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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 1452 by tim, Mon Aug 23 15:11:36 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 + #include "Quaternion.hpp"
18 + #include "Mat4x4d.hpp"
19  
20 < class Verlet : public Integrator {
20 > using namespace std;
21 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
22 > const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
23 > const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
24 > const int maxIteration = 300;
25 > const double tol = 1.0e-6;
26  
27 + class VelVerletConsFramework;
28 + template<typename T = BaseIntegrator> class Integrator : public T {
29 +
30   public:
31 <  Verlet( SimInfo &info, ForceFields* the_ff );
32 <  ~Verlet();
31 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
32 >  virtual ~Integrator();
33    void integrate( void );
34 +  virtual double  getConservedQuantity(void);
35 +  virtual string getAdditionalParameters(void);
36  
37 < private:
18 <  
19 <  void move_a( double dt );
20 <  void move_b( double dt );
37 > protected:
38  
39 +  virtual void integrateStep( int calcPot, int calcStress );
40 +  //virtual void preMove( void );
41 +  virtual void moveA( void );
42 +  virtual void moveB( void );
43 +  //virtual void constrainA( void );
44 +  //virtual void constrainB( void );
45 +  virtual int  readyCheck( void ) { return 1; }
46 +
47 +  virtual void resetIntegrator( void ) { }
48 +
49 +  virtual void calcForce( int calcPot, int calcStress );
50 +  virtual void thermalize();
51 +
52 +  virtual bool stopIntegrator() {return false;}
53 +
54 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
55 +
56 +  //void checkConstraints( void );
57 +  void rotate( int axes1, int axes2, double angle, double j[3],
58 +         double A[3][3] );
59 +
60 +  void printQuaternion(StuntDouble* sd);
61 +  Mat4x4d getS(const Quaternion& q);
62 +
63    ForceFields* myFF;
64  
65 <  SimInfo *entry_plug; // all the info we'll ever need
66 <  int c_natoms;  /* the number of atoms */
67 <  Atom **c_atoms; /* array of atom pointers */
65 >  SimInfo *info; // all the info we'll ever need
66 >  vector<StuntDouble*> integrableObjects;
67 >  int nAtoms;  /* the number of atoms */
68 >  int oldAtoms;
69 >  Atom **atoms; /* array of atom pointers */
70    Molecule* molecules;
71    int nMols;
72  
73 <  int c_is_constrained; /*boolean to know whether the systems contains
74 <                          constraints. */
75 <  int c_n_constrained; /*counter for number of constraints */
76 <  int *c_constrained_i; /* the i of a constraint pair */
77 <  int *c_constrained_j; /* the j of a constraint pair */
78 <  double *c_constrained_dsqr; /* the square of the constraint distance */
79 <  double *c_mass; /* the array of masses */
80 <  short is_first; /*boolean for the first time integrate is called */
81 <  double c_box_x;
82 <  double c_box_y;
83 <  double c_box_z;
73 >  VelVerletConsFramework* consFramework;
74 >
75 >  //int isConstrained; // boolean to know whether the systems contains constraints.
76 >  //int nConstrained;  // counter for number of constraints
77 >  //int *constrainedA; // the i of a constraint pair
78 >  //int *constrainedB; // the j of a constraint pair
79 >  //double *constrainedDsqr; // the square of the constraint distance
80 >
81 >  //int* moving; // tells whether we are moving atom i
82 >  //int* moved;  // tells whether we have moved atom i
83 >  //double* oldPos; // pre constrained positions
84 >
85 >  short isFirst; /*boolean for the first time integrate is called */
86 >
87 >  double dt;
88 >  double dt2;
89 >
90 >  Thermo *tStats;
91 >  StatWriter*  statOut;
92 >  DumpWriter*  dumpOut;
93 >
94   };
95  
96 < class Symplectic : public Integrator {
97 <  
96 > typedef Integrator<BaseIntegrator> RealIntegrator;
97 >
98 > // ansi instantiation
99 > // template class Integrator<BaseIntegrator>;
100 >
101 >
102 > template<typename T> class NVE : public T {
103 >
104   public:
105 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
106 <  ~Symplectic();
105 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
106 >    T( theInfo, the_ff ){}
107 >  virtual ~NVE(){}
108 > };
109 >
110 >
111 > template<typename T> class NVT : public T {
112 >
113 > public:
114 >
115 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
116 >  virtual ~NVT();
117 >
118 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
119 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
120 >  void setChiTolerance(double tol) {chiTolerance = tol;}
121 >  virtual double  getConservedQuantity(void);
122 >  virtual string getAdditionalParameters(void);
123 >
124 > protected:
125 >
126 >  virtual void moveA( void );
127 >  virtual void moveB( void );
128 >
129 >  virtual int readyCheck();
130 >
131 >  virtual void resetIntegrator( void );
132 >
133 >  // chi is a propagated degree of freedom.
134 >
135 >  double chi;
136 >
137 >  //integral of chi(t)dt
138 >  double integralOfChidt;
139 >
140 >  // targetTemp must be set.  tauThermostat must also be set;
141 >
142 >  double targetTemp;
143 >  double tauThermostat;
144 >
145 >  short int have_tau_thermostat, have_target_temp;
146 >
147 >  double *oldVel;
148 >  double *oldJi;
149 >
150 >  double chiTolerance;
151 >  short int have_chi_tolerance;
152 >
153 > };
154 >
155 >
156 >
157 > template<typename T> class NPT : public T{
158 >
159 > public:
160 >
161 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
162 >  virtual ~NPT();
163 >
164 >  virtual void integrateStep( int calcPot, int calcStress ){
165 >    calcStress = 1;
166 >    T::integrateStep( calcPot, calcStress );
167 >  }
168 >
169 >  virtual double getConservedQuantity(void) = 0;
170 >  virtual string getAdditionalParameters(void) = 0;
171    
172 <  void integrate( void );
172 >  double myTauThermo( void ) { return tauThermostat; }
173 >  double myTauBaro( void ) { return tauBarostat; }
174  
175 < private:
175 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
180 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
181 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
182  
183 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
183 > protected:
184  
185 <  SimInfo* entry_plug;
186 <  ForceFields* myFF;
185 >  virtual void  moveA( void );
186 >  virtual void moveB( void );
187  
188 <  Molecule* molecules;
60 <  int nMols;
188 >  virtual int readyCheck();
189  
190 <  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 */
190 >  virtual void resetIntegrator( void );
191  
192 <  short int isFirst;
192 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
193 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
194 >  virtual void getPosScale(double pos[3], double COM[3],
195 >                           int index, double sc[3]) = 0;
196  
197 <  SRI **srInteractions; /* array of SRI pointers */
198 <  int nSRI; /* the number of short range interactions */
197 >  virtual void calcVelScale( void ) = 0;
198 >
199 >  virtual bool chiConverged( void );
200 >  virtual bool etaConverged( void ) = 0;
201 >
202 >  virtual void evolveChiA( void );
203 >  virtual void evolveEtaA( void ) = 0;
204 >  virtual void evolveChiB( void );
205 >  virtual void evolveEtaB( void ) = 0;
206 >
207 >  virtual void scaleSimBox( void ) = 0;
208 >
209 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
210 >
211 >  // chi and eta are the propagated degrees of freedom
212 >
213 >  double oldChi;
214 >  double prevChi;
215 >  double chi;
216 >  double NkBT;
217 >  double fkBT;
218 >
219 >  double tt2, tb2;
220 >  double instaTemp, instaPress, instaVol;
221 >  double press[3][3];
222 >
223 >  int Nparticles;
224 >
225 >  double integralOfChidt;
226 >
227 >  // targetTemp, targetPressure, and tauBarostat must be set.
228 >  // One of qmass or tauThermostat must be set;
229 >
230 >  double targetTemp;
231 >  double targetPressure;
232 >  double tauThermostat;
233 >  double tauBarostat;
234 >
235 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
236 >  short int have_target_pressure;
237 >
238 >  double *oldPos;
239 >  double *oldVel;
240 >  double *oldJi;
241 >
242 >  double chiTolerance;
243 >  short int have_chi_tolerance;
244 >  double posIterTolerance;
245 >  short int have_pos_iter_tolerance;
246 >  double etaTolerance;
247 >  short int have_eta_tolerance;
248 >
249 > };
250 >
251 > template<typename T> class NPTi : public T{
252 >
253 > public:
254 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
255 >  ~NPTi();
256 >
257 >  virtual double getConservedQuantity(void);
258 >  virtual void resetIntegrator(void);
259 >  virtual string getAdditionalParameters(void);
260 > protected:
261 >
262 >
263 >
264 >  virtual void evolveEtaA(void);
265 >  virtual void evolveEtaB(void);
266 >
267 >  virtual bool etaConverged( void );
268 >
269 >  virtual void scaleSimBox( void );
270 >
271 >  virtual void getVelScaleA( double sc[3], double vel[3] );
272 >  virtual void getVelScaleB( double sc[3], int index );
273 >  virtual void getPosScale(double pos[3], double COM[3],
274 >                           int index, double sc[3]);
275 >
276 >  virtual void calcVelScale( void );
277 >
278 >  double eta, oldEta, prevEta;
279 >  double vScale;
280 > };
281 >
282 > template<typename T> class NPTf : public T{
283 >
284 > public:
285 >
286 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
287 >  virtual ~NPTf();
288 >
289 >  virtual double getConservedQuantity(void);
290 >  virtual string getAdditionalParameters(void);
291 >  virtual void resetIntegrator(void);
292 >
293 > protected:
294 >
295 >  virtual void evolveEtaA(void);
296 >  virtual void evolveEtaB(void);
297 >
298 >  virtual bool etaConverged( void );
299 >
300 >  virtual void scaleSimBox( void );
301 >
302 >  virtual void getVelScaleA( double sc[3], double vel[3] );
303 >  virtual void getVelScaleB( double sc[3], int index );
304 >  virtual void getPosScale(double pos[3], double COM[3],
305 >                           int index, double sc[3]);
306 >
307 >  virtual void calcVelScale( void );
308 >
309 >  double eta[3][3];
310 >  double oldEta[3][3];
311 >  double prevEta[3][3];
312 >  double vScale[3][3];
313 > };
314 >
315 > template<typename T> class NPTxyz : public T{
316 >
317 > public:
318 >
319 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
320 >  virtual ~NPTxyz();
321 >
322 >  virtual double getConservedQuantity(void);
323 >  virtual string getAdditionalParameters(void);
324 >  virtual void resetIntegrator(void);
325 >
326 > protected:
327 >
328 >  virtual void evolveEtaA(void);
329 >  virtual void evolveEtaB(void);
330 >
331 >  virtual bool etaConverged( void );
332 >
333 >  virtual void scaleSimBox( void );
334 >
335 >  virtual void getVelScaleA( double sc[3], double vel[3] );
336 >  virtual void getVelScaleB( double sc[3], int index );
337 >  virtual void getPosScale(double pos[3], double COM[3],
338 >                           int index, double sc[3]);
339 >
340 >  virtual void calcVelScale( void );
341 >
342 >  double eta[3][3];
343 >  double oldEta[3][3];
344 >  double prevEta[3][3];
345 >  double vScale[3][3];
346 > };
347 >
348 >
349 > template<typename T> class ZConstraint : public T {
350 >
351 >  public:
352 >  class ForceSubtractionPolicy{
353 >    public:
354 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
355 >
356 >      virtual void update() = 0;
357 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
358 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
359 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
360 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
361 >
362 >   protected:
363 >     ZConstraint<T>* zconsIntegrator;
364 >  };
365 >
366 >  class PolicyByNumber : public ForceSubtractionPolicy{
367 >
368 >    public:
369 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
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 >      int totNumOfMovingAtoms;
378 >  };
379 >
380 >  class PolicyByMass : public ForceSubtractionPolicy{
381 >
382 >    public:
383 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
384 >
385 >      virtual void update();
386 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
387 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
388 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
389 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
390 >
391 >   private:
392 >     double totMassOfMovingAtoms;
393 >  };
394 >
395 > public:
396 >
397 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
398 >  ~ZConstraint();
399 >
400 >  void setZConsTime(double time)                  {this->zconsTime = time;}
401 >  void getZConsTime()                             {return zconsTime;}
402 >
403 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
404 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
405 >
406 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
407 >  string getZConsOutput()                         {return zconsOutput;}
408 >
409 >  virtual void integrate();
410 >
411 >
412 > #ifdef IS_MPI
413 >  virtual void update();                      //which is called to indicate the molecules' migration
414 > #endif
415 >
416 >  enum ZConsState {zcsMoving, zcsFixed};
417 >
418 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
419 >  vector<ZConsState> states;                 //state of z-constraint molecules
420 >
421 >
422 >
423 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
424 >  double totalMassOfUncons;                //total mas of unconstraint molecules
425 >
426 >
427 > protected:
428 >
429 >
430 >
431 >  virtual void calcForce( int calcPot, int calcStress );
432 >  virtual void thermalize(void);
433 >
434 >  void zeroOutVel();
435 >  void doZconstraintForce();
436 >  void doHarmonic(vector<double>& resPos);
437 >  bool checkZConsState();
438 >
439 >  bool haveFixedZMols();
440 >  bool haveMovingZMols();
441 >
442 >  double calcZSys();
443 >
444 >  int isZConstraintMol(Molecule* mol);
445 >
446 >
447 >  double zconsTime;                              //sample time
448 >  double zconsTol;                                 //tolerance of z-contratint
449 >  double zForceConst;                           //base force constant term
450 >                                                          //which is estimate by OOPSE
451 >
452 >
453 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
454 >  vector<double> kz;                              //force constant array
455 >
456 >  vector<double> zPos;                          //
457 >
458 >
459 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
460 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 >
462 >
463 >  vector<ZConsParaItem>* parameters; //
464 >
465 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466 >
467 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
468 >  vector<double> fz;
469 >  vector<double> curZPos;
470 >
471 >  bool usingSMD;
472 >  vector<double> prevCantPos;
473 >  vector<double> cantPos;
474 >  vector<double> cantVel;
475 >
476 >  double zconsFixTime;  
477 >  double zconsGap;
478 >  bool hasZConsGap;
479 >  vector<double> endFixTime;
480    
481 +  int whichDirection;                           //constraint direction
482 +
483 + private:
484 +
485 +  string zconsOutput;                         //filename of zconstraint output
486 +  ZConsWriter* fzOut;                         //z-constraint writer
487 +
488 +  double curZconsTime;
489 +
490 +  double calcMovingMolsCOMVel();
491 +  double calcSysCOMVel();
492 +  double calcTotalForce();
493 +  void updateZPos();
494 +  void updateCantPos();
495 +  
496 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
497 +  friend class ForceSubtractionPolicy;
498 +
499   };
500  
501 +
502 + //Sympletic quaternion Scheme Integrator
503 + //Reference:
504 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
505 + //Symplectic quaternion Scheme for biophysical molecular dynamics
506 + //116(20), 8649, J. Chem. Phys. (2002)
507 + template<typename T> class SQSIntegrator : public T{
508 +  public:
509 +    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
510 +    virtual void moveA();
511 +    virtual void moveB();
512 +  protected:
513 +    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
514 +    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
515 +  private:
516 +    Quaternion getPk(int i, const Vector4d& q);
517 +    Mat4x4d getS(const Quaternion& q);
518 +    vector<Quaternion> q;
519 +    vector<Vector4d> p_qua;
520 +    vector<double> I0;
521 +
522 +                Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
523 +                Vector4d j2p(const Vector4d& j, Mat4x4d& m);
524 + };
525   #endif

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