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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 50 | Line 50 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
50      }
51    }
52  
53 <  oldVel = new double[3*nAtoms];
54 <  oldJi = new double[3*nAtoms];
53 >  oldVel = new double[3*integrableObjects.size()];
54 >  oldJi = new double[3*integrableObjects.size()];
55   }
56  
57   template<typename T> NVT<T>::~NVT() {
# Line 73 | Line 73 | template<typename T> void NVT<T>::moveA() {
73  
74    instTemp = tStats->getTemperature();
75  
76 <  for( i=0; i<nAtoms; i++ ){
76 >  for( i=0; i < integrableObjects.size(); i++ ){
77  
78 <    atoms[i]->getVel( vel );
79 <    atoms[i]->getPos( pos );
80 <    atoms[i]->getFrc( frc );
78 >    integrableObjects[i]->getVel( vel );
79 >    integrableObjects[i]->getPos( pos );
80 >    integrableObjects[i]->getFrc( frc );
81  
82 <    mass = atoms[i]->getMass();
82 >    mass = integrableObjects[i]->getMass();
83  
84      for (j=0; j < 3; j++) {
85        // velocity half step  (use chi from previous step here):
# Line 88 | Line 88 | template<typename T> void NVT<T>::moveA() {
88        pos[j] += dt * vel[j];
89      }
90  
91 <    atoms[i]->setVel( vel );
92 <    atoms[i]->setPos( pos );
91 >    integrableObjects[i]->setVel( vel );
92 >    integrableObjects[i]->setPos( pos );
93  
94 <    if( atoms[i]->isDirectional() ){
94 >    if( integrableObjects[i]->isDirectional() ){
95  
96 –      dAtom = (DirectionalAtom *)atoms[i];
97 –
96        // get and convert the torque to body frame
97  
98 <      dAtom->getTrq( Tb );
99 <      dAtom->lab2Body( Tb );
98 >      integrableObjects[i]->getTrq( Tb );
99 >      integrableObjects[i]->lab2Body( Tb );
100  
101        // get the angular momentum, and propagate a half step
102  
103 <      dAtom->getJ( ji );
103 >      integrableObjects[i]->getJ( ji );
104  
105        for (j=0; j < 3; j++)
106          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
107  
108 <      this->rotationPropagation( dAtom, ji );
108 >      this->rotationPropagation( integrableObjects[i], ji );
109  
110 <      dAtom->setJ( ji );
110 >      integrableObjects[i]->setJ( ji );
111      }
112    }
113  
114 <  if (nConstrained){
117 <    constrainA();
118 <  }
114 >  consFramework->doConstrainA();
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 +  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
120 +  
121    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
122    integralOfChidt += chi*dt2;
123  
# Line 127 | Line 125 | template<typename T> void NVT<T>::moveB( void ){
125  
126   template<typename T> void NVT<T>::moveB( void ){
127    int i, j, k;
130 –  DirectionalAtom* dAtom;
128    double Tb[3], ji[3];
129    double vel[3], frc[3];
130    double mass;
# Line 138 | Line 135 | template<typename T> void NVT<T>::moveB( void ){
135  
136    oldChi = chi;
137  
138 <  for( i=0; i<nAtoms; i++ ){
138 >  for( i=0; i < integrableObjects.size(); i++ ){
139  
140 <    atoms[i]->getVel( vel );
140 >    integrableObjects[i]->getVel( vel );
141  
142      for (j=0; j < 3; j++)
143        oldVel[3*i + j]  = vel[j];
144  
145 <    if( atoms[i]->isDirectional() ){
149 <
150 <      dAtom = (DirectionalAtom *)atoms[i];
145 >    if( integrableObjects[i]->isDirectional() ){
146  
147 <      dAtom->getJ( ji );
147 >      integrableObjects[i]->getJ( ji );
148  
149        for (j=0; j < 3; j++)
150          oldJi[3*i + j] = ji[j];
# Line 169 | Line 164 | template<typename T> void NVT<T>::moveB( void ){
164      chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
165        (tauThermostat*tauThermostat);
166  
167 <    for( i=0; i<nAtoms; i++ ){
167 >    for( i=0; i < integrableObjects.size(); i++ ){
168  
169 <      atoms[i]->getFrc( frc );
170 <      atoms[i]->getVel(vel);
169 >      integrableObjects[i]->getFrc( frc );
170 >      integrableObjects[i]->getVel(vel);
171  
172 <      mass = atoms[i]->getMass();
172 >      mass = integrableObjects[i]->getMass();
173  
174        // velocity half step
175        for (j=0; j < 3; j++)
176          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
177  
178 <      atoms[i]->setVel( vel );
178 >      integrableObjects[i]->setVel( vel );
179  
180 <      if( atoms[i]->isDirectional() ){
180 >      if( integrableObjects[i]->isDirectional() ){
181  
187 –        dAtom = (DirectionalAtom *)atoms[i];
188 –
182          // get and convert the torque to body frame
183  
184 <        dAtom->getTrq( Tb );
185 <        dAtom->lab2Body( Tb );
184 >        integrableObjects[i]->getTrq( Tb );
185 >        integrableObjects[i]->lab2Body( Tb );
186  
187          for (j=0; j < 3; j++)
188            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
189  
190 <        dAtom->setJ( ji );
190 >        integrableObjects[i]->setJ( ji );
191        }
192      }
193  
194 <    if (nConstrained){
202 <      constrainB();
203 <    }
194 >    consFramework->doConstrainB();
195  
196      if (fabs(prevChi - chi) <= chiTolerance) break;
197    }
# Line 225 | Line 216 | template<typename T> int NVT<T>::readyCheck() {
216  
217    if (!have_target_temp) {
218      sprintf( painCave.errMsg,
219 <             "NVT error: You can't use the NVT integrator without a targetTemp!\n"
219 >             "You can't use the NVT integrator without a targetTemp!\n"
220               );
221      painCave.isFatal = 1;
222 +    painCave.severity = OOPSE_ERROR;
223      simError();
224      return -1;
225    }
# Line 236 | Line 228 | template<typename T> int NVT<T>::readyCheck() {
228  
229    if (!have_tau_thermostat) {
230      sprintf( painCave.errMsg,
231 <             "NVT error: If you use the constant temperature\n"
232 <             "   integrator, you must set tauThermostat.\n");
231 >             "If you use the constant temperature\n"
232 >             "\tintegrator, you must set tauThermostat.\n");
233 >    painCave.severity = OOPSE_ERROR;
234      painCave.isFatal = 1;
235      simError();
236      return -1;
# Line 245 | Line 238 | template<typename T> int NVT<T>::readyCheck() {
238  
239    if (!have_chi_tolerance) {
240      sprintf( painCave.errMsg,
241 <             "NVT warning: setting chi tolerance to 1e-6\n");
241 >             "In NVT integrator: setting chi tolerance to 1e-6\n");
242      chiTolerance = 1e-6;
243      have_chi_tolerance = 1;
244 +    painCave.severity = OOPSE_INFO;
245      painCave.isFatal = 0;
246      simError();
247    }
# Line 264 | Line 258 | template<typename T> double NVT<T>::getConservedQuanti
258    double thermostat_kinetic;
259    double thermostat_potential;
260  
261 <  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
261 >  fkBT = (double)(info->ndf) * kB * targetTemp;
262  
263    Energy = tStats->getTotalE();
264  

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