| 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 |
|
|
| 139 |
|
// routine derived via viral theorem description in: |
| 140 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 141 |
|
|
| 142 |
< |
return 0.0; |
| 142 |
> |
const double convert = 4.184e-4; |
| 143 |
> |
double mtot; |
| 144 |
> |
double vcom[3]; |
| 145 |
> |
double p_local, p_sum, p_mol, virial; |
| 146 |
> |
double theBox[3]; |
| 147 |
> |
double* tau; |
| 148 |
> |
int i, nMols; |
| 149 |
> |
Molecule* molecules; |
| 150 |
> |
|
| 151 |
> |
nMols = entry_plug->n_mol; |
| 152 |
> |
molecules = entry_plug->molecules; |
| 153 |
> |
tau = entry_plug->tau; |
| 154 |
> |
|
| 155 |
> |
// use velocities of molecular centers of mass and molecular masses: |
| 156 |
> |
p_local = 0.0; |
| 157 |
> |
for (i=0; i < nMols; i++) { |
| 158 |
> |
molecules[i].getCOMvel(mtot, vcom); |
| 159 |
> |
p_local += mtot* (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]); |
| 160 |
> |
} |
| 161 |
> |
|
| 162 |
> |
// Get total for entire system from MPI. |
| 163 |
> |
#ifdef IS_MPI |
| 164 |
> |
MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 165 |
> |
#else |
| 166 |
> |
p_sum = p_local; |
| 167 |
> |
#endif // is_mpi |
| 168 |
> |
|
| 169 |
> |
virial = tau[0] + tau[4] + tau[8]; |
| 170 |
> |
entry_plug->getBox(theBox); |
| 171 |
> |
|
| 172 |
> |
p_mol = (p_sum - virial*convert) / (3.0 * theBox[0] * theBox[1]* theBox[2]); |
| 173 |
> |
|
| 174 |
> |
return p_mol; |
| 175 |
|
} |
| 176 |
|
|
| 177 |
|
void Thermo::velocitize() { |
| 185 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 186 |
|
double av2; |
| 187 |
|
double kebar; |
| 189 |
– |
int ndf, ndf_local; // number of degrees of freedom |
| 190 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 188 |
|
int n_atoms; |
| 189 |
|
Atom** atoms; |
| 190 |
|
DirectionalAtom* dAtom; |
| 198 |
|
n_oriented = entry_plug->n_oriented; |
| 199 |
|
n_constraints = entry_plug->n_constraints; |
| 200 |
|
|
| 201 |
< |
kebar = kb * temperature * (double)this->getNDF() / |
| 202 |
< |
( 2.0 * (double)this->getNDFraw() ); |
| 201 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 202 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 203 |
|
|
| 204 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 205 |
|
|
