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root/group/trunk/OOPSE-4/src/applications/staticProps/StaticPropsCmd.c

Comparing trunk/OOPSE-4/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 2242 by tim, Fri May 27 21:11:24 2005 UTC vs.
Revision 3009 by gezelter, Wed Sep 20 20:13:40 2006 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.16
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd
4	>	gengetopt -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"
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->LegendreL_given = 0 ;
52	+	args_info->rcut_given = 0 ;
53	+	args_info->zoffset_given = 0 ;
54	+	args_info->sele1_given = 0 ;
55	+	args_info->sele2_given = 0 ;
56	+	args_info->sele3_given = 0 ;
57	+	args_info->refsele_given = 0 ;
58	+	args_info->molname_given = 0 ;
59	+	args_info->begin_given = 0 ;
60	+	args_info->end_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->staticProps_group_counter = 0 ;
74	+	}
75	+
76	+	static
77	+	void clear_args (struct gengetopt_args_info *args_info)
78	+	{
79	+	args_info->input_arg = NULL;
80	+	args_info->input_orig = NULL;
81	+	args_info->output_arg = NULL;
82	+	args_info->output_orig = NULL;
83	+	args_info->step_arg = 1;
84	+	args_info->step_orig = NULL;
85	+	args_info->nbins_arg = 100;
86	+	args_info->nbins_orig = NULL;
87	+	args_info->nbins_x_arg = 100;
88	+	args_info->nbins_x_orig = NULL;
89	+	args_info->nbins_y_arg = 100;
90	+	args_info->nbins_y_orig = NULL;
91	+	args_info->nanglebins_arg = 50;
92	+	args_info->nanglebins_orig = NULL;
93	+	args_info->length_orig = NULL;
94	+	args_info->LegendreL_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	+
111	+	}
112	+
113		void
114		cmdline_parser_print_version (void)
115		{
#	Line 32 | Line 120 | cmdline_parser_print_help (void)
120		cmdline_parser_print_help (void)
121		{
122		cmdline_parser_print_version ();
123	<	printf("\n"
124	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
125	<	printf("\n");
126	<	printf("  -h, --help                      Print help and exit\n");
127	<	printf("  -V, --version                   Print version and exit\n");
128	<	printf("  -i, --input=filename            input dump file\n");
129	<	printf("  -o, --output=filename           output file name\n");
130	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
131	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
132	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
133	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
134	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
135	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
136	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
137	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
138	<	printf("      --molname=STRING            molecule name\n");
139	<	printf("      --begin=INT                 begin interanl index\n");
140	<	printf("      --end=INT                   end internal index\n");
141	<	printf("\n");
142	<	printf(" Group: staticProps  an option of this group is required\n");
143	<	printf("      --gofr                      g(r)\n");
144	<	printf("      --r_theta                   g(r, cos(theta))\n");
145	<	printf("      --r_omega                   g(r, cos(omega))\n");
146	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
147	<	printf("      --gxyz                      g(x, y, z)\n");
148	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
149	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
150	<	printf("      --density                   density plot (--sele1 must be specified)\n");
123	>	printf("\nUsage: StaticProps [OPTIONS]...\n\n");
124	>	printf("%s\n","  -h, --help                    Print help and exit");
125	>	printf("%s\n","  -V, --version                 Print version and exit");
126	>	printf("%s\n","  -i, --input=filename          input dump file");
127	>	printf("%s\n","  -o, --output=filename         output file name");
128	>	printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
129	>	printf("%s\n","  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')");
130	>	printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
131	>	printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
132	>	printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
133	>	printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
134	>	printf("%s\n","  -l, --LegendreL=INT           Order of Legendre Polynomial (used for Bond \n                                  Order calculations)");
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","\n Group: staticProps\n   an option of this group is required");
145	>	printf("%s\n","      --bo                      bond order parameter (--rcut and --LegendreL \n                                  must be specified");
146	>	printf("%s\n","  -g, --gofr                    g(r)");
147	>	printf("%s\n","      --r_theta                 g(r, cos(theta))");
148	>	printf("%s\n","      --r_omega                 g(r, cos(omega))");
149	>	printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
150	>	printf("%s\n","      --gxyz                    g(x, y, z)");
151	>	printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
152	>	printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
153	>	printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
154	>	printf("%s\n","  -d, --density                 density plot");
155	>	printf("%s\n","      --slab_density            slab density");
156	>	printf("%s\n","      --hxy                     hxy");
157	>
158		}
159
160	+	void
161	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
162	+	{
163	+	clear_given (args_info);
164	+	clear_args (args_info);
165	+	}
166
167	<	static char *gengetopt_strdup (const char *s);
167	>	static void
168	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
169	>	{
170	>
171	>	if (args_info->input_arg)
172	>	{
173	>	free (args_info->input_arg); /* free previous argument */
174	>	args_info->input_arg = 0;
175	>	}
176	>	if (args_info->input_orig)
177	>	{
178	>	free (args_info->input_orig); /* free previous argument */
179	>	args_info->input_orig = 0;
180	>	}
181	>	if (args_info->output_arg)
182	>	{
183	>	free (args_info->output_arg); /* free previous argument */
184	>	args_info->output_arg = 0;
185	>	}
186	>	if (args_info->output_orig)
187	>	{
188	>	free (args_info->output_orig); /* free previous argument */
189	>	args_info->output_orig = 0;
190	>	}
191	>	if (args_info->step_orig)
192	>	{
193	>	free (args_info->step_orig); /* free previous argument */
194	>	args_info->step_orig = 0;
195	>	}
196	>	if (args_info->nbins_orig)
197	>	{
198	>	free (args_info->nbins_orig); /* free previous argument */
199	>	args_info->nbins_orig = 0;
200	>	}
201	>	if (args_info->nbins_x_orig)
202	>	{
203	>	free (args_info->nbins_x_orig); /* free previous argument */
204	>	args_info->nbins_x_orig = 0;
205	>	}
206	>	if (args_info->nbins_y_orig)
207	>	{
208	>	free (args_info->nbins_y_orig); /* free previous argument */
209	>	args_info->nbins_y_orig = 0;
210	>	}
211	>	if (args_info->nanglebins_orig)
212	>	{
213	>	free (args_info->nanglebins_orig); /* free previous argument */
214	>	args_info->nanglebins_orig = 0;
215	>	}
216	>	if (args_info->length_orig)
217	>	{
218	>	free (args_info->length_orig); /* free previous argument */
219	>	args_info->length_orig = 0;
220	>	}
221	>	if (args_info->LegendreL_orig)
222	>	{
223	>	free (args_info->LegendreL_orig); /* free previous argument */
224	>	args_info->LegendreL_orig = 0;
225	>	}
226	>	if (args_info->rcut_orig)
227	>	{
228	>	free (args_info->rcut_orig); /* free previous argument */
229	>	args_info->rcut_orig = 0;
230	>	}
231	>	if (args_info->zoffset_orig)
232	>	{
233	>	free (args_info->zoffset_orig); /* free previous argument */
234	>	args_info->zoffset_orig = 0;
235	>	}
236	>	if (args_info->sele1_arg)
237	>	{
238	>	free (args_info->sele1_arg); /* free previous argument */
239	>	args_info->sele1_arg = 0;
240	>	}
241	>	if (args_info->sele1_orig)
242	>	{
243	>	free (args_info->sele1_orig); /* free previous argument */
244	>	args_info->sele1_orig = 0;
245	>	}
246	>	if (args_info->sele2_arg)
247	>	{
248	>	free (args_info->sele2_arg); /* free previous argument */
249	>	args_info->sele2_arg = 0;
250	>	}
251	>	if (args_info->sele2_orig)
252	>	{
253	>	free (args_info->sele2_orig); /* free previous argument */
254	>	args_info->sele2_orig = 0;
255	>	}
256	>	if (args_info->sele3_arg)
257	>	{
258	>	free (args_info->sele3_arg); /* free previous argument */
259	>	args_info->sele3_arg = 0;
260	>	}
261	>	if (args_info->sele3_orig)
262	>	{
263	>	free (args_info->sele3_orig); /* free previous argument */
264	>	args_info->sele3_orig = 0;
265	>	}
266	>	if (args_info->refsele_arg)
267	>	{
268	>	free (args_info->refsele_arg); /* free previous argument */
269	>	args_info->refsele_arg = 0;
270	>	}
271	>	if (args_info->refsele_orig)
272	>	{
273	>	free (args_info->refsele_orig); /* free previous argument */
274	>	args_info->refsele_orig = 0;
275	>	}
276	>	if (args_info->molname_arg)
277	>	{
278	>	free (args_info->molname_arg); /* free previous argument */
279	>	args_info->molname_arg = 0;
280	>	}
281	>	if (args_info->molname_orig)
282	>	{
283	>	free (args_info->molname_orig); /* free previous argument */
284	>	args_info->molname_orig = 0;
285	>	}
286	>	if (args_info->begin_orig)
287	>	{
288	>	free (args_info->begin_orig); /* free previous argument */
289	>	args_info->begin_orig = 0;
290	>	}
291	>	if (args_info->end_orig)
292	>	{
293	>	free (args_info->end_orig); /* free previous argument */
294	>	args_info->end_orig = 0;
295	>	}
296	>
297	>	clear_given (args_info);
298	>	}
299	>
300	>	int
301	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
302	>	{
303	>	FILE *outfile;
304	>	int i = 0;
305	>
306	>	outfile = fopen(filename, "w");
307	>
308	>	if (!outfile)
309	>	{
310	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
311	>	return EXIT_FAILURE;
312	>	}
313	>
314	>	if (args_info->help_given) {
315	>	fprintf(outfile, "%s\n", "help");
316	>	}
317	>	if (args_info->version_given) {
318	>	fprintf(outfile, "%s\n", "version");
319	>	}
320	>	if (args_info->input_given) {
321	>	if (args_info->input_orig) {
322	>	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
323	>	} else {
324	>	fprintf(outfile, "%s\n", "input");
325	>	}
326	>	}
327	>	if (args_info->output_given) {
328	>	if (args_info->output_orig) {
329	>	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
330	>	} else {
331	>	fprintf(outfile, "%s\n", "output");
332	>	}
333	>	}
334	>	if (args_info->step_given) {
335	>	if (args_info->step_orig) {
336	>	fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
337	>	} else {
338	>	fprintf(outfile, "%s\n", "step");
339	>	}
340	>	}
341	>	if (args_info->nbins_given) {
342	>	if (args_info->nbins_orig) {
343	>	fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
344	>	} else {
345	>	fprintf(outfile, "%s\n", "nbins");
346	>	}
347	>	}
348	>	if (args_info->nbins_x_given) {
349	>	if (args_info->nbins_x_orig) {
350	>	fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
351	>	} else {
352	>	fprintf(outfile, "%s\n", "nbins_x");
353	>	}
354	>	}
355	>	if (args_info->nbins_y_given) {
356	>	if (args_info->nbins_y_orig) {
357	>	fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
358	>	} else {
359	>	fprintf(outfile, "%s\n", "nbins_y");
360	>	}
361	>	}
362	>	if (args_info->nanglebins_given) {
363	>	if (args_info->nanglebins_orig) {
364	>	fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
365	>	} else {
366	>	fprintf(outfile, "%s\n", "nanglebins");
367	>	}
368	>	}
369	>	if (args_info->length_given) {
370	>	if (args_info->length_orig) {
371	>	fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
372	>	} else {
373	>	fprintf(outfile, "%s\n", "length");
374	>	}
375	>	}
376	>	if (args_info->LegendreL_given) {
377	>	if (args_info->LegendreL_orig) {
378	>	fprintf(outfile, "%s=\"%s\"\n", "LegendreL", args_info->LegendreL_orig);
379	>	} else {
380	>	fprintf(outfile, "%s\n", "LegendreL");
381	>	}
382	>	}
383	>	if (args_info->rcut_given) {
384	>	if (args_info->rcut_orig) {
385	>	fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
386	>	} else {
387	>	fprintf(outfile, "%s\n", "rcut");
388	>	}
389	>	}
390	>	if (args_info->zoffset_given) {
391	>	if (args_info->zoffset_orig) {
392	>	fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
393	>	} else {
394	>	fprintf(outfile, "%s\n", "zoffset");
395	>	}
396	>	}
397	>	if (args_info->sele1_given) {
398	>	if (args_info->sele1_orig) {
399	>	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
400	>	} else {
401	>	fprintf(outfile, "%s\n", "sele1");
402	>	}
403	>	}
404	>	if (args_info->sele2_given) {
405	>	if (args_info->sele2_orig) {
406	>	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
407	>	} else {
408	>	fprintf(outfile, "%s\n", "sele2");
409	>	}
410	>	}
411	>	if (args_info->sele3_given) {
412	>	if (args_info->sele3_orig) {
413	>	fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
414	>	} else {
415	>	fprintf(outfile, "%s\n", "sele3");
416	>	}
417	>	}
418	>	if (args_info->refsele_given) {
419	>	if (args_info->refsele_orig) {
420	>	fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
421	>	} else {
422	>	fprintf(outfile, "%s\n", "refsele");
423	>	}
424	>	}
425	>	if (args_info->molname_given) {
426	>	if (args_info->molname_orig) {
427	>	fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
428	>	} else {
429	>	fprintf(outfile, "%s\n", "molname");
430	>	}
431	>	}
432	>	if (args_info->begin_given) {
433	>	if (args_info->begin_orig) {
434	>	fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
435	>	} else {
436	>	fprintf(outfile, "%s\n", "begin");
437	>	}
438	>	}
439	>	if (args_info->end_given) {
440	>	if (args_info->end_orig) {
441	>	fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
442	>	} else {
443	>	fprintf(outfile, "%s\n", "end");
444	>	}
445	>	}
446	>	if (args_info->bo_given) {
447	>	fprintf(outfile, "%s\n", "bo");
448	>	}
449	>	if (args_info->gofr_given) {
450	>	fprintf(outfile, "%s\n", "gofr");
451	>	}
452	>	if (args_info->r_theta_given) {
453	>	fprintf(outfile, "%s\n", "r_theta");
454	>	}
455	>	if (args_info->r_omega_given) {
456	>	fprintf(outfile, "%s\n", "r_omega");
457	>	}
458	>	if (args_info->theta_omega_given) {
459	>	fprintf(outfile, "%s\n", "theta_omega");
460	>	}
461	>	if (args_info->gxyz_given) {
462	>	fprintf(outfile, "%s\n", "gxyz");
463	>	}
464	>	if (args_info->p2_given) {
465	>	fprintf(outfile, "%s\n", "p2");
466	>	}
467	>	if (args_info->rp2_given) {
468	>	fprintf(outfile, "%s\n", "rp2");
469	>	}
470	>	if (args_info->scd_given) {
471	>	fprintf(outfile, "%s\n", "scd");
472	>	}
473	>	if (args_info->density_given) {
474	>	fprintf(outfile, "%s\n", "density");
475	>	}
476	>	if (args_info->slab_density_given) {
477	>	fprintf(outfile, "%s\n", "slab_density");
478	>	}
479	>	if (args_info->hxy_given) {
480	>	fprintf(outfile, "%s\n", "hxy");
481	>	}
482	>
483	>	fclose (outfile);
484
485	+	i = EXIT_SUCCESS;
486	+	return i;
487	+	}
488	+
489	+	void
490	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
491	+	{
492	+	cmdline_parser_release (args_info);
493	+	}
494	+
495	+
496		/* gengetopt_strdup() */
497		/* strdup.c replacement of strdup, which is not standard */
498		char *
499		gengetopt_strdup (const char *s)
500		{
501	<	char *result = (char*)malloc(strlen(s) + 1);
501	>	char *result = NULL;
502	>	if (!s)
503	>	return result;
504	>
505	>	result = (char*)malloc(strlen(s) + 1);
506		if (result == (char*)0)
507		return (char*)0;
508		strcpy(result, s);
509		return result;
510		}
511
512	<	int
513	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
512	>	static void
513	>	reset_group_staticProps(struct gengetopt_args_info *args_info);
514	>
515	>	static void
516	>	reset_group_staticProps(struct gengetopt_args_info *args_info)
517		{
518	<	int c;        /* Character of the parsed option.  */
519	<	int missing_required_options = 0;
85	<	int staticProps_group_counter = 0;
518	>	if (! args_info->staticProps_group_counter)
519	>	return;
520
521	<
88	<	args_info->help_given = 0 ;
89	<	args_info->version_given = 0 ;
90	<	args_info->input_given = 0 ;
91	<	args_info->output_given = 0 ;
92	<	args_info->step_given = 0 ;
93	<	args_info->nrbins_given = 0 ;
94	<	args_info->nanglebins_given = 0 ;
95	<	args_info->length_given = 0 ;
96	<	args_info->sele1_given = 0 ;
97	<	args_info->sele2_given = 0 ;
98	<	args_info->sele3_given = 0 ;
99	<	args_info->refsele_given = 0 ;
100	<	args_info->molname_given = 0 ;
101	<	args_info->begin_given = 0 ;
102	<	args_info->end_given = 0 ;
521	>	args_info->bo_given = 0 ;
522		args_info->gofr_given = 0 ;
523		args_info->r_theta_given = 0 ;
524		args_info->r_omega_given = 0 ;
525		args_info->theta_omega_given = 0 ;
526		args_info->gxyz_given = 0 ;
527		args_info->p2_given = 0 ;
528	+	args_info->rp2_given = 0 ;
529		args_info->scd_given = 0 ;
530		args_info->density_given = 0 ;
531	<	#define clear_args() { \
532	<	args_info->input_arg = NULL; \
533	<	args_info->output_arg = NULL; \
534	<	args_info->step_arg = 1 ;\
115	<	args_info->nrbins_arg = 100 ;\
116	<	args_info->nanglebins_arg = 50 ;\
117	<	args_info->sele1_arg = NULL; \
118	<	args_info->sele2_arg = NULL; \
119	<	args_info->sele3_arg = NULL; \
120	<	args_info->refsele_arg = NULL; \
121	<	args_info->molname_arg = NULL; \
531	>	args_info->slab_density_given = 0 ;
532	>	args_info->hxy_given = 0 ;
533	>
534	>	args_info->staticProps_group_counter = 0;
535		}
536
537	<	clear_args();
537	>	int
538	>	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
539	>	{
540	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
541	>	}
542
543	+	int
544	+	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
545	+	{
546	+	int result;
547	+
548	+	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
549	+
550	+	if (result == EXIT_FAILURE)
551	+	{
552	+	cmdline_parser_free (args_info);
553	+	exit (EXIT_FAILURE);
554	+	}
555	+
556	+	return result;
557	+	}
558	+
559	+	int
560	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
561	+	{
562	+	int result = EXIT_SUCCESS;
563	+
564	+	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
565	+	result = EXIT_FAILURE;
566	+
567	+	if (result == EXIT_FAILURE)
568	+	{
569	+	cmdline_parser_free (args_info);
570	+	exit (EXIT_FAILURE);
571	+	}
572	+
573	+	return result;
574	+	}
575	+
576	+	int
577	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
578	+	{
579	+	int error = 0;
580	+
581	+	if (! args_info->input_given)
582	+	{
583	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
584	+	error = 1;
585	+	}
586	+	if (args_info->staticProps_group_counter == 0)
587	+	{
588	+	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 : ""));
589	+	error = 1;
590	+	}
591	+
592	+
593	+	return error;
594	+	}
595	+
596	+	int
597	+	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)
598	+	{
599	+	int c;        /* Character of the parsed option.  */
600	+
601	+	int error = 0;
602	+	struct gengetopt_args_info local_args_info;
603	+
604	+	if (initialize)
605	+	cmdline_parser_init (args_info);
606	+
607	+	cmdline_parser_init (&local_args_info);
608	+
609		optarg = 0;
610	<	optind = 1;
610	>	optind = 0;
611		opterr = 1;
612		optopt = '?';
613
#	Line 139 | Line 622 | cmdline_parser (int argc, char * const *argv, struct g
622		{ "input",      1, NULL, 'i' },
623		{ "output",     1, NULL, 'o' },
624		{ "step",       1, NULL, 'n' },
625	<	{ "nrbins",     1, NULL, 'r' },
625	>	{ "nbins",      1, NULL, 'b' },
626	>	{ "nbins_x",    1, NULL, 'x' },
627	>	{ "nbins_y",    1, NULL, 'y' },
628		{ "nanglebins", 1, NULL, 'a' },
629	<	{ "length",     1, NULL, 'l' },
629	>	{ "length",     1, NULL, 0 },
630	>	{ "LegendreL",  1, NULL, 'l' },
631	>	{ "rcut",       1, NULL, 'c' },
632	>	{ "zoffset",    1, NULL, 'z' },
633		{ "sele1",      1, NULL, 0 },
634		{ "sele2",      1, NULL, 0 },
635		{ "sele3",      1, NULL, 0 },
#	Line 149 | Line 637 | cmdline_parser (int argc, char * const *argv, struct g
637		{ "molname",    1, NULL, 0 },
638		{ "begin",      1, NULL, 0 },
639		{ "end",        1, NULL, 0 },
640	<	{ "gofr",       0, NULL, 0 },
640	>	{ "bo", 0, NULL, 0 },
641	>	{ "gofr",       0, NULL, 'g' },
642		{ "r_theta",    0, NULL, 0 },
643		{ "r_omega",    0, NULL, 0 },
644		{ "theta_omega",        0, NULL, 0 },
645		{ "gxyz",       0, NULL, 0 },
646	<	{ "p2", 0, NULL, 0 },
647	<	{ "scd",        0, NULL, 0 },
648	<	{ "density",    0, NULL, 0 },
646	>	{ "p2", 0, NULL, 'p' },
647	>	{ "rp2",        0, NULL, 0 },
648	>	{ "scd",        0, NULL, 's' },
649	>	{ "density",    0, NULL, 'd' },
650	>	{ "slab_density",       0, NULL, 0 },
651	>	{ "hxy",        0, NULL, 0 },
652		{ NULL, 0, NULL, 0 }
653		};
654
655		stop_char = 0;
656	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
656	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:l:c:z:gpsd", long_options, &option_index);
657
658		if (c == -1) break;       /* Exit from `while (1)' loop.  */
659
660		switch (c)
661		{
662		case 'h':       /* Print help and exit.  */
171	–	clear_args ();
663		cmdline_parser_print_help ();
664	+	cmdline_parser_free (&local_args_info);
665		exit (EXIT_SUCCESS);
666
667		case 'V':       /* Print version and exit.  */
176	–	clear_args ();
668		cmdline_parser_print_version ();
669	+	cmdline_parser_free (&local_args_info);
670		exit (EXIT_SUCCESS);
671
672		case 'i':       /* input dump file.  */
673	<	if (args_info->input_given)
673	>	if (local_args_info.input_given)
674		{
675	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
676	<	clear_args ();
185	<	exit (EXIT_FAILURE);
675	>	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
676	>	goto failure;
677		}
678	+	if (args_info->input_given && ! override)
679	+	continue;
680	+	local_args_info.input_given = 1;
681		args_info->input_given = 1;
682	+	if (args_info->input_arg)
683	+	free (args_info->input_arg); /* free previous string */
684		args_info->input_arg = gengetopt_strdup (optarg);
685	+	if (args_info->input_orig)
686	+	free (args_info->input_orig); /* free previous string */
687	+	args_info->input_orig = gengetopt_strdup (optarg);
688		break;
689
690		case 'o':       /* output file name.  */
691	<	if (args_info->output_given)
691	>	if (local_args_info.output_given)
692		{
693	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
694	<	clear_args ();
196	<	exit (EXIT_FAILURE);
693	>	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
694	>	goto failure;
695		}
696	+	if (args_info->output_given && ! override)
697	+	continue;
698	+	local_args_info.output_given = 1;
699		args_info->output_given = 1;
700	+	if (args_info->output_arg)
701	+	free (args_info->output_arg); /* free previous string */
702		args_info->output_arg = gengetopt_strdup (optarg);
703	+	if (args_info->output_orig)
704	+	free (args_info->output_orig); /* free previous string */
705	+	args_info->output_orig = gengetopt_strdup (optarg);
706		break;
707
708		case 'n':       /* process every n frame.  */
709	<	if (args_info->step_given)
709	>	if (local_args_info.step_given)
710		{
711	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
712	<	clear_args ();
207	<	exit (EXIT_FAILURE);
711	>	fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
712	>	goto failure;
713		}
714	+	if (args_info->step_given && ! override)
715	+	continue;
716	+	local_args_info.step_given = 1;
717		args_info->step_given = 1;
718	<	args_info->step_arg = strtol (optarg,&stop_char,0);
718	>	args_info->step_arg = strtol (optarg, &stop_char, 0);
719	>	if (!(stop_char && *stop_char == '\0')) {
720	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
721	>	goto failure;
722	>	}
723	>	if (args_info->step_orig)
724	>	free (args_info->step_orig); /* free previous string */
725	>	args_info->step_orig = gengetopt_strdup (optarg);
726		break;
727
728	<	case 'r':       /* number of bins for distance.  */
729	<	if (args_info->nrbins_given)
728	>	case 'b':       /* number of bins (general purpose).  */
729	>	if (local_args_info.nbins_given)
730		{
731	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
732	<	clear_args ();
218	<	exit (EXIT_FAILURE);
731	>	fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
732	>	goto failure;
733		}
734	<	args_info->nrbins_given = 1;
735	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
734	>	if (args_info->nbins_given && ! override)
735	>	continue;
736	>	local_args_info.nbins_given = 1;
737	>	args_info->nbins_given = 1;
738	>	args_info->nbins_arg = strtol (optarg, &stop_char, 0);
739	>	if (!(stop_char && *stop_char == '\0')) {
740	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
741	>	goto failure;
742	>	}
743	>	if (args_info->nbins_orig)
744	>	free (args_info->nbins_orig); /* free previous string */
745	>	args_info->nbins_orig = gengetopt_strdup (optarg);
746		break;
747
748	+	case 'x':       /* number of bins in x axis.  */
749	+	if (local_args_info.nbins_x_given)
750	+	{
751	+	fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
752	+	goto failure;
753	+	}
754	+	if (args_info->nbins_x_given && ! override)
755	+	continue;
756	+	local_args_info.nbins_x_given = 1;
757	+	args_info->nbins_x_given = 1;
758	+	args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
759	+	if (!(stop_char && *stop_char == '\0')) {
760	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
761	+	goto failure;
762	+	}
763	+	if (args_info->nbins_x_orig)
764	+	free (args_info->nbins_x_orig); /* free previous string */
765	+	args_info->nbins_x_orig = gengetopt_strdup (optarg);
766	+	break;
767	+
768	+	case 'y':       /* number of bins in y axis.  */
769	+	if (local_args_info.nbins_y_given)
770	+	{
771	+	fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
772	+	goto failure;
773	+	}
774	+	if (args_info->nbins_y_given && ! override)
775	+	continue;
776	+	local_args_info.nbins_y_given = 1;
777	+	args_info->nbins_y_given = 1;
778	+	args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
779	+	if (!(stop_char && *stop_char == '\0')) {
780	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
781	+	goto failure;
782	+	}
783	+	if (args_info->nbins_y_orig)
784	+	free (args_info->nbins_y_orig); /* free previous string */
785	+	args_info->nbins_y_orig = gengetopt_strdup (optarg);
786	+	break;
787	+
788		case 'a':       /* number of bins for cos(angle).  */
789	<	if (args_info->nanglebins_given)
789	>	if (local_args_info.nanglebins_given)
790		{
791	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
792	<	clear_args ();
229	<	exit (EXIT_FAILURE);
791	>	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
792	>	goto failure;
793		}
794	+	if (args_info->nanglebins_given && ! override)
795	+	continue;
796	+	local_args_info.nanglebins_given = 1;
797		args_info->nanglebins_given = 1;
798	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
798	>	args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
799	>	if (!(stop_char && *stop_char == '\0')) {
800	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
801	>	goto failure;
802	>	}
803	>	if (args_info->nanglebins_orig)
804	>	free (args_info->nanglebins_orig); /* free previous string */
805	>	args_info->nanglebins_orig = gengetopt_strdup (optarg);
806		break;
807
808	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
809	<	if (args_info->length_given)
808	>	case 'l':       /* Order of Legendre Polynomial (used for Bond Order calculations).  */
809	>	if (local_args_info.LegendreL_given)
810		{
811	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
812	<	clear_args ();
240	<	exit (EXIT_FAILURE);
811	>	fprintf (stderr, "%s: `--LegendreL' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
812	>	goto failure;
813		}
814	<	args_info->length_given = 1;
815	<	args_info->length_arg = strtod (optarg, NULL);
814	>	if (args_info->LegendreL_given && ! override)
815	>	continue;
816	>	local_args_info.LegendreL_given = 1;
817	>	args_info->LegendreL_given = 1;
818	>	args_info->LegendreL_arg = strtol (optarg, &stop_char, 0);
819	>	if (!(stop_char && *stop_char == '\0')) {
820	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
821	>	goto failure;
822	>	}
823	>	if (args_info->LegendreL_orig)
824	>	free (args_info->LegendreL_orig); /* free previous string */
825	>	args_info->LegendreL_orig = gengetopt_strdup (optarg);
826		break;
827
828	+	case 'c':       /* cutoff radius (rcut).  */
829	+	if (local_args_info.rcut_given)
830	+	{
831	+	fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
832	+	goto failure;
833	+	}
834	+	if (args_info->rcut_given && ! override)
835	+	continue;
836	+	local_args_info.rcut_given = 1;
837	+	args_info->rcut_given = 1;
838	+	args_info->rcut_arg = strtod (optarg, &stop_char);
839	+	if (!(stop_char && *stop_char == '\0')) {
840	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
841	+	goto failure;
842	+	}
843	+	if (args_info->rcut_orig)
844	+	free (args_info->rcut_orig); /* free previous string */
845	+	args_info->rcut_orig = gengetopt_strdup (optarg);
846	+	break;
847
848	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
849	+	if (local_args_info.zoffset_given)
850	+	{
851	+	fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
852	+	goto failure;
853	+	}
854	+	if (args_info->zoffset_given && ! override)
855	+	continue;
856	+	local_args_info.zoffset_given = 1;
857	+	args_info->zoffset_given = 1;
858	+	args_info->zoffset_arg = strtod (optarg, &stop_char);
859	+	if (!(stop_char && *stop_char == '\0')) {
860	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
861	+	goto failure;
862	+	}
863	+	if (args_info->zoffset_orig)
864	+	free (args_info->zoffset_orig); /* free previous string */
865	+	args_info->zoffset_orig = gengetopt_strdup (optarg);
866	+	break;
867	+
868	+	case 'g':       /* g(r).  */
869	+	if (local_args_info.gofr_given)
870	+	{
871	+	fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
872	+	goto failure;
873	+	}
874	+	if (args_info->gofr_given && ! override)
875	+	continue;
876	+	local_args_info.gofr_given = 1;
877	+	args_info->gofr_given = 1;
878	+	if (args_info->staticProps_group_counter && override)
879	+	reset_group_staticProps (args_info);
880	+	args_info->staticProps_group_counter += 1;
881	+	break;
882	+
883	+	case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
884	+	if (local_args_info.p2_given)
885	+	{
886	+	fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
887	+	goto failure;
888	+	}
889	+	if (args_info->p2_given && ! override)
890	+	continue;
891	+	local_args_info.p2_given = 1;
892	+	args_info->p2_given = 1;
893	+	if (args_info->staticProps_group_counter && override)
894	+	reset_group_staticProps (args_info);
895	+	args_info->staticProps_group_counter += 1;
896	+	break;
897	+
898	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
899	+	if (local_args_info.scd_given)
900	+	{
901	+	fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
902	+	goto failure;
903	+	}
904	+	if (args_info->scd_given && ! override)
905	+	continue;
906	+	local_args_info.scd_given = 1;
907	+	args_info->scd_given = 1;
908	+	if (args_info->staticProps_group_counter && override)
909	+	reset_group_staticProps (args_info);
910	+	args_info->staticProps_group_counter += 1;
911	+	break;
912	+
913	+	case 'd':       /* density plot.  */
914	+	if (local_args_info.density_given)
915	+	{
916	+	fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	+	goto failure;
918	+	}
919	+	if (args_info->density_given && ! override)
920	+	continue;
921	+	local_args_info.density_given = 1;
922	+	args_info->density_given = 1;
923	+	if (args_info->staticProps_group_counter && override)
924	+	reset_group_staticProps (args_info);
925	+	args_info->staticProps_group_counter += 1;
926	+	break;
927	+
928	+
929		case 0: /* Long option with no short option */
930	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
931	+	if (strcmp (long_options[option_index].name, "length") == 0)
932	+	{
933	+	if (local_args_info.length_given)
934	+	{
935	+	fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
936	+	goto failure;
937	+	}
938	+	if (args_info->length_given && ! override)
939	+	continue;
940	+	local_args_info.length_given = 1;
941	+	args_info->length_given = 1;
942	+	args_info->length_arg = strtod (optarg, &stop_char);
943	+	if (!(stop_char && *stop_char == '\0')) {
944	+	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
945	+	goto failure;
946	+	}
947	+	if (args_info->length_orig)
948	+	free (args_info->length_orig); /* free previous string */
949	+	args_info->length_orig = gengetopt_strdup (optarg);
950	+	}
951		/* select the first stuntdouble set.  */
952	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
952	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
953		{
954	<	if (args_info->sele1_given)
954	>	if (local_args_info.sele1_given)
955		{
956	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
957	<	clear_args ();
255	<	exit (EXIT_FAILURE);
956	>	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
957	>	goto failure;
958		}
959	+	if (args_info->sele1_given && ! override)
960	+	continue;
961	+	local_args_info.sele1_given = 1;
962		args_info->sele1_given = 1;
963	+	if (args_info->sele1_arg)
964	+	free (args_info->sele1_arg); /* free previous string */
965		args_info->sele1_arg = gengetopt_strdup (optarg);
966	<	break;
966	>	if (args_info->sele1_orig)
967	>	free (args_info->sele1_orig); /* free previous string */
968	>	args_info->sele1_orig = gengetopt_strdup (optarg);
969		}
261	–
970		/* select the second stuntdouble set.  */
971		else if (strcmp (long_options[option_index].name, "sele2") == 0)
972		{
973	<	if (args_info->sele2_given)
973	>	if (local_args_info.sele2_given)
974		{
975	<	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
976	<	clear_args ();
269	<	exit (EXIT_FAILURE);
975	>	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
976	>	goto failure;
977		}
978	+	if (args_info->sele2_given && ! override)
979	+	continue;
980	+	local_args_info.sele2_given = 1;
981		args_info->sele2_given = 1;
982	+	if (args_info->sele2_arg)
983	+	free (args_info->sele2_arg); /* free previous string */
984		args_info->sele2_arg = gengetopt_strdup (optarg);
985	<	break;
985	>	if (args_info->sele2_orig)
986	>	free (args_info->sele2_orig); /* free previous string */
987	>	args_info->sele2_orig = gengetopt_strdup (optarg);
988		}
275	–
989		/* select the third stuntdouble set.  */
990		else if (strcmp (long_options[option_index].name, "sele3") == 0)
991		{
992	<	if (args_info->sele3_given)
992	>	if (local_args_info.sele3_given)
993		{
994	<	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
995	<	clear_args ();
283	<	exit (EXIT_FAILURE);
994	>	fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
995	>	goto failure;
996		}
997	+	if (args_info->sele3_given && ! override)
998	+	continue;
999	+	local_args_info.sele3_given = 1;
1000		args_info->sele3_given = 1;
1001	+	if (args_info->sele3_arg)
1002	+	free (args_info->sele3_arg); /* free previous string */
1003		args_info->sele3_arg = gengetopt_strdup (optarg);
1004	<	break;
1004	>	if (args_info->sele3_orig)
1005	>	free (args_info->sele3_orig); /* free previous string */
1006	>	args_info->sele3_orig = gengetopt_strdup (optarg);
1007		}
289	–
1008		/* select reference (use and only use with --gxyz).  */
1009		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1010		{
1011	<	if (args_info->refsele_given)
1011	>	if (local_args_info.refsele_given)
1012		{
1013	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1014	<	clear_args ();
297	<	exit (EXIT_FAILURE);
1013	>	fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1014	>	goto failure;
1015		}
1016	+	if (args_info->refsele_given && ! override)
1017	+	continue;
1018	+	local_args_info.refsele_given = 1;
1019		args_info->refsele_given = 1;
1020	+	if (args_info->refsele_arg)
1021	+	free (args_info->refsele_arg); /* free previous string */
1022		args_info->refsele_arg = gengetopt_strdup (optarg);
1023	<	break;
1023	>	if (args_info->refsele_orig)
1024	>	free (args_info->refsele_orig); /* free previous string */
1025	>	args_info->refsele_orig = gengetopt_strdup (optarg);
1026		}
303	–
1027		/* molecule name.  */
1028		else if (strcmp (long_options[option_index].name, "molname") == 0)
1029		{
1030	<	if (args_info->molname_given)
1030	>	if (local_args_info.molname_given)
1031		{
1032	<	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1033	<	clear_args ();
311	<	exit (EXIT_FAILURE);
1032	>	fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1033	>	goto failure;
1034		}
1035	+	if (args_info->molname_given && ! override)
1036	+	continue;
1037	+	local_args_info.molname_given = 1;
1038		args_info->molname_given = 1;
1039	+	if (args_info->molname_arg)
1040	+	free (args_info->molname_arg); /* free previous string */
1041		args_info->molname_arg = gengetopt_strdup (optarg);
1042	<	break;
1042	>	if (args_info->molname_orig)
1043	>	free (args_info->molname_orig); /* free previous string */
1044	>	args_info->molname_orig = gengetopt_strdup (optarg);
1045		}
1046	<
318	<	/* begin interanl index.  */
1046	>	/* begin internal index.  */
1047		else if (strcmp (long_options[option_index].name, "begin") == 0)
1048		{
1049	<	if (args_info->begin_given)
1049	>	if (local_args_info.begin_given)
1050		{
1051	<	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1052	<	clear_args ();
325	<	exit (EXIT_FAILURE);
1051	>	fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1052	>	goto failure;
1053		}
1054	+	if (args_info->begin_given && ! override)
1055	+	continue;
1056	+	local_args_info.begin_given = 1;
1057		args_info->begin_given = 1;
1058	<	args_info->begin_arg = strtol (optarg,&stop_char,0);
1059	<	break;
1058	>	args_info->begin_arg = strtol (optarg, &stop_char, 0);
1059	>	if (!(stop_char && *stop_char == '\0')) {
1060	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1061	>	goto failure;
1062	>	}
1063	>	if (args_info->begin_orig)
1064	>	free (args_info->begin_orig); /* free previous string */
1065	>	args_info->begin_orig = gengetopt_strdup (optarg);
1066		}
331	–
1067		/* end internal index.  */
1068		else if (strcmp (long_options[option_index].name, "end") == 0)
1069		{
1070	<	if (args_info->end_given)
1070	>	if (local_args_info.end_given)
1071		{
1072	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1073	<	clear_args ();
339	<	exit (EXIT_FAILURE);
1072	>	fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1073	>	goto failure;
1074		}
1075	+	if (args_info->end_given && ! override)
1076	+	continue;
1077	+	local_args_info.end_given = 1;
1078		args_info->end_given = 1;
1079	<	args_info->end_arg = strtol (optarg,&stop_char,0);
1080	<	break;
1079	>	args_info->end_arg = strtol (optarg, &stop_char, 0);
1080	>	if (!(stop_char && *stop_char == '\0')) {
1081	>	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1082	>	goto failure;
1083	>	}
1084	>	if (args_info->end_orig)
1085	>	free (args_info->end_orig); /* free previous string */
1086	>	args_info->end_orig = gengetopt_strdup (optarg);
1087		}
1088	<
1089	<	/* g(r).  */
347	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1088	>	/* bond order parameter (--rcut and --LegendreL must be specified.  */
1089	>	else if (strcmp (long_options[option_index].name, "bo") == 0)
1090		{
1091	<	if (args_info->gofr_given)
1091	>	if (local_args_info.bo_given)
1092		{
1093	<	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1094	<	clear_args ();
353	<	exit (EXIT_FAILURE);
1093	>	fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1094	>	goto failure;
1095		}
1096	<	args_info->gofr_given = 1; staticProps_group_counter += 1;
1097	<
1096	>	if (args_info->bo_given && ! override)
1097	>	continue;
1098	>	local_args_info.bo_given = 1;
1099	>	args_info->bo_given = 1;
1100	>	if (args_info->staticProps_group_counter && override)
1101	>	reset_group_staticProps (args_info);
1102	>	args_info->staticProps_group_counter += 1;
1103		break;
1104		}
359	–
1105		/* g(r, cos(theta)).  */
1106		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1107		{
1108	<	if (args_info->r_theta_given)
1108	>	if (local_args_info.r_theta_given)
1109		{
1110	<	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1111	<	clear_args ();
367	<	exit (EXIT_FAILURE);
1110	>	fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1111	>	goto failure;
1112		}
1113	<	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1114	<
1113	>	if (args_info->r_theta_given && ! override)
1114	>	continue;
1115	>	local_args_info.r_theta_given = 1;
1116	>	args_info->r_theta_given = 1;
1117	>	if (args_info->staticProps_group_counter && override)
1118	>	reset_group_staticProps (args_info);
1119	>	args_info->staticProps_group_counter += 1;
1120		break;
1121		}
373	–
1122		/* g(r, cos(omega)).  */
1123		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1124		{
1125	<	if (args_info->r_omega_given)
1125	>	if (local_args_info.r_omega_given)
1126		{
1127	<	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1128	<	clear_args ();
381	<	exit (EXIT_FAILURE);
1127	>	fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1128	>	goto failure;
1129		}
1130	<	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1131	<
1130	>	if (args_info->r_omega_given && ! override)
1131	>	continue;
1132	>	local_args_info.r_omega_given = 1;
1133	>	args_info->r_omega_given = 1;
1134	>	if (args_info->staticProps_group_counter && override)
1135	>	reset_group_staticProps (args_info);
1136	>	args_info->staticProps_group_counter += 1;
1137		break;
1138		}
387	–
1139		/* g(cos(theta), cos(omega)).  */
1140		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1141		{
1142	<	if (args_info->theta_omega_given)
1142	>	if (local_args_info.theta_omega_given)
1143		{
1144	<	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1145	<	clear_args ();
395	<	exit (EXIT_FAILURE);
1144	>	fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1145	>	goto failure;
1146		}
1147	<	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1148	<
1147	>	if (args_info->theta_omega_given && ! override)
1148	>	continue;
1149	>	local_args_info.theta_omega_given = 1;
1150	>	args_info->theta_omega_given = 1;
1151	>	if (args_info->staticProps_group_counter && override)
1152	>	reset_group_staticProps (args_info);
1153	>	args_info->staticProps_group_counter += 1;
1154		break;
1155		}
401	–
1156		/* g(x, y, z).  */
1157		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1158		{
1159	<	if (args_info->gxyz_given)
1159	>	if (local_args_info.gxyz_given)
1160		{
1161	<	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1162	<	clear_args ();
409	<	exit (EXIT_FAILURE);
1161	>	fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1162	>	goto failure;
1163		}
1164	<	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1165	<
1164	>	if (args_info->gxyz_given && ! override)
1165	>	continue;
1166	>	local_args_info.gxyz_given = 1;
1167	>	args_info->gxyz_given = 1;
1168	>	if (args_info->staticProps_group_counter && override)
1169	>	reset_group_staticProps (args_info);
1170	>	args_info->staticProps_group_counter += 1;
1171		break;
1172		}
1173	<
1174	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
417	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1173	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1174	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1175		{
1176	<	if (args_info->p2_given)
1176	>	if (local_args_info.rp2_given)
1177		{
1178	<	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1179	<	clear_args ();
423	<	exit (EXIT_FAILURE);
1178	>	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1179	>	goto failure;
1180		}
1181	<	args_info->p2_given = 1; staticProps_group_counter += 1;
1182	<
1181	>	if (args_info->rp2_given && ! override)
1182	>	continue;
1183	>	local_args_info.rp2_given = 1;
1184	>	args_info->rp2_given = 1;
1185	>	if (args_info->staticProps_group_counter && override)
1186	>	reset_group_staticProps (args_info);
1187	>	args_info->staticProps_group_counter += 1;
1188		break;
1189		}
1190	<
1191	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
431	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1190	>	/* slab density.  */
1191	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1192		{
1193	<	if (args_info->scd_given)
1193	>	if (local_args_info.slab_density_given)
1194		{
1195	<	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1196	<	clear_args ();
437	<	exit (EXIT_FAILURE);
1195	>	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1196	>	goto failure;
1197		}
1198	<	args_info->scd_given = 1; staticProps_group_counter += 1;
1199	<
1198	>	if (args_info->slab_density_given && ! override)
1199	>	continue;
1200	>	local_args_info.slab_density_given = 1;
1201	>	args_info->slab_density_given = 1;
1202	>	if (args_info->staticProps_group_counter && override)
1203	>	reset_group_staticProps (args_info);
1204	>	args_info->staticProps_group_counter += 1;
1205		break;
1206		}
1207	<
1208	<	/* density plot (--sele1 must be specified).  */
445	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1207	>	/* hxy.  */
1208	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1209		{
1210	<	if (args_info->density_given)
1210	>	if (local_args_info.hxy_given)
1211		{
1212	<	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1213	<	clear_args ();
451	<	exit (EXIT_FAILURE);
1212	>	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1213	>	goto failure;
1214		}
1215	<	args_info->density_given = 1; staticProps_group_counter += 1;
1216	<
1215	>	if (args_info->hxy_given && ! override)
1216	>	continue;
1217	>	local_args_info.hxy_given = 1;
1218	>	args_info->hxy_given = 1;
1219	>	if (args_info->staticProps_group_counter && override)
1220	>	reset_group_staticProps (args_info);
1221	>	args_info->staticProps_group_counter += 1;
1222		break;
1223		}
1224
1225	<
1225	>	break;
1226		case '?':       /* Invalid option.  */
1227		/* `getopt_long' already printed an error message.  */
1228	<	exit (EXIT_FAILURE);
1228	>	goto failure;
1229
1230		default:        /* bug: option not considered.  */
1231	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1231	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1232		abort ();
1233		} /* switch */
1234		} /* while */
1235
1236	<	if ( staticProps_group_counter != 1)
1236	>	if (args_info->staticProps_group_counter > 1)
1237		{
1238	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1239	<	missing_required_options = 1;
1238	>	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 : ""));
1239	>	error = 1;
1240		}
1241
1242
1243	<	if (! args_info->input_given)
1243	>
1244	>	if (check_required)
1245		{
1246	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
479	<	missing_required_options = 1;
1246	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1247		}
481	–	if ( missing_required_options )
482	–	exit (EXIT_FAILURE);
1248
1249	+	cmdline_parser_release (&local_args_info);
1250	+
1251	+	if ( error )
1252	+	return (EXIT_FAILURE);
1253	+
1254		return 0;
1255	+
1256	+	failure:
1257	+
1258	+	cmdline_parser_release (&local_args_info);
1259	+	return (EXIT_FAILURE);
1260		}

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