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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC

# Line 6 | Line 6
6   #include "AbstractClasses.hpp"
7   #include "SimInfo.hpp"
8   #include "ForceFields.hpp"
9 < #include "ExtendedSystem.hpp"
9 > #include "Thermo.hpp"
10 > #include "ReadWrite.hpp"
11  
12 < class Verlet : public Integrator {
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 <  Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es );
21 <  ~Verlet();
20 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
21 >  virtual ~Integrator();
22    void integrate( void );
23  
24 < private:
24 >
25 > protected:
26    
27 <  void move_a( double dt );
28 <  void move_b( double dt );
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 >  
35 >  void checkConstraints( void );
36 >  void rotate( int axes1, int axes2, double angle, double j[3],
37 >               double A[9] );
38  
39 +
40    ForceFields* myFF;
24 –  ExtendedSystem* myES;
41  
42 <  SimInfo *entry_plug; // all the info we'll ever need
43 <  int c_natoms;  /* the number of atoms */
44 <  Atom **c_atoms; /* array of atom pointers */
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 c_is_constrained; /*boolean to know whether the systems contains
50 <                          constraints. */
51 <  int c_n_constrained; /*counter for number of constraints */
52 <  int *c_constrained_i; /* the i of a constraint pair */
53 <  int *c_constrained_j; /* the j of a constraint pair */
54 <  double *c_constrained_dsqr; /* the square of the constraint distance */
55 <  double *c_mass; /* the array of masses */
56 <  short is_first; /*boolean for the first time integrate is called */
57 <  double c_box_x;
58 <  double c_box_y;
42 <  double c_box_z;
43 < };
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 < class Symplectic : public Integrator {
60 >  short isFirst; /*boolean for the first time integrate is called */
61    
62 +  double dt;
63 +  double dt2;
64 +
65 +  double* pos;
66 +  double* vel;
67 +  double* frc;
68 +  double* trq;
69 +  double* Amat;
70 +
71 +  Thermo *tStats;
72 +  StatWriter*  statOut;
73 +  DumpWriter*  dumpOut;
74 +  
75 + };
76 +
77 + class NVE : public Integrator{
78 +
79   public:
80 <  Symplectic( SimInfo* the_entry_plug,  
81 <              ForceFields* the_ff,
82 <              ExtendedSystem* the_es);
83 <  ~Symplectic();
80 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
81 >    Integrator( theInfo, the_ff ){}
82 >  virtual ~NVE(){}
83 >
84    
53 –  void integrate( void );
85  
86 < private:
86 > };
87  
88 <  void rotate( int axes1, int axes2, double angle, double j[3],
58 <               double A[3][3] );
88 > class NVT : public Integrator{
89  
90 <  SimInfo* entry_plug;
61 <  ForceFields* myFF;
62 <  ExtendedSystem* myES;
90 > public:
91  
92 <  Molecule* molecules;
93 <  int nMols;
92 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
93 >  virtual ~NVT() {}
94  
95 <  int is_constrained; /*boolean to know whether the systems contains
96 <                          constraints. */
69 <  int n_constrained; /*counter for number of constraints */
70 <  int *constrained_i; /* the i of a constraint pair */
71 <  int *constrained_j; /* the j of a constraint pair */
72 <  double *constrained_dsqr; /* the square of the constraint distance */
73 <  double *mass; /* the array of masses */
95 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
96 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
97  
98 <  short int isFirst;
98 > protected:
99  
100 <  SRI **srInteractions; /* array of SRI pointers */
101 <  int nSRI; /* the number of short range interactions */
100 >  virtual void moveA( void );
101 >  virtual void moveB( void );
102 >
103 >  virtual int readyCheck();
104 >
105 >  // chi is a propagated degree of freedom.
106 >
107 >  double chi;
108 >
109 >  // targetTemp must be set.  tauThermostat must also be set;
110 >
111 >  double targetTemp;
112 >  double tauThermostat;
113    
114 +  short int have_tau_thermostat, have_target_temp;
115 +
116   };
117  
118 +
119 + class NPTi : public Integrator{
120 +
121 + public:
122 +
123 +  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
124 +  virtual ~NPTi() {};
125 +
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;}
129 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
130 +
131 + protected:
132 +
133 +  virtual void  moveA( void );
134 +  virtual void moveB( void );
135 +
136 +  virtual int readyCheck();
137 +
138 +  // chi and eta are the propagated degrees of freedom
139 +
140 +  double chi;
141 +  double eta;
142 +  double NkBT;
143 +
144 +  // targetTemp, targetPressure, and tauBarostat must be set.  
145 +  // One of qmass or tauThermostat must be set;
146 +
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;
154 +
155 + };
156 +
157   #endif

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