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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 768 by mmeineke, Wed Sep 17 14:22:15 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 <  zeta = 0.0;
17 >  chi = 0.0;
18    have_tau_thermostat = 0;
19    have_target_temp = 0;
20 <  have_qmass = 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;
26 <  int atomIndex, aMatIndex;
34 >  int i, j;
35    DirectionalAtom* dAtom;
36 <  double Tb[3];
37 <  double ji[3];
38 <  double ke;
39 <  double angle;
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;
42  
43 <  ke = tStats->getKinetic() * eConvert;
35 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
43 >  // We need the temperature at time = t for the chi update below:
44  
45 +  instTemp = tStats->getTemperature();
46 +  
47    for( i=0; i<nAtoms; i++ ){
38 –    atomIndex = i * 3;
39 –    aMatIndex = i * 9;
40 –    
41 –    // velocity half step
42 –    for( j=atomIndex; j<(atomIndex+3); j++ )
43 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
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 53 | Line 68 | void NVT::moveA() {
68            
69        // get and convert the torque to body frame
70        
71 <      Tb[0] = dAtom->getTx();
57 <      Tb[1] = dAtom->getTy();
58 <      Tb[2] = dAtom->getTz();
59 <      
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        
68 –      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
69 –      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
70 –      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
71 –      
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] );
98 <    }
99 <    
107 >      dAtom->setJ( ji );
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 < void NVT::moveB( void ){
125 <  int i,j,k;
105 <  int atomIndex;
124 > template<typename T> void NVT<T>::moveB( void ){
125 >  int i, j, k;
126    DirectionalAtom* dAtom;
127 <  double Tb[3];
128 <  double ji[3];
129 <  double ke;
130 <  
127 >  double Tb[3], ji[3];
128 >  double vel[3], frc[3];
129 >  double mass;
130 >  double instTemp;
131 >  double oldChi, prevChi;
132  
133 <  ke = tStats->getKinetic() * eConvert;
134 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
135 <  
133 >  // Set things up for the iteration:
134 >
135 >  oldChi = chi;
136 >
137    for( i=0; i<nAtoms; i++ ){
138 <    atomIndex = i * 3;
139 <    
140 <    // velocity half step
141 <    for( j=atomIndex; j<(atomIndex+3); j++ )
142 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
143 <    
138 >
139 >    atoms[i]->getVel( vel );
140 >
141 >    for (j=0; j < 3; j++)
142 >      oldVel[3*i + j]  = vel[j];
143 >
144      if( atoms[i]->isDirectional() ){
145 <      
145 >
146        dAtom = (DirectionalAtom *)atoms[i];
147 +
148 +      dAtom->getJ( ji );
149 +
150 +      for (j=0; j < 3; j++)
151 +        oldJi[3*i + j] = ji[j];
152 +
153 +    }
154 +  }
155 +
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 <      // get and convert the torque to body frame
173 >      mass = atoms[i]->getMass();
174        
175 <      Tb[0] = dAtom->getTx();
176 <      Tb[1] = dAtom->getTy();
177 <      Tb[2] = dAtom->getTz();
175 >      // velocity half step
176 >      for (j=0; j < 3; j++)
177 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
178        
179 <      dAtom->lab2Body( Tb );
179 >      atoms[i]->setVel( vel );
180        
181 <      // get the angular momentum, and complete the angular momentum
182 <      // half step
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 <      ji[0] = dAtom->getJx();
194 <      ji[1] = dAtom->getJy();
139 <      ji[2] = dAtom->getJz();
140 <      
141 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
143 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
144 <      
145 <      dAtom->setJx( ji[0] );
146 <      dAtom->setJy( ji[1] );
147 <      dAtom->setJz( ji[2] );
193 >        dAtom->setJ( ji );
194 >      }
195      }
196 +
197 +    if (nConstrained){
198 +      constrainB();
199 +    }
200 +
201 +    if (fabs(prevChi - chi) <= chiTolerance) break;
202    }
203 +  
204 +  integralOfChidt += dt2*chi;
205   }
206  
207 < int NVT::readyCheck() {
208 <
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 >
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 162 | Line 227 | int NVT::readyCheck() {
227      simError();
228      return -1;
229    }
230 <    
231 <  // Next check to see that we have a reasonable number of degrees of freedom
232 <  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
233 <  // are also fatal.
169 <
170 <  if (info->ndf > 0) {
171 <    NkBT = (double)info->ndf * kB * targetTemp;
172 <  } else {
230 >  
231 >  // We must set tauThermostat.
232 >  
233 >  if (!have_tau_thermostat) {
234      sprintf( painCave.errMsg,
235 <             "NVT error: We got a silly number of degrees of freedom!\n"
236 <             );
235 >             "NVT error: If you use the constant temperature\n"
236 >             "   integrator, you must set tauThermostat.\n");
237      painCave.isFatal = 1;
238      simError();
239      return -1;
240 <  }
180 <    
181 <  // We have our choice on setting qmass or tauThermostat.  One of them
182 <  // must be set.
240 >  }    
241  
242 <  if (!have_qmass) {
243 <    if (have_tau_thermostat) {
244 <      sprintf( painCave.errMsg,
245 <               "NVT info: Setting qMass = %lf\n", tauThermostat * NkBT);
246 <      this->setQmass(tauThermostat * NkBT);      
247 <      painCave.isFatal = 0;
248 <      simError();
249 <    } else {
250 <      sprintf( painCave.errMsg,
251 <               "NVT error: If you use the constant temperature\n"
252 <               "   integrator, you must set either tauThermostat or qMass.\n");
195 <      painCave.isFatal = 1;
196 <      simError();
197 <      return -1;
198 <    }
199 <  }
200 <  
201 <  return 1;
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 E_NVT;
259 +
260 +  //HNVE
261 +  conservedQuantity = tStats->getTotalE();
262 +  //HNVE
263 +  
264 +  E_NVT =  (info->getNDF() * kB * targetTemp *
265 +                (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert;
266 +
267 +  conservedQuantity += E_NVT;
268 +
269 +  //cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl;
270 +
271 +  return conservedQuantity;
272 + }

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