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"

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 );


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[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;}

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;

};


template<typename T> class NPTi : public T{

public:

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

  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();

  // 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;

};

template<typename T> class NPTim : public T{

public:

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

  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();

  Molecule* myMolecules;
  Atom** myAtoms;

  // 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;

};

template<typename T> class NPTf : public T{

public:

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

  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();

  // 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;

};

template<typename T> class NPTfm : public T{

public:

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

  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();

  Molecule* myMolecules;
  Atom** myAtoms;

  // 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:	645
Committed:	Tue Jul 22 19:54:52 2003 UTC (20 years, 11 months ago) by tim
File size:	7255 byte(s)
Log Message:	* empty log message *
#	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	377
13	mmeineke	561	const double kB = 8.31451e-7;// boltzmann constant amuAng^2fs^-2/K
14			const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
15	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
16	mmeineke	561	const int maxIteration = 300;
17			const double tol = 1.0e-6;
18
19	mmeineke	377
20	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
21
22	mmeineke	377	public:
23	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
24	mmeineke	548	virtual ~Integrator();
25	mmeineke	377	void integrate( void );
26
27
28	mmeineke	540	protected:
29	mmeineke	377
30	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
31	mmeineke	548	virtual void preMove( void );
32	mmeineke	540	virtual void moveA( void );
33			virtual void moveB( void );
34			virtual void constrainA( void );
35			virtual void constrainB( void );
36	mmeineke	559	virtual int readyCheck( void ) { return 1; }
37	mmeineke	377
38	mmeineke	540	void checkConstraints( void );
39	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
40	gezelter	600	double A[3][3] );
41	mmeineke	377
42	mmeineke	540
43	mmeineke	377	ForceFields* myFF;
44
45	mmeineke	540	SimInfo *info; // all the info we'll ever need
46			int nAtoms; /* the number of atoms */
47	mmeineke	548	int oldAtoms;
48	mmeineke	540	Atom *atoms; / array of atom pointers */
49	mmeineke	423	Molecule* molecules;
50			int nMols;
51
52	mmeineke	548	int isConstrained; // boolean to know whether the systems contains
53			// constraints.
54			int nConstrained; // counter for number of constraints
55			int *constrainedA; // the i of a constraint pair
56			int *constrainedB; // the j of a constraint pair
57			double *constrainedDsqr; // the square of the constraint distance
58
59			int* moving; // tells whether we are moving atom i
60			int* moved; // tells whether we have moved atom i
61	mmeineke	561	double* oldPos; // pre constrained positions
62	mmeineke	548
63	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
64
65			double dt;
66	mmeineke	541	double dt2;
67	gezelter	560
68	mmeineke	540	Thermo *tStats;
69			StatWriter* statOut;
70			DumpWriter* dumpOut;
71	mmeineke	377
72			};
73
74	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
75	mmeineke	540
76	tim	645	template<typename T> class NVE : public T {
77
78	mmeineke	561	public:
79			NVE ( SimInfo theInfo, ForceFields the_ff ):
80	tim	645	T( theInfo, the_ff ){}
81			virtual ~NVE(){}
82			};
83	mmeineke	555
84
85	tim	645	template<typename T> class NVT : public T {
86	mmeineke	555
87	gezelter	560	public:
88
89	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
90			virtual ~NVT() {}
91	mmeineke	540
92	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
93			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
94
95	mmeineke	540	protected:
96	gezelter	560
97	mmeineke	561	virtual void moveA( void );
98			virtual void moveB( void );
99	mmeineke	540
100	mmeineke	561	virtual int readyCheck();
101	gezelter	560
102	gezelter	565	// chi is a propagated degree of freedom.
103	gezelter	560
104	gezelter	565	double chi;
105	gezelter	560
106	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
107	gezelter	560
108			double targetTemp;
109			double tauThermostat;
110	mmeineke	561
111	gezelter	565	short int have_tau_thermostat, have_target_temp;
112	gezelter	560
113	mmeineke	540	};
114
115
116
117	tim	645	template<typename T> class NPTi : public T{
118
119	gezelter	560	public:
120
121	gezelter	574	NPTi ( SimInfo theInfo, ForceFields the_ff);
122			virtual ~NPTi() {};
123	gezelter	560
124	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
125			calcStress = 1;
126	tim	645	T::integrateStep( calcPot, calcStress );
127	mmeineke	594	}
128
129	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
130			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
131			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
132			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
133
134			protected:
135
136	mmeineke	561	virtual void moveA( void );
137			virtual void moveB( void );
138	gezelter	560
139	mmeineke	561	virtual int readyCheck();
140	gezelter	560
141	gezelter	565	// chi and eta are the propagated degrees of freedom
142	gezelter	560
143	gezelter	565	double chi;
144			double eta;
145	gezelter	574	double NkBT;
146	gezelter	560
147			// targetTemp, targetPressure, and tauBarostat must be set.
148			// One of qmass or tauThermostat must be set;
149
150			double targetTemp;
151			double targetPressure;
152			double tauThermostat;
153			double tauBarostat;
154
155			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
156	gezelter	565	short int have_target_pressure;
157	gezelter	560
158			};
159
160	tim	645	template<typename T> class NPTim : public T{
161	gezelter	596
162			public:
163
164			NPTim ( SimInfo theInfo, ForceFields the_ff);
165			virtual ~NPTim() {};
166
167			virtual void integrateStep( int calcPot, int calcStress ){
168			calcStress = 1;
169	tim	645	T::integrateStep( calcPot, calcStress );
170	gezelter	596	}
171
172			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
173			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
174			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
175			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
176
177			protected:
178
179	gezelter	604	virtual void moveA( void );
180	gezelter	596	virtual void moveB( void );
181
182			virtual int readyCheck();
183
184	gezelter	604	Molecule* myMolecules;
185			Atom** myAtoms;
186
187	gezelter	596	// chi and eta are the propagated degrees of freedom
188
189			double chi;
190			double eta;
191			double NkBT;
192
193			// targetTemp, targetPressure, and tauBarostat must be set.
194			// One of qmass or tauThermostat must be set;
195
196			double targetTemp;
197			double targetPressure;
198			double tauThermostat;
199			double tauBarostat;
200
201			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202			short int have_target_pressure;
203
204			};
205
206	tim	645	template<typename T> class NPTf : public T{
207	gezelter	576
208			public:
209
210			NPTf ( SimInfo theInfo, ForceFields the_ff);
211			virtual ~NPTf() {};
212
213	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
214			calcStress = 1;
215	tim	645	T::integrateStep( calcPot, calcStress );
216	mmeineke	594	}
217
218	gezelter	576	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
222
223			protected:
224
225			virtual void moveA( void );
226			virtual void moveB( void );
227
228			virtual int readyCheck();
229
230			// chi and eta are the propagated degrees of freedom
231
232			double chi;
233	gezelter	588	double eta[3][3];
234	gezelter	576	double NkBT;
235
236			// targetTemp, targetPressure, and tauBarostat must be set.
237			// One of qmass or tauThermostat must be set;
238
239			double targetTemp;
240			double targetPressure;
241			double tauThermostat;
242			double tauBarostat;
243
244			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
245			short int have_target_pressure;
246
247			};
248
249	tim	645	template<typename T> class NPTfm : public T{
250	gezelter	596
251			public:
252
253			NPTfm ( SimInfo theInfo, ForceFields the_ff);
254			virtual ~NPTfm() {};
255
256			virtual void integrateStep( int calcPot, int calcStress ){
257			calcStress = 1;
258	tim	645	T::integrateStep( calcPot, calcStress );
259	gezelter	596	}
260
261			void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
262			void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264			void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
265
266			protected:
267
268			virtual void moveA( void );
269			virtual void moveB( void );
270
271			virtual int readyCheck();
272
273	gezelter	605	Molecule* myMolecules;
274			Atom** myAtoms;
275
276	gezelter	596	// chi and eta are the propagated degrees of freedom
277
278			double chi;
279			double eta[3][3];
280			double NkBT;
281
282			// targetTemp, targetPressure, and tauBarostat must be set.
283			// One of qmass or tauThermostat must be set;
284
285			double targetTemp;
286			double targetPressure;
287			double tauThermostat;
288			double tauBarostat;
289
290			short int have_tau_thermostat, have_tau_barostat, have_target_temp;
291			short int have_target_pressure;
292
293			};
294
295	mmeineke	377	#endif