16 |
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#include "mpiSimulation.hpp" |
17 |
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#endif // is_mpi |
18 |
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|
19 |
< |
|
20 |
< |
#define BASE_SEED 123456789 |
21 |
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|
22 |
< |
Thermo::Thermo( SimInfo* the_entry_plug ) { |
23 |
< |
entry_plug = the_entry_plug; |
24 |
< |
int baseSeed = BASE_SEED; |
19 |
> |
Thermo::Thermo( SimInfo* the_info ) { |
20 |
> |
info = the_info; |
21 |
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int baseSeed = the_info->getSeed(); |
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|
23 |
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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double Thermo::getKinetic(){ |
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|
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
33 |
< |
double vx2, vy2, vz2; |
34 |
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double kinetic, v_sqr; |
35 |
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int kl; |
36 |
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double jx2, jy2, jz2; // the square of the angular momentums |
33 |
> |
double kinetic; |
34 |
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double amass; |
35 |
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double aVel[3], aJ[3], I[3][3]; |
36 |
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int j, kl; |
37 |
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|
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DirectionalAtom *dAtom; |
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|
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Atom** atoms; |
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|
44 |
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|
45 |
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n_atoms = entry_plug->n_atoms; |
46 |
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atoms = entry_plug->atoms; |
45 |
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n_atoms = info->n_atoms; |
46 |
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atoms = info->atoms; |
47 |
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|
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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for( kl=0; kl < n_atoms; kl++ ){ |
51 |
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|
52 |
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atoms[kl]->getVel(aVel); |
53 |
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amass = atoms[kl]->getMass(); |
54 |
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|
55 |
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for (j=0; j < 3; j++) |
56 |
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kinetic += amass * aVel[j] * aVel[j]; |
57 |
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|
55 |
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vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
56 |
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vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
57 |
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vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
58 |
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|
59 |
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v_sqr = vx2 + vy2 + vz2; |
60 |
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kinetic += atoms[kl]->getMass() * v_sqr; |
61 |
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|
58 |
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if( atoms[kl]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[kl]; |
61 |
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|
62 |
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dAtom->getJ( aJ ); |
63 |
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dAtom->getI( I ); |
64 |
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|
65 |
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jx2 = dAtom->getJx() * dAtom->getJx(); |
66 |
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jy2 = dAtom->getJy() * dAtom->getJy(); |
68 |
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jz2 = dAtom->getJz() * dAtom->getJz(); |
65 |
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for (j=0; j<3; j++) |
66 |
> |
kinetic += aJ[j]*aJ[j] / I[j][j]; |
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|
70 |
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kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
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+ (jz2 / dAtom->getIzz()); |
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} |
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} |
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#ifdef IS_MPI |
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int el, nSRI; |
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Molecule* molecules; |
87 |
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|
88 |
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molecules = entry_plug->molecules; |
89 |
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nSRI = entry_plug->n_SRI; |
88 |
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molecules = info->molecules; |
89 |
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nSRI = info->n_SRI; |
90 |
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|
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potential_local = 0.0; |
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potential = 0.0; |
93 |
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potential_local += entry_plug->lrPot; |
93 |
> |
potential_local += info->lrPot; |
94 |
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|
95 |
< |
for( el=0; el<entry_plug->n_mol; el++ ){ |
95 |
> |
for( el=0; el<info->n_mol; el++ ){ |
96 |
|
potential_local += molecules[el].getPotential(); |
97 |
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} |
98 |
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|
126 |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
127 |
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double temperature; |
128 |
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|
129 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
129 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
131 |
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} |
132 |
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|
134 |
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|
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
136 |
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double u, p, v; |
137 |
< |
double press[9]; |
137 |
> |
double press[3][3]; |
138 |
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|
139 |
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u = this->getTotalE(); |
140 |
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|
141 |
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this->getPressureTensor(press); |
142 |
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p = (press[0] + press[4] + press[8]) / 3.0; |
142 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
143 |
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|
144 |
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v = this->getVolume(); |
145 |
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|
147 |
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} |
148 |
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|
149 |
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double Thermo::getVolume() { |
154 |
– |
double theBox[3]; |
150 |
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|
151 |
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entry_plug->getBox(theBox); |
157 |
< |
return (theBox[0] * theBox[1] * theBox[2]); |
151 |
> |
return info->boxVol; |
152 |
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} |
153 |
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|
154 |
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double Thermo::getPressure() { |
155 |
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// returns the pressure in units of atm |
155 |
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|
156 |
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// Relies on the calculation of the full molecular pressure tensor |
157 |
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|
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const double p_convert = 1.63882576e8; |
159 |
< |
double press[9]; |
159 |
> |
double press[3][3]; |
160 |
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double pressure; |
161 |
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|
162 |
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this->getPressureTensor(press); |
163 |
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|
164 |
< |
pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
164 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
165 |
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|
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return pressure; |
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} |
168 |
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|
169 |
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double Thermo::getPressureX() { |
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|
171 |
< |
void Thermo::getPressureTensor(double press[9]){ |
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// 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 |
> |
|
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return pressureX; |
182 |
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} |
183 |
> |
|
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> |
double Thermo::getPressureY() { |
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|
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> |
// 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; |
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} |
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 |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
217 |
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// routine derived via viral theorem description in: |
218 |
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// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
222 |
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double molmass, volume; |
223 |
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double vcom[3]; |
224 |
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double p_local[9], p_global[9]; |
225 |
< |
double theBox[3]; |
187 |
< |
double* tau; |
188 |
< |
int i, nMols; |
225 |
> |
int i, j, k, nMols; |
226 |
|
Molecule* molecules; |
227 |
|
|
228 |
< |
nMols = entry_plug->n_mol; |
229 |
< |
molecules = entry_plug->molecules; |
230 |
< |
tau = entry_plug->tau; |
228 |
> |
nMols = info->n_mol; |
229 |
> |
molecules = info->molecules; |
230 |
> |
//tau = info->tau; |
231 |
|
|
232 |
|
// use velocities of molecular centers of mass and molecular masses: |
233 |
|
for (i=0; i < 9; i++) { |
259 |
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} |
260 |
|
#endif // is_mpi |
261 |
|
|
262 |
< |
entry_plug->getBox(theBox); |
262 |
> |
volume = this->getVolume(); |
263 |
|
|
264 |
< |
volume = theBox[0] * theBox[1] * theBox[2]; |
264 |
> |
for(i = 0; i < 3; i++) { |
265 |
> |
for (j = 0; j < 3; j++) { |
266 |
> |
k = 3*i + j; |
267 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
268 |
|
|
269 |
< |
for(i=0; i<9; i++) { |
230 |
< |
press[i] = (p_global[i] - tau[i]*e_convert) / volume; |
269 |
> |
} |
270 |
|
} |
271 |
|
} |
272 |
|
|
273 |
|
void Thermo::velocitize() { |
274 |
|
|
275 |
|
double x,y; |
276 |
< |
double vx, vy, vz; |
277 |
< |
double jx, jy, jz; |
239 |
< |
int i, vr, vd; // velocity randomizer loop counters |
276 |
> |
double aVel[3], aJ[3], I[3][3]; |
277 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
278 |
|
double vdrift[3]; |
279 |
|
double vbar; |
280 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
287 |
|
int n_oriented; |
288 |
|
int n_constraints; |
289 |
|
|
290 |
< |
atoms = entry_plug->atoms; |
291 |
< |
n_atoms = entry_plug->n_atoms; |
292 |
< |
temperature = entry_plug->target_temp; |
293 |
< |
n_oriented = entry_plug->n_oriented; |
294 |
< |
n_constraints = entry_plug->n_constraints; |
290 |
> |
atoms = info->atoms; |
291 |
> |
n_atoms = info->n_atoms; |
292 |
> |
temperature = info->target_temp; |
293 |
> |
n_oriented = info->n_oriented; |
294 |
> |
n_constraints = info->n_constraints; |
295 |
|
|
296 |
< |
kebar = kb * temperature * (double)entry_plug->ndf / |
297 |
< |
( 2.0 * (double)entry_plug->ndfRaw ); |
296 |
> |
kebar = kb * temperature * (double)info->ndf / |
297 |
> |
( 2.0 * (double)info->ndfRaw ); |
298 |
|
|
299 |
|
for(vr = 0; vr < n_atoms; vr++){ |
300 |
|
|
308 |
|
// picks random velocities from a gaussian distribution |
309 |
|
// centered on vbar |
310 |
|
|
311 |
< |
vx = vbar * gaussStream->getGaussian(); |
312 |
< |
vy = vbar * gaussStream->getGaussian(); |
313 |
< |
vz = vbar * gaussStream->getGaussian(); |
311 |
> |
for (j=0; j<3; j++) |
312 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
313 |
> |
|
314 |
> |
atoms[vr]->setVel( aVel ); |
315 |
|
|
277 |
– |
atoms[vr]->set_vx( vx ); |
278 |
– |
atoms[vr]->set_vy( vy ); |
279 |
– |
atoms[vr]->set_vz( vz ); |
316 |
|
} |
317 |
|
|
318 |
|
// Get the Center of Mass drift velocity. |
324 |
|
|
325 |
|
for(vd = 0; vd < n_atoms; vd++){ |
326 |
|
|
327 |
< |
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]; |
327 |
> |
atoms[vd]->getVel(aVel); |
328 |
|
|
329 |
< |
atoms[vd]->set_vx(vx); |
330 |
< |
atoms[vd]->set_vy(vy); |
331 |
< |
atoms[vd]->set_vz(vz); |
329 |
> |
for (j=0; j < 3; j++) |
330 |
> |
aVel[j] -= vdrift[j]; |
331 |
> |
|
332 |
> |
atoms[vd]->setVel( aVel ); |
333 |
|
} |
334 |
|
if( n_oriented ){ |
335 |
|
|
338 |
|
if( atoms[i]->isDirectional() ){ |
339 |
|
|
340 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
341 |
+ |
dAtom->getI( I ); |
342 |
+ |
|
343 |
+ |
for (j = 0 ; j < 3; j++) { |
344 |
|
|
345 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
346 |
< |
jx = vbar * gaussStream->getGaussian(); |
345 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
346 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
347 |
|
|
348 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
349 |
< |
jy = vbar * gaussStream->getGaussian(); |
350 |
< |
|
351 |
< |
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 ); |
348 |
> |
} |
349 |
> |
|
350 |
> |
dAtom->setJ( aJ ); |
351 |
> |
|
352 |
|
} |
353 |
|
} |
354 |
|
} |
357 |
|
void Thermo::getCOMVel(double vdrift[3]){ |
358 |
|
|
359 |
|
double mtot, mtot_local; |
360 |
+ |
double aVel[3], amass; |
361 |
|
double vdrift_local[3]; |
362 |
< |
int vd, n_atoms; |
362 |
> |
int vd, n_atoms, j; |
363 |
|
Atom** atoms; |
364 |
|
|
365 |
|
// We are very careless here with the distinction between n_atoms and n_local |
366 |
|
// We should really fix this before someone pokes an eye out. |
367 |
|
|
368 |
< |
n_atoms = entry_plug->n_atoms; |
369 |
< |
atoms = entry_plug->atoms; |
368 |
> |
n_atoms = info->n_atoms; |
369 |
> |
atoms = info->atoms; |
370 |
|
|
371 |
|
mtot_local = 0.0; |
372 |
|
vdrift_local[0] = 0.0; |
375 |
|
|
376 |
|
for(vd = 0; vd < n_atoms; vd++){ |
377 |
|
|
378 |
< |
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
379 |
< |
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
380 |
< |
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
378 |
> |
amass = atoms[vd]->getMass(); |
379 |
> |
atoms[vd]->getVel( aVel ); |
380 |
> |
|
381 |
> |
for(j = 0; j < 3; j++) |
382 |
> |
vdrift_local[j] += aVel[j] * amass; |
383 |
|
|
384 |
< |
mtot_local += atoms[vd]->getMass(); |
384 |
> |
mtot_local += amass; |
385 |
|
} |
386 |
|
|
387 |
|
#ifdef IS_MPI |