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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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22
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	–
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 "Dump2XYZCmd.h"
23
24	+	const char *gengetopt_args_info_purpose = "";
25	+
26	+	const char *gengetopt_args_info_usage = "Usage: Dump2XYZ [OPTIONS]... [FILES]...";
27	+
28	+	const char *gengetopt_args_info_description = "";
29	+
30	+	const char *gengetopt_args_info_help[] = {
31	+	"  -h, --help                    Print help and exit",
32	+	"  -V, --version                 Print version and exit",
33	+	"  -i, --input=filename          input dump file",
34	+	"  -o, --output=filename         output file name",
35	+	"  -n, --frame=INT               print every n frame  (default=`1')",
36	+	"  -w, --water                   skip the the waters  (default=off)",
37	+	"  -m, --periodicBox             map to the periodic box  (default=off)",
38	+	"  -z, --zconstraint             replace the atom types of zconstraint molecules \n                                   (default=off)",
39	+	"  -r, --rigidbody               add a pseudo COM atom to rigidbody  \n                                  (default=off)",
40	+	"  -t, --watertype               replace the atom type of water model  \n                                  (default=on)",
41	+	"  -s, --selection=selection script\n                                general selection syntax",
42	+	"      --originsele=selection script\n                                select origin",
43	+	"      --refsele=selection script\n                                select reference",
44	+	"      --repeatX=INT             The number of images to repeat in the x \n                                  direction  (default=`0')",
45	+	"      --repeatY=INT             The number of images to repeat in the y \n                                  direction  (default=`0')",
46	+	"      --repeatZ=INT             The number of images to repeat in the z \n                                  direction  (default=`0')",
47	+	"  -b, --basetype                Convert to base atom type  (default=off)",
48	+	"  -v, --velocities              Print velocities in xyz file  (default=off)",
49	+	"  -f, --forces                  Print forces xyz file  (default=off)",
50	+	"  -u, --vectors                 Print vectors (dipoles, etc) in xyz file  \n                                  (default=off)",
51	+	"  -c, --charges                 Print charges in xyz file  (default=off)",
52	+	0
53	+	};
54	+
55	+	typedef enum {ARG_NO
56	+	, ARG_FLAG
57	+	, ARG_STRING
58	+	, ARG_INT
59	+	} cmdline_parser_arg_type;
60	+
61	+	static
62	+	void clear_given (struct gengetopt_args_info *args_info);
63	+	static
64	+	void clear_args (struct gengetopt_args_info *args_info);
65	+
66	+	static int
67	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
68	+	struct cmdline_parser_params *params, const char *additional_error);
69	+
70	+	static int
71	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
72	+
73	+	static char *
74	+	gengetopt_strdup (const char *s);
75	+
76	+	static
77	+	void clear_given (struct gengetopt_args_info *args_info)
78	+	{
79	+	args_info->help_given = 0 ;
80	+	args_info->version_given = 0 ;
81	+	args_info->input_given = 0 ;
82	+	args_info->output_given = 0 ;
83	+	args_info->frame_given = 0 ;
84	+	args_info->water_given = 0 ;
85	+	args_info->periodicBox_given = 0 ;
86	+	args_info->zconstraint_given = 0 ;
87	+	args_info->rigidbody_given = 0 ;
88	+	args_info->watertype_given = 0 ;
89	+	args_info->selection_given = 0 ;
90	+	args_info->originsele_given = 0 ;
91	+	args_info->refsele_given = 0 ;
92	+	args_info->repeatX_given = 0 ;
93	+	args_info->repeatY_given = 0 ;
94	+	args_info->repeatZ_given = 0 ;
95	+	args_info->basetype_given = 0 ;
96	+	args_info->velocities_given = 0 ;
97	+	args_info->forces_given = 0 ;
98	+	args_info->vectors_given = 0 ;
99	+	args_info->charges_given = 0 ;
100	+	}
101	+
102	+	static
103	+	void clear_args (struct gengetopt_args_info *args_info)
104	+	{
105	+	args_info->input_arg = NULL;
106	+	args_info->input_orig = NULL;
107	+	args_info->output_arg = NULL;
108	+	args_info->output_orig = NULL;
109	+	args_info->frame_arg = 1;
110	+	args_info->frame_orig = NULL;
111	+	args_info->water_flag = 0;
112	+	args_info->periodicBox_flag = 0;
113	+	args_info->zconstraint_flag = 0;
114	+	args_info->rigidbody_flag = 0;
115	+	args_info->watertype_flag = 1;
116	+	args_info->selection_arg = NULL;
117	+	args_info->selection_orig = NULL;
118	+	args_info->originsele_arg = NULL;
119	+	args_info->originsele_orig = NULL;
120	+	args_info->refsele_arg = NULL;
121	+	args_info->refsele_orig = NULL;
122	+	args_info->repeatX_arg = 0;
123	+	args_info->repeatX_orig = NULL;
124	+	args_info->repeatY_arg = 0;
125	+	args_info->repeatY_orig = NULL;
126	+	args_info->repeatZ_arg = 0;
127	+	args_info->repeatZ_orig = NULL;
128	+	args_info->basetype_flag = 0;
129	+	args_info->velocities_flag = 0;
130	+	args_info->forces_flag = 0;
131	+	args_info->vectors_flag = 0;
132	+	args_info->charges_flag = 0;
133	+
134	+	}
135	+
136	+	static
137	+	void init_args_info(struct gengetopt_args_info *args_info)
138	+	{
139	+
140	+
141	+	args_info->help_help = gengetopt_args_info_help[0] ;
142	+	args_info->version_help = gengetopt_args_info_help[1] ;
143	+	args_info->input_help = gengetopt_args_info_help[2] ;
144	+	args_info->output_help = gengetopt_args_info_help[3] ;
145	+	args_info->frame_help = gengetopt_args_info_help[4] ;
146	+	args_info->water_help = gengetopt_args_info_help[5] ;
147	+	args_info->periodicBox_help = gengetopt_args_info_help[6] ;
148	+	args_info->zconstraint_help = gengetopt_args_info_help[7] ;
149	+	args_info->rigidbody_help = gengetopt_args_info_help[8] ;
150	+	args_info->watertype_help = gengetopt_args_info_help[9] ;
151	+	args_info->selection_help = gengetopt_args_info_help[10] ;
152	+	args_info->originsele_help = gengetopt_args_info_help[11] ;
153	+	args_info->refsele_help = gengetopt_args_info_help[12] ;
154	+	args_info->repeatX_help = gengetopt_args_info_help[13] ;
155	+	args_info->repeatY_help = gengetopt_args_info_help[14] ;
156	+	args_info->repeatZ_help = gengetopt_args_info_help[15] ;
157	+	args_info->basetype_help = gengetopt_args_info_help[16] ;
158	+	args_info->velocities_help = gengetopt_args_info_help[17] ;
159	+	args_info->forces_help = gengetopt_args_info_help[18] ;
160	+	args_info->vectors_help = gengetopt_args_info_help[19] ;
161	+	args_info->charges_help = gengetopt_args_info_help[20] ;
162	+
163	+	}
164	+
165		void
166		cmdline_parser_print_version (void)
167		{
168		printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
169		}
170
171	+	static void print_help_common(void) {
172	+	cmdline_parser_print_version ();
173	+
174	+	if (strlen(gengetopt_args_info_purpose) > 0)
175	+	printf("\n%s\n", gengetopt_args_info_purpose);
176	+
177	+	if (strlen(gengetopt_args_info_usage) > 0)
178	+	printf("\n%s\n", gengetopt_args_info_usage);
179	+
180	+	printf("\n");
181	+
182	+	if (strlen(gengetopt_args_info_description) > 0)
183	+	printf("%s\n", gengetopt_args_info_description);
184	+	}
185	+
186		void
187		cmdline_parser_print_help (void)
188		{
189	<	cmdline_parser_print_version ();
190	<	printf("\n"
191	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
192	<	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");
189	>	int i = 0;
190	>	print_help_common();
191	>	while (gengetopt_args_info_help[i])
192	>	printf("%s\n", gengetopt_args_info_help[i++]);
193		}
194
195	+	void
196	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
197	+	{
198	+	clear_given (args_info);
199	+	clear_args (args_info);
200	+	init_args_info (args_info);
201
202	<	static char *gengetopt_strdup (const char *s);
202	>	args_info->inputs = NULL;
203	>	args_info->inputs_num = 0;
204	>	}
205
206	<	/* gengetopt_strdup() */
207	<	/* strdup.c replacement of strdup, which is not standard */
206	>	void
207	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
208	>	{
209	>	if (params)
210	>	{
211	>	params->override = 0;
212	>	params->initialize = 1;
213	>	params->check_required = 1;
214	>	params->check_ambiguity = 0;
215	>	params->print_errors = 1;
216	>	}
217	>	}
218	>
219	>	struct cmdline_parser_params *
220	>	cmdline_parser_params_create(void)
221	>	{
222	>	struct cmdline_parser_params *params =
223	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
224	>	cmdline_parser_params_init(params);
225	>	return params;
226	>	}
227	>
228	>	static void
229	>	free_string_field (char **s)
230	>	{
231	>	if (*s)
232	>	{
233	>	free (*s);
234	>	*s = 0;
235	>	}
236	>	}
237	>
238	>
239	>	static void
240	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
241	>	{
242	>	unsigned int i;
243	>	free_string_field (&(args_info->input_arg));
244	>	free_string_field (&(args_info->input_orig));
245	>	free_string_field (&(args_info->output_arg));
246	>	free_string_field (&(args_info->output_orig));
247	>	free_string_field (&(args_info->frame_orig));
248	>	free_string_field (&(args_info->selection_arg));
249	>	free_string_field (&(args_info->selection_orig));
250	>	free_string_field (&(args_info->originsele_arg));
251	>	free_string_field (&(args_info->originsele_orig));
252	>	free_string_field (&(args_info->refsele_arg));
253	>	free_string_field (&(args_info->refsele_orig));
254	>	free_string_field (&(args_info->repeatX_orig));
255	>	free_string_field (&(args_info->repeatY_orig));
256	>	free_string_field (&(args_info->repeatZ_orig));
257	>
258	>
259	>	for (i = 0; i < args_info->inputs_num; ++i)
260	>	free (args_info->inputs [i]);
261	>
262	>	if (args_info->inputs_num)
263	>	free (args_info->inputs);
264	>
265	>	clear_given (args_info);
266	>	}
267	>
268	>
269	>	static void
270	>	write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
271	>	{
272	>	if (arg) {
273	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
274	>	} else {
275	>	fprintf(outfile, "%s\n", opt);
276	>	}
277	>	}
278	>
279	>
280	>	int
281	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
282	>	{
283	>	int i = 0;
284	>
285	>	if (!outfile)
286	>	{
287	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
288	>	return EXIT_FAILURE;
289	>	}
290	>
291	>	if (args_info->help_given)
292	>	write_into_file(outfile, "help", 0, 0 );
293	>	if (args_info->version_given)
294	>	write_into_file(outfile, "version", 0, 0 );
295	>	if (args_info->input_given)
296	>	write_into_file(outfile, "input", args_info->input_orig, 0);
297	>	if (args_info->output_given)
298	>	write_into_file(outfile, "output", args_info->output_orig, 0);
299	>	if (args_info->frame_given)
300	>	write_into_file(outfile, "frame", args_info->frame_orig, 0);
301	>	if (args_info->water_given)
302	>	write_into_file(outfile, "water", 0, 0 );
303	>	if (args_info->periodicBox_given)
304	>	write_into_file(outfile, "periodicBox", 0, 0 );
305	>	if (args_info->zconstraint_given)
306	>	write_into_file(outfile, "zconstraint", 0, 0 );
307	>	if (args_info->rigidbody_given)
308	>	write_into_file(outfile, "rigidbody", 0, 0 );
309	>	if (args_info->watertype_given)
310	>	write_into_file(outfile, "watertype", 0, 0 );
311	>	if (args_info->selection_given)
312	>	write_into_file(outfile, "selection", args_info->selection_orig, 0);
313	>	if (args_info->originsele_given)
314	>	write_into_file(outfile, "originsele", args_info->originsele_orig, 0);
315	>	if (args_info->refsele_given)
316	>	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
317	>	if (args_info->repeatX_given)
318	>	write_into_file(outfile, "repeatX", args_info->repeatX_orig, 0);
319	>	if (args_info->repeatY_given)
320	>	write_into_file(outfile, "repeatY", args_info->repeatY_orig, 0);
321	>	if (args_info->repeatZ_given)
322	>	write_into_file(outfile, "repeatZ", args_info->repeatZ_orig, 0);
323	>	if (args_info->basetype_given)
324	>	write_into_file(outfile, "basetype", 0, 0 );
325	>	if (args_info->velocities_given)
326	>	write_into_file(outfile, "velocities", 0, 0 );
327	>	if (args_info->forces_given)
328	>	write_into_file(outfile, "forces", 0, 0 );
329	>	if (args_info->vectors_given)
330	>	write_into_file(outfile, "vectors", 0, 0 );
331	>	if (args_info->charges_given)
332	>	write_into_file(outfile, "charges", 0, 0 );
333	>
334	>
335	>	i = EXIT_SUCCESS;
336	>	return i;
337	>	}
338	>
339	>	int
340	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
341	>	{
342	>	FILE *outfile;
343	>	int i = 0;
344	>
345	>	outfile = fopen(filename, "w");
346	>
347	>	if (!outfile)
348	>	{
349	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
350	>	return EXIT_FAILURE;
351	>	}
352	>
353	>	i = cmdline_parser_dump(outfile, args_info);
354	>	fclose (outfile);
355	>
356	>	return i;
357	>	}
358	>
359	>	void
360	>	cmdline_parser_free (struct gengetopt_args_info *args_info)
361	>	{
362	>	cmdline_parser_release (args_info);
363	>	}
364	>
365	>	/** @brief replacement of strdup, which is not standard */
366		char *
367		gengetopt_strdup (const char *s)
368		{
369	<	char *result = (char*)malloc(strlen(s) + 1);
369	>	char *result = NULL;
370	>	if (!s)
371	>	return result;
372	>
373	>	result = (char*)malloc(strlen(s) + 1);
374		if (result == (char*)0)
375		return (char*)0;
376		strcpy(result, s);
#	Line 78 | Line 380 | cmdline_parser (int argc, char * const *argv, struct g
380		int
381		cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
382		{
383	<	int c;        /* Character of the parsed option.  */
384	<	int i;        /* Counter */
385	<	struct ignore_list
386	<	{
387	<	char * ignore_arg;
388	<	struct ignore_list * next;
389	<	};
390	<	struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
383	>	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
384	>	}
385	>
386	>	int
387	>	cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
388	>	struct cmdline_parser_params *params)
389	>	{
390	>	int result;
391	>	result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
392	>
393	>	if (result == EXIT_FAILURE)
394	>	{
395	>	cmdline_parser_free (args_info);
396	>	exit (EXIT_FAILURE);
397	>	}
398
399	<	int missing_required_options = 0;
399	>	return result;
400	>	}
401
402	<	args_info->help_given = 0 ;
403	<	args_info->version_given = 0 ;
404	<	args_info->input_given = 0 ;
405	<	args_info->output_given = 0 ;
406	<	args_info->frame_given = 0 ;
407	<	args_info->dipole_given = 0 ;
408	<	args_info->water_given = 0 ;
409	<	args_info->periodicBox_given = 0 ;
410	<	args_info->zconstraint_given = 0 ;
411	<	args_info->rigidbody_given = 0 ;
412	<	args_info->watertype_given = 0 ;
413	<	args_info->ignore_given = 0 ;
414	<	args_info->selection_given = 0 ;
415	<	args_info->repeatX_given = 0 ;
416	<	args_info->repeatY_given = 0 ;
417	<	args_info->repeatZ_given = 0 ;
418	<	#define clear_args() { \
419	<	args_info->input_arg = NULL; \
420	<	args_info->output_arg = NULL; \
421	<	args_info->frame_arg = 1 ;\
422	<	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 ;\
402	>	int
403	>	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
404	>	{
405	>	int result;
406	>	struct cmdline_parser_params params;
407	>
408	>	params.override = override;
409	>	params.initialize = initialize;
410	>	params.check_required = check_required;
411	>	params.check_ambiguity = 0;
412	>	params.print_errors = 1;
413	>
414	>	result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
415	>
416	>	if (result == EXIT_FAILURE)
417	>	{
418	>	cmdline_parser_free (args_info);
419	>	exit (EXIT_FAILURE);
420	>	}
421	>
422	>	return result;
423		}
424
425	<	clear_args();
425	>	int
426	>	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
427	>	{
428	>	int result = EXIT_SUCCESS;
429	>
430	>	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
431	>	result = EXIT_FAILURE;
432	>
433	>	if (result == EXIT_FAILURE)
434	>	{
435	>	cmdline_parser_free (args_info);
436	>	exit (EXIT_FAILURE);
437	>	}
438	>
439	>	return result;
440	>	}
441	>
442	>	int
443	>	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
444	>	{
445	>	int error = 0;
446	>
447	>	/* checks for required options */
448	>	if (! args_info->input_given)
449	>	{
450	>	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
451	>	error = 1;
452	>	}
453	>
454	>
455	>	/* checks for dependences among options */
456	>
457	>	return error;
458	>	}
459	>
460	>
461	>	static char *package_name = 0;
462	>
463	>	/**
464	>	* @brief updates an option
465	>	* @param field the generic pointer to the field to update
466	>	* @param orig_field the pointer to the orig field
467	>	* @param field_given the pointer to the number of occurrence of this option
468	>	* @param prev_given the pointer to the number of occurrence already seen
469	>	* @param value the argument for this option (if null no arg was specified)
470	>	* @param possible_values the possible values for this option (if specified)
471	>	* @param default_value the default value (in case the option only accepts fixed values)
472	>	* @param arg_type the type of this option
473	>	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
474	>	* @param override @see cmdline_parser_params.override
475	>	* @param no_free whether to free a possible previous value
476	>	* @param multiple_option whether this is a multiple option
477	>	* @param long_opt the corresponding long option
478	>	* @param short_opt the corresponding short option (or '-' if none)
479	>	* @param additional_error possible further error specification
480	>	*/
481	>	static
482	>	int update_arg(void *field, char **orig_field,
483	>	unsigned int *field_given, unsigned int *prev_given,
484	>	char *value, char *possible_values[], const char *default_value,
485	>	cmdline_parser_arg_type arg_type,
486	>	int check_ambiguity, int override,
487	>	int no_free, int multiple_option,
488	>	const char *long_opt, char short_opt,
489	>	const char *additional_error)
490	>	{
491	>	char *stop_char = 0;
492	>	const char *val = value;
493	>	int found;
494	>	char **string_field;
495	>
496	>	stop_char = 0;
497	>	found = 0;
498	>
499	>	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
500	>	{
501	>	if (short_opt != '-')
502	>	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
503	>	package_name, long_opt, short_opt,
504	>	(additional_error ? additional_error : ""));
505	>	else
506	>	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
507	>	package_name, long_opt,
508	>	(additional_error ? additional_error : ""));
509	>	return 1; /* failure */
510	>	}
511
512	+
513	+	if (field_given && *field_given && ! override)
514	+	return 0;
515	+	if (prev_given)
516	+	(*prev_given)++;
517	+	if (field_given)
518	+	(*field_given)++;
519	+	if (possible_values)
520	+	val = possible_values[found];
521	+
522	+	switch(arg_type) {
523	+	case ARG_FLAG:
524	+	*((int *)field) = !*((int *)field);
525	+	break;
526	+	case ARG_INT:
527	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
528	+	break;
529	+	case ARG_STRING:
530	+	if (val) {
531	+	string_field = (char **)field;
532	+	if (!no_free && *string_field)
533	+	free (*string_field); /* free previous string */
534	+	*string_field = gengetopt_strdup (val);
535	+	}
536	+	break;
537	+	default:
538	+	break;
539	+	};
540	+
541	+	/* check numeric conversion */
542	+	switch(arg_type) {
543	+	case ARG_INT:
544	+	if (val && !(stop_char && *stop_char == '\0')) {
545	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
546	+	return 1; /* failure */
547	+	}
548	+	break;
549	+	default:
550	+	;
551	+	};
552	+
553	+	/* store the original value */
554	+	switch(arg_type) {
555	+	case ARG_NO:
556	+	case ARG_FLAG:
557	+	break;
558	+	default:
559	+	if (value && orig_field) {
560	+	if (no_free) {
561	+	*orig_field = value;
562	+	} else {
563	+	if (*orig_field)
564	+	free (*orig_field); /* free previous string */
565	+	*orig_field = gengetopt_strdup (value);
566	+	}
567	+	}
568	+	};
569	+
570	+	return 0; /* OK */
571	+	}
572	+
573	+
574	+	int
575	+	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
576	+	struct cmdline_parser_params *params, const char *additional_error)
577	+	{
578	+	int c;        /* Character of the parsed option.  */
579	+
580	+	int error = 0;
581	+	struct gengetopt_args_info local_args_info;
582	+
583	+	int override;
584	+	int initialize;
585	+	int check_required;
586	+	int check_ambiguity;
587	+
588	+	package_name = argv[0];
589	+
590	+	override = params->override;
591	+	initialize = params->initialize;
592	+	check_required = params->check_required;
593	+	check_ambiguity = params->check_ambiguity;
594	+
595	+	if (initialize)
596	+	cmdline_parser_init (args_info);
597	+
598	+	cmdline_parser_init (&local_args_info);
599	+
600		optarg = 0;
601	<	optind = 1;
602	<	opterr = 1;
601	>	optind = 0;
602	>	opterr = params->print_errors;
603		optopt = '?';
604
605		while (1)
606		{
607		int option_index = 0;
135	–	char *stop_char;
608
609		static struct option long_options[] = {
610		{ "help",       0, NULL, 'h' },
#	Line 140 | Line 612 | cmdline_parser (int argc, char * const *argv, struct g
612		{ "input",      1, NULL, 'i' },
613		{ "output",     1, NULL, 'o' },
614		{ "frame",      1, NULL, 'n' },
143	–	{ "dipole",     0, NULL, 'd' },
615		{ "water",      0, NULL, 'w' },
616		{ "periodicBox",        0, NULL, 'm' },
617		{ "zconstraint",        0, NULL, 'z' },
618		{ "rigidbody",  0, NULL, 'r' },
619		{ "watertype",  0, NULL, 't' },
149	–	{ "ignore",     1, NULL, 'g' },
620		{ "selection",  1, NULL, 's' },
621	+	{ "originsele", 1, NULL, 0 },
622	+	{ "refsele",    1, NULL, 0 },
623		{ "repeatX",    1, NULL, 0 },
624		{ "repeatY",    1, NULL, 0 },
625		{ "repeatZ",    1, NULL, 0 },
626	+	{ "basetype",   0, NULL, 'b' },
627	+	{ "velocities", 0, NULL, 'v' },
628	+	{ "forces",     0, NULL, 'f' },
629	+	{ "vectors",    0, NULL, 'u' },
630	+	{ "charges",    0, NULL, 'c' },
631		{ NULL, 0, NULL, 0 }
632		};
633
634	<	stop_char = 0;
158	<	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
634	>	c = getopt_long (argc, argv, "hVi:o:n:wmzrts:bvfuc", long_options, &option_index);
635
636		if (c == -1) break;       /* Exit from `while (1)' loop.  */
637
638		switch (c)
639		{
640		case 'h':       /* Print help and exit.  */
165	–	clear_args ();
641		cmdline_parser_print_help ();
642	+	cmdline_parser_free (&local_args_info);
643		exit (EXIT_SUCCESS);
644
645		case 'V':       /* Print version and exit.  */
170	–	clear_args ();
646		cmdline_parser_print_version ();
647	+	cmdline_parser_free (&local_args_info);
648		exit (EXIT_SUCCESS);
649
650		case 'i':       /* input dump file.  */
651	<	if (args_info->input_given)
652	<	{
653	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
654	<	clear_args ();
655	<	exit (EXIT_FAILURE);
656	<	}
657	<	args_info->input_given = 1;
658	<	args_info->input_arg = gengetopt_strdup (optarg);
651	>
652	>
653	>	if (update_arg( (void *)&(args_info->input_arg),
654	>	&(args_info->input_orig), &(args_info->input_given),
655	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
656	>	check_ambiguity, override, 0, 0,
657	>	"input", 'i',
658	>	additional_error))
659	>	goto failure;
660	>
661		break;
184	–
662		case 'o':       /* output file name.  */
663	<	if (args_info->output_given)
664	<	{
665	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
666	<	clear_args ();
667	<	exit (EXIT_FAILURE);
668	<	}
669	<	args_info->output_given = 1;
670	<	args_info->output_arg = gengetopt_strdup (optarg);
663	>
664	>
665	>	if (update_arg( (void *)&(args_info->output_arg),
666	>	&(args_info->output_orig), &(args_info->output_given),
667	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
668	>	check_ambiguity, override, 0, 0,
669	>	"output", 'o',
670	>	additional_error))
671	>	goto failure;
672	>
673		break;
195	–
674		case 'n':       /* print every n frame.  */
675	<	if (args_info->frame_given)
676	<	{
677	<	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
678	<	clear_args ();
679	<	exit (EXIT_FAILURE);
680	<	}
681	<	args_info->frame_given = 1;
682	<	args_info->frame_arg = strtol (optarg,&stop_char,0);
675	>
676	>
677	>	if (update_arg( (void *)&(args_info->frame_arg),
678	>	&(args_info->frame_orig), &(args_info->frame_given),
679	>	&(local_args_info.frame_given), optarg, 0, "1", ARG_INT,
680	>	check_ambiguity, override, 0, 0,
681	>	"frame", 'n',
682	>	additional_error))
683	>	goto failure;
684	>
685		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	–
686		case 'w':       /* skip the the waters.  */
687	<	if (args_info->water_given)
688	<	{
689	<	fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
690	<	clear_args ();
691	<	exit (EXIT_FAILURE);
692	<	}
693	<	args_info->water_given = 1;
694	<	args_info->water_flag = !(args_info->water_flag);
687	>
688	>
689	>	if (update_arg((void *)&(args_info->water_flag), 0, &(args_info->water_given),
690	>	&(local_args_info.water_given), optarg, 0, 0, ARG_FLAG,
691	>	check_ambiguity, override, 1, 0, "water", 'w',
692	>	additional_error))
693	>	goto failure;
694	>
695		break;
228	–
696		case 'm':       /* map to the periodic box.  */
697	<	if (args_info->periodicBox_given)
698	<	{
699	<	fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
700	<	clear_args ();
701	<	exit (EXIT_FAILURE);
702	<	}
703	<	args_info->periodicBox_given = 1;
704	<	args_info->periodicBox_flag = !(args_info->periodicBox_flag);
697	>
698	>
699	>	if (update_arg((void *)&(args_info->periodicBox_flag), 0, &(args_info->periodicBox_given),
700	>	&(local_args_info.periodicBox_given), optarg, 0, 0, ARG_FLAG,
701	>	check_ambiguity, override, 1, 0, "periodicBox", 'm',
702	>	additional_error))
703	>	goto failure;
704	>
705		break;
239	–
706		case 'z':       /* replace the atom types of zconstraint molecules.  */
707	<	if (args_info->zconstraint_given)
708	<	{
709	<	fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
710	<	clear_args ();
711	<	exit (EXIT_FAILURE);
712	<	}
713	<	args_info->zconstraint_given = 1;
714	<	args_info->zconstraint_flag = !(args_info->zconstraint_flag);
707	>
708	>
709	>	if (update_arg((void *)&(args_info->zconstraint_flag), 0, &(args_info->zconstraint_given),
710	>	&(local_args_info.zconstraint_given), optarg, 0, 0, ARG_FLAG,
711	>	check_ambiguity, override, 1, 0, "zconstraint", 'z',
712	>	additional_error))
713	>	goto failure;
714	>
715		break;
250	–
716		case 'r':       /* add a pseudo COM atom to rigidbody.  */
717	<	if (args_info->rigidbody_given)
718	<	{
719	<	fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
720	<	clear_args ();
721	<	exit (EXIT_FAILURE);
722	<	}
723	<	args_info->rigidbody_given = 1;
724	<	args_info->rigidbody_flag = !(args_info->rigidbody_flag);
717	>
718	>
719	>	if (update_arg((void *)&(args_info->rigidbody_flag), 0, &(args_info->rigidbody_given),
720	>	&(local_args_info.rigidbody_given), optarg, 0, 0, ARG_FLAG,
721	>	check_ambiguity, override, 1, 0, "rigidbody", 'r',
722	>	additional_error))
723	>	goto failure;
724	>
725		break;
261	–
726		case 't':       /* replace the atom type of water model.  */
727	<	if (args_info->watertype_given)
728	<	{
729	<	fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
730	<	clear_args ();
731	<	exit (EXIT_FAILURE);
732	<	}
733	<	args_info->watertype_given = 1;
734	<	args_info->watertype_flag = !(args_info->watertype_flag);
727	>
728	>
729	>	if (update_arg((void *)&(args_info->watertype_flag), 0, &(args_info->watertype_given),
730	>	&(local_args_info.watertype_given), optarg, 0, 0, ARG_FLAG,
731	>	check_ambiguity, override, 1, 0, "watertype", 't',
732	>	additional_error))
733	>	goto failure;
734	>
735		break;
736	<
737	<	case 'g':       /* ignore the atom types.  */
738	<	args_info->ignore_given++;
739	<	ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
740	<	ignore_new->next = ignore_list;
741	<	ignore_list = ignore_new;
742	<	ignore_new->ignore_arg = gengetopt_strdup (optarg);
736	>	case 's':       /* general selection syntax.  */
737	>
738	>
739	>	if (update_arg( (void *)&(args_info->selection_arg),
740	>	&(args_info->selection_orig), &(args_info->selection_given),
741	>	&(local_args_info.selection_given), optarg, 0, 0, ARG_STRING,
742	>	check_ambiguity, override, 0, 0,
743	>	"selection", 's',
744	>	additional_error))
745	>	goto failure;
746	>
747		break;
748	<
749	<	case 's':       /* general selection syntax:\n
750	<	select DMPC -- select DMPC molecule\n \
751	<	select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
752	<	select 5 -- select stuntdobule whose global index is 5\n \
753	<	select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
754	<	select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule .  */
755	<	if (args_info->selection_given)
756	<	{
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);
748	>	case 'b':       /* Convert to base atom type.  */
749	>
750	>
751	>	if (update_arg((void *)&(args_info->basetype_flag), 0, &(args_info->basetype_given),
752	>	&(local_args_info.basetype_given), optarg, 0, 0, ARG_FLAG,
753	>	check_ambiguity, override, 1, 0, "basetype", 'b',
754	>	additional_error))
755	>	goto failure;
756	>
757		break;
758	+	case 'v':       /* Print velocities in xyz file.  */
759	+
760	+
761	+	if (update_arg((void *)&(args_info->velocities_flag), 0, &(args_info->velocities_given),
762	+	&(local_args_info.velocities_given), optarg, 0, 0, ARG_FLAG,
763	+	check_ambiguity, override, 1, 0, "velocities", 'v',
764	+	additional_error))
765	+	goto failure;
766	+
767	+	break;
768	+	case 'f':       /* Print forces xyz file.  */
769	+
770	+
771	+	if (update_arg((void *)&(args_info->forces_flag), 0, &(args_info->forces_given),
772	+	&(local_args_info.forces_given), optarg, 0, 0, ARG_FLAG,
773	+	check_ambiguity, override, 1, 0, "forces", 'f',
774	+	additional_error))
775	+	goto failure;
776	+
777	+	break;
778	+	case 'u':       /* Print vectors (dipoles, etc) in xyz file.  */
779	+
780	+
781	+	if (update_arg((void *)&(args_info->vectors_flag), 0, &(args_info->vectors_given),
782	+	&(local_args_info.vectors_given), optarg, 0, 0, ARG_FLAG,
783	+	check_ambiguity, override, 1, 0, "vectors", 'u',
784	+	additional_error))
785	+	goto failure;
786	+
787	+	break;
788	+	case 'c':       /* Print charges in xyz file.  */
789	+
790	+
791	+	if (update_arg((void *)&(args_info->charges_flag), 0, &(args_info->charges_given),
792	+	&(local_args_info.charges_given), optarg, 0, 0, ARG_FLAG,
793	+	check_ambiguity, override, 1, 0, "charges", 'c',
794	+	additional_error))
795	+	goto failure;
796	+
797	+	break;
798
297	–
799		case 0: /* Long option with no short option */
800	<	/* The number of images to repeat in the x direction.  */
801	<	if (strcmp (long_options[option_index].name, "repeatX") == 0)
800	>	/* select origin.  */
801	>	if (strcmp (long_options[option_index].name, "originsele") == 0)
802		{
803	<	if (args_info->repeatX_given)
804	<	{
805	<	fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
806	<	clear_args ();
807	<	exit (EXIT_FAILURE);
808	<	}
809	<	args_info->repeatX_given = 1;
810	<	args_info->repeatX_arg = strtol (optarg,&stop_char,0);
811	<	break;
803	>
804	>
805	>	if (update_arg( (void *)&(args_info->originsele_arg),
806	>	&(args_info->originsele_orig), &(args_info->originsele_given),
807	>	&(local_args_info.originsele_given), optarg, 0, 0, ARG_STRING,
808	>	check_ambiguity, override, 0, 0,
809	>	"originsele", '-',
810	>	additional_error))
811	>	goto failure;
812	>
813		}
814	+	/* select reference.  */
815	+	else if (strcmp (long_options[option_index].name, "refsele") == 0)
816	+	{
817
818	+
819	+	if (update_arg( (void *)&(args_info->refsele_arg),
820	+	&(args_info->refsele_orig), &(args_info->refsele_given),
821	+	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
822	+	check_ambiguity, override, 0, 0,
823	+	"refsele", '-',
824	+	additional_error))
825	+	goto failure;
826	+
827	+	}
828	+	/* The number of images to repeat in the x direction.  */
829	+	else if (strcmp (long_options[option_index].name, "repeatX") == 0)
830	+	{
831	+
832	+
833	+	if (update_arg( (void *)&(args_info->repeatX_arg),
834	+	&(args_info->repeatX_orig), &(args_info->repeatX_given),
835	+	&(local_args_info.repeatX_given), optarg, 0, "0", ARG_INT,
836	+	check_ambiguity, override, 0, 0,
837	+	"repeatX", '-',
838	+	additional_error))
839	+	goto failure;
840	+
841	+	}
842		/* The number of images to repeat in the y direction.  */
843		else if (strcmp (long_options[option_index].name, "repeatY") == 0)
844		{
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	–	}
845
846	+
847	+	if (update_arg( (void *)&(args_info->repeatY_arg),
848	+	&(args_info->repeatY_orig), &(args_info->repeatY_given),
849	+	&(local_args_info.repeatY_given), optarg, 0, "0", ARG_INT,
850	+	check_ambiguity, override, 0, 0,
851	+	"repeatY", '-',
852	+	additional_error))
853	+	goto failure;
854	+
855	+	}
856		/* The number of images to repeat in the z direction.  */
857		else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
858		{
859	<	if (args_info->repeatZ_given)
860	<	{
861	<	fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
862	<	clear_args ();
863	<	exit (EXIT_FAILURE);
864	<	}
865	<	args_info->repeatZ_given = 1;
866	<	args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
867	<	break;
859	>
860	>
861	>	if (update_arg( (void *)&(args_info->repeatZ_arg),
862	>	&(args_info->repeatZ_orig), &(args_info->repeatZ_given),
863	>	&(local_args_info.repeatZ_given), optarg, 0, "0", ARG_INT,
864	>	check_ambiguity, override, 0, 0,
865	>	"repeatZ", '-',
866	>	additional_error))
867	>	goto failure;
868	>
869		}
870
871	<
871	>	break;
872		case '?':       /* Invalid option.  */
873		/* `getopt_long' already printed an error message.  */
874	<	exit (EXIT_FAILURE);
874	>	goto failure;
875
876		default:        /* bug: option not considered.  */
877	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
877	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
878		abort ();
879		} /* switch */
880		} /* while */
881
882
883	<	if (! args_info->input_given)
883	>
884	>	if (check_required)
885		{
886	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
356	<	missing_required_options = 1;
886	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
887		}
358	–	if ( missing_required_options )
359	–	exit (EXIT_FAILURE);
888
889	<	if (args_info->ignore_given)
889	>	cmdline_parser_release (&local_args_info);
890	>
891	>	if ( error )
892	>	return (EXIT_FAILURE);
893	>
894	>	if (optind < argc)
895		{
896	<	args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
897	<	for (i = 0; i < args_info->ignore_given; i++)
898	<	{
899	<	args_info->ignore_arg [i] = ignore_list->ignore_arg;
900	<	ignore_list = ignore_list->next;
896	>	int i = 0 ;
897	>	int found_prog_name = 0;
898	>	/* whether program name, i.e., argv[0], is in the remaining args
899	>	(this may happen with some implementations of getopt,
900	>	but surely not with the one included by gengetopt) */
901	>
902	>	i = optind;
903	>	while (i < argc)
904	>	if (argv[i++] == argv[0]) {
905	>	found_prog_name = 1;
906	>	break;
907		}
908	+	i = 0;
909	+
910	+	args_info->inputs_num = argc - optind - found_prog_name;
911	+	args_info->inputs =
912	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
913	+	while (optind < argc)
914	+	if (argv[optind++] != argv[0])
915	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
916		}
917	<
917	>
918		return 0;
919	+
920	+	failure:
921	+
922	+	cmdline_parser_release (&local_args_info);
923	+	return (EXIT_FAILURE);
924		}

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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