applications/dump2Xyz/Dump2XYZCmd.c

/*
  File autogenerated by gengetopt version 2.11
  generated with the following command:
  /home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd 

  The developers of gengetopt consider the fixed text that goes in all
  gengetopt output files to be in the public domain:
  we make no copyright claims on it.
*/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>

/* If we use autoconf.  */
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

#include "getopt.h"

#include "Dump2XYZCmd.h"

void
cmdline_parser_print_version (void)
{
  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
}

void
cmdline_parser_print_help (void)
{
  cmdline_parser_print_version ();
  printf("\n"
  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
  printf("\n");
  printf("  -h, --help                        Print help and exit\n");
  printf("  -V, --version                     Print version and exit\n");
  printf("  -i, --input=filename              input dump file\n");
  printf("  -o, --output=filename             output file name\n");
  printf("  -n, --frame=INT                   print every n frame  (default=`1')\n");
  printf("  -d, --dipole                      print the dipole moments  (default=off)\n");
  printf("  -w, --water                       skip the the waters  (default=off)\n");
  printf("  -m, --periodicBox                 map to the periodic box  (default=off)\n");
  printf("  -z, --zconstraint                 replace the atom types of zconstraint \n                                      molecules  (default=off)\n");
  printf("  -r, --rigidbody                   add a pseudo COM atom to rigidbody  \n                                      (default=off)\n");
  printf("  -t, --watertype                   replace the atom type of water model  \n                                      (default=on)\n");
  printf("  -g, --ignore=atomtype             ignore the atom types\n");
  printf("  -s, --selection=selection script  selection syntax:\n"                                      
         "                                    select DMPC -- select DMPC molecule\n"                     
         "                                    select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n"           
         "                                    select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n" 
         "                                    select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n"  
         "                                    select 5 -- select stuntdobule whose global index is 5\n"                                       
         "                                    select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n" 
         "                                    select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n");
  printf("      --repeatX=INT                 The number of images to repeat in the x \n                                      direction  (default=`0')\n");
  printf("      --repeatY=INT                 The number of images to repeat in the y \n                                      direction  (default=`0')\n");
  printf("      --repeatZ=INT                 The number of images to repeat in the z \n                                      direction  (default=`0')\n");
}


static char *gengetopt_strdup (const char *s);

/* gengetopt_strdup() */
/* strdup.c replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = (char*)malloc(strlen(s) + 1);
  if (result == (char*)0)
    return (char*)0;
  strcpy(result, s);
  return result;
}

int
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
{
  int c;        /* Character of the parsed option.  */
  int i;        /* Counter */
  struct ignore_list
  {
    char * ignore_arg;
    struct ignore_list * next;
  };
  struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
  
  int missing_required_options = 0;

  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->input_given = 0 ;
  args_info->output_given = 0 ;
  args_info->frame_given = 0 ;
  args_info->dipole_given = 0 ;
  args_info->water_given = 0 ;
  args_info->periodicBox_given = 0 ;
  args_info->zconstraint_given = 0 ;
  args_info->rigidbody_given = 0 ;
  args_info->watertype_given = 0 ;
  args_info->ignore_given = 0 ;
  args_info->selection_given = 0 ;
  args_info->repeatX_given = 0 ;
  args_info->repeatY_given = 0 ;
  args_info->repeatZ_given = 0 ;
#define clear_args() { \
  args_info->input_arg = NULL; \
  args_info->output_arg = NULL; \
  args_info->frame_arg = 1 ;\
  args_info->dipole_flag = 0;\
  args_info->water_flag = 0;\
  args_info->periodicBox_flag = 0;\
  args_info->zconstraint_flag = 0;\
  args_info->rigidbody_flag = 0;\
  args_info->watertype_flag = 1;\
  args_info->ignore_arg = NULL; \
  args_info->selection_arg = NULL; \
  args_info->repeatX_arg = 0 ;\
  args_info->repeatY_arg = 0 ;\
  args_info->repeatZ_arg = 0 ;\
}

  clear_args();

  optarg = 0;
  optind = 1;
  opterr = 1;
  optopt = '?';

  while (1)
    {
      int option_index = 0;
      char *stop_char;

      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "input",      1, NULL, 'i' },
        { "output",     1, NULL, 'o' },
        { "frame",      1, NULL, 'n' },
        { "dipole",     0, NULL, 'd' },
        { "water",      0, NULL, 'w' },
        { "periodicBox",        0, NULL, 'm' },
        { "zconstraint",        0, NULL, 'z' },
        { "rigidbody",  0, NULL, 'r' },
        { "watertype",  0, NULL, 't' },
        { "ignore",     1, NULL, 'g' },
        { "selection",  1, NULL, 's' },
        { "repeatX",    1, NULL, 0 },
        { "repeatY",    1, NULL, 0 },
        { "repeatZ",    1, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);

      if (c == -1) break;       /* Exit from `while (1)' loop.  */

      switch (c)
        {
        case 'h':       /* Print help and exit.  */
          clear_args ();
          cmdline_parser_print_help ();
          exit (EXIT_SUCCESS);

        case 'V':       /* Print version and exit.  */
          clear_args ();
          cmdline_parser_print_version ();
          exit (EXIT_SUCCESS);

        case 'i':       /* input dump file.  */
          if (args_info->input_given)
            {
              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->input_given = 1;
          args_info->input_arg = gengetopt_strdup (optarg);
          break;

        case 'o':       /* output file name.  */
          if (args_info->output_given)
            {
              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->output_given = 1;
          args_info->output_arg = gengetopt_strdup (optarg);
          break;

        case 'n':       /* print every n frame.  */
          if (args_info->frame_given)
            {
              fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->frame_given = 1;
          args_info->frame_arg = strtol (optarg,&stop_char,0);
          break;

        case 'd':       /* print the dipole moments.  */
          if (args_info->dipole_given)
            {
              fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->dipole_given = 1;
          args_info->dipole_flag = !(args_info->dipole_flag);
          break;

        case 'w':       /* skip the the waters.  */
          if (args_info->water_given)
            {
              fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->water_given = 1;
          args_info->water_flag = !(args_info->water_flag);
          break;

        case 'm':       /* map to the periodic box.  */
          if (args_info->periodicBox_given)
            {
              fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->periodicBox_given = 1;
          args_info->periodicBox_flag = !(args_info->periodicBox_flag);
          break;

        case 'z':       /* replace the atom types of zconstraint molecules.  */
          if (args_info->zconstraint_given)
            {
              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->zconstraint_given = 1;
          args_info->zconstraint_flag = !(args_info->zconstraint_flag);
          break;

        case 'r':       /* add a pseudo COM atom to rigidbody.  */
          if (args_info->rigidbody_given)
            {
              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->rigidbody_given = 1;
          args_info->rigidbody_flag = !(args_info->rigidbody_flag);
          break;

        case 't':       /* replace the atom type of water model.  */
          if (args_info->watertype_given)
            {
              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->watertype_given = 1;
          args_info->watertype_flag = !(args_info->watertype_flag);
          break;

        case 'g':       /* ignore the atom types.  */
          args_info->ignore_given++;
          ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
          ignore_new->next = ignore_list;
          ignore_list = ignore_new;
          ignore_new->ignore_arg = gengetopt_strdup (optarg);
          break;

        case 's':       /* general selection syntax:\n
select DMPC -- select DMPC molecule\n \
select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
select 5 -- select stuntdobule whose global index is 5\n \
select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule .  */
          if (args_info->selection_given)
            {
              fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
              clear_args ();
              exit (EXIT_FAILURE);
            }
          args_info->selection_given = 1;
          args_info->selection_arg = gengetopt_strdup (optarg);
          break;


        case 0: /* Long option with no short option */
          /* The number of images to repeat in the x direction.  */
          if (strcmp (long_options[option_index].name, "repeatX") == 0)
          {
            if (args_info->repeatX_given)
              {
                fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
                clear_args ();
                exit (EXIT_FAILURE);
              }
            args_info->repeatX_given = 1;
            args_info->repeatX_arg = strtol (optarg,&stop_char,0);
            break;
          }
          
          /* The number of images to repeat in the y direction.  */
          else if (strcmp (long_options[option_index].name, "repeatY") == 0)
          {
            if (args_info->repeatY_given)
              {
                fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
                clear_args ();
                exit (EXIT_FAILURE);
              }
            args_info->repeatY_given = 1;
            args_info->repeatY_arg = strtol (optarg,&stop_char,0);
            break;
          }
          
          /* The number of images to repeat in the z direction.  */
          else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
          {
            if (args_info->repeatZ_given)
              {
                fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
                clear_args ();
                exit (EXIT_FAILURE);
              }
            args_info->repeatZ_given = 1;
            args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
            break;
          }
          

        case '?':       /* Invalid option.  */
          /* `getopt_long' already printed an error message.  */
          exit (EXIT_FAILURE);

        default:        /* bug: option not considered.  */
          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
          abort ();
        } /* switch */
    } /* while */


  if (! args_info->input_given)
    {
      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
      missing_required_options = 1;
    }
  if ( missing_required_options )
    exit (EXIT_FAILURE);

  if (args_info->ignore_given)
    {
      args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
      for (i = 0; i < args_info->ignore_given; i++)
        {
          args_info->ignore_arg [i] = ignore_list->ignore_arg;
          ignore_list = ignore_list->next;
        }
    }
  
  return 0;
}
Revision:	1986
Committed:	Mon Feb 7 21:11:22 2005 UTC (19 years, 5 months ago) by tim
Content type:	text/plain
File size:	13952 byte(s)
Log Message:	update help info for Dump2XYZ
#	Content
1	/*
2	File autogenerated by gengetopt version 2.11
3	generated with the following command:
4	/home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd
5
6	The developers of gengetopt consider the fixed text that goes in all
7	gengetopt output files to be in the public domain:
8	we make no copyright claims on it.
9	*/
10
11
12	#include <stdio.h>
13	#include <stdlib.h>
14	#include <string.h>
15
16	/* If we use autoconf. */
17	#ifdef HAVE_CONFIG_H
18	#include "config.h"
19	#endif
20
21	#include "getopt.h"
22
23	#include "Dump2XYZCmd.h"
24
25	void
26	cmdline_parser_print_version (void)
27	{
28	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	}
30
31	void
32	cmdline_parser_print_help (void)
33	{
34	cmdline_parser_print_version ();
35	printf("\n"
36	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	printf("\n");
38	printf(" -h, --help Print help and exit\n");
39	printf(" -V, --version Print version and exit\n");
40	printf(" -i, --input=filename input dump file\n");
41	printf(" -o, --output=filename output file name\n");
42	printf(" -n, --frame=INT print every n frame (default=`1')\n");
43	printf(" -d, --dipole print the dipole moments (default=off)\n");
44	printf(" -w, --water skip the the waters (default=off)\n");
45	printf(" -m, --periodicBox map to the periodic box (default=off)\n");
46	printf(" -z, --zconstraint replace the atom types of zconstraint \n molecules (default=off)\n");
47	printf(" -r, --rigidbody add a pseudo COM atom to rigidbody \n (default=off)\n");
48	printf(" -t, --watertype replace the atom type of water model \n (default=on)\n");
49	printf(" -g, --ignore=atomtype ignore the atom types\n");
50	printf(" -s, --selection=selection script selection syntax:\n"
51	" select DMPC -- select DMPC molecule\n"
52	" select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n"
53	" select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n"
54	" select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n"
55	" select 5 -- select stuntdobule whose global index is 5\n"
56	" select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n"
57	" select DMPC.DMPC_RB_. --select atoms belong to rigid body inside DMPC molecule \n");
58	printf(" --repeatX=INT The number of images to repeat in the x \n direction (default=`0')\n");
59	printf(" --repeatY=INT The number of images to repeat in the y \n direction (default=`0')\n");
60	printf(" --repeatZ=INT The number of images to repeat in the z \n direction (default=`0')\n");
61	}
62
63
64	static char gengetopt_strdup (const char s);
65
66	/* gengetopt_strdup() */
67	/* strdup.c replacement of strdup, which is not standard */
68	char *
69	gengetopt_strdup (const char *s)
70	{
71	char result = (char)malloc(strlen(s) + 1);
72	if (result == (char*)0)
73	return (char*)0;
74	strcpy(result, s);
75	return result;
76	}
77
78	int
79	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
80	{
81	int c; /* Character of the parsed option. */
82	int i; /* Counter */
83	struct ignore_list
84	{
85	char * ignore_arg;
86	struct ignore_list * next;
87	};
88	struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
89
90	int missing_required_options = 0;
91
92	args_info->help_given = 0 ;
93	args_info->version_given = 0 ;
94	args_info->input_given = 0 ;
95	args_info->output_given = 0 ;
96	args_info->frame_given = 0 ;
97	args_info->dipole_given = 0 ;
98	args_info->water_given = 0 ;
99	args_info->periodicBox_given = 0 ;
100	args_info->zconstraint_given = 0 ;
101	args_info->rigidbody_given = 0 ;
102	args_info->watertype_given = 0 ;
103	args_info->ignore_given = 0 ;
104	args_info->selection_given = 0 ;
105	args_info->repeatX_given = 0 ;
106	args_info->repeatY_given = 0 ;
107	args_info->repeatZ_given = 0 ;
108	#define clear_args() { \
109	args_info->input_arg = NULL; \
110	args_info->output_arg = NULL; \
111	args_info->frame_arg = 1 ;\
112	args_info->dipole_flag = 0;\
113	args_info->water_flag = 0;\
114	args_info->periodicBox_flag = 0;\
115	args_info->zconstraint_flag = 0;\
116	args_info->rigidbody_flag = 0;\
117	args_info->watertype_flag = 1;\
118	args_info->ignore_arg = NULL; \
119	args_info->selection_arg = NULL; \
120	args_info->repeatX_arg = 0 ;\
121	args_info->repeatY_arg = 0 ;\
122	args_info->repeatZ_arg = 0 ;\
123	}
124
125	clear_args();
126
127	optarg = 0;
128	optind = 1;
129	opterr = 1;
130	optopt = '?';
131
132	while (1)
133	{
134	int option_index = 0;
135	char *stop_char;
136
137	static struct option long_options[] = {
138	{ "help", 0, NULL, 'h' },
139	{ "version", 0, NULL, 'V' },
140	{ "input", 1, NULL, 'i' },
141	{ "output", 1, NULL, 'o' },
142	{ "frame", 1, NULL, 'n' },
143	{ "dipole", 0, NULL, 'd' },
144	{ "water", 0, NULL, 'w' },
145	{ "periodicBox", 0, NULL, 'm' },
146	{ "zconstraint", 0, NULL, 'z' },
147	{ "rigidbody", 0, NULL, 'r' },
148	{ "watertype", 0, NULL, 't' },
149	{ "ignore", 1, NULL, 'g' },
150	{ "selection", 1, NULL, 's' },
151	{ "repeatX", 1, NULL, 0 },
152	{ "repeatY", 1, NULL, 0 },
153	{ "repeatZ", 1, NULL, 0 },
154	{ NULL, 0, NULL, 0 }
155	};
156
157	stop_char = 0;
158	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
159
160	if (c == -1) break; /* Exit from `while (1)' loop. */
161
162	switch (c)
163	{
164	case 'h': /* Print help and exit. */
165	clear_args ();
166	cmdline_parser_print_help ();
167	exit (EXIT_SUCCESS);
168
169	case 'V': /* Print version and exit. */
170	clear_args ();
171	cmdline_parser_print_version ();
172	exit (EXIT_SUCCESS);
173
174	case 'i': /* input dump file. */
175	if (args_info->input_given)
176	{
177	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
178	clear_args ();
179	exit (EXIT_FAILURE);
180	}
181	args_info->input_given = 1;
182	args_info->input_arg = gengetopt_strdup (optarg);
183	break;
184
185	case 'o': /* output file name. */
186	if (args_info->output_given)
187	{
188	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
189	clear_args ();
190	exit (EXIT_FAILURE);
191	}
192	args_info->output_given = 1;
193	args_info->output_arg = gengetopt_strdup (optarg);
194	break;
195
196	case 'n': /* print every n frame. */
197	if (args_info->frame_given)
198	{
199	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
200	clear_args ();
201	exit (EXIT_FAILURE);
202	}
203	args_info->frame_given = 1;
204	args_info->frame_arg = strtol (optarg,&stop_char,0);
205	break;
206
207	case 'd': /* print the dipole moments. */
208	if (args_info->dipole_given)
209	{
210	fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
211	clear_args ();
212	exit (EXIT_FAILURE);
213	}
214	args_info->dipole_given = 1;
215	args_info->dipole_flag = !(args_info->dipole_flag);
216	break;
217
218	case 'w': /* skip the the waters. */
219	if (args_info->water_given)
220	{
221	fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
222	clear_args ();
223	exit (EXIT_FAILURE);
224	}
225	args_info->water_given = 1;
226	args_info->water_flag = !(args_info->water_flag);
227	break;
228
229	case 'm': /* map to the periodic box. */
230	if (args_info->periodicBox_given)
231	{
232	fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
233	clear_args ();
234	exit (EXIT_FAILURE);
235	}
236	args_info->periodicBox_given = 1;
237	args_info->periodicBox_flag = !(args_info->periodicBox_flag);
238	break;
239
240	case 'z': /* replace the atom types of zconstraint molecules. */
241	if (args_info->zconstraint_given)
242	{
243	fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
244	clear_args ();
245	exit (EXIT_FAILURE);
246	}
247	args_info->zconstraint_given = 1;
248	args_info->zconstraint_flag = !(args_info->zconstraint_flag);
249	break;
250
251	case 'r': /* add a pseudo COM atom to rigidbody. */
252	if (args_info->rigidbody_given)
253	{
254	fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
255	clear_args ();
256	exit (EXIT_FAILURE);
257	}
258	args_info->rigidbody_given = 1;
259	args_info->rigidbody_flag = !(args_info->rigidbody_flag);
260	break;
261
262	case 't': /* replace the atom type of water model. */
263	if (args_info->watertype_given)
264	{
265	fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
266	clear_args ();
267	exit (EXIT_FAILURE);
268	}
269	args_info->watertype_given = 1;
270	args_info->watertype_flag = !(args_info->watertype_flag);
271	break;
272
273	case 'g': /* ignore the atom types. */
274	args_info->ignore_given++;
275	ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
276	ignore_new->next = ignore_list;
277	ignore_list = ignore_new;
278	ignore_new->ignore_arg = gengetopt_strdup (optarg);
279	break;
280
281	case 's': /* general selection syntax:\n
282	select DMPC -- select DMPC molecule\n \
283	select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
284	select 5 -- select stuntdobule whose global index is 5\n \
285	select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
286	select DMPC.DMPC_RB_. --select atoms belong to rigid body inside DMPC molecule . */
287	if (args_info->selection_given)
288	{
289	fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
290	clear_args ();
291	exit (EXIT_FAILURE);
292	}
293	args_info->selection_given = 1;
294	args_info->selection_arg = gengetopt_strdup (optarg);
295	break;
296
297
298	case 0: /* Long option with no short option */
299	/* The number of images to repeat in the x direction. */
300	if (strcmp (long_options[option_index].name, "repeatX") == 0)
301	{
302	if (args_info->repeatX_given)
303	{
304	fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
305	clear_args ();
306	exit (EXIT_FAILURE);
307	}
308	args_info->repeatX_given = 1;
309	args_info->repeatX_arg = strtol (optarg,&stop_char,0);
310	break;
311	}
312
313	/* The number of images to repeat in the y direction. */
314	else if (strcmp (long_options[option_index].name, "repeatY") == 0)
315	{
316	if (args_info->repeatY_given)
317	{
318	fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
319	clear_args ();
320	exit (EXIT_FAILURE);
321	}
322	args_info->repeatY_given = 1;
323	args_info->repeatY_arg = strtol (optarg,&stop_char,0);
324	break;
325	}
326
327	/* The number of images to repeat in the z direction. */
328	else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
329	{
330	if (args_info->repeatZ_given)
331	{
332	fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
333	clear_args ();
334	exit (EXIT_FAILURE);
335	}
336	args_info->repeatZ_given = 1;
337	args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
338	break;
339	}
340
341
342	case '?': /* Invalid option. */
343	/* `getopt_long' already printed an error message. */
344	exit (EXIT_FAILURE);
345
346	default: /* bug: option not considered. */
347	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
348	abort ();
349	} /* switch */
350	} /* while */
351
352
353	if (! args_info->input_given)
354	{
355	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
356	missing_required_options = 1;
357	}
358	if ( missing_required_options )
359	exit (EXIT_FAILURE);
360
361	if (args_info->ignore_given)
362	{
363	args_info->ignore_arg = (char * ) malloc (args_info->ignore_given sizeof (char *));
364	for (i = 0; i < args_info->ignore_given; i++)
365	{
366	args_info->ignore_arg [i] = ignore_list->ignore_arg;
367	ignore_list = ignore_list->next;
368	}
369	}
370
371	return 0;
372	}