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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 594 by mmeineke, Fri Jul 11 22:34:48 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 > 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 <  Verlet( SimInfo &info, ForceFields* the_ff );
22 <  ~Verlet();
21 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
22 >  virtual ~Integrator();
23    void integrate( void );
24  
25 < private:
25 >
26 > protected:
27    
28 <  void move_a( double dt );
29 <  void move_b( double dt );
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 >  
36 >  void checkConstraints( void );
37 >  void rotate( int axes1, int axes2, double angle, double j[3],
38 >               double A[3][3] );
39  
40 +
41    ForceFields* myFF;
42  
43 <  SimInfo *entry_plug; // all the info we'll ever need
44 <  int c_natoms;  /* the number of atoms */
45 <  Atom **c_atoms; /* array of atom pointers */
46 <  SRI **c_sr_interactions; /* array of SRI pointers */
47 <  int c_n_SRI; /* the number of short range interactions */
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 c_is_constrained; /*boolean to know whether the systems contains
51 <                          constraints. */
52 <  int c_n_constrained; /*counter for number of constraints */
53 <  int *c_constrained_i; /* the i of a constraint pair */
54 <  int *c_constrained_j; /* the j of a constraint pair */
55 <  double *c_constrained_dsqr; /* the square of the constraint distance */
56 <  double *c_mass; /* the array of masses */
57 <  short is_first; /*boolean for the first time integrate is called */
58 <  double c_box_x;
59 <  double c_box_y;
40 <  double c_box_z;
41 < };
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 < class Symplectic : public Integrator {
61 >  short isFirst; /*boolean for the first time integrate is called */
62    
63 +  double dt;
64 +  double dt2;
65 +
66 +  double* pos;
67 +  double* vel;
68 +  double* frc;
69 +  double* trq;
70 +  double* Amat;
71 +
72 +  Thermo *tStats;
73 +  StatWriter*  statOut;
74 +  DumpWriter*  dumpOut;
75 +  
76 + };
77 +
78 + class NVE : public Integrator{
79 +
80   public:
81 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
82 <  ~Symplectic();
81 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
82 >    Integrator( theInfo, the_ff ){}
83 >  virtual ~NVE(){}
84 >
85    
49 –  void integrate( void );
86  
87 < private:
87 > };
88  
89 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
89 > class NVT : public Integrator{
90  
91 <  SimInfo* entry_plug;
57 <  ForceFields* myFF;
91 > public:
92  
93 <  int is_constrained; /*boolean to know whether the systems contains
94 <                          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 */
93 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 >  virtual ~NVT() {}
95  
96 <  short int isFirst;
96 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98  
99 <  SRI **srInteractions; /* array of SRI pointers */
100 <  int nSRI; /* the number of short range interactions */
99 > protected:
100 >
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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