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#ifndef _INTEGRATOR_H_ |
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#define _INTEGRATOR_H_ |
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#include <string> |
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#include <vector> |
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "ZConsWriter.hpp" |
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using namespace std; |
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const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
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const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm |
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const int maxIteration = 300; |
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const double tol = 1.0e-6; |
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class Integrator : public BaseIntegrator { |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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public: |
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Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
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virtual ~Integrator(); |
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void integrate( void ); |
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virtual double getConservedQuantity(void); |
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protected: |
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virtual void integrateStep( int calcPot, int calcStress ); |
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virtual void preMove( void ); |
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virtual void moveA( void ); |
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virtual void constrainA( void ); |
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virtual void constrainB( void ); |
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virtual int readyCheck( void ) { return 1; } |
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|
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virtual void resetIntegrator( void ) { } |
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|
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(); |
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virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
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|
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void checkConstraints( void ); |
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void rotate( int axes1, int axes2, double angle, double j[3], |
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double A[9] ); |
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double A[3][3] ); |
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ForceFields* myFF; |
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SimInfo *info; // all the info we'll ever need |
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int nMols; |
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int isConstrained; // boolean to know whether the systems contains |
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// constraints. |
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// constraints. |
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int nConstrained; // counter for number of constraints |
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int *constrainedA; // the i of a constraint pair |
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int *constrainedB; // the j of a constraint pair |
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double dt; |
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double dt2; |
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double* pos; |
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double* vel; |
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double* frc; |
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double* trq; |
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double* Amat; |
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|
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Thermo *tStats; |
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StatWriter* statOut; |
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DumpWriter* dumpOut; |
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}; |
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class NVE : public Integrator{ |
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typedef Integrator<BaseIntegrator> RealIntegrator; |
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template<typename T> class NVE : public T { |
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|
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public: |
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NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
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Integrator( theInfo, the_ff ){} |
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virtual ~NVE(){} |
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T( theInfo, the_ff ){} |
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virtual ~NVE(){} |
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}; |
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class NVT : public Integrator{ |
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template<typename T> class NVT : public T { |
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public: |
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NVT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NVT() {} |
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virtual ~NVT(); |
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
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void setChiTolerance(double tol) {chiTolerance = tol;} |
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virtual double getConservedQuantity(void); |
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protected: |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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|
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// chi is a propagated degree of freedom. |
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double chi; |
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//integral of chi(t)dt |
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double integralOfChidt; |
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|
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// targetTemp must be set. tauThermostat must also be set; |
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double targetTemp; |
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short int have_tau_thermostat, have_target_temp; |
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double *oldVel; |
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double *oldJi; |
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|
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double chiTolerance; |
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short int have_chi_tolerance; |
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|
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}; |
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class NPTi : public Integrator{ |
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template<typename T> class NPT : public T{ |
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|
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public: |
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NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTi() {}; |
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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPT(); |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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T::integrateStep( calcPot, calcStress ); |
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} |
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virtual double getConservedQuantity(void) = 0; |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTauBarostat(double tb) {tauBarostat = tb; 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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void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;} |
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void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;} |
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protected: |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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|
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virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
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virtual void getVelScaleB( double sc[3], int index ) = 0; |
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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]) = 0; |
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|
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virtual bool chiConverged( void ); |
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virtual bool etaConverged( void ) = 0; |
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|
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virtual void evolveChiA( void ); |
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virtual void evolveEtaA( void ) = 0; |
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virtual void evolveChiB( void ); |
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virtual void evolveEtaB( void ) = 0; |
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|
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virtual void scaleSimBox( void ) = 0; |
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|
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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|
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// chi and eta are the propagated degrees of freedom |
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|
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double oldChi; |
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double prevChi; |
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double chi; |
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double eta; |
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double NkBT; |
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double fkBT; |
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|
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double tt2, tb2; |
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double instaTemp, instaPress, instaVol; |
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double press[3][3]; |
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|
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int Nparticles; |
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|
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double integralOfChidt; |
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|
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// targetTemp, targetPressure, and tauBarostat must be set. |
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// One of qmass or tauThermostat must be set; |
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short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
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short int have_target_pressure; |
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double *oldPos; |
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double *oldVel; |
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double *oldJi; |
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|
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double chiTolerance; |
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short int have_chi_tolerance; |
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double posIterTolerance; |
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short int have_pos_iter_tolerance; |
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double etaTolerance; |
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short int have_eta_tolerance; |
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|
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}; |
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class NPTf : public Integrator{ |
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template<typename T> class NPTi : public T{ |
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|
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public: |
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NPTi( SimInfo *theInfo, ForceFields* the_ff); |
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~NPTi(); |
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|
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virtual double getConservedQuantity(void); |
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virtual void resetIntegrator(void); |
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|
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protected: |
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|
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|
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|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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|
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virtual void getVelScaleA( double sc[3], double vel[3] ); |
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virtual void getVelScaleB( double sc[3], int index ); |
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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]); |
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|
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double eta, oldEta, prevEta; |
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}; |
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|
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template<typename T> class NPTzm : public T{ |
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|
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public: |
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|
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NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTzm() {}; |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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T::integrateStep( calcPot, calcStress ); |
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} |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTauBarostat(double tb) {tauBarostat = tb; 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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protected: |
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|
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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|
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virtual int readyCheck(); |
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|
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virtual void resetIntegrator( void ); |
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|
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Molecule* myMolecules; |
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Atom** myAtoms; |
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|
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// chi and eta are the propagated degrees of freedom |
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|
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double chi; |
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double eta; |
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double etaZ; |
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double NkBT; |
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|
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// targetTemp, targetPressure, and tauBarostat must be set. |
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// One of qmass or tauThermostat must be set; |
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|
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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; |
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|
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}; |
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|
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template<typename T> class NPTf : public T{ |
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|
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public: |
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|
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NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTf() {}; |
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virtual ~NPTf(); |
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|
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virtual double getConservedQuantity(void); |
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virtual void resetIntegrator(void); |
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|
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protected: |
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|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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|
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virtual void getVelScaleA( double sc[3], double vel[3] ); |
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virtual void getVelScaleB( double sc[3], int index ); |
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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]); |
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|
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double eta[3][3]; |
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double oldEta[3][3]; |
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double prevEta[3][3]; |
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}; |
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|
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template<typename T> class NPTxym : public T{ |
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|
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public: |
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|
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NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTxym() {}; |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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T::integrateStep( calcPot, calcStress ); |
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} |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
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|
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protected: |
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|
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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|
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virtual int readyCheck(); |
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|
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virtual void resetIntegrator( void ); |
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|
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Molecule* myMolecules; |
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Atom** myAtoms; |
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|
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// chi and eta are the propagated degrees of freedom |
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|
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double chi; |
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double eta; |
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double etaX; |
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double etaY; |
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double NkBT; |
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|
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// targetTemp, targetPressure, and tauBarostat must be set. |
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// One of qmass or tauThermostat must be set; |
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|
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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; |
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|
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}; |
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|
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|
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template<typename T> class NPTfm : public T{ |
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|
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public: |
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|
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NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTfm() {}; |
391 |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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T::integrateStep( calcPot, calcStress ); |
395 |
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accIntegralOfChidt(); |
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} |
397 |
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|
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virtual double getConservedQuantity(void); |
399 |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
401 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
402 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
403 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
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+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
405 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
406 |
+ |
|
407 |
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protected: |
408 |
+ |
|
409 |
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virtual void moveA( void ); |
410 |
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virtual void moveB( void ); |
411 |
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|
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+ |
virtual void resetIntegrator( void ); |
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|
414 |
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virtual int readyCheck(); |
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|
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
417 |
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|
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Molecule* myMolecules; |
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+ |
Atom** myAtoms; |
420 |
+ |
|
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// chi and eta are the propagated degrees of freedom |
422 |
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|
423 |
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double chi; |
424 |
< |
double eta[9]; |
424 |
> |
double eta[3][3]; |
425 |
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double NkBT; |
426 |
+ |
double integralOfChidt; |
427 |
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|
428 |
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// targetTemp, targetPressure, and tauBarostat must be set. |
429 |
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// One of qmass or tauThermostat must be set; |
435 |
|
|
436 |
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short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
437 |
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short int have_target_pressure; |
438 |
+ |
double chiTolerance; |
439 |
+ |
short int have_chi_tolerance; |
440 |
+ |
double posIterTolerance; |
441 |
+ |
short int have_pos_iter_tolerance; |
442 |
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|
443 |
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}; |
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|
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+ |
|
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template<typename T> class NPTpr : public T{ |
447 |
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|
448 |
+ |
public: |
449 |
+ |
|
450 |
+ |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
451 |
+ |
virtual ~NPTpr() {}; |
452 |
+ |
|
453 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
454 |
+ |
calcStress = 1; |
455 |
+ |
T::integrateStep( calcPot, calcStress ); |
456 |
+ |
} |
457 |
+ |
|
458 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
459 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
460 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
461 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
462 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
463 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
464 |
+ |
|
465 |
+ |
protected: |
466 |
+ |
|
467 |
+ |
virtual void moveA( void ); |
468 |
+ |
virtual void moveB( void ); |
469 |
+ |
|
470 |
+ |
virtual int readyCheck(); |
471 |
+ |
|
472 |
+ |
virtual void resetIntegrator( void ); |
473 |
+ |
|
474 |
+ |
// chi and eta are the propagated degrees of freedom |
475 |
+ |
|
476 |
+ |
double chi; |
477 |
+ |
double eta[3][3]; |
478 |
+ |
double NkBT; |
479 |
+ |
|
480 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
481 |
+ |
// One of qmass or tauThermostat must be set; |
482 |
+ |
|
483 |
+ |
double targetTemp; |
484 |
+ |
double targetPressure; |
485 |
+ |
double tauThermostat; |
486 |
+ |
double tauBarostat; |
487 |
+ |
|
488 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
489 |
+ |
short int have_target_pressure; |
490 |
+ |
double chiTolerance; |
491 |
+ |
short int have_chi_tolerance; |
492 |
+ |
double posIterTolerance; |
493 |
+ |
short int have_pos_iter_tolerance; |
494 |
+ |
|
495 |
+ |
}; |
496 |
+ |
|
497 |
+ |
|
498 |
+ |
template<typename T> class ZConstraint : public T { |
499 |
+ |
|
500 |
+ |
public: |
501 |
+ |
class ForceSubtractionPolicy{ |
502 |
+ |
public: |
503 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
504 |
+ |
|
505 |
+ |
virtual void update() = 0; |
506 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
507 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
508 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
509 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
510 |
+ |
|
511 |
+ |
protected: |
512 |
+ |
ZConstraint<T>* zconsIntegrator;; |
513 |
+ |
}; |
514 |
+ |
|
515 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
516 |
+ |
|
517 |
+ |
public: |
518 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
519 |
+ |
virtual void update(); |
520 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
521 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
522 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
523 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
524 |
+ |
|
525 |
+ |
private: |
526 |
+ |
int totNumOfMovingAtoms; |
527 |
+ |
}; |
528 |
+ |
|
529 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
530 |
+ |
|
531 |
+ |
public: |
532 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
533 |
+ |
|
534 |
+ |
virtual void update(); |
535 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
536 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
537 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
538 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
539 |
+ |
|
540 |
+ |
private: |
541 |
+ |
double totMassOfMovingAtoms; |
542 |
+ |
}; |
543 |
+ |
|
544 |
+ |
public: |
545 |
+ |
|
546 |
+ |
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
547 |
+ |
~ZConstraint(); |
548 |
+ |
|
549 |
+ |
void setZConsTime(double time) {this->zconsTime = time;} |
550 |
+ |
void getZConsTime() {return zconsTime;} |
551 |
+ |
|
552 |
+ |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
553 |
+ |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
554 |
+ |
|
555 |
+ |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
556 |
+ |
string getZConsOutput() {return zconsOutput;} |
557 |
+ |
|
558 |
+ |
virtual void integrate(); |
559 |
+ |
|
560 |
+ |
|
561 |
+ |
#ifdef IS_MPI |
562 |
+ |
virtual void update(); //which is called to indicate the molecules' migration |
563 |
|
#endif |
564 |
+ |
|
565 |
+ |
protected: |
566 |
+ |
|
567 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
568 |
+ |
|
569 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
570 |
+ |
virtual void thermalize(void); |
571 |
+ |
|
572 |
+ |
void zeroOutVel(); |
573 |
+ |
void doZconstraintForce(); |
574 |
+ |
void doHarmonic(); |
575 |
+ |
bool checkZConsState(); |
576 |
+ |
|
577 |
+ |
bool haveFixedZMols(); |
578 |
+ |
bool haveMovingZMols(); |
579 |
+ |
|
580 |
+ |
double calcZSys(); |
581 |
+ |
|
582 |
+ |
int isZConstraintMol(Molecule* mol); |
583 |
+ |
|
584 |
+ |
|
585 |
+ |
double zconsTime; //sample time |
586 |
+ |
double zconsTol; //tolerance of z-contratint |
587 |
+ |
double zForceConst; //base force constant term |
588 |
+ |
//which is estimate by OOPSE |
589 |
+ |
|
590 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
591 |
+ |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
592 |
+ |
vector<double> kz; //force constant array |
593 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
594 |
+ |
vector<double> zPos; // |
595 |
+ |
|
596 |
+ |
|
597 |
+ |
vector<Molecule*> unconsMols; //unconstraint molecules array |
598 |
+ |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
599 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
600 |
+ |
|
601 |
+ |
vector<ZConsParaItem>* parameters; // |
602 |
+ |
|
603 |
+ |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
604 |
+ |
|
605 |
+ |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
606 |
+ |
double* fz; |
607 |
+ |
double* curZPos; |
608 |
+ |
|
609 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
610 |
+ |
|
611 |
+ |
int whichDirection; //constraint direction |
612 |
+ |
|
613 |
+ |
private: |
614 |
+ |
|
615 |
+ |
string zconsOutput; //filename of zconstraint output |
616 |
+ |
ZConsWriter* fzOut; //z-constraint writer |
617 |
+ |
|
618 |
+ |
double curZconsTime; |
619 |
+ |
|
620 |
+ |
double calcMovingMolsCOMVel(); |
621 |
+ |
double calcSysCOMVel(); |
622 |
+ |
double calcTotalForce(); |
623 |
+ |
|
624 |
+ |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
625 |
+ |
friend class ForceSubtractionPolicy; |
626 |
+ |
|
627 |
+ |
}; |
628 |
+ |
|
629 |
+ |
#endif |