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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

# Line 1 | Line 1
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"
# Line 9 | Line 11
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 amu*Ang^2*fs^-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 amu*fs^-2*Ang^-1 -> atm
# Line 23 | Line 27 | template<typename T = BaseIntegrator> class Integrator
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
27 –
32   protected:
33 <  
33 >
34    virtual void integrateStep( int calcPot, int calcStress );
35    virtual void preMove( void );
36    virtual void moveA( void );
# Line 34 | Line 38 | template<typename T = BaseIntegrator> class Integrator
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void resetIntegrator( void ) { }
43 +
44 +  virtual void calcForce( int calcPot, int calcStress );  
45 +  virtual void thermalize();
46    
47 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
48 +
49    void checkConstraints( void );
50    void rotate( int axes1, int axes2, double angle, double j[3],
51 <               double A[3][3] );
52 <
42 <
51 >         double A[3][3] );
52 >        
53    ForceFields* myFF;
54  
55    SimInfo *info; // all the info we'll ever need
# Line 50 | Line 60 | template<typename T = BaseIntegrator> class Integrator
60    int nMols;
61  
62    int isConstrained; // boolean to know whether the systems contains
63 <                     // constraints.
63 >         // constraints.
64    int nConstrained;  // counter for number of constraints
65    int *constrainedA; // the i of a constraint pair
66    int *constrainedB; // the j of a constraint pair
# Line 87 | Line 97 | template<typename T> class NVT : public T { (public)
97   public:
98  
99    NVT ( SimInfo *theInfo, ForceFields* the_ff);
100 <  virtual ~NVT() {}
100 >  virtual ~NVT();
101  
102    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
103    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
104 +  void setChiTolerance(double tol) {chiTolerance = tol;}
105 +  virtual double  getConservedQuantity(void);
106  
107   protected:
108  
# Line 99 | Line 111 | template<typename T> class NVT : public T { (public)
111  
112    virtual int readyCheck();
113  
114 +  virtual void resetIntegrator( void );
115 +
116    // chi is a propagated degree of freedom.
117  
118    double chi;
119  
120 +  //integral of chi(t)dt
121 +  double integralOfChidt;
122 +
123    // targetTemp must be set.  tauThermostat must also be set;
124  
125    double targetTemp;
# Line 110 | Line 127 | template<typename T> class NVT : public T { (public)
127    
128    short int have_tau_thermostat, have_target_temp;
129  
130 +  double *oldVel;
131 +  double *oldJi;
132 +
133 +  double chiTolerance;
134 +  short int have_chi_tolerance;
135 +
136   };
137  
138  
139  
140 < template<typename T> class NPTi : public T{
140 > template<typename T> class NPT : public T{
141  
142   public:
143  
144 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
145 <  virtual ~NPTi() {};
146 <
144 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
145 >  virtual ~NPT();
146 >  
147    virtual void integrateStep( int calcPot, int calcStress ){
148      calcStress = 1;
149      T::integrateStep( calcPot, calcStress );
150    }
151  
152 +  virtual double getConservedQuantity(void) = 0;
153 +
154    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
155    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
156    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
157    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
158 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
159 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
160 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
161  
162   protected:
163  
# Line 138 | Line 166 | template<typename T> class NPTi : public T{ (protected
166  
167    virtual int readyCheck();
168  
169 +  virtual void resetIntegrator( void );
170 +
171 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
172 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
173 +  virtual void getPosScale(double pos[3], double COM[3],
174 +                           int index, double sc[3]) = 0;
175 +
176 +  virtual bool chiConverged( void );
177 +  virtual bool etaConverged( void ) = 0;
178 +  
179 +  virtual void evolveChiA( void );
180 +  virtual void evolveEtaA( void ) = 0;
181 +  virtual void evolveChiB( void );
182 +  virtual void evolveEtaB( void ) = 0;
183 +
184 +  virtual void scaleSimBox( void ) = 0;
185 +
186 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
187 +
188    // chi and eta are the propagated degrees of freedom
189  
190 +  double oldChi;
191 +  double prevChi;
192    double chi;
144 –  double eta;
193    double NkBT;
194 +  double fkBT;
195  
196 +  double tt2, tb2;
197 +  double instaTemp, instaPress, instaVol;
198 +  double press[3][3];
199 +
200 +  int Nparticles;
201 +
202 +  double integralOfChidt;
203 +
204    // targetTemp, targetPressure, and tauBarostat must be set.  
205    // One of qmass or tauThermostat must be set;
206  
# Line 155 | Line 212 | template<typename T> class NPTi : public T{ (protected
212    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213    short int have_target_pressure;
214  
215 < };
215 >  double *oldPos;
216 >  double *oldVel;
217 >  double *oldJi;
218  
219 < template<typename T> class NPTim : public T{
219 >  double chiTolerance;
220 >  short int have_chi_tolerance;
221 >  double posIterTolerance;
222 >  short int have_pos_iter_tolerance;
223 >  double etaTolerance;
224 >  short int have_eta_tolerance;
225  
226 + };
227 +
228 + template<typename T> class NPTi : public T{
229 +  
230   public:
231 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
232 +  ~NPTi();
233  
234 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
235 <  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;}
234 >  virtual double getConservedQuantity(void);
235 >  virtual void resetIntegrator(void);
236  
237   protected:
238  
239 <  virtual void moveA( void );
180 <  virtual void moveB( void );
239 >
240  
241 <  virtual int readyCheck();
241 >  virtual void evolveEtaA(void);
242 >  virtual void evolveEtaB(void);
243  
244 <  Molecule* myMolecules;
185 <  Atom** myAtoms;
244 >  virtual bool etaConverged( void );
245  
246 <  // chi and eta are the propagated degrees of freedom
246 >  virtual void scaleSimBox( void );
247  
248 <  double chi;
249 <  double eta;
250 <  double NkBT;
248 >  virtual void getVelScaleA( double sc[3], double vel[3] );
249 >  virtual void getVelScaleB( double sc[3], int index );
250 >  virtual void getPosScale(double pos[3], double COM[3],
251 >                           int index, double sc[3]);
252  
253 <  // 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 <
253 >  double eta, oldEta, prevEta;
254   };
255  
256   template<typename T> class NPTf : public T{
# Line 208 | Line 258 | template<typename T> class NPTf : public T{ (public)
258   public:
259  
260    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTf() {};
261 >  virtual ~NPTf();
262  
263 <  virtual void integrateStep( int calcPot, int calcStress ){
264 <    calcStress = 1;
215 <    T::integrateStep( calcPot, calcStress );
216 <  }
263 >  virtual double getConservedQuantity(void);
264 >  virtual void resetIntegrator(void);
265  
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 –
266   protected:
267  
268 <  virtual void  moveA( void );
269 <  virtual void moveB( void );
268 >  virtual void evolveEtaA(void);
269 >  virtual void evolveEtaB(void);
270  
271 <  virtual int readyCheck();
271 >  virtual bool etaConverged( void );
272  
273 <  // chi and eta are the propagated degrees of freedom
273 >  virtual void scaleSimBox( void );
274  
275 <  double chi;
275 >  virtual void getVelScaleA( double sc[3], double vel[3] );
276 >  virtual void getVelScaleB( double sc[3], int index );
277 >  virtual void getPosScale(double pos[3], double COM[3],
278 >                           int index, double sc[3]);
279 >
280    double eta[3][3];
281 <  double NkBT;
281 >  double oldEta[3][3];
282 >  double prevEta[3][3];
283 > };
284  
285 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
285 > template<typename T> class NPTxyz : public T{
286  
287 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
287 > public:
288  
289 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
290 <  short int have_target_pressure;
289 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
290 >  virtual ~NPTxyz();
291 >
292 >  virtual double getConservedQuantity(void);
293 >  virtual void resetIntegrator(void);
294  
295 + protected:
296 +
297 +  virtual void evolveEtaA(void);
298 +  virtual void evolveEtaB(void);
299 +
300 +  virtual bool etaConverged( void );
301 +
302 +  virtual void scaleSimBox( void );
303 +
304 +  virtual void getVelScaleA( double sc[3], double vel[3] );
305 +  virtual void getVelScaleB( double sc[3], int index );
306 +  virtual void getPosScale(double pos[3], double COM[3],
307 +                           int index, double sc[3]);
308 +
309 +  double eta[3][3];
310 +  double oldEta[3][3];
311 +  double prevEta[3][3];
312   };
313  
249 – template<typename T> class NPTfm : public T{
314  
315 + template<typename T> class ZConstraint : public T {
316 +  
317 +  public:
318 +  class ForceSubtractionPolicy{
319 +    public:
320 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
321 +
322 +      virtual void update() = 0;    
323 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
324 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
325 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
326 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
327 +    
328 +   protected:
329 +     ZConstraint<T>* zconsIntegrator;
330 +  };
331 +
332 +  class PolicyByNumber : public ForceSubtractionPolicy{
333 +
334 +    public:
335 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
336 +      virtual void update();    
337 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
338 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
339 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
340 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
341 +    
342 +    private:
343 +      int totNumOfMovingAtoms;
344 +  };
345 +
346 +  class PolicyByMass : public ForceSubtractionPolicy{
347 +
348 +    public:
349 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
350 +      
351 +      virtual void update();    
352 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
353 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
354 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
355 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
356 +
357 +   private:
358 +     double totMassOfMovingAtoms;
359 +  };
360 +
361   public:
362  
363 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
364 <  virtual ~NPTfm() {};
363 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
364 >  ~ZConstraint();
365 >    
366 >  void setZConsTime(double time)                  {this->zconsTime = time;}
367 >  void getZConsTime()                             {return zconsTime;}
368 >  
369 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
370 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
371 >  
372 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
373 >  string getZConsOutput()                         {return zconsOutput;}
374 >  
375 >  virtual void integrate();
376 >  
377  
378 <  virtual void integrateStep( int calcPot, int calcStress ){
379 <    calcStress = 1;
380 <    T::integrateStep( calcPot, calcStress );
259 <  }
378 > #ifdef IS_MPI
379 >  virtual void update();                      //which is called to indicate the molecules' migration
380 > #endif
381  
382 <  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;}
382 >  enum ZConsState {zcsMoving, zcsFixed};  
383  
384 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
385 +  vector<ZConsState> states;                 //state of z-constraint molecules
386 +
387 +
388 +
389 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
390 +  double totalMassOfUncons;                //total mas of unconstraint molecules
391 +
392 +
393   protected:
394  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
395  
396 <  virtual int readyCheck();
396 >
397 >  virtual void calcForce( int calcPot, int calcStress );
398 >  virtual void thermalize(void);
399 >  
400 >  void zeroOutVel();
401 >  void doZconstraintForce();
402 >  void doHarmonic();
403 >  bool checkZConsState();
404  
405 <  Molecule* myMolecules;
406 <  Atom** myAtoms;
405 >  bool haveFixedZMols();
406 >  bool haveMovingZMols();
407  
408 <  // chi and eta are the propagated degrees of freedom
408 >  double calcZSys();
409  
410 <  double chi;
279 <  double eta[3][3];
280 <  double NkBT;
410 >  int isZConstraintMol(Molecule* mol);
411  
282 –  // targetTemp, targetPressure, and tauBarostat must be set.  
283 –  // One of qmass or tauThermostat must be set;
412  
413 <  double targetTemp;
414 <  double targetPressure;
415 <  double tauThermostat;
416 <  double tauBarostat;
413 >  double zconsTime;                              //sample time
414 >  double zconsTol;                                 //tolerance of z-contratint
415 >  double zForceConst;                           //base force constant term
416 >                                                          //which is estimate by OOPSE
417 >  
418  
419 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
420 <  short int have_target_pressure;
419 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
420 >  vector<double> kz;                              //force constant array
421  
422 +  vector<double> zPos;                          //
423 +  
424 +  
425 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
426 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
427 +
428 +
429 +  vector<ZConsParaItem>* parameters; //
430 +  
431 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
432 +
433 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
434 +  double* fz;
435 +  double* curZPos;
436 +  
437 +
438 +
439 +  int whichDirection;                           //constraint direction
440 +  
441 + private:
442 +  
443 +  string zconsOutput;                         //filename of zconstraint output
444 +  ZConsWriter* fzOut;                         //z-constraint writer
445 +
446 +  double curZconsTime;                      
447 +
448 +  double calcMovingMolsCOMVel();
449 +  double calcSysCOMVel();
450 +  double calcTotalForce();
451 +  
452 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
453 +  friend class ForceSubtractionPolicy;
454 +
455   };
456  
457   #endif

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