| 129 |
|
|
| 130 |
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 131 |
|
double temperature; |
| 132 |
– |
int ndf_local, ndf; |
| 132 |
|
|
| 133 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 135 |
< |
- entry_plug->n_constraints; |
| 136 |
< |
|
| 137 |
< |
#ifdef IS_MPI |
| 138 |
< |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 139 |
< |
#else |
| 140 |
< |
ndf = ndf_local; |
| 141 |
< |
#endif |
| 142 |
< |
|
| 143 |
< |
ndf = ndf - 3; |
| 144 |
< |
|
| 145 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
| 133 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
| 134 |
|
return temperature; |
| 135 |
|
} |
| 136 |
|
|
| 153 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 154 |
|
double av2; |
| 155 |
|
double kebar; |
| 168 |
– |
int ndf, ndf_local; // number of degrees of freedom |
| 169 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 156 |
|
int n_atoms; |
| 157 |
|
Atom** atoms; |
| 158 |
|
DirectionalAtom* dAtom; |
| 166 |
|
n_oriented = entry_plug->n_oriented; |
| 167 |
|
n_constraints = entry_plug->n_constraints; |
| 168 |
|
|
| 169 |
< |
// Raw degrees of freedom that we have to set |
| 170 |
< |
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; |
| 169 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 170 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 171 |
|
|
| 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 |
– |
|
| 172 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 173 |
|
|
| 174 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
| 224 |
|
|
| 225 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 226 |
|
jy = vbar * gaussStream->getGaussian(); |
| 227 |
< |
|
| 227 |
> |
|
| 228 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 229 |
|
jz = vbar * gaussStream->getGaussian(); |
| 230 |
|
|
