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 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;

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;

};

/*
template<typename T> class SingleZConstrain : public T{


};
*/

template<typename T> class NonEquMD : public T {
  public:
    

};


//
template<typename T> class SingleZConstraint : public T{
  public:
    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
    ~SingleZConstraint();
    
    bool stopIntegrator();
    
  protected:
    
};

//Steered Molecular Dynamics, curret implement only support one steered molecule
 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 );  
    bool stopIntegrator();
  private:
    
};

//By using state pattern, Coordinate Drive is responsible for switching back and forth between
//Driven Molecular Dynamics and ZConstraint Method. 
template<typename T> class CoordinateDriver : public T {
  public:
    typedef T ParentIntegrator;

    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
    ~CoordinateDriver();
    
    virtual void integrate();

  private:    
    BaseIntegrator* zconsIntegrator;
    BaseIntegrator* drivenIntegrator;
    
};

#endif
Revision:	1141
Committed:	Wed Apr 28 23:09:32 2004 UTC (20 years, 2 months ago) by tim
File size:	14290 byte(s)
Log Message:	keep the previous position of cantilever in SMD
#	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 bool stopIntegrator() {return false;}
49
50	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51
52	void checkConstraints( void );
53	void rotate( int axes1, int axes2, double angle, double j[3],
54	double A[3][3] );
55
56	ForceFields* myFF;
57
58	SimInfo *info; // all the info we'll ever need
59	vector<StuntDouble*> integrableObjects;
60	int nAtoms; /* the number of atoms */
61	int oldAtoms;
62	Atom *atoms; / array of atom pointers */
63	Molecule* molecules;
64	int nMols;
65
66	int isConstrained; // boolean to know whether the systems contains
67	// constraints.
68	int nConstrained; // counter for number of constraints
69	int *constrainedA; // the i of a constraint pair
70	int *constrainedB; // the j of a constraint pair
71	double *constrainedDsqr; // the square of the constraint distance
72
73	int* moving; // tells whether we are moving atom i
74	int* moved; // tells whether we have moved atom i
75	double* oldPos; // pre constrained positions
76
77	short isFirst; /boolean for the first time integrate is called /
78
79	double dt;
80	double dt2;
81
82	Thermo *tStats;
83	StatWriter* statOut;
84	DumpWriter* dumpOut;
85
86	};
87
88	typedef Integrator<BaseIntegrator> RealIntegrator;
89
90	template<typename T> class NVE : public T {
91
92	public:
93	NVE ( SimInfo theInfo, ForceFields the_ff ):
94	T( theInfo, the_ff ){}
95	virtual ~NVE(){}
96	};
97
98
99	template<typename T> class NVT : public T {
100
101	public:
102
103	NVT ( SimInfo theInfo, ForceFields the_ff);
104	virtual ~NVT();
105
106	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
107	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108	void setChiTolerance(double tol) {chiTolerance = tol;}
109	virtual double getConservedQuantity(void);
110	virtual string getAdditionalParameters(void);
111
112	protected:
113
114	virtual void moveA( void );
115	virtual void moveB( void );
116
117	virtual int readyCheck();
118
119	virtual void resetIntegrator( void );
120
121	// chi is a propagated degree of freedom.
122
123	double chi;
124
125	//integral of chi(t)dt
126	double integralOfChidt;
127
128	// targetTemp must be set. tauThermostat must also be set;
129
130	double targetTemp;
131	double tauThermostat;
132
133	short int have_tau_thermostat, have_target_temp;
134
135	double *oldVel;
136	double *oldJi;
137
138	double chiTolerance;
139	short int have_chi_tolerance;
140
141	};
142
143
144
145	template<typename T> class NPT : public T{
146
147	public:
148
149	NPT ( SimInfo theInfo, ForceFields the_ff);
150	virtual ~NPT();
151
152	virtual void integrateStep( int calcPot, int calcStress ){
153	calcStress = 1;
154	T::integrateStep( calcPot, calcStress );
155	}
156
157	virtual double getConservedQuantity(void) = 0;
158	virtual string getAdditionalParameters(void) = 0;
159
160	double myTauThermo( void ) { return tauThermostat; }
161	double myTauBaro( void ) { return tauBarostat; }
162
163	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
165	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170
171	protected:
172
173	virtual void moveA( void );
174	virtual void moveB( void );
175
176	virtual int readyCheck();
177
178	virtual void resetIntegrator( void );
179
180	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181	virtual void getVelScaleB( double sc[3], int index ) = 0;
182	virtual void getPosScale(double pos[3], double COM[3],
183	int index, double sc[3]) = 0;
184
185	virtual void calcVelScale( void ) = 0;
186
187	virtual bool chiConverged( void );
188	virtual bool etaConverged( void ) = 0;
189
190	virtual void evolveChiA( void );
191	virtual void evolveEtaA( void ) = 0;
192	virtual void evolveChiB( void );
193	virtual void evolveEtaB( void ) = 0;
194
195	virtual void scaleSimBox( void ) = 0;
196
197	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198
199	// chi and eta are the propagated degrees of freedom
200
201	double oldChi;
202	double prevChi;
203	double chi;
204	double NkBT;
205	double fkBT;
206
207	double tt2, tb2;
208	double instaTemp, instaPress, instaVol;
209	double press[3][3];
210
211	int Nparticles;
212
213	double integralOfChidt;
214
215	// targetTemp, targetPressure, and tauBarostat must be set.
216	// One of qmass or tauThermostat must be set;
217
218	double targetTemp;
219	double targetPressure;
220	double tauThermostat;
221	double tauBarostat;
222
223	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224	short int have_target_pressure;
225
226	double *oldPos;
227	double *oldVel;
228	double *oldJi;
229
230	double chiTolerance;
231	short int have_chi_tolerance;
232	double posIterTolerance;
233	short int have_pos_iter_tolerance;
234	double etaTolerance;
235	short int have_eta_tolerance;
236
237	};
238
239	template<typename T> class NPTi : public T{
240
241	public:
242	NPTi( SimInfo theInfo, ForceFields the_ff);
243	~NPTi();
244
245	virtual double getConservedQuantity(void);
246	virtual void resetIntegrator(void);
247	virtual string getAdditionalParameters(void);
248	protected:
249
250
251
252	virtual void evolveEtaA(void);
253	virtual void evolveEtaB(void);
254
255	virtual bool etaConverged( void );
256
257	virtual void scaleSimBox( void );
258
259	virtual void getVelScaleA( double sc[3], double vel[3] );
260	virtual void getVelScaleB( double sc[3], int index );
261	virtual void getPosScale(double pos[3], double COM[3],
262	int index, double sc[3]);
263
264	virtual void calcVelScale( void );
265
266	double eta, oldEta, prevEta;
267	double vScale;
268	};
269
270	template<typename T> class NPTf : public T{
271
272	public:
273
274	NPTf ( SimInfo theInfo, ForceFields the_ff);
275	virtual ~NPTf();
276
277	virtual double getConservedQuantity(void);
278	virtual string getAdditionalParameters(void);
279	virtual void resetIntegrator(void);
280
281	protected:
282
283	virtual void evolveEtaA(void);
284	virtual void evolveEtaB(void);
285
286	virtual bool etaConverged( void );
287
288	virtual void scaleSimBox( void );
289
290	virtual void getVelScaleA( double sc[3], double vel[3] );
291	virtual void getVelScaleB( double sc[3], int index );
292	virtual void getPosScale(double pos[3], double COM[3],
293	int index, double sc[3]);
294
295	virtual void calcVelScale( void );
296
297	double eta[3][3];
298	double oldEta[3][3];
299	double prevEta[3][3];
300	double vScale[3][3];
301	};
302
303	template<typename T> class NPTxyz : public T{
304
305	public:
306
307	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
308	virtual ~NPTxyz();
309
310	virtual double getConservedQuantity(void);
311	virtual string getAdditionalParameters(void);
312	virtual void resetIntegrator(void);
313
314	protected:
315
316	virtual void evolveEtaA(void);
317	virtual void evolveEtaB(void);
318
319	virtual bool etaConverged( void );
320
321	virtual void scaleSimBox( void );
322
323	virtual void getVelScaleA( double sc[3], double vel[3] );
324	virtual void getVelScaleB( double sc[3], int index );
325	virtual void getPosScale(double pos[3], double COM[3],
326	int index, double sc[3]);
327
328	virtual void calcVelScale( void );
329
330	double eta[3][3];
331	double oldEta[3][3];
332	double prevEta[3][3];
333	double vScale[3][3];
334	};
335
336
337	template<typename T> class ZConstraint : public T {
338
339	public:
340	class ForceSubtractionPolicy{
341	public:
342	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343
344	virtual void update() = 0;
345	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349
350	protected:
351	ZConstraint<T>* zconsIntegrator;
352	};
353
354	class PolicyByNumber : public ForceSubtractionPolicy{
355
356	public:
357	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358	virtual void update();
359	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363
364	private:
365	int totNumOfMovingAtoms;
366	};
367
368	class PolicyByMass : public ForceSubtractionPolicy{
369
370	public:
371	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372
373	virtual void update();
374	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
377	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
378
379	private:
380	double totMassOfMovingAtoms;
381	};
382
383	public:
384
385	ZConstraint( SimInfo theInfo, ForceFields the_ff);
386	~ZConstraint();
387
388	void setZConsTime(double time) {this->zconsTime = time;}
389	void getZConsTime() {return zconsTime;}
390
391	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
393
394	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
395	string getZConsOutput() {return zconsOutput;}
396
397	virtual void integrate();
398
399
400	#ifdef IS_MPI
401	virtual void update(); //which is called to indicate the molecules' migration
402	#endif
403
404	enum ZConsState {zcsMoving, zcsFixed};
405
406	vector<Molecule*> zconsMols; //z-constraint molecules array
407	vector<ZConsState> states; //state of z-constraint molecules
408
409
410
411	int totNumOfUnconsAtoms; //total number of uncontraint atoms
412	double totalMassOfUncons; //total mas of unconstraint molecules
413
414
415	protected:
416
417
418
419	virtual void calcForce( int calcPot, int calcStress );
420	virtual void thermalize(void);
421
422	void zeroOutVel();
423	void doZconstraintForce();
424	void doHarmonic(vector<double>& resPos);
425	bool checkZConsState();
426
427	bool haveFixedZMols();
428	bool haveMovingZMols();
429
430	double calcZSys();
431
432	int isZConstraintMol(Molecule* mol);
433
434
435	double zconsTime; //sample time
436	double zconsTol; //tolerance of z-contratint
437	double zForceConst; //base force constant term
438	//which is estimate by OOPSE
439
440
441	vector<double> massOfZConsMols; //mass of z-constraint molecule
442	vector<double> kz; //force constant array
443
444	vector<double> zPos; //
445
446
447	vector<Molecule*> unconsMols; //unconstraint molecules array
448	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
449
450
451	vector<ZConsParaItem>* parameters; //
452
453	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
454
455	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
456	vector<double> fz;
457	vector<double> curZPos;
458
459	bool usingSMD;
460	vector<double> prevCantPos;
461	vector<double> cantPos;
462	vector<double> cantVel;
463
464	double zconsFixTime;
465	double zconsGap;
466	bool hasZConsGap;
467	vector<double> endFixTime;
468
469	int whichDirection; //constraint direction
470
471	private:
472
473	string zconsOutput; //filename of zconstraint output
474	ZConsWriter* fzOut; //z-constraint writer
475
476	double curZconsTime;
477
478	double calcMovingMolsCOMVel();
479	double calcSysCOMVel();
480	double calcTotalForce();
481	void updateZPos();
482	void updateCantPos();
483
484	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
485	friend class ForceSubtractionPolicy;
486
487	};
488
489	/*
490	template<typename T> class SingleZConstrain : public T{
491
492
493	};
494	*/
495
496	template<typename T> class NonEquMD : public T {
497	public:
498
499
500
501	};
502
503
504	//
505	template<typename T> class SingleZConstraint : public T{
506	public:
507	SingleZConstraint(SimInfo theInfo, ForceFields the_ff);
508	~SingleZConstraint();
509
510	bool stopIntegrator();
511
512	protected:
513
514	};
515
516	//Steered Molecular Dynamics, curret implement only support one steered molecule
517	template<typename T> class SMD : public T{
518	public:
519	SMD( SimInfo theInfo, ForceFields the_ff);
520	~SMD();
521
522	virtual void integrate();
523	virtual void calcForce( int calcPot, int calcStress );
524	bool stopIntegrator();
525	private:
526
527	};
528
529	//By using state pattern, Coordinate Drive is responsible for switching back and forth between
530	//Driven Molecular Dynamics and ZConstraint Method.
531	template<typename T> class CoordinateDriver : public T {
532	public:
533	typedef T ParentIntegrator;
534
535	CoordinateDriver(SimInfo, ForceFields, BaseIntegrator, BaseIntegrator);
536	~CoordinateDriver();
537
538	virtual void integrate();
539
540	private:
541	BaseIntegrator* zconsIntegrator;
542	BaseIntegrator* drivenIntegrator;
543
544	};
545
546	#endif