OOPSE/libmdtools/Integrator.hpp

#ifndef _INTEGRATOR_H_
#define _INTEGRATOR_H_

#include "Atom.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"

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 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 );


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; }
  
  void checkConstraints( void );
  void rotate( int axes1, int axes2, double angle, double j[3], 
               double A[9] );


  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;

  double* pos;
  double* vel;
  double* frc;
  double* trq;
  double* Amat;

  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 setQmass(double q) {qmass = q; have_qmass = 1;}
  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}

protected:

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

  virtual int readyCheck();

  // zeta is a propagated degree of freedom.

  double zeta;

  // targetTemp must be set.  One of qmass or tauThermostat must be set;

  double qmass;
  double targetTemp;
  double tauThermostat;

  double NkBT;
  
  short int have_tau_thermostat, have_target_temp, have_qmass;

};


class NPT : public Integrator{

public:

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

  void setQmass(double q) {qmass = q; have_qmass = 1;}
  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();

  Atom** atoms;

  // zeta and epsilonDot are the propagated degrees of freedom.

  double zeta;
  double epsilonDot;

  // targetTemp, targetPressure, and tauBarostat must be set.  
  // One of qmass or tauThermostat must be set;

  double qmass;
  double targetTemp;
  double targetPressure;
  double tauThermostat;
  double tauBarostat;

  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
  short int have_target_pressure, have_qmass;

};

#endif
Revision:	561
Committed:	Fri Jun 20 20:29:36 2003 UTC (21 years ago) by mmeineke
File size:	3833 byte(s)
Log Message:	Most of the integrator and NVT seem to be working now.
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4			#include "Atom.hpp"
5			#include "SRI.hpp"
6			#include "AbstractClasses.hpp"
7			#include "SimInfo.hpp"
8			#include "ForceFields.hpp"
9	mmeineke	540	#include "Thermo.hpp"
10			#include "ReadWrite.hpp"
11	mmeineke	377
12	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
13			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
14			const int maxIteration = 300;
15			const double tol = 1.0e-6;
16
17	mmeineke	540	class Integrator : public BaseIntegrator {
18	mmeineke	377
19			public:
20	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
21	mmeineke	548	virtual ~Integrator();
22	mmeineke	377	void integrate( void );
23
24
25	mmeineke	540	protected:
26	mmeineke	377
27	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
28	mmeineke	548	virtual void preMove( void );
29	mmeineke	540	virtual void moveA( void );
30			virtual void moveB( void );
31			virtual void constrainA( void );
32			virtual void constrainB( void );
33	mmeineke	559	virtual int readyCheck( void ) { return 1; }
34	mmeineke	377
35	mmeineke	540	void checkConstraints( void );
36	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
37	mmeineke	561	double A[9] );
38	mmeineke	377
39	mmeineke	540
40	mmeineke	377	ForceFields* myFF;
41
42	mmeineke	540	SimInfo *info; // all the info we'll ever need
43			int nAtoms; /* the number of atoms */
44	mmeineke	548	int oldAtoms;
45	mmeineke	540	Atom *atoms; / array of atom pointers */
46	mmeineke	423	Molecule* molecules;
47			int nMols;
48
49	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
50			// constraints.
51			int nConstrained; // counter for number of constraints
52			int *constrainedA; // the i of a constraint pair
53			int *constrainedB; // the j of a constraint pair
54			double *constrainedDsqr; // the square of the constraint distance
55
56			int* moving; // tells whether we are moving atom i
57			int* moved; // tells whether we have moved atom i
58	mmeineke	561	double* oldPos; // pre constrained positions
59	mmeineke	548
60	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
61
62			double dt;
63	mmeineke	541	double dt2;
64	gezelter	560
65	mmeineke	541	double* pos;
66			double* vel;
67			double* frc;
68			double* trq;
69			double* Amat;
70	mmeineke	377
71	mmeineke	540	Thermo *tStats;
72			StatWriter* statOut;
73			DumpWriter* dumpOut;
74	mmeineke	377
75			};
76
77	mmeineke	555	class NVE : public Integrator{
78	mmeineke	540
79	mmeineke	561	public:
80			NVE ( SimInfo theInfo, ForceFields the_ff ):
81	mmeineke	555	Integrator( theInfo, the_ff ){}
82			virtual ~NVE(){}
83
84
85
86			};
87
88	mmeineke	540	class NVT : public Integrator{
89
90	gezelter	560	public:
91
92	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
93			virtual ~NVT() {}
94	mmeineke	540
95	gezelter	560	void setQmass(double q) {qmass = q; have_qmass = 1;}
96			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98
99	mmeineke	540	protected:
100	gezelter	560
101	mmeineke	561	virtual void moveA( void );
102			virtual void moveB( void );
103	mmeineke	540
104	mmeineke	561	virtual int readyCheck();
105	gezelter	560
106			// zeta is a propagated degree of freedom.
107
108			double zeta;
109
110			// targetTemp must be set. One of qmass or tauThermostat must be set;
111
112			double qmass;
113			double targetTemp;
114			double tauThermostat;
115
116	mmeineke	561	double NkBT;
117
118	gezelter	560	short int have_tau_thermostat, have_target_temp, have_qmass;
119
120	mmeineke	540	};
121
122
123	gezelter	560	class NPT : public Integrator{
124	mmeineke	540
125	gezelter	560	public:
126
127	mmeineke	561	NPT ( SimInfo theInfo, ForceFields the_ff);
128	gezelter	560	virtual ~NPT();
129
130			void setQmass(double q) {qmass = q; have_qmass = 1;}
131			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
132			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
133			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
134			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
135
136			protected:
137
138	mmeineke	561	virtual void moveA( void );
139			virtual void moveB( void );
140	gezelter	560
141	mmeineke	561	virtual int readyCheck();
142	gezelter	560
143			Atom** atoms;
144
145			// zeta and epsilonDot are the propagated degrees of freedom.
146
147			double zeta;
148			double epsilonDot;
149
150			// targetTemp, targetPressure, and tauBarostat must be set.
151			// One of qmass or tauThermostat must be set;
152
153			double qmass;
154			double targetTemp;
155			double targetPressure;
156			double tauThermostat;
157			double tauBarostat;
158
159			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
160			short int have_target_pressure, have_qmass;
161
162			};
163
164	mmeineke	377	#endif