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root/OpenMD/trunk/src/applications/dump2Xyz/Dump2XYZCmd.cpp

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZCmd.c (file contents), Revision 302 by tim, Mon Feb 7 21:11:22 2005 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZCmd.c (file contents), Revision 1630 by gezelter, Wed Sep 14 21:40:12 2011 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd
4	>	gengetopt -F Dump2XYZCmd -u
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
8		we make no copyright claims on it.
9		*/
10
11	+	/* 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	<	/* If we use autoconf.  */
21	<	#ifdef HAVE_CONFIG_H
18	<	#include "config.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22		#endif
23
24	<	#include "getopt.h"
24	>	#include <getopt.h>
25
26		#include "Dump2XYZCmd.h"
27
28	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
28	>	const char *gengetopt_args_info_purpose = "";
29
30	<	void
32	<	cmdline_parser_print_help (void)
33	<	{
34	<	cmdline_parser_print_version ();
35	<	printf("\n"
36	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	<	printf("\n");
38	<	printf("  -h, --help                        Print help and exit\n");
39	<	printf("  -V, --version                     Print version and exit\n");
40	<	printf("  -i, --input=filename              input dump file\n");
41	<	printf("  -o, --output=filename             output file name\n");
42	<	printf("  -n, --frame=INT                   print every n frame  (default=`1')\n");
43	<	printf("  -d, --dipole                      print the dipole moments  (default=off)\n");
44	<	printf("  -w, --water                       skip the the waters  (default=off)\n");
45	<	printf("  -m, --periodicBox                 map to the periodic box  (default=off)\n");
46	<	printf("  -z, --zconstraint                 replace the atom types of zconstraint \n                                      molecules  (default=off)\n");
47	<	printf("  -r, --rigidbody                   add a pseudo COM atom to rigidbody  \n                                      (default=off)\n");
48	<	printf("  -t, --watertype                   replace the atom type of water model  \n                                      (default=on)\n");
49	<	printf("  -g, --ignore=atomtype             ignore the atom types\n");
50	<	printf("  -s, --selection=selection script  selection syntax:\n"
51	<	"                                    select DMPC -- select DMPC molecule\n"
52	<	"                                    select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n"
53	<	"                                    select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n"
54	<	"                                    select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n"
55	<	"                                    select 5 -- select stuntdobule whose global index is 5\n"
56	<	"                                    select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n"
57	<	"                                    select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n");
58	<	printf("      --repeatX=INT                 The number of images to repeat in the x \n                                      direction  (default=`0')\n");
59	<	printf("      --repeatY=INT                 The number of images to repeat in the y \n                                      direction  (default=`0')\n");
60	<	printf("      --repeatZ=INT                 The number of images to repeat in the z \n                                      direction  (default=`0')\n");
61	<	}
30	>	const char *gengetopt_args_info_usage = "Usage: Dump2XYZ [OPTIONS]... [FILES]...";
31
32	+	const char *gengetopt_args_info_description = "";
33
34	<	static char *gengetopt_strdup (const char *s);
34	>	const char *gengetopt_args_info_help[] = {
35	>	"  -h, --help                    Print help and exit",
36	>	"  -V, --version                 Print version and exit",
37	>	"  -i, --input=filename          input dump file",
38	>	"  -o, --output=filename         output file name",
39	>	"  -n, --frame=INT               print every n frame  (default=`1')",
40	>	"  -w, --water                   skip the the waters  (default=off)",
41	>	"  -m, --periodicBox             map to the periodic box  (default=off)",
42	>	"  -z, --zconstraint             replace the atom types of zconstraint molecules \n                                   (default=off)",
43	>	"  -r, --rigidbody               add a pseudo COM atom to rigidbody  \n                                  (default=off)",
44	>	"  -t, --watertype               replace the atom type of water model  \n                                  (default=on)",
45	>	"  -s, --selection=selection script\n                                general selection syntax",
46	>	"      --originsele=selection script\n                                select origin",
47	>	"      --refsele=selection script\n                                select reference",
48	>	"      --repeatX=INT             The number of images to repeat in the x \n                                  direction  (default=`0')",
49	>	"      --repeatY=INT             The number of images to repeat in the y \n                                  direction  (default=`0')",
50	>	"      --repeatZ=INT             The number of images to repeat in the z \n                                  direction  (default=`0')",
51	>	"  -b, --basetype                Convert to base atom type  (default=off)",
52	>	"  -v, --velocities              Print velocities in xyz file  (default=off)",
53	>	"  -f, --forces                  Print forces xyz file  (default=off)",
54	>	"  -u, --vectors                 Print vectors (dipoles, etc) in xyz file  \n                                  (default=off)",
55	>	"  -c, --charges                 Print charges in xyz file  (default=off)",
56	>	0
57	>	};
58
59	<	/* gengetopt_strdup() */
60	<	/* strdup.c replacement of strdup, which is not standard */
61	<	char *
62	<	gengetopt_strdup (const char *s)
63	<	{
71	<	char *result = (char*)malloc(strlen(s) + 1);
72	<	if (result == (char*)0)
73	<	return (char*)0;
74	<	strcpy(result, s);
75	<	return result;
76	<	}
59	>	typedef enum {ARG_NO
60	>	, ARG_FLAG
61	>	, ARG_STRING
62	>	, ARG_INT
63	>	} cmdline_parser_arg_type;
64
65	<	int
66	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
67	<	{
68	<	int c;        /* Character of the parsed option.  */
82	<	int i;        /* Counter */
83	<	struct ignore_list
84	<	{
85	<	char * ignore_arg;
86	<	struct ignore_list * next;
87	<	};
88	<	struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
89	<
90	<	int missing_required_options = 0;
65	>	static
66	>	void clear_given (struct gengetopt_args_info *args_info);
67	>	static
68	>	void clear_args (struct gengetopt_args_info *args_info);
69
70	+	static int
71	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
72	+	struct cmdline_parser_params *params, const char *additional_error);
73	+
74	+	static int
75	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
76	+
77	+	static char *
78	+	gengetopt_strdup (const char *s);
79	+
80	+	static
81	+	void clear_given (struct gengetopt_args_info *args_info)
82	+	{
83		args_info->help_given = 0 ;
84		args_info->version_given = 0 ;
85		args_info->input_given = 0 ;
86		args_info->output_given = 0 ;
87		args_info->frame_given = 0 ;
97	–	args_info->dipole_given = 0 ;
88		args_info->water_given = 0 ;
89		args_info->periodicBox_given = 0 ;
90		args_info->zconstraint_given = 0 ;
91		args_info->rigidbody_given = 0 ;
92		args_info->watertype_given = 0 ;
103	–	args_info->ignore_given = 0 ;
93		args_info->selection_given = 0 ;
94	+	args_info->originsele_given = 0 ;
95	+	args_info->refsele_given = 0 ;
96		args_info->repeatX_given = 0 ;
97		args_info->repeatY_given = 0 ;
98		args_info->repeatZ_given = 0 ;
99	<	#define clear_args() { \
100	<	args_info->input_arg = NULL; \
101	<	args_info->output_arg = NULL; \
102	<	args_info->frame_arg = 1 ;\
103	<	args_info->dipole_flag = 0;\
113	<	args_info->water_flag = 0;\
114	<	args_info->periodicBox_flag = 0;\
115	<	args_info->zconstraint_flag = 0;\
116	<	args_info->rigidbody_flag = 0;\
117	<	args_info->watertype_flag = 1;\
118	<	args_info->ignore_arg = NULL; \
119	<	args_info->selection_arg = NULL; \
120	<	args_info->repeatX_arg = 0 ;\
121	<	args_info->repeatY_arg = 0 ;\
122	<	args_info->repeatZ_arg = 0 ;\
99	>	args_info->basetype_given = 0 ;
100	>	args_info->velocities_given = 0 ;
101	>	args_info->forces_given = 0 ;
102	>	args_info->vectors_given = 0 ;
103	>	args_info->charges_given = 0 ;
104		}
105
106	<	clear_args();
106	>	static
107	>	void clear_args (struct gengetopt_args_info *args_info)
108	>	{
109	>	FIX_UNUSED (args_info);
110	>	args_info->input_arg = NULL;
111	>	args_info->input_orig = NULL;
112	>	args_info->output_arg = NULL;
113	>	args_info->output_orig = NULL;
114	>	args_info->frame_arg = 1;
115	>	args_info->frame_orig = NULL;
116	>	args_info->water_flag = 0;
117	>	args_info->periodicBox_flag = 0;
118	>	args_info->zconstraint_flag = 0;
119	>	args_info->rigidbody_flag = 0;
120	>	args_info->watertype_flag = 1;
121	>	args_info->selection_arg = NULL;
122	>	args_info->selection_orig = NULL;
123	>	args_info->originsele_arg = NULL;
124	>	args_info->originsele_orig = NULL;
125	>	args_info->refsele_arg = NULL;
126	>	args_info->refsele_orig = NULL;
127	>	args_info->repeatX_arg = 0;
128	>	args_info->repeatX_orig = NULL;
129	>	args_info->repeatY_arg = 0;
130	>	args_info->repeatY_orig = NULL;
131	>	args_info->repeatZ_arg = 0;
132	>	args_info->repeatZ_orig = NULL;
133	>	args_info->basetype_flag = 0;
134	>	args_info->velocities_flag = 0;
135	>	args_info->forces_flag = 0;
136	>	args_info->vectors_flag = 0;
137	>	args_info->charges_flag = 0;
138	>
139	>	}
140
141	+	static
142	+	void init_args_info(struct gengetopt_args_info *args_info)
143	+	{
144	+
145	+
146	+	args_info->help_help = gengetopt_args_info_help[0] ;
147	+	args_info->version_help = gengetopt_args_info_help[1] ;
148	+	args_info->input_help = gengetopt_args_info_help[2] ;
149	+	args_info->output_help = gengetopt_args_info_help[3] ;
150	+	args_info->frame_help = gengetopt_args_info_help[4] ;
151	+	args_info->water_help = gengetopt_args_info_help[5] ;
152	+	args_info->periodicBox_help = gengetopt_args_info_help[6] ;
153	+	args_info->zconstraint_help = gengetopt_args_info_help[7] ;
154	+	args_info->rigidbody_help = gengetopt_args_info_help[8] ;
155	+	args_info->watertype_help = gengetopt_args_info_help[9] ;
156	+	args_info->selection_help = gengetopt_args_info_help[10] ;
157	+	args_info->originsele_help = gengetopt_args_info_help[11] ;
158	+	args_info->refsele_help = gengetopt_args_info_help[12] ;
159	+	args_info->repeatX_help = gengetopt_args_info_help[13] ;
160	+	args_info->repeatY_help = gengetopt_args_info_help[14] ;
161	+	args_info->repeatZ_help = gengetopt_args_info_help[15] ;
162	+	args_info->basetype_help = gengetopt_args_info_help[16] ;
163	+	args_info->velocities_help = gengetopt_args_info_help[17] ;
164	+	args_info->forces_help = gengetopt_args_info_help[18] ;
165	+	args_info->vectors_help = gengetopt_args_info_help[19] ;
166	+	args_info->charges_help = gengetopt_args_info_help[20] ;
167	+
168	+	}
169	+
170	+	void
171	+	cmdline_parser_print_version (void)
172	+	{
173	+	printf ("%s %s\n",
174	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
175	+	CMDLINE_PARSER_VERSION);
176	+	}
177	+
178	+	static void print_help_common(void) {
179	+	cmdline_parser_print_version ();
180	+
181	+	if (strlen(gengetopt_args_info_purpose) > 0)
182	+	printf("\n%s\n", gengetopt_args_info_purpose);
183	+
184	+	if (strlen(gengetopt_args_info_usage) > 0)
185	+	printf("\n%s\n", gengetopt_args_info_usage);
186	+
187	+	printf("\n");
188	+
189	+	if (strlen(gengetopt_args_info_description) > 0)
190	+	printf("%s\n\n", gengetopt_args_info_description);
191	+	}
192	+
193	+	void
194	+	cmdline_parser_print_help (void)
195	+	{
196	+	int i = 0;
197	+	print_help_common();
198	+	while (gengetopt_args_info_help[i])
199	+	printf("%s\n", gengetopt_args_info_help[i++]);
200	+	}
201	+
202	+	void
203	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
204	+	{
205	+	clear_given (args_info);
206	+	clear_args (args_info);
207	+	init_args_info (args_info);
208	+
209	+	args_info->inputs = 0;
210	+	args_info->inputs_num = 0;
211	+	}
212	+
213	+	void
214	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
215	+	{
216	+	if (params)
217	+	{
218	+	params->override = 0;
219	+	params->initialize = 1;
220	+	params->check_required = 1;
221	+	params->check_ambiguity = 0;
222	+	params->print_errors = 1;
223	+	}
224	+	}
225	+
226	+	struct cmdline_parser_params *
227	+	cmdline_parser_params_create(void)
228	+	{
229	+	struct cmdline_parser_params *params =
230	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
231	+	cmdline_parser_params_init(params);
232	+	return params;
233	+	}
234	+
235	+	static void
236	+	free_string_field (char **s)
237	+	{
238	+	if (*s)
239	+	{
240	+	free (*s);
241	+	*s = 0;
242	+	}
243	+	}
244	+
245	+
246	+	static void
247	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
248	+	{
249	+	unsigned int i;
250	+	free_string_field (&(args_info->input_arg));
251	+	free_string_field (&(args_info->input_orig));
252	+	free_string_field (&(args_info->output_arg));
253	+	free_string_field (&(args_info->output_orig));
254	+	free_string_field (&(args_info->frame_orig));
255	+	free_string_field (&(args_info->selection_arg));
256	+	free_string_field (&(args_info->selection_orig));
257	+	free_string_field (&(args_info->originsele_arg));
258	+	free_string_field (&(args_info->originsele_orig));
259	+	free_string_field (&(args_info->refsele_arg));
260	+	free_string_field (&(args_info->refsele_orig));
261	+	free_string_field (&(args_info->repeatX_orig));
262	+	free_string_field (&(args_info->repeatY_orig));
263	+	free_string_field (&(args_info->repeatZ_orig));
264	+
265	+
266	+	for (i = 0; i < args_info->inputs_num; ++i)
267	+	free (args_info->inputs [i]);
268	+
269	+	if (args_info->inputs_num)
270	+	free (args_info->inputs);
271	+
272	+	clear_given (args_info);
273	+	}
274	+
275	+
276	+	static void
277	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
278	+	{
279	+	FIX_UNUSED (values);
280	+	if (arg) {
281	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
282	+	} else {
283	+	fprintf(outfile, "%s\n", opt);
284	+	}
285	+	}
286	+
287	+
288	+	int
289	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
290	+	{
291	+	int i = 0;
292	+
293	+	if (!outfile)
294	+	{
295	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
296	+	return EXIT_FAILURE;
297	+	}
298	+
299	+	if (args_info->help_given)
300	+	write_into_file(outfile, "help", 0, 0 );
301	+	if (args_info->version_given)
302	+	write_into_file(outfile, "version", 0, 0 );
303	+	if (args_info->input_given)
304	+	write_into_file(outfile, "input", args_info->input_orig, 0);
305	+	if (args_info->output_given)
306	+	write_into_file(outfile, "output", args_info->output_orig, 0);
307	+	if (args_info->frame_given)
308	+	write_into_file(outfile, "frame", args_info->frame_orig, 0);
309	+	if (args_info->water_given)
310	+	write_into_file(outfile, "water", 0, 0 );
311	+	if (args_info->periodicBox_given)
312	+	write_into_file(outfile, "periodicBox", 0, 0 );
313	+	if (args_info->zconstraint_given)
314	+	write_into_file(outfile, "zconstraint", 0, 0 );
315	+	if (args_info->rigidbody_given)
316	+	write_into_file(outfile, "rigidbody", 0, 0 );
317	+	if (args_info->watertype_given)
318	+	write_into_file(outfile, "watertype", 0, 0 );
319	+	if (args_info->selection_given)
320	+	write_into_file(outfile, "selection", args_info->selection_orig, 0);
321	+	if (args_info->originsele_given)
322	+	write_into_file(outfile, "originsele", args_info->originsele_orig, 0);
323	+	if (args_info->refsele_given)
324	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
325	+	if (args_info->repeatX_given)
326	+	write_into_file(outfile, "repeatX", args_info->repeatX_orig, 0);
327	+	if (args_info->repeatY_given)
328	+	write_into_file(outfile, "repeatY", args_info->repeatY_orig, 0);
329	+	if (args_info->repeatZ_given)
330	+	write_into_file(outfile, "repeatZ", args_info->repeatZ_orig, 0);
331	+	if (args_info->basetype_given)
332	+	write_into_file(outfile, "basetype", 0, 0 );
333	+	if (args_info->velocities_given)
334	+	write_into_file(outfile, "velocities", 0, 0 );
335	+	if (args_info->forces_given)
336	+	write_into_file(outfile, "forces", 0, 0 );
337	+	if (args_info->vectors_given)
338	+	write_into_file(outfile, "vectors", 0, 0 );
339	+	if (args_info->charges_given)
340	+	write_into_file(outfile, "charges", 0, 0 );
341	+
342	+
343	+	i = EXIT_SUCCESS;
344	+	return i;
345	+	}
346	+
347	+	int
348	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
349	+	{
350	+	FILE *outfile;
351	+	int i = 0;
352	+
353	+	outfile = fopen(filename, "w");
354	+
355	+	if (!outfile)
356	+	{
357	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
358	+	return EXIT_FAILURE;
359	+	}
360	+
361	+	i = cmdline_parser_dump(outfile, args_info);
362	+	fclose (outfile);
363	+
364	+	return i;
365	+	}
366	+
367	+	void
368	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
369	+	{
370	+	cmdline_parser_release (args_info);
371	+	}
372	+
373	+	/** @brief replacement of strdup, which is not standard */
374	+	char *
375	+	gengetopt_strdup (const char *s)
376	+	{
377	+	char *result = 0;
378	+	if (!s)
379	+	return result;
380	+
381	+	result = (char*)malloc(strlen(s) + 1);
382	+	if (result == (char*)0)
383	+	return (char*)0;
384	+	strcpy(result, s);
385	+	return result;
386	+	}
387	+
388	+	int
389	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
390	+	{
391	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
392	+	}
393	+
394	+	int
395	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
396	+	struct cmdline_parser_params *params)
397	+	{
398	+	int result;
399	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
400	+
401	+	if (result == EXIT_FAILURE)
402	+	{
403	+	cmdline_parser_free (args_info);
404	+	exit (EXIT_FAILURE);
405	+	}
406	+
407	+	return result;
408	+	}
409	+
410	+	int
411	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
412	+	{
413	+	int result;
414	+	struct cmdline_parser_params params;
415	+
416	+	params.override = override;
417	+	params.initialize = initialize;
418	+	params.check_required = check_required;
419	+	params.check_ambiguity = 0;
420	+	params.print_errors = 1;
421	+
422	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
423	+
424	+	if (result == EXIT_FAILURE)
425	+	{
426	+	cmdline_parser_free (args_info);
427	+	exit (EXIT_FAILURE);
428	+	}
429	+
430	+	return result;
431	+	}
432	+
433	+	int
434	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
435	+	{
436	+	int result = EXIT_SUCCESS;
437	+
438	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
439	+	result = EXIT_FAILURE;
440	+
441	+	if (result == EXIT_FAILURE)
442	+	{
443	+	cmdline_parser_free (args_info);
444	+	exit (EXIT_FAILURE);
445	+	}
446	+
447	+	return result;
448	+	}
449	+
450	+	int
451	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
452	+	{
453	+	int error = 0;
454	+	FIX_UNUSED (additional_error);
455	+
456	+	/* checks for required options */
457	+	if (! args_info->input_given)
458	+	{
459	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
460	+	error = 1;
461	+	}
462	+
463	+
464	+	/* checks for dependences among options */
465	+
466	+	return error;
467	+	}
468	+
469	+
470	+	static char *package_name = 0;
471	+
472	+	/**
473	+	* @brief updates an option
474	+	* @param field the generic pointer to the field to update
475	+	* @param orig_field the pointer to the orig field
476	+	* @param field_given the pointer to the number of occurrence of this option
477	+	* @param prev_given the pointer to the number of occurrence already seen
478	+	* @param value the argument for this option (if null no arg was specified)
479	+	* @param possible_values the possible values for this option (if specified)
480	+	* @param default_value the default value (in case the option only accepts fixed values)
481	+	* @param arg_type the type of this option
482	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
483	+	* @param override @see cmdline_parser_params.override
484	+	* @param no_free whether to free a possible previous value
485	+	* @param multiple_option whether this is a multiple option
486	+	* @param long_opt the corresponding long option
487	+	* @param short_opt the corresponding short option (or '-' if none)
488	+	* @param additional_error possible further error specification
489	+	*/
490	+	static
491	+	int update_arg(void *field, char **orig_field,
492	+	unsigned int *field_given, unsigned int *prev_given,
493	+	char *value, const char *possible_values[],
494	+	const char *default_value,
495	+	cmdline_parser_arg_type arg_type,
496	+	int check_ambiguity, int override,
497	+	int no_free, int multiple_option,
498	+	const char *long_opt, char short_opt,
499	+	const char *additional_error)
500	+	{
501	+	char *stop_char = 0;
502	+	const char *val = value;
503	+	int found;
504	+	char **string_field;
505	+	FIX_UNUSED (field);
506	+
507	+	stop_char = 0;
508	+	found = 0;
509	+
510	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
511	+	{
512	+	if (short_opt != '-')
513	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
514	+	package_name, long_opt, short_opt,
515	+	(additional_error ? additional_error : ""));
516	+	else
517	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
518	+	package_name, long_opt,
519	+	(additional_error ? additional_error : ""));
520	+	return 1; /* failure */
521	+	}
522	+
523	+	FIX_UNUSED (default_value);
524	+
525	+	if (field_given && *field_given && ! override)
526	+	return 0;
527	+	if (prev_given)
528	+	(*prev_given)++;
529	+	if (field_given)
530	+	(*field_given)++;
531	+	if (possible_values)
532	+	val = possible_values[found];
533	+
534	+	switch(arg_type) {
535	+	case ARG_FLAG:
536	+	*((int *)field) = !*((int *)field);
537	+	break;
538	+	case ARG_INT:
539	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
540	+	break;
541	+	case ARG_STRING:
542	+	if (val) {
543	+	string_field = (char **)field;
544	+	if (!no_free && *string_field)
545	+	free (*string_field); /* free previous string */
546	+	*string_field = gengetopt_strdup (val);
547	+	}
548	+	break;
549	+	default:
550	+	break;
551	+	};
552	+
553	+	/* check numeric conversion */
554	+	switch(arg_type) {
555	+	case ARG_INT:
556	+	if (val && !(stop_char && *stop_char == '\0')) {
557	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
558	+	return 1; /* failure */
559	+	}
560	+	break;
561	+	default:
562	+	;
563	+	};
564	+
565	+	/* store the original value */
566	+	switch(arg_type) {
567	+	case ARG_NO:
568	+	case ARG_FLAG:
569	+	break;
570	+	default:
571	+	if (value && orig_field) {
572	+	if (no_free) {
573	+	*orig_field = value;
574	+	} else {
575	+	if (*orig_field)
576	+	free (*orig_field); /* free previous string */
577	+	*orig_field = gengetopt_strdup (value);
578	+	}
579	+	}
580	+	};
581	+
582	+	return 0; /* OK */
583	+	}
584	+
585	+
586	+	int
587	+	cmdline_parser_internal (
588	+	int argc, char **argv, struct gengetopt_args_info *args_info,
589	+	struct cmdline_parser_params *params, const char *additional_error)
590	+	{
591	+	int c;        /* Character of the parsed option.  */
592	+
593	+	int error = 0;
594	+	struct gengetopt_args_info local_args_info;
595	+
596	+	int override;
597	+	int initialize;
598	+	int check_required;
599	+	int check_ambiguity;
600	+
601	+	package_name = argv[0];
602	+
603	+	override = params->override;
604	+	initialize = params->initialize;
605	+	check_required = params->check_required;
606	+	check_ambiguity = params->check_ambiguity;
607	+
608	+	if (initialize)
609	+	cmdline_parser_init (args_info);
610	+
611	+	cmdline_parser_init (&local_args_info);
612	+
613		optarg = 0;
614	<	optind = 1;
615	<	opterr = 1;
614	>	optind = 0;
615	>	opterr = params->print_errors;
616		optopt = '?';
617
618		while (1)
619		{
620		int option_index = 0;
135	–	char *stop_char;
621
622		static struct option long_options[] = {
623		{ "help",       0, NULL, 'h' },
#	Line 140 | Line 625 | cmdline_parser (int argc, char * const *argv, struct g
625		{ "input",      1, NULL, 'i' },
626		{ "output",     1, NULL, 'o' },
627		{ "frame",      1, NULL, 'n' },
143	–	{ "dipole",     0, NULL, 'd' },
628		{ "water",      0, NULL, 'w' },
629		{ "periodicBox",        0, NULL, 'm' },
630		{ "zconstraint",        0, NULL, 'z' },
631		{ "rigidbody",  0, NULL, 'r' },
632		{ "watertype",  0, NULL, 't' },
149	–	{ "ignore",     1, NULL, 'g' },
633		{ "selection",  1, NULL, 's' },
634	+	{ "originsele", 1, NULL, 0 },
635	+	{ "refsele",    1, NULL, 0 },
636		{ "repeatX",    1, NULL, 0 },
637		{ "repeatY",    1, NULL, 0 },
638		{ "repeatZ",    1, NULL, 0 },
639	<	{ NULL, 0, NULL, 0 }
639	>	{ "basetype",   0, NULL, 'b' },
640	>	{ "velocities", 0, NULL, 'v' },
641	>	{ "forces",     0, NULL, 'f' },
642	>	{ "vectors",    0, NULL, 'u' },
643	>	{ "charges",    0, NULL, 'c' },
644	>	{ 0,  0, 0, 0 }
645		};
646
647	<	stop_char = 0;
158	<	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
647	>	c = getopt_long (argc, argv, "hVi:o:n:wmzrts:bvfuc", long_options, &option_index);
648
649		if (c == -1) break;       /* Exit from `while (1)' loop.  */
650
651		switch (c)
652		{
653		case 'h':       /* Print help and exit.  */
165	–	clear_args ();
654		cmdline_parser_print_help ();
655	+	cmdline_parser_free (&local_args_info);
656		exit (EXIT_SUCCESS);
657
658		case 'V':       /* Print version and exit.  */
170	–	clear_args ();
659		cmdline_parser_print_version ();
660	+	cmdline_parser_free (&local_args_info);
661		exit (EXIT_SUCCESS);
662
663		case 'i':       /* input dump file.  */
664	<	if (args_info->input_given)
665	<	{
666	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
667	<	clear_args ();
668	<	exit (EXIT_FAILURE);
669	<	}
670	<	args_info->input_given = 1;
671	<	args_info->input_arg = gengetopt_strdup (optarg);
664	>
665	>
666	>	if (update_arg( (void *)&(args_info->input_arg),
667	>	&(args_info->input_orig), &(args_info->input_given),
668	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
669	>	check_ambiguity, override, 0, 0,
670	>	"input", 'i',
671	>	additional_error))
672	>	goto failure;
673	>
674		break;
184	–
675		case 'o':       /* output file name.  */
676	<	if (args_info->output_given)
677	<	{
678	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
679	<	clear_args ();
680	<	exit (EXIT_FAILURE);
681	<	}
682	<	args_info->output_given = 1;
683	<	args_info->output_arg = gengetopt_strdup (optarg);
676	>
677	>
678	>	if (update_arg( (void *)&(args_info->output_arg),
679	>	&(args_info->output_orig), &(args_info->output_given),
680	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
681	>	check_ambiguity, override, 0, 0,
682	>	"output", 'o',
683	>	additional_error))
684	>	goto failure;
685	>
686		break;
195	–
687		case 'n':       /* print every n frame.  */
688	<	if (args_info->frame_given)
689	<	{
690	<	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
691	<	clear_args ();
692	<	exit (EXIT_FAILURE);
693	<	}
694	<	args_info->frame_given = 1;
695	<	args_info->frame_arg = strtol (optarg,&stop_char,0);
688	>
689	>
690	>	if (update_arg( (void *)&(args_info->frame_arg),
691	>	&(args_info->frame_orig), &(args_info->frame_given),
692	>	&(local_args_info.frame_given), optarg, 0, "1", ARG_INT,
693	>	check_ambiguity, override, 0, 0,
694	>	"frame", 'n',
695	>	additional_error))
696	>	goto failure;
697	>
698		break;
206	–
207	–	case 'd':       /* print the dipole moments.  */
208	–	if (args_info->dipole_given)
209	–	{
210	–	fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
211	–	clear_args ();
212	–	exit (EXIT_FAILURE);
213	–	}
214	–	args_info->dipole_given = 1;
215	–	args_info->dipole_flag = !(args_info->dipole_flag);
216	–	break;
217	–
699		case 'w':       /* skip the the waters.  */
700	<	if (args_info->water_given)
701	<	{
702	<	fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
703	<	clear_args ();
704	<	exit (EXIT_FAILURE);
705	<	}
706	<	args_info->water_given = 1;
707	<	args_info->water_flag = !(args_info->water_flag);
700	>
701	>
702	>	if (update_arg((void *)&(args_info->water_flag), 0, &(args_info->water_given),
703	>	&(local_args_info.water_given), optarg, 0, 0, ARG_FLAG,
704	>	check_ambiguity, override, 1, 0, "water", 'w',
705	>	additional_error))
706	>	goto failure;
707	>
708		break;
228	–
709		case 'm':       /* map to the periodic box.  */
710	<	if (args_info->periodicBox_given)
711	<	{
712	<	fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
713	<	clear_args ();
714	<	exit (EXIT_FAILURE);
715	<	}
716	<	args_info->periodicBox_given = 1;
717	<	args_info->periodicBox_flag = !(args_info->periodicBox_flag);
710	>
711	>
712	>	if (update_arg((void *)&(args_info->periodicBox_flag), 0, &(args_info->periodicBox_given),
713	>	&(local_args_info.periodicBox_given), optarg, 0, 0, ARG_FLAG,
714	>	check_ambiguity, override, 1, 0, "periodicBox", 'm',
715	>	additional_error))
716	>	goto failure;
717	>
718		break;
239	–
719		case 'z':       /* replace the atom types of zconstraint molecules.  */
720	<	if (args_info->zconstraint_given)
721	<	{
722	<	fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
723	<	clear_args ();
724	<	exit (EXIT_FAILURE);
725	<	}
726	<	args_info->zconstraint_given = 1;
727	<	args_info->zconstraint_flag = !(args_info->zconstraint_flag);
720	>
721	>
722	>	if (update_arg((void *)&(args_info->zconstraint_flag), 0, &(args_info->zconstraint_given),
723	>	&(local_args_info.zconstraint_given), optarg, 0, 0, ARG_FLAG,
724	>	check_ambiguity, override, 1, 0, "zconstraint", 'z',
725	>	additional_error))
726	>	goto failure;
727	>
728		break;
250	–
729		case 'r':       /* add a pseudo COM atom to rigidbody.  */
730	<	if (args_info->rigidbody_given)
731	<	{
732	<	fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
733	<	clear_args ();
734	<	exit (EXIT_FAILURE);
735	<	}
736	<	args_info->rigidbody_given = 1;
737	<	args_info->rigidbody_flag = !(args_info->rigidbody_flag);
730	>
731	>
732	>	if (update_arg((void *)&(args_info->rigidbody_flag), 0, &(args_info->rigidbody_given),
733	>	&(local_args_info.rigidbody_given), optarg, 0, 0, ARG_FLAG,
734	>	check_ambiguity, override, 1, 0, "rigidbody", 'r',
735	>	additional_error))
736	>	goto failure;
737	>
738		break;
261	–
739		case 't':       /* replace the atom type of water model.  */
740	<	if (args_info->watertype_given)
741	<	{
742	<	fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
743	<	clear_args ();
744	<	exit (EXIT_FAILURE);
745	<	}
746	<	args_info->watertype_given = 1;
747	<	args_info->watertype_flag = !(args_info->watertype_flag);
740	>
741	>
742	>	if (update_arg((void *)&(args_info->watertype_flag), 0, &(args_info->watertype_given),
743	>	&(local_args_info.watertype_given), optarg, 0, 0, ARG_FLAG,
744	>	check_ambiguity, override, 1, 0, "watertype", 't',
745	>	additional_error))
746	>	goto failure;
747	>
748		break;
749	<
750	<	case 'g':       /* ignore the atom types.  */
751	<	args_info->ignore_given++;
752	<	ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
753	<	ignore_new->next = ignore_list;
754	<	ignore_list = ignore_new;
755	<	ignore_new->ignore_arg = gengetopt_strdup (optarg);
749	>	case 's':       /* general selection syntax.  */
750	>
751	>
752	>	if (update_arg( (void *)&(args_info->selection_arg),
753	>	&(args_info->selection_orig), &(args_info->selection_given),
754	>	&(local_args_info.selection_given), optarg, 0, 0, ARG_STRING,
755	>	check_ambiguity, override, 0, 0,
756	>	"selection", 's',
757	>	additional_error))
758	>	goto failure;
759	>
760		break;
761	<
762	<	case 's':       /* general selection syntax:\n
763	<	select DMPC -- select DMPC molecule\n \
764	<	select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
765	<	select 5 -- select stuntdobule whose global index is 5\n \
766	<	select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
767	<	select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule .  */
768	<	if (args_info->selection_given)
769	<	{
289	<	fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
290	<	clear_args ();
291	<	exit (EXIT_FAILURE);
292	<	}
293	<	args_info->selection_given = 1;
294	<	args_info->selection_arg = gengetopt_strdup (optarg);
761	>	case 'b':       /* Convert to base atom type.  */
762	>
763	>
764	>	if (update_arg((void *)&(args_info->basetype_flag), 0, &(args_info->basetype_given),
765	>	&(local_args_info.basetype_given), optarg, 0, 0, ARG_FLAG,
766	>	check_ambiguity, override, 1, 0, "basetype", 'b',
767	>	additional_error))
768	>	goto failure;
769	>
770		break;
771	+	case 'v':       /* Print velocities in xyz file.  */
772	+
773	+
774	+	if (update_arg((void *)&(args_info->velocities_flag), 0, &(args_info->velocities_given),
775	+	&(local_args_info.velocities_given), optarg, 0, 0, ARG_FLAG,
776	+	check_ambiguity, override, 1, 0, "velocities", 'v',
777	+	additional_error))
778	+	goto failure;
779	+
780	+	break;
781	+	case 'f':       /* Print forces xyz file.  */
782	+
783	+
784	+	if (update_arg((void *)&(args_info->forces_flag), 0, &(args_info->forces_given),
785	+	&(local_args_info.forces_given), optarg, 0, 0, ARG_FLAG,
786	+	check_ambiguity, override, 1, 0, "forces", 'f',
787	+	additional_error))
788	+	goto failure;
789	+
790	+	break;
791	+	case 'u':       /* Print vectors (dipoles, etc) in xyz file.  */
792	+
793	+
794	+	if (update_arg((void *)&(args_info->vectors_flag), 0, &(args_info->vectors_given),
795	+	&(local_args_info.vectors_given), optarg, 0, 0, ARG_FLAG,
796	+	check_ambiguity, override, 1, 0, "vectors", 'u',
797	+	additional_error))
798	+	goto failure;
799	+
800	+	break;
801	+	case 'c':       /* Print charges in xyz file.  */
802	+
803	+
804	+	if (update_arg((void *)&(args_info->charges_flag), 0, &(args_info->charges_given),
805	+	&(local_args_info.charges_given), optarg, 0, 0, ARG_FLAG,
806	+	check_ambiguity, override, 1, 0, "charges", 'c',
807	+	additional_error))
808	+	goto failure;
809	+
810	+	break;
811
297	–
812		case 0: /* Long option with no short option */
813	<	/* The number of images to repeat in the x direction.  */
814	<	if (strcmp (long_options[option_index].name, "repeatX") == 0)
813	>	/* select origin.  */
814	>	if (strcmp (long_options[option_index].name, "originsele") == 0)
815		{
816	<	if (args_info->repeatX_given)
817	<	{
818	<	fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
819	<	clear_args ();
820	<	exit (EXIT_FAILURE);
821	<	}
822	<	args_info->repeatX_given = 1;
823	<	args_info->repeatX_arg = strtol (optarg,&stop_char,0);
824	<	break;
816	>
817	>
818	>	if (update_arg( (void *)&(args_info->originsele_arg),
819	>	&(args_info->originsele_orig), &(args_info->originsele_given),
820	>	&(local_args_info.originsele_given), optarg, 0, 0, ARG_STRING,
821	>	check_ambiguity, override, 0, 0,
822	>	"originsele", '-',
823	>	additional_error))
824	>	goto failure;
825	>
826		}
827	+	/* select reference.  */
828	+	else if (strcmp (long_options[option_index].name, "refsele") == 0)
829	+	{
830
831	+
832	+	if (update_arg( (void *)&(args_info->refsele_arg),
833	+	&(args_info->refsele_orig), &(args_info->refsele_given),
834	+	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
835	+	check_ambiguity, override, 0, 0,
836	+	"refsele", '-',
837	+	additional_error))
838	+	goto failure;
839	+
840	+	}
841	+	/* The number of images to repeat in the x direction.  */
842	+	else if (strcmp (long_options[option_index].name, "repeatX") == 0)
843	+	{
844	+
845	+
846	+	if (update_arg( (void *)&(args_info->repeatX_arg),
847	+	&(args_info->repeatX_orig), &(args_info->repeatX_given),
848	+	&(local_args_info.repeatX_given), optarg, 0, "0", ARG_INT,
849	+	check_ambiguity, override, 0, 0,
850	+	"repeatX", '-',
851	+	additional_error))
852	+	goto failure;
853	+
854	+	}
855		/* The number of images to repeat in the y direction.  */
856		else if (strcmp (long_options[option_index].name, "repeatY") == 0)
857		{
316	–	if (args_info->repeatY_given)
317	–	{
318	–	fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
319	–	clear_args ();
320	–	exit (EXIT_FAILURE);
321	–	}
322	–	args_info->repeatY_given = 1;
323	–	args_info->repeatY_arg = strtol (optarg,&stop_char,0);
324	–	break;
325	–	}
858
859	+
860	+	if (update_arg( (void *)&(args_info->repeatY_arg),
861	+	&(args_info->repeatY_orig), &(args_info->repeatY_given),
862	+	&(local_args_info.repeatY_given), optarg, 0, "0", ARG_INT,
863	+	check_ambiguity, override, 0, 0,
864	+	"repeatY", '-',
865	+	additional_error))
866	+	goto failure;
867	+
868	+	}
869		/* The number of images to repeat in the z direction.  */
870		else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
871		{
872	<	if (args_info->repeatZ_given)
873	<	{
874	<	fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
875	<	clear_args ();
876	<	exit (EXIT_FAILURE);
877	<	}
878	<	args_info->repeatZ_given = 1;
879	<	args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
880	<	break;
872	>
873	>
874	>	if (update_arg( (void *)&(args_info->repeatZ_arg),
875	>	&(args_info->repeatZ_orig), &(args_info->repeatZ_given),
876	>	&(local_args_info.repeatZ_given), optarg, 0, "0", ARG_INT,
877	>	check_ambiguity, override, 0, 0,
878	>	"repeatZ", '-',
879	>	additional_error))
880	>	goto failure;
881	>
882		}
883
884	<
884	>	break;
885		case '?':       /* Invalid option.  */
886		/* `getopt_long' already printed an error message.  */
887	<	exit (EXIT_FAILURE);
887	>	goto failure;
888
889		default:        /* bug: option not considered.  */
890	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
890	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
891		abort ();
892		} /* switch */
893		} /* while */
894
895
896	<	if (! args_info->input_given)
896	>
897	>	if (check_required)
898		{
899	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
356	<	missing_required_options = 1;
899	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
900		}
358	–	if ( missing_required_options )
359	–	exit (EXIT_FAILURE);
901
902	<	if (args_info->ignore_given)
902	>	cmdline_parser_release (&local_args_info);
903	>
904	>	if ( error )
905	>	return (EXIT_FAILURE);
906	>
907	>	if (optind < argc)
908		{
909	<	args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
910	<	for (i = 0; i < args_info->ignore_given; i++)
911	<	{
912	<	args_info->ignore_arg [i] = ignore_list->ignore_arg;
913	<	ignore_list = ignore_list->next;
909	>	int i = 0 ;
910	>	int found_prog_name = 0;
911	>	/* whether program name, i.e., argv[0], is in the remaining args
912	>	(this may happen with some implementations of getopt,
913	>	but surely not with the one included by gengetopt) */
914	>
915	>	i = optind;
916	>	while (i < argc)
917	>	if (argv[i++] == argv[0]) {
918	>	found_prog_name = 1;
919	>	break;
920		}
921	+	i = 0;
922	+
923	+	args_info->inputs_num = argc - optind - found_prog_name;
924	+	args_info->inputs =
925	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
926	+	while (optind < argc)
927	+	if (argv[optind++] != argv[0])
928	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
929		}
930	<
930	>
931		return 0;
932	+
933	+	failure:
934	+
935	+	cmdline_parser_release (&local_args_info);
936	+	return (EXIT_FAILURE);
937		}

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZCmd.c (property svn:keywords), Revision 302 by tim, Mon Feb 7 21:11:22 2005 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZCmd.c (property svn:keywords), Revision 1630 by gezelter, Wed Sep 14 21:40:12 2011 UTC

#	Line 0 | Line 1
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