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("      --originsele=selection script  select origin\n");
  printf("      --refsele=selection script     select reference\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->originsele_given = 0 ;
  args_info->refsele_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->originsele_arg = NULL; \
  args_info->refsele_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' },
        { "originsele", 1, NULL, 0 },
        { "refsele",    1, NULL, 0 },
        { "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(now only support select atoms within a specified range).  */
          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 */
          /* select origin.  */
          if (strcmp (long_options[option_index].name, "originsele") == 0)
          {
            if (args_info->originsele_given)
              {
                fprintf (stderr, "%s: `--originsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
                clear_args ();
                exit (EXIT_FAILURE);
              }
            args_info->originsele_given = 1;
            args_info->originsele_arg = gengetopt_strdup (optarg);
            break;
          }
          
          /* select reference.  */
          else if (strcmp (long_options[option_index].name, "refsele") == 0)
          {
            if (args_info->refsele_given)
              {
                fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
                clear_args ();
                exit (EXIT_FAILURE);
              }
            args_info->refsele_given = 1;
            args_info->refsele_arg = gengetopt_strdup (optarg);
            break;
          }
          
          /* The number of images to repeat in the x direction.  */
          else 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:	369
Committed:	Fri Feb 18 23:07:32 2005 UTC (20 years, 3 months ago) by tim
Content type:	text/plain
Original Path:	*trunk/src/applications/dump2Xyz/Dump2XYZCmd.c*
File size:	15086 byte(s)
Log Message:	adding LipidTransVisitor, GofXyz is working now
#	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	369	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	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	369	printf(" --originsele=selection script select origin\n");
60			printf(" --refsele=selection script select reference\n");
61			printf(" --repeatX=INT The number of images to repeat in the x \n direction (default=`0')\n");
62			printf(" --repeatY=INT The number of images to repeat in the y \n direction (default=`0')\n");
63			printf(" --repeatZ=INT The number of images to repeat in the z \n direction (default=`0')\n");
64	tim	12	}
65
66
67			static char gengetopt_strdup (const char s);
68
69			/* gengetopt_strdup() */
70			/* strdup.c replacement of strdup, which is not standard */
71			char *
72			gengetopt_strdup (const char *s)
73			{
74			char result = (char)malloc(strlen(s) + 1);
75			if (result == (char*)0)
76			return (char*)0;
77			strcpy(result, s);
78			return result;
79			}
80
81			int
82			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
83			{
84			int c; /* Character of the parsed option. */
85			int i; /* Counter */
86			struct ignore_list
87			{
88			char * ignore_arg;
89			struct ignore_list * next;
90			};
91			struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
92
93			int missing_required_options = 0;
94
95			args_info->help_given = 0 ;
96			args_info->version_given = 0 ;
97			args_info->input_given = 0 ;
98			args_info->output_given = 0 ;
99			args_info->frame_given = 0 ;
100			args_info->dipole_given = 0 ;
101			args_info->water_given = 0 ;
102			args_info->periodicBox_given = 0 ;
103			args_info->zconstraint_given = 0 ;
104			args_info->rigidbody_given = 0 ;
105			args_info->watertype_given = 0 ;
106			args_info->ignore_given = 0 ;
107	tim	291	args_info->selection_given = 0 ;
108	tim	369	args_info->originsele_given = 0 ;
109			args_info->refsele_given = 0 ;
110	tim	12	args_info->repeatX_given = 0 ;
111			args_info->repeatY_given = 0 ;
112			args_info->repeatZ_given = 0 ;
113			#define clear_args() { \
114			args_info->input_arg = NULL; \
115			args_info->output_arg = NULL; \
116			args_info->frame_arg = 1 ;\
117			args_info->dipole_flag = 0;\
118			args_info->water_flag = 0;\
119			args_info->periodicBox_flag = 0;\
120			args_info->zconstraint_flag = 0;\
121			args_info->rigidbody_flag = 0;\
122			args_info->watertype_flag = 1;\
123			args_info->ignore_arg = NULL; \
124	tim	291	args_info->selection_arg = NULL; \
125	tim	369	args_info->originsele_arg = NULL; \
126			args_info->refsele_arg = NULL; \
127	tim	12	args_info->repeatX_arg = 0 ;\
128			args_info->repeatY_arg = 0 ;\
129			args_info->repeatZ_arg = 0 ;\
130			}
131
132			clear_args();
133
134			optarg = 0;
135			optind = 1;
136			opterr = 1;
137			optopt = '?';
138
139			while (1)
140			{
141			int option_index = 0;
142			char *stop_char;
143
144			static struct option long_options[] = {
145			{ "help", 0, NULL, 'h' },
146			{ "version", 0, NULL, 'V' },
147			{ "input", 1, NULL, 'i' },
148			{ "output", 1, NULL, 'o' },
149			{ "frame", 1, NULL, 'n' },
150			{ "dipole", 0, NULL, 'd' },
151			{ "water", 0, NULL, 'w' },
152			{ "periodicBox", 0, NULL, 'm' },
153			{ "zconstraint", 0, NULL, 'z' },
154			{ "rigidbody", 0, NULL, 'r' },
155			{ "watertype", 0, NULL, 't' },
156	tim	291	{ "ignore", 1, NULL, 'g' },
157			{ "selection", 1, NULL, 's' },
158	tim	369	{ "originsele", 1, NULL, 0 },
159			{ "refsele", 1, NULL, 0 },
160	tim	12	{ "repeatX", 1, NULL, 0 },
161			{ "repeatY", 1, NULL, 0 },
162			{ "repeatZ", 1, NULL, 0 },
163			{ NULL, 0, NULL, 0 }
164			};
165
166			stop_char = 0;
167	tim	291	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
168	tim	12
169			if (c == -1) break; /* Exit from `while (1)' loop. */
170
171			switch (c)
172			{
173			case 'h': /* Print help and exit. */
174			clear_args ();
175			cmdline_parser_print_help ();
176			exit (EXIT_SUCCESS);
177
178			case 'V': /* Print version and exit. */
179			clear_args ();
180			cmdline_parser_print_version ();
181			exit (EXIT_SUCCESS);
182
183			case 'i': /* input dump file. */
184			if (args_info->input_given)
185			{
186			fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
187			clear_args ();
188			exit (EXIT_FAILURE);
189			}
190			args_info->input_given = 1;
191			args_info->input_arg = gengetopt_strdup (optarg);
192			break;
193
194			case 'o': /* output file name. */
195			if (args_info->output_given)
196			{
197			fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
198			clear_args ();
199			exit (EXIT_FAILURE);
200			}
201			args_info->output_given = 1;
202			args_info->output_arg = gengetopt_strdup (optarg);
203			break;
204
205			case 'n': /* print every n frame. */
206			if (args_info->frame_given)
207			{
208			fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
209			clear_args ();
210			exit (EXIT_FAILURE);
211			}
212			args_info->frame_given = 1;
213			args_info->frame_arg = strtol (optarg,&stop_char,0);
214			break;
215
216			case 'd': /* print the dipole moments. */
217			if (args_info->dipole_given)
218			{
219			fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
220			clear_args ();
221			exit (EXIT_FAILURE);
222			}
223			args_info->dipole_given = 1;
224			args_info->dipole_flag = !(args_info->dipole_flag);
225			break;
226
227			case 'w': /* skip the the waters. */
228			if (args_info->water_given)
229			{
230			fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
231			clear_args ();
232			exit (EXIT_FAILURE);
233			}
234			args_info->water_given = 1;
235			args_info->water_flag = !(args_info->water_flag);
236			break;
237
238			case 'm': /* map to the periodic box. */
239			if (args_info->periodicBox_given)
240			{
241			fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
242			clear_args ();
243			exit (EXIT_FAILURE);
244			}
245			args_info->periodicBox_given = 1;
246			args_info->periodicBox_flag = !(args_info->periodicBox_flag);
247			break;
248
249			case 'z': /* replace the atom types of zconstraint molecules. */
250			if (args_info->zconstraint_given)
251			{
252			fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
253			clear_args ();
254			exit (EXIT_FAILURE);
255			}
256			args_info->zconstraint_given = 1;
257			args_info->zconstraint_flag = !(args_info->zconstraint_flag);
258			break;
259
260			case 'r': /* add a pseudo COM atom to rigidbody. */
261			if (args_info->rigidbody_given)
262			{
263			fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
264			clear_args ();
265			exit (EXIT_FAILURE);
266			}
267			args_info->rigidbody_given = 1;
268			args_info->rigidbody_flag = !(args_info->rigidbody_flag);
269			break;
270
271			case 't': /* replace the atom type of water model. */
272			if (args_info->watertype_given)
273			{
274			fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
275			clear_args ();
276			exit (EXIT_FAILURE);
277			}
278			args_info->watertype_given = 1;
279			args_info->watertype_flag = !(args_info->watertype_flag);
280			break;
281
282	tim	291	case 'g': /* ignore the atom types. */
283	tim	12	args_info->ignore_given++;
284			ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
285			ignore_new->next = ignore_list;
286			ignore_list = ignore_new;
287			ignore_new->ignore_arg = gengetopt_strdup (optarg);
288			break;
289
290	tim	369	case 's': /* general selection syntax(now only support select atoms within a specified range). */
291	tim	291	if (args_info->selection_given)
292			{
293			fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
294			clear_args ();
295			exit (EXIT_FAILURE);
296			}
297			args_info->selection_given = 1;
298			args_info->selection_arg = gengetopt_strdup (optarg);
299			break;
300	tim	12
301	tim	291
302	tim	12	case 0: /* Long option with no short option */
303	tim	369	/* select origin. */
304			if (strcmp (long_options[option_index].name, "originsele") == 0)
305			{
306			if (args_info->originsele_given)
307			{
308			fprintf (stderr, "%s: `--originsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
309			clear_args ();
310			exit (EXIT_FAILURE);
311			}
312			args_info->originsele_given = 1;
313			args_info->originsele_arg = gengetopt_strdup (optarg);
314			break;
315			}
316
317			/* select reference. */
318			else if (strcmp (long_options[option_index].name, "refsele") == 0)
319			{
320			if (args_info->refsele_given)
321			{
322			fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
323			clear_args ();
324			exit (EXIT_FAILURE);
325			}
326			args_info->refsele_given = 1;
327			args_info->refsele_arg = gengetopt_strdup (optarg);
328			break;
329			}
330
331	tim	12	/* The number of images to repeat in the x direction. */
332	tim	369	else if (strcmp (long_options[option_index].name, "repeatX") == 0)
333	tim	12	{
334			if (args_info->repeatX_given)
335			{
336			fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
337			clear_args ();
338			exit (EXIT_FAILURE);
339			}
340			args_info->repeatX_given = 1;
341			args_info->repeatX_arg = strtol (optarg,&stop_char,0);
342			break;
343			}
344
345			/* The number of images to repeat in the y direction. */
346			else if (strcmp (long_options[option_index].name, "repeatY") == 0)
347			{
348			if (args_info->repeatY_given)
349			{
350			fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
351			clear_args ();
352			exit (EXIT_FAILURE);
353			}
354			args_info->repeatY_given = 1;
355			args_info->repeatY_arg = strtol (optarg,&stop_char,0);
356			break;
357			}
358
359			/* The number of images to repeat in the z direction. */
360			else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
361			{
362			if (args_info->repeatZ_given)
363			{
364			fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
365			clear_args ();
366			exit (EXIT_FAILURE);
367			}
368			args_info->repeatZ_given = 1;
369			args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
370			break;
371			}
372
373
374			case '?': /* Invalid option. */
375			/* `getopt_long' already printed an error message. */
376			exit (EXIT_FAILURE);
377
378			default: /* bug: option not considered. */
379			fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
380			abort ();
381			} /* switch */
382			} /* while */
383
384
385			if (! args_info->input_given)
386			{
387			fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
388			missing_required_options = 1;
389			}
390			if ( missing_required_options )
391			exit (EXIT_FAILURE);
392
393			if (args_info->ignore_given)
394			{
395			args_info->ignore_arg = (char * ) malloc (args_info->ignore_given sizeof (char *));
396			for (i = 0; i < args_info->ignore_given; i++)
397			{
398			args_info->ignore_arg [i] = ignore_list->ignore_arg;
399			ignore_list = ignore_list->next;
400			}
401			}
402
403			return 0;
404			}