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 );


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 calcForce( int calcPot, int calcStress );  
  virtual void thermalize();
  
  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;

};

template<typename T> class ZConstraint : public T {

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;
  double zconsTol;
  double zForceConst;
  
  vector<Molecule*> zconsMols;
  vector<double> massOfZConsMols;
  vector<double> kz;
  vector<ZConsState> states; 
  vector<double> zPos;
  
  
  vector<Molecule*> unconsMols;
  vector<double> massOfUnconsMols;
  double totalMassOfUncons;

  vector<ZConsParaItem>* parameters;
  
  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels

  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
  double* fz;
  
  int totNumOfUnconsAtoms;

  int whichDirection;                           //constraint direction 
  
private:
  
  string zconsOutput;
  ZConsWriter* fzOut;


};

#endif
Revision:	682
Committed:	Tue Aug 12 17:51:33 2003 UTC (20 years, 10 months ago) by tim
File size:	9227 byte(s)
Log Message:	added harmonical potential to z-constraint method
#	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
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 calcForce( int calcPot, int calcStress );
43	virtual void thermalize();
44
45	void checkConstraints( void );
46	void rotate( int axes1, int axes2, double angle, double j[3],
47	double A[3][3] );
48
49	ForceFields* myFF;
50
51	SimInfo *info; // all the info we'll ever need
52	int nAtoms; /* the number of atoms */
53	int oldAtoms;
54	Atom *atoms; / array of atom pointers */
55	Molecule* molecules;
56	int nMols;
57
58	int isConstrained; // boolean to know whether the systems contains
59	// constraints.
60	int nConstrained; // counter for number of constraints
61	int *constrainedA; // the i of a constraint pair
62	int *constrainedB; // the j of a constraint pair
63	double *constrainedDsqr; // the square of the constraint distance
64
65	int* moving; // tells whether we are moving atom i
66	int* moved; // tells whether we have moved atom i
67	double* oldPos; // pre constrained positions
68
69	short isFirst; /boolean for the first time integrate is called /
70
71	double dt;
72	double dt2;
73
74	Thermo *tStats;
75	StatWriter* statOut;
76	DumpWriter* dumpOut;
77
78	};
79
80	typedef Integrator<BaseIntegrator> RealIntegrator;
81
82	template<typename T> class NVE : public T {
83
84	public:
85	NVE ( SimInfo theInfo, ForceFields the_ff ):
86	T( theInfo, the_ff ){}
87	virtual ~NVE(){}
88	};
89
90
91	template<typename T> class NVT : public T {
92
93	public:
94
95	NVT ( SimInfo theInfo, ForceFields the_ff);
96	virtual ~NVT() {}
97
98	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100
101	protected:
102
103	virtual void moveA( void );
104	virtual void moveB( void );
105
106	virtual int readyCheck();
107
108	// chi is a propagated degree of freedom.
109
110	double chi;
111
112	// targetTemp must be set. tauThermostat must also be set;
113
114	double targetTemp;
115	double tauThermostat;
116
117	short int have_tau_thermostat, have_target_temp;
118
119	};
120
121
122
123	template<typename T> class NPTi : public T{
124
125	public:
126
127	NPTi ( SimInfo theInfo, ForceFields the_ff);
128	virtual ~NPTi() {};
129
130	virtual void integrateStep( int calcPot, int calcStress ){
131	calcStress = 1;
132	T::integrateStep( calcPot, calcStress );
133	}
134
135	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
136	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
137	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
138	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
139
140	protected:
141
142	virtual void moveA( void );
143	virtual void moveB( void );
144
145	virtual int readyCheck();
146
147	// chi and eta are the propagated degrees of freedom
148
149	double chi;
150	double eta;
151	double NkBT;
152
153	// targetTemp, targetPressure, and tauBarostat must be set.
154	// One of qmass or tauThermostat must be set;
155
156	double targetTemp;
157	double targetPressure;
158	double tauThermostat;
159	double tauBarostat;
160
161	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
162	short int have_target_pressure;
163
164	};
165
166	template<typename T> class NPTim : public T{
167
168	public:
169
170	NPTim ( SimInfo theInfo, ForceFields the_ff);
171	virtual ~NPTim() {};
172
173	virtual void integrateStep( int calcPot, int calcStress ){
174	calcStress = 1;
175	T::integrateStep( calcPot, calcStress );
176	}
177
178	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182
183	protected:
184
185	virtual void moveA( void );
186	virtual void moveB( void );
187
188	virtual int readyCheck();
189
190	Molecule* myMolecules;
191	Atom** myAtoms;
192
193	// chi and eta are the propagated degrees of freedom
194
195	double chi;
196	double eta;
197	double NkBT;
198
199	// targetTemp, targetPressure, and tauBarostat must be set.
200	// One of qmass or tauThermostat must be set;
201
202	double targetTemp;
203	double targetPressure;
204	double tauThermostat;
205	double tauBarostat;
206
207	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
208	short int have_target_pressure;
209
210	};
211
212	template<typename T> class NPTf : public T{
213
214	public:
215
216	NPTf ( SimInfo theInfo, ForceFields the_ff);
217	virtual ~NPTf() {};
218
219	virtual void integrateStep( int calcPot, int calcStress ){
220	calcStress = 1;
221	T::integrateStep( calcPot, calcStress );
222	}
223
224	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228
229	protected:
230
231	virtual void moveA( void );
232	virtual void moveB( void );
233
234	virtual int readyCheck();
235
236	// chi and eta are the propagated degrees of freedom
237
238	double chi;
239	double eta[3][3];
240	double NkBT;
241
242	// targetTemp, targetPressure, and tauBarostat must be set.
243	// One of qmass or tauThermostat must be set;
244
245	double targetTemp;
246	double targetPressure;
247	double tauThermostat;
248	double tauBarostat;
249
250	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251	short int have_target_pressure;
252
253	};
254
255	template<typename T> class NPTfm : public T{
256
257	public:
258
259	NPTfm ( SimInfo theInfo, ForceFields the_ff);
260	virtual ~NPTfm() {};
261
262	virtual void integrateStep( int calcPot, int calcStress ){
263	calcStress = 1;
264	T::integrateStep( calcPot, calcStress );
265	}
266
267	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268	void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269	void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270	void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271
272	protected:
273
274	virtual void moveA( void );
275	virtual void moveB( void );
276
277	virtual int readyCheck();
278
279	Molecule* myMolecules;
280	Atom** myAtoms;
281
282	// chi and eta are the propagated degrees of freedom
283
284	double chi;
285	double eta[3][3];
286	double NkBT;
287
288	// targetTemp, targetPressure, and tauBarostat must be set.
289	// One of qmass or tauThermostat must be set;
290
291	double targetTemp;
292	double targetPressure;
293	double tauThermostat;
294	double tauBarostat;
295
296	short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297	short int have_target_pressure;
298
299	};
300
301	template<typename T> class ZConstraint : public T {
302
303	public:
304
305	ZConstraint( SimInfo theInfo, ForceFields the_ff);
306	~ZConstraint();
307
308	void setZConsTime(double time) {this->zconsTime = time;}
309	void getZConsTime() {return zconsTime;}
310
311	void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
312	void getIndexOfAllZConsMols() {return indexOfAllZConsMols;}
313
314	void setZConsOutput(const char * fileName) {zconsOutput = fileName;}
315	string getZConsOutput() {return zconsOutput;}
316
317	virtual void integrate();
318
319
320	#ifdef IS_MPI
321	virtual void update(); //which is called to indicate the molecules' migration
322	#endif
323
324	protected:
325
326	enum ZConsState {zcsMoving, zcsFixed};
327
328
329
330	virtual void calcForce( int calcPot, int calcStress );
331	virtual void thermalize(void);
332
333	void zeroOutVel();
334	void doZconstraintForce();
335	void doHarmonic();
336	bool checkZConsState();
337
338	bool haveFixedZMols();
339	bool haveMovingZMols();
340
341	double calcZSys();
342
343	int isZConstraintMol(Molecule* mol);
344
345
346	double zconsTime;
347	double zconsTol;
348	double zForceConst;
349
350	vector<Molecule*> zconsMols;
351	vector<double> massOfZConsMols;
352	vector<double> kz;
353	vector<ZConsState> states;
354	vector<double> zPos;
355
356
357	vector<Molecule*> unconsMols;
358	vector<double> massOfUnconsMols;
359	double totalMassOfUncons;
360
361	vector<ZConsParaItem>* parameters;
362
363	vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
364
365	int* indexOfZConsMols; //index of local Z-Constraint Molecules
366	double* fz;
367
368	int totNumOfUnconsAtoms;
369
370	int whichDirection; //constraint direction
371
372	private:
373
374	string zconsOutput;
375	ZConsWriter* fzOut;
376
377
378	};
379
380	#endif