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); |
104 |
|
double rij2 = rij * rij; |
105 |
|
double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
106 |
|
Mat3x3d tmpMat; |
107 |
< |
tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; |
107 |
> |
tmpMat = outProduct(Rij, Rij) / rij2; |
108 |
|
double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
109 |
|
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
110 |
|
}else { |
119 |
|
|
120 |
|
//invert B Matrix |
121 |
|
invertMatrix(B, C); |
122 |
+ |
|
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) { |
132 |
|
Mat3x3d Xitt; |
133 |
|
Mat3x3d Xirr; |
134 |
|
Mat3x3d Xitr; |
135 |
+ |
|
136 |
+ |
//calculate the total volume |
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); |
141 |
+ |
} |
142 |
|
|
143 |
|
for (std::size_t i = 0; i < nbeads; ++i) { |
144 |
|
for (std::size_t j = 0; j < nbeads; ++j) { |
146 |
|
C.getSubMatrix(i*3, j*3, Cij); |
147 |
|
|
148 |
|
Xitt += Cij; |
149 |
< |
Xirr += U[i] * Cij; |
150 |
< |
Xitr += U[i] * Cij * U[j]; |
149 |
> |
Xitr += U[i] * Cij; |
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); |
141 |
< |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
142 |
< |
Xi.setSubMatrix(3, 0, Xitr); |
143 |
< |
Xi.setSubMatrix(3, 3, Xirr); |
144 |
< |
//invertMatrix(Xi, Do); |
145 |
< |
double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
146 |
< |
//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 |
163 |
|
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
164 |
|
|
165 |
< |
Mat3x3d XirrInv(0.0); |
154 |
< |
Mat3x3d XirrCopy; |
155 |
< |
XirrCopy = Xirr; |
165 |
> |
const static Mat3x3d zeroMat(0.0); |
166 |
|
|
167 |
|
Mat3x3d XittInv(0.0); |
168 |
< |
Mat3x3d XittCopy; |
169 |
< |
XittCopy = Xitt; |
170 |
< |
invertMatrix(XittCopy, XittInv); |
168 |
> |
XittInv = Xitt.inverse(); |
169 |
> |
|
170 |
> |
Mat3x3d XirrInv; |
171 |
> |
XirrInv = Xirr.inverse(); |
172 |
|
|
173 |
|
Mat3x3d tmp; |
174 |
|
Mat3x3d tmpInv; |
175 |
|
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
176 |
+ |
tmpInv = tmp.inverse(); |
177 |
|
|
178 |
< |
const static Mat3x3d zeroMat(0.0); |
179 |
< |
if (!invertMatrix(tmp, tmpInv)) { |
168 |
< |
tmpInv = zeroMat; |
169 |
< |
} |
170 |
< |
|
171 |
< |
Dott = kt * tmpInv; |
172 |
< |
Dotr = -kt*XirrInv * Xitr * tmpInv; |
173 |
< |
|
174 |
< |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
178 |
> |
Dott = tmpInv; |
179 |
> |
Dotr = -XirrInv * Xitr * tmpInv; |
180 |
|
|
181 |
< |
if(!invertMatrix(tmp, tmpInv)) { |
182 |
< |
tmpInv = zeroMat; |
183 |
< |
} |
184 |
< |
Dorr = kt * tmpInv; |
181 |
> |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
182 |
> |
tmpInv = tmp.inverse(); |
183 |
> |
|
184 |
> |
Dorr = tmpInv; |
185 |
|
|
181 |
– |
//Do.getSubMatrix(0, 0 , Dott); |
182 |
– |
//Do.getSubMatrix(3, 0, Dotr); |
183 |
– |
//Do.getSubMatrix(3, 3, Dorr); |
184 |
– |
|
186 |
|
//calculate center of diffusion |
187 |
|
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
188 |
|
tmp(0, 1) = - Dorr(0, 1); |
199 |
|
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
200 |
|
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
201 |
|
|
202 |
< |
if(!invertMatrix(tmp, tmpInv)) { |
202 |
< |
tmpInv = zeroMat; |
203 |
< |
} |
202 |
> |
tmpInv = tmp.inverse(); |
203 |
|
|
204 |
|
Vector3d rod = tmpInv * tmpVec; |
205 |
|
|
214 |
|
Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
215 |
|
Ddrr = Dorr; |
216 |
|
Ddtr = Dotr + Dorr * Uod; |
218 |
– |
|
219 |
– |
props_.diffCenter = rod; |
220 |
– |
props_.transDiff = Ddtt; |
221 |
– |
props_.transRotDiff = Ddtr; |
222 |
– |
props_.rotDiff = Ddrr; |
217 |
|
|
218 |
< |
return true; |
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 |
> |
invertMatrix(Dd, Xid); |
225 |
> |
|
226 |
> |
Ddtt *= kt; |
227 |
> |
Ddtr *=kt; |
228 |
> |
Ddrr *= kt; |
229 |
> |
|
230 |
> |
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
231 |
> |
Xid *= OOPSEConstant::kb*temperature_/kt; |
232 |
> |
|
233 |
> |
props_.diffCenter = rod; |
234 |
> |
props_.Ddtt = Ddtt; |
235 |
> |
props_.Ddtr = Ddtr; |
236 |
> |
props_.Ddrr = Ddrr; |
237 |
> |
Xid.getSubMatrix(0, 0, props_.Xidtt); |
238 |
> |
Xid.getSubMatrix(0, 3, props_.Xidrt); |
239 |
> |
Xid.getSubMatrix(3, 0, props_.Xidtr); |
240 |
> |
Xid.getSubMatrix(3, 3, props_.Xidrr); |
241 |
> |
|
242 |
> |
|
243 |
> |
std::cout << "viscosity = " << viscosity_ << std::endl; |
244 |
> |
std::cout << "temperature = " << temperature_ << std::endl; |
245 |
> |
std::cout << "center of diffusion :" << std::endl; |
246 |
> |
std::cout << rod << std::endl; |
247 |
> |
std::cout << "diffusion tensor at center of diffusion " << std::endl; |
248 |
> |
std::cout << "translation(A^2/fs) :" << std::endl; |
249 |
> |
std::cout << Ddtt << std::endl; |
250 |
> |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
251 |
> |
std::cout << Ddtr << std::endl; |
252 |
> |
std::cout << "rotation(A^4/fs):" << std::endl; |
253 |
> |
std::cout << Ddrr << std::endl; |
254 |
> |
|
255 |
> |
std::cout << "resistance tensor at center of diffusion " << std::endl; |
256 |
> |
std::cout << "translation(kcal*fs*mol^-1*Ang^-2) :" << std::endl; |
257 |
> |
std::cout << props_.Xidtt << std::endl; |
258 |
> |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
259 |
> |
std::cout << props_.Xidrt << std::endl; |
260 |
> |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
261 |
> |
std::cout << props_.Xidtr << std::endl; |
262 |
> |
std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
263 |
> |
std::cout << props_.Xidrr << std::endl; |
264 |
> |
|
265 |
> |
|
266 |
|
} |
267 |
|
|
268 |
|
void HydrodynamicsModel::writeBeads(std::ostream& os) { |
276 |
|
} |
277 |
|
|
278 |
|
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
238 |
– |
os << "//viscosity = " << viscosity_ << std::endl; |
239 |
– |
os << "//temperature = " << temperature_<< std::endl; |
240 |
– |
std::vector<BeadParam>::iterator iter; |
241 |
– |
os << sd_->getType() << "\n"; |
279 |
|
|
280 |
< |
os << "//diffusion center" << std::endl; |
281 |
< |
os << props_.diffCenter << std::endl; |
280 |
> |
os << sd_->getType() << "\t"; |
281 |
> |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
282 |
|
|
283 |
< |
os << "//translational diffusion tensor" << std::endl; |
284 |
< |
os << props_.transDiff << std::endl; |
283 |
> |
os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t" |
284 |
> |
<< props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t" |
285 |
> |
<< props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t"; |
286 |
> |
|
287 |
> |
os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t" |
288 |
> |
<< props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t" |
289 |
> |
<< props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t"; |
290 |
|
|
291 |
< |
os << "//translational diffusion tensor" << std::endl; |
292 |
< |
os << props_.transRotDiff << std::endl; |
291 |
> |
os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t" |
292 |
> |
<< props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t" |
293 |
> |
<< props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t"; |
294 |
|
|
295 |
< |
os << "//rotational diffusion tensor" << std::endl; |
296 |
< |
os << props_.rotDiff << std::endl; |
297 |
< |
|
255 |
< |
/* |
256 |
< |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n" |
295 |
> |
os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t" |
296 |
> |
<< props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t" |
297 |
> |
<< props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t"; |
298 |
|
|
299 |
< |
os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t" |
300 |
< |
<< props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t" |
301 |
< |
<< props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n"; |
299 |
> |
os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t" |
300 |
> |
<< props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t" |
301 |
> |
<< props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t"; |
302 |
|
|
303 |
< |
os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t" |
304 |
< |
<< props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t" |
305 |
< |
<< props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t" |
303 |
> |
os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t" |
304 |
> |
<< props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t" |
305 |
> |
<< props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t"; |
306 |
|
|
307 |
< |
os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t" |
308 |
< |
<< props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t" |
309 |
< |
<< props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";" |
310 |
< |
<< std::endl; |
270 |
< |
*/ |
307 |
> |
os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t" |
308 |
> |
<< props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t" |
309 |
> |
<< props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl; |
310 |
> |
|
311 |
|
} |
312 |
|
|
313 |
|
} |