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;


class Integrator : public  BaseIntegrator{
  
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;

};

class NVE : public Integrator {

public:
  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
    Integrator( theInfo, the_ff ){}
  virtual ~NVE(){}
};


class NVT : public Integrator {

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;

};


class NPT : public Integrator{

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 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;

};

class NPTi : public NPT{

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]);

  double eta, oldEta, prevEta;
};

class NPTf : public NPT{

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]);

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[3][3];
};

class NPTxyz : public NPT{

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]);

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[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;

// };

#endif
Revision:	849
Committed:	Fri Oct 31 21:06:47 2003 UTC (21 years, 9 months ago) by mmeineke
File size:	12607 byte(s)
Log Message:	started work on template removal.
#	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	mmeineke	849	// #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	mmeineke	849	class Integrator : public BaseIntegrator{
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	mmeineke	849	class NVE : public Integrator {
86	mmeineke	540
87	mmeineke	561	public:
88			NVE ( SimInfo theInfo, ForceFields the_ff ):
89	mmeineke	849	Integrator( theInfo, the_ff ){}
90	tim	837	virtual ~NVE(){}
91	tim	645	};
92	mmeineke	555
93
94	mmeineke	849	class NVT : public Integrator {
95	mmeineke	555
96	gezelter	560	public:
97
98	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
99	tim	763	virtual ~NVT();
100	mmeineke	540
101	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
102			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
103	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
104			virtual double getConservedQuantity(void);
105	tim	837	virtual string getAdditionalParameters(void);
106	gezelter	560
107	mmeineke	540	protected:
108	gezelter	560
109	mmeineke	561	virtual void moveA( void );
110			virtual void moveB( void );
111	mmeineke	540
112	mmeineke	561	virtual int readyCheck();
113	gezelter	560
114	mmeineke	746	virtual void resetIntegrator( void );
115
116	gezelter	565	// chi is a propagated degree of freedom.
117	gezelter	560
118	gezelter	565	double chi;
119	gezelter	560
120	tim	763	//integral of chi(t)dt
121			double integralOfChidt;
122
123	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
124	gezelter	560
125			double targetTemp;
126			double tauThermostat;
127	tim	837
128	gezelter	565	short int have_tau_thermostat, have_target_temp;
129	gezelter	560
130	tim	763	double *oldVel;
131			double *oldJi;
132
133			double chiTolerance;
134			short int have_chi_tolerance;
135
136	mmeineke	540	};
137
138
139
140	mmeineke	849	class NPT : public Integrator{
141	tim	645
142	gezelter	560	public:
143
144	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
145			virtual ~NPT();
146	tim	837
147	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
148			calcStress = 1;
149	tim	645	T::integrateStep( calcPot, calcStress );
150	mmeineke	594	}
151
152	mmeineke	778	virtual double getConservedQuantity(void) = 0;
153	tim	837	virtual string getAdditionalParameters(void) = 0;
154	mmeineke	843
155			double myTauThermo( void ) { return tauThermostat; }
156			double myTauBaro( void ) { return tauBarostat; }
157
158	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
159			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
160			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
161			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
162	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
163			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
164			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
165	gezelter	560
166			protected:
167
168	mmeineke	561	virtual void moveA( void );
169			virtual void moveB( void );
170	gezelter	560
171	mmeineke	561	virtual int readyCheck();
172	gezelter	560
173	mmeineke	746	virtual void resetIntegrator( void );
174
175	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
176			virtual void getVelScaleB( double sc[3], int index ) = 0;
177	tim	837	virtual void getPosScale(double pos[3], double COM[3],
178	mmeineke	778	int index, double sc[3]) = 0;
179
180			virtual bool chiConverged( void );
181			virtual bool etaConverged( void ) = 0;
182	tim	837
183	mmeineke	778	virtual void evolveChiA( void );
184			virtual void evolveEtaA( void ) = 0;
185			virtual void evolveChiB( void );
186			virtual void evolveEtaB( void ) = 0;
187
188			virtual void scaleSimBox( void ) = 0;
189
190	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
191
192	gezelter	565	// chi and eta are the propagated degrees of freedom
193	gezelter	560
194	mmeineke	778	double oldChi;
195			double prevChi;
196	gezelter	565	double chi;
197	gezelter	574	double NkBT;
198	tim	763	double fkBT;
199	gezelter	560
200	mmeineke	778	double tt2, tb2;
201			double instaTemp, instaPress, instaVol;
202	mmeineke	780	double press[3][3];
203	mmeineke	778
204	tim	763	int Nparticles;
205
206			double integralOfChidt;
207
208	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
209	gezelter	560	// One of qmass or tauThermostat must be set;
210
211			double targetTemp;
212			double targetPressure;
213			double tauThermostat;
214			double tauBarostat;
215
216			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
217	gezelter	565	short int have_target_pressure;
218	gezelter	560
219	tim	763	double *oldPos;
220			double *oldVel;
221			double *oldJi;
222
223			double chiTolerance;
224			short int have_chi_tolerance;
225			double posIterTolerance;
226			short int have_pos_iter_tolerance;
227			double etaTolerance;
228			short int have_eta_tolerance;
229
230	gezelter	560	};
231
232	mmeineke	849	class NPTi : public NPT{
233	tim	837
234	mmeineke	778	public:
235			NPTi( SimInfo theInfo, ForceFields the_ff);
236			~NPTi();
237
238			virtual double getConservedQuantity(void);
239			virtual void resetIntegrator(void);
240	tim	837	virtual string getAdditionalParameters(void);
241	mmeineke	778	protected:
242
243
244	tim	837
245	mmeineke	778	virtual void evolveEtaA(void);
246			virtual void evolveEtaB(void);
247
248			virtual bool etaConverged( void );
249
250			virtual void scaleSimBox( void );
251
252			virtual void getVelScaleA( double sc[3], double vel[3] );
253			virtual void getVelScaleB( double sc[3], int index );
254	tim	837	virtual void getPosScale(double pos[3], double COM[3],
255	mmeineke	778	int index, double sc[3]);
256
257			double eta, oldEta, prevEta;
258			};
259
260	mmeineke	849	class NPTf : public NPT{
261	gezelter	576
262			public:
263
264			NPTf ( SimInfo theInfo, ForceFields the_ff);
265	tim	767	virtual ~NPTf();
266	gezelter	576
267	tim	763	virtual double getConservedQuantity(void);
268	tim	837	virtual string getAdditionalParameters(void);
269	mmeineke	780	virtual void resetIntegrator(void);
270	mmeineke	594
271	gezelter	576	protected:
272
273	mmeineke	780	virtual void evolveEtaA(void);
274			virtual void evolveEtaB(void);
275	gezelter	576
276	mmeineke	780	virtual bool etaConverged( void );
277	mmeineke	746
278	mmeineke	780	virtual void scaleSimBox( void );
279	gezelter	576
280	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
281			virtual void getVelScaleB( double sc[3], int index );
282	tim	837	virtual void getPosScale(double pos[3], double COM[3],
283	mmeineke	780	int index, double sc[3]);
284	tim	763
285	gezelter	588	double eta[3][3];
286	mmeineke	780	double oldEta[3][3];
287			double prevEta[3][3];
288	gezelter	576	};
289
290	mmeineke	849	class NPTxyz : public NPT{
291	mmeineke	755
292			public:
293
294	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
295			virtual ~NPTxyz();
296	mmeineke	755
297	mmeineke	812	virtual double getConservedQuantity(void);
298	tim	837	virtual string getAdditionalParameters(void);
299	mmeineke	812	virtual void resetIntegrator(void);
300	mmeineke	755
301			protected:
302
303	mmeineke	812	virtual void evolveEtaA(void);
304			virtual void evolveEtaB(void);
305	mmeineke	755
306	mmeineke	812	virtual bool etaConverged( void );
307	mmeineke	755
308	mmeineke	812	virtual void scaleSimBox( void );
309	mmeineke	755
310	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
311			virtual void getVelScaleB( double sc[3], int index );
312	tim	837	virtual void getPosScale(double pos[3], double COM[3],
313	mmeineke	812	int index, double sc[3]);
314	mmeineke	755
315	mmeineke	812	double eta[3][3];
316			double oldEta[3][3];
317			double prevEta[3][3];
318			};
319	mmeineke	755
320
321	mmeineke	849	// template<typename T> class ZConstraint : public T {
322	tim	837
323	mmeineke	849	// public:
324			// class ForceSubtractionPolicy{
325			// public:
326			// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
327	tim	658
328	mmeineke	849	// virtual void update() = 0;
329			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
330			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
331			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
333	tim	837
334	mmeineke	849	// protected:
335			// ZConstraint<T>* zconsIntegrator;
336			// };
337	tim	699
338	mmeineke	849	// class PolicyByNumber : public ForceSubtractionPolicy{
339	gezelter	747
340	mmeineke	849	// public:
341			// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
342			// virtual void update();
343			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
344			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
345			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
346			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
347	tim	837
348	mmeineke	849	// private:
349			// int totNumOfMovingAtoms;
350			// };
351	tim	699
352	mmeineke	849	// class PolicyByMass : public ForceSubtractionPolicy{
353	gezelter	747
354	mmeineke	849	// public:
355			// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
356	tim	837
357	mmeineke	849	// virtual void update();
358			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
359			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
360			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
361			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
362	tim	699
363	mmeineke	849	// private:
364			// double totMassOfMovingAtoms;
365			// };
366	tim	699
367	mmeineke	849	// public:
368	tim	658
369	mmeineke	849	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
370			// ~ZConstraint();
371	tim	837
372	mmeineke	849	// void setZConsTime(double time) {this->zconsTime = time;}
373			// void getZConsTime() {return zconsTime;}
374	tim	837
375	mmeineke	849	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
376			// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
377	tim	837
378	mmeineke	849	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
379			// string getZConsOutput() {return zconsOutput;}
380	tim	837
381	mmeineke	849	// virtual void integrate();
382	tim	658
383	tim	837
384	mmeineke	849	// #ifdef IS_MPI
385			// virtual void update(); //which is called to indicate the molecules' migration
386			// #endif
387	tim	658
388	mmeineke	849	// enum ZConsState {zcsMoving, zcsFixed};
389	mmeineke	790
390	mmeineke	849	// vector<Molecule*> zconsMols; //z-constraint molecules array
391			// vector<ZConsState> states; //state of z-constraint molecules
392	mmeineke	790
393
394	tim	837
395	mmeineke	849	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
396			// double totalMassOfUncons; //total mas of unconstraint molecules
397	mmeineke	790
398
399	mmeineke	849	// protected:
400	tim	658
401	mmeineke	790
402	tim	837
403	mmeineke	849	// virtual void calcForce( int calcPot, int calcStress );
404			// virtual void thermalize(void);
405	tim	837
406	mmeineke	849	// void zeroOutVel();
407			// void doZconstraintForce();
408			// void doHarmonic();
409			// bool checkZConsState();
410	tim	677
411	mmeineke	849	// bool haveFixedZMols();
412			// bool haveMovingZMols();
413	tim	677
414	mmeineke	849	// double calcZSys();
415	tim	677
416	mmeineke	849	// int isZConstraintMol(Molecule* mol);
417	tim	677
418
419	mmeineke	849	// double zconsTime; //sample time
420			// double zconsTol; //tolerance of z-contratint
421			// double zForceConst; //base force constant term
422			// //which is estimate by OOPSE
423	mmeineke	790
424	tim	837
425	mmeineke	849	// vector<double> massOfZConsMols; //mass of z-constraint molecule
426			// vector<double> kz; //force constant array
427	mmeineke	790
428	mmeineke	849	// vector<double> zPos; //
429	tim	837
430
431	mmeineke	849	// vector<Molecule*> unconsMols; //unconstraint molecules array
432			// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
433	tim	682
434	mmeineke	790
435	mmeineke	849	// vector<ZConsParaItem>* parameters; //
436	tim	837
437	mmeineke	849	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
438	tim	677
439	mmeineke	849	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
440			// double* fz;
441			// double* curZPos;
442	tim	677
443	mmeineke	790
444	tim	837
445	mmeineke	849	// int whichDirection; //constraint direction
446	tim	837
447	mmeineke	849	// private:
448	tim	837
449	mmeineke	849	// string zconsOutput; //filename of zconstraint output
450			// ZConsWriter* fzOut; //z-constraint writer
451	tim	677
452	mmeineke	849	// double curZconsTime;
453	tim	699
454	mmeineke	849	// double calcMovingMolsCOMVel();
455			// double calcSysCOMVel();
456			// double calcTotalForce();
457	tim	837
458	mmeineke	849	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
459			// friend class ForceSubtractionPolicy;
460	tim	677
461	mmeineke	849	// };
462	tim	658
463			#endif