| 77 |
|
/** create the molecules belong to current processor*/ |
| 78 |
|
virtual void createMolecules(); |
| 79 |
|
|
| 80 |
< |
/** Sets the global index for atoms, rigidbodies and cutoff groups */ |
| 80 |
> |
/** |
| 81 |
> |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 82 |
> |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 83 |
> |
* global index to the global index of the groups (or molecules) they belong to. |
| 84 |
> |
* These array are never changed during the simulation. |
| 85 |
> |
*/ |
| 86 |
|
void setGlobalIndex(); |
| 87 |
|
|
| 88 |
|
private: |
| 94 |
|
/** Initialize fortran, mainly set the cutoff radius and setup*/ |
| 95 |
|
void initFortran(SimInfo* info); |
| 96 |
|
|
| 97 |
+ |
/** Figure out the cutoff radius and pass it to fortran */ |
| 98 |
+ |
void setCutoff(SimInfo* info); |
| 99 |
+ |
|
| 100 |
|
std::string mdFileName_; //save the meta-data file name which may be used later |
| 101 |
|
}; |
| 102 |
|
|
