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namespace oopse { |
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< |
Ellipsoid::Ellipsoid(Vector3d origin, double rMajor, double rMinor,Mat3x3d rotMat) |
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> |
Ellipsoid::Ellipsoid(Vector3d origin, RealType rMajor, RealType rMinor,Mat3x3d rotMat) |
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: origin_(origin), rMajor_(rMajor), rMinor_(rMinor), rotMat_(rotMat) { |
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} |
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bool Ellipsoid::isInterior(Vector3d pos) { |
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Vector3d r = pos - origin_; |
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Vector3d rbody = rotMat_ * r; |
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< |
double xovera = rbody[0]/rMajor_; |
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< |
double yovera = rbody[1]/rMajor_; |
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< |
double zoverb = rbody[2]/rMinor_; |
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> |
RealType xovera = rbody[0]/rMajor_; |
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> |
RealType yovera = rbody[1]/rMajor_; |
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> |
RealType zoverb = rbody[2]/rMinor_; |
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bool result; |
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if (xovera*xovera + yovera*yovera + zoverb*zoverb < 1) |
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std::pair<Vector3d, Vector3d> boundary; |
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//make a cubic box |
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double rad = rMajor_ > rMinor_ ? rMajor_ : rMinor_; |
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> |
RealType rad = rMajor_ > rMinor_ ? rMajor_ : rMinor_; |
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Vector3d r(rad, rad, rad); |
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boundary.first = origin_ - r; |
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boundary.second = origin_ + r; |
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return boundary; |
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} |
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< |
HydroProps Ellipsoid::getHydroProps(double viscosity, double temperature) { |
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> |
HydroProp* Ellipsoid::getHydroProp(RealType viscosity, RealType temperature) { |
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< |
double a = rMinor_; |
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double b = rMajor_; |
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double a2 = a * a; |
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double b2 = b* b; |
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> |
RealType a = rMinor_; |
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> |
RealType b = rMajor_; |
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> |
RealType a2 = a * a; |
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> |
RealType b2 = b* b; |
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double p = a /b; |
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double S; |
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RealType p = a /b; |
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RealType S; |
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if (p > 1.0) { //prolate |
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S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b); |
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} else { //oblate |
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S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a); |
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} |
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< |
double P = 1.0/(a2 - b2) * (S - 2.0/a); |
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double Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
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//RealType P = 1.0/(a2 - b2) * (S - 2.0/a); |
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> |
//RealType Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
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< |
double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
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< |
double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
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< |
double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
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< |
double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
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RealType transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
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RealType transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
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RealType rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
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RealType rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
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< |
HydroProps props; |
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> |
Mat6x6d Xi, XiCopy, D; |
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< |
props.Xi(0,0) = transMajor; |
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props.Xi(1,1) = transMajor; |
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props.Xi(2,2) = transMinor; |
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props.Xi(3,3) = rotMajor; |
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props.Xi(4,4) = rotMajor; |
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< |
props.Xi(5,5) = rotMinor; |
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Xi(0,0) = transMajor; |
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Xi(1,1) = transMajor; |
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Xi(2,2) = transMinor; |
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Xi(3,3) = rotMajor; |
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Xi(4,4) = rotMajor; |
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Xi(5,5) = rotMinor; |
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< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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< |
props.Xi *= convertConstant; |
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> |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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> |
Xi *= convertConstant; |
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< |
Mat6x6d XiCopy = props.Xi; |
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< |
invertMatrix(XiCopy, props.D); |
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< |
double kt = OOPSEConstant::kB * temperature; |
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props.D *= kt; |
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props.Xi *= OOPSEConstant::kb * temperature; |
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> |
XiCopy = Xi; |
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> |
invertMatrix(XiCopy, D); |
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> |
RealType kt = OOPSEConstant::kB * temperature; |
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> |
D *= kt; |
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> |
Xi *= OOPSEConstant::kb * temperature; |
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< |
return props; |
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> |
HydroProp* hprop = new HydroProp(V3Zero, Xi, D); |
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return hprop; |
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} |
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} |
