17 |
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#include "mpiSimulation.hpp" |
18 |
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#endif // is_mpi |
19 |
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|
20 |
+ |
inline double roundMe( double x ){ |
21 |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
22 |
+ |
} |
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|
24 |
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Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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int baseSeed = the_info->getSeed(); |
200 |
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const double e_convert = 4.184e-4; |
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|
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double molmass, volume; |
203 |
< |
double vcom[3], pcom[3], fcom[3], scaled[3]; |
203 |
> |
double vcom[3]; |
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double p_local[9], p_global[9]; |
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< |
int i, j, k, nMols; |
202 |
< |
Molecule* molecules; |
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> |
int i, j, k; |
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|
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nMols = info->n_mol; |
205 |
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molecules = info->molecules; |
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//tau = info->tau; |
207 |
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|
208 |
< |
// use velocities of molecular centers of mass and molecular masses: |
208 |
> |
|
209 |
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for (i=0; i < 9; i++) { |
210 |
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p_local[i] = 0.0; |
211 |
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p_global[i] = 0.0; |
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} |
213 |
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|
214 |
+ |
// use velocities of integrableObjects and their masses: |
215 |
+ |
|
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for (i=0; i < info->integrableObjects.size(); i++) { |
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|
218 |
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molmass = info->integrableObjects[i]->getMass(); |
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info->integrableObjects[i]->getVel(vcom); |
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< |
info->integrableObjects[i]->getPos(pcom); |
222 |
< |
info->integrableObjects[i]->getFrc(fcom); |
223 |
< |
|
224 |
< |
matVecMul3(info->HmatInv, pcom, scaled); |
225 |
< |
|
226 |
< |
for(j=0; j<3; j++) |
227 |
< |
scaled[j] -= roundMe(scaled[j]); |
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< |
|
229 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
230 |
< |
|
229 |
< |
matVecMul3(info->Hmat, scaled, pcom); |
221 |
> |
|
222 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
223 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
224 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
225 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
226 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
227 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
228 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
229 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
230 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
231 |
|
|
231 |
– |
p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert; |
232 |
– |
p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert; |
233 |
– |
p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert; |
234 |
– |
p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert; |
235 |
– |
p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert; |
236 |
– |
p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert; |
237 |
– |
p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert; |
238 |
– |
p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert; |
239 |
– |
p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert; |
240 |
– |
|
232 |
|
} |
233 |
|
|
234 |
|
// Get total for entire system from MPI. |
235 |
< |
|
235 |
> |
|
236 |
|
#ifdef IS_MPI |
237 |
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MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
238 |
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#else |
246 |
|
for(i = 0; i < 3; i++) { |
247 |
|
for (j = 0; j < 3; j++) { |
248 |
|
k = 3*i + j; |
249 |
< |
press[i][j] = p_global[k] / volume; |
259 |
< |
|
249 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
250 |
|
} |
251 |
|
} |
252 |
|
} |
437 |
|
|
438 |
|
info->integrableObjects[vd]->setVel( aVel ); |
439 |
|
} |
440 |
< |
} |
440 |
> |
} |