| 30 |
|
|
| 31 |
|
double tau[9]; // the stress tensor |
| 32 |
|
|
| 33 |
< |
unsigned int n_bonds; // number of bends |
| 34 |
< |
unsigned int n_bends; // number of bends |
| 35 |
< |
unsigned int n_torsions; // number of torsions |
| 36 |
< |
unsigned int n_oriented; // number of of atoms with orientation |
| 37 |
< |
unsigned int ndf; // number of actual degrees of freedom |
| 38 |
< |
unsigned int ndfRaw; // number of settable degrees of freedom |
| 39 |
< |
unsigned int ndfTrans; // number of translational degrees of freedom |
| 40 |
< |
unsigned int nZconstraints; // the number of zConstraints |
| 33 |
> |
int n_bonds; // number of bends |
| 34 |
> |
int n_bends; // number of bends |
| 35 |
> |
int n_torsions; // number of torsions |
| 36 |
> |
int n_oriented; // number of of atoms with orientation |
| 37 |
> |
int ndf; // number of actual degrees of freedom |
| 38 |
> |
int ndfRaw; // number of settable degrees of freedom |
| 39 |
> |
int ndfTrans; // number of translational degrees of freedom |
| 40 |
> |
int nZconstraints; // the number of zConstraints |
| 41 |
|
|
| 42 |
< |
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
| 43 |
< |
unsigned int resetIntegrator; // boolean to reset the integrator |
| 42 |
> |
int setTemp; // boolean to set the temperature at each sampleTime |
| 43 |
> |
int resetIntegrator; // boolean to reset the integrator |
| 44 |
|
|
| 45 |
< |
unsigned int n_dipoles; // number of dipoles |
| 45 |
> |
int n_dipoles; // number of dipoles |
| 46 |
|
|
| 47 |
|
|
| 48 |
|
int n_exclude; // the # of pairs excluded from long range forces |
| 57 |
|
|
| 58 |
|
int n_constraints; // the number of constraints on the system |
| 59 |
|
|
| 60 |
< |
unsigned int n_SRI; // the number of short range interactions |
| 60 |
> |
int n_SRI; // the number of short range interactions |
| 61 |
|
|
| 62 |
|
double lrPot; // the potential energy from the long range calculations. |
| 63 |
|
|
| 162 |
|
double matDet3(double m[3][3]); |
| 163 |
|
double matTrace3(double m[3][3]); |
| 164 |
|
|
| 165 |
+ |
void crossProduct3(double a[3],double b[3], double out[3]); |
| 166 |
+ |
double dotProduct3(double a[3], double b[3]); |
| 167 |
+ |
double length3(double a[3]); |
| 168 |
+ |
|
| 169 |
|
SimState* getConfiguration( void ) { return myConfiguration; } |
| 170 |
|
|
| 171 |
|
void addProperty(GenericData* prop); |
| 189 |
|
double ecr; // the electrostatic cutoff radius |
| 190 |
|
double est; // the electrostatic skin thickness |
| 191 |
|
double maxCutoff; |
| 192 |
+ |
|
| 193 |
+ |
double distXY; |
| 194 |
+ |
double distYZ; |
| 195 |
+ |
double distZX; |
| 196 |
|
|
| 197 |
|
void calcHmatInv( void ); |
| 198 |
|
void calcBoxL(); |
| 199 |
+ |
double calcMaxCutOff(); |
| 200 |
|
void checkCutOffs( void ); |
| 201 |
|
|
| 202 |
|
// private function to initialize the fortran side of the simulation |
