ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZCmd.c
(Generate patch)

Comparing trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZCmd.c (file contents):
Revision 1988 by tim, Mon Feb 7 22:38:35 2005 UTC vs.
Revision 2053 by tim, Fri Feb 18 23:07:32 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"                                      
38 >  printf("  -h, --help                         Print help and exit\n");
39 >  printf("  -V, --version                      Print version and exit\n");
40 >  printf("  -i, --input=filename               input dump file\n");
41 >  printf("  -o, --output=filename              output file name\n");
42 >  printf("  -n, --frame=INT                    print every n frame  (default=`1')\n");
43 >  printf("  -d, --dipole                       print the dipole moments  (default=off)\n");
44 >  printf("  -w, --water                        skip the the waters  (default=off)\n");
45 >  printf("  -m, --periodicBox                  map to the periodic box  (default=off)\n");
46 >  printf("  -z, --zconstraint                  replace the atom types of zconstraint \n                                       molecules  (default=off)\n");
47 >  printf("  -r, --rigidbody                    add a pseudo COM atom to rigidbody  \n                                       (default=off)\n");
48 >  printf("  -t, --watertype                    replace the atom type of water model  \n                                       (default=on)\n");
49 >  printf("  -g, --ignore=atomtype              ignore the atom types\n");
50 >  printf("  -s, --selection=selection script  selection syntax:\n"
51 >         "                                    select DMPC -- select DMPC molecule\n"
52 >         "                                    select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule(same as above)\n"
53 >         "                                    select not DMPC -- select all atoms and all rigidbodies do not belong to DMPC molecule\n"
54 >         "                                    select C* and 4 to 7 -- select stuntdoubles which match C* and which index is between [4, 7)\n"
55 >         "                                    select 5 -- select stuntdobule whose global index is 5\n"
56           "                                    select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n"
57           "                                    select DMPC.3 -- select stuntdouble which internal index is 3\n"
58           "                                    select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule \n");
59 <  printf("      --repeatX=INT                 The number of images to repeat in the x \n                                      direction  (default=`0')\n");
60 <  printf("      --repeatY=INT                 The number of images to repeat in the y \n                                      direction  (default=`0')\n");
61 <  printf("      --repeatZ=INT                 The number of images to repeat in the z \n                                      direction  (default=`0')\n");
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  
# Line 103 | Line 105 | cmdline_parser (int argc, char * const *argv, struct g
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 ;
# Line 118 | Line 122 | cmdline_parser (int argc, char * const *argv, struct g
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 ;\
# Line 149 | Line 155 | cmdline_parser (int argc, char * const *argv, struct g
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 },
# Line 279 | Line 287 | cmdline_parser (int argc, char * const *argv, struct g
287            ignore_new->ignore_arg = gengetopt_strdup (optarg);
288            break;
289  
290 <        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 .  */
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);
# Line 297 | Line 300 | select DMPC.DMPC_RB_*.* --select atoms belong to rigid
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 <          if (strcmp (long_options[option_index].name, "repeatX") == 0)
332 >          else if (strcmp (long_options[option_index].name, "repeatX") == 0)
333            {
334              if (args_info->repeatX_given)
335                {

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines