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#include "math/LU.hpp" |
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#include "math/DynamicRectMatrix.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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namespace oopse { |
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/** |
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* Reference: |
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* Comparison of Different Modeling and Computational Procedures. |
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* Biophysical Journal, 75(6), 3044, 1999 |
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*/ |
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bool HydrodynamicsModel::calcHydrodyanmicsProps(double eta) { |
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|
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HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){ |
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DynamicProperty::const_iterator iter; |
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|
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iter = extraParams.find("Viscosity"); |
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if (iter != extraParams.end()) { |
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boost::any param = iter->second; |
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viscosity_ = boost::any_cast<double>(param); |
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}else { |
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std::cout << "HydrodynamicsModel Error\n" ; |
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} |
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|
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iter = extraParams.find("Temperature"); |
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if (iter != extraParams.end()) { |
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boost::any param = iter->second; |
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temperature_ = boost::any_cast<double>(param); |
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}else { |
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std::cout << "HydrodynamicsModel Error\n" ; |
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} |
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} |
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|
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bool HydrodynamicsModel::calcHydrodyanmicsProps() { |
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if (!createBeads(beads_)) { |
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std::cout << "can not create beads" << std::endl; |
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return false; |
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} |
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|
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|
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//calcResistanceTensor(); |
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calcDiffusionTensor(); |
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return true; |
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} |
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|
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void HydrodynamicsModel::calcResistanceTensor() { |
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} |
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|
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void HydrodynamicsModel::calcDiffusionTensor() { |
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int nbeads = beads_.size(); |
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DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
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DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
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Mat3x3d I; |
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I(0, 0) = 1.0; |
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I(1, 1) = 1.0; |
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I(2, 2) = 1.0; |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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Mat3x3d Tij; |
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double rij2 = rij * rij; |
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double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
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Mat3x3d tmpMat; |
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tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; |
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double constant = 8.0 * NumericConstant::PI * eta * rij; |
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tmpMat = outProduct(Rij, Rij) / rij2; |
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double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
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Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
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}else { |
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double constant = 1.0 / (6.0 * NumericConstant::PI * eta * beads_[i].radius); |
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double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
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Tij(0, 0) = constant; |
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Tij(1, 1) = constant; |
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Tij(2, 2) = constant; |
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|
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//invert B Matrix |
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invertMatrix(B, C); |
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|
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|
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//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
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std::vector<Mat3x3d> U; |
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for (int i = 0; i < nbeads; ++i) { |
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Mat3x3d Xitt; |
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Mat3x3d Xirr; |
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Mat3x3d Xitr; |
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|
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//calculate the total volume |
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|
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double volume = 0.0; |
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for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
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volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
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} |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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C.getSubMatrix(i*3, j*3, Cij); |
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|
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Xitt += Cij; |
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< |
Xirr += U[i] * Cij; |
150 |
< |
Xitr += U[i] * Cij * U[j]; |
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Xitr += U[i] * Cij; |
150 |
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Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I; |
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} |
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} |
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|
154 |
< |
//invert Xi to get Diffusion Tensor at arbitrary origin O |
155 |
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RectMatrix<double, 6, 6> Xi; |
156 |
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RectMatrix<double, 6, 6> Do; |
157 |
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Xi.setSubMatrix(0, 0, Xitt); |
116 |
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Xi.setSubMatrix(0, 3, Xitr.transpose()); |
117 |
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Xi.setSubMatrix(3, 0, Xitr); |
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Xi.setSubMatrix(3, 3, Xitt); |
119 |
< |
invertMatrix(Xi, Do); |
154 |
> |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
155 |
> |
Xitt *= convertConstant; |
156 |
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Xitr *= convertConstant; |
157 |
> |
Xirr *= convertConstant; |
158 |
|
|
159 |
+ |
double kt = OOPSEConstant::kB * temperature_; |
160 |
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|
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Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
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Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
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Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
124 |
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Do.getSubMatrix(0, 0 , Dott); |
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Do.getSubMatrix(3, 0, Dotr); |
126 |
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Do.getSubMatrix(3, 3, Dorr); |
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|
|
165 |
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const static Mat3x3d zeroMat(0.0); |
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|
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Mat3x3d XittInv(0.0); |
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XittInv = Xitt.inverse(); |
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|
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Mat3x3d XirrInv; |
171 |
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XirrInv = Xirr.inverse(); |
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|
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Mat3x3d tmp; |
174 |
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Mat3x3d tmpInv; |
175 |
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tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
176 |
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tmpInv = tmp.inverse(); |
177 |
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|
178 |
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Dott = tmpInv; |
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Dotr = -XirrInv * Xitr * tmpInv; |
180 |
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|
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tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
182 |
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tmpInv = tmp.inverse(); |
183 |
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|
184 |
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Dorr = tmpInv; |
185 |
+ |
|
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|
//calculate center of diffusion |
187 |
< |
Mat3x3d tmpMat; |
188 |
< |
tmpMat(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
189 |
< |
tmpMat(0, 1) = - Dorr(0, 1); |
190 |
< |
tmpMat(0, 2) = -Dorr(0, 2); |
191 |
< |
tmpMat(1, 0) = -Dorr(0, 1); |
192 |
< |
tmpMat(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
193 |
< |
tmpMat(1, 2) = -Dorr(1, 2); |
194 |
< |
tmpMat(2, 0) = -Dorr(0, 2); |
195 |
< |
tmpMat(2, 1) = -Dorr(1, 2); |
138 |
< |
tmpMat(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
187 |
> |
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
188 |
> |
tmp(0, 1) = - Dorr(0, 1); |
189 |
> |
tmp(0, 2) = -Dorr(0, 2); |
190 |
> |
tmp(1, 0) = -Dorr(0, 1); |
191 |
> |
tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
192 |
> |
tmp(1, 2) = -Dorr(1, 2); |
193 |
> |
tmp(2, 0) = -Dorr(0, 2); |
194 |
> |
tmp(2, 1) = -Dorr(1, 2); |
195 |
> |
tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
196 |
|
|
197 |
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Vector3d tmpVec; |
198 |
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tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
199 |
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tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
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tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
144 |
– |
|
145 |
– |
Vector3d rod = tmpMat.inverse() * tmpVec; |
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|
|
202 |
+ |
tmpInv = tmp.inverse(); |
203 |
+ |
|
204 |
+ |
Vector3d rod = tmpInv * tmpVec; |
205 |
+ |
|
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//calculate Diffusion Tensor at center of diffusion |
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Mat3x3d Uod; |
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Uod.setupSkewMat(rod); |
214 |
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Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
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Ddrr = Dorr; |
216 |
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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) { |
270 |
+ |
std::vector<BeadParam>::iterator iter; |
271 |
+ |
os << beads_.size() << std::endl; |
272 |
+ |
os << "Generated by Hydro" << std::endl; |
273 |
+ |
for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
274 |
+ |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
275 |
+ |
} |
276 |
|
|
277 |
|
} |
278 |
|
|
279 |
|
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
280 |
|
|
281 |
+ |
os << sd_->getType() << "\t"; |
282 |
+ |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
283 |
+ |
|
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 << 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 << 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_.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_.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_.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 |
|
} |