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.3 -- select stuntdouble which internal index is 3\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:	1988
Committed:	Mon Feb 7 22:38:35 2005 UTC (19 years, 5 months ago) by tim
Content type:	text/plain
File size:	14062 byte(s)
Log Message:	update help info
#	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.3 -- select stuntdouble which internal index is 3\n"
58	" select DMPC.DMPC_RB_. --select atoms belong to rigid body inside DMPC molecule \n");
59	printf(" --repeatX=INT The number of images to repeat in the x \n direction (default=`0')\n");
60	printf(" --repeatY=INT The number of images to repeat in the y \n direction (default=`0')\n");
61	printf(" --repeatZ=INT The number of images to repeat in the z \n direction (default=`0')\n");
62	}
63
64
65	static char gengetopt_strdup (const char s);
66
67	/* gengetopt_strdup() */
68	/* strdup.c replacement of strdup, which is not standard */
69	char *
70	gengetopt_strdup (const char *s)
71	{
72	char result = (char)malloc(strlen(s) + 1);
73	if (result == (char*)0)
74	return (char*)0;
75	strcpy(result, s);
76	return result;
77	}
78
79	int
80	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
81	{
82	int c; /* Character of the parsed option. */
83	int i; /* Counter */
84	struct ignore_list
85	{
86	char * ignore_arg;
87	struct ignore_list * next;
88	};
89	struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
90
91	int missing_required_options = 0;
92
93	args_info->help_given = 0 ;
94	args_info->version_given = 0 ;
95	args_info->input_given = 0 ;
96	args_info->output_given = 0 ;
97	args_info->frame_given = 0 ;
98	args_info->dipole_given = 0 ;
99	args_info->water_given = 0 ;
100	args_info->periodicBox_given = 0 ;
101	args_info->zconstraint_given = 0 ;
102	args_info->rigidbody_given = 0 ;
103	args_info->watertype_given = 0 ;
104	args_info->ignore_given = 0 ;
105	args_info->selection_given = 0 ;
106	args_info->repeatX_given = 0 ;
107	args_info->repeatY_given = 0 ;
108	args_info->repeatZ_given = 0 ;
109	#define clear_args() { \
110	args_info->input_arg = NULL; \
111	args_info->output_arg = NULL; \
112	args_info->frame_arg = 1 ;\
113	args_info->dipole_flag = 0;\
114	args_info->water_flag = 0;\
115	args_info->periodicBox_flag = 0;\
116	args_info->zconstraint_flag = 0;\
117	args_info->rigidbody_flag = 0;\
118	args_info->watertype_flag = 1;\
119	args_info->ignore_arg = NULL; \
120	args_info->selection_arg = NULL; \
121	args_info->repeatX_arg = 0 ;\
122	args_info->repeatY_arg = 0 ;\
123	args_info->repeatZ_arg = 0 ;\
124	}
125
126	clear_args();
127
128	optarg = 0;
129	optind = 1;
130	opterr = 1;
131	optopt = '?';
132
133	while (1)
134	{
135	int option_index = 0;
136	char *stop_char;
137
138	static struct option long_options[] = {
139	{ "help", 0, NULL, 'h' },
140	{ "version", 0, NULL, 'V' },
141	{ "input", 1, NULL, 'i' },
142	{ "output", 1, NULL, 'o' },
143	{ "frame", 1, NULL, 'n' },
144	{ "dipole", 0, NULL, 'd' },
145	{ "water", 0, NULL, 'w' },
146	{ "periodicBox", 0, NULL, 'm' },
147	{ "zconstraint", 0, NULL, 'z' },
148	{ "rigidbody", 0, NULL, 'r' },
149	{ "watertype", 0, NULL, 't' },
150	{ "ignore", 1, NULL, 'g' },
151	{ "selection", 1, NULL, 's' },
152	{ "repeatX", 1, NULL, 0 },
153	{ "repeatY", 1, NULL, 0 },
154	{ "repeatZ", 1, NULL, 0 },
155	{ NULL, 0, NULL, 0 }
156	};
157
158	stop_char = 0;
159	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
160
161	if (c == -1) break; /* Exit from `while (1)' loop. */
162
163	switch (c)
164	{
165	case 'h': /* Print help and exit. */
166	clear_args ();
167	cmdline_parser_print_help ();
168	exit (EXIT_SUCCESS);
169
170	case 'V': /* Print version and exit. */
171	clear_args ();
172	cmdline_parser_print_version ();
173	exit (EXIT_SUCCESS);
174
175	case 'i': /* input dump file. */
176	if (args_info->input_given)
177	{
178	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
179	clear_args ();
180	exit (EXIT_FAILURE);
181	}
182	args_info->input_given = 1;
183	args_info->input_arg = gengetopt_strdup (optarg);
184	break;
185
186	case 'o': /* output file name. */
187	if (args_info->output_given)
188	{
189	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
190	clear_args ();
191	exit (EXIT_FAILURE);
192	}
193	args_info->output_given = 1;
194	args_info->output_arg = gengetopt_strdup (optarg);
195	break;
196
197	case 'n': /* print every n frame. */
198	if (args_info->frame_given)
199	{
200	fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
201	clear_args ();
202	exit (EXIT_FAILURE);
203	}
204	args_info->frame_given = 1;
205	args_info->frame_arg = strtol (optarg,&stop_char,0);
206	break;
207
208	case 'd': /* print the dipole moments. */
209	if (args_info->dipole_given)
210	{
211	fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
212	clear_args ();
213	exit (EXIT_FAILURE);
214	}
215	args_info->dipole_given = 1;
216	args_info->dipole_flag = !(args_info->dipole_flag);
217	break;
218
219	case 'w': /* skip the the waters. */
220	if (args_info->water_given)
221	{
222	fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
223	clear_args ();
224	exit (EXIT_FAILURE);
225	}
226	args_info->water_given = 1;
227	args_info->water_flag = !(args_info->water_flag);
228	break;
229
230	case 'm': /* map to the periodic box. */
231	if (args_info->periodicBox_given)
232	{
233	fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
234	clear_args ();
235	exit (EXIT_FAILURE);
236	}
237	args_info->periodicBox_given = 1;
238	args_info->periodicBox_flag = !(args_info->periodicBox_flag);
239	break;
240
241	case 'z': /* replace the atom types of zconstraint molecules. */
242	if (args_info->zconstraint_given)
243	{
244	fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
245	clear_args ();
246	exit (EXIT_FAILURE);
247	}
248	args_info->zconstraint_given = 1;
249	args_info->zconstraint_flag = !(args_info->zconstraint_flag);
250	break;
251
252	case 'r': /* add a pseudo COM atom to rigidbody. */
253	if (args_info->rigidbody_given)
254	{
255	fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
256	clear_args ();
257	exit (EXIT_FAILURE);
258	}
259	args_info->rigidbody_given = 1;
260	args_info->rigidbody_flag = !(args_info->rigidbody_flag);
261	break;
262
263	case 't': /* replace the atom type of water model. */
264	if (args_info->watertype_given)
265	{
266	fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
267	clear_args ();
268	exit (EXIT_FAILURE);
269	}
270	args_info->watertype_given = 1;
271	args_info->watertype_flag = !(args_info->watertype_flag);
272	break;
273
274	case 'g': /* ignore the atom types. */
275	args_info->ignore_given++;
276	ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
277	ignore_new->next = ignore_list;
278	ignore_list = ignore_new;
279	ignore_new->ignore_arg = gengetopt_strdup (optarg);
280	break;
281
282	case 's': /* general selection syntax:\n
283	select DMPC -- select DMPC molecule\n \
284	select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
285	select 5 -- select stuntdobule whose global index is 5\n \
286	select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
287	select DMPC.DMPC_RB_. --select atoms belong to rigid body inside DMPC molecule . */
288	if (args_info->selection_given)
289	{
290	fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
291	clear_args ();
292	exit (EXIT_FAILURE);
293	}
294	args_info->selection_given = 1;
295	args_info->selection_arg = gengetopt_strdup (optarg);
296	break;
297
298
299	case 0: /* Long option with no short option */
300	/* The number of images to repeat in the x direction. */
301	if (strcmp (long_options[option_index].name, "repeatX") == 0)
302	{
303	if (args_info->repeatX_given)
304	{
305	fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
306	clear_args ();
307	exit (EXIT_FAILURE);
308	}
309	args_info->repeatX_given = 1;
310	args_info->repeatX_arg = strtol (optarg,&stop_char,0);
311	break;
312	}
313
314	/* The number of images to repeat in the y direction. */
315	else if (strcmp (long_options[option_index].name, "repeatY") == 0)
316	{
317	if (args_info->repeatY_given)
318	{
319	fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
320	clear_args ();
321	exit (EXIT_FAILURE);
322	}
323	args_info->repeatY_given = 1;
324	args_info->repeatY_arg = strtol (optarg,&stop_char,0);
325	break;
326	}
327
328	/* The number of images to repeat in the z direction. */
329	else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
330	{
331	if (args_info->repeatZ_given)
332	{
333	fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
334	clear_args ();
335	exit (EXIT_FAILURE);
336	}
337	args_info->repeatZ_given = 1;
338	args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
339	break;
340	}
341
342
343	case '?': /* Invalid option. */
344	/* `getopt_long' already printed an error message. */
345	exit (EXIT_FAILURE);
346
347	default: /* bug: option not considered. */
348	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
349	abort ();
350	} /* switch */
351	} /* while */
352
353
354	if (! args_info->input_given)
355	{
356	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
357	missing_required_options = 1;
358	}
359	if ( missing_required_options )
360	exit (EXIT_FAILURE);
361
362	if (args_info->ignore_given)
363	{
364	args_info->ignore_arg = (char * ) malloc (args_info->ignore_given sizeof (char *));
365	for (i = 0; i < args_info->ignore_given; i++)
366	{
367	args_info->ignore_arg [i] = ignore_list->ignore_arg;
368	ignore_list = ignore_list->next;
369	}
370	}
371
372	return 0;
373	}