77 |
|
std::cout << "can not create beads" << std::endl; |
78 |
|
return false; |
79 |
|
} |
80 |
< |
|
80 |
> |
|
81 |
> |
//calcResistanceTensor(); |
82 |
> |
calcDiffusionTensor(); |
83 |
> |
return true; |
84 |
> |
} |
85 |
> |
|
86 |
> |
void HydrodynamicsModel::calcResistanceTensor() { |
87 |
> |
} |
88 |
> |
|
89 |
> |
void HydrodynamicsModel::calcDiffusionTensor() { |
90 |
|
int nbeads = beads_.size(); |
91 |
|
DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
92 |
|
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
114 |
|
Tij(2, 2) = constant; |
115 |
|
} |
116 |
|
B.setSubMatrix(i*3, j*3, Tij); |
108 |
– |
std::cout << Tij << std::endl; |
117 |
|
} |
118 |
|
} |
119 |
|
|
112 |
– |
std::cout << "B=\n" |
113 |
– |
<< B << std::endl; |
120 |
|
//invert B Matrix |
121 |
|
invertMatrix(B, C); |
122 |
|
|
117 |
– |
std::cout << "C=\n" |
118 |
– |
<< C << std::endl; |
119 |
– |
|
123 |
|
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
124 |
|
std::vector<Mat3x3d> U; |
125 |
|
for (int i = 0; i < nbeads; ++i) { |
137 |
|
|
138 |
|
double volume = 0.0; |
139 |
|
for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
140 |
< |
volume = 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
140 |
> |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
141 |
|
} |
142 |
|
|
143 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
147 |
|
|
148 |
|
Xitt += Cij; |
149 |
|
Xitr += U[i] * Cij; |
150 |
< |
Xirr += -U[i] * Cij * U[j]; |
148 |
< |
//Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I; |
150 |
> |
Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I; |
151 |
|
} |
152 |
|
} |
153 |
|
|
154 |
< |
//invert Xi to get Diffusion Tensor at arbitrary origin O |
155 |
< |
RectMatrix<double, 6, 6> Xi; |
156 |
< |
RectMatrix<double, 6, 6> Do; |
157 |
< |
Xi.setSubMatrix(0, 0, Xitt); |
156 |
< |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
157 |
< |
Xi.setSubMatrix(3, 0, Xitr); |
158 |
< |
Xi.setSubMatrix(3, 3, Xirr); |
159 |
< |
//invertMatrix(Xi, Do); |
160 |
< |
double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
161 |
< |
//Do *= kt; |
154 |
> |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
155 |
> |
Xitt *= convertConstant; |
156 |
> |
Xitr *= convertConstant; |
157 |
> |
Xirr *= convertConstant; |
158 |
|
|
159 |
+ |
double kt = OOPSEConstant::kB * temperature_; |
160 |
|
|
161 |
|
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
162 |
|
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
167 |
|
Mat3x3d XittInv(0.0); |
168 |
|
XittInv = Xitt.inverse(); |
169 |
|
|
173 |
– |
//Xirr may not be inverted,if it one of the diagonal element is zero, for example |
174 |
– |
//( a11 a12 0) |
175 |
– |
//( a21 a22 0) |
176 |
– |
//( 0 0 0) |
170 |
|
Mat3x3d XirrInv; |
171 |
|
XirrInv = Xirr.inverse(); |
172 |
|
|
175 |
|
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
176 |
|
tmpInv = tmp.inverse(); |
177 |
|
|
178 |
< |
Dott = kt * tmpInv; |
179 |
< |
Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8; |
180 |
< |
|
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*1.0E16; |
184 |
> |
Dorr = tmpInv; |
185 |
|
|
193 |
– |
//Do.getSubMatrix(0, 0 , Dott); |
194 |
– |
//Do.getSubMatrix(3, 0, Dotr); |
195 |
– |
//Do.getSubMatrix(3, 3, Dorr); |
196 |
– |
|
186 |
|
//calculate center of diffusion |
187 |
|
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
188 |
|
tmp(0, 1) = - Dorr(0, 1); |
214 |
|
Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
215 |
|
Ddrr = Dorr; |
216 |
|
Ddtr = Dotr + Dorr * Uod; |
217 |
< |
|
217 |
> |
|
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 |
> |
|
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_.transDiff = Ddtt; |
236 |
< |
props_.transRotDiff = Ddtr; |
237 |
< |
props_.rotDiff = Ddrr; |
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 |
< |
return true; |
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; |
249 |
> |
std::cout << "translation(A^2/fs) :" << std::endl; |
250 |
> |
std::cout << Ddtt << std::endl; |
251 |
> |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
252 |
> |
std::cout << Ddtr << std::endl; |
253 |
> |
std::cout << "rotation(A^4/fs):" << std::endl; |
254 |
> |
std::cout << Ddrr << std::endl; |
255 |
> |
|
256 |
> |
std::cout << "resistance tensor at center of diffusion " << std::endl; |
257 |
> |
std::cout << "translation(kcal*fs*mol^-1*Ang^-2) :" << std::endl; |
258 |
> |
std::cout << props_.Xidtt << std::endl; |
259 |
> |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
260 |
> |
std::cout << props_.Xidrt << std::endl; |
261 |
> |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
262 |
> |
std::cout << props_.Xidtr << std::endl; |
263 |
> |
std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
264 |
> |
std::cout << props_.Xidrr << std::endl; |
265 |
> |
|
266 |
> |
|
267 |
|
} |
268 |
|
|
269 |
|
void HydrodynamicsModel::writeBeads(std::ostream& os) { |
277 |
|
} |
278 |
|
|
279 |
|
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
248 |
– |
os << "//viscosity = " << viscosity_ << std::endl; |
249 |
– |
os << "//temperature = " << temperature_<< std::endl; |
250 |
– |
std::vector<BeadParam>::iterator iter; |
251 |
– |
os << sd_->getType() << "\n"; |
280 |
|
|
281 |
< |
os << "//diffusion center" << std::endl; |
282 |
< |
os << props_.diffCenter << std::endl; |
281 |
> |
os << sd_->getType() << "\t"; |
282 |
> |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
283 |
|
|
284 |
< |
os << "//translational diffusion tensor" << std::endl; |
285 |
< |
os << props_.transDiff << std::endl; |
284 |
> |
os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t" |
285 |
> |
<< props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t" |
286 |
> |
<< props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t"; |
287 |
> |
|
288 |
> |
os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t" |
289 |
> |
<< props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t" |
290 |
> |
<< props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t"; |
291 |
|
|
292 |
< |
os << "//translation-rotation coupling diffusion tensor" << std::endl; |
293 |
< |
os << props_.transRotDiff << std::endl; |
292 |
> |
os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t" |
293 |
> |
<< props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t" |
294 |
> |
<< props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t"; |
295 |
|
|
296 |
< |
os << "//rotational diffusion tensor" << std::endl; |
297 |
< |
os << props_.rotDiff << std::endl; |
298 |
< |
|
265 |
< |
/* |
266 |
< |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n" |
296 |
> |
os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t" |
297 |
> |
<< props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t" |
298 |
> |
<< props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t"; |
299 |
|
|
300 |
< |
os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t" |
301 |
< |
<< props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t" |
302 |
< |
<< props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n"; |
300 |
> |
os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t" |
301 |
> |
<< props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t" |
302 |
> |
<< props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t"; |
303 |
|
|
304 |
< |
os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t" |
305 |
< |
<< props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t" |
306 |
< |
<< props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t" |
304 |
> |
os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t" |
305 |
> |
<< props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t" |
306 |
> |
<< props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t"; |
307 |
|
|
308 |
< |
os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t" |
309 |
< |
<< props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t" |
310 |
< |
<< props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";" |
311 |
< |
<< std::endl; |
280 |
< |
*/ |
308 |
> |
os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t" |
309 |
> |
<< props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t" |
310 |
> |
<< props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl; |
311 |
> |
|
312 |
|
} |
313 |
|
|
314 |
|
} |