OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include <string>
#include <vector>
#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;


template<typename T = BaseIntegrator> class Integrator : public T {

public:
  Integrator( SimInfo *theInfo, ForceFields* the_ff );
  virtual ~Integrator();
  void integrate( void );
  virtual double  getConservedQuantity(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;
  
};

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);

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;

  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;

};

template<typename T> class NPTi : public T{
  
public:
  NPTi( SimInfo *theInfo, ForceFields* the_ff);
  ~NPTi();

  virtual double getConservedQuantity(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, oldEta, prevEta;
};

template<typename T> class NPTzm : public T{

public:

  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTzm() {};

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

  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;}

protected:

  virtual void moveA( void );
  virtual void moveB( void );

  virtual int readyCheck();

  virtual void resetIntegrator( void );

  Molecule* myMolecules;
  Atom** myAtoms;

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta;
  double etaZ;
  double NkBT;

  // 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;

};

template<typename T> class NPTf : public T{

public:

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

  virtual double getConservedQuantity(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 NPTxym : public T{

public:

  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
  virtual ~NPTxym() {};

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

  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;}

protected:

  virtual void moveA( void );
  virtual void moveB( void );

  virtual int readyCheck();

  virtual void resetIntegrator( void );

  Molecule* myMolecules;
  Atom** myAtoms;

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta;
  double etaX;
  double etaY;
  double NkBT;

  // 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;

};

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

protected:

  enum ZConsState {zcsMoving, zcsFixed};  
 
  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<Molecule*> zconsMols;              //z-constraint molecules array
  vector<double> massOfZConsMols;       //mass of z-constraint molecule 
  vector<double> kz;                              //force constant array
  vector<ZConsState> states;                 //state of z-constraint molecules
  vector<double> zPos;                          //
  
  
  vector<Molecule*> unconsMols;           //unconstraint molecules array
  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
  double totalMassOfUncons;                //total mas 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 totNumOfUnconsAtoms;              //total number of uncontraint atoms

  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:	782
Committed:	Tue Sep 23 20:34:31 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	13976 byte(s)
Log Message:	Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include <string>
5	#include <vector>
6	#include "Atom.hpp"
7	#include "Molecule.hpp"
8	#include "SRI.hpp"
9	#include "AbstractClasses.hpp"
10	#include "SimInfo.hpp"
11	#include "ForceFields.hpp"
12	#include "Thermo.hpp"
13	#include "ReadWrite.hpp"
14	#include "ZConsWriter.hpp"
15
16	using namespace std;
17	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
18	const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	const int maxIteration = 300;
21	const double tol = 1.0e-6;
22
23
24	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	public:
27	Integrator( SimInfo theInfo, ForceFields the_ff );
28	virtual ~Integrator();
29	void integrate( void );
30	virtual double getConservedQuantity(void);
31
32	protected:
33
34	virtual void integrateStep( int calcPot, int calcStress );
35	virtual void preMove( void );
36	virtual void moveA( void );
37	virtual void moveB( void );
38	virtual void constrainA( void );
39	virtual void constrainB( void );
40	virtual int readyCheck( void ) { return 1; }
41
42	virtual void resetIntegrator( void ) { }
43
44	virtual void calcForce( int calcPot, int calcStress );
45	virtual void thermalize();
46
47	virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48
49	void checkConstraints( void );
50	void rotate( int axes1, int axes2, double angle, double j[3],
51	double A[3][3] );
52
53	ForceFields* myFF;
54
55	SimInfo *info; // all the info we'll ever need
56	int nAtoms; /* the number of atoms */
57	int oldAtoms;
58	Atom *atoms; / array of atom pointers */
59	Molecule* molecules;
60	int nMols;
61
62	int isConstrained; // boolean to know whether the systems contains
63	// constraints.
64	int nConstrained; // counter for number of constraints
65	int *constrainedA; // the i of a constraint pair
66	int *constrainedB; // the j of a constraint pair
67	double *constrainedDsqr; // the square of the constraint distance
68
69	int* moving; // tells whether we are moving atom i
70	int* moved; // tells whether we have moved atom i
71	double* oldPos; // pre constrained positions
72
73	short isFirst; /boolean for the first time integrate is called /
74
75	double dt;
76	double dt2;
77
78	Thermo *tStats;
79	StatWriter* statOut;
80	DumpWriter* dumpOut;
81
82	};
83
84	typedef Integrator<BaseIntegrator> RealIntegrator;
85
86	template<typename T> class NVE : public T {
87
88	public:
89	NVE ( SimInfo theInfo, ForceFields the_ff ):
90	T( theInfo, the_ff ){}
91	virtual ~NVE(){}
92	};
93
94
95	template<typename T> class NVT : public T {
96
97	public:
98
99	NVT ( SimInfo theInfo, ForceFields the_ff);
100	virtual ~NVT();
101
102	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104	void setChiTolerance(double tol) {chiTolerance = tol;}
105	virtual double getConservedQuantity(void);
106
107	protected:
108
109	virtual void moveA( void );
110	virtual void moveB( void );
111
112	virtual int readyCheck();
113
114	virtual void resetIntegrator( void );
115
116	// chi is a propagated degree of freedom.
117
118	double chi;
119
120	//integral of chi(t)dt
121	double integralOfChidt;
122
123	// targetTemp must be set. tauThermostat must also be set;
124
125	double targetTemp;
126	double tauThermostat;
127
128	short int have_tau_thermostat, have_target_temp;
129
130	double *oldVel;
131	double *oldJi;
132
133	double chiTolerance;
134	short int have_chi_tolerance;
135
136	};
137
138
139
140	template<typename T> class NPT : public T{
141
142	public:
143
144	NPT ( SimInfo theInfo, ForceFields the_ff);
145	virtual ~NPT();
146
147	virtual void integrateStep( int calcPot, int calcStress ){
148	calcStress = 1;
149	T::integrateStep( calcPot, calcStress );
150	}
151
152	virtual double getConservedQuantity(void) = 0;
153
154	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158	void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159	void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160	void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161
162	protected:
163
164	virtual void moveA( void );
165	virtual void moveB( void );
166
167	virtual int readyCheck();
168
169	virtual void resetIntegrator( void );
170
171	virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172	virtual void getVelScaleB( double sc[3], int index ) = 0;
173	virtual void getPosScale(double pos[3], double COM[3],
174	int index, double sc[3]) = 0;
175
176	virtual bool chiConverged( void );
177	virtual bool etaConverged( void ) = 0;
178
179	virtual void evolveChiA( void );
180	virtual void evolveEtaA( void ) = 0;
181	virtual void evolveChiB( void );
182	virtual void evolveEtaB( void ) = 0;
183
184	virtual void scaleSimBox( void ) = 0;
185
186	void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187
188	// chi and eta are the propagated degrees of freedom
189
190	double oldChi;
191	double prevChi;
192	double chi;
193	double NkBT;
194	double fkBT;
195
196	double tt2, tb2;
197	double instaTemp, instaPress, instaVol;
198	double press[3][3];
199
200	int Nparticles;
201
202	double integralOfChidt;
203
204	// targetTemp, targetPressure, and tauBarostat must be set.
205	// One of qmass or tauThermostat must be set;
206
207	double targetTemp;
208	double targetPressure;
209	double tauThermostat;
210	double tauBarostat;
211
212	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213	short int have_target_pressure;
214
215	double *oldPos;
216	double *oldVel;
217	double *oldJi;
218
219	double chiTolerance;
220	short int have_chi_tolerance;
221	double posIterTolerance;
222	short int have_pos_iter_tolerance;
223	double etaTolerance;
224	short int have_eta_tolerance;
225
226	};
227
228	template<typename T> class NPTi : public T{
229
230	public:
231	NPTi( SimInfo theInfo, ForceFields the_ff);
232	~NPTi();
233
234	virtual double getConservedQuantity(void);
235	virtual void resetIntegrator(void);
236
237	protected:
238
239
240
241	virtual void evolveEtaA(void);
242	virtual void evolveEtaB(void);
243
244	virtual bool etaConverged( void );
245
246	virtual void scaleSimBox( void );
247
248	virtual void getVelScaleA( double sc[3], double vel[3] );
249	virtual void getVelScaleB( double sc[3], int index );
250	virtual void getPosScale(double pos[3], double COM[3],
251	int index, double sc[3]);
252
253	double eta, oldEta, prevEta;
254	};
255
256	template<typename T> class NPTzm : public T{
257
258	public:
259
260	NPTzm ( SimInfo theInfo, ForceFields the_ff);
261	virtual ~NPTzm() {};
262
263	virtual void integrateStep( int calcPot, int calcStress ){
264	calcStress = 1;
265	T::integrateStep( calcPot, calcStress );
266	}
267
268	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272
273	protected:
274
275	virtual void moveA( void );
276	virtual void moveB( void );
277
278	virtual int readyCheck();
279
280	virtual void resetIntegrator( void );
281
282	Molecule* myMolecules;
283	Atom** myAtoms;
284
285	// chi and eta are the propagated degrees of freedom
286
287	double chi;
288	double eta;
289	double etaZ;
290	double NkBT;
291
292	// targetTemp, targetPressure, and tauBarostat must be set.
293	// One of qmass or tauThermostat must be set;
294
295	double targetTemp;
296	double targetPressure;
297	double tauThermostat;
298	double tauBarostat;
299
300	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301	short int have_target_pressure;
302
303	};
304
305	template<typename T> class NPTf : public T{
306
307	public:
308
309	NPTf ( SimInfo theInfo, ForceFields the_ff);
310	virtual ~NPTf();
311
312	virtual double getConservedQuantity(void);
313	virtual void resetIntegrator(void);
314
315	protected:
316
317	virtual void evolveEtaA(void);
318	virtual void evolveEtaB(void);
319
320	virtual bool etaConverged( void );
321
322	virtual void scaleSimBox( void );
323
324	virtual void getVelScaleA( double sc[3], double vel[3] );
325	virtual void getVelScaleB( double sc[3], int index );
326	virtual void getPosScale(double pos[3], double COM[3],
327	int index, double sc[3]);
328
329	double eta[3][3];
330	double oldEta[3][3];
331	double prevEta[3][3];
332	};
333
334	template<typename T> class NPTxym : public T{
335
336	public:
337
338	NPTxym ( SimInfo theInfo, ForceFields the_ff);
339	virtual ~NPTxym() {};
340
341	virtual void integrateStep( int calcPot, int calcStress ){
342	calcStress = 1;
343	T::integrateStep( calcPot, calcStress );
344	}
345
346	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
350
351	protected:
352
353	virtual void moveA( void );
354	virtual void moveB( void );
355
356	virtual int readyCheck();
357
358	virtual void resetIntegrator( void );
359
360	Molecule* myMolecules;
361	Atom** myAtoms;
362
363	// chi and eta are the propagated degrees of freedom
364
365	double chi;
366	double eta;
367	double etaX;
368	double etaY;
369	double NkBT;
370
371	// targetTemp, targetPressure, and tauBarostat must be set.
372	// One of qmass or tauThermostat must be set;
373
374	double targetTemp;
375	double targetPressure;
376	double tauThermostat;
377	double tauBarostat;
378
379	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380	short int have_target_pressure;
381
382	};
383
384	template<typename T> class ZConstraint : public T {
385
386	public:
387	class ForceSubtractionPolicy{
388	public:
389	ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
390
391	virtual void update() = 0;
392	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
393	virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
394	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
395	virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
396
397	protected:
398	ZConstraint<T>* zconsIntegrator;;
399	};
400
401	class PolicyByNumber : public ForceSubtractionPolicy{
402
403	public:
404	PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
405	virtual void update();
406	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
407	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
408	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
409	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
410
411	private:
412	int totNumOfMovingAtoms;
413	};
414
415	class PolicyByMass : public ForceSubtractionPolicy{
416
417	public:
418	PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
419
420	virtual void update();
421	virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
422	virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
423	virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
424	virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
425
426	private:
427	double totMassOfMovingAtoms;
428	};
429
430	public:
431
432	ZConstraint( SimInfo theInfo, ForceFields the_ff);
433	~ZConstraint();
434
435	void setZConsTime(double time) {this->zconsTime = time;}
436	void getZConsTime() {return zconsTime;}
437
438	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
439	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
440
441	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
442	string getZConsOutput() {return zconsOutput;}
443
444	virtual void integrate();
445
446
447	#ifdef IS_MPI
448	virtual void update(); //which is called to indicate the molecules' migration
449	#endif
450
451	protected:
452
453	enum ZConsState {zcsMoving, zcsFixed};
454
455	virtual void calcForce( int calcPot, int calcStress );
456	virtual void thermalize(void);
457
458	void zeroOutVel();
459	void doZconstraintForce();
460	void doHarmonic();
461	bool checkZConsState();
462
463	bool haveFixedZMols();
464	bool haveMovingZMols();
465
466	double calcZSys();
467
468	int isZConstraintMol(Molecule* mol);
469
470
471	double zconsTime; //sample time
472	double zconsTol; //tolerance of z-contratint
473	double zForceConst; //base force constant term
474	//which is estimate by OOPSE
475
476	vector<Molecule*> zconsMols; //z-constraint molecules array
477	vector<double> massOfZConsMols; //mass of z-constraint molecule
478	vector<double> kz; //force constant array
479	vector<ZConsState> states; //state of z-constraint molecules
480	vector<double> zPos; //
481
482
483	vector<Molecule*> unconsMols; //unconstraint molecules array
484	vector<double> massOfUnconsMols; //mass array of unconstraint molecules
485	double totalMassOfUncons; //total mas of unconstraint molecules
486
487	vector<ZConsParaItem>* parameters; //
488
489	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
490
491	int* indexOfZConsMols; //index of local Z-Constraint Molecules
492	double* fz;
493	double* curZPos;
494
495	int totNumOfUnconsAtoms; //total number of uncontraint atoms
496
497	int whichDirection; //constraint direction
498
499	private:
500
501	string zconsOutput; //filename of zconstraint output
502	ZConsWriter* fzOut; //z-constraint writer
503
504	double curZconsTime;
505
506	double calcMovingMolsCOMVel();
507	double calcSysCOMVel();
508	double calcTotalForce();
509
510	ForceSubtractionPolicy* forcePolicy; //force subtraction policy
511	friend class ForceSubtractionPolicy;
512
513	};
514
515	#endif