ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

# Line 4 | Line 4
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"
# Line 20 | Line 21 | const double tol = 1.0e-6;
21   const int maxIteration = 300;
22   const double tol = 1.0e-6;
23  
23 –
24   template<typename T = BaseIntegrator> class Integrator : public T {
25  
26   public:
# Line 28 | Line 28 | template<typename T = BaseIntegrator> class Integrator
28    virtual ~Integrator();
29    void integrate( void );
30    virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
33   protected:
34  
# Line 40 | Line 41 | template<typename T = BaseIntegrator> class Integrator
41    virtual int  readyCheck( void ) { return 1; }
42  
43    virtual void resetIntegrator( void ) { }
44 <
45 <  virtual void calcForce( int calcPot, int calcStress );  
44 >
45 >  virtual void calcForce( int calcPot, int calcStress );
46    virtual void thermalize();
46 –  
47 –  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
47  
48 +  virtual bool stopIntegrator() {return false;}
49 +
50 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51 +
52    void checkConstraints( void );
53 <  void rotate( int axes1, int axes2, double angle, double j[3],
53 >  void rotate( int axes1, int axes2, double angle, double j[3],
54           double A[3][3] );
55 <        
55 >
56    ForceFields* myFF;
57  
58    SimInfo *info; // all the info we'll ever need
59 +  vector<StuntDouble*> integrableObjects;
60    int nAtoms;  /* the number of atoms */
61    int oldAtoms;
62    Atom **atoms; /* array of atom pointers */
# Line 61 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65  
66    int isConstrained; // boolean to know whether the systems contains
67           // constraints.
68 <  int nConstrained;  // counter for number of constraints
69 <  int *constrainedA; // the i of a constraint pair
70 <  int *constrainedB; // the j of a constraint pair
71 <  double *constrainedDsqr; // the square of the constraint distance
72 <  
68 >  int nConstrained;  // counter for number of constraints
69 >  int *constrainedA; // the i of a constraint pair
70 >  int *constrainedB; // the j of a constraint pair
71 >  double *constrainedDsqr; // the square of the constraint distance
72 >
73    int* moving; // tells whether we are moving atom i
74    int* moved;  // tells whether we have moved atom i
75 <  double* oldPos; // pre constrained positions
75 >  double* oldPos; // pre constrained positions
76  
77    short isFirst; /*boolean for the first time integrate is called */
78 <  
78 >
79    double dt;
80    double dt2;
81  
82    Thermo *tStats;
83    StatWriter*  statOut;
84    DumpWriter*  dumpOut;
85 <  
85 >
86   };
87  
88   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 88 | Line 92 | template<typename T> class NVE : public T { (public)
92   public:
93    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94      T( theInfo, the_ff ){}
95 <  virtual ~NVE(){}  
95 >  virtual ~NVE(){}
96   };
97  
98  
# Line 103 | Line 107 | template<typename T> class NVT : public T { (public)
107    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108    void setChiTolerance(double tol) {chiTolerance = tol;}
109    virtual double  getConservedQuantity(void);
110 +  virtual string getAdditionalParameters(void);
111  
112   protected:
113  
# Line 124 | Line 129 | template<typename T> class NVT : public T { (public)
129  
130    double targetTemp;
131    double tauThermostat;
132 <  
132 >
133    short int have_tau_thermostat, have_target_temp;
134  
135    double *oldVel;
# Line 143 | Line 148 | template<typename T> class NPT : public T{ (public)
148  
149    NPT ( SimInfo *theInfo, ForceFields* the_ff);
150    virtual ~NPT();
151 <  
151 >
152    virtual void integrateStep( int calcPot, int calcStress ){
153      calcStress = 1;
154      T::integrateStep( calcPot, calcStress );
155    }
156  
157    virtual double getConservedQuantity(void) = 0;
158 +  virtual string getAdditionalParameters(void) = 0;
159 +  
160 +  double myTauThermo( void ) { return tauThermostat; }
161 +  double myTauBaro( void ) { return tauBarostat; }
162  
163    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 170 | Line 179 | template<typename T> class NPT : public T{ (public)
179  
180    virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181    virtual void getVelScaleB( double sc[3], int index ) = 0;
182 <  virtual void getPosScale(double pos[3], double COM[3],
182 >  virtual void getPosScale(double pos[3], double COM[3],
183                             int index, double sc[3]) = 0;
184  
185 +  virtual void calcVelScale( void ) = 0;
186 +
187    virtual bool chiConverged( void );
188    virtual bool etaConverged( void ) = 0;
189 <  
189 >
190    virtual void evolveChiA( void );
191    virtual void evolveEtaA( void ) = 0;
192    virtual void evolveChiB( void );
# Line 201 | Line 212 | template<typename T> class NPT : public T{ (public)
212  
213    double integralOfChidt;
214  
215 <  // targetTemp, targetPressure, and tauBarostat must be set.  
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216    // One of qmass or tauThermostat must be set;
217  
218    double targetTemp;
# Line 226 | Line 237 | template<typename T> class NPTi : public T{
237   };
238  
239   template<typename T> class NPTi : public T{
240 <  
240 >
241   public:
242    NPTi( SimInfo *theInfo, ForceFields* the_ff);
243    ~NPTi();
244  
245    virtual double getConservedQuantity(void);
246    virtual void resetIntegrator(void);
247 <
247 >  virtual string getAdditionalParameters(void);
248   protected:
249  
239 –
250  
251 +
252    virtual void evolveEtaA(void);
253    virtual void evolveEtaB(void);
254  
# Line 247 | Line 258 | template<typename T> class NPTi : public T{
258  
259    virtual void getVelScaleA( double sc[3], double vel[3] );
260    virtual void getVelScaleB( double sc[3], int index );
261 <  virtual void getPosScale(double pos[3], double COM[3],
261 >  virtual void getPosScale(double pos[3], double COM[3],
262                             int index, double sc[3]);
263  
264 <  double eta, oldEta, prevEta;
254 < };
255 <
256 < template<typename T> class NPTzm : public T{
257 <
258 < public:
259 <
260 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
261 <  virtual ~NPTzm() {};
262 <
263 <  virtual void integrateStep( int calcPot, int calcStress ){
264 <    calcStress = 1;
265 <    T::integrateStep( calcPot, calcStress );
266 <  }
267 <
268 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272 <
273 < protected:
274 <
275 <  virtual void moveA( void );
276 <  virtual void moveB( void );
264 >  virtual void calcVelScale( void );
265  
266 <  virtual int readyCheck();
267 <
280 <  virtual void resetIntegrator( void );
281 <
282 <  Molecule* myMolecules;
283 <  Atom** myAtoms;
284 <
285 <  // chi and eta are the propagated degrees of freedom
286 <
287 <  double chi;
288 <  double eta;
289 <  double etaZ;
290 <  double NkBT;
291 <
292 <  // targetTemp, targetPressure, and tauBarostat must be set.  
293 <  // One of qmass or tauThermostat must be set;
294 <
295 <  double targetTemp;
296 <  double targetPressure;
297 <  double tauThermostat;
298 <  double tauBarostat;
299 <
300 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301 <  short int have_target_pressure;
302 <
266 >  double eta, oldEta, prevEta;
267 >  double vScale;
268   };
269  
270   template<typename T> class NPTf : public T{
# Line 310 | Line 275 | template<typename T> class NPTf : public T{ (public)
275    virtual ~NPTf();
276  
277    virtual double getConservedQuantity(void);
278 +  virtual string getAdditionalParameters(void);
279    virtual void resetIntegrator(void);
280  
281   protected:
# Line 323 | Line 289 | template<typename T> class NPTf : public T{ (public)
289  
290    virtual void getVelScaleA( double sc[3], double vel[3] );
291    virtual void getVelScaleB( double sc[3], int index );
292 <  virtual void getPosScale(double pos[3], double COM[3],
292 >  virtual void getPosScale(double pos[3], double COM[3],
293                             int index, double sc[3]);
294  
295 +  virtual void calcVelScale( void );
296 +
297    double eta[3][3];
298    double oldEta[3][3];
299    double prevEta[3][3];
300 +  double vScale[3][3];
301   };
302  
303 < template<typename T> class NPTxym : public T{
303 > template<typename T> class NPTxyz : public T{
304  
305   public:
306  
307 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
308 <  virtual ~NPTxym() {};
307 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
308 >  virtual ~NPTxyz();
309  
310 <  virtual void integrateStep( int calcPot, int calcStress ){
311 <    calcStress = 1;
312 <    T::integrateStep( calcPot, calcStress );
344 <  }
310 >  virtual double getConservedQuantity(void);
311 >  virtual string getAdditionalParameters(void);
312 >  virtual void resetIntegrator(void);
313  
346 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
350 –
314   protected:
315  
316 <  virtual void moveA( void );
317 <  virtual void moveB( void );
316 >  virtual void evolveEtaA(void);
317 >  virtual void evolveEtaB(void);
318  
319 <  virtual int readyCheck();
319 >  virtual bool etaConverged( void );
320  
321 <  virtual void resetIntegrator( void );
321 >  virtual void scaleSimBox( void );
322  
323 <  Molecule* myMolecules;
324 <  Atom** myAtoms;
323 >  virtual void getVelScaleA( double sc[3], double vel[3] );
324 >  virtual void getVelScaleB( double sc[3], int index );
325 >  virtual void getPosScale(double pos[3], double COM[3],
326 >                           int index, double sc[3]);
327  
328 <  // chi and eta are the propagated degrees of freedom
328 >  virtual void calcVelScale( void );
329  
330 <  double chi;
331 <  double eta;
332 <  double etaX;
333 <  double etaY;
369 <  double NkBT;
370 <
371 <  // targetTemp, targetPressure, and tauBarostat must be set.  
372 <  // One of qmass or tauThermostat must be set;
373 <
374 <  double targetTemp;
375 <  double targetPressure;
376 <  double tauThermostat;
377 <  double tauBarostat;
378 <
379 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380 <  short int have_target_pressure;
381 <
330 >  double eta[3][3];
331 >  double oldEta[3][3];
332 >  double prevEta[3][3];
333 >  double vScale[3][3];
334   };
335  
336 +
337   template<typename T> class ZConstraint : public T {
338 <  
339 <  public:
338 >
339 >  public:
340    class ForceSubtractionPolicy{
341      public:
342        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343  
344 <      virtual void update() = 0;    
344 >      virtual void update() = 0;
345        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349 <    
349 >
350     protected:
351       ZConstraint<T>* zconsIntegrator;
352    };
# Line 401 | Line 354 | template<typename T> class ZConstraint : public T {
354    class PolicyByNumber : public ForceSubtractionPolicy{
355  
356      public:
357 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
358 <      virtual void update();    
357 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >      virtual void update();
359        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363 <    
363 >
364      private:
365        int totNumOfMovingAtoms;
366    };
# Line 415 | Line 368 | template<typename T> class ZConstraint : public T {
368    class PolicyByMass : public ForceSubtractionPolicy{
369  
370      public:
371 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
372 <      
373 <      virtual void update();    
371 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372 >
373 >      virtual void update();
374        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 431 | Line 384 | template<typename T> class ZConstraint : public T {
384  
385    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386    ~ZConstraint();
387 <    
387 >
388    void setZConsTime(double time)                  {this->zconsTime = time;}
389    void getZConsTime()                             {return zconsTime;}
390 <  
390 >
391    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393 <  
393 >
394    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395    string getZConsOutput()                         {return zconsOutput;}
396 <  
396 >
397    virtual void integrate();
445 –  
398  
399 +
400   #ifdef IS_MPI
401    virtual void update();                      //which is called to indicate the molecules' migration
402   #endif
403  
404 <  enum ZConsState {zcsMoving, zcsFixed};  
404 >  enum ZConsState {zcsMoving, zcsFixed};
405  
406    vector<Molecule*> zconsMols;              //z-constraint molecules array
407    vector<ZConsState> states;                 //state of z-constraint molecules
408  
456 –
409  
410 +
411    int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412    double totalMassOfUncons;                //total mas of unconstraint molecules
413  
# Line 462 | Line 415 | template<typename T> class ZConstraint : public T {
415   protected:
416  
417  
418 <
419 <  virtual void calcForce( int calcPot, int calcStress );
418 >
419 >  virtual void calcForce( int calcPot, int calcStress );
420    virtual void thermalize(void);
421 <  
421 >
422    void zeroOutVel();
423    void doZconstraintForce();
424 <  void doHarmonic();
424 >  void doHarmonic(vector<double>& resPos);
425    bool checkZConsState();
426  
427    bool haveFixedZMols();
# Line 483 | Line 436 | template<typename T> class ZConstraint : public T {
436    double zconsTol;                                 //tolerance of z-contratint
437    double zForceConst;                           //base force constant term
438                                                            //which is estimate by OOPSE
486 –  
439  
440 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
440 >
441 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442    vector<double> kz;                              //force constant array
443  
444    vector<double> zPos;                          //
445 <  
446 <  
445 >
446 >
447    vector<Molecule*> unconsMols;           //unconstraint molecules array
448    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
449  
450  
451    vector<ZConsParaItem>* parameters; //
452 <  
452 >
453    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454  
455 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
456 <  double* fz;
457 <  double* curZPos;
505 <  
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458  
459 +  bool usingSMD;
460 +  vector<double> cantPos;
461 +  vector<double> cantVel;
462  
463 <  int whichDirection;                           //constraint direction
463 >  double zconsFixTime;  
464 >  double zconsGap;
465 >  bool hasZConsGap;
466 >  vector<double> endFixTime;
467    
468 +  int whichDirection;                           //constraint direction
469 +
470   private:
471 <  
471 >
472    string zconsOutput;                         //filename of zconstraint output
473    ZConsWriter* fzOut;                         //z-constraint writer
474  
475 <  double curZconsTime;                      
475 >  double curZconsTime;
476  
477    double calcMovingMolsCOMVel();
478    double calcSysCOMVel();
479    double calcTotalForce();
480 +  void updateZPos();
481 +  void updateCantPos();
482    
483    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
484    friend class ForceSubtractionPolicy;
485  
486   };
487  
488 + /*
489 + template<typename T> class SingleZConstrain : public T{
490 +
491 +
492 + };
493 + */
494 +
495 + template<typename T> class NonEquMD : public T {
496 +  public:
497 +    
498 +
499 +
500 + };
501 +
502 +
503 + //
504 + template<typename T> class SingleZConstraint : public T{
505 +  public:
506 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
507 +    ~SingleZConstraint();
508 +    
509 +    bool stopIntegrator();
510 +    
511 +  protected:
512 +    
513 + };
514 +
515 + //Steered Molecular Dynamics, curret implement only support one steered molecule
516 + template<typename T> class SMD : public T{
517 +  public:
518 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
519 +    ~SMD();
520 +  
521 +    virtual void integrate();
522 +    virtual void calcForce( int calcPot, int calcStress );  
523 +    bool stopIntegrator();
524 +  private:
525 +    
526 + };
527 +
528 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
529 + //Driven Molecular Dynamics and ZConstraint Method.
530 + template<typename T> class CoordinateDriver : public T {
531 +  public:
532 +    typedef T ParentIntegrator;
533 +
534 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
535 +    ~CoordinateDriver();
536 +    
537 +    virtual void integrate();
538 +
539 +  private:    
540 +    BaseIntegrator* zconsIntegrator;
541 +    BaseIntegrator* drivenIntegrator;
542 +    
543 + };
544 +
545   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines