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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 1330 by gezelter, Fri Jul 16 16:29:44 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 VelVerletConsFramework;
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 */
63 <  SRI **c_sr_interactions; /* array of SRI pointers */
64 <  int c_n_SRI; /* the number of short range interactions */
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 >  VelVerletConsFramework* consFramework;
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 >
97 > template<typename T> class NVE : public T {
98 >
99   public:
100 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
101 <  ~Symplectic();
100 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
101 >    T( theInfo, the_ff ){}
102 >  virtual ~NVE(){}
103 > };
104 >
105 >
106 > template<typename T> class NVT : public T {
107 >
108 > public:
109 >
110 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
111 >  virtual ~NVT();
112 >
113 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
114 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
115 >  void setChiTolerance(double tol) {chiTolerance = tol;}
116 >  virtual double  getConservedQuantity(void);
117 >  virtual string getAdditionalParameters(void);
118 >
119 > protected:
120 >
121 >  virtual void moveA( void );
122 >  virtual void moveB( void );
123 >
124 >  virtual int readyCheck();
125 >
126 >  virtual void resetIntegrator( void );
127 >
128 >  // chi is a propagated degree of freedom.
129 >
130 >  double chi;
131 >
132 >  //integral of chi(t)dt
133 >  double integralOfChidt;
134 >
135 >  // targetTemp must be set.  tauThermostat must also be set;
136 >
137 >  double targetTemp;
138 >  double tauThermostat;
139 >
140 >  short int have_tau_thermostat, have_target_temp;
141 >
142 >  double *oldVel;
143 >  double *oldJi;
144 >
145 >  double chiTolerance;
146 >  short int have_chi_tolerance;
147 >
148 > };
149 >
150 >
151 >
152 > template<typename T> class NPT : public T{
153 >
154 > public:
155 >
156 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
157 >  virtual ~NPT();
158 >
159 >  virtual void integrateStep( int calcPot, int calcStress ){
160 >    calcStress = 1;
161 >    T::integrateStep( calcPot, calcStress );
162 >  }
163 >
164 >  virtual double getConservedQuantity(void) = 0;
165 >  virtual string getAdditionalParameters(void) = 0;
166    
167 <  void integrate( void );
167 >  double myTauThermo( void ) { return tauThermostat; }
168 >  double myTauBaro( void ) { return tauBarostat; }
169  
170 < private:
170 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
175 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
176 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
177  
178 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
178 > protected:
179  
180 <  SimInfo* entry_plug;
181 <  ForceFields* myFF;
180 >  virtual void  moveA( void );
181 >  virtual void moveB( void );
182  
183 <  int is_constrained; /*boolean to know whether the systems contains
60 <                          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 */
183 >  virtual int readyCheck();
184  
185 <  short int isFirst;
185 >  virtual void resetIntegrator( void );
186  
187 <  SRI **srInteractions; /* array of SRI pointers */
188 <  int nSRI; /* the number of short range interactions */
187 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
188 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
189 >  virtual void getPosScale(double pos[3], double COM[3],
190 >                           int index, double sc[3]) = 0;
191 >
192 >  virtual void calcVelScale( void ) = 0;
193 >
194 >  virtual bool chiConverged( void );
195 >  virtual bool etaConverged( void ) = 0;
196 >
197 >  virtual void evolveChiA( void );
198 >  virtual void evolveEtaA( void ) = 0;
199 >  virtual void evolveChiB( void );
200 >  virtual void evolveEtaB( void ) = 0;
201 >
202 >  virtual void scaleSimBox( void ) = 0;
203 >
204 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
205 >
206 >  // chi and eta are the propagated degrees of freedom
207 >
208 >  double oldChi;
209 >  double prevChi;
210 >  double chi;
211 >  double NkBT;
212 >  double fkBT;
213 >
214 >  double tt2, tb2;
215 >  double instaTemp, instaPress, instaVol;
216 >  double press[3][3];
217 >
218 >  int Nparticles;
219 >
220 >  double integralOfChidt;
221 >
222 >  // targetTemp, targetPressure, and tauBarostat must be set.
223 >  // One of qmass or tauThermostat must be set;
224 >
225 >  double targetTemp;
226 >  double targetPressure;
227 >  double tauThermostat;
228 >  double tauBarostat;
229 >
230 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
231 >  short int have_target_pressure;
232 >
233 >  double *oldPos;
234 >  double *oldVel;
235 >  double *oldJi;
236 >
237 >  double chiTolerance;
238 >  short int have_chi_tolerance;
239 >  double posIterTolerance;
240 >  short int have_pos_iter_tolerance;
241 >  double etaTolerance;
242 >  short int have_eta_tolerance;
243 >
244 > };
245 >
246 > template<typename T> class NPTi : public T{
247 >
248 > public:
249 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
250 >  ~NPTi();
251 >
252 >  virtual double getConservedQuantity(void);
253 >  virtual void resetIntegrator(void);
254 >  virtual string getAdditionalParameters(void);
255 > protected:
256 >
257 >
258 >
259 >  virtual void evolveEtaA(void);
260 >  virtual void evolveEtaB(void);
261 >
262 >  virtual bool etaConverged( void );
263 >
264 >  virtual void scaleSimBox( void );
265 >
266 >  virtual void getVelScaleA( double sc[3], double vel[3] );
267 >  virtual void getVelScaleB( double sc[3], int index );
268 >  virtual void getPosScale(double pos[3], double COM[3],
269 >                           int index, double sc[3]);
270 >
271 >  virtual void calcVelScale( void );
272 >
273 >  double eta, oldEta, prevEta;
274 >  double vScale;
275 > };
276 >
277 > template<typename T> class NPTf : public T{
278 >
279 > public:
280 >
281 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
282 >  virtual ~NPTf();
283 >
284 >  virtual double getConservedQuantity(void);
285 >  virtual string getAdditionalParameters(void);
286 >  virtual void resetIntegrator(void);
287 >
288 > protected:
289 >
290 >  virtual void evolveEtaA(void);
291 >  virtual void evolveEtaB(void);
292 >
293 >  virtual bool etaConverged( void );
294 >
295 >  virtual void scaleSimBox( void );
296 >
297 >  virtual void getVelScaleA( double sc[3], double vel[3] );
298 >  virtual void getVelScaleB( double sc[3], int index );
299 >  virtual void getPosScale(double pos[3], double COM[3],
300 >                           int index, double sc[3]);
301 >
302 >  virtual void calcVelScale( void );
303 >
304 >  double eta[3][3];
305 >  double oldEta[3][3];
306 >  double prevEta[3][3];
307 >  double vScale[3][3];
308 > };
309 >
310 > template<typename T> class NPTxyz : public T{
311 >
312 > public:
313 >
314 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
315 >  virtual ~NPTxyz();
316 >
317 >  virtual double getConservedQuantity(void);
318 >  virtual string getAdditionalParameters(void);
319 >  virtual void resetIntegrator(void);
320 >
321 > protected:
322 >
323 >  virtual void evolveEtaA(void);
324 >  virtual void evolveEtaB(void);
325 >
326 >  virtual bool etaConverged( void );
327 >
328 >  virtual void scaleSimBox( void );
329 >
330 >  virtual void getVelScaleA( double sc[3], double vel[3] );
331 >  virtual void getVelScaleB( double sc[3], int index );
332 >  virtual void getPosScale(double pos[3], double COM[3],
333 >                           int index, double sc[3]);
334 >
335 >  virtual void calcVelScale( void );
336 >
337 >  double eta[3][3];
338 >  double oldEta[3][3];
339 >  double prevEta[3][3];
340 >  double vScale[3][3];
341 > };
342 >
343 >
344 > template<typename T> class ZConstraint : public T {
345 >
346 >  public:
347 >  class ForceSubtractionPolicy{
348 >    public:
349 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
350 >
351 >      virtual void update() = 0;
352 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
354 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
356 >
357 >   protected:
358 >     ZConstraint<T>* zconsIntegrator;
359 >  };
360 >
361 >  class PolicyByNumber : public ForceSubtractionPolicy{
362 >
363 >    public:
364 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
365 >      virtual void update();
366 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
367 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
368 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
369 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
370 >
371 >    private:
372 >      int totNumOfMovingAtoms;
373 >  };
374 >
375 >  class PolicyByMass : public ForceSubtractionPolicy{
376 >
377 >    public:
378 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
379 >
380 >      virtual void update();
381 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385 >
386 >   private:
387 >     double totMassOfMovingAtoms;
388 >  };
389 >
390 > public:
391 >
392 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
393 >  ~ZConstraint();
394 >
395 >  void setZConsTime(double time)                  {this->zconsTime = time;}
396 >  void getZConsTime()                             {return zconsTime;}
397 >
398 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
400 >
401 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
402 >  string getZConsOutput()                         {return zconsOutput;}
403 >
404 >  virtual void integrate();
405 >
406 >
407 > #ifdef IS_MPI
408 >  virtual void update();                      //which is called to indicate the molecules' migration
409 > #endif
410 >
411 >  enum ZConsState {zcsMoving, zcsFixed};
412 >
413 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
414 >  vector<ZConsState> states;                 //state of z-constraint molecules
415 >
416 >
417 >
418 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
419 >  double totalMassOfUncons;                //total mas of unconstraint molecules
420 >
421 >
422 > protected:
423 >
424 >
425 >
426 >  virtual void calcForce( int calcPot, int calcStress );
427 >  virtual void thermalize(void);
428 >
429 >  void zeroOutVel();
430 >  void doZconstraintForce();
431 >  void doHarmonic(vector<double>& resPos);
432 >  bool checkZConsState();
433 >
434 >  bool haveFixedZMols();
435 >  bool haveMovingZMols();
436 >
437 >  double calcZSys();
438 >
439 >  int isZConstraintMol(Molecule* mol);
440 >
441 >
442 >  double zconsTime;                              //sample time
443 >  double zconsTol;                                 //tolerance of z-contratint
444 >  double zForceConst;                           //base force constant term
445 >                                                          //which is estimate by OOPSE
446 >
447 >
448 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
449 >  vector<double> kz;                              //force constant array
450 >
451 >  vector<double> zPos;                          //
452 >
453 >
454 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
455 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
456 >
457 >
458 >  vector<ZConsParaItem>* parameters; //
459 >
460 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
461 >
462 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
463 >  vector<double> fz;
464 >  vector<double> curZPos;
465 >
466 >  bool usingSMD;
467 >  vector<double> prevCantPos;
468 >  vector<double> cantPos;
469 >  vector<double> cantVel;
470 >
471 >  double zconsFixTime;  
472 >  double zconsGap;
473 >  bool hasZConsGap;
474 >  vector<double> endFixTime;
475    
476 +  int whichDirection;                           //constraint direction
477 +
478 + private:
479 +
480 +  string zconsOutput;                         //filename of zconstraint output
481 +  ZConsWriter* fzOut;                         //z-constraint writer
482 +
483 +  double curZconsTime;
484 +
485 +  double calcMovingMolsCOMVel();
486 +  double calcSysCOMVel();
487 +  double calcTotalForce();
488 +  void updateZPos();
489 +  void updateCantPos();
490 +  
491 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
492 +  friend class ForceSubtractionPolicy;
493 +
494   };
495  
496 +
497 + //Sympletic quaternion Scheme Integrator
498 + //Reference:
499 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500 + //Symplectic quaternion Scheme for biophysical molecular dynamics
501 + //116(20), 8649, J. Chem. Phys. (2002)
502 + template<typename T> class SQSIntegrator : public T{
503 +  public:
504 +    virtual void moveA();
505 +    virtual void moveB();
506 +  protected:
507 +    void freeRotor();
508 +    void rotate(int k, double dt);
509 +    
510 + };
511   #endif

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