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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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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 moveB( 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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virtual void resetIntegrator( void ) { } |
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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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void checkConstraints( void ); |
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void rotate( int axes1, int axes2, double angle, double j[3], |
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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 nAtoms; /* the number of atoms */ |
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int oldAtoms; |
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Atom **atoms; /* array of atom pointers */ |
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Molecule* molecules; |
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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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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 *constrainedDsqr; // the square of the constraint distance |
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int* moving; // tells whether we are moving atom i |
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int* moved; // tells whether we have moved atom i |
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double* oldPos; // pre constrained positions |
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short isFirst; /*boolean for the first time integrate is called */ |
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double dt; |
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double dt2; |
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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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typedef Integrator<BaseIntegrator> RealIntegrator; |
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template<typename T> class NVE : public T { |
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public: |
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NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
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T( theInfo, the_ff ){} |
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virtual ~NVE(){} |
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}; |
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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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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 void moveA( void ); |
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virtual void moveB( void ); |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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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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// targetTemp must be set. tauThermostat must also be set; |
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double targetTemp; |
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double tauThermostat; |
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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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double chiTolerance; |
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short int have_chi_tolerance; |
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}; |
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template<typename T> class NPT : public T{ |
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public: |
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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPT(); |
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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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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 void moveA( void ); |
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virtual void moveB( void ); |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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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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virtual bool chiConverged( void ); |
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virtual bool etaConverged( void ) = 0; |
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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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virtual void scaleSimBox( void ) = 0; |
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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// chi and eta are the propagated degrees of freedom |
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double oldChi; |
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double prevChi; |
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double chi; |
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double NkBT; |
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double fkBT; |
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double tt2, tb2; |
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double instaTemp, instaPress, instaVol; |
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int Nparticles; |
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double integralOfChidt; |
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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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double targetTemp; |
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double targetPressure; |
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double tauThermostat; |
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double tauBarostat; |
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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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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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template<typename T> class NPTi : public T{ |
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public: |
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NPTi( SimInfo *theInfo, ForceFields* the_ff); |
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~NPTi(); |
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virtual double getConservedQuantity(void); |
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virtual void resetIntegrator(void); |
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protected: |
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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virtual bool etaConverged( void ); |
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virtual void scaleSimBox( void ); |
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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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double eta, oldEta, prevEta; |
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}; |
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template<typename T> class NPTim : public T{ |
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public: |
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NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTim() {} |
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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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accIntegralOfChidt(); |
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} |
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virtual double getConservedQuantity(void); |
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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;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
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protected: |
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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Molecule* myMolecules; |
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Atom** myAtoms; |
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// chi and eta are the propagated degrees of freedom |
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double chi; |
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double eta; |
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double NkBT; |
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double integralOfChidt; |
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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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double targetTemp; |
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double targetPressure; |
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double tauThermostat; |
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double tauBarostat; |
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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 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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}; |
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template<typename T> class NPTzm : public T{ |
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public: |
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NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTzm() {}; |
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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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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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protected: |
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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virtual int readyCheck(); |
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virtual void resetIntegrator( void ); |
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Molecule* myMolecules; |
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Atom** myAtoms; |
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// chi and eta are the propagated degrees of freedom |
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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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// targetTemp, targetPressure, and tauBarostat must be set. |
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// One of qmass or tauThermostat must be set; |
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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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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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template<typename T> class NPTf : public T{ |
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public: |
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NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTf(); |
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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); |
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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;} |
382 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
383 |
tim |
763 |
void setChiTolerance(double tol) {chiTolerance = tol;} |
384 |
|
|
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
385 |
gezelter |
576 |
|
386 |
|
|
protected: |
387 |
|
|
|
388 |
|
|
virtual void moveA( void ); |
389 |
|
|
virtual void moveB( void ); |
390 |
|
|
|
391 |
mmeineke |
746 |
virtual void resetIntegrator( void ); |
392 |
|
|
|
393 |
gezelter |
576 |
virtual int readyCheck(); |
394 |
|
|
|
395 |
tim |
763 |
|
396 |
gezelter |
576 |
// chi and eta are the propagated degrees of freedom |
397 |
|
|
|
398 |
|
|
double chi; |
399 |
gezelter |
588 |
double eta[3][3]; |
400 |
gezelter |
576 |
double NkBT; |
401 |
tim |
767 |
double fkBT; |
402 |
gezelter |
576 |
|
403 |
tim |
767 |
int Nparticles; |
404 |
|
|
|
405 |
|
|
double *oldPos; |
406 |
|
|
double *oldVel; |
407 |
|
|
double *oldJi; |
408 |
|
|
|
409 |
tim |
763 |
double integralOfChidt; |
410 |
|
|
|
411 |
gezelter |
576 |
// targetTemp, targetPressure, and tauBarostat must be set. |
412 |
|
|
// One of qmass or tauThermostat must be set; |
413 |
|
|
|
414 |
|
|
double targetTemp; |
415 |
|
|
double targetPressure; |
416 |
|
|
double tauThermostat; |
417 |
|
|
double tauBarostat; |
418 |
|
|
|
419 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
420 |
|
|
short int have_target_pressure; |
421 |
tim |
763 |
double chiTolerance; |
422 |
|
|
short int have_chi_tolerance; |
423 |
|
|
double posIterTolerance; |
424 |
|
|
short int have_pos_iter_tolerance; |
425 |
tim |
767 |
double etaTolerance; |
426 |
|
|
short int have_eta_tolerance; |
427 |
gezelter |
576 |
}; |
428 |
|
|
|
429 |
mmeineke |
755 |
template<typename T> class NPTxym : public T{ |
430 |
|
|
|
431 |
|
|
public: |
432 |
|
|
|
433 |
|
|
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
434 |
|
|
virtual ~NPTxym() {}; |
435 |
|
|
|
436 |
|
|
virtual void integrateStep( int calcPot, int calcStress ){ |
437 |
|
|
calcStress = 1; |
438 |
|
|
T::integrateStep( calcPot, calcStress ); |
439 |
|
|
} |
440 |
|
|
|
441 |
|
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
442 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
443 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
444 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
445 |
|
|
|
446 |
|
|
protected: |
447 |
|
|
|
448 |
|
|
virtual void moveA( void ); |
449 |
|
|
virtual void moveB( void ); |
450 |
|
|
|
451 |
|
|
virtual int readyCheck(); |
452 |
|
|
|
453 |
|
|
virtual void resetIntegrator( void ); |
454 |
|
|
|
455 |
|
|
Molecule* myMolecules; |
456 |
|
|
Atom** myAtoms; |
457 |
|
|
|
458 |
|
|
// chi and eta are the propagated degrees of freedom |
459 |
|
|
|
460 |
|
|
double chi; |
461 |
|
|
double eta; |
462 |
|
|
double etaX; |
463 |
|
|
double etaY; |
464 |
|
|
double NkBT; |
465 |
|
|
|
466 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
467 |
|
|
// One of qmass or tauThermostat must be set; |
468 |
|
|
|
469 |
|
|
double targetTemp; |
470 |
|
|
double targetPressure; |
471 |
|
|
double tauThermostat; |
472 |
|
|
double tauBarostat; |
473 |
|
|
|
474 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
475 |
|
|
short int have_target_pressure; |
476 |
|
|
|
477 |
|
|
}; |
478 |
|
|
|
479 |
|
|
|
480 |
tim |
645 |
template<typename T> class NPTfm : public T{ |
481 |
gezelter |
596 |
|
482 |
|
|
public: |
483 |
|
|
|
484 |
|
|
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
485 |
|
|
virtual ~NPTfm() {}; |
486 |
|
|
|
487 |
|
|
virtual void integrateStep( int calcPot, int calcStress ){ |
488 |
|
|
calcStress = 1; |
489 |
tim |
645 |
T::integrateStep( calcPot, calcStress ); |
490 |
tim |
763 |
accIntegralOfChidt(); |
491 |
gezelter |
596 |
} |
492 |
|
|
|
493 |
tim |
763 |
virtual double getConservedQuantity(void); |
494 |
|
|
|
495 |
gezelter |
596 |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
496 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
497 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
498 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
499 |
tim |
763 |
void setChiTolerance(double tol) {chiTolerance = tol;} |
500 |
|
|
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
501 |
gezelter |
596 |
|
502 |
|
|
protected: |
503 |
|
|
|
504 |
|
|
virtual void moveA( void ); |
505 |
|
|
virtual void moveB( void ); |
506 |
|
|
|
507 |
mmeineke |
746 |
virtual void resetIntegrator( void ); |
508 |
|
|
|
509 |
gezelter |
596 |
virtual int readyCheck(); |
510 |
|
|
|
511 |
tim |
763 |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
512 |
|
|
|
513 |
gezelter |
605 |
Molecule* myMolecules; |
514 |
|
|
Atom** myAtoms; |
515 |
|
|
|
516 |
gezelter |
596 |
// chi and eta are the propagated degrees of freedom |
517 |
|
|
|
518 |
|
|
double chi; |
519 |
|
|
double eta[3][3]; |
520 |
|
|
double NkBT; |
521 |
tim |
763 |
double integralOfChidt; |
522 |
gezelter |
596 |
|
523 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
524 |
|
|
// One of qmass or tauThermostat must be set; |
525 |
|
|
|
526 |
|
|
double targetTemp; |
527 |
|
|
double targetPressure; |
528 |
|
|
double tauThermostat; |
529 |
|
|
double tauBarostat; |
530 |
|
|
|
531 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
532 |
|
|
short int have_target_pressure; |
533 |
tim |
763 |
double chiTolerance; |
534 |
|
|
short int have_chi_tolerance; |
535 |
|
|
double posIterTolerance; |
536 |
|
|
short int have_pos_iter_tolerance; |
537 |
gezelter |
596 |
|
538 |
|
|
}; |
539 |
|
|
|
540 |
gezelter |
718 |
|
541 |
|
|
template<typename T> class NPTpr : public T{ |
542 |
|
|
|
543 |
|
|
public: |
544 |
|
|
|
545 |
|
|
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
546 |
|
|
virtual ~NPTpr() {}; |
547 |
|
|
|
548 |
|
|
virtual void integrateStep( int calcPot, int calcStress ){ |
549 |
|
|
calcStress = 1; |
550 |
|
|
T::integrateStep( calcPot, calcStress ); |
551 |
|
|
} |
552 |
|
|
|
553 |
|
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
554 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
555 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
556 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
557 |
tim |
763 |
void setChiTolerance(double tol) {chiTolerance = tol;} |
558 |
|
|
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
559 |
gezelter |
718 |
|
560 |
|
|
protected: |
561 |
|
|
|
562 |
|
|
virtual void moveA( void ); |
563 |
|
|
virtual void moveB( void ); |
564 |
|
|
|
565 |
|
|
virtual int readyCheck(); |
566 |
|
|
|
567 |
mmeineke |
746 |
virtual void resetIntegrator( void ); |
568 |
|
|
|
569 |
gezelter |
718 |
// chi and eta are the propagated degrees of freedom |
570 |
|
|
|
571 |
|
|
double chi; |
572 |
|
|
double eta[3][3]; |
573 |
|
|
double NkBT; |
574 |
|
|
|
575 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
576 |
|
|
// One of qmass or tauThermostat must be set; |
577 |
|
|
|
578 |
|
|
double targetTemp; |
579 |
|
|
double targetPressure; |
580 |
|
|
double tauThermostat; |
581 |
|
|
double tauBarostat; |
582 |
|
|
|
583 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
584 |
|
|
short int have_target_pressure; |
585 |
tim |
763 |
double chiTolerance; |
586 |
|
|
short int have_chi_tolerance; |
587 |
|
|
double posIterTolerance; |
588 |
|
|
short int have_pos_iter_tolerance; |
589 |
gezelter |
718 |
|
590 |
|
|
}; |
591 |
|
|
|
592 |
|
|
|
593 |
tim |
658 |
template<typename T> class ZConstraint : public T { |
594 |
tim |
701 |
|
595 |
|
|
public: |
596 |
tim |
738 |
class ForceSubtractionPolicy{ |
597 |
tim |
699 |
public: |
598 |
tim |
738 |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
599 |
tim |
658 |
|
600 |
tim |
701 |
virtual void update() = 0; |
601 |
tim |
699 |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
602 |
|
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
603 |
tim |
701 |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
604 |
|
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
605 |
|
|
|
606 |
|
|
protected: |
607 |
|
|
ZConstraint<T>* zconsIntegrator;; |
608 |
tim |
699 |
}; |
609 |
|
|
|
610 |
tim |
738 |
class PolicyByNumber : public ForceSubtractionPolicy{ |
611 |
gezelter |
747 |
|
612 |
tim |
699 |
public: |
613 |
tim |
738 |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
614 |
tim |
701 |
virtual void update(); |
615 |
tim |
699 |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
616 |
|
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
617 |
tim |
701 |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
618 |
|
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
619 |
|
|
|
620 |
tim |
699 |
private: |
621 |
tim |
763 |
int totNumOfMovingAtoms; |
622 |
tim |
699 |
}; |
623 |
|
|
|
624 |
tim |
738 |
class PolicyByMass : public ForceSubtractionPolicy{ |
625 |
gezelter |
747 |
|
626 |
tim |
699 |
public: |
627 |
tim |
738 |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
628 |
tim |
701 |
|
629 |
|
|
virtual void update(); |
630 |
tim |
699 |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
631 |
|
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
632 |
tim |
701 |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
633 |
|
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
634 |
tim |
699 |
|
635 |
tim |
701 |
private: |
636 |
|
|
double totMassOfMovingAtoms; |
637 |
tim |
699 |
}; |
638 |
|
|
|
639 |
tim |
658 |
public: |
640 |
|
|
|
641 |
|
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
642 |
|
|
~ZConstraint(); |
643 |
tim |
677 |
|
644 |
tim |
658 |
void setZConsTime(double time) {this->zconsTime = time;} |
645 |
|
|
void getZConsTime() {return zconsTime;} |
646 |
|
|
|
647 |
tim |
701 |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
648 |
|
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
649 |
tim |
658 |
|
650 |
tim |
701 |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
651 |
tim |
658 |
string getZConsOutput() {return zconsOutput;} |
652 |
tim |
677 |
|
653 |
|
|
virtual void integrate(); |
654 |
|
|
|
655 |
tim |
658 |
|
656 |
|
|
#ifdef IS_MPI |
657 |
tim |
701 |
virtual void update(); //which is called to indicate the molecules' migration |
658 |
mmeineke |
377 |
#endif |
659 |
tim |
658 |
|
660 |
|
|
protected: |
661 |
|
|
|
662 |
tim |
701 |
enum ZConsState {zcsMoving, zcsFixed}; |
663 |
tim |
677 |
|
664 |
|
|
virtual void calcForce( int calcPot, int calcStress ); |
665 |
|
|
virtual void thermalize(void); |
666 |
|
|
|
667 |
|
|
void zeroOutVel(); |
668 |
|
|
void doZconstraintForce(); |
669 |
tim |
682 |
void doHarmonic(); |
670 |
tim |
677 |
bool checkZConsState(); |
671 |
|
|
|
672 |
|
|
bool haveFixedZMols(); |
673 |
|
|
bool haveMovingZMols(); |
674 |
|
|
|
675 |
|
|
double calcZSys(); |
676 |
|
|
|
677 |
|
|
int isZConstraintMol(Molecule* mol); |
678 |
|
|
|
679 |
|
|
|
680 |
tim |
701 |
double zconsTime; //sample time |
681 |
|
|
double zconsTol; //tolerance of z-contratint |
682 |
|
|
double zForceConst; //base force constant term |
683 |
|
|
//which is estimate by OOPSE |
684 |
tim |
658 |
|
685 |
tim |
701 |
vector<Molecule*> zconsMols; //z-constraint molecules array |
686 |
|
|
vector<double> massOfZConsMols; //mass of z-constraint molecule |
687 |
|
|
vector<double> kz; //force constant array |
688 |
|
|
vector<ZConsState> states; //state of z-constraint molecules |
689 |
|
|
vector<double> zPos; // |
690 |
tim |
658 |
|
691 |
tim |
677 |
|
692 |
tim |
701 |
vector<Molecule*> unconsMols; //unconstraint molecules array |
693 |
|
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
694 |
|
|
double totalMassOfUncons; //total mas of unconstraint molecules |
695 |
tim |
682 |
|
696 |
tim |
701 |
vector<ZConsParaItem>* parameters; // |
697 |
tim |
658 |
|
698 |
|
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
699 |
tim |
677 |
|
700 |
|
|
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
701 |
tim |
658 |
double* fz; |
702 |
tim |
699 |
double* curZPos; |
703 |
tim |
658 |
|
704 |
tim |
701 |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
705 |
tim |
677 |
|
706 |
|
|
int whichDirection; //constraint direction |
707 |
|
|
|
708 |
tim |
658 |
private: |
709 |
tim |
677 |
|
710 |
tim |
701 |
string zconsOutput; //filename of zconstraint output |
711 |
|
|
ZConsWriter* fzOut; //z-constraint writer |
712 |
tim |
677 |
|
713 |
tim |
701 |
double curZconsTime; |
714 |
tim |
699 |
|
715 |
tim |
696 |
double calcMovingMolsCOMVel(); |
716 |
|
|
double calcSysCOMVel(); |
717 |
|
|
double calcTotalForce(); |
718 |
tim |
701 |
|
719 |
gezelter |
747 |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
720 |
tim |
738 |
friend class ForceSubtractionPolicy; |
721 |
tim |
677 |
|
722 |
tim |
658 |
}; |
723 |
|
|
|
724 |
|
|
#endif |