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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 843 by mmeineke, Wed Oct 29 20:41:39 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 +  virtual string getAdditionalParameters(void);
32  
33 < private:
18 <  
19 <  void move_a( double dt );
20 <  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;
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 */
59 <  SRI **c_sr_interactions; /* array of SRI pointers */
60 <  int c_n_SRI; /* the number of short range interactions */
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,  ForceFields* the_ff );
91 <  ~Symplectic();
92 <  
93 <  void integrate( void );
90 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91 >    T( theInfo, the_ff ){}
92 >  virtual ~NVE(){}
93 > };
94  
51 – private:
95  
96 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
96 > template<typename T> class NVT : public T {
97  
98 <  SimInfo* entry_plug;
57 <  ForceFields* myFF;
98 > public:
99  
100 <  int is_constrained; /*boolean to know whether the systems contains
101 <                          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 */
100 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
101 >  virtual ~NVT();
102  
103 <  short int isFirst;
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 <  SRI **srInteractions; /* array of SRI pointers */
110 <  int nSRI; /* the number of short range interactions */
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 +  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 bool chiConverged( void );
183 +  virtual bool etaConverged( void ) = 0;
184 +
185 +  virtual void evolveChiA( void );
186 +  virtual void evolveEtaA( void ) = 0;
187 +  virtual void evolveChiB( void );
188 +  virtual void evolveEtaB( void ) = 0;
189 +
190 +  virtual void scaleSimBox( void ) = 0;
191 +
192 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
193 +
194 +  // chi and eta are the propagated degrees of freedom
195 +
196 +  double oldChi;
197 +  double prevChi;
198 +  double chi;
199 +  double NkBT;
200 +  double fkBT;
201 +
202 +  double tt2, tb2;
203 +  double instaTemp, instaPress, instaVol;
204 +  double press[3][3];
205 +
206 +  int Nparticles;
207 +
208 +  double integralOfChidt;
209 +
210 +  // targetTemp, targetPressure, and tauBarostat must be set.
211 +  // One of qmass or tauThermostat must be set;
212 +
213 +  double targetTemp;
214 +  double targetPressure;
215 +  double tauThermostat;
216 +  double tauBarostat;
217 +
218 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
219 +  short int have_target_pressure;
220 +
221 +  double *oldPos;
222 +  double *oldVel;
223 +  double *oldJi;
224 +
225 +  double chiTolerance;
226 +  short int have_chi_tolerance;
227 +  double posIterTolerance;
228 +  short int have_pos_iter_tolerance;
229 +  double etaTolerance;
230 +  short int have_eta_tolerance;
231 +
232   };
233  
234 + template<typename T> class NPTi : public T{
235 +
236 + public:
237 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
238 +  ~NPTi();
239 +
240 +  virtual double getConservedQuantity(void);
241 +  virtual void resetIntegrator(void);
242 +  virtual string getAdditionalParameters(void);
243 + protected:
244 +
245 +
246 +
247 +  virtual void evolveEtaA(void);
248 +  virtual void evolveEtaB(void);
249 +
250 +  virtual bool etaConverged( void );
251 +
252 +  virtual void scaleSimBox( void );
253 +
254 +  virtual void getVelScaleA( double sc[3], double vel[3] );
255 +  virtual void getVelScaleB( double sc[3], int index );
256 +  virtual void getPosScale(double pos[3], double COM[3],
257 +                           int index, double sc[3]);
258 +
259 +  double eta, oldEta, prevEta;
260 + };
261 +
262 + template<typename T> class NPTf : public T{
263 +
264 + public:
265 +
266 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
267 +  virtual ~NPTf();
268 +
269 +  virtual double getConservedQuantity(void);
270 +  virtual string getAdditionalParameters(void);
271 +  virtual void resetIntegrator(void);
272 +
273 + protected:
274 +
275 +  virtual void evolveEtaA(void);
276 +  virtual void evolveEtaB(void);
277 +
278 +  virtual bool etaConverged( void );
279 +
280 +  virtual void scaleSimBox( void );
281 +
282 +  virtual void getVelScaleA( double sc[3], double vel[3] );
283 +  virtual void getVelScaleB( double sc[3], int index );
284 +  virtual void getPosScale(double pos[3], double COM[3],
285 +                           int index, double sc[3]);
286 +
287 +  double eta[3][3];
288 +  double oldEta[3][3];
289 +  double prevEta[3][3];
290 + };
291 +
292 + template<typename T> class NPTxyz : public T{
293 +
294 + public:
295 +
296 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
297 +  virtual ~NPTxyz();
298 +
299 +  virtual double getConservedQuantity(void);
300 +  virtual string getAdditionalParameters(void);
301 +  virtual void resetIntegrator(void);
302 +
303 + protected:
304 +
305 +  virtual void evolveEtaA(void);
306 +  virtual void evolveEtaB(void);
307 +
308 +  virtual bool etaConverged( void );
309 +
310 +  virtual void scaleSimBox( void );
311 +
312 +  virtual void getVelScaleA( double sc[3], double vel[3] );
313 +  virtual void getVelScaleB( double sc[3], int index );
314 +  virtual void getPosScale(double pos[3], double COM[3],
315 +                           int index, double sc[3]);
316 +
317 +  double eta[3][3];
318 +  double oldEta[3][3];
319 +  double prevEta[3][3];
320 + };
321 +
322 +
323 + template<typename T> class ZConstraint : public T {
324 +
325 +  public:
326 +  class ForceSubtractionPolicy{
327 +    public:
328 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
329 +
330 +      virtual void update() = 0;
331 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
333 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
335 +
336 +   protected:
337 +     ZConstraint<T>* zconsIntegrator;
338 +  };
339 +
340 +  class PolicyByNumber : public ForceSubtractionPolicy{
341 +
342 +    public:
343 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
344 +      virtual void update();
345 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
346 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
347 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
348 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
349 +
350 +    private:
351 +      int totNumOfMovingAtoms;
352 +  };
353 +
354 +  class PolicyByMass : public ForceSubtractionPolicy{
355 +
356 +    public:
357 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 +
359 +      virtual void update();
360 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
361 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
362 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
363 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
364 +
365 +   private:
366 +     double totMassOfMovingAtoms;
367 +  };
368 +
369 + public:
370 +
371 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
372 +  ~ZConstraint();
373 +
374 +  void setZConsTime(double time)                  {this->zconsTime = time;}
375 +  void getZConsTime()                             {return zconsTime;}
376 +
377 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
378 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
379 +
380 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
381 +  string getZConsOutput()                         {return zconsOutput;}
382 +
383 +  virtual void integrate();
384 +
385 +
386 + #ifdef IS_MPI
387 +  virtual void update();                      //which is called to indicate the molecules' migration
388   #endif
389 +
390 +  enum ZConsState {zcsMoving, zcsFixed};
391 +
392 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
393 +  vector<ZConsState> states;                 //state of z-constraint molecules
394 +
395 +
396 +
397 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
398 +  double totalMassOfUncons;                //total mas of unconstraint molecules
399 +
400 +
401 + protected:
402 +
403 +
404 +
405 +  virtual void calcForce( int calcPot, int calcStress );
406 +  virtual void thermalize(void);
407 +
408 +  void zeroOutVel();
409 +  void doZconstraintForce();
410 +  void doHarmonic();
411 +  bool checkZConsState();
412 +
413 +  bool haveFixedZMols();
414 +  bool haveMovingZMols();
415 +
416 +  double calcZSys();
417 +
418 +  int isZConstraintMol(Molecule* mol);
419 +
420 +
421 +  double zconsTime;                              //sample time
422 +  double zconsTol;                                 //tolerance of z-contratint
423 +  double zForceConst;                           //base force constant term
424 +                                                          //which is estimate by OOPSE
425 +
426 +
427 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
428 +  vector<double> kz;                              //force constant array
429 +
430 +  vector<double> zPos;                          //
431 +
432 +
433 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
434 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
435 +
436 +
437 +  vector<ZConsParaItem>* parameters; //
438 +
439 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
440 +
441 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
442 +  double* fz;
443 +  double* curZPos;
444 +
445 +
446 +
447 +  int whichDirection;                           //constraint direction
448 +
449 + private:
450 +
451 +  string zconsOutput;                         //filename of zconstraint output
452 +  ZConsWriter* fzOut;                         //z-constraint writer
453 +
454 +  double curZconsTime;
455 +
456 +  double calcMovingMolsCOMVel();
457 +  double calcSysCOMVel();
458 +  double calcTotalForce();
459 +
460 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
461 +  friend class ForceSubtractionPolicy;
462 +
463 + };
464 +
465 + #endif

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