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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.
trunk/src/applications/dump2Xyz/Dump2XYZCmd.cpp (file contents), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 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	>	#ifdef WIN32
25	>	#include "utils/wingetopt.h"
26	>	#else
27	>	#include <getopt.h>
28	>	#endif
29
30		#include "Dump2XYZCmd.h"
31
32	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
32	>	const char *gengetopt_args_info_purpose = "";
33
34	<	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	<	}
34	>	const char *gengetopt_args_info_usage = "Usage: Dump2XYZ [OPTIONS]... [FILES]...";
35
36	+	const char *gengetopt_args_info_description = "";
37
38	<	static char *gengetopt_strdup (const char *s);
38	>	const char *gengetopt_args_info_help[] = {
39	>	"  -h, --help                    Print help and exit",
40	>	"  -V, --version                 Print version and exit",
41	>	"  -i, --input=filename          input dump file",
42	>	"  -o, --output=filename         output file name",
43	>	"  -n, --frame=INT               print every n frame  (default=`1')",
44	>	"  -w, --water                   skip the the waters  (default=off)",
45	>	"  -m, --periodicBox             map to the periodic box  (default=off)",
46	>	"  -z, --zconstraint             replace the atom types of zconstraint molecules \n                                   (default=off)",
47	>	"  -r, --rigidbody               add a pseudo COM atom to rigidbody  \n                                  (default=off)",
48	>	"  -t, --watertype               replace the atom type of water model  \n                                  (default=on)",
49	>	"  -s, --selection=selection script\n                                general selection syntax",
50	>	"      --originsele=selection script\n                                select origin",
51	>	"      --refsele=selection script\n                                select reference",
52	>	"      --repeatX=INT             The number of images to repeat in the x \n                                  direction  (default=`0')",
53	>	"      --repeatY=INT             The number of images to repeat in the y \n                                  direction  (default=`0')",
54	>	"      --repeatZ=INT             The number of images to repeat in the z \n                                  direction  (default=`0')",
55	>	"  -b, --basetype                Convert to base atom type  (default=off)",
56	>	"  -v, --velocities              Print velocities in xyz file  (default=off)",
57	>	"  -f, --forces                  Print forces xyz file  (default=off)",
58	>	"  -u, --vectors                 Print vectors (dipoles, etc) in xyz file  \n                                  (default=off)",
59	>	"  -c, --charges                 Print charges in xyz file  (default=off)",
60	>	0
61	>	};
62
63	<	/* gengetopt_strdup() */
64	<	/* strdup.c replacement of strdup, which is not standard */
65	<	char *
66	<	gengetopt_strdup (const char *s)
67	<	{
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	<	}
63	>	typedef enum {ARG_NO
64	>	, ARG_FLAG
65	>	, ARG_STRING
66	>	, ARG_INT
67	>	} cmdline_parser_arg_type;
68
69	<	int
70	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
71	<	{
72	<	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;
69	>	static
70	>	void clear_given (struct gengetopt_args_info *args_info);
71	>	static
72	>	void clear_args (struct gengetopt_args_info *args_info);
73
74	+	static int
75	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
76	+	struct cmdline_parser_params *params, const char *additional_error);
77	+
78	+	static int
79	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
80	+
81	+	static char *
82	+	gengetopt_strdup (const char *s);
83	+
84	+	static
85	+	void clear_given (struct gengetopt_args_info *args_info)
86	+	{
87		args_info->help_given = 0 ;
88		args_info->version_given = 0 ;
89		args_info->input_given = 0 ;
90		args_info->output_given = 0 ;
91		args_info->frame_given = 0 ;
97	–	args_info->dipole_given = 0 ;
92		args_info->water_given = 0 ;
93		args_info->periodicBox_given = 0 ;
94		args_info->zconstraint_given = 0 ;
95		args_info->rigidbody_given = 0 ;
96		args_info->watertype_given = 0 ;
103	–	args_info->ignore_given = 0 ;
97		args_info->selection_given = 0 ;
98	+	args_info->originsele_given = 0 ;
99	+	args_info->refsele_given = 0 ;
100		args_info->repeatX_given = 0 ;
101		args_info->repeatY_given = 0 ;
102		args_info->repeatZ_given = 0 ;
103	<	#define clear_args() { \
104	<	args_info->input_arg = NULL; \
105	<	args_info->output_arg = NULL; \
106	<	args_info->frame_arg = 1 ;\
107	<	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 ;\
103	>	args_info->basetype_given = 0 ;
104	>	args_info->velocities_given = 0 ;
105	>	args_info->forces_given = 0 ;
106	>	args_info->vectors_given = 0 ;
107	>	args_info->charges_given = 0 ;
108		}
109
110	<	clear_args();
110	>	static
111	>	void clear_args (struct gengetopt_args_info *args_info)
112	>	{
113	>	FIX_UNUSED (args_info);
114	>	args_info->input_arg = NULL;
115	>	args_info->input_orig = NULL;
116	>	args_info->output_arg = NULL;
117	>	args_info->output_orig = NULL;
118	>	args_info->frame_arg = 1;
119	>	args_info->frame_orig = NULL;
120	>	args_info->water_flag = 0;
121	>	args_info->periodicBox_flag = 0;
122	>	args_info->zconstraint_flag = 0;
123	>	args_info->rigidbody_flag = 0;
124	>	args_info->watertype_flag = 1;
125	>	args_info->selection_arg = NULL;
126	>	args_info->selection_orig = NULL;
127	>	args_info->originsele_arg = NULL;
128	>	args_info->originsele_orig = NULL;
129	>	args_info->refsele_arg = NULL;
130	>	args_info->refsele_orig = NULL;
131	>	args_info->repeatX_arg = 0;
132	>	args_info->repeatX_orig = NULL;
133	>	args_info->repeatY_arg = 0;
134	>	args_info->repeatY_orig = NULL;
135	>	args_info->repeatZ_arg = 0;
136	>	args_info->repeatZ_orig = NULL;
137	>	args_info->basetype_flag = 0;
138	>	args_info->velocities_flag = 0;
139	>	args_info->forces_flag = 0;
140	>	args_info->vectors_flag = 0;
141	>	args_info->charges_flag = 0;
142	>
143	>	}
144
145	+	static
146	+	void init_args_info(struct gengetopt_args_info *args_info)
147	+	{
148	+
149	+
150	+	args_info->help_help = gengetopt_args_info_help[0] ;
151	+	args_info->version_help = gengetopt_args_info_help[1] ;
152	+	args_info->input_help = gengetopt_args_info_help[2] ;
153	+	args_info->output_help = gengetopt_args_info_help[3] ;
154	+	args_info->frame_help = gengetopt_args_info_help[4] ;
155	+	args_info->water_help = gengetopt_args_info_help[5] ;
156	+	args_info->periodicBox_help = gengetopt_args_info_help[6] ;
157	+	args_info->zconstraint_help = gengetopt_args_info_help[7] ;
158	+	args_info->rigidbody_help = gengetopt_args_info_help[8] ;
159	+	args_info->watertype_help = gengetopt_args_info_help[9] ;
160	+	args_info->selection_help = gengetopt_args_info_help[10] ;
161	+	args_info->originsele_help = gengetopt_args_info_help[11] ;
162	+	args_info->refsele_help = gengetopt_args_info_help[12] ;
163	+	args_info->repeatX_help = gengetopt_args_info_help[13] ;
164	+	args_info->repeatY_help = gengetopt_args_info_help[14] ;
165	+	args_info->repeatZ_help = gengetopt_args_info_help[15] ;
166	+	args_info->basetype_help = gengetopt_args_info_help[16] ;
167	+	args_info->velocities_help = gengetopt_args_info_help[17] ;
168	+	args_info->forces_help = gengetopt_args_info_help[18] ;
169	+	args_info->vectors_help = gengetopt_args_info_help[19] ;
170	+	args_info->charges_help = gengetopt_args_info_help[20] ;
171	+
172	+	}
173	+
174	+	void
175	+	cmdline_parser_print_version (void)
176	+	{
177	+	printf ("%s %s\n",
178	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
179	+	CMDLINE_PARSER_VERSION);
180	+	}
181	+
182	+	static void print_help_common(void) {
183	+	cmdline_parser_print_version ();
184	+
185	+	if (strlen(gengetopt_args_info_purpose) > 0)
186	+	printf("\n%s\n", gengetopt_args_info_purpose);
187	+
188	+	if (strlen(gengetopt_args_info_usage) > 0)
189	+	printf("\n%s\n", gengetopt_args_info_usage);
190	+
191	+	printf("\n");
192	+
193	+	if (strlen(gengetopt_args_info_description) > 0)
194	+	printf("%s\n\n", gengetopt_args_info_description);
195	+	}
196	+
197	+	void
198	+	cmdline_parser_print_help (void)
199	+	{
200	+	int i = 0;
201	+	print_help_common();
202	+	while (gengetopt_args_info_help[i])
203	+	printf("%s\n", gengetopt_args_info_help[i++]);
204	+	}
205	+
206	+	void
207	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
208	+	{
209	+	clear_given (args_info);
210	+	clear_args (args_info);
211	+	init_args_info (args_info);
212	+
213	+	args_info->inputs = 0;
214	+	args_info->inputs_num = 0;
215	+	}
216	+
217	+	void
218	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
219	+	{
220	+	if (params)
221	+	{
222	+	params->override = 0;
223	+	params->initialize = 1;
224	+	params->check_required = 1;
225	+	params->check_ambiguity = 0;
226	+	params->print_errors = 1;
227	+	}
228	+	}
229	+
230	+	struct cmdline_parser_params *
231	+	cmdline_parser_params_create(void)
232	+	{
233	+	struct cmdline_parser_params *params =
234	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
235	+	cmdline_parser_params_init(params);
236	+	return params;
237	+	}
238	+
239	+	static void
240	+	free_string_field (char **s)
241	+	{
242	+	if (*s)
243	+	{
244	+	free (*s);
245	+	*s = 0;
246	+	}
247	+	}
248	+
249	+
250	+	static void
251	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
252	+	{
253	+	unsigned int i;
254	+	free_string_field (&(args_info->input_arg));
255	+	free_string_field (&(args_info->input_orig));
256	+	free_string_field (&(args_info->output_arg));
257	+	free_string_field (&(args_info->output_orig));
258	+	free_string_field (&(args_info->frame_orig));
259	+	free_string_field (&(args_info->selection_arg));
260	+	free_string_field (&(args_info->selection_orig));
261	+	free_string_field (&(args_info->originsele_arg));
262	+	free_string_field (&(args_info->originsele_orig));
263	+	free_string_field (&(args_info->refsele_arg));
264	+	free_string_field (&(args_info->refsele_orig));
265	+	free_string_field (&(args_info->repeatX_orig));
266	+	free_string_field (&(args_info->repeatY_orig));
267	+	free_string_field (&(args_info->repeatZ_orig));
268	+
269	+
270	+	for (i = 0; i < args_info->inputs_num; ++i)
271	+	free (args_info->inputs [i]);
272	+
273	+	if (args_info->inputs_num)
274	+	free (args_info->inputs);
275	+
276	+	clear_given (args_info);
277	+	}
278	+
279	+
280	+	static void
281	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
282	+	{
283	+	FIX_UNUSED (values);
284	+	if (arg) {
285	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
286	+	} else {
287	+	fprintf(outfile, "%s\n", opt);
288	+	}
289	+	}
290	+
291	+
292	+	int
293	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
294	+	{
295	+	int i = 0;
296	+
297	+	if (!outfile)
298	+	{
299	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
300	+	return EXIT_FAILURE;
301	+	}
302	+
303	+	if (args_info->help_given)
304	+	write_into_file(outfile, "help", 0, 0 );
305	+	if (args_info->version_given)
306	+	write_into_file(outfile, "version", 0, 0 );
307	+	if (args_info->input_given)
308	+	write_into_file(outfile, "input", args_info->input_orig, 0);
309	+	if (args_info->output_given)
310	+	write_into_file(outfile, "output", args_info->output_orig, 0);
311	+	if (args_info->frame_given)
312	+	write_into_file(outfile, "frame", args_info->frame_orig, 0);
313	+	if (args_info->water_given)
314	+	write_into_file(outfile, "water", 0, 0 );
315	+	if (args_info->periodicBox_given)
316	+	write_into_file(outfile, "periodicBox", 0, 0 );
317	+	if (args_info->zconstraint_given)
318	+	write_into_file(outfile, "zconstraint", 0, 0 );
319	+	if (args_info->rigidbody_given)
320	+	write_into_file(outfile, "rigidbody", 0, 0 );
321	+	if (args_info->watertype_given)
322	+	write_into_file(outfile, "watertype", 0, 0 );
323	+	if (args_info->selection_given)
324	+	write_into_file(outfile, "selection", args_info->selection_orig, 0);
325	+	if (args_info->originsele_given)
326	+	write_into_file(outfile, "originsele", args_info->originsele_orig, 0);
327	+	if (args_info->refsele_given)
328	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
329	+	if (args_info->repeatX_given)
330	+	write_into_file(outfile, "repeatX", args_info->repeatX_orig, 0);
331	+	if (args_info->repeatY_given)
332	+	write_into_file(outfile, "repeatY", args_info->repeatY_orig, 0);
333	+	if (args_info->repeatZ_given)
334	+	write_into_file(outfile, "repeatZ", args_info->repeatZ_orig, 0);
335	+	if (args_info->basetype_given)
336	+	write_into_file(outfile, "basetype", 0, 0 );
337	+	if (args_info->velocities_given)
338	+	write_into_file(outfile, "velocities", 0, 0 );
339	+	if (args_info->forces_given)
340	+	write_into_file(outfile, "forces", 0, 0 );
341	+	if (args_info->vectors_given)
342	+	write_into_file(outfile, "vectors", 0, 0 );
343	+	if (args_info->charges_given)
344	+	write_into_file(outfile, "charges", 0, 0 );
345	+
346	+
347	+	i = EXIT_SUCCESS;
348	+	return i;
349	+	}
350	+
351	+	int
352	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
353	+	{
354	+	FILE *outfile;
355	+	int i = 0;
356	+
357	+	outfile = fopen(filename, "w");
358	+
359	+	if (!outfile)
360	+	{
361	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
362	+	return EXIT_FAILURE;
363	+	}
364	+
365	+	i = cmdline_parser_dump(outfile, args_info);
366	+	fclose (outfile);
367	+
368	+	return i;
369	+	}
370	+
371	+	void
372	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
373	+	{
374	+	cmdline_parser_release (args_info);
375	+	}
376	+
377	+	/** @brief replacement of strdup, which is not standard */
378	+	char *
379	+	gengetopt_strdup (const char *s)
380	+	{
381	+	char *result = 0;
382	+	if (!s)
383	+	return result;
384	+
385	+	result = (char*)malloc(strlen(s) + 1);
386	+	if (result == (char*)0)
387	+	return (char*)0;
388	+	strcpy(result, s);
389	+	return result;
390	+	}
391	+
392	+	int
393	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
394	+	{
395	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
396	+	}
397	+
398	+	int
399	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
400	+	struct cmdline_parser_params *params)
401	+	{
402	+	int result;
403	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
404	+
405	+	if (result == EXIT_FAILURE)
406	+	{
407	+	cmdline_parser_free (args_info);
408	+	exit (EXIT_FAILURE);
409	+	}
410	+
411	+	return result;
412	+	}
413	+
414	+	int
415	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
416	+	{
417	+	int result;
418	+	struct cmdline_parser_params params;
419	+
420	+	params.override = override;
421	+	params.initialize = initialize;
422	+	params.check_required = check_required;
423	+	params.check_ambiguity = 0;
424	+	params.print_errors = 1;
425	+
426	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
427	+
428	+	if (result == EXIT_FAILURE)
429	+	{
430	+	cmdline_parser_free (args_info);
431	+	exit (EXIT_FAILURE);
432	+	}
433	+
434	+	return result;
435	+	}
436	+
437	+	int
438	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
439	+	{
440	+	int result = EXIT_SUCCESS;
441	+
442	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
443	+	result = EXIT_FAILURE;
444	+
445	+	if (result == EXIT_FAILURE)
446	+	{
447	+	cmdline_parser_free (args_info);
448	+	exit (EXIT_FAILURE);
449	+	}
450	+
451	+	return result;
452	+	}
453	+
454	+	int
455	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
456	+	{
457	+	int error = 0;
458	+	FIX_UNUSED (additional_error);
459	+
460	+	/* checks for required options */
461	+	if (! args_info->input_given)
462	+	{
463	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
464	+	error = 1;
465	+	}
466	+
467	+
468	+	/* checks for dependences among options */
469	+
470	+	return error;
471	+	}
472	+
473	+
474	+	static char *package_name = 0;
475	+
476	+	/**
477	+	* @brief updates an option
478	+	* @param field the generic pointer to the field to update
479	+	* @param orig_field the pointer to the orig field
480	+	* @param field_given the pointer to the number of occurrence of this option
481	+	* @param prev_given the pointer to the number of occurrence already seen
482	+	* @param value the argument for this option (if null no arg was specified)
483	+	* @param possible_values the possible values for this option (if specified)
484	+	* @param default_value the default value (in case the option only accepts fixed values)
485	+	* @param arg_type the type of this option
486	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
487	+	* @param override @see cmdline_parser_params.override
488	+	* @param no_free whether to free a possible previous value
489	+	* @param multiple_option whether this is a multiple option
490	+	* @param long_opt the corresponding long option
491	+	* @param short_opt the corresponding short option (or '-' if none)
492	+	* @param additional_error possible further error specification
493	+	*/
494	+	static
495	+	int update_arg(void *field, char **orig_field,
496	+	unsigned int *field_given, unsigned int *prev_given,
497	+	char *value, const char *possible_values[],
498	+	const char *default_value,
499	+	cmdline_parser_arg_type arg_type,
500	+	int check_ambiguity, int override,
501	+	int no_free, int multiple_option,
502	+	const char *long_opt, char short_opt,
503	+	const char *additional_error)
504	+	{
505	+	char *stop_char = 0;
506	+	const char *val = value;
507	+	int found;
508	+	char **string_field;
509	+	FIX_UNUSED (field);
510	+
511	+	stop_char = 0;
512	+	found = 0;
513	+
514	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
515	+	{
516	+	if (short_opt != '-')
517	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
518	+	package_name, long_opt, short_opt,
519	+	(additional_error ? additional_error : ""));
520	+	else
521	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
522	+	package_name, long_opt,
523	+	(additional_error ? additional_error : ""));
524	+	return 1; /* failure */
525	+	}
526	+
527	+	FIX_UNUSED (default_value);
528	+
529	+	if (field_given && *field_given && ! override)
530	+	return 0;
531	+	if (prev_given)
532	+	(*prev_given)++;
533	+	if (field_given)
534	+	(*field_given)++;
535	+	if (possible_values)
536	+	val = possible_values[found];
537	+
538	+	switch(arg_type) {
539	+	case ARG_FLAG:
540	+	*((int *)field) = !*((int *)field);
541	+	break;
542	+	case ARG_INT:
543	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
544	+	break;
545	+	case ARG_STRING:
546	+	if (val) {
547	+	string_field = (char **)field;
548	+	if (!no_free && *string_field)
549	+	free (*string_field); /* free previous string */
550	+	*string_field = gengetopt_strdup (val);
551	+	}
552	+	break;
553	+	default:
554	+	break;
555	+	};
556	+
557	+	/* check numeric conversion */
558	+	switch(arg_type) {
559	+	case ARG_INT:
560	+	if (val && !(stop_char && *stop_char == '\0')) {
561	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
562	+	return 1; /* failure */
563	+	}
564	+	break;
565	+	default:
566	+	;
567	+	};
568	+
569	+	/* store the original value */
570	+	switch(arg_type) {
571	+	case ARG_NO:
572	+	case ARG_FLAG:
573	+	break;
574	+	default:
575	+	if (value && orig_field) {
576	+	if (no_free) {
577	+	*orig_field = value;
578	+	} else {
579	+	if (*orig_field)
580	+	free (*orig_field); /* free previous string */
581	+	*orig_field = gengetopt_strdup (value);
582	+	}
583	+	}
584	+	};
585	+
586	+	return 0; /* OK */
587	+	}
588	+
589	+
590	+	int
591	+	cmdline_parser_internal (
592	+	int argc, char **argv, struct gengetopt_args_info *args_info,
593	+	struct cmdline_parser_params *params, const char *additional_error)
594	+	{
595	+	int c;        /* Character of the parsed option.  */
596	+
597	+	int error = 0;
598	+	struct gengetopt_args_info local_args_info;
599	+
600	+	int override;
601	+	int initialize;
602	+	int check_required;
603	+	int check_ambiguity;
604	+
605	+	package_name = argv[0];
606	+
607	+	override = params->override;
608	+	initialize = params->initialize;
609	+	check_required = params->check_required;
610	+	check_ambiguity = params->check_ambiguity;
611	+
612	+	if (initialize)
613	+	cmdline_parser_init (args_info);
614	+
615	+	cmdline_parser_init (&local_args_info);
616	+
617		optarg = 0;
618	<	optind = 1;
619	<	opterr = 1;
618	>	optind = 0;
619	>	opterr = params->print_errors;
620		optopt = '?';
621
622		while (1)
623		{
624		int option_index = 0;
135	–	char *stop_char;
625
626		static struct option long_options[] = {
627		{ "help",       0, NULL, 'h' },
#	Line 140 | Line 629 | cmdline_parser (int argc, char * const *argv, struct g
629		{ "input",      1, NULL, 'i' },
630		{ "output",     1, NULL, 'o' },
631		{ "frame",      1, NULL, 'n' },
143	–	{ "dipole",     0, NULL, 'd' },
632		{ "water",      0, NULL, 'w' },
633		{ "periodicBox",        0, NULL, 'm' },
634		{ "zconstraint",        0, NULL, 'z' },
635		{ "rigidbody",  0, NULL, 'r' },
636		{ "watertype",  0, NULL, 't' },
149	–	{ "ignore",     1, NULL, 'g' },
637		{ "selection",  1, NULL, 's' },
638	+	{ "originsele", 1, NULL, 0 },
639	+	{ "refsele",    1, NULL, 0 },
640		{ "repeatX",    1, NULL, 0 },
641		{ "repeatY",    1, NULL, 0 },
642		{ "repeatZ",    1, NULL, 0 },
643	<	{ NULL, 0, NULL, 0 }
643	>	{ "basetype",   0, NULL, 'b' },
644	>	{ "velocities", 0, NULL, 'v' },
645	>	{ "forces",     0, NULL, 'f' },
646	>	{ "vectors",    0, NULL, 'u' },
647	>	{ "charges",    0, NULL, 'c' },
648	>	{ 0,  0, 0, 0 }
649		};
650
651	<	stop_char = 0;
158	<	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
651	>	c = getopt_long (argc, argv, "hVi:o:n:wmzrts:bvfuc", long_options, &option_index);
652
653		if (c == -1) break;       /* Exit from `while (1)' loop.  */
654
655		switch (c)
656		{
657		case 'h':       /* Print help and exit.  */
165	–	clear_args ();
658		cmdline_parser_print_help ();
659	+	cmdline_parser_free (&local_args_info);
660		exit (EXIT_SUCCESS);
661
662		case 'V':       /* Print version and exit.  */
170	–	clear_args ();
663		cmdline_parser_print_version ();
664	+	cmdline_parser_free (&local_args_info);
665		exit (EXIT_SUCCESS);
666
667		case 'i':       /* input dump file.  */
668	<	if (args_info->input_given)
669	<	{
670	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
671	<	clear_args ();
672	<	exit (EXIT_FAILURE);
673	<	}
674	<	args_info->input_given = 1;
675	<	args_info->input_arg = gengetopt_strdup (optarg);
668	>
669	>
670	>	if (update_arg( (void *)&(args_info->input_arg),
671	>	&(args_info->input_orig), &(args_info->input_given),
672	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
673	>	check_ambiguity, override, 0, 0,
674	>	"input", 'i',
675	>	additional_error))
676	>	goto failure;
677	>
678		break;
184	–
679		case 'o':       /* output file name.  */
680	<	if (args_info->output_given)
681	<	{
682	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
683	<	clear_args ();
684	<	exit (EXIT_FAILURE);
685	<	}
686	<	args_info->output_given = 1;
687	<	args_info->output_arg = gengetopt_strdup (optarg);
680	>
681	>
682	>	if (update_arg( (void *)&(args_info->output_arg),
683	>	&(args_info->output_orig), &(args_info->output_given),
684	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
685	>	check_ambiguity, override, 0, 0,
686	>	"output", 'o',
687	>	additional_error))
688	>	goto failure;
689	>
690		break;
195	–
691		case 'n':       /* print every n frame.  */
692	<	if (args_info->frame_given)
693	<	{
694	<	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
695	<	clear_args ();
696	<	exit (EXIT_FAILURE);
697	<	}
698	<	args_info->frame_given = 1;
699	<	args_info->frame_arg = strtol (optarg,&stop_char,0);
692	>
693	>
694	>	if (update_arg( (void *)&(args_info->frame_arg),
695	>	&(args_info->frame_orig), &(args_info->frame_given),
696	>	&(local_args_info.frame_given), optarg, 0, "1", ARG_INT,
697	>	check_ambiguity, override, 0, 0,
698	>	"frame", 'n',
699	>	additional_error))
700	>	goto failure;
701	>
702		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	–
703		case 'w':       /* skip the the waters.  */
704	<	if (args_info->water_given)
705	<	{
706	<	fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
707	<	clear_args ();
708	<	exit (EXIT_FAILURE);
709	<	}
710	<	args_info->water_given = 1;
711	<	args_info->water_flag = !(args_info->water_flag);
704	>
705	>
706	>	if (update_arg((void *)&(args_info->water_flag), 0, &(args_info->water_given),
707	>	&(local_args_info.water_given), optarg, 0, 0, ARG_FLAG,
708	>	check_ambiguity, override, 1, 0, "water", 'w',
709	>	additional_error))
710	>	goto failure;
711	>
712		break;
228	–
713		case 'm':       /* map to the periodic box.  */
714	<	if (args_info->periodicBox_given)
715	<	{
716	<	fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
717	<	clear_args ();
718	<	exit (EXIT_FAILURE);
719	<	}
720	<	args_info->periodicBox_given = 1;
721	<	args_info->periodicBox_flag = !(args_info->periodicBox_flag);
714	>
715	>
716	>	if (update_arg((void *)&(args_info->periodicBox_flag), 0, &(args_info->periodicBox_given),
717	>	&(local_args_info.periodicBox_given), optarg, 0, 0, ARG_FLAG,
718	>	check_ambiguity, override, 1, 0, "periodicBox", 'm',
719	>	additional_error))
720	>	goto failure;
721	>
722		break;
239	–
723		case 'z':       /* replace the atom types of zconstraint molecules.  */
724	<	if (args_info->zconstraint_given)
725	<	{
726	<	fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
727	<	clear_args ();
728	<	exit (EXIT_FAILURE);
729	<	}
730	<	args_info->zconstraint_given = 1;
731	<	args_info->zconstraint_flag = !(args_info->zconstraint_flag);
724	>
725	>
726	>	if (update_arg((void *)&(args_info->zconstraint_flag), 0, &(args_info->zconstraint_given),
727	>	&(local_args_info.zconstraint_given), optarg, 0, 0, ARG_FLAG,
728	>	check_ambiguity, override, 1, 0, "zconstraint", 'z',
729	>	additional_error))
730	>	goto failure;
731	>
732		break;
250	–
733		case 'r':       /* add a pseudo COM atom to rigidbody.  */
734	<	if (args_info->rigidbody_given)
735	<	{
736	<	fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
737	<	clear_args ();
738	<	exit (EXIT_FAILURE);
739	<	}
740	<	args_info->rigidbody_given = 1;
741	<	args_info->rigidbody_flag = !(args_info->rigidbody_flag);
734	>
735	>
736	>	if (update_arg((void *)&(args_info->rigidbody_flag), 0, &(args_info->rigidbody_given),
737	>	&(local_args_info.rigidbody_given), optarg, 0, 0, ARG_FLAG,
738	>	check_ambiguity, override, 1, 0, "rigidbody", 'r',
739	>	additional_error))
740	>	goto failure;
741	>
742		break;
261	–
743		case 't':       /* replace the atom type of water model.  */
744	<	if (args_info->watertype_given)
745	<	{
746	<	fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
747	<	clear_args ();
748	<	exit (EXIT_FAILURE);
749	<	}
750	<	args_info->watertype_given = 1;
751	<	args_info->watertype_flag = !(args_info->watertype_flag);
744	>
745	>
746	>	if (update_arg((void *)&(args_info->watertype_flag), 0, &(args_info->watertype_given),
747	>	&(local_args_info.watertype_given), optarg, 0, 0, ARG_FLAG,
748	>	check_ambiguity, override, 1, 0, "watertype", 't',
749	>	additional_error))
750	>	goto failure;
751	>
752		break;
753	<
754	<	case 'g':       /* ignore the atom types.  */
755	<	args_info->ignore_given++;
756	<	ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
757	<	ignore_new->next = ignore_list;
758	<	ignore_list = ignore_new;
759	<	ignore_new->ignore_arg = gengetopt_strdup (optarg);
753	>	case 's':       /* general selection syntax.  */
754	>
755	>
756	>	if (update_arg( (void *)&(args_info->selection_arg),
757	>	&(args_info->selection_orig), &(args_info->selection_given),
758	>	&(local_args_info.selection_given), optarg, 0, 0, ARG_STRING,
759	>	check_ambiguity, override, 0, 0,
760	>	"selection", 's',
761	>	additional_error))
762	>	goto failure;
763	>
764		break;
765	<
766	<	case 's':       /* general selection syntax:\n
767	<	select DMPC -- select DMPC molecule\n \
768	<	select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
769	<	select 5 -- select stuntdobule whose global index is 5\n \
770	<	select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
771	<	select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule .  */
772	<	if (args_info->selection_given)
773	<	{
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);
765	>	case 'b':       /* Convert to base atom type.  */
766	>
767	>
768	>	if (update_arg((void *)&(args_info->basetype_flag), 0, &(args_info->basetype_given),
769	>	&(local_args_info.basetype_given), optarg, 0, 0, ARG_FLAG,
770	>	check_ambiguity, override, 1, 0, "basetype", 'b',
771	>	additional_error))
772	>	goto failure;
773	>
774		break;
775	+	case 'v':       /* Print velocities in xyz file.  */
776	+
777	+
778	+	if (update_arg((void *)&(args_info->velocities_flag), 0, &(args_info->velocities_given),
779	+	&(local_args_info.velocities_given), optarg, 0, 0, ARG_FLAG,
780	+	check_ambiguity, override, 1, 0, "velocities", 'v',
781	+	additional_error))
782	+	goto failure;
783	+
784	+	break;
785	+	case 'f':       /* Print forces xyz file.  */
786	+
787	+
788	+	if (update_arg((void *)&(args_info->forces_flag), 0, &(args_info->forces_given),
789	+	&(local_args_info.forces_given), optarg, 0, 0, ARG_FLAG,
790	+	check_ambiguity, override, 1, 0, "forces", 'f',
791	+	additional_error))
792	+	goto failure;
793	+
794	+	break;
795	+	case 'u':       /* Print vectors (dipoles, etc) in xyz file.  */
796	+
797	+
798	+	if (update_arg((void *)&(args_info->vectors_flag), 0, &(args_info->vectors_given),
799	+	&(local_args_info.vectors_given), optarg, 0, 0, ARG_FLAG,
800	+	check_ambiguity, override, 1, 0, "vectors", 'u',
801	+	additional_error))
802	+	goto failure;
803	+
804	+	break;
805	+	case 'c':       /* Print charges in xyz file.  */
806	+
807	+
808	+	if (update_arg((void *)&(args_info->charges_flag), 0, &(args_info->charges_given),
809	+	&(local_args_info.charges_given), optarg, 0, 0, ARG_FLAG,
810	+	check_ambiguity, override, 1, 0, "charges", 'c',
811	+	additional_error))
812	+	goto failure;
813	+
814	+	break;
815
297	–
816		case 0: /* Long option with no short option */
817	<	/* The number of images to repeat in the x direction.  */
818	<	if (strcmp (long_options[option_index].name, "repeatX") == 0)
817	>	/* select origin.  */
818	>	if (strcmp (long_options[option_index].name, "originsele") == 0)
819		{
820	<	if (args_info->repeatX_given)
821	<	{
822	<	fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
823	<	clear_args ();
824	<	exit (EXIT_FAILURE);
825	<	}
826	<	args_info->repeatX_given = 1;
827	<	args_info->repeatX_arg = strtol (optarg,&stop_char,0);
828	<	break;
820	>
821	>
822	>	if (update_arg( (void *)&(args_info->originsele_arg),
823	>	&(args_info->originsele_orig), &(args_info->originsele_given),
824	>	&(local_args_info.originsele_given), optarg, 0, 0, ARG_STRING,
825	>	check_ambiguity, override, 0, 0,
826	>	"originsele", '-',
827	>	additional_error))
828	>	goto failure;
829	>
830		}
831	+	/* select reference.  */
832	+	else if (strcmp (long_options[option_index].name, "refsele") == 0)
833	+	{
834
835	+
836	+	if (update_arg( (void *)&(args_info->refsele_arg),
837	+	&(args_info->refsele_orig), &(args_info->refsele_given),
838	+	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
839	+	check_ambiguity, override, 0, 0,
840	+	"refsele", '-',
841	+	additional_error))
842	+	goto failure;
843	+
844	+	}
845	+	/* The number of images to repeat in the x direction.  */
846	+	else if (strcmp (long_options[option_index].name, "repeatX") == 0)
847	+	{
848	+
849	+
850	+	if (update_arg( (void *)&(args_info->repeatX_arg),
851	+	&(args_info->repeatX_orig), &(args_info->repeatX_given),
852	+	&(local_args_info.repeatX_given), optarg, 0, "0", ARG_INT,
853	+	check_ambiguity, override, 0, 0,
854	+	"repeatX", '-',
855	+	additional_error))
856	+	goto failure;
857	+
858	+	}
859		/* The number of images to repeat in the y direction.  */
860		else if (strcmp (long_options[option_index].name, "repeatY") == 0)
861		{
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	–	}
862
863	+
864	+	if (update_arg( (void *)&(args_info->repeatY_arg),
865	+	&(args_info->repeatY_orig), &(args_info->repeatY_given),
866	+	&(local_args_info.repeatY_given), optarg, 0, "0", ARG_INT,
867	+	check_ambiguity, override, 0, 0,
868	+	"repeatY", '-',
869	+	additional_error))
870	+	goto failure;
871	+
872	+	}
873		/* The number of images to repeat in the z direction.  */
874		else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
875		{
876	<	if (args_info->repeatZ_given)
877	<	{
878	<	fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
879	<	clear_args ();
880	<	exit (EXIT_FAILURE);
881	<	}
882	<	args_info->repeatZ_given = 1;
883	<	args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
884	<	break;
876	>
877	>
878	>	if (update_arg( (void *)&(args_info->repeatZ_arg),
879	>	&(args_info->repeatZ_orig), &(args_info->repeatZ_given),
880	>	&(local_args_info.repeatZ_given), optarg, 0, "0", ARG_INT,
881	>	check_ambiguity, override, 0, 0,
882	>	"repeatZ", '-',
883	>	additional_error))
884	>	goto failure;
885	>
886		}
887
888	<
888	>	break;
889		case '?':       /* Invalid option.  */
890		/* `getopt_long' already printed an error message.  */
891	<	exit (EXIT_FAILURE);
891	>	goto failure;
892
893		default:        /* bug: option not considered.  */
894	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
894	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
895		abort ();
896		} /* switch */
897		} /* while */
898
899
900	<	if (! args_info->input_given)
900	>
901	>	if (check_required)
902		{
903	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
356	<	missing_required_options = 1;
903	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
904		}
358	–	if ( missing_required_options )
359	–	exit (EXIT_FAILURE);
905
906	<	if (args_info->ignore_given)
906	>	cmdline_parser_release (&local_args_info);
907	>
908	>	if ( error )
909	>	return (EXIT_FAILURE);
910	>
911	>	if (optind < argc)
912		{
913	<	args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
914	<	for (i = 0; i < args_info->ignore_given; i++)
915	<	{
916	<	args_info->ignore_arg [i] = ignore_list->ignore_arg;
917	<	ignore_list = ignore_list->next;
913	>	int i = 0 ;
914	>	int found_prog_name = 0;
915	>	/* whether program name, i.e., argv[0], is in the remaining args
916	>	(this may happen with some implementations of getopt,
917	>	but surely not with the one included by gengetopt) */
918	>
919	>	i = optind;
920	>	while (i < argc)
921	>	if (argv[i++] == argv[0]) {
922	>	found_prog_name = 1;
923	>	break;
924		}
925	+	i = 0;
926	+
927	+	args_info->inputs_num = argc - optind - found_prog_name;
928	+	args_info->inputs =
929	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
930	+	while (optind < argc)
931	+	if (argv[optind++] != argv[0])
932	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
933		}
934	<
934	>
935		return 0;
936	+
937	+	failure:
938	+
939	+	cmdline_parser_release (&local_args_info);
940	+	return (EXIT_FAILURE);
941		}

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZCmd.c (property svn:keywords), Revision 302 by tim, Mon Feb 7 21:11:22 2005 UTC vs.
trunk/src/applications/dump2Xyz/Dump2XYZCmd.cpp (property svn:keywords), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

#	Line 0 | Line 1
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