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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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 12 | Line 13
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15   #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18   using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
23 –
25   template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
# Line 45 | Line 46 | template<typename T = BaseIntegrator> class Integrator
46    virtual void calcForce( int calcPot, int calcStress );
47    virtual void thermalize();
48  
49 <  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49 >  virtual bool stopIntegrator() {return false;}
50  
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53    void checkConstraints( void );
54    void rotate( int axes1, int axes2, double angle, double j[3],
55           double A[3][3] );
# Line 54 | Line 57 | template<typename T = BaseIntegrator> class Integrator
57    ForceFields* myFF;
58  
59    SimInfo *info; // all the info we'll ever need
60 +  vector<StuntDouble*> integrableObjects;
61    int nAtoms;  /* the number of atoms */
62    int oldAtoms;
63    Atom **atoms; /* array of atom pointers */
# Line 83 | Line 87 | typedef Integrator<BaseIntegrator> RealIntegrator;
87   };
88  
89   typedef Integrator<BaseIntegrator> RealIntegrator;
90 +
91 + // ansi instantiation
92 + template class Integrator<BaseIntegrator>;
93  
94   template<typename T> class NVE : public T {
95  
# Line 418 | Line 425 | template<typename T> class ZConstraint : public T { (p
425  
426    void zeroOutVel();
427    void doZconstraintForce();
428 <  void doHarmonic();
428 >  void doHarmonic(vector<double>& resPos);
429    bool checkZConsState();
430  
431    bool haveFixedZMols();
# Line 449 | Line 456 | template<typename T> class ZConstraint : public T { (p
456  
457    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458  
459 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 <  double* fz;
461 <  double* curZPos;
455 <
459 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 >  vector<double> fz;
461 >  vector<double> curZPos;
462  
463 +  bool usingSMD;
464 +  vector<double> prevCantPos;
465 +  vector<double> cantPos;
466 +  vector<double> cantVel;
467  
468 +  double zconsFixTime;  
469 +  double zconsGap;
470 +  bool hasZConsGap;
471 +  vector<double> endFixTime;
472 +  
473    int whichDirection;                           //constraint direction
474  
475   private:
# Line 467 | Line 482 | template<typename T> class ZConstraint : public T { (p
482    double calcMovingMolsCOMVel();
483    double calcSysCOMVel();
484    double calcTotalForce();
485 <
485 >  void updateZPos();
486 >  void updateCantPos();
487 >  
488    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489    friend class ForceSubtractionPolicy;
490  

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