56 |
|
|
57 |
|
double lrPot; // the potential energy from the long range calculations. |
58 |
|
|
59 |
< |
double Hmat[9]; // the periodic boundry conditions. The Hmat is the |
60 |
< |
// column vectors of the x, y, and z box vectors. |
61 |
< |
// |
62 |
< |
// h1 h2 h3 |
63 |
< |
// [ Xx Yx Zx ] |
64 |
< |
// [ Xy Yy Zy ] |
65 |
< |
// [ Xz Yz Zz ] |
66 |
< |
// |
67 |
< |
// to preserve compatibility with Fortran the |
68 |
< |
// ordering in the array is as follows: |
69 |
< |
// |
70 |
< |
// [ 0 3 6 ] |
71 |
< |
// [ 1 4 7 ] |
72 |
< |
// [ 2 5 8 ] |
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 |
|
|
74 |
– |
double HmatI[9]; // the inverted Hmat; |
68 |
|
double boxLx, boxLy, boxLz; // the box Lengths |
69 |
< |
double boxVol, orthoRhombic; |
69 |
> |
double boxVol; |
70 |
> |
int orthoRhombic; |
71 |
|
|
72 |
|
|
73 |
|
|
123 |
|
int getNDFraw(); |
124 |
|
|
125 |
|
void setBox( double newBox[3] ); |
126 |
< |
void setBoxM( double newBox[9] ); |
127 |
< |
void getBoxM( double theBox[9] ); |
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 |
+ |
double matDet3(double m[3][3]); |
136 |
+ |
|
137 |
|
private: |
138 |
|
|
139 |
< |
void calcHmatI( void ); |
139 |
> |
void calcHmatInv( void ); |
140 |
|
void calcBoxL(); |
141 |
|
|
142 |
|
// private function to initialize the fortran side of the simulation |