| 56 |
|
|
| 57 |
|
double lrPot; // the potential energy from the long range calculations. |
| 58 |
|
|
| 59 |
< |
double box_x, box_y, box_z; // the periodic boundry conditions |
| 59 |
> |
double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
| 60 |
> |
// column vectors of the x, y, and z box vectors. |
| 61 |
> |
// h1 h2 h3 |
| 62 |
> |
// [ Xx Yx Zx ] |
| 63 |
> |
// [ Xy Yy Zy ] |
| 64 |
> |
// [ Xz Yz Zz ] |
| 65 |
> |
// |
| 66 |
> |
double HmatInv[3][3]; |
| 67 |
> |
|
| 68 |
> |
double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
| 69 |
> |
double boxVol; |
| 70 |
> |
int orthoRhombic; |
| 71 |
> |
|
| 72 |
> |
|
| 73 |
> |
|
| 74 |
|
double rList, rCut; // variables for the neighborlist |
| 75 |
|
|
| 76 |
|
int usePBC; // whether we use periodic boundry conditions. |
| 123 |
|
int getNDFraw(); |
| 124 |
|
|
| 125 |
|
void setBox( double newBox[3] ); |
| 126 |
< |
void getBox( double theBox[3] ); |
| 126 |
> |
void setBoxM( double newBox[3][3] ); |
| 127 |
> |
void getBoxM( double theBox[3][3] ); |
| 128 |
> |
void scaleBox( double scale ); |
| 129 |
|
|
| 130 |
+ |
void wrapVector( double thePos[3] ); |
| 131 |
+ |
|
| 132 |
+ |
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
| 133 |
+ |
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
| 134 |
+ |
void invertMat3(double in[3][3], double out[3][3]); |
| 135 |
+ |
void transposeMat3(double in[3][3], double out[3][3]); |
| 136 |
+ |
void printMat3(double A[3][3]); |
| 137 |
+ |
void printMat9(double A[9]); |
| 138 |
+ |
double matDet3(double m[3][3]); |
| 139 |
+ |
|
| 140 |
|
private: |
| 141 |
|
|
| 142 |
+ |
void calcHmatInv( void ); |
| 143 |
+ |
void calcBoxL(); |
| 144 |
+ |
|
| 145 |
|
// private function to initialize the fortran side of the simulation |
| 146 |
|
void (*setFsimulation) setFortranSimList; |
| 147 |
|
|
