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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC

# Line 6 | Line 6
6   #include "AbstractClasses.hpp"
7   #include "SimInfo.hpp"
8   #include "ForceFields.hpp"
9 + #include "Thermo.hpp"
10 + #include "ReadWrite.hpp"
11  
12 < class Verlet : public Integrator {
12 > class Integrator : public BaseIntegrator {
13  
14   public:
15 <  Verlet( SimInfo &info, ForceFields* the_ff );
16 <  ~Verlet();
15 >  Integrator( SimInfo &theInfo, ForceFields* the_ff );
16 >  virtual ~Integrator();
17    void integrate( void );
18  
19 < private:
19 >
20 > protected:
21    
22 <  void move_a( double dt );
23 <  void move_b( double dt );
22 >  virtual void integrateStep( int calcPot, int calcStress );
23 >  virtual void preMove( void );
24 >  virtual void moveA( void );
25 >  virtual void moveB( void );
26 >  virtual void constrainA( void );
27 >  virtual void constrainB( void );
28 >  virtual int  readyCheck( void ) { return 1; }
29 >  
30 >  void checkConstraints( void );
31 >  void rotate( int axes1, int axes2, double angle, double j[3],
32 >               double A[3][3] );
33  
34 +
35    ForceFields* myFF;
36  
37 <  SimInfo *entry_plug; // all the info we'll ever need
38 <  int c_natoms;  /* the number of atoms */
39 <  Atom **c_atoms; /* array of atom pointers */
40 <  SRI **c_sr_interactions; /* array of SRI pointers */
41 <  int c_n_SRI; /* the number of short range interactions */
37 >  SimInfo *info; // all the info we'll ever need
38 >  int nAtoms;  /* the number of atoms */
39 >  int oldAtoms;
40 >  Atom **atoms; /* array of atom pointers */
41 >  Molecule* molecules;
42 >  int nMols;
43  
44 <  int c_is_constrained; /*boolean to know whether the systems contains
45 <                          constraints. */
46 <  int c_n_constrained; /*counter for number of constraints */
47 <  int *c_constrained_i; /* the i of a constraint pair */
48 <  int *c_constrained_j; /* the j of a constraint pair */
49 <  double *c_constrained_dsqr; /* the square of the constraint distance */
50 <  double *c_mass; /* the array of masses */
51 <  short is_first; /*boolean for the first time integrate is called */
52 <  double c_box_x;
53 <  double c_box_y;
54 <  double c_box_z;
44 >  int isConstrained; // boolean to know whether the systems contains
45 >                     // constraints.
46 >  int nConstrained;  // counter for number of constraints
47 >  int *constrainedA; // the i of a constraint pair
48 >  int *constrainedB; // the j of a constraint pair
49 >  double *constrainedDsqr; // the square of the constraint distance
50 >  
51 >  int* moving; // tells whether we are moving atom i
52 >  int* moved;  // tells whether we have moved atom i
53 >  double* prePos; // pre constrained positions
54 >
55 >  short isFirst; /*boolean for the first time integrate is called */
56 >  
57 >  double dt;
58 >  double dt2;
59 >
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;
68 >  double* trq;
69 >  double* Amat;
70 >
71 >  Thermo *tStats;
72 >  StatWriter*  statOut;
73 >  DumpWriter*  dumpOut;
74 >  
75   };
76  
77 < class Symplectic : public Integrator {
77 > class NVE : public Integrator{
78 >
79 >  NVE ( void ):
80 >    Integrator( theInfo, the_ff ){}
81 >  virtual ~NVE(){}
82 >
83    
84 +
85 + };
86 +
87 + class NVT : public Integrator{
88 +
89   public:
46 –  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
47 –  ~Symplectic();
48 –  
49 –  void integrate( void );
90  
91 < private:
91 >  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
92 >    Integrator( theInfo, the_ff );
93 >  virtual ~NVT();
94  
95 <  void rotate( int axes1, int axes2, double angle, double j[3],
96 <               double A[3][3] );
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 <  SimInfo* entry_plug;
57 <  ForceFields* myFF;
99 > protected:
100  
101 <  int is_constrained; /*boolean to know whether the systems contains
102 <                          constraints. */
61 <  int n_constrained; /*counter for number of constraints */
62 <  int *constrained_i; /* the i of a constraint pair */
63 <  int *constrained_j; /* the j of a constraint pair */
64 <  double *constrained_dsqr; /* the square of the constraint distance */
65 <  double *mass; /* the array of masses */
101 >  virtual moveA( void );
102 >  virtual moveB( void );
103  
104 <  short int isFirst;
104 >  int readyCheck();
105  
106 <  SRI **srInteractions; /* array of SRI pointers */
107 <  int nSRI; /* the number of short range interactions */
108 <  
106 >  Atom** atoms;
107 >
108 >  // zeta is a propagated degree of freedom.
109 >
110 >  double zeta;
111 >
112 >  // targetTemp must be set.  One of qmass or tauThermostat must be set;
113 >
114 >  double qmass;
115 >  double targetTemp;
116 >  double tauThermostat;
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 +    Integrator( theInfo, the_ff );
129 +  virtual ~NPT();
130 +
131 +  void setQmass(double q) {qmass = q; have_qmass = 1;}
132 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
133 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
134 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
135 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
136 +
137 + protected:
138 +
139 +  virtual moveA( void );
140 +  virtual moveB( void );
141 +
142 +  int readyCheck();
143 +
144 +  Atom** atoms;
145 +
146 +  // zeta and epsilonDot are the propagated degrees of freedom.
147 +
148 +  double zeta;
149 +  double epsilonDot;
150 +
151 +  // targetTemp, targetPressure, and tauBarostat must be set.  
152 +  // One of qmass or tauThermostat must be set;
153 +
154 +  double qmass;
155 +  double targetTemp;
156 +  double targetPressure;
157 +  double tauThermostat;
158 +  double tauBarostat;
159 +
160 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
161 +  short int have_target_pressure, have_qmass;
162 +
163 + };
164 +
165   #endif

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