ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 596 by gezelter, Mon Jul 14 15:04:55 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 –  
66    double* pos;
67    double* vel;
68    double* frc;
# Line 76 | Line 77 | class NVE : public Integrator{
77  
78   class NVE : public Integrator{
79  
80 <  NVE ( void ):
80 > public:
81 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
82      Integrator( theInfo, the_ff ){}
83    virtual ~NVE(){}
84  
# Line 88 | Line 90 | class NVT : public Integrator{ (public)
90  
91   public:
92  
93 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
94 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
93 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 >  virtual ~NVT() {}
95  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
96    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98  
99   protected:
100  
101 <  virtual moveA( void );
102 <  virtual moveB( void );
101 >  virtual void moveA( void );
102 >  virtual void moveB( void );
103  
104 <  int readyCheck();
104 >  virtual int readyCheck();
105  
106 <  Atom** atoms;
106 >  // chi is a propagated degree of freedom.
107  
108 <  // zeta is a propagated degree of freedom.
108 >  double chi;
109  
110 <  double zeta;
110 >  // targetTemp must be set.  tauThermostat must also be set;
111  
112 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
112 >  double targetTemp;
113 >  double tauThermostat;
114 >  
115 >  short int have_tau_thermostat, have_target_temp;
116  
117 <  double qmass;
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_target_temp, have_qmass;
158 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
159 >  short int have_target_pressure;
160  
161   };
162  
163 + class NPTim : public Integrator{
164  
165 < class NPT : public Integrator{
165 > public:
166  
167 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
168 +  virtual ~NPTim() {};
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;
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 + class NPTf : public Integrator{
207 +
208   public:
209  
210 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
211 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
210 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
211 >  virtual ~NPTf() {};
212  
213 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
213 >  virtual void integrateStep( int calcPot, int calcStress ){
214 >    calcStress = 1;
215 >    Integrator::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;}
# Line 136 | Line 222 | class NPT : public Integrator{ (protected)
222  
223   protected:
224  
225 <  virtual moveA( void );
226 <  virtual moveB( void );
225 >  virtual void  moveA( void );
226 >  virtual void moveB( void );
227  
228 <  int readyCheck();
228 >  virtual int readyCheck();
229  
230 <  Atom** atoms;
230 >  // chi and eta are the propagated degrees of freedom
231  
232 <  // zeta and epsilonDot are the propagated degrees of freedom.
232 >  double chi;
233 >  double eta[3][3];
234 >  double NkBT;
235  
236 <  double zeta;
237 <  double epsilonDot;
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 + class NPTfm : public Integrator{
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 +    Integrator::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 +  // chi and eta are the propagated degrees of freedom
274 +
275 +  double chi;
276 +  double eta[3][3];
277 +  double NkBT;
278 +
279    // targetTemp, targetPressure, and tauBarostat must be set.  
280    // One of qmass or tauThermostat must be set;
281  
154 –  double qmass;
282    double targetTemp;
283    double targetPressure;
284    double tauThermostat;
285    double tauBarostat;
286  
287    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure, have_qmass;
288 >  short int have_target_pressure;
289  
290   };
291  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines