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 boxLx, boxLy, boxLz; // the box Lengths |
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. |
98 |
|
|
99 |
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
100 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
101 |
< |
Integrator *the_integrator; // the integrator of the simulation |
101 |
> |
BaseIntegrator *the_integrator; // the integrator of the simulation |
102 |
|
|
103 |
|
char finalName[300]; // the name of the eor file to be written |
104 |
|
char sampleName[300]; // the name of the dump file to be written |
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 |
+ |
double matDet3(double m[3][3]); |
136 |
+ |
|
137 |
|
private: |
138 |
|
|
139 |
+ |
void calcHmatInv( void ); |
140 |
+ |
void calcBoxL(); |
141 |
+ |
|
142 |
|
// private function to initialize the fortran side of the simulation |
143 |
|
void (*setFsimulation) setFortranSimList; |
144 |
|
|