| 125 |
|
return total; |
| 126 |
|
} |
| 127 |
|
|
| 128 |
< |
double Thermo::getTemperature(){ |
| 129 |
< |
|
| 130 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 131 |
< |
double temperature; |
| 128 |
> |
int Thermo::getNDF(){ |
| 129 |
|
int ndf_local, ndf; |
| 130 |
|
|
| 131 |
|
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 138 |
|
#endif |
| 139 |
|
|
| 140 |
|
ndf = ndf - 3; |
| 141 |
+ |
|
| 142 |
+ |
return ndf; |
| 143 |
+ |
} |
| 144 |
+ |
|
| 145 |
+ |
int Thermo::getNDFraw() { |
| 146 |
+ |
int ndfRaw_local, ndfRaw; |
| 147 |
+ |
|
| 148 |
+ |
// Raw degrees of freedom that we have to set |
| 149 |
+ |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 150 |
|
|
| 151 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
| 151 |
> |
#ifdef IS_MPI |
| 152 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 153 |
> |
#else |
| 154 |
> |
ndfRaw = ndfRaw_local; |
| 155 |
> |
#endif |
| 156 |
> |
|
| 157 |
> |
return ndfRaw; |
| 158 |
> |
} |
| 159 |
> |
|
| 160 |
> |
|
| 161 |
> |
double Thermo::getTemperature(){ |
| 162 |
> |
|
| 163 |
> |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 164 |
> |
double temperature; |
| 165 |
> |
|
| 166 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb ); |
| 167 |
|
return temperature; |
| 168 |
|
} |
| 169 |
|
|
| 201 |
|
n_oriented = entry_plug->n_oriented; |
| 202 |
|
n_constraints = entry_plug->n_constraints; |
| 203 |
|
|
| 204 |
< |
// Raw degrees of freedom that we have to set |
| 205 |
< |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 185 |
< |
|
| 186 |
< |
// Degrees of freedom that can contain kinetic energy |
| 187 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 188 |
< |
- entry_plug->n_constraints; |
| 204 |
> |
kebar = kb * temperature * (double)this->getNDF() / |
| 205 |
> |
( 2.0 * (double)this->getNDFraw() ); |
| 206 |
|
|
| 190 |
– |
#ifdef IS_MPI |
| 191 |
– |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 192 |
– |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 193 |
– |
#else |
| 194 |
– |
ndfRaw = ndfRaw_local; |
| 195 |
– |
ndf = ndf_local; |
| 196 |
– |
#endif |
| 197 |
– |
ndf = ndf - 3; |
| 198 |
– |
|
| 199 |
– |
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
| 200 |
– |
|
| 207 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 208 |
|
|
| 209 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
| 259 |
|
|
| 260 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 261 |
|
jy = vbar * gaussStream->getGaussian(); |
| 262 |
< |
|
| 262 |
> |
|
| 263 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 264 |
|
jz = vbar * gaussStream->getGaussian(); |
| 265 |
|
|
