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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 559 by mmeineke, Thu Jun 19 22:02:44 2003 UTC vs.
Revision 597 by mmeineke, Mon Jul 14 21:28:54 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  
25  
26   protected:
21 –
27    
28    virtual void integrateStep( int calcPot, int calcStress );
29    virtual void preMove( void );
# Line 30 | Line 35 | class Integrator : public BaseIntegrator { (protected)
35    
36    void checkConstraints( void );
37    void rotate( int axes1, int axes2, double angle, double j[3],
38 <               double A[3][3] );
38 >               double A[9] );
39  
40  
41    ForceFields* myFF;
# Line 51 | 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;
60 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
65  
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –
65 –  
66    double* pos;
67    double* vel;
68    double* frc;
69    double* trq;
70    double* Amat;
71 –  
71  
73 –
72    Thermo *tStats;
73    StatWriter*  statOut;
74    DumpWriter*  dumpOut;
# Line 79 | 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 89 | Line 88 | class NVT : public Integrator{
88  
89   class NVT : public Integrator{
90  
91 <  NVT ( SimInfo &theInfo, ForceFields* the_ff ) :
93 <    Integrator( theInfo, the_ff );
94 <  virtual ~NVT();
91 > public:
92  
93 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 +  virtual ~NVT() {}
95 +
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:
97 –  virtual moveA( void );
98 –  virtual moveB( void );
100  
101 < };
101 >  virtual void moveA( void );
102 >  virtual void moveB( void );
103  
104 +  virtual int readyCheck();
105 +
106 +  // chi is a propagated degree of freedom.
107 +
108 +  double chi;
109 +
110 +  // targetTemp must be set.  tauThermostat must also be set;
111 +
112 +  double targetTemp;
113 +  double tauThermostat;
114    
115 +  short int have_tau_thermostat, have_target_temp;
116  
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_tau_barostat, have_target_temp;
159 +  short int have_target_pressure;
160 +
161 + };
162 +
163 + class NPTim : public Integrator{
164 +
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 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
211 +  virtual ~NPTf() {};
212 +
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;}
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 + 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 +
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;
289 +
290 + };
291 +
292   #endif

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