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);

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);

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;

  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;

};

template<typename T> class NPTi : public T{
  
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;
};

template<typename T> class NPTf : public T{

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];
};

template<typename T> class NPTxyz : public T{

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:	812
Committed:	Wed Oct 22 21:17:32 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	12235 byte(s)
Log Message:	added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
#	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	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	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
85	mmeineke	540
86	tim	645	template<typename T> class NVE : public T {
87
88	mmeineke	561	public:
89			NVE ( SimInfo theInfo, ForceFields the_ff ):
90	tim	645	T( theInfo, the_ff ){}
91			virtual ~NVE(){}
92			};
93	mmeineke	555
94
95	tim	645	template<typename T> class NVT : public T {
96	mmeineke	555
97	gezelter	560	public:
98
99	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
100	tim	763	virtual ~NVT();
101	mmeineke	540
102	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
105			virtual double getConservedQuantity(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	mmeineke	561
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	778	template<typename T> class NPT : public T{
141	tim	645
142	gezelter	560	public:
143
144	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
145			virtual ~NPT();
146	tim	763
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	763
154	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161	gezelter	560
162			protected:
163
164	mmeineke	561	virtual void moveA( void );
165			virtual void moveB( void );
166	gezelter	560
167	mmeineke	561	virtual int readyCheck();
168	gezelter	560
169	mmeineke	746	virtual void resetIntegrator( void );
170
171	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172			virtual void getVelScaleB( double sc[3], int index ) = 0;
173			virtual void getPosScale(double pos[3], double COM[3],
174			int index, double sc[3]) = 0;
175
176			virtual bool chiConverged( void );
177			virtual bool etaConverged( void ) = 0;
178
179			virtual void evolveChiA( void );
180			virtual void evolveEtaA( void ) = 0;
181			virtual void evolveChiB( void );
182			virtual void evolveEtaB( void ) = 0;
183
184			virtual void scaleSimBox( void ) = 0;
185
186	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187
188	gezelter	565	// chi and eta are the propagated degrees of freedom
189	gezelter	560
190	mmeineke	778	double oldChi;
191			double prevChi;
192	gezelter	565	double chi;
193	gezelter	574	double NkBT;
194	tim	763	double fkBT;
195	gezelter	560
196	mmeineke	778	double tt2, tb2;
197			double instaTemp, instaPress, instaVol;
198	mmeineke	780	double press[3][3];
199	mmeineke	778
200	tim	763	int Nparticles;
201
202			double integralOfChidt;
203
204	gezelter	560	// targetTemp, targetPressure, and tauBarostat must be set.
205			// One of qmass or tauThermostat must be set;
206
207			double targetTemp;
208			double targetPressure;
209			double tauThermostat;
210			double tauBarostat;
211
212			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213	gezelter	565	short int have_target_pressure;
214	gezelter	560
215	tim	763	double *oldPos;
216			double *oldVel;
217			double *oldJi;
218
219			double chiTolerance;
220			short int have_chi_tolerance;
221			double posIterTolerance;
222			short int have_pos_iter_tolerance;
223			double etaTolerance;
224			short int have_eta_tolerance;
225
226	gezelter	560	};
227
228	mmeineke	778	template<typename T> class NPTi : public T{
229
230			public:
231			NPTi( SimInfo theInfo, ForceFields the_ff);
232			~NPTi();
233
234			virtual double getConservedQuantity(void);
235			virtual void resetIntegrator(void);
236
237			protected:
238
239
240
241			virtual void evolveEtaA(void);
242			virtual void evolveEtaB(void);
243
244			virtual bool etaConverged( void );
245
246			virtual void scaleSimBox( void );
247
248			virtual void getVelScaleA( double sc[3], double vel[3] );
249			virtual void getVelScaleB( double sc[3], int index );
250			virtual void getPosScale(double pos[3], double COM[3],
251			int index, double sc[3]);
252
253			double eta, oldEta, prevEta;
254			};
255
256	tim	645	template<typename T> class NPTf : public T{
257	gezelter	576
258			public:
259
260			NPTf ( SimInfo theInfo, ForceFields the_ff);
261	tim	767	virtual ~NPTf();
262	gezelter	576
263	tim	763	virtual double getConservedQuantity(void);
264	mmeineke	780	virtual void resetIntegrator(void);
265	mmeineke	594
266	gezelter	576	protected:
267
268	mmeineke	780	virtual void evolveEtaA(void);
269			virtual void evolveEtaB(void);
270	gezelter	576
271	mmeineke	780	virtual bool etaConverged( void );
272	mmeineke	746
273	mmeineke	780	virtual void scaleSimBox( void );
274	gezelter	576
275	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
276			virtual void getVelScaleB( double sc[3], int index );
277			virtual void getPosScale(double pos[3], double COM[3],
278			int index, double sc[3]);
279	tim	763
280	gezelter	588	double eta[3][3];
281	mmeineke	780	double oldEta[3][3];
282			double prevEta[3][3];
283	gezelter	576	};
284
285	mmeineke	812	template<typename T> class NPTxyz : public T{
286	mmeineke	755
287			public:
288
289	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
290			virtual ~NPTxyz();
291	mmeineke	755
292	mmeineke	812	virtual double getConservedQuantity(void);
293			virtual void resetIntegrator(void);
294	mmeineke	755
295			protected:
296
297	mmeineke	812	virtual void evolveEtaA(void);
298			virtual void evolveEtaB(void);
299	mmeineke	755
300	mmeineke	812	virtual bool etaConverged( void );
301	mmeineke	755
302	mmeineke	812	virtual void scaleSimBox( void );
303	mmeineke	755
304	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
305			virtual void getVelScaleB( double sc[3], int index );
306			virtual void getPosScale(double pos[3], double COM[3],
307			int index, double sc[3]);
308	mmeineke	755
309	mmeineke	812	double eta[3][3];
310			double oldEta[3][3];
311			double prevEta[3][3];
312			};
313	mmeineke	755
314
315	tim	658	template<typename T> class ZConstraint : public T {
316	tim	701
317			public:
318	tim	738	class ForceSubtractionPolicy{
319	tim	699	public:
320	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
321	tim	658
322	tim	701	virtual void update() = 0;
323	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
324			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
325	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
326			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
327
328			protected:
329	mmeineke	788	ZConstraint<T>* zconsIntegrator;
330	tim	699	};
331
332	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
333	gezelter	747
334	tim	699	public:
335	tim	738	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
336	tim	701	virtual void update();
337	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
338			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
339	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
340			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
341
342	tim	699	private:
343	tim	763	int totNumOfMovingAtoms;
344	tim	699	};
345
346	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
347	gezelter	747
348	tim	699	public:
349	tim	738	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
350	tim	701
351			virtual void update();
352	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
353			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
354	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
355			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
356	tim	699
357	tim	701	private:
358			double totMassOfMovingAtoms;
359	tim	699	};
360
361	tim	658	public:
362
363			ZConstraint( SimInfo theInfo, ForceFields the_ff);
364			~ZConstraint();
365	tim	677
366	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
367			void getZConsTime() {return zconsTime;}
368
369	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
370			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
371	tim	658
372	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
373	tim	658	string getZConsOutput() {return zconsOutput;}
374	tim	677
375			virtual void integrate();
376
377	tim	658
378			#ifdef IS_MPI
379	tim	701	virtual void update(); //which is called to indicate the molecules' migration
380	mmeineke	377	#endif
381	tim	658
382	mmeineke	790	enum ZConsState {zcsMoving, zcsFixed};
383
384			vector<Molecule*> zconsMols; //z-constraint molecules array
385			vector<ZConsState> states; //state of z-constraint molecules
386
387
388
389			int totNumOfUnconsAtoms; //total number of uncontraint atoms
390			double totalMassOfUncons; //total mas of unconstraint molecules
391
392
393	tim	658	protected:
394
395	mmeineke	790
396	tim	677
397			virtual void calcForce( int calcPot, int calcStress );
398			virtual void thermalize(void);
399
400			void zeroOutVel();
401			void doZconstraintForce();
402	tim	682	void doHarmonic();
403	tim	677	bool checkZConsState();
404
405			bool haveFixedZMols();
406			bool haveMovingZMols();
407
408			double calcZSys();
409
410			int isZConstraintMol(Molecule* mol);
411
412
413	tim	701	double zconsTime; //sample time
414			double zconsTol; //tolerance of z-contratint
415			double zForceConst; //base force constant term
416			//which is estimate by OOPSE
417	tim	658
418	mmeineke	790
419	tim	701	vector<double> massOfZConsMols; //mass of z-constraint molecule
420			vector<double> kz; //force constant array
421	mmeineke	790
422	tim	701	vector<double> zPos; //
423	tim	658
424	tim	677
425	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
426			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
427	tim	682
428	mmeineke	790
429	tim	701	vector<ZConsParaItem>* parameters; //
430	tim	658
431			vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
432	tim	677
433			int* indexOfZConsMols; //index of local Z-Constraint Molecules
434	tim	658	double* fz;
435	tim	699	double* curZPos;
436	tim	658
437	tim	677
438	mmeineke	790
439	tim	677	int whichDirection; //constraint direction
440
441	tim	658	private:
442	tim	677
443	tim	701	string zconsOutput; //filename of zconstraint output
444			ZConsWriter* fzOut; //z-constraint writer
445	tim	677
446	tim	701	double curZconsTime;
447	tim	699
448	tim	696	double calcMovingMolsCOMVel();
449			double calcSysCOMVel();
450			double calcTotalForce();
451	tim	701
452	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
453	tim	738	friend class ForceSubtractionPolicy;
454	tim	677
455	tim	658	};
456
457			#endif