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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 "ExtendedSystem.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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|
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class Verlet : public Integrator { |
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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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|
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public: |
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Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es ); |
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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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virtual double getConservedQuantity(void); |
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virtual string getAdditionalParameters(void); |
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private: |
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|
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void move_a( double dt ); |
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void move_b( double dt ); |
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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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|
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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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|
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virtual bool stopIntegrator() {return false;} |
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|
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virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
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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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|
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ForceFields* myFF; |
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ExtendedSystem* myES; |
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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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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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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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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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|
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short isFirst; /*boolean for the first time integrate is called */ |
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|
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double dt; |
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double dt2; |
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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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}; |
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class Symplectic : public Integrator { |
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typedef Integrator<BaseIntegrator> RealIntegrator; |
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|
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template<typename T> class NVE : public T { |
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|
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public: |
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Symplectic( SimInfo* the_entry_plug, |
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ForceFields* the_ff, |
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ExtendedSystem* the_es); |
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~Symplectic(); |
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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double targetTemp; |
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double tauThermostat; |
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|
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short int have_tau_thermostat, have_target_temp; |
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|
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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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template<typename T> class NPT : public T{ |
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public: |
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|
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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPT(); |
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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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virtual double getConservedQuantity(void) = 0; |
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virtual string getAdditionalParameters(void) = 0; |
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void integrate( void ); |
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double myTauThermo( void ) { return tauThermostat; } |
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double myTauBaro( void ) { return tauBarostat; } |
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private: |
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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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void rotate( int axes1, int axes2, double angle, double j[3], |
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double A[3][3] ); |
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protected: |
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SimInfo* entry_plug; |
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ForceFields* myFF; |
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ExtendedSystem* myES; |
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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Molecule* molecules; |
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int nMols; |
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virtual int readyCheck(); |
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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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virtual void resetIntegrator( void ); |
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short int isFirst; |
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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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SRI **srInteractions; /* array of SRI pointers */ |
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int nSRI; /* the number of short range interactions */ |
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virtual void calcVelScale( void ) = 0; |
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|
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virtual bool chiConverged( void ); |
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virtual bool etaConverged( void ) = 0; |
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|
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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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|
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virtual void scaleSimBox( void ) = 0; |
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|
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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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|
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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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|
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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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|
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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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}; |
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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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|
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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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|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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|
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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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|
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virtual void calcVelScale( void ); |
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|
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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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|
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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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|
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protected: |
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|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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|
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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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|
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virtual void calcVelScale( void ); |
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|
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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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|
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NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTxyz(); |
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|
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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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|
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protected: |
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|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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|
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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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|
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virtual void calcVelScale( void ); |
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|
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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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|
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template<typename T> class ZConstraint : public T { |
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|
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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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|
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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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|
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protected: |
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ZConstraint<T>* zconsIntegrator; |
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}; |
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|
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class PolicyByNumber : public ForceSubtractionPolicy{ |
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|
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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) ; |
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virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
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virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
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|
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private: |
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int totNumOfMovingAtoms; |
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}; |
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|
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class PolicyByMass : public ForceSubtractionPolicy{ |
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|
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public: |
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PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
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|
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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) ; |
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virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
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virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
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|
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private: |
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double totMassOfMovingAtoms; |
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}; |
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|
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public: |
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|
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ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
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~ZConstraint(); |
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|
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void setZConsTime(double time) {this->zconsTime = time;} |
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void getZConsTime() {return zconsTime;} |
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|
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void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
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void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
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|
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void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
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string getZConsOutput() {return zconsOutput;} |
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|
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virtual void integrate(); |
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|
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|
400 |
> |
#ifdef IS_MPI |
401 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
402 |
> |
#endif |
403 |
> |
|
404 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
405 |
> |
|
406 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
407 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
408 |
> |
|
409 |
> |
|
410 |
> |
|
411 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
412 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
413 |
> |
|
414 |
> |
|
415 |
> |
protected: |
416 |
> |
|
417 |
> |
|
418 |
> |
|
419 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
420 |
> |
virtual void thermalize(void); |
421 |
> |
|
422 |
> |
void zeroOutVel(); |
423 |
> |
void doZconstraintForce(); |
424 |
> |
void doHarmonic(vector<double>& resPos); |
425 |
> |
bool checkZConsState(); |
426 |
> |
|
427 |
> |
bool haveFixedZMols(); |
428 |
> |
bool haveMovingZMols(); |
429 |
> |
|
430 |
> |
double calcZSys(); |
431 |
> |
|
432 |
> |
int isZConstraintMol(Molecule* mol); |
433 |
> |
|
434 |
> |
|
435 |
> |
double zconsTime; //sample time |
436 |
> |
double zconsTol; //tolerance of z-contratint |
437 |
> |
double zForceConst; //base force constant term |
438 |
> |
//which is estimate by OOPSE |
439 |
> |
|
440 |
> |
|
441 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
442 |
> |
vector<double> kz; //force constant array |
443 |
> |
|
444 |
> |
vector<double> zPos; // |
445 |
> |
|
446 |
> |
|
447 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
448 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
449 |
> |
|
450 |
> |
|
451 |
> |
vector<ZConsParaItem>* parameters; // |
452 |
> |
|
453 |
> |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
454 |
> |
|
455 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
456 |
> |
vector<double> fz; |
457 |
> |
vector<double> curZPos; |
458 |
> |
|
459 |
> |
bool usingSMD; |
460 |
> |
vector<double> cantPos; |
461 |
> |
vector<double> cantVel; |
462 |
> |
|
463 |
> |
double zconsFixTime; |
464 |
> |
double zconsGap; |
465 |
> |
bool hasZConsGap; |
466 |
> |
vector<double> endFixTime; |
467 |
|
|
468 |
+ |
int whichDirection; //constraint direction |
469 |
+ |
|
470 |
+ |
private: |
471 |
+ |
|
472 |
+ |
string zconsOutput; //filename of zconstraint output |
473 |
+ |
ZConsWriter* fzOut; //z-constraint writer |
474 |
+ |
|
475 |
+ |
double curZconsTime; |
476 |
+ |
|
477 |
+ |
double calcMovingMolsCOMVel(); |
478 |
+ |
double calcSysCOMVel(); |
479 |
+ |
double calcTotalForce(); |
480 |
+ |
void updateZPos(); |
481 |
+ |
void updateCantPos(); |
482 |
+ |
|
483 |
+ |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
484 |
+ |
friend class ForceSubtractionPolicy; |
485 |
+ |
|
486 |
|
}; |
487 |
|
|
488 |
+ |
/* |
489 |
+ |
template<typename T> class SingleZConstrain : public T{ |
490 |
+ |
|
491 |
+ |
|
492 |
+ |
}; |
493 |
+ |
*/ |
494 |
+ |
|
495 |
+ |
template<typename T> class NonEquMD : public T { |
496 |
+ |
public: |
497 |
+ |
|
498 |
+ |
|
499 |
+ |
|
500 |
+ |
}; |
501 |
+ |
|
502 |
+ |
|
503 |
+ |
// |
504 |
+ |
template<typename T> class SingleZConstraint : public T{ |
505 |
+ |
public: |
506 |
+ |
SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff); |
507 |
+ |
~SingleZConstraint(); |
508 |
+ |
|
509 |
+ |
bool stopIntegrator(); |
510 |
+ |
|
511 |
+ |
protected: |
512 |
+ |
|
513 |
+ |
}; |
514 |
+ |
|
515 |
+ |
//Steered Molecular Dynamics, curret implement only support one steered molecule |
516 |
+ |
template<typename T> class SMD : public T{ |
517 |
+ |
public: |
518 |
+ |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
519 |
+ |
~SMD(); |
520 |
+ |
|
521 |
+ |
virtual void integrate(); |
522 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
523 |
+ |
bool stopIntegrator(); |
524 |
+ |
private: |
525 |
+ |
|
526 |
+ |
}; |
527 |
+ |
|
528 |
+ |
//By using state pattern, Coordinate Drive is responsible for switching back and forth between |
529 |
+ |
//Driven Molecular Dynamics and ZConstraint Method. |
530 |
+ |
template<typename T> class CoordinateDriver : public T { |
531 |
+ |
public: |
532 |
+ |
typedef T ParentIntegrator; |
533 |
+ |
|
534 |
+ |
CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*); |
535 |
+ |
~CoordinateDriver(); |
536 |
+ |
|
537 |
+ |
virtual void integrate(); |
538 |
+ |
|
539 |
+ |
private: |
540 |
+ |
BaseIntegrator* zconsIntegrator; |
541 |
+ |
BaseIntegrator* drivenIntegrator; |
542 |
+ |
|
543 |
+ |
}; |
544 |
+ |
|
545 |
|
#endif |