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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
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|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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#include "math/LU.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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Ellipsoid::Ellipsoid(Vector3d origin, double rMajor, double rMinor,Mat3x3d rotMat) |
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: origin_(origin), rMajor_(rMajor), rMinor_(rMinor), rotMat_(rotMat) { |
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|
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Ellipsoid::Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial, |
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Mat3x3d rotMat) : origin_(origin), rAxial_(rAxial), |
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rEquatorial_(rEquatorial), |
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rotMat_(rotMat) { |
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> |
if (rAxial_ > rEquatorial_) { |
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> |
rMajor_ = rAxial_; |
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> |
rMinor_ = rEquatorial_; |
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> |
} else { |
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rMajor_ = rEquatorial_; |
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> |
rMinor_ = rAxial_; |
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} |
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} |
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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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> |
|
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> |
RealType xoverb = rbody[0]/rEquatorial_; |
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> |
RealType yoverb = rbody[1]/rEquatorial_; |
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RealType zovera = rbody[2]/rAxial_; |
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|
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bool result; |
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< |
if (xovera*xovera + yovera*yovera + zoverb*zoverb < 1) |
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if (xoverb*xoverb + yoverb*yoverb + zovera*zovera < 1) |
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result = true; |
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else |
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result = false; |
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|
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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 = rAxial_ > rEquatorial_ ? rAxial_ : rEquatorial_; |
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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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|
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< |
HydroProps Ellipsoid::getHydroProps(double viscosity, double temperature) { |
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> |
HydroProp* Ellipsoid::getHydroProp(RealType viscosity, |
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> |
RealType temperature) { |
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|
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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 = rAxial_; |
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> |
RealType b = rEquatorial_; |
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> |
RealType a2 = a * a; |
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> |
RealType b2 = b * b; |
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|
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< |
double p = a /b; |
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< |
double S; |
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if (p > 1.0) { //prolate |
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> |
RealType p = a / b; |
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> |
RealType S; |
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> |
if (p > 1.0) { |
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> |
// Ellipsoid is 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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> |
} else { |
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> |
// Ellipsoid is oblate: |
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S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a); |
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} |
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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 pi = NumericConstant::PI; |
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> |
RealType XittA = 16.0 * pi * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
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> |
RealType XittB = 32.0 * pi * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
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> |
RealType XirrA = 32.0/3.0 * pi * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
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> |
RealType XirrB = 32.0/3.0 * pi * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
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|
|
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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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|
|
| 115 |
+ |
Mat6x6d Xi, XiCopy, D; |
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|
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< |
HydroProps props; |
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> |
Xi(0,0) = XittB; |
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> |
Xi(1,1) = XittB; |
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> |
Xi(2,2) = XittA; |
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> |
Xi(3,3) = XirrB; |
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> |
Xi(4,4) = XirrB; |
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> |
Xi(5,5) = XirrA; |
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> |
|
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> |
Xi *= PhysicalConstants::viscoConvert; |
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|
|
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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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< |
|
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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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< |
|
| 115 |
< |
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; |
| 126 |
> |
XiCopy = Xi; |
| 127 |
> |
invertMatrix(XiCopy, D); |
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> |
RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
| 129 |
> |
D *= kt; |
| 130 |
|
|
| 131 |
< |
return props; |
| 131 |
> |
HydroProp* hprop = new HydroProp(V3Zero, Xi, D); |
| 132 |
|
|
| 133 |
+ |
return hprop; |
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+ |
|
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|
} |
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|
} |
