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 RattleFramework;
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;

  RattleFramework* rattle;

  //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:	1254
Committed:	Wed Jun 9 16:16:33 2004 UTC (21 years, 4 months ago) by tim
File size:	13701 byte(s)
Log Message:	1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3) these classes use anonymous union and struct to support double[3], double[3][3] and double[4] 2. adding roll constraint algorithm
#	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 RattleFramework;
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	RattleFramework* rattle;
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	template<typename T> class NVE : public T {
97
98	public:
99	NVE ( SimInfo theInfo, ForceFields the_ff ):
100	T( theInfo, the_ff ){}
101	virtual ~NVE(){}
102	};
103
104
105	template<typename T> class NVT : public T {
106
107	public:
108
109	NVT ( SimInfo theInfo, ForceFields the_ff);
110	virtual ~NVT();
111
112	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
113	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
114	void setChiTolerance(double tol) {chiTolerance = tol;}
115	virtual double getConservedQuantity(void);
116	virtual string getAdditionalParameters(void);
117
118	protected:
119
120	virtual void moveA( void );
121	virtual void moveB( void );
122
123	virtual int readyCheck();
124
125	virtual void resetIntegrator( void );
126
127	// chi is a propagated degree of freedom.
128
129	double chi;
130
131	//integral of chi(t)dt
132	double integralOfChidt;
133
134	// targetTemp must be set. tauThermostat must also be set;
135
136	double targetTemp;
137	double tauThermostat;
138
139	short int have_tau_thermostat, have_target_temp;
140
141	double *oldVel;
142	double *oldJi;
143
144	double chiTolerance;
145	short int have_chi_tolerance;
146
147	};
148
149
150
151	template<typename T> class NPT : public T{
152
153	public:
154
155	NPT ( SimInfo theInfo, ForceFields the_ff);
156	virtual ~NPT();
157
158	virtual void integrateStep( int calcPot, int calcStress ){
159	calcStress = 1;
160	T::integrateStep( calcPot, calcStress );
161	}
162
163	virtual double getConservedQuantity(void) = 0;
164	virtual string getAdditionalParameters(void) = 0;
165
166	double myTauThermo( void ) { return tauThermostat; }
167	double myTauBaro( void ) { return tauBarostat; }
168
169	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
174	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
175	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
176
177	protected:
178
179	virtual void moveA( void );
180	virtual void moveB( void );
181
182	virtual int readyCheck();
183
184	virtual void resetIntegrator( void );
185
186	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
187	virtual void getVelScaleB( double sc[3], int index ) = 0;
188	virtual void getPosScale(double pos[3], double COM[3],
189	int index, double sc[3]) = 0;
190
191	virtual void calcVelScale( void ) = 0;
192
193	virtual bool chiConverged( void );
194	virtual bool etaConverged( void ) = 0;
195
196	virtual void evolveChiA( void );
197	virtual void evolveEtaA( void ) = 0;
198	virtual void evolveChiB( void );
199	virtual void evolveEtaB( void ) = 0;
200
201	virtual void scaleSimBox( void ) = 0;
202
203	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
204
205	// chi and eta are the propagated degrees of freedom
206
207	double oldChi;
208	double prevChi;
209	double chi;
210	double NkBT;
211	double fkBT;
212
213	double tt2, tb2;
214	double instaTemp, instaPress, instaVol;
215	double press[3][3];
216
217	int Nparticles;
218
219	double integralOfChidt;
220
221	// targetTemp, targetPressure, and tauBarostat must be set.
222	// One of qmass or tauThermostat must be set;
223
224	double targetTemp;
225	double targetPressure;
226	double tauThermostat;
227	double tauBarostat;
228
229	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
230	short int have_target_pressure;
231
232	double *oldPos;
233	double *oldVel;
234	double *oldJi;
235
236	double chiTolerance;
237	short int have_chi_tolerance;
238	double posIterTolerance;
239	short int have_pos_iter_tolerance;
240	double etaTolerance;
241	short int have_eta_tolerance;
242
243	};
244
245	template<typename T> class NPTi : public T{
246
247	public:
248	NPTi( SimInfo theInfo, ForceFields the_ff);
249	~NPTi();
250
251	virtual double getConservedQuantity(void);
252	virtual void resetIntegrator(void);
253	virtual string getAdditionalParameters(void);
254	protected:
255
256
257
258	virtual void evolveEtaA(void);
259	virtual void evolveEtaB(void);
260
261	virtual bool etaConverged( void );
262
263	virtual void scaleSimBox( void );
264
265	virtual void getVelScaleA( double sc[3], double vel[3] );
266	virtual void getVelScaleB( double sc[3], int index );
267	virtual void getPosScale(double pos[3], double COM[3],
268	int index, double sc[3]);
269
270	virtual void calcVelScale( void );
271
272	double eta, oldEta, prevEta;
273	double vScale;
274	};
275
276	template<typename T> class NPTf : public T{
277
278	public:
279
280	NPTf ( SimInfo theInfo, ForceFields the_ff);
281	virtual ~NPTf();
282
283	virtual double getConservedQuantity(void);
284	virtual string getAdditionalParameters(void);
285	virtual void resetIntegrator(void);
286
287	protected:
288
289	virtual void evolveEtaA(void);
290	virtual void evolveEtaB(void);
291
292	virtual bool etaConverged( void );
293
294	virtual void scaleSimBox( void );
295
296	virtual void getVelScaleA( double sc[3], double vel[3] );
297	virtual void getVelScaleB( double sc[3], int index );
298	virtual void getPosScale(double pos[3], double COM[3],
299	int index, double sc[3]);
300
301	virtual void calcVelScale( void );
302
303	double eta[3][3];
304	double oldEta[3][3];
305	double prevEta[3][3];
306	double vScale[3][3];
307	};
308
309	template<typename T> class NPTxyz : public T{
310
311	public:
312
313	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
314	virtual ~NPTxyz();
315
316	virtual double getConservedQuantity(void);
317	virtual string getAdditionalParameters(void);
318	virtual void resetIntegrator(void);
319
320	protected:
321
322	virtual void evolveEtaA(void);
323	virtual void evolveEtaB(void);
324
325	virtual bool etaConverged( void );
326
327	virtual void scaleSimBox( void );
328
329	virtual void getVelScaleA( double sc[3], double vel[3] );
330	virtual void getVelScaleB( double sc[3], int index );
331	virtual void getPosScale(double pos[3], double COM[3],
332	int index, double sc[3]);
333
334	virtual void calcVelScale( void );
335
336	double eta[3][3];
337	double oldEta[3][3];
338	double prevEta[3][3];
339	double vScale[3][3];
340	};
341
342
343	template<typename T> class ZConstraint : public T {
344
345	public:
346	class ForceSubtractionPolicy{
347	public:
348	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349
350	virtual void update() = 0;
351	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
353	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
354	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
355
356	protected:
357	ZConstraint<T>* zconsIntegrator;
358	};
359
360	class PolicyByNumber : public ForceSubtractionPolicy{
361
362	public:
363	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
364	virtual void update();
365	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
366	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
367	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
368	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
369
370	private:
371	int totNumOfMovingAtoms;
372	};
373
374	class PolicyByMass : public ForceSubtractionPolicy{
375
376	public:
377	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
378
379	virtual void update();
380	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
381	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
382	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
383	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
384
385	private:
386	double totMassOfMovingAtoms;
387	};
388
389	public:
390
391	ZConstraint( SimInfo theInfo, ForceFields the_ff);
392	~ZConstraint();
393
394	void setZConsTime(double time) {this->zconsTime = time;}
395	void getZConsTime() {return zconsTime;}
396
397	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
398	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
399
400	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
401	string getZConsOutput() {return zconsOutput;}
402
403	virtual void integrate();
404
405
406	#ifdef IS_MPI
407	virtual void update(); //which is called to indicate the molecules' migration
408	#endif
409
410	enum ZConsState {zcsMoving, zcsFixed};
411
412	vector<Molecule*> zconsMols; //z-constraint molecules array
413	vector<ZConsState> states; //state of z-constraint molecules
414
415
416
417	int totNumOfUnconsAtoms; //total number of uncontraint atoms
418	double totalMassOfUncons; //total mas of unconstraint molecules
419
420
421	protected:
422
423
424
425	virtual void calcForce( int calcPot, int calcStress );
426	virtual void thermalize(void);
427
428	void zeroOutVel();
429	void doZconstraintForce();
430	void doHarmonic(vector<double>& resPos);
431	bool checkZConsState();
432
433	bool haveFixedZMols();
434	bool haveMovingZMols();
435
436	double calcZSys();
437
438	int isZConstraintMol(Molecule* mol);
439
440
441	double zconsTime; //sample time
442	double zconsTol; //tolerance of z-contratint
443	double zForceConst; //base force constant term
444	//which is estimate by OOPSE
445
446
447	vector<double> massOfZConsMols; //mass of z-constraint molecule
448	vector<double> kz; //force constant array
449
450	vector<double> zPos; //
451
452
453	vector<Molecule*> unconsMols; //unconstraint molecules array
454	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
455
456
457	vector<ZConsParaItem>* parameters; //
458
459	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
460
461	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
462	vector<double> fz;
463	vector<double> curZPos;
464
465	bool usingSMD;
466	vector<double> prevCantPos;
467	vector<double> cantPos;
468	vector<double> cantVel;
469
470	double zconsFixTime;
471	double zconsGap;
472	bool hasZConsGap;
473	vector<double> endFixTime;
474
475	int whichDirection; //constraint direction
476
477	private:
478
479	string zconsOutput; //filename of zconstraint output
480	ZConsWriter* fzOut; //z-constraint writer
481
482	double curZconsTime;
483
484	double calcMovingMolsCOMVel();
485	double calcSysCOMVel();
486	double calcTotalForce();
487	void updateZPos();
488	void updateCantPos();
489
490	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
491	friend class ForceSubtractionPolicy;
492
493	};
494
495
496	//Sympletic quaternion Scheme Integrator
497	//Reference:
498	// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
499	//Symplectic quaternion Scheme for biophysical molecular dynamics
500	//116(20), 8649, J. Chem. Phys. (2002)
501	template<typename T> class SQSIntegrator : public T{
502	public:
503	virtual void moveA();
504	virtual void moveB();
505	protected:
506	void freeRotor();
507	void rotate(int k, double dt);
508
509	};
510	#endif