| 10 |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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+ |
#include "MatVec3.h" |
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|
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#ifdef IS_MPI |
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#define __C |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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|
| 20 |
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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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; |
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double vcom[3]; |
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> |
double vcom[3], pcom[3], fcom[3], scaled[3]; |
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double p_local[9], p_global[9]; |
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int i, j, k, nMols; |
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Molecule* molecules; |
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p_global[i] = 0.0; |
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} |
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|
| 218 |
< |
for (i=0; i < nMols; i++) { |
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molmass = molecules[i].getCOMvel(vcom); |
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> |
for (i=0; i < info->integrableObjects.size(); i++) { |
| 219 |
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|
| 220 |
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molmass = info->integrableObjects[i]->getMass(); |
| 221 |
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|
| 222 |
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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); |
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|
| 226 |
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matVecMul3(info->HmatInv, pcom, scaled); |
| 227 |
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|
| 228 |
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for(j=0; j<3; j++) |
| 229 |
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scaled[j] -= roundMe(scaled[j]); |
| 230 |
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|
| 231 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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|
| 233 |
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matVecMul3(info->Hmat, scaled, pcom); |
| 234 |
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|
| 235 |
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p_local[0] += molmass * (vcom[0] * vcom[0]); |
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p_local[1] += molmass * (vcom[0] * vcom[1]); |
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p_local[2] += molmass * (vcom[0] * vcom[2]); |
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p_local[6] += molmass * (vcom[2] * vcom[0]); |
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p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 243 |
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p_local[8] += molmass * (vcom[2] * vcom[2]); |
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+ |
|
| 245 |
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} |
| 246 |
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|
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// Get total for entire system from MPI. |
| 260 |
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for (j = 0; j < 3; j++) { |
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k = 3*i + j; |
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press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
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|
| 263 |
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} |
| 264 |
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} |
| 265 |
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} |
| 450 |
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|
| 451 |
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info->integrableObjects[vd]->setVel( aVel ); |
| 452 |
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} |
| 453 |
< |
} |
| 453 |
> |
} |
