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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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|
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class Verlet : public Integrator { |
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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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public: |
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Verlet( SimInfo &info, ForceFields* the_ff ); |
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~Verlet(); |
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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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private: |
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protected: |
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void move_a( double dt ); |
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void move_b( double dt ); |
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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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|
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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 *entry_plug; // all the info we'll ever need |
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int c_natoms; /* the number of atoms */ |
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Atom **c_atoms; /* array of atom pointers */ |
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SRI **c_sr_interactions; /* array of SRI pointers */ |
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int c_n_SRI; /* the number of short range interactions */ |
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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 c_is_constrained; /*boolean to know whether the systems contains |
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constraints. */ |
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int c_n_constrained; /*counter for number of constraints */ |
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int *c_constrained_i; /* the i of a constraint pair */ |
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int *c_constrained_j; /* the j of a constraint pair */ |
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double *c_constrained_dsqr; /* the square of the constraint distance */ |
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double *c_mass; /* the array of masses */ |
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short is_first; /*boolean for the first time integrate is called */ |
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double c_box_x; |
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double c_box_y; |
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double c_box_z; |
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}; |
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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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|
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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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class Symplectic : public Integrator { |
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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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|
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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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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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public: |
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Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ); |
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~Symplectic(); |
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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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void integrate( void ); |
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private: |
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}; |
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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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class NVT : public Integrator{ |
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SimInfo* entry_plug; |
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ForceFields* myFF; |
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public: |
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int is_constrained; /*boolean to know whether the systems contains |
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constraints. */ |
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int n_constrained; /*counter for number of constraints */ |
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int *constrained_i; /* the i of a constraint pair */ |
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int *constrained_j; /* the j of a constraint pair */ |
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double *constrained_dsqr; /* the square of the constraint distance */ |
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double *mass; /* the array of masses */ |
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NVT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NVT() {} |
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short int isFirst; |
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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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SRI **srInteractions; /* array of SRI pointers */ |
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int nSRI; /* the number of short range interactions */ |
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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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virtual int readyCheck(); |
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// chi is a propagated degree of freedom. |
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|
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double chi; |
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// targetTemp must be set. tauThermostat must also be set; |
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|
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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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class NPTi : public Integrator{ |
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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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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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Integrator::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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// 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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|
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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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class NPTim : public Integrator{ |
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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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Integrator::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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// 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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|
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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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class NPTf : public Integrator{ |
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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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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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Integrator::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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// 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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// 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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class NPTfm : public Integrator{ |
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public: |
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|
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NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTfm() {}; |
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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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Integrator::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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// 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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// 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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#endif |