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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC

# Line 9 | Line 9
9   #include "Thermo.hpp"
10   #include "ReadWrite.hpp"
11  
12 + const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
13 + const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
14 + const int maxIteration = 300;
15 + const double tol = 1.0e-6;
16 +
17   class Integrator : public BaseIntegrator {
18  
19   public:
20 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
20 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
21    virtual ~Integrator();
22    void integrate( void );
23  
# Line 29 | Line 34 | class Integrator : public BaseIntegrator { (protected)
34    
35    void checkConstraints( void );
36    void rotate( int axes1, int axes2, double angle, double j[3],
37 <               double A[3][3] );
37 >               double A[9] );
38  
39  
40    ForceFields* myFF;
# Line 50 | Line 55 | class Integrator : public BaseIntegrator { (protected)
55    
56    int* moving; // tells whether we are moving atom i
57    int* moved;  // tells whether we have moved atom i
58 <  double* prePos; // pre constrained positions
58 >  double* oldPos; // pre constrained positions
59  
60    short isFirst; /*boolean for the first time integrate is called */
61    
62    double dt;
63    double dt2;
64  
60 –  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
61 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –  
65    double* pos;
66    double* vel;
67    double* frc;
# Line 76 | Line 76 | class NVE : public Integrator{
76  
77   class NVE : public Integrator{
78  
79 <  NVE ( void ):
79 > public:
80 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
81      Integrator( theInfo, the_ff ){}
82    virtual ~NVE(){}
83  
# Line 88 | Line 89 | class NVT : public Integrator{ (public)
89  
90   public:
91  
92 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
93 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
92 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
93 >  virtual ~NVT() {}
94  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
95    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
96    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
97  
98   protected:
99  
100 <  virtual moveA( void );
101 <  virtual moveB( void );
100 >  virtual void moveA( void );
101 >  virtual void moveB( void );
102  
103 <  int readyCheck();
103 >  virtual int readyCheck();
104  
105 <  Atom** atoms;
105 >  // chi is a propagated degree of freedom.
106  
107 <  // zeta is a propagated degree of freedom.
107 >  double chi;
108  
109 <  double zeta;
109 >  // targetTemp must be set.  tauThermostat must also be set;
110  
112 –  // targetTemp must be set.  One of qmass or tauThermostat must be set;
113 –
114 –  double qmass;
111    double targetTemp;
112    double tauThermostat;
113 +  
114 +  short int have_tau_thermostat, have_target_temp;
115  
118 –  short int have_tau_thermostat, have_target_temp, have_qmass;
119 –
116   };
117  
118  
119 < class NPT : public Integrator{
119 > class NPTi : public Integrator{
120  
121   public:
122  
123 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
124 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
123 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
124 >  virtual ~NPTi() {};
125  
131 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
126    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
127    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
128    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 136 | Line 130 | class NPT : public Integrator{ (protected)
130  
131   protected:
132  
133 <  virtual moveA( void );
134 <  virtual moveB( void );
133 >  virtual void  moveA( void );
134 >  virtual void moveB( void );
135  
136 <  int readyCheck();
136 >  virtual int readyCheck();
137  
138 <  Atom** atoms;
138 >  // chi and eta are the propagated degrees of freedom
139  
140 <  // zeta and epsilonDot are the propagated degrees of freedom.
140 >  double chi;
141 >  double eta;
142 >  double NkBT;
143  
148 –  double zeta;
149 –  double epsilonDot;
150 –
144    // targetTemp, targetPressure, and tauBarostat must be set.  
145    // One of qmass or tauThermostat must be set;
146  
154 –  double qmass;
147    double targetTemp;
148    double targetPressure;
149    double tauThermostat;
150    double tauBarostat;
151  
152    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
153 <  short int have_target_pressure, have_qmass;
153 >  short int have_target_pressure;
154  
155   };
156  

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