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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 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"
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 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 );
28 <  ~Verlet();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31  
32 < private:
32 > protected:
33 >
34 >  virtual void integrateStep( int calcPot, int calcStress );
35 >  virtual void preMove( void );
36 >  virtual void moveA( void );
37 >  virtual void moveB( void );
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 <  void move_a( double dt );
20 <  void move_b( double dt );
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 +        
53    ForceFields* myFF;
54  
55 <  SimInfo *entry_plug; // all the info we'll ever need
56 <  int c_natoms;  /* the number of atoms */
57 <  Atom **c_atoms; /* array of atom pointers */
58 <  SRI **c_sr_interactions; /* array of SRI pointers */
59 <  int c_n_SRI; /* the number of short range interactions */
55 >  SimInfo *info; // all the info we'll ever need
56 >  int nAtoms;  /* the number of atoms */
57 >  int oldAtoms;
58 >  Atom **atoms; /* array of atom pointers */
59 >  Molecule* molecules;
60 >  int nMols;
61  
62 <  int c_is_constrained; /*boolean to know whether the systems contains
63 <                          constraints. */
64 <  int c_n_constrained; /*counter for number of constraints */
65 <  int *c_constrained_i; /* the i of a constraint pair */
66 <  int *c_constrained_j; /* the j of a constraint pair */
67 <  double *c_constrained_dsqr; /* the square of the constraint distance */
68 <  double *c_mass; /* the array of masses */
69 <  short is_first; /*boolean for the first time integrate is called */
70 <  double c_box_x;
71 <  double c_box_y;
72 <  double c_box_z;
62 >  int isConstrained; // boolean to know whether the systems contains
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
67 >  double *constrainedDsqr; // the square of the constraint distance
68 >  
69 >  int* moving; // tells whether we are moving atom i
70 >  int* moved;  // tells whether we have moved atom i
71 >  double* oldPos; // pre constrained positions
72 >
73 >  short isFirst; /*boolean for the first time integrate is called */
74 >  
75 >  double dt;
76 >  double dt2;
77 >
78 >  Thermo *tStats;
79 >  StatWriter*  statOut;
80 >  DumpWriter*  dumpOut;
81 >  
82   };
83  
84 < class Symplectic : public Integrator {
84 > typedef Integrator<BaseIntegrator> RealIntegrator;
85 >
86 > template<typename T> class NVE : public T {
87 >
88 > public:
89 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
90 >    T( theInfo, the_ff ){}
91 >  virtual ~NVE(){}  
92 > };
93 >
94 >
95 > template<typename T> class NVT : public T {
96 >
97 > public:
98 >
99 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
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 >
109 >  virtual void moveA( void );
110 >  virtual void moveB( void );
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;
126 >  double tauThermostat;
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 NPT : public T{
141 +
142   public:
143 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
144 <  ~Symplectic();
143 >
144 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
145 >  virtual ~NPT();
146    
147 <  void integrate( void );
147 >  virtual void integrateStep( int calcPot, int calcStress ){
148 >    calcStress = 1;
149 >    T::integrateStep( calcPot, calcStress );
150 >  }
151  
152 < private:
152 >  virtual double getConservedQuantity(void) = 0;
153  
154 <  void rotate( int axes1, int axes2, double angle, double j[3],
155 <               double A[3][3] );
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 <  SimInfo* entry_plug;
57 <  ForceFields* myFF;
162 > protected:
163  
164 <  int is_constrained; /*boolean to know whether the systems contains
165 <                          constraints. */
61 <  int n_constrained; /*counter for number of constraints */
62 <  int *constrained_i; /* the i of a constraint pair */
63 <  int *constrained_j; /* the j of a constraint pair */
64 <  double *constrained_dsqr; /* the square of the constraint distance */
65 <  double *mass; /* the array of masses */
164 >  virtual void  moveA( void );
165 >  virtual void moveB( void );
166  
167 <  short int isFirst;
167 >  virtual int readyCheck();
168  
169 <  SRI **srInteractions; /* array of SRI pointers */
170 <  int nSRI; /* the number of short range interactions */
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;
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 +
207 +  double targetTemp;
208 +  double targetPressure;
209 +  double tauThermostat;
210 +  double tauBarostat;
211 +
212 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
213 +  short int have_target_pressure;
214 +
215 +  double *oldPos;
216 +  double *oldVel;
217 +  double *oldJi;
218 +
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 +  virtual double getConservedQuantity(void);
235 +  virtual void resetIntegrator(void);
236 +
237 + protected:
238 +
239 +
240 +
241 +  virtual void evolveEtaA(void);
242 +  virtual void evolveEtaB(void);
243 +
244 +  virtual bool etaConverged( void );
245 +
246 +  virtual void scaleSimBox( void );
247 +
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 +  double eta, oldEta, prevEta;
254 + };
255 +
256 + template<typename T> class NPTf : public T{
257 +
258 + public:
259 +
260 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
261 +  virtual ~NPTf();
262 +
263 +  virtual double getConservedQuantity(void);
264 +  virtual void resetIntegrator(void);
265 +
266 + protected:
267 +
268 +  virtual void evolveEtaA(void);
269 +  virtual void evolveEtaB(void);
270 +
271 +  virtual bool etaConverged( void );
272 +
273 +  virtual void scaleSimBox( void );
274 +
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 oldEta[3][3];
282 +  double prevEta[3][3];
283 + };
284 +
285 + template<typename T> class NPTxyz : public T{
286 +
287 + public:
288 +
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 +
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 +  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 + #ifdef IS_MPI
379 +  virtual void update();                      //which is called to indicate the molecules' migration
380   #endif
381 +
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 +
395 +
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 +  bool haveFixedZMols();
406 +  bool haveMovingZMols();
407 +
408 +  double calcZSys();
409 +
410 +  int isZConstraintMol(Molecule* mol);
411 +
412 +
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 +  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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