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 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();

  // 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();

  // 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();

  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 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 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();

  // 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 ForceSubstractionPolicy{
    public:
      ForceSubstractionPolicy(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 : ForceSubstractionPolicy{
    public:
      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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 :ForceSubstractionPolicy{
    public:
      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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();
  
  ForceSubstractionPolicy* forcePolicy; //force substration policy
  friend class ForceSubstractionPolicy;

};

#endif
Revision:	718
Committed:	Mon Aug 25 21:51:30 2003 UTC (20 years, 10 months ago) by gezelter
File size:	13054 byte(s)
Log Message:	* empty log message *
#	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 calcForce( int calcPot, int calcStress );
43	virtual void thermalize();
44
45	void checkConstraints( void );
46	void rotate( int axes1, int axes2, double angle, double j[3],
47	double A[3][3] );
48
49	ForceFields* myFF;
50
51	SimInfo *info; // all the info we'll ever need
52	int nAtoms; /* the number of atoms */
53	int oldAtoms;
54	Atom *atoms; / array of atom pointers */
55	Molecule* molecules;
56	int nMols;
57
58	int isConstrained; // boolean to know whether the systems contains
59	// constraints.
60	int nConstrained; // counter for number of constraints
61	int *constrainedA; // the i of a constraint pair
62	int *constrainedB; // the j of a constraint pair
63	double *constrainedDsqr; // the square of the constraint distance
64
65	int* moving; // tells whether we are moving atom i
66	int* moved; // tells whether we have moved atom i
67	double* oldPos; // pre constrained positions
68
69	short isFirst; /boolean for the first time integrate is called /
70
71	double dt;
72	double dt2;
73
74	Thermo *tStats;
75	StatWriter* statOut;
76	DumpWriter* dumpOut;
77
78	};
79
80	typedef Integrator<BaseIntegrator> RealIntegrator;
81
82	template<typename T> class NVE : public T {
83
84	public:
85	NVE ( SimInfo theInfo, ForceFields the_ff ):
86	T( theInfo, the_ff ){}
87	virtual ~NVE(){}
88	};
89
90
91	template<typename T> class NVT : public T {
92
93	public:
94
95	NVT ( SimInfo theInfo, ForceFields the_ff);
96	virtual ~NVT() {}
97
98	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100
101	protected:
102
103	virtual void moveA( void );
104	virtual void moveB( void );
105
106	virtual int readyCheck();
107
108	// chi is a propagated degree of freedom.
109
110	double chi;
111
112	// targetTemp must be set. tauThermostat must also be set;
113
114	double targetTemp;
115	double tauThermostat;
116
117	short int have_tau_thermostat, have_target_temp;
118
119	};
120
121
122
123	template<typename T> class NPTi : public T{
124
125	public:
126
127	NPTi ( SimInfo theInfo, ForceFields the_ff);
128	virtual ~NPTi() {};
129
130	virtual void integrateStep( int calcPot, int calcStress ){
131	calcStress = 1;
132	T::integrateStep( calcPot, calcStress );
133	}
134
135	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
136	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
137	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
138	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
139
140	protected:
141
142	virtual void moveA( void );
143	virtual void moveB( void );
144
145	virtual int readyCheck();
146
147	// chi and eta are the propagated degrees of freedom
148
149	double chi;
150	double eta;
151	double NkBT;
152
153	// targetTemp, targetPressure, and tauBarostat must be set.
154	// One of qmass or tauThermostat must be set;
155
156	double targetTemp;
157	double targetPressure;
158	double tauThermostat;
159	double tauBarostat;
160
161	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
162	short int have_target_pressure;
163
164	};
165
166	template<typename T> class NPTim : public T{
167
168	public:
169
170	NPTim ( SimInfo theInfo, ForceFields the_ff);
171	virtual ~NPTim() {};
172
173	virtual void integrateStep( int calcPot, int calcStress ){
174	calcStress = 1;
175	T::integrateStep( calcPot, calcStress );
176	}
177
178	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182
183	protected:
184
185	virtual void moveA( void );
186	virtual void moveB( void );
187
188	virtual int readyCheck();
189
190	Molecule* myMolecules;
191	Atom** myAtoms;
192
193	// chi and eta are the propagated degrees of freedom
194
195	double chi;
196	double eta;
197	double NkBT;
198
199	// targetTemp, targetPressure, and tauBarostat must be set.
200	// One of qmass or tauThermostat must be set;
201
202	double targetTemp;
203	double targetPressure;
204	double tauThermostat;
205	double tauBarostat;
206
207	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
208	short int have_target_pressure;
209
210	};
211
212	template<typename T> class NPTf : public T{
213
214	public:
215
216	NPTf ( SimInfo theInfo, ForceFields the_ff);
217	virtual ~NPTf() {};
218
219	virtual void integrateStep( int calcPot, int calcStress ){
220	calcStress = 1;
221	T::integrateStep( calcPot, calcStress );
222	}
223
224	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228
229	protected:
230
231	virtual void moveA( void );
232	virtual void moveB( void );
233
234	virtual int readyCheck();
235
236	// chi and eta are the propagated degrees of freedom
237
238	double chi;
239	double eta[3][3];
240	double NkBT;
241
242	// targetTemp, targetPressure, and tauBarostat must be set.
243	// One of qmass or tauThermostat must be set;
244
245	double targetTemp;
246	double targetPressure;
247	double tauThermostat;
248	double tauBarostat;
249
250	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251	short int have_target_pressure;
252
253	};
254
255	template<typename T> class NPTfm : public T{
256
257	public:
258
259	NPTfm ( SimInfo theInfo, ForceFields the_ff);
260	virtual ~NPTfm() {};
261
262	virtual void integrateStep( int calcPot, int calcStress ){
263	calcStress = 1;
264	T::integrateStep( calcPot, calcStress );
265	}
266
267	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271
272	protected:
273
274	virtual void moveA( void );
275	virtual void moveB( void );
276
277	virtual int readyCheck();
278
279	Molecule* myMolecules;
280	Atom** myAtoms;
281
282	// chi and eta are the propagated degrees of freedom
283
284	double chi;
285	double eta[3][3];
286	double NkBT;
287
288	// targetTemp, targetPressure, and tauBarostat must be set.
289	// One of qmass or tauThermostat must be set;
290
291	double targetTemp;
292	double targetPressure;
293	double tauThermostat;
294	double tauBarostat;
295
296	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297	short int have_target_pressure;
298
299	};
300
301
302	template<typename T> class NPTpr : public T{
303
304	public:
305
306	NPTpr ( SimInfo theInfo, ForceFields the_ff);
307	virtual ~NPTpr() {};
308
309	virtual void integrateStep( int calcPot, int calcStress ){
310	calcStress = 1;
311	T::integrateStep( calcPot, calcStress );
312	}
313
314	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
315	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
316	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
317	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
318
319	protected:
320
321	virtual void moveA( void );
322	virtual void moveB( void );
323
324	virtual int readyCheck();
325
326	// chi and eta are the propagated degrees of freedom
327
328	double chi;
329	double eta[3][3];
330	double NkBT;
331
332	// targetTemp, targetPressure, and tauBarostat must be set.
333	// One of qmass or tauThermostat must be set;
334
335	double targetTemp;
336	double targetPressure;
337	double tauThermostat;
338	double tauBarostat;
339
340	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
341	short int have_target_pressure;
342
343	};
344
345
346	template<typename T> class ZConstraint : public T {
347
348	public:
349	class ForceSubstractionPolicy{
350	public:
351	ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
352
353	virtual void update() = 0;
354	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
356	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
357	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
358
359	protected:
360	ZConstraint<T>* zconsIntegrator;;
361	};
362
363	class PolicyByNumber : ForceSubstractionPolicy{
364	public:
365	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}
366	virtual void update();
367	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
368	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
369	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
370	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
371
372	private:
373	int totNumOfMovingAtoms;
374	};
375
376	class PolicyByMass :ForceSubstractionPolicy{
377	public:
378	PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}
379
380	virtual void update();
381	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385
386	private:
387	double totMassOfMovingAtoms;
388	};
389
390	public:
391
392	ZConstraint( SimInfo theInfo, ForceFields the_ff);
393	~ZConstraint();
394
395	void setZConsTime(double time) {this->zconsTime = time;}
396	void getZConsTime() {return zconsTime;}
397
398	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
400
401	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
402	string getZConsOutput() {return zconsOutput;}
403
404	virtual void integrate();
405
406
407	#ifdef IS_MPI
408	virtual void update(); //which is called to indicate the molecules' migration
409	#endif
410
411	protected:
412
413	enum ZConsState {zcsMoving, zcsFixed};
414
415	virtual void calcForce( int calcPot, int calcStress );
416	virtual void thermalize(void);
417
418	void zeroOutVel();
419	void doZconstraintForce();
420	void doHarmonic();
421	bool checkZConsState();
422
423	bool haveFixedZMols();
424	bool haveMovingZMols();
425
426	double calcZSys();
427
428	int isZConstraintMol(Molecule* mol);
429
430
431	double zconsTime; //sample time
432	double zconsTol; //tolerance of z-contratint
433	double zForceConst; //base force constant term
434	//which is estimate by OOPSE
435
436	vector<Molecule*> zconsMols; //z-constraint molecules array
437	vector<double> massOfZConsMols; //mass of z-constraint molecule
438	vector<double> kz; //force constant array
439	vector<ZConsState> states; //state of z-constraint molecules
440	vector<double> zPos; //
441
442
443	vector<Molecule*> unconsMols; //unconstraint molecules array
444	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
445	double totalMassOfUncons; //total mas of unconstraint molecules
446
447	vector<ZConsParaItem>* parameters; //
448
449	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
450
451	int* indexOfZConsMols; //index of local Z-Constraint Molecules
452	double* fz;
453	double* curZPos;
454
455	int totNumOfUnconsAtoms; //total number of uncontraint atoms
456
457	int whichDirection; //constraint direction
458
459	private:
460
461	string zconsOutput; //filename of zconstraint output
462	ZConsWriter* fzOut; //z-constraint writer
463
464	double curZconsTime;
465
466	double calcMovingMolsCOMVel();
467	double calcSysCOMVel();
468	double calcTotalForce();
469
470	ForceSubstractionPolicy* forcePolicy; //force substration policy
471	friend class ForceSubstractionPolicy;
472
473	};
474
475	#endif