| 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 ); |
| 130 |
|
return temperature; |
| 131 |
|
} |
| 132 |
|
|
| 133 |
– |
double Thermo::getEnthalpy() { |
| 134 |
– |
|
| 135 |
– |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 136 |
– |
double u, p, v; |
| 137 |
– |
double press[3][3]; |
| 138 |
– |
|
| 139 |
– |
u = this->getTotalE(); |
| 140 |
– |
|
| 141 |
– |
this->getPressureTensor(press); |
| 142 |
– |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 143 |
– |
|
| 144 |
– |
v = this->getVolume(); |
| 145 |
– |
|
| 146 |
– |
return (u + (p*v)/e_convert); |
| 147 |
– |
} |
| 148 |
– |
|
| 133 |
|
double Thermo::getVolume() { |
| 134 |
|
|
| 135 |
|
return info->boxVol; |
| 256 |
|
|
| 257 |
|
void Thermo::velocitize() { |
| 258 |
|
|
| 275 |
– |
double x,y; |
| 259 |
|
double aVel[3], aJ[3], I[3][3]; |
| 260 |
|
int i, j, vr, vd; // velocity randomizer loop counters |
| 261 |
|
double vdrift[3]; |
| 276 |
|
n_oriented = info->n_oriented; |
| 277 |
|
n_constraints = info->n_constraints; |
| 278 |
|
|
| 279 |
< |
kebar = kb * temperature * (double)info->ndf / |
| 280 |
< |
( 2.0 * (double)info->ndfRaw ); |
| 279 |
> |
kebar = kb * temperature * (double)info->ndfRaw / |
| 280 |
> |
( 2.0 * (double)info->ndf ); |
| 281 |
|
|
| 282 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 283 |
|
|
| 382 |
|
} |
| 383 |
|
|
| 384 |
|
} |
| 385 |
+ |
|
| 386 |
+ |
void Thermo::getCOM(double COM[3]){ |
| 387 |
+ |
|
| 388 |
+ |
double mtot, mtot_local; |
| 389 |
+ |
double aPos[3], amass; |
| 390 |
+ |
double COM_local[3]; |
| 391 |
+ |
int i, n_atoms, j; |
| 392 |
+ |
Atom** atoms; |
| 393 |
|
|
| 394 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
| 395 |
+ |
// We should really fix this before someone pokes an eye out. |
| 396 |
+ |
|
| 397 |
+ |
n_atoms = info->n_atoms; |
| 398 |
+ |
atoms = info->atoms; |
| 399 |
+ |
|
| 400 |
+ |
mtot_local = 0.0; |
| 401 |
+ |
COM_local[0] = 0.0; |
| 402 |
+ |
COM_local[1] = 0.0; |
| 403 |
+ |
COM_local[2] = 0.0; |
| 404 |
+ |
|
| 405 |
+ |
for(i = 0; i < n_atoms; i++){ |
| 406 |
+ |
|
| 407 |
+ |
amass = atoms[i]->getMass(); |
| 408 |
+ |
atoms[i]->getPos( aPos ); |
| 409 |
+ |
|
| 410 |
+ |
for(j = 0; j < 3; j++) |
| 411 |
+ |
COM_local[j] += aPos[j] * amass; |
| 412 |
+ |
|
| 413 |
+ |
mtot_local += amass; |
| 414 |
+ |
} |
| 415 |
+ |
|
| 416 |
+ |
#ifdef IS_MPI |
| 417 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 418 |
+ |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 419 |
+ |
#else |
| 420 |
+ |
mtot = mtot_local; |
| 421 |
+ |
for(i = 0; i < 3; i++) { |
| 422 |
+ |
COM[i] = COM_local[i]; |
| 423 |
+ |
} |
| 424 |
+ |
#endif |
| 425 |
+ |
|
| 426 |
+ |
for (i = 0; i < 3; i++) { |
| 427 |
+ |
COM[i] = COM[i] / mtot; |
| 428 |
+ |
} |
| 429 |
+ |
} |
