| 175 |
|
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
| 176 |
|
tmpInv = tmp.inverse(); |
| 177 |
|
|
| 178 |
< |
Dott = kt*tmpInv; |
| 179 |
< |
Dotr = -kt*XirrInv * Xitr * tmpInv; |
| 178 |
> |
Dott = tmpInv; |
| 179 |
> |
Dotr = -XirrInv * Xitr * tmpInv; |
| 180 |
|
|
| 181 |
|
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
| 182 |
|
tmpInv = tmp.inverse(); |
| 183 |
|
|
| 184 |
< |
Dorr = kt * tmpInv; |
| 184 |
> |
Dorr = tmpInv; |
| 185 |
|
|
| 186 |
|
//calculate center of diffusion |
| 187 |
|
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
| 227 |
|
Dd.setSubMatrix(3, 3, Ddrr); |
| 228 |
|
SquareMatrix<double, 6> Xid; |
| 229 |
|
invertMatrix(Dd, Xid); |
| 230 |
+ |
|
| 231 |
+ |
Ddtt *= kt; |
| 232 |
+ |
Ddtr *=kt; |
| 233 |
+ |
Ddrr *= kt; |
| 234 |
|
|
| 235 |
|
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
| 236 |
< |
Xid *= OOPSEConstant::kb*temperature_; |
| 236 |
> |
Xid *= OOPSEConstant::kb*temperature_/kt; |
| 237 |
|
|
| 238 |
|
Xid.getSubMatrix(0, 0, props_.Xidtt); |
| 239 |
|
Xid.getSubMatrix(0, 3, props_.Xidrt); |
| 241 |
|
Xid.getSubMatrix(3, 3, props_.Xidrr); |
| 242 |
|
|
| 243 |
|
|
| 244 |
+ |
std::cout << "viscosity = " << viscosity_ << std::endl; |
| 245 |
+ |
std::cout << "temperature = " << temperature_ << std::endl; |
| 246 |
|
std::cout << "center of diffusion :" << std::endl; |
| 247 |
|
std::cout << rod << std::endl; |
| 248 |
|
std::cout << "diffusion tensor at center of diffusion " << std::endl; |
