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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
Revision 769 by tim, Fri Sep 19 14:22:29 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 +  if (nConstrained){
113 +    constrainA();
114 +  }
115 +
116 +  // Finally, evolve chi a half step (just like a velocity) using
117 +  // temperature at time t, not time t+dt/2
118 +
119 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
120 +  integralOfChidt += chi*dt2;
121 +
122   }
123  
124   template<typename T> void NVT<T>::moveB( void ){
125 <  int i, j;
125 >  int i, j, k;
126    DirectionalAtom* dAtom;
127    double Tb[3], ji[3];
128    double vel[3], frc[3];
129    double mass;
111 –
130    double instTemp;
131 <  
132 <  instTemp = tStats->getTemperature();
133 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
134 <  
131 >  double oldChi, prevChi;
132 >
133 >  // Set things up for the iteration:
134 >
135 >  oldChi = chi;
136 >
137    for( i=0; i<nAtoms; i++ ){
138  
139      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
140  
141 <    mass = atoms[i]->getMass();
141 >    for (j=0; j < 3; j++)
142 >      oldVel[3*i + j]  = vel[j];
143  
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 –
144      if( atoms[i]->isDirectional() ){
145  
146        dAtom = (DirectionalAtom *)atoms[i];
147  
148 <      // get and convert the torque to body frame      
148 >      dAtom->getJ( ji );
149  
150 <      dAtom->getTrq( Tb );
151 <      dAtom->lab2Body( Tb );
150 >      for (j=0; j < 3; j++)
151 >        oldJi[3*i + j] = ji[j];
152  
153 <      // get the angular momentum, and propagate a half step
153 >    }
154 >  }
155  
156 <      dAtom->getJ( ji );
156 >  // do the iteration:
157  
158 +  for (k=0; k < 4; k++) {
159 +    
160 +    instTemp = tStats->getTemperature();
161 +
162 +    // evolve chi another half step using the temperature at t + dt/2
163 +
164 +    prevChi = chi;
165 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
166 +      (tauThermostat*tauThermostat);
167 +  
168 +    for( i=0; i<nAtoms; i++ ){
169 +
170 +      atoms[i]->getFrc( frc );
171 +      atoms[i]->getVel(vel);
172 +      
173 +      mass = atoms[i]->getMass();
174 +      
175 +      // velocity half step
176        for (j=0; j < 3; j++)
177 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
177 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
178        
179 +      atoms[i]->setVel( vel );
180 +      
181 +      if( atoms[i]->isDirectional() ){
182 +        
183 +        dAtom = (DirectionalAtom *)atoms[i];
184 +        
185 +        // get and convert the torque to body frame      
186 +        
187 +        dAtom->getTrq( Tb );
188 +        dAtom->lab2Body( Tb );      
189 +            
190 +        for (j=0; j < 3; j++)
191 +          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
192 +      
193 +        dAtom->setJ( ji );
194 +      }
195 +    }
196  
197 <      dAtom->setJ( ji );
197 >    if (nConstrained){
198 >      constrainB();
199      }
200 +
201 +    if (fabs(prevChi - chi) <= chiTolerance) break;
202    }
203 +  
204 +  integralOfChidt += dt2*chi;
205   }
206  
207 + template<typename T> void NVT<T>::resetIntegrator( void ){
208 +  
209 +  chi = 0.0;
210 +  integralOfChidt = 0.0;
211 + }
212 +
213   template<typename T> int NVT<T>::readyCheck() {
214 <
214 >
215 >  //check parent's readyCheck() first
216 >  if (T::readyCheck() == -1)
217 >    return -1;
218 >  
219    // First check to see if we have a target temperature.
220    // Not having one is fatal.
221    
# Line 173 | Line 238 | template<typename T> int NVT<T>::readyCheck() {
238      simError();
239      return -1;
240    }    
241 <  return 1;
241 >
242 >  if (!have_chi_tolerance) {
243 >    sprintf( painCave.errMsg,
244 >             "NVT warning: setting chi tolerance to 1e-6\n");
245 >    chiTolerance = 1e-6;
246 >    have_chi_tolerance = 1;
247 >    painCave.isFatal = 0;
248 >    simError();
249 >  }    
250 >
251 >  return 1;    
252 >
253   }
254 +
255 + template<typename T> double NVT<T>::getConservedQuantity(void){
256 +
257 +  double conservedQuantity;
258 +  double fkBT;
259 +  double Energy;
260 +  double thermostat_kinetic;
261 +  double thermostat_potential;
262 +
263 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
264 +
265 +  Energy = tStats->getTotalE();
266 +
267 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268 +    (2.0 * eConvert);
269 +
270 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
271 +
272 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
273 +  
274 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
275 +      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
276 +
277 +  return conservedQuantity;
278 + }

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