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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC

# Line 2 | Line 2
2   #define _INTEGRATOR_H_
3  
4   #include "Atom.hpp"
5 + #include "Molecule.hpp"
6   #include "SRI.hpp"
7   #include "AbstractClasses.hpp"
8   #include "SimInfo.hpp"
9   #include "ForceFields.hpp"
10 + #include "Thermo.hpp"
11 + #include "ReadWrite.hpp"
12  
13 < class Verlet : public Integrator {
13 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
14 > const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
15 > const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
16 > const int maxIteration = 300;
17 > const double tol = 1.0e-6;
18  
19 +
20 + template<typename T = BaseIntegrator> class Integrator : public T {
21 +
22   public:
23 <  Verlet( SimInfo &info, ForceFields* the_ff );
24 <  ~Verlet();
23 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
24 >  virtual ~Integrator();
25    void integrate( void );
26  
27 < private:
27 >
28 > protected:
29    
30 <  void move_a( double dt );
31 <  void move_b( double dt );
30 >  virtual void integrateStep( int calcPot, int calcStress );
31 >  virtual void preMove( void );
32 >  virtual void moveA( void );
33 >  virtual void moveB( void );
34 >  virtual void constrainA( void );
35 >  virtual void constrainB( void );
36 >  virtual int  readyCheck( void ) { return 1; }
37 >  
38 >  void checkConstraints( void );
39 >  void rotate( int axes1, int axes2, double angle, double j[3],
40 >               double A[3][3] );
41  
42 +
43    ForceFields* myFF;
44  
45 <  SimInfo *entry_plug; // all the info we'll ever need
46 <  int c_natoms;  /* the number of atoms */
47 <  Atom **c_atoms; /* array of atom pointers */
45 >  SimInfo *info; // all the info we'll ever need
46 >  int nAtoms;  /* the number of atoms */
47 >  int oldAtoms;
48 >  Atom **atoms; /* array of atom pointers */
49    Molecule* molecules;
50    int nMols;
51  
52 <  int c_is_constrained; /*boolean to know whether the systems contains
53 <                          constraints. */
54 <  int c_n_constrained; /*counter for number of constraints */
55 <  int *c_constrained_i; /* the i of a constraint pair */
56 <  int *c_constrained_j; /* the j of a constraint pair */
57 <  double *c_constrained_dsqr; /* the square of the constraint distance */
58 <  double *c_mass; /* the array of masses */
59 <  short is_first; /*boolean for the first time integrate is called */
60 <  double c_box_x;
61 <  double c_box_y;
40 <  double c_box_z;
41 < };
52 >  int isConstrained; // boolean to know whether the systems contains
53 >                     // constraints.
54 >  int nConstrained;  // counter for number of constraints
55 >  int *constrainedA; // the i of a constraint pair
56 >  int *constrainedB; // the j of a constraint pair
57 >  double *constrainedDsqr; // the square of the constraint distance
58 >  
59 >  int* moving; // tells whether we are moving atom i
60 >  int* moved;  // tells whether we have moved atom i
61 >  double* oldPos; // pre constrained positions
62  
63 < class Symplectic : public Integrator {
63 >  short isFirst; /*boolean for the first time integrate is called */
64    
65 < public:
66 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
67 <  ~Symplectic();
65 >  double dt;
66 >  double dt2;
67 >
68 >  Thermo *tStats;
69 >  StatWriter*  statOut;
70 >  DumpWriter*  dumpOut;
71    
72 <  void integrate( void );
72 > };
73  
74 < private:
74 > typedef Integrator<BaseIntegrator> RealIntegrator;
75  
76 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
76 > template<typename T> class NVE : public T {
77  
78 <  SimInfo* entry_plug;
79 <  ForceFields* myFF;
78 > public:
79 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
80 >    T( theInfo, the_ff ){}
81 >  virtual ~NVE(){}  
82 > };
83  
59 –  Molecule* molecules;
60 –  int nMols;
84  
85 <  int is_constrained; /*boolean to know whether the systems contains
63 <                          constraints. */
64 <  int n_constrained; /*counter for number of constraints */
65 <  int *constrained_i; /* the i of a constraint pair */
66 <  int *constrained_j; /* the j of a constraint pair */
67 <  double *constrained_dsqr; /* the square of the constraint distance */
68 <  double *mass; /* the array of masses */
85 > template<typename T> class NVT : public T {
86  
87 <  short int isFirst;
87 > public:
88  
89 <  SRI **srInteractions; /* array of SRI pointers */
90 <  int nSRI; /* the number of short range interactions */
89 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
90 >  virtual ~NVT() {}
91 >
92 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
93 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
94 >
95 > protected:
96 >
97 >  virtual void moveA( void );
98 >  virtual void moveB( void );
99 >
100 >  virtual int readyCheck();
101 >
102 >  // chi is a propagated degree of freedom.
103 >
104 >  double chi;
105 >
106 >  // targetTemp must be set.  tauThermostat must also be set;
107 >
108 >  double targetTemp;
109 >  double tauThermostat;
110    
111 +  short int have_tau_thermostat, have_target_temp;
112 +
113   };
114  
115 +
116 +
117 + template<typename T> class NPTi : public T{
118 +
119 + public:
120 +
121 +  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
122 +  virtual ~NPTi() {};
123 +
124 +  virtual void integrateStep( int calcPot, int calcStress ){
125 +    calcStress = 1;
126 +    T::integrateStep( calcPot, calcStress );
127 +  }
128 +
129 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
130 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
131 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
132 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
133 +
134 + protected:
135 +
136 +  virtual void  moveA( void );
137 +  virtual void moveB( void );
138 +
139 +  virtual int readyCheck();
140 +
141 +  // chi and eta are the propagated degrees of freedom
142 +
143 +  double chi;
144 +  double eta;
145 +  double NkBT;
146 +
147 +  // targetTemp, targetPressure, and tauBarostat must be set.  
148 +  // One of qmass or tauThermostat must be set;
149 +
150 +  double targetTemp;
151 +  double targetPressure;
152 +  double tauThermostat;
153 +  double tauBarostat;
154 +
155 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
156 +  short int have_target_pressure;
157 +
158 + };
159 +
160 + template<typename T> class NPTim : public T{
161 +
162 + public:
163 +
164 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
165 +  virtual ~NPTim() {};
166 +
167 +  virtual void integrateStep( int calcPot, int calcStress ){
168 +    calcStress = 1;
169 +    T::integrateStep( calcPot, calcStress );
170 +  }
171 +
172 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
173 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
174 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
175 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
176 +
177 + protected:
178 +
179 +  virtual void moveA( void );
180 +  virtual void moveB( void );
181 +
182 +  virtual int readyCheck();
183 +
184 +  Molecule* myMolecules;
185 +  Atom** myAtoms;
186 +
187 +  // chi and eta are the propagated degrees of freedom
188 +
189 +  double chi;
190 +  double eta;
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 + template<typename T> class NPTf : public T{
207 +
208 + public:
209 +
210 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
211 +  virtual ~NPTf() {};
212 +
213 +  virtual void integrateStep( int calcPot, int calcStress ){
214 +    calcStress = 1;
215 +    T::integrateStep( calcPot, calcStress );
216 +  }
217 +
218 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
222 +
223 + protected:
224 +
225 +  virtual void  moveA( void );
226 +  virtual void moveB( void );
227 +
228 +  virtual int readyCheck();
229 +
230 +  // chi and eta are the propagated degrees of freedom
231 +
232 +  double chi;
233 +  double eta[3][3];
234 +  double NkBT;
235 +
236 +  // targetTemp, targetPressure, and tauBarostat must be set.  
237 +  // One of qmass or tauThermostat must be set;
238 +
239 +  double targetTemp;
240 +  double targetPressure;
241 +  double tauThermostat;
242 +  double tauBarostat;
243 +
244 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
245 +  short int have_target_pressure;
246 +
247 + };
248 +
249 + template<typename T> class NPTfm : public T{
250 +
251 + public:
252 +
253 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
254 +  virtual ~NPTfm() {};
255 +
256 +  virtual void integrateStep( int calcPot, int calcStress ){
257 +    calcStress = 1;
258 +    T::integrateStep( calcPot, calcStress );
259 +  }
260 +
261 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
262 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
265 +
266 + protected:
267 +
268 +  virtual void  moveA( void );
269 +  virtual void moveB( void );
270 +
271 +  virtual int readyCheck();
272 +
273 +  Molecule* myMolecules;
274 +  Atom** myAtoms;
275 +
276 +  // chi and eta are the propagated degrees of freedom
277 +
278 +  double chi;
279 +  double eta[3][3];
280 +  double NkBT;
281 +
282 +  // targetTemp, targetPressure, and tauBarostat must be set.  
283 +  // One of qmass or tauThermostat must be set;
284 +
285 +  double targetTemp;
286 +  double targetPressure;
287 +  double tauThermostat;
288 +  double tauBarostat;
289 +
290 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
291 +  short int have_target_pressure;
292 +
293 + };
294 +
295   #endif

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