| 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 |
|
|
| 38 |
|
unsigned int n_dipoles; // number of dipoles |
| 39 |
< |
double rRF; // the reaction field cut off radius |
| 39 |
> |
double ecr; // the electrostatic cutoff radius |
| 40 |
> |
double est; // the electrostatic skin thickness |
| 41 |
|
double dielectric; // the dielectric of the medium for reaction field |
| 42 |
|
|
| 43 |
|
int n_exclude; // the # of pairs excluded from long range forces |
| 44 |
< |
int *excludes; // the pairs themselves |
| 44 |
> |
Exclude** excludes; // the pairs themselves |
| 45 |
|
|
| 46 |
|
int nGlobalExcludes; |
| 47 |
|
int* globalExcludes; // same as above, but these guys participate in |
| 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 |
|
|
| 55 |
|
unsigned int n_SRI; // the number of short range interactions |
| 52 |
– |
SRI **sr_interactions;// the array of short range force objects |
| 56 |
|
|
| 57 |
|
double lrPot; // the potential energy from the long range calculations. |
| 58 |
|
|
| 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 |
