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#include "Thermo.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#ifdef IS_MPI |
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#define __C |
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//#include "mpiSimulation.hpp" |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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#define BASE_SEED 123456789 |
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Thermo::Thermo( SimInfo* the_entry_plug ) { |
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potential_local = 0.0; |
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potential_local += entry_plug->lrPot; |
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for( el=0; el<nSRI; el++ ){ |
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potential_local += sris[el]->get_potential(); |
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for( el=0; el<entry_plug->n_mol; el++ ){ |
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potential_local += entry_plug->molecules[el]->get_potential(); |
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} |
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// Get total potential for entire system from MPI. |
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double vx, vy, vz; |
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double jx, jy, jz; |
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int i, vr, vd; // velocity randomizer loop counters |
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double *vdrift; |
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double vdrift[3]; |
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double vbar; |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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double av2; |
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double kebar; |
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int ndf; // number of degrees of freedom |
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int ndfRaw; // the raw number of degrees of freedom |
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int ndf, ndf_local; // number of degrees of freedom |
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int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
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int n_atoms; |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
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n_oriented = entry_plug->n_oriented; |
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n_constraints = entry_plug->n_constraints; |
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// Raw degrees of freedom that we have to set |
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ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
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|
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ndfRaw = 3 * n_atoms + 3 * n_oriented; |
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ndf = ndfRaw - n_constraints - 3; |
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// Degrees of freedom that can contain kinetic energy |
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ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
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- entry_plug->n_constraints; |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
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MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); |
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#else |
| 186 |
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ndfRaw = ndfRaw_local; |
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ndf = ndf_local; |
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> |
#endif |
| 189 |
> |
ndf = ndf - 3; |
| 190 |
> |
|
| 191 |
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kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
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| 193 |
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for(vr = 0; vr < n_atoms; vr++){ |
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// Get the Center of Mass drift velocity. |
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< |
vdrift = getCOMVel(); |
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getCOMVel(vdrift); |
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// Corrects for the center of mass drift. |
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// sums all the momentum and divides by total mass. |
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} |
| 258 |
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} |
| 259 |
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|
| 260 |
< |
double* Thermo::getCOMVel(){ |
| 260 |
> |
void Thermo::getCOMVel(double vdrift[3]){ |
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| 262 |
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double mtot, mtot_local; |
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double* vdrift; |
| 263 |
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double vdrift_local[3]; |
| 264 |
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int vd, n_atoms; |
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Atom** atoms; |
| 266 |
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|
| 251 |
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vdrift = new double[3]; |
| 267 |
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// We are very careless here with the distinction between n_atoms and n_local |
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// We should really fix this before someone pokes an eye out. |
| 269 |
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|
| 286 |
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| 287 |
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#ifdef IS_MPI |
| 288 |
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MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
| 289 |
< |
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 289 |
> |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 290 |
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#else |
| 291 |
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mtot = mtot_local; |
| 292 |
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for(vd = 0; vd < 3; vd++) { |
| 298 |
|
vdrift[vd] = vdrift[vd] / mtot; |
| 299 |
|
} |
| 300 |
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|
| 286 |
– |
return vdrift; |
| 301 |
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} |
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