| 123 |
|
|
| 124 |
|
double Thermo::getTemperature(){ |
| 125 |
|
|
| 126 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 126 |
> |
const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
| 127 |
|
double temperature; |
| 128 |
|
|
| 129 |
|
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
| 166 |
|
return pressure; |
| 167 |
|
} |
| 168 |
|
|
| 169 |
+ |
double Thermo::getPressureX() { |
| 170 |
|
|
| 171 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
| 172 |
+ |
|
| 173 |
+ |
const double p_convert = 1.63882576e8; |
| 174 |
+ |
double press[3][3]; |
| 175 |
+ |
double pressureX; |
| 176 |
+ |
|
| 177 |
+ |
this->getPressureTensor(press); |
| 178 |
+ |
|
| 179 |
+ |
pressureX = p_convert * press[0][0]; |
| 180 |
+ |
|
| 181 |
+ |
return pressureX; |
| 182 |
+ |
} |
| 183 |
+ |
|
| 184 |
+ |
double Thermo::getPressureY() { |
| 185 |
+ |
|
| 186 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
| 187 |
+ |
|
| 188 |
+ |
const double p_convert = 1.63882576e8; |
| 189 |
+ |
double press[3][3]; |
| 190 |
+ |
double pressureY; |
| 191 |
+ |
|
| 192 |
+ |
this->getPressureTensor(press); |
| 193 |
+ |
|
| 194 |
+ |
pressureY = p_convert * press[1][1]; |
| 195 |
+ |
|
| 196 |
+ |
return pressureY; |
| 197 |
+ |
} |
| 198 |
+ |
|
| 199 |
+ |
double Thermo::getPressureZ() { |
| 200 |
+ |
|
| 201 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
| 202 |
+ |
|
| 203 |
+ |
const double p_convert = 1.63882576e8; |
| 204 |
+ |
double press[3][3]; |
| 205 |
+ |
double pressureZ; |
| 206 |
+ |
|
| 207 |
+ |
this->getPressureTensor(press); |
| 208 |
+ |
|
| 209 |
+ |
pressureZ = p_convert * press[2][2]; |
| 210 |
+ |
|
| 211 |
+ |
return pressureZ; |
| 212 |
+ |
} |
| 213 |
+ |
|
| 214 |
+ |
|
| 215 |
|
void Thermo::getPressureTensor(double press[3][3]){ |
| 216 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 217 |
|
// routine derived via viral theorem description in: |
| 293 |
|
n_oriented = info->n_oriented; |
| 294 |
|
n_constraints = info->n_constraints; |
| 295 |
|
|
| 296 |
< |
kebar = kb * temperature * (double)info->ndf / |
| 297 |
< |
( 2.0 * (double)info->ndfRaw ); |
| 296 |
> |
kebar = kb * temperature * (double)info->ndfRaw / |
| 297 |
> |
( 2.0 * (double)info->ndf ); |
| 298 |
|
|
| 299 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 300 |
|
|
| 400 |
|
|
| 401 |
|
} |
| 402 |
|
|
| 403 |
+ |
void Thermo::getCOM(double COM[3]){ |
| 404 |
+ |
|
| 405 |
+ |
double mtot, mtot_local; |
| 406 |
+ |
double aPos[3], amass; |
| 407 |
+ |
double COM_local[3]; |
| 408 |
+ |
int i, n_atoms, j; |
| 409 |
+ |
Atom** atoms; |
| 410 |
+ |
|
| 411 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
| 412 |
+ |
// We should really fix this before someone pokes an eye out. |
| 413 |
+ |
|
| 414 |
+ |
n_atoms = info->n_atoms; |
| 415 |
+ |
atoms = info->atoms; |
| 416 |
+ |
|
| 417 |
+ |
mtot_local = 0.0; |
| 418 |
+ |
COM_local[0] = 0.0; |
| 419 |
+ |
COM_local[1] = 0.0; |
| 420 |
+ |
COM_local[2] = 0.0; |
| 421 |
+ |
|
| 422 |
+ |
for(i = 0; i < n_atoms; i++){ |
| 423 |
+ |
|
| 424 |
+ |
amass = atoms[i]->getMass(); |
| 425 |
+ |
atoms[i]->getPos( aPos ); |
| 426 |
+ |
|
| 427 |
+ |
for(j = 0; j < 3; j++) |
| 428 |
+ |
COM_local[j] += aPos[j] * amass; |
| 429 |
+ |
|
| 430 |
+ |
mtot_local += amass; |
| 431 |
+ |
} |
| 432 |
+ |
|
| 433 |
+ |
#ifdef IS_MPI |
| 434 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 435 |
+ |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 436 |
+ |
#else |
| 437 |
+ |
mtot = mtot_local; |
| 438 |
+ |
for(i = 0; i < 3; i++) { |
| 439 |
+ |
COM[i] = COM_local[i]; |
| 440 |
+ |
} |
| 441 |
+ |
#endif |
| 442 |
+ |
|
| 443 |
+ |
for (i = 0; i < 3; i++) { |
| 444 |
+ |
COM[i] = COM[i] / mtot; |
| 445 |
+ |
} |
| 446 |
+ |
} |
