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root/OpenMD/trunk/src/applications/dump2Xyz/Dump2XYZCmd.c
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Comparing trunk/src/applications/dump2Xyz/Dump2XYZCmd.c (file contents):
Revision 302 by tim, Mon Feb 7 21:11:22 2005 UTC vs.
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC

# Line 35 | Line 35 | cmdline_parser_print_help (void)
35    printf("\n"
36    "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37    printf("\n");
38 <  printf("  -h, --help                        Print help and exit\n");
39 <  printf("  -V, --version                     Print version and exit\n");
40 <  printf("  -i, --input=filename              input dump file\n");
41 <  printf("  -o, --output=filename             output file name\n");
42 <  printf("  -n, --frame=INT                   print every n frame  (default=`1')\n");
43 <  printf("  -d, --dipole                      print the dipole moments  (default=off)\n");
44 <  printf("  -w, --water                       skip the the waters  (default=off)\n");
45 <  printf("  -m, --periodicBox                 map to the periodic box  (default=off)\n");
46 <  printf("  -z, --zconstraint                 replace the atom types of zconstraint \n                                      molecules  (default=off)\n");
47 <  printf("  -r, --rigidbody                   add a pseudo COM atom to rigidbody  \n                                      (default=off)\n");
48 <  printf("  -t, --watertype                   replace the atom type of water model  \n                                      (default=on)\n");
49 <  printf("  -g, --ignore=atomtype             ignore the atom types\n");
50 <  printf("  -s, --selection=selection script  selection syntax:\n"                                      
51 <         "                                    select DMPC -- select DMPC molecule\n"                    
52 <         "                                    select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n"          
53 <         "                                    select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n"
54 <         "                                    select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n"  
55 <         "                                    select 5 -- select stuntdobule whose global index is 5\n"                                      
56 <         "                                    select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n"
57 <         "                                    select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n");
58 <  printf("      --repeatX=INT                 The number of images to repeat in the x \n                                      direction  (default=`0')\n");
59 <  printf("      --repeatY=INT                 The number of images to repeat in the y \n                                      direction  (default=`0')\n");
60 <  printf("      --repeatZ=INT                 The number of images to repeat in the z \n                                      direction  (default=`0')\n");
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("  -w, --water                        skip the the waters  (default=off)\n");
44 >  printf("  -m, --periodicBox                  map to the periodic box  (default=off)\n");
45 >  printf("  -z, --zconstraint                  replace the atom types of zconstraint \n                                       molecules  (default=off)\n");
46 >  printf("  -r, --rigidbody                    add a pseudo COM atom to rigidbody  \n                                       (default=off)\n");
47 >  printf("  -t, --watertype                    replace the atom type of water model  \n                                       (default=on)\n");
48 >  printf("  -s, --selection=selection script   general selection syntax(now only support \n                                       select atoms within a specified range)\n");
49 >  printf("      --originsele=selection script  select origin\n");
50 >  printf("      --refsele=selection script     select reference\n");
51 >  printf("      --repeatX=INT                  The number of images to repeat in the x \n                                       direction  (default=`0')\n");
52 >  printf("      --repeatY=INT                  The number of images to repeat in the y \n                                       direction  (default=`0')\n");
53 >  printf("      --repeatZ=INT                  The number of images to repeat in the z \n                                       direction  (default=`0')\n");
54   }
55  
56  
# Line 79 | Line 72 | cmdline_parser (int argc, char * const *argv, struct g
72   cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
73   {
74    int c;        /* Character of the parsed option.  */
82 –  int i;        /* Counter */
83 –  struct ignore_list
84 –  {
85 –    char * ignore_arg;
86 –    struct ignore_list * next;
87 –  };
88 –  struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
89 –  
75    int missing_required_options = 0;
76  
77    args_info->help_given = 0 ;
# Line 94 | Line 79 | cmdline_parser (int argc, char * const *argv, struct g
79    args_info->input_given = 0 ;
80    args_info->output_given = 0 ;
81    args_info->frame_given = 0 ;
97 –  args_info->dipole_given = 0 ;
82    args_info->water_given = 0 ;
83    args_info->periodicBox_given = 0 ;
84    args_info->zconstraint_given = 0 ;
85    args_info->rigidbody_given = 0 ;
86    args_info->watertype_given = 0 ;
103 –  args_info->ignore_given = 0 ;
87    args_info->selection_given = 0 ;
88 +  args_info->originsele_given = 0 ;
89 +  args_info->refsele_given = 0 ;
90    args_info->repeatX_given = 0 ;
91    args_info->repeatY_given = 0 ;
92    args_info->repeatZ_given = 0 ;
# Line 109 | Line 94 | cmdline_parser (int argc, char * const *argv, struct g
94    args_info->input_arg = NULL; \
95    args_info->output_arg = NULL; \
96    args_info->frame_arg = 1 ;\
112 –  args_info->dipole_flag = 0;\
97    args_info->water_flag = 0;\
98    args_info->periodicBox_flag = 0;\
99    args_info->zconstraint_flag = 0;\
100    args_info->rigidbody_flag = 0;\
101    args_info->watertype_flag = 1;\
118 –  args_info->ignore_arg = NULL; \
102    args_info->selection_arg = NULL; \
103 +  args_info->originsele_arg = NULL; \
104 +  args_info->refsele_arg = NULL; \
105    args_info->repeatX_arg = 0 ;\
106    args_info->repeatY_arg = 0 ;\
107    args_info->repeatZ_arg = 0 ;\
# Line 140 | Line 125 | cmdline_parser (int argc, char * const *argv, struct g
125          { "input",      1, NULL, 'i' },
126          { "output",     1, NULL, 'o' },
127          { "frame",      1, NULL, 'n' },
143 –        { "dipole",     0, NULL, 'd' },
128          { "water",      0, NULL, 'w' },
129          { "periodicBox",        0, NULL, 'm' },
130          { "zconstraint",        0, NULL, 'z' },
131          { "rigidbody",  0, NULL, 'r' },
132          { "watertype",  0, NULL, 't' },
149 –        { "ignore",     1, NULL, 'g' },
133          { "selection",  1, NULL, 's' },
134 +        { "originsele", 1, NULL, 0 },
135 +        { "refsele",    1, NULL, 0 },
136          { "repeatX",    1, NULL, 0 },
137          { "repeatY",    1, NULL, 0 },
138          { "repeatZ",    1, NULL, 0 },
# Line 155 | Line 140 | cmdline_parser (int argc, char * const *argv, struct g
140        };
141  
142        stop_char = 0;
143 <      c = getopt_long (argc, argv, "hVi:o:n:dwmzrtg:s:", long_options, &option_index);
143 >      c = getopt_long (argc, argv, "hVi:o:n:wmzrts:", long_options, &option_index);
144  
145        if (c == -1) break;       /* Exit from `while (1)' loop.  */
146  
# Line 204 | Line 189 | cmdline_parser (int argc, char * const *argv, struct g
189            args_info->frame_arg = strtol (optarg,&stop_char,0);
190            break;
191  
207 –        case 'd':       /* print the dipole moments.  */
208 –          if (args_info->dipole_given)
209 –            {
210 –              fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
211 –              clear_args ();
212 –              exit (EXIT_FAILURE);
213 –            }
214 –          args_info->dipole_given = 1;
215 –          args_info->dipole_flag = !(args_info->dipole_flag);
216 –          break;
217 –
192          case 'w':       /* skip the the waters.  */
193            if (args_info->water_given)
194              {
# Line 270 | Line 244 | cmdline_parser (int argc, char * const *argv, struct g
244            args_info->watertype_flag = !(args_info->watertype_flag);
245            break;
246  
247 <        case 'g':       /* ignore the atom types.  */
274 <          args_info->ignore_given++;
275 <          ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
276 <          ignore_new->next = ignore_list;
277 <          ignore_list = ignore_new;
278 <          ignore_new->ignore_arg = gengetopt_strdup (optarg);
279 <          break;
280 <
281 <        case 's':       /* general selection syntax:\n
282 < select DMPC -- select DMPC molecule\n \
283 < select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \
284 < select 5 -- select stuntdobule whose global index is 5\n \
285 < select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \
286 < select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule .  */
247 >        case 's':       /* general selection syntax(now only support select atoms within a specified range).  */
248            if (args_info->selection_given)
249              {
250                fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
# Line 296 | Line 257 | select DMPC.DMPC_RB_*.* --select atoms belong to rigid
257  
258  
259          case 0: /* Long option with no short option */
260 +          /* select origin.  */
261 +          if (strcmp (long_options[option_index].name, "originsele") == 0)
262 +          {
263 +            if (args_info->originsele_given)
264 +              {
265 +                fprintf (stderr, "%s: `--originsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
266 +                clear_args ();
267 +                exit (EXIT_FAILURE);
268 +              }
269 +            args_info->originsele_given = 1;
270 +            args_info->originsele_arg = gengetopt_strdup (optarg);
271 +            break;
272 +          }
273 +          
274 +          /* select reference.  */
275 +          else if (strcmp (long_options[option_index].name, "refsele") == 0)
276 +          {
277 +            if (args_info->refsele_given)
278 +              {
279 +                fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
280 +                clear_args ();
281 +                exit (EXIT_FAILURE);
282 +              }
283 +            args_info->refsele_given = 1;
284 +            args_info->refsele_arg = gengetopt_strdup (optarg);
285 +            break;
286 +          }
287 +          
288            /* The number of images to repeat in the x direction.  */
289 <          if (strcmp (long_options[option_index].name, "repeatX") == 0)
289 >          else if (strcmp (long_options[option_index].name, "repeatX") == 0)
290            {
291              if (args_info->repeatX_given)
292                {
# Line 358 | Line 347 | select DMPC.DMPC_RB_*.* --select atoms belong to rigid
347    if ( missing_required_options )
348      exit (EXIT_FAILURE);
349  
361 –  if (args_info->ignore_given)
362 –    {
363 –      args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
364 –      for (i = 0; i < args_info->ignore_given; i++)
365 –        {
366 –          args_info->ignore_arg [i] = ignore_list->ignore_arg;
367 –          ignore_list = ignore_list->next;
368 –        }
369 –    }
370 –  
350    return 0;
351   }

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