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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 763 by tim, Mon Sep 15 16:52:02 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 A[3][3], I[3][3];
38 >  double angle, mass;
39 >  double vel[3], pos[3], frc[3];
40 >
41    double instTemp;
30 –  double angle;
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    
36 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
37 –
47    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);
48  
49 <    // position whole step    
50 <    for( j=atomIndex; j<(atomIndex+3); j++ )
49 >    atoms[i]->getVel( vel );
50 >    atoms[i]->getPos( pos );
51 >    atoms[i]->getFrc( frc );
52 >
53 >    mass = atoms[i]->getMass();
54 >
55 >    for (j=0; j < 3; j++) {
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];
60 +    }
61  
62 +    atoms[i]->setVel( vel );
63 +    atoms[i]->setPos( pos );
64    
65      if( atoms[i]->isDirectional() ){
66  
# Line 54 | Line 68 | void NVT::moveA() {
68            
69        // get and convert the torque to body frame
70        
71 <      Tb[0] = dAtom->getTx();
58 <      Tb[1] = dAtom->getTy();
59 <      Tb[2] = dAtom->getTz();
60 <      
71 >      dAtom->getTrq( Tb );
72        dAtom->lab2Body( Tb );
73        
74        // get the angular momentum, and propagate a half step
75  
76 <      ji[0] = dAtom->getJx();
77 <      ji[1] = dAtom->getJy();
78 <      ji[2] = dAtom->getJz();
76 >      dAtom->getJ( ji );
77 >
78 >      for (j=0; j < 3; j++)
79 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
80        
69 –      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);
72 –      
81        // use the angular velocities to propagate the rotation matrix a
82        // full time step
83 <      
83 >
84 >      dAtom->getA(A);
85 >      dAtom->getI(I);
86 >    
87        // rotate about the x-axis      
88 <      angle = dt2 * ji[0] / dAtom->getIxx();
89 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
90 <      
88 >      angle = dt2 * ji[0] / I[0][0];
89 >      this->rotate( 1, 2, angle, ji, A );
90 >
91        // rotate about the y-axis
92 <      angle = dt2 * ji[1] / dAtom->getIyy();
93 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
92 >      angle = dt2 * ji[1] / I[1][1];
93 >      this->rotate( 2, 0, angle, ji, A );
94        
95        // rotate about the z-axis
96 <      angle = dt * ji[2] / dAtom->getIzz();
97 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
96 >      angle = dt * ji[2] / I[2][2];
97 >      this->rotate( 0, 1, angle, ji, A);
98        
99        // rotate about the y-axis
100 <      angle = dt2 * ji[1] / dAtom->getIyy();
101 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
100 >      angle = dt2 * ji[1] / I[1][1];
101 >      this->rotate( 2, 0, angle, ji, A );
102        
103         // rotate about the x-axis
104 <      angle = dt2 * ji[0] / dAtom->getIxx();
105 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
104 >      angle = dt2 * ji[0] / I[0][0];
105 >      this->rotate( 1, 2, angle, ji, A );
106        
107 <      dAtom->setJx( ji[0] );
108 <      dAtom->setJy( ji[1] );
109 <      dAtom->setJz( ji[2] );
99 <    }
100 <    
107 >      dAtom->setJ( ji );
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 < void NVT::moveB( void ){
121 <  int i,j,k;
106 <  int atomIndex;
120 > template<typename T> void NVT<T>::moveB( void ){
121 >  int i, j, k;
122    DirectionalAtom* dAtom;
123 <  double Tb[3];
124 <  double ji[3];
123 >  double Tb[3], ji[3];
124 >  double vel[3], frc[3];
125 >  double mass;
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 <    atomIndex = i * 3;
135 <    
136 <    // velocity half step
137 <    for( j=atomIndex; j<(atomIndex+3); j++ )
138 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
139 <    
134 >
135 >    atoms[i]->getVel( vel );
136 >
137 >    for (j=0; j < 3; j++)
138 >      oldVel[3*i + j]  = vel[j];
139 >
140      if( atoms[i]->isDirectional() ){
141 <      
141 >
142        dAtom = (DirectionalAtom *)atoms[i];
143 +
144 +      dAtom->getJ( ji );
145 +
146 +      for (j=0; j < 3; j++)
147 +        oldJi[3*i + j] = ji[j];
148 +
149 +    }
150 +  }
151 +
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 <      // get and convert the torque to body frame
169 >      mass = atoms[i]->getMass();
170        
171 <      Tb[0] = dAtom->getTx();
172 <      Tb[1] = dAtom->getTy();
173 <      Tb[2] = dAtom->getTz();
171 >      // velocity half step
172 >      for (j=0; j < 3; j++)
173 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
174        
175 <      dAtom->lab2Body( Tb );
175 >      atoms[i]->setVel( vel );
176        
177 <      // get the angular momentum, and complete the angular momentum
178 <      // half step
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 <      ji[0] = dAtom->getJx();
190 <      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] );
189 >        dAtom->setJ( ji );
190 >      }
191      }
192 +
193 +    if (fabs(prevChi - chi) <= chiTolerance) break;
194    }
195 +  
196 +  integralOfChidt += dt2*chi;
197   }
198  
199 < int NVT::readyCheck() {
200 <
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() {
206 >
207 >  //check parent's readyCheck() first
208 >  if (T::readyCheck() == -1)
209 >    return -1;
210 >  
211    // First check to see if we have a target temperature.
212    // Not having one is fatal.
213    
# Line 173 | Line 230 | int NVT::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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