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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, 24107 (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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#ifndef BRAINS_THERMO_HPP |
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#include "primitives/Atom.hpp" |
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#include "brains/SimInfo.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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class Thermo{ |
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|
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public: |
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|
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Thermo( SimInfo* info) : info_(info) {} |
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Thermo( SimInfo* info ) : info_(info) {} |
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|
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// note: all the following energies are in kcal/mol |
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|
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+ |
RealType getTranslationalKinetic(); // the translational kinetic energy |
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+ |
RealType getRotationalKinetic(); // the rotational kinetic energy |
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RealType getKinetic(); // the total kinetic energy |
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RealType getPotential(); // the total potential energy |
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RealType getTotalE(); // gets the total energy |
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> |
RealType getTotalEnergy(); // gets the total energy |
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|
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RealType getTemperature(); // gives the instant temp. in K |
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> |
RealType getTemperature(); // Gives the instant temp. in K |
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> |
RealType getElectronicTemperature(); // gives the instant electronic temperature in K |
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|
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RealType getPressure(); // gives the instant pressure in atm; |
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RealType getPressureX() { return getPressure(0); } |
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RealType getPressureY() { return getPressure(1); } |
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RealType getPressureZ() { return getPressure(2); } |
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|
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Mat3x3d getPressureTensor(); // gives the pressure tensor in amu*fs^-2*Ang^-1 |
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|
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// gives the pressure tensor in amu*fs^-2*Ang^-1 |
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Mat3x3d getPressureTensor(); |
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RealType getVolume(); // gives the volume in Ang^3 |
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+ |
|
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// accumulate and return the simulation box dipole moment in C*m |
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Vector3d getSystemDipole(); |
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Vector3d getHeatFlux(); |
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+ |
|
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/** Returns the center of the mass of the whole system.*/ |
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Vector3d getCom(); |
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|
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/** Returns the velocity of center of mass of the whole system.*/ |
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Vector3d getComVel(); |
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|
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/** Returns the center of the mass and Center of Mass velocity of |
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the whole system.*/ |
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void getComAll(Vector3d& com,Vector3d& comVel); |
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|
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/** Returns intertia tensor for the entire system and system |
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Angular Momentum.*/ |
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void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
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|
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void saveStat(); |
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/** Returns system angular momentum */ |
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> |
Vector3d getAngularMomentum(); |
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|
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> |
/** Returns volume of system as estimated by an ellipsoid defined |
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by the radii of gyration */ |
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> |
RealType getGyrationalVolume(); |
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> |
|
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/** Overloaded version of gyrational volume that also returns |
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> |
det(I) so dV/dr can be calculated */ |
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void getGyrationalVolume(RealType &vol, RealType &detI); |
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|
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RealType getHullVolume(); |
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> |
|
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> |
RealType getTaggedAtomPairDistance(); |
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|
|
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private: |
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RealType getPressure(int direction); |
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|
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> |
private: |
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> |
private: |
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SimInfo* info_; |
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}; |
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|
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< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
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#endif |
