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

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (file contents), Revision 1069 by chuckv, Fri Oct 13 20:16:59 2006 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 2.15
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	gengetopt -u -i nanoparticleBuilder.ggo -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	–	char *ShellRadius_orig;
39	–	struct ShellRadius_list * next;
40	–	};
41	–
42	–	struct molFraction_list
43	–	{
44	–	double molFraction_arg;
45	–	char *molFraction_orig;
46	–	struct molFraction_list * next;
47	–	};
48	–
49	–	struct vacancyRadius_list
50	–	{
51	–	double vacancyRadius_arg;
52	–	char *vacancyRadius_orig;
53	–	struct vacancyRadius_list * next;
54	–	};
55	–
65		static char *
66		gengetopt_strdup (const char *s);
67
#	Line 62 | 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->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->output_orig = NULL;
89	<	args_info->latticeCnst_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;
91	>	args_info->shellRadius_arg = NULL;
92	>	args_info->shellRadius_orig = NULL;
93		args_info->molFraction_arg = NULL;
94		args_info->molFraction_orig = NULL;
95	<	args_info->vacancyPCT_orig = NULL;
96	<	args_info->vacancyRadius_arg = NULL;
97	<	args_info->vacancyRadius_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");
103	<	printf("%s\n","  -V, --version               Print version and exit");
104	<	printf("%s\n","  -o, --output=STRING         Output file name");
105	<	printf("%s\n","      --latticeCnst=DOUBLE    Lattice spacing in Angstroms for cubic lattice.");
106	<	printf("%s\n","      --radius=DOUBLE         Nanoparticle radius in Angstroms");
107	<	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.");
108	<	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.");
109	<	printf("%s\n","      --vacancyPCT=DOUBLE     Percentage of vacancies to build");
110	<	printf("%s\n","      --vacancyRadius=DOUBLE  Radius arround core-shell where vacancies should \n                                be located.");
111	<
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 116 | 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_params_init(struct cmdline_parser_params *params)
168	+	{
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	+	}
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	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
189	>	free_string_field (char **s)
190		{
191	<
128	<	unsigned int i;
129	<	if (args_info->output_arg)
191	>	if (*s)
192		{
193	<	free (args_info->output_arg); /* free previous argument */
194	<	args_info->output_arg = 0;
193	>	free (*s);
194	>	*s = 0;
195		}
196	<	if (args_info->output_orig)
197	<	{
198	<	free (args_info->output_orig); /* free previous argument */
199	<	args_info->output_orig = 0;
200	<	}
201	<	if (args_info->latticeCnst_orig)
202	<	{
203	<	free (args_info->latticeCnst_orig); /* free previous argument */
204	<	args_info->latticeCnst_orig = 0;
205	<	}
206	<	if (args_info->radius_orig)
207	<	{
208	<	free (args_info->radius_orig); /* free previous argument */
209	<	args_info->radius_orig = 0;
210	<	}
211	<	if (args_info->ShellRadius_arg)
212	<	{
213	<	for (i = 0; i < args_info->ShellRadius_given; ++i)
214	<	{
215	<	if (args_info->ShellRadius_orig [i])
216	<	{
217	<	free (args_info->ShellRadius_orig [i]); /* free previous argument */
218	<	args_info->ShellRadius_orig [i] = 0;
219	<	}
220	<	}
221	<	free (args_info->ShellRadius_arg); /* free previous argument */
222	<	args_info->ShellRadius_arg = 0;
223	<	free (args_info->ShellRadius_orig); /* free previous argument */
224	<	args_info->ShellRadius_orig = 0;
225	<	}
226	<	if (args_info->molFraction_arg)
227	<	{
228	<	for (i = 0; i < args_info->molFraction_given; ++i)
229	<	{
230	<	if (args_info->molFraction_orig [i])
231	<	{
232	<	free (args_info->molFraction_orig [i]); /* free previous argument */
233	<	args_info->molFraction_orig [i] = 0;
234	<	}
235	<	}
236	<	free (args_info->molFraction_arg); /* free previous argument */
237	<	args_info->molFraction_arg = 0;
238	<	free (args_info->molFraction_orig); /* free previous argument */
239	<	args_info->molFraction_orig = 0;
240	<	}
241	<	if (args_info->vacancyPCT_orig)
242	<	{
243	<	free (args_info->vacancyPCT_orig); /* free previous argument */
244	<	args_info->vacancyPCT_orig = 0;
245	<	}
246	<	if (args_info->vacancyRadius_arg)
247	<	{
248	<	for (i = 0; i < args_info->vacancyRadius_given; ++i)
249	<	{
250	<	if (args_info->vacancyRadius_orig [i])
251	<	{
252	<	free (args_info->vacancyRadius_orig [i]); /* free previous argument */
253	<	args_info->vacancyRadius_orig [i] = 0;
254	<	}
255	<	}
256	<	free (args_info->vacancyRadius_arg); /* free previous argument */
257	<	args_info->vacancyRadius_arg = 0;
258	<	free (args_info->vacancyRadius_orig); /* free previous argument */
197	<	args_info->vacancyRadius_orig = 0;
198	<	}
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	+
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;
#	Line 220 | Line 337 | cmdline_parser_file_save(const char *filename, struct
337		return EXIT_FAILURE;
338		}
339
340	<	if (args_info->help_given) {
224	<	fprintf(outfile, "%s\n", "help");
225	<	}
226	<	if (args_info->version_given) {
227	<	fprintf(outfile, "%s\n", "version");
228	<	}
229	<	if (args_info->output_given) {
230	<	if (args_info->output_orig) {
231	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
232	<	} else {
233	<	fprintf(outfile, "%s\n", "output");
234	<	}
235	<	}
236	<	if (args_info->latticeCnst_given) {
237	<	if (args_info->latticeCnst_orig) {
238	<	fprintf(outfile, "%s=\"%s\"\n", "latticeCnst", args_info->latticeCnst_orig);
239	<	} else {
240	<	fprintf(outfile, "%s\n", "latticeCnst");
241	<	}
242	<	}
243	<	if (args_info->radius_given) {
244	<	if (args_info->radius_orig) {
245	<	fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
246	<	} else {
247	<	fprintf(outfile, "%s\n", "radius");
248	<	}
249	<	}
250	<	if (args_info->ShellRadius_orig)
251	<	{
252	<	for (i = 0; i < args_info->ShellRadius_given; ++i)
253	<	{
254	<	if (args_info->ShellRadius_orig [i])
255	<	{
256	<	fprintf(outfile, "%s=\"%s\"\n", "ShellRadius", args_info->ShellRadius_orig [i]);
257	<	}
258	<	}
259	<	}
260	<	if (args_info->molFraction_orig)
261	<	{
262	<	for (i = 0; i < args_info->molFraction_given; ++i)
263	<	{
264	<	if (args_info->molFraction_orig [i])
265	<	{
266	<	fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]);
267	<	}
268	<	}
269	<	}
270	<	if (args_info->vacancyPCT_given) {
271	<	if (args_info->vacancyPCT_orig) {
272	<	fprintf(outfile, "%s=\"%s\"\n", "vacancyPCT", args_info->vacancyPCT_orig);
273	<	} else {
274	<	fprintf(outfile, "%s\n", "vacancyPCT");
275	<	}
276	<	}
277	<	if (args_info->vacancyRadius_orig)
278	<	{
279	<	for (i = 0; i < args_info->vacancyRadius_given; ++i)
280	<	{
281	<	if (args_info->vacancyRadius_orig [i])
282	<	{
283	<	fprintf(outfile, "%s=\"%s\"\n", "vacancyRadius", args_info->vacancyRadius_orig [i]);
284	<	}
285	<	}
286	<	}
287	<
340	>	i = cmdline_parser_dump(outfile, args_info);
341		fclose (outfile);
342
290	–	i = EXIT_SUCCESS;
343		return i;
344		}
345
#	Line 297 | Line 349 | cmdline_parser_free (struct gengetopt_args_info *args_
349		cmdline_parser_release (args_info);
350		}
351
352	<
301	<	/* gengetopt_strdup() */
302	<	/* strdup.c replacement of strdup, which is not standard */
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 317 | 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 380 | 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 396 | 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	+
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	+	char *stop_char = 0;
634	+	const char *val = value;
635	+	int found;
636	+	char **string_field;
637	+	FIX_UNUSED (field);
638	+
639	+	stop_char = 0;
640	+	found = 0;
641	+
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 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
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.  */
418	–	char *multi_token, *multi_next; /* for multiple options */
851
852	<	int i;        /* Counter */
853	<
422	<	struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
423	<	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
424	<	struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
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 431 | 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;
441	–	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	<	{ "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
456	–	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 471 | Line 911 | cmdline_parser_internal (int argc, char * const *argv,
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)
484	<	free (args_info->output_arg); /* free previous string */
485	<	args_info->output_arg = gengetopt_strdup (optarg);
486	<	if (args_info->output_orig)
487	<	free (args_info->output_orig); /* free previous string */
488	<	args_info->output_orig = 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
491	–
926		case 0: /* Long option with no short option */
927		/* Lattice spacing in Angstroms for cubic lattice..  */
928	<	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;
504	<	args_info->latticeCnst_given = 1;
505	<	args_info->latticeCnst_arg = strtod (optarg, &stop_char);
506	<	if (!(stop_char && *stop_char == '\0')) {
507	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
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	<	}
510	<	if (args_info->latticeCnst_orig)
511	<	free (args_info->latticeCnst_orig); /* free previous string */
512	<	args_info->latticeCnst_orig = gengetopt_strdup (optarg);
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;
525	<	args_info->radius_given = 1;
526	<	args_info->radius_arg = strtod (optarg, &stop_char);
527	<	if (!(stop_char && *stop_char == '\0')) {
528	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
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	<	}
531	<	if (args_info->radius_orig)
532	<	free (args_info->radius_orig); /* free previous string */
533	<	args_info->radius_orig = gengetopt_strdup (optarg);
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		{
538	–	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
543	–	while (1)
544	–	{
545	–	ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
546	–	ShellRadius_new->next = ShellRadius_list;
547	–	ShellRadius_list = ShellRadius_new;
548	–	ShellRadius_new->ShellRadius_arg = strtod (multi_token, &stop_char);
549	–	if (!(stop_char && *stop_char == '\0')) {
550	–	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
551	–	goto failure;
552	–	}
553	–	ShellRadius_new->ShellRadius_orig = multi_token;
554	–
555	–	if (multi_next)
556	–	{
557	–	multi_token = get_multiple_arg_token(multi_next);
558	–	multi_next = get_multiple_arg_token_next (multi_next);
559	–	local_args_info.ShellRadius_given++;
560	–	}
561	–	else
562	–	break;
563	–	}
564	–	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		{
569	–	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;
578	<	molFraction_list = molFraction_new;
579	<	molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
580	<	if (!(stop_char && *stop_char == '\0')) {
581	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
582	<	goto failure;
583	<	}
584	<	molFraction_new->molFraction_orig = 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	<	}
595	<	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;
608	<	args_info->vacancyPCT_given = 1;
609	<	args_info->vacancyPCT_arg = strtod (optarg, &stop_char);
610	<	if (!(stop_char && *stop_char == '\0')) {
611	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
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	<	}
614	<	if (args_info->vacancyPCT_orig)
615	<	free (args_info->vacancyPCT_orig); /* free previous string */
616	<	args_info->vacancyPCT_orig = gengetopt_strdup (optarg);
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		{
621	–	local_args_info.vacancyRadius_given++;
1008
623	–	multi_token = get_multiple_arg_token(optarg);
624	–	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, &stop_char);
1016	<	if (!(stop_char && *stop_char == '\0')) {
633	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
634	<	goto failure;
635	<	}
636	<	vacancyRadius_new->vacancyRadius_orig = 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
638	–	if (multi_next)
639	–	{
640	–	multi_token = get_multiple_arg_token(multi_next);
641	–	multi_next = get_multiple_arg_token_next (multi_next);
642	–	local_args_info.vacancyRadius_given++;
643	–	}
644	–	else
645	–	break;
646	–	}
647	–	break;
1018		}
1019
1020		break;
#	Line 659 | 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	<	args_info->ShellRadius_orig = (char **) realloc (args_info->ShellRadius_orig, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (char *));
1037	<	for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
1038	<	{
1039	<	tmp = ShellRadius_list;
670	<	args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
671	<	args_info->ShellRadius_orig [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_orig;
672	<	ShellRadius_list = ShellRadius_list->next;
673	<	free (tmp);
674	<	}
675	<	}
676	<
677	<	if (local_args_info.molFraction_given && molFraction_list)
678	<	{
679	<	struct molFraction_list *tmp;
680	<	args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double));
681	<	args_info->molFraction_orig = (char **) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (char *));
682	<	for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
683	<	{
684	<	tmp = molFraction_list;
685	<	args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
686	<	args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
687	<	molFraction_list = molFraction_list->next;
688	<	free (tmp);
689	<	}
690	<	}
691	<
692	<	if (local_args_info.vacancyRadius_given && vacancyRadius_list)
693	<	{
694	<	struct vacancyRadius_list *tmp;
695	<	args_info->vacancyRadius_arg = (double *) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (double));
696	<	args_info->vacancyRadius_orig = (char **) realloc (args_info->vacancyRadius_orig, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (char *));
697	<	for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
698	<	{
699	<	tmp = vacancyRadius_list;
700	<	args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
701	<	args_info->vacancyRadius_orig [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_orig;
702	<	vacancyRadius_list = vacancyRadius_list->next;
703	<	free (tmp);
704	<	}
705	<	}
706	<
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;
712	–	args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
713	–	local_args_info.vacancyRadius_given = 0;
1045
1046		if (check_required)
1047		{
#	Line 725 | 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	<	{
741	<	struct ShellRadius_list *tmp;
742	<	while (ShellRadius_list)
743	<	{
744	<	tmp = ShellRadius_list;
745	<	free (ShellRadius_list->ShellRadius_orig);
746	<	ShellRadius_list = ShellRadius_list->next;
747	<	free (tmp);
748	<	}
749	<	}
750	<	if (molFraction_list)
751	<	{
752	<	struct molFraction_list *tmp;
753	<	while (molFraction_list)
754	<	{
755	<	tmp = molFraction_list;
756	<	free (molFraction_list->molFraction_orig);
757	<	molFraction_list = molFraction_list->next;
758	<	free (tmp);
759	<	}
760	<	}
761	<	if (vacancyRadius_list)
762	<	{
763	<	struct vacancyRadius_list *tmp;
764	<	while (vacancyRadius_list)
765	<	{
766	<	tmp = vacancyRadius_list;
767	<	free (vacancyRadius_list->vacancyRadius_orig);
768	<	vacancyRadius_list = vacancyRadius_list->next;
769	<	free (tmp);
770	<	}
771	<	}
1083	>	free_list (shellRadius_list, 0 );
1084	>	free_list (molFraction_list, 0 );
1085
1086		cmdline_parser_release (&local_args_info);
1087		return (EXIT_FAILURE);

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (property svn:keywords), Revision 1069 by chuckv, Fri Oct 13 20:16:59 2006 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