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"

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( 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;

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> 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;

};

/*
//Steered Molecular Dynamics
 template<typename T> class SMD : public T{
  public:
    SMD( SimInfo *theInfo, ForceFields* the_ff);
    ~SMD();
  
   virtual void integrate();
  virtual void calcForce( int calcPot, int calcStress );   
};
*/
#endif
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	13275 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	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
17	using namespace std;
18	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
19	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
21	const int maxIteration = 300;
22	const double tol = 1.0e-6;
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( StuntDouble* sd, 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	vector<StuntDouble*> integrableObjects;
58	int nAtoms; /* the number of atoms */
59	int oldAtoms;
60	Atom *atoms; / array of atom pointers */
61	Molecule* molecules;
62	int nMols;
63
64	int isConstrained; // boolean to know whether the systems contains
65	// constraints.
66	int nConstrained; // counter for number of constraints
67	int *constrainedA; // the i of a constraint pair
68	int *constrainedB; // the j of a constraint pair
69	double *constrainedDsqr; // the square of the constraint distance
70
71	int* moving; // tells whether we are moving atom i
72	int* moved; // tells whether we have moved atom i
73	double* oldPos; // pre constrained positions
74
75	short isFirst; /boolean for the first time integrate is called /
76
77	double dt;
78	double dt2;
79
80	Thermo *tStats;
81	StatWriter* statOut;
82	DumpWriter* dumpOut;
83
84	};
85
86	typedef Integrator<BaseIntegrator> RealIntegrator;
87
88	template<typename T> class NVE : public T {
89
90	public:
91	NVE ( SimInfo theInfo, ForceFields the_ff ):
92	T( theInfo, the_ff ){}
93	virtual ~NVE(){}
94	};
95
96
97	template<typename T> class NVT : public T {
98
99	public:
100
101	NVT ( SimInfo theInfo, ForceFields the_ff);
102	virtual ~NVT();
103
104	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
105	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
106	void setChiTolerance(double tol) {chiTolerance = tol;}
107	virtual double getConservedQuantity(void);
108	virtual string getAdditionalParameters(void);
109
110	protected:
111
112	virtual void moveA( void );
113	virtual void moveB( void );
114
115	virtual int readyCheck();
116
117	virtual void resetIntegrator( void );
118
119	// chi is a propagated degree of freedom.
120
121	double chi;
122
123	//integral of chi(t)dt
124	double integralOfChidt;
125
126	// targetTemp must be set. tauThermostat must also be set;
127
128	double targetTemp;
129	double tauThermostat;
130
131	short int have_tau_thermostat, have_target_temp;
132
133	double *oldVel;
134	double *oldJi;
135
136	double chiTolerance;
137	short int have_chi_tolerance;
138
139	};
140
141
142
143	template<typename T> class NPT : public T{
144
145	public:
146
147	NPT ( SimInfo theInfo, ForceFields the_ff);
148	virtual ~NPT();
149
150	virtual void integrateStep( int calcPot, int calcStress ){
151	calcStress = 1;
152	T::integrateStep( calcPot, calcStress );
153	}
154
155	virtual double getConservedQuantity(void) = 0;
156	virtual string getAdditionalParameters(void) = 0;
157
158	double myTauThermo( void ) { return tauThermostat; }
159	double myTauBaro( void ) { return tauBarostat; }
160
161	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
162	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
163	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
164	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
165	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
166	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
167	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
168
169	protected:
170
171	virtual void moveA( void );
172	virtual void moveB( void );
173
174	virtual int readyCheck();
175
176	virtual void resetIntegrator( void );
177
178	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
179	virtual void getVelScaleB( double sc[3], int index ) = 0;
180	virtual void getPosScale(double pos[3], double COM[3],
181	int index, double sc[3]) = 0;
182
183	virtual void calcVelScale( void ) = 0;
184
185	virtual bool chiConverged( void );
186	virtual bool etaConverged( void ) = 0;
187
188	virtual void evolveChiA( void );
189	virtual void evolveEtaA( void ) = 0;
190	virtual void evolveChiB( void );
191	virtual void evolveEtaB( void ) = 0;
192
193	virtual void scaleSimBox( void ) = 0;
194
195	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
196
197	// chi and eta are the propagated degrees of freedom
198
199	double oldChi;
200	double prevChi;
201	double chi;
202	double NkBT;
203	double fkBT;
204
205	double tt2, tb2;
206	double instaTemp, instaPress, instaVol;
207	double press[3][3];
208
209	int Nparticles;
210
211	double integralOfChidt;
212
213	// targetTemp, targetPressure, and tauBarostat must be set.
214	// One of qmass or tauThermostat must be set;
215
216	double targetTemp;
217	double targetPressure;
218	double tauThermostat;
219	double tauBarostat;
220
221	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
222	short int have_target_pressure;
223
224	double *oldPos;
225	double *oldVel;
226	double *oldJi;
227
228	double chiTolerance;
229	short int have_chi_tolerance;
230	double posIterTolerance;
231	short int have_pos_iter_tolerance;
232	double etaTolerance;
233	short int have_eta_tolerance;
234
235	};
236
237	template<typename T> class NPTi : public T{
238
239	public:
240	NPTi( SimInfo theInfo, ForceFields the_ff);
241	~NPTi();
242
243	virtual double getConservedQuantity(void);
244	virtual void resetIntegrator(void);
245	virtual string getAdditionalParameters(void);
246	protected:
247
248
249
250	virtual void evolveEtaA(void);
251	virtual void evolveEtaB(void);
252
253	virtual bool etaConverged( void );
254
255	virtual void scaleSimBox( void );
256
257	virtual void getVelScaleA( double sc[3], double vel[3] );
258	virtual void getVelScaleB( double sc[3], int index );
259	virtual void getPosScale(double pos[3], double COM[3],
260	int index, double sc[3]);
261
262	virtual void calcVelScale( void );
263
264	double eta, oldEta, prevEta;
265	double vScale;
266	};
267
268	template<typename T> class NPTf : public T{
269
270	public:
271
272	NPTf ( SimInfo theInfo, ForceFields the_ff);
273	virtual ~NPTf();
274
275	virtual double getConservedQuantity(void);
276	virtual string getAdditionalParameters(void);
277	virtual void resetIntegrator(void);
278
279	protected:
280
281	virtual void evolveEtaA(void);
282	virtual void evolveEtaB(void);
283
284	virtual bool etaConverged( void );
285
286	virtual void scaleSimBox( void );
287
288	virtual void getVelScaleA( double sc[3], double vel[3] );
289	virtual void getVelScaleB( double sc[3], int index );
290	virtual void getPosScale(double pos[3], double COM[3],
291	int index, double sc[3]);
292
293	virtual void calcVelScale( void );
294
295	double eta[3][3];
296	double oldEta[3][3];
297	double prevEta[3][3];
298	double vScale[3][3];
299	};
300
301	template<typename T> class NPTxyz : public T{
302
303	public:
304
305	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
306	virtual ~NPTxyz();
307
308	virtual double getConservedQuantity(void);
309	virtual string getAdditionalParameters(void);
310	virtual void resetIntegrator(void);
311
312	protected:
313
314	virtual void evolveEtaA(void);
315	virtual void evolveEtaB(void);
316
317	virtual bool etaConverged( void );
318
319	virtual void scaleSimBox( void );
320
321	virtual void getVelScaleA( double sc[3], double vel[3] );
322	virtual void getVelScaleB( double sc[3], int index );
323	virtual void getPosScale(double pos[3], double COM[3],
324	int index, double sc[3]);
325
326	virtual void calcVelScale( void );
327
328	double eta[3][3];
329	double oldEta[3][3];
330	double prevEta[3][3];
331	double vScale[3][3];
332	};
333
334
335	template<typename T> class ZConstraint : public T {
336
337	public:
338	class ForceSubtractionPolicy{
339	public:
340	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
341
342	virtual void update() = 0;
343	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
344	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
345	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
347
348	protected:
349	ZConstraint<T>* zconsIntegrator;
350	};
351
352	class PolicyByNumber : public ForceSubtractionPolicy{
353
354	public:
355	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
356	virtual void update();
357	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
358	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
359	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
360	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
361
362	private:
363	int totNumOfMovingAtoms;
364	};
365
366	class PolicyByMass : public ForceSubtractionPolicy{
367
368	public:
369	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370
371	virtual void update();
372	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
373	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
374	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
375	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
376
377	private:
378	double totMassOfMovingAtoms;
379	};
380
381	public:
382
383	ZConstraint( SimInfo theInfo, ForceFields the_ff);
384	~ZConstraint();
385
386	void setZConsTime(double time) {this->zconsTime = time;}
387	void getZConsTime() {return zconsTime;}
388
389	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
390	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
391
392	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
393	string getZConsOutput() {return zconsOutput;}
394
395	virtual void integrate();
396
397
398	#ifdef IS_MPI
399	virtual void update(); //which is called to indicate the molecules' migration
400	#endif
401
402	enum ZConsState {zcsMoving, zcsFixed};
403
404	vector<Molecule*> zconsMols; //z-constraint molecules array
405	vector<ZConsState> states; //state of z-constraint molecules
406
407
408
409	int totNumOfUnconsAtoms; //total number of uncontraint atoms
410	double totalMassOfUncons; //total mas of unconstraint molecules
411
412
413	protected:
414
415
416
417	virtual void calcForce( int calcPot, int calcStress );
418	virtual void thermalize(void);
419
420	void zeroOutVel();
421	void doZconstraintForce();
422	void doHarmonic(vector<double>& resPos);
423	bool checkZConsState();
424
425	bool haveFixedZMols();
426	bool haveMovingZMols();
427
428	double calcZSys();
429
430	int isZConstraintMol(Molecule* mol);
431
432
433	double zconsTime; //sample time
434	double zconsTol; //tolerance of z-contratint
435	double zForceConst; //base force constant term
436	//which is estimate by OOPSE
437
438
439	vector<double> massOfZConsMols; //mass of z-constraint molecule
440	vector<double> kz; //force constant array
441
442	vector<double> zPos; //
443
444
445	vector<Molecule*> unconsMols; //unconstraint molecules array
446	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
447
448
449	vector<ZConsParaItem>* parameters; //
450
451	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
452
453	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
454	vector<double> fz;
455	vector<double> curZPos;
456
457	bool usingSMD;
458	vector<double> cantPos;
459	vector<double> cantVel;
460
461	double zconsFixTime;
462	double zconsGap;
463	bool hasZConsGap;
464	vector<double> endFixTime;
465
466	int whichDirection; //constraint direction
467
468	private:
469
470	string zconsOutput; //filename of zconstraint output
471	ZConsWriter* fzOut; //z-constraint writer
472
473	double curZconsTime;
474
475	double calcMovingMolsCOMVel();
476	double calcSysCOMVel();
477	double calcTotalForce();
478	void updateZPos();
479	void updateCantPos();
480
481	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
482	friend class ForceSubtractionPolicy;
483
484	};
485
486	/*
487	//Steered Molecular Dynamics
488	template<typename T> class SMD : public T{
489	public:
490	SMD( SimInfo theInfo, ForceFields the_ff);
491	~SMD();
492
493	virtual void integrate();
494	virtual void calcForce( int calcPot, int calcStress );
495	};
496	*/
497	#endif