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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 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC

# Line 9 | Line 9 | class Integrator : public BaseIntegrator {
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 double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
15 + const int maxIteration = 300;
16 + const double tol = 1.0e-6;
17 +
18   class Integrator : public BaseIntegrator {
19  
20   public:
21 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
21 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
22    virtual ~Integrator();
23    void integrate( void );
24  
# Line 29 | Line 35 | class Integrator : public BaseIntegrator { (protected)
35    
36    void checkConstraints( void );
37    void rotate( int axes1, int axes2, double angle, double j[3],
38 <               double A[3][3] );
38 >               double A[9] );
39  
40  
41    ForceFields* myFF;
# Line 50 | Line 56 | class Integrator : public BaseIntegrator { (protected)
56    
57    int* moving; // tells whether we are moving atom i
58    int* moved;  // tells whether we have moved atom i
59 <  double* prePos; // pre constrained positions
59 >  double* oldPos; // pre constrained positions
60  
61    short isFirst; /*boolean for the first time integrate is called */
62    
63    double dt;
64    double dt2;
65  
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 –  
66    double* pos;
67    double* vel;
68    double* frc;
# Line 76 | Line 77 | class NVE : public Integrator{
77  
78   class NVE : public Integrator{
79  
80 <  NVE ( void ):
80 > public:
81 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
82      Integrator( theInfo, the_ff ){}
83    virtual ~NVE(){}
84  
# Line 88 | Line 90 | class NVT : public Integrator{ (public)
90  
91   public:
92  
93 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
94 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
93 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 >  virtual ~NVT() {}
95  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
96    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98  
99   protected:
100  
101 <  virtual moveA( void );
102 <  virtual moveB( void );
101 >  virtual void moveA( void );
102 >  virtual void moveB( void );
103  
104 <  int readyCheck();
104 >  virtual int readyCheck();
105  
106 <  Atom** atoms;
106 >  // chi is a propagated degree of freedom.
107  
108 <  // zeta is a propagated degree of freedom.
108 >  double chi;
109  
110 <  double zeta;
110 >  // targetTemp must be set.  tauThermostat must also be set;
111  
112 –  // targetTemp must be set.  One of qmass or tauThermostat must be set;
113 –
114 –  double qmass;
112    double targetTemp;
113    double tauThermostat;
114 +  
115 +  short int have_tau_thermostat, have_target_temp;
116  
118 –  short int have_tau_thermostat, have_target_temp, have_qmass;
119 –
117   };
118  
119  
120 < class NPT : public Integrator{
120 > class NPTi : public Integrator{
121  
122   public:
123  
124 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
125 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
124 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
125 >  virtual ~NPTi() {};
126  
131 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
127    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
128    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
129    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 136 | Line 131 | class NPT : public Integrator{ (protected)
131  
132   protected:
133  
134 <  virtual moveA( void );
135 <  virtual moveB( void );
134 >  virtual void  moveA( void );
135 >  virtual void moveB( void );
136  
137 <  int readyCheck();
137 >  virtual int readyCheck();
138  
139 <  Atom** atoms;
139 >  // chi and eta are the propagated degrees of freedom
140  
141 <  // zeta and epsilonDot are the propagated degrees of freedom.
141 >  double chi;
142 >  double eta;
143 >  double NkBT;
144  
145 <  double zeta;
146 <  double epsilonDot;
145 >  // targetTemp, targetPressure, and tauBarostat must be set.  
146 >  // One of qmass or tauThermostat must be set;
147  
148 +  double targetTemp;
149 +  double targetPressure;
150 +  double tauThermostat;
151 +  double tauBarostat;
152 +
153 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
154 +  short int have_target_pressure;
155 +
156 + };
157 +
158 + class NPTf : public Integrator{
159 +
160 + public:
161 +
162 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
163 +  virtual ~NPTf() {};
164 +
165 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
166 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
167 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
168 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
169 +
170 + protected:
171 +
172 +  virtual void  moveA( void );
173 +  virtual void moveB( void );
174 +
175 +  virtual int readyCheck();
176 +
177 +  // chi and eta are the propagated degrees of freedom
178 +
179 +  double chi;
180 +  double eta[9];
181 +  double NkBT;
182 +
183    // targetTemp, targetPressure, and tauBarostat must be set.  
184    // One of qmass or tauThermostat must be set;
185  
154 –  double qmass;
186    double targetTemp;
187    double targetPressure;
188    double tauThermostat;
189    double tauBarostat;
190  
191    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
192 <  short int have_target_pressure, have_qmass;
192 >  short int have_target_pressure;
193  
194   };
195  

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