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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 565 by gezelter, Tue Jun 24 22:51:57 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

# Line 11 | Line 11 | NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
11  
12   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
13  
14 < NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 <  Integrator( theInfo, the_ff )
14 > template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 >  T( theInfo, the_ff )
16   {
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 < void NVT::moveA() {
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,k;
25 <  int atomIndex, aMatIndex;
34 >  int i, j;
35    DirectionalAtom* dAtom;
36 <  double Tb[3];
37 <  double ji[3];
36 >  double Tb[3], ji[3];
37 >  double mass;
38 >  double vel[3], pos[3], frc[3];
39 >
40    double instTemp;
30 –  double angle;
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    
36 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
37 –
46    for( i=0; i<nAtoms; i++ ){
39 –    atomIndex = i * 3;
40 –    aMatIndex = i * 9;
41 –    
42 –    // velocity half step
43 –    for( j=atomIndex; j<(atomIndex+3); j++ )
44 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
47  
48 <    // position whole step    
49 <    for( j=atomIndex; j<(atomIndex+3); j++ )
48 >    atoms[i]->getVel( vel );
49 >    atoms[i]->getPos( pos );
50 >    atoms[i]->getFrc( frc );
51 >
52 >    mass = atoms[i]->getMass();
53 >
54 >    for (j=0; j < 3; j++) {
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];
59 +    }
60  
61 +    atoms[i]->setVel( vel );
62 +    atoms[i]->setPos( pos );
63    
64      if( atoms[i]->isDirectional() ){
65  
# Line 54 | Line 67 | void NVT::moveA() {
67            
68        // get and convert the torque to body frame
69        
70 <      Tb[0] = dAtom->getTx();
58 <      Tb[1] = dAtom->getTy();
59 <      Tb[2] = dAtom->getTz();
60 <      
70 >      dAtom->getTrq( Tb );
71        dAtom->lab2Body( Tb );
72        
73        // get the angular momentum, and propagate a half step
74  
75 <      ji[0] = dAtom->getJx();
76 <      ji[1] = dAtom->getJy();
77 <      ji[2] = dAtom->getJz();
75 >      dAtom->getJ( ji );
76 >
77 >      for (j=0; j < 3; j++)
78 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
79        
80 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
70 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
71 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
80 >      this->rotationPropagation( dAtom, ji );
81        
82 <      // use the angular velocities to propagate the rotation matrix a
83 <      // full time step
75 <      
76 <      // rotate about the x-axis      
77 <      angle = dt2 * ji[0] / dAtom->getIxx();
78 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
79 <      
80 <      // rotate about the y-axis
81 <      angle = dt2 * ji[1] / dAtom->getIyy();
82 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
83 <      
84 <      // rotate about the z-axis
85 <      angle = dt * ji[2] / dAtom->getIzz();
86 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
87 <      
88 <      // rotate about the y-axis
89 <      angle = dt2 * ji[1] / dAtom->getIyy();
90 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
91 <      
92 <       // rotate about the x-axis
93 <      angle = dt2 * ji[0] / dAtom->getIxx();
94 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
95 <      
96 <      dAtom->setJx( ji[0] );
97 <      dAtom->setJy( ji[1] );
98 <      dAtom->setJz( ji[2] );
99 <    }
100 <    
82 >      dAtom->setJ( ji );
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 < void NVT::moveB( void ){
99 <  int i,j,k;
106 <  int atomIndex;
98 > template<typename T> void NVT<T>::moveB( void ){
99 >  int i, j, k;
100    DirectionalAtom* dAtom;
101 <  double Tb[3];
102 <  double ji[3];
101 >  double Tb[3], ji[3];
102 >  double vel[3], frc[3];
103 >  double mass;
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 <    atomIndex = i * 3;
113 <    
114 <    // velocity half step
115 <    for( j=atomIndex; j<(atomIndex+3); j++ )
116 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
117 <    
112 >
113 >    atoms[i]->getVel( vel );
114 >
115 >    for (j=0; j < 3; j++)
116 >      oldVel[3*i + j]  = vel[j];
117 >
118      if( atoms[i]->isDirectional() ){
119 <      
119 >
120        dAtom = (DirectionalAtom *)atoms[i];
121 +
122 +      dAtom->getJ( ji );
123 +
124 +      for (j=0; j < 3; j++)
125 +        oldJi[3*i + j] = ji[j];
126 +
127 +    }
128 +  }
129 +
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 <      // get and convert the torque to body frame
147 >      mass = atoms[i]->getMass();
148        
149 <      Tb[0] = dAtom->getTx();
150 <      Tb[1] = dAtom->getTy();
151 <      Tb[2] = dAtom->getTz();
149 >      // velocity half step
150 >      for (j=0; j < 3; j++)
151 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
152        
153 <      dAtom->lab2Body( Tb );
153 >      atoms[i]->setVel( vel );
154        
155 <      // get the angular momentum, and complete the angular momentum
156 <      // half step
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 <      ji[0] = dAtom->getJx();
168 <      ji[1] = dAtom->getJy();
139 <      ji[2] = dAtom->getJz();
140 <      
141 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
143 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
144 <      
145 <      dAtom->setJx( ji[0] );
146 <      dAtom->setJy( ji[1] );
147 <      dAtom->setJz( ji[2] );
167 >        dAtom->setJ( ji );
168 >      }
169      }
170 +
171 +    if (nConstrained){
172 +      constrainB();
173 +    }
174 +
175 +    if (fabs(prevChi - chi) <= chiTolerance) break;
176    }
177 +  
178 +  integralOfChidt += dt2*chi;
179   }
180  
181 < int NVT::readyCheck() {
182 <
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 >
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 | int NVT::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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