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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 2539 by tim, Mon Jan 9 22:14:32 2006 UTC vs.
Revision 3076 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/program/gengetopt-2.11/src/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"
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, --step=INT                  process every n frame  (default=`1')\n");
132	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
133	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
134	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
135	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
136	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
137	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
138	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
139	<	printf("      --molname=STRING            molecule name\n");
140	<	printf("      --begin=INT                 begin interanl index\n");
141	<	printf("      --end=INT                   end internal index\n");
142	<	printf("\n");
143	<	printf(" Group: staticProps  an option of this group is required\n");
144	<	printf("      --gofr                      g(r)\n");
145	<	printf("      --r_theta                   g(r, cos(theta))\n");
146	<	printf("      --r_omega                   g(r, cos(omega))\n");
147	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
148	<	printf("      --gxyz                      g(x, y, z)\n");
149	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
150	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
151	<	printf("      --density                   density plot (--sele1 must be specified)\n");
152	<	printf("      --slab_density              slab density (--sele1 must be specified)\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;
86	<	int staticProps_group_counter = 0;
523	>	if (! args_info->staticProps_group_counter)
524	>	return;
525
526	<
89	<	args_info->help_given = 0 ;
90	<	args_info->version_given = 0 ;
91	<	args_info->input_given = 0 ;
92	<	args_info->output_given = 0 ;
93	<	args_info->step_given = 0 ;
94	<	args_info->nrbins_given = 0 ;
95	<	args_info->nanglebins_given = 0 ;
96	<	args_info->length_given = 0 ;
97	<	args_info->sele1_given = 0 ;
98	<	args_info->sele2_given = 0 ;
99	<	args_info->sele3_given = 0 ;
100	<	args_info->refsele_given = 0 ;
101	<	args_info->molname_given = 0 ;
102	<	args_info->begin_given = 0 ;
103	<	args_info->end_given = 0 ;
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->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	<	#define clear_args() { \
538	<	args_info->input_arg = NULL; \
539	<	args_info->output_arg = NULL; \
540	<	args_info->step_arg = 1 ;\
117	<	args_info->nrbins_arg = 100 ;\
118	<	args_info->nanglebins_arg = 50 ;\
119	<	args_info->sele1_arg = NULL; \
120	<	args_info->sele2_arg = NULL; \
121	<	args_info->sele3_arg = NULL; \
122	<	args_info->refsele_arg = NULL; \
123	<	args_info->molname_arg = NULL; \
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 141 | Line 628 | cmdline_parser (int argc, char * const *argv, struct g
628		{ "input",      1, NULL, 'i' },
629		{ "output",     1, NULL, 'o' },
630		{ "step",       1, NULL, 'n' },
631	<	{ "nrbins",     1, NULL, 'r' },
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		{ "sele3",      1, NULL, 0 },
#	Line 151 | Line 642 | cmdline_parser (int argc, char * const *argv, struct g
642		{ "molname",    1, NULL, 0 },
643		{ "begin",      1, NULL, 0 },
644		{ "end",        1, NULL, 0 },
645	<	{ "gofr",       0, 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		{ "gxyz",       0, NULL, 0 },
652	<	{ "p2", 0, NULL, 0 },
653	<	{ "scd",        0, NULL, 0 },
654	<	{ "density",    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:r: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.  */
174	–	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.  */
179	–	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 ();
188	<	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 ();
199	<	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':       /* process every n frame.  */
716	<	if (args_info->step_given)
716	>	if (local_args_info.step_given)
717		{
718	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
719	<	clear_args ();
210	<	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	+	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);
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 'r':       /* number of bins for distance.  */
736	<	if (args_info->nrbins_given)
735	>	case 'b':       /* number of bins (general purpose).  */
736	>	if (local_args_info.nbins_given)
737		{
738	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
739	<	clear_args ();
221	<	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->nrbins_given = 1;
742	<	args_info->nrbins_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 ();
232	<	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 (Defaults to 1/2 smallest length of first frame).  */
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 ();
243	<	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	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
918	+	if (strcmp (long_options[option_index].name, "length") == 0)
919	+	{
920	+	if (local_args_info.length_given)
921	+	{
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	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
939	>	else if (strcmp (long_options[option_index].name, "sele1") == 0)
940		{
941	<	if (args_info->sele1_given)
941	>	if (local_args_info.sele1_given)
942		{
943	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
944	<	clear_args ();
258	<	exit (EXIT_FAILURE);
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		}
264	–
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 ();
272	<	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		}
278	–
976		/* select the third stuntdouble set.  */
977		else if (strcmp (long_options[option_index].name, "sele3") == 0)
978		{
979	<	if (args_info->sele3_given)
979	>	if (local_args_info.sele3_given)
980		{
981	<	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
982	<	clear_args ();
286	<	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	+	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	<	break;
991	>	if (args_info->sele3_orig)
992	>	free (args_info->sele3_orig); /* free previous string */
993	>	args_info->sele3_orig = gengetopt_strdup (optarg);
994		}
292	–
995		/* select reference (use and only use with --gxyz).  */
996		else if (strcmp (long_options[option_index].name, "refsele") == 0)
997		{
998	<	if (args_info->refsele_given)
998	>	if (local_args_info.refsele_given)
999		{
1000	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1001	<	clear_args ();
300	<	exit (EXIT_FAILURE);
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	<	break;
1010	>	if (args_info->refsele_orig)
1011	>	free (args_info->refsele_orig); /* free previous string */
1012	>	args_info->refsele_orig = gengetopt_strdup (optarg);
1013		}
306	–
1014		/* molecule name.  */
1015		else if (strcmp (long_options[option_index].name, "molname") == 0)
1016		{
1017	<	if (args_info->molname_given)
1017	>	if (local_args_info.molname_given)
1018		{
1019	<	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1020	<	clear_args ();
314	<	exit (EXIT_FAILURE);
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	<	break;
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	<
321	<	/* begin interanl index.  */
1033	>	/* begin internal index.  */
1034		else if (strcmp (long_options[option_index].name, "begin") == 0)
1035		{
1036	<	if (args_info->begin_given)
1036	>	if (local_args_info.begin_given)
1037		{
1038	<	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1039	<	clear_args ();
328	<	exit (EXIT_FAILURE);
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	<	break;
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		}
334	–
1054		/* end internal index.  */
1055		else if (strcmp (long_options[option_index].name, "end") == 0)
1056		{
1057	<	if (args_info->end_given)
1057	>	if (local_args_info.end_given)
1058		{
1059	<	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1060	<	clear_args ();
342	<	exit (EXIT_FAILURE);
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	<	break;
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	<
1076	<	/* g(r).  */
350	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1075	>	/* nanoparticle radius.  */
1076	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1077		{
1078	<	if (args_info->gofr_given)
1078	>	if (local_args_info.radius_given)
1079		{
1080	<	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1081	<	clear_args ();
356	<	exit (EXIT_FAILURE);
1080	>	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1081	>	goto failure;
1082		}
1083	<	args_info->gofr_given = 1; staticProps_group_counter += 1;
1084	<
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		}
362	–
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 ();
370	<	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		}
376	–
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 ();
384	<	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		}
390	–
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 ();
398	<	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		}
404	–
1164		/* g(x, y, z).  */
1165		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1166		{
1167	<	if (args_info->gxyz_given)
1167	>	if (local_args_info.gxyz_given)
1168		{
1169	<	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1170	<	clear_args ();
412	<	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->gxyz_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	<
1182	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
420	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1181	>	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1182	>	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1183		{
1184	<	if (args_info->p2_given)
1184	>	if (local_args_info.rp2_given)
1185		{
1186	<	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1187	<	clear_args ();
426	<	exit (EXIT_FAILURE);
1186	>	fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1187	>	goto failure;
1188		}
1189	<	args_info->p2_given = 1; staticProps_group_counter += 1;
1190	<
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	<
1199	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
434	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1198	>	/* slab density.  */
1199	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1200		{
1201	<	if (args_info->scd_given)
1201	>	if (local_args_info.slab_density_given)
1202		{
1203	<	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1204	<	clear_args ();
440	<	exit (EXIT_FAILURE);
1203	>	fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1204	>	goto failure;
1205		}
1206	<	args_info->scd_given = 1; staticProps_group_counter += 1;
1207	<
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	<
1216	<	/* density plot (--sele1 must be specified).  */
448	<	else if (strcmp (long_options[option_index].name, "density") == 0)
1215	>	/* hxy.  */
1216	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1217		{
1218	<	if (args_info->density_given)
1218	>	if (local_args_info.hxy_given)
1219		{
1220	<	fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1221	<	clear_args ();
454	<	exit (EXIT_FAILURE);
1220	>	fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1221	>	goto failure;
1222		}
1223	<	args_info->density_given = 1; staticProps_group_counter += 1;
1224	<
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	<
1233	<	/* slab density (--sele1 must be specified).  */
462	<	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1232	>	/* rho of R.  */
1233	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1234		{
1235	<	if (args_info->slab_density_given)
1235	>	if (local_args_info.rho_r_given)
1236		{
1237	<	fprintf (stderr, "%s: `--slab_density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1238	<	clear_args ();
468	<	exit (EXIT_FAILURE);
1237	>	fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1238	>	goto failure;
1239		}
1240	<	args_info->slab_density_given = 1; staticProps_group_counter += 1;
1241	<
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);
496	<	missing_required_options = 1;
1271	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1272		}
498	–	if ( missing_required_options )
499	–	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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