OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#include "Atom.hpp"
#include "Molecule.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "ZConsWriter.hpp"

using namespace std;
const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
const int maxIteration = 300;
const double tol = 1.0e-6;


template<typename T = BaseIntegrator> class Integrator : public T {

public:
  Integrator( SimInfo *theInfo, ForceFields* the_ff );
  virtual ~Integrator();
  void integrate( void );
  virtual double  getConservedQuantity(void);
  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 void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );

  void checkConstraints( void );
  void rotate( int axes1, int axes2, double angle, double j[3],
         double A[3][3] );

  ForceFields* myFF;

  SimInfo *info; // all the info we'll ever need
  int nAtoms;  /* the number of atoms */
  int oldAtoms;
  Atom **atoms; /* array of atom pointers */
  Molecule* molecules;
  int nMols;

  int isConstrained; // boolean to know whether the systems contains
         // constraints.
  int nConstrained;  // counter for number of constraints
  int *constrainedA; // the i of a constraint pair
  int *constrainedB; // the j of a constraint pair
  double *constrainedDsqr; // the square of the constraint distance

  int* moving; // tells whether we are moving atom i
  int* moved;  // tells whether we have moved atom i
  double* oldPos; // pre constrained positions

  short isFirst; /*boolean for the first time integrate is called */

  double dt;
  double dt2;

  Thermo *tStats;
  StatWriter*  statOut;
  DumpWriter*  dumpOut;

};

typedef Integrator<BaseIntegrator> RealIntegrator;

template<typename T> class NVE : public T {

public:
  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
    T( theInfo, the_ff ){}
  virtual ~NVE(){}
};


template<typename T> class NVT : public T {

public:

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

  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
  void setChiTolerance(double tol) {chiTolerance = tol;}
  virtual double  getConservedQuantity(void);
  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();
  bool checkZConsState();

  bool haveFixedZMols();
  bool haveMovingZMols();

  double calcZSys();

  int isZConstraintMol(Molecule* mol);


  double zconsTime;                              //sample time
  double zconsTol;                                 //tolerance of z-contratint
  double zForceConst;                           //base force constant term
                                                          //which is estimate by OOPSE


  vector<double> massOfZConsMols;       //mass of z-constraint molecule
  vector<double> kz;                              //force constant array

  vector<double> zPos;                          //


  vector<Molecule*> unconsMols;           //unconstraint molecules array
  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules


  vector<ZConsParaItem>* parameters; //

  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels

  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
  double* fz;
  double* curZPos;


  int whichDirection;                           //constraint direction

private:

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

  double curZconsTime;

  double calcMovingMolsCOMVel();
  double calcSysCOMVel();
  double calcTotalForce();

  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
  friend class ForceSubtractionPolicy;

};

#endif
Revision:	857
Committed:	Fri Nov 7 17:09:48 2003 UTC (21 years, 11 months ago) by mmeineke
File size:	12715 byte(s)
Log Message:	moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
#	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	virtual double getConservedQuantity(void);
31	virtual string getAdditionalParameters(void);
32
33	protected:
34
35	virtual void integrateStep( int calcPot, int calcStress );
36	virtual void preMove( void );
37	virtual void moveA( void );
38	virtual void moveB( void );
39	virtual void constrainA( void );
40	virtual void constrainB( void );
41	virtual int readyCheck( void ) { return 1; }
42
43	virtual void resetIntegrator( void ) { }
44
45	virtual void calcForce( int calcPot, int calcStress );
46	virtual void thermalize();
47
48	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49
50	void checkConstraints( void );
51	void rotate( int axes1, int axes2, double angle, double j[3],
52	double A[3][3] );
53
54	ForceFields* myFF;
55
56	SimInfo *info; // all the info we'll ever need
57	int nAtoms; /* the number of atoms */
58	int oldAtoms;
59	Atom *atoms; / array of atom pointers */
60	Molecule* molecules;
61	int nMols;
62
63	int isConstrained; // boolean to know whether the systems contains
64	// constraints.
65	int nConstrained; // counter for number of constraints
66	int *constrainedA; // the i of a constraint pair
67	int *constrainedB; // the j of a constraint pair
68	double *constrainedDsqr; // the square of the constraint distance
69
70	int* moving; // tells whether we are moving atom i
71	int* moved; // tells whether we have moved atom i
72	double* oldPos; // pre constrained positions
73
74	short isFirst; /boolean for the first time integrate is called /
75
76	double dt;
77	double dt2;
78
79	Thermo *tStats;
80	StatWriter* statOut;
81	DumpWriter* dumpOut;
82
83	};
84
85	typedef Integrator<BaseIntegrator> RealIntegrator;
86
87	template<typename T> class NVE : public T {
88
89	public:
90	NVE ( SimInfo theInfo, ForceFields the_ff ):
91	T( theInfo, the_ff ){}
92	virtual ~NVE(){}
93	};
94
95
96	template<typename T> class NVT : public T {
97
98	public:
99
100	NVT ( SimInfo theInfo, ForceFields the_ff);
101	virtual ~NVT();
102
103	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
104	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105	void setChiTolerance(double tol) {chiTolerance = tol;}
106	virtual double getConservedQuantity(void);
107	virtual string getAdditionalParameters(void);
108
109	protected:
110
111	virtual void moveA( void );
112	virtual void moveB( void );
113
114	virtual int readyCheck();
115
116	virtual void resetIntegrator( void );
117
118	// chi is a propagated degree of freedom.
119
120	double chi;
121
122	//integral of chi(t)dt
123	double integralOfChidt;
124
125	// targetTemp must be set. tauThermostat must also be set;
126
127	double targetTemp;
128	double tauThermostat;
129
130	short int have_tau_thermostat, have_target_temp;
131
132	double *oldVel;
133	double *oldJi;
134
135	double chiTolerance;
136	short int have_chi_tolerance;
137
138	};
139
140
141
142	template<typename T> class NPT : public T{
143
144	public:
145
146	NPT ( SimInfo theInfo, ForceFields the_ff);
147	virtual ~NPT();
148
149	virtual void integrateStep( int calcPot, int calcStress ){
150	calcStress = 1;
151	T::integrateStep( calcPot, calcStress );
152	}
153
154	virtual double getConservedQuantity(void) = 0;
155	virtual string getAdditionalParameters(void) = 0;
156
157	double myTauThermo( void ) { return tauThermostat; }
158	double myTauBaro( void ) { return tauBarostat; }
159
160	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167
168	protected:
169
170	virtual void moveA( void );
171	virtual void moveB( void );
172
173	virtual int readyCheck();
174
175	virtual void resetIntegrator( void );
176
177	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178	virtual void getVelScaleB( double sc[3], int index ) = 0;
179	virtual void getPosScale(double pos[3], double COM[3],
180	int index, double sc[3]) = 0;
181
182	virtual void calcVelScale( void ) = 0;
183
184	virtual bool chiConverged( void );
185	virtual bool etaConverged( void ) = 0;
186
187	virtual void evolveChiA( void );
188	virtual void evolveEtaA( void ) = 0;
189	virtual void evolveChiB( void );
190	virtual void evolveEtaB( void ) = 0;
191
192	virtual void scaleSimBox( void ) = 0;
193
194	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
195
196	// chi and eta are the propagated degrees of freedom
197
198	double oldChi;
199	double prevChi;
200	double chi;
201	double NkBT;
202	double fkBT;
203
204	double tt2, tb2;
205	double instaTemp, instaPress, instaVol;
206	double press[3][3];
207
208	int Nparticles;
209
210	double integralOfChidt;
211
212	// targetTemp, targetPressure, and tauBarostat must be set.
213	// One of qmass or tauThermostat must be set;
214
215	double targetTemp;
216	double targetPressure;
217	double tauThermostat;
218	double tauBarostat;
219
220	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
221	short int have_target_pressure;
222
223	double *oldPos;
224	double *oldVel;
225	double *oldJi;
226
227	double chiTolerance;
228	short int have_chi_tolerance;
229	double posIterTolerance;
230	short int have_pos_iter_tolerance;
231	double etaTolerance;
232	short int have_eta_tolerance;
233
234	};
235
236	template<typename T> class NPTi : public T{
237
238	public:
239	NPTi( SimInfo theInfo, ForceFields the_ff);
240	~NPTi();
241
242	virtual double getConservedQuantity(void);
243	virtual void resetIntegrator(void);
244	virtual string getAdditionalParameters(void);
245	protected:
246
247
248
249	virtual void evolveEtaA(void);
250	virtual void evolveEtaB(void);
251
252	virtual bool etaConverged( void );
253
254	virtual void scaleSimBox( void );
255
256	virtual void getVelScaleA( double sc[3], double vel[3] );
257	virtual void getVelScaleB( double sc[3], int index );
258	virtual void getPosScale(double pos[3], double COM[3],
259	int index, double sc[3]);
260
261	virtual void calcVelScale( void );
262
263	double eta, oldEta, prevEta;
264	double vScale;
265	};
266
267	template<typename T> class NPTf : public T{
268
269	public:
270
271	NPTf ( SimInfo theInfo, ForceFields the_ff);
272	virtual ~NPTf();
273
274	virtual double getConservedQuantity(void);
275	virtual string getAdditionalParameters(void);
276	virtual void resetIntegrator(void);
277
278	protected:
279
280	virtual void evolveEtaA(void);
281	virtual void evolveEtaB(void);
282
283	virtual bool etaConverged( void );
284
285	virtual void scaleSimBox( void );
286
287	virtual void getVelScaleA( double sc[3], double vel[3] );
288	virtual void getVelScaleB( double sc[3], int index );
289	virtual void getPosScale(double pos[3], double COM[3],
290	int index, double sc[3]);
291
292	virtual void calcVelScale( void );
293
294	double eta[3][3];
295	double oldEta[3][3];
296	double prevEta[3][3];
297	double vScale[3][3];
298	};
299
300	template<typename T> class NPTxyz : public T{
301
302	public:
303
304	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
305	virtual ~NPTxyz();
306
307	virtual double getConservedQuantity(void);
308	virtual string getAdditionalParameters(void);
309	virtual void resetIntegrator(void);
310
311	protected:
312
313	virtual void evolveEtaA(void);
314	virtual void evolveEtaB(void);
315
316	virtual bool etaConverged( void );
317
318	virtual void scaleSimBox( void );
319
320	virtual void getVelScaleA( double sc[3], double vel[3] );
321	virtual void getVelScaleB( double sc[3], int index );
322	virtual void getPosScale(double pos[3], double COM[3],
323	int index, double sc[3]);
324
325	virtual void calcVelScale( void );
326
327	double eta[3][3];
328	double oldEta[3][3];
329	double prevEta[3][3];
330	double vScale[3][3];
331	};
332
333
334	template<typename T> class ZConstraint : public T {
335
336	public:
337	class ForceSubtractionPolicy{
338	public:
339	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
340
341	virtual void update() = 0;
342	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
343	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
344	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346
347	protected:
348	ZConstraint<T>* zconsIntegrator;
349	};
350
351	class PolicyByNumber : public ForceSubtractionPolicy{
352
353	public:
354	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
355	virtual void update();
356	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
357	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
358	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
359	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360
361	private:
362	int totNumOfMovingAtoms;
363	};
364
365	class PolicyByMass : public ForceSubtractionPolicy{
366
367	public:
368	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
369
370	virtual void update();
371	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375
376	private:
377	double totMassOfMovingAtoms;
378	};
379
380	public:
381
382	ZConstraint( SimInfo theInfo, ForceFields the_ff);
383	~ZConstraint();
384
385	void setZConsTime(double time) {this->zconsTime = time;}
386	void getZConsTime() {return zconsTime;}
387
388	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
390
391	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
392	string getZConsOutput() {return zconsOutput;}
393
394	virtual void integrate();
395
396
397	#ifdef IS_MPI
398	virtual void update(); //which is called to indicate the molecules' migration
399	#endif
400
401	enum ZConsState {zcsMoving, zcsFixed};
402
403	vector<Molecule*> zconsMols; //z-constraint molecules array
404	vector<ZConsState> states; //state of z-constraint molecules
405
406
407
408	int totNumOfUnconsAtoms; //total number of uncontraint atoms
409	double totalMassOfUncons; //total mas of unconstraint molecules
410
411
412	protected:
413
414
415
416	virtual void calcForce( int calcPot, int calcStress );
417	virtual void thermalize(void);
418
419	void zeroOutVel();
420	void doZconstraintForce();
421	void doHarmonic();
422	bool checkZConsState();
423
424	bool haveFixedZMols();
425	bool haveMovingZMols();
426
427	double calcZSys();
428
429	int isZConstraintMol(Molecule* mol);
430
431
432	double zconsTime; //sample time
433	double zconsTol; //tolerance of z-contratint
434	double zForceConst; //base force constant term
435	//which is estimate by OOPSE
436
437
438	vector<double> massOfZConsMols; //mass of z-constraint molecule
439	vector<double> kz; //force constant array
440
441	vector<double> zPos; //
442
443
444	vector<Molecule*> unconsMols; //unconstraint molecules array
445	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
446
447
448	vector<ZConsParaItem>* parameters; //
449
450	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
451
452	int* indexOfZConsMols; //index of local Z-Constraint Molecules
453	double* fz;
454	double* curZPos;
455
456
457
458	int whichDirection; //constraint direction
459
460	private:
461
462	string zconsOutput; //filename of zconstraint output
463	ZConsWriter* fzOut; //z-constraint writer
464
465	double curZconsTime;
466
467	double calcMovingMolsCOMVel();
468	double calcSysCOMVel();
469	double calcTotalForce();
470
471	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
472	friend class ForceSubtractionPolicy;
473
474	};
475
476	#endif