| 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" |
| 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: |
| 45 |
|
virtual void calcForce( int calcPot, int calcStress ); |
| 46 |
|
virtual void thermalize(); |
| 47 |
|
|
| 48 |
< |
virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
| 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], |
| 54 |
|
double A[3][3] ); |
| 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 */ |
| 87 |
|
|
| 88 |
|
typedef Integrator<BaseIntegrator> RealIntegrator; |
| 89 |
|
|
| 90 |
+ |
// ansi instantiation |
| 91 |
+ |
template class Integrator<BaseIntegrator>; |
| 92 |
+ |
|
| 93 |
|
template<typename T> class NVE : public T { |
| 94 |
|
|
| 95 |
|
public: |
| 424 |
|
|
| 425 |
|
void zeroOutVel(); |
| 426 |
|
void doZconstraintForce(); |
| 427 |
< |
void doHarmonic(); |
| 427 |
> |
void doHarmonic(vector<double>& resPos); |
| 428 |
|
bool checkZConsState(); |
| 429 |
|
|
| 430 |
|
bool haveFixedZMols(); |
| 455 |
|
|
| 456 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
| 457 |
|
|
| 458 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
| 459 |
< |
double* fz; |
| 460 |
< |
double* curZPos; |
| 458 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
| 459 |
> |
vector<double> fz; |
| 460 |
> |
vector<double> curZPos; |
| 461 |
|
|
| 462 |
+ |
bool usingSMD; |
| 463 |
+ |
vector<double> prevCantPos; |
| 464 |
+ |
vector<double> cantPos; |
| 465 |
+ |
vector<double> cantVel; |
| 466 |
|
|
| 467 |
< |
|
| 467 |
> |
double zconsFixTime; |
| 468 |
> |
double zconsGap; |
| 469 |
> |
bool hasZConsGap; |
| 470 |
> |
vector<double> endFixTime; |
| 471 |
> |
|
| 472 |
|
int whichDirection; //constraint direction |
| 473 |
|
|
| 474 |
|
private: |
| 481 |
|
double calcMovingMolsCOMVel(); |
| 482 |
|
double calcSysCOMVel(); |
| 483 |
|
double calcTotalForce(); |
| 484 |
< |
|
| 484 |
> |
void updateZPos(); |
| 485 |
> |
void updateCantPos(); |
| 486 |
> |
|
| 487 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
| 488 |
|
friend class ForceSubtractionPolicy; |
| 489 |
|
|
| 490 |
|
}; |
| 491 |
|
|
| 492 |
|
/* |
| 493 |
< |
class OOPSEMinimizerBase : public RealIntegrator { |
| 478 |
< |
public: |
| 493 |
> |
template<typename T> class SingleZConstrain : public T{ |
| 494 |
|
|
| 495 |
< |
OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff ); |
| 496 |
< |
virtual ~OOPSEMinimizerBase(); |
| 495 |
> |
|
| 496 |
> |
}; |
| 497 |
> |
*/ |
| 498 |
> |
|
| 499 |
> |
template<typename T> class NonEquMD : public T { |
| 500 |
> |
public: |
| 501 |
|
|
| 502 |
< |
double calcGradient(vector<double>& x, vector<double>& grad); |
| 503 |
< |
void setCoor(vector<double>& x); |
| 504 |
< |
vector<double> getCoor(); |
| 505 |
< |
void output(vector<double>& x, int iteration); |
| 506 |
< |
int getDim() {return dim;} |
| 507 |
< |
void constraintMove(); |
| 508 |
< |
void shakeF(); |
| 509 |
< |
void shakeR(); |
| 502 |
> |
|
| 503 |
> |
|
| 504 |
> |
}; |
| 505 |
> |
|
| 506 |
> |
|
| 507 |
> |
// |
| 508 |
> |
template<typename T> class SingleZConstraint : public T{ |
| 509 |
> |
public: |
| 510 |
> |
SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff); |
| 511 |
> |
~SingleZConstraint(); |
| 512 |
> |
|
| 513 |
> |
bool stopIntegrator(); |
| 514 |
> |
|
| 515 |
|
protected: |
| 516 |
|
|
| 493 |
– |
int dim; |
| 494 |
– |
void calcDim(); |
| 517 |
|
}; |
| 518 |
|
|
| 519 |
< |
//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{ |
| 520 |
< |
// public: |
| 521 |
< |
// void writeOutput(); |
| 522 |
< |
//}; |
| 523 |
< |
*/ |
| 519 |
> |
//Steered Molecular Dynamics, curret implement only support one steered molecule |
| 520 |
> |
template<typename T> class SMD : public T{ |
| 521 |
> |
public: |
| 522 |
> |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
| 523 |
> |
~SMD(); |
| 524 |
> |
|
| 525 |
> |
virtual void integrate(); |
| 526 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
| 527 |
> |
bool stopIntegrator(); |
| 528 |
> |
private: |
| 529 |
> |
|
| 530 |
> |
}; |
| 531 |
> |
|
| 532 |
> |
//By using state pattern, Coordinate Drive is responsible for switching back and forth between |
| 533 |
> |
//Driven Molecular Dynamics and ZConstraint Method. |
| 534 |
> |
template<typename T> class CoordinateDriver : public T { |
| 535 |
> |
public: |
| 536 |
> |
typedef T ParentIntegrator; |
| 537 |
> |
|
| 538 |
> |
CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*); |
| 539 |
> |
~CoordinateDriver(); |
| 540 |
> |
|
| 541 |
> |
virtual void integrate(); |
| 542 |
> |
|
| 543 |
> |
private: |
| 544 |
> |
BaseIntegrator* zconsIntegrator; |
| 545 |
> |
BaseIntegrator* drivenIntegrator; |
| 546 |
> |
|
| 547 |
> |
}; |
| 548 |
> |
|
| 549 |
|
#endif |
