[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/Integrator.hpp

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

+#ifndef _INTEGRATOR_H_
+#define _INTEGRATOR_H_
-+
+#include <string>
-+
+#include <vector>
+#include "Atom.hpp"
-+
+#include "StuntDouble.hpp"
-+
+#include "Molecule.hpp"
+#include "SRI.hpp"
+#include "AbstractClasses.hpp"
+#include "SimInfo.hpp"
+#include "ForceFields.hpp"
+#include "Thermo.hpp"
+#include "ReadWrite.hpp"
-+
+#include "ZConsWriter.hpp"
-+
+#include "Restraints.hpp"
-+
+#include "Quaternion.hpp"
-+
+#include "Mat4x4d.hpp"
-+
+using namespace std;
+const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
+const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
-+
+const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
+const int maxIteration = 300;
+const double tol = 1.0e-6;
-<
+class Integrator : public BaseIntegrator {
->
+class VelVerletConsFramework;
->
+template<typename T = BaseIntegrator> class Integrator : public T {
+public:
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
+  virtual ~Integrator();
+  void integrate( void );
-+
+  virtual double  getConservedQuantity(void);
-+
+  virtual string getAdditionalParameters(void);
-–
+protected:
-<
->
+  virtual void integrateStep( int calcPot, int calcStress );
-<
+  virtual void preMove( void );
->
+  //virtual void preMove( void );
+  virtual void moveA( void );
+  virtual void moveB( void );
-<
+  virtual void constrainA( void );
-<
+  virtual void constrainB( void );
->
+  //virtual void constrainA( void );
->
+  //virtual void constrainB( void );
+  virtual int  readyCheck( void ) { return 1; }
-–
-–
+  void checkConstraints( void );
-–
+  void rotate( int axes1, int axes2, double angle, double j[3],
-–
+               double A[9] );
-+
+  virtual void resetIntegrator( void ) { }
-+
+  virtual void calcForce( int calcPot, int calcStress );
-+
+  virtual void thermalize();
-+
-+
+  virtual bool stopIntegrator() {return false;}
-+
-+
+  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
-+
-+
+  //void checkConstraints( void );
-+
+  void rotate( int axes1, int axes2, double angle, double j[3],
-+
+         double A[3][3] );
-+
-+
+  void printQuaternion(StuntDouble* sd);
-+
+  Mat4x4d getS(const Quaternion& q);
-+
+  ForceFields* myFF;
+  SimInfo *info; // all the info we'll ever need
-+
+  vector<StuntDouble*> integrableObjects;
+  int nAtoms;  /* the number of atoms */
+  int oldAtoms;
+  Atom **atoms; /* array of atom pointers */
+  Molecule* molecules;
+  int nMols;
-<
+  int isConstrained; // boolean to know whether the systems contains
-<
+                     // constraints.
-<
+  int nConstrained;  // counter for number of constraints
-<
+  int *constrainedA; // the i of a constraint pair
-<
+  int *constrainedB; // the j of a constraint pair
-<
+  double *constrainedDsqr; // the square of the constraint distance
-<
-<
+  int* moving; // tells whether we are moving atom i
-<
+  int* moved;  // tells whether we have moved atom i
-<
+  double* oldPos; // pre constrained positions
->
+  VelVerletConsFramework* consFramework;
-+
+  //int isConstrained; // boolean to know whether the systems contains constraints.
-+
+  //int nConstrained;  // counter for number of constraints
-+
+  //int *constrainedA; // the i of a constraint pair
-+
+  //int *constrainedB; // the j of a constraint pair
-+
+  //double *constrainedDsqr; // the square of the constraint distance
-+
-+
+  //int* moving; // tells whether we are moving atom i
-+
+  //int* moved;  // tells whether we have moved atom i
-+
+  //double* oldPos; // pre constrained positions
-+
+  short isFirst; /*boolean for the first time integrate is called */
-<
->
+  double dt;
+  double dt2;
-–
+  double* pos;
-–
+  double* vel;
-–
+  double* frc;
-–
+  double* trq;
-–
+  double* Amat;
-–
+  Thermo *tStats;
+  StatWriter*  statOut;
+  DumpWriter*  dumpOut;
-<
->
+};
-<
+class NVE : public Integrator{
->
+typedef Integrator<BaseIntegrator> RealIntegrator;
-+
+// ansi instantiation
-+
+// template class Integrator<BaseIntegrator>;
-+
-+
-+
+template<typename T> class NVE : public T {
-+
+public:
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
-<
+    Integrator( theInfo, the_ff ){}
->
+    T( theInfo, the_ff ){}
+  virtual ~NVE(){}
-–
-–
-–
+};
-–
+class NVT : public Integrator{
-+
+template<typename T> class NVT : public T {
-+
+public:
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
-<
+  virtual ~NVT() {}
->
+  virtual ~NVT();
+  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
+  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-+
+  void setChiTolerance(double tol) {chiTolerance = tol;}
-+
+  virtual double  getConservedQuantity(void);
-+
+  virtual string getAdditionalParameters(void);
+protected:
+  virtual int readyCheck();
-+
+  virtual void resetIntegrator( void );
-+
+  // chi is a propagated degree of freedom.
+  double chi;
-+
+  //integral of chi(t)dt
-+
+  double integralOfChidt;
-+
+  // targetTemp must be set.  tauThermostat must also be set;
+  double targetTemp;
+  double tauThermostat;
-<
->
+  short int have_tau_thermostat, have_target_temp;
-+
+  double *oldVel;
-+
+  double *oldJi;
-+
-+
+  double chiTolerance;
-+
+  short int have_chi_tolerance;
-+
+};
-–
+class NPT : public Integrator{
-+
+template<typename T> class NPT : public T{
-+
+public:
+  NPT ( SimInfo *theInfo, ForceFields* the_ff);
-<
+  virtual ~NPT() {};
->
+  virtual ~NPT();
-+
+  virtual void integrateStep( int calcPot, int calcStress ){
-+
+    calcStress = 1;
-+
+    T::integrateStep( calcPot, calcStress );
-+
+  }
-+
-+
+  virtual double getConservedQuantity(void) = 0;
-+
+  virtual string getAdditionalParameters(void) = 0;
-+
-+
+  double myTauThermo( void ) { return tauThermostat; }
-+
+  double myTauBaro( void ) { return tauBarostat; }
-+
+  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
+  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
+  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
+  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
-+
+  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
-+
+  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
-+
+  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
+protected:
+  virtual int readyCheck();
-+
+  virtual void resetIntegrator( void );
-+
-+
+  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
-+
+  virtual void getVelScaleB( double sc[3], int index ) = 0;
-+
+  virtual void getPosScale(double pos[3], double COM[3],
-+
+                           int index, double sc[3]) = 0;
-+
-+
+  virtual void calcVelScale( void ) = 0;
-+
-+
+  virtual bool chiConverged( void );
-+
+  virtual bool etaConverged( void ) = 0;
-+
-+
+  virtual void evolveChiA( void );
-+
+  virtual void evolveEtaA( void ) = 0;
-+
+  virtual void evolveChiB( void );
-+
+  virtual void evolveEtaB( void ) = 0;
-+
-+
+  virtual void scaleSimBox( void ) = 0;
-+
-+
+  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
-+
+  // chi and eta are the propagated degrees of freedom
-+
+  double oldChi;
-+
+  double prevChi;
+  double chi;
-<
+  double eta;
->
+  double NkBT;
->
+  double fkBT;
-<
+  // targetTemp, targetPressure, and tauBarostat must be set.
->
+  double tt2, tb2;
->
+  double instaTemp, instaPress, instaVol;
->
+  double press[3][3];
->
->
+  int Nparticles;
->
->
+  double integralOfChidt;
->
->
+  // targetTemp, targetPressure, and tauBarostat must be set.
+  // One of qmass or tauThermostat must be set;
+  double targetTemp;
+  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
+  short int have_target_pressure;
-+
+  double *oldPos;
-+
+  double *oldVel;
-+
+  double *oldJi;
-+
-+
+  double chiTolerance;
-+
+  short int have_chi_tolerance;
-+
+  double posIterTolerance;
-+
+  short int have_pos_iter_tolerance;
-+
+  double etaTolerance;
-+
+  short int have_eta_tolerance;
-+
+};
-+
+template<typename T> class NPTi : public T{
-+
-+
+public:
-+
+  NPTi( SimInfo *theInfo, ForceFields* the_ff);
-+
+  ~NPTi();
-+
-+
+  virtual double getConservedQuantity(void);
-+
+  virtual void resetIntegrator(void);
-+
+  virtual string getAdditionalParameters(void);
-+
+protected:
-+
-+
-+
-+
+  virtual void evolveEtaA(void);
-+
+  virtual void evolveEtaB(void);
-+
-+
+  virtual bool etaConverged( void );
-+
-+
+  virtual void scaleSimBox( void );
-+
-+
+  virtual void getVelScaleA( double sc[3], double vel[3] );
-+
+  virtual void getVelScaleB( double sc[3], int index );
-+
+  virtual void getPosScale(double pos[3], double COM[3],
-+
+                           int index, double sc[3]);
-+
-+
+  virtual void calcVelScale( void );
-+
-+
+  double eta, oldEta, prevEta;
-+
+  double vScale;
-+
+};
-+
-+
+template<typename T> class NPTf : public T{
-+
-+
+public:
-+
-+
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
-+
+  virtual ~NPTf();
-+
-+
+  virtual double getConservedQuantity(void);
-+
+  virtual string getAdditionalParameters(void);
-+
+  virtual void resetIntegrator(void);
-+
-+
+protected:
-+
-+
+  virtual void evolveEtaA(void);
-+
+  virtual void evolveEtaB(void);
-+
-+
+  virtual bool etaConverged( void );
-+
-+
+  virtual void scaleSimBox( void );
-+
-+
+  virtual void getVelScaleA( double sc[3], double vel[3] );
-+
+  virtual void getVelScaleB( double sc[3], int index );
-+
+  virtual void getPosScale(double pos[3], double COM[3],
-+
+                           int index, double sc[3]);
-+
-+
+  virtual void calcVelScale( void );
-+
-+
+  double eta[3][3];
-+
+  double oldEta[3][3];
-+
+  double prevEta[3][3];
-+
+  double vScale[3][3];
-+
+};
-+
-+
+template<typename T> class NPTxyz : public T{
-+
-+
+public:
-+
-+
+  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
-+
+  virtual ~NPTxyz();
-+
-+
+  virtual double getConservedQuantity(void);
-+
+  virtual string getAdditionalParameters(void);
-+
+  virtual void resetIntegrator(void);
-+
-+
+protected:
-+
-+
+  virtual void evolveEtaA(void);
-+
+  virtual void evolveEtaB(void);
-+
-+
+  virtual bool etaConverged( void );
-+
-+
+  virtual void scaleSimBox( void );
-+
-+
+  virtual void getVelScaleA( double sc[3], double vel[3] );
-+
+  virtual void getVelScaleB( double sc[3], int index );
-+
+  virtual void getPosScale(double pos[3], double COM[3],
-+
+                           int index, double sc[3]);
-+
-+
+  virtual void calcVelScale( void );
-+
-+
+  double eta[3][3];
-+
+  double oldEta[3][3];
-+
+  double prevEta[3][3];
-+
+  double vScale[3][3];
-+
+};
-+
-+
-+
+template<typename T> class ZConstraint : public T {
-+
-+
+  public:
-+
+  class ForceSubtractionPolicy{
-+
+    public:
-+
+      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
-+
-+
+      virtual void update() = 0;
-+
+      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
-+
+      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
-+
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
-+
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
-+
-+
+   protected:
-+
+     ZConstraint<T>* zconsIntegrator;
-+
+  };
-+
-+
+  class PolicyByNumber : public ForceSubtractionPolicy{
-+
-+
+    public:
-+
+      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
-+
+      virtual void update();
-+
+      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
-+
+      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
-+
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
-+
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
-+
-+
+    private:
-+
+      int totNumOfMovingAtoms;
-+
+  };
-+
-+
+  class PolicyByMass : public ForceSubtractionPolicy{
-+
-+
+    public:
-+
+      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
-+
-+
+      virtual void update();
-+
+      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
-+
+      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
-+
+      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
-+
+      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
-+
-+
+   private:
-+
+     double totMassOfMovingAtoms;
-+
+  };
-+
-+
+public:
-+
-+
+  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
-+
+  ~ZConstraint();
-+
-+
+  void setZConsTime(double time)                  {this->zconsTime = time;}
-+
+  void getZConsTime()                             {return zconsTime;}
-+
-+
+  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
-+
+  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
-+
-+
+  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
-+
+  string getZConsOutput()                         {return zconsOutput;}
-+
-+
+  virtual void integrate();
-+
-+
-+
+#ifdef IS_MPI
-+
+  virtual void update();                      //which is called to indicate the molecules' migration
+#endif
-+
-+
+  enum ZConsState {zcsMoving, zcsFixed};
-+
-+
+  vector<Molecule*> zconsMols;              //z-constraint molecules array
-+
+  vector<ZConsState> states;                 //state of z-constraint molecules
-+
-+
-+
-+
+  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
-+
+  double totalMassOfUncons;                //total mas of unconstraint molecules
-+
-+
-+
+protected:
-+
-+
-+
-+
+  virtual void calcForce( int calcPot, int calcStress );
-+
+  virtual void thermalize(void);
-+
-+
+  void zeroOutVel();
-+
+  void doZconstraintForce();
-+
+  void doHarmonic(vector<double>& resPos);
-+
+  bool checkZConsState();
-+
-+
+  bool haveFixedZMols();
-+
+  bool haveMovingZMols();
-+
-+
+  double calcZSys();
-+
-+
+  int isZConstraintMol(Molecule* mol);
-+
-+
-+
+  double zconsTime;                              //sample time
-+
+  double zconsTol;                                 //tolerance of z-contratint
-+
+  double zForceConst;                           //base force constant term
-+
+                                                          //which is estimate by OOPSE
-+
-+
-+
+  vector<double> massOfZConsMols;       //mass of z-constraint molecule
-+
+  vector<double> kz;                              //force constant array
-+
-+
+  vector<double> zPos;                          //
-+
-+
-+
+  vector<Molecule*> unconsMols;           //unconstraint molecules array
-+
+  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
-+
-+
-+
+  vector<ZConsParaItem>* parameters; //
-+
-+
+  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
-+
-+
+  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
-+
+  vector<double> fz;
-+
+  vector<double> curZPos;
-+
-+
+  bool usingSMD;
-+
+  vector<double> prevCantPos;
-+
+  vector<double> cantPos;
-+
+  vector<double> cantVel;
-+
-+
+  double zconsFixTime;
-+
+  double zconsGap;
-+
+  bool hasZConsGap;
-+
+  vector<double> endFixTime;
-+
-+
+  int whichDirection;                           //constraint direction
-+
-+
+private:
-+
-+
+  string zconsOutput;                         //filename of zconstraint output
-+
+  ZConsWriter* fzOut;                         //z-constraint writer
-+
-+
+  double curZconsTime;
-+
-+
+  double calcMovingMolsCOMVel();
-+
+  double calcSysCOMVel();
-+
+  double calcTotalForce();
-+
+  void updateZPos();
-+
+  void updateCantPos();
-+
-+
+  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
-+
+  friend class ForceSubtractionPolicy;
-+
-+
+};
-+
-+
-+
+//Sympletic quaternion Scheme Integrator
-+
+//Reference:
-+
+// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
-+
+//Symplectic quaternion Scheme for biophysical molecular dynamics
-+
+//116(20), 8649, J. Chem. Phys. (2002)
-+
+template<typename T> class SQSIntegrator : public T{
-+
+  public:
-+
+    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
-+
+    virtual void moveA();
-+
+    virtual void moveB();
-+
+  protected:
-+
+    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
-+
+    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
-+
+  private:
-+
+    Quaternion getPk(int i, const Vector4d& q);
-+
+    Mat4x4d getS(const Quaternion& q);
-+
+    vector<Quaternion> q;
-+
+    vector<Vector4d> p_qua;
-+
+    vector<double> I0;
-+
-+
+                Vector4d p2j(const Vector4d& p, Mat4x4d& m);
-+
+                Vector4d j2p(const Vector4d& j, Mat4x4d& m);
-+
+};
-+
+#endif

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
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+Changed lines

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents): Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC vs. Revision 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 2004 UTC