| 134 |
|
return temperature; |
| 135 |
|
} |
| 136 |
|
|
| 137 |
< |
double Thermo::getPressure(){ |
| 138 |
< |
// returns pressure in units amu*fs^-2*Ang^-1 |
| 137 |
> |
double Thermo::getEnthalpy() { |
| 138 |
> |
|
| 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 |
> |
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 |
> |
|
| 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 |
|
const double e_convert = 4.184e-4; |
| 191 |
< |
const double p_convert = 1.63882576e8; |
| 192 |
< |
double molmass; |
| 191 |
> |
|
| 192 |
> |
double molmass, volume; |
| 193 |
|
double vcom[3]; |
| 194 |
< |
double p_local, p_sum, p_mol, virial; |
| 194 |
> |
double p_local[9], p_global[9]; |
| 195 |
|
double theBox[3]; |
| 196 |
< |
double* tau; |
| 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; |
| 202 |
> |
//tau = entry_plug->tau; |
| 203 |
|
|
| 204 |
|
// use velocities of molecular centers of mass and molecular masses: |
| 205 |
< |
p_local = 0.0; |
| 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 |
< |
p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass; |
| 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_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 227 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 228 |
|
#else |
| 229 |
< |
p_sum = p_local; |
| 229 |
> |
for (i=0; i<9; i++) { |
| 230 |
> |
p_global[i] = p_local[i]; |
| 231 |
> |
} |
| 232 |
|
#endif // is_mpi |
| 233 |
|
|
| 234 |
< |
virial = tau[0] + tau[4] + tau[8]; |
| 172 |
< |
entry_plug->getBox(theBox); |
| 234 |
> |
volume = entry_plug->boxVol; |
| 235 |
|
|
| 236 |
< |
p_mol = p_convert * (p_sum - virial*e_convert) / |
| 237 |
< |
(3.0 * theBox[0] * theBox[1]* theBox[2]); |
| 238 |
< |
|
| 177 |
< |
return p_mol; |
| 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() { |
