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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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 "StuntDouble.hpp"
8 + #include "Molecule.hpp"
9   #include "SRI.hpp"
10   #include "AbstractClasses.hpp"
11   #include "SimInfo.hpp"
12   #include "ForceFields.hpp"
13 < #include "ExtendedSystem.hpp"
13 > #include "Thermo.hpp"
14 > #include "ReadWrite.hpp"
15 > #include "ZConsWriter.hpp"
16 > #include "Restraints.hpp"
17  
18 < class Verlet : public Integrator {
18 > using namespace std;
19 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
20 > const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21 > const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
22 > const int maxIteration = 300;
23 > const double tol = 1.0e-6;
24  
25 + template<typename T = BaseIntegrator> class Integrator : public T {
26 +
27   public:
28 <  Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es );
29 <  ~Verlet();
28 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
29 >  virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
34 < private:
19 <  
20 <  void move_a( double dt );
21 <  void move_b( double dt );
34 > protected:
35  
36 +  virtual void integrateStep( int calcPot, int calcStress );
37 +  virtual void preMove( void );
38 +  virtual void moveA( void );
39 +  virtual void moveB( void );
40 +  virtual void constrainA( void );
41 +  virtual void constrainB( void );
42 +  virtual int  readyCheck( void ) { return 1; }
43 +
44 +  virtual void resetIntegrator( void ) { }
45 +
46 +  virtual void calcForce( int calcPot, int calcStress );
47 +  virtual void thermalize();
48 +
49 +  virtual bool stopIntegrator() {return false;}
50 +
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53 +  void checkConstraints( void );
54 +  void rotate( int axes1, int axes2, double angle, double j[3],
55 +         double A[3][3] );
56 +
57    ForceFields* myFF;
24 –  ExtendedSystem* myES;
58  
59 <  SimInfo *entry_plug; // all the info we'll ever need
60 <  int c_natoms;  /* the number of atoms */
61 <  Atom **c_atoms; /* array of atom pointers */
59 >  SimInfo *info; // all the info we'll ever need
60 >  vector<StuntDouble*> integrableObjects;
61 >  int nAtoms;  /* the number of atoms */
62 >  int oldAtoms;
63 >  Atom **atoms; /* array of atom pointers */
64    Molecule* molecules;
65    int nMols;
66  
67 <  int c_is_constrained; /*boolean to know whether the systems contains
68 <                          constraints. */
69 <  int c_n_constrained; /*counter for number of constraints */
70 <  int *c_constrained_i; /* the i of a constraint pair */
71 <  int *c_constrained_j; /* the j of a constraint pair */
72 <  double *c_constrained_dsqr; /* the square of the constraint distance */
73 <  double *c_mass; /* the array of masses */
74 <  short is_first; /*boolean for the first time integrate is called */
75 <  double c_box_x;
76 <  double c_box_y;
77 <  double c_box_z;
67 >  int isConstrained; // boolean to know whether the systems contains
68 >         // constraints.
69 >  int nConstrained;  // counter for number of constraints
70 >  int *constrainedA; // the i of a constraint pair
71 >  int *constrainedB; // the j of a constraint pair
72 >  double *constrainedDsqr; // the square of the constraint distance
73 >
74 >  int* moving; // tells whether we are moving atom i
75 >  int* moved;  // tells whether we have moved atom i
76 >  double* oldPos; // pre constrained positions
77 >
78 >  short isFirst; /*boolean for the first time integrate is called */
79 >
80 >  double dt;
81 >  double dt2;
82 >
83 >  Thermo *tStats;
84 >  StatWriter*  statOut;
85 >  DumpWriter*  dumpOut;
86 >
87   };
88  
89 < class Symplectic : public Integrator {
90 <  
89 > typedef Integrator<BaseIntegrator> RealIntegrator;
90 >
91 > // ansi instantiation
92 > template class Integrator<BaseIntegrator>;
93 >
94 > template<typename T> class NVE : public T {
95 >
96   public:
97 <  Symplectic( SimInfo* the_entry_plug,  
98 <              ForceFields* the_ff,
99 <              ExtendedSystem* the_es);
100 <  ~Symplectic();
97 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
98 >    T( theInfo, the_ff ){}
99 >  virtual ~NVE(){}
100 > };
101 >
102 >
103 > template<typename T> class NVT : public T {
104 >
105 > public:
106 >
107 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
108 >  virtual ~NVT();
109 >
110 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
111 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112 >  void setChiTolerance(double tol) {chiTolerance = tol;}
113 >  virtual double  getConservedQuantity(void);
114 >  virtual string getAdditionalParameters(void);
115 >
116 > protected:
117 >
118 >  virtual void moveA( void );
119 >  virtual void moveB( void );
120 >
121 >  virtual int readyCheck();
122 >
123 >  virtual void resetIntegrator( void );
124 >
125 >  // chi is a propagated degree of freedom.
126 >
127 >  double chi;
128 >
129 >  //integral of chi(t)dt
130 >  double integralOfChidt;
131 >
132 >  // targetTemp must be set.  tauThermostat must also be set;
133 >
134 >  double targetTemp;
135 >  double tauThermostat;
136 >
137 >  short int have_tau_thermostat, have_target_temp;
138 >
139 >  double *oldVel;
140 >  double *oldJi;
141 >
142 >  double chiTolerance;
143 >  short int have_chi_tolerance;
144 >
145 > };
146 >
147 >
148 >
149 > template<typename T> class NPT : public T{
150 >
151 > public:
152 >
153 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
154 >  virtual ~NPT();
155 >
156 >  virtual void integrateStep( int calcPot, int calcStress ){
157 >    calcStress = 1;
158 >    T::integrateStep( calcPot, calcStress );
159 >  }
160 >
161 >  virtual double getConservedQuantity(void) = 0;
162 >  virtual string getAdditionalParameters(void) = 0;
163    
164 <  void integrate( void );
164 >  double myTauThermo( void ) { return tauThermostat; }
165 >  double myTauBaro( void ) { return tauBarostat; }
166  
167 < private:
167 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174  
175 <  void rotate( int axes1, int axes2, double angle, double j[3],
58 <               double A[3][3] );
175 > protected:
176  
177 <  SimInfo* entry_plug;
178 <  ForceFields* myFF;
62 <  ExtendedSystem* myES;
177 >  virtual void  moveA( void );
178 >  virtual void moveB( void );
179  
180 <  Molecule* molecules;
65 <  int nMols;
180 >  virtual int readyCheck();
181  
182 <  int is_constrained; /*boolean to know whether the systems contains
68 <                          constraints. */
69 <  int n_constrained; /*counter for number of constraints */
70 <  int *constrained_i; /* the i of a constraint pair */
71 <  int *constrained_j; /* the j of a constraint pair */
72 <  double *constrained_dsqr; /* the square of the constraint distance */
73 <  double *mass; /* the array of masses */
182 >  virtual void resetIntegrator( void );
183  
184 <  short int isFirst;
184 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
186 >  virtual void getPosScale(double pos[3], double COM[3],
187 >                           int index, double sc[3]) = 0;
188  
189 <  SRI **srInteractions; /* array of SRI pointers */
190 <  int nSRI; /* the number of short range interactions */
189 >  virtual void calcVelScale( void ) = 0;
190 >
191 >  virtual bool chiConverged( void );
192 >  virtual bool etaConverged( void ) = 0;
193 >
194 >  virtual void evolveChiA( void );
195 >  virtual void evolveEtaA( void ) = 0;
196 >  virtual void evolveChiB( void );
197 >  virtual void evolveEtaB( void ) = 0;
198 >
199 >  virtual void scaleSimBox( void ) = 0;
200 >
201 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202 >
203 >  // chi and eta are the propagated degrees of freedom
204 >
205 >  double oldChi;
206 >  double prevChi;
207 >  double chi;
208 >  double NkBT;
209 >  double fkBT;
210 >
211 >  double tt2, tb2;
212 >  double instaTemp, instaPress, instaVol;
213 >  double press[3][3];
214 >
215 >  int Nparticles;
216 >
217 >  double integralOfChidt;
218 >
219 >  // targetTemp, targetPressure, and tauBarostat must be set.
220 >  // One of qmass or tauThermostat must be set;
221 >
222 >  double targetTemp;
223 >  double targetPressure;
224 >  double tauThermostat;
225 >  double tauBarostat;
226 >
227 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228 >  short int have_target_pressure;
229 >
230 >  double *oldPos;
231 >  double *oldVel;
232 >  double *oldJi;
233 >
234 >  double chiTolerance;
235 >  short int have_chi_tolerance;
236 >  double posIterTolerance;
237 >  short int have_pos_iter_tolerance;
238 >  double etaTolerance;
239 >  short int have_eta_tolerance;
240 >
241 > };
242 >
243 > template<typename T> class NPTi : public T{
244 >
245 > public:
246 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
247 >  ~NPTi();
248 >
249 >  virtual double getConservedQuantity(void);
250 >  virtual void resetIntegrator(void);
251 >  virtual string getAdditionalParameters(void);
252 > protected:
253 >
254 >
255 >
256 >  virtual void evolveEtaA(void);
257 >  virtual void evolveEtaB(void);
258 >
259 >  virtual bool etaConverged( void );
260 >
261 >  virtual void scaleSimBox( void );
262 >
263 >  virtual void getVelScaleA( double sc[3], double vel[3] );
264 >  virtual void getVelScaleB( double sc[3], int index );
265 >  virtual void getPosScale(double pos[3], double COM[3],
266 >                           int index, double sc[3]);
267 >
268 >  virtual void calcVelScale( void );
269 >
270 >  double eta, oldEta, prevEta;
271 >  double vScale;
272 > };
273 >
274 > template<typename T> class NPTf : public T{
275 >
276 > public:
277 >
278 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
279 >  virtual ~NPTf();
280 >
281 >  virtual double getConservedQuantity(void);
282 >  virtual string getAdditionalParameters(void);
283 >  virtual void resetIntegrator(void);
284 >
285 > protected:
286 >
287 >  virtual void evolveEtaA(void);
288 >  virtual void evolveEtaB(void);
289 >
290 >  virtual bool etaConverged( void );
291 >
292 >  virtual void scaleSimBox( void );
293 >
294 >  virtual void getVelScaleA( double sc[3], double vel[3] );
295 >  virtual void getVelScaleB( double sc[3], int index );
296 >  virtual void getPosScale(double pos[3], double COM[3],
297 >                           int index, double sc[3]);
298 >
299 >  virtual void calcVelScale( void );
300 >
301 >  double eta[3][3];
302 >  double oldEta[3][3];
303 >  double prevEta[3][3];
304 >  double vScale[3][3];
305 > };
306 >
307 > template<typename T> class NPTxyz : public T{
308 >
309 > public:
310 >
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313 >
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317 >
318 > protected:
319 >
320 >  virtual void evolveEtaA(void);
321 >  virtual void evolveEtaB(void);
322 >
323 >  virtual bool etaConverged( void );
324 >
325 >  virtual void scaleSimBox( void );
326 >
327 >  virtual void getVelScaleA( double sc[3], double vel[3] );
328 >  virtual void getVelScaleB( double sc[3], int index );
329 >  virtual void getPosScale(double pos[3], double COM[3],
330 >                           int index, double sc[3]);
331 >
332 >  virtual void calcVelScale( void );
333 >
334 >  double eta[3][3];
335 >  double oldEta[3][3];
336 >  double prevEta[3][3];
337 >  double vScale[3][3];
338 > };
339 >
340 >
341 > template<typename T> class ZConstraint : public T {
342 >
343 >  public:
344 >  class ForceSubtractionPolicy{
345 >    public:
346 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347 >
348 >      virtual void update() = 0;
349 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353 >
354 >   protected:
355 >     ZConstraint<T>* zconsIntegrator;
356 >  };
357 >
358 >  class PolicyByNumber : public ForceSubtractionPolicy{
359 >
360 >    public:
361 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362 >      virtual void update();
363 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367 >
368 >    private:
369 >      int totNumOfMovingAtoms;
370 >  };
371 >
372 >  class PolicyByMass : public ForceSubtractionPolicy{
373 >
374 >    public:
375 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376 >
377 >      virtual void update();
378 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
381 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382 >
383 >   private:
384 >     double totMassOfMovingAtoms;
385 >  };
386 >
387 > public:
388 >
389 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
390 >  ~ZConstraint();
391 >
392 >  void setZConsTime(double time)                  {this->zconsTime = time;}
393 >  void getZConsTime()                             {return zconsTime;}
394 >
395 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
397 >
398 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
399 >  string getZConsOutput()                         {return zconsOutput;}
400 >
401 >  virtual void integrate();
402 >
403 >
404 > #ifdef IS_MPI
405 >  virtual void update();                      //which is called to indicate the molecules' migration
406 > #endif
407 >
408 >  enum ZConsState {zcsMoving, zcsFixed};
409 >
410 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
411 >  vector<ZConsState> states;                 //state of z-constraint molecules
412 >
413 >
414 >
415 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
416 >  double totalMassOfUncons;                //total mas of unconstraint molecules
417 >
418 >
419 > protected:
420 >
421 >
422 >
423 >  virtual void calcForce( int calcPot, int calcStress );
424 >  virtual void thermalize(void);
425 >
426 >  void zeroOutVel();
427 >  void doZconstraintForce();
428 >  void doHarmonic(vector<double>& resPos);
429 >  bool checkZConsState();
430 >
431 >  bool haveFixedZMols();
432 >  bool haveMovingZMols();
433 >
434 >  double calcZSys();
435 >
436 >  int isZConstraintMol(Molecule* mol);
437 >
438 >
439 >  double zconsTime;                              //sample time
440 >  double zconsTol;                                 //tolerance of z-contratint
441 >  double zForceConst;                           //base force constant term
442 >                                                          //which is estimate by OOPSE
443 >
444 >
445 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 >  vector<double> kz;                              //force constant array
447 >
448 >  vector<double> zPos;                          //
449 >
450 >
451 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
452 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
453 >
454 >
455 >  vector<ZConsParaItem>* parameters; //
456 >
457 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458 >
459 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 >  vector<double> fz;
461 >  vector<double> curZPos;
462 >
463 >  bool usingSMD;
464 >  vector<double> prevCantPos;
465 >  vector<double> cantPos;
466 >  vector<double> cantVel;
467 >
468 >  double zconsFixTime;  
469 >  double zconsGap;
470 >  bool hasZConsGap;
471 >  vector<double> endFixTime;
472    
473 +  int whichDirection;                           //constraint direction
474 +
475 + private:
476 +
477 +  string zconsOutput;                         //filename of zconstraint output
478 +  ZConsWriter* fzOut;                         //z-constraint writer
479 +
480 +  double curZconsTime;
481 +
482 +  double calcMovingMolsCOMVel();
483 +  double calcSysCOMVel();
484 +  double calcTotalForce();
485 +  void updateZPos();
486 +  void updateCantPos();
487 +  
488 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489 +  friend class ForceSubtractionPolicy;
490 +
491   };
492  
493   #endif

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