| 27 |
|
char * input_arg; /* input dump file. */ |
| 28 |
|
char * output_arg; /* output file name. */ |
| 29 |
|
int frame_arg; /* print every n frame (default='1'). */ |
| 30 |
– |
int dipole_flag; /* print the dipole moments (default=off). */ |
| 30 |
|
int water_flag; /* skip the the waters (default=off). */ |
| 31 |
|
int periodicBox_flag; /* map to the periodic box (default=off). */ |
| 32 |
|
int zconstraint_flag; /* replace the atom types of zconstraint molecules (default=off). */ |
| 33 |
|
int rigidbody_flag; /* add a pseudo COM atom to rigidbody (default=off). */ |
| 34 |
|
int watertype_flag; /* replace the atom type of water model (default=on). */ |
| 35 |
< |
char ** ignore_arg; /* ignore the atom types. */ |
| 36 |
< |
char * selection_arg; /* general selection syntax:\n |
| 37 |
< |
select DMPC -- select DMPC molecule\n \ |
| 39 |
< |
select DMPC.* -- select all atoms and all rigidbodies belong to DMPC molecule\n \ |
| 40 |
< |
select 5 -- select stuntdobule whose global index is 5\n \ |
| 41 |
< |
select within (5.0, HDP or PO4) -- select stuntdoubles which is within 5 A to HDP or PO4\n \ |
| 42 |
< |
select DMPC.DMPC_RB_*.* --select atoms belong to rigid body inside DMPC molecule . */ |
| 35 |
> |
char * selection_arg; /* general selection syntax. */ |
| 36 |
> |
char * originsele_arg; /* select origin. */ |
| 37 |
> |
char * refsele_arg; /* select reference. */ |
| 38 |
|
int repeatX_arg; /* The number of images to repeat in the x direction (default='0'). */ |
| 39 |
|
int repeatY_arg; /* The number of images to repeat in the y direction (default='0'). */ |
| 40 |
|
int repeatZ_arg; /* The number of images to repeat in the z direction (default='0'). */ |
| 41 |
+ |
char * gb_arg; /* Replace the Gay-Berne atom with four linear atoms. */ |
| 42 |
+ |
int basetype_flag; /* Convert to base atom type (default=off). */ |
| 43 |
|
|
| 44 |
|
int help_given ; /* Whether help was given. */ |
| 45 |
|
int version_given ; /* Whether version was given. */ |
| 46 |
|
int input_given ; /* Whether input was given. */ |
| 47 |
|
int output_given ; /* Whether output was given. */ |
| 48 |
|
int frame_given ; /* Whether frame was given. */ |
| 52 |
– |
int dipole_given ; /* Whether dipole was given. */ |
| 49 |
|
int water_given ; /* Whether water was given. */ |
| 50 |
|
int periodicBox_given ; /* Whether periodicBox was given. */ |
| 51 |
|
int zconstraint_given ; /* Whether zconstraint was given. */ |
| 52 |
|
int rigidbody_given ; /* Whether rigidbody was given. */ |
| 53 |
|
int watertype_given ; /* Whether watertype was given. */ |
| 58 |
– |
int ignore_given ; /* Whether ignore was given. */ |
| 54 |
|
int selection_given ; /* Whether selection was given. */ |
| 55 |
+ |
int originsele_given ; /* Whether originsele was given. */ |
| 56 |
+ |
int refsele_given ; /* Whether refsele was given. */ |
| 57 |
|
int repeatX_given ; /* Whether repeatX was given. */ |
| 58 |
|
int repeatY_given ; /* Whether repeatY was given. */ |
| 59 |
|
int repeatZ_given ; /* Whether repeatZ was given. */ |
| 60 |
+ |
int gb_given ; /* Whether gb was given. */ |
| 61 |
+ |
int basetype_given ; /* Whether basetype was given. */ |
| 62 |
|
|
| 63 |
|
} ; |
| 64 |
|
|
