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"
#include "Quaternion.hpp"
#include "Mat4x4d.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] );

  void printQuaternion(StuntDouble* sd);
  Mat4x4d getS(const Quaternion& q);

  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:
    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
    virtual void moveA();
    virtual void moveB();
  protected:
    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
  private:
    Quaternion getPk(int i, const Vector4d& q);
    Mat4x4d getS(const Quaternion& q);
    vector<Quaternion> q;
    vector<Vector4d> p_qua;
    vector<double> I0;

                Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
                Vector4d j2p(const Vector4d& j, Mat4x4d& m);
};
#endif
Revision:	1452
Committed:	Mon Aug 23 15:11:36 2004 UTC (19 years, 10 months ago) by tim
File size:	14280 byte(s)
Log Message:	* empty log message *
#	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	#include "Quaternion.hpp"
18	#include "Mat4x4d.hpp"
19
20	using namespace std;
21	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
22	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
23	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
24	const int maxIteration = 300;
25	const double tol = 1.0e-6;
26
27	class VelVerletConsFramework;
28	template<typename T = BaseIntegrator> class Integrator : public T {
29
30	public:
31	Integrator( SimInfo theInfo, ForceFields the_ff );
32	virtual ~Integrator();
33	void integrate( void );
34	virtual double getConservedQuantity(void);
35	virtual string getAdditionalParameters(void);
36
37	protected:
38
39	virtual void integrateStep( int calcPot, int calcStress );
40	//virtual void preMove( void );
41	virtual void moveA( void );
42	virtual void moveB( void );
43	//virtual void constrainA( void );
44	//virtual void constrainB( void );
45	virtual int readyCheck( void ) { return 1; }
46
47	virtual void resetIntegrator( void ) { }
48
49	virtual void calcForce( int calcPot, int calcStress );
50	virtual void thermalize();
51
52	virtual bool stopIntegrator() {return false;}
53
54	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
55
56	//void checkConstraints( void );
57	void rotate( int axes1, int axes2, double angle, double j[3],
58	double A[3][3] );
59
60	void printQuaternion(StuntDouble* sd);
61	Mat4x4d getS(const Quaternion& q);
62
63	ForceFields* myFF;
64
65	SimInfo *info; // all the info we'll ever need
66	vector<StuntDouble*> integrableObjects;
67	int nAtoms; /* the number of atoms */
68	int oldAtoms;
69	Atom *atoms; / array of atom pointers */
70	Molecule* molecules;
71	int nMols;
72
73	VelVerletConsFramework* consFramework;
74
75	//int isConstrained; // boolean to know whether the systems contains constraints.
76	//int nConstrained; // counter for number of constraints
77	//int *constrainedA; // the i of a constraint pair
78	//int *constrainedB; // the j of a constraint pair
79	//double *constrainedDsqr; // the square of the constraint distance
80
81	//int* moving; // tells whether we are moving atom i
82	//int* moved; // tells whether we have moved atom i
83	//double* oldPos; // pre constrained positions
84
85	short isFirst; /boolean for the first time integrate is called /
86
87	double dt;
88	double dt2;
89
90	Thermo *tStats;
91	StatWriter* statOut;
92	DumpWriter* dumpOut;
93
94	};
95
96	typedef Integrator<BaseIntegrator> RealIntegrator;
97
98	// ansi instantiation
99	// template class Integrator<BaseIntegrator>;
100
101
102	template<typename T> class NVE : public T {
103
104	public:
105	NVE ( SimInfo theInfo, ForceFields the_ff ):
106	T( theInfo, the_ff ){}
107	virtual ~NVE(){}
108	};
109
110
111	template<typename T> class NVT : public T {
112
113	public:
114
115	NVT ( SimInfo theInfo, ForceFields the_ff);
116	virtual ~NVT();
117
118	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
119	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
120	void setChiTolerance(double tol) {chiTolerance = tol;}
121	virtual double getConservedQuantity(void);
122	virtual string getAdditionalParameters(void);
123
124	protected:
125
126	virtual void moveA( void );
127	virtual void moveB( void );
128
129	virtual int readyCheck();
130
131	virtual void resetIntegrator( void );
132
133	// chi is a propagated degree of freedom.
134
135	double chi;
136
137	//integral of chi(t)dt
138	double integralOfChidt;
139
140	// targetTemp must be set. tauThermostat must also be set;
141
142	double targetTemp;
143	double tauThermostat;
144
145	short int have_tau_thermostat, have_target_temp;
146
147	double *oldVel;
148	double *oldJi;
149
150	double chiTolerance;
151	short int have_chi_tolerance;
152
153	};
154
155
156
157	template<typename T> class NPT : public T{
158
159	public:
160
161	NPT ( SimInfo theInfo, ForceFields the_ff);
162	virtual ~NPT();
163
164	virtual void integrateStep( int calcPot, int calcStress ){
165	calcStress = 1;
166	T::integrateStep( calcPot, calcStress );
167	}
168
169	virtual double getConservedQuantity(void) = 0;
170	virtual string getAdditionalParameters(void) = 0;
171
172	double myTauThermo( void ) { return tauThermostat; }
173	double myTauBaro( void ) { return tauBarostat; }
174
175	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
180	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
181	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
182
183	protected:
184
185	virtual void moveA( void );
186	virtual void moveB( void );
187
188	virtual int readyCheck();
189
190	virtual void resetIntegrator( void );
191
192	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
193	virtual void getVelScaleB( double sc[3], int index ) = 0;
194	virtual void getPosScale(double pos[3], double COM[3],
195	int index, double sc[3]) = 0;
196
197	virtual void calcVelScale( void ) = 0;
198
199	virtual bool chiConverged( void );
200	virtual bool etaConverged( void ) = 0;
201
202	virtual void evolveChiA( void );
203	virtual void evolveEtaA( void ) = 0;
204	virtual void evolveChiB( void );
205	virtual void evolveEtaB( void ) = 0;
206
207	virtual void scaleSimBox( void ) = 0;
208
209	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
210
211	// chi and eta are the propagated degrees of freedom
212
213	double oldChi;
214	double prevChi;
215	double chi;
216	double NkBT;
217	double fkBT;
218
219	double tt2, tb2;
220	double instaTemp, instaPress, instaVol;
221	double press[3][3];
222
223	int Nparticles;
224
225	double integralOfChidt;
226
227	// targetTemp, targetPressure, and tauBarostat must be set.
228	// One of qmass or tauThermostat must be set;
229
230	double targetTemp;
231	double targetPressure;
232	double tauThermostat;
233	double tauBarostat;
234
235	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
236	short int have_target_pressure;
237
238	double *oldPos;
239	double *oldVel;
240	double *oldJi;
241
242	double chiTolerance;
243	short int have_chi_tolerance;
244	double posIterTolerance;
245	short int have_pos_iter_tolerance;
246	double etaTolerance;
247	short int have_eta_tolerance;
248
249	};
250
251	template<typename T> class NPTi : public T{
252
253	public:
254	NPTi( SimInfo theInfo, ForceFields the_ff);
255	~NPTi();
256
257	virtual double getConservedQuantity(void);
258	virtual void resetIntegrator(void);
259	virtual string getAdditionalParameters(void);
260	protected:
261
262
263
264	virtual void evolveEtaA(void);
265	virtual void evolveEtaB(void);
266
267	virtual bool etaConverged( void );
268
269	virtual void scaleSimBox( void );
270
271	virtual void getVelScaleA( double sc[3], double vel[3] );
272	virtual void getVelScaleB( double sc[3], int index );
273	virtual void getPosScale(double pos[3], double COM[3],
274	int index, double sc[3]);
275
276	virtual void calcVelScale( void );
277
278	double eta, oldEta, prevEta;
279	double vScale;
280	};
281
282	template<typename T> class NPTf : public T{
283
284	public:
285
286	NPTf ( SimInfo theInfo, ForceFields the_ff);
287	virtual ~NPTf();
288
289	virtual double getConservedQuantity(void);
290	virtual string getAdditionalParameters(void);
291	virtual void resetIntegrator(void);
292
293	protected:
294
295	virtual void evolveEtaA(void);
296	virtual void evolveEtaB(void);
297
298	virtual bool etaConverged( void );
299
300	virtual void scaleSimBox( void );
301
302	virtual void getVelScaleA( double sc[3], double vel[3] );
303	virtual void getVelScaleB( double sc[3], int index );
304	virtual void getPosScale(double pos[3], double COM[3],
305	int index, double sc[3]);
306
307	virtual void calcVelScale( void );
308
309	double eta[3][3];
310	double oldEta[3][3];
311	double prevEta[3][3];
312	double vScale[3][3];
313	};
314
315	template<typename T> class NPTxyz : public T{
316
317	public:
318
319	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
320	virtual ~NPTxyz();
321
322	virtual double getConservedQuantity(void);
323	virtual string getAdditionalParameters(void);
324	virtual void resetIntegrator(void);
325
326	protected:
327
328	virtual void evolveEtaA(void);
329	virtual void evolveEtaB(void);
330
331	virtual bool etaConverged( void );
332
333	virtual void scaleSimBox( void );
334
335	virtual void getVelScaleA( double sc[3], double vel[3] );
336	virtual void getVelScaleB( double sc[3], int index );
337	virtual void getPosScale(double pos[3], double COM[3],
338	int index, double sc[3]);
339
340	virtual void calcVelScale( void );
341
342	double eta[3][3];
343	double oldEta[3][3];
344	double prevEta[3][3];
345	double vScale[3][3];
346	};
347
348
349	template<typename T> class ZConstraint : public T {
350
351	public:
352	class ForceSubtractionPolicy{
353	public:
354	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
355
356	virtual void update() = 0;
357	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
358	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
359	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
360	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
361
362	protected:
363	ZConstraint<T>* zconsIntegrator;
364	};
365
366	class PolicyByNumber : public ForceSubtractionPolicy{
367
368	public:
369	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370	virtual void update();
371	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375
376	private:
377	int totNumOfMovingAtoms;
378	};
379
380	class PolicyByMass : public ForceSubtractionPolicy{
381
382	public:
383	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
384
385	virtual void update();
386	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
387	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
388	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
389	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
390
391	private:
392	double totMassOfMovingAtoms;
393	};
394
395	public:
396
397	ZConstraint( SimInfo theInfo, ForceFields the_ff);
398	~ZConstraint();
399
400	void setZConsTime(double time) {this->zconsTime = time;}
401	void getZConsTime() {return zconsTime;}
402
403	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
404	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
405
406	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
407	string getZConsOutput() {return zconsOutput;}
408
409	virtual void integrate();
410
411
412	#ifdef IS_MPI
413	virtual void update(); //which is called to indicate the molecules' migration
414	#endif
415
416	enum ZConsState {zcsMoving, zcsFixed};
417
418	vector<Molecule*> zconsMols; //z-constraint molecules array
419	vector<ZConsState> states; //state of z-constraint molecules
420
421
422
423	int totNumOfUnconsAtoms; //total number of uncontraint atoms
424	double totalMassOfUncons; //total mas of unconstraint molecules
425
426
427	protected:
428
429
430
431	virtual void calcForce( int calcPot, int calcStress );
432	virtual void thermalize(void);
433
434	void zeroOutVel();
435	void doZconstraintForce();
436	void doHarmonic(vector<double>& resPos);
437	bool checkZConsState();
438
439	bool haveFixedZMols();
440	bool haveMovingZMols();
441
442	double calcZSys();
443
444	int isZConstraintMol(Molecule* mol);
445
446
447	double zconsTime; //sample time
448	double zconsTol; //tolerance of z-contratint
449	double zForceConst; //base force constant term
450	//which is estimate by OOPSE
451
452
453	vector<double> massOfZConsMols; //mass of z-constraint molecule
454	vector<double> kz; //force constant array
455
456	vector<double> zPos; //
457
458
459	vector<Molecule*> unconsMols; //unconstraint molecules array
460	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
461
462
463	vector<ZConsParaItem>* parameters; //
464
465	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
466
467	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
468	vector<double> fz;
469	vector<double> curZPos;
470
471	bool usingSMD;
472	vector<double> prevCantPos;
473	vector<double> cantPos;
474	vector<double> cantVel;
475
476	double zconsFixTime;
477	double zconsGap;
478	bool hasZConsGap;
479	vector<double> endFixTime;
480
481	int whichDirection; //constraint direction
482
483	private:
484
485	string zconsOutput; //filename of zconstraint output
486	ZConsWriter* fzOut; //z-constraint writer
487
488	double curZconsTime;
489
490	double calcMovingMolsCOMVel();
491	double calcSysCOMVel();
492	double calcTotalForce();
493	void updateZPos();
494	void updateCantPos();
495
496	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
497	friend class ForceSubtractionPolicy;
498
499	};
500
501
502	//Sympletic quaternion Scheme Integrator
503	//Reference:
504	// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
505	//Symplectic quaternion Scheme for biophysical molecular dynamics
506	//116(20), 8649, J. Chem. Phys. (2002)
507	template<typename T> class SQSIntegrator : public T{
508	public:
509	SQSIntegrator( SimInfo theInfo, ForceFields the_ff );
510	virtual void moveA();
511	virtual void moveB();
512	protected:
513	void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
514	void rotate(int k, double dt, Quaternion& q, Vector4d& qdot, double Ik);
515	private:
516	Quaternion getPk(int i, const Vector4d& q);
517	Mat4x4d getS(const Quaternion& q);
518	vector<Quaternion> q;
519	vector<Vector4d> p_qua;
520	vector<double> I0;
521
522	Vector4d p2j(const Vector4d& p, Mat4x4d& m);
523	Vector4d j2p(const Vector4d& j, Mat4x4d& m);
524	};
525	#endif