src/integrators/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#include "primitives/Atom.hpp"
#include "primitives/StuntDouble.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/SRI.hpp"
#include "primitives/AbstractClasses.hpp"
#include "brains/SimInfo.hpp"
#include "UseTheForce/ForceFields.hpp"
#include "brains/Thermo.hpp"
#include "io/ReadWrite.hpp"
#include "io/ZConsWriter.hpp"
#include "restraints/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;


  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;
  RestraintWriter* restOut;
  RestraintReader* initRestraints;

};

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:	1772
Committed:	Tue Nov 23 22:48:31 2004 UTC (19 years, 7 months ago) by chrisfen
File size:	13822 byte(s)
Log Message:	Improvements to restraints
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "primitives/Atom.hpp"
7	#include "primitives/StuntDouble.hpp"
8	#include "primitives/Molecule.hpp"
9	#include "primitives/SRI.hpp"
10	#include "primitives/AbstractClasses.hpp"
11	#include "brains/SimInfo.hpp"
12	#include "UseTheForce/ForceFields.hpp"
13	#include "brains/Thermo.hpp"
14	#include "io/ReadWrite.hpp"
15	#include "io/ZConsWriter.hpp"
16	#include "restraints/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
69	int isConstrained; // boolean to know whether the systems contains constraints.
70	int nConstrained; // counter for number of constraints
71	int *constrainedA; // the i of a constraint pair
72	int *constrainedB; // the j of a constraint pair
73	double *constrainedDsqr; // the square of the constraint distance
74
75	int* moving; // tells whether we are moving atom i
76	int* moved; // tells whether we have moved atom i
77	double* oldPos; // pre constrained positions
78
79	short isFirst; /boolean for the first time integrate is called /
80
81	double dt;
82	double dt2;
83
84	Thermo *tStats;
85	StatWriter* statOut;
86	DumpWriter* dumpOut;
87	RestraintWriter* restOut;
88	RestraintReader* initRestraints;
89
90	};
91
92	typedef Integrator<BaseIntegrator> RealIntegrator;
93
94	// ansi instantiation
95	// template class Integrator<BaseIntegrator>;
96
97
98	template<typename T> class NVE : public T {
99
100	public:
101	NVE ( SimInfo theInfo, ForceFields the_ff ):
102	T( theInfo, the_ff ){}
103	virtual ~NVE(){}
104	};
105
106
107	template<typename T> class NVT : public T {
108
109	public:
110
111	NVT ( SimInfo theInfo, ForceFields the_ff);
112	virtual ~NVT();
113
114	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
115	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
116	void setChiTolerance(double tol) {chiTolerance = tol;}
117	virtual double getConservedQuantity(void);
118	virtual string getAdditionalParameters(void);
119
120	protected:
121
122	virtual void moveA( void );
123	virtual void moveB( void );
124
125	virtual int readyCheck();
126
127	virtual void resetIntegrator( void );
128
129	// chi is a propagated degree of freedom.
130
131	double chi;
132
133	//integral of chi(t)dt
134	double integralOfChidt;
135
136	// targetTemp must be set. tauThermostat must also be set;
137
138	double targetTemp;
139	double tauThermostat;
140
141	short int have_tau_thermostat, have_target_temp;
142
143	double *oldVel;
144	double *oldJi;
145
146	double chiTolerance;
147	short int have_chi_tolerance;
148
149	};
150
151
152
153	template<typename T> class NPT : public T{
154
155	public:
156
157	NPT ( SimInfo theInfo, ForceFields the_ff);
158	virtual ~NPT();
159
160	virtual void integrateStep( int calcPot, int calcStress ){
161	calcStress = 1;
162	T::integrateStep( calcPot, calcStress );
163	}
164
165	virtual double getConservedQuantity(void) = 0;
166	virtual string getAdditionalParameters(void) = 0;
167
168	double myTauThermo( void ) { return tauThermostat; }
169	double myTauBaro( void ) { return tauBarostat; }
170
171	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
172	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
173	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
174	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
175	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
176	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
177	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
178
179	protected:
180
181	virtual void moveA( void );
182	virtual void moveB( void );
183
184	virtual int readyCheck();
185
186	virtual void resetIntegrator( void );
187
188	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
189	virtual void getVelScaleB( double sc[3], int index ) = 0;
190	virtual void getPosScale(double pos[3], double COM[3],
191	int index, double sc[3]) = 0;
192
193	virtual void calcVelScale( void ) = 0;
194
195	virtual bool chiConverged( void );
196	virtual bool etaConverged( void ) = 0;
197
198	virtual void evolveChiA( void );
199	virtual void evolveEtaA( void ) = 0;
200	virtual void evolveChiB( void );
201	virtual void evolveEtaB( void ) = 0;
202
203	virtual void scaleSimBox( void ) = 0;
204
205	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
206
207	// chi and eta are the propagated degrees of freedom
208
209	double oldChi;
210	double prevChi;
211	double chi;
212	double NkBT;
213	double fkBT;
214
215	double tt2, tb2;
216	double instaTemp, instaPress, instaVol;
217	double press[3][3];
218
219	int Nparticles;
220
221	double integralOfChidt;
222
223	// targetTemp, targetPressure, and tauBarostat must be set.
224	// One of qmass or tauThermostat must be set;
225
226	double targetTemp;
227	double targetPressure;
228	double tauThermostat;
229	double tauBarostat;
230
231	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
232	short int have_target_pressure;
233
234	double *oldPos;
235	double *oldVel;
236	double *oldJi;
237
238	double chiTolerance;
239	short int have_chi_tolerance;
240	double posIterTolerance;
241	short int have_pos_iter_tolerance;
242	double etaTolerance;
243	short int have_eta_tolerance;
244
245	};
246
247	template<typename T> class NPTi : public T{
248
249	public:
250	NPTi( SimInfo theInfo, ForceFields the_ff);
251	~NPTi();
252
253	virtual double getConservedQuantity(void);
254	virtual void resetIntegrator(void);
255	virtual string getAdditionalParameters(void);
256	protected:
257
258
259
260	virtual void evolveEtaA(void);
261	virtual void evolveEtaB(void);
262
263	virtual bool etaConverged( void );
264
265	virtual void scaleSimBox( void );
266
267	virtual void getVelScaleA( double sc[3], double vel[3] );
268	virtual void getVelScaleB( double sc[3], int index );
269	virtual void getPosScale(double pos[3], double COM[3],
270	int index, double sc[3]);
271
272	virtual void calcVelScale( void );
273
274	double eta, oldEta, prevEta;
275	double vScale;
276	};
277
278	template<typename T> class NPTf : public T{
279
280	public:
281
282	NPTf ( SimInfo theInfo, ForceFields the_ff);
283	virtual ~NPTf();
284
285	virtual double getConservedQuantity(void);
286	virtual string getAdditionalParameters(void);
287	virtual void resetIntegrator(void);
288
289	protected:
290
291	virtual void evolveEtaA(void);
292	virtual void evolveEtaB(void);
293
294	virtual bool etaConverged( void );
295
296	virtual void scaleSimBox( void );
297
298	virtual void getVelScaleA( double sc[3], double vel[3] );
299	virtual void getVelScaleB( double sc[3], int index );
300	virtual void getPosScale(double pos[3], double COM[3],
301	int index, double sc[3]);
302
303	virtual void calcVelScale( void );
304
305	double eta[3][3];
306	double oldEta[3][3];
307	double prevEta[3][3];
308	double vScale[3][3];
309	};
310
311	template<typename T> class NPTxyz : public T{
312
313	public:
314
315	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
316	virtual ~NPTxyz();
317
318	virtual double getConservedQuantity(void);
319	virtual string getAdditionalParameters(void);
320	virtual void resetIntegrator(void);
321
322	protected:
323
324	virtual void evolveEtaA(void);
325	virtual void evolveEtaB(void);
326
327	virtual bool etaConverged( void );
328
329	virtual void scaleSimBox( void );
330
331	virtual void getVelScaleA( double sc[3], double vel[3] );
332	virtual void getVelScaleB( double sc[3], int index );
333	virtual void getPosScale(double pos[3], double COM[3],
334	int index, double sc[3]);
335
336	virtual void calcVelScale( void );
337
338	double eta[3][3];
339	double oldEta[3][3];
340	double prevEta[3][3];
341	double vScale[3][3];
342	};
343
344
345	template<typename T> class ZConstraint : public T {
346
347	public:
348	class ForceSubtractionPolicy{
349	public:
350	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
351
352	virtual void update() = 0;
353	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
354	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
355	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
356	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
357
358	protected:
359	ZConstraint<T>* zconsIntegrator;
360	};
361
362	class PolicyByNumber : public ForceSubtractionPolicy{
363
364	public:
365	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
366	virtual void update();
367	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
368	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
369	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
370	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
371
372	private:
373	int totNumOfMovingAtoms;
374	};
375
376	class PolicyByMass : public ForceSubtractionPolicy{
377
378	public:
379	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
380
381	virtual void update();
382	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
383	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
384	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
385	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
386
387	private:
388	double totMassOfMovingAtoms;
389	};
390
391	public:
392
393	ZConstraint( SimInfo theInfo, ForceFields the_ff);
394	~ZConstraint();
395
396	void setZConsTime(double time) {this->zconsTime = time;}
397	void getZConsTime() {return zconsTime;}
398
399	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
400	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
401
402	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
403	string getZConsOutput() {return zconsOutput;}
404
405	virtual void integrate();
406
407
408	#ifdef IS_MPI
409	virtual void update(); //which is called to indicate the molecules' migration
410	#endif
411
412	enum ZConsState {zcsMoving, zcsFixed};
413
414	vector<Molecule*> zconsMols; //z-constraint molecules array
415	vector<ZConsState> states; //state of z-constraint molecules
416
417
418
419	int totNumOfUnconsAtoms; //total number of uncontraint atoms
420	double totalMassOfUncons; //total mas of unconstraint molecules
421
422
423	protected:
424
425
426
427	virtual void calcForce( int calcPot, int calcStress );
428	virtual void thermalize(void);
429
430	void zeroOutVel();
431	void doZconstraintForce();
432	void doHarmonic(vector<double>& resPos);
433	bool checkZConsState();
434
435	bool haveFixedZMols();
436	bool haveMovingZMols();
437
438	double calcZSys();
439
440	int isZConstraintMol(Molecule* mol);
441
442
443	double zconsTime; //sample time
444	double zconsTol; //tolerance of z-contratint
445	double zForceConst; //base force constant term
446	//which is estimate by OOPSE
447
448
449	vector<double> massOfZConsMols; //mass of z-constraint molecule
450	vector<double> kz; //force constant array
451
452	vector<double> zPos; //
453
454
455	vector<Molecule*> unconsMols; //unconstraint molecules array
456	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
457
458
459	vector<ZConsParaItem>* parameters; //
460
461	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
462
463	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
464	vector<double> fz;
465	vector<double> curZPos;
466
467	bool usingSMD;
468	vector<double> prevCantPos;
469	vector<double> cantPos;
470	vector<double> cantVel;
471
472	double zconsFixTime;
473	double zconsGap;
474	bool hasZConsGap;
475	vector<double> endFixTime;
476
477	int whichDirection; //constraint direction
478
479	private:
480
481	string zconsOutput; //filename of zconstraint output
482	ZConsWriter* fzOut; //z-constraint writer
483
484	double curZconsTime;
485
486	double calcMovingMolsCOMVel();
487	double calcSysCOMVel();
488	double calcTotalForce();
489	void updateZPos();
490	void updateCantPos();
491
492	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
493	friend class ForceSubtractionPolicy;
494
495	};
496
497
498	//Sympletic quaternion Scheme Integrator
499	//Reference:
500	// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
501	//Symplectic quaternion Scheme for biophysical molecular dynamics
502	//116(20), 8649, J. Chem. Phys. (2002)
503	template<typename T> class SQSIntegrator : public T{
504	public:
505	virtual void moveA();
506	virtual void moveB();
507	protected:
508	void freeRotor();
509	void rotate(int k, double dt);
510
511	};
512	#endif