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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 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 "ExtendedSystem.hpp"
12 > #include "Thermo.hpp"
13 > #include "ReadWrite.hpp"
14 > #include "ZConsWriter.hpp"
15  
16 < class Verlet : public Integrator {
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 <  Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es );
28 <  ~Verlet();
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  
33 < private:
19 <  
20 <  void move_a( double dt );
21 <  void move_b( double dt );
33 > protected:
34  
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 +  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;
24 –  ExtendedSystem* myES;
55  
56 <  SimInfo *entry_plug; // all the info we'll ever need
57 <  int c_natoms;  /* the number of atoms */
58 <  Atom **c_atoms; /* array of atom pointers */
56 >  SimInfo *info; // all the info we'll ever need
57 >  int nAtoms;  /* the number of atoms */
58 >  int oldAtoms;
59 >  Atom **atoms; /* array of atom pointers */
60    Molecule* molecules;
61    int nMols;
62  
63 <  int c_is_constrained; /*boolean to know whether the systems contains
64 <                          constraints. */
65 <  int c_n_constrained; /*counter for number of constraints */
66 <  int *c_constrained_i; /* the i of a constraint pair */
67 <  int *c_constrained_j; /* the j of a constraint pair */
68 <  double *c_constrained_dsqr; /* the square of the constraint distance */
69 <  double *c_mass; /* the array of masses */
70 <  short is_first; /*boolean for the first time integrate is called */
71 <  double c_box_x;
72 <  double c_box_y;
73 <  double c_box_z;
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 >
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
73 >
74 >  short isFirst; /*boolean for the first time integrate is called */
75 >
76 >  double dt;
77 >  double dt2;
78 >
79 >  Thermo *tStats;
80 >  StatWriter*  statOut;
81 >  DumpWriter*  dumpOut;
82 >
83   };
84  
85 < class Symplectic : public Integrator {
86 <  
85 > typedef Integrator<BaseIntegrator> RealIntegrator;
86 >
87 > template<typename T> class NVE : public T {
88 >
89   public:
90 <  Symplectic( SimInfo* the_entry_plug,  
91 <              ForceFields* the_ff,
92 <              ExtendedSystem* the_es);
93 <  ~Symplectic();
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 >
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 <  void integrate( void );
157 >  double myTauThermo( void ) { return tauThermostat; }
158 >  double myTauBaro( void ) { return tauBarostat; }
159  
160 < private:
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 <  void rotate( int axes1, int axes2, double angle, double j[3],
58 <               double A[3][3] );
168 > protected:
169  
170 <  SimInfo* entry_plug;
171 <  ForceFields* myFF;
62 <  ExtendedSystem* myES;
170 >  virtual void  moveA( void );
171 >  virtual void moveB( void );
172  
173 <  Molecule* molecules;
65 <  int nMols;
173 >  virtual int readyCheck();
174  
175 <  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 */
175 >  virtual void resetIntegrator( void );
176  
177 <  short int isFirst;
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 <  SRI **srInteractions; /* array of SRI pointers */
183 <  int nSRI; /* the number of short range interactions */
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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