14 |
|
NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff): |
15 |
|
Integrator( 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 |
|
} |
21 |
|
|
22 |
|
void NVT::moveA() { |
26 |
|
DirectionalAtom* dAtom; |
27 |
|
double Tb[3]; |
28 |
|
double ji[3]; |
29 |
< |
double ke; |
29 |
> |
double instTemp; |
30 |
|
double angle; |
31 |
|
|
32 |
+ |
instTemp = tStats->getTemperature(); |
33 |
|
|
34 |
< |
ke = tStats->getKinetic() * eConvert; |
35 |
< |
zeta += dt2 * ( (2.0 * ke - NkBT) / qmass ); |
34 |
> |
// first evolve chi a half step |
35 |
> |
|
36 |
> |
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
37 |
|
|
38 |
|
for( i=0; i<nAtoms; i++ ){ |
39 |
|
atomIndex = i * 3; |
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]*zeta); |
44 |
> |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi); |
45 |
|
|
46 |
|
// position whole step |
47 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
66 |
|
ji[1] = dAtom->getJy(); |
67 |
|
ji[2] = dAtom->getJz(); |
68 |
|
|
69 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta); |
70 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta); |
71 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta); |
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 |
|
|
73 |
|
// use the angular velocities to propagate the rotation matrix a |
74 |
|
// full time step |
107 |
|
DirectionalAtom* dAtom; |
108 |
|
double Tb[3]; |
109 |
|
double ji[3]; |
110 |
< |
double ke; |
110 |
> |
double instTemp; |
111 |
|
|
112 |
< |
|
113 |
< |
ke = tStats->getKinetic() * eConvert; |
113 |
< |
zeta += dt2 * ( (2.0 * ke - NkBT) / qmass ); |
112 |
> |
instTemp = tStats->getTemperature(); |
113 |
> |
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
114 |
|
|
115 |
|
for( i=0; i<nAtoms; i++ ){ |
116 |
|
atomIndex = i * 3; |
117 |
|
|
118 |
|
// velocity half step |
119 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
120 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta); |
120 |
> |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi); |
121 |
|
|
122 |
|
if( atoms[i]->isDirectional() ){ |
123 |
|
|
138 |
|
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); |
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] ); |
162 |
|
simError(); |
163 |
|
return -1; |
164 |
|
} |
165 |
< |
|
166 |
< |
// Next check to see that we have a reasonable number of degrees of freedom |
167 |
< |
// and then set NkBT if we do have it. Unreasonable numbers of DOFs |
168 |
< |
// are also fatal. |
169 |
< |
|
170 |
< |
if (info->ndf > 0) { |
171 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
172 |
< |
} else { |
165 |
> |
|
166 |
> |
// We must set tauThermostat. |
167 |
> |
|
168 |
> |
if (!have_tau_thermostat) { |
169 |
|
sprintf( painCave.errMsg, |
170 |
< |
"NVT error: We got a silly number of degrees of freedom!\n" |
171 |
< |
); |
170 |
> |
"NVT error: If you use the constant temperature\n" |
171 |
> |
" integrator, you must set tauThermostat.\n"); |
172 |
|
painCave.isFatal = 1; |
173 |
|
simError(); |
174 |
|
return -1; |
175 |
< |
} |
180 |
< |
|
181 |
< |
// We have our choice on setting qmass or tauThermostat. One of them |
182 |
< |
// must be set. |
183 |
< |
|
184 |
< |
if (!have_qmass) { |
185 |
< |
if (have_tau_thermostat) { |
186 |
< |
sprintf( painCave.errMsg, |
187 |
< |
"NVT info: Setting qMass = %lf\n", tauThermostat * NkBT); |
188 |
< |
this->setQmass(tauThermostat * NkBT); |
189 |
< |
painCave.isFatal = 0; |
190 |
< |
simError(); |
191 |
< |
} else { |
192 |
< |
sprintf( painCave.errMsg, |
193 |
< |
"NVT error: If you use the constant temperature\n" |
194 |
< |
" integrator, you must set either tauThermostat or qMass.\n"); |
195 |
< |
painCave.isFatal = 1; |
196 |
< |
simError(); |
197 |
< |
return -1; |
198 |
< |
} |
199 |
< |
} |
200 |
< |
|
175 |
> |
} |
176 |
|
return 1; |
177 |
|
} |
178 |
|
|