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 char* 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;


  char addParams[100];
};

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 char* 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 char* 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 char* 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 char* 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:	851
Committed:	Wed Nov 5 19:18:17 2003 UTC (21 years, 9 months ago) by mmeineke
File size:	12658 byte(s)
Log Message:	some work on trying to find the compression bug
#	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	mmeineke	851	virtual char* 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	851
82			char addParams[100];
83	mmeineke	377	};
84
85	mmeineke	849	class NVE : public Integrator {
86	mmeineke	540
87	mmeineke	561	public:
88			NVE ( SimInfo theInfo, ForceFields the_ff ):
89	mmeineke	849	Integrator( theInfo, the_ff ){}
90	tim	837	virtual ~NVE(){}
91	tim	645	};
92	mmeineke	555
93
94	mmeineke	849	class NVT : public Integrator {
95	mmeineke	555
96	gezelter	560	public:
97
98	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
99	tim	763	virtual ~NVT();
100	mmeineke	540
101	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
102			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
103	tim	763	void setChiTolerance(double tol) {chiTolerance = tol;}
104			virtual double getConservedQuantity(void);
105	mmeineke	850	virtual char* getAdditionalParameters(void);
106	gezelter	560
107	mmeineke	540	protected:
108	gezelter	560
109	mmeineke	561	virtual void moveA( void );
110			virtual void moveB( void );
111	mmeineke	540
112	mmeineke	561	virtual int readyCheck();
113	gezelter	560
114	mmeineke	746	virtual void resetIntegrator( void );
115
116	gezelter	565	// chi is a propagated degree of freedom.
117	gezelter	560
118	gezelter	565	double chi;
119	gezelter	560
120	tim	763	//integral of chi(t)dt
121			double integralOfChidt;
122
123	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
124	gezelter	560
125			double targetTemp;
126			double tauThermostat;
127	tim	837
128	gezelter	565	short int have_tau_thermostat, have_target_temp;
129	gezelter	560
130	tim	763	double *oldVel;
131			double *oldJi;
132
133			double chiTolerance;
134			short int have_chi_tolerance;
135
136	mmeineke	850	char addParamBuffer[1000];
137
138	mmeineke	540	};
139
140
141
142	mmeineke	849	class NPT : public Integrator{
143	tim	645
144	gezelter	560	public:
145
146	mmeineke	778	NPT ( SimInfo theInfo, ForceFields the_ff);
147			virtual ~NPT();
148	tim	837
149	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
150			calcStress = 1;
151	mmeineke	850	Integrator::integrateStep( calcPot, calcStress );
152	mmeineke	594	}
153
154	mmeineke	778	virtual double getConservedQuantity(void) = 0;
155	mmeineke	851	virtual char* getAdditionalParameters(void) = 0;
156	mmeineke	843
157			double myTauThermo( void ) { return tauThermostat; }
158			double myTauBaro( void ) { return tauBarostat; }
159
160	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164	tim	763	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165			void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166			void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167	gezelter	560
168			protected:
169
170	mmeineke	561	virtual void moveA( void );
171			virtual void moveB( void );
172	gezelter	560
173	mmeineke	561	virtual int readyCheck();
174	gezelter	560
175	mmeineke	746	virtual void resetIntegrator( void );
176
177	mmeineke	778	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178			virtual void getVelScaleB( double sc[3], int index ) = 0;
179	tim	837	virtual void getPosScale(double pos[3], double COM[3],
180	mmeineke	778	int index, double sc[3]) = 0;
181
182			virtual bool chiConverged( void );
183			virtual bool etaConverged( void ) = 0;
184	tim	837
185	mmeineke	778	virtual void evolveChiA( void );
186			virtual void evolveEtaA( void ) = 0;
187			virtual void evolveChiB( void );
188			virtual void evolveEtaB( void ) = 0;
189
190			virtual void scaleSimBox( void ) = 0;
191
192	tim	763	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
193
194	gezelter	565	// chi and eta are the propagated degrees of freedom
195	gezelter	560
196	mmeineke	778	double oldChi;
197			double prevChi;
198	gezelter	565	double chi;
199	gezelter	574	double NkBT;
200	tim	763	double fkBT;
201	gezelter	560
202	mmeineke	778	double tt2, tb2;
203			double instaTemp, instaPress, instaVol;
204	mmeineke	780	double press[3][3];
205	mmeineke	778
206	tim	763	int Nparticles;
207
208			double integralOfChidt;
209
210	tim	837	// targetTemp, targetPressure, and tauBarostat must be set.
211	gezelter	560	// One of qmass or tauThermostat must be set;
212
213			double targetTemp;
214			double targetPressure;
215			double tauThermostat;
216			double tauBarostat;
217
218			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
219	gezelter	565	short int have_target_pressure;
220	gezelter	560
221	tim	763	double *oldPos;
222			double *oldVel;
223			double *oldJi;
224
225			double chiTolerance;
226			short int have_chi_tolerance;
227			double posIterTolerance;
228			short int have_pos_iter_tolerance;
229			double etaTolerance;
230			short int have_eta_tolerance;
231
232	mmeineke	850	char addParamBuffer[1000];
233
234	gezelter	560	};
235
236	mmeineke	849	class NPTi : public NPT{
237	tim	837
238	mmeineke	778	public:
239			NPTi( SimInfo theInfo, ForceFields the_ff);
240			~NPTi();
241
242			virtual double getConservedQuantity(void);
243			virtual void resetIntegrator(void);
244	mmeineke	851	virtual char* getAdditionalParameters(void);
245	mmeineke	778	protected:
246
247
248	tim	837
249	mmeineke	778	virtual void evolveEtaA(void);
250			virtual void evolveEtaB(void);
251
252			virtual bool etaConverged( void );
253
254			virtual void scaleSimBox( void );
255
256			virtual void getVelScaleA( double sc[3], double vel[3] );
257			virtual void getVelScaleB( double sc[3], int index );
258	tim	837	virtual void getPosScale(double pos[3], double COM[3],
259	mmeineke	778	int index, double sc[3]);
260
261			double eta, oldEta, prevEta;
262			};
263
264	mmeineke	849	class NPTf : public NPT{
265	gezelter	576
266			public:
267
268			NPTf ( SimInfo theInfo, ForceFields the_ff);
269	tim	767	virtual ~NPTf();
270	gezelter	576
271	tim	763	virtual double getConservedQuantity(void);
272	mmeineke	851	virtual char* getAdditionalParameters(void);
273	mmeineke	780	virtual void resetIntegrator(void);
274	mmeineke	594
275	gezelter	576	protected:
276
277	mmeineke	780	virtual void evolveEtaA(void);
278			virtual void evolveEtaB(void);
279	gezelter	576
280	mmeineke	780	virtual bool etaConverged( void );
281	mmeineke	746
282	mmeineke	780	virtual void scaleSimBox( void );
283	gezelter	576
284	mmeineke	780	virtual void getVelScaleA( double sc[3], double vel[3] );
285			virtual void getVelScaleB( double sc[3], int index );
286	tim	837	virtual void getPosScale(double pos[3], double COM[3],
287	mmeineke	780	int index, double sc[3]);
288	tim	763
289	gezelter	588	double eta[3][3];
290	mmeineke	780	double oldEta[3][3];
291			double prevEta[3][3];
292	gezelter	576	};
293
294	mmeineke	849	class NPTxyz : public NPT{
295	mmeineke	755
296			public:
297
298	mmeineke	812	NPTxyz ( SimInfo theInfo, ForceFields the_ff);
299			virtual ~NPTxyz();
300	mmeineke	755
301	mmeineke	812	virtual double getConservedQuantity(void);
302	mmeineke	851	virtual char* getAdditionalParameters(void);
303	mmeineke	812	virtual void resetIntegrator(void);
304	mmeineke	755
305			protected:
306
307	mmeineke	812	virtual void evolveEtaA(void);
308			virtual void evolveEtaB(void);
309	mmeineke	755
310	mmeineke	812	virtual bool etaConverged( void );
311	mmeineke	755
312	mmeineke	812	virtual void scaleSimBox( void );
313	mmeineke	755
314	mmeineke	812	virtual void getVelScaleA( double sc[3], double vel[3] );
315			virtual void getVelScaleB( double sc[3], int index );
316	tim	837	virtual void getPosScale(double pos[3], double COM[3],
317	mmeineke	812	int index, double sc[3]);
318	mmeineke	755
319	mmeineke	812	double eta[3][3];
320			double oldEta[3][3];
321			double prevEta[3][3];
322			};
323	mmeineke	755
324
325	mmeineke	849	// template<typename T> class ZConstraint : public T {
326	tim	837
327	mmeineke	849	// public:
328			// class ForceSubtractionPolicy{
329			// public:
330			// ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
331	tim	658
332	mmeineke	849	// virtual void update() = 0;
333			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
335			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
336			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
337	tim	837
338	mmeineke	849	// protected:
339			// ZConstraint<T>* zconsIntegrator;
340			// };
341	tim	699
342	mmeineke	849	// class PolicyByNumber : public ForceSubtractionPolicy{
343	gezelter	747
344	mmeineke	849	// public:
345			// PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
346			// virtual void update();
347			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
348			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
349			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
350			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
351	tim	837
352	mmeineke	849	// private:
353			// int totNumOfMovingAtoms;
354			// };
355	tim	699
356	mmeineke	849	// class PolicyByMass : public ForceSubtractionPolicy{
357	gezelter	747
358	mmeineke	849	// public:
359			// PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
360	tim	837
361	mmeineke	849	// virtual void update();
362			// virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
363			// virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
364			// virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
365			// virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
366	tim	699
367	mmeineke	849	// private:
368			// double totMassOfMovingAtoms;
369			// };
370	tim	699
371	mmeineke	849	// public:
372	tim	658
373	mmeineke	849	// ZConstraint( SimInfo theInfo, ForceFields the_ff);
374			// ~ZConstraint();
375	tim	837
376	mmeineke	849	// void setZConsTime(double time) {this->zconsTime = time;}
377			// void getZConsTime() {return zconsTime;}
378	tim	837
379	mmeineke	849	// void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
380			// void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
381	tim	837
382	mmeineke	849	// void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
383			// string getZConsOutput() {return zconsOutput;}
384	tim	837
385	mmeineke	849	// virtual void integrate();
386	tim	658
387	tim	837
388	mmeineke	849	// #ifdef IS_MPI
389			// virtual void update(); //which is called to indicate the molecules' migration
390			// #endif
391	tim	658
392	mmeineke	849	// enum ZConsState {zcsMoving, zcsFixed};
393	mmeineke	790
394	mmeineke	849	// vector<Molecule*> zconsMols; //z-constraint molecules array
395			// vector<ZConsState> states; //state of z-constraint molecules
396	mmeineke	790
397
398	tim	837
399	mmeineke	849	// int totNumOfUnconsAtoms; //total number of uncontraint atoms
400			// double totalMassOfUncons; //total mas of unconstraint molecules
401	mmeineke	790
402
403	mmeineke	849	// protected:
404	tim	658
405	mmeineke	790
406	tim	837
407	mmeineke	849	// virtual void calcForce( int calcPot, int calcStress );
408			// virtual void thermalize(void);
409	tim	837
410	mmeineke	849	// void zeroOutVel();
411			// void doZconstraintForce();
412			// void doHarmonic();
413			// bool checkZConsState();
414	tim	677
415	mmeineke	849	// bool haveFixedZMols();
416			// bool haveMovingZMols();
417	tim	677
418	mmeineke	849	// double calcZSys();
419	tim	677
420	mmeineke	849	// int isZConstraintMol(Molecule* mol);
421	tim	677
422
423	mmeineke	849	// double zconsTime; //sample time
424			// double zconsTol; //tolerance of z-contratint
425			// double zForceConst; //base force constant term
426			// //which is estimate by OOPSE
427	mmeineke	790
428	tim	837
429	mmeineke	849	// vector<double> massOfZConsMols; //mass of z-constraint molecule
430			// vector<double> kz; //force constant array
431	mmeineke	790
432	mmeineke	849	// vector<double> zPos; //
433	tim	837
434
435	mmeineke	849	// vector<Molecule*> unconsMols; //unconstraint molecules array
436			// vector<double> massOfUnconsMols; //mass array of unconstraint molecules
437	tim	682
438	mmeineke	790
439	mmeineke	849	// vector<ZConsParaItem>* parameters; //
440	tim	837
441	mmeineke	849	// vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
442	tim	677
443	mmeineke	849	// int* indexOfZConsMols; //index of local Z-Constraint Molecules
444			// double* fz;
445			// double* curZPos;
446	tim	677
447	mmeineke	790
448	tim	837
449	mmeineke	849	// int whichDirection; //constraint direction
450	tim	837
451	mmeineke	849	// private:
452	tim	837
453	mmeineke	849	// string zconsOutput; //filename of zconstraint output
454			// ZConsWriter* fzOut; //z-constraint writer
455	tim	677
456	mmeineke	849	// double curZconsTime;
457	tim	699
458	mmeineke	849	// double calcMovingMolsCOMVel();
459			// double calcSysCOMVel();
460			// double calcTotalForce();
461	tim	837
462	mmeineke	849	// ForceSubtractionPolicy* forcePolicy; //force subtraction policy
463			// friend class ForceSubtractionPolicy;
464	tim	677
465	mmeineke	849	// };
466	tim	658
467			#endif