| 33 |
|
double Thermo::getKinetic(){ |
| 34 |
|
|
| 35 |
|
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 36 |
< |
double vx2, vy2, vz2; |
| 37 |
< |
double kinetic, v_sqr; |
| 38 |
< |
int kl; |
| 39 |
< |
double jx2, jy2, jz2; // the square of the angular momentums |
| 36 |
> |
double kinetic; |
| 37 |
> |
double amass; |
| 38 |
> |
double aVel[3], aJ[3], I[3][3]; |
| 39 |
> |
int j, kl; |
| 40 |
|
|
| 41 |
|
DirectionalAtom *dAtom; |
| 42 |
|
|
| 51 |
|
kinetic = 0.0; |
| 52 |
|
kinetic_global = 0.0; |
| 53 |
|
for( kl=0; kl < n_atoms; kl++ ){ |
| 54 |
+ |
|
| 55 |
+ |
atoms[kl]->getVel(aVel); |
| 56 |
+ |
amass = atoms[kl]->getMass(); |
| 57 |
+ |
|
| 58 |
+ |
for (j=0; j < 3; j++) |
| 59 |
+ |
kinetic += amass * aVel[j] * aVel[j]; |
| 60 |
|
|
| 55 |
– |
vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
| 56 |
– |
vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
| 57 |
– |
vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
| 58 |
– |
|
| 59 |
– |
v_sqr = vx2 + vy2 + vz2; |
| 60 |
– |
kinetic += atoms[kl]->getMass() * v_sqr; |
| 61 |
– |
|
| 61 |
|
if( atoms[kl]->isDirectional() ){ |
| 62 |
|
|
| 63 |
|
dAtom = (DirectionalAtom *)atoms[kl]; |
| 64 |
+ |
|
| 65 |
+ |
dAtom->getJ( aJ ); |
| 66 |
+ |
dAtom->getI( I ); |
| 67 |
|
|
| 68 |
< |
jx2 = dAtom->getJx() * dAtom->getJx(); |
| 69 |
< |
jy2 = dAtom->getJy() * dAtom->getJy(); |
| 68 |
< |
jz2 = dAtom->getJz() * dAtom->getJz(); |
| 68 |
> |
for (j=0; j<3; j++) |
| 69 |
> |
kinetic += aJ[j]*aJ[j] / I[j][j]; |
| 70 |
|
|
| 70 |
– |
kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
| 71 |
– |
+ (jz2 / dAtom->getIzz()); |
| 71 |
|
} |
| 72 |
|
} |
| 73 |
|
#ifdef IS_MPI |
| 137 |
|
|
| 138 |
|
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 139 |
|
double u, p, v; |
| 140 |
< |
double press[9]; |
| 140 |
> |
double press[3][3]; |
| 141 |
|
|
| 142 |
|
u = this->getTotalE(); |
| 143 |
|
|
| 144 |
|
this->getPressureTensor(press); |
| 145 |
< |
p = (press[0] + press[4] + press[8]) / 3.0; |
| 145 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 146 |
|
|
| 147 |
|
v = this->getVolume(); |
| 148 |
|
|
| 150 |
|
} |
| 151 |
|
|
| 152 |
|
double Thermo::getVolume() { |
| 154 |
– |
double theBox[3]; |
| 153 |
|
|
| 154 |
< |
entry_plug->getBox(theBox); |
| 157 |
< |
return (theBox[0] * theBox[1] * theBox[2]); |
| 154 |
> |
return entry_plug->boxVol; |
| 155 |
|
} |
| 156 |
|
|
| 157 |
|
double Thermo::getPressure() { |
| 158 |
< |
// returns the pressure in units of atm |
| 158 |
> |
|
| 159 |
|
// Relies on the calculation of the full molecular pressure tensor |
| 160 |
|
|
| 161 |
|
const double p_convert = 1.63882576e8; |
| 162 |
< |
double press[9]; |
| 162 |
> |
double press[3][3]; |
| 163 |
|
double pressure; |
| 164 |
|
|
| 165 |
|
this->getPressureTensor(press); |
| 166 |
|
|
| 167 |
< |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
| 167 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 168 |
|
|
| 169 |
|
return pressure; |
| 170 |
|
} |
| 171 |
|
|
| 172 |
|
|
| 173 |
< |
void Thermo::getPressureTensor(double press[9]){ |
| 173 |
> |
void Thermo::getPressureTensor(double press[3][3]){ |
| 174 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 175 |
|
// routine derived via viral theorem description in: |
| 176 |
|
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 180 |
|
double molmass, volume; |
| 181 |
|
double vcom[3]; |
| 182 |
|
double p_local[9], p_global[9]; |
| 183 |
< |
double theBox[3]; |
| 187 |
< |
//double* tau; |
| 188 |
< |
int i, nMols; |
| 183 |
> |
int i, j, k, l, nMols; |
| 184 |
|
Molecule* molecules; |
| 185 |
|
|
| 186 |
|
nMols = entry_plug->n_mol; |
| 217 |
|
} |
| 218 |
|
#endif // is_mpi |
| 219 |
|
|
| 220 |
< |
entry_plug->getBox(theBox); |
| 220 |
> |
volume = entry_plug->boxVol; |
| 221 |
|
|
| 222 |
< |
volume = theBox[0] * theBox[1] * theBox[2]; |
| 223 |
< |
|
| 224 |
< |
for(i=0; i<9; i++) { |
| 225 |
< |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
| 222 |
> |
for(i = 0; i < 3; i++) { |
| 223 |
> |
for (j = 0; j < 3; j++) { |
| 224 |
> |
k = 3*i + j; |
| 225 |
> |
l = 3*j + i; |
| 226 |
> |
press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume; |
| 227 |
> |
} |
| 228 |
|
} |
| 229 |
|
} |
| 230 |
|
|
| 231 |
|
void Thermo::velocitize() { |
| 232 |
|
|
| 233 |
|
double x,y; |
| 234 |
< |
double vx, vy, vz; |
| 235 |
< |
double jx, jy, jz; |
| 239 |
< |
int i, vr, vd; // velocity randomizer loop counters |
| 234 |
> |
double aVel[3], aJ[3], I[3][3]; |
| 235 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
| 236 |
|
double vdrift[3]; |
| 237 |
|
double vbar; |
| 238 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 266 |
|
// picks random velocities from a gaussian distribution |
| 267 |
|
// centered on vbar |
| 268 |
|
|
| 269 |
< |
vx = vbar * gaussStream->getGaussian(); |
| 270 |
< |
vy = vbar * gaussStream->getGaussian(); |
| 271 |
< |
vz = vbar * gaussStream->getGaussian(); |
| 269 |
> |
for (j=0; j<3; j++) |
| 270 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
| 271 |
> |
|
| 272 |
> |
atoms[vr]->setVel( aVel ); |
| 273 |
|
|
| 277 |
– |
atoms[vr]->set_vx( vx ); |
| 278 |
– |
atoms[vr]->set_vy( vy ); |
| 279 |
– |
atoms[vr]->set_vz( vz ); |
| 274 |
|
} |
| 275 |
|
|
| 276 |
|
// Get the Center of Mass drift velocity. |
| 282 |
|
|
| 283 |
|
for(vd = 0; vd < n_atoms; vd++){ |
| 284 |
|
|
| 285 |
< |
vx = atoms[vd]->get_vx(); |
| 292 |
< |
vy = atoms[vd]->get_vy(); |
| 293 |
< |
vz = atoms[vd]->get_vz(); |
| 294 |
< |
|
| 295 |
< |
vx -= vdrift[0]; |
| 296 |
< |
vy -= vdrift[1]; |
| 297 |
< |
vz -= vdrift[2]; |
| 285 |
> |
atoms[vd]->getVel(aVel); |
| 286 |
|
|
| 287 |
< |
atoms[vd]->set_vx(vx); |
| 288 |
< |
atoms[vd]->set_vy(vy); |
| 289 |
< |
atoms[vd]->set_vz(vz); |
| 287 |
> |
for (j=0; j < 3; j++) |
| 288 |
> |
aVel[j] -= vdrift[j]; |
| 289 |
> |
|
| 290 |
> |
atoms[vd]->setVel( aVel ); |
| 291 |
|
} |
| 292 |
|
if( n_oriented ){ |
| 293 |
|
|
| 296 |
|
if( atoms[i]->isDirectional() ){ |
| 297 |
|
|
| 298 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 299 |
+ |
dAtom->getI( I ); |
| 300 |
+ |
|
| 301 |
+ |
for (j = 0 ; j < 3; j++) { |
| 302 |
|
|
| 303 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
| 304 |
< |
jx = vbar * gaussStream->getGaussian(); |
| 303 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 304 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 305 |
|
|
| 306 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 307 |
< |
jy = vbar * gaussStream->getGaussian(); |
| 308 |
< |
|
| 309 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 318 |
< |
jz = vbar * gaussStream->getGaussian(); |
| 319 |
< |
|
| 320 |
< |
dAtom->setJx( jx ); |
| 321 |
< |
dAtom->setJy( jy ); |
| 322 |
< |
dAtom->setJz( jz ); |
| 306 |
> |
} |
| 307 |
> |
|
| 308 |
> |
dAtom->setJ( aJ ); |
| 309 |
> |
|
| 310 |
|
} |
| 311 |
|
} |
| 312 |
|
} |
| 315 |
|
void Thermo::getCOMVel(double vdrift[3]){ |
| 316 |
|
|
| 317 |
|
double mtot, mtot_local; |
| 318 |
+ |
double aVel[3], amass; |
| 319 |
|
double vdrift_local[3]; |
| 320 |
< |
int vd, n_atoms; |
| 320 |
> |
int vd, n_atoms, j; |
| 321 |
|
Atom** atoms; |
| 322 |
|
|
| 323 |
|
// We are very careless here with the distinction between n_atoms and n_local |
| 333 |
|
|
| 334 |
|
for(vd = 0; vd < n_atoms; vd++){ |
| 335 |
|
|
| 336 |
< |
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
| 337 |
< |
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
| 338 |
< |
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
| 336 |
> |
amass = atoms[vd]->getMass(); |
| 337 |
> |
atoms[vd]->getVel( aVel ); |
| 338 |
> |
|
| 339 |
> |
for(j = 0; j < 3; j++) |
| 340 |
> |
vdrift_local[j] += aVel[j] * amass; |
| 341 |
|
|
| 342 |
< |
mtot_local += atoms[vd]->getMass(); |
| 342 |
> |
mtot_local += amass; |
| 343 |
|
} |
| 344 |
|
|
| 345 |
|
#ifdef IS_MPI |
