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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 6 | Line 6
6   #include "Thermo.hpp"
7   #include "ReadWrite.hpp"
8   #include "Integrator.hpp"
9 < #include "NVT.hpp"
10 <
9 > #include "simError.h"
10 >
11 >
12   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
13  
14 < NVT::NVT() {
15 <  zeta = 0.0;
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_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;
23 <  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 <  ke = tStats->getKinetic() * eConvert;
29 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
41 >  double instTemp;
42  
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++ ){
32 –    atomIndex = i * 3;
33 –    aMatIndex = i * 9;
34 –    
35 –    // velocity half step
36 –    for( j=atomIndex; j<(atomIndex+3); j++ )
37 –      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 47 | Line 68 | void NVT::moveA() {
68            
69        // get and convert the torque to body frame
70        
71 <      Tb[0] = dAtom->getTx();
51 <      Tb[1] = dAtom->getTy();
52 <      Tb[2] = dAtom->getTz();
53 <      
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        
62 –      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
63 –      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
64 –      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
65 –      
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] );
92 <    }
93 <    
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 Integrator::moveB( void ){
121 <  int i,j,k;
99 <  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 >  double oldChi, prevChi;
128  
129 <  ke = tStats->getKinetic() * eConvert;
130 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
131 <  
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]*zeta);
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();
131 <      ji[2] = dAtom->getJz();
132 <      
133 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
134 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
135 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
136 <      
137 <      jx2 = ji[0] * ji[0];
138 <      jy2 = ji[1] * ji[1];
139 <      jz2 = ji[2] * ji[2];
140 <      
141 <      dAtom->setJx( ji[0] );
142 <      dAtom->setJy( ji[1] );
143 <      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 <  double NkBT;
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 159 | Line 219 | int NVT::readyCheck() {
219      simError();
220      return -1;
221    }
222 <    
223 <  // Next check to see that we have a reasonable number of degrees of freedom
224 <  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
225 <  // are also fatal.
166 <
167 <  if (entry_plug->ndf > 0) {
168 <    NkBT = (double)entry_plug->ndf * kB * targetTemp;
169 <  } else {
222 >  
223 >  // We must set tauThermostat.
224 >  
225 >  if (!have_tau_thermostat) {
226      sprintf( painCave.errMsg,
227 <             "NVT error: We got a silly number of degrees of freedom!\n"
228 <             );
227 >             "NVT error: If you use the constant temperature\n"
228 >             "   integrator, you must set tauThermostat.\n");
229      painCave.isFatal = 1;
230      simError();
231      return -1;
232 <  }
177 <    
178 <  // We have our choice on setting qmass or tauThermostat.  One of them
179 <  // must be set.
232 >  }    
233  
234 <  if (!have_qmass) {
235 <    if (have_tau_thermostat) {
236 <      sprintf( painCave.errMsg,
237 <               "NVT info: Setting qMass = %d\n", tauThermostat * NkBT);
238 <      this->setQmass(tauThermostat * NkBT);      
239 <      painCave.isFatal = 0;
240 <      simError();
241 <    } else {
242 <      sprintf( painCave.errMsg,
243 <               "NVT error: If you use the constant temperature\n"
244 <               "   integrator, you must set either tauThermostat or qMass.\n");
192 <      painCave.isFatal = 1;
193 <      simError();
194 <      return -1;
195 <    }
196 <  }
197 <  
198 <  return 1;
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 < #endif
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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