| 69 |
|
public: |
| 70 |
|
|
| 71 |
|
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), |
| 72 |
< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 72 |
> |
currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 73 |
|
|
| 74 |
|
} |
| 75 |
|
|
| 76 |
|
Snapshot(int nAtoms, int nRigidbodies, int storageLayout) |
| 77 |
|
: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout), |
| 78 |
< |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 78 |
> |
currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) { |
| 79 |
|
|
| 80 |
|
} |
| 81 |
|
|
| 111 |
|
/** Sets the H-Matrix */ |
| 112 |
|
void setHmat(const Mat3x3d& m); |
| 113 |
|
|
| 114 |
< |
double getVolume() { |
| 114 |
> |
RealType getVolume() { |
| 115 |
|
return hmat_.determinant(); |
| 116 |
|
} |
| 117 |
|
|
| 122 |
|
|
| 123 |
|
/** Wrapping the vector according to periodic boundary condition*/ |
| 124 |
|
void wrapVector(Vector3d& v); |
| 125 |
< |
|
| 125 |
> |
Vector3d getCOM(); |
| 126 |
> |
Vector3d getCOMvel(); |
| 127 |
> |
Vector3d getCOMw(); |
| 128 |
|
|
| 129 |
< |
double getTime() { |
| 129 |
> |
RealType getTime() { |
| 130 |
|
return currentTime_; |
| 131 |
|
} |
| 132 |
|
|
| 133 |
< |
void increaseTime(double dt) { |
| 133 |
> |
void increaseTime(RealType dt) { |
| 134 |
|
setTime(getTime() + dt); |
| 135 |
|
} |
| 136 |
|
|
| 137 |
< |
void setTime(double time) { |
| 137 |
> |
void setTime(RealType time) { |
| 138 |
|
currentTime_ =time; |
| 139 |
|
//time at statData is redundant |
| 140 |
|
statData[Stats::TIME] = currentTime_; |
| 141 |
|
} |
| 142 |
|
|
| 143 |
< |
double getChi() { |
| 143 |
> |
RealType getChi() { |
| 144 |
|
return chi_; |
| 145 |
|
} |
| 146 |
|
|
| 147 |
< |
void setChi(double chi) { |
| 147 |
> |
void setChi(RealType chi) { |
| 148 |
|
chi_ = chi; |
| 149 |
|
} |
| 150 |
|
|
| 151 |
< |
double getIntegralOfChiDt() { |
| 151 |
> |
RealType getIntegralOfChiDt() { |
| 152 |
|
return integralOfChiDt_; |
| 153 |
|
} |
| 154 |
|
|
| 155 |
< |
void setIntegralOfChiDt(double integralOfChiDt) { |
| 155 |
> |
void setIntegralOfChiDt(RealType integralOfChiDt) { |
| 156 |
|
integralOfChiDt_ = integralOfChiDt; |
| 157 |
|
} |
| 158 |
|
|
| 159 |
+ |
|
| 160 |
+ |
void setOrthoTolerance(RealType orthoTolerance) { |
| 161 |
+ |
orthoTolerance_ = orthoTolerance; |
| 162 |
+ |
} |
| 163 |
+ |
|
| 164 |
|
Mat3x3d getEta() { |
| 165 |
|
return eta_; |
| 166 |
|
} |
| 168 |
|
void setEta(const Mat3x3d& eta) { |
| 169 |
|
eta_ = eta; |
| 170 |
|
} |
| 171 |
< |
|
| 171 |
> |
|
| 172 |
> |
bool hasCOM() { |
| 173 |
> |
return hasCOM_; |
| 174 |
> |
} |
| 175 |
> |
|
| 176 |
> |
void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
| 177 |
> |
COM_ = COM; |
| 178 |
> |
COMvel_ = COMvel; |
| 179 |
> |
COMw_ = COMw; |
| 180 |
> |
hasCOM_ = true; |
| 181 |
> |
} |
| 182 |
> |
|
| 183 |
|
DataStorage atomData; |
| 184 |
|
DataStorage rigidbodyData; |
| 185 |
|
Stats statData; |
| 186 |
|
|
| 187 |
|
private: |
| 188 |
< |
double currentTime_; |
| 188 |
> |
RealType currentTime_; |
| 189 |
|
|
| 190 |
|
Mat3x3d hmat_; |
| 191 |
|
Mat3x3d invHmat_; |
| 192 |
+ |
RealType orthoTolerance_; |
| 193 |
|
int orthoRhombic_; |
| 194 |
|
|
| 195 |
< |
double chi_; |
| 196 |
< |
double integralOfChiDt_; |
| 195 |
> |
RealType chi_; |
| 196 |
> |
RealType integralOfChiDt_; |
| 197 |
|
Mat3x3d eta_; |
| 198 |
+ |
Vector3d COM_; |
| 199 |
+ |
Vector3d COMvel_; |
| 200 |
+ |
Vector3d COMw_; |
| 201 |
+ |
bool hasCOM_; |
| 202 |
|
|
| 203 |
|
int id_; /**< identification number of the snapshot */ |
| 204 |
|
}; |
