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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 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"
# Line 9 | Line 10 | class Integrator : public BaseIntegrator {
10   #include "Thermo.hpp"
11   #include "ReadWrite.hpp"
12  
13 < class Integrator : public BaseIntegrator {
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 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
23 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
24    virtual ~Integrator();
25    void integrate( void );
26  
# Line 50 | Line 58 | class Integrator : public BaseIntegrator { (protected)
58    
59    int* moving; // tells whether we are moving atom i
60    int* moved;  // tells whether we have moved atom i
61 <  double* prePos; // pre constrained positions
61 >  double* oldPos; // pre constrained positions
62  
63    short isFirst; /*boolean for the first time integrate is called */
64    
65    double dt;
66    double dt2;
67  
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 –
68    Thermo *tStats;
69    StatWriter*  statOut;
70    DumpWriter*  dumpOut;
71    
72   };
73  
74 < class NVE : public Integrator{
74 > typedef Integrator<BaseIntegrator> RealIntegrator;
75  
76 <  NVE ( void ):
80 <    Integrator( theInfo, the_ff ){}
81 <  virtual ~NVE(){}
76 > template<typename T> class NVE : public T {
77  
78 + public:
79 +  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
80 +    T( theInfo, the_ff ){}
81 +  virtual ~NVE(){}  
82 + };
83 +
84 +
85 + template<typename T> class NVT : public T {
86 +
87 + public:
88 +
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  
87 – class NVT : public Integrator{
115  
116 +
117 + template<typename T> class NPTi : public T{
118 +
119   public:
120  
121 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
122 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
121 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
122 >  virtual ~NPTi() {};
123  
124 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
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 moveA( void );
137 <  virtual moveB( void );
136 >  virtual void  moveA( void );
137 >  virtual void moveB( void );
138  
139 <  int readyCheck();
139 >  virtual int readyCheck();
140  
141 <  Atom** atoms;
141 >  // chi and eta are the propagated degrees of freedom
142  
143 <  // zeta is a propagated degree of freedom.
143 >  double chi;
144 >  double eta;
145 >  double NkBT;
146  
147 <  double zeta;
147 >  // targetTemp, targetPressure, and tauBarostat must be set.  
148 >  // One of qmass or tauThermostat must be set;
149  
150 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
150 >  double targetTemp;
151 >  double targetPressure;
152 >  double tauThermostat;
153 >  double tauBarostat;
154  
155 <  double qmass;
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_target_temp, have_qmass;
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 < class NPT : public Integrator{
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 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
254 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
253 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
254 >  virtual ~NPTfm() {};
255  
256 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
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;}
# Line 136 | Line 265 | class NPT : public Integrator{ (protected)
265  
266   protected:
267  
268 <  virtual moveA( void );
269 <  virtual moveB( void );
268 >  virtual void  moveA( void );
269 >  virtual void moveB( void );
270  
271 <  int readyCheck();
271 >  virtual int readyCheck();
272  
273 <  Atom** atoms;
273 >  Molecule* myMolecules;
274 >  Atom** myAtoms;
275  
276 <  // zeta and epsilonDot are the propagated degrees of freedom.
276 >  // chi and eta are the propagated degrees of freedom
277  
278 <  double zeta;
279 <  double epsilonDot;
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  
154 –  double qmass;
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, have_qmass;
291 >  short int have_target_pressure;
292  
293   };
294  

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