OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#include "Atom.hpp"
#include "StuntDouble.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"
#include "Restraints.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);
  virtual string getAdditionalParameters(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 bool stopIntegrator() {return false;}

  virtual void rotationPropagation( StuntDouble* sd, 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
  vector<StuntDouble*> integrableObjects;
  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;

// ansi instantiation
template class Integrator<BaseIntegrator>;

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);
  virtual string getAdditionalParameters(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;
  virtual string getAdditionalParameters(void) = 0;
  
  double myTauThermo( void ) { return tauThermostat; }
  double myTauBaro( void ) { return tauBarostat; }

  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 void calcVelScale( void ) = 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);
  virtual string getAdditionalParameters(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]);

  virtual void calcVelScale( void );

  double eta, oldEta, prevEta;
  double vScale;
};

template<typename T> class NPTf : public T{

public:

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

  virtual double getConservedQuantity(void);
  virtual string getAdditionalParameters(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]);

  virtual void calcVelScale( void );

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[3][3];
  double vScale[3][3];
};

template<typename T> class NPTxyz : public T{

public:

  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTxyz();

  virtual double getConservedQuantity(void);
  virtual string getAdditionalParameters(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]);

  virtual void calcVelScale( void );

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[3][3];
  double vScale[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(vector<double>& resPos);
  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

  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
  vector<double> fz;
  vector<double> curZPos;

  bool usingSMD;
  vector<double> prevCantPos;
  vector<double> cantPos;
  vector<double> cantVel;

  double zconsFixTime;  
  double zconsGap;
  bool hasZConsGap;
  vector<double> endFixTime;
  
  int whichDirection;                           //constraint direction

private:

  string zconsOutput;                         //filename of zconstraint output
  ZConsWriter* fzOut;                         //z-constraint writer

  double curZconsTime;

  double calcMovingMolsCOMVel();
  double calcSysCOMVel();
  double calcTotalForce();
  void updateZPos();
  void updateCantPos();
  
  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
  friend class ForceSubtractionPolicy;

};

#endif
Revision:	1198
Committed:	Thu May 27 00:48:12 2004 UTC (20 years, 1 month ago) by tim
File size:	13201 byte(s)
Log Message:	in the progress of fixing MPI version of cutoff group
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "Atom.hpp"
7	#include "StuntDouble.hpp"
8	#include "Molecule.hpp"
9	#include "SRI.hpp"
10	#include "AbstractClasses.hpp"
11	#include "SimInfo.hpp"
12	#include "ForceFields.hpp"
13	#include "Thermo.hpp"
14	#include "ReadWrite.hpp"
15	#include "ZConsWriter.hpp"
16	#include "Restraints.hpp"
17
18	using namespace std;
19	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
20	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
22	const int maxIteration = 300;
23	const double tol = 1.0e-6;
24
25	template<typename T = BaseIntegrator> class Integrator : public T {
26
27	public:
28	Integrator( SimInfo theInfo, ForceFields the_ff );
29	virtual ~Integrator();
30	void integrate( void );
31	virtual double getConservedQuantity(void);
32	virtual string getAdditionalParameters(void);
33
34	protected:
35
36	virtual void integrateStep( int calcPot, int calcStress );
37	virtual void preMove( void );
38	virtual void moveA( void );
39	virtual void moveB( void );
40	virtual void constrainA( void );
41	virtual void constrainB( void );
42	virtual int readyCheck( void ) { return 1; }
43
44	virtual void resetIntegrator( void ) { }
45
46	virtual void calcForce( int calcPot, int calcStress );
47	virtual void thermalize();
48
49	virtual bool stopIntegrator() {return false;}
50
51	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52
53	void checkConstraints( void );
54	void rotate( int axes1, int axes2, double angle, double j[3],
55	double A[3][3] );
56
57	ForceFields* myFF;
58
59	SimInfo *info; // all the info we'll ever need
60	vector<StuntDouble*> integrableObjects;
61	int nAtoms; /* the number of atoms */
62	int oldAtoms;
63	Atom *atoms; / array of atom pointers */
64	Molecule* molecules;
65	int nMols;
66
67	int isConstrained; // boolean to know whether the systems contains
68	// constraints.
69	int nConstrained; // counter for number of constraints
70	int *constrainedA; // the i of a constraint pair
71	int *constrainedB; // the j of a constraint pair
72	double *constrainedDsqr; // the square of the constraint distance
73
74	int* moving; // tells whether we are moving atom i
75	int* moved; // tells whether we have moved atom i
76	double* oldPos; // pre constrained positions
77
78	short isFirst; /boolean for the first time integrate is called /
79
80	double dt;
81	double dt2;
82
83	Thermo *tStats;
84	StatWriter* statOut;
85	DumpWriter* dumpOut;
86
87	};
88
89	typedef Integrator<BaseIntegrator> RealIntegrator;
90
91	// ansi instantiation
92	template class Integrator<BaseIntegrator>;
93
94	template<typename T> class NVE : public T {
95
96	public:
97	NVE ( SimInfo theInfo, ForceFields the_ff ):
98	T( theInfo, the_ff ){}
99	virtual ~NVE(){}
100	};
101
102
103	template<typename T> class NVT : public T {
104
105	public:
106
107	NVT ( SimInfo theInfo, ForceFields the_ff);
108	virtual ~NVT();
109
110	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
111	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112	void setChiTolerance(double tol) {chiTolerance = tol;}
113	virtual double getConservedQuantity(void);
114	virtual string getAdditionalParameters(void);
115
116	protected:
117
118	virtual void moveA( void );
119	virtual void moveB( void );
120
121	virtual int readyCheck();
122
123	virtual void resetIntegrator( void );
124
125	// chi is a propagated degree of freedom.
126
127	double chi;
128
129	//integral of chi(t)dt
130	double integralOfChidt;
131
132	// targetTemp must be set. tauThermostat must also be set;
133
134	double targetTemp;
135	double tauThermostat;
136
137	short int have_tau_thermostat, have_target_temp;
138
139	double *oldVel;
140	double *oldJi;
141
142	double chiTolerance;
143	short int have_chi_tolerance;
144
145	};
146
147
148
149	template<typename T> class NPT : public T{
150
151	public:
152
153	NPT ( SimInfo theInfo, ForceFields the_ff);
154	virtual ~NPT();
155
156	virtual void integrateStep( int calcPot, int calcStress ){
157	calcStress = 1;
158	T::integrateStep( calcPot, calcStress );
159	}
160
161	virtual double getConservedQuantity(void) = 0;
162	virtual string getAdditionalParameters(void) = 0;
163
164	double myTauThermo( void ) { return tauThermostat; }
165	double myTauBaro( void ) { return tauBarostat; }
166
167	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174
175	protected:
176
177	virtual void moveA( void );
178	virtual void moveB( void );
179
180	virtual int readyCheck();
181
182	virtual void resetIntegrator( void );
183
184	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185	virtual void getVelScaleB( double sc[3], int index ) = 0;
186	virtual void getPosScale(double pos[3], double COM[3],
187	int index, double sc[3]) = 0;
188
189	virtual void calcVelScale( void ) = 0;
190
191	virtual bool chiConverged( void );
192	virtual bool etaConverged( void ) = 0;
193
194	virtual void evolveChiA( void );
195	virtual void evolveEtaA( void ) = 0;
196	virtual void evolveChiB( void );
197	virtual void evolveEtaB( void ) = 0;
198
199	virtual void scaleSimBox( void ) = 0;
200
201	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202
203	// chi and eta are the propagated degrees of freedom
204
205	double oldChi;
206	double prevChi;
207	double chi;
208	double NkBT;
209	double fkBT;
210
211	double tt2, tb2;
212	double instaTemp, instaPress, instaVol;
213	double press[3][3];
214
215	int Nparticles;
216
217	double integralOfChidt;
218
219	// targetTemp, targetPressure, and tauBarostat must be set.
220	// One of qmass or tauThermostat must be set;
221
222	double targetTemp;
223	double targetPressure;
224	double tauThermostat;
225	double tauBarostat;
226
227	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228	short int have_target_pressure;
229
230	double *oldPos;
231	double *oldVel;
232	double *oldJi;
233
234	double chiTolerance;
235	short int have_chi_tolerance;
236	double posIterTolerance;
237	short int have_pos_iter_tolerance;
238	double etaTolerance;
239	short int have_eta_tolerance;
240
241	};
242
243	template<typename T> class NPTi : public T{
244
245	public:
246	NPTi( SimInfo theInfo, ForceFields the_ff);
247	~NPTi();
248
249	virtual double getConservedQuantity(void);
250	virtual void resetIntegrator(void);
251	virtual string getAdditionalParameters(void);
252	protected:
253
254
255
256	virtual void evolveEtaA(void);
257	virtual void evolveEtaB(void);
258
259	virtual bool etaConverged( void );
260
261	virtual void scaleSimBox( void );
262
263	virtual void getVelScaleA( double sc[3], double vel[3] );
264	virtual void getVelScaleB( double sc[3], int index );
265	virtual void getPosScale(double pos[3], double COM[3],
266	int index, double sc[3]);
267
268	virtual void calcVelScale( void );
269
270	double eta, oldEta, prevEta;
271	double vScale;
272	};
273
274	template<typename T> class NPTf : public T{
275
276	public:
277
278	NPTf ( SimInfo theInfo, ForceFields the_ff);
279	virtual ~NPTf();
280
281	virtual double getConservedQuantity(void);
282	virtual string getAdditionalParameters(void);
283	virtual void resetIntegrator(void);
284
285	protected:
286
287	virtual void evolveEtaA(void);
288	virtual void evolveEtaB(void);
289
290	virtual bool etaConverged( void );
291
292	virtual void scaleSimBox( void );
293
294	virtual void getVelScaleA( double sc[3], double vel[3] );
295	virtual void getVelScaleB( double sc[3], int index );
296	virtual void getPosScale(double pos[3], double COM[3],
297	int index, double sc[3]);
298
299	virtual void calcVelScale( void );
300
301	double eta[3][3];
302	double oldEta[3][3];
303	double prevEta[3][3];
304	double vScale[3][3];
305	};
306
307	template<typename T> class NPTxyz : public T{
308
309	public:
310
311	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
312	virtual ~NPTxyz();
313
314	virtual double getConservedQuantity(void);
315	virtual string getAdditionalParameters(void);
316	virtual void resetIntegrator(void);
317
318	protected:
319
320	virtual void evolveEtaA(void);
321	virtual void evolveEtaB(void);
322
323	virtual bool etaConverged( void );
324
325	virtual void scaleSimBox( void );
326
327	virtual void getVelScaleA( double sc[3], double vel[3] );
328	virtual void getVelScaleB( double sc[3], int index );
329	virtual void getPosScale(double pos[3], double COM[3],
330	int index, double sc[3]);
331
332	virtual void calcVelScale( void );
333
334	double eta[3][3];
335	double oldEta[3][3];
336	double prevEta[3][3];
337	double vScale[3][3];
338	};
339
340
341	template<typename T> class ZConstraint : public T {
342
343	public:
344	class ForceSubtractionPolicy{
345	public:
346	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347
348	virtual void update() = 0;
349	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353
354	protected:
355	ZConstraint<T>* zconsIntegrator;
356	};
357
358	class PolicyByNumber : public ForceSubtractionPolicy{
359
360	public:
361	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362	virtual void update();
363	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367
368	private:
369	int totNumOfMovingAtoms;
370	};
371
372	class PolicyByMass : public ForceSubtractionPolicy{
373
374	public:
375	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376
377	virtual void update();
378	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
381	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382
383	private:
384	double totMassOfMovingAtoms;
385	};
386
387	public:
388
389	ZConstraint( SimInfo theInfo, ForceFields the_ff);
390	~ZConstraint();
391
392	void setZConsTime(double time) {this->zconsTime = time;}
393	void getZConsTime() {return zconsTime;}
394
395	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
397
398	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
399	string getZConsOutput() {return zconsOutput;}
400
401	virtual void integrate();
402
403
404	#ifdef IS_MPI
405	virtual void update(); //which is called to indicate the molecules' migration
406	#endif
407
408	enum ZConsState {zcsMoving, zcsFixed};
409
410	vector<Molecule*> zconsMols; //z-constraint molecules array
411	vector<ZConsState> states; //state of z-constraint molecules
412
413
414
415	int totNumOfUnconsAtoms; //total number of uncontraint atoms
416	double totalMassOfUncons; //total mas of unconstraint molecules
417
418
419	protected:
420
421
422
423	virtual void calcForce( int calcPot, int calcStress );
424	virtual void thermalize(void);
425
426	void zeroOutVel();
427	void doZconstraintForce();
428	void doHarmonic(vector<double>& resPos);
429	bool checkZConsState();
430
431	bool haveFixedZMols();
432	bool haveMovingZMols();
433
434	double calcZSys();
435
436	int isZConstraintMol(Molecule* mol);
437
438
439	double zconsTime; //sample time
440	double zconsTol; //tolerance of z-contratint
441	double zForceConst; //base force constant term
442	//which is estimate by OOPSE
443
444
445	vector<double> massOfZConsMols; //mass of z-constraint molecule
446	vector<double> kz; //force constant array
447
448	vector<double> zPos; //
449
450
451	vector<Molecule*> unconsMols; //unconstraint molecules array
452	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
453
454
455	vector<ZConsParaItem>* parameters; //
456
457	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
458
459	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
460	vector<double> fz;
461	vector<double> curZPos;
462
463	bool usingSMD;
464	vector<double> prevCantPos;
465	vector<double> cantPos;
466	vector<double> cantVel;
467
468	double zconsFixTime;
469	double zconsGap;
470	bool hasZConsGap;
471	vector<double> endFixTime;
472
473	int whichDirection; //constraint direction
474
475	private:
476
477	string zconsOutput; //filename of zconstraint output
478	ZConsWriter* fzOut; //z-constraint writer
479
480	double curZconsTime;
481
482	double calcMovingMolsCOMVel();
483	double calcSysCOMVel();
484	double calcTotalForce();
485	void updateZPos();
486	void updateCantPos();
487
488	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489	friend class ForceSubtractionPolicy;
490
491	};
492
493	#endif