	}
335	+	}
336	+	if (args_info->step_given) {
337	+	if (args_info->step_orig) {
338	+	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
339	+	} else {
340	+	fprintf(outfile, "%s\n", "step");
341	+	}
342	+	}
343	+	if (args_info->nbins_given) {
344	+	if (args_info->nbins_orig) {
345	+	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
346	+	} else {
347	+	fprintf(outfile, "%s\n", "nbins");
348	+	}
349	+	}
350	+	if (args_info->nbins_x_given) {
351	+	if (args_info->nbins_x_orig) {
352	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
353	+	} else {
354	+	fprintf(outfile, "%s\n", "nbins_x");
355	+	}
356	+	}
357	+	if (args_info->nbins_y_given) {
358	+	if (args_info->nbins_y_orig) {
359	+	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
360	+	} else {
361	+	fprintf(outfile, "%s\n", "nbins_y");
362	+	}
363	+	}
364	+	if (args_info->nanglebins_given) {
365	+	if (args_info->nanglebins_orig) {
366	+	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
367	+	} else {
368	+	fprintf(outfile, "%s\n", "nanglebins");
369	+	}
370	+	}
371	+	if (args_info->length_given) {
372	+	if (args_info->length_orig) {
373	+	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
374	+	} else {
375	+	fprintf(outfile, "%s\n", "length");
376	+	}
377	+	}
378	+	if (args_info->rcut_given) {
379	+	if (args_info->rcut_orig) {
380	+	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
381	+	} else {
382	+	fprintf(outfile, "%s\n", "rcut");
383	+	}
384	+	}
385	+	if (args_info->zoffset_given) {
386	+	if (args_info->zoffset_orig) {
387	+	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
388	+	} else {
389	+	fprintf(outfile, "%s\n", "zoffset");
390	+	}
391	+	}
392	+	if (args_info->sele1_given) {
393	+	if (args_info->sele1_orig) {
394	+	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
395	+	} else {
396	+	fprintf(outfile, "%s\n", "sele1");
397	+	}
398	+	}
399	+	if (args_info->sele2_given) {
400	+	if (args_info->sele2_orig) {
401	+	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
402	+	} else {
403	+	fprintf(outfile, "%s\n", "sele2");
404	+	}
405	+	}
406	+	if (args_info->sele3_given) {
407	+	if (args_info->sele3_orig) {
408	+	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
409	+	} else {
410	+	fprintf(outfile, "%s\n", "sele3");
411	+	}
412	+	}
413	+	if (args_info->refsele_given) {
414	+	if (args_info->refsele_orig) {
415	+	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
416	+	} else {
417	+	fprintf(outfile, "%s\n", "refsele");
418	+	}
419	+	}
420	+	if (args_info->molname_given) {
421	+	if (args_info->molname_orig) {
422	+	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
423	+	} else {
424	+	fprintf(outfile, "%s\n", "molname");
425	+	}
426	+	}
427	+	if (args_info->begin_given) {
428	+	if (args_info->begin_orig) {
429	+	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
430	+	} else {
431	+	fprintf(outfile, "%s\n", "begin");
432	+	}
433	+	}
434	+	if (args_info->end_given) {
435	+	if (args_info->end_orig) {
436	+	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
437	+	} else {
438	+	fprintf(outfile, "%s\n", "end");
439	+	}
440	+	}
441	+	if (args_info->radius_given) {
442	+	if (args_info->radius_orig) {
443	+	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
444	+	} else {
445	+	fprintf(outfile, "%s\n", "radius");
446	+	}
447	+	}
448	+	if (args_info->bo_given) {
449	+	fprintf(outfile, "%s\n", "bo");
450	+	}
451	+	if (args_info->gofr_given) {
452	+	fprintf(outfile, "%s\n", "gofr");
453	+	}
454	+	if (args_info->r_theta_given) {
455	+	fprintf(outfile, "%s\n", "r_theta");
456	+	}
457	+	if (args_info->r_omega_given) {
458	+	fprintf(outfile, "%s\n", "r_omega");
459	+	}
460	+	if (args_info->theta_omega_given) {
461	+	fprintf(outfile, "%s\n", "theta_omega");
462	+	}
463	+	if (args_info->gxyz_given) {
464	+	fprintf(outfile, "%s\n", "gxyz");
465	+	}
466	+	if (args_info->p2_given) {
467	+	fprintf(outfile, "%s\n", "p2");
468	+	}
469	+	if (args_info->rp2_given) {
470	+	fprintf(outfile, "%s\n", "rp2");
471	+	}
472	+	if (args_info->scd_given) {
473	+	fprintf(outfile, "%s\n", "scd");
474	+	}
475	+	if (args_info->density_given) {
476	+	fprintf(outfile, "%s\n", "density");
477	+	}
478	+	if (args_info->slab_density_given) {
479	+	fprintf(outfile, "%s\n", "slab_density");
480	+	}
481	+	if (args_info->hxy_given) {
482	+	fprintf(outfile, "%s\n", "hxy");
483	+	}
484	+	if (args_info->rho_r_given) {
485	+	fprintf(outfile, "%s\n", "rho_r");
486	+	}
487	+
488	+	fclose (outfile);
489	+
490	+	i = EXIT_SUCCESS;
491	+	return i;
492	+	}
493	+
494	+	void
495	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
496	+	{
497	+	cmdline_parser_release (args_info);
498	+	}
499	+
500	+
501		/* gengetopt_strdup() */
502		/* strdup.c replacement of strdup, which is not standard */
503		char *
504		gengetopt_strdup (const char *s)
505		{
506	<	char *result = (char*)malloc(strlen(s) + 1);
506	>	char *result = NULL;
507	>	if (!s)
508	>	return result;
509	>
510	>	result = (char*)malloc(strlen(s) + 1);
511		if (result == (char*)0)
512		return (char*)0;
513		strcpy(result, s);
514		return result;
515		}
516
517	<	int
518	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
517	>	static void
518	>	reset_group_staticProps(struct gengetopt_args_info *args_info);
519	>
520	>	static void
521	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
522		{
523	<	int c;        /* Character of the parsed option.  */
524	<	int missing_required_options = 0;
77	<	int staticProps_group_counter = 0;
523	>	if (! args_info->staticProps_group_counter)
524	>	return;
525
526	<
80	<	args_info->help_given = 0 ;
81	<	args_info->version_given = 0 ;
82	<	args_info->input_given = 0 ;
83	<	args_info->output_given = 0 ;
84	<	args_info->frame_given = 0 ;
85	<	args_info->ndistebins_given = 0 ;
86	<	args_info->nanglebins_given = 0 ;
87	<	args_info->length_given = 0 ;
88	<	args_info->sele1_given = 0 ;
89	<	args_info->sele2_given = 0 ;
526	>	args_info->bo_given = 0 ;
527		args_info->gofr_given = 0 ;
528		args_info->r_theta_given = 0 ;
529		args_info->r_omega_given = 0 ;
530		args_info->theta_omega_given = 0 ;
531	<	args_info->xyz_given = 0 ;
532	<	#define clear_args() { \
533	<	args_info->input_arg = NULL; \
534	<	args_info->output_arg = NULL; \
535	<	args_info->frame_arg = 1 ;\
536	<	args_info->ndistebins_arg = 50 ;\
537	<	args_info->nanglebins_arg = 50 ;\
538	<	args_info->sele1_arg = NULL; \
539	<	args_info->sele2_arg = NULL; \
531	>	args_info->gxyz_given = 0 ;
532	>	args_info->p2_given = 0 ;
533	>	args_info->rp2_given = 0 ;
534	>	args_info->scd_given = 0 ;
535	>	args_info->density_given = 0 ;
536	>	args_info->slab_density_given = 0 ;
537	>	args_info->hxy_given = 0 ;
538	>	args_info->rho_r_given = 0 ;
539	>
540	>	args_info->staticProps_group_counter = 0;
541		}
542
543	<	clear_args();
543	>	int
544	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
545	>	{
546	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
547	>	}
548
549	+	int
550	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
551	+	{
552	+	int result;
553	+
554	+	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
555	+
556	+	if (result == EXIT_FAILURE)
557	+	{
558	+	cmdline_parser_free (args_info);
559	+	exit (EXIT_FAILURE);
560	+	}
561	+
562	+	return result;
563	+	}
564	+
565	+	int
566	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
567	+	{
568	+	int result = EXIT_SUCCESS;
569	+
570	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
571	+	result = EXIT_FAILURE;
572	+
573	+	if (result == EXIT_FAILURE)
574	+	{
575	+	cmdline_parser_free (args_info);
576	+	exit (EXIT_FAILURE);
577	+	}
578	+
579	+	return result;
580	+	}
581	+
582	+	int
583	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
584	+	{
585	+	int error = 0;
586	+
587	+	if (! args_info->input_given)
588	+	{
589	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
590	+	error = 1;
591	+	}
592	+	if (args_info->staticProps_group_counter == 0)
593	+	{
594	+	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 : ""));
595	+	error = 1;
596	+	}
597	+
598	+
599	+	return error;
600	+	}
601	+
602	+	int
603	+	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)
604	+	{
605	+	int c;        /* Character of the parsed option.  */
606	+
607	+	int error = 0;
608	+	struct gengetopt_args_info local_args_info;
609	+
610	+	if (initialize)
611	+	cmdline_parser_init (args_info);
612	+
613	+	cmdline_parser_init (&local_args_info);
614	+
615		optarg = 0;
616		optind = 1;
617		opterr = 1;
#	Line 119 | Line 627 | cmdline_parser (int argc, char * const *argv, struct g
627		{ "version",    0, NULL, 'V' },
628		{ "input",      1, NULL, 'i' },
629		{ "output",     1, NULL, 'o' },
630	<	{ "frame",      1, NULL, 'n' },
631	<	{ "ndistebins", 1, NULL, 'd' },
630	>	{ "step",       1, NULL, 'n' },
631	>	{ "nbins",      1, NULL, 'b' },
632	>	{ "nbins_x",    1, NULL, 'x' },
633	>	{ "nbins_y",    1, NULL, 'y' },
634		{ "nanglebins", 1, NULL, 'a' },
635	<	{ "length",     1, NULL, 'l' },
635	>	{ "length",     1, NULL, 0 },
636	>	{ "rcut",       1, NULL, 'c' },
637	>	{ "zoffset",    1, NULL, 'z' },
638		{ "sele1",      1, NULL, 0 },
639		{ "sele2",      1, NULL, 0 },
640	<	{ "gofr",       0, NULL, 0 },
640	>	{ "sele3",      1, NULL, 0 },
641	>	{ "refsele",    1, NULL, 0 },
642	>	{ "molname",    1, NULL, 0 },
643	>	{ "begin",      1, NULL, 0 },
644	>	{ "end",        1, NULL, 0 },
645	>	{ "radius",     1, NULL, 0 },
646	>	{ "bo", 0, NULL, 0 },
647	>	{ "gofr",       0, NULL, 'g' },
648		{ "r_theta",    0, NULL, 0 },
649		{ "r_omega",    0, NULL, 0 },
650		{ "theta_omega",        0, NULL, 0 },
651	<	{ "xyz",        0, NULL, 0 },
651	>	{ "gxyz",       0, NULL, 0 },
652	>	{ "p2", 0, NULL, 'p' },
653	>	{ "rp2",        0, NULL, 0 },
654	>	{ "scd",        0, NULL, 's' },
655	>	{ "density",    0, NULL, 'd' },
656	>	{ "slab_density",       0, NULL, 0 },
657	>	{ "hxy",        0, NULL, 0 },
658	>	{ "rho_r",      0, NULL, 0 },
659		{ NULL, 0, NULL, 0 }
660		};
661
662		stop_char = 0;
663	<	c = getopt_long (argc, argv, "hVi:o:n:d:a:l:", long_options, &option_index);
663	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
664
665		if (c == -1) break;       /* Exit from `while (1)' loop.  */
666
667		switch (c)
668		{
669		case 'h':       /* Print help and exit.  */
144	–	clear_args ();
670		cmdline_parser_print_help ();
671	+	cmdline_parser_free (&local_args_info);
672		exit (EXIT_SUCCESS);
673
674		case 'V':       /* Print version and exit.  */
149	–	clear_args ();
675		cmdline_parser_print_version ();
676	+	cmdline_parser_free (&local_args_info);
677		exit (EXIT_SUCCESS);
678
679		case 'i':       /* input dump file.  */
680	<	if (args_info->input_given)
680	>	if (local_args_info.input_given)
681		{
682	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
683	<	clear_args ();
158	<	exit (EXIT_FAILURE);
682	>	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
683	>	goto failure;
684		}
685	+	if (args_info->input_given && ! override)
686	+	continue;
687	+	local_args_info.input_given = 1;
688		args_info->input_given = 1;
689	+	if (args_info->input_arg)
690	+	free (args_info->input_arg); /* free previous string */
691		args_info->input_arg = gengetopt_strdup (optarg);
692	+	if (args_info->input_orig)
693	+	free (args_info->input_orig); /* free previous string */
694	+	args_info->input_orig = gengetopt_strdup (optarg);
695		break;
696
697		case 'o':       /* output file name.  */
698	<	if (args_info->output_given)
698	>	if (local_args_info.output_given)
699		{
700	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
701	<	clear_args ();
169	<	exit (EXIT_FAILURE);
700	>	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
701	>	goto failure;
702		}
703	+	if (args_info->output_given && ! override)
704	+	continue;
705	+	local_args_info.output_given = 1;
706		args_info->output_given = 1;
707	+	if (args_info->output_arg)
708	+	free (args_info->output_arg); /* free previous string */
709		args_info->output_arg = gengetopt_strdup (optarg);
710	+	if (args_info->output_orig)
711	+	free (args_info->output_orig); /* free previous string */
712	+	args_info->output_orig = gengetopt_strdup (optarg);
713		break;
714
715	<	case 'n':       /* print every n frame.  */
716	<	if (args_info->frame_given)
715	>	case 'n':       /* process every n frame.  */
716	>	if (local_args_info.step_given)
717		{
718	<	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
719	<	clear_args ();
180	<	exit (EXIT_FAILURE);
718	>	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
719	>	goto failure;
720		}
721	<	args_info->frame_given = 1;
722	<	args_info->frame_arg = strtol (optarg,&stop_char,0);
721	>	if (args_info->step_given && ! override)
722	>	continue;
723	>	local_args_info.step_given = 1;
724	>	args_info->step_given = 1;
725	>	args_info->step_arg = strtol (optarg, &stop_char, 0);
726	>	if (!(stop_char && *stop_char == '\0')) {
727	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
728	>	goto failure;
729	>	}
730	>	if (args_info->step_orig)
731	>	free (args_info->step_orig); /* free previous string */
732	>	args_info->step_orig = gengetopt_strdup (optarg);
733		break;
734
735	<	case 'd':       /* number of bins for distance.  */
736	<	if (args_info->ndistebins_given)
735	>	case 'b':       /* number of bins (general purpose).  */
736	>	if (local_args_info.nbins_given)
737		{
738	<	fprintf (stderr, "%s: `--ndistebins' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
739	<	clear_args ();
191	<	exit (EXIT_FAILURE);
738	>	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
739	>	goto failure;
740		}
741	<	args_info->ndistebins_given = 1;
742	<	args_info->ndistebins_arg = strtol (optarg,&stop_char,0);
741	>	if (args_info->nbins_given && ! override)
742	>	continue;
743	>	local_args_info.nbins_given = 1;
744	>	args_info->nbins_given = 1;
745	>	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
746	>	if (!(stop_char && *stop_char == '\0')) {
747	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
748	>	goto failure;
749	>	}
750	>	if (args_info->nbins_orig)
751	>	free (args_info->nbins_orig); /* free previous string */
752	>	args_info->nbins_orig = gengetopt_strdup (optarg);
753		break;
754
755	+	case 'x':       /* number of bins in x axis.  */
756	+	if (local_args_info.nbins_x_given)
757	+	{
758	+	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
759	+	goto failure;
760	+	}
761	+	if (args_info->nbins_x_given && ! override)
762	+	continue;
763	+	local_args_info.nbins_x_given = 1;
764	+	args_info->nbins_x_given = 1;
765	+	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
766	+	if (!(stop_char && *stop_char == '\0')) {
767	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
768	+	goto failure;
769	+	}
770	+	if (args_info->nbins_x_orig)
771	+	free (args_info->nbins_x_orig); /* free previous string */
772	+	args_info->nbins_x_orig = gengetopt_strdup (optarg);
773	+	break;
774	+
775	+	case 'y':       /* number of bins in y axis.  */
776	+	if (local_args_info.nbins_y_given)
777	+	{
778	+	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
779	+	goto failure;
780	+	}
781	+	if (args_info->nbins_y_given && ! override)
782	+	continue;
783	+	local_args_info.nbins_y_given = 1;
784	+	args_info->nbins_y_given = 1;
785	+	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
786	+	if (!(stop_char && *stop_char == '\0')) {
787	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
788	+	goto failure;
789	+	}
790	+	if (args_info->nbins_y_orig)
791	+	free (args_info->nbins_y_orig); /* free previous string */
792	+	args_info->nbins_y_orig = gengetopt_strdup (optarg);
793	+	break;
794	+
795		case 'a':       /* number of bins for cos(angle).  */
796	<	if (args_info->nanglebins_given)
796	>	if (local_args_info.nanglebins_given)
797		{
798	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
799	<	clear_args ();
202	<	exit (EXIT_FAILURE);
798	>	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
799	>	goto failure;
800		}
801	+	if (args_info->nanglebins_given && ! override)
802	+	continue;
803	+	local_args_info.nanglebins_given = 1;
804		args_info->nanglebins_given = 1;
805	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
805	>	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
806	>	if (!(stop_char && *stop_char == '\0')) {
807	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
808	>	goto failure;
809	>	}
810	>	if (args_info->nanglebins_orig)
811	>	free (args_info->nanglebins_orig); /* free previous string */
812	>	args_info->nanglebins_orig = gengetopt_strdup (optarg);
813		break;
814
815	<	case 'l':       /* maximum length.  */
816	<	if (args_info->length_given)
815	>	case 'c':       /* cutoff radius (rcut).  */
816	>	if (local_args_info.rcut_given)
817		{
818	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
819	<	clear_args ();
213	<	exit (EXIT_FAILURE);
818	>	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
819	>	goto failure;
820		}
821	<	args_info->length_given = 1;
822	<	args_info->length_arg = strtod (optarg, NULL);
821	>	if (args_info->rcut_given && ! override)
822	>	continue;
823	>	local_args_info.rcut_given = 1;
824	>	args_info->rcut_given = 1;
825	>	args_info->rcut_arg = strtod (optarg, &stop_char);
826	>	if (!(stop_char && *stop_char == '\0')) {
827	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
828	>	goto failure;
829	>	}
830	>	if (args_info->rcut_orig)
831	>	free (args_info->rcut_orig); /* free previous string */
832	>	args_info->rcut_orig = gengetopt_strdup (optarg);
833		break;
834
835	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
836	+	if (local_args_info.zoffset_given)
837	+	{
838	+	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
839	+	goto failure;
840	+	}
841	+	if (args_info->zoffset_given && ! override)
842	+	continue;
843	+	local_args_info.zoffset_given = 1;
844	+	args_info->zoffset_given = 1;
845	+	args_info->zoffset_arg = strtod (optarg, &stop_char);
846	+	if (!(stop_char && *stop_char == '\0')) {
847	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
848	+	goto failure;
849	+	}
850	+	if (args_info->zoffset_orig)
851	+	free (args_info->zoffset_orig); /* free previous string */
852	+	args_info->zoffset_orig = gengetopt_strdup (optarg);
853	+	break;
854
855	+	case 'g':       /* g(r).  */
856	+	if (local_args_info.gofr_given)
857	+	{
858	+	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
859	+	goto failure;
860	+	}
861	+	if (args_info->gofr_given && ! override)
862	+	continue;
863	+	local_args_info.gofr_given = 1;
864	+	args_info->gofr_given = 1;
865	+	if (args_info->staticProps_group_counter && override)
866	+	reset_group_staticProps (args_info);
867	+	args_info->staticProps_group_counter += 1;
868	+	break;
869	+
870	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
871	+	if (local_args_info.p2_given)
872	+	{
873	+	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
874	+	goto failure;
875	+	}
876	+	if (args_info->p2_given && ! override)
877	+	continue;
878	+	local_args_info.p2_given = 1;
879	+	args_info->p2_given = 1;
880	+	if (args_info->staticProps_group_counter && override)
881	+	reset_group_staticProps (args_info);
882	+	args_info->staticProps_group_counter += 1;
883	+	break;
884	+
885	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
886	+	if (local_args_info.scd_given)
887	+	{
888	+	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
889	+	goto failure;
890	+	}
891	+	if (args_info->scd_given && ! override)
892	+	continue;
893	+	local_args_info.scd_given = 1;
894	+	args_info->scd_given = 1;
895	+	if (args_info->staticProps_group_counter && override)
896	+	reset_group_staticProps (args_info);
897	+	args_info->staticProps_group_counter += 1;
898	+	break;
899	+
900	+	case 'd':       /* density plot.  */
901	+	if (local_args_info.density_given)
902	+	{
903	+	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
904	+	goto failure;
905	+	}
906	+	if (args_info->density_given && ! override)
907	+	continue;
908	+	local_args_info.density_given = 1;
909	+	args_info->density_given = 1;
910	+	if (args_info->staticProps_group_counter && override)
911	+	reset_group_staticProps (args_info);
912	+	args_info->staticProps_group_counter += 1;
913	+	break;
914	+
915	+
916		case 0: /* Long option with no short option */
917	<	/* select first stuntdouble set.  */
918	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
917	>	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
918	>	if (strcmp (long_options[option_index].name, "length") == 0)
919		{
920	<	if (args_info->sele1_given)
920	>	if (local_args_info.length_given)
921		{
922	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
923	<	clear_args ();
228	<	exit (EXIT_FAILURE);
922	>	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
923	>	goto failure;
924		}
925	+	if (args_info->length_given && ! override)
926	+	continue;
927	+	local_args_info.length_given = 1;
928	+	args_info->length_given = 1;
929	+	args_info->length_arg = strtod (optarg, &stop_char);
930	+	if (!(stop_char && *stop_char == '\0')) {
931	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
932	+	goto failure;
933	+	}
934	+	if (args_info->length_orig)
935	+	free (args_info->length_orig); /* free previous string */
936	+	args_info->length_orig = gengetopt_strdup (optarg);
937	+	}
938	+	/* select the first stuntdouble set.  */
939	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
940	+	{
941	+	if (local_args_info.sele1_given)
942	+	{
943	+	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
944	+	goto failure;
945	+	}
946	+	if (args_info->sele1_given && ! override)
947	+	continue;
948	+	local_args_info.sele1_given = 1;
949		args_info->sele1_given = 1;
950	+	if (args_info->sele1_arg)
951	+	free (args_info->sele1_arg); /* free previous string */
952		args_info->sele1_arg = gengetopt_strdup (optarg);
953	<	break;
953	>	if (args_info->sele1_orig)
954	>	free (args_info->sele1_orig); /* free previous string */
955	>	args_info->sele1_orig = gengetopt_strdup (optarg);
956		}
957	<
235	<	/* select second stuntdouble set.  */
957	>	/* select the second stuntdouble set.  */
958		else if (strcmp (long_options[option_index].name, "sele2") == 0)
959		{
960	<	if (args_info->sele2_given)
960	>	if (local_args_info.sele2_given)
961		{
962	<	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
963	<	clear_args ();
242	<	exit (EXIT_FAILURE);
962	>	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
963	>	goto failure;
964		}
965	+	if (args_info->sele2_given && ! override)
966	+	continue;
967	+	local_args_info.sele2_given = 1;
968		args_info->sele2_given = 1;
969	+	if (args_info->sele2_arg)
970	+	free (args_info->sele2_arg); /* free previous string */
971		args_info->sele2_arg = gengetopt_strdup (optarg);
972	<	break;
972	>	if (args_info->sele2_orig)
973	>	free (args_info->sele2_orig); /* free previous string */
974	>	args_info->sele2_orig = gengetopt_strdup (optarg);
975		}
976	<
977	<	/* g(r).  */
250	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
976	>	/* select the third stuntdouble set.  */
977	>	else if (strcmp (long_options[option_index].name, "sele3") == 0)
978		{
979	<	if (args_info->gofr_given)
979	>	if (local_args_info.sele3_given)
980		{
981	<	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
982	<	clear_args ();
256	<	exit (EXIT_FAILURE);
981	>	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
982	>	goto failure;
983		}
984	<	args_info->gofr_given = 1; staticProps_group_counter += 1;
985	<
984	>	if (args_info->sele3_given && ! override)
985	>	continue;
986	>	local_args_info.sele3_given = 1;
987	>	args_info->sele3_given = 1;
988	>	if (args_info->sele3_arg)
989	>	free (args_info->sele3_arg); /* free previous string */
990	>	args_info->sele3_arg = gengetopt_strdup (optarg);
991	>	if (args_info->sele3_orig)
992	>	free (args_info->sele3_orig); /* free previous string */
993	>	args_info->sele3_orig = gengetopt_strdup (optarg);
994	>	}
995	>	/* select reference (use and only use with --gxyz).  */
996	>	else if (strcmp (long_options[option_index].name, "refsele") == 0)
997	>	{
998	>	if (local_args_info.refsele_given)
999	>	{
1000	>	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001	>	goto failure;
1002	>	}
1003	>	if (args_info->refsele_given && ! override)
1004	>	continue;
1005	>	local_args_info.refsele_given = 1;
1006	>	args_info->refsele_given = 1;
1007	>	if (args_info->refsele_arg)
1008	>	free (args_info->refsele_arg); /* free previous string */
1009	>	args_info->refsele_arg = gengetopt_strdup (optarg);
1010	>	if (args_info->refsele_orig)
1011	>	free (args_info->refsele_orig); /* free previous string */
1012	>	args_info->refsele_orig = gengetopt_strdup (optarg);
1013	>	}
1014	>	/* molecule name.  */
1015	>	else if (strcmp (long_options[option_index].name, "molname") == 0)
1016	>	{
1017	>	if (local_args_info.molname_given)
1018	>	{
1019	>	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1020	>	goto failure;
1021	>	}
1022	>	if (args_info->molname_given && ! override)
1023	>	continue;
1024	>	local_args_info.molname_given = 1;
1025	>	args_info->molname_given = 1;
1026	>	if (args_info->molname_arg)
1027	>	free (args_info->molname_arg); /* free previous string */
1028	>	args_info->molname_arg = gengetopt_strdup (optarg);
1029	>	if (args_info->molname_orig)
1030	>	free (args_info->molname_orig); /* free previous string */
1031	>	args_info->molname_orig = gengetopt_strdup (optarg);
1032	>	}
1033	>	/* begin internal index.  */
1034	>	else if (strcmp (long_options[option_index].name, "begin") == 0)
1035	>	{
1036	>	if (local_args_info.begin_given)
1037	>	{
1038	>	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1039	>	goto failure;
1040	>	}
1041	>	if (args_info->begin_given && ! override)
1042	>	continue;
1043	>	local_args_info.begin_given = 1;
1044	>	args_info->begin_given = 1;
1045	>	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1046	>	if (!(stop_char && *stop_char == '\0')) {
1047	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1048	>	goto failure;
1049	>	}
1050	>	if (args_info->begin_orig)
1051	>	free (args_info->begin_orig); /* free previous string */
1052	>	args_info->begin_orig = gengetopt_strdup (optarg);
1053	>	}
1054	>	/* end internal index.  */
1055	>	else if (strcmp (long_options[option_index].name, "end") == 0)
1056	>	{
1057	>	if (local_args_info.end_given)
1058	>	{
1059	>	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1060	>	goto failure;
1061	>	}
1062	>	if (args_info->end_given && ! override)
1063	>	continue;
1064	>	local_args_info.end_given = 1;
1065	>	args_info->end_given = 1;
1066	>	args_info->end_arg = strtol (optarg, &stop_char, 0);
1067	>	if (!(stop_char && *stop_char == '\0')) {
1068	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1069	>	goto failure;
1070	>	}
1071	>	if (args_info->end_orig)
1072	>	free (args_info->end_orig); /* free previous string */
1073	>	args_info->end_orig = gengetopt_strdup (optarg);
1074	>	}
1075	>	/* nanoparticle radius.  */
1076	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1077	>	{
1078	>	if (local_args_info.radius_given)
1079	>	{
1080	>	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1081	>	goto failure;
1082	>	}
1083	>	if (args_info->radius_given && ! override)
1084	>	continue;
1085	>	local_args_info.radius_given = 1;
1086	>	args_info->radius_given = 1;
1087	>	args_info->radius_arg = strtod (optarg, &stop_char);
1088	>	if (!(stop_char && *stop_char == '\0')) {
1089	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1090	>	goto failure;
1091	>	}
1092	>	if (args_info->radius_orig)
1093	>	free (args_info->radius_orig); /* free previous string */
1094	>	args_info->radius_orig = gengetopt_strdup (optarg);
1095	>	}
1096	>	/* bond order parameter (--rcut must be specified.  */
1097	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1098	>	{
1099	>	if (local_args_info.bo_given)
1100	>	{
1101	>	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1102	>	goto failure;
1103	>	}
1104	>	if (args_info->bo_given && ! override)
1105	>	continue;
1106	>	local_args_info.bo_given = 1;
1107	>	args_info->bo_given = 1;
1108	>	if (args_info->staticProps_group_counter && override)
1109	>	reset_group_staticProps (args_info);
1110	>	args_info->staticProps_group_counter += 1;
1111		break;
1112		}
262	–
1113		/* g(r, cos(theta)).  */
1114		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1115		{
1116	<	if (args_info->r_theta_given)
1116	>	if (local_args_info.r_theta_given)
1117		{
1118	<	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1119	<	clear_args ();
270	<	exit (EXIT_FAILURE);
1118	>	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1119	>	goto failure;
1120		}
1121	<	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1122	<
1121	>	if (args_info->r_theta_given && ! override)
1122	>	continue;
1123	>	local_args_info.r_theta_given = 1;
1124	>	args_info->r_theta_given = 1;
1125	>	if (args_info->staticProps_group_counter && override)
1126	>	reset_group_staticProps (args_info);
1127	>	args_info->staticProps_group_counter += 1;
1128		break;
1129		}
276	–
1130		/* g(r, cos(omega)).  */
1131		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1132		{
1133	<	if (args_info->r_omega_given)
1133	>	if (local_args_info.r_omega_given)
1134		{
1135	<	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1136	<	clear_args ();
284	<	exit (EXIT_FAILURE);
1135	>	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1136	>	goto failure;
1137		}
1138	<	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1139	<
1138	>	if (args_info->r_omega_given && ! override)
1139	>	continue;
1140	>	local_args_info.r_omega_given = 1;
1141	>	args_info->r_omega_given = 1;
1142	>	if (args_info->staticProps_group_counter && override)
1143	>	reset_group_staticProps (args_info);
1144	>	args_info->staticProps_group_counter += 1;
1145		break;
1146		}
290	–
1147		/* g(cos(theta), cos(omega)).  */
1148		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1149		{
1150	<	if (args_info->theta_omega_given)
1150	>	if (local_args_info.theta_omega_given)
1151		{
1152	<	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1153	<	clear_args ();
298	<	exit (EXIT_FAILURE);
1152	>	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1153	>	goto failure;
1154		}
1155	<	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1156	<
1155	>	if (args_info->theta_omega_given && ! override)
1156	>	continue;
1157	>	local_args_info.theta_omega_given = 1;
1158	>	args_info->theta_omega_given = 1;
1159	>	if (args_info->staticProps_group_counter && override)
1160	>	reset_group_staticProps (args_info);
1161	>	args_info->staticProps_group_counter += 1;
1162		break;
1163		}
304	–
1164		/* g(x, y, z).  */
1165	<	else if (strcmp (long_options[option_index].name, "xyz") == 0)
1165	>	else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1166		{
1167	<	if (args_info->xyz_given)
1167	>	if (local_args_info.gxyz_given)
1168		{
1169	<	fprintf (stderr, "%s: `--xyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1170	<	clear_args ();
312	<	exit (EXIT_FAILURE);
1169	>	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1170	>	goto failure;
1171		}
1172	<	args_info->xyz_given = 1; staticProps_group_counter += 1;
1173	<
1172	>	if (args_info->gxyz_given && ! override)
1173	>	continue;
1174	>	local_args_info.gxyz_given = 1;
1175	>	args_info->gxyz_given = 1;
1176	>	if (args_info->staticProps_group_counter && override)
1177	>	reset_group_staticProps (args_info);
1178	>	args_info->staticProps_group_counter += 1;
1179		break;
1180		}
1181	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1182	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1183	+	{
1184	+	if (local_args_info.rp2_given)
1185	+	{
1186	+	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1187	+	goto failure;
1188	+	}
1189	+	if (args_info->rp2_given && ! override)
1190	+	continue;
1191	+	local_args_info.rp2_given = 1;
1192	+	args_info->rp2_given = 1;
1193	+	if (args_info->staticProps_group_counter && override)
1194	+	reset_group_staticProps (args_info);
1195	+	args_info->staticProps_group_counter += 1;
1196	+	break;
1197	+	}
1198	+	/* slab density.  */
1199	+	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1200	+	{
1201	+	if (local_args_info.slab_density_given)
1202	+	{
1203	+	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1204	+	goto failure;
1205	+	}
1206	+	if (args_info->slab_density_given && ! override)
1207	+	continue;
1208	+	local_args_info.slab_density_given = 1;
1209	+	args_info->slab_density_given = 1;
1210	+	if (args_info->staticProps_group_counter && override)
1211	+	reset_group_staticProps (args_info);
1212	+	args_info->staticProps_group_counter += 1;
1213	+	break;
1214	+	}
1215	+	/* hxy.  */
1216	+	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1217	+	{
1218	+	if (local_args_info.hxy_given)
1219	+	{
1220	+	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1221	+	goto failure;
1222	+	}
1223	+	if (args_info->hxy_given && ! override)
1224	+	continue;
1225	+	local_args_info.hxy_given = 1;
1226	+	args_info->hxy_given = 1;
1227	+	if (args_info->staticProps_group_counter && override)
1228	+	reset_group_staticProps (args_info);
1229	+	args_info->staticProps_group_counter += 1;
1230	+	break;
1231	+	}
1232	+	/* rho of R.  */
1233	+	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1234	+	{
1235	+	if (local_args_info.rho_r_given)
1236	+	{
1237	+	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1238	+	goto failure;
1239	+	}
1240	+	if (args_info->rho_r_given && ! override)
1241	+	continue;
1242	+	local_args_info.rho_r_given = 1;
1243	+	args_info->rho_r_given = 1;
1244	+	if (args_info->staticProps_group_counter && override)
1245	+	reset_group_staticProps (args_info);
1246	+	args_info->staticProps_group_counter += 1;
1247	+	break;
1248	+	}
1249
1250	<
1250	>	break;
1251		case '?':       /* Invalid option.  */
1252		/* `getopt_long' already printed an error message.  */
1253	<	exit (EXIT_FAILURE);
1253	>	goto failure;
1254
1255		default:        /* bug: option not considered.  */
1256	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1256	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1257		abort ();
1258		} /* switch */
1259		} /* while */
1260
1261	<	if ( staticProps_group_counter != 1)
1261	>	if (args_info->staticProps_group_counter > 1)
1262		{
1263	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1264	<	missing_required_options = 1;
1263	>	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 : ""));
1264	>	error = 1;
1265		}
1266
1267
1268	<	if (! args_info->input_given)
1268	>
1269	>	if (check_required)
1270		{
1271	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
340	<	missing_required_options = 1;
1271	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1272		}
342	–	if (! args_info->length_given)
343	–	{
344	–	fprintf (stderr, "%s: '--length' ('-l') option required\n", CMDLINE_PARSER_PACKAGE);
345	–	missing_required_options = 1;
346	–	}
347	–	if ( missing_required_options )
348	–	exit (EXIT_FAILURE);
1273
1274	+	cmdline_parser_release (&local_args_info);
1275	+
1276	+	if ( error )
1277	+	return (EXIT_FAILURE);
1278	+
1279		return 0;
1280	+
1281	+	failure:
1282	+
1283	+	cmdline_parser_release (&local_args_info);
1284	+	return (EXIT_FAILURE);
1285		}

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