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); |
215 |
|
Ddrr = Dorr; |
216 |
|
Ddtr = Dotr + Dorr * Uod; |
217 |
|
|
218 |
– |
props_.diffCenter = rod; |
219 |
– |
props_.Ddtt = Ddtt; |
220 |
– |
props_.Ddtr = Ddtr; |
221 |
– |
props_.Ddrr = Ddrr; |
222 |
– |
|
218 |
|
SquareMatrix<double, 6> Dd; |
219 |
|
Dd.setSubMatrix(0, 0, Ddtt); |
220 |
|
Dd.setSubMatrix(0, 3, Ddtr.transpose()); |
221 |
|
Dd.setSubMatrix(3, 0, Ddtr); |
222 |
|
Dd.setSubMatrix(3, 3, Ddrr); |
223 |
|
SquareMatrix<double, 6> Xid; |
224 |
+ |
Ddtt *= kt; |
225 |
+ |
Ddtr *=kt; |
226 |
+ |
Ddrr *= kt; |
227 |
|
invertMatrix(Dd, Xid); |
228 |
|
|
231 |
– |
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
232 |
– |
Xid *= OOPSEConstant::kb*temperature_; |
229 |
|
|
230 |
+ |
|
231 |
+ |
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
232 |
+ |
//Xid /= OOPSEConstant::energyConvert; |
233 |
+ |
Xid *= OOPSEConstant::kb * temperature_; |
234 |
+ |
props_.diffCenter = rod; |
235 |
+ |
props_.Ddtt = Ddtt; |
236 |
+ |
props_.Ddtr = Ddtr; |
237 |
+ |
props_.Ddrr = Ddrr; |
238 |
|
Xid.getSubMatrix(0, 0, props_.Xidtt); |
239 |
|
Xid.getSubMatrix(0, 3, props_.Xidrt); |
240 |
|
Xid.getSubMatrix(3, 0, props_.Xidtr); |
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; |