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"
#include "Restraints.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 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 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;

  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;

  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;

};


//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:
    virtual void moveA();
    virtual void moveB();
  protected:
    void freeRotor();
    void rotate(int k, double dt);
    
};
#endif
Revision:	1330
Committed:	Fri Jul 16 16:29:44 2004 UTC (20 years, 1 month ago) by gezelter
File size:	13726 byte(s)
Log Message:	Minor changes
#	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	chrisfen	1180	#include "Restraints.hpp"
17	mmeineke	377
18	tim	658	using namespace std;
19	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
20			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
22	mmeineke	561	const int maxIteration = 300;
23			const double tol = 1.0e-6;
24
25	tim	1268	class VelVerletConsFramework;
26	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
27
28	mmeineke	377	public:
29	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
30	mmeineke	548	virtual ~Integrator();
31	mmeineke	377	void integrate( void );
32	tim	763	virtual double getConservedQuantity(void);
33	tim	837	virtual string getAdditionalParameters(void);
34	mmeineke	377
35	mmeineke	540	protected:
36	mmeineke	778
37	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
38	tim	1234	//virtual void preMove( void );
39	mmeineke	540	virtual void moveA( void );
40			virtual void moveB( void );
41	tim	1234	//virtual void constrainA( void );
42			//virtual void constrainB( void );
43	mmeineke	559	virtual int readyCheck( void ) { return 1; }
44	tim	677
45	mmeineke	746	virtual void resetIntegrator( void ) { }
46	tim	837
47			virtual void calcForce( int calcPot, int calcStress );
48	tim	677	virtual void thermalize();
49	tim	837
50	tim	1108	virtual bool stopIntegrator() {return false;}
51
52	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53	mmeineke	778
54	tim	1234	//void checkConstraints( void );
55	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
56	tim	701	double A[3][3] );
57	tim	837
58	mmeineke	377	ForceFields* myFF;
59
60	mmeineke	540	SimInfo *info; // all the info we'll ever need
61	gezelter	1097	vector<StuntDouble*> integrableObjects;
62	mmeineke	540	int nAtoms; /* the number of atoms */
63	mmeineke	548	int oldAtoms;
64	mmeineke	540	Atom *atoms; / array of atom pointers */
65	mmeineke	423	Molecule* molecules;
66			int nMols;
67
68	tim	1268	VelVerletConsFramework* consFramework;
69	tim	837
70	tim	1234	//int isConstrained; // boolean to know whether the systems contains constraints.
71			//int nConstrained; // counter for number of constraints
72			//int *constrainedA; // the i of a constraint pair
73			//int *constrainedB; // the j of a constraint pair
74			//double *constrainedDsqr; // the square of the constraint distance
75	mmeineke	548
76	tim	1234	//int* moving; // tells whether we are moving atom i
77			//int* moved; // tells whether we have moved atom i
78			//double* oldPos; // pre constrained positions
79
80	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
81	tim	837
82	mmeineke	540	double dt;
83	mmeineke	541	double dt2;
84	gezelter	560
85	mmeineke	540	Thermo *tStats;
86			StatWriter* statOut;
87			DumpWriter* dumpOut;
88	tim	837
89	mmeineke	377	};
90
91	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
92	mmeineke	540
93	tim	1161	// ansi instantiation
94	gezelter	1323	// template class Integrator<BaseIntegrator>;
95	tim	1161
96	gezelter	1330
97	tim	645	template<typename T> class NVE : public T {
98
99	mmeineke	561	public:
100			NVE ( SimInfo theInfo, ForceFields the_ff ):
101	tim	645	T( theInfo, the_ff ){}
102	tim	837	virtual ~NVE(){}
103	tim	645	};
104	mmeineke	555
105
106	tim	645	template<typename T> class NVT : public T {
107	mmeineke	555
108	gezelter	560	public:
109
110	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
111	tim	763	virtual ~NVT();
112	mmeineke	540
113	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
114			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
115	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
116			virtual double getConservedQuantity(void);
117	tim	837	virtual string getAdditionalParameters(void);
118	gezelter	560
119	mmeineke	540	protected:
120	gezelter	560
121	mmeineke	561	virtual void moveA( void );
122			virtual void moveB( void );
123	mmeineke	540
124	mmeineke	561	virtual int readyCheck();
125	gezelter	560
126	mmeineke	746	virtual void resetIntegrator( void );
127
128	gezelter	565	// chi is a propagated degree of freedom.
129	gezelter	560
130	gezelter	565	double chi;
131	gezelter	560
132	tim	763	//integral of chi(t)dt
133			double integralOfChidt;
134
135	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
136	gezelter	560
137			double targetTemp;
138			double tauThermostat;
139	tim	837
140	gezelter	565	short int have_tau_thermostat, have_target_temp;
141	gezelter	560
142	tim	763	double *oldVel;
143			double *oldJi;
144
145			double chiTolerance;
146			short int have_chi_tolerance;
147
148	mmeineke	540	};
149
150
151
152	mmeineke	778	template<typename T> class NPT : public T{
153	tim	645
154	gezelter	560	public:
155
156	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
157			virtual ~NPT();
158	tim	837
159	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
160			calcStress = 1;
161	tim	645	T::integrateStep( calcPot, calcStress );
162	mmeineke	594	}
163
164	mmeineke	778	virtual double getConservedQuantity(void) = 0;
165	tim	837	virtual string getAdditionalParameters(void) = 0;
166	mmeineke	843
167			double myTauThermo( void ) { return tauThermostat; }
168			double myTauBaro( void ) { return tauBarostat; }
169
170	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
175			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
176			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
177	gezelter	560
178			protected:
179
180	mmeineke	561	virtual void moveA( void );
181			virtual void moveB( void );
182	gezelter	560
183	mmeineke	561	virtual int readyCheck();
184	gezelter	560
185	mmeineke	746	virtual void resetIntegrator( void );
186
187	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
188			virtual void getVelScaleB( double sc[3], int index ) = 0;
189	tim	837	virtual void getPosScale(double pos[3], double COM[3],
190	mmeineke	778	int index, double sc[3]) = 0;
191
192	mmeineke	857	virtual void calcVelScale( void ) = 0;
193
194	mmeineke	778	virtual bool chiConverged( void );
195			virtual bool etaConverged( void ) = 0;
196	tim	837
197	mmeineke	778	virtual void evolveChiA( void );
198			virtual void evolveEtaA( void ) = 0;
199			virtual void evolveChiB( void );
200			virtual void evolveEtaB( void ) = 0;
201
202			virtual void scaleSimBox( void ) = 0;
203
204	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
205
206	gezelter	565	// chi and eta are the propagated degrees of freedom
207	gezelter	560
208	mmeineke	778	double oldChi;
209			double prevChi;
210	gezelter	565	double chi;
211	gezelter	574	double NkBT;
212	tim	763	double fkBT;
213	gezelter	560
214	mmeineke	778	double tt2, tb2;
215			double instaTemp, instaPress, instaVol;
216	mmeineke	780	double press[3][3];
217	mmeineke	778
218	tim	763	int Nparticles;
219
220			double integralOfChidt;
221
222	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
223	gezelter	560	// One of qmass or tauThermostat must be set;
224
225			double targetTemp;
226			double targetPressure;
227			double tauThermostat;
228			double tauBarostat;
229
230			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
231	gezelter	565	short int have_target_pressure;
232	gezelter	560
233	tim	763	double *oldPos;
234			double *oldVel;
235			double *oldJi;
236
237			double chiTolerance;
238			short int have_chi_tolerance;
239			double posIterTolerance;
240			short int have_pos_iter_tolerance;
241			double etaTolerance;
242			short int have_eta_tolerance;
243
244	gezelter	560	};
245
246	mmeineke	778	template<typename T> class NPTi : public T{
247	tim	837
248	mmeineke	778	public:
249			NPTi( SimInfo theInfo, ForceFields the_ff);
250			~NPTi();
251
252			virtual double getConservedQuantity(void);
253			virtual void resetIntegrator(void);
254	tim	837	virtual string getAdditionalParameters(void);
255	mmeineke	778	protected:
256
257
258	tim	837
259	mmeineke	778	virtual void evolveEtaA(void);
260			virtual void evolveEtaB(void);
261
262			virtual bool etaConverged( void );
263
264			virtual void scaleSimBox( void );
265
266			virtual void getVelScaleA( double sc[3], double vel[3] );
267			virtual void getVelScaleB( double sc[3], int index );
268	tim	837	virtual void getPosScale(double pos[3], double COM[3],
269	mmeineke	778	int index, double sc[3]);
270
271	mmeineke	857	virtual void calcVelScale( void );
272
273	mmeineke	778	double eta, oldEta, prevEta;
274	mmeineke	857	double vScale;
275	mmeineke	778	};
276
277	tim	645	template<typename T> class NPTf : public T{
278	gezelter	576
279			public:
280
281			NPTf ( SimInfo theInfo, ForceFields the_ff);
282	tim	767	virtual ~NPTf();
283	gezelter	576
284	tim	763	virtual double getConservedQuantity(void);
285	tim	837	virtual string getAdditionalParameters(void);
286	mmeineke	780	virtual void resetIntegrator(void);
287	mmeineke	594
288	gezelter	576	protected:
289
290	mmeineke	780	virtual void evolveEtaA(void);
291			virtual void evolveEtaB(void);
292	gezelter	576
293	mmeineke	780	virtual bool etaConverged( void );
294	mmeineke	746
295	mmeineke	780	virtual void scaleSimBox( void );
296	gezelter	576
297	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
298			virtual void getVelScaleB( double sc[3], int index );
299	tim	837	virtual void getPosScale(double pos[3], double COM[3],
300	mmeineke	780	int index, double sc[3]);
301	tim	763
302	mmeineke	857	virtual void calcVelScale( void );
303
304	gezelter	588	double eta[3][3];
305	mmeineke	780	double oldEta[3][3];
306			double prevEta[3][3];
307	mmeineke	857	double vScale[3][3];
308	gezelter	576	};
309
310	mmeineke	812	template<typename T> class NPTxyz : public T{
311	mmeineke	755
312			public:
313
314	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
315			virtual ~NPTxyz();
316	mmeineke	755
317	mmeineke	812	virtual double getConservedQuantity(void);
318	tim	837	virtual string getAdditionalParameters(void);
319	mmeineke	812	virtual void resetIntegrator(void);
320	mmeineke	755
321			protected:
322
323	mmeineke	812	virtual void evolveEtaA(void);
324			virtual void evolveEtaB(void);
325	mmeineke	755
326	mmeineke	812	virtual bool etaConverged( void );
327	mmeineke	755
328	mmeineke	812	virtual void scaleSimBox( void );
329	mmeineke	755
330	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
331			virtual void getVelScaleB( double sc[3], int index );
332	tim	837	virtual void getPosScale(double pos[3], double COM[3],
333	mmeineke	812	int index, double sc[3]);
334	mmeineke	755
335	mmeineke	857	virtual void calcVelScale( void );
336
337	mmeineke	812	double eta[3][3];
338			double oldEta[3][3];
339			double prevEta[3][3];
340	mmeineke	857	double vScale[3][3];
341	mmeineke	812	};
342	mmeineke	755
343
344	tim	658	template<typename T> class ZConstraint : public T {
345	tim	837
346			public:
347	tim	738	class ForceSubtractionPolicy{
348	tim	699	public:
349	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
350	tim	658
351	tim	837	virtual void update() = 0;
352	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
354	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
356	tim	837
357	tim	701	protected:
358	mmeineke	788	ZConstraint<T>* zconsIntegrator;
359	tim	699	};
360
361	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
362	gezelter	747
363	tim	699	public:
364	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
365			virtual void update();
366	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
367			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
368	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
369			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
370	tim	837
371	tim	699	private:
372	tim	763	int totNumOfMovingAtoms;
373	tim	699	};
374
375	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
376	gezelter	747
377	tim	699	public:
378	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
379
380			virtual void update();
381	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385	tim	699
386	tim	701	private:
387			double totMassOfMovingAtoms;
388	tim	699	};
389
390	tim	658	public:
391
392			ZConstraint( SimInfo theInfo, ForceFields the_ff);
393			~ZConstraint();
394	tim	837
395	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
396			void getZConsTime() {return zconsTime;}
397	tim	837
398	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
400	tim	837
401	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
402	tim	658	string getZConsOutput() {return zconsOutput;}
403	tim	837
404	tim	677	virtual void integrate();
405	tim	658
406	tim	837
407	tim	658	#ifdef IS_MPI
408	tim	701	virtual void update(); //which is called to indicate the molecules' migration
409	mmeineke	377	#endif
410	tim	658
411	tim	837	enum ZConsState {zcsMoving, zcsFixed};
412	mmeineke	790
413			vector<Molecule*> zconsMols; //z-constraint molecules array
414			vector<ZConsState> states; //state of z-constraint molecules
415
416
417	tim	837
418	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
419			double totalMassOfUncons; //total mas of unconstraint molecules
420
421
422	tim	658	protected:
423
424	mmeineke	790
425	tim	837
426			virtual void calcForce( int calcPot, int calcStress );
427	tim	677	virtual void thermalize(void);
428	tim	837
429	tim	677	void zeroOutVel();
430			void doZconstraintForce();
431	tim	1093	void doHarmonic(vector<double>& resPos);
432	tim	677	bool checkZConsState();
433
434			bool haveFixedZMols();
435			bool haveMovingZMols();
436
437			double calcZSys();
438
439			int isZConstraintMol(Molecule* mol);
440
441
442	tim	701	double zconsTime; //sample time
443			double zconsTol; //tolerance of z-contratint
444			double zForceConst; //base force constant term
445			//which is estimate by OOPSE
446	mmeineke	790
447	tim	837
448			vector<double> massOfZConsMols; //mass of z-constraint molecule
449	tim	701	vector<double> kz; //force constant array
450	mmeineke	790
451	tim	701	vector<double> zPos; //
452	tim	837
453
454	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
455			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
456	tim	682
457	mmeineke	790
458	tim	701	vector<ZConsParaItem>* parameters; //
459	tim	837
460	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
461	tim	677
462	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
463			vector<double> fz;
464			vector<double> curZPos;
465	tim	677
466	tim	1093	bool usingSMD;
467	tim	1141	vector<double> prevCantPos;
468	tim	1093	vector<double> cantPos;
469			vector<double> cantVel;
470
471	tim	1091	double zconsFixTime;
472			double zconsGap;
473			bool hasZConsGap;
474			vector<double> endFixTime;
475
476	tim	837	int whichDirection; //constraint direction
477
478	tim	658	private:
479	tim	837
480	tim	701	string zconsOutput; //filename of zconstraint output
481			ZConsWriter* fzOut; //z-constraint writer
482	tim	677
483	tim	837	double curZconsTime;
484	tim	699
485	tim	696	double calcMovingMolsCOMVel();
486			double calcSysCOMVel();
487			double calcTotalForce();
488	tim	1091	void updateZPos();
489	tim	1093	void updateCantPos();
490
491	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
492	tim	738	friend class ForceSubtractionPolicy;
493	tim	677
494	tim	658	};
495
496	tim	1254
497			//Sympletic quaternion Scheme Integrator
498			//Reference:
499			// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500			//Symplectic quaternion Scheme for biophysical molecular dynamics
501			//116(20), 8649, J. Chem. Phys. (2002)
502			template<typename T> class SQSIntegrator : public T{
503			public:
504			virtual void moveA();
505			virtual void moveB();
506			protected:
507			void freeRotor();
508			void rotate(int k, double dt);
509
510			};
511	tim	658	#endif