| 30 |
|
unsigned int n_bends; // number of bends |
| 31 |
|
unsigned int n_torsions; // number of torsions |
| 32 |
|
unsigned int n_oriented; // number of of atoms with orientation |
| 33 |
+ |
unsigned int ndf; // number of actual degrees of freedom |
| 34 |
+ |
unsigned int ndfRaw; // number of settable degrees of freedom |
| 35 |
|
|
| 36 |
|
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
| 37 |
|
|
| 48 |
|
// no long range forces. |
| 49 |
|
|
| 50 |
|
int* identArray; // array of unique identifiers for the atoms |
| 51 |
+ |
int* molMembershipArray; // map of atom numbers onto molecule numbers |
| 52 |
|
|
| 53 |
|
int n_constraints; // the number of constraints on the system |
| 54 |
|
|
| 84 |
|
|
| 85 |
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
| 86 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
| 87 |
< |
Integrator *the_integrator; // the integrator of the simulation |
| 87 |
> |
BaseIntegrator *the_integrator; // the integrator of the simulation |
| 88 |
|
|
| 89 |
|
char finalName[300]; // the name of the eor file to be written |
| 90 |
|
char sampleName[300]; // the name of the dump file to be written |
| 105 |
|
setFortranBoxSize = fBox; |
| 106 |
|
} |
| 107 |
|
|
| 108 |
+ |
int getNDF(); |
| 109 |
+ |
int getNDFraw(); |
| 110 |
+ |
|
| 111 |
+ |
void setBox( double newBox[3] ); |
| 112 |
+ |
void getBox( double theBox[3] ); |
| 113 |
+ |
|
| 114 |
|
private: |
| 115 |
|
|
| 116 |
|
// private function to initialize the fortran side of the simulation |
