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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.
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp (file contents), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.15
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	+	#ifdef WIN32
25	+	#include "utils/wingetopt.h"
26	+	#else
27	+	#include <getopt.h>
28	+	#endif
29	+
30		#include "nanoparticleBuilderCmd.h"
31
32	+	const char *gengetopt_args_info_purpose = "Builds spherical random or core-shell nanoparticles and outputs an OpenMD \nstartup file";
33	+
34	+	const char *gengetopt_args_info_usage = "Usage: nanoparticleBuilder [OPTIONS]... [FILES]...";
35	+
36	+	const char *gengetopt_args_info_description = "";
37	+
38	+	const char *gengetopt_args_info_help[] = {
39	+	"  -h, --help                    Print help and exit",
40	+	"  -V, --version                 Print version and exit",
41	+	"  -o, --output=STRING           Output file name",
42	+	"      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.",
43	+	"      --radius=DOUBLE           Nanoparticle radius in Angstroms",
44	+	"      --shellRadius=DOUBLE      Radius containing within it only molecules of a \n                                  specific component. Specified for each \n                                  component > 1 in the template file.",
45	+	"      --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.",
46	+	"      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within \n                                  vacancy range",
47	+	"      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
48	+	"      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
49	+	0
50	+	};
51	+
52	+	typedef enum {ARG_NO
53	+	, ARG_STRING
54	+	, ARG_DOUBLE
55	+	} cmdline_parser_arg_type;
56	+
57		static
58		void clear_given (struct gengetopt_args_info *args_info);
59		static
60		void clear_args (struct gengetopt_args_info *args_info);
61
62		static int
63	<	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);
63	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
64	>	struct cmdline_parser_params *params, const char *additional_error);
65
66		static int
67		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
68
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	–
69		static char *
70		gengetopt_strdup (const char *s);
71
#	Line 62 | Line 75 | void clear_given (struct gengetopt_args_info *args_inf
75		args_info->help_given = 0 ;
76		args_info->version_given = 0 ;
77		args_info->output_given = 0 ;
78	<	args_info->latticeCnst_given = 0 ;
78	>	args_info->latticeConstant_given = 0 ;
79		args_info->radius_given = 0 ;
80	<	args_info->ShellRadius_given = 0 ;
80	>	args_info->shellRadius_given = 0 ;
81		args_info->molFraction_given = 0 ;
82	<	args_info->vacancyPCT_given = 0 ;
83	<	args_info->vacancyRadius_given = 0 ;
82	>	args_info->vacancyPercent_given = 0 ;
83	>	args_info->vacancyInnerRadius_given = 0 ;
84	>	args_info->vacancyOuterRadius_given = 0 ;
85		}
86
87		static
88		void clear_args (struct gengetopt_args_info *args_info)
89		{
90	+	FIX_UNUSED (args_info);
91		args_info->output_arg = NULL;
92		args_info->output_orig = NULL;
93	<	args_info->latticeCnst_orig = NULL;
93	>	args_info->latticeConstant_orig = NULL;
94		args_info->radius_orig = NULL;
95	<	args_info->ShellRadius_arg = NULL;
96	<	args_info->ShellRadius_orig = NULL;
95	>	args_info->shellRadius_arg = NULL;
96	>	args_info->shellRadius_orig = NULL;
97		args_info->molFraction_arg = NULL;
98		args_info->molFraction_orig = NULL;
99	<	args_info->vacancyPCT_orig = NULL;
100	<	args_info->vacancyRadius_arg = NULL;
101	<	args_info->vacancyRadius_orig = NULL;
99	>	args_info->vacancyPercent_orig = NULL;
100	>	args_info->vacancyInnerRadius_orig = NULL;
101	>	args_info->vacancyOuterRadius_orig = NULL;
102
103		}
104
105	+	static
106	+	void init_args_info(struct gengetopt_args_info *args_info)
107	+	{
108	+
109	+
110	+	args_info->help_help = gengetopt_args_info_help[0] ;
111	+	args_info->version_help = gengetopt_args_info_help[1] ;
112	+	args_info->output_help = gengetopt_args_info_help[2] ;
113	+	args_info->latticeConstant_help = gengetopt_args_info_help[3] ;
114	+	args_info->radius_help = gengetopt_args_info_help[4] ;
115	+	args_info->shellRadius_help = gengetopt_args_info_help[5] ;
116	+	args_info->shellRadius_min = 0;
117	+	args_info->shellRadius_max = 0;
118	+	args_info->molFraction_help = gengetopt_args_info_help[6] ;
119	+	args_info->molFraction_min = 0;
120	+	args_info->molFraction_max = 0;
121	+	args_info->vacancyPercent_help = gengetopt_args_info_help[7] ;
122	+	args_info->vacancyInnerRadius_help = gengetopt_args_info_help[8] ;
123	+	args_info->vacancyOuterRadius_help = gengetopt_args_info_help[9] ;
124	+
125	+	}
126	+
127		void
128		cmdline_parser_print_version (void)
129		{
130	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
130	>	printf ("%s %s\n",
131	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
132	>	CMDLINE_PARSER_VERSION);
133		}
134
135	+	static void print_help_common(void) {
136	+	cmdline_parser_print_version ();
137	+
138	+	if (strlen(gengetopt_args_info_purpose) > 0)
139	+	printf("\n%s\n", gengetopt_args_info_purpose);
140	+
141	+	if (strlen(gengetopt_args_info_usage) > 0)
142	+	printf("\n%s\n", gengetopt_args_info_usage);
143	+
144	+	printf("\n");
145	+
146	+	if (strlen(gengetopt_args_info_description) > 0)
147	+	printf("%s\n\n", gengetopt_args_info_description);
148	+	}
149	+
150		void
151		cmdline_parser_print_help (void)
152		{
153	<	cmdline_parser_print_version ();
154	<	printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
155	<	printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
156	<	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	<
153	>	int i = 0;
154	>	print_help_common();
155	>	while (gengetopt_args_info_help[i])
156	>	printf("%s\n", gengetopt_args_info_help[i++]);
157		}
158
159		void
#	Line 116 | Line 161 | cmdline_parser_init (struct gengetopt_args_info *args_
161		{
162		clear_given (args_info);
163		clear_args (args_info);
164	+	init_args_info (args_info);
165
166	<	args_info->inputs = NULL;
166	>	args_info->inputs = 0;
167		args_info->inputs_num = 0;
168		}
169
170	+	void
171	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
172	+	{
173	+	if (params)
174	+	{
175	+	params->override = 0;
176	+	params->initialize = 1;
177	+	params->check_required = 1;
178	+	params->check_ambiguity = 0;
179	+	params->print_errors = 1;
180	+	}
181	+	}
182	+
183	+	struct cmdline_parser_params *
184	+	cmdline_parser_params_create(void)
185	+	{
186	+	struct cmdline_parser_params *params =
187	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
188	+	cmdline_parser_params_init(params);
189	+	return params;
190	+	}
191	+
192		static void
193	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
193	>	free_string_field (char **s)
194		{
195	<
128	<	unsigned int i;
129	<	if (args_info->output_arg)
195	>	if (*s)
196		{
197	<	free (args_info->output_arg); /* free previous argument */
198	<	args_info->output_arg = 0;
197	>	free (*s);
198	>	*s = 0;
199		}
200	<	if (args_info->output_orig)
201	<	{
202	<	free (args_info->output_orig); /* free previous argument */
203	<	args_info->output_orig = 0;
204	<	}
205	<	if (args_info->latticeCnst_orig)
206	<	{
207	<	free (args_info->latticeCnst_orig); /* free previous argument */
208	<	args_info->latticeCnst_orig = 0;
209	<	}
210	<	if (args_info->radius_orig)
211	<	{
212	<	free (args_info->radius_orig); /* free previous argument */
213	<	args_info->radius_orig = 0;
214	<	}
215	<	if (args_info->ShellRadius_arg)
216	<	{
217	<	for (i = 0; i < args_info->ShellRadius_given; ++i)
218	<	{
219	<	if (args_info->ShellRadius_orig [i])
220	<	{
221	<	free (args_info->ShellRadius_orig [i]); /* free previous argument */
222	<	args_info->ShellRadius_orig [i] = 0;
223	<	}
224	<	}
225	<	free (args_info->ShellRadius_arg); /* free previous argument */
226	<	args_info->ShellRadius_arg = 0;
227	<	free (args_info->ShellRadius_orig); /* free previous argument */
228	<	args_info->ShellRadius_orig = 0;
229	<	}
230	<	if (args_info->molFraction_arg)
231	<	{
232	<	for (i = 0; i < args_info->molFraction_given; ++i)
233	<	{
234	<	if (args_info->molFraction_orig [i])
235	<	{
236	<	free (args_info->molFraction_orig [i]); /* free previous argument */
237	<	args_info->molFraction_orig [i] = 0;
238	<	}
239	<	}
240	<	free (args_info->molFraction_arg); /* free previous argument */
241	<	args_info->molFraction_arg = 0;
242	<	free (args_info->molFraction_orig); /* free previous argument */
243	<	args_info->molFraction_orig = 0;
244	<	}
245	<	if (args_info->vacancyPCT_orig)
246	<	{
247	<	free (args_info->vacancyPCT_orig); /* free previous argument */
248	<	args_info->vacancyPCT_orig = 0;
249	<	}
250	<	if (args_info->vacancyRadius_arg)
251	<	{
252	<	for (i = 0; i < args_info->vacancyRadius_given; ++i)
253	<	{
254	<	if (args_info->vacancyRadius_orig [i])
255	<	{
256	<	free (args_info->vacancyRadius_orig [i]); /* free previous argument */
257	<	args_info->vacancyRadius_orig [i] = 0;
258	<	}
259	<	}
260	<	free (args_info->vacancyRadius_arg); /* free previous argument */
261	<	args_info->vacancyRadius_arg = 0;
262	<	free (args_info->vacancyRadius_orig); /* free previous argument */
197	<	args_info->vacancyRadius_orig = 0;
198	<	}
200	>	}
201	>
202	>	/** @brief generic value variable */
203	>	union generic_value {
204	>	double double_arg;
205	>	char *string_arg;
206	>	const char *default_string_arg;
207	>	};
208	>
209	>	/** @brief holds temporary values for multiple options */
210	>	struct generic_list
211	>	{
212	>	union generic_value arg;
213	>	char *orig;
214	>	struct generic_list *next;
215	>	};
216	>
217	>	/**
218	>	* @brief add a node at the head of the list
219	>	*/
220	>	static void add_node(struct generic_list **list) {
221	>	struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
222	>	new_node->next = *list;
223	>	*list = new_node;
224	>	new_node->arg.string_arg = 0;
225	>	new_node->orig = 0;
226	>	}
227	>
228	>	/**
229	>	* The passed arg parameter is NOT set to 0 from this function
230	>	*/
231	>	static void
232	>	free_multiple_field(unsigned int len, void *arg, char ***orig)
233	>	{
234	>	unsigned int i;
235	>	if (arg) {
236	>	for (i = 0; i < len; ++i)
237	>	{
238	>	free_string_field(&((*orig)[i]));
239	>	}
240	>
241	>	free (arg);
242	>	free (*orig);
243	>	*orig = 0;
244	>	}
245	>	}
246	>
247	>
248	>	static void
249	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
250	>	{
251	>	unsigned int i;
252	>	free_string_field (&(args_info->output_arg));
253	>	free_string_field (&(args_info->output_orig));
254	>	free_string_field (&(args_info->latticeConstant_orig));
255	>	free_string_field (&(args_info->radius_orig));
256	>	free_multiple_field (args_info->shellRadius_given, (void *)(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
257	>	args_info->shellRadius_arg = 0;
258	>	free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
259	>	args_info->molFraction_arg = 0;
260	>	free_string_field (&(args_info->vacancyPercent_orig));
261	>	free_string_field (&(args_info->vacancyInnerRadius_orig));
262	>	free_string_field (&(args_info->vacancyOuterRadius_orig));
263
264	+
265		for (i = 0; i < args_info->inputs_num; ++i)
266		free (args_info->inputs [i]);
267	<
267	>
268		if (args_info->inputs_num)
269		free (args_info->inputs);
270	<
270	>
271		clear_given (args_info);
272	+	}
273	+
274	+
275	+	static void
276	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
277	+	{
278	+	FIX_UNUSED (values);
279	+	if (arg) {
280	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
281	+	} else {
282	+	fprintf(outfile, "%s\n", opt);
283	+	}
284	+	}
285	+
286	+	static void
287	+	write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
288	+	{
289	+	int i;
290	+
291	+	for (i = 0; i < len; ++i)
292	+	write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
293		}
294
295		int
296	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
297	+	{
298	+	int i = 0;
299	+
300	+	if (!outfile)
301	+	{
302	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
303	+	return EXIT_FAILURE;
304	+	}
305	+
306	+	if (args_info->help_given)
307	+	write_into_file(outfile, "help", 0, 0 );
308	+	if (args_info->version_given)
309	+	write_into_file(outfile, "version", 0, 0 );
310	+	if (args_info->output_given)
311	+	write_into_file(outfile, "output", args_info->output_orig, 0);
312	+	if (args_info->latticeConstant_given)
313	+	write_into_file(outfile, "latticeConstant", args_info->latticeConstant_orig, 0);
314	+	if (args_info->radius_given)
315	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
316	+	write_multiple_into_file(outfile, args_info->shellRadius_given, "shellRadius", args_info->shellRadius_orig, 0);
317	+	write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0);
318	+	if (args_info->vacancyPercent_given)
319	+	write_into_file(outfile, "vacancyPercent", args_info->vacancyPercent_orig, 0);
320	+	if (args_info->vacancyInnerRadius_given)
321	+	write_into_file(outfile, "vacancyInnerRadius", args_info->vacancyInnerRadius_orig, 0);
322	+	if (args_info->vacancyOuterRadius_given)
323	+	write_into_file(outfile, "vacancyOuterRadius", args_info->vacancyOuterRadius_orig, 0);
324	+
325	+
326	+	i = EXIT_SUCCESS;
327	+	return i;
328	+	}
329	+
330	+	int
331		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
332		{
333		FILE *outfile;
#	Line 220 | Line 341 | cmdline_parser_file_save(const char *filename, struct
341		return EXIT_FAILURE;
342		}
343
344	<	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	<
344	>	i = cmdline_parser_dump(outfile, args_info);
345		fclose (outfile);
346
290	–	i = EXIT_SUCCESS;
347		return i;
348		}
349
#	Line 297 | Line 353 | cmdline_parser_free (struct gengetopt_args_info *args_
353		cmdline_parser_release (args_info);
354		}
355
356	<
301	<	/* gengetopt_strdup() */
302	<	/* strdup.c replacement of strdup, which is not standard */
356	>	/** @brief replacement of strdup, which is not standard */
357		char *
358		gengetopt_strdup (const char *s)
359		{
360	<	char *result = NULL;
360	>	char *result = 0;
361		if (!s)
362		return result;
363
#	Line 317 | Line 371 | get_multiple_arg_token(const char *arg)
371		static char *
372		get_multiple_arg_token(const char *arg)
373		{
374	<	char *tok, *ret;
375	<	size_t len;
374	>	const char *tok;
375	>	char *ret;
376	>	size_t len, num_of_escape, i, j;
377
378		if (!arg)
379	<	return NULL;
379	>	return 0;
380
381		tok = strchr (arg, ',');
382	+	num_of_escape = 0;
383
384	+	/* make sure it is not escaped */
385	+	while (tok)
386	+	{
387	+	if (*(tok-1) == '\\')
388	+	{
389	+	/* find the next one */
390	+	tok = strchr (tok+1, ',');
391	+	++num_of_escape;
392	+	}
393	+	else
394	+	break;
395	+	}
396	+
397		if (tok)
398		len = (size_t)(tok - arg + 1);
399		else
400		len = strlen (arg) + 1;
401
402	+	len -= num_of_escape;
403	+
404		ret = (char *) malloc (len);
405	<	strncpy (ret, arg, len-1);
405	>
406	>	i = 0;
407	>	j = 0;
408	>	while (arg[i] && (j < len-1))
409	>	{
410	>	if (arg[i] == '\\' &&
411	>	arg[ i + 1 ] &&
412	>	arg[ i + 1 ] == ',')
413	>	++i;
414	>
415	>	ret[j++] = arg[i++];
416	>	}
417	>
418		ret[len-1] = '\0';
419
420		return ret;
421		}
422
423	<	static char *
423	>	static const char *
424		get_multiple_arg_token_next(const char *arg)
425		{
426	<	char *tok;
426	>	const char *tok;
427
428		if (!arg)
429	<	return NULL;
429	>	return 0;
430
431		tok = strchr (arg, ',');
432
433	+	/* make sure it is not escaped */
434	+	while (tok)
435	+	{
436	+	if (*(tok-1) == '\\')
437	+	{
438	+	/* find the next one */
439	+	tok = strchr (tok+1, ',');
440	+	}
441	+	else
442	+	break;
443	+	}
444	+
445		if (! tok || strlen(tok) == 1)
446		return 0;
447
448		return tok+1;
449		}
450
451	+	static int
452	+	check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
453	+
454		int
455	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
455	>	check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc)
456		{
457	+	int error = 0;
458	+
459	+	if (option_given && (min > 0 || max > 0))
460	+	{
461	+	if (min > 0 && max > 0)
462	+	{
463	+	if (min == max)
464	+	{
465	+	/* specific occurrences */
466	+	if (option_given != (unsigned int) min)
467	+	{
468	+	fprintf (stderr, "%s: %s option occurrences must be %d\n",
469	+	prog_name, option_desc, min);
470	+	error = 1;
471	+	}
472	+	}
473	+	else if (option_given < (unsigned int) min
474	+	|| option_given > (unsigned int) max)
475	+	{
476	+	/* range occurrences */
477	+	fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
478	+	prog_name, option_desc, min, max);
479	+	error = 1;
480	+	}
481	+	}
482	+	else if (min > 0)
483	+	{
484	+	/* at least check */
485	+	if (option_given < min)
486	+	{
487	+	fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
488	+	prog_name, option_desc, min);
489	+	error = 1;
490	+	}
491	+	}
492	+	else if (max > 0)
493	+	{
494	+	/* at most check */
495	+	if (option_given > max)
496	+	{
497	+	fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
498	+	prog_name, option_desc, max);
499	+	error = 1;
500	+	}
501	+	}
502	+	}
503	+
504	+	return error;
505	+	}
506	+	int
507	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
508	+	{
509		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
510		}
511
512		int
513	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
513	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
514	>	struct cmdline_parser_params *params)
515		{
516		int result;
517	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
518
519	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
519	>	if (result == EXIT_FAILURE)
520	>	{
521	>	cmdline_parser_free (args_info);
522	>	exit (EXIT_FAILURE);
523	>	}
524	>
525	>	return result;
526	>	}
527
528	+	int
529	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
530	+	{
531	+	int result;
532	+	struct cmdline_parser_params params;
533	+
534	+	params.override = override;
535	+	params.initialize = initialize;
536	+	params.check_required = check_required;
537	+	params.check_ambiguity = 0;
538	+	params.print_errors = 1;
539	+
540	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
541	+
542		if (result == EXIT_FAILURE)
543		{
544		cmdline_parser_free (args_info);
#	Line 380 | Line 553 | cmdline_parser_required (struct gengetopt_args_info *a
553		{
554		int result = EXIT_SUCCESS;
555
556	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
556	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
557		result = EXIT_FAILURE;
558
559		if (result == EXIT_FAILURE)
#	Line 396 | Line 569 | cmdline_parser_required2 (struct gengetopt_args_info *
569		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
570		{
571		int error = 0;
572	+	FIX_UNUSED (additional_error);
573
574	<	if (! args_info->latticeCnst_given)
574	>	/* checks for required options */
575	>	if (! args_info->output_given)
576		{
577	<	fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
577	>	fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
578		error = 1;
579		}
580	+
581	+	if (! args_info->latticeConstant_given)
582	+	{
583	+	fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
584	+	error = 1;
585	+	}
586	+
587		if (! args_info->radius_given)
588		{
589		fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
590		error = 1;
591		}
592	+
593	+	if (check_multiple_option_occurrences(prog_name, args_info->shellRadius_given, args_info->shellRadius_min, args_info->shellRadius_max, "'--shellRadius'"))
594	+	error = 1;
595	+
596	+	if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'"))
597	+	error = 1;
598	+
599	+
600	+	/* checks for dependences among options */
601
602		return error;
603		}
604
605	+
606	+	static char *package_name = 0;
607	+
608	+	/**
609	+	* @brief updates an option
610	+	* @param field the generic pointer to the field to update
611	+	* @param orig_field the pointer to the orig field
612	+	* @param field_given the pointer to the number of occurrence of this option
613	+	* @param prev_given the pointer to the number of occurrence already seen
614	+	* @param value the argument for this option (if null no arg was specified)
615	+	* @param possible_values the possible values for this option (if specified)
616	+	* @param default_value the default value (in case the option only accepts fixed values)
617	+	* @param arg_type the type of this option
618	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
619	+	* @param override @see cmdline_parser_params.override
620	+	* @param no_free whether to free a possible previous value
621	+	* @param multiple_option whether this is a multiple option
622	+	* @param long_opt the corresponding long option
623	+	* @param short_opt the corresponding short option (or '-' if none)
624	+	* @param additional_error possible further error specification
625	+	*/
626	+	static
627	+	int update_arg(void *field, char **orig_field,
628	+	unsigned int *field_given, unsigned int *prev_given,
629	+	char *value, const char *possible_values[],
630	+	const char *default_value,
631	+	cmdline_parser_arg_type arg_type,
632	+	int check_ambiguity, int override,
633	+	int no_free, int multiple_option,
634	+	const char *long_opt, char short_opt,
635	+	const char *additional_error)
636	+	{
637	+	char *stop_char = 0;
638	+	const char *val = value;
639	+	int found;
640	+	char **string_field;
641	+	FIX_UNUSED (field);
642	+
643	+	stop_char = 0;
644	+	found = 0;
645	+
646	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
647	+	{
648	+	if (short_opt != '-')
649	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
650	+	package_name, long_opt, short_opt,
651	+	(additional_error ? additional_error : ""));
652	+	else
653	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
654	+	package_name, long_opt,
655	+	(additional_error ? additional_error : ""));
656	+	return 1; /* failure */
657	+	}
658	+
659	+	FIX_UNUSED (default_value);
660	+
661	+	if (field_given && *field_given && ! override)
662	+	return 0;
663	+	if (prev_given)
664	+	(*prev_given)++;
665	+	if (field_given)
666	+	(*field_given)++;
667	+	if (possible_values)
668	+	val = possible_values[found];
669	+
670	+	switch(arg_type) {
671	+	case ARG_DOUBLE:
672	+	if (val) *((double *)field) = strtod (val, &stop_char);
673	+	break;
674	+	case ARG_STRING:
675	+	if (val) {
676	+	string_field = (char **)field;
677	+	if (!no_free && *string_field)
678	+	free (*string_field); /* free previous string */
679	+	*string_field = gengetopt_strdup (val);
680	+	}
681	+	break;
682	+	default:
683	+	break;
684	+	};
685	+
686	+	/* check numeric conversion */
687	+	switch(arg_type) {
688	+	case ARG_DOUBLE:
689	+	if (val && !(stop_char && *stop_char == '\0')) {
690	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
691	+	return 1; /* failure */
692	+	}
693	+	break;
694	+	default:
695	+	;
696	+	};
697	+
698	+	/* store the original value */
699	+	switch(arg_type) {
700	+	case ARG_NO:
701	+	break;
702	+	default:
703	+	if (value && orig_field) {
704	+	if (no_free) {
705	+	*orig_field = value;
706	+	} else {
707	+	if (*orig_field)
708	+	free (*orig_field); /* free previous string */
709	+	*orig_field = gengetopt_strdup (value);
710	+	}
711	+	}
712	+	};
713	+
714	+	return 0; /* OK */
715	+	}
716	+
717	+	/**
718	+	* @brief store information about a multiple option in a temporary list
719	+	* @param list where to (temporarily) store multiple options
720	+	*/
721	+	static
722	+	int update_multiple_arg_temp(struct generic_list **list,
723	+	unsigned int *prev_given, const char *val,
724	+	const char *possible_values[], const char *default_value,
725	+	cmdline_parser_arg_type arg_type,
726	+	const char *long_opt, char short_opt,
727	+	const char *additional_error)
728	+	{
729	+	/* store single arguments */
730	+	char *multi_token;
731	+	const char *multi_next;
732	+
733	+	if (arg_type == ARG_NO) {
734	+	(*prev_given)++;
735	+	return 0; /* OK */
736	+	}
737	+
738	+	multi_token = get_multiple_arg_token(val);
739	+	multi_next = get_multiple_arg_token_next (val);
740	+
741	+	while (1)
742	+	{
743	+	add_node (list);
744	+	if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
745	+	prev_given, multi_token, possible_values, default_value,
746	+	arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
747	+	if (multi_token) free(multi_token);
748	+	return 1; /* failure */
749	+	}
750	+
751	+	if (multi_next)
752	+	{
753	+	multi_token = get_multiple_arg_token(multi_next);
754	+	multi_next = get_multiple_arg_token_next (multi_next);
755	+	}
756	+	else
757	+	break;
758	+	}
759	+
760	+	return 0; /* OK */
761	+	}
762	+
763	+	/**
764	+	* @brief free the passed list (including possible string argument)
765	+	*/
766	+	static
767	+	void free_list(struct generic_list *list, short string_arg)
768	+	{
769	+	if (list) {
770	+	struct generic_list *tmp;
771	+	while (list)
772	+	{
773	+	tmp = list;
774	+	if (string_arg && list->arg.string_arg)
775	+	free (list->arg.string_arg);
776	+	if (list->orig)
777	+	free (list->orig);
778	+	list = list->next;
779	+	free (tmp);
780	+	}
781	+	}
782	+	}
783	+
784	+	/**
785	+	* @brief updates a multiple option starting from the passed list
786	+	*/
787	+	static
788	+	void update_multiple_arg(void *field, char ***orig_field,
789	+	unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
790	+	cmdline_parser_arg_type arg_type,
791	+	struct generic_list *list)
792	+	{
793	+	int i;
794	+	struct generic_list *tmp;
795	+
796	+	if (prev_given && list) {
797	+	*orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
798	+
799	+	switch(arg_type) {
800	+	case ARG_DOUBLE:
801	+	*((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
802	+	case ARG_STRING:
803	+	*((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
804	+	default:
805	+	break;
806	+	};
807	+
808	+	for (i = (prev_given - 1); i >= 0; --i)
809	+	{
810	+	tmp = list;
811	+
812	+	switch(arg_type) {
813	+	case ARG_DOUBLE:
814	+	(*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
815	+	case ARG_STRING:
816	+	(*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
817	+	default:
818	+	break;
819	+	}
820	+	(*orig_field) [i + field_given] = list->orig;
821	+	list = list->next;
822	+	free (tmp);
823	+	}
824	+	} else { /* set the default value */
825	+	if (default_value && ! field_given) {
826	+	switch(arg_type) {
827	+	case ARG_DOUBLE:
828	+	if (! *((double **)field)) {
829	+	*((double **)field) = (double *)malloc (sizeof (double));
830	+	(*((double **)field))[0] = default_value->double_arg;
831	+	}
832	+	break;
833	+	case ARG_STRING:
834	+	if (! *((char ***)field)) {
835	+	*((char ***)field) = (char **)malloc (sizeof (char *));
836	+	(*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
837	+	}
838	+	break;
839	+	default: break;
840	+	}
841	+	if (!(*orig_field)) {
842	+	*orig_field = (char **) malloc (sizeof (char *));
843	+	(*orig_field)[0] = 0;
844	+	}
845	+	}
846	+	}
847	+	}
848	+
849		int
850	<	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)
850	>	cmdline_parser_internal (
851	>	int argc, char **argv, struct gengetopt_args_info *args_info,
852	>	struct cmdline_parser_params *params, const char *additional_error)
853		{
854		int c;        /* Character of the parsed option.  */
418	–	char *multi_token, *multi_next; /* for multiple options */
855
856	<	int i;        /* Counter */
857	<
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;
856	>	struct generic_list * shellRadius_list = NULL;
857	>	struct generic_list * molFraction_list = NULL;
858		int error = 0;
859		struct gengetopt_args_info local_args_info;
860	+
861	+	int override;
862	+	int initialize;
863	+	int check_required;
864	+	int check_ambiguity;
865	+
866	+	package_name = argv[0];
867	+
868	+	override = params->override;
869	+	initialize = params->initialize;
870	+	check_required = params->check_required;
871	+	check_ambiguity = params->check_ambiguity;
872
873		if (initialize)
874		cmdline_parser_init (args_info);
#	Line 431 | Line 876 | cmdline_parser_internal (int argc, char * const *argv,
876		cmdline_parser_init (&local_args_info);
877
878		optarg = 0;
879	<	optind = 1;
880	<	opterr = 1;
879	>	optind = 0;
880	>	opterr = params->print_errors;
881		optopt = '?';
882
883		while (1)
884		{
885		int option_index = 0;
441	–	char *stop_char;
886
887		static struct option long_options[] = {
888		{ "help",       0, NULL, 'h' },
889		{ "version",    0, NULL, 'V' },
890		{ "output",     1, NULL, 'o' },
891	<	{ "latticeCnst",        1, NULL, 0 },
891	>	{ "latticeConstant",    1, NULL, 0 },
892		{ "radius",     1, NULL, 0 },
893	<	{ "ShellRadius",        1, NULL, 0 },
893	>	{ "shellRadius",        1, NULL, 0 },
894		{ "molFraction",        1, NULL, 0 },
895	<	{ "vacancyPCT", 1, NULL, 0 },
896	<	{ "vacancyRadius",      1, NULL, 0 },
897	<	{ NULL, 0, NULL, 0 }
895	>	{ "vacancyPercent",     1, NULL, 0 },
896	>	{ "vacancyInnerRadius", 1, NULL, 0 },
897	>	{ "vacancyOuterRadius", 1, NULL, 0 },
898	>	{ 0,  0, 0, 0 }
899		};
900
456	–	stop_char = 0;
901		c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
902
903		if (c == -1) break;       /* Exit from `while (1)' loop.  */
#	Line 471 | Line 915 | cmdline_parser_internal (int argc, char * const *argv,
915		exit (EXIT_SUCCESS);
916
917		case 'o':       /* Output file name.  */
918	<	if (local_args_info.output_given)
919	<	{
920	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
921	<	goto failure;
922	<	}
923	<	if (args_info->output_given && ! override)
924	<	continue;
925	<	local_args_info.output_given = 1;
926	<	args_info->output_given = 1;
927	<	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);
918	>
919	>
920	>	if (update_arg( (void *)&(args_info->output_arg),
921	>	&(args_info->output_orig), &(args_info->output_given),
922	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
923	>	check_ambiguity, override, 0, 0,
924	>	"output", 'o',
925	>	additional_error))
926	>	goto failure;
927	>
928		break;
929
491	–
930		case 0: /* Long option with no short option */
931		/* Lattice spacing in Angstroms for cubic lattice..  */
932	<	if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
932	>	if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
933		{
934	<	if (local_args_info.latticeCnst_given)
935	<	{
936	<	fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
937	<	goto failure;
938	<	}
939	<	if (args_info->latticeCnst_given && ! override)
940	<	continue;
941	<	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);
934	>
935	>
936	>	if (update_arg( (void *)&(args_info->latticeConstant_arg),
937	>	&(args_info->latticeConstant_orig), &(args_info->latticeConstant_given),
938	>	&(local_args_info.latticeConstant_given), optarg, 0, 0, ARG_DOUBLE,
939	>	check_ambiguity, override, 0, 0,
940	>	"latticeConstant", '-',
941	>	additional_error))
942		goto failure;
943	<	}
510	<	if (args_info->latticeCnst_orig)
511	<	free (args_info->latticeCnst_orig); /* free previous string */
512	<	args_info->latticeCnst_orig = gengetopt_strdup (optarg);
943	>
944		}
945		/* Nanoparticle radius in Angstroms.  */
946		else if (strcmp (long_options[option_index].name, "radius") == 0)
947		{
948	<	if (local_args_info.radius_given)
949	<	{
950	<	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
951	<	goto failure;
952	<	}
953	<	if (args_info->radius_given && ! override)
954	<	continue;
955	<	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);
948	>
949	>
950	>	if (update_arg( (void *)&(args_info->radius_arg),
951	>	&(args_info->radius_orig), &(args_info->radius_given),
952	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
953	>	check_ambiguity, override, 0, 0,
954	>	"radius", '-',
955	>	additional_error))
956		goto failure;
957	<	}
531	<	if (args_info->radius_orig)
532	<	free (args_info->radius_orig); /* free previous string */
533	<	args_info->radius_orig = gengetopt_strdup (optarg);
957	>
958		}
959	<	/* 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..  */
960	<	else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
959	>	/* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file..  */
960	>	else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
961		{
538	–	local_args_info.ShellRadius_given++;
962
963	<	multi_token = get_multiple_arg_token(optarg);
964	<	multi_next = get_multiple_arg_token_next (optarg);
963	>	if (update_multiple_arg_temp(&shellRadius_list,
964	>	&(local_args_info.shellRadius_given), optarg, 0, 0, ARG_DOUBLE,
965	>	"shellRadius", '-',
966	>	additional_error))
967	>	goto failure;
968
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;
969		}
970	<	/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
970	>	/* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file..  */
971		else if (strcmp (long_options[option_index].name, "molFraction") == 0)
972		{
569	–	local_args_info.molFraction_given++;
973
974	<	multi_token = get_multiple_arg_token(optarg);
975	<	multi_next = get_multiple_arg_token_next (optarg);
974	>	if (update_multiple_arg_temp(&molFraction_list,
975	>	&(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE,
976	>	"molFraction", '-',
977	>	additional_error))
978	>	goto failure;
979
980	<	while (1)
981	<	{
982	<	molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
983	<	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;
980	>	}
981	>	/* Percentage of atoms to remove from within vacancy range.  */
982	>	else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
983	>	{
984
985	<	if (multi_next)
986	<	{
987	<	multi_token = get_multiple_arg_token(multi_next);
988	<	multi_next = get_multiple_arg_token_next (multi_next);
989	<	local_args_info.molFraction_given++;
990	<	}
991	<	else
992	<	break;
993	<	}
595	<	break;
985	>
986	>	if (update_arg( (void *)&(args_info->vacancyPercent_arg),
987	>	&(args_info->vacancyPercent_orig), &(args_info->vacancyPercent_given),
988	>	&(local_args_info.vacancyPercent_given), optarg, 0, 0, ARG_DOUBLE,
989	>	check_ambiguity, override, 0, 0,
990	>	"vacancyPercent", '-',
991	>	additional_error))
992	>	goto failure;
993	>
994		}
995	<	/* Percentage of vacancies to build.  */
996	<	else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
995	>	/* Radius arround core-shell where vacancies should be located..  */
996	>	else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
997		{
998	<	if (local_args_info.vacancyPCT_given)
999	<	{
1000	<	fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001	<	goto failure;
1002	<	}
1003	<	if (args_info->vacancyPCT_given && ! override)
1004	<	continue;
1005	<	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);
998	>
999	>
1000	>	if (update_arg( (void *)&(args_info->vacancyInnerRadius_arg),
1001	>	&(args_info->vacancyInnerRadius_orig), &(args_info->vacancyInnerRadius_given),
1002	>	&(local_args_info.vacancyInnerRadius_given), optarg, 0, 0, ARG_DOUBLE,
1003	>	check_ambiguity, override, 0, 0,
1004	>	"vacancyInnerRadius", '-',
1005	>	additional_error))
1006		goto failure;
1007	<	}
614	<	if (args_info->vacancyPCT_orig)
615	<	free (args_info->vacancyPCT_orig); /* free previous string */
616	<	args_info->vacancyPCT_orig = gengetopt_strdup (optarg);
1007	>
1008		}
1009		/* Radius arround core-shell where vacancies should be located..  */
1010	<	else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
1010	>	else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
1011		{
621	–	local_args_info.vacancyRadius_given++;
1012
623	–	multi_token = get_multiple_arg_token(optarg);
624	–	multi_next = get_multiple_arg_token_next (optarg);
1013
1014	<	while (1)
1015	<	{
1016	<	vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
1017	<	vacancyRadius_new->next = vacancyRadius_list;
1018	<	vacancyRadius_list = vacancyRadius_new;
1019	<	vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, &stop_char);
1020	<	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;
1014	>	if (update_arg( (void *)&(args_info->vacancyOuterRadius_arg),
1015	>	&(args_info->vacancyOuterRadius_orig), &(args_info->vacancyOuterRadius_given),
1016	>	&(local_args_info.vacancyOuterRadius_given), optarg, 0, 0, ARG_DOUBLE,
1017	>	check_ambiguity, override, 0, 0,
1018	>	"vacancyOuterRadius", '-',
1019	>	additional_error))
1020	>	goto failure;
1021
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;
1022		}
1023
1024		break;
#	Line 659 | Line 1033 | cmdline_parser_internal (int argc, char * const *argv,
1033		} /* while */
1034
1035
1036	<	if (local_args_info.ShellRadius_given && ShellRadius_list)
1037	<	{
1038	<	struct ShellRadius_list *tmp;
1039	<	args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double));
1040	<	args_info->ShellRadius_orig = (char **) realloc (args_info->ShellRadius_orig, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (char *));
1041	<	for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
1042	<	{
1043	<	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	<
1036	>	update_multiple_arg((void *)&(args_info->shellRadius_arg),
1037	>	&(args_info->shellRadius_orig), args_info->shellRadius_given,
1038	>	local_args_info.shellRadius_given, 0,
1039	>	ARG_DOUBLE, shellRadius_list);
1040	>	update_multiple_arg((void *)&(args_info->molFraction_arg),
1041	>	&(args_info->molFraction_orig), args_info->molFraction_given,
1042	>	local_args_info.molFraction_given, 0,
1043	>	ARG_DOUBLE, molFraction_list);
1044
1045	<	args_info->ShellRadius_given += local_args_info.ShellRadius_given;
1046	<	local_args_info.ShellRadius_given = 0;
1045	>	args_info->shellRadius_given += local_args_info.shellRadius_given;
1046	>	local_args_info.shellRadius_given = 0;
1047		args_info->molFraction_given += local_args_info.molFraction_given;
1048		local_args_info.molFraction_given = 0;
712	–	args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
713	–	local_args_info.vacancyRadius_given = 0;
1049
1050		if (check_required)
1051		{
#	Line 725 | Line 1060 | cmdline_parser_internal (int argc, char * const *argv,
1060		if (optind < argc)
1061		{
1062		int i = 0 ;
1063	+	int found_prog_name = 0;
1064	+	/* whether program name, i.e., argv[0], is in the remaining args
1065	+	(this may happen with some implementations of getopt,
1066	+	but surely not with the one included by gengetopt) */
1067
1068	<	args_info->inputs_num = argc - optind ;
1068	>	i = optind;
1069	>	while (i < argc)
1070	>	if (argv[i++] == argv[0]) {
1071	>	found_prog_name = 1;
1072	>	break;
1073	>	}
1074	>	i = 0;
1075	>
1076	>	args_info->inputs_num = argc - optind - found_prog_name;
1077		args_info->inputs =
1078		(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1079		while (optind < argc)
1080	<	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
1080	>	if (argv[optind++] != argv[0])
1081	>	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1082		}
1083
1084		return 0;
1085
1086		failure:
1087	<	if (ShellRadius_list)
1088	<	{
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	<	}
1087	>	free_list (shellRadius_list, 0 );
1088	>	free_list (molFraction_list, 0 );
1089
1090		cmdline_parser_release (&local_args_info);
1091		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.
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp (property svn:keywords), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

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

Diff Legend

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