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"

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 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;

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> 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;

};

/*
//Steered Molecular Dynamics
 template<typename T> class SMD : public T{
  public:
    SMD( SimInfo *theInfo, ForceFields* the_ff);
    ~SMD();
  
   virtual void integrate();
  virtual void calcForce( int calcPot, int calcStress );   
};
*/
#endif
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	13275 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	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	mmeineke	377
17	tim	658	using namespace std;
18	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
19			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
21	mmeineke	561	const int maxIteration = 300;
22			const double tol = 1.0e-6;
23
24	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	mmeineke	377	public:
27	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
28	mmeineke	548	virtual ~Integrator();
29	mmeineke	377	void integrate( void );
30	tim	763	virtual double getConservedQuantity(void);
31	tim	837	virtual string getAdditionalParameters(void);
32	mmeineke	377
33	mmeineke	540	protected:
34	mmeineke	778
35	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
36	mmeineke	548	virtual void preMove( void );
37	mmeineke	540	virtual void moveA( void );
38			virtual void moveB( void );
39			virtual void constrainA( void );
40			virtual void constrainB( void );
41	mmeineke	559	virtual int readyCheck( void ) { return 1; }
42	tim	677
43	mmeineke	746	virtual void resetIntegrator( void ) { }
44	tim	837
45			virtual void calcForce( int calcPot, int calcStress );
46	tim	677	virtual void thermalize();
47	tim	837
48	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
49	mmeineke	778
50	mmeineke	540	void checkConstraints( void );
51	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
52	tim	701	double A[3][3] );
53	tim	837
54	mmeineke	377	ForceFields* myFF;
55
56	mmeineke	540	SimInfo *info; // all the info we'll ever need
57	gezelter	1097	vector<StuntDouble*> integrableObjects;
58	mmeineke	540	int nAtoms; /* the number of atoms */
59	mmeineke	548	int oldAtoms;
60	mmeineke	540	Atom *atoms; / array of atom pointers */
61	mmeineke	423	Molecule* molecules;
62			int nMols;
63
64	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
65	tim	701	// constraints.
66	tim	837	int nConstrained; // counter for number of constraints
67			int *constrainedA; // the i of a constraint pair
68			int *constrainedB; // the j of a constraint pair
69			double *constrainedDsqr; // the square of the constraint distance
70
71	mmeineke	548	int* moving; // tells whether we are moving atom i
72			int* moved; // tells whether we have moved atom i
73	tim	837	double* oldPos; // pre constrained positions
74	mmeineke	548
75	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
76	tim	837
77	mmeineke	540	double dt;
78	mmeineke	541	double dt2;
79	gezelter	560
80	mmeineke	540	Thermo *tStats;
81			StatWriter* statOut;
82			DumpWriter* dumpOut;
83	tim	837
84	mmeineke	377	};
85
86	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
87	mmeineke	540
88	tim	645	template<typename T> class NVE : public T {
89
90	mmeineke	561	public:
91			NVE ( SimInfo theInfo, ForceFields the_ff ):
92	tim	645	T( theInfo, the_ff ){}
93	tim	837	virtual ~NVE(){}
94	tim	645	};
95	mmeineke	555
96
97	tim	645	template<typename T> class NVT : public T {
98	mmeineke	555
99	gezelter	560	public:
100
101	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
102	tim	763	virtual ~NVT();
103	mmeineke	540
104	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
105			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
106	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
107			virtual double getConservedQuantity(void);
108	tim	837	virtual string getAdditionalParameters(void);
109	gezelter	560
110	mmeineke	540	protected:
111	gezelter	560
112	mmeineke	561	virtual void moveA( void );
113			virtual void moveB( void );
114	mmeineke	540
115	mmeineke	561	virtual int readyCheck();
116	gezelter	560
117	mmeineke	746	virtual void resetIntegrator( void );
118
119	gezelter	565	// chi is a propagated degree of freedom.
120	gezelter	560
121	gezelter	565	double chi;
122	gezelter	560
123	tim	763	//integral of chi(t)dt
124			double integralOfChidt;
125
126	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
127	gezelter	560
128			double targetTemp;
129			double tauThermostat;
130	tim	837
131	gezelter	565	short int have_tau_thermostat, have_target_temp;
132	gezelter	560
133	tim	763	double *oldVel;
134			double *oldJi;
135
136			double chiTolerance;
137			short int have_chi_tolerance;
138
139	mmeineke	540	};
140
141
142
143	mmeineke	778	template<typename T> class NPT : public T{
144	tim	645
145	gezelter	560	public:
146
147	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
148			virtual ~NPT();
149	tim	837
150	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
151			calcStress = 1;
152	tim	645	T::integrateStep( calcPot, calcStress );
153	mmeineke	594	}
154
155	mmeineke	778	virtual double getConservedQuantity(void) = 0;
156	tim	837	virtual string getAdditionalParameters(void) = 0;
157	mmeineke	843
158			double myTauThermo( void ) { return tauThermostat; }
159			double myTauBaro( void ) { return tauBarostat; }
160
161	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
162			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
163			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
164			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
165	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
166			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
167			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
168	gezelter	560
169			protected:
170
171	mmeineke	561	virtual void moveA( void );
172			virtual void moveB( void );
173	gezelter	560
174	mmeineke	561	virtual int readyCheck();
175	gezelter	560
176	mmeineke	746	virtual void resetIntegrator( void );
177
178	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
179			virtual void getVelScaleB( double sc[3], int index ) = 0;
180	tim	837	virtual void getPosScale(double pos[3], double COM[3],
181	mmeineke	778	int index, double sc[3]) = 0;
182
183	mmeineke	857	virtual void calcVelScale( void ) = 0;
184
185	mmeineke	778	virtual bool chiConverged( void );
186			virtual bool etaConverged( void ) = 0;
187	tim	837
188	mmeineke	778	virtual void evolveChiA( void );
189			virtual void evolveEtaA( void ) = 0;
190			virtual void evolveChiB( void );
191			virtual void evolveEtaB( void ) = 0;
192
193			virtual void scaleSimBox( void ) = 0;
194
195	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
196
197	gezelter	565	// chi and eta are the propagated degrees of freedom
198	gezelter	560
199	mmeineke	778	double oldChi;
200			double prevChi;
201	gezelter	565	double chi;
202	gezelter	574	double NkBT;
203	tim	763	double fkBT;
204	gezelter	560
205	mmeineke	778	double tt2, tb2;
206			double instaTemp, instaPress, instaVol;
207	mmeineke	780	double press[3][3];
208	mmeineke	778
209	tim	763	int Nparticles;
210
211			double integralOfChidt;
212
213	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
214	gezelter	560	// One of qmass or tauThermostat must be set;
215
216			double targetTemp;
217			double targetPressure;
218			double tauThermostat;
219			double tauBarostat;
220
221			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
222	gezelter	565	short int have_target_pressure;
223	gezelter	560
224	tim	763	double *oldPos;
225			double *oldVel;
226			double *oldJi;
227
228			double chiTolerance;
229			short int have_chi_tolerance;
230			double posIterTolerance;
231			short int have_pos_iter_tolerance;
232			double etaTolerance;
233			short int have_eta_tolerance;
234
235	gezelter	560	};
236
237	mmeineke	778	template<typename T> class NPTi : public T{
238	tim	837
239	mmeineke	778	public:
240			NPTi( SimInfo theInfo, ForceFields the_ff);
241			~NPTi();
242
243			virtual double getConservedQuantity(void);
244			virtual void resetIntegrator(void);
245	tim	837	virtual string getAdditionalParameters(void);
246	mmeineke	778	protected:
247
248
249	tim	837
250	mmeineke	778	virtual void evolveEtaA(void);
251			virtual void evolveEtaB(void);
252
253			virtual bool etaConverged( void );
254
255			virtual void scaleSimBox( void );
256
257			virtual void getVelScaleA( double sc[3], double vel[3] );
258			virtual void getVelScaleB( double sc[3], int index );
259	tim	837	virtual void getPosScale(double pos[3], double COM[3],
260	mmeineke	778	int index, double sc[3]);
261
262	mmeineke	857	virtual void calcVelScale( void );
263
264	mmeineke	778	double eta, oldEta, prevEta;
265	mmeineke	857	double vScale;
266	mmeineke	778	};
267
268	tim	645	template<typename T> class NPTf : public T{
269	gezelter	576
270			public:
271
272			NPTf ( SimInfo theInfo, ForceFields the_ff);
273	tim	767	virtual ~NPTf();
274	gezelter	576
275	tim	763	virtual double getConservedQuantity(void);
276	tim	837	virtual string getAdditionalParameters(void);
277	mmeineke	780	virtual void resetIntegrator(void);
278	mmeineke	594
279	gezelter	576	protected:
280
281	mmeineke	780	virtual void evolveEtaA(void);
282			virtual void evolveEtaB(void);
283	gezelter	576
284	mmeineke	780	virtual bool etaConverged( void );
285	mmeineke	746
286	mmeineke	780	virtual void scaleSimBox( void );
287	gezelter	576
288	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
289			virtual void getVelScaleB( double sc[3], int index );
290	tim	837	virtual void getPosScale(double pos[3], double COM[3],
291	mmeineke	780	int index, double sc[3]);
292	tim	763
293	mmeineke	857	virtual void calcVelScale( void );
294
295	gezelter	588	double eta[3][3];
296	mmeineke	780	double oldEta[3][3];
297			double prevEta[3][3];
298	mmeineke	857	double vScale[3][3];
299	gezelter	576	};
300
301	mmeineke	812	template<typename T> class NPTxyz : public T{
302	mmeineke	755
303			public:
304
305	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
306			virtual ~NPTxyz();
307	mmeineke	755
308	mmeineke	812	virtual double getConservedQuantity(void);
309	tim	837	virtual string getAdditionalParameters(void);
310	mmeineke	812	virtual void resetIntegrator(void);
311	mmeineke	755
312			protected:
313
314	mmeineke	812	virtual void evolveEtaA(void);
315			virtual void evolveEtaB(void);
316	mmeineke	755
317	mmeineke	812	virtual bool etaConverged( void );
318	mmeineke	755
319	mmeineke	812	virtual void scaleSimBox( void );
320	mmeineke	755
321	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
322			virtual void getVelScaleB( double sc[3], int index );
323	tim	837	virtual void getPosScale(double pos[3], double COM[3],
324	mmeineke	812	int index, double sc[3]);
325	mmeineke	755
326	mmeineke	857	virtual void calcVelScale( void );
327
328	mmeineke	812	double eta[3][3];
329			double oldEta[3][3];
330			double prevEta[3][3];
331	mmeineke	857	double vScale[3][3];
332	mmeineke	812	};
333	mmeineke	755
334
335	tim	658	template<typename T> class ZConstraint : public T {
336	tim	837
337			public:
338	tim	738	class ForceSubtractionPolicy{
339	tim	699	public:
340	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
341	tim	658
342	tim	837	virtual void update() = 0;
343	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
344			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
345	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
347	tim	837
348	tim	701	protected:
349	mmeineke	788	ZConstraint<T>* zconsIntegrator;
350	tim	699	};
351
352	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
353	gezelter	747
354	tim	699	public:
355	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
356			virtual void update();
357	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
358			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
359	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
360			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
361	tim	837
362	tim	699	private:
363	tim	763	int totNumOfMovingAtoms;
364	tim	699	};
365
366	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
367	gezelter	747
368	tim	699	public:
369	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370
371			virtual void update();
372	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
373			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
374	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
375			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
376	tim	699
377	tim	701	private:
378			double totMassOfMovingAtoms;
379	tim	699	};
380
381	tim	658	public:
382
383			ZConstraint( SimInfo theInfo, ForceFields the_ff);
384			~ZConstraint();
385	tim	837
386	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
387			void getZConsTime() {return zconsTime;}
388	tim	837
389	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
390			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
391	tim	837
392	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
393	tim	658	string getZConsOutput() {return zconsOutput;}
394	tim	837
395	tim	677	virtual void integrate();
396	tim	658
397	tim	837
398	tim	658	#ifdef IS_MPI
399	tim	701	virtual void update(); //which is called to indicate the molecules' migration
400	mmeineke	377	#endif
401	tim	658
402	tim	837	enum ZConsState {zcsMoving, zcsFixed};
403	mmeineke	790
404			vector<Molecule*> zconsMols; //z-constraint molecules array
405			vector<ZConsState> states; //state of z-constraint molecules
406
407
408	tim	837
409	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
410			double totalMassOfUncons; //total mas of unconstraint molecules
411
412
413	tim	658	protected:
414
415	mmeineke	790
416	tim	837
417			virtual void calcForce( int calcPot, int calcStress );
418	tim	677	virtual void thermalize(void);
419	tim	837
420	tim	677	void zeroOutVel();
421			void doZconstraintForce();
422	tim	1093	void doHarmonic(vector<double>& resPos);
423	tim	677	bool checkZConsState();
424
425			bool haveFixedZMols();
426			bool haveMovingZMols();
427
428			double calcZSys();
429
430			int isZConstraintMol(Molecule* mol);
431
432
433	tim	701	double zconsTime; //sample time
434			double zconsTol; //tolerance of z-contratint
435			double zForceConst; //base force constant term
436			//which is estimate by OOPSE
437	mmeineke	790
438	tim	837
439			vector<double> massOfZConsMols; //mass of z-constraint molecule
440	tim	701	vector<double> kz; //force constant array
441	mmeineke	790
442	tim	701	vector<double> zPos; //
443	tim	837
444
445	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
446			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
447	tim	682
448	mmeineke	790
449	tim	701	vector<ZConsParaItem>* parameters; //
450	tim	837
451	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
452	tim	677
453	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
454			vector<double> fz;
455			vector<double> curZPos;
456	tim	677
457	tim	1093	bool usingSMD;
458			vector<double> cantPos;
459			vector<double> cantVel;
460
461	tim	1091	double zconsFixTime;
462			double zconsGap;
463			bool hasZConsGap;
464			vector<double> endFixTime;
465
466	tim	837	int whichDirection; //constraint direction
467
468	tim	658	private:
469	tim	837
470	tim	701	string zconsOutput; //filename of zconstraint output
471			ZConsWriter* fzOut; //z-constraint writer
472	tim	677
473	tim	837	double curZconsTime;
474	tim	699
475	tim	696	double calcMovingMolsCOMVel();
476			double calcSysCOMVel();
477			double calcTotalForce();
478	tim	1091	void updateZPos();
479	tim	1093	void updateCantPos();
480
481	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
482	tim	738	friend class ForceSubtractionPolicy;
483	tim	677
484	tim	658	};
485
486	tim	1064	/*
487	tim	1091	//Steered Molecular Dynamics
488			template<typename T> class SMD : public T{
489	tim	969	public:
490	tim	1091	SMD( SimInfo theInfo, ForceFields the_ff);
491			~SMD();
492
493			virtual void integrate();
494			virtual void calcForce( int calcPot, int calcStress );
495	tim	969	};
496	tim	1091	*/
497	tim	658	#endif