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 |
180 |
|
double molmass, volume; |
181 |
|
double vcom[3]; |
182 |
|
double p_local[9], p_global[9]; |
183 |
< |
int i, j, k, 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 |
< |
volume = entry_plug->boxVol; |
220 |
> |
volume = this->getVolume(); |
221 |
|
|
222 |
|
for(i = 0; i < 3; i++) { |
223 |
|
for (j = 0; j < 3; j++) { |
224 |
|
k = 3*i + j; |
225 |
< |
press[i][j] = (p_global[k] - entry_plug->tau[k]*e_convert) / volume; |
225 |
> |
press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume; |
226 |
|
} |
227 |
|
} |
228 |
|
} |
230 |
|
void Thermo::velocitize() { |
231 |
|
|
232 |
|
double x,y; |
233 |
< |
double vx, vy, vz; |
234 |
< |
double jx, jy, jz; |
236 |
< |
int i, vr, vd; // velocity randomizer loop counters |
233 |
> |
double aVel[3], aJ[3], I[3][3]; |
234 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
235 |
|
double vdrift[3]; |
236 |
|
double vbar; |
237 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
265 |
|
// picks random velocities from a gaussian distribution |
266 |
|
// centered on vbar |
267 |
|
|
268 |
< |
vx = vbar * gaussStream->getGaussian(); |
269 |
< |
vy = vbar * gaussStream->getGaussian(); |
270 |
< |
vz = vbar * gaussStream->getGaussian(); |
268 |
> |
for (j=0; j<3; j++) |
269 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
270 |
> |
|
271 |
> |
atoms[vr]->setVel( aVel ); |
272 |
|
|
274 |
– |
atoms[vr]->set_vx( vx ); |
275 |
– |
atoms[vr]->set_vy( vy ); |
276 |
– |
atoms[vr]->set_vz( vz ); |
273 |
|
} |
274 |
|
|
275 |
|
// Get the Center of Mass drift velocity. |
281 |
|
|
282 |
|
for(vd = 0; vd < n_atoms; vd++){ |
283 |
|
|
284 |
< |
vx = atoms[vd]->get_vx(); |
289 |
< |
vy = atoms[vd]->get_vy(); |
290 |
< |
vz = atoms[vd]->get_vz(); |
291 |
< |
|
292 |
< |
vx -= vdrift[0]; |
293 |
< |
vy -= vdrift[1]; |
294 |
< |
vz -= vdrift[2]; |
284 |
> |
atoms[vd]->getVel(aVel); |
285 |
|
|
286 |
< |
atoms[vd]->set_vx(vx); |
287 |
< |
atoms[vd]->set_vy(vy); |
288 |
< |
atoms[vd]->set_vz(vz); |
286 |
> |
for (j=0; j < 3; j++) |
287 |
> |
aVel[j] -= vdrift[j]; |
288 |
> |
|
289 |
> |
atoms[vd]->setVel( aVel ); |
290 |
|
} |
291 |
|
if( n_oriented ){ |
292 |
|
|
295 |
|
if( atoms[i]->isDirectional() ){ |
296 |
|
|
297 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
298 |
+ |
dAtom->getI( I ); |
299 |
+ |
|
300 |
+ |
for (j = 0 ; j < 3; j++) { |
301 |
|
|
302 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
303 |
< |
jx = vbar * gaussStream->getGaussian(); |
302 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
303 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
304 |
|
|
305 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
306 |
< |
jy = vbar * gaussStream->getGaussian(); |
307 |
< |
|
308 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
315 |
< |
jz = vbar * gaussStream->getGaussian(); |
316 |
< |
|
317 |
< |
dAtom->setJx( jx ); |
318 |
< |
dAtom->setJy( jy ); |
319 |
< |
dAtom->setJz( jz ); |
305 |
> |
} |
306 |
> |
|
307 |
> |
dAtom->setJ( aJ ); |
308 |
> |
|
309 |
|
} |
310 |
|
} |
311 |
|
} |
314 |
|
void Thermo::getCOMVel(double vdrift[3]){ |
315 |
|
|
316 |
|
double mtot, mtot_local; |
317 |
+ |
double aVel[3], amass; |
318 |
|
double vdrift_local[3]; |
319 |
< |
int vd, n_atoms; |
319 |
> |
int vd, n_atoms, j; |
320 |
|
Atom** atoms; |
321 |
|
|
322 |
|
// We are very careless here with the distinction between n_atoms and n_local |
332 |
|
|
333 |
|
for(vd = 0; vd < n_atoms; vd++){ |
334 |
|
|
335 |
< |
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
336 |
< |
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
337 |
< |
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
335 |
> |
amass = atoms[vd]->getMass(); |
336 |
> |
atoms[vd]->getVel( aVel ); |
337 |
> |
|
338 |
> |
for(j = 0; j < 3; j++) |
339 |
> |
vdrift_local[j] += aVel[j] * amass; |
340 |
|
|
341 |
< |
mtot_local += atoms[vd]->getMass(); |
341 |
> |
mtot_local += amass; |
342 |
|
} |
343 |
|
|
344 |
|
#ifdef IS_MPI |