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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC vs.
Revision 561 by mmeineke, Fri Jun 20 20:29:36 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 int maxIteration = 300;
15 + const double tol = 1.0e-6;
16 +
17   class Integrator : public BaseIntegrator {
18  
19   public:
20 <  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
21 <  virtual ~Symplectic();
20 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
21 >  virtual ~Integrator();
22    void integrate( void );
23  
24  
25   protected:
21 –
26    
27    virtual void integrateStep( int calcPot, int calcStress );
28 +  virtual void preMove( void );
29    virtual void moveA( void );
30    virtual void moveB( void );
31    virtual void constrainA( void );
32    virtual void constrainB( void );
33 +  virtual int  readyCheck( void ) { return 1; }
34    
29 –  
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;
41  
42    SimInfo *info; // all the info we'll ever need
43    int nAtoms;  /* the number of atoms */
44 +  int oldAtoms;
45    Atom **atoms; /* array of atom pointers */
46    Molecule* molecules;
47    int nMols;
48  
49 <  int isConstrained; /*boolean to know whether the systems contains
50 <                       constraints. */
51 <  int nConstrained; /*counter for number of constraints */
52 <  int *constrainedI; /* the i of a constraint pair */
53 <  int *constrainedJ; /* the j of a constraint pair */
54 <  double *constrainedDsqr; /* the square of the constraint distance */
49 >  int isConstrained; // boolean to know whether the systems contains
50 >                     // constraints.
51 >  int nConstrained;  // counter for number of constraints
52 >  int *constrainedA; // the i of a constraint pair
53 >  int *constrainedB; // the j of a constraint pair
54 >  double *constrainedDsqr; // the square of the constraint distance
55 >  
56 >  int* moving; // tells whether we are moving atom i
57 >  int* moved;  // tells whether we have moved atom i
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;
53 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
64  
55 –  
65    double* pos;
66    double* vel;
67    double* frc;
68    double* trq;
69    double* Amat;
61 –  
70  
63 –
71    Thermo *tStats;
72    StatWriter*  statOut;
73    DumpWriter*  dumpOut;
74    
75   };
76  
77 + class NVE : public Integrator{
78  
79 + public:
80 +  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
81 +    Integrator( theInfo, the_ff ){}
82 +  virtual ~NVE(){}
83 +
84 +  
85 +
86 + };
87 +
88   class NVT : public Integrator{
89  
90 <  NVT ( void );
74 <  virtual ~NVT();
90 > public:
91  
92 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
93 +  virtual ~NVT() {}
94 +
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:
77 –  virtual moveA( void );
78 –  virtual moveB( void );
100  
101 < };
101 >  virtual void moveA( void );
102 >  virtual void moveB( void );
103  
104 +  virtual int readyCheck();
105 +
106 +  // zeta is a propagated degree of freedom.
107 +
108 +  double zeta;
109 +
110 +  // targetTemp must be set.  One of qmass or tauThermostat must be set;
111 +
112 +  double qmass;
113 +  double targetTemp;
114 +  double tauThermostat;
115 +
116 +  double NkBT;
117    
118 +  short int have_tau_thermostat, have_target_temp, have_qmass;
119  
120 + };
121  
122 +
123 + class NPT : public Integrator{
124 +
125 + public:
126 +
127 +  NPT ( SimInfo *theInfo, ForceFields* the_ff);
128 +  virtual ~NPT();
129 +
130 +  void setQmass(double q) {qmass = q; have_qmass = 1;}
131 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
132 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
133 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
134 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
135 +
136 + protected:
137 +
138 +  virtual void  moveA( void );
139 +  virtual void moveB( void );
140 +
141 +  virtual int readyCheck();
142 +
143 +  Atom** atoms;
144 +
145 +  // zeta and epsilonDot are the propagated degrees of freedom.
146 +
147 +  double zeta;
148 +  double epsilonDot;
149 +
150 +  // targetTemp, targetPressure, and tauBarostat must be set.  
151 +  // One of qmass or tauThermostat must be set;
152 +
153 +  double qmass;
154 +  double targetTemp;
155 +  double targetPressure;
156 +  double tauThermostat;
157 +  double tauBarostat;
158 +
159 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
160 +  short int have_target_pressure, have_qmass;
161 +
162 + };
163 +
164   #endif

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