| 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 |
| 134 |
< |
- entry_plug->n_constraints; |
| 133 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
| 134 |
> |
return temperature; |
| 135 |
> |
} |
| 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 |
| 137 |
> |
double Thermo::getEnthalpy() { |
| 138 |
|
|
| 139 |
< |
ndf = ndf - 3; |
| 139 |
> |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 140 |
> |
double u, p, v; |
| 141 |
> |
double press[9]; |
| 142 |
> |
|
| 143 |
> |
u = this->getTotalE(); |
| 144 |
> |
|
| 145 |
> |
this->getPressureTensor(press); |
| 146 |
> |
p = (press[0] + press[4] + press[8]) / 3.0; |
| 147 |
> |
|
| 148 |
> |
v = this->getVolume(); |
| 149 |
> |
|
| 150 |
> |
return (u + (p*v)/e_convert); |
| 151 |
> |
} |
| 152 |
> |
|
| 153 |
> |
double Thermo::getVolume() { |
| 154 |
> |
|
| 155 |
> |
double volume; |
| 156 |
> |
double Hmat[9]; |
| 157 |
> |
|
| 158 |
> |
entry_plug->getBoxM(Hmat); |
| 159 |
> |
|
| 160 |
> |
// volume = h1 (dot) h2 (cross) h3 |
| 161 |
> |
|
| 162 |
> |
volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
| 163 |
> |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
| 164 |
> |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
| 165 |
> |
|
| 166 |
> |
return volume; |
| 167 |
> |
} |
| 168 |
> |
|
| 169 |
> |
double Thermo::getPressure() { |
| 170 |
> |
|
| 171 |
> |
// Relies on the calculation of the full molecular pressure tensor |
| 172 |
|
|
| 173 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
| 174 |
< |
return temperature; |
| 173 |
> |
const double p_convert = 1.63882576e8; |
| 174 |
> |
double press[9]; |
| 175 |
> |
double pressure; |
| 176 |
> |
|
| 177 |
> |
this->getPressureTensor(press); |
| 178 |
> |
|
| 179 |
> |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
| 180 |
> |
|
| 181 |
> |
return pressure; |
| 182 |
|
} |
| 183 |
|
|
| 184 |
< |
double Thermo::getPressure(){ |
| 185 |
< |
// returns pressure in units amu*fs^-2*Ang^-1 |
| 184 |
> |
|
| 185 |
> |
void Thermo::getPressureTensor(double press[9]){ |
| 186 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 187 |
|
// routine derived via viral theorem description in: |
| 188 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 189 |
|
|
| 190 |
< |
return 0.0; |
| 190 |
> |
const double e_convert = 4.184e-4; |
| 191 |
> |
|
| 192 |
> |
double molmass, volume; |
| 193 |
> |
double vcom[3]; |
| 194 |
> |
double p_local[9], p_global[9]; |
| 195 |
> |
double theBox[3]; |
| 196 |
> |
//double* tau; |
| 197 |
> |
int i, nMols; |
| 198 |
> |
Molecule* molecules; |
| 199 |
> |
|
| 200 |
> |
nMols = entry_plug->n_mol; |
| 201 |
> |
molecules = entry_plug->molecules; |
| 202 |
> |
//tau = entry_plug->tau; |
| 203 |
> |
|
| 204 |
> |
// use velocities of molecular centers of mass and molecular masses: |
| 205 |
> |
for (i=0; i < 9; i++) { |
| 206 |
> |
p_local[i] = 0.0; |
| 207 |
> |
p_global[i] = 0.0; |
| 208 |
> |
} |
| 209 |
> |
|
| 210 |
> |
for (i=0; i < nMols; i++) { |
| 211 |
> |
molmass = molecules[i].getCOMvel(vcom); |
| 212 |
> |
|
| 213 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
| 214 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 215 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
| 216 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
| 217 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 218 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
| 219 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 220 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 221 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 222 |
> |
} |
| 223 |
> |
|
| 224 |
> |
// Get total for entire system from MPI. |
| 225 |
> |
|
| 226 |
> |
#ifdef IS_MPI |
| 227 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 228 |
> |
#else |
| 229 |
> |
for (i=0; i<9; i++) { |
| 230 |
> |
p_global[i] = p_local[i]; |
| 231 |
> |
} |
| 232 |
> |
#endif // is_mpi |
| 233 |
> |
|
| 234 |
> |
volume = entry_plug->boxVol; |
| 235 |
> |
|
| 236 |
> |
for(i=0; i<9; i++) { |
| 237 |
> |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
| 238 |
> |
} |
| 239 |
|
} |
| 240 |
|
|
| 241 |
|
void Thermo::velocitize() { |
| 249 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 250 |
|
double av2; |
| 251 |
|
double kebar; |
| 168 |
– |
int ndf, ndf_local; // number of degrees of freedom |
| 169 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 252 |
|
int n_atoms; |
| 253 |
|
Atom** atoms; |
| 254 |
|
DirectionalAtom* dAtom; |
| 262 |
|
n_oriented = entry_plug->n_oriented; |
| 263 |
|
n_constraints = entry_plug->n_constraints; |
| 264 |
|
|
| 265 |
< |
// Raw degrees of freedom that we have to set |
| 266 |
< |
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; |
| 265 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 266 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 267 |
|
|
| 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 |
– |
|
| 268 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 269 |
|
|
| 270 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
| 320 |
|
|
| 321 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 322 |
|
jy = vbar * gaussStream->getGaussian(); |
| 323 |
< |
|
| 323 |
> |
|
| 324 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 325 |
|
jz = vbar * gaussStream->getGaussian(); |
| 326 |
|
|
