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 NPTzm : public T{

public:

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

  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 etaZ;
  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 NPTxym : public T{

public:

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

  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 etaX;
  double etaY;
  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 subtraction policy
  friend class ForceSubtractionPolicy;

};

#endif
Revision:	755
Committed:	Tue Sep 9 20:35:25 2003 UTC (20 years, 10 months ago) by mmeineke
File size:	15752 byte(s)
Log Message:	updated the ChangeLog added two new NPT integrators, they still need work.
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "Atom.hpp"
7	#include "Molecule.hpp"
8	#include "SRI.hpp"
9	#include "AbstractClasses.hpp"
10	#include "SimInfo.hpp"
11	#include "ForceFields.hpp"
12	#include "Thermo.hpp"
13	#include "ReadWrite.hpp"
14	#include "ZConsWriter.hpp"
15
16	using namespace std;
17	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	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	const int maxIteration = 300;
21	const double tol = 1.0e-6;
22
23
24	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	public:
27	Integrator( SimInfo theInfo, ForceFields the_ff );
28	virtual ~Integrator();
29	void integrate( void );
30
31
32	protected:
33
34	virtual void integrateStep( int calcPot, int calcStress );
35	virtual void preMove( void );
36	virtual void moveA( void );
37	virtual void moveB( void );
38	virtual void constrainA( void );
39	virtual void constrainB( void );
40	virtual int readyCheck( void ) { return 1; }
41
42	virtual void resetIntegrator( void ) { }
43
44	virtual void calcForce( int calcPot, int calcStress );
45	virtual void thermalize();
46
47	void checkConstraints( void );
48	void rotate( int axes1, int axes2, double angle, double j[3],
49	double A[3][3] );
50
51	ForceFields* myFF;
52
53	SimInfo *info; // all the info we'll ever need
54	int nAtoms; /* the number of atoms */
55	int oldAtoms;
56	Atom *atoms; / array of atom pointers */
57	Molecule* molecules;
58	int nMols;
59
60	int isConstrained; // boolean to know whether the systems contains
61	// constraints.
62	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	double* oldPos; // pre constrained positions
70
71	short isFirst; /boolean for the first time integrate is called /
72
73	double dt;
74	double dt2;
75
76	Thermo *tStats;
77	StatWriter* statOut;
78	DumpWriter* dumpOut;
79
80	};
81
82	typedef Integrator<BaseIntegrator> RealIntegrator;
83
84	template<typename T> class NVE : public T {
85
86	public:
87	NVE ( SimInfo theInfo, ForceFields the_ff ):
88	T( theInfo, the_ff ){}
89	virtual ~NVE(){}
90	};
91
92
93	template<typename T> class NVT : public T {
94
95	public:
96
97	NVT ( SimInfo theInfo, ForceFields the_ff);
98	virtual ~NVT() {}
99
100	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102
103	protected:
104
105	virtual void moveA( void );
106	virtual void moveB( void );
107
108	virtual int readyCheck();
109
110	virtual void resetIntegrator( void );
111
112	// chi is a propagated degree of freedom.
113
114	double chi;
115
116	// targetTemp must be set. tauThermostat must also be set;
117
118	double targetTemp;
119	double tauThermostat;
120
121	short int have_tau_thermostat, have_target_temp;
122
123	};
124
125
126
127	template<typename T> class NPTi : public T{
128
129	public:
130
131	NPTi ( SimInfo theInfo, ForceFields the_ff);
132	virtual ~NPTi() {};
133
134	virtual void integrateStep( int calcPot, int calcStress ){
135	calcStress = 1;
136	T::integrateStep( calcPot, calcStress );
137	}
138
139	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	virtual void moveA( void );
147	virtual void moveB( void );
148
149	virtual int readyCheck();
150
151	virtual void resetIntegrator( void );
152
153	// chi and eta are the propagated degrees of freedom
154
155	double chi;
156	double eta;
157	double NkBT;
158
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	short int have_target_pressure;
169
170	};
171
172	template<typename T> class NPTim : public T{
173
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	T::integrateStep( calcPot, calcStress );
182	}
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	virtual void moveA( void );
192	virtual void moveB( void );
193
194	virtual int readyCheck();
195
196	virtual void resetIntegrator( void );
197
198	Molecule* myMolecules;
199	Atom** myAtoms;
200
201	// 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	template<typename T> class NPTzm : public T{
221
222	public:
223
224	NPTzm ( SimInfo theInfo, ForceFields the_ff);
225	virtual ~NPTzm() {};
226
227	virtual void integrateStep( int calcPot, int calcStress ){
228	calcStress = 1;
229	T::integrateStep( calcPot, calcStress );
230	}
231
232	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	virtual int readyCheck();
243
244	virtual void resetIntegrator( void );
245
246	Molecule* myMolecules;
247	Atom** myAtoms;
248
249	// chi and eta are the propagated degrees of freedom
250
251	double chi;
252	double eta;
253	double etaZ;
254	double NkBT;
255
256	// targetTemp, targetPressure, and tauBarostat must be set.
257	// One of qmass or tauThermostat must be set;
258
259	double targetTemp;
260	double targetPressure;
261	double tauThermostat;
262	double tauBarostat;
263
264	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
265	short int have_target_pressure;
266
267	};
268
269	template<typename T> class NPTf : public T{
270
271	public:
272
273	NPTf ( SimInfo theInfo, ForceFields the_ff);
274	virtual ~NPTf() {};
275
276	virtual void integrateStep( int calcPot, int calcStress ){
277	calcStress = 1;
278	T::integrateStep( calcPot, calcStress );
279	}
280
281	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
283	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
284	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
285
286	protected:
287
288	virtual void moveA( void );
289	virtual void moveB( void );
290
291	virtual void resetIntegrator( void );
292
293	virtual int readyCheck();
294
295	// chi and eta are the propagated degrees of freedom
296
297	double chi;
298	double eta[3][3];
299	double NkBT;
300
301	// targetTemp, targetPressure, and tauBarostat must be set.
302	// One of qmass or tauThermostat must be set;
303
304	double targetTemp;
305	double targetPressure;
306	double tauThermostat;
307	double tauBarostat;
308
309	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
310	short int have_target_pressure;
311
312	};
313
314	template<typename T> class NPTxym : public T{
315
316	public:
317
318	NPTxym ( SimInfo theInfo, ForceFields the_ff);
319	virtual ~NPTxym() {};
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	virtual void resetIntegrator( void );
339
340	Molecule* myMolecules;
341	Atom** myAtoms;
342
343	// chi and eta are the propagated degrees of freedom
344
345	double chi;
346	double eta;
347	double etaX;
348	double etaY;
349	double NkBT;
350
351	// targetTemp, targetPressure, and tauBarostat must be set.
352	// One of qmass or tauThermostat must be set;
353
354	double targetTemp;
355	double targetPressure;
356	double tauThermostat;
357	double tauBarostat;
358
359	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
360	short int have_target_pressure;
361
362	};
363
364
365	template<typename T> class NPTfm : public T{
366
367	public:
368
369	NPTfm ( SimInfo theInfo, ForceFields the_ff);
370	virtual ~NPTfm() {};
371
372	virtual void integrateStep( int calcPot, int calcStress ){
373	calcStress = 1;
374	T::integrateStep( calcPot, calcStress );
375	}
376
377	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
378	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
379	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
380	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
381
382	protected:
383
384	virtual void moveA( void );
385	virtual void moveB( void );
386
387	virtual void resetIntegrator( void );
388
389	virtual int readyCheck();
390
391	Molecule* myMolecules;
392	Atom** myAtoms;
393
394	// chi and eta are the propagated degrees of freedom
395
396	double chi;
397	double eta[3][3];
398	double NkBT;
399
400	// targetTemp, targetPressure, and tauBarostat must be set.
401	// One of qmass or tauThermostat must be set;
402
403	double targetTemp;
404	double targetPressure;
405	double tauThermostat;
406	double tauBarostat;
407
408	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
409	short int have_target_pressure;
410
411	};
412
413
414	template<typename T> class NPTpr : public T{
415
416	public:
417
418	NPTpr ( SimInfo theInfo, ForceFields the_ff);
419	virtual ~NPTpr() {};
420
421	virtual void integrateStep( int calcPot, int calcStress ){
422	calcStress = 1;
423	T::integrateStep( calcPot, calcStress );
424	}
425
426	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
427	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
428	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
429	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
430
431	protected:
432
433	virtual void moveA( void );
434	virtual void moveB( void );
435
436	virtual int readyCheck();
437
438	virtual void resetIntegrator( void );
439
440	// chi and eta are the propagated degrees of freedom
441
442	double chi;
443	double eta[3][3];
444	double NkBT;
445
446	// targetTemp, targetPressure, and tauBarostat must be set.
447	// One of qmass or tauThermostat must be set;
448
449	double targetTemp;
450	double targetPressure;
451	double tauThermostat;
452	double tauBarostat;
453
454	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
455	short int have_target_pressure;
456
457	};
458
459
460	template<typename T> class ZConstraint : public T {
461
462	public:
463	class ForceSubtractionPolicy{
464	public:
465	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
466
467	virtual void update() = 0;
468	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
469	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
470	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
471	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
472
473	protected:
474	ZConstraint<T>* zconsIntegrator;;
475	};
476
477	class PolicyByNumber : public ForceSubtractionPolicy{
478
479	public:
480	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
481	virtual void update();
482	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
483	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
484	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
485	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
486
487	private:
488	int totNumOfMovingAtoms;
489	};
490
491	class PolicyByMass : public ForceSubtractionPolicy{
492
493	public:
494	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
495
496	virtual void update();
497	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
498	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
499	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
500	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
501
502	private:
503	double totMassOfMovingAtoms;
504	};
505
506	public:
507
508	ZConstraint( SimInfo theInfo, ForceFields the_ff);
509	~ZConstraint();
510
511	void setZConsTime(double time) {this->zconsTime = time;}
512	void getZConsTime() {return zconsTime;}
513
514	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
515	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
516
517	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
518	string getZConsOutput() {return zconsOutput;}
519
520	virtual void integrate();
521
522
523	#ifdef IS_MPI
524	virtual void update(); //which is called to indicate the molecules' migration
525	#endif
526
527	protected:
528
529	enum ZConsState {zcsMoving, zcsFixed};
530
531	virtual void calcForce( int calcPot, int calcStress );
532	virtual void thermalize(void);
533
534	void zeroOutVel();
535	void doZconstraintForce();
536	void doHarmonic();
537	bool checkZConsState();
538
539	bool haveFixedZMols();
540	bool haveMovingZMols();
541
542	double calcZSys();
543
544	int isZConstraintMol(Molecule* mol);
545
546
547	double zconsTime; //sample time
548	double zconsTol; //tolerance of z-contratint
549	double zForceConst; //base force constant term
550	//which is estimate by OOPSE
551
552	vector<Molecule*> zconsMols; //z-constraint molecules array
553	vector<double> massOfZConsMols; //mass of z-constraint molecule
554	vector<double> kz; //force constant array
555	vector<ZConsState> states; //state of z-constraint molecules
556	vector<double> zPos; //
557
558
559	vector<Molecule*> unconsMols; //unconstraint molecules array
560	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
561	double totalMassOfUncons; //total mas of unconstraint molecules
562
563	vector<ZConsParaItem>* parameters; //
564
565	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
566
567	int* indexOfZConsMols; //index of local Z-Constraint Molecules
568	double* fz;
569	double* curZPos;
570
571	int totNumOfUnconsAtoms; //total number of uncontraint atoms
572
573	int whichDirection; //constraint direction
574
575	private:
576
577	string zconsOutput; //filename of zconstraint output
578	ZConsWriter* fzOut; //z-constraint writer
579
580	double curZconsTime;
581
582	double calcMovingMolsCOMVel();
583	double calcSysCOMVel();
584	double calcTotalForce();
585
586	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
587	friend class ForceSubtractionPolicy;
588
589	};
590
591	#endif