| 152 |
|
double vx, vy, vz; |
| 153 |
|
double jx, jy, jz; |
| 154 |
|
int i, vr, vd; // velocity randomizer loop counters |
| 155 |
< |
double *vdrift; |
| 155 |
> |
double vdrift[3]; |
| 156 |
|
double vbar; |
| 157 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 158 |
|
double av2; |
| 159 |
|
double kebar; |
| 160 |
< |
int ndf; // number of degrees of freedom |
| 161 |
< |
int ndfRaw; // the raw number of degrees of freedom |
| 160 |
> |
int ndf, ndf_local; // number of degrees of freedom |
| 161 |
> |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 162 |
|
int n_atoms; |
| 163 |
|
Atom** atoms; |
| 164 |
|
DirectionalAtom* dAtom; |
| 172 |
|
n_oriented = entry_plug->n_oriented; |
| 173 |
|
n_constraints = entry_plug->n_constraints; |
| 174 |
|
|
| 175 |
+ |
// Raw degrees of freedom that we have to set |
| 176 |
+ |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 177 |
|
|
| 178 |
< |
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
| 179 |
< |
ndf = ndfRaw - n_constraints - 3; |
| 178 |
> |
// Degrees of freedom that can contain kinetic energy |
| 179 |
> |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 180 |
> |
- entry_plug->n_constraints; |
| 181 |
> |
|
| 182 |
> |
#ifdef IS_MPI |
| 183 |
> |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
| 184 |
> |
MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); |
| 185 |
> |
#else |
| 186 |
> |
ndfRaw = ndfRaw_local; |
| 187 |
> |
ndf = ndf_local; |
| 188 |
> |
#endif |
| 189 |
> |
ndf = ndf - 3; |
| 190 |
> |
|
| 191 |
|
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
| 192 |
|
|
| 193 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 213 |
|
|
| 214 |
|
// Get the Center of Mass drift velocity. |
| 215 |
|
|
| 216 |
< |
vdrift = getCOMVel(); |
| 216 |
> |
getCOMVel(vdrift); |
| 217 |
|
|
| 218 |
|
// Corrects for the center of mass drift. |
| 219 |
|
// sums all the momentum and divides by total mass. |
| 257 |
|
} |
| 258 |
|
} |
| 259 |
|
|
| 260 |
< |
double* Thermo::getCOMVel(){ |
| 260 |
> |
void Thermo::getCOMVel(double vdrift[3]){ |
| 261 |
|
|
| 262 |
|
double mtot, mtot_local; |
| 250 |
– |
double* vdrift; |
| 263 |
|
double vdrift_local[3]; |
| 264 |
|
int vd, n_atoms; |
| 265 |
|
Atom** atoms; |
| 266 |
|
|
| 255 |
– |
vdrift = new double[3]; |
| 267 |
|
// We are very careless here with the distinction between n_atoms and n_local |
| 268 |
|
// We should really fix this before someone pokes an eye out. |
| 269 |
|
|
| 286 |
|
|
| 287 |
|
#ifdef IS_MPI |
| 288 |
|
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
| 289 |
< |
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 289 |
> |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 290 |
|
#else |
| 291 |
|
mtot = mtot_local; |
| 292 |
|
for(vd = 0; vd < 3; vd++) { |
| 298 |
|
vdrift[vd] = vdrift[vd] / mtot; |
| 299 |
|
} |
| 300 |
|
|
| 290 |
– |
return vdrift; |
| 301 |
|
} |
| 302 |
|
|
