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 |
|
|