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 *
#	Content
1	#ifndef _INTEGRATOR_H_
2	#define _INTEGRATOR_H_
3
4	#include "Atom.hpp"
5	#include "Molecule.hpp"
6	#include "SRI.hpp"
7	#include "AbstractClasses.hpp"
8	#include "SimInfo.hpp"
9	#include "ForceFields.hpp"
10	#include "Thermo.hpp"
11	#include "ReadWrite.hpp"
12
13	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	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
16	const int maxIteration = 300;
17	const double tol = 1.0e-6;
18
19
20	template<typename T = BaseIntegrator> class Integrator : public T {
21
22	public:
23	Integrator( SimInfo theInfo, ForceFields the_ff );
24	virtual ~Integrator();
25	void integrate( void );
26
27
28	protected:
29
30	virtual void integrateStep( int calcPot, int calcStress );
31	virtual void preMove( void );
32	virtual void moveA( void );
33	virtual void moveB( void );
34	virtual void constrainA( void );
35	virtual void constrainB( void );
36	virtual int readyCheck( void ) { return 1; }
37
38	void checkConstraints( void );
39	void rotate( int axes1, int axes2, double angle, double j[3],
40	double A[3][3] );
41
42
43	ForceFields* myFF;
44
45	SimInfo *info; // all the info we'll ever need
46	int nAtoms; /* the number of atoms */
47	int oldAtoms;
48	Atom *atoms; / array of atom pointers */
49	Molecule* molecules;
50	int nMols;
51
52	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	double* oldPos; // pre constrained positions
62
63	short isFirst; /boolean for the first time integrate is called /
64
65	double dt;
66	double dt2;
67
68	Thermo *tStats;
69	StatWriter* statOut;
70	DumpWriter* dumpOut;
71
72	};
73
74	typedef Integrator<BaseIntegrator> RealIntegrator;
75
76	template<typename T> class NVE : public T {
77
78	public:
79	NVE ( SimInfo theInfo, ForceFields the_ff ):
80	T( theInfo, the_ff ){}
81	virtual ~NVE(){}
82	};
83
84
85	template<typename T> class NVT : public T {
86
87	public:
88
89	NVT ( SimInfo theInfo, ForceFields the_ff);
90	virtual ~NVT() {}
91
92	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
93	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
94
95	protected:
96
97	virtual void moveA( void );
98	virtual void moveB( void );
99
100	virtual int readyCheck();
101
102	// chi is a propagated degree of freedom.
103
104	double chi;
105
106	// targetTemp must be set. tauThermostat must also be set;
107
108	double targetTemp;
109	double tauThermostat;
110
111	short int have_tau_thermostat, have_target_temp;
112
113	};
114
115
116
117	template<typename T> class NPTi : public T{
118
119	public:
120
121	NPTi ( SimInfo theInfo, ForceFields the_ff);
122	virtual ~NPTi() {};
123
124	virtual void integrateStep( int calcPot, int calcStress ){
125	calcStress = 1;
126	T::integrateStep( calcPot, calcStress );
127	}
128
129	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	virtual void moveA( void );
137	virtual void moveB( void );
138
139	virtual int readyCheck();
140
141	// chi and eta are the propagated degrees of freedom
142
143	double chi;
144	double eta;
145	double NkBT;
146
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	short int have_target_pressure;
157
158	};
159
160	template<typename T> class NPTim : public T{
161
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	T::integrateStep( calcPot, calcStress );
170	}
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	virtual void moveA( void );
180	virtual void moveB( void );
181
182	virtual int readyCheck();
183
184	Molecule* myMolecules;
185	Atom** myAtoms;
186
187	// 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	template<typename T> class NPTf : public T{
207
208	public:
209
210	NPTf ( SimInfo theInfo, ForceFields the_ff);
211	virtual ~NPTf() {};
212
213	virtual void integrateStep( int calcPot, int calcStress ){
214	calcStress = 1;
215	T::integrateStep( calcPot, calcStress );
216	}
217
218	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	double eta[3][3];
234	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	template<typename T> class NPTfm : public T{
250
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	T::integrateStep( calcPot, calcStress );
259	}
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	Molecule* myMolecules;
274	Atom** myAtoms;
275
276	// 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	#endif