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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 600 by gezelter, Mon Jul 14 22:38:13 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 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"
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 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
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
18 – class Integrator : public BaseIntegrator {
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 +  virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
25 –
33   protected:
34 <  
34 >
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
# Line 32 | Line 39 | class Integrator : public BaseIntegrator { (protected)
39    virtual void constrainA( void );
40    virtual void constrainB( void );
41    virtual int  readyCheck( void ) { return 1; }
35 –  
36 –  void checkConstraints( void );
37 –  void rotate( int axes1, int axes2, double angle, double j[3],
38 –               double A[3][3] );
42  
43 +  virtual void resetIntegrator( void ) { }
44  
45 +  virtual void calcForce( int calcPot, int calcStress );
46 +  virtual void thermalize();
47 +
48 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49 +
50 +  void checkConstraints( void );
51 +  void rotate( int axes1, int axes2, double angle, double j[3],
52 +         double A[3][3] );
53 +
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
# Line 48 | Line 61 | class Integrator : public BaseIntegrator { (protected)
61    int nMols;
62  
63    int isConstrained; // boolean to know whether the systems contains
64 <                     // constraints.
65 <  int nConstrained;  // counter for number of constraints
66 <  int *constrainedA; // the i of a constraint pair
67 <  int *constrainedB; // the j of a constraint pair
68 <  double *constrainedDsqr; // the square of the constraint distance
69 <  
64 >         // constraints.
65 >  int nConstrained;  // counter for number of constraints
66 >  int *constrainedA; // the i of a constraint pair
67 >  int *constrainedB; // the j of a constraint pair
68 >  double *constrainedDsqr; // the square of the constraint distance
69 >
70    int* moving; // tells whether we are moving atom i
71    int* moved;  // tells whether we have moved atom i
72 <  double* oldPos; // pre constrained positions
72 >  double* oldPos; // pre constrained positions
73  
74    short isFirst; /*boolean for the first time integrate is called */
75 <  
75 >
76    double dt;
77    double dt2;
78  
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85 < class NVE : public Integrator{
85 > typedef Integrator<BaseIntegrator> RealIntegrator;
86  
87 + template<typename T> class NVE : public T {
88 +
89   public:
90    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91 <    Integrator( theInfo, the_ff ){}
91 >    T( theInfo, the_ff ){}
92    virtual ~NVE(){}
78 –
79 –  
80 –
93   };
94  
83 – class NVT : public Integrator{
95  
96 + template<typename T> class NVT : public T {
97 +
98   public:
99  
100    NVT ( SimInfo *theInfo, ForceFields* the_ff);
101 <  virtual ~NVT() {}
101 >  virtual ~NVT();
102  
103    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
104    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105 +  void setChiTolerance(double tol) {chiTolerance = tol;}
106 +  virtual double  getConservedQuantity(void);
107 +  virtual string getAdditionalParameters(void);
108  
109   protected:
110  
# Line 97 | Line 113 | class NVT : public Integrator{ (protected)
113  
114    virtual int readyCheck();
115  
116 +  virtual void resetIntegrator( void );
117 +
118    // chi is a propagated degree of freedom.
119  
120    double chi;
121  
122 +  //integral of chi(t)dt
123 +  double integralOfChidt;
124 +
125    // targetTemp must be set.  tauThermostat must also be set;
126  
127    double targetTemp;
128    double tauThermostat;
129 <  
129 >
130    short int have_tau_thermostat, have_target_temp;
131  
132 +  double *oldVel;
133 +  double *oldJi;
134 +
135 +  double chiTolerance;
136 +  short int have_chi_tolerance;
137 +
138   };
139  
140  
114 – class NPTi : public Integrator{
141  
142 + template<typename T> class NPT : public T{
143 +
144   public:
145  
146 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
147 <  virtual ~NPTi() {};
146 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
147 >  virtual ~NPT();
148  
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151 <    Integrator::integrateStep( calcPot, calcStress );
151 >    T::integrateStep( calcPot, calcStress );
152    }
153  
154 +  virtual double getConservedQuantity(void) = 0;
155 +  virtual string getAdditionalParameters(void) = 0;
156    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
157    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
158    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
159    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
160 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
161 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
162 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
163  
164   protected:
165  
# Line 135 | Line 168 | class NPTi : public Integrator{ (protected)
168  
169    virtual int readyCheck();
170  
171 <  // chi and eta are the propagated degrees of freedom
171 >  virtual void resetIntegrator( void );
172  
173 <  double chi;
174 <  double eta;
175 <  double NkBT;
173 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
174 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
175 >  virtual void getPosScale(double pos[3], double COM[3],
176 >                           int index, double sc[3]) = 0;
177  
178 <  // targetTemp, targetPressure, and tauBarostat must be set.  
179 <  // One of qmass or tauThermostat must be set;
178 >  virtual bool chiConverged( void );
179 >  virtual bool etaConverged( void ) = 0;
180  
181 <  double targetTemp;
182 <  double targetPressure;
183 <  double tauThermostat;
184 <  double tauBarostat;
181 >  virtual void evolveChiA( void );
182 >  virtual void evolveEtaA( void ) = 0;
183 >  virtual void evolveChiB( void );
184 >  virtual void evolveEtaB( void ) = 0;
185  
186 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
153 <  short int have_target_pressure;
154 <
155 < };
156 <
157 < class NPTim : public Integrator{
186 >  virtual void scaleSimBox( void ) = 0;
187  
188 < public:
188 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
189  
161 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
162 –  virtual ~NPTim() {};
163 –
164 –  virtual void integrateStep( int calcPot, int calcStress ){
165 –    calcStress = 1;
166 –    Integrator::integrateStep( calcPot, calcStress );
167 –  }
168 –
169 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173 –
174 – protected:
175 –
176 –  virtual void  moveA( void );
177 –  virtual void moveB( void );
178 –
179 –  virtual int readyCheck();
180 –
190    // chi and eta are the propagated degrees of freedom
191  
192 +  double oldChi;
193 +  double prevChi;
194    double chi;
184 –  double eta;
195    double NkBT;
196 +  double fkBT;
197  
198 <  // targetTemp, targetPressure, and tauBarostat must be set.  
198 >  double tt2, tb2;
199 >  double instaTemp, instaPress, instaVol;
200 >  double press[3][3];
201 >
202 >  int Nparticles;
203 >
204 >  double integralOfChidt;
205 >
206 >  // targetTemp, targetPressure, and tauBarostat must be set.
207    // One of qmass or tauThermostat must be set;
208  
209    double targetTemp;
# Line 195 | Line 214 | class NPTim : public Integrator{ (protected)
214    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
215    short int have_target_pressure;
216  
217 +  double *oldPos;
218 +  double *oldVel;
219 +  double *oldJi;
220 +
221 +  double chiTolerance;
222 +  short int have_chi_tolerance;
223 +  double posIterTolerance;
224 +  short int have_pos_iter_tolerance;
225 +  double etaTolerance;
226 +  short int have_eta_tolerance;
227 +
228   };
229  
230 < class NPTf : public Integrator{
230 > template<typename T> class NPTi : public T{
231  
232   public:
233 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
234 +  ~NPTi();
235  
236 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
237 <  virtual ~NPTf() {};
236 >  virtual double getConservedQuantity(void);
237 >  virtual void resetIntegrator(void);
238 >  virtual string getAdditionalParameters(void);
239 > protected:
240  
207 –  virtual void integrateStep( int calcPot, int calcStress ){
208 –    calcStress = 1;
209 –    Integrator::integrateStep( calcPot, calcStress );
210 –  }
241  
212 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
213 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
214 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
215 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
242  
243 +  virtual void evolveEtaA(void);
244 +  virtual void evolveEtaB(void);
245 +
246 +  virtual bool etaConverged( void );
247 +
248 +  virtual void scaleSimBox( void );
249 +
250 +  virtual void getVelScaleA( double sc[3], double vel[3] );
251 +  virtual void getVelScaleB( double sc[3], int index );
252 +  virtual void getPosScale(double pos[3], double COM[3],
253 +                           int index, double sc[3]);
254 +
255 +  double eta, oldEta, prevEta;
256 + };
257 +
258 + template<typename T> class NPTf : public T{
259 +
260 + public:
261 +
262 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
263 +  virtual ~NPTf();
264 +
265 +  virtual double getConservedQuantity(void);
266 +  virtual string getAdditionalParameters(void);
267 +  virtual void resetIntegrator(void);
268 +
269   protected:
270  
271 <  virtual void  moveA( void );
272 <  virtual void moveB( void );
271 >  virtual void evolveEtaA(void);
272 >  virtual void evolveEtaB(void);
273  
274 <  virtual int readyCheck();
274 >  virtual bool etaConverged( void );
275  
276 <  // chi and eta are the propagated degrees of freedom
276 >  virtual void scaleSimBox( void );
277  
278 <  double chi;
279 <  double eta[3][3];
280 <  double NkBT;
278 >  virtual void getVelScaleA( double sc[3], double vel[3] );
279 >  virtual void getVelScaleB( double sc[3], int index );
280 >  virtual void getPosScale(double pos[3], double COM[3],
281 >                           int index, double sc[3]);
282  
283 <  // targetTemp, targetPressure, and tauBarostat must be set.  
284 <  // One of qmass or tauThermostat must be set;
283 >  double eta[3][3];
284 >  double oldEta[3][3];
285 >  double prevEta[3][3];
286 > };
287  
288 <  double targetTemp;
234 <  double targetPressure;
235 <  double tauThermostat;
236 <  double tauBarostat;
288 > template<typename T> class NPTxyz : public T{
289  
290 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
239 <  short int have_target_pressure;
290 > public:
291  
292 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
293 +  virtual ~NPTxyz();
294 +
295 +  virtual double getConservedQuantity(void);
296 +  virtual string getAdditionalParameters(void);
297 +  virtual void resetIntegrator(void);
298 +
299 + protected:
300 +
301 +  virtual void evolveEtaA(void);
302 +  virtual void evolveEtaB(void);
303 +
304 +  virtual bool etaConverged( void );
305 +
306 +  virtual void scaleSimBox( void );
307 +
308 +  virtual void getVelScaleA( double sc[3], double vel[3] );
309 +  virtual void getVelScaleB( double sc[3], int index );
310 +  virtual void getPosScale(double pos[3], double COM[3],
311 +                           int index, double sc[3]);
312 +
313 +  double eta[3][3];
314 +  double oldEta[3][3];
315 +  double prevEta[3][3];
316   };
317  
243 – class NPTfm : public Integrator{
318  
319 + template<typename T> class ZConstraint : public T {
320 +
321 +  public:
322 +  class ForceSubtractionPolicy{
323 +    public:
324 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
325 +
326 +      virtual void update() = 0;
327 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
328 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
329 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
330 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
331 +
332 +   protected:
333 +     ZConstraint<T>* zconsIntegrator;
334 +  };
335 +
336 +  class PolicyByNumber : public ForceSubtractionPolicy{
337 +
338 +    public:
339 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
340 +      virtual void update();
341 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
342 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
343 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
344 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
345 +
346 +    private:
347 +      int totNumOfMovingAtoms;
348 +  };
349 +
350 +  class PolicyByMass : public ForceSubtractionPolicy{
351 +
352 +    public:
353 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
354 +
355 +      virtual void update();
356 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
357 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
358 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
359 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360 +
361 +   private:
362 +     double totMassOfMovingAtoms;
363 +  };
364 +
365   public:
366  
367 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
368 <  virtual ~NPTfm() {};
367 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
368 >  ~ZConstraint();
369  
370 <  virtual void integrateStep( int calcPot, int calcStress ){
371 <    calcStress = 1;
252 <    Integrator::integrateStep( calcPot, calcStress );
253 <  }
370 >  void setZConsTime(double time)                  {this->zconsTime = time;}
371 >  void getZConsTime()                             {return zconsTime;}
372  
373 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
374 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
257 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
258 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
373 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
374 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
375  
376 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
377 +  string getZConsOutput()                         {return zconsOutput;}
378 +
379 +  virtual void integrate();
380 +
381 +
382 + #ifdef IS_MPI
383 +  virtual void update();                      //which is called to indicate the molecules' migration
384 + #endif
385 +
386 +  enum ZConsState {zcsMoving, zcsFixed};
387 +
388 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
389 +  vector<ZConsState> states;                 //state of z-constraint molecules
390 +
391 +
392 +
393 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
394 +  double totalMassOfUncons;                //total mas of unconstraint molecules
395 +
396 +
397   protected:
398  
262 –  virtual void  moveA( void );
263 –  virtual void moveB( void );
399  
265 –  virtual int readyCheck();
400  
401 <  // chi and eta are the propagated degrees of freedom
401 >  virtual void calcForce( int calcPot, int calcStress );
402 >  virtual void thermalize(void);
403  
404 <  double chi;
405 <  double eta[3][3];
406 <  double NkBT;
404 >  void zeroOutVel();
405 >  void doZconstraintForce();
406 >  void doHarmonic();
407 >  bool checkZConsState();
408  
409 <  // targetTemp, targetPressure, and tauBarostat must be set.  
410 <  // One of qmass or tauThermostat must be set;
409 >  bool haveFixedZMols();
410 >  bool haveMovingZMols();
411  
412 <  double targetTemp;
277 <  double targetPressure;
278 <  double tauThermostat;
279 <  double tauBarostat;
412 >  double calcZSys();
413  
414 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
282 <  short int have_target_pressure;
414 >  int isZConstraintMol(Molecule* mol);
415  
416 +
417 +  double zconsTime;                              //sample time
418 +  double zconsTol;                                 //tolerance of z-contratint
419 +  double zForceConst;                           //base force constant term
420 +                                                          //which is estimate by OOPSE
421 +
422 +
423 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
424 +  vector<double> kz;                              //force constant array
425 +
426 +  vector<double> zPos;                          //
427 +
428 +
429 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
430 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
431 +
432 +
433 +  vector<ZConsParaItem>* parameters; //
434 +
435 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
436 +
437 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
438 +  double* fz;
439 +  double* curZPos;
440 +
441 +
442 +
443 +  int whichDirection;                           //constraint direction
444 +
445 + private:
446 +
447 +  string zconsOutput;                         //filename of zconstraint output
448 +  ZConsWriter* fzOut;                         //z-constraint writer
449 +
450 +  double curZconsTime;
451 +
452 +  double calcMovingMolsCOMVel();
453 +  double calcSysCOMVel();
454 +  double calcTotalForce();
455 +
456 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
457 +  friend class ForceSubtractionPolicy;
458 +
459   };
460  
461   #endif

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