| 36 |
|
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
| 37 |
|
|
| 38 |
|
unsigned int n_dipoles; // number of dipoles |
| 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 |
| 39 |
|
|
| 40 |
+ |
|
| 41 |
|
int n_exclude; // the # of pairs excluded from long range forces |
| 42 |
|
Exclude** excludes; // the pairs themselves |
| 43 |
|
|
| 54 |
|
|
| 55 |
|
double lrPot; // the potential energy from the long range calculations. |
| 56 |
|
|
| 57 |
< |
double Hmat[9]; // the periodic boundry conditions. The Hmat is the |
| 58 |
< |
// column vectors of the x, y, and z box vectors. |
| 59 |
< |
// |
| 60 |
< |
// h1 h2 h3 |
| 61 |
< |
// [ Xx Yx Zx ] |
| 62 |
< |
// [ Xy Yy Zy ] |
| 63 |
< |
// [ Xz Yz Zz ] |
| 64 |
< |
// |
| 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 ] |
| 57 |
> |
double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
| 58 |
> |
// column vectors of the x, y, and z box vectors. |
| 59 |
> |
// h1 h2 h3 |
| 60 |
> |
// [ Xx Yx Zx ] |
| 61 |
> |
// [ Xy Yy Zy ] |
| 62 |
> |
// [ Xz Yz Zz ] |
| 63 |
> |
// |
| 64 |
> |
double HmatInv[3][3]; |
| 65 |
|
|
| 66 |
< |
double HmatI[9]; // the inverted Hmat; |
| 67 |
< |
double boxLx, boxLy, boxLz; // the box Lengths |
| 68 |
< |
double boxVol, orthoRhombic; |
| 66 |
> |
double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
| 67 |
> |
double boxVol; |
| 68 |
> |
int orthoRhombic; |
| 69 |
|
|
| 70 |
|
|
| 71 |
+ |
double dielectric; // the dielectric of the medium for reaction field |
| 72 |
|
|
| 80 |
– |
double rList, rCut; // variables for the neighborlist |
| 73 |
|
|
| 74 |
|
int usePBC; // whether we use periodic boundry conditions. |
| 75 |
|
int useLJ; |
| 112 |
|
// sets the internal function pointer to fortran. |
| 113 |
|
|
| 114 |
|
void setInternal( void (*fSetup) setFortranSimList, |
| 115 |
< |
void (*fBox) setFortranBoxList ){ |
| 115 |
> |
void (*fBox) setFortranBoxList, |
| 116 |
> |
void (*fCut) notifyFortranCutOffList ){ |
| 117 |
|
setFsimulation = fSetup; |
| 118 |
|
setFortranBoxSize = fBox; |
| 119 |
+ |
notifyFortranCutOffs = fCut; |
| 120 |
|
} |
| 121 |
|
|
| 122 |
|
int getNDF(); |
| 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 setRcut( double theRcut ); |
| 131 |
> |
void setEcr( double theEcr ); |
| 132 |
> |
void setEcr( double theEcr, double theEst ); |
| 133 |
|
|
| 134 |
+ |
double getRcut( void ) { return rCut; } |
| 135 |
+ |
double getRlist( void ) { return rList; } |
| 136 |
+ |
double getEcr( void ) { return ecr; } |
| 137 |
+ |
double getEst( void ) { return est; } |
| 138 |
+ |
|
| 139 |
+ |
|
| 140 |
|
void wrapVector( double thePos[3] ); |
| 141 |
|
|
| 142 |
+ |
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
| 143 |
+ |
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
| 144 |
+ |
void invertMat3(double in[3][3], double out[3][3]); |
| 145 |
+ |
void transposeMat3(double in[3][3], double out[3][3]); |
| 146 |
+ |
void printMat3(double A[3][3]); |
| 147 |
+ |
void printMat9(double A[9]); |
| 148 |
+ |
double matDet3(double m[3][3]); |
| 149 |
+ |
|
| 150 |
|
private: |
| 151 |
+ |
|
| 152 |
+ |
double origRcut, origEcr; |
| 153 |
+ |
int boxIsInit, haveOrigRcut, haveOrigEcr; |
| 154 |
+ |
|
| 155 |
+ |
double oldEcr; |
| 156 |
+ |
double oldRcut; |
| 157 |
+ |
|
| 158 |
+ |
double rList, rCut; // variables for the neighborlist |
| 159 |
+ |
double ecr; // the electrostatic cutoff radius |
| 160 |
+ |
double est; // the electrostatic skin thickness |
| 161 |
+ |
double maxCutoff; |
| 162 |
|
|
| 163 |
< |
void calcHmatI( void ); |
| 163 |
> |
void calcHmatInv( void ); |
| 164 |
|
void calcBoxL(); |
| 165 |
+ |
void checkCutOffs( void ); |
| 166 |
|
|
| 167 |
|
// private function to initialize the fortran side of the simulation |
| 168 |
|
void (*setFsimulation) setFortranSimList; |
| 169 |
|
|
| 170 |
|
void (*setFortranBoxSize) setFortranBoxList; |
| 171 |
+ |
|
| 172 |
+ |
void (*notifyFortranCutOffs) notifyFortranCutOffList; |
| 173 |
+ |
|
| 174 |
|
}; |
| 175 |
|
|
| 176 |
|
|
