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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 1254 by tim, Wed Jun 9 16:16:33 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 "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 + class RattleFramework;
26 + template<typename T = BaseIntegrator> class Integrator : public T {
27 +
28   public:
29 <  Verlet( SimInfo &info, ForceFields* the_ff );
30 <  ~Verlet();
29 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
30 >  virtual ~Integrator();
31    void integrate( void );
32 +  virtual double  getConservedQuantity(void);
33 +  virtual string getAdditionalParameters(void);
34  
35 < private:
18 <  
19 <  void move_a( double dt );
20 <  void move_b( double dt );
35 > protected:
36  
37 +  virtual void integrateStep( int calcPot, int calcStress );
38 +  //virtual void preMove( void );
39 +  virtual void moveA( void );
40 +  virtual void moveB( void );
41 +  //virtual void constrainA( void );
42 +  //virtual void constrainB( void );
43 +  virtual int  readyCheck( void ) { return 1; }
44 +
45 +  virtual void resetIntegrator( void ) { }
46 +
47 +  virtual void calcForce( int calcPot, int calcStress );
48 +  virtual void thermalize();
49 +
50 +  virtual bool stopIntegrator() {return false;}
51 +
52 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53 +
54 +  //void checkConstraints( void );
55 +  void rotate( int axes1, int axes2, double angle, double j[3],
56 +         double A[3][3] );
57 +
58    ForceFields* myFF;
59  
60 <  SimInfo *entry_plug; // all the info we'll ever need
61 <  int c_natoms;  /* the number of atoms */
62 <  Atom **c_atoms; /* array of atom pointers */
60 >  SimInfo *info; // all the info we'll ever need
61 >  vector<StuntDouble*> integrableObjects;
62 >  int nAtoms;  /* the number of atoms */
63 >  int oldAtoms;
64 >  Atom **atoms; /* array of atom pointers */
65    Molecule* molecules;
66    int nMols;
67  
68 <  int c_is_constrained; /*boolean to know whether the systems contains
69 <                          constraints. */
70 <  int c_n_constrained; /*counter for number of constraints */
71 <  int *c_constrained_i; /* the i of a constraint pair */
72 <  int *c_constrained_j; /* the j of a constraint pair */
73 <  double *c_constrained_dsqr; /* the square of the constraint distance */
74 <  double *c_mass; /* the array of masses */
75 <  short is_first; /*boolean for the first time integrate is called */
76 <  double c_box_x;
77 <  double c_box_y;
78 <  double c_box_z;
68 >  RattleFramework* rattle;
69 >
70 >  //int isConstrained; // boolean to know whether the systems contains constraints.
71 >  //int nConstrained;  // counter for number of constraints
72 >  //int *constrainedA; // the i of a constraint pair
73 >  //int *constrainedB; // the j of a constraint pair
74 >  //double *constrainedDsqr; // the square of the constraint distance
75 >
76 >  //int* moving; // tells whether we are moving atom i
77 >  //int* moved;  // tells whether we have moved atom i
78 >  //double* oldPos; // pre constrained positions
79 >
80 >  short isFirst; /*boolean for the first time integrate is called */
81 >
82 >  double dt;
83 >  double dt2;
84 >
85 >  Thermo *tStats;
86 >  StatWriter*  statOut;
87 >  DumpWriter*  dumpOut;
88 >
89   };
90  
91 < class Symplectic : public Integrator {
92 <  
91 > typedef Integrator<BaseIntegrator> RealIntegrator;
92 >
93 > // ansi instantiation
94 > template class Integrator<BaseIntegrator>;
95 >
96 > template<typename T> class NVE : public T {
97 >
98   public:
99 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
100 <  ~Symplectic();
99 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
100 >    T( theInfo, the_ff ){}
101 >  virtual ~NVE(){}
102 > };
103 >
104 >
105 > template<typename T> class NVT : public T {
106 >
107 > public:
108 >
109 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
110 >  virtual ~NVT();
111 >
112 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
113 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
114 >  void setChiTolerance(double tol) {chiTolerance = tol;}
115 >  virtual double  getConservedQuantity(void);
116 >  virtual string getAdditionalParameters(void);
117 >
118 > protected:
119 >
120 >  virtual void moveA( void );
121 >  virtual void moveB( void );
122 >
123 >  virtual int readyCheck();
124 >
125 >  virtual void resetIntegrator( void );
126 >
127 >  // chi is a propagated degree of freedom.
128 >
129 >  double chi;
130 >
131 >  //integral of chi(t)dt
132 >  double integralOfChidt;
133 >
134 >  // targetTemp must be set.  tauThermostat must also be set;
135 >
136 >  double targetTemp;
137 >  double tauThermostat;
138 >
139 >  short int have_tau_thermostat, have_target_temp;
140 >
141 >  double *oldVel;
142 >  double *oldJi;
143 >
144 >  double chiTolerance;
145 >  short int have_chi_tolerance;
146 >
147 > };
148 >
149 >
150 >
151 > template<typename T> class NPT : public T{
152 >
153 > public:
154 >
155 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
156 >  virtual ~NPT();
157 >
158 >  virtual void integrateStep( int calcPot, int calcStress ){
159 >    calcStress = 1;
160 >    T::integrateStep( calcPot, calcStress );
161 >  }
162 >
163 >  virtual double getConservedQuantity(void) = 0;
164 >  virtual string getAdditionalParameters(void) = 0;
165    
166 <  void integrate( void );
166 >  double myTauThermo( void ) { return tauThermostat; }
167 >  double myTauBaro( void ) { return tauBarostat; }
168  
169 < private:
169 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
174 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
175 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
176  
177 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
177 > protected:
178  
179 <  SimInfo* entry_plug;
180 <  ForceFields* myFF;
179 >  virtual void  moveA( void );
180 >  virtual void moveB( void );
181  
182 <  Molecule* molecules;
60 <  int nMols;
182 >  virtual int readyCheck();
183  
184 <  int is_constrained; /*boolean to know whether the systems contains
63 <                          constraints. */
64 <  int n_constrained; /*counter for number of constraints */
65 <  int *constrained_i; /* the i of a constraint pair */
66 <  int *constrained_j; /* the j of a constraint pair */
67 <  double *constrained_dsqr; /* the square of the constraint distance */
68 <  double *mass; /* the array of masses */
184 >  virtual void resetIntegrator( void );
185  
186 <  short int isFirst;
186 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
187 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
188 >  virtual void getPosScale(double pos[3], double COM[3],
189 >                           int index, double sc[3]) = 0;
190  
191 <  SRI **srInteractions; /* array of SRI pointers */
192 <  int nSRI; /* the number of short range interactions */
191 >  virtual void calcVelScale( void ) = 0;
192 >
193 >  virtual bool chiConverged( void );
194 >  virtual bool etaConverged( void ) = 0;
195 >
196 >  virtual void evolveChiA( void );
197 >  virtual void evolveEtaA( void ) = 0;
198 >  virtual void evolveChiB( void );
199 >  virtual void evolveEtaB( void ) = 0;
200 >
201 >  virtual void scaleSimBox( void ) = 0;
202 >
203 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
204 >
205 >  // chi and eta are the propagated degrees of freedom
206 >
207 >  double oldChi;
208 >  double prevChi;
209 >  double chi;
210 >  double NkBT;
211 >  double fkBT;
212 >
213 >  double tt2, tb2;
214 >  double instaTemp, instaPress, instaVol;
215 >  double press[3][3];
216 >
217 >  int Nparticles;
218 >
219 >  double integralOfChidt;
220 >
221 >  // targetTemp, targetPressure, and tauBarostat must be set.
222 >  // One of qmass or tauThermostat must be set;
223 >
224 >  double targetTemp;
225 >  double targetPressure;
226 >  double tauThermostat;
227 >  double tauBarostat;
228 >
229 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
230 >  short int have_target_pressure;
231 >
232 >  double *oldPos;
233 >  double *oldVel;
234 >  double *oldJi;
235 >
236 >  double chiTolerance;
237 >  short int have_chi_tolerance;
238 >  double posIterTolerance;
239 >  short int have_pos_iter_tolerance;
240 >  double etaTolerance;
241 >  short int have_eta_tolerance;
242 >
243 > };
244 >
245 > template<typename T> class NPTi : public T{
246 >
247 > public:
248 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
249 >  ~NPTi();
250 >
251 >  virtual double getConservedQuantity(void);
252 >  virtual void resetIntegrator(void);
253 >  virtual string getAdditionalParameters(void);
254 > protected:
255 >
256 >
257 >
258 >  virtual void evolveEtaA(void);
259 >  virtual void evolveEtaB(void);
260 >
261 >  virtual bool etaConverged( void );
262 >
263 >  virtual void scaleSimBox( void );
264 >
265 >  virtual void getVelScaleA( double sc[3], double vel[3] );
266 >  virtual void getVelScaleB( double sc[3], int index );
267 >  virtual void getPosScale(double pos[3], double COM[3],
268 >                           int index, double sc[3]);
269 >
270 >  virtual void calcVelScale( void );
271 >
272 >  double eta, oldEta, prevEta;
273 >  double vScale;
274 > };
275 >
276 > template<typename T> class NPTf : public T{
277 >
278 > public:
279 >
280 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
281 >  virtual ~NPTf();
282 >
283 >  virtual double getConservedQuantity(void);
284 >  virtual string getAdditionalParameters(void);
285 >  virtual void resetIntegrator(void);
286 >
287 > protected:
288 >
289 >  virtual void evolveEtaA(void);
290 >  virtual void evolveEtaB(void);
291 >
292 >  virtual bool etaConverged( void );
293 >
294 >  virtual void scaleSimBox( void );
295 >
296 >  virtual void getVelScaleA( double sc[3], double vel[3] );
297 >  virtual void getVelScaleB( double sc[3], int index );
298 >  virtual void getPosScale(double pos[3], double COM[3],
299 >                           int index, double sc[3]);
300 >
301 >  virtual void calcVelScale( void );
302 >
303 >  double eta[3][3];
304 >  double oldEta[3][3];
305 >  double prevEta[3][3];
306 >  double vScale[3][3];
307 > };
308 >
309 > template<typename T> class NPTxyz : public T{
310 >
311 > public:
312 >
313 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
314 >  virtual ~NPTxyz();
315 >
316 >  virtual double getConservedQuantity(void);
317 >  virtual string getAdditionalParameters(void);
318 >  virtual void resetIntegrator(void);
319 >
320 > protected:
321 >
322 >  virtual void evolveEtaA(void);
323 >  virtual void evolveEtaB(void);
324 >
325 >  virtual bool etaConverged( void );
326 >
327 >  virtual void scaleSimBox( void );
328 >
329 >  virtual void getVelScaleA( double sc[3], double vel[3] );
330 >  virtual void getVelScaleB( double sc[3], int index );
331 >  virtual void getPosScale(double pos[3], double COM[3],
332 >                           int index, double sc[3]);
333 >
334 >  virtual void calcVelScale( void );
335 >
336 >  double eta[3][3];
337 >  double oldEta[3][3];
338 >  double prevEta[3][3];
339 >  double vScale[3][3];
340 > };
341 >
342 >
343 > template<typename T> class ZConstraint : public T {
344 >
345 >  public:
346 >  class ForceSubtractionPolicy{
347 >    public:
348 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349 >
350 >      virtual void update() = 0;
351 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
353 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
354 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
355 >
356 >   protected:
357 >     ZConstraint<T>* zconsIntegrator;
358 >  };
359 >
360 >  class PolicyByNumber : public ForceSubtractionPolicy{
361 >
362 >    public:
363 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
364 >      virtual void update();
365 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
366 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
367 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
368 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
369 >
370 >    private:
371 >      int totNumOfMovingAtoms;
372 >  };
373 >
374 >  class PolicyByMass : public ForceSubtractionPolicy{
375 >
376 >    public:
377 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
378 >
379 >      virtual void update();
380 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
381 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
382 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
383 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
384 >
385 >   private:
386 >     double totMassOfMovingAtoms;
387 >  };
388 >
389 > public:
390 >
391 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
392 >  ~ZConstraint();
393 >
394 >  void setZConsTime(double time)                  {this->zconsTime = time;}
395 >  void getZConsTime()                             {return zconsTime;}
396 >
397 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
398 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
399 >
400 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
401 >  string getZConsOutput()                         {return zconsOutput;}
402 >
403 >  virtual void integrate();
404 >
405 >
406 > #ifdef IS_MPI
407 >  virtual void update();                      //which is called to indicate the molecules' migration
408 > #endif
409 >
410 >  enum ZConsState {zcsMoving, zcsFixed};
411 >
412 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
413 >  vector<ZConsState> states;                 //state of z-constraint molecules
414 >
415 >
416 >
417 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
418 >  double totalMassOfUncons;                //total mas of unconstraint molecules
419 >
420 >
421 > protected:
422 >
423 >
424 >
425 >  virtual void calcForce( int calcPot, int calcStress );
426 >  virtual void thermalize(void);
427 >
428 >  void zeroOutVel();
429 >  void doZconstraintForce();
430 >  void doHarmonic(vector<double>& resPos);
431 >  bool checkZConsState();
432 >
433 >  bool haveFixedZMols();
434 >  bool haveMovingZMols();
435 >
436 >  double calcZSys();
437 >
438 >  int isZConstraintMol(Molecule* mol);
439 >
440 >
441 >  double zconsTime;                              //sample time
442 >  double zconsTol;                                 //tolerance of z-contratint
443 >  double zForceConst;                           //base force constant term
444 >                                                          //which is estimate by OOPSE
445 >
446 >
447 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
448 >  vector<double> kz;                              //force constant array
449 >
450 >  vector<double> zPos;                          //
451 >
452 >
453 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
454 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
455 >
456 >
457 >  vector<ZConsParaItem>* parameters; //
458 >
459 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
460 >
461 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
462 >  vector<double> fz;
463 >  vector<double> curZPos;
464 >
465 >  bool usingSMD;
466 >  vector<double> prevCantPos;
467 >  vector<double> cantPos;
468 >  vector<double> cantVel;
469 >
470 >  double zconsFixTime;  
471 >  double zconsGap;
472 >  bool hasZConsGap;
473 >  vector<double> endFixTime;
474    
475 +  int whichDirection;                           //constraint direction
476 +
477 + private:
478 +
479 +  string zconsOutput;                         //filename of zconstraint output
480 +  ZConsWriter* fzOut;                         //z-constraint writer
481 +
482 +  double curZconsTime;
483 +
484 +  double calcMovingMolsCOMVel();
485 +  double calcSysCOMVel();
486 +  double calcTotalForce();
487 +  void updateZPos();
488 +  void updateCantPos();
489 +  
490 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
491 +  friend class ForceSubtractionPolicy;
492 +
493   };
494  
495 +
496 + //Sympletic quaternion Scheme Integrator
497 + //Reference:
498 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
499 + //Symplectic quaternion Scheme for biophysical molecular dynamics
500 + //116(20), 8649, J. Chem. Phys. (2002)
501 + template<typename T> class SQSIntegrator : public T{
502 +  public:
503 +    virtual void moveA();
504 +    virtual void moveB();
505 +  protected:
506 +    void freeRotor();
507 +    void rotate(int k, double dt);
508 +    
509 + };
510   #endif

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