125 |
|
return total; |
126 |
|
} |
127 |
|
|
128 |
– |
int Thermo::getNDF(){ |
129 |
– |
int ndf_local, ndf; |
130 |
– |
|
131 |
– |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
132 |
– |
- entry_plug->n_constraints; |
133 |
– |
|
134 |
– |
#ifdef IS_MPI |
135 |
– |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
136 |
– |
#else |
137 |
– |
ndf = ndf_local; |
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 |
– |
#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 |
– |
|
128 |
|
double Thermo::getTemperature(){ |
129 |
|
|
130 |
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
131 |
|
double temperature; |
132 |
|
|
133 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * 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; |
189 |
– |
int ndf, ndf_local; // number of degrees of freedom |
190 |
– |
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 |
< |
kebar = kb * temperature * (double)this->getNDF() / |
170 |
< |
( 2.0 * (double)this->getNDFraw() ); |
169 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
170 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
171 |
|
|
172 |
|
for(vr = 0; vr < n_atoms; vr++){ |
173 |
|
|