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root/OpenMD/trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp

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trunk/src/applications/dynamicProps/DynamicPropsCmd.c (file contents), Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 UTC vs.
trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp (file contents), Revision 2024 by gezelter, Thu Oct 16 19:13:51 2014 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 DynamicProps.ggo -F DynamicPropsCmd
4	>	gengetopt --file-name=DynamicPropsCmd --unamed-opts
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 "DynamicPropsCmd.h"
31
32	+	const char *gengetopt_args_info_purpose = "";
33	+
34	+	const char *gengetopt_args_info_usage = "Usage: DynamicProps [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	+	"  -i, --input=filename          input dump file",
42	+	"  -o, --output=filename         output file name",
43	+	"      --sele1=selection script  select first stuntdouble set",
44	+	"      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)",
45	+	"      --order=INT               Lengendre Polynomial Order",
46	+	"  -z, --nzbins=INT              Number of Z bins  (default=`100')",
47	+	"  -m, --memory=memory specification\n                                Available memory (defaults to 2G)  \n                                  (default=`2G')",
48	+	"\n Group: dynamicProps\n   an option of this group is required",
49	+	"  -s, --selecorr                selection correlation function",
50	+	"  -r, --rcorr                   rmsd",
51	+	"  -v, --vcorr                   velocity correlation function",
52	+	"      --vcorrZ                  velocity correlation function along z-axis",
53	+	"      --vcorrR                  velocity correlation function projected \n                                  radially",
54	+	"  -d, --dcorr                   dipole correlation function",
55	+	"  -l, --lcorr                   Lengendre correlation function",
56	+	"      --lcorrZ                  Lengendre correlation function binned by Z",
57	+	"      --cohZ                    Lengendre correlation function for OH bond \n                                  vectors binned by Z",
58	+	"  -M, --sdcorr                  System dipole correlation function",
59	+	"      --r_rcorr                 Radial rmsd",
60	+	"      --thetacorr               Angular rmsd",
61	+	"      --drcorr                  Directional rmsd for particles with unit \n                                  vectors",
62	+	"      --helfandEcorr            Helfand moment for thermal conductvity",
63	+	"  -p, --momentum                Helfand momentum for viscosity",
64	+	"      --stresscorr              Stress tensor correlation function",
65	+	"  -b, --bondcorr                Bond extension correlation function",
66	+	"  -f, --freqfluccorr            Frequency Fluctuation correlation function",
67	+	0
68	+	};
69	+
70	+	typedef enum {ARG_NO
71	+	, ARG_STRING
72	+	, ARG_INT
73	+	} cmdline_parser_arg_type;
74	+
75		static
76		void clear_given (struct gengetopt_args_info *args_info);
77		static
78		void clear_args (struct gengetopt_args_info *args_info);
79
80		static int
81	<	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);
81	>	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
82	>	struct cmdline_parser_params *params, const char *additional_error);
83
84		static int
85		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
#	Line 45 | Line 97 | void clear_given (struct gengetopt_args_info *args_inf
97		args_info->sele1_given = 0 ;
98		args_info->sele2_given = 0 ;
99		args_info->order_given = 0 ;
100	+	args_info->nzbins_given = 0 ;
101	+	args_info->memory_given = 0 ;
102	+	args_info->selecorr_given = 0 ;
103		args_info->rcorr_given = 0 ;
104		args_info->vcorr_given = 0 ;
105	+	args_info->vcorrZ_given = 0 ;
106	+	args_info->vcorrR_given = 0 ;
107		args_info->dcorr_given = 0 ;
108		args_info->lcorr_given = 0 ;
109	+	args_info->lcorrZ_given = 0 ;
110	+	args_info->cohZ_given = 0 ;
111	+	args_info->sdcorr_given = 0 ;
112		args_info->r_rcorr_given = 0 ;
113		args_info->thetacorr_given = 0 ;
114	+	args_info->drcorr_given = 0 ;
115	+	args_info->helfandEcorr_given = 0 ;
116	+	args_info->momentum_given = 0 ;
117	+	args_info->stresscorr_given = 0 ;
118	+	args_info->bondcorr_given = 0 ;
119	+	args_info->freqfluccorr_given = 0 ;
120		args_info->dynamicProps_group_counter = 0 ;
121		}
122
123		static
124		void clear_args (struct gengetopt_args_info *args_info)
125		{
126	+	FIX_UNUSED (args_info);
127		args_info->input_arg = NULL;
128		args_info->input_orig = NULL;
129		args_info->output_arg = NULL;
#	Line 66 | Line 133 | void clear_args (struct gengetopt_args_info *args_info
133		args_info->sele2_arg = NULL;
134		args_info->sele2_orig = NULL;
135		args_info->order_orig = NULL;
136	+	args_info->nzbins_arg = 100;
137	+	args_info->nzbins_orig = NULL;
138	+	args_info->memory_arg = gengetopt_strdup ("2G");
139	+	args_info->memory_orig = NULL;
140
141		}
142
143	+	static
144	+	void init_args_info(struct gengetopt_args_info *args_info)
145	+	{
146	+
147	+
148	+	args_info->help_help = gengetopt_args_info_help[0] ;
149	+	args_info->version_help = gengetopt_args_info_help[1] ;
150	+	args_info->input_help = gengetopt_args_info_help[2] ;
151	+	args_info->output_help = gengetopt_args_info_help[3] ;
152	+	args_info->sele1_help = gengetopt_args_info_help[4] ;
153	+	args_info->sele2_help = gengetopt_args_info_help[5] ;
154	+	args_info->order_help = gengetopt_args_info_help[6] ;
155	+	args_info->nzbins_help = gengetopt_args_info_help[7] ;
156	+	args_info->memory_help = gengetopt_args_info_help[8] ;
157	+	args_info->selecorr_help = gengetopt_args_info_help[10] ;
158	+	args_info->rcorr_help = gengetopt_args_info_help[11] ;
159	+	args_info->vcorr_help = gengetopt_args_info_help[12] ;
160	+	args_info->vcorrZ_help = gengetopt_args_info_help[13] ;
161	+	args_info->vcorrR_help = gengetopt_args_info_help[14] ;
162	+	args_info->dcorr_help = gengetopt_args_info_help[15] ;
163	+	args_info->lcorr_help = gengetopt_args_info_help[16] ;
164	+	args_info->lcorrZ_help = gengetopt_args_info_help[17] ;
165	+	args_info->cohZ_help = gengetopt_args_info_help[18] ;
166	+	args_info->sdcorr_help = gengetopt_args_info_help[19] ;
167	+	args_info->r_rcorr_help = gengetopt_args_info_help[20] ;
168	+	args_info->thetacorr_help = gengetopt_args_info_help[21] ;
169	+	args_info->drcorr_help = gengetopt_args_info_help[22] ;
170	+	args_info->helfandEcorr_help = gengetopt_args_info_help[23] ;
171	+	args_info->momentum_help = gengetopt_args_info_help[24] ;
172	+	args_info->stresscorr_help = gengetopt_args_info_help[25] ;
173	+	args_info->bondcorr_help = gengetopt_args_info_help[26] ;
174	+	args_info->freqfluccorr_help = gengetopt_args_info_help[27] ;
175	+
176	+	}
177	+
178		void
179		cmdline_parser_print_version (void)
180		{
181	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
181	>	printf ("%s %s\n",
182	>	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
183	>	CMDLINE_PARSER_VERSION);
184		}
185
186	+	static void print_help_common(void) {
187	+	cmdline_parser_print_version ();
188	+
189	+	if (strlen(gengetopt_args_info_purpose) > 0)
190	+	printf("\n%s\n", gengetopt_args_info_purpose);
191	+
192	+	if (strlen(gengetopt_args_info_usage) > 0)
193	+	printf("\n%s\n", gengetopt_args_info_usage);
194	+
195	+	printf("\n");
196	+
197	+	if (strlen(gengetopt_args_info_description) > 0)
198	+	printf("%s\n\n", gengetopt_args_info_description);
199	+	}
200	+
201		void
202		cmdline_parser_print_help (void)
203		{
204	<	cmdline_parser_print_version ();
205	<	printf("\nUsage: DynamicProps [OPTIONS]... [FILES]...\n\n");
206	<	printf("%s\n","  -h, --help                    Print help and exit");
207	<	printf("%s\n","  -V, --version                 Print version and exit");
85	<	printf("%s\n","  -i, --input=filename          input dump file");
86	<	printf("%s\n","  -o, --output=filename         output file name");
87	<	printf("%s\n","      --sele1=selection script  select first stuntdouble set");
88	<	printf("%s\n","      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)");
89	<	printf("%s\n","      --order=INT               Lengendre Polynomial Order");
90	<	printf("%s\n","\n Group: dynamicProps\n   an option of this group is required");
91	<	printf("%s\n","  -r, --rcorr                   rmsd");
92	<	printf("%s\n","  -v, --vcorr                   velocity correlation function");
93	<	printf("%s\n","  -d, --dcorr                   dipole correlation function");
94	<	printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
95	<	printf("%s\n","      --r_rcorr                 Radial rmsd");
96	<	printf("%s\n","      --thetacorr               Angular rmsd");
97	<
204	>	int i = 0;
205	>	print_help_common();
206	>	while (gengetopt_args_info_help[i])
207	>	printf("%s\n", gengetopt_args_info_help[i++]);
208		}
209
210		void
#	Line 102 | Line 212 | cmdline_parser_init (struct gengetopt_args_info *args_
212		{
213		clear_given (args_info);
214		clear_args (args_info);
215	+	init_args_info (args_info);
216
217	<	args_info->inputs = NULL;
217	>	args_info->inputs = 0;
218		args_info->inputs_num = 0;
219		}
220
221	+	void
222	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
223	+	{
224	+	if (params)
225	+	{
226	+	params->override = 0;
227	+	params->initialize = 1;
228	+	params->check_required = 1;
229	+	params->check_ambiguity = 0;
230	+	params->print_errors = 1;
231	+	}
232	+	}
233	+
234	+	struct cmdline_parser_params *
235	+	cmdline_parser_params_create(void)
236	+	{
237	+	struct cmdline_parser_params *params =
238	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
239	+	cmdline_parser_params_init(params);
240	+	return params;
241	+	}
242	+
243		static void
244	<	cmdline_parser_release (struct gengetopt_args_info *args_info)
244	>	free_string_field (char **s)
245		{
246	<
114	<	unsigned int i;
115	<	if (args_info->input_arg)
246	>	if (*s)
247		{
248	<	free (args_info->input_arg); /* free previous argument */
249	<	args_info->input_arg = 0;
248	>	free (*s);
249	>	*s = 0;
250		}
251	<	if (args_info->input_orig)
252	<	{
253	<	free (args_info->input_orig); /* free previous argument */
254	<	args_info->input_orig = 0;
255	<	}
256	<	if (args_info->output_arg)
257	<	{
258	<	free (args_info->output_arg); /* free previous argument */
259	<	args_info->output_arg = 0;
260	<	}
261	<	if (args_info->output_orig)
262	<	{
263	<	free (args_info->output_orig); /* free previous argument */
264	<	args_info->output_orig = 0;
265	<	}
266	<	if (args_info->sele1_arg)
267	<	{
268	<	free (args_info->sele1_arg); /* free previous argument */
269	<	args_info->sele1_arg = 0;
139	<	}
140	<	if (args_info->sele1_orig)
141	<	{
142	<	free (args_info->sele1_orig); /* free previous argument */
143	<	args_info->sele1_orig = 0;
144	<	}
145	<	if (args_info->sele2_arg)
146	<	{
147	<	free (args_info->sele2_arg); /* free previous argument */
148	<	args_info->sele2_arg = 0;
149	<	}
150	<	if (args_info->sele2_orig)
151	<	{
152	<	free (args_info->sele2_orig); /* free previous argument */
153	<	args_info->sele2_orig = 0;
154	<	}
155	<	if (args_info->order_orig)
156	<	{
157	<	free (args_info->order_orig); /* free previous argument */
158	<	args_info->order_orig = 0;
159	<	}
251	>	}
252	>
253	>
254	>	static void
255	>	cmdline_parser_release (struct gengetopt_args_info *args_info)
256	>	{
257	>	unsigned int i;
258	>	free_string_field (&(args_info->input_arg));
259	>	free_string_field (&(args_info->input_orig));
260	>	free_string_field (&(args_info->output_arg));
261	>	free_string_field (&(args_info->output_orig));
262	>	free_string_field (&(args_info->sele1_arg));
263	>	free_string_field (&(args_info->sele1_orig));
264	>	free_string_field (&(args_info->sele2_arg));
265	>	free_string_field (&(args_info->sele2_orig));
266	>	free_string_field (&(args_info->order_orig));
267	>	free_string_field (&(args_info->nzbins_orig));
268	>	free_string_field (&(args_info->memory_arg));
269	>	free_string_field (&(args_info->memory_orig));
270
271	+
272		for (i = 0; i < args_info->inputs_num; ++i)
273		free (args_info->inputs [i]);
274	<
274	>
275		if (args_info->inputs_num)
276		free (args_info->inputs);
277	<
277	>
278		clear_given (args_info);
279		}
280
281	+
282	+	static void
283	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
284	+	{
285	+	FIX_UNUSED (values);
286	+	if (arg) {
287	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
288	+	} else {
289	+	fprintf(outfile, "%s\n", opt);
290	+	}
291	+	}
292	+
293	+
294		int
295	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
296	+	{
297	+	int i = 0;
298	+
299	+	if (!outfile)
300	+	{
301	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
302	+	return EXIT_FAILURE;
303	+	}
304	+
305	+	if (args_info->help_given)
306	+	write_into_file(outfile, "help", 0, 0 );
307	+	if (args_info->version_given)
308	+	write_into_file(outfile, "version", 0, 0 );
309	+	if (args_info->input_given)
310	+	write_into_file(outfile, "input", args_info->input_orig, 0);
311	+	if (args_info->output_given)
312	+	write_into_file(outfile, "output", args_info->output_orig, 0);
313	+	if (args_info->sele1_given)
314	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
315	+	if (args_info->sele2_given)
316	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
317	+	if (args_info->order_given)
318	+	write_into_file(outfile, "order", args_info->order_orig, 0);
319	+	if (args_info->nzbins_given)
320	+	write_into_file(outfile, "nzbins", args_info->nzbins_orig, 0);
321	+	if (args_info->memory_given)
322	+	write_into_file(outfile, "memory", args_info->memory_orig, 0);
323	+	if (args_info->selecorr_given)
324	+	write_into_file(outfile, "selecorr", 0, 0 );
325	+	if (args_info->rcorr_given)
326	+	write_into_file(outfile, "rcorr", 0, 0 );
327	+	if (args_info->vcorr_given)
328	+	write_into_file(outfile, "vcorr", 0, 0 );
329	+	if (args_info->vcorrZ_given)
330	+	write_into_file(outfile, "vcorrZ", 0, 0 );
331	+	if (args_info->vcorrR_given)
332	+	write_into_file(outfile, "vcorrR", 0, 0 );
333	+	if (args_info->dcorr_given)
334	+	write_into_file(outfile, "dcorr", 0, 0 );
335	+	if (args_info->lcorr_given)
336	+	write_into_file(outfile, "lcorr", 0, 0 );
337	+	if (args_info->lcorrZ_given)
338	+	write_into_file(outfile, "lcorrZ", 0, 0 );
339	+	if (args_info->cohZ_given)
340	+	write_into_file(outfile, "cohZ", 0, 0 );
341	+	if (args_info->sdcorr_given)
342	+	write_into_file(outfile, "sdcorr", 0, 0 );
343	+	if (args_info->r_rcorr_given)
344	+	write_into_file(outfile, "r_rcorr", 0, 0 );
345	+	if (args_info->thetacorr_given)
346	+	write_into_file(outfile, "thetacorr", 0, 0 );
347	+	if (args_info->drcorr_given)
348	+	write_into_file(outfile, "drcorr", 0, 0 );
349	+	if (args_info->helfandEcorr_given)
350	+	write_into_file(outfile, "helfandEcorr", 0, 0 );
351	+	if (args_info->momentum_given)
352	+	write_into_file(outfile, "momentum", 0, 0 );
353	+	if (args_info->stresscorr_given)
354	+	write_into_file(outfile, "stresscorr", 0, 0 );
355	+	if (args_info->bondcorr_given)
356	+	write_into_file(outfile, "bondcorr", 0, 0 );
357	+	if (args_info->freqfluccorr_given)
358	+	write_into_file(outfile, "freqfluccorr", 0, 0 );
359	+
360	+
361	+	i = EXIT_SUCCESS;
362	+	return i;
363	+	}
364	+
365	+	int
366		cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
367		{
368		FILE *outfile;
#	Line 181 | Line 376 | cmdline_parser_file_save(const char *filename, struct
376		return EXIT_FAILURE;
377		}
378
379	<	if (args_info->help_given) {
185	<	fprintf(outfile, "%s\n", "help");
186	<	}
187	<	if (args_info->version_given) {
188	<	fprintf(outfile, "%s\n", "version");
189	<	}
190	<	if (args_info->input_given) {
191	<	if (args_info->input_orig) {
192	<	fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
193	<	} else {
194	<	fprintf(outfile, "%s\n", "input");
195	<	}
196	<	}
197	<	if (args_info->output_given) {
198	<	if (args_info->output_orig) {
199	<	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
200	<	} else {
201	<	fprintf(outfile, "%s\n", "output");
202	<	}
203	<	}
204	<	if (args_info->sele1_given) {
205	<	if (args_info->sele1_orig) {
206	<	fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
207	<	} else {
208	<	fprintf(outfile, "%s\n", "sele1");
209	<	}
210	<	}
211	<	if (args_info->sele2_given) {
212	<	if (args_info->sele2_orig) {
213	<	fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
214	<	} else {
215	<	fprintf(outfile, "%s\n", "sele2");
216	<	}
217	<	}
218	<	if (args_info->order_given) {
219	<	if (args_info->order_orig) {
220	<	fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
221	<	} else {
222	<	fprintf(outfile, "%s\n", "order");
223	<	}
224	<	}
225	<	if (args_info->rcorr_given) {
226	<	fprintf(outfile, "%s\n", "rcorr");
227	<	}
228	<	if (args_info->vcorr_given) {
229	<	fprintf(outfile, "%s\n", "vcorr");
230	<	}
231	<	if (args_info->dcorr_given) {
232	<	fprintf(outfile, "%s\n", "dcorr");
233	<	}
234	<	if (args_info->lcorr_given) {
235	<	fprintf(outfile, "%s\n", "lcorr");
236	<	}
237	<	if (args_info->r_rcorr_given) {
238	<	fprintf(outfile, "%s\n", "r_rcorr");
239	<	}
240	<	if (args_info->thetacorr_given) {
241	<	fprintf(outfile, "%s\n", "thetacorr");
242	<	}
243	<
379	>	i = cmdline_parser_dump(outfile, args_info);
380		fclose (outfile);
381
246	–	i = EXIT_SUCCESS;
382		return i;
383		}
384
#	Line 253 | Line 388 | cmdline_parser_free (struct gengetopt_args_info *args_
388		cmdline_parser_release (args_info);
389		}
390
391	<
257	<	/* gengetopt_strdup() */
258	<	/* strdup.c replacement of strdup, which is not standard */
391	>	/** @brief replacement of strdup, which is not standard */
392		char *
393		gengetopt_strdup (const char *s)
394		{
395	<	char *result = NULL;
395	>	char *result = 0;
396		if (!s)
397		return result;
398
#	Line 271 | Line 404 | static void
404		}
405
406		static void
274	–	reset_group_dynamicProps(struct gengetopt_args_info *args_info);
275	–
276	–	static void
407		reset_group_dynamicProps(struct gengetopt_args_info *args_info)
408		{
409		if (! args_info->dynamicProps_group_counter)
410		return;
411
412	+	args_info->selecorr_given = 0 ;
413		args_info->rcorr_given = 0 ;
414		args_info->vcorr_given = 0 ;
415	+	args_info->vcorrZ_given = 0 ;
416	+	args_info->vcorrR_given = 0 ;
417		args_info->dcorr_given = 0 ;
418		args_info->lcorr_given = 0 ;
419	+	args_info->lcorrZ_given = 0 ;
420	+	args_info->cohZ_given = 0 ;
421	+	args_info->sdcorr_given = 0 ;
422		args_info->r_rcorr_given = 0 ;
423		args_info->thetacorr_given = 0 ;
424	+	args_info->drcorr_given = 0 ;
425	+	args_info->helfandEcorr_given = 0 ;
426	+	args_info->momentum_given = 0 ;
427	+	args_info->stresscorr_given = 0 ;
428	+	args_info->bondcorr_given = 0 ;
429	+	args_info->freqfluccorr_given = 0 ;
430
431		args_info->dynamicProps_group_counter = 0;
432		}
433
434		int
435	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
435	>	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
436		{
437		return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
438		}
439
440		int
441	<	cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
441	>	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
442	>	struct cmdline_parser_params *params)
443		{
444		int result;
445	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
446
447	<	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
447	>	if (result == EXIT_FAILURE)
448	>	{
449	>	cmdline_parser_free (args_info);
450	>	exit (EXIT_FAILURE);
451	>	}
452	>
453	>	return result;
454	>	}
455
456	+	int
457	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
458	+	{
459	+	int result;
460	+	struct cmdline_parser_params params;
461	+
462	+	params.override = override;
463	+	params.initialize = initialize;
464	+	params.check_required = check_required;
465	+	params.check_ambiguity = 0;
466	+	params.print_errors = 1;
467	+
468	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
469	+
470		if (result == EXIT_FAILURE)
471		{
472		cmdline_parser_free (args_info);
#	Line 316 | Line 481 | cmdline_parser_required (struct gengetopt_args_info *a
481		{
482		int result = EXIT_SUCCESS;
483
484	<	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
484	>	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
485		result = EXIT_FAILURE;
486
487		if (result == EXIT_FAILURE)
#	Line 332 | Line 497 | cmdline_parser_required2 (struct gengetopt_args_info *
497		cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
498		{
499		int error = 0;
500	+	FIX_UNUSED (additional_error);
501
502	+	/* checks for required options */
503		if (! args_info->input_given)
504		{
505		fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
506		error = 1;
507		}
508	+
509		if (args_info->dynamicProps_group_counter == 0)
510		{
511	<	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
511	>	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
512		error = 1;
513		}
514
515
516	+	/* checks for dependences among options */
517	+
518		return error;
519		}
520
521	+
522	+	static char *package_name = 0;
523	+
524	+	/**
525	+	* @brief updates an option
526	+	* @param field the generic pointer to the field to update
527	+	* @param orig_field the pointer to the orig field
528	+	* @param field_given the pointer to the number of occurrence of this option
529	+	* @param prev_given the pointer to the number of occurrence already seen
530	+	* @param value the argument for this option (if null no arg was specified)
531	+	* @param possible_values the possible values for this option (if specified)
532	+	* @param default_value the default value (in case the option only accepts fixed values)
533	+	* @param arg_type the type of this option
534	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
535	+	* @param override @see cmdline_parser_params.override
536	+	* @param no_free whether to free a possible previous value
537	+	* @param multiple_option whether this is a multiple option
538	+	* @param long_opt the corresponding long option
539	+	* @param short_opt the corresponding short option (or '-' if none)
540	+	* @param additional_error possible further error specification
541	+	*/
542	+	static
543	+	int update_arg(void *field, char **orig_field,
544	+	unsigned int *field_given, unsigned int *prev_given,
545	+	char *value, const char *possible_values[],
546	+	const char *default_value,
547	+	cmdline_parser_arg_type arg_type,
548	+	int check_ambiguity, int override,
549	+	int no_free, int multiple_option,
550	+	const char *long_opt, char short_opt,
551	+	const char *additional_error)
552	+	{
553	+	char *stop_char = 0;
554	+	const char *val = value;
555	+	int found;
556	+	char **string_field;
557	+	FIX_UNUSED (field);
558	+
559	+	stop_char = 0;
560	+	found = 0;
561	+
562	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
563	+	{
564	+	if (short_opt != '-')
565	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
566	+	package_name, long_opt, short_opt,
567	+	(additional_error ? additional_error : ""));
568	+	else
569	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
570	+	package_name, long_opt,
571	+	(additional_error ? additional_error : ""));
572	+	return 1; /* failure */
573	+	}
574	+
575	+	FIX_UNUSED (default_value);
576	+
577	+	if (field_given && *field_given && ! override)
578	+	return 0;
579	+	if (prev_given)
580	+	(*prev_given)++;
581	+	if (field_given)
582	+	(*field_given)++;
583	+	if (possible_values)
584	+	val = possible_values[found];
585	+
586	+	switch(arg_type) {
587	+	case ARG_INT:
588	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
589	+	break;
590	+	case ARG_STRING:
591	+	if (val) {
592	+	string_field = (char **)field;
593	+	if (!no_free && *string_field)
594	+	free (*string_field); /* free previous string */
595	+	*string_field = gengetopt_strdup (val);
596	+	}
597	+	break;
598	+	default:
599	+	break;
600	+	};
601	+
602	+	/* check numeric conversion */
603	+	switch(arg_type) {
604	+	case ARG_INT:
605	+	if (val && !(stop_char && *stop_char == '\0')) {
606	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
607	+	return 1; /* failure */
608	+	}
609	+	break;
610	+	default:
611	+	;
612	+	};
613	+
614	+	/* store the original value */
615	+	switch(arg_type) {
616	+	case ARG_NO:
617	+	break;
618	+	default:
619	+	if (value && orig_field) {
620	+	if (no_free) {
621	+	*orig_field = value;
622	+	} else {
623	+	if (*orig_field)
624	+	free (*orig_field); /* free previous string */
625	+	*orig_field = gengetopt_strdup (value);
626	+	}
627	+	}
628	+	};
629	+
630	+	return 0; /* OK */
631	+	}
632	+
633	+
634		int
635	<	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)
635	>	cmdline_parser_internal (
636	>	int argc, char **argv, struct gengetopt_args_info *args_info,
637	>	struct cmdline_parser_params *params, const char *additional_error)
638		{
639		int c;        /* Character of the parsed option.  */
640
641		int error = 0;
642		struct gengetopt_args_info local_args_info;
643	+
644	+	int override;
645	+	int initialize;
646	+	int check_required;
647	+	int check_ambiguity;
648	+
649	+	package_name = argv[0];
650	+
651	+	override = params->override;
652	+	initialize = params->initialize;
653	+	check_required = params->check_required;
654	+	check_ambiguity = params->check_ambiguity;
655
656		if (initialize)
657		cmdline_parser_init (args_info);
#	Line 362 | Line 659 | cmdline_parser_internal (int argc, char * const *argv,
659		cmdline_parser_init (&local_args_info);
660
661		optarg = 0;
662	<	optind = 1;
663	<	opterr = 1;
662	>	optind = 0;
663	>	opterr = params->print_errors;
664		optopt = '?';
665
666		while (1)
667		{
668		int option_index = 0;
372	–	char *stop_char;
669
670		static struct option long_options[] = {
671		{ "help",       0, NULL, 'h' },
#	Line 379 | Line 675 | cmdline_parser_internal (int argc, char * const *argv,
675		{ "sele1",      1, NULL, 0 },
676		{ "sele2",      1, NULL, 0 },
677		{ "order",      1, NULL, 0 },
678	+	{ "nzbins",     1, NULL, 'z' },
679	+	{ "memory",     1, NULL, 'm' },
680	+	{ "selecorr",   0, NULL, 's' },
681		{ "rcorr",      0, NULL, 'r' },
682		{ "vcorr",      0, NULL, 'v' },
683	+	{ "vcorrZ",     0, NULL, 0 },
684	+	{ "vcorrR",     0, NULL, 0 },
685		{ "dcorr",      0, NULL, 'd' },
686		{ "lcorr",      0, NULL, 'l' },
687	+	{ "lcorrZ",     0, NULL, 0 },
688	+	{ "cohZ",       0, NULL, 0 },
689	+	{ "sdcorr",     0, NULL, 'M' },
690		{ "r_rcorr",    0, NULL, 0 },
691		{ "thetacorr",  0, NULL, 0 },
692	<	{ NULL, 0, NULL, 0 }
692	>	{ "drcorr",     0, NULL, 0 },
693	>	{ "helfandEcorr",       0, NULL, 0 },
694	>	{ "momentum",   0, NULL, 'p' },
695	>	{ "stresscorr", 0, NULL, 0 },
696	>	{ "bondcorr",   0, NULL, 'b' },
697	>	{ "freqfluccorr",       0, NULL, 'f' },
698	>	{ 0,  0, 0, 0 }
699		};
700
701	<	stop_char = 0;
392	<	c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);
701	>	c = getopt_long (argc, argv, "hVi:o:z:m:srvdlMpbf", long_options, &option_index);
702
703		if (c == -1) break;       /* Exit from `while (1)' loop.  */
704
#	Line 406 | Line 715 | cmdline_parser_internal (int argc, char * const *argv,
715		exit (EXIT_SUCCESS);
716
717		case 'i':       /* input dump file.  */
718	<	if (local_args_info.input_given)
719	<	{
720	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
721	<	goto failure;
722	<	}
723	<	if (args_info->input_given && ! override)
724	<	continue;
725	<	local_args_info.input_given = 1;
726	<	args_info->input_given = 1;
727	<	if (args_info->input_arg)
419	<	free (args_info->input_arg); /* free previous string */
420	<	args_info->input_arg = gengetopt_strdup (optarg);
421	<	if (args_info->input_orig)
422	<	free (args_info->input_orig); /* free previous string */
423	<	args_info->input_orig = gengetopt_strdup (optarg);
718	>
719	>
720	>	if (update_arg( (void *)&(args_info->input_arg),
721	>	&(args_info->input_orig), &(args_info->input_given),
722	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
723	>	check_ambiguity, override, 0, 0,
724	>	"input", 'i',
725	>	additional_error))
726	>	goto failure;
727	>
728		break;
425	–
729		case 'o':       /* output file name.  */
730	<	if (local_args_info.output_given)
731	<	{
732	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
733	<	goto failure;
734	<	}
735	<	if (args_info->output_given && ! override)
736	<	continue;
737	<	local_args_info.output_given = 1;
738	<	args_info->output_given = 1;
739	<	if (args_info->output_arg)
437	<	free (args_info->output_arg); /* free previous string */
438	<	args_info->output_arg = gengetopt_strdup (optarg);
439	<	if (args_info->output_orig)
440	<	free (args_info->output_orig); /* free previous string */
441	<	args_info->output_orig = gengetopt_strdup (optarg);
730	>
731	>
732	>	if (update_arg( (void *)&(args_info->output_arg),
733	>	&(args_info->output_orig), &(args_info->output_given),
734	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
735	>	check_ambiguity, override, 0, 0,
736	>	"output", 'o',
737	>	additional_error))
738	>	goto failure;
739	>
740		break;
741	<
741	>	case 'z':       /* Number of Z bins.  */
742	>
743	>
744	>	if (update_arg( (void *)&(args_info->nzbins_arg),
745	>	&(args_info->nzbins_orig), &(args_info->nzbins_given),
746	>	&(local_args_info.nzbins_given), optarg, 0, "100", ARG_INT,
747	>	check_ambiguity, override, 0, 0,
748	>	"nzbins", 'z',
749	>	additional_error))
750	>	goto failure;
751	>
752	>	break;
753	>	case 'm':       /* Available memory (defaults to 2G).  */
754	>
755	>
756	>	if (update_arg( (void *)&(args_info->memory_arg),
757	>	&(args_info->memory_orig), &(args_info->memory_given),
758	>	&(local_args_info.memory_given), optarg, 0, "2G", ARG_STRING,
759	>	check_ambiguity, override, 0, 0,
760	>	"memory", 'm',
761	>	additional_error))
762	>	goto failure;
763	>
764	>	break;
765	>	case 's':       /* selection correlation function.  */
766	>
767	>	if (args_info->dynamicProps_group_counter && override)
768	>	reset_group_dynamicProps (args_info);
769	>	args_info->dynamicProps_group_counter += 1;
770	>
771	>	if (update_arg( 0 ,
772	>	0 , &(args_info->selecorr_given),
773	>	&(local_args_info.selecorr_given), optarg, 0, 0, ARG_NO,
774	>	check_ambiguity, override, 0, 0,
775	>	"selecorr", 's',
776	>	additional_error))
777	>	goto failure;
778	>
779	>	break;
780		case 'r':       /* rmsd.  */
781	<	if (local_args_info.rcorr_given)
446	<	{
447	<	fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
448	<	goto failure;
449	<	}
450	<	if (args_info->rcorr_given && ! override)
451	<	continue;
452	<	local_args_info.rcorr_given = 1;
453	<	args_info->rcorr_given = 1;
781	>
782		if (args_info->dynamicProps_group_counter && override)
783		reset_group_dynamicProps (args_info);
784		args_info->dynamicProps_group_counter += 1;
785	+
786	+	if (update_arg( 0 ,
787	+	0 , &(args_info->rcorr_given),
788	+	&(local_args_info.rcorr_given), optarg, 0, 0, ARG_NO,
789	+	check_ambiguity, override, 0, 0,
790	+	"rcorr", 'r',
791	+	additional_error))
792	+	goto failure;
793	+
794		break;
458	–
795		case 'v':       /* velocity correlation function.  */
796	<	if (local_args_info.vcorr_given)
461	<	{
462	<	fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
463	<	goto failure;
464	<	}
465	<	if (args_info->vcorr_given && ! override)
466	<	continue;
467	<	local_args_info.vcorr_given = 1;
468	<	args_info->vcorr_given = 1;
796	>
797		if (args_info->dynamicProps_group_counter && override)
798		reset_group_dynamicProps (args_info);
799		args_info->dynamicProps_group_counter += 1;
800	+
801	+	if (update_arg( 0 ,
802	+	0 , &(args_info->vcorr_given),
803	+	&(local_args_info.vcorr_given), optarg, 0, 0, ARG_NO,
804	+	check_ambiguity, override, 0, 0,
805	+	"vcorr", 'v',
806	+	additional_error))
807	+	goto failure;
808	+
809		break;
473	–
810		case 'd':       /* dipole correlation function.  */
811	<	if (local_args_info.dcorr_given)
476	<	{
477	<	fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
478	<	goto failure;
479	<	}
480	<	if (args_info->dcorr_given && ! override)
481	<	continue;
482	<	local_args_info.dcorr_given = 1;
483	<	args_info->dcorr_given = 1;
811	>
812		if (args_info->dynamicProps_group_counter && override)
813		reset_group_dynamicProps (args_info);
814		args_info->dynamicProps_group_counter += 1;
815	+
816	+	if (update_arg( 0 ,
817	+	0 , &(args_info->dcorr_given),
818	+	&(local_args_info.dcorr_given), optarg, 0, 0, ARG_NO,
819	+	check_ambiguity, override, 0, 0,
820	+	"dcorr", 'd',
821	+	additional_error))
822	+	goto failure;
823	+
824		break;
488	–
825		case 'l':       /* Lengendre correlation function.  */
826	<	if (local_args_info.lcorr_given)
491	<	{
492	<	fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
493	<	goto failure;
494	<	}
495	<	if (args_info->lcorr_given && ! override)
496	<	continue;
497	<	local_args_info.lcorr_given = 1;
498	<	args_info->lcorr_given = 1;
826	>
827		if (args_info->dynamicProps_group_counter && override)
828		reset_group_dynamicProps (args_info);
829		args_info->dynamicProps_group_counter += 1;
830	+
831	+	if (update_arg( 0 ,
832	+	0 , &(args_info->lcorr_given),
833	+	&(local_args_info.lcorr_given), optarg, 0, 0, ARG_NO,
834	+	check_ambiguity, override, 0, 0,
835	+	"lcorr", 'l',
836	+	additional_error))
837	+	goto failure;
838	+
839		break;
840	<
840	>	case 'M':       /* System dipole correlation function.  */
841	>
842	>	if (args_info->dynamicProps_group_counter && override)
843	>	reset_group_dynamicProps (args_info);
844	>	args_info->dynamicProps_group_counter += 1;
845	>
846	>	if (update_arg( 0 ,
847	>	0 , &(args_info->sdcorr_given),
848	>	&(local_args_info.sdcorr_given), optarg, 0, 0, ARG_NO,
849	>	check_ambiguity, override, 0, 0,
850	>	"sdcorr", 'M',
851	>	additional_error))
852	>	goto failure;
853	>
854	>	break;
855	>	case 'p':       /* Helfand momentum for viscosity.  */
856	>
857	>	if (args_info->dynamicProps_group_counter && override)
858	>	reset_group_dynamicProps (args_info);
859	>	args_info->dynamicProps_group_counter += 1;
860	>
861	>	if (update_arg( 0 ,
862	>	0 , &(args_info->momentum_given),
863	>	&(local_args_info.momentum_given), optarg, 0, 0, ARG_NO,
864	>	check_ambiguity, override, 0, 0,
865	>	"momentum", 'p',
866	>	additional_error))
867	>	goto failure;
868	>
869	>	break;
870	>	case 'b':       /* Bond extension correlation function.  */
871	>
872	>	if (args_info->dynamicProps_group_counter && override)
873	>	reset_group_dynamicProps (args_info);
874	>	args_info->dynamicProps_group_counter += 1;
875	>
876	>	if (update_arg( 0 ,
877	>	0 , &(args_info->bondcorr_given),
878	>	&(local_args_info.bondcorr_given), optarg, 0, 0, ARG_NO,
879	>	check_ambiguity, override, 0, 0,
880	>	"bondcorr", 'b',
881	>	additional_error))
882	>	goto failure;
883	>
884	>	break;
885	>	case 'f':       /* Frequency Fluctuation correlation function.  */
886	>
887	>	if (args_info->dynamicProps_group_counter && override)
888	>	reset_group_dynamicProps (args_info);
889	>	args_info->dynamicProps_group_counter += 1;
890	>
891	>	if (update_arg( 0 ,
892	>	0 , &(args_info->freqfluccorr_given),
893	>	&(local_args_info.freqfluccorr_given), optarg, 0, 0, ARG_NO,
894	>	check_ambiguity, override, 0, 0,
895	>	"freqfluccorr", 'f',
896	>	additional_error))
897	>	goto failure;
898	>
899	>	break;
900
901		case 0: /* Long option with no short option */
902		/* select first stuntdouble set.  */
903		if (strcmp (long_options[option_index].name, "sele1") == 0)
904		{
905	<	if (local_args_info.sele1_given)
906	<	{
907	<	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
908	<	goto failure;
909	<	}
910	<	if (args_info->sele1_given && ! override)
911	<	continue;
912	<	local_args_info.sele1_given = 1;
913	<	args_info->sele1_given = 1;
914	<	if (args_info->sele1_arg)
519	<	free (args_info->sele1_arg); /* free previous string */
520	<	args_info->sele1_arg = gengetopt_strdup (optarg);
521	<	if (args_info->sele1_orig)
522	<	free (args_info->sele1_orig); /* free previous string */
523	<	args_info->sele1_orig = gengetopt_strdup (optarg);
905	>
906	>
907	>	if (update_arg( (void *)&(args_info->sele1_arg),
908	>	&(args_info->sele1_orig), &(args_info->sele1_given),
909	>	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
910	>	check_ambiguity, override, 0, 0,
911	>	"sele1", '-',
912	>	additional_error))
913	>	goto failure;
914	>
915		}
916		/* select second stuntdouble set (if sele2 is not set, use script from sele1).  */
917		else if (strcmp (long_options[option_index].name, "sele2") == 0)
918		{
919	<	if (local_args_info.sele2_given)
920	<	{
921	<	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
922	<	goto failure;
923	<	}
924	<	if (args_info->sele2_given && ! override)
925	<	continue;
926	<	local_args_info.sele2_given = 1;
927	<	args_info->sele2_given = 1;
928	<	if (args_info->sele2_arg)
538	<	free (args_info->sele2_arg); /* free previous string */
539	<	args_info->sele2_arg = gengetopt_strdup (optarg);
540	<	if (args_info->sele2_orig)
541	<	free (args_info->sele2_orig); /* free previous string */
542	<	args_info->sele2_orig = gengetopt_strdup (optarg);
919	>
920	>
921	>	if (update_arg( (void *)&(args_info->sele2_arg),
922	>	&(args_info->sele2_orig), &(args_info->sele2_given),
923	>	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
924	>	check_ambiguity, override, 0, 0,
925	>	"sele2", '-',
926	>	additional_error))
927	>	goto failure;
928	>
929		}
930		/* Lengendre Polynomial Order.  */
931		else if (strcmp (long_options[option_index].name, "order") == 0)
932		{
933	<	if (local_args_info.order_given)
934	<	{
935	<	fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
936	<	goto failure;
937	<	}
938	<	if (args_info->order_given && ! override)
939	<	continue;
940	<	local_args_info.order_given = 1;
555	<	args_info->order_given = 1;
556	<	args_info->order_arg = strtol (optarg, &stop_char, 0);
557	<	if (!(stop_char && *stop_char == '\0')) {
558	<	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
933	>
934	>
935	>	if (update_arg( (void *)&(args_info->order_arg),
936	>	&(args_info->order_orig), &(args_info->order_given),
937	>	&(local_args_info.order_given), optarg, 0, 0, ARG_INT,
938	>	check_ambiguity, override, 0, 0,
939	>	"order", '-',
940	>	additional_error))
941		goto failure;
942	<	}
561	<	if (args_info->order_orig)
562	<	free (args_info->order_orig); /* free previous string */
563	<	args_info->order_orig = gengetopt_strdup (optarg);
942	>
943		}
944	+	/* velocity correlation function along z-axis.  */
945	+	else if (strcmp (long_options[option_index].name, "vcorrZ") == 0)
946	+	{
947	+
948	+	if (args_info->dynamicProps_group_counter && override)
949	+	reset_group_dynamicProps (args_info);
950	+	args_info->dynamicProps_group_counter += 1;
951	+
952	+	if (update_arg( 0 ,
953	+	0 , &(args_info->vcorrZ_given),
954	+	&(local_args_info.vcorrZ_given), optarg, 0, 0, ARG_NO,
955	+	check_ambiguity, override, 0, 0,
956	+	"vcorrZ", '-',
957	+	additional_error))
958	+	goto failure;
959	+
960	+	}
961	+	/* velocity correlation function projected radially.  */
962	+	else if (strcmp (long_options[option_index].name, "vcorrR") == 0)
963	+	{
964	+
965	+	if (args_info->dynamicProps_group_counter && override)
966	+	reset_group_dynamicProps (args_info);
967	+	args_info->dynamicProps_group_counter += 1;
968	+
969	+	if (update_arg( 0 ,
970	+	0 , &(args_info->vcorrR_given),
971	+	&(local_args_info.vcorrR_given), optarg, 0, 0, ARG_NO,
972	+	check_ambiguity, override, 0, 0,
973	+	"vcorrR", '-',
974	+	additional_error))
975	+	goto failure;
976	+
977	+	}
978	+	/* Lengendre correlation function binned by Z.  */
979	+	else if (strcmp (long_options[option_index].name, "lcorrZ") == 0)
980	+	{
981	+
982	+	if (args_info->dynamicProps_group_counter && override)
983	+	reset_group_dynamicProps (args_info);
984	+	args_info->dynamicProps_group_counter += 1;
985	+
986	+	if (update_arg( 0 ,
987	+	0 , &(args_info->lcorrZ_given),
988	+	&(local_args_info.lcorrZ_given), optarg, 0, 0, ARG_NO,
989	+	check_ambiguity, override, 0, 0,
990	+	"lcorrZ", '-',
991	+	additional_error))
992	+	goto failure;
993	+
994	+	}
995	+	/* Lengendre correlation function for OH bond vectors binned by Z.  */
996	+	else if (strcmp (long_options[option_index].name, "cohZ") == 0)
997	+	{
998	+
999	+	if (args_info->dynamicProps_group_counter && override)
1000	+	reset_group_dynamicProps (args_info);
1001	+	args_info->dynamicProps_group_counter += 1;
1002	+
1003	+	if (update_arg( 0 ,
1004	+	0 , &(args_info->cohZ_given),
1005	+	&(local_args_info.cohZ_given), optarg, 0, 0, ARG_NO,
1006	+	check_ambiguity, override, 0, 0,
1007	+	"cohZ", '-',
1008	+	additional_error))
1009	+	goto failure;
1010	+
1011	+	}
1012		/* Radial rmsd.  */
1013		else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
1014		{
1015	<	if (local_args_info.r_rcorr_given)
569	<	{
570	<	fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
571	<	goto failure;
572	<	}
573	<	if (args_info->r_rcorr_given && ! override)
574	<	continue;
575	<	local_args_info.r_rcorr_given = 1;
576	<	args_info->r_rcorr_given = 1;
1015	>
1016		if (args_info->dynamicProps_group_counter && override)
1017		reset_group_dynamicProps (args_info);
1018		args_info->dynamicProps_group_counter += 1;
1019	<	break;
1019	>
1020	>	if (update_arg( 0 ,
1021	>	0 , &(args_info->r_rcorr_given),
1022	>	&(local_args_info.r_rcorr_given), optarg, 0, 0, ARG_NO,
1023	>	check_ambiguity, override, 0, 0,
1024	>	"r_rcorr", '-',
1025	>	additional_error))
1026	>	goto failure;
1027	>
1028		}
1029		/* Angular rmsd.  */
1030		else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
1031		{
1032	<	if (local_args_info.thetacorr_given)
586	<	{
587	<	fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
588	<	goto failure;
589	<	}
590	<	if (args_info->thetacorr_given && ! override)
591	<	continue;
592	<	local_args_info.thetacorr_given = 1;
593	<	args_info->thetacorr_given = 1;
1032	>
1033		if (args_info->dynamicProps_group_counter && override)
1034		reset_group_dynamicProps (args_info);
1035		args_info->dynamicProps_group_counter += 1;
1036	<	break;
1036	>
1037	>	if (update_arg( 0 ,
1038	>	0 , &(args_info->thetacorr_given),
1039	>	&(local_args_info.thetacorr_given), optarg, 0, 0, ARG_NO,
1040	>	check_ambiguity, override, 0, 0,
1041	>	"thetacorr", '-',
1042	>	additional_error))
1043	>	goto failure;
1044	>
1045		}
1046	+	/* Directional rmsd for particles with unit vectors.  */
1047	+	else if (strcmp (long_options[option_index].name, "drcorr") == 0)
1048	+	{
1049
1050	+	if (args_info->dynamicProps_group_counter && override)
1051	+	reset_group_dynamicProps (args_info);
1052	+	args_info->dynamicProps_group_counter += 1;
1053	+
1054	+	if (update_arg( 0 ,
1055	+	0 , &(args_info->drcorr_given),
1056	+	&(local_args_info.drcorr_given), optarg, 0, 0, ARG_NO,
1057	+	check_ambiguity, override, 0, 0,
1058	+	"drcorr", '-',
1059	+	additional_error))
1060	+	goto failure;
1061	+
1062	+	}
1063	+	/* Helfand moment for thermal conductvity.  */
1064	+	else if (strcmp (long_options[option_index].name, "helfandEcorr") == 0)
1065	+	{
1066	+
1067	+	if (args_info->dynamicProps_group_counter && override)
1068	+	reset_group_dynamicProps (args_info);
1069	+	args_info->dynamicProps_group_counter += 1;
1070	+
1071	+	if (update_arg( 0 ,
1072	+	0 , &(args_info->helfandEcorr_given),
1073	+	&(local_args_info.helfandEcorr_given), optarg, 0, 0, ARG_NO,
1074	+	check_ambiguity, override, 0, 0,
1075	+	"helfandEcorr", '-',
1076	+	additional_error))
1077	+	goto failure;
1078	+
1079	+	}
1080	+	/* Stress tensor correlation function.  */
1081	+	else if (strcmp (long_options[option_index].name, "stresscorr") == 0)
1082	+	{
1083	+
1084	+	if (args_info->dynamicProps_group_counter && override)
1085	+	reset_group_dynamicProps (args_info);
1086	+	args_info->dynamicProps_group_counter += 1;
1087	+
1088	+	if (update_arg( 0 ,
1089	+	0 , &(args_info->stresscorr_given),
1090	+	&(local_args_info.stresscorr_given), optarg, 0, 0, ARG_NO,
1091	+	check_ambiguity, override, 0, 0,
1092	+	"stresscorr", '-',
1093	+	additional_error))
1094	+	goto failure;
1095	+
1096	+	}
1097	+
1098		break;
1099		case '?':       /* Invalid option.  */
1100		/* `getopt_long' already printed an error message.  */
#	Line 610 | Line 1108 | cmdline_parser_internal (int argc, char * const *argv,
1108
1109		if (args_info->dynamicProps_group_counter > 1)
1110		{
1111	<	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
1111	>	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
1112		error = 1;
1113		}
1114
#	Line 629 | Line 1127 | cmdline_parser_internal (int argc, char * const *argv,
1127		if (optind < argc)
1128		{
1129		int i = 0 ;
1130	+	int found_prog_name = 0;
1131	+	/* whether program name, i.e., argv[0], is in the remaining args
1132	+	(this may happen with some implementations of getopt,
1133	+	but surely not with the one included by gengetopt) */
1134
1135	<	args_info->inputs_num = argc - optind ;
1135	>	i = optind;
1136	>	while (i < argc)
1137	>	if (argv[i++] == argv[0]) {
1138	>	found_prog_name = 1;
1139	>	break;
1140	>	}
1141	>	i = 0;
1142	>
1143	>	args_info->inputs_num = argc - optind - found_prog_name;
1144		args_info->inputs =
1145		(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1146		while (optind < argc)
1147	<	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
1147	>	if (argv[optind++] != argv[0])
1148	>	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1149		}
1150
1151		return 0;

Comparing:
trunk/src/applications/dynamicProps/DynamicPropsCmd.c (property svn:keywords), Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 UTC vs.
trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp (property svn:keywords), Revision 2024 by gezelter, Thu Oct 16 19:13:51 2014 UTC

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

Diff Legend

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+	Added lines
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