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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 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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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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|
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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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|
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class NPTi : 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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virtual ~NPTi() {}; |
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virtual ~NPTi(); |
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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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/* accIntegralOfChidt(); */ |
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} |
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virtual double getConservedQuantity(void); |
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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 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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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 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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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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|
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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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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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double volume; |
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|
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}; |
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|
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template<typename T> class NPTim : public T{ |
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|
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public: |
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|
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NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTim() {} |
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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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accIntegralOfChidt(); |
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} |
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|
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virtual double getConservedQuantity(void); |
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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;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
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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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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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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 NkBT; |
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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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|
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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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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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}; |
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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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|
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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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|
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virtual double getConservedQuantity(void); |
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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;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
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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 void resetIntegrator( void ); |
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|
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virtual int readyCheck(); |
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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 chi; |
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double eta[3][3]; |
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double NkBT; |
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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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|
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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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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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}; |
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|
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template<typename T> class NPTxym : public T{ |
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|
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public: |
379 |
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|
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NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTxym() {}; |
382 |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
384 |
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calcStress = 1; |
385 |
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T::integrateStep( calcPot, calcStress ); |
386 |
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} |
387 |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
389 |
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void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
390 |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
391 |
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void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
392 |
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|
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protected: |
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|
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virtual void moveA( void ); |
396 |
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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 |
406 |
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|
407 |
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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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|
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}; |
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|
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|
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template<typename T> class NPTfm : public T{ |
428 |
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|
429 |
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public: |
430 |
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|
431 |
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NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
432 |
+ |
virtual ~NPTfm() {}; |
433 |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
435 |
+ |
calcStress = 1; |
436 |
+ |
T::integrateStep( calcPot, calcStress ); |
437 |
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accIntegralOfChidt(); |
438 |
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} |
439 |
+ |
|
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virtual double getConservedQuantity(void); |
441 |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
443 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
444 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
445 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
446 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
447 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
448 |
+ |
|
449 |
+ |
protected: |
450 |
+ |
|
451 |
+ |
virtual void moveA( void ); |
452 |
+ |
virtual void moveB( void ); |
453 |
+ |
|
454 |
+ |
virtual void resetIntegrator( void ); |
455 |
+ |
|
456 |
+ |
virtual int readyCheck(); |
457 |
+ |
|
458 |
+ |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
459 |
+ |
|
460 |
+ |
Molecule* myMolecules; |
461 |
+ |
Atom** myAtoms; |
462 |
+ |
|
463 |
+ |
// chi and eta are the propagated degrees of freedom |
464 |
+ |
|
465 |
+ |
double chi; |
466 |
+ |
double eta[3][3]; |
467 |
+ |
double NkBT; |
468 |
+ |
double integralOfChidt; |
469 |
+ |
|
470 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
471 |
+ |
// One of qmass or tauThermostat must be set; |
472 |
+ |
|
473 |
+ |
double targetTemp; |
474 |
+ |
double targetPressure; |
475 |
+ |
double tauThermostat; |
476 |
+ |
double tauBarostat; |
477 |
+ |
|
478 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
479 |
+ |
short int have_target_pressure; |
480 |
+ |
double chiTolerance; |
481 |
+ |
short int have_chi_tolerance; |
482 |
+ |
double posIterTolerance; |
483 |
+ |
short int have_pos_iter_tolerance; |
484 |
+ |
|
485 |
+ |
}; |
486 |
+ |
|
487 |
+ |
|
488 |
+ |
template<typename T> class NPTpr : public T{ |
489 |
+ |
|
490 |
+ |
public: |
491 |
+ |
|
492 |
+ |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
493 |
+ |
virtual ~NPTpr() {}; |
494 |
+ |
|
495 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
496 |
+ |
calcStress = 1; |
497 |
+ |
T::integrateStep( calcPot, calcStress ); |
498 |
+ |
} |
499 |
+ |
|
500 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
501 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
502 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
503 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
504 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
505 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
506 |
+ |
|
507 |
+ |
protected: |
508 |
+ |
|
509 |
+ |
virtual void moveA( void ); |
510 |
+ |
virtual void moveB( void ); |
511 |
+ |
|
512 |
+ |
virtual int readyCheck(); |
513 |
+ |
|
514 |
+ |
virtual void resetIntegrator( void ); |
515 |
+ |
|
516 |
+ |
// chi and eta are the propagated degrees of freedom |
517 |
+ |
|
518 |
+ |
double chi; |
519 |
+ |
double eta[3][3]; |
520 |
+ |
double NkBT; |
521 |
+ |
|
522 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
523 |
+ |
// One of qmass or tauThermostat must be set; |
524 |
+ |
|
525 |
+ |
double targetTemp; |
526 |
+ |
double targetPressure; |
527 |
+ |
double tauThermostat; |
528 |
+ |
double tauBarostat; |
529 |
+ |
|
530 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
531 |
+ |
short int have_target_pressure; |
532 |
+ |
double chiTolerance; |
533 |
+ |
short int have_chi_tolerance; |
534 |
+ |
double posIterTolerance; |
535 |
+ |
short int have_pos_iter_tolerance; |
536 |
+ |
|
537 |
+ |
}; |
538 |
+ |
|
539 |
+ |
|
540 |
+ |
template<typename T> class ZConstraint : public T { |
541 |
+ |
|
542 |
+ |
public: |
543 |
+ |
class ForceSubtractionPolicy{ |
544 |
+ |
public: |
545 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
546 |
+ |
|
547 |
+ |
virtual void update() = 0; |
548 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
549 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
550 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
551 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
552 |
+ |
|
553 |
+ |
protected: |
554 |
+ |
ZConstraint<T>* zconsIntegrator;; |
555 |
+ |
}; |
556 |
+ |
|
557 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
558 |
+ |
|
559 |
+ |
public: |
560 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
561 |
+ |
virtual void update(); |
562 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
563 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
564 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
565 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
566 |
+ |
|
567 |
+ |
private: |
568 |
+ |
int totNumOfMovingAtoms; |
569 |
+ |
}; |
570 |
+ |
|
571 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
572 |
+ |
|
573 |
+ |
public: |
574 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
575 |
+ |
|
576 |
+ |
virtual void update(); |
577 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
578 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
579 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
580 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
581 |
+ |
|
582 |
+ |
private: |
583 |
+ |
double totMassOfMovingAtoms; |
584 |
+ |
}; |
585 |
+ |
|
586 |
+ |
public: |
587 |
+ |
|
588 |
+ |
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
589 |
+ |
~ZConstraint(); |
590 |
+ |
|
591 |
+ |
void setZConsTime(double time) {this->zconsTime = time;} |
592 |
+ |
void getZConsTime() {return zconsTime;} |
593 |
+ |
|
594 |
+ |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
595 |
+ |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
596 |
+ |
|
597 |
+ |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
598 |
+ |
string getZConsOutput() {return zconsOutput;} |
599 |
+ |
|
600 |
+ |
virtual void integrate(); |
601 |
+ |
|
602 |
+ |
|
603 |
+ |
#ifdef IS_MPI |
604 |
+ |
virtual void update(); //which is called to indicate the molecules' migration |
605 |
|
#endif |
606 |
+ |
|
607 |
+ |
protected: |
608 |
+ |
|
609 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
610 |
+ |
|
611 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
612 |
+ |
virtual void thermalize(void); |
613 |
+ |
|
614 |
+ |
void zeroOutVel(); |
615 |
+ |
void doZconstraintForce(); |
616 |
+ |
void doHarmonic(); |
617 |
+ |
bool checkZConsState(); |
618 |
+ |
|
619 |
+ |
bool haveFixedZMols(); |
620 |
+ |
bool haveMovingZMols(); |
621 |
+ |
|
622 |
+ |
double calcZSys(); |
623 |
+ |
|
624 |
+ |
int isZConstraintMol(Molecule* mol); |
625 |
+ |
|
626 |
+ |
|
627 |
+ |
double zconsTime; //sample time |
628 |
+ |
double zconsTol; //tolerance of z-contratint |
629 |
+ |
double zForceConst; //base force constant term |
630 |
+ |
//which is estimate by OOPSE |
631 |
+ |
|
632 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
633 |
+ |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
634 |
+ |
vector<double> kz; //force constant array |
635 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
636 |
+ |
vector<double> zPos; // |
637 |
+ |
|
638 |
+ |
|
639 |
+ |
vector<Molecule*> unconsMols; //unconstraint molecules array |
640 |
+ |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
641 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
642 |
+ |
|
643 |
+ |
vector<ZConsParaItem>* parameters; // |
644 |
+ |
|
645 |
+ |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
646 |
+ |
|
647 |
+ |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
648 |
+ |
double* fz; |
649 |
+ |
double* curZPos; |
650 |
+ |
|
651 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
652 |
+ |
|
653 |
+ |
int whichDirection; //constraint direction |
654 |
+ |
|
655 |
+ |
private: |
656 |
+ |
|
657 |
+ |
string zconsOutput; //filename of zconstraint output |
658 |
+ |
ZConsWriter* fzOut; //z-constraint writer |
659 |
+ |
|
660 |
+ |
double curZconsTime; |
661 |
+ |
|
662 |
+ |
double calcMovingMolsCOMVel(); |
663 |
+ |
double calcSysCOMVel(); |
664 |
+ |
double calcTotalForce(); |
665 |
+ |
|
666 |
+ |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
667 |
+ |
friend class ForceSubtractionPolicy; |
668 |
+ |
|
669 |
+ |
}; |
670 |
+ |
|
671 |
+ |
#endif |