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;

  double calcCOMVel();
  double calcCOMVel2();

};

#endif
Revision:	693
Committed:	Wed Aug 13 19:21:53 2003 UTC (20 years, 10 months ago) by tim
File size:	9274 byte(s)
Log Message:	harmonic potential & z-contraint method
#	User	Rev	Content
1	mmeineke	377	#ifndef _INTEGRATOR_H_
2			#define _INTEGRATOR_H_
3
4	tim	658	#include <string>
5			#include <vector>
6	mmeineke	377	#include "Atom.hpp"
7	gezelter	604	#include "Molecule.hpp"
8	mmeineke	377	#include "SRI.hpp"
9			#include "AbstractClasses.hpp"
10			#include "SimInfo.hpp"
11			#include "ForceFields.hpp"
12	mmeineke	540	#include "Thermo.hpp"
13			#include "ReadWrite.hpp"
14	tim	658	#include "ZConsWriter.hpp"
15	mmeineke	377
16	tim	658	using namespace std;
17	mmeineke	561	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	mmeineke	586	const double p_convert = 1.63882576e8; //converts amufs^-2Ang^-1 -> atm
20	mmeineke	561	const int maxIteration = 300;
21			const double tol = 1.0e-6;
22
23	mmeineke	377
24	tim	645	template<typename T = BaseIntegrator> class Integrator : public T {
25
26	mmeineke	377	public:
27	mmeineke	561	Integrator( SimInfo theInfo, ForceFields the_ff );
28	mmeineke	548	virtual ~Integrator();
29	mmeineke	377	void integrate( void );
30
31
32	mmeineke	540	protected:
33	mmeineke	377
34	mmeineke	540	virtual void integrateStep( int calcPot, int calcStress );
35	mmeineke	548	virtual void preMove( void );
36	mmeineke	540	virtual void moveA( void );
37			virtual void moveB( void );
38			virtual void constrainA( void );
39			virtual void constrainB( void );
40	mmeineke	559	virtual int readyCheck( void ) { return 1; }
41	tim	677
42			virtual void calcForce( int calcPot, int calcStress );
43			virtual void thermalize();
44	mmeineke	377
45	mmeineke	540	void checkConstraints( void );
46	mmeineke	377	void rotate( int axes1, int axes2, double angle, double j[3],
47	gezelter	600	double A[3][3] );
48	tim	677
49	mmeineke	377	ForceFields* myFF;
50
51	mmeineke	540	SimInfo *info; // all the info we'll ever need
52			int nAtoms; /* the number of atoms */
53	mmeineke	548	int oldAtoms;
54	mmeineke	540	Atom *atoms; / array of atom pointers */
55	mmeineke	423	Molecule* molecules;
56			int nMols;
57
58	mmeineke	548	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	mmeineke	561	double* oldPos; // pre constrained positions
68	mmeineke	548
69	mmeineke	540	short isFirst; /boolean for the first time integrate is called /
70
71			double dt;
72	mmeineke	541	double dt2;
73	gezelter	560
74	mmeineke	540	Thermo *tStats;
75			StatWriter* statOut;
76			DumpWriter* dumpOut;
77	mmeineke	377
78			};
79
80	tim	645	typedef Integrator<BaseIntegrator> RealIntegrator;
81	mmeineke	540
82	tim	645	template<typename T> class NVE : public T {
83
84	mmeineke	561	public:
85			NVE ( SimInfo theInfo, ForceFields the_ff ):
86	tim	645	T( theInfo, the_ff ){}
87			virtual ~NVE(){}
88			};
89	mmeineke	555
90
91	tim	645	template<typename T> class NVT : public T {
92	mmeineke	555
93	gezelter	560	public:
94
95	mmeineke	561	NVT ( SimInfo theInfo, ForceFields the_ff);
96			virtual ~NVT() {}
97	mmeineke	540
98	gezelter	560	void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99			void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100
101	mmeineke	540	protected:
102	gezelter	560
103	mmeineke	561	virtual void moveA( void );
104			virtual void moveB( void );
105	mmeineke	540
106	mmeineke	561	virtual int readyCheck();
107	gezelter	560
108	gezelter	565	// chi is a propagated degree of freedom.
109	gezelter	560
110	gezelter	565	double chi;
111	gezelter	560
112	gezelter	565	// targetTemp must be set. tauThermostat must also be set;
113	gezelter	560
114			double targetTemp;
115			double tauThermostat;
116	mmeineke	561
117	gezelter	565	short int have_tau_thermostat, have_target_temp;
118	gezelter	560
119	mmeineke	540	};
120
121
122
123	tim	645	template<typename T> class NPTi : public T{
124
125	gezelter	560	public:
126
127	gezelter	574	NPTi ( SimInfo theInfo, ForceFields the_ff);
128			virtual ~NPTi() {};
129	gezelter	560
130	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
131			calcStress = 1;
132	tim	645	T::integrateStep( calcPot, calcStress );
133	mmeineke	594	}
134
135	gezelter	560	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	mmeineke	561	virtual void moveA( void );
143			virtual void moveB( void );
144	gezelter	560
145	mmeineke	561	virtual int readyCheck();
146	gezelter	560
147	gezelter	565	// chi and eta are the propagated degrees of freedom
148	gezelter	560
149	gezelter	565	double chi;
150			double eta;
151	gezelter	574	double NkBT;
152	gezelter	560
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	gezelter	565	short int have_target_pressure;
163	gezelter	560
164			};
165
166	tim	645	template<typename T> class NPTim : public T{
167	gezelter	596
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	tim	645	T::integrateStep( calcPot, calcStress );
176	gezelter	596	}
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	gezelter	604	virtual void moveA( void );
186	gezelter	596	virtual void moveB( void );
187
188			virtual int readyCheck();
189
190	gezelter	604	Molecule* myMolecules;
191			Atom** myAtoms;
192
193	gezelter	596	// 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	tim	645	template<typename T> class NPTf : public T{
213	gezelter	576
214			public:
215
216			NPTf ( SimInfo theInfo, ForceFields the_ff);
217			virtual ~NPTf() {};
218
219	mmeineke	594	virtual void integrateStep( int calcPot, int calcStress ){
220			calcStress = 1;
221	tim	645	T::integrateStep( calcPot, calcStress );
222	mmeineke	594	}
223
224	gezelter	576	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	gezelter	588	double eta[3][3];
240	gezelter	576	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	tim	645	template<typename T> class NPTfm : public T{
256	gezelter	596
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	tim	645	T::integrateStep( calcPot, calcStress );
265	gezelter	596	}
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	gezelter	605	Molecule* myMolecules;
280			Atom** myAtoms;
281
282	gezelter	596	// 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	tim	658	template<typename T> class ZConstraint : public T {
302
303			public:
304
305			ZConstraint( SimInfo theInfo, ForceFields the_ff);
306			~ZConstraint();
307	tim	677
308	tim	658	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	tim	677
317			virtual void integrate();
318
319	tim	658
320			#ifdef IS_MPI
321			virtual void update(); //which is called to indicate the molecules' migration
322	mmeineke	377	#endif
323	tim	658
324			protected:
325
326	tim	677	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	tim	682	void doHarmonic();
336	tim	677	bool checkZConsState();
337
338			bool haveFixedZMols();
339			bool haveMovingZMols();
340
341			double calcZSys();
342
343			int isZConstraintMol(Molecule* mol);
344
345
346	tim	658	double zconsTime;
347	tim	682	double zconsTol;
348			double zForceConst;
349	tim	658
350			vector<Molecule*> zconsMols;
351			vector<double> massOfZConsMols;
352	tim	677	vector<double> kz;
353			vector<ZConsState> states;
354	tim	682	vector<double> zPos;
355	tim	658
356	tim	677
357	tim	658	vector<Molecule*> unconsMols;
358			vector<double> massOfUnconsMols;
359			double totalMassOfUncons;
360	tim	682
361			vector<ZConsParaItem>* parameters;
362	tim	658
363			vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels
364	tim	677
365			int* indexOfZConsMols; //index of local Z-Constraint Molecules
366	tim	658	double* fz;
367
368	tim	677	int totNumOfUnconsAtoms;
369
370			int whichDirection; //constraint direction
371
372	tim	658	private:
373	tim	677
374	tim	658	string zconsOutput;
375			ZConsWriter* fzOut;
376	tim	677
377	tim	693	double calcCOMVel();
378			double calcCOMVel2();
379	tim	677
380	tim	658	};
381
382			#endif