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#ifndef _EXTENDEDSYSTEM_H_ |
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#define _EXTENDEDSYSTEM_H_ |
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|
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#include <math.h> |
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|
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SimInfo.hpp" |
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|
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class ExtendedSystem{ |
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public: |
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|
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ExtendedSystem(SimInfo* the_entry_plug); |
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virtual ~ExtendedSystem() {} |
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|
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void setQmass(double q) {qmass = q; have_qmass = 1;} |
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTauBarostat(double tt) {tauBarostat = tt; have_tau_barostat = 1;} |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
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void setTargetPressure(double tp) {targetPressure=tp;have_target_pressure=1;} |
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|
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void NoseHooverNVT(double dt, double ke); |
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void NoseHooverAndersonNPT(double dt, double ke, double p_tensor[9]); |
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void ConstantStress(double dt, double ke, double p_tensor[9]); |
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void AffineTransform(double oldBox[3], double newBox[3]); |
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|
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protected: |
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|
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SimInfo* entry_plug; |
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|
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short int NVTready(); |
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short int NPTready(); |
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|
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// |
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int nAtoms; |
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int nMols; |
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int nOriented; |
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int ndf; |
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|
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Molecule* molecules; |
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Atom** atoms; |
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|
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// zeta and epsilonDot are propagated |
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double zeta; |
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double epsilonDot; |
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double epsilonDotX; |
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double epsilonDotY; |
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double epsilonDotZ; |
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|
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// qmass, tauRelax, targetTemp, and targetPressure are parameters that |
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// must be set |
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double qmass; |
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double targetTemp; |
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double targetPressure; |
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double tauThermostat; |
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double tauBarostat; |
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|
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short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
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short int have_target_pressure, have_qmass; |
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|
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}; |
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#endif |
