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#ifndef __THERMO_H__ |
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#define __THERMO_H__ |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#ifndef BRAINS_THERMO_HPP |
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#define BRAINS_THERMO_HPP |
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "SimInfo.hpp" |
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#include "randomSPRNG.hpp" |
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#include "primitives/Atom.hpp" |
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#include "brains/SimInfo.hpp" |
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class Thermo{ |
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namespace OpenMD { |
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public: |
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Thermo( SimInfo* the_info ); |
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~Thermo(); |
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class Thermo{ |
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// note: all the following energies are in kcal/mol |
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public: |
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double getKinetic(); // the total kinetic energy |
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double getPotential(); // the total potential energy |
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double getTotalE(); // gets the total energy |
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Thermo( SimInfo* info) : info_(info) {} |
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double getTemperature(); // gives the instant temp. in K |
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// note: all the following energies are in kcal/mol |
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double getPressure(); // gives the instant pressure in atm; |
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double getPressureX(); // gives the instant pressure in atm; |
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double getPressureY(); // gives the instant pressure in atm; |
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double getPressureZ(); // gives the instant pressure in atm; |
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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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void getPressureTensor(double press[3][3]); // gives the pressure |
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// tensor in |
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// amu*fs^-2*Ang^-1 |
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double getVolume(); // gives the volume in Ang^3 |
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RealType getTemperature(); // gives the instant temp. in K |
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int getNDF(); // get the number of degrees of freedom in the system |
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int getNDFraw(); // get the number of raw degrees of freedom in the system |
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// i.e. don't subtract constraints or system COM. |
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void velocitize(); // set the temperature to the target temp in SimInfo |
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// NOTE: srand48 should be seeded before calling. |
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void getCOMVel(double vdrift[3]); |
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void getCOM(double COM[3]); |
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void removeCOMdrift(); |
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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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private: |
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SimInfo* info; |
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gaussianSPRNG *gaussStream; |
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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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// accumulate and return the simulation box dipole moment in C*m |
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Vector3d getBoxDipole(); |
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void saveStat(); |
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private: |
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RealType getPressure(int direction); |
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SimInfo* info_; |
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}; |
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} //end namespace OpenMD |
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#endif |
