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("      --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:	2053
Committed:	Fri Feb 18 23:07:32 2005 UTC (19 years, 4 months ago) by tim
Content type:	text/plain
File size:	15086 byte(s)
Log Message:	adding LipidTransVisitor, GofXyz is working now
#	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(" --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	}
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	args_info->selection_given = 0 ;
108	args_info->originsele_given = 0 ;
109	args_info->refsele_given = 0 ;
110	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	args_info->selection_arg = NULL; \
125	args_info->originsele_arg = NULL; \
126	args_info->refsele_arg = NULL; \
127	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	{ "ignore", 1, NULL, 'g' },
157	{ "selection", 1, NULL, 's' },
158	{ "originsele", 1, NULL, 0 },
159	{ "refsele", 1, NULL, 0 },
160	{ "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	c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
168
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	case 'g': /* ignore the atom types. */
283	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	case 's': /* general selection syntax(now only support select atoms within a specified range). */
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
301
302	case 0: /* Long option with no short option */
303	/* 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	/* The number of images to repeat in the x direction. */
332	else if (strcmp (long_options[option_index].name, "repeatX") == 0)
333	{
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	}