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 );


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();
  
  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;}

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;

  // targetTemp must be set.  tauThermostat must also be set;

  double targetTemp;
  double tauThermostat;
  
  short int have_tau_thermostat, have_target_temp;

};


template<typename T> class NPTi : public T{

public:

  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTi() {};

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    T::integrateStep( calcPot, calcStress );
  }

  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;}

protected:

  virtual void  moveA( void );
  virtual void moveB( void );

  virtual int readyCheck();

  virtual void resetIntegrator( void );

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta;
  double NkBT;

  // 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;

};

template<typename T> class NPTim : public T{

public:

  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTim() {};

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    T::integrateStep( calcPot, calcStress );
  }

  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;}

protected:

  virtual void moveA( void );
  virtual void moveB( void );

  virtual int readyCheck();

  virtual void resetIntegrator( void );

  Molecule* myMolecules;
  Atom** myAtoms;

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta;
  double NkBT;

  // 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;

};

template<typename T> class NPTf : public T{

public:

  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTf() {};

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    T::integrateStep( calcPot, calcStress );
  }

  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;}

protected:

  virtual void  moveA( void );
  virtual void moveB( void );

  virtual void resetIntegrator( void );

  virtual int readyCheck();

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta[3][3];
  double NkBT;

  // 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;

};

template<typename T> class NPTfm : public T{

public:

  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTfm() {};

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    T::integrateStep( calcPot, calcStress );
  }

  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;}

protected:

  virtual void  moveA( void );
  virtual void moveB( void );

  virtual void resetIntegrator( void );

  virtual int readyCheck();

  Molecule* myMolecules;
  Atom** myAtoms;

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta[3][3];
  double NkBT;

  // 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;

};


template<typename T> class NPTpr : public T{

public:

  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTpr() {};

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    T::integrateStep( calcPot, calcStress );
  }

  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;}

protected:

  virtual void  moveA( void );
  virtual void moveB( void );

  virtual int readyCheck();

  virtual void resetIntegrator( void );

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta[3][3];
  double NkBT;

  // 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;

};


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

protected:

  enum ZConsState {zcsMoving, zcsFixed};  
 
  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<Molecule*> zconsMols;              //z-constraint molecules array
  vector<double> massOfZConsMols;       //mass of z-constraint molecule 
  vector<double> kz;                              //force constant array
  vector<ZConsState> states;                 //state of z-constraint molecules
  vector<double> zPos;                          //
  
  
  vector<Molecule*> unconsMols;           //unconstraint molecules array
  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
  double totalMassOfUncons;                //total mas 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 totNumOfUnconsAtoms;              //total number of uncontraint atoms

  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 substration policy
  friend class ForceSubtractionPolicy;

};

#endif
Revision:	746
Committed:	Thu Sep 4 21:48:35 2003 UTC (20 years, 10 months ago) by mmeineke
File size:	13351 byte(s)
Log Message:	added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
#	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
31
32	mmeineke	540	protected:
33	mmeineke	377
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
44	tim	677	virtual void calcForce( int calcPot, int calcStress );
45			virtual void thermalize();
46	mmeineke	377
47	mmeineke	540	void checkConstraints( void );
48	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
49	tim	701	double A[3][3] );
50
51	mmeineke	377	ForceFields* myFF;
52
53	mmeineke	540	SimInfo *info; // all the info we'll ever need
54			int nAtoms; /* the number of atoms */
55	mmeineke	548	int oldAtoms;
56	mmeineke	540	Atom *atoms; / array of atom pointers */
57	mmeineke	423	Molecule* molecules;
58			int nMols;
59
60	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
61	tim	701	// constraints.
62	mmeineke	548	int nConstrained; // counter for number of constraints
63			int *constrainedA; // the i of a constraint pair
64			int *constrainedB; // the j of a constraint pair
65			double *constrainedDsqr; // the square of the constraint distance
66
67			int* moving; // tells whether we are moving atom i
68			int* moved; // tells whether we have moved atom i
69	mmeineke	561	double* oldPos; // pre constrained positions
70	mmeineke	548
71	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
72
73			double dt;
74	mmeineke	541	double dt2;
75	gezelter	560
76	mmeineke	540	Thermo *tStats;
77			StatWriter* statOut;
78			DumpWriter* dumpOut;
79	mmeineke	377
80			};
81
82	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
83	mmeineke	540
84	tim	645	template<typename T> class NVE : public T {
85
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	tim	645	template<typename T> class NVT : public T {
94	mmeineke	555
95	gezelter	560	public:
96
97	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
98			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
103	mmeineke	540	protected:
104	gezelter	560
105	mmeineke	561	virtual void moveA( void );
106			virtual void moveB( void );
107	mmeineke	540
108	mmeineke	561	virtual int readyCheck();
109	gezelter	560
110	mmeineke	746	virtual void resetIntegrator( void );
111
112	gezelter	565	// chi is a propagated degree of freedom.
113	gezelter	560
114	gezelter	565	double chi;
115	gezelter	560
116	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
117	gezelter	560
118			double targetTemp;
119			double tauThermostat;
120	mmeineke	561
121	gezelter	565	short int have_tau_thermostat, have_target_temp;
122	gezelter	560
123	mmeineke	540	};
124
125
126
127	tim	645	template<typename T> class NPTi : public T{
128
129	gezelter	560	public:
130
131	gezelter	574	NPTi ( SimInfo theInfo, ForceFields the_ff);
132			virtual ~NPTi() {};
133	gezelter	560
134	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
135			calcStress = 1;
136	tim	645	T::integrateStep( calcPot, calcStress );
137	mmeineke	594	}
138
139	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
140			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
141			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
142			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
143
144			protected:
145
146	mmeineke	561	virtual void moveA( void );
147			virtual void moveB( void );
148	gezelter	560
149	mmeineke	561	virtual int readyCheck();
150	gezelter	560
151	mmeineke	746	virtual void resetIntegrator( void );
152
153	gezelter	565	// chi and eta are the propagated degrees of freedom
154	gezelter	560
155	gezelter	565	double chi;
156			double eta;
157	gezelter	574	double NkBT;
158	gezelter	560
159			// targetTemp, targetPressure, and tauBarostat must be set.
160			// One of qmass or tauThermostat must be set;
161
162			double targetTemp;
163			double targetPressure;
164			double tauThermostat;
165			double tauBarostat;
166
167			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
168	gezelter	565	short int have_target_pressure;
169	gezelter	560
170			};
171
172	tim	645	template<typename T> class NPTim : public T{
173	gezelter	596
174			public:
175
176			NPTim ( SimInfo theInfo, ForceFields the_ff);
177			virtual ~NPTim() {};
178
179			virtual void integrateStep( int calcPot, int calcStress ){
180			calcStress = 1;
181	tim	645	T::integrateStep( calcPot, calcStress );
182	gezelter	596	}
183
184			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
185			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
186			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
187			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
188
189			protected:
190
191	gezelter	604	virtual void moveA( void );
192	gezelter	596	virtual void moveB( void );
193
194			virtual int readyCheck();
195
196	mmeineke	746	virtual void resetIntegrator( void );
197
198	gezelter	604	Molecule* myMolecules;
199			Atom** myAtoms;
200
201	gezelter	596	// chi and eta are the propagated degrees of freedom
202
203			double chi;
204			double eta;
205			double NkBT;
206
207			// targetTemp, targetPressure, and tauBarostat must be set.
208			// One of qmass or tauThermostat must be set;
209
210			double targetTemp;
211			double targetPressure;
212			double tauThermostat;
213			double tauBarostat;
214
215			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
216			short int have_target_pressure;
217
218			};
219
220	tim	645	template<typename T> class NPTf : public T{
221	gezelter	576
222			public:
223
224			NPTf ( SimInfo theInfo, ForceFields the_ff);
225			virtual ~NPTf() {};
226
227	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
228			calcStress = 1;
229	tim	645	T::integrateStep( calcPot, calcStress );
230	mmeineke	594	}
231
232	gezelter	576	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
233			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
234			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
235			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
236
237			protected:
238
239			virtual void moveA( void );
240			virtual void moveB( void );
241
242	mmeineke	746	virtual void resetIntegrator( void );
243
244	gezelter	576	virtual int readyCheck();
245
246			// chi and eta are the propagated degrees of freedom
247
248			double chi;
249	gezelter	588	double eta[3][3];
250	gezelter	576	double NkBT;
251
252			// targetTemp, targetPressure, and tauBarostat must be set.
253			// One of qmass or tauThermostat must be set;
254
255			double targetTemp;
256			double targetPressure;
257			double tauThermostat;
258			double tauBarostat;
259
260			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261			short int have_target_pressure;
262
263			};
264
265	tim	645	template<typename T> class NPTfm : public T{
266	gezelter	596
267			public:
268
269			NPTfm ( SimInfo theInfo, ForceFields the_ff);
270			virtual ~NPTfm() {};
271
272			virtual void integrateStep( int calcPot, int calcStress ){
273			calcStress = 1;
274	tim	645	T::integrateStep( calcPot, calcStress );
275	gezelter	596	}
276
277			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
278			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
279			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
280			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
281
282			protected:
283
284			virtual void moveA( void );
285			virtual void moveB( void );
286
287	mmeineke	746	virtual void resetIntegrator( void );
288
289	gezelter	596	virtual int readyCheck();
290
291	gezelter	605	Molecule* myMolecules;
292			Atom** myAtoms;
293
294	gezelter	596	// chi and eta are the propagated degrees of freedom
295
296			double chi;
297			double eta[3][3];
298			double NkBT;
299
300			// targetTemp, targetPressure, and tauBarostat must be set.
301			// One of qmass or tauThermostat must be set;
302
303			double targetTemp;
304			double targetPressure;
305			double tauThermostat;
306			double tauBarostat;
307
308			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
309			short int have_target_pressure;
310
311			};
312
313	gezelter	718
314			template<typename T> class NPTpr : public T{
315
316			public:
317
318			NPTpr ( SimInfo theInfo, ForceFields the_ff);
319			virtual ~NPTpr() {};
320
321			virtual void integrateStep( int calcPot, int calcStress ){
322			calcStress = 1;
323			T::integrateStep( calcPot, calcStress );
324			}
325
326			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
327			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
328			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
329			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
330
331			protected:
332
333			virtual void moveA( void );
334			virtual void moveB( void );
335
336			virtual int readyCheck();
337
338	mmeineke	746	virtual void resetIntegrator( void );
339
340	gezelter	718	// chi and eta are the propagated degrees of freedom
341
342			double chi;
343			double eta[3][3];
344			double NkBT;
345
346			// targetTemp, targetPressure, and tauBarostat must be set.
347			// One of qmass or tauThermostat must be set;
348
349			double targetTemp;
350			double targetPressure;
351			double tauThermostat;
352			double tauBarostat;
353
354			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
355			short int have_target_pressure;
356
357			};
358
359
360	tim	658	template<typename T> class ZConstraint : public T {
361	tim	701
362			public:
363	tim	738	class ForceSubtractionPolicy{
364	tim	699	public:
365	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
366	tim	658
367	tim	701	virtual void update() = 0;
368	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
369			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
370	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
371			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
372
373			protected:
374			ZConstraint<T>* zconsIntegrator;;
375	tim	699	};
376
377	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
378	tim	699	public:
379	tim	738	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
380	tim	701	virtual void update();
381	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385
386	tim	699	private:
387	tim	701	int totNumOfMovingAtoms;
388	tim	699	};
389
390	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
391	tim	699	public:
392	tim	738	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
393	tim	701
394			virtual void update();
395	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
396			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
397	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
398			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
399	tim	699
400	tim	701	private:
401			double totMassOfMovingAtoms;
402	tim	699	};
403
404	tim	658	public:
405
406			ZConstraint( SimInfo theInfo, ForceFields the_ff);
407			~ZConstraint();
408	tim	677
409	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
410			void getZConsTime() {return zconsTime;}
411
412	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
413			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
414	tim	658
415	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
416	tim	658	string getZConsOutput() {return zconsOutput;}
417	tim	677
418			virtual void integrate();
419
420	tim	658
421			#ifdef IS_MPI
422	tim	701	virtual void update(); //which is called to indicate the molecules' migration
423	mmeineke	377	#endif
424	tim	658
425			protected:
426
427	tim	701	enum ZConsState {zcsMoving, zcsFixed};
428	tim	677
429			virtual void calcForce( int calcPot, int calcStress );
430			virtual void thermalize(void);
431
432			void zeroOutVel();
433			void doZconstraintForce();
434	tim	682	void doHarmonic();
435	tim	677	bool checkZConsState();
436
437			bool haveFixedZMols();
438			bool haveMovingZMols();
439
440			double calcZSys();
441
442			int isZConstraintMol(Molecule* mol);
443
444
445	tim	701	double zconsTime; //sample time
446			double zconsTol; //tolerance of z-contratint
447			double zForceConst; //base force constant term
448			//which is estimate by OOPSE
449	tim	658
450	tim	701	vector<Molecule*> zconsMols; //z-constraint molecules array
451			vector<double> massOfZConsMols; //mass of z-constraint molecule
452			vector<double> kz; //force constant array
453			vector<ZConsState> states; //state of z-constraint molecules
454			vector<double> zPos; //
455	tim	658
456	tim	677
457	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
458			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
459			double totalMassOfUncons; //total mas of unconstraint molecules
460	tim	682
461	tim	701	vector<ZConsParaItem>* parameters; //
462	tim	658
463			vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
464	tim	677
465			int* indexOfZConsMols; //index of local Z-Constraint Molecules
466	tim	658	double* fz;
467	tim	699	double* curZPos;
468	tim	658
469	tim	701	int totNumOfUnconsAtoms; //total number of uncontraint atoms
470	tim	677
471			int whichDirection; //constraint direction
472
473	tim	658	private:
474	tim	677
475	tim	701	string zconsOutput; //filename of zconstraint output
476			ZConsWriter* fzOut; //z-constraint writer
477	tim	677
478	tim	701	double curZconsTime;
479	tim	699
480	tim	696	double calcMovingMolsCOMVel();
481			double calcSysCOMVel();
482			double calcTotalForce();
483	tim	701
484	tim	738	ForceSubtractionPolicy* forcePolicy; //force substration policy
485			friend class ForceSubtractionPolicy;
486	tim	677
487	tim	658	};
488
489			#endif