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;

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;

};

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;

};

#endif
Revision:	1198
Committed:	Thu May 27 00:48:12 2004 UTC (20 years, 1 month ago) by tim
File size:	13201 byte(s)
Log Message:	in the progress of fixing MPI version of cutoff group
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4	tim	658	#include <string>
5			#include <vector>
6	mmeineke	377	#include "Atom.hpp"
7	gezelter	1097	#include "StuntDouble.hpp"
8	gezelter	604	#include "Molecule.hpp"
9	mmeineke	377	#include "SRI.hpp"
10			#include "AbstractClasses.hpp"
11			#include "SimInfo.hpp"
12			#include "ForceFields.hpp"
13	mmeineke	540	#include "Thermo.hpp"
14			#include "ReadWrite.hpp"
15	tim	658	#include "ZConsWriter.hpp"
16	chrisfen	1180	#include "Restraints.hpp"
17	mmeineke	377
18	tim	658	using namespace std;
19	mmeineke	561	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	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
22	mmeineke	561	const int maxIteration = 300;
23			const double tol = 1.0e-6;
24
25	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
26
27	mmeineke	377	public:
28	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
29	mmeineke	548	virtual ~Integrator();
30	mmeineke	377	void integrate( void );
31	tim	763	virtual double getConservedQuantity(void);
32	tim	837	virtual string getAdditionalParameters(void);
33	mmeineke	377
34	mmeineke	540	protected:
35	mmeineke	778
36	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
37	mmeineke	548	virtual void preMove( void );
38	mmeineke	540	virtual void moveA( void );
39			virtual void moveB( void );
40			virtual void constrainA( void );
41			virtual void constrainB( void );
42	mmeineke	559	virtual int readyCheck( void ) { return 1; }
43	tim	677
44	mmeineke	746	virtual void resetIntegrator( void ) { }
45	tim	837
46			virtual void calcForce( int calcPot, int calcStress );
47	tim	677	virtual void thermalize();
48	tim	837
49	tim	1108	virtual bool stopIntegrator() {return false;}
50
51	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52	mmeineke	778
53	mmeineke	540	void checkConstraints( void );
54	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
55	tim	701	double A[3][3] );
56	tim	837
57	mmeineke	377	ForceFields* myFF;
58
59	mmeineke	540	SimInfo *info; // all the info we'll ever need
60	gezelter	1097	vector<StuntDouble*> integrableObjects;
61	mmeineke	540	int nAtoms; /* the number of atoms */
62	mmeineke	548	int oldAtoms;
63	mmeineke	540	Atom *atoms; / array of atom pointers */
64	mmeineke	423	Molecule* molecules;
65			int nMols;
66
67	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
68	tim	701	// constraints.
69	tim	837	int nConstrained; // counter for number of constraints
70			int *constrainedA; // the i of a constraint pair
71			int *constrainedB; // the j of a constraint pair
72			double *constrainedDsqr; // the square of the constraint distance
73
74	mmeineke	548	int* moving; // tells whether we are moving atom i
75			int* moved; // tells whether we have moved atom i
76	tim	837	double* oldPos; // pre constrained positions
77	mmeineke	548
78	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
79	tim	837
80	mmeineke	540	double dt;
81	mmeineke	541	double dt2;
82	gezelter	560
83	mmeineke	540	Thermo *tStats;
84			StatWriter* statOut;
85			DumpWriter* dumpOut;
86	tim	837
87	mmeineke	377	};
88
89	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
90	mmeineke	540
91	tim	1161	// ansi instantiation
92			template class Integrator<BaseIntegrator>;
93
94	tim	645	template<typename T> class NVE : public T {
95
96	mmeineke	561	public:
97			NVE ( SimInfo theInfo, ForceFields the_ff ):
98	tim	645	T( theInfo, the_ff ){}
99	tim	837	virtual ~NVE(){}
100	tim	645	};
101	mmeineke	555
102
103	tim	645	template<typename T> class NVT : public T {
104	mmeineke	555
105	gezelter	560	public:
106
107	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
108	tim	763	virtual ~NVT();
109	mmeineke	540
110	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
111			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
113			virtual double getConservedQuantity(void);
114	tim	837	virtual string getAdditionalParameters(void);
115	gezelter	560
116	mmeineke	540	protected:
117	gezelter	560
118	mmeineke	561	virtual void moveA( void );
119			virtual void moveB( void );
120	mmeineke	540
121	mmeineke	561	virtual int readyCheck();
122	gezelter	560
123	mmeineke	746	virtual void resetIntegrator( void );
124
125	gezelter	565	// chi is a propagated degree of freedom.
126	gezelter	560
127	gezelter	565	double chi;
128	gezelter	560
129	tim	763	//integral of chi(t)dt
130			double integralOfChidt;
131
132	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
133	gezelter	560
134			double targetTemp;
135			double tauThermostat;
136	tim	837
137	gezelter	565	short int have_tau_thermostat, have_target_temp;
138	gezelter	560
139	tim	763	double *oldVel;
140			double *oldJi;
141
142			double chiTolerance;
143			short int have_chi_tolerance;
144
145	mmeineke	540	};
146
147
148
149	mmeineke	778	template<typename T> class NPT : public T{
150	tim	645
151	gezelter	560	public:
152
153	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
154			virtual ~NPT();
155	tim	837
156	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
157			calcStress = 1;
158	tim	645	T::integrateStep( calcPot, calcStress );
159	mmeineke	594	}
160
161	mmeineke	778	virtual double getConservedQuantity(void) = 0;
162	tim	837	virtual string getAdditionalParameters(void) = 0;
163	mmeineke	843
164			double myTauThermo( void ) { return tauThermostat; }
165			double myTauBaro( void ) { return tauBarostat; }
166
167	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174	gezelter	560
175			protected:
176
177	mmeineke	561	virtual void moveA( void );
178			virtual void moveB( void );
179	gezelter	560
180	mmeineke	561	virtual int readyCheck();
181	gezelter	560
182	mmeineke	746	virtual void resetIntegrator( void );
183
184	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185			virtual void getVelScaleB( double sc[3], int index ) = 0;
186	tim	837	virtual void getPosScale(double pos[3], double COM[3],
187	mmeineke	778	int index, double sc[3]) = 0;
188
189	mmeineke	857	virtual void calcVelScale( void ) = 0;
190
191	mmeineke	778	virtual bool chiConverged( void );
192			virtual bool etaConverged( void ) = 0;
193	tim	837
194	mmeineke	778	virtual void evolveChiA( void );
195			virtual void evolveEtaA( void ) = 0;
196			virtual void evolveChiB( void );
197			virtual void evolveEtaB( void ) = 0;
198
199			virtual void scaleSimBox( void ) = 0;
200
201	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202
203	gezelter	565	// chi and eta are the propagated degrees of freedom
204	gezelter	560
205	mmeineke	778	double oldChi;
206			double prevChi;
207	gezelter	565	double chi;
208	gezelter	574	double NkBT;
209	tim	763	double fkBT;
210	gezelter	560
211	mmeineke	778	double tt2, tb2;
212			double instaTemp, instaPress, instaVol;
213	mmeineke	780	double press[3][3];
214	mmeineke	778
215	tim	763	int Nparticles;
216
217			double integralOfChidt;
218
219	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
220	gezelter	560	// One of qmass or tauThermostat must be set;
221
222			double targetTemp;
223			double targetPressure;
224			double tauThermostat;
225			double tauBarostat;
226
227			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228	gezelter	565	short int have_target_pressure;
229	gezelter	560
230	tim	763	double *oldPos;
231			double *oldVel;
232			double *oldJi;
233
234			double chiTolerance;
235			short int have_chi_tolerance;
236			double posIterTolerance;
237			short int have_pos_iter_tolerance;
238			double etaTolerance;
239			short int have_eta_tolerance;
240
241	gezelter	560	};
242
243	mmeineke	778	template<typename T> class NPTi : public T{
244	tim	837
245	mmeineke	778	public:
246			NPTi( SimInfo theInfo, ForceFields the_ff);
247			~NPTi();
248
249			virtual double getConservedQuantity(void);
250			virtual void resetIntegrator(void);
251	tim	837	virtual string getAdditionalParameters(void);
252	mmeineke	778	protected:
253
254
255	tim	837
256	mmeineke	778	virtual void evolveEtaA(void);
257			virtual void evolveEtaB(void);
258
259			virtual bool etaConverged( void );
260
261			virtual void scaleSimBox( void );
262
263			virtual void getVelScaleA( double sc[3], double vel[3] );
264			virtual void getVelScaleB( double sc[3], int index );
265	tim	837	virtual void getPosScale(double pos[3], double COM[3],
266	mmeineke	778	int index, double sc[3]);
267
268	mmeineke	857	virtual void calcVelScale( void );
269
270	mmeineke	778	double eta, oldEta, prevEta;
271	mmeineke	857	double vScale;
272	mmeineke	778	};
273
274	tim	645	template<typename T> class NPTf : public T{
275	gezelter	576
276			public:
277
278			NPTf ( SimInfo theInfo, ForceFields the_ff);
279	tim	767	virtual ~NPTf();
280	gezelter	576
281	tim	763	virtual double getConservedQuantity(void);
282	tim	837	virtual string getAdditionalParameters(void);
283	mmeineke	780	virtual void resetIntegrator(void);
284	mmeineke	594
285	gezelter	576	protected:
286
287	mmeineke	780	virtual void evolveEtaA(void);
288			virtual void evolveEtaB(void);
289	gezelter	576
290	mmeineke	780	virtual bool etaConverged( void );
291	mmeineke	746
292	mmeineke	780	virtual void scaleSimBox( void );
293	gezelter	576
294	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
295			virtual void getVelScaleB( double sc[3], int index );
296	tim	837	virtual void getPosScale(double pos[3], double COM[3],
297	mmeineke	780	int index, double sc[3]);
298	tim	763
299	mmeineke	857	virtual void calcVelScale( void );
300
301	gezelter	588	double eta[3][3];
302	mmeineke	780	double oldEta[3][3];
303			double prevEta[3][3];
304	mmeineke	857	double vScale[3][3];
305	gezelter	576	};
306
307	mmeineke	812	template<typename T> class NPTxyz : public T{
308	mmeineke	755
309			public:
310
311	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
312			virtual ~NPTxyz();
313	mmeineke	755
314	mmeineke	812	virtual double getConservedQuantity(void);
315	tim	837	virtual string getAdditionalParameters(void);
316	mmeineke	812	virtual void resetIntegrator(void);
317	mmeineke	755
318			protected:
319
320	mmeineke	812	virtual void evolveEtaA(void);
321			virtual void evolveEtaB(void);
322	mmeineke	755
323	mmeineke	812	virtual bool etaConverged( void );
324	mmeineke	755
325	mmeineke	812	virtual void scaleSimBox( void );
326	mmeineke	755
327	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
328			virtual void getVelScaleB( double sc[3], int index );
329	tim	837	virtual void getPosScale(double pos[3], double COM[3],
330	mmeineke	812	int index, double sc[3]);
331	mmeineke	755
332	mmeineke	857	virtual void calcVelScale( void );
333
334	mmeineke	812	double eta[3][3];
335			double oldEta[3][3];
336			double prevEta[3][3];
337	mmeineke	857	double vScale[3][3];
338	mmeineke	812	};
339	mmeineke	755
340
341	tim	658	template<typename T> class ZConstraint : public T {
342	tim	837
343			public:
344	tim	738	class ForceSubtractionPolicy{
345	tim	699	public:
346	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347	tim	658
348	tim	837	virtual void update() = 0;
349	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353	tim	837
354	tim	701	protected:
355	mmeineke	788	ZConstraint<T>* zconsIntegrator;
356	tim	699	};
357
358	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
359	gezelter	747
360	tim	699	public:
361	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362			virtual void update();
363	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367	tim	837
368	tim	699	private:
369	tim	763	int totNumOfMovingAtoms;
370	tim	699	};
371
372	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
373	gezelter	747
374	tim	699	public:
375	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376
377			virtual void update();
378	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
381			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382	tim	699
383	tim	701	private:
384			double totMassOfMovingAtoms;
385	tim	699	};
386
387	tim	658	public:
388
389			ZConstraint( SimInfo theInfo, ForceFields the_ff);
390			~ZConstraint();
391	tim	837
392	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
393			void getZConsTime() {return zconsTime;}
394	tim	837
395	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
397	tim	837
398	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
399	tim	658	string getZConsOutput() {return zconsOutput;}
400	tim	837
401	tim	677	virtual void integrate();
402	tim	658
403	tim	837
404	tim	658	#ifdef IS_MPI
405	tim	701	virtual void update(); //which is called to indicate the molecules' migration
406	mmeineke	377	#endif
407	tim	658
408	tim	837	enum ZConsState {zcsMoving, zcsFixed};
409	mmeineke	790
410			vector<Molecule*> zconsMols; //z-constraint molecules array
411			vector<ZConsState> states; //state of z-constraint molecules
412
413
414	tim	837
415	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
416			double totalMassOfUncons; //total mas of unconstraint molecules
417
418
419	tim	658	protected:
420
421	mmeineke	790
422	tim	837
423			virtual void calcForce( int calcPot, int calcStress );
424	tim	677	virtual void thermalize(void);
425	tim	837
426	tim	677	void zeroOutVel();
427			void doZconstraintForce();
428	tim	1093	void doHarmonic(vector<double>& resPos);
429	tim	677	bool checkZConsState();
430
431			bool haveFixedZMols();
432			bool haveMovingZMols();
433
434			double calcZSys();
435
436			int isZConstraintMol(Molecule* mol);
437
438
439	tim	701	double zconsTime; //sample time
440			double zconsTol; //tolerance of z-contratint
441			double zForceConst; //base force constant term
442			//which is estimate by OOPSE
443	mmeineke	790
444	tim	837
445			vector<double> massOfZConsMols; //mass of z-constraint molecule
446	tim	701	vector<double> kz; //force constant array
447	mmeineke	790
448	tim	701	vector<double> zPos; //
449	tim	837
450
451	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
452			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
453	tim	682
454	mmeineke	790
455	tim	701	vector<ZConsParaItem>* parameters; //
456	tim	837
457	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
458	tim	677
459	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
460			vector<double> fz;
461			vector<double> curZPos;
462	tim	677
463	tim	1093	bool usingSMD;
464	tim	1141	vector<double> prevCantPos;
465	tim	1093	vector<double> cantPos;
466			vector<double> cantVel;
467
468	tim	1091	double zconsFixTime;
469			double zconsGap;
470			bool hasZConsGap;
471			vector<double> endFixTime;
472
473	tim	837	int whichDirection; //constraint direction
474
475	tim	658	private:
476	tim	837
477	tim	701	string zconsOutput; //filename of zconstraint output
478			ZConsWriter* fzOut; //z-constraint writer
479	tim	677
480	tim	837	double curZconsTime;
481	tim	699
482	tim	696	double calcMovingMolsCOMVel();
483			double calcSysCOMVel();
484			double calcTotalForce();
485	tim	1091	void updateZPos();
486	tim	1093	void updateCantPos();
487
488	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489	tim	738	friend class ForceSubtractionPolicy;
490	tim	677
491	tim	658	};
492
493			#endif