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 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 );


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 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();

  // chi is a propagated degree of freedom.

  double chi;

  // targetTemp must be set.  tauThermostat must also be set;

  double targetTemp;
  double tauThermostat;
  
  short int have_tau_thermostat, have_target_temp;

};


class NPTi : public Integrator{

public:

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

  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();

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta;
  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;

};

class NPTf : public Integrator{

public:

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

  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();

  // chi and eta are the propagated degrees of freedom

  double chi;
  double eta[3][3];
  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;

};

#endif
Revision:	588
Committed:	Thu Jul 10 17:10:56 2003 UTC (21 years ago) by gezelter
File size:	4650 byte(s)
Log Message:	Bunch of 1-d array -> 2-d array stuff
#	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	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
15	mmeineke	561	const int maxIteration = 300;
16			const double tol = 1.0e-6;
17
18	mmeineke	540	class Integrator : public BaseIntegrator {
19	mmeineke	377
20			public:
21	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
22	mmeineke	548	virtual ~Integrator();
23	mmeineke	377	void integrate( void );
24
25
26	mmeineke	540	protected:
27	mmeineke	377
28	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
29	mmeineke	548	virtual void preMove( void );
30	mmeineke	540	virtual void moveA( void );
31			virtual void moveB( void );
32			virtual void constrainA( void );
33			virtual void constrainB( void );
34	mmeineke	559	virtual int readyCheck( void ) { return 1; }
35	mmeineke	377
36	mmeineke	540	void checkConstraints( void );
37	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
38	mmeineke	561	double A[9] );
39	mmeineke	377
40	mmeineke	540
41	mmeineke	377	ForceFields* myFF;
42
43	mmeineke	540	SimInfo *info; // all the info we'll ever need
44			int nAtoms; /* the number of atoms */
45	mmeineke	548	int oldAtoms;
46	mmeineke	540	Atom *atoms; / array of atom pointers */
47	mmeineke	423	Molecule* molecules;
48			int nMols;
49
50	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
51			// constraints.
52			int nConstrained; // counter for number of constraints
53			int *constrainedA; // the i of a constraint pair
54			int *constrainedB; // the j of a constraint pair
55			double *constrainedDsqr; // the square of the constraint distance
56
57			int* moving; // tells whether we are moving atom i
58			int* moved; // tells whether we have moved atom i
59	mmeineke	561	double* oldPos; // pre constrained positions
60	mmeineke	548
61	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
62
63			double dt;
64	mmeineke	541	double dt2;
65	gezelter	560
66	mmeineke	541	double* pos;
67			double* vel;
68			double* frc;
69			double* trq;
70			double* Amat;
71	mmeineke	377
72	mmeineke	540	Thermo *tStats;
73			StatWriter* statOut;
74			DumpWriter* dumpOut;
75	mmeineke	377
76			};
77
78	mmeineke	555	class NVE : public Integrator{
79	mmeineke	540
80	mmeineke	561	public:
81			NVE ( SimInfo theInfo, ForceFields the_ff ):
82	mmeineke	555	Integrator( theInfo, the_ff ){}
83			virtual ~NVE(){}
84
85
86
87			};
88
89	mmeineke	540	class NVT : public Integrator{
90
91	gezelter	560	public:
92
93	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
94			virtual ~NVT() {}
95	mmeineke	540
96	gezelter	560	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	gezelter	565	// chi is a propagated degree of freedom.
107	gezelter	560
108	gezelter	565	double chi;
109	gezelter	560
110	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
111	gezelter	560
112			double targetTemp;
113			double tauThermostat;
114	mmeineke	561
115	gezelter	565	short int have_tau_thermostat, have_target_temp;
116	gezelter	560
117	mmeineke	540	};
118
119
120	gezelter	574	class NPTi : public Integrator{
121	mmeineke	540
122	gezelter	560	public:
123
124	gezelter	574	NPTi ( SimInfo theInfo, ForceFields the_ff);
125			virtual ~NPTi() {};
126	gezelter	560
127			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
128			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
129			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
130			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
131
132			protected:
133
134	mmeineke	561	virtual void moveA( void );
135			virtual void moveB( void );
136	gezelter	560
137	mmeineke	561	virtual int readyCheck();
138	gezelter	560
139	gezelter	565	// chi and eta are the propagated degrees of freedom
140	gezelter	560
141	gezelter	565	double chi;
142			double eta;
143	gezelter	574	double NkBT;
144	gezelter	560
145			// targetTemp, targetPressure, and tauBarostat must be set.
146			// One of qmass or tauThermostat must be set;
147
148			double targetTemp;
149			double targetPressure;
150			double tauThermostat;
151			double tauBarostat;
152
153			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
154	gezelter	565	short int have_target_pressure;
155	gezelter	560
156			};
157
158	gezelter	576	class NPTf : public Integrator{
159
160			public:
161
162			NPTf ( SimInfo theInfo, ForceFields the_ff);
163			virtual ~NPTf() {};
164
165			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
166			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
167			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
168			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
169
170			protected:
171
172			virtual void moveA( void );
173			virtual void moveB( void );
174
175			virtual int readyCheck();
176
177			// chi and eta are the propagated degrees of freedom
178
179			double chi;
180	gezelter	588	double eta[3][3];
181	gezelter	576	double NkBT;
182
183			// targetTemp, targetPressure, and tauBarostat must be set.
184			// One of qmass or tauThermostat must be set;
185
186			double targetTemp;
187			double targetPressure;
188			double tauThermostat;
189			double tauBarostat;
190
191			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
192			short int have_target_pressure;
193
194			};
195
196	mmeineke	377	#endif