OOPSE/libmdtools/Integrator.hpp

#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"

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:
  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 moveA( void );
  virtual void moveB( void );
  virtual void constrainA( void );
  virtual void constrainB( void );
  virtual int  readyCheck( void ) { return 1; }

  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] );

  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

  short isFirst; /*boolean for the first time integrate is called */

  double dt;
  double dt2;

  Thermo *tStats;
  StatWriter*  statOut;
  DumpWriter*  dumpOut;

};

typedef Integrator<BaseIntegrator> RealIntegrator;

// ansi instantiation
template class Integrator<BaseIntegrator>;

template<typename T> class NVE : public T {

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;}
  void setChiTolerance(double tol) {chiTolerance = tol;}
  virtual double  getConservedQuantity(void);
  virtual string getAdditionalParameters(void);

protected:

  virtual void moveA( void );
  virtual void moveB( void );

  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;

};


template<typename T> class NPT : public T{

public:

  NPT ( SimInfo *theInfo, ForceFields* the_ff);
  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 void  moveA( void );
  virtual void moveB( void );

  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 NkBT;
  double fkBT;

  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;
  double targetPressure;
  double tauThermostat;
  double tauBarostat;

  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;

};

/*
template<typename T> class SingleZConstrain : public T{


};
*/

template<typename T> class NonEquMD : public T {
  public:
    

};


//
template<typename T> class SingleZConstraint : public T{
  public:
    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
    ~SingleZConstraint();
    
    bool stopIntegrator();
    
  protected:
    
};

//Steered Molecular Dynamics, curret implement only support one steered molecule
 template<typename T> class SMD : public T{
  public:
    SMD( SimInfo *theInfo, ForceFields* the_ff);
    ~SMD();
  
    virtual void integrate();
    virtual void calcForce( int calcPot, int calcStress );  
    bool stopIntegrator();
  private:
    
};

//By using state pattern, Coordinate Drive is responsible for switching back and forth between
//Driven Molecular Dynamics and ZConstraint Method. 
template<typename T> class CoordinateDriver : public T {
  public:
    typedef T ParentIntegrator;

    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
    ~CoordinateDriver();
    
    virtual void integrate();

  private:    
    BaseIntegrator* zconsIntegrator;
    BaseIntegrator* drivenIntegrator;
    
};

#endif
Revision:	1161
Committed:	Tue May 11 21:44:05 2004 UTC (20 years, 4 months ago) by tim
File size:	14356 byte(s)
Log Message:	adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4	tim	658	#include <string>
5			#include <vector>
6	mmeineke	377	#include "Atom.hpp"
7	gezelter	1097	#include "StuntDouble.hpp"
8	gezelter	604	#include "Molecule.hpp"
9	mmeineke	377	#include "SRI.hpp"
10			#include "AbstractClasses.hpp"
11			#include "SimInfo.hpp"
12			#include "ForceFields.hpp"
13	mmeineke	540	#include "Thermo.hpp"
14			#include "ReadWrite.hpp"
15	tim	658	#include "ZConsWriter.hpp"
16	mmeineke	377
17	tim	658	using namespace std;
18	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
19			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
21	mmeineke	561	const int maxIteration = 300;
22			const double tol = 1.0e-6;
23
24	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	mmeineke	377	public:
27	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
28	mmeineke	548	virtual ~Integrator();
29	mmeineke	377	void integrate( void );
30	tim	763	virtual double getConservedQuantity(void);
31	tim	837	virtual string getAdditionalParameters(void);
32	mmeineke	377
33	mmeineke	540	protected:
34	mmeineke	778
35	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
36	mmeineke	548	virtual void preMove( void );
37	mmeineke	540	virtual void moveA( void );
38			virtual void moveB( void );
39			virtual void constrainA( void );
40			virtual void constrainB( void );
41	mmeineke	559	virtual int readyCheck( void ) { return 1; }
42	tim	677
43	mmeineke	746	virtual void resetIntegrator( void ) { }
44	tim	837
45			virtual void calcForce( int calcPot, int calcStress );
46	tim	677	virtual void thermalize();
47	tim	837
48	tim	1108	virtual bool stopIntegrator() {return false;}
49
50	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51	mmeineke	778
52	mmeineke	540	void checkConstraints( void );
53	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
54	tim	701	double A[3][3] );
55	tim	837
56	mmeineke	377	ForceFields* myFF;
57
58	mmeineke	540	SimInfo *info; // all the info we'll ever need
59	gezelter	1097	vector<StuntDouble*> integrableObjects;
60	mmeineke	540	int nAtoms; /* the number of atoms */
61	mmeineke	548	int oldAtoms;
62	mmeineke	540	Atom *atoms; / array of atom pointers */
63	mmeineke	423	Molecule* molecules;
64			int nMols;
65
66	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
67	tim	701	// constraints.
68	tim	837	int nConstrained; // counter for number of constraints
69			int *constrainedA; // the i of a constraint pair
70			int *constrainedB; // the j of a constraint pair
71			double *constrainedDsqr; // the square of the constraint distance
72
73	mmeineke	548	int* moving; // tells whether we are moving atom i
74			int* moved; // tells whether we have moved atom i
75	tim	837	double* oldPos; // pre constrained positions
76	mmeineke	548
77	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
78	tim	837
79	mmeineke	540	double dt;
80	mmeineke	541	double dt2;
81	gezelter	560
82	mmeineke	540	Thermo *tStats;
83			StatWriter* statOut;
84			DumpWriter* dumpOut;
85	tim	837
86	mmeineke	377	};
87
88	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
89	mmeineke	540
90	tim	1161	// ansi instantiation
91			template class Integrator<BaseIntegrator>;
92
93	tim	645	template<typename T> class NVE : public T {
94
95	mmeineke	561	public:
96			NVE ( SimInfo theInfo, ForceFields the_ff ):
97	tim	645	T( theInfo, the_ff ){}
98	tim	837	virtual ~NVE(){}
99	tim	645	};
100	mmeineke	555
101
102	tim	645	template<typename T> class NVT : public T {
103	mmeineke	555
104	gezelter	560	public:
105
106	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
107	tim	763	virtual ~NVT();
108	mmeineke	540
109	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
110			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
111	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
112			virtual double getConservedQuantity(void);
113	tim	837	virtual string getAdditionalParameters(void);
114	gezelter	560
115	mmeineke	540	protected:
116	gezelter	560
117	mmeineke	561	virtual void moveA( void );
118			virtual void moveB( void );
119	mmeineke	540
120	mmeineke	561	virtual int readyCheck();
121	gezelter	560
122	mmeineke	746	virtual void resetIntegrator( void );
123
124	gezelter	565	// chi is a propagated degree of freedom.
125	gezelter	560
126	gezelter	565	double chi;
127	gezelter	560
128	tim	763	//integral of chi(t)dt
129			double integralOfChidt;
130
131	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
132	gezelter	560
133			double targetTemp;
134			double tauThermostat;
135	tim	837
136	gezelter	565	short int have_tau_thermostat, have_target_temp;
137	gezelter	560
138	tim	763	double *oldVel;
139			double *oldJi;
140
141			double chiTolerance;
142			short int have_chi_tolerance;
143
144	mmeineke	540	};
145
146
147
148	mmeineke	778	template<typename T> class NPT : public T{
149	tim	645
150	gezelter	560	public:
151
152	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
153			virtual ~NPT();
154	tim	837
155	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
156			calcStress = 1;
157	tim	645	T::integrateStep( calcPot, calcStress );
158	mmeineke	594	}
159
160	mmeineke	778	virtual double getConservedQuantity(void) = 0;
161	tim	837	virtual string getAdditionalParameters(void) = 0;
162	mmeineke	843
163			double myTauThermo( void ) { return tauThermostat; }
164			double myTauBaro( void ) { return tauBarostat; }
165
166	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
167			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
168			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
169			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
170	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
171			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
172			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
173	gezelter	560
174			protected:
175
176	mmeineke	561	virtual void moveA( void );
177			virtual void moveB( void );
178	gezelter	560
179	mmeineke	561	virtual int readyCheck();
180	gezelter	560
181	mmeineke	746	virtual void resetIntegrator( void );
182
183	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
184			virtual void getVelScaleB( double sc[3], int index ) = 0;
185	tim	837	virtual void getPosScale(double pos[3], double COM[3],
186	mmeineke	778	int index, double sc[3]) = 0;
187
188	mmeineke	857	virtual void calcVelScale( void ) = 0;
189
190	mmeineke	778	virtual bool chiConverged( void );
191			virtual bool etaConverged( void ) = 0;
192	tim	837
193	mmeineke	778	virtual void evolveChiA( void );
194			virtual void evolveEtaA( void ) = 0;
195			virtual void evolveChiB( void );
196			virtual void evolveEtaB( void ) = 0;
197
198			virtual void scaleSimBox( void ) = 0;
199
200	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
201
202	gezelter	565	// chi and eta are the propagated degrees of freedom
203	gezelter	560
204	mmeineke	778	double oldChi;
205			double prevChi;
206	gezelter	565	double chi;
207	gezelter	574	double NkBT;
208	tim	763	double fkBT;
209	gezelter	560
210	mmeineke	778	double tt2, tb2;
211			double instaTemp, instaPress, instaVol;
212	mmeineke	780	double press[3][3];
213	mmeineke	778
214	tim	763	int Nparticles;
215
216			double integralOfChidt;
217
218	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
219	gezelter	560	// One of qmass or tauThermostat must be set;
220
221			double targetTemp;
222			double targetPressure;
223			double tauThermostat;
224			double tauBarostat;
225
226			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
227	gezelter	565	short int have_target_pressure;
228	gezelter	560
229	tim	763	double *oldPos;
230			double *oldVel;
231			double *oldJi;
232
233			double chiTolerance;
234			short int have_chi_tolerance;
235			double posIterTolerance;
236			short int have_pos_iter_tolerance;
237			double etaTolerance;
238			short int have_eta_tolerance;
239
240	gezelter	560	};
241
242	mmeineke	778	template<typename T> class NPTi : public T{
243	tim	837
244	mmeineke	778	public:
245			NPTi( SimInfo theInfo, ForceFields the_ff);
246			~NPTi();
247
248			virtual double getConservedQuantity(void);
249			virtual void resetIntegrator(void);
250	tim	837	virtual string getAdditionalParameters(void);
251	mmeineke	778	protected:
252
253
254	tim	837
255	mmeineke	778	virtual void evolveEtaA(void);
256			virtual void evolveEtaB(void);
257
258			virtual bool etaConverged( void );
259
260			virtual void scaleSimBox( void );
261
262			virtual void getVelScaleA( double sc[3], double vel[3] );
263			virtual void getVelScaleB( double sc[3], int index );
264	tim	837	virtual void getPosScale(double pos[3], double COM[3],
265	mmeineke	778	int index, double sc[3]);
266
267	mmeineke	857	virtual void calcVelScale( void );
268
269	mmeineke	778	double eta, oldEta, prevEta;
270	mmeineke	857	double vScale;
271	mmeineke	778	};
272
273	tim	645	template<typename T> class NPTf : public T{
274	gezelter	576
275			public:
276
277			NPTf ( SimInfo theInfo, ForceFields the_ff);
278	tim	767	virtual ~NPTf();
279	gezelter	576
280	tim	763	virtual double getConservedQuantity(void);
281	tim	837	virtual string getAdditionalParameters(void);
282	mmeineke	780	virtual void resetIntegrator(void);
283	mmeineke	594
284	gezelter	576	protected:
285
286	mmeineke	780	virtual void evolveEtaA(void);
287			virtual void evolveEtaB(void);
288	gezelter	576
289	mmeineke	780	virtual bool etaConverged( void );
290	mmeineke	746
291	mmeineke	780	virtual void scaleSimBox( void );
292	gezelter	576
293	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
294			virtual void getVelScaleB( double sc[3], int index );
295	tim	837	virtual void getPosScale(double pos[3], double COM[3],
296	mmeineke	780	int index, double sc[3]);
297	tim	763
298	mmeineke	857	virtual void calcVelScale( void );
299
300	gezelter	588	double eta[3][3];
301	mmeineke	780	double oldEta[3][3];
302			double prevEta[3][3];
303	mmeineke	857	double vScale[3][3];
304	gezelter	576	};
305
306	mmeineke	812	template<typename T> class NPTxyz : public T{
307	mmeineke	755
308			public:
309
310	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
311			virtual ~NPTxyz();
312	mmeineke	755
313	mmeineke	812	virtual double getConservedQuantity(void);
314	tim	837	virtual string getAdditionalParameters(void);
315	mmeineke	812	virtual void resetIntegrator(void);
316	mmeineke	755
317			protected:
318
319	mmeineke	812	virtual void evolveEtaA(void);
320			virtual void evolveEtaB(void);
321	mmeineke	755
322	mmeineke	812	virtual bool etaConverged( void );
323	mmeineke	755
324	mmeineke	812	virtual void scaleSimBox( void );
325	mmeineke	755
326	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
327			virtual void getVelScaleB( double sc[3], int index );
328	tim	837	virtual void getPosScale(double pos[3], double COM[3],
329	mmeineke	812	int index, double sc[3]);
330	mmeineke	755
331	mmeineke	857	virtual void calcVelScale( void );
332
333	mmeineke	812	double eta[3][3];
334			double oldEta[3][3];
335			double prevEta[3][3];
336	mmeineke	857	double vScale[3][3];
337	mmeineke	812	};
338	mmeineke	755
339
340	tim	658	template<typename T> class ZConstraint : public T {
341	tim	837
342			public:
343	tim	738	class ForceSubtractionPolicy{
344	tim	699	public:
345	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
346	tim	658
347	tim	837	virtual void update() = 0;
348	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
349			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
350	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
352	tim	837
353	tim	701	protected:
354	mmeineke	788	ZConstraint<T>* zconsIntegrator;
355	tim	699	};
356
357	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
358	gezelter	747
359	tim	699	public:
360	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
361			virtual void update();
362	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
363			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
364	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
365			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
366	tim	837
367	tim	699	private:
368	tim	763	int totNumOfMovingAtoms;
369	tim	699	};
370
371	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
372	gezelter	747
373	tim	699	public:
374	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
375
376			virtual void update();
377	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
378			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
379	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
380			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
381	tim	699
382	tim	701	private:
383			double totMassOfMovingAtoms;
384	tim	699	};
385
386	tim	658	public:
387
388			ZConstraint( SimInfo theInfo, ForceFields the_ff);
389			~ZConstraint();
390	tim	837
391	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
392			void getZConsTime() {return zconsTime;}
393	tim	837
394	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
395			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
396	tim	837
397	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
398	tim	658	string getZConsOutput() {return zconsOutput;}
399	tim	837
400	tim	677	virtual void integrate();
401	tim	658
402	tim	837
403	tim	658	#ifdef IS_MPI
404	tim	701	virtual void update(); //which is called to indicate the molecules' migration
405	mmeineke	377	#endif
406	tim	658
407	tim	837	enum ZConsState {zcsMoving, zcsFixed};
408	mmeineke	790
409			vector<Molecule*> zconsMols; //z-constraint molecules array
410			vector<ZConsState> states; //state of z-constraint molecules
411
412
413	tim	837
414	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
415			double totalMassOfUncons; //total mas of unconstraint molecules
416
417
418	tim	658	protected:
419
420	mmeineke	790
421	tim	837
422			virtual void calcForce( int calcPot, int calcStress );
423	tim	677	virtual void thermalize(void);
424	tim	837
425	tim	677	void zeroOutVel();
426			void doZconstraintForce();
427	tim	1093	void doHarmonic(vector<double>& resPos);
428	tim	677	bool checkZConsState();
429
430			bool haveFixedZMols();
431			bool haveMovingZMols();
432
433			double calcZSys();
434
435			int isZConstraintMol(Molecule* mol);
436
437
438	tim	701	double zconsTime; //sample time
439			double zconsTol; //tolerance of z-contratint
440			double zForceConst; //base force constant term
441			//which is estimate by OOPSE
442	mmeineke	790
443	tim	837
444			vector<double> massOfZConsMols; //mass of z-constraint molecule
445	tim	701	vector<double> kz; //force constant array
446	mmeineke	790
447	tim	701	vector<double> zPos; //
448	tim	837
449
450	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
451			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
452	tim	682
453	mmeineke	790
454	tim	701	vector<ZConsParaItem>* parameters; //
455	tim	837
456	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
457	tim	677
458	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
459			vector<double> fz;
460			vector<double> curZPos;
461	tim	677
462	tim	1093	bool usingSMD;
463	tim	1141	vector<double> prevCantPos;
464	tim	1093	vector<double> cantPos;
465			vector<double> cantVel;
466
467	tim	1091	double zconsFixTime;
468			double zconsGap;
469			bool hasZConsGap;
470			vector<double> endFixTime;
471
472	tim	837	int whichDirection; //constraint direction
473
474	tim	658	private:
475	tim	837
476	tim	701	string zconsOutput; //filename of zconstraint output
477			ZConsWriter* fzOut; //z-constraint writer
478	tim	677
479	tim	837	double curZconsTime;
480	tim	699
481	tim	696	double calcMovingMolsCOMVel();
482			double calcSysCOMVel();
483			double calcTotalForce();
484	tim	1091	void updateZPos();
485	tim	1093	void updateCantPos();
486
487	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488	tim	738	friend class ForceSubtractionPolicy;
489	tim	677
490	tim	658	};
491
492	tim	1064	/*
493	tim	1108	template<typename T> class SingleZConstrain : public T{
494
495
496			};
497			*/
498
499			template<typename T> class NonEquMD : public T {
500			public:
501
502
503
504			};
505
506
507			//
508			template<typename T> class SingleZConstraint : public T{
509			public:
510			SingleZConstraint(SimInfo theInfo, ForceFields the_ff);
511			~SingleZConstraint();
512
513			bool stopIntegrator();
514
515			protected:
516
517			};
518
519			//Steered Molecular Dynamics, curret implement only support one steered molecule
520	tim	1091	template<typename T> class SMD : public T{
521	tim	969	public:
522	tim	1091	SMD( SimInfo theInfo, ForceFields the_ff);
523			~SMD();
524
525	tim	1108	virtual void integrate();
526			virtual void calcForce( int calcPot, int calcStress );
527			bool stopIntegrator();
528			private:
529
530	tim	969	};
531	tim	1108
532			//By using state pattern, Coordinate Drive is responsible for switching back and forth between
533			//Driven Molecular Dynamics and ZConstraint Method.
534			template<typename T> class CoordinateDriver : public T {
535			public:
536			typedef T ParentIntegrator;
537
538			CoordinateDriver(SimInfo, ForceFields, BaseIntegrator, BaseIntegrator);
539			~CoordinateDriver();
540
541			virtual void integrate();
542
543			private:
544			BaseIntegrator* zconsIntegrator;
545			BaseIntegrator* drivenIntegrator;
546
547			};
548
549	tim	658	#endif