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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 778 by mmeineke, Fri Sep 19 20:00:27 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;
35    DirectionalAtom* dAtom;
36    double Tb[3], ji[3];
37 <  double A[3][3], I[3][3];
28 <  double angle, mass;
37 >  double mass;
38    double vel[3], pos[3], frc[3];
39  
40    double instTemp;
41  
42 <  instTemp = tStats->getTemperature();
42 >  // We need the temperature at time = t for the chi update below:
43  
44 <  // first evolve chi a half step
44 >  instTemp = tStats->getTemperature();
45    
37 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 –
46    for( i=0; i<nAtoms; i++ ){
47  
48      atoms[i]->getVel( vel );
# Line 45 | Line 52 | template<typename T> void NVT<T>::moveA() {
52      mass = atoms[i]->getMass();
53  
54      for (j=0; j < 3; j++) {
55 <      // velocity half step
55 >      // velocity half step  (use chi from previous step here):
56        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
57        // position whole step
58        pos[j] += dt * vel[j];
# Line 70 | Line 77 | template<typename T> void NVT<T>::moveA() {
77        for (j=0; j < 3; j++)
78          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
79        
80 <      // use the angular velocities to propagate the rotation matrix a
74 <      // full time step
75 <
76 <      dAtom->getA(A);
77 <      dAtom->getI(I);
78 <    
79 <      // rotate about the x-axis      
80 <      angle = dt2 * ji[0] / I[0][0];
81 <      this->rotate( 1, 2, angle, ji, A );
82 <
83 <      // rotate about the y-axis
84 <      angle = dt2 * ji[1] / I[1][1];
85 <      this->rotate( 2, 0, angle, ji, A );
80 >      this->rotationPropagation( dAtom, ji );
81        
87 –      // rotate about the z-axis
88 –      angle = dt * ji[2] / I[2][2];
89 –      this->rotate( 0, 1, angle, ji, A);
90 –      
91 –      // rotate about the y-axis
92 –      angle = dt2 * ji[1] / I[1][1];
93 –      this->rotate( 2, 0, angle, ji, A );
94 –      
95 –       // rotate about the x-axis
96 –      angle = dt2 * ji[0] / I[0][0];
97 –      this->rotate( 1, 2, angle, ji, A );
98 –      
82        dAtom->setJ( ji );
100 –      dAtom->setA( A  );    
83      }    
84    }
85 +  
86 +  if (nConstrained){
87 +    constrainA();
88 +  }
89 +
90 +  // Finally, evolve chi a half step (just like a velocity) using
91 +  // temperature at time t, not time t+dt/2
92 +
93 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
94 +  integralOfChidt += chi*dt2;
95 +
96   }
97  
98   template<typename T> void NVT<T>::moveB( void ){
99 <  int i, j;
99 >  int i, j, k;
100    DirectionalAtom* dAtom;
101    double Tb[3], ji[3];
102    double vel[3], frc[3];
103    double mass;
111 –
104    double instTemp;
105 <  
106 <  instTemp = tStats->getTemperature();
107 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
108 <  
105 >  double oldChi, prevChi;
106 >
107 >  // Set things up for the iteration:
108 >
109 >  oldChi = chi;
110 >
111    for( i=0; i<nAtoms; i++ ){
112  
113      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
114  
115 <    mass = atoms[i]->getMass();
115 >    for (j=0; j < 3; j++)
116 >      oldVel[3*i + j]  = vel[j];
117  
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 –
118      if( atoms[i]->isDirectional() ){
119  
120        dAtom = (DirectionalAtom *)atoms[i];
121  
122 <      // get and convert the torque to body frame      
122 >      dAtom->getJ( ji );
123  
124 <      dAtom->getTrq( Tb );
125 <      dAtom->lab2Body( Tb );
124 >      for (j=0; j < 3; j++)
125 >        oldJi[3*i + j] = ji[j];
126  
127 <      // get the angular momentum, and propagate a half step
127 >    }
128 >  }
129  
130 <      dAtom->getJ( ji );
130 >  // do the iteration:
131  
132 +  for (k=0; k < 4; k++) {
133 +    
134 +    instTemp = tStats->getTemperature();
135 +
136 +    // evolve chi another half step using the temperature at t + dt/2
137 +
138 +    prevChi = chi;
139 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
140 +      (tauThermostat*tauThermostat);
141 +  
142 +    for( i=0; i<nAtoms; i++ ){
143 +
144 +      atoms[i]->getFrc( frc );
145 +      atoms[i]->getVel(vel);
146 +      
147 +      mass = atoms[i]->getMass();
148 +      
149 +      // velocity half step
150        for (j=0; j < 3; j++)
151 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
151 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
152        
153 +      atoms[i]->setVel( vel );
154 +      
155 +      if( atoms[i]->isDirectional() ){
156 +        
157 +        dAtom = (DirectionalAtom *)atoms[i];
158 +        
159 +        // get and convert the torque to body frame      
160 +        
161 +        dAtom->getTrq( Tb );
162 +        dAtom->lab2Body( Tb );      
163 +            
164 +        for (j=0; j < 3; j++)
165 +          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
166 +      
167 +        dAtom->setJ( ji );
168 +      }
169 +    }
170  
171 <      dAtom->setJ( ji );
171 >    if (nConstrained){
172 >      constrainB();
173      }
174 +
175 +    if (fabs(prevChi - chi) <= chiTolerance) break;
176    }
177 +  
178 +  integralOfChidt += dt2*chi;
179   }
180  
181 + template<typename T> void NVT<T>::resetIntegrator( void ){
182 +  
183 +  chi = 0.0;
184 +  integralOfChidt = 0.0;
185 + }
186 +
187   template<typename T> int NVT<T>::readyCheck() {
188 <
188 >
189 >  //check parent's readyCheck() first
190 >  if (T::readyCheck() == -1)
191 >    return -1;
192 >  
193    // First check to see if we have a target temperature.
194    // Not having one is fatal.
195    
# Line 173 | Line 212 | template<typename T> int NVT<T>::readyCheck() {
212      simError();
213      return -1;
214    }    
215 <  return 1;
215 >
216 >  if (!have_chi_tolerance) {
217 >    sprintf( painCave.errMsg,
218 >             "NVT warning: setting chi tolerance to 1e-6\n");
219 >    chiTolerance = 1e-6;
220 >    have_chi_tolerance = 1;
221 >    painCave.isFatal = 0;
222 >    simError();
223 >  }    
224 >
225 >  return 1;    
226 >
227   }
228 +
229 + template<typename T> double NVT<T>::getConservedQuantity(void){
230 +
231 +  double conservedQuantity;
232 +  double fkBT;
233 +  double Energy;
234 +  double thermostat_kinetic;
235 +  double thermostat_potential;
236 +
237 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
238 +
239 +  Energy = tStats->getTotalE();
240 +
241 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
242 +    (2.0 * eConvert);
243 +
244 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
245 +
246 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
247 +  
248 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
249 +      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
250 +
251 +  return conservedQuantity;
252 + }

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