| 43 |
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#include "math/LU.hpp" |
| 44 |
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#include "math/DynamicRectMatrix.hpp" |
| 45 |
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#include "math/SquareMatrix3.hpp" |
| 46 |
+ |
#include "utils/OOPSEConstant.hpp" |
| 47 |
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namespace oopse { |
| 48 |
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/** |
| 49 |
|
* Reference: |
| 51 |
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* Comparison of Different Modeling and Computational Procedures. |
| 52 |
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* Biophysical Journal, 75(6), 3044, 1999 |
| 53 |
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*/ |
| 54 |
< |
bool HydrodynamicsModel::calcHydrodyanmicsProps(double eta) { |
| 54 |
> |
|
| 55 |
> |
HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){ |
| 56 |
> |
DynamicProperty::const_iterator iter; |
| 57 |
> |
|
| 58 |
> |
iter = extraParams.find("Viscosity"); |
| 59 |
> |
if (iter != extraParams.end()) { |
| 60 |
> |
boost::any param = iter->second; |
| 61 |
> |
viscosity_ = boost::any_cast<double>(param); |
| 62 |
> |
}else { |
| 63 |
> |
std::cout << "HydrodynamicsModel Error\n" ; |
| 64 |
> |
} |
| 65 |
> |
|
| 66 |
> |
iter = extraParams.find("Temperature"); |
| 67 |
> |
if (iter != extraParams.end()) { |
| 68 |
> |
boost::any param = iter->second; |
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> |
temperature_ = boost::any_cast<double>(param); |
| 70 |
> |
}else { |
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> |
std::cout << "HydrodynamicsModel Error\n" ; |
| 72 |
> |
} |
| 73 |
> |
} |
| 74 |
> |
|
| 75 |
> |
bool HydrodynamicsModel::calcHydrodyanmicsProps() { |
| 76 |
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if (!createBeads(beads_)) { |
| 77 |
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std::cout << "can not create beads" << std::endl; |
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return false; |
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} |
| 80 |
< |
|
| 80 |
> |
|
| 81 |
> |
//calcResistanceTensor(); |
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> |
calcDiffusionTensor(); |
| 83 |
> |
return true; |
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> |
} |
| 85 |
> |
|
| 86 |
> |
void HydrodynamicsModel::calcResistanceTensor() { |
| 87 |
> |
} |
| 88 |
> |
|
| 89 |
> |
void HydrodynamicsModel::calcDiffusionTensor() { |
| 90 |
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int nbeads = beads_.size(); |
| 91 |
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DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
| 92 |
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DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
| 93 |
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Mat3x3d I; |
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+ |
I(0, 0) = 1.0; |
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+ |
I(1, 1) = 1.0; |
| 96 |
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I(2, 2) = 1.0; |
| 97 |
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|
| 98 |
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for (std::size_t i = 0; i < nbeads; ++i) { |
| 99 |
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for (std::size_t j = 0; j < nbeads; ++j) { |
| 100 |
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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; |
| 106 |
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Mat3x3d tmpMat; |
| 107 |
< |
tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; |
| 108 |
< |
double constant = 8.0 * NumericConstant::PI * eta * rij; |
| 107 |
> |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 108 |
> |
double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
| 109 |
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Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 110 |
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}else { |
| 111 |
< |
double constant = 1.0 / (6.0 * NumericConstant::PI * eta * beads_[i].radius); |
| 111 |
> |
double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
| 112 |
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Tij(0, 0) = constant; |
| 113 |
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Tij(1, 1) = constant; |
| 114 |
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Tij(2, 2) = constant; |
| 119 |
|
|
| 120 |
|
//invert B Matrix |
| 121 |
|
invertMatrix(B, C); |
| 122 |
< |
|
| 122 |
> |
|
| 123 |
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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; |
| 125 |
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for (int i = 0; i < nbeads; ++i) { |
| 132 |
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Mat3x3d Xitt; |
| 133 |
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Mat3x3d Xirr; |
| 134 |
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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); |
| 116 |
< |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
| 117 |
< |
Xi.setSubMatrix(3, 0, Xitr); |
| 118 |
< |
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 |
> |
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 |
| 124 |
– |
Do.getSubMatrix(0, 0 , Dott); |
| 125 |
– |
Do.getSubMatrix(3, 0, Dotr); |
| 126 |
– |
Do.getSubMatrix(3, 3, Dorr); |
| 164 |
|
|
| 165 |
+ |
const static Mat3x3d zeroMat(0.0); |
| 166 |
+ |
|
| 167 |
+ |
Mat3x3d XittInv(0.0); |
| 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 |
+ |
Dott = tmpInv; |
| 179 |
+ |
Dotr = -XirrInv * Xitr * tmpInv; |
| 180 |
+ |
|
| 181 |
+ |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
| 182 |
+ |
tmpInv = tmp.inverse(); |
| 183 |
+ |
|
| 184 |
+ |
Dorr = tmpInv; |
| 185 |
+ |
|
| 186 |
|
//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 |
|
Vector3d tmpVec; |
| 198 |
|
tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
| 199 |
|
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
| 200 |
|
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
| 144 |
– |
|
| 145 |
– |
Vector3d rod = tmpMat.inverse() * tmpVec; |
| 201 |
|
|
| 202 |
+ |
tmpInv = tmp.inverse(); |
| 203 |
+ |
|
| 204 |
+ |
Vector3d rod = tmpInv * tmpVec; |
| 205 |
+ |
|
| 206 |
|
//calculate Diffusion Tensor at center of diffusion |
| 207 |
|
Mat3x3d Uod; |
| 208 |
|
Uod.setupSkewMat(rod); |
| 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 |
> |
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_.transDiff = Ddtt; |
| 235 |
< |
props_.transRotDiff = Ddtr; |
| 236 |
< |
props_.rotDiff = Ddrr; |
| 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 |
< |
return true; |
| 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) { |
| 269 |
+ |
std::vector<BeadParam>::iterator iter; |
| 270 |
+ |
os << beads_.size() << std::endl; |
| 271 |
+ |
os << "Generated by Hydro" << std::endl; |
| 272 |
+ |
for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
| 273 |
+ |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
| 274 |
+ |
} |
| 275 |
|
|
| 276 |
|
} |
| 277 |
|
|
| 278 |
|
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
| 279 |
|
|
| 280 |
+ |
os << sd_->getType() << "\t"; |
| 281 |
+ |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
| 282 |
+ |
|
| 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 << 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 << 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_.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_.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_.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 |
|
} |
