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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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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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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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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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// chi is a propagated degree of freedom. |
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double chi; |
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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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}; |
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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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virtual ~NPTi() {}; |
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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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// 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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// 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 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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} |
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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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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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// 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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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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// chi and eta are the propagated degrees of freedom |
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double chi; |
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double eta[3][3]; |
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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 NPTfm : public T{ |
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public: |
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NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTfm() {}; |
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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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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[3][3]; |
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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 ZConstraint : public T { |
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public: |
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ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
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~ZConstraint(); |
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virtual void integrateStep( int calcPot, int calcStress ); |
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void setZConsTime(double time) {this->zconsTime = time;} |
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void getZConsTime() {return zconsTime;} |
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void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
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void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
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void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
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string getZConsOutput() {return zconsOutput;} |
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#ifdef IS_MPI |
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virtual void update(); //which is called to indicate the molecules' migration |
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#endif |
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protected: |
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double zconsTime; |
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void resetZ(void); |
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vector<Molecule*> zconsMols; |
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vector<double> massOfZConsMols; |
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vector<Molecule*> unconsMols; |
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vector<double> massOfUnconsMols; |
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double totalMassOfUncons; |
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vector<double> allRefZ; |
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vector<double> refZ; |
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vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
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int* indexOfZConsMols; //index of local Z-Constraint Molecules |
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double* fz; |
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private: |
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int isZConstraintMol(Molecule* mol); |
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string zconsOutput; |
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ZConsWriter* fzOut; |
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}; |
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#endif |
