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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 17 | Line 17 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
17    chi = 0.0;
18    have_tau_thermostat = 0;
19    have_target_temp = 0;
20 +  have_chi_tolerance = 0;
21 +  integralOfChidt = 0.0;
22 +
23 +  oldVel = new double[3*nAtoms];
24 +  oldJi = new double[3*nAtoms];
25   }
26  
27 + template<typename T> NVT<T>::~NVT() {
28 +  delete[] oldVel;
29 +  delete[] oldJi;
30 + }
31 +
32   template<typename T> void NVT<T>::moveA() {
33    
34    int i, j;
# Line 30 | Line 40 | template<typename T> void NVT<T>::moveA() {
40  
41    double instTemp;
42  
43 <  instTemp = tStats->getTemperature();
43 >  // We need the temperature at time = t for the chi update below:
44  
45 <  // first evolve chi a half step
45 >  instTemp = tStats->getTemperature();
46    
37 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 –
47    for( i=0; i<nAtoms; i++ ){
48  
49      atoms[i]->getVel( vel );
# Line 45 | Line 53 | template<typename T> void NVT<T>::moveA() {
53      mass = atoms[i]->getMass();
54  
55      for (j=0; j < 3; j++) {
56 <      // velocity half step
56 >      // velocity half step  (use chi from previous step here):
57        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
58        // position whole step
59        pos[j] += dt * vel[j];
# Line 100 | Line 108 | template<typename T> void NVT<T>::moveA() {
108        dAtom->setA( A  );    
109      }    
110    }
111 +
112 +  // Finally, evolve chi a half step (just like a velocity) using
113 +  // temperature at time t, not time t+dt/2
114 +
115 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
116 +  integralOfChidt += chi*dt2;
117 +
118   }
119  
120   template<typename T> void NVT<T>::moveB( void ){
121 <  int i, j;
121 >  int i, j, k;
122    DirectionalAtom* dAtom;
123    double Tb[3], ji[3];
124    double vel[3], frc[3];
125    double mass;
111 –
126    double instTemp;
127 <  
128 <  instTemp = tStats->getTemperature();
129 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
130 <  
127 >  double oldChi, prevChi;
128 >
129 >  // Set things up for the iteration:
130 >
131 >  oldChi = chi;
132 >
133    for( i=0; i<nAtoms; i++ ){
134  
135      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
136  
137 <    mass = atoms[i]->getMass();
137 >    for (j=0; j < 3; j++)
138 >      oldVel[3*i + j]  = vel[j];
139  
124 –    // velocity half step
125 –    for (j=0; j < 3; j++)
126 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
127 –    
128 –    atoms[i]->setVel( vel );
129 –
140      if( atoms[i]->isDirectional() ){
141  
142        dAtom = (DirectionalAtom *)atoms[i];
143  
144 <      // get and convert the torque to body frame      
144 >      dAtom->getJ( ji );
145  
146 <      dAtom->getTrq( Tb );
147 <      dAtom->lab2Body( Tb );
146 >      for (j=0; j < 3; j++)
147 >        oldJi[3*i + j] = ji[j];
148  
149 <      // get the angular momentum, and propagate a half step
149 >    }
150 >  }
151  
152 <      dAtom->getJ( ji );
152 >  // do the iteration:
153  
154 +  for (k=0; k < 4; k++) {
155 +    
156 +    instTemp = tStats->getTemperature();
157 +
158 +    // evolve chi another half step using the temperature at t + dt/2
159 +
160 +    prevChi = chi;
161 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
162 +      (tauThermostat*tauThermostat);
163 +  
164 +    for( i=0; i<nAtoms; i++ ){
165 +
166 +      atoms[i]->getFrc( frc );
167 +      atoms[i]->getVel(vel);
168 +      
169 +      mass = atoms[i]->getMass();
170 +      
171 +      // velocity half step
172        for (j=0; j < 3; j++)
173 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
173 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
174        
175 <
176 <      dAtom->setJ( ji );
175 >      atoms[i]->setVel( vel );
176 >      
177 >      if( atoms[i]->isDirectional() ){
178 >        
179 >        dAtom = (DirectionalAtom *)atoms[i];
180 >        
181 >        // get and convert the torque to body frame      
182 >        
183 >        dAtom->getTrq( Tb );
184 >        dAtom->lab2Body( Tb );      
185 >            
186 >        for (j=0; j < 3; j++)
187 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
188 >      
189 >        dAtom->setJ( ji );
190 >      }
191      }
192 +
193 +    if (fabs(prevChi - chi) <= chiTolerance) break;
194    }
195 +  
196 +  integralOfChidt += dt2*chi;
197   }
198  
199   template<typename T> void NVT<T>::resetIntegrator( void ){
200    
201    chi = 0.0;
202 +  integralOfChidt = 0.0;
203   }
204  
205   template<typename T> int NVT<T>::readyCheck() {
# Line 182 | Line 230 | template<typename T> int NVT<T>::readyCheck() {
230      simError();
231      return -1;
232    }    
233 <  return 1;
233 >
234 >  if (!have_chi_tolerance) {
235 >    sprintf( painCave.errMsg,
236 >             "NVT warning: setting chi tolerance to 1e-6\n");
237 >    chiTolerance = 1e-6;
238 >    have_chi_tolerance = 1;
239 >    painCave.isFatal = 0;
240 >    simError();
241 >  }    
242 >
243 >  return 1;    
244 >
245   }
246 +
247 + template<typename T> double NVT<T>::getConservedQuantity(void){
248 +
249 +  double conservedQuantity;
250 +  double E_NVT;
251 +
252 +  //HNVE
253 +  conservedQuantity = tStats->getTotalE();
254 +  //HNVE
255 +  
256 +  E_NVT =  (info->getNDF() * kB * targetTemp *
257 +                (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert;
258 +
259 +  conservedQuantity += E_NVT;
260 +
261 +  //cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl;
262 +
263 +  return conservedQuantity;
264 + }

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