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;

class RattleFramework;
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;

  RattleFramework* rattle;

  //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:	1248
Committed:	Fri Jun 4 19:30:05 2004 UTC (20 years, 1 month ago) by tim
File size:	13266 byte(s)
Log Message:	constraint algorithm for minimization is working
#	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	1234	class RattleFramework;
26	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
27
28	mmeineke	377	public:
29	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
30	mmeineke	548	virtual ~Integrator();
31	mmeineke	377	void integrate( void );
32	tim	763	virtual double getConservedQuantity(void);
33	tim	837	virtual string getAdditionalParameters(void);
34	mmeineke	377
35	mmeineke	540	protected:
36	mmeineke	778
37	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
38	tim	1234	//virtual void preMove( void );
39	mmeineke	540	virtual void moveA( void );
40			virtual void moveB( void );
41	tim	1234	//virtual void constrainA( void );
42			//virtual void constrainB( void );
43	mmeineke	559	virtual int readyCheck( void ) { return 1; }
44	tim	677
45	mmeineke	746	virtual void resetIntegrator( void ) { }
46	tim	837
47			virtual void calcForce( int calcPot, int calcStress );
48	tim	677	virtual void thermalize();
49	tim	837
50	tim	1108	virtual bool stopIntegrator() {return false;}
51
52	gezelter	1097	virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53	mmeineke	778
54	tim	1234	//void checkConstraints( void );
55	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
56	tim	701	double A[3][3] );
57	tim	837
58	mmeineke	377	ForceFields* myFF;
59
60	mmeineke	540	SimInfo *info; // all the info we'll ever need
61	gezelter	1097	vector<StuntDouble*> integrableObjects;
62	mmeineke	540	int nAtoms; /* the number of atoms */
63	mmeineke	548	int oldAtoms;
64	mmeineke	540	Atom *atoms; / array of atom pointers */
65	mmeineke	423	Molecule* molecules;
66			int nMols;
67
68	tim	1234	RattleFramework* rattle;
69	tim	837
70	tim	1234	//int isConstrained; // boolean to know whether the systems contains constraints.
71			//int nConstrained; // counter for number of constraints
72			//int *constrainedA; // the i of a constraint pair
73			//int *constrainedB; // the j of a constraint pair
74			//double *constrainedDsqr; // the square of the constraint distance
75	mmeineke	548
76	tim	1234	//int* moving; // tells whether we are moving atom i
77			//int* moved; // tells whether we have moved atom i
78			//double* oldPos; // pre constrained positions
79
80	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
81	tim	837
82	mmeineke	540	double dt;
83	mmeineke	541	double dt2;
84	gezelter	560
85	mmeineke	540	Thermo *tStats;
86			StatWriter* statOut;
87			DumpWriter* dumpOut;
88	tim	837
89	mmeineke	377	};
90
91	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
92	mmeineke	540
93	tim	1161	// ansi instantiation
94	tim	1248	//template class Integrator<BaseIntegrator>;
95	tim	1161
96	tim	645	template<typename T> class NVE : public T {
97
98	mmeineke	561	public:
99			NVE ( SimInfo theInfo, ForceFields the_ff ):
100	tim	645	T( theInfo, the_ff ){}
101	tim	837	virtual ~NVE(){}
102	tim	645	};
103	mmeineke	555
104
105	tim	645	template<typename T> class NVT : public T {
106	mmeineke	555
107	gezelter	560	public:
108
109	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
110	tim	763	virtual ~NVT();
111	mmeineke	540
112	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
113			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
114	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
115			virtual double getConservedQuantity(void);
116	tim	837	virtual string getAdditionalParameters(void);
117	gezelter	560
118	mmeineke	540	protected:
119	gezelter	560
120	mmeineke	561	virtual void moveA( void );
121			virtual void moveB( void );
122	mmeineke	540
123	mmeineke	561	virtual int readyCheck();
124	gezelter	560
125	mmeineke	746	virtual void resetIntegrator( void );
126
127	gezelter	565	// chi is a propagated degree of freedom.
128	gezelter	560
129	gezelter	565	double chi;
130	gezelter	560
131	tim	763	//integral of chi(t)dt
132			double integralOfChidt;
133
134	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
135	gezelter	560
136			double targetTemp;
137			double tauThermostat;
138	tim	837
139	gezelter	565	short int have_tau_thermostat, have_target_temp;
140	gezelter	560
141	tim	763	double *oldVel;
142			double *oldJi;
143
144			double chiTolerance;
145			short int have_chi_tolerance;
146
147	mmeineke	540	};
148
149
150
151	mmeineke	778	template<typename T> class NPT : public T{
152	tim	645
153	gezelter	560	public:
154
155	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
156			virtual ~NPT();
157	tim	837
158	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
159			calcStress = 1;
160	tim	645	T::integrateStep( calcPot, calcStress );
161	mmeineke	594	}
162
163	mmeineke	778	virtual double getConservedQuantity(void) = 0;
164	tim	837	virtual string getAdditionalParameters(void) = 0;
165	mmeineke	843
166			double myTauThermo( void ) { return tauThermostat; }
167			double myTauBaro( void ) { return tauBarostat; }
168
169	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
174			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
175			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
176	gezelter	560
177			protected:
178
179	mmeineke	561	virtual void moveA( void );
180			virtual void moveB( void );
181	gezelter	560
182	mmeineke	561	virtual int readyCheck();
183	gezelter	560
184	mmeineke	746	virtual void resetIntegrator( void );
185
186	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
187			virtual void getVelScaleB( double sc[3], int index ) = 0;
188	tim	837	virtual void getPosScale(double pos[3], double COM[3],
189	mmeineke	778	int index, double sc[3]) = 0;
190
191	mmeineke	857	virtual void calcVelScale( void ) = 0;
192
193	mmeineke	778	virtual bool chiConverged( void );
194			virtual bool etaConverged( void ) = 0;
195	tim	837
196	mmeineke	778	virtual void evolveChiA( void );
197			virtual void evolveEtaA( void ) = 0;
198			virtual void evolveChiB( void );
199			virtual void evolveEtaB( void ) = 0;
200
201			virtual void scaleSimBox( void ) = 0;
202
203	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
204
205	gezelter	565	// chi and eta are the propagated degrees of freedom
206	gezelter	560
207	mmeineke	778	double oldChi;
208			double prevChi;
209	gezelter	565	double chi;
210	gezelter	574	double NkBT;
211	tim	763	double fkBT;
212	gezelter	560
213	mmeineke	778	double tt2, tb2;
214			double instaTemp, instaPress, instaVol;
215	mmeineke	780	double press[3][3];
216	mmeineke	778
217	tim	763	int Nparticles;
218
219			double integralOfChidt;
220
221	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
222	gezelter	560	// One of qmass or tauThermostat must be set;
223
224			double targetTemp;
225			double targetPressure;
226			double tauThermostat;
227			double tauBarostat;
228
229			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
230	gezelter	565	short int have_target_pressure;
231	gezelter	560
232	tim	763	double *oldPos;
233			double *oldVel;
234			double *oldJi;
235
236			double chiTolerance;
237			short int have_chi_tolerance;
238			double posIterTolerance;
239			short int have_pos_iter_tolerance;
240			double etaTolerance;
241			short int have_eta_tolerance;
242
243	gezelter	560	};
244
245	mmeineke	778	template<typename T> class NPTi : public T{
246	tim	837
247	mmeineke	778	public:
248			NPTi( SimInfo theInfo, ForceFields the_ff);
249			~NPTi();
250
251			virtual double getConservedQuantity(void);
252			virtual void resetIntegrator(void);
253	tim	837	virtual string getAdditionalParameters(void);
254	mmeineke	778	protected:
255
256
257	tim	837
258	mmeineke	778	virtual void evolveEtaA(void);
259			virtual void evolveEtaB(void);
260
261			virtual bool etaConverged( void );
262
263			virtual void scaleSimBox( void );
264
265			virtual void getVelScaleA( double sc[3], double vel[3] );
266			virtual void getVelScaleB( double sc[3], int index );
267	tim	837	virtual void getPosScale(double pos[3], double COM[3],
268	mmeineke	778	int index, double sc[3]);
269
270	mmeineke	857	virtual void calcVelScale( void );
271
272	mmeineke	778	double eta, oldEta, prevEta;
273	mmeineke	857	double vScale;
274	mmeineke	778	};
275
276	tim	645	template<typename T> class NPTf : public T{
277	gezelter	576
278			public:
279
280			NPTf ( SimInfo theInfo, ForceFields the_ff);
281	tim	767	virtual ~NPTf();
282	gezelter	576
283	tim	763	virtual double getConservedQuantity(void);
284	tim	837	virtual string getAdditionalParameters(void);
285	mmeineke	780	virtual void resetIntegrator(void);
286	mmeineke	594
287	gezelter	576	protected:
288
289	mmeineke	780	virtual void evolveEtaA(void);
290			virtual void evolveEtaB(void);
291	gezelter	576
292	mmeineke	780	virtual bool etaConverged( void );
293	mmeineke	746
294	mmeineke	780	virtual void scaleSimBox( void );
295	gezelter	576
296	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
297			virtual void getVelScaleB( double sc[3], int index );
298	tim	837	virtual void getPosScale(double pos[3], double COM[3],
299	mmeineke	780	int index, double sc[3]);
300	tim	763
301	mmeineke	857	virtual void calcVelScale( void );
302
303	gezelter	588	double eta[3][3];
304	mmeineke	780	double oldEta[3][3];
305			double prevEta[3][3];
306	mmeineke	857	double vScale[3][3];
307	gezelter	576	};
308
309	mmeineke	812	template<typename T> class NPTxyz : public T{
310	mmeineke	755
311			public:
312
313	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
314			virtual ~NPTxyz();
315	mmeineke	755
316	mmeineke	812	virtual double getConservedQuantity(void);
317	tim	837	virtual string getAdditionalParameters(void);
318	mmeineke	812	virtual void resetIntegrator(void);
319	mmeineke	755
320			protected:
321
322	mmeineke	812	virtual void evolveEtaA(void);
323			virtual void evolveEtaB(void);
324	mmeineke	755
325	mmeineke	812	virtual bool etaConverged( void );
326	mmeineke	755
327	mmeineke	812	virtual void scaleSimBox( void );
328	mmeineke	755
329	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
330			virtual void getVelScaleB( double sc[3], int index );
331	tim	837	virtual void getPosScale(double pos[3], double COM[3],
332	mmeineke	812	int index, double sc[3]);
333	mmeineke	755
334	mmeineke	857	virtual void calcVelScale( void );
335
336	mmeineke	812	double eta[3][3];
337			double oldEta[3][3];
338			double prevEta[3][3];
339	mmeineke	857	double vScale[3][3];
340	mmeineke	812	};
341	mmeineke	755
342
343	tim	658	template<typename T> class ZConstraint : public T {
344	tim	837
345			public:
346	tim	738	class ForceSubtractionPolicy{
347	tim	699	public:
348	tim	738	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349	tim	658
350	tim	837	virtual void update() = 0;
351	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352			virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
353	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
354			virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
355	tim	837
356	tim	701	protected:
357	mmeineke	788	ZConstraint<T>* zconsIntegrator;
358	tim	699	};
359
360	tim	738	class PolicyByNumber : public ForceSubtractionPolicy{
361	gezelter	747
362	tim	699	public:
363	tim	837	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
364			virtual void update();
365	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
366			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
367	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
368			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
369	tim	837
370	tim	699	private:
371	tim	763	int totNumOfMovingAtoms;
372	tim	699	};
373
374	tim	738	class PolicyByMass : public ForceSubtractionPolicy{
375	gezelter	747
376	tim	699	public:
377	tim	837	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
378
379			virtual void update();
380	tim	699	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
381			virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
382	tim	701	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
383			virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
384	tim	699
385	tim	701	private:
386			double totMassOfMovingAtoms;
387	tim	699	};
388
389	tim	658	public:
390
391			ZConstraint( SimInfo theInfo, ForceFields the_ff);
392			~ZConstraint();
393	tim	837
394	tim	658	void setZConsTime(double time) {this->zconsTime = time;}
395			void getZConsTime() {return zconsTime;}
396	tim	837
397	tim	701	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
398			void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
399	tim	837
400	tim	701	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
401	tim	658	string getZConsOutput() {return zconsOutput;}
402	tim	837
403	tim	677	virtual void integrate();
404	tim	658
405	tim	837
406	tim	658	#ifdef IS_MPI
407	tim	701	virtual void update(); //which is called to indicate the molecules' migration
408	mmeineke	377	#endif
409	tim	658
410	tim	837	enum ZConsState {zcsMoving, zcsFixed};
411	mmeineke	790
412			vector<Molecule*> zconsMols; //z-constraint molecules array
413			vector<ZConsState> states; //state of z-constraint molecules
414
415
416	tim	837
417	mmeineke	790	int totNumOfUnconsAtoms; //total number of uncontraint atoms
418			double totalMassOfUncons; //total mas of unconstraint molecules
419
420
421	tim	658	protected:
422
423	mmeineke	790
424	tim	837
425			virtual void calcForce( int calcPot, int calcStress );
426	tim	677	virtual void thermalize(void);
427	tim	837
428	tim	677	void zeroOutVel();
429			void doZconstraintForce();
430	tim	1093	void doHarmonic(vector<double>& resPos);
431	tim	677	bool checkZConsState();
432
433			bool haveFixedZMols();
434			bool haveMovingZMols();
435
436			double calcZSys();
437
438			int isZConstraintMol(Molecule* mol);
439
440
441	tim	701	double zconsTime; //sample time
442			double zconsTol; //tolerance of z-contratint
443			double zForceConst; //base force constant term
444			//which is estimate by OOPSE
445	mmeineke	790
446	tim	837
447			vector<double> massOfZConsMols; //mass of z-constraint molecule
448	tim	701	vector<double> kz; //force constant array
449	mmeineke	790
450	tim	701	vector<double> zPos; //
451	tim	837
452
453	tim	701	vector<Molecule*> unconsMols; //unconstraint molecules array
454			vector<double> massOfUnconsMols; //mass array of unconstraint molecules
455	tim	682
456	mmeineke	790
457	tim	701	vector<ZConsParaItem>* parameters; //
458	tim	837
459	tim	658	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
460	tim	677
461	tim	1093	vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules
462			vector<double> fz;
463			vector<double> curZPos;
464	tim	677
465	tim	1093	bool usingSMD;
466	tim	1141	vector<double> prevCantPos;
467	tim	1093	vector<double> cantPos;
468			vector<double> cantVel;
469
470	tim	1091	double zconsFixTime;
471			double zconsGap;
472			bool hasZConsGap;
473			vector<double> endFixTime;
474
475	tim	837	int whichDirection; //constraint direction
476
477	tim	658	private:
478	tim	837
479	tim	701	string zconsOutput; //filename of zconstraint output
480			ZConsWriter* fzOut; //z-constraint writer
481	tim	677
482	tim	837	double curZconsTime;
483	tim	699
484	tim	696	double calcMovingMolsCOMVel();
485			double calcSysCOMVel();
486			double calcTotalForce();
487	tim	1091	void updateZPos();
488	tim	1093	void updateCantPos();
489
490	gezelter	747	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
491	tim	738	friend class ForceSubtractionPolicy;
492	tim	677
493	tim	658	};
494
495			#endif