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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 548 by mmeineke, Wed Jun 4 21:06:45 2003 UTC vs.
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 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 < class Integrator : public BaseIntegrator {
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  
23 +
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
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  
19 –
33   protected:
34  
22 –  
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
38    virtual void moveB( void );
39    virtual void constrainA( void );
40    virtual void constrainB( void );
41 <  
30 <  
31 <  void checkConstraints( void );
32 <  void rotate( int axes1, int axes2, double angle, double j[3],
33 <               double A[3][3] );
41 >  virtual int  readyCheck( void ) { return 1; }
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 43 | 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* prePos; // 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;
60 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
78  
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –
65 –  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –  
72 –
73 –
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85 + typedef Integrator<BaseIntegrator> RealIntegrator;
86  
87 < class NVT : public Integrator{
87 > template<typename T> class NVE : public T {
88  
89 <  NVT ( void );
89 > public:
90 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91 >    T( theInfo, the_ff ){}
92 >  virtual ~NVE(){}
93 > };
94 >
95 >
96 > template<typename T> class NVT : public T {
97 >
98 > public:
99 >
100 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
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 <  virtual moveA( void );
111 <  virtual moveB( void );
110 >
111 >  virtual void moveA( void );
112 >  virtual void moveB( void );
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 >
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 >
141 >
142 > template<typename T> class NPT : public T{
143 >
144 > public:
145 >
146 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
147 >  virtual ~NPT();
148 >
149 >  virtual void integrateStep( int calcPot, int calcStress ){
150 >    calcStress = 1;
151 >    T::integrateStep( calcPot, calcStress );
152 >  }
153 >
154 >  virtual double getConservedQuantity(void) = 0;
155 >  virtual string getAdditionalParameters(void) = 0;
156 >  
157 >  double myTauThermo( void ) { return tauThermostat; }
158 >  double myTauBaro( void ) { return tauBarostat; }
159 >
160 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167 >
168 > protected:
169 >
170 >  virtual void  moveA( void );
171 >  virtual void moveB( void );
172 >
173 >  virtual int readyCheck();
174 >
175 >  virtual void resetIntegrator( void );
176 >
177 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
179 >  virtual void getPosScale(double pos[3], double COM[3],
180 >                           int index, double sc[3]) = 0;
181 >
182 >  virtual void calcVelScale( void ) = 0;
183 >
184 >  virtual bool chiConverged( void );
185 >  virtual bool etaConverged( void ) = 0;
186 >
187 >  virtual void evolveChiA( void );
188 >  virtual void evolveEtaA( void ) = 0;
189 >  virtual void evolveChiB( void );
190 >  virtual void evolveEtaB( void ) = 0;
191 >
192 >  virtual void scaleSimBox( void ) = 0;
193 >
194 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
195 >
196 >  // chi and eta are the propagated degrees of freedom
197 >
198 >  double oldChi;
199 >  double prevChi;
200 >  double chi;
201 >  double NkBT;
202 >  double fkBT;
203 >
204 >  double tt2, tb2;
205 >  double instaTemp, instaPress, instaVol;
206 >  double press[3][3];
207 >
208 >  int Nparticles;
209 >
210 >  double integralOfChidt;
211 >
212 >  // targetTemp, targetPressure, and tauBarostat must be set.
213 >  // One of qmass or tauThermostat must be set;
214 >
215 >  double targetTemp;
216 >  double targetPressure;
217 >  double tauThermostat;
218 >  double tauBarostat;
219 >
220 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
221 >  short int have_target_pressure;
222 >
223 >  double *oldPos;
224 >  double *oldVel;
225 >  double *oldJi;
226 >
227 >  double chiTolerance;
228 >  short int have_chi_tolerance;
229 >  double posIterTolerance;
230 >  short int have_pos_iter_tolerance;
231 >  double etaTolerance;
232 >  short int have_eta_tolerance;
233 >
234 > };
235 >
236 > template<typename T> class NPTi : public T{
237 >
238 > public:
239 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
240 >  ~NPTi();
241 >
242 >  virtual double getConservedQuantity(void);
243 >  virtual void resetIntegrator(void);
244 >  virtual string getAdditionalParameters(void);
245 > protected:
246 >
247 >
248 >
249 >  virtual void evolveEtaA(void);
250 >  virtual void evolveEtaB(void);
251 >
252 >  virtual bool etaConverged( void );
253  
254 +  virtual void scaleSimBox( void );
255 +
256 +  virtual void getVelScaleA( double sc[3], double vel[3] );
257 +  virtual void getVelScaleB( double sc[3], int index );
258 +  virtual void getPosScale(double pos[3], double COM[3],
259 +                           int index, double sc[3]);
260 +
261 +  virtual void calcVelScale( void );
262 +
263 +  double eta, oldEta, prevEta;
264 +  double vScale;
265   };
266  
267 + template<typename T> class NPTf : public T{
268 +
269 + public:
270 +
271 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
272 +  virtual ~NPTf();
273 +
274 +  virtual double getConservedQuantity(void);
275 +  virtual string getAdditionalParameters(void);
276 +  virtual void resetIntegrator(void);
277 +
278 + protected:
279 +
280 +  virtual void evolveEtaA(void);
281 +  virtual void evolveEtaB(void);
282 +
283 +  virtual bool etaConverged( void );
284 +
285 +  virtual void scaleSimBox( void );
286 +
287 +  virtual void getVelScaleA( double sc[3], double vel[3] );
288 +  virtual void getVelScaleB( double sc[3], int index );
289 +  virtual void getPosScale(double pos[3], double COM[3],
290 +                           int index, double sc[3]);
291 +
292 +  virtual void calcVelScale( void );
293 +
294 +  double eta[3][3];
295 +  double oldEta[3][3];
296 +  double prevEta[3][3];
297 +  double vScale[3][3];
298 + };
299 +
300 + template<typename T> class NPTxyz : public T{
301 +
302 + public:
303 +
304 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
305 +  virtual ~NPTxyz();
306 +
307 +  virtual double getConservedQuantity(void);
308 +  virtual string getAdditionalParameters(void);
309 +  virtual void resetIntegrator(void);
310 +
311 + protected:
312 +
313 +  virtual void evolveEtaA(void);
314 +  virtual void evolveEtaB(void);
315 +
316 +  virtual bool etaConverged( void );
317 +
318 +  virtual void scaleSimBox( void );
319 +
320 +  virtual void getVelScaleA( double sc[3], double vel[3] );
321 +  virtual void getVelScaleB( double sc[3], int index );
322 +  virtual void getPosScale(double pos[3], double COM[3],
323 +                           int index, double sc[3]);
324 +
325 +  virtual void calcVelScale( void );
326 +
327 +  double eta[3][3];
328 +  double oldEta[3][3];
329 +  double prevEta[3][3];
330 +  double vScale[3][3];
331 + };
332 +
333 +
334 + template<typename T> class ZConstraint : public T {
335 +
336 +  public:
337 +  class ForceSubtractionPolicy{
338 +    public:
339 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
340 +
341 +      virtual void update() = 0;
342 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
343 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
344 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346 +
347 +   protected:
348 +     ZConstraint<T>* zconsIntegrator;
349 +  };
350 +
351 +  class PolicyByNumber : public ForceSubtractionPolicy{
352 +
353 +    public:
354 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
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 +      int totNumOfMovingAtoms;
363 +  };
364 +
365 +  class PolicyByMass : public ForceSubtractionPolicy{
366 +
367 +    public:
368 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
369 +
370 +      virtual void update();
371 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375 +
376 +   private:
377 +     double totMassOfMovingAtoms;
378 +  };
379 +
380 + public:
381 +
382 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
383 +  ~ZConstraint();
384 +
385 +  void setZConsTime(double time)                  {this->zconsTime = time;}
386 +  void getZConsTime()                             {return zconsTime;}
387 +
388 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
390 +
391 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
392 +  string getZConsOutput()                         {return zconsOutput;}
393 +
394 +  virtual void integrate();
395 +
396 +
397 + #ifdef IS_MPI
398 +  virtual void update();                      //which is called to indicate the molecules' migration
399 + #endif
400 +
401 +  enum ZConsState {zcsMoving, zcsFixed};
402 +
403 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
404 +  vector<ZConsState> states;                 //state of z-constraint molecules
405 +
406 +
407 +
408 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
409 +  double totalMassOfUncons;                //total mas of unconstraint molecules
410 +
411 +
412 + protected:
413 +
414 +
415 +
416 +  virtual void calcForce( int calcPot, int calcStress );
417 +  virtual void thermalize(void);
418 +
419 +  void zeroOutVel();
420 +  void doZconstraintForce();
421 +  void doHarmonic();
422 +  bool checkZConsState();
423 +
424 +  bool haveFixedZMols();
425 +  bool haveMovingZMols();
426 +
427 +  double calcZSys();
428 +
429 +  int isZConstraintMol(Molecule* mol);
430 +
431 +
432 +  double zconsTime;                              //sample time
433 +  double zconsTol;                                 //tolerance of z-contratint
434 +  double zForceConst;                           //base force constant term
435 +                                                          //which is estimate by OOPSE
436 +
437 +
438 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
439 +  vector<double> kz;                              //force constant array
440 +
441 +  vector<double> zPos;                          //
442 +
443 +
444 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
445 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
446 +
447 +
448 +  vector<ZConsParaItem>* parameters; //
449 +
450 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
451 +
452 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
453 +  double* fz;
454 +  double* curZPos;
455 +
456 +  double zconsFixTime;  
457 +  double zconsGap;
458 +  bool hasZConsGap;
459 +  vector<double> endFixTime;
460    
461 +  int whichDirection;                           //constraint direction
462  
463 + private:
464  
465 +  string zconsOutput;                         //filename of zconstraint output
466 +  ZConsWriter* fzOut;                         //z-constraint writer
467 +
468 +  double curZconsTime;
469 +
470 +  double calcMovingMolsCOMVel();
471 +  double calcSysCOMVel();
472 +  double calcTotalForce();
473 +  void updateZPos();
474 +
475 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
476 +  friend class ForceSubtractionPolicy;
477 +
478 + };
479 +
480 + /*
481 + //Steered Molecular Dynamics
482 + template<typename T> class SMD : public T{
483 +  public:
484 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
485 +    ~SMD();
486 +  
487 +   virtual void integrate();
488 +  virtual void calcForce( int calcPot, int calcStress );  
489 + };
490 + */
491   #endif

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