ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (file contents), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.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 2.13
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	gengetopt -u -F nanoparticleBuilderCmd
4	>	gengetopt -F nanoparticleBuilderCmd -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:
#	Line 17 | Line 17
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	#include "getopt.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22	>	#endif
23
24	+	#include <getopt.h>
25	+
26		#include "nanoparticleBuilderCmd.h"
27
28	+	const char *gengetopt_args_info_purpose = "Builds spherical random or core-shell nanoparticles and outputs an OpenMD \nstartup file";
29	+
30	+	const char *gengetopt_args_info_usage = "Usage: nanoparticleBuilder [OPTIONS]... [FILES]...";
31	+
32	+	const char *gengetopt_args_info_description = "";
33	+
34	+	const char *gengetopt_args_info_help[] = {
35	+	"  -h, --help                    Print help and exit",
36	+	"  -V, --version                 Print version and exit",
37	+	"  -o, --output=STRING           Output file name",
38	+	"      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.",
39	+	"      --radius=DOUBLE           Nanoparticle radius in Angstroms",
40	+	"      --shellRadius=DOUBLE      Radius containing within it only molecules of a \n                                  specific component. Specified for each \n                                  component > 1 in the template file.",
41	+	"      --molFraction=DOUBLE      Builds a multi-component random alloy \n                                  nanoparticle. A mole Fraction must be \n                                  specified for each component > 1 in the \n                                  template file.",
42	+	"      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within \n                                  vacancy range",
43	+	"      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
44	+	"      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
45	+	0
46	+	};
47	+
48	+	typedef enum {ARG_NO
49	+	, ARG_STRING
50	+	, ARG_DOUBLE
51	+	} cmdline_parser_arg_type;
52	+
53		static
54		void clear_given (struct gengetopt_args_info *args_info);
55		static
56		void clear_args (struct gengetopt_args_info *args_info);
57
58		static int
59	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
59	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
60	>	struct cmdline_parser_params *params, const char *additional_error);
61
62		static int
63		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
64
35	–	struct ShellRadius_list
36	–	{
37	–	double ShellRadius_arg;
38	–	struct ShellRadius_list * next;
39	–	};
40	–
41	–	struct molFraction_list
42	–	{
43	–	double molFraction_arg;
44	–	struct molFraction_list * next;
45	–	};
46	–
47	–	struct vacancyRadius_list
48	–	{
49	–	double vacancyRadius_arg;
50	–	struct vacancyRadius_list * next;
51	–	};
52	–
65		static char *
66		gengetopt_strdup (const char *s);
67
#	Line 59 | Line 71 | void clear_given (struct gengetopt_args_info *args_inf
71		args_info->help_given = 0 ;
72		args_info->version_given = 0 ;
73		args_info->output_given = 0 ;
74	<	args_info->latticetype_given = 0 ;
63	<	args_info->latticeCnst_given = 0 ;
74	>	args_info->latticeConstant_given = 0 ;
75		args_info->radius_given = 0 ;
76	<	args_info->ShellRadius_given = 0 ;
76	>	args_info->shellRadius_given = 0 ;
77		args_info->molFraction_given = 0 ;
78	<	args_info->vacancyPCT_given = 0 ;
79	<	args_info->vacancyRadius_given = 0 ;
78	>	args_info->vacancyPercent_given = 0 ;
79	>	args_info->vacancyInnerRadius_given = 0 ;
80	>	args_info->vacancyOuterRadius_given = 0 ;
81		}
82
83		static
84		void clear_args (struct gengetopt_args_info *args_info)
85		{
86	+	FIX_UNUSED (args_info);
87		args_info->output_arg = NULL;
88	<	args_info->latticetype_arg = gengetopt_strdup ("fcc");
89	<	args_info->ShellRadius_arg = NULL;
88	>	args_info->output_orig = NULL;
89	>	args_info->latticeConstant_orig = NULL;
90	>	args_info->radius_orig = NULL;
91	>	args_info->shellRadius_arg = NULL;
92	>	args_info->shellRadius_orig = NULL;
93		args_info->molFraction_arg = NULL;
94	<	args_info->vacancyRadius_arg = NULL;
94	>	args_info->molFraction_orig = NULL;
95	>	args_info->vacancyPercent_orig = NULL;
96	>	args_info->vacancyInnerRadius_orig = NULL;
97	>	args_info->vacancyOuterRadius_orig = NULL;
98	>
99		}
100
101	+	static
102	+	void init_args_info(struct gengetopt_args_info *args_info)
103	+	{
104	+
105	+
106	+	args_info->help_help = gengetopt_args_info_help[0] ;
107	+	args_info->version_help = gengetopt_args_info_help[1] ;
108	+	args_info->output_help = gengetopt_args_info_help[2] ;
109	+	args_info->latticeConstant_help = gengetopt_args_info_help[3] ;
110	+	args_info->radius_help = gengetopt_args_info_help[4] ;
111	+	args_info->shellRadius_help = gengetopt_args_info_help[5] ;
112	+	args_info->shellRadius_min = 0;
113	+	args_info->shellRadius_max = 0;
114	+	args_info->molFraction_help = gengetopt_args_info_help[6] ;
115	+	args_info->molFraction_min = 0;
116	+	args_info->molFraction_max = 0;
117	+	args_info->vacancyPercent_help = gengetopt_args_info_help[7] ;
118	+	args_info->vacancyInnerRadius_help = gengetopt_args_info_help[8] ;
119	+	args_info->vacancyOuterRadius_help = gengetopt_args_info_help[9] ;
120	+
121	+	}
122	+
123		void
124		cmdline_parser_print_version (void)
125		{
126	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
126	>	printf ("%s %s\n",
127	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
128	>	CMDLINE_PARSER_VERSION);
129		}
130
131	+	static void print_help_common(void) {
132	+	cmdline_parser_print_version ();
133	+
134	+	if (strlen(gengetopt_args_info_purpose) > 0)
135	+	printf("\n%s\n", gengetopt_args_info_purpose);
136	+
137	+	if (strlen(gengetopt_args_info_usage) > 0)
138	+	printf("\n%s\n", gengetopt_args_info_usage);
139	+
140	+	printf("\n");
141	+
142	+	if (strlen(gengetopt_args_info_description) > 0)
143	+	printf("%s\n\n", gengetopt_args_info_description);
144	+	}
145	+
146		void
147		cmdline_parser_print_help (void)
148		{
149	<	cmdline_parser_print_version ();
150	<	printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
151	<	printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
152	<	printf("%s\n","  -h, --help                  Print help and exit");
94	<	printf("%s\n","  -V, --version               Print version and exit");
95	<	printf("%s\n","  -o, --output=STRING         Output file name");
96	<	printf("%s\n","      --latticetype=STRING    Lattice type string. Valid types are fcc,hcp,bcc. \n                                 (default=`fcc')");
97	<	printf("%s\n","      --latticeCnst=DOUBLE    Lattice spacing in Angstroms for cubic lattice.");
98	<	printf("%s\n","      --radius=DOUBLE         Nanoparticle radius in Angstroms");
99	<	printf("%s\n","      --ShellRadius=DOUBLE    Radius from the center of the particle to start a \n                                new shell in multi-component core-shell \n                                particle. Specified for each component > 1 in \n                                md file.");
100	<	printf("%s\n","      --molFraction=DOUBLE    (Default) Builds a multi-component random mixed \n                                nanoparticle. Mole Fraction must be specified \n                                for each componet > 1 in MD file.");
101	<	printf("%s\n","      --vacancyPCT=DOUBLE     Percentage of vacancies to build");
102	<	printf("%s\n","      --vacancyRadius=DOUBLE  Radius arround core-shell where vacancies should \n                                be located.");
103	<
149	>	int i = 0;
150	>	print_help_common();
151	>	while (gengetopt_args_info_help[i])
152	>	printf("%s\n", gengetopt_args_info_help[i++]);
153		}
154
155		void
#	Line 108 | Line 157 | cmdline_parser_init (struct gengetopt_args_info *args_
157		{
158		clear_given (args_info);
159		clear_args (args_info);
160	+	init_args_info (args_info);
161
162	<	args_info->inputs = NULL;
162	>	args_info->inputs = 0;
163		args_info->inputs_num = 0;
164		}
165
166		void
167	<	cmdline_parser_free (struct gengetopt_args_info *args_info)
167	>	cmdline_parser_params_init(struct cmdline_parser_params *params)
168		{
169	<
170	<	unsigned int i;
171	<	if (args_info->output_arg)
172	<	{
173	<	free (args_info->output_arg); /* free previous argument */
174	<	args_info->output_arg = 0;
169	>	if (params)
170	>	{
171	>	params->override = 0;
172	>	params->initialize = 1;
173	>	params->check_required = 1;
174	>	params->check_ambiguity = 0;
175	>	params->print_errors = 1;
176		}
177	<	if (args_info->latticetype_arg)
177	>	}
178	>
179	>	struct cmdline_parser_params *
180	>	cmdline_parser_params_create(void)
181	>	{
182	>	struct cmdline_parser_params *params =
183	>	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
184	>	cmdline_parser_params_init(params);
185	>	return params;
186	>	}
187	>
188	>	static void
189	>	free_string_field (char **s)
190	>	{
191	>	if (*s)
192		{
193	<	free (args_info->latticetype_arg); /* free previous argument */
194	<	args_info->latticetype_arg = 0;
193	>	free (*s);
194	>	*s = 0;
195		}
196	<	if (args_info->ShellRadius_arg)
197	<	{
198	<	free (args_info->ShellRadius_arg); /* free previous argument */
199	<	args_info->ShellRadius_arg = 0;
200	<	}
201	<	if (args_info->molFraction_arg)
202	<	{
203	<	free (args_info->molFraction_arg); /* free previous argument */
204	<	args_info->molFraction_arg = 0;
205	<	}
206	<	if (args_info->vacancyRadius_arg)
207	<	{
208	<	free (args_info->vacancyRadius_arg); /* free previous argument */
209	<	args_info->vacancyRadius_arg = 0;
210	<	}
196	>	}
197	>
198	>	/** @brief generic value variable */
199	>	union generic_value {
200	>	double double_arg;
201	>	char *string_arg;
202	>	const char *default_string_arg;
203	>	};
204	>
205	>	/** @brief holds temporary values for multiple options */
206	>	struct generic_list
207	>	{
208	>	union generic_value arg;
209	>	char *orig;
210	>	struct generic_list *next;
211	>	};
212	>
213	>	/**
214	>	* @brief add a node at the head of the list
215	>	*/
216	>	static void add_node(struct generic_list **list) {
217	>	struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
218	>	new_node->next = *list;
219	>	*list = new_node;
220	>	new_node->arg.string_arg = 0;
221	>	new_node->orig = 0;
222	>	}
223	>
224	>	/**
225	>	* The passed arg parameter is NOT set to 0 from this function
226	>	*/
227	>	static void
228	>	free_multiple_field(unsigned int len, void *arg, char ***orig)
229	>	{
230	>	unsigned int i;
231	>	if (arg) {
232	>	for (i = 0; i < len; ++i)
233	>	{
234	>	free_string_field(&((*orig)[i]));
235	>	}
236	>
237	>	free (arg);
238	>	free (*orig);
239	>	*orig = 0;
240	>	}
241	>	}
242	>
243	>
244	>	static void
245	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
246	>	{
247	>	unsigned int i;
248	>	free_string_field (&(args_info->output_arg));
249	>	free_string_field (&(args_info->output_orig));
250	>	free_string_field (&(args_info->latticeConstant_orig));
251	>	free_string_field (&(args_info->radius_orig));
252	>	free_multiple_field (args_info->shellRadius_given, (void *)(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
253	>	args_info->shellRadius_arg = 0;
254	>	free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
255	>	args_info->molFraction_arg = 0;
256	>	free_string_field (&(args_info->vacancyPercent_orig));
257	>	free_string_field (&(args_info->vacancyInnerRadius_orig));
258	>	free_string_field (&(args_info->vacancyOuterRadius_orig));
259
260	+
261		for (i = 0; i < args_info->inputs_num; ++i)
262		free (args_info->inputs [i]);
263	<
263	>
264		if (args_info->inputs_num)
265		free (args_info->inputs);
266	<
266	>
267		clear_given (args_info);
268		}
269
270	<	/* gengetopt_strdup() */
271	<	/* strdup.c replacement of strdup, which is not standard */
270	>
271	>	static void
272	>	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
273	>	{
274	>	FIX_UNUSED (values);
275	>	if (arg) {
276	>	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
277	>	} else {
278	>	fprintf(outfile, "%s\n", opt);
279	>	}
280	>	}
281	>
282	>	static void
283	>	write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
284	>	{
285	>	int i;
286	>
287	>	for (i = 0; i < len; ++i)
288	>	write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
289	>	}
290	>
291	>	int
292	>	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
293	>	{
294	>	int i = 0;
295	>
296	>	if (!outfile)
297	>	{
298	>	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
299	>	return EXIT_FAILURE;
300	>	}
301	>
302	>	if (args_info->help_given)
303	>	write_into_file(outfile, "help", 0, 0 );
304	>	if (args_info->version_given)
305	>	write_into_file(outfile, "version", 0, 0 );
306	>	if (args_info->output_given)
307	>	write_into_file(outfile, "output", args_info->output_orig, 0);
308	>	if (args_info->latticeConstant_given)
309	>	write_into_file(outfile, "latticeConstant", args_info->latticeConstant_orig, 0);
310	>	if (args_info->radius_given)
311	>	write_into_file(outfile, "radius", args_info->radius_orig, 0);
312	>	write_multiple_into_file(outfile, args_info->shellRadius_given, "shellRadius", args_info->shellRadius_orig, 0);
313	>	write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0);
314	>	if (args_info->vacancyPercent_given)
315	>	write_into_file(outfile, "vacancyPercent", args_info->vacancyPercent_orig, 0);
316	>	if (args_info->vacancyInnerRadius_given)
317	>	write_into_file(outfile, "vacancyInnerRadius", args_info->vacancyInnerRadius_orig, 0);
318	>	if (args_info->vacancyOuterRadius_given)
319	>	write_into_file(outfile, "vacancyOuterRadius", args_info->vacancyOuterRadius_orig, 0);
320	>
321	>
322	>	i = EXIT_SUCCESS;
323	>	return i;
324	>	}
325	>
326	>	int
327	>	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
328	>	{
329	>	FILE *outfile;
330	>	int i = 0;
331	>
332	>	outfile = fopen(filename, "w");
333	>
334	>	if (!outfile)
335	>	{
336	>	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
337	>	return EXIT_FAILURE;
338	>	}
339	>
340	>	i = cmdline_parser_dump(outfile, args_info);
341	>	fclose (outfile);
342	>
343	>	return i;
344	>	}
345	>
346	>	void
347	>	cmdline_parser_free (struct gengetopt_args_info *args_info)
348	>	{
349	>	cmdline_parser_release (args_info);
350	>	}
351	>
352	>	/** @brief replacement of strdup, which is not standard */
353		char *
354		gengetopt_strdup (const char *s)
355		{
356	<	char *result = NULL;
356	>	char *result = 0;
357		if (!s)
358		return result;
359
#	Line 172 | Line 367 | get_multiple_arg_token(const char *arg)
367		static char *
368		get_multiple_arg_token(const char *arg)
369		{
370	<	char *tok, *ret;
371	<	size_t len;
370	>	const char *tok;
371	>	char *ret;
372	>	size_t len, num_of_escape, i, j;
373
374		if (!arg)
375	<	return NULL;
375	>	return 0;
376
377		tok = strchr (arg, ',');
378	+	num_of_escape = 0;
379
380	+	/* make sure it is not escaped */
381	+	while (tok)
382	+	{
383	+	if (*(tok-1) == '\\')
384	+	{
385	+	/* find the next one */
386	+	tok = strchr (tok+1, ',');
387	+	++num_of_escape;
388	+	}
389	+	else
390	+	break;
391	+	}
392	+
393		if (tok)
394		len = (size_t)(tok - arg + 1);
395		else
396		len = strlen (arg) + 1;
397
398	+	len -= num_of_escape;
399	+
400		ret = (char *) malloc (len);
401	<	strncpy (ret, arg, len-1);
401	>
402	>	i = 0;
403	>	j = 0;
404	>	while (arg[i] && (j < len-1))
405	>	{
406	>	if (arg[i] == '\\' &&
407	>	arg[ i + 1 ] &&
408	>	arg[ i + 1 ] == ',')
409	>	++i;
410	>
411	>	ret[j++] = arg[i++];
412	>	}
413	>
414		ret[len-1] = '\0';
415
416		return ret;
417		}
418
419	<	static char *
419	>	static const char *
420		get_multiple_arg_token_next(const char *arg)
421		{
422	<	char *tok;
422	>	const char *tok;
423
424		if (!arg)
425	<	return NULL;
425	>	return 0;
426
427		tok = strchr (arg, ',');
428
429	+	/* make sure it is not escaped */
430	+	while (tok)
431	+	{
432	+	if (*(tok-1) == '\\')
433	+	{
434	+	/* find the next one */
435	+	tok = strchr (tok+1, ',');
436	+	}
437	+	else
438	+	break;
439	+	}
440	+
441		if (! tok || strlen(tok) == 1)
442		return 0;
443
444		return tok+1;
445		}
446
447	+	static int
448	+	check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
449	+
450		int
451	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
451	>	check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc)
452		{
453	+	int error = 0;
454	+
455	+	if (option_given && (min > 0 || max > 0))
456	+	{
457	+	if (min > 0 && max > 0)
458	+	{
459	+	if (min == max)
460	+	{
461	+	/* specific occurrences */
462	+	if (option_given != (unsigned int) min)
463	+	{
464	+	fprintf (stderr, "%s: %s option occurrences must be %d\n",
465	+	prog_name, option_desc, min);
466	+	error = 1;
467	+	}
468	+	}
469	+	else if (option_given < (unsigned int) min
470	+	|| option_given > (unsigned int) max)
471	+	{
472	+	/* range occurrences */
473	+	fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
474	+	prog_name, option_desc, min, max);
475	+	error = 1;
476	+	}
477	+	}
478	+	else if (min > 0)
479	+	{
480	+	/* at least check */
481	+	if (option_given < min)
482	+	{
483	+	fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
484	+	prog_name, option_desc, min);
485	+	error = 1;
486	+	}
487	+	}
488	+	else if (max > 0)
489	+	{
490	+	/* at most check */
491	+	if (option_given > max)
492	+	{
493	+	fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
494	+	prog_name, option_desc, max);
495	+	error = 1;
496	+	}
497	+	}
498	+	}
499	+
500	+	return error;
501	+	}
502	+	int
503	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
504	+	{
505		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
506		}
507
508		int
509	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
509	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
510	>	struct cmdline_parser_params *params)
511		{
512		int result;
513	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
514
515	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
515	>	if (result == EXIT_FAILURE)
516	>	{
517	>	cmdline_parser_free (args_info);
518	>	exit (EXIT_FAILURE);
519	>	}
520	>
521	>	return result;
522	>	}
523
524	+	int
525	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
526	+	{
527	+	int result;
528	+	struct cmdline_parser_params params;
529	+
530	+	params.override = override;
531	+	params.initialize = initialize;
532	+	params.check_required = check_required;
533	+	params.check_ambiguity = 0;
534	+	params.print_errors = 1;
535	+
536	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
537	+
538		if (result == EXIT_FAILURE)
539		{
540		cmdline_parser_free (args_info);
#	Line 235 | Line 549 | cmdline_parser_required (struct gengetopt_args_info *a
549		{
550		int result = EXIT_SUCCESS;
551
552	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
552	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
553		result = EXIT_FAILURE;
554
555		if (result == EXIT_FAILURE)
#	Line 251 | Line 565 | cmdline_parser_required2 (struct gengetopt_args_info *
565		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
566		{
567		int error = 0;
568	+	FIX_UNUSED (additional_error);
569
570	<	if (! args_info->latticeCnst_given)
570	>	/* checks for required options */
571	>	if (! args_info->output_given)
572		{
573	<	fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
573	>	fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
574		error = 1;
575		}
576	+
577	+	if (! args_info->latticeConstant_given)
578	+	{
579	+	fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
580	+	error = 1;
581	+	}
582	+
583		if (! args_info->radius_given)
584		{
585		fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
586		error = 1;
587		}
588	+
589	+	if (check_multiple_option_occurrences(prog_name, args_info->shellRadius_given, args_info->shellRadius_min, args_info->shellRadius_max, "'--shellRadius'"))
590	+	error = 1;
591	+
592	+	if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'"))
593	+	error = 1;
594	+
595	+
596	+	/* checks for dependences among options */
597
598		return error;
599		}
600
601	<	int
602	<	cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
601	>
602	>	static char *package_name = 0;
603	>
604	>	/**
605	>	* @brief updates an option
606	>	* @param field the generic pointer to the field to update
607	>	* @param orig_field the pointer to the orig field
608	>	* @param field_given the pointer to the number of occurrence of this option
609	>	* @param prev_given the pointer to the number of occurrence already seen
610	>	* @param value the argument for this option (if null no arg was specified)
611	>	* @param possible_values the possible values for this option (if specified)
612	>	* @param default_value the default value (in case the option only accepts fixed values)
613	>	* @param arg_type the type of this option
614	>	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
615	>	* @param override @see cmdline_parser_params.override
616	>	* @param no_free whether to free a possible previous value
617	>	* @param multiple_option whether this is a multiple option
618	>	* @param long_opt the corresponding long option
619	>	* @param short_opt the corresponding short option (or '-' if none)
620	>	* @param additional_error possible further error specification
621	>	*/
622	>	static
623	>	int update_arg(void *field, char **orig_field,
624	>	unsigned int *field_given, unsigned int *prev_given,
625	>	char *value, const char *possible_values[],
626	>	const char *default_value,
627	>	cmdline_parser_arg_type arg_type,
628	>	int check_ambiguity, int override,
629	>	int no_free, int multiple_option,
630	>	const char *long_opt, char short_opt,
631	>	const char *additional_error)
632		{
633	<	int c;        /* Character of the parsed option.  */
634	<	char *multi_token, *multi_next; /* for multiple options */
633	>	char *stop_char = 0;
634	>	const char *val = value;
635	>	int found;
636	>	char **string_field;
637	>	FIX_UNUSED (field);
638
639	<	int i;        /* Counter */
639	>	stop_char = 0;
640	>	found = 0;
641
642	<	struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
643	<	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
644	<	struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
642	>	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
643	>	{
644	>	if (short_opt != '-')
645	>	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
646	>	package_name, long_opt, short_opt,
647	>	(additional_error ? additional_error : ""));
648	>	else
649	>	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
650	>	package_name, long_opt,
651	>	(additional_error ? additional_error : ""));
652	>	return 1; /* failure */
653	>	}
654	>
655	>	FIX_UNUSED (default_value);
656	>
657	>	if (field_given && *field_given && ! override)
658	>	return 0;
659	>	if (prev_given)
660	>	(*prev_given)++;
661	>	if (field_given)
662	>	(*field_given)++;
663	>	if (possible_values)
664	>	val = possible_values[found];
665	>
666	>	switch(arg_type) {
667	>	case ARG_DOUBLE:
668	>	if (val) *((double *)field) = strtod (val, &stop_char);
669	>	break;
670	>	case ARG_STRING:
671	>	if (val) {
672	>	string_field = (char **)field;
673	>	if (!no_free && *string_field)
674	>	free (*string_field); /* free previous string */
675	>	*string_field = gengetopt_strdup (val);
676	>	}
677	>	break;
678	>	default:
679	>	break;
680	>	};
681	>
682	>	/* check numeric conversion */
683	>	switch(arg_type) {
684	>	case ARG_DOUBLE:
685	>	if (val && !(stop_char && *stop_char == '\0')) {
686	>	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
687	>	return 1; /* failure */
688	>	}
689	>	break;
690	>	default:
691	>	;
692	>	};
693	>
694	>	/* store the original value */
695	>	switch(arg_type) {
696	>	case ARG_NO:
697	>	break;
698	>	default:
699	>	if (value && orig_field) {
700	>	if (no_free) {
701	>	*orig_field = value;
702	>	} else {
703	>	if (*orig_field)
704	>	free (*orig_field); /* free previous string */
705	>	*orig_field = gengetopt_strdup (value);
706	>	}
707	>	}
708	>	};
709	>
710	>	return 0; /* OK */
711	>	}
712	>
713	>	/**
714	>	* @brief store information about a multiple option in a temporary list
715	>	* @param list where to (temporarily) store multiple options
716	>	*/
717	>	static
718	>	int update_multiple_arg_temp(struct generic_list **list,
719	>	unsigned int *prev_given, const char *val,
720	>	const char *possible_values[], const char *default_value,
721	>	cmdline_parser_arg_type arg_type,
722	>	const char *long_opt, char short_opt,
723	>	const char *additional_error)
724	>	{
725	>	/* store single arguments */
726	>	char *multi_token;
727	>	const char *multi_next;
728	>
729	>	if (arg_type == ARG_NO) {
730	>	(*prev_given)++;
731	>	return 0; /* OK */
732	>	}
733	>
734	>	multi_token = get_multiple_arg_token(val);
735	>	multi_next = get_multiple_arg_token_next (val);
736	>
737	>	while (1)
738	>	{
739	>	add_node (list);
740	>	if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
741	>	prev_given, multi_token, possible_values, default_value,
742	>	arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
743	>	if (multi_token) free(multi_token);
744	>	return 1; /* failure */
745	>	}
746	>
747	>	if (multi_next)
748	>	{
749	>	multi_token = get_multiple_arg_token(multi_next);
750	>	multi_next = get_multiple_arg_token_next (multi_next);
751	>	}
752	>	else
753	>	break;
754	>	}
755	>
756	>	return 0; /* OK */
757	>	}
758	>
759	>	/**
760	>	* @brief free the passed list (including possible string argument)
761	>	*/
762	>	static
763	>	void free_list(struct generic_list *list, short string_arg)
764	>	{
765	>	if (list) {
766	>	struct generic_list *tmp;
767	>	while (list)
768	>	{
769	>	tmp = list;
770	>	if (string_arg && list->arg.string_arg)
771	>	free (list->arg.string_arg);
772	>	if (list->orig)
773	>	free (list->orig);
774	>	list = list->next;
775	>	free (tmp);
776	>	}
777	>	}
778	>	}
779	>
780	>	/**
781	>	* @brief updates a multiple option starting from the passed list
782	>	*/
783	>	static
784	>	void update_multiple_arg(void *field, char ***orig_field,
785	>	unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
786	>	cmdline_parser_arg_type arg_type,
787	>	struct generic_list *list)
788	>	{
789	>	int i;
790	>	struct generic_list *tmp;
791	>
792	>	if (prev_given && list) {
793	>	*orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
794	>
795	>	switch(arg_type) {
796	>	case ARG_DOUBLE:
797	>	*((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
798	>	case ARG_STRING:
799	>	*((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
800	>	default:
801	>	break;
802	>	};
803	>
804	>	for (i = (prev_given - 1); i >= 0; --i)
805	>	{
806	>	tmp = list;
807	>
808	>	switch(arg_type) {
809	>	case ARG_DOUBLE:
810	>	(*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
811	>	case ARG_STRING:
812	>	(*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
813	>	default:
814	>	break;
815	>	}
816	>	(*orig_field) [i + field_given] = list->orig;
817	>	list = list->next;
818	>	free (tmp);
819	>	}
820	>	} else { /* set the default value */
821	>	if (default_value && ! field_given) {
822	>	switch(arg_type) {
823	>	case ARG_DOUBLE:
824	>	if (! *((double **)field)) {
825	>	*((double **)field) = (double *)malloc (sizeof (double));
826	>	(*((double **)field))[0] = default_value->double_arg;
827	>	}
828	>	break;
829	>	case ARG_STRING:
830	>	if (! *((char ***)field)) {
831	>	*((char ***)field) = (char **)malloc (sizeof (char *));
832	>	(*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
833	>	}
834	>	break;
835	>	default: break;
836	>	}
837	>	if (!(*orig_field)) {
838	>	*orig_field = (char **) malloc (sizeof (char *));
839	>	(*orig_field)[0] = 0;
840	>	}
841	>	}
842	>	}
843	>	}
844	>
845	>	int
846	>	cmdline_parser_internal (
847	>	int argc, char **argv, struct gengetopt_args_info *args_info,
848	>	struct cmdline_parser_params *params, const char *additional_error)
849	>	{
850	>	int c;        /* Character of the parsed option.  */
851	>
852	>	struct generic_list * shellRadius_list = NULL;
853	>	struct generic_list * molFraction_list = NULL;
854		int error = 0;
855		struct gengetopt_args_info local_args_info;
856	+
857	+	int override;
858	+	int initialize;
859	+	int check_required;
860	+	int check_ambiguity;
861	+
862	+	package_name = argv[0];
863	+
864	+	override = params->override;
865	+	initialize = params->initialize;
866	+	check_required = params->check_required;
867	+	check_ambiguity = params->check_ambiguity;
868
869		if (initialize)
870		cmdline_parser_init (args_info);
#	Line 286 | Line 872 | cmdline_parser_internal (int argc, char * const *argv,
872		cmdline_parser_init (&local_args_info);
873
874		optarg = 0;
875	<	optind = 1;
876	<	opterr = 1;
875	>	optind = 0;
876	>	opterr = params->print_errors;
877		optopt = '?';
878
879		while (1)
880		{
881		int option_index = 0;
296	–	char *stop_char;
882
883		static struct option long_options[] = {
884		{ "help",       0, NULL, 'h' },
885		{ "version",    0, NULL, 'V' },
886		{ "output",     1, NULL, 'o' },
887	<	{ "latticetype",        1, NULL, 0 },
303	<	{ "latticeCnst",        1, NULL, 0 },
887	>	{ "latticeConstant",    1, NULL, 0 },
888		{ "radius",     1, NULL, 0 },
889	<	{ "ShellRadius",        1, NULL, 0 },
889	>	{ "shellRadius",        1, NULL, 0 },
890		{ "molFraction",        1, NULL, 0 },
891	<	{ "vacancyPCT", 1, NULL, 0 },
892	<	{ "vacancyRadius",      1, NULL, 0 },
893	<	{ NULL, 0, NULL, 0 }
891	>	{ "vacancyPercent",     1, NULL, 0 },
892	>	{ "vacancyInnerRadius", 1, NULL, 0 },
893	>	{ "vacancyOuterRadius", 1, NULL, 0 },
894	>	{ 0,  0, 0, 0 }
895		};
896
312	–	stop_char = 0;
897		c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
898
899		if (c == -1) break;       /* Exit from `while (1)' loop.  */
#	Line 318 | Line 902 | cmdline_parser_internal (int argc, char * const *argv,
902		{
903		case 'h':       /* Print help and exit.  */
904		cmdline_parser_print_help ();
905	+	cmdline_parser_free (&local_args_info);
906		exit (EXIT_SUCCESS);
907
908		case 'V':       /* Print version and exit.  */
909		cmdline_parser_print_version ();
910	+	cmdline_parser_free (&local_args_info);
911		exit (EXIT_SUCCESS);
912
913		case 'o':       /* Output file name.  */
914	<	if (local_args_info.output_given)
915	<	{
916	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
917	<	goto failure;
918	<	}
919	<	if (args_info->output_given && ! override)
920	<	continue;
921	<	local_args_info.output_given = 1;
922	<	args_info->output_given = 1;
923	<	if (args_info->output_arg)
338	<	free (args_info->output_arg); /* free previous string */
339	<	args_info->output_arg = gengetopt_strdup (optarg);
914	>
915	>
916	>	if (update_arg( (void *)&(args_info->output_arg),
917	>	&(args_info->output_orig), &(args_info->output_given),
918	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
919	>	check_ambiguity, override, 0, 0,
920	>	"output", 'o',
921	>	additional_error))
922	>	goto failure;
923	>
924		break;
925
342	–
926		case 0: /* Long option with no short option */
344	–	/* Lattice type string. Valid types are fcc,hcp,bcc..  */
345	–	if (strcmp (long_options[option_index].name, "latticetype") == 0)
346	–	{
347	–	if (local_args_info.latticetype_given)
348	–	{
349	–	fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
350	–	goto failure;
351	–	}
352	–	if (args_info->latticetype_given && ! override)
353	–	continue;
354	–	local_args_info.latticetype_given = 1;
355	–	args_info->latticetype_given = 1;
356	–	if (args_info->latticetype_arg)
357	–	free (args_info->latticetype_arg); /* free previous string */
358	–	args_info->latticetype_arg = gengetopt_strdup (optarg);
359	–	}
927		/* Lattice spacing in Angstroms for cubic lattice..  */
928	<	else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
928	>	if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
929		{
930	<	if (local_args_info.latticeCnst_given)
931	<	{
932	<	fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
933	<	goto failure;
934	<	}
935	<	if (args_info->latticeCnst_given && ! override)
936	<	continue;
937	<	local_args_info.latticeCnst_given = 1;
938	<	args_info->latticeCnst_given = 1;
939	<	args_info->latticeCnst_arg = strtod (optarg, NULL);
930	>
931	>
932	>	if (update_arg( (void *)&(args_info->latticeConstant_arg),
933	>	&(args_info->latticeConstant_orig), &(args_info->latticeConstant_given),
934	>	&(local_args_info.latticeConstant_given), optarg, 0, 0, ARG_DOUBLE,
935	>	check_ambiguity, override, 0, 0,
936	>	"latticeConstant", '-',
937	>	additional_error))
938	>	goto failure;
939	>
940		}
941		/* Nanoparticle radius in Angstroms.  */
942		else if (strcmp (long_options[option_index].name, "radius") == 0)
943		{
944	<	if (local_args_info.radius_given)
945	<	{
946	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
947	<	goto failure;
948	<	}
949	<	if (args_info->radius_given && ! override)
950	<	continue;
951	<	local_args_info.radius_given = 1;
952	<	args_info->radius_given = 1;
953	<	args_info->radius_arg = strtod (optarg, NULL);
944	>
945	>
946	>	if (update_arg( (void *)&(args_info->radius_arg),
947	>	&(args_info->radius_orig), &(args_info->radius_given),
948	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
949	>	check_ambiguity, override, 0, 0,
950	>	"radius", '-',
951	>	additional_error))
952	>	goto failure;
953	>
954		}
955	<	/* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file..  */
956	<	else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
955	>	/* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file..  */
956	>	else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
957		{
391	–	local_args_info.ShellRadius_given++;
958
959	<	multi_token = get_multiple_arg_token(optarg);
960	<	multi_next = get_multiple_arg_token_next (optarg);
959	>	if (update_multiple_arg_temp(&shellRadius_list,
960	>	&(local_args_info.shellRadius_given), optarg, 0, 0, ARG_DOUBLE,
961	>	"shellRadius", '-',
962	>	additional_error))
963	>	goto failure;
964
396	–	while (1)
397	–	{
398	–	ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
399	–	ShellRadius_new->next = ShellRadius_list;
400	–	ShellRadius_list = ShellRadius_new;
401	–	ShellRadius_new->ShellRadius_arg = strtod (multi_token, NULL);
402	–	free (multi_token);
403	–
404	–	if (multi_next)
405	–	{
406	–	multi_token = get_multiple_arg_token(multi_next);
407	–	multi_next = get_multiple_arg_token_next (multi_next);
408	–	local_args_info.ShellRadius_given++;
409	–	}
410	–	else
411	–	break;
412	–	}
413	–	break;
965		}
966	<	/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
966	>	/* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file..  */
967		else if (strcmp (long_options[option_index].name, "molFraction") == 0)
968		{
418	–	local_args_info.molFraction_given++;
969
970	<	multi_token = get_multiple_arg_token(optarg);
971	<	multi_next = get_multiple_arg_token_next (optarg);
970	>	if (update_multiple_arg_temp(&molFraction_list,
971	>	&(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE,
972	>	"molFraction", '-',
973	>	additional_error))
974	>	goto failure;
975
976	<	while (1)
977	<	{
978	<	molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
979	<	molFraction_new->next = molFraction_list;
427	<	molFraction_list = molFraction_new;
428	<	molFraction_new->molFraction_arg = strtod (multi_token, NULL);
429	<	free (multi_token);
976	>	}
977	>	/* Percentage of atoms to remove from within vacancy range.  */
978	>	else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
979	>	{
980
981	<	if (multi_next)
982	<	{
983	<	multi_token = get_multiple_arg_token(multi_next);
984	<	multi_next = get_multiple_arg_token_next (multi_next);
985	<	local_args_info.molFraction_given++;
986	<	}
987	<	else
988	<	break;
989	<	}
440	<	break;
981	>
982	>	if (update_arg( (void *)&(args_info->vacancyPercent_arg),
983	>	&(args_info->vacancyPercent_orig), &(args_info->vacancyPercent_given),
984	>	&(local_args_info.vacancyPercent_given), optarg, 0, 0, ARG_DOUBLE,
985	>	check_ambiguity, override, 0, 0,
986	>	"vacancyPercent", '-',
987	>	additional_error))
988	>	goto failure;
989	>
990		}
991	<	/* Percentage of vacancies to build.  */
992	<	else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
991	>	/* Radius arround core-shell where vacancies should be located..  */
992	>	else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
993		{
994	<	if (local_args_info.vacancyPCT_given)
995	<	{
996	<	fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
997	<	goto failure;
998	<	}
999	<	if (args_info->vacancyPCT_given && ! override)
1000	<	continue;
1001	<	local_args_info.vacancyPCT_given = 1;
1002	<	args_info->vacancyPCT_given = 1;
1003	<	args_info->vacancyPCT_arg = strtod (optarg, NULL);
994	>
995	>
996	>	if (update_arg( (void *)&(args_info->vacancyInnerRadius_arg),
997	>	&(args_info->vacancyInnerRadius_orig), &(args_info->vacancyInnerRadius_given),
998	>	&(local_args_info.vacancyInnerRadius_given), optarg, 0, 0, ARG_DOUBLE,
999	>	check_ambiguity, override, 0, 0,
1000	>	"vacancyInnerRadius", '-',
1001	>	additional_error))
1002	>	goto failure;
1003	>
1004		}
1005		/* Radius arround core-shell where vacancies should be located..  */
1006	<	else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
1006	>	else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
1007		{
459	–	local_args_info.vacancyRadius_given++;
1008
461	–	multi_token = get_multiple_arg_token(optarg);
462	–	multi_next = get_multiple_arg_token_next (optarg);
1009
1010	<	while (1)
1011	<	{
1012	<	vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
1013	<	vacancyRadius_new->next = vacancyRadius_list;
1014	<	vacancyRadius_list = vacancyRadius_new;
1015	<	vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
1016	<	free (multi_token);
1010	>	if (update_arg( (void *)&(args_info->vacancyOuterRadius_arg),
1011	>	&(args_info->vacancyOuterRadius_orig), &(args_info->vacancyOuterRadius_given),
1012	>	&(local_args_info.vacancyOuterRadius_given), optarg, 0, 0, ARG_DOUBLE,
1013	>	check_ambiguity, override, 0, 0,
1014	>	"vacancyOuterRadius", '-',
1015	>	additional_error))
1016	>	goto failure;
1017
472	–	if (multi_next)
473	–	{
474	–	multi_token = get_multiple_arg_token(multi_next);
475	–	multi_next = get_multiple_arg_token_next (multi_next);
476	–	local_args_info.vacancyRadius_given++;
477	–	}
478	–	else
479	–	break;
480	–	}
481	–	break;
1018		}
1019
1020		break;
#	Line 493 | Line 1029 | cmdline_parser_internal (int argc, char * const *argv,
1029		} /* while */
1030
1031
1032	<	if (local_args_info.ShellRadius_given && ShellRadius_list)
1033	<	{
1034	<	struct ShellRadius_list *tmp;
1035	<	args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double));
1036	<	for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
1037	<	{
1038	<	tmp = ShellRadius_list;
1039	<	args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
504	<	ShellRadius_list = ShellRadius_list->next;
505	<	free (tmp);
506	<	}
507	<	}
508	<
509	<	if (local_args_info.molFraction_given && molFraction_list)
510	<	{
511	<	struct molFraction_list *tmp;
512	<	args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double));
513	<	for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
514	<	{
515	<	tmp = molFraction_list;
516	<	args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
517	<	molFraction_list = molFraction_list->next;
518	<	free (tmp);
519	<	}
520	<	}
521	<
522	<	if (local_args_info.vacancyRadius_given && vacancyRadius_list)
523	<	{
524	<	struct vacancyRadius_list *tmp;
525	<	args_info->vacancyRadius_arg = (double *) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (double));
526	<	for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
527	<	{
528	<	tmp = vacancyRadius_list;
529	<	args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
530	<	vacancyRadius_list = vacancyRadius_list->next;
531	<	free (tmp);
532	<	}
533	<	}
534	<
1032	>	update_multiple_arg((void *)&(args_info->shellRadius_arg),
1033	>	&(args_info->shellRadius_orig), args_info->shellRadius_given,
1034	>	local_args_info.shellRadius_given, 0,
1035	>	ARG_DOUBLE, shellRadius_list);
1036	>	update_multiple_arg((void *)&(args_info->molFraction_arg),
1037	>	&(args_info->molFraction_orig), args_info->molFraction_given,
1038	>	local_args_info.molFraction_given, 0,
1039	>	ARG_DOUBLE, molFraction_list);
1040
1041	<	args_info->ShellRadius_given += local_args_info.ShellRadius_given;
1042	<	local_args_info.ShellRadius_given = 0;
1041	>	args_info->shellRadius_given += local_args_info.shellRadius_given;
1042	>	local_args_info.shellRadius_given = 0;
1043		args_info->molFraction_given += local_args_info.molFraction_given;
1044		local_args_info.molFraction_given = 0;
540	–	args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
541	–	local_args_info.vacancyRadius_given = 0;
1045
1046		if (check_required)
1047		{
1048		error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1049		}
1050
1051	<	cmdline_parser_free (&local_args_info);
1051	>	cmdline_parser_release (&local_args_info);
1052
1053		if ( error )
1054		return (EXIT_FAILURE);
#	Line 553 | Line 1056 | cmdline_parser_internal (int argc, char * const *argv,
1056		if (optind < argc)
1057		{
1058		int i = 0 ;
1059	+	int found_prog_name = 0;
1060	+	/* whether program name, i.e., argv[0], is in the remaining args
1061	+	(this may happen with some implementations of getopt,
1062	+	but surely not with the one included by gengetopt) */
1063
1064	<	args_info->inputs_num = argc - optind ;
1064	>	i = optind;
1065	>	while (i < argc)
1066	>	if (argv[i++] == argv[0]) {
1067	>	found_prog_name = 1;
1068	>	break;
1069	>	}
1070	>	i = 0;
1071	>
1072	>	args_info->inputs_num = argc - optind - found_prog_name;
1073		args_info->inputs =
1074		(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1075		while (optind < argc)
1076	<	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
1076	>	if (argv[optind++] != argv[0])
1077	>	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1078		}
1079
1080		return 0;
1081
1082		failure:
1083	<	if (ShellRadius_list)
1084	<	{
569	<	struct ShellRadius_list *tmp;
570	<	while (ShellRadius_list)
571	<	{
572	<	tmp = ShellRadius_list;
573	<	ShellRadius_list = ShellRadius_list->next;
574	<	free (tmp);
575	<	}
576	<	}
577	<	if (molFraction_list)
578	<	{
579	<	struct molFraction_list *tmp;
580	<	while (molFraction_list)
581	<	{
582	<	tmp = molFraction_list;
583	<	molFraction_list = molFraction_list->next;
584	<	free (tmp);
585	<	}
586	<	}
587	<	if (vacancyRadius_list)
588	<	{
589	<	struct vacancyRadius_list *tmp;
590	<	while (vacancyRadius_list)
591	<	{
592	<	tmp = vacancyRadius_list;
593	<	vacancyRadius_list = vacancyRadius_list->next;
594	<	free (tmp);
595	<	}
596	<	}
1083	>	free_list (shellRadius_list, 0 );
1084	>	free_list (molFraction_list, 0 );
1085
1086	<	cmdline_parser_free (&local_args_info);
1086	>	cmdline_parser_release (&local_args_info);
1087		return (EXIT_FAILURE);
1088		}

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (property svn:keywords), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (property svn:keywords), Revision 1630 by gezelter, Wed Sep 14 21:40:12 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines