applications/dump2Xyz/Dump2XYZCmd.cpp

/*
  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:	304
Committed:	Mon Feb 7 22:38:35 2005 UTC (20 years, 3 months ago) by tim
Content type:	text/plain
Original Path:	*trunk/src/applications/dump2Xyz/Dump2XYZCmd.c*
File size:	14062 byte(s)
Log Message:	update help info
#	User	Rev	Content
1	tim	12	/*
2			File autogenerated by gengetopt version 2.11
3			generated with the following command:
4	tim	302	/home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd
5	tim	12
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	tim	291	#include "Dump2XYZCmd.h"
24	tim	12
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	tim	291	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	tim	302	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	tim	304	" 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	tim	302	" select DMPC.DMPC_RB_. --select atoms belong to rigid body inside DMPC molecule \n");
59	tim	291	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	tim	12	}
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	tim	291	args_info->selection_given = 0 ;
106	tim	12	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	tim	291	args_info->selection_arg = NULL; \
121	tim	12	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	tim	291	{ "ignore", 1, NULL, 'g' },
151			{ "selection", 1, NULL, 's' },
152	tim	12	{ "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	tim	291	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
160	tim	12
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	tim	291	case 'g': /* ignore the atom types. */
275	tim	12	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	tim	302	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	tim	291	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	tim	12
298	tim	291
299	tim	12	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			}