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"
#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 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] );

  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;

  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:
    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
Revision:	1452
Committed:	Mon Aug 23 15:11:36 2004 UTC (20 years ago) by tim
File size:	14280 byte(s)
Log Message:	* empty log message *
#	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	tim	1452	#include "Quaternion.hpp"
18			#include "Mat4x4d.hpp"
19	mmeineke	377
20	tim	658	using namespace std;
21	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
22			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
23	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
24	mmeineke	561	const int maxIteration = 300;
25			const double tol = 1.0e-6;
26
27	tim	1268	class VelVerletConsFramework;
28	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
29
30	mmeineke	377	public:
31	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
32	mmeineke	548	virtual ~Integrator();
33	mmeineke	377	void integrate( void );
34	tim	763	virtual double getConservedQuantity(void);
35	tim	837	virtual string getAdditionalParameters(void);
36	mmeineke	377
37	mmeineke	540	protected:
38	mmeineke	778
39	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
40	tim	1234	//virtual void preMove( void );
41	mmeineke	540	virtual void moveA( void );
42			virtual void moveB( void );
43	tim	1234	//virtual void constrainA( void );
44			//virtual void constrainB( void );
45	mmeineke	559	virtual int readyCheck( void ) { return 1; }
46	tim	677
47	mmeineke	746	virtual void resetIntegrator( void ) { }
48	tim	837
49			virtual void calcForce( int calcPot, int calcStress );
50	tim	677	virtual void thermalize();
51	tim	837
52	tim	1108	virtual bool stopIntegrator() {return false;}
53
54	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
55	mmeineke	778
56	tim	1234	//void checkConstraints( void );
57	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
58	tim	701	double A[3][3] );
59	tim	837
60	tim	1452	void printQuaternion(StuntDouble* sd);
61			Mat4x4d getS(const Quaternion& q);
62
63	mmeineke	377	ForceFields* myFF;
64
65	mmeineke	540	SimInfo *info; // all the info we'll ever need
66	gezelter	1097	vector<StuntDouble*> integrableObjects;
67	mmeineke	540	int nAtoms; /* the number of atoms */
68	mmeineke	548	int oldAtoms;
69	mmeineke	540	Atom *atoms; / array of atom pointers */
70	mmeineke	423	Molecule* molecules;
71			int nMols;
72
73	tim	1268	VelVerletConsFramework* consFramework;
74	tim	837
75	tim	1234	//int isConstrained; // boolean to know whether the systems contains constraints.
76			//int nConstrained; // counter for number of constraints
77			//int *constrainedA; // the i of a constraint pair
78			//int *constrainedB; // the j of a constraint pair
79			//double *constrainedDsqr; // the square of the constraint distance
80	mmeineke	548
81	tim	1234	//int* moving; // tells whether we are moving atom i
82			//int* moved; // tells whether we have moved atom i
83			//double* oldPos; // pre constrained positions
84
85	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
86	tim	837
87	mmeineke	540	double dt;
88	mmeineke	541	double dt2;
89	gezelter	560
90	mmeineke	540	Thermo *tStats;
91			StatWriter* statOut;
92			DumpWriter* dumpOut;
93	tim	837
94	mmeineke	377	};
95
96	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
97	mmeineke	540
98	tim	1161	// ansi instantiation
99	gezelter	1323	// template class Integrator<BaseIntegrator>;
100	tim	1161
101	gezelter	1330
102	tim	645	template<typename T> class NVE : public T {
103
104	mmeineke	561	public:
105			NVE ( SimInfo theInfo, ForceFields the_ff ):
106	tim	645	T( theInfo, the_ff ){}
107	tim	837	virtual ~NVE(){}
108	tim	645	};
109	mmeineke	555
110
111	tim	645	template<typename T> class NVT : public T {
112	mmeineke	555
113	gezelter	560	public:
114
115	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
116	tim	763	virtual ~NVT();
117	mmeineke	540
118	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
119			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
120	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
121			virtual double getConservedQuantity(void);
122	tim	837	virtual string getAdditionalParameters(void);
123	gezelter	560
124	mmeineke	540	protected:
125	gezelter	560
126	mmeineke	561	virtual void moveA( void );
127			virtual void moveB( void );
128	mmeineke	540
129	mmeineke	561	virtual int readyCheck();
130	gezelter	560
131	mmeineke	746	virtual void resetIntegrator( void );
132
133	gezelter	565	// chi is a propagated degree of freedom.
134	gezelter	560
135	gezelter	565	double chi;
136	gezelter	560
137	tim	763	//integral of chi(t)dt
138			double integralOfChidt;
139
140	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
141	gezelter	560
142			double targetTemp;
143			double tauThermostat;
144	tim	837
145	gezelter	565	short int have_tau_thermostat, have_target_temp;
146	gezelter	560
147	tim	763	double *oldVel;
148			double *oldJi;
149
150			double chiTolerance;
151			short int have_chi_tolerance;
152
153	mmeineke	540	};
154
155
156
157	mmeineke	778	template<typename T> class NPT : public T{
158	tim	645
159	gezelter	560	public:
160
161	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
162			virtual ~NPT();
163	tim	837
164	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
165			calcStress = 1;
166	tim	645	T::integrateStep( calcPot, calcStress );
167	mmeineke	594	}
168
169	mmeineke	778	virtual double getConservedQuantity(void) = 0;
170	tim	837	virtual string getAdditionalParameters(void) = 0;
171	mmeineke	843
172			double myTauThermo( void ) { return tauThermostat; }
173			double myTauBaro( void ) { return tauBarostat; }
174
175	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
180			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
181			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
182	gezelter	560
183			protected:
184
185	mmeineke	561	virtual void moveA( void );
186			virtual void moveB( void );
187	gezelter	560
188	mmeineke	561	virtual int readyCheck();
189	gezelter	560
190	mmeineke	746	virtual void resetIntegrator( void );
191
192	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
193			virtual void getVelScaleB( double sc[3], int index ) = 0;
194	tim	837	virtual void getPosScale(double pos[3], double COM[3],
195	mmeineke	778	int index, double sc[3]) = 0;
196
197	mmeineke	857	virtual void calcVelScale( void ) = 0;
198
199	mmeineke	778	virtual bool chiConverged( void );
200			virtual bool etaConverged( void ) = 0;
201	tim	837
202	mmeineke	778	virtual void evolveChiA( void );
203			virtual void evolveEtaA( void ) = 0;
204			virtual void evolveChiB( void );
205			virtual void evolveEtaB( void ) = 0;
206
207			virtual void scaleSimBox( void ) = 0;
208
209	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
210
211	gezelter	565	// chi and eta are the propagated degrees of freedom
212	gezelter	560
213	mmeineke	778	double oldChi;
214			double prevChi;
215	gezelter	565	double chi;
216	gezelter	574	double NkBT;
217	tim	763	double fkBT;
218	gezelter	560
219	mmeineke	778	double tt2, tb2;
220			double instaTemp, instaPress, instaVol;
221	mmeineke	780	double press[3][3];
222	mmeineke	778
223	tim	763	int Nparticles;
224
225			double integralOfChidt;
226
227	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
228	gezelter	560	// One of qmass or tauThermostat must be set;
229
230			double targetTemp;
231			double targetPressure;
232			double tauThermostat;
233			double tauBarostat;
234
235			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
236	gezelter	565	short int have_target_pressure;
237	gezelter	560
238	tim	763	double *oldPos;
239			double *oldVel;
240			double *oldJi;
241
242			double chiTolerance;
243			short int have_chi_tolerance;
244			double posIterTolerance;
245			short int have_pos_iter_tolerance;
246			double etaTolerance;
247			short int have_eta_tolerance;
248
249	gezelter	560	};
250
251	mmeineke	778	template<typename T> class NPTi : public T{
252	tim	837
253	mmeineke	778	public:
254			NPTi( SimInfo theInfo, ForceFields the_ff);
255			~NPTi();
256
257			virtual double getConservedQuantity(void);
258			virtual void resetIntegrator(void);
259	tim	837	virtual string getAdditionalParameters(void);
260	mmeineke	778	protected:
261
262
263	tim	837
264	mmeineke	778	virtual void evolveEtaA(void);
265			virtual void evolveEtaB(void);
266
267			virtual bool etaConverged( void );
268
269			virtual void scaleSimBox( void );
270
271			virtual void getVelScaleA( double sc[3], double vel[3] );
272			virtual void getVelScaleB( double sc[3], int index );
273	tim	837	virtual void getPosScale(double pos[3], double COM[3],
274	mmeineke	778	int index, double sc[3]);
275
276	mmeineke	857	virtual void calcVelScale( void );
277
278	mmeineke	778	double eta, oldEta, prevEta;
279	mmeineke	857	double vScale;
280	mmeineke	778	};
281
282	tim	645	template<typename T> class NPTf : public T{
283	gezelter	576
284			public:
285
286			NPTf ( SimInfo theInfo, ForceFields the_ff);
287	tim	767	virtual ~NPTf();
288	gezelter	576
289	tim	763	virtual double getConservedQuantity(void);
290	tim	837	virtual string getAdditionalParameters(void);
291	mmeineke	780	virtual void resetIntegrator(void);
292	mmeineke	594
293	gezelter	576	protected:
294
295	mmeineke	780	virtual void evolveEtaA(void);
296			virtual void evolveEtaB(void);
297	gezelter	576
298	mmeineke	780	virtual bool etaConverged( void );
299	mmeineke	746
300	mmeineke	780	virtual void scaleSimBox( void );
301	gezelter	576
302	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
303			virtual void getVelScaleB( double sc[3], int index );
304	tim	837	virtual void getPosScale(double pos[3], double COM[3],
305	mmeineke	780	int index, double sc[3]);
306	tim	763
307	mmeineke	857	virtual void calcVelScale( void );
308
309	gezelter	588	double eta[3][3];
310	mmeineke	780	double oldEta[3][3];
311			double prevEta[3][3];
312	mmeineke	857	double vScale[3][3];
313	gezelter	576	};
314
315	mmeineke	812	template<typename T> class NPTxyz : public T{
316	mmeineke	755
317			public:
318
319	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
320			virtual ~NPTxyz();
321	mmeineke	755
322	mmeineke	812	virtual double getConservedQuantity(void);
323	tim	837	virtual string getAdditionalParameters(void);
324	mmeineke	812	virtual void resetIntegrator(void);
325	mmeineke	755
326			protected:
327
328	mmeineke	812	virtual void evolveEtaA(void);
329			virtual void evolveEtaB(void);
330	mmeineke	755
331	mmeineke	812	virtual bool etaConverged( void );
332	mmeineke	755
333	mmeineke	812	virtual void scaleSimBox( void );
334	mmeineke	755
335	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
336			virtual void getVelScaleB( double sc[3], int index );
337	tim	837	virtual void getPosScale(double pos[3], double COM[3],
338	mmeineke	812	int index, double sc[3]);
339	mmeineke	755
340	mmeineke	857	virtual void calcVelScale( void );
341
342	mmeineke	812	double eta[3][3];
343			double oldEta[3][3];
344			double prevEta[3][3];
345	mmeineke	857	double vScale[3][3];
346	mmeineke	812	};
347	mmeineke	755
348
349	tim	658	template<typename T> class ZConstraint : public T {
350	tim	837
351			public:
352	tim	738	class ForceSubtractionPolicy{
353	tim	699	public:
354	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
355	tim	658
356	tim	837	virtual void update() = 0;
357	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
358			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
359	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
360			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
361	tim	837
362	tim	701	protected:
363	mmeineke	788	ZConstraint<T>* zconsIntegrator;
364	tim	699	};
365
366	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
367	gezelter	747
368	tim	699	public:
369	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370			virtual void update();
371	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375	tim	837
376	tim	699	private:
377	tim	763	int totNumOfMovingAtoms;
378	tim	699	};
379
380	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
381	gezelter	747
382	tim	699	public:
383	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
384
385			virtual void update();
386	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
387			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
388	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
389			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
390	tim	699
391	tim	701	private:
392			double totMassOfMovingAtoms;
393	tim	699	};
394
395	tim	658	public:
396
397			ZConstraint( SimInfo theInfo, ForceFields the_ff);
398			~ZConstraint();
399	tim	837
400	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
401			void getZConsTime() {return zconsTime;}
402	tim	837
403	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
404			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
405	tim	837
406	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
407	tim	658	string getZConsOutput() {return zconsOutput;}
408	tim	837
409	tim	677	virtual void integrate();
410	tim	658
411	tim	837
412	tim	658	#ifdef IS_MPI
413	tim	701	virtual void update(); //which is called to indicate the molecules' migration
414	mmeineke	377	#endif
415	tim	658
416	tim	837	enum ZConsState {zcsMoving, zcsFixed};
417	mmeineke	790
418			vector<Molecule*> zconsMols; //z-constraint molecules array
419			vector<ZConsState> states; //state of z-constraint molecules
420
421
422	tim	837
423	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
424			double totalMassOfUncons; //total mas of unconstraint molecules
425
426
427	tim	658	protected:
428
429	mmeineke	790
430	tim	837
431			virtual void calcForce( int calcPot, int calcStress );
432	tim	677	virtual void thermalize(void);
433	tim	837
434	tim	677	void zeroOutVel();
435			void doZconstraintForce();
436	tim	1093	void doHarmonic(vector<double>& resPos);
437	tim	677	bool checkZConsState();
438
439			bool haveFixedZMols();
440			bool haveMovingZMols();
441
442			double calcZSys();
443
444			int isZConstraintMol(Molecule* mol);
445
446
447	tim	701	double zconsTime; //sample time
448			double zconsTol; //tolerance of z-contratint
449			double zForceConst; //base force constant term
450			//which is estimate by OOPSE
451	mmeineke	790
452	tim	837
453			vector<double> massOfZConsMols; //mass of z-constraint molecule
454	tim	701	vector<double> kz; //force constant array
455	mmeineke	790
456	tim	701	vector<double> zPos; //
457	tim	837
458
459	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
460			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
461	tim	682
462	mmeineke	790
463	tim	701	vector<ZConsParaItem>* parameters; //
464	tim	837
465	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
466	tim	677
467	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
468			vector<double> fz;
469			vector<double> curZPos;
470	tim	677
471	tim	1093	bool usingSMD;
472	tim	1141	vector<double> prevCantPos;
473	tim	1093	vector<double> cantPos;
474			vector<double> cantVel;
475
476	tim	1091	double zconsFixTime;
477			double zconsGap;
478			bool hasZConsGap;
479			vector<double> endFixTime;
480
481	tim	837	int whichDirection; //constraint direction
482
483	tim	658	private:
484	tim	837
485	tim	701	string zconsOutput; //filename of zconstraint output
486			ZConsWriter* fzOut; //z-constraint writer
487	tim	677
488	tim	837	double curZconsTime;
489	tim	699
490	tim	696	double calcMovingMolsCOMVel();
491			double calcSysCOMVel();
492			double calcTotalForce();
493	tim	1091	void updateZPos();
494	tim	1093	void updateCantPos();
495
496	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
497	tim	738	friend class ForceSubtractionPolicy;
498	tim	677
499	tim	658	};
500
501	tim	1254
502			//Sympletic quaternion Scheme Integrator
503			//Reference:
504			// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
505			//Symplectic quaternion Scheme for biophysical molecular dynamics
506			//116(20), 8649, J. Chem. Phys. (2002)
507			template<typename T> class SQSIntegrator : public T{
508			public:
509	tim	1452	SQSIntegrator( SimInfo theInfo, ForceFields the_ff );
510	tim	1254	virtual void moveA();
511			virtual void moveB();
512			protected:
513	tim	1452	void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
514			void rotate(int k, double dt, Quaternion& q, Vector4d& qdot, double Ik);
515			private:
516			Quaternion getPk(int i, const Vector4d& q);
517			Mat4x4d getS(const Quaternion& q);
518			vector<Quaternion> q;
519			vector<Vector4d> p_qua;
520			vector<double> I0;
521
522			Vector4d p2j(const Vector4d& p, Mat4x4d& m);
523			Vector4d j2p(const Vector4d& j, Mat4x4d& m);
524	tim	1254	};
525	tim	658	#endif