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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 "StuntDouble.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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#include "Restraints.hpp" |
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|
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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 RattleFramework; |
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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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virtual string getAdditionalParameters(void); |
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protected: |
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|
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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 bool stopIntegrator() {return false;} |
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virtual void rotationPropagation( StuntDouble* sd, 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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vector<StuntDouble*> integrableObjects; |
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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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RattleFramework* rattle; |
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//int isConstrained; // boolean to know whether the systems contains 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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// ansi instantiation |
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template class Integrator<BaseIntegrator>; |
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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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virtual string getAdditionalParameters(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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virtual string getAdditionalParameters(void) = 0; |
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double myTauThermo( void ) { return tauThermostat; } |
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double myTauBaro( void ) { return tauBarostat; } |
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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 void calcVelScale( void ) = 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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double press[3][3]; |
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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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virtual string getAdditionalParameters(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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virtual void calcVelScale( void ); |
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double eta, oldEta, prevEta; |
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double vScale; |
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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 double getConservedQuantity(void); |
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virtual string getAdditionalParameters(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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virtual void calcVelScale( void ); |
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double eta[3][3]; |
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double oldEta[3][3]; |
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double prevEta[3][3]; |
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double vScale[3][3]; |
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}; |
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template<typename T> class NPTxyz : public T{ |
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public: |
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NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTxyz(); |
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virtual double getConservedQuantity(void); |
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virtual string getAdditionalParameters(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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virtual void calcVelScale( void ); |
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double eta[3][3]; |
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double oldEta[3][3]; |
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double prevEta[3][3]; |
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double vScale[3][3]; |
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}; |
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template<typename T> class ZConstraint : public T { |
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public: |
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class ForceSubtractionPolicy{ |
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public: |
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ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
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virtual void update() = 0; |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
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virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
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virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
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virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
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protected: |
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ZConstraint<T>* zconsIntegrator; |
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}; |
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class PolicyByNumber : public ForceSubtractionPolicy{ |
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public: |
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PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
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virtual void update(); |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
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virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
367 |
tim |
701 |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
368 |
|
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
369 |
tim |
837 |
|
370 |
tim |
699 |
private: |
371 |
tim |
763 |
int totNumOfMovingAtoms; |
372 |
tim |
699 |
}; |
373 |
|
|
|
374 |
tim |
738 |
class PolicyByMass : public ForceSubtractionPolicy{ |
375 |
gezelter |
747 |
|
376 |
tim |
699 |
public: |
377 |
tim |
837 |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
378 |
|
|
|
379 |
|
|
virtual void update(); |
380 |
tim |
699 |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
381 |
|
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
382 |
tim |
701 |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
383 |
|
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
384 |
tim |
699 |
|
385 |
tim |
701 |
private: |
386 |
|
|
double totMassOfMovingAtoms; |
387 |
tim |
699 |
}; |
388 |
|
|
|
389 |
tim |
658 |
public: |
390 |
|
|
|
391 |
|
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
392 |
|
|
~ZConstraint(); |
393 |
tim |
837 |
|
394 |
tim |
658 |
void setZConsTime(double time) {this->zconsTime = time;} |
395 |
|
|
void getZConsTime() {return zconsTime;} |
396 |
tim |
837 |
|
397 |
tim |
701 |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
398 |
|
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
399 |
tim |
837 |
|
400 |
tim |
701 |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
401 |
tim |
658 |
string getZConsOutput() {return zconsOutput;} |
402 |
tim |
837 |
|
403 |
tim |
677 |
virtual void integrate(); |
404 |
tim |
658 |
|
405 |
tim |
837 |
|
406 |
tim |
658 |
#ifdef IS_MPI |
407 |
tim |
701 |
virtual void update(); //which is called to indicate the molecules' migration |
408 |
mmeineke |
377 |
#endif |
409 |
tim |
658 |
|
410 |
tim |
837 |
enum ZConsState {zcsMoving, zcsFixed}; |
411 |
mmeineke |
790 |
|
412 |
|
|
vector<Molecule*> zconsMols; //z-constraint molecules array |
413 |
|
|
vector<ZConsState> states; //state of z-constraint molecules |
414 |
|
|
|
415 |
|
|
|
416 |
tim |
837 |
|
417 |
mmeineke |
790 |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
418 |
|
|
double totalMassOfUncons; //total mas of unconstraint molecules |
419 |
|
|
|
420 |
|
|
|
421 |
tim |
658 |
protected: |
422 |
|
|
|
423 |
mmeineke |
790 |
|
424 |
tim |
837 |
|
425 |
|
|
virtual void calcForce( int calcPot, int calcStress ); |
426 |
tim |
677 |
virtual void thermalize(void); |
427 |
tim |
837 |
|
428 |
tim |
677 |
void zeroOutVel(); |
429 |
|
|
void doZconstraintForce(); |
430 |
tim |
1093 |
void doHarmonic(vector<double>& resPos); |
431 |
tim |
677 |
bool checkZConsState(); |
432 |
|
|
|
433 |
|
|
bool haveFixedZMols(); |
434 |
|
|
bool haveMovingZMols(); |
435 |
|
|
|
436 |
|
|
double calcZSys(); |
437 |
|
|
|
438 |
|
|
int isZConstraintMol(Molecule* mol); |
439 |
|
|
|
440 |
|
|
|
441 |
tim |
701 |
double zconsTime; //sample time |
442 |
|
|
double zconsTol; //tolerance of z-contratint |
443 |
|
|
double zForceConst; //base force constant term |
444 |
|
|
//which is estimate by OOPSE |
445 |
mmeineke |
790 |
|
446 |
tim |
837 |
|
447 |
|
|
vector<double> massOfZConsMols; //mass of z-constraint molecule |
448 |
tim |
701 |
vector<double> kz; //force constant array |
449 |
mmeineke |
790 |
|
450 |
tim |
701 |
vector<double> zPos; // |
451 |
tim |
837 |
|
452 |
|
|
|
453 |
tim |
701 |
vector<Molecule*> unconsMols; //unconstraint molecules array |
454 |
|
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
455 |
tim |
682 |
|
456 |
mmeineke |
790 |
|
457 |
tim |
701 |
vector<ZConsParaItem>* parameters; // |
458 |
tim |
837 |
|
459 |
tim |
658 |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
460 |
tim |
677 |
|
461 |
tim |
1093 |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
462 |
|
|
vector<double> fz; |
463 |
|
|
vector<double> curZPos; |
464 |
tim |
677 |
|
465 |
tim |
1093 |
bool usingSMD; |
466 |
tim |
1141 |
vector<double> prevCantPos; |
467 |
tim |
1093 |
vector<double> cantPos; |
468 |
|
|
vector<double> cantVel; |
469 |
|
|
|
470 |
tim |
1091 |
double zconsFixTime; |
471 |
|
|
double zconsGap; |
472 |
|
|
bool hasZConsGap; |
473 |
|
|
vector<double> endFixTime; |
474 |
|
|
|
475 |
tim |
837 |
int whichDirection; //constraint direction |
476 |
|
|
|
477 |
tim |
658 |
private: |
478 |
tim |
837 |
|
479 |
tim |
701 |
string zconsOutput; //filename of zconstraint output |
480 |
|
|
ZConsWriter* fzOut; //z-constraint writer |
481 |
tim |
677 |
|
482 |
tim |
837 |
double curZconsTime; |
483 |
tim |
699 |
|
484 |
tim |
696 |
double calcMovingMolsCOMVel(); |
485 |
|
|
double calcSysCOMVel(); |
486 |
|
|
double calcTotalForce(); |
487 |
tim |
1091 |
void updateZPos(); |
488 |
tim |
1093 |
void updateCantPos(); |
489 |
|
|
|
490 |
gezelter |
747 |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
491 |
tim |
738 |
friend class ForceSubtractionPolicy; |
492 |
tim |
677 |
|
493 |
tim |
658 |
}; |
494 |
|
|
|
495 |
|
|
#endif |