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
#	User	Rev	Content
1	gezelter	1490	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4			#include <string>
5			#include <vector>
6	tim	1492	#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	gezelter	1490
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	chrisfen	1772	RestraintWriter* restOut;
88			RestraintReader* initRestraints;
89	gezelter	1490
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