OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#include "Atom.hpp"
#include "Molecule.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "ZConsWriter.hpp"

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 void rotationPropagation( DirectionalAtom* dAtom, 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
  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;

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();
  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

  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
  double* fz;
  double* curZPos;


  int whichDirection;                           //constraint direction

private:

  string zconsOutput;                         //filename of zconstraint output
  ZConsWriter* fzOut;                         //z-constraint writer

  double curZconsTime;

  double calcMovingMolsCOMVel();
  double calcSysCOMVel();
  double calcTotalForce();

  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
  friend class ForceSubtractionPolicy;

};

/*
class OOPSEMinimizerBase : public RealIntegrator {
  public:

    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
    virtual ~OOPSEMinimizerBase();
    
    double calcGradient(vector<double>& x, vector<double>& grad);
    void setCoor(vector<double>& x);
    vector<double> getCoor();
    void output(vector<double>& x, int iteration);
    int getDim() {return dim;}
    void constraintMove();
    void shakeF();
    void shakeR();
  protected:
    
    int dim;
    void calcDim();
};

//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
//  public:
//    void writeOutput();
//};
*/  
#endif
Revision:	1064
Committed:	Tue Feb 24 15:44:45 2004 UTC (20 years, 4 months ago) by tim
File size:	13363 byte(s)
Log Message:	Using inherit instead of compose to implement Minimizer both versions are working
#	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	604	#include "Molecule.hpp"
8	mmeineke	377	#include "SRI.hpp"
9			#include "AbstractClasses.hpp"
10			#include "SimInfo.hpp"
11			#include "ForceFields.hpp"
12	mmeineke	540	#include "Thermo.hpp"
13			#include "ReadWrite.hpp"
14	tim	658	#include "ZConsWriter.hpp"
15	mmeineke	377
16	tim	658	using namespace std;
17	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
18			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	mmeineke	561	const int maxIteration = 300;
21			const double tol = 1.0e-6;
22
23	mmeineke	377
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	mmeineke	778	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49
50	mmeineke	540	void checkConstraints( void );
51	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
52	tim	701	double A[3][3] );
53	tim	837
54	mmeineke	377	ForceFields* myFF;
55
56	mmeineke	540	SimInfo *info; // all the info we'll ever need
57			int nAtoms; /* the number of atoms */
58	mmeineke	548	int oldAtoms;
59	mmeineke	540	Atom *atoms; / array of atom pointers */
60	mmeineke	423	Molecule* molecules;
61			int nMols;
62
63	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
64	tim	701	// constraints.
65	tim	837	int nConstrained; // counter for number of constraints
66			int *constrainedA; // the i of a constraint pair
67			int *constrainedB; // the j of a constraint pair
68			double *constrainedDsqr; // the square of the constraint distance
69
70	mmeineke	548	int* moving; // tells whether we are moving atom i
71			int* moved; // tells whether we have moved atom i
72	tim	837	double* oldPos; // pre constrained positions
73	mmeineke	548
74	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
75	tim	837
76	mmeineke	540	double dt;
77	mmeineke	541	double dt2;
78	gezelter	560
79	mmeineke	540	Thermo *tStats;
80			StatWriter* statOut;
81			DumpWriter* dumpOut;
82	tim	837
83	mmeineke	377	};
84
85	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
86	mmeineke	540
87	tim	645	template<typename T> class NVE : public T {
88
89	mmeineke	561	public:
90			NVE ( SimInfo theInfo, ForceFields the_ff ):
91	tim	645	T( theInfo, the_ff ){}
92	tim	837	virtual ~NVE(){}
93	tim	645	};
94	mmeineke	555
95
96	tim	645	template<typename T> class NVT : public T {
97	mmeineke	555
98	gezelter	560	public:
99
100	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
101	tim	763	virtual ~NVT();
102	mmeineke	540
103	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
104			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
106			virtual double getConservedQuantity(void);
107	tim	837	virtual string getAdditionalParameters(void);
108	gezelter	560
109	mmeineke	540	protected:
110	gezelter	560
111	mmeineke	561	virtual void moveA( void );
112			virtual void moveB( void );
113	mmeineke	540
114	mmeineke	561	virtual int readyCheck();
115	gezelter	560
116	mmeineke	746	virtual void resetIntegrator( void );
117
118	gezelter	565	// chi is a propagated degree of freedom.
119	gezelter	560
120	gezelter	565	double chi;
121	gezelter	560
122	tim	763	//integral of chi(t)dt
123			double integralOfChidt;
124
125	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
126	gezelter	560
127			double targetTemp;
128			double tauThermostat;
129	tim	837
130	gezelter	565	short int have_tau_thermostat, have_target_temp;
131	gezelter	560
132	tim	763	double *oldVel;
133			double *oldJi;
134
135			double chiTolerance;
136			short int have_chi_tolerance;
137
138	mmeineke	540	};
139
140
141
142	mmeineke	778	template<typename T> class NPT : public T{
143	tim	645
144	gezelter	560	public:
145
146	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
147			virtual ~NPT();
148	tim	837
149	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
150			calcStress = 1;
151	tim	645	T::integrateStep( calcPot, calcStress );
152	mmeineke	594	}
153
154	mmeineke	778	virtual double getConservedQuantity(void) = 0;
155	tim	837	virtual string getAdditionalParameters(void) = 0;
156	mmeineke	843
157			double myTauThermo( void ) { return tauThermostat; }
158			double myTauBaro( void ) { return tauBarostat; }
159
160	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167	gezelter	560
168			protected:
169
170	mmeineke	561	virtual void moveA( void );
171			virtual void moveB( void );
172	gezelter	560
173	mmeineke	561	virtual int readyCheck();
174	gezelter	560
175	mmeineke	746	virtual void resetIntegrator( void );
176
177	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178			virtual void getVelScaleB( double sc[3], int index ) = 0;
179	tim	837	virtual void getPosScale(double pos[3], double COM[3],
180	mmeineke	778	int index, double sc[3]) = 0;
181
182	mmeineke	857	virtual void calcVelScale( void ) = 0;
183
184	mmeineke	778	virtual bool chiConverged( void );
185			virtual bool etaConverged( void ) = 0;
186	tim	837
187	mmeineke	778	virtual void evolveChiA( void );
188			virtual void evolveEtaA( void ) = 0;
189			virtual void evolveChiB( void );
190			virtual void evolveEtaB( void ) = 0;
191
192			virtual void scaleSimBox( void ) = 0;
193
194	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
195
196	gezelter	565	// chi and eta are the propagated degrees of freedom
197	gezelter	560
198	mmeineke	778	double oldChi;
199			double prevChi;
200	gezelter	565	double chi;
201	gezelter	574	double NkBT;
202	tim	763	double fkBT;
203	gezelter	560
204	mmeineke	778	double tt2, tb2;
205			double instaTemp, instaPress, instaVol;
206	mmeineke	780	double press[3][3];
207	mmeineke	778
208	tim	763	int Nparticles;
209
210			double integralOfChidt;
211
212	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
213	gezelter	560	// One of qmass or tauThermostat must be set;
214
215			double targetTemp;
216			double targetPressure;
217			double tauThermostat;
218			double tauBarostat;
219
220			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
221	gezelter	565	short int have_target_pressure;
222	gezelter	560
223	tim	763	double *oldPos;
224			double *oldVel;
225			double *oldJi;
226
227			double chiTolerance;
228			short int have_chi_tolerance;
229			double posIterTolerance;
230			short int have_pos_iter_tolerance;
231			double etaTolerance;
232			short int have_eta_tolerance;
233
234	gezelter	560	};
235
236	mmeineke	778	template<typename T> class NPTi : public T{
237	tim	837
238	mmeineke	778	public:
239			NPTi( SimInfo theInfo, ForceFields the_ff);
240			~NPTi();
241
242			virtual double getConservedQuantity(void);
243			virtual void resetIntegrator(void);
244	tim	837	virtual string getAdditionalParameters(void);
245	mmeineke	778	protected:
246
247
248	tim	837
249	mmeineke	778	virtual void evolveEtaA(void);
250			virtual void evolveEtaB(void);
251
252			virtual bool etaConverged( void );
253
254			virtual void scaleSimBox( void );
255
256			virtual void getVelScaleA( double sc[3], double vel[3] );
257			virtual void getVelScaleB( double sc[3], int index );
258	tim	837	virtual void getPosScale(double pos[3], double COM[3],
259	mmeineke	778	int index, double sc[3]);
260
261	mmeineke	857	virtual void calcVelScale( void );
262
263	mmeineke	778	double eta, oldEta, prevEta;
264	mmeineke	857	double vScale;
265	mmeineke	778	};
266
267	tim	645	template<typename T> class NPTf : public T{
268	gezelter	576
269			public:
270
271			NPTf ( SimInfo theInfo, ForceFields the_ff);
272	tim	767	virtual ~NPTf();
273	gezelter	576
274	tim	763	virtual double getConservedQuantity(void);
275	tim	837	virtual string getAdditionalParameters(void);
276	mmeineke	780	virtual void resetIntegrator(void);
277	mmeineke	594
278	gezelter	576	protected:
279
280	mmeineke	780	virtual void evolveEtaA(void);
281			virtual void evolveEtaB(void);
282	gezelter	576
283	mmeineke	780	virtual bool etaConverged( void );
284	mmeineke	746
285	mmeineke	780	virtual void scaleSimBox( void );
286	gezelter	576
287	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
288			virtual void getVelScaleB( double sc[3], int index );
289	tim	837	virtual void getPosScale(double pos[3], double COM[3],
290	mmeineke	780	int index, double sc[3]);
291	tim	763
292	mmeineke	857	virtual void calcVelScale( void );
293
294	gezelter	588	double eta[3][3];
295	mmeineke	780	double oldEta[3][3];
296			double prevEta[3][3];
297	mmeineke	857	double vScale[3][3];
298	gezelter	576	};
299
300	mmeineke	812	template<typename T> class NPTxyz : public T{
301	mmeineke	755
302			public:
303
304	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
305			virtual ~NPTxyz();
306	mmeineke	755
307	mmeineke	812	virtual double getConservedQuantity(void);
308	tim	837	virtual string getAdditionalParameters(void);
309	mmeineke	812	virtual void resetIntegrator(void);
310	mmeineke	755
311			protected:
312
313	mmeineke	812	virtual void evolveEtaA(void);
314			virtual void evolveEtaB(void);
315	mmeineke	755
316	mmeineke	812	virtual bool etaConverged( void );
317	mmeineke	755
318	mmeineke	812	virtual void scaleSimBox( void );
319	mmeineke	755
320	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
321			virtual void getVelScaleB( double sc[3], int index );
322	tim	837	virtual void getPosScale(double pos[3], double COM[3],
323	mmeineke	812	int index, double sc[3]);
324	mmeineke	755
325	mmeineke	857	virtual void calcVelScale( void );
326
327	mmeineke	812	double eta[3][3];
328			double oldEta[3][3];
329			double prevEta[3][3];
330	mmeineke	857	double vScale[3][3];
331	mmeineke	812	};
332	mmeineke	755
333
334	tim	658	template<typename T> class ZConstraint : public T {
335	tim	837
336			public:
337	tim	738	class ForceSubtractionPolicy{
338	tim	699	public:
339	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
340	tim	658
341	tim	837	virtual void update() = 0;
342	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
343			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
344	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346	tim	837
347	tim	701	protected:
348	mmeineke	788	ZConstraint<T>* zconsIntegrator;
349	tim	699	};
350
351	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
352	gezelter	747
353	tim	699	public:
354	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
355			virtual void update();
356	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
357			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
358	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
359			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360	tim	837
361	tim	699	private:
362	tim	763	int totNumOfMovingAtoms;
363	tim	699	};
364
365	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
366	gezelter	747
367	tim	699	public:
368	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
369
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	699
376	tim	701	private:
377			double totMassOfMovingAtoms;
378	tim	699	};
379
380	tim	658	public:
381
382			ZConstraint( SimInfo theInfo, ForceFields the_ff);
383			~ZConstraint();
384	tim	837
385	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
386			void getZConsTime() {return zconsTime;}
387	tim	837
388	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
390	tim	837
391	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
392	tim	658	string getZConsOutput() {return zconsOutput;}
393	tim	837
394	tim	677	virtual void integrate();
395	tim	658
396	tim	837
397	tim	658	#ifdef IS_MPI
398	tim	701	virtual void update(); //which is called to indicate the molecules' migration
399	mmeineke	377	#endif
400	tim	658
401	tim	837	enum ZConsState {zcsMoving, zcsFixed};
402	mmeineke	790
403			vector<Molecule*> zconsMols; //z-constraint molecules array
404			vector<ZConsState> states; //state of z-constraint molecules
405
406
407	tim	837
408	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
409			double totalMassOfUncons; //total mas of unconstraint molecules
410
411
412	tim	658	protected:
413
414	mmeineke	790
415	tim	837
416			virtual void calcForce( int calcPot, int calcStress );
417	tim	677	virtual void thermalize(void);
418	tim	837
419	tim	677	void zeroOutVel();
420			void doZconstraintForce();
421	tim	682	void doHarmonic();
422	tim	677	bool checkZConsState();
423
424			bool haveFixedZMols();
425			bool haveMovingZMols();
426
427			double calcZSys();
428
429			int isZConstraintMol(Molecule* mol);
430
431
432	tim	701	double zconsTime; //sample time
433			double zconsTol; //tolerance of z-contratint
434			double zForceConst; //base force constant term
435			//which is estimate by OOPSE
436	mmeineke	790
437	tim	837
438			vector<double> massOfZConsMols; //mass of z-constraint molecule
439	tim	701	vector<double> kz; //force constant array
440	mmeineke	790
441	tim	701	vector<double> zPos; //
442	tim	837
443
444	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
445			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
446	tim	682
447	mmeineke	790
448	tim	701	vector<ZConsParaItem>* parameters; //
449	tim	837
450	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
451	tim	677
452	tim	837	int* indexOfZConsMols; //index of local Z-Constraint Molecules
453	tim	658	double* fz;
454	tim	699	double* curZPos;
455	tim	677
456	mmeineke	790
457	tim	837
458			int whichDirection; //constraint direction
459
460	tim	658	private:
461	tim	837
462	tim	701	string zconsOutput; //filename of zconstraint output
463			ZConsWriter* fzOut; //z-constraint writer
464	tim	677
465	tim	837	double curZconsTime;
466	tim	699
467	tim	696	double calcMovingMolsCOMVel();
468			double calcSysCOMVel();
469			double calcTotalForce();
470	tim	837
471	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
472	tim	738	friend class ForceSubtractionPolicy;
473	tim	677
474	tim	658	};
475
476	tim	1064	/*
477	tim	969	class OOPSEMinimizerBase : public RealIntegrator {
478			public:
479
480			OOPSEMinimizerBase ( SimInfo theInfo, ForceFields the_ff );
481			virtual ~OOPSEMinimizerBase();
482
483	tim	1010	double calcGradient(vector<double>& x, vector<double>& grad);
484	tim	1035	void setCoor(vector<double>& x);
485			vector<double> getCoor();
486	tim	1031	void output(vector<double>& x, int iteration);
487			int getDim() {return dim;}
488	tim	1057	void constraintMove();
489			void shakeF();
490			void shakeR();
491	tim	1031	protected:
492	tim	969
493	tim	1031	int dim;
494			void calcDim();
495	tim	969	};
496
497	tim	1031	//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
498			// public:
499			// void writeOutput();
500			//};
501	tim	1064	*/
502	tim	658	#endif