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;

class VelVerletConsFramework;
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;

  VelVerletConsFramework* consFramework;

  //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;

};


//Sympletic quaternion Scheme Integrator
//Reference:
// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
//Symplectic quaternion Scheme for biophysical molecular dynamics
//116(20), 8649, J. Chem. Phys. (2002)
template<typename T> class SQSIntegrator : public T{
  public:
    virtual void moveA();
    virtual void moveB();
  protected:
    void freeRotor();
    void rotate(int k, double dt);
    
};
#endif
Revision:	1330
Committed:	Fri Jul 16 16:29:44 2004 UTC (20 years, 9 months ago) by gezelter
File size:	13726 byte(s)
Log Message:	Minor changes
#	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	class VelVerletConsFramework;
26	template<typename T = BaseIntegrator> class Integrator : public T {
27
28	public:
29	Integrator( SimInfo theInfo, ForceFields the_ff );
30	virtual ~Integrator();
31	void integrate( void );
32	virtual double getConservedQuantity(void);
33	virtual string getAdditionalParameters(void);
34
35	protected:
36
37	virtual void integrateStep( int calcPot, int calcStress );
38	//virtual void preMove( void );
39	virtual void moveA( void );
40	virtual void moveB( void );
41	//virtual void constrainA( void );
42	//virtual void constrainB( void );
43	virtual int readyCheck( void ) { return 1; }
44
45	virtual void resetIntegrator( void ) { }
46
47	virtual void calcForce( int calcPot, int calcStress );
48	virtual void thermalize();
49
50	virtual bool stopIntegrator() {return false;}
51
52	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53
54	//void checkConstraints( void );
55	void rotate( int axes1, int axes2, double angle, double j[3],
56	double A[3][3] );
57
58	ForceFields* myFF;
59
60	SimInfo *info; // all the info we'll ever need
61	vector<StuntDouble*> integrableObjects;
62	int nAtoms; /* the number of atoms */
63	int oldAtoms;
64	Atom *atoms; / array of atom pointers */
65	Molecule* molecules;
66	int nMols;
67
68	VelVerletConsFramework* consFramework;
69
70	//int isConstrained; // boolean to know whether the systems contains constraints.
71	//int nConstrained; // counter for number of constraints
72	//int *constrainedA; // the i of a constraint pair
73	//int *constrainedB; // the j of a constraint pair
74	//double *constrainedDsqr; // the square of the constraint distance
75
76	//int* moving; // tells whether we are moving atom i
77	//int* moved; // tells whether we have moved atom i
78	//double* oldPos; // pre constrained positions
79
80	short isFirst; /boolean for the first time integrate is called /
81
82	double dt;
83	double dt2;
84
85	Thermo *tStats;
86	StatWriter* statOut;
87	DumpWriter* dumpOut;
88
89	};
90
91	typedef Integrator<BaseIntegrator> RealIntegrator;
92
93	// ansi instantiation
94	// template class Integrator<BaseIntegrator>;
95
96
97	template<typename T> class NVE : public T {
98
99	public:
100	NVE ( SimInfo theInfo, ForceFields the_ff ):
101	T( theInfo, the_ff ){}
102	virtual ~NVE(){}
103	};
104
105
106	template<typename T> class NVT : public T {
107
108	public:
109
110	NVT ( SimInfo theInfo, ForceFields the_ff);
111	virtual ~NVT();
112
113	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
114	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
115	void setChiTolerance(double tol) {chiTolerance = tol;}
116	virtual double getConservedQuantity(void);
117	virtual string getAdditionalParameters(void);
118
119	protected:
120
121	virtual void moveA( void );
122	virtual void moveB( void );
123
124	virtual int readyCheck();
125
126	virtual void resetIntegrator( void );
127
128	// chi is a propagated degree of freedom.
129
130	double chi;
131
132	//integral of chi(t)dt
133	double integralOfChidt;
134
135	// targetTemp must be set. tauThermostat must also be set;
136
137	double targetTemp;
138	double tauThermostat;
139
140	short int have_tau_thermostat, have_target_temp;
141
142	double *oldVel;
143	double *oldJi;
144
145	double chiTolerance;
146	short int have_chi_tolerance;
147
148	};
149
150
151
152	template<typename T> class NPT : public T{
153
154	public:
155
156	NPT ( SimInfo theInfo, ForceFields the_ff);
157	virtual ~NPT();
158
159	virtual void integrateStep( int calcPot, int calcStress ){
160	calcStress = 1;
161	T::integrateStep( calcPot, calcStress );
162	}
163
164	virtual double getConservedQuantity(void) = 0;
165	virtual string getAdditionalParameters(void) = 0;
166
167	double myTauThermo( void ) { return tauThermostat; }
168	double myTauBaro( void ) { return tauBarostat; }
169
170	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
175	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
176	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
177
178	protected:
179
180	virtual void moveA( void );
181	virtual void moveB( void );
182
183	virtual int readyCheck();
184
185	virtual void resetIntegrator( void );
186
187	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
188	virtual void getVelScaleB( double sc[3], int index ) = 0;
189	virtual void getPosScale(double pos[3], double COM[3],
190	int index, double sc[3]) = 0;
191
192	virtual void calcVelScale( void ) = 0;
193
194	virtual bool chiConverged( void );
195	virtual bool etaConverged( void ) = 0;
196
197	virtual void evolveChiA( void );
198	virtual void evolveEtaA( void ) = 0;
199	virtual void evolveChiB( void );
200	virtual void evolveEtaB( void ) = 0;
201
202	virtual void scaleSimBox( void ) = 0;
203
204	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
205
206	// chi and eta are the propagated degrees of freedom
207
208	double oldChi;
209	double prevChi;
210	double chi;
211	double NkBT;
212	double fkBT;
213
214	double tt2, tb2;
215	double instaTemp, instaPress, instaVol;
216	double press[3][3];
217
218	int Nparticles;
219
220	double integralOfChidt;
221
222	// targetTemp, targetPressure, and tauBarostat must be set.
223	// One of qmass or tauThermostat must be set;
224
225	double targetTemp;
226	double targetPressure;
227	double tauThermostat;
228	double tauBarostat;
229
230	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
231	short int have_target_pressure;
232
233	double *oldPos;
234	double *oldVel;
235	double *oldJi;
236
237	double chiTolerance;
238	short int have_chi_tolerance;
239	double posIterTolerance;
240	short int have_pos_iter_tolerance;
241	double etaTolerance;
242	short int have_eta_tolerance;
243
244	};
245
246	template<typename T> class NPTi : public T{
247
248	public:
249	NPTi( SimInfo theInfo, ForceFields the_ff);
250	~NPTi();
251
252	virtual double getConservedQuantity(void);
253	virtual void resetIntegrator(void);
254	virtual string getAdditionalParameters(void);
255	protected:
256
257
258
259	virtual void evolveEtaA(void);
260	virtual void evolveEtaB(void);
261
262	virtual bool etaConverged( void );
263
264	virtual void scaleSimBox( void );
265
266	virtual void getVelScaleA( double sc[3], double vel[3] );
267	virtual void getVelScaleB( double sc[3], int index );
268	virtual void getPosScale(double pos[3], double COM[3],
269	int index, double sc[3]);
270
271	virtual void calcVelScale( void );
272
273	double eta, oldEta, prevEta;
274	double vScale;
275	};
276
277	template<typename T> class NPTf : public T{
278
279	public:
280
281	NPTf ( SimInfo theInfo, ForceFields the_ff);
282	virtual ~NPTf();
283
284	virtual double getConservedQuantity(void);
285	virtual string getAdditionalParameters(void);
286	virtual void resetIntegrator(void);
287
288	protected:
289
290	virtual void evolveEtaA(void);
291	virtual void evolveEtaB(void);
292
293	virtual bool etaConverged( void );
294
295	virtual void scaleSimBox( void );
296
297	virtual void getVelScaleA( double sc[3], double vel[3] );
298	virtual void getVelScaleB( double sc[3], int index );
299	virtual void getPosScale(double pos[3], double COM[3],
300	int index, double sc[3]);
301
302	virtual void calcVelScale( void );
303
304	double eta[3][3];
305	double oldEta[3][3];
306	double prevEta[3][3];
307	double vScale[3][3];
308	};
309
310	template<typename T> class NPTxyz : public T{
311
312	public:
313
314	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
315	virtual ~NPTxyz();
316
317	virtual double getConservedQuantity(void);
318	virtual string getAdditionalParameters(void);
319	virtual void resetIntegrator(void);
320
321	protected:
322
323	virtual void evolveEtaA(void);
324	virtual void evolveEtaB(void);
325
326	virtual bool etaConverged( void );
327
328	virtual void scaleSimBox( void );
329
330	virtual void getVelScaleA( double sc[3], double vel[3] );
331	virtual void getVelScaleB( double sc[3], int index );
332	virtual void getPosScale(double pos[3], double COM[3],
333	int index, double sc[3]);
334
335	virtual void calcVelScale( void );
336
337	double eta[3][3];
338	double oldEta[3][3];
339	double prevEta[3][3];
340	double vScale[3][3];
341	};
342
343
344	template<typename T> class ZConstraint : public T {
345
346	public:
347	class ForceSubtractionPolicy{
348	public:
349	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
350
351	virtual void update() = 0;
352	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
354	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
356
357	protected:
358	ZConstraint<T>* zconsIntegrator;
359	};
360
361	class PolicyByNumber : public ForceSubtractionPolicy{
362
363	public:
364	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
365	virtual void update();
366	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
367	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
368	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
369	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
370
371	private:
372	int totNumOfMovingAtoms;
373	};
374
375	class PolicyByMass : public ForceSubtractionPolicy{
376
377	public:
378	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
379
380	virtual void update();
381	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385
386	private:
387	double totMassOfMovingAtoms;
388	};
389
390	public:
391
392	ZConstraint( SimInfo theInfo, ForceFields the_ff);
393	~ZConstraint();
394
395	void setZConsTime(double time) {this->zconsTime = time;}
396	void getZConsTime() {return zconsTime;}
397
398	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
400
401	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
402	string getZConsOutput() {return zconsOutput;}
403
404	virtual void integrate();
405
406
407	#ifdef IS_MPI
408	virtual void update(); //which is called to indicate the molecules' migration
409	#endif
410
411	enum ZConsState {zcsMoving, zcsFixed};
412
413	vector<Molecule*> zconsMols; //z-constraint molecules array
414	vector<ZConsState> states; //state of z-constraint molecules
415
416
417
418	int totNumOfUnconsAtoms; //total number of uncontraint atoms
419	double totalMassOfUncons; //total mas of unconstraint molecules
420
421
422	protected:
423
424
425
426	virtual void calcForce( int calcPot, int calcStress );
427	virtual void thermalize(void);
428
429	void zeroOutVel();
430	void doZconstraintForce();
431	void doHarmonic(vector<double>& resPos);
432	bool checkZConsState();
433
434	bool haveFixedZMols();
435	bool haveMovingZMols();
436
437	double calcZSys();
438
439	int isZConstraintMol(Molecule* mol);
440
441
442	double zconsTime; //sample time
443	double zconsTol; //tolerance of z-contratint
444	double zForceConst; //base force constant term
445	//which is estimate by OOPSE
446
447
448	vector<double> massOfZConsMols; //mass of z-constraint molecule
449	vector<double> kz; //force constant array
450
451	vector<double> zPos; //
452
453
454	vector<Molecule*> unconsMols; //unconstraint molecules array
455	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
456
457
458	vector<ZConsParaItem>* parameters; //
459
460	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
461
462	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
463	vector<double> fz;
464	vector<double> curZPos;
465
466	bool usingSMD;
467	vector<double> prevCantPos;
468	vector<double> cantPos;
469	vector<double> cantVel;
470
471	double zconsFixTime;
472	double zconsGap;
473	bool hasZConsGap;
474	vector<double> endFixTime;
475
476	int whichDirection; //constraint direction
477
478	private:
479
480	string zconsOutput; //filename of zconstraint output
481	ZConsWriter* fzOut; //z-constraint writer
482
483	double curZconsTime;
484
485	double calcMovingMolsCOMVel();
486	double calcSysCOMVel();
487	double calcTotalForce();
488	void updateZPos();
489	void updateCantPos();
490
491	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
492	friend class ForceSubtractionPolicy;
493
494	};
495
496
497	//Sympletic quaternion Scheme Integrator
498	//Reference:
499	// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500	//Symplectic quaternion Scheme for biophysical molecular dynamics
501	//116(20), 8649, J. Chem. Phys. (2002)
502	template<typename T> class SQSIntegrator : public T{
503	public:
504	virtual void moveA();
505	virtual void moveB();
506	protected:
507	void freeRotor();
508	void rotate(int k, double dt);
509
510	};
511	#endif