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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 576 by gezelter, Tue Jul 8 21:10:16 2003 UTC vs.
Revision 604 by gezelter, Tue Jul 15 03:08:00 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 11 | Line 12 | const double eConvert = 4.184e-4; // converts kcal/mol
12  
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  
# Line 34 | Line 36 | class Integrator : public BaseIntegrator { (protected)
36    
37    void checkConstraints( void );
38    void rotate( int axes1, int axes2, double angle, double j[3],
39 <               double A[9] );
39 >               double A[3][3] );
40  
41  
42    ForceFields* myFF;
# Line 62 | Line 64 | class Integrator : public BaseIntegrator { (protected)
64    double dt;
65    double dt2;
66  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
67    Thermo *tStats;
68    StatWriter*  statOut;
69    DumpWriter*  dumpOut;
# Line 123 | Line 119 | class NPTi : public Integrator{ (public)
119    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
120    virtual ~NPTi() {};
121  
122 +  virtual void integrateStep( int calcPot, int calcStress ){
123 +    calcStress = 1;
124 +    Integrator::integrateStep( calcPot, calcStress );
125 +  }
126 +
127    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
128    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
129    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 154 | Line 155 | class NPTi : public Integrator{ (public)
155  
156   };
157  
158 + class NPTim : public Integrator{
159 +
160 + public:
161 +
162 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
163 +  virtual ~NPTim() {};
164 +
165 +  virtual void integrateStep( int calcPot, int calcStress ){
166 +    calcStress = 1;
167 +    Integrator::integrateStep( calcPot, calcStress );
168 +  }
169 +
170 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174 +
175 + protected:
176 +
177 +  virtual void moveA( void );
178 +  virtual void moveB( void );
179 +
180 +  virtual int readyCheck();
181 +
182 +  Molecule* myMolecules;
183 +  Atom** myAtoms;
184 +
185 +  // chi and eta are the propagated degrees of freedom
186 +
187 +  double chi;
188 +  double eta;
189 +  double NkBT;
190 +
191 +  // targetTemp, targetPressure, and tauBarostat must be set.  
192 +  // One of qmass or tauThermostat must be set;
193 +
194 +  double targetTemp;
195 +  double targetPressure;
196 +  double tauThermostat;
197 +  double tauBarostat;
198 +
199 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
200 +  short int have_target_pressure;
201 +
202 + };
203 +
204   class NPTf : public Integrator{
205  
206   public:
# Line 161 | Line 208 | class NPTf : public Integrator{ (public)
208    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
209    virtual ~NPTf() {};
210  
211 +  virtual void integrateStep( int calcPot, int calcStress ){
212 +    calcStress = 1;
213 +    Integrator::integrateStep( calcPot, calcStress );
214 +  }
215 +
216    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
217    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
218    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 176 | Line 228 | class NPTf : public Integrator{ (public)
228    // chi and eta are the propagated degrees of freedom
229  
230    double chi;
231 <  double eta[9];
231 >  double eta[3][3];
232    double NkBT;
233  
234    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 192 | Line 244 | class NPTf : public Integrator{ (public)
244  
245   };
246  
247 + class NPTfm : public Integrator{
248 +
249 + public:
250 +
251 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
252 +  virtual ~NPTfm() {};
253 +
254 +  virtual void integrateStep( int calcPot, int calcStress ){
255 +    calcStress = 1;
256 +    Integrator::integrateStep( calcPot, calcStress );
257 +  }
258 +
259 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
260 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
261 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
262 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
263 +
264 + protected:
265 +
266 +  virtual void  moveA( void );
267 +  virtual void moveB( void );
268 +
269 +  virtual int readyCheck();
270 +
271 +  // chi and eta are the propagated degrees of freedom
272 +
273 +  double chi;
274 +  double eta[3][3];
275 +  double NkBT;
276 +
277 +  // targetTemp, targetPressure, and tauBarostat must be set.  
278 +  // One of qmass or tauThermostat must be set;
279 +
280 +  double targetTemp;
281 +  double targetPressure;
282 +  double tauThermostat;
283 +  double tauBarostat;
284 +
285 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
286 +  short int have_target_pressure;
287 +
288 + };
289 +
290   #endif

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