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

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC

+#ifndef _INTEGRATOR_H_
+#define _INTEGRATOR_H_
-+
+#include <string>
-+
+#include <vector>
+#include "Atom.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"
-<
+class Integrator : public BaseIntegrator {
->
+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;
-+
-+
+template<typename T = BaseIntegrator> class Integrator : public T {
-+
+public:
-<
+  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
-<
+  virtual ~Symplectic();
->
+  Integrator( SimInfo *theInfo, ForceFields* the_ff );
->
+  virtual ~Integrator();
+  void integrate( void );
+protected:
-–
+  virtual void integrateStep( int calcPot, int calcStress );
-+
+  virtual void preMove( void );
+  virtual void moveA( void );
+  virtual void moveB( void );
+  virtual void constrainA( void );
+  virtual void constrainB( void );
-+
+  virtual int  readyCheck( void ) { return 1; }
-+
-+
+  virtual void calcForce( int calcPot, int calcStress );
-+
+  virtual void thermalize();
-–
+  void checkConstraints( void );
+  void rotate( int axes1, int axes2, double angle, double j[3],
+               double A[3][3] );
-<
-<
->
+  ForceFields* myFF;
+  SimInfo *info; // all the info we'll ever need
+  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 *constrainedI; /* the i of a constraint pair */
-<
+  int *constrainedJ; /* the j of a constraint pair */
-<
+  double *constrainedDsqr; /* the square of the constraint distance */
->
+  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;
-–
+  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
-–
-–
+  double* pos;
-–
+  double* vel;
-–
+  double* frc;
-–
+  double* trq;
-–
+  double* Amat;
-–
-–
-–
+  Thermo *tStats;
+  StatWriter*  statOut;
+  DumpWriter*  dumpOut;
+};
-+
+typedef Integrator<BaseIntegrator> RealIntegrator;
-<
+class NVT : public Integrator{
->
+template<typename T> class NVE : public T {
-<
+  NVT ( void );
-<
+  virtual ~NVT();
->
+public:
->
+  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
->
+    T( theInfo, the_ff ){}
->
+  virtual ~NVE(){}
->
+};
-+
-+
+template<typename T> class NVT : public T {
-+
-+
+public:
-+
-+
+  NVT ( SimInfo *theInfo, ForceFields* the_ff);
-+
+  virtual ~NVT() {}
-+
-+
+  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
-+
+  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
-+
+protected:
-<
+  virtual moveA( void );
-<
+  virtual moveB( void );
->
->
+  virtual void moveA( void );
->
+  virtual void moveB( void );
->
->
+  virtual int readyCheck();
->
->
+  // chi is a propagated degree of freedom.
->
->
+  double chi;
->
->
+  // targetTemp must be set.  tauThermostat must also be set;
->
->
+  double targetTemp;
->
+  double tauThermostat;
->
->
+  short int have_tau_thermostat, have_target_temp;
->
->
+};
->
->
->
->
+template<typename T> class NPTi : public T{
->
->
+public:
->
->
+  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
->
+  virtual ~NPTi() {};
->
->
+  virtual void integrateStep( int calcPot, int calcStress ){
->
+    calcStress = 1;
->
+    T::integrateStep( calcPot, calcStress );
->
+  }
->
->
+  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;}
->
->
+protected:
->
->
+  virtual void  moveA( void );
->
+  virtual void moveB( void );
->
->
+  virtual int readyCheck();
->
->
+  // chi and eta are the propagated degrees of freedom
->
->
+  double chi;
->
+  double eta;
->
+  double NkBT;
->
->
+  // targetTemp, targetPressure, and tauBarostat must be set.
->
+  // One of qmass or tauThermostat must be set;
->
->
+  double targetTemp;
->
+  double targetPressure;
->
+  double tauThermostat;
->
+  double tauBarostat;
->
->
+  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
->
+  short int have_target_pressure;
->
->
+};
->
->
+template<typename T> class NPTim : public T{
->
->
+public:
->
->
+  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
->
+  virtual ~NPTim() {};
->
->
+  virtual void integrateStep( int calcPot, int calcStress ){
->
+    calcStress = 1;
->
+    T::integrateStep( calcPot, calcStress );
->
+  }
->
->
+  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;}
->
->
+protected:
->
->
+  virtual void moveA( void );
->
+  virtual void moveB( void );
->
->
+  virtual int readyCheck();
->
->
+  Molecule* myMolecules;
->
+  Atom** myAtoms;
->
->
+  // chi and eta are the propagated degrees of freedom
->
->
+  double chi;
->
+  double eta;
->
+  double NkBT;
->
->
+  // targetTemp, targetPressure, and tauBarostat must be set.
->
+  // One of qmass or tauThermostat must be set;
->
->
+  double targetTemp;
->
+  double targetPressure;
->
+  double tauThermostat;
->
+  double tauBarostat;
->
->
+  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
->
+  short int have_target_pressure;
->
->
+};
->
->
+template<typename T> class NPTf : public T{
->
->
+public:
->
->
+  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
->
+  virtual ~NPTf() {};
->
->
+  virtual void integrateStep( int calcPot, int calcStress ){
->
+    calcStress = 1;
->
+    T::integrateStep( calcPot, calcStress );
->
+  }
->
->
+  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;}
-+
+protected:
-+
-+
+  virtual void  moveA( void );
-+
+  virtual void moveB( void );
-+
-+
+  virtual int readyCheck();
-+
-+
+  // chi and eta are the propagated degrees of freedom
-+
-+
+  double chi;
-+
+  double eta[3][3];
-+
+  double NkBT;
-+
-+
+  // targetTemp, targetPressure, and tauBarostat must be set.
-+
+  // One of qmass or tauThermostat must be set;
-+
-+
+  double targetTemp;
-+
+  double targetPressure;
-+
+  double tauThermostat;
-+
+  double tauBarostat;
-+
-+
+  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-+
+  short int have_target_pressure;
-+
+};
-+
+template<typename T> class NPTfm : public T{
-+
-+
+public:
-+
-+
+  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
-+
+  virtual ~NPTfm() {};
-+
-+
+  virtual void integrateStep( int calcPot, int calcStress ){
-+
+    calcStress = 1;
-+
+    T::integrateStep( calcPot, calcStress );
-+
+  }
-+
-+
+  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;}
-+
-+
+protected:
-+
-+
+  virtual void  moveA( void );
-+
+  virtual void moveB( void );
-+
-+
+  virtual int readyCheck();
-+
-+
+  Molecule* myMolecules;
-+
+  Atom** myAtoms;
-+
-+
+  // chi and eta are the propagated degrees of freedom
-+
-+
+  double chi;
-+
+  double eta[3][3];
-+
+  double NkBT;
-+
-+
+  // targetTemp, targetPressure, and tauBarostat must be set.
-+
+  // One of qmass or tauThermostat must be set;
-+
-+
+  double targetTemp;
-+
+  double targetPressure;
-+
+  double tauThermostat;
-+
+  double tauBarostat;
-+
-+
+  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
-+
+  short int have_target_pressure;
-+
-+
+};
-+
-+
+template<typename T> class ZConstraint : public T {
-+
-+
+  public:
-+
+  class ForceSubstractionPolicy{
-+
+    public:
-+
+      ForceSubstractionPolicy(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 : ForceSubstractionPolicy{
-+
+    public:
-+
+                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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 :ForceSubstractionPolicy{
-+
+    public:
-+
+      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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
-+
+protected:
-+
-+
+  enum ZConsState {zcsMoving, zcsFixed};
-+
-+
-+
-+
+  virtual void calcForce( int calcPot, int calcStress );
-+
+  virtual void thermalize(void);
-+
-+
+  void zeroOutVel();
-+
+  void doZconstraintForce();
-+
+  void doHarmonic();
-+
+  bool checkZConsState();
-+
-+
+  bool haveFixedZMols();
-+
+  bool haveMovingZMols();
-+
-+
+  double calcZSys();
-+
-+
+  int isZConstraintMol(Molecule* mol);
-+
-+
-+
+  double zconsTime;
-+
+  double zconsTol;
-+
+  double zForceConst;
-+
-+
+  vector<Molecule*> zconsMols;
-+
+  vector<double> massOfZConsMols;
-+
+  vector<double> kz;
-+
+  vector<ZConsState> states;
-+
+  vector<double> zPos;
-+
-+
-+
+  vector<Molecule*> unconsMols;
-+
+  vector<double> massOfUnconsMols;
-+
+  double totalMassOfUncons;
-+
-+
+  vector<ZConsParaItem>* parameters;
-+
-+
+  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
-+
-+
+  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
-+
+  double* fz;
-+
+  double* curZPos;
-+
-+
+  int totNumOfUnconsAtoms;
-+
-+
+  int whichDirection;                           //constraint direction
-+
-+
+private:
-+
-+
+  string zconsOutput;
-+
+  ZConsWriter* fzOut;
-+
-+
+  double curZconsTime;
-+
-+
+  double calcMovingMolsCOMVel();
-+
+  double calcSysCOMVel();
-+
+  double calcTotalForce();
-+
-+
+  ForceSubstractionPolicy* forcePolicy;
-+
+  friend class ForceSubstractionPolicy;
-+
-+
+};
-+
+#endif

Diff Legend

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

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents): Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC vs. Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC