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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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#include "simError.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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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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|
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|
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#define BASE_SEED 123456789 |
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|
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Thermo::Thermo( SimInfo* the_entry_plug ) { |
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double potential_local; |
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double potential; |
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int el, nSRI; |
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< |
SRI** sris; |
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Molecule* molecules; |
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|
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sris = entry_plug->sr_interactions; |
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molecules = entry_plug->molecules; |
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nSRI = entry_plug->n_SRI; |
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|
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potential_local = 0.0; |
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potential = 0.0; |
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potential_local += entry_plug->lrPot; |
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|
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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 += molecules[el].getPotential(); |
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} |
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|
| 103 |
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot |
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<< "; pot_local = " << potential_local |
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<< "; pot = " << potential << "\n"; |
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*/ |
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#endif |
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|
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// Get total potential for entire system from MPI. |
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
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potential = potential_local; |
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#endif // is_mpi |
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|
| 118 |
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
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*/ |
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#endif |
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|
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return potential; |
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} |
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|
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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 |
| 177 |
< |
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; |
| 190 |
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|
| 191 |
+ |
// Raw degrees of freedom that we have to set |
| 192 |
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ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 193 |
|
|
| 194 |
< |
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
| 195 |
< |
ndf = ndfRaw - n_constraints - 3; |
| 194 |
> |
// Degrees of freedom that can contain kinetic energy |
| 195 |
> |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 196 |
> |
- entry_plug->n_constraints; |
| 197 |
> |
|
| 198 |
> |
#ifdef IS_MPI |
| 199 |
> |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
| 200 |
> |
MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); |
| 201 |
> |
#else |
| 202 |
> |
ndfRaw = ndfRaw_local; |
| 203 |
> |
ndf = ndf_local; |
| 204 |
> |
#endif |
| 205 |
> |
ndf = ndf - 3; |
| 206 |
> |
|
| 207 |
|
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
| 208 |
|
|
| 209 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 229 |
|
|
| 230 |
|
// Get the Center of Mass drift velocity. |
| 231 |
|
|
| 232 |
< |
vdrift = getCOMVel(); |
| 232 |
> |
getCOMVel(vdrift); |
| 233 |
|
|
| 234 |
|
// Corrects for the center of mass drift. |
| 235 |
|
// sums all the momentum and divides by total mass. |
| 273 |
|
} |
| 274 |
|
} |
| 275 |
|
|
| 276 |
< |
double* Thermo::getCOMVel(){ |
| 276 |
> |
void Thermo::getCOMVel(double vdrift[3]){ |
| 277 |
|
|
| 278 |
|
double mtot, mtot_local; |
| 246 |
– |
double* vdrift; |
| 279 |
|
double vdrift_local[3]; |
| 280 |
|
int vd, n_atoms; |
| 281 |
|
Atom** atoms; |
| 282 |
|
|
| 251 |
– |
vdrift = new double[3]; |
| 283 |
|
// We are very careless here with the distinction between n_atoms and n_local |
| 284 |
|
// We should really fix this before someone pokes an eye out. |
| 285 |
|
|
| 302 |
|
|
| 303 |
|
#ifdef IS_MPI |
| 304 |
|
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
| 305 |
< |
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 305 |
> |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 306 |
|
#else |
| 307 |
|
mtot = mtot_local; |
| 308 |
|
for(vd = 0; vd < 3; vd++) { |
| 314 |
|
vdrift[vd] = vdrift[vd] / mtot; |
| 315 |
|
} |
| 316 |
|
|
| 286 |
– |
return vdrift; |
| 317 |
|
} |
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|
