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);

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 ):
    T( 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);

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;

  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);

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 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 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:	833
Committed:	Tue Oct 28 17:08:18 2003 UTC (21 years, 6 months ago) by mmeineke
File size:	12338 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	mmeineke	833	// #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	833	// #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	833	class Integrator : public BaseIntegrator {
25	tim	645
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	mmeineke	377
32	mmeineke	540	protected:
33	mmeineke	778
34	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
35	mmeineke	548	virtual void preMove( void );
36	mmeineke	540	virtual void moveA( void );
37			virtual void moveB( void );
38			virtual void constrainA( void );
39			virtual void constrainB( void );
40	mmeineke	559	virtual int readyCheck( void ) { return 1; }
41	tim	677
42	mmeineke	746	virtual void resetIntegrator( void ) { }
43	tim	763
44	tim	677	virtual void calcForce( int calcPot, int calcStress );
45			virtual void thermalize();
46	mmeineke	377
47	mmeineke	778	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48
49	mmeineke	540	void checkConstraints( void );
50	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
51	tim	701	double A[3][3] );
52
53	mmeineke	377	ForceFields* myFF;
54
55	mmeineke	540	SimInfo *info; // all the info we'll ever need
56			int nAtoms; /* the number of atoms */
57	mmeineke	548	int oldAtoms;
58	mmeineke	540	Atom *atoms; / array of atom pointers */
59	mmeineke	423	Molecule* molecules;
60			int nMols;
61
62	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
63	tim	701	// constraints.
64	mmeineke	548	int nConstrained; // counter for number of constraints
65			int *constrainedA; // the i of a constraint pair
66			int *constrainedB; // the j of a constraint pair
67			double *constrainedDsqr; // the square of the constraint distance
68
69			int* moving; // tells whether we are moving atom i
70			int* moved; // tells whether we have moved atom i
71	mmeineke	561	double* oldPos; // pre constrained positions
72	mmeineke	548
73	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
74
75			double dt;
76	mmeineke	541	double dt2;
77	gezelter	560
78	mmeineke	540	Thermo *tStats;
79			StatWriter* statOut;
80			DumpWriter* dumpOut;
81	mmeineke	377
82			};
83
84	mmeineke	833	class NVE : public Integrator {
85	mmeineke	540
86	mmeineke	561	public:
87			NVE ( SimInfo theInfo, ForceFields the_ff ):
88	tim	645	T( theInfo, the_ff ){}
89			virtual ~NVE(){}
90			};
91	mmeineke	555
92
93	mmeineke	833	class NVT : public Integrator {
94	mmeineke	555
95	gezelter	560	public:
96
97	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
98	tim	763	virtual ~NVT();
99	mmeineke	540
100	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
103			virtual double getConservedQuantity(void);
104	gezelter	560
105	mmeineke	540	protected:
106	gezelter	560
107	mmeineke	561	virtual void moveA( void );
108			virtual void moveB( void );
109	mmeineke	540
110	mmeineke	561	virtual int readyCheck();
111	gezelter	560
112	mmeineke	746	virtual void resetIntegrator( void );
113
114	gezelter	565	// chi is a propagated degree of freedom.
115	gezelter	560
116	gezelter	565	double chi;
117	gezelter	560
118	tim	763	//integral of chi(t)dt
119			double integralOfChidt;
120
121	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
122	gezelter	560
123			double targetTemp;
124			double tauThermostat;
125	mmeineke	561
126	gezelter	565	short int have_tau_thermostat, have_target_temp;
127	gezelter	560
128	tim	763	double *oldVel;
129			double *oldJi;
130
131			double chiTolerance;
132			short int have_chi_tolerance;
133
134	mmeineke	540	};
135
136
137
138	mmeineke	833	class NPT : public Integrator{
139	tim	645
140	gezelter	560	public:
141
142	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
143			virtual ~NPT();
144	tim	763
145	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
146			calcStress = 1;
147	tim	645	T::integrateStep( calcPot, calcStress );
148	mmeineke	594	}
149
150	mmeineke	778	virtual double getConservedQuantity(void) = 0;
151	tim	763
152	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
153			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
154			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
155			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
156	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
157			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
158			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
159	gezelter	560
160			protected:
161
162	mmeineke	561	virtual void moveA( void );
163			virtual void moveB( void );
164	gezelter	560
165	mmeineke	561	virtual int readyCheck();
166	gezelter	560
167	mmeineke	746	virtual void resetIntegrator( void );
168
169	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
170			virtual void getVelScaleB( double sc[3], int index ) = 0;
171			virtual void getPosScale(double pos[3], double COM[3],
172			int index, double sc[3]) = 0;
173
174			virtual bool chiConverged( void );
175			virtual bool etaConverged( void ) = 0;
176
177			virtual void evolveChiA( void );
178			virtual void evolveEtaA( void ) = 0;
179			virtual void evolveChiB( void );
180			virtual void evolveEtaB( void ) = 0;
181
182			virtual void scaleSimBox( void ) = 0;
183
184	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
185
186	gezelter	565	// chi and eta are the propagated degrees of freedom
187	gezelter	560
188	mmeineke	778	double oldChi;
189			double prevChi;
190	gezelter	565	double chi;
191	gezelter	574	double NkBT;
192	tim	763	double fkBT;
193	gezelter	560
194	mmeineke	778	double tt2, tb2;
195			double instaTemp, instaPress, instaVol;
196	mmeineke	780	double press[3][3];
197	mmeineke	778
198	tim	763	int Nparticles;
199
200			double integralOfChidt;
201
202	gezelter	560	// targetTemp, targetPressure, and tauBarostat must be set.
203			// One of qmass or tauThermostat must be set;
204
205			double targetTemp;
206			double targetPressure;
207			double tauThermostat;
208			double tauBarostat;
209
210			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
211	gezelter	565	short int have_target_pressure;
212	gezelter	560
213	tim	763	double *oldPos;
214			double *oldVel;
215			double *oldJi;
216
217			double chiTolerance;
218			short int have_chi_tolerance;
219			double posIterTolerance;
220			short int have_pos_iter_tolerance;
221			double etaTolerance;
222			short int have_eta_tolerance;
223
224	gezelter	560	};
225
226	mmeineke	833	class NPTi : public NPT{
227	mmeineke	778
228			public:
229			NPTi( SimInfo theInfo, ForceFields the_ff);
230			~NPTi();
231
232			virtual double getConservedQuantity(void);
233			virtual void resetIntegrator(void);
234
235			protected:
236
237
238
239			virtual void evolveEtaA(void);
240			virtual void evolveEtaB(void);
241
242			virtual bool etaConverged( void );
243
244			virtual void scaleSimBox( void );
245
246			virtual void getVelScaleA( double sc[3], double vel[3] );
247			virtual void getVelScaleB( double sc[3], int index );
248			virtual void getPosScale(double pos[3], double COM[3],
249			int index, double sc[3]);
250
251			double eta, oldEta, prevEta;
252			};
253
254	mmeineke	833	class NPTf : public NPT{
255	gezelter	576
256			public:
257
258			NPTf ( SimInfo theInfo, ForceFields the_ff);
259	tim	767	virtual ~NPTf();
260	gezelter	576
261	tim	763	virtual double getConservedQuantity(void);
262	mmeineke	780	virtual void resetIntegrator(void);
263	mmeineke	594
264	gezelter	576	protected:
265
266	mmeineke	780	virtual void evolveEtaA(void);
267			virtual void evolveEtaB(void);
268	gezelter	576
269	mmeineke	780	virtual bool etaConverged( void );
270	mmeineke	746
271	mmeineke	780	virtual void scaleSimBox( void );
272	gezelter	576
273	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
274			virtual void getVelScaleB( double sc[3], int index );
275			virtual void getPosScale(double pos[3], double COM[3],
276			int index, double sc[3]);
277	tim	763
278	gezelter	588	double eta[3][3];
279	mmeineke	780	double oldEta[3][3];
280			double prevEta[3][3];
281	gezelter	576	};
282
283	mmeineke	833	class NPTxyz : public NPT{
284	mmeineke	755
285			public:
286
287	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
288			virtual ~NPTxyz();
289	mmeineke	755
290	mmeineke	812	virtual double getConservedQuantity(void);
291			virtual void resetIntegrator(void);
292	mmeineke	755
293			protected:
294
295	mmeineke	812	virtual void evolveEtaA(void);
296			virtual void evolveEtaB(void);
297	mmeineke	755
298	mmeineke	812	virtual bool etaConverged( void );
299	mmeineke	755
300	mmeineke	812	virtual void scaleSimBox( void );
301	mmeineke	755
302	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
303			virtual void getVelScaleB( double sc[3], int index );
304			virtual void getPosScale(double pos[3], double COM[3],
305			int index, double sc[3]);
306	mmeineke	755
307	mmeineke	812	double eta[3][3];
308			double oldEta[3][3];
309			double prevEta[3][3];
310			};
311	mmeineke	755
312
313	mmeineke	833	// template<typename T> class ZConstraint : public T {
314	tim	701
315	mmeineke	833	// public:
316			// class ForceSubtractionPolicy{
317			// public:
318			// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
319	tim	658
320	mmeineke	833	// virtual void update() = 0;
321			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
322			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
323			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
324			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
325	tim	701
326	mmeineke	833	// protected:
327			// ZConstraint<T>* zconsIntegrator;
328			// };
329	tim	699
330	mmeineke	833	// class PolicyByNumber : public ForceSubtractionPolicy{
331	gezelter	747
332	mmeineke	833	// public:
333			// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
334			// virtual void update();
335			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
336			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
337			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
338			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
339	tim	701
340	mmeineke	833	// private:
341			// int totNumOfMovingAtoms;
342			// };
343	tim	699
344	mmeineke	833	// class PolicyByMass : public ForceSubtractionPolicy{
345	gezelter	747
346	mmeineke	833	// public:
347			// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
348	tim	701
349	mmeineke	833	// virtual void update();
350			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
351			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
352			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
353			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
354	tim	699
355	mmeineke	833	// private:
356			// double totMassOfMovingAtoms;
357			// };
358	tim	699
359	mmeineke	833	// public:
360	tim	658
361	mmeineke	833	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
362			// ~ZConstraint();
363	tim	677
364	mmeineke	833	// void setZConsTime(double time) {this->zconsTime = time;}
365			// void getZConsTime() {return zconsTime;}
366	tim	658
367	mmeineke	833	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
368			// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
369	tim	658
370	mmeineke	833	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
371			// string getZConsOutput() {return zconsOutput;}
372	tim	677
373	mmeineke	833	// virtual void integrate();
374	tim	677
375	tim	658
376	mmeineke	833	// #ifdef IS_MPI
377			// virtual void update(); //which is called to indicate the molecules' migration
378			// #endif
379	tim	658
380	mmeineke	833	// enum ZConsState {zcsMoving, zcsFixed};
381	mmeineke	790
382	mmeineke	833	// vector<Molecule*> zconsMols; //z-constraint molecules array
383			// vector<ZConsState> states; //state of z-constraint molecules
384	mmeineke	790
385
386
387	mmeineke	833	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
388			// double totalMassOfUncons; //total mas of unconstraint molecules
389	mmeineke	790
390
391	mmeineke	833	// protected:
392	tim	658
393	mmeineke	790
394	tim	677
395	mmeineke	833	// virtual void calcForce( int calcPot, int calcStress );
396			// virtual void thermalize(void);
397	tim	677
398	mmeineke	833	// void zeroOutVel();
399			// void doZconstraintForce();
400			// void doHarmonic();
401			// bool checkZConsState();
402	tim	677
403	mmeineke	833	// bool haveFixedZMols();
404			// bool haveMovingZMols();
405	tim	677
406	mmeineke	833	// double calcZSys();
407	tim	677
408	mmeineke	833	// int isZConstraintMol(Molecule* mol);
409	tim	677
410
411	mmeineke	833	// double zconsTime; //sample time
412			// double zconsTol; //tolerance of z-contratint
413			// double zForceConst; //base force constant term
414			// //which is estimate by OOPSE
415	tim	658
416	mmeineke	790
417	mmeineke	833	// vector<double> massOfZConsMols; //mass of z-constraint molecule
418			// vector<double> kz; //force constant array
419	mmeineke	790
420	mmeineke	833	// vector<double> zPos; //
421	tim	658
422	tim	677
423	mmeineke	833	// vector<Molecule*> unconsMols; //unconstraint molecules array
424			// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
425	tim	682
426	mmeineke	790
427	mmeineke	833	// vector<ZConsParaItem>* parameters; //
428	tim	658
429	mmeineke	833	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
430	tim	677
431	mmeineke	833	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
432			// double* fz;
433			// double* curZPos;
434	tim	658
435	tim	677
436	mmeineke	790
437	mmeineke	833	// int whichDirection; //constraint direction
438	tim	677
439	mmeineke	833	// private:
440	tim	677
441	mmeineke	833	// string zconsOutput; //filename of zconstraint output
442			// ZConsWriter* fzOut; //z-constraint writer
443	tim	677
444	mmeineke	833	// double curZconsTime;
445	tim	699
446	mmeineke	833	// double calcMovingMolsCOMVel();
447			// double calcSysCOMVel();
448			// double calcTotalForce();
449	tim	701
450	mmeineke	833	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
451			// friend class ForceSubtractionPolicy;
452	tim	677
453	mmeineke	833	// };
454	tim	658
455			#endif