77 |
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/** 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 |
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|
88 |
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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 |
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