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 |
124 |
|
return total; |
125 |
|
} |
126 |
|
|
127 |
< |
int Thermo::getNDF(){ |
128 |
< |
int ndf_local, ndf; |
127 |
> |
double Thermo::getTemperature(){ |
128 |
> |
|
129 |
> |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
130 |
> |
double temperature; |
131 |
|
|
132 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
133 |
< |
- entry_plug->n_constraints; |
132 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
133 |
> |
return temperature; |
134 |
> |
} |
135 |
|
|
136 |
< |
#ifdef IS_MPI |
135 |
< |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
136 |
< |
#else |
137 |
< |
ndf = ndf_local; |
138 |
< |
#endif |
136 |
> |
double Thermo::getEnthalpy() { |
137 |
|
|
138 |
< |
ndf = ndf - 3; |
138 |
> |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
139 |
> |
double u, p, v; |
140 |
> |
double press[3][3]; |
141 |
|
|
142 |
< |
return ndf; |
143 |
< |
} |
142 |
> |
u = this->getTotalE(); |
143 |
|
|
144 |
< |
int Thermo::getNDFraw() { |
145 |
< |
int ndfRaw_local, ndfRaw; |
144 |
> |
this->getPressureTensor(press); |
145 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
146 |
|
|
147 |
< |
// Raw degrees of freedom that we have to set |
149 |
< |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
150 |
< |
|
151 |
< |
#ifdef IS_MPI |
152 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
153 |
< |
#else |
154 |
< |
ndfRaw = ndfRaw_local; |
155 |
< |
#endif |
147 |
> |
v = this->getVolume(); |
148 |
|
|
149 |
< |
return ndfRaw; |
149 |
> |
return (u + (p*v)/e_convert); |
150 |
|
} |
151 |
|
|
152 |
+ |
double Thermo::getVolume() { |
153 |
|
|
154 |
< |
double Thermo::getTemperature(){ |
154 |
> |
return entry_plug->boxVol; |
155 |
> |
} |
156 |
|
|
157 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
158 |
< |
double temperature; |
157 |
> |
double Thermo::getPressure() { |
158 |
> |
|
159 |
> |
// Relies on the calculation of the full molecular pressure tensor |
160 |
|
|
161 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb ); |
162 |
< |
return temperature; |
161 |
> |
const double p_convert = 1.63882576e8; |
162 |
> |
double press[3][3]; |
163 |
> |
double pressure; |
164 |
> |
|
165 |
> |
this->getPressureTensor(press); |
166 |
> |
|
167 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
168 |
> |
|
169 |
> |
return pressure; |
170 |
|
} |
171 |
|
|
172 |
< |
double Thermo::getPressure(){ |
173 |
< |
// returns pressure in units amu*fs^-2*Ang^-1 |
172 |
> |
|
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 |
177 |
|
|
178 |
< |
return 0.0; |
178 |
> |
const double e_convert = 4.184e-4; |
179 |
> |
|
180 |
> |
double molmass, volume; |
181 |
> |
double vcom[3]; |
182 |
> |
double p_local[9], p_global[9]; |
183 |
> |
int i, j, k, l, nMols; |
184 |
> |
Molecule* molecules; |
185 |
> |
|
186 |
> |
nMols = entry_plug->n_mol; |
187 |
> |
molecules = entry_plug->molecules; |
188 |
> |
//tau = entry_plug->tau; |
189 |
> |
|
190 |
> |
// use velocities of molecular centers of mass and molecular masses: |
191 |
> |
for (i=0; i < 9; i++) { |
192 |
> |
p_local[i] = 0.0; |
193 |
> |
p_global[i] = 0.0; |
194 |
> |
} |
195 |
> |
|
196 |
> |
for (i=0; i < nMols; i++) { |
197 |
> |
molmass = molecules[i].getCOMvel(vcom); |
198 |
> |
|
199 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
200 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
201 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
202 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
203 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
204 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
205 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
206 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
207 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
208 |
> |
} |
209 |
> |
|
210 |
> |
// Get total for entire system from MPI. |
211 |
> |
|
212 |
> |
#ifdef IS_MPI |
213 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
214 |
> |
#else |
215 |
> |
for (i=0; i<9; i++) { |
216 |
> |
p_global[i] = p_local[i]; |
217 |
> |
} |
218 |
> |
#endif // is_mpi |
219 |
> |
|
220 |
> |
volume = entry_plug->boxVol; |
221 |
> |
|
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; |
183 |
< |
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. |
239 |
|
double av2; |
240 |
|
double kebar; |
189 |
– |
int ndf, ndf_local; // number of degrees of freedom |
190 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
241 |
|
int n_atoms; |
242 |
|
Atom** atoms; |
243 |
|
DirectionalAtom* dAtom; |
251 |
|
n_oriented = entry_plug->n_oriented; |
252 |
|
n_constraints = entry_plug->n_constraints; |
253 |
|
|
254 |
< |
kebar = kb * temperature * (double)this->getNDF() / |
255 |
< |
( 2.0 * (double)this->getNDFraw() ); |
254 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
255 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
256 |
|
|
257 |
|
for(vr = 0; vr < n_atoms; vr++){ |
258 |
|
|
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 |
|
|
223 |
– |
atoms[vr]->set_vx( vx ); |
224 |
– |
atoms[vr]->set_vy( vy ); |
225 |
– |
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(); |
238 |
< |
vy = atoms[vd]->get_vy(); |
239 |
< |
vz = atoms[vd]->get_vz(); |
240 |
< |
|
241 |
< |
vx -= vdrift[0]; |
242 |
< |
vy -= vdrift[1]; |
243 |
< |
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() ); |
264 |
< |
jz = vbar * gaussStream->getGaussian(); |
265 |
< |
|
266 |
< |
dAtom->setJx( jx ); |
267 |
< |
dAtom->setJy( jy ); |
268 |
< |
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 |