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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 594 by mmeineke, Fri Jul 11 22:34:48 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 <  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
22 <  virtual ~Symplectic();
21 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
22 >  virtual ~Integrator();
23    void integrate( void );
24  
25  
26   protected:
21 –
27    
28    virtual void integrateStep( int calcPot, int calcStress );
29 +  virtual void preMove( void );
30    virtual void moveA( void );
31    virtual void moveB( void );
32    virtual void constrainA( void );
33    virtual void constrainB( void );
34 +  virtual int  readyCheck( void ) { return 1; }
35    
29 –  
36    void checkConstraints( void );
37    void rotate( int axes1, int axes2, double angle, double j[3],
38                 double A[3][3] );
# Line 36 | Line 42 | class Integrator : public BaseIntegrator { (protected)
42  
43    SimInfo *info; // all the info we'll ever need
44    int nAtoms;  /* the number of atoms */
45 +  int oldAtoms;
46    Atom **atoms; /* array of atom pointers */
47    Molecule* molecules;
48    int nMols;
49  
50 <  int isConstrained; /*boolean to know whether the systems contains
51 <                       constraints. */
52 <  int nConstrained; /*counter for number of constraints */
53 <  int *constrainedI; /* the i of a constraint pair */
54 <  int *constrainedJ; /* the j of a constraint pair */
55 <  double *constrainedDsqr; /* the square of the constraint distance */
50 >  int isConstrained; // boolean to know whether the systems contains
51 >                     // constraints.
52 >  int nConstrained;  // counter for number of constraints
53 >  int *constrainedA; // the i of a constraint pair
54 >  int *constrainedB; // the j of a constraint pair
55 >  double *constrainedDsqr; // the square of the constraint distance
56 >  
57 >  int* moving; // tells whether we are moving atom i
58 >  int* moved;  // tells whether we have moved atom i
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;
53 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
65  
55 –  
66    double* pos;
67    double* vel;
68    double* frc;
69    double* trq;
70    double* Amat;
61 –  
71  
63 –
72    Thermo *tStats;
73    StatWriter*  statOut;
74    DumpWriter*  dumpOut;
75    
76   };
77  
78 + class NVE : public Integrator{
79  
80 + public:
81 +  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
82 +    Integrator( theInfo, the_ff ){}
83 +  virtual ~NVE(){}
84 +
85 +  
86 +
87 + };
88 +
89   class NVT : public Integrator{
90  
91 <  NVT ( void );
74 <  virtual ~NVT();
91 > public:
92  
93 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 +  virtual ~NVT() {}
95 +
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 +  // chi is a propagated degree of freedom.
107 +
108 +  double chi;
109 +
110 +  // targetTemp must be set.  tauThermostat must also be set;
111 +
112 +  double targetTemp;
113 +  double tauThermostat;
114    
115 +  short int have_tau_thermostat, have_target_temp;
116  
117 + };
118  
119 +
120 + class NPTi : public Integrator{
121 +
122 + public:
123 +
124 +  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
125 +  virtual ~NPTi() {};
126 +
127 +  virtual void integrateStep( int calcPot, int calcStress ){
128 +    calcStress = 1;
129 +    Integrator::integrateStep( calcPot, calcStress );
130 +  }
131 +
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 void  moveA( void );
140 +  virtual void moveB( void );
141 +
142 +  virtual int readyCheck();
143 +
144 +  // chi and eta are the propagated degrees of freedom
145 +
146 +  double chi;
147 +  double eta;
148 +  double NkBT;
149 +
150 +  // targetTemp, targetPressure, and tauBarostat must be set.  
151 +  // One of qmass or tauThermostat must be set;
152 +
153 +  double targetTemp;
154 +  double targetPressure;
155 +  double tauThermostat;
156 +  double tauBarostat;
157 +
158 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
159 +  short int have_target_pressure;
160 +
161 + };
162 +
163 + class NPTf : public Integrator{
164 +
165 + public:
166 +
167 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
168 +  virtual ~NPTf() {};
169 +
170 +  virtual void integrateStep( int calcPot, int calcStress ){
171 +    calcStress = 1;
172 +    Integrator::integrateStep( calcPot, calcStress );
173 +  }
174 +
175 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 +
180 + protected:
181 +
182 +  virtual void  moveA( void );
183 +  virtual void moveB( void );
184 +
185 +  virtual int readyCheck();
186 +
187 +  // chi and eta are the propagated degrees of freedom
188 +
189 +  double chi;
190 +  double eta[3][3];
191 +  double NkBT;
192 +
193 +  // targetTemp, targetPressure, and tauBarostat must be set.  
194 +  // One of qmass or tauThermostat must be set;
195 +
196 +  double targetTemp;
197 +  double targetPressure;
198 +  double tauThermostat;
199 +  double tauBarostat;
200 +
201 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202 +  short int have_target_pressure;
203 +
204 + };
205 +
206   #endif

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