| 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]; |
| 141 |
> |
double press[3][3]; |
| 142 |
|
|
| 143 |
|
u = this->getTotalE(); |
| 144 |
|
|
| 145 |
|
this->getPressureTensor(press); |
| 146 |
< |
p = (press[0] + press[4] + press[8]) / 3.0; |
| 146 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 147 |
|
|
| 148 |
|
v = this->getVolume(); |
| 149 |
|
|
| 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; |
| 155 |
> |
return entry_plug->boxVol; |
| 156 |
|
} |
| 157 |
|
|
| 158 |
|
double Thermo::getPressure() { |
| 160 |
|
// Relies on the calculation of the full molecular pressure tensor |
| 161 |
|
|
| 162 |
|
const double p_convert = 1.63882576e8; |
| 163 |
< |
double press[9]; |
| 163 |
> |
double press[3][3]; |
| 164 |
|
double pressure; |
| 165 |
|
|
| 166 |
|
this->getPressureTensor(press); |
| 167 |
|
|
| 168 |
< |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
| 168 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 169 |
|
|
| 170 |
|
return pressure; |
| 171 |
|
} |
| 172 |
|
|
| 173 |
|
|
| 174 |
< |
void Thermo::getPressureTensor(double press[9]){ |
| 174 |
> |
void Thermo::getPressureTensor(double press[3][3]){ |
| 175 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 176 |
|
// routine derived via viral theorem description in: |
| 177 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 181 |
|
double molmass, volume; |
| 182 |
|
double vcom[3]; |
| 183 |
|
double p_local[9], p_global[9]; |
| 184 |
< |
double theBox[3]; |
| 196 |
< |
//double* tau; |
| 197 |
< |
int i, nMols; |
| 184 |
> |
int i, j, k, nMols; |
| 185 |
|
Molecule* molecules; |
| 186 |
|
|
| 187 |
|
nMols = entry_plug->n_mol; |
| 220 |
|
|
| 221 |
|
volume = entry_plug->boxVol; |
| 222 |
|
|
| 223 |
< |
for(i=0; i<9; i++) { |
| 224 |
< |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
| 223 |
> |
for(i = 0; i < 3; i++) { |
| 224 |
> |
for (j = 0; j < 3; j++) { |
| 225 |
> |
k = 3*i + j; |
| 226 |
> |
press[i][j] = (p_global[k] - entry_plug->tau[k]*e_convert) / volume; |
| 227 |
> |
} |
| 228 |
|
} |
| 229 |
|
} |
| 230 |
|
|
