| 10 |
|
#include "Thermo.hpp" |
| 11 |
|
#include "SRI.hpp" |
| 12 |
|
#include "Integrator.hpp" |
| 13 |
+ |
#include "simError.h" |
| 14 |
+ |
|
| 15 |
+ |
#ifdef IS_MPI |
| 16 |
|
#define __C |
| 17 |
< |
//#include "mpiSimulation.hpp" |
| 17 |
> |
#include "mpiSimulation.hpp" |
| 18 |
> |
#endif // is_mpi |
| 19 |
|
|
| 20 |
+ |
|
| 21 |
|
#define BASE_SEED 123456789 |
| 22 |
|
|
| 23 |
|
Thermo::Thermo( SimInfo* the_entry_plug ) { |
| 87 |
|
double potential_local; |
| 88 |
|
double potential; |
| 89 |
|
int el, nSRI; |
| 90 |
< |
SRI** sris; |
| 90 |
> |
Molecule* molecules; |
| 91 |
|
|
| 92 |
< |
sris = entry_plug->sr_interactions; |
| 92 |
> |
molecules = entry_plug->molecules; |
| 93 |
|
nSRI = entry_plug->n_SRI; |
| 94 |
|
|
| 95 |
|
potential_local = 0.0; |
| 96 |
+ |
potential = 0.0; |
| 97 |
|
potential_local += entry_plug->lrPot; |
| 98 |
|
|
| 99 |
< |
for( el=0; el<nSRI; el++ ){ |
| 100 |
< |
potential_local += sris[el]->get_potential(); |
| 99 |
> |
for( el=0; el<entry_plug->n_mol; el++ ){ |
| 100 |
> |
potential_local += molecules[el].getPotential(); |
| 101 |
|
} |
| 102 |
|
|
| 103 |
+ |
#ifdef IS_MPI |
| 104 |
+ |
/* |
| 105 |
+ |
std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot |
| 106 |
+ |
<< "; pot_local = " << potential_local |
| 107 |
+ |
<< "; pot = " << potential << "\n"; |
| 108 |
+ |
*/ |
| 109 |
+ |
#endif |
| 110 |
+ |
|
| 111 |
|
// Get total potential for entire system from MPI. |
| 112 |
|
#ifdef IS_MPI |
| 113 |
|
MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
| 115 |
|
potential = potential_local; |
| 116 |
|
#endif // is_mpi |
| 117 |
|
|
| 118 |
+ |
#ifdef IS_MPI |
| 119 |
+ |
/* |
| 120 |
+ |
std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
| 121 |
+ |
*/ |
| 122 |
+ |
#endif |
| 123 |
+ |
|
| 124 |
|
return potential; |
| 125 |
|
} |
| 126 |
|
|
| 168 |
|
double vx, vy, vz; |
| 169 |
|
double jx, jy, jz; |
| 170 |
|
int i, vr, vd; // velocity randomizer loop counters |
| 171 |
< |
double *vdrift; |
| 171 |
> |
double vdrift[3]; |
| 172 |
|
double vbar; |
| 173 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 174 |
|
double av2; |
| 175 |
|
double kebar; |
| 176 |
< |
int ndf; // number of degrees of freedom |
| 177 |
< |
int ndfRaw; // the raw number of degrees of freedom |
| 176 |
> |
int ndf, ndf_local; // number of degrees of freedom |
| 177 |
> |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 178 |
|
int n_atoms; |
| 179 |
|
Atom** atoms; |
| 180 |
|
DirectionalAtom* dAtom; |
| 188 |
|
n_oriented = entry_plug->n_oriented; |
| 189 |
|
n_constraints = entry_plug->n_constraints; |
| 190 |
|
|
| 191 |
+ |
// Raw degrees of freedom that we have to set |
| 192 |
+ |
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++){ |
| 212 |
|
|
| 213 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
| 214 |
|
vbar = sqrt( av2 ); |
| 215 |
< |
|
| 215 |
> |
|
| 216 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
| 217 |
|
|
| 218 |
|
// picks random velocities from a gaussian distribution |
| 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 |
|
} |
| 318 |
|
|
