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 |
|
|