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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 600 by gezelter, Mon Jul 14 22:38:13 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 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
21 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
22    virtual ~Integrator();
23    void integrate( void );
24  
# Line 50 | Line 56 | class Integrator : public BaseIntegrator { (protected)
56    
57    int* moving; // tells whether we are moving atom i
58    int* moved;  // tells whether we have moved atom i
59 <  double* prePos; // pre constrained positions
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;
65  
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 –
66    Thermo *tStats;
67    StatWriter*  statOut;
68    DumpWriter*  dumpOut;
# Line 76 | Line 71 | class NVE : public Integrator{
71  
72   class NVE : public Integrator{
73  
74 <  NVE ( void ):
74 > public:
75 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
76      Integrator( theInfo, the_ff ){}
77    virtual ~NVE(){}
78  
# Line 88 | Line 84 | class NVT : public Integrator{ (public)
84  
85   public:
86  
87 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
88 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
87 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
88 >  virtual ~NVT() {}
89  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
90    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
91    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
92  
93   protected:
94  
95 <  virtual moveA( void );
96 <  virtual moveB( void );
95 >  virtual void moveA( void );
96 >  virtual void moveB( void );
97  
98 <  int readyCheck();
98 >  virtual int readyCheck();
99  
100 <  Atom** atoms;
100 >  // chi is a propagated degree of freedom.
101  
102 <  // zeta is a propagated degree of freedom.
102 >  double chi;
103  
104 <  double zeta;
104 >  // targetTemp must be set.  tauThermostat must also be set;
105  
106 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
106 >  double targetTemp;
107 >  double tauThermostat;
108 >  
109 >  short int have_tau_thermostat, have_target_temp;
110  
111 <  double qmass;
111 > };
112 >
113 >
114 > class NPTi : public Integrator{
115 >
116 > public:
117 >
118 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
119 >  virtual ~NPTi() {};
120 >
121 >  virtual void integrateStep( int calcPot, int calcStress ){
122 >    calcStress = 1;
123 >    Integrator::integrateStep( calcPot, calcStress );
124 >  }
125 >
126 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
127 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
128 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
129 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
130 >
131 > protected:
132 >
133 >  virtual void  moveA( void );
134 >  virtual void moveB( void );
135 >
136 >  virtual int readyCheck();
137 >
138 >  // chi and eta are the propagated degrees of freedom
139 >
140 >  double chi;
141 >  double eta;
142 >  double NkBT;
143 >
144 >  // targetTemp, targetPressure, and tauBarostat must be set.  
145 >  // One of qmass or tauThermostat must be set;
146 >
147    double targetTemp;
148 +  double targetPressure;
149    double tauThermostat;
150 +  double tauBarostat;
151  
152 <  short int have_tau_thermostat, have_target_temp, have_qmass;
152 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
153 >  short int have_target_pressure;
154  
155   };
156  
157 + class NPTim : public Integrator{
158  
159 < class NPT : public Integrator{
159 > public:
160  
161 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
162 +  virtual ~NPTim() {};
163 +
164 +  virtual void integrateStep( int calcPot, int calcStress ){
165 +    calcStress = 1;
166 +    Integrator::integrateStep( calcPot, calcStress );
167 +  }
168 +
169 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173 +
174 + protected:
175 +
176 +  virtual void  moveA( void );
177 +  virtual void moveB( void );
178 +
179 +  virtual int readyCheck();
180 +
181 +  // chi and eta are the propagated degrees of freedom
182 +
183 +  double chi;
184 +  double eta;
185 +  double NkBT;
186 +
187 +  // targetTemp, targetPressure, and tauBarostat must be set.  
188 +  // One of qmass or tauThermostat must be set;
189 +
190 +  double targetTemp;
191 +  double targetPressure;
192 +  double tauThermostat;
193 +  double tauBarostat;
194 +
195 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
196 +  short int have_target_pressure;
197 +
198 + };
199 +
200 + class NPTf : public Integrator{
201 +
202   public:
203  
204 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
205 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
204 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
205 >  virtual ~NPTf() {};
206  
207 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
207 >  virtual void integrateStep( int calcPot, int calcStress ){
208 >    calcStress = 1;
209 >    Integrator::integrateStep( calcPot, calcStress );
210 >  }
211 >
212    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
213    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
214    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 136 | Line 216 | class NPT : public Integrator{ (protected)
216  
217   protected:
218  
219 <  virtual moveA( void );
220 <  virtual moveB( void );
219 >  virtual void  moveA( void );
220 >  virtual void moveB( void );
221  
222 <  int readyCheck();
222 >  virtual int readyCheck();
223  
224 <  Atom** atoms;
224 >  // chi and eta are the propagated degrees of freedom
225  
226 <  // zeta and epsilonDot are the propagated degrees of freedom.
226 >  double chi;
227 >  double eta[3][3];
228 >  double NkBT;
229  
230 <  double zeta;
231 <  double epsilonDot;
230 >  // targetTemp, targetPressure, and tauBarostat must be set.  
231 >  // One of qmass or tauThermostat must be set;
232  
233 +  double targetTemp;
234 +  double targetPressure;
235 +  double tauThermostat;
236 +  double tauBarostat;
237 +
238 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
239 +  short int have_target_pressure;
240 +
241 + };
242 +
243 + class NPTfm : public Integrator{
244 +
245 + public:
246 +
247 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
248 +  virtual ~NPTfm() {};
249 +
250 +  virtual void integrateStep( int calcPot, int calcStress ){
251 +    calcStress = 1;
252 +    Integrator::integrateStep( calcPot, calcStress );
253 +  }
254 +
255 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
256 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
257 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
258 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
259 +
260 + protected:
261 +
262 +  virtual void  moveA( void );
263 +  virtual void moveB( void );
264 +
265 +  virtual int readyCheck();
266 +
267 +  // chi and eta are the propagated degrees of freedom
268 +
269 +  double chi;
270 +  double eta[3][3];
271 +  double NkBT;
272 +
273    // targetTemp, targetPressure, and tauBarostat must be set.  
274    // One of qmass or tauThermostat must be set;
275  
154 –  double qmass;
276    double targetTemp;
277    double targetPressure;
278    double tauThermostat;
279    double tauBarostat;
280  
281    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
282 <  short int have_target_pressure, have_qmass;
282 >  short int have_target_pressure;
283  
284   };
285  

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