OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include "Atom.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;


class Integrator : public  BaseIntegrator{
  
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( DirectionalAtom* dAtom, 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
  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;

};

class NVE : public Integrator {

public:
  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
    Integrator( theInfo, the_ff ){}
  virtual ~NVE(){}
};


class NVT : public Integrator {

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 char* 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;

  char addParamBuffer[1000];

};


class NPT : public Integrator{

public:

  NPT ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPT();

  virtual void integrateStep( int calcPot, int calcStress ){
    calcStress = 1;
    Integrator::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 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;

  char addParamBuffer[1000];

};

class NPTi : public NPT{

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]);

  double eta, oldEta, prevEta;
};

class NPTf : public NPT{

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]);

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[3][3];
};

class NPTxyz : public NPT{

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]);

  double eta[3][3];
  double oldEta[3][3];
  double prevEta[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();
//   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

//   int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
//   double* fz;
//   double* curZPos;


//   int whichDirection;                           //constraint direction

// private:

//   string zconsOutput;                         //filename of zconstraint output
//   ZConsWriter* fzOut;                         //z-constraint writer

//   double curZconsTime;

//   double calcMovingMolsCOMVel();
//   double calcSysCOMVel();
//   double calcTotalForce();

//   ForceSubtractionPolicy* forcePolicy; //force subtraction policy
//   friend class ForceSubtractionPolicy;

// };

#endif
Revision:	850
Committed:	Mon Nov 3 22:07:17 2003 UTC (21 years, 9 months ago) by mmeineke
File size:	12639 byte(s)
Log Message:	begun work on removing templates and most of standard template library from OOPSE.
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4			#include "Atom.hpp"
5	gezelter	604	#include "Molecule.hpp"
6	mmeineke	377	#include "SRI.hpp"
7			#include "AbstractClasses.hpp"
8			#include "SimInfo.hpp"
9			#include "ForceFields.hpp"
10	mmeineke	540	#include "Thermo.hpp"
11			#include "ReadWrite.hpp"
12	mmeineke	849	// #include "ZConsWriter.hpp"
13	mmeineke	377
14	tim	658	using namespace std;
15	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
16			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
17	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
18	mmeineke	561	const int maxIteration = 300;
19			const double tol = 1.0e-6;
20
21	mmeineke	377
22	mmeineke	849	class Integrator : public BaseIntegrator{
23
24	mmeineke	377	public:
25	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
26	mmeineke	548	virtual ~Integrator();
27	mmeineke	377	void integrate( void );
28	tim	763	virtual double getConservedQuantity(void);
29	tim	837	virtual string getAdditionalParameters(void);
30	mmeineke	377
31	mmeineke	540	protected:
32	mmeineke	778
33	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
34	mmeineke	548	virtual void preMove( void );
35	mmeineke	540	virtual void moveA( void );
36			virtual void moveB( void );
37			virtual void constrainA( void );
38			virtual void constrainB( void );
39	mmeineke	559	virtual int readyCheck( void ) { return 1; }
40	tim	677
41	mmeineke	746	virtual void resetIntegrator( void ) { }
42	tim	837
43			virtual void calcForce( int calcPot, int calcStress );
44	tim	677	virtual void thermalize();
45	tim	837
46	mmeineke	778	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
47
48	mmeineke	540	void checkConstraints( void );
49	tim	837	void rotate( int axes1, int axes2, double angle, double j[3],
50	tim	701	double A[3][3] );
51	tim	837
52	mmeineke	377	ForceFields* myFF;
53
54	mmeineke	540	SimInfo *info; // all the info we'll ever need
55			int nAtoms; /* the number of atoms */
56	mmeineke	548	int oldAtoms;
57	mmeineke	540	Atom *atoms; / array of atom pointers */
58	mmeineke	423	Molecule* molecules;
59			int nMols;
60
61	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
62	tim	701	// constraints.
63	tim	837	int nConstrained; // counter for number of constraints
64			int *constrainedA; // the i of a constraint pair
65			int *constrainedB; // the j of a constraint pair
66			double *constrainedDsqr; // the square of the constraint distance
67
68	mmeineke	548	int* moving; // tells whether we are moving atom i
69			int* moved; // tells whether we have moved atom i
70	tim	837	double* oldPos; // pre constrained positions
71	mmeineke	548
72	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
73	tim	837
74	mmeineke	540	double dt;
75	mmeineke	541	double dt2;
76	gezelter	560
77	mmeineke	540	Thermo *tStats;
78			StatWriter* statOut;
79			DumpWriter* dumpOut;
80	tim	837
81	mmeineke	377	};
82
83	mmeineke	849	class NVE : public Integrator {
84	mmeineke	540
85	mmeineke	561	public:
86			NVE ( SimInfo theInfo, ForceFields the_ff ):
87	mmeineke	849	Integrator( theInfo, the_ff ){}
88	tim	837	virtual ~NVE(){}
89	tim	645	};
90	mmeineke	555
91
92	mmeineke	849	class NVT : public Integrator {
93	mmeineke	555
94	gezelter	560	public:
95
96	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
97	tim	763	virtual ~NVT();
98	mmeineke	540
99	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
100			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
101	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
102			virtual double getConservedQuantity(void);
103	mmeineke	850	virtual char* getAdditionalParameters(void);
104	gezelter	560
105	mmeineke	540	protected:
106	gezelter	560
107	mmeineke	561	virtual void moveA( void );
108			virtual void moveB( void );
109	mmeineke	540
110	mmeineke	561	virtual int readyCheck();
111	gezelter	560
112	mmeineke	746	virtual void resetIntegrator( void );
113
114	gezelter	565	// chi is a propagated degree of freedom.
115	gezelter	560
116	gezelter	565	double chi;
117	gezelter	560
118	tim	763	//integral of chi(t)dt
119			double integralOfChidt;
120
121	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
122	gezelter	560
123			double targetTemp;
124			double tauThermostat;
125	tim	837
126	gezelter	565	short int have_tau_thermostat, have_target_temp;
127	gezelter	560
128	tim	763	double *oldVel;
129			double *oldJi;
130
131			double chiTolerance;
132			short int have_chi_tolerance;
133
134	mmeineke	850	char addParamBuffer[1000];
135
136	mmeineke	540	};
137
138
139
140	mmeineke	849	class NPT : public Integrator{
141	tim	645
142	gezelter	560	public:
143
144	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
145			virtual ~NPT();
146	tim	837
147	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
148			calcStress = 1;
149	mmeineke	850	Integrator::integrateStep( calcPot, calcStress );
150	mmeineke	594	}
151
152	mmeineke	778	virtual double getConservedQuantity(void) = 0;
153	tim	837	virtual string getAdditionalParameters(void) = 0;
154	mmeineke	843
155			double myTauThermo( void ) { return tauThermostat; }
156			double myTauBaro( void ) { return tauBarostat; }
157
158	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
159			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
160			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
161			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
162	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
163			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
164			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
165	gezelter	560
166			protected:
167
168	mmeineke	561	virtual void moveA( void );
169			virtual void moveB( void );
170	gezelter	560
171	mmeineke	561	virtual int readyCheck();
172	gezelter	560
173	mmeineke	746	virtual void resetIntegrator( void );
174
175	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
176			virtual void getVelScaleB( double sc[3], int index ) = 0;
177	tim	837	virtual void getPosScale(double pos[3], double COM[3],
178	mmeineke	778	int index, double sc[3]) = 0;
179
180			virtual bool chiConverged( void );
181			virtual bool etaConverged( void ) = 0;
182	tim	837
183	mmeineke	778	virtual void evolveChiA( void );
184			virtual void evolveEtaA( void ) = 0;
185			virtual void evolveChiB( void );
186			virtual void evolveEtaB( void ) = 0;
187
188			virtual void scaleSimBox( void ) = 0;
189
190	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
191
192	gezelter	565	// chi and eta are the propagated degrees of freedom
193	gezelter	560
194	mmeineke	778	double oldChi;
195			double prevChi;
196	gezelter	565	double chi;
197	gezelter	574	double NkBT;
198	tim	763	double fkBT;
199	gezelter	560
200	mmeineke	778	double tt2, tb2;
201			double instaTemp, instaPress, instaVol;
202	mmeineke	780	double press[3][3];
203	mmeineke	778
204	tim	763	int Nparticles;
205
206			double integralOfChidt;
207
208	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
209	gezelter	560	// One of qmass or tauThermostat must be set;
210
211			double targetTemp;
212			double targetPressure;
213			double tauThermostat;
214			double tauBarostat;
215
216			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
217	gezelter	565	short int have_target_pressure;
218	gezelter	560
219	tim	763	double *oldPos;
220			double *oldVel;
221			double *oldJi;
222
223			double chiTolerance;
224			short int have_chi_tolerance;
225			double posIterTolerance;
226			short int have_pos_iter_tolerance;
227			double etaTolerance;
228			short int have_eta_tolerance;
229
230	mmeineke	850	char addParamBuffer[1000];
231
232	gezelter	560	};
233
234	mmeineke	849	class NPTi : public NPT{
235	tim	837
236	mmeineke	778	public:
237			NPTi( SimInfo theInfo, ForceFields the_ff);
238			~NPTi();
239
240			virtual double getConservedQuantity(void);
241			virtual void resetIntegrator(void);
242	tim	837	virtual string getAdditionalParameters(void);
243	mmeineke	778	protected:
244
245
246	tim	837
247	mmeineke	778	virtual void evolveEtaA(void);
248			virtual void evolveEtaB(void);
249
250			virtual bool etaConverged( void );
251
252			virtual void scaleSimBox( void );
253
254			virtual void getVelScaleA( double sc[3], double vel[3] );
255			virtual void getVelScaleB( double sc[3], int index );
256	tim	837	virtual void getPosScale(double pos[3], double COM[3],
257	mmeineke	778	int index, double sc[3]);
258
259			double eta, oldEta, prevEta;
260			};
261
262	mmeineke	849	class NPTf : public NPT{
263	gezelter	576
264			public:
265
266			NPTf ( SimInfo theInfo, ForceFields the_ff);
267	tim	767	virtual ~NPTf();
268	gezelter	576
269	tim	763	virtual double getConservedQuantity(void);
270	tim	837	virtual string getAdditionalParameters(void);
271	mmeineke	780	virtual void resetIntegrator(void);
272	mmeineke	594
273	gezelter	576	protected:
274
275	mmeineke	780	virtual void evolveEtaA(void);
276			virtual void evolveEtaB(void);
277	gezelter	576
278	mmeineke	780	virtual bool etaConverged( void );
279	mmeineke	746
280	mmeineke	780	virtual void scaleSimBox( void );
281	gezelter	576
282	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
283			virtual void getVelScaleB( double sc[3], int index );
284	tim	837	virtual void getPosScale(double pos[3], double COM[3],
285	mmeineke	780	int index, double sc[3]);
286	tim	763
287	gezelter	588	double eta[3][3];
288	mmeineke	780	double oldEta[3][3];
289			double prevEta[3][3];
290	gezelter	576	};
291
292	mmeineke	849	class NPTxyz : public NPT{
293	mmeineke	755
294			public:
295
296	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
297			virtual ~NPTxyz();
298	mmeineke	755
299	mmeineke	812	virtual double getConservedQuantity(void);
300	tim	837	virtual string getAdditionalParameters(void);
301	mmeineke	812	virtual void resetIntegrator(void);
302	mmeineke	755
303			protected:
304
305	mmeineke	812	virtual void evolveEtaA(void);
306			virtual void evolveEtaB(void);
307	mmeineke	755
308	mmeineke	812	virtual bool etaConverged( void );
309	mmeineke	755
310	mmeineke	812	virtual void scaleSimBox( void );
311	mmeineke	755
312	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
313			virtual void getVelScaleB( double sc[3], int index );
314	tim	837	virtual void getPosScale(double pos[3], double COM[3],
315	mmeineke	812	int index, double sc[3]);
316	mmeineke	755
317	mmeineke	812	double eta[3][3];
318			double oldEta[3][3];
319			double prevEta[3][3];
320			};
321	mmeineke	755
322
323	mmeineke	849	// template<typename T> class ZConstraint : public T {
324	tim	837
325	mmeineke	849	// public:
326			// class ForceSubtractionPolicy{
327			// public:
328			// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
329	tim	658
330	mmeineke	849	// virtual void update() = 0;
331			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
333			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
335	tim	837
336	mmeineke	849	// protected:
337			// ZConstraint<T>* zconsIntegrator;
338			// };
339	tim	699
340	mmeineke	849	// class PolicyByNumber : public ForceSubtractionPolicy{
341	gezelter	747
342	mmeineke	849	// public:
343			// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
344			// virtual void update();
345			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
346			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
347			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
348			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
349	tim	837
350	mmeineke	849	// private:
351			// int totNumOfMovingAtoms;
352			// };
353	tim	699
354	mmeineke	849	// class PolicyByMass : public ForceSubtractionPolicy{
355	gezelter	747
356	mmeineke	849	// public:
357			// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358	tim	837
359	mmeineke	849	// virtual void update();
360			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
361			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
362			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
363			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
364	tim	699
365	mmeineke	849	// private:
366			// double totMassOfMovingAtoms;
367			// };
368	tim	699
369	mmeineke	849	// public:
370	tim	658
371	mmeineke	849	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
372			// ~ZConstraint();
373	tim	837
374	mmeineke	849	// void setZConsTime(double time) {this->zconsTime = time;}
375			// void getZConsTime() {return zconsTime;}
376	tim	837
377	mmeineke	849	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
378			// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
379	tim	837
380	mmeineke	849	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
381			// string getZConsOutput() {return zconsOutput;}
382	tim	837
383	mmeineke	849	// virtual void integrate();
384	tim	658
385	tim	837
386	mmeineke	849	// #ifdef IS_MPI
387			// virtual void update(); //which is called to indicate the molecules' migration
388			// #endif
389	tim	658
390	mmeineke	849	// enum ZConsState {zcsMoving, zcsFixed};
391	mmeineke	790
392	mmeineke	849	// vector<Molecule*> zconsMols; //z-constraint molecules array
393			// vector<ZConsState> states; //state of z-constraint molecules
394	mmeineke	790
395
396	tim	837
397	mmeineke	849	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
398			// double totalMassOfUncons; //total mas of unconstraint molecules
399	mmeineke	790
400
401	mmeineke	849	// protected:
402	tim	658
403	mmeineke	790
404	tim	837
405	mmeineke	849	// virtual void calcForce( int calcPot, int calcStress );
406			// virtual void thermalize(void);
407	tim	837
408	mmeineke	849	// void zeroOutVel();
409			// void doZconstraintForce();
410			// void doHarmonic();
411			// bool checkZConsState();
412	tim	677
413	mmeineke	849	// bool haveFixedZMols();
414			// bool haveMovingZMols();
415	tim	677
416	mmeineke	849	// double calcZSys();
417	tim	677
418	mmeineke	849	// int isZConstraintMol(Molecule* mol);
419	tim	677
420
421	mmeineke	849	// double zconsTime; //sample time
422			// double zconsTol; //tolerance of z-contratint
423			// double zForceConst; //base force constant term
424			// //which is estimate by OOPSE
425	mmeineke	790
426	tim	837
427	mmeineke	849	// vector<double> massOfZConsMols; //mass of z-constraint molecule
428			// vector<double> kz; //force constant array
429	mmeineke	790
430	mmeineke	849	// vector<double> zPos; //
431	tim	837
432
433	mmeineke	849	// vector<Molecule*> unconsMols; //unconstraint molecules array
434			// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
435	tim	682
436	mmeineke	790
437	mmeineke	849	// vector<ZConsParaItem>* parameters; //
438	tim	837
439	mmeineke	849	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
440	tim	677
441	mmeineke	849	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
442			// double* fz;
443			// double* curZPos;
444	tim	677
445	mmeineke	790
446	tim	837
447	mmeineke	849	// int whichDirection; //constraint direction
448	tim	837
449	mmeineke	849	// private:
450	tim	837
451	mmeineke	849	// string zconsOutput; //filename of zconstraint output
452			// ZConsWriter* fzOut; //z-constraint writer
453	tim	677
454	mmeineke	849	// double curZconsTime;
455	tim	699
456	mmeineke	849	// double calcMovingMolsCOMVel();
457			// double calcSysCOMVel();
458			// double calcTotalForce();
459	tim	837
460	mmeineke	849	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
461			// friend class ForceSubtractionPolicy;
462	tim	677
463	mmeineke	849	// };
464	tim	658
465			#endif