17 |
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#include "mpiSimulation.hpp" |
18 |
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#endif // is_mpi |
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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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} |
23 |
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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(); |
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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]; |
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> |
double vcom[3]; |
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double p_local[9], p_global[9]; |
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< |
int i, j, k, nMols; |
202 |
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Molecule* molecules; |
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int i, j, k; |
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|
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nMols = info->n_mol; |
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molecules = info->molecules; |
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//tau = info->tau; |
207 |
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|
208 |
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// use velocities of molecular centers of mass and molecular masses: |
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for (i=0; i < 9; i++) { |
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p_local[i] = 0.0; |
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p_global[i] = 0.0; |
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} |
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|
212 |
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// use velocities of integrableObjects and their masses: |
213 |
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|
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for (i=0; i < info->integrableObjects.size(); i++) { |
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|
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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); |
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info->integrableObjects[i]->getFrc(fcom); |
221 |
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|
222 |
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matVecMul3(info->HmatInv, pcom, scaled); |
223 |
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|
224 |
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for(j=0; j<3; j++) |
225 |
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scaled[j] -= roundMe(scaled[j]); |
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|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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|
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matVecMul3(info->Hmat, scaled, pcom); |
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|
220 |
< |
p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert; |
221 |
< |
p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert; |
222 |
< |
p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert; |
223 |
< |
p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert; |
224 |
< |
p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert; |
225 |
< |
p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert; |
226 |
< |
p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert; |
227 |
< |
p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert; |
228 |
< |
p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert; |
229 |
< |
|
220 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
221 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
222 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
223 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
224 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
225 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
226 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
227 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
228 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
229 |
> |
|
230 |
|
} |
231 |
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|
232 |
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// Get total for entire system from MPI. |
233 |
< |
|
233 |
> |
|
234 |
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#ifdef IS_MPI |
235 |
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MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
236 |
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#else |
241 |
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|
242 |
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volume = this->getVolume(); |
243 |
|
|
244 |
+ |
|
245 |
+ |
|
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 |
> |
} |