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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 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 84 | Line 88 | typedef Integrator<BaseIntegrator> RealIntegrator;
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  
96   public:
# Line 153 | Line 160 | template<typename T> class NPT : public T{ (public)
160  
161    virtual double getConservedQuantity(void) = 0;
162    virtual string getAdditionalParameters(void) = 0;
163 +  
164 +  double myTauThermo( void ) { return tauThermostat; }
165 +  double myTauBaro( void ) { return tauBarostat; }
166 +
167    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 175 | Line 186 | template<typename T> class NPT : public T{ (public)
186    virtual void getPosScale(double pos[3], double COM[3],
187                             int index, double sc[3]) = 0;
188  
189 +  virtual void calcVelScale( void ) = 0;
190 +
191    virtual bool chiConverged( void );
192    virtual bool etaConverged( void ) = 0;
193  
# Line 252 | Line 265 | template<typename T> class NPTi : public T{ (protected
265    virtual void getPosScale(double pos[3], double COM[3],
266                             int index, double sc[3]);
267  
268 +  virtual void calcVelScale( void );
269 +
270    double eta, oldEta, prevEta;
271 +  double vScale;
272   };
273  
274   template<typename T> class NPTf : public T{
# Line 280 | Line 296 | template<typename T> class NPTf : public T{ (protected
296    virtual void getPosScale(double pos[3], double COM[3],
297                             int index, double sc[3]);
298  
299 +  virtual void calcVelScale( void );
300 +
301    double eta[3][3];
302    double oldEta[3][3];
303    double prevEta[3][3];
304 +  double vScale[3][3];
305   };
306  
307   template<typename T> class NPTxyz : public T{
# Line 310 | Line 329 | template<typename T> class NPTxyz : public T{ (protect
329    virtual void getPosScale(double pos[3], double COM[3],
330                             int index, double sc[3]);
331  
332 +  virtual void calcVelScale( void );
333 +
334    double eta[3][3];
335    double oldEta[3][3];
336    double prevEta[3][3];
337 +  double vScale[3][3];
338   };
339  
340  
# Line 403 | 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 434 | 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;
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 <
468 >  double zconsFixTime;  
469 >  double zconsGap;
470 >  bool hasZConsGap;
471 >  vector<double> endFixTime;
472 >  
473    int whichDirection;                           //constraint direction
474  
475   private:
# Line 452 | 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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