| 1 |
|
#include <cmath> |
| 2 |
+ |
#include <mpi++.h> |
| 3 |
|
|
| 4 |
|
#include "Thermo.hpp" |
| 5 |
|
#include "SRI.hpp" |
| 18 |
|
DirectionalAtom *dAtom; |
| 19 |
|
|
| 20 |
|
int n_atoms; |
| 21 |
+ |
double kinetic_global; |
| 22 |
|
Atom** atoms; |
| 23 |
+ |
|
| 24 |
|
|
| 25 |
|
n_atoms = entry_plug->n_atoms; |
| 26 |
|
atoms = entry_plug->atoms; |
| 27 |
|
|
| 28 |
|
kinetic = 0.0; |
| 29 |
+ |
kinetic_global = 0.0; |
| 30 |
|
for( kl=0; kl < n_atoms; kl++ ){ |
| 31 |
|
|
| 32 |
|
vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
| 48 |
|
+ (jz2 / dAtom->getIzz()); |
| 49 |
|
} |
| 50 |
|
} |
| 51 |
< |
|
| 51 |
> |
#ifdef IS_MPI |
| 52 |
> |
MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
| 53 |
> |
kinetic = kinetic_global; |
| 54 |
> |
#endif |
| 55 |
> |
|
| 56 |
|
kinetic = kinetic * 0.5 / e_convert; |
| 57 |
|
|
| 58 |
|
return kinetic; |
| 61 |
|
double Thermo::getPotential(){ |
| 62 |
|
|
| 63 |
|
double potential; |
| 64 |
+ |
double potential_global; |
| 65 |
|
int el, nSRI; |
| 66 |
|
SRI** sris; |
| 67 |
|
|
| 69 |
|
nSRI = entry_plug->n_SRI; |
| 70 |
|
|
| 71 |
|
potential = 0.0; |
| 72 |
< |
|
| 72 |
> |
potential_global = 0.0; |
| 73 |
|
potential += entry_plug->longRange->get_potential();; |
| 74 |
|
|
| 75 |
|
// std::cerr << "long range potential: " << potential << "\n"; |
| 67 |
– |
|
| 76 |
|
for( el=0; el<nSRI; el++ ){ |
| 77 |
|
|
| 78 |
|
potential += sris[el]->get_potential(); |
| 79 |
|
} |
| 80 |
|
|
| 81 |
+ |
// Get total potential for entire system from MPI. |
| 82 |
+ |
#ifdef IS_MPI |
| 83 |
+ |
MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM); |
| 84 |
+ |
potential = potential_global; |
| 85 |
+ |
#endif |
| 86 |
+ |
|
| 87 |
|
return potential; |
| 88 |
|
} |
| 89 |
|
|
| 109 |
|
|
| 110 |
|
double Thermo::getPressure(){ |
| 111 |
|
|
| 112 |
< |
const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
| 113 |
< |
const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
| 114 |
< |
const double conv_A_m = 1.0E-10; //convert A -> m |
| 112 |
> |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
| 113 |
> |
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
| 114 |
> |
// const double conv_A_m = 1.0E-10; //convert A -> m |
| 115 |
|
|
| 116 |
|
return 0.0; |
| 117 |
|
} |
| 159 |
|
|
| 160 |
|
// picks random velocities from a gaussian distribution |
| 161 |
|
// centered on vbar |
| 162 |
< |
|
| 162 |
> |
#ifndef USE_SPRNG |
| 163 |
> |
/* If we are using mpi, we need to use the SPRNG random |
| 164 |
> |
generator. The non drand48 generator will just repeat |
| 165 |
> |
the same numbers for every node creating a non-gaussian |
| 166 |
> |
distribution for the simulation. drand48 is fine for the |
| 167 |
> |
single processor version of the code, but SPRNG should |
| 168 |
> |
still be preferred for consistency. |
| 169 |
> |
*/ |
| 170 |
> |
#ifdef IS_MPI |
| 171 |
> |
#error "SPRNG random number generator must be used for MPI" |
| 172 |
> |
#else |
| 173 |
> |
#warning "Using drand48 for random number generation" |
| 174 |
> |
#endif |
| 175 |
|
x = drand48(); |
| 176 |
|
y = drand48(); |
| 177 |
|
vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
| 183 |
|
x = drand48(); |
| 184 |
|
y = drand48(); |
| 185 |
|
vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
| 186 |
< |
|
| 186 |
> |
#endif |
| 187 |
> |
|
| 188 |
> |
#ifdef USE_SPRNG |
| 189 |
> |
vx = vbar * entry_plug->gaussStream->getGaussian(); |
| 190 |
> |
vy = vbar * entry_plug->gaussStream->getGaussian(); |
| 191 |
> |
vz = vbar * entry_plug->gaussStream->getGaussian(); |
| 192 |
> |
#endif |
| 193 |
> |
|
| 194 |
|
atoms[vr]->set_vx( vx ); |
| 195 |
|
atoms[vr]->set_vy( vy ); |
| 196 |
|
atoms[vr]->set_vz( vz ); |
| 238 |
|
if( atoms[i]->isDirectional() ){ |
| 239 |
|
|
| 240 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 241 |
+ |
#ifdef IS_MPI |
| 242 |
+ |
#error "SPRNG random number generator must be used for MPI" |
| 243 |
+ |
#else |
| 244 |
+ |
#warning "Using drand48 for random number generation" |
| 245 |
+ |
#endif |
| 246 |
|
|
| 247 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
| 248 |
|
x = drand48(); |
| 258 |
|
x = drand48(); |
| 259 |
|
y = drand48(); |
| 260 |
|
jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
| 261 |
+ |
#endif |
| 262 |
+ |
#ifdef USE_SPRNG |
| 263 |
+ |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
| 264 |
+ |
jx = vbar * entry_plug->gaussStream->getGaussian(); |
| 265 |
+ |
|
| 266 |
+ |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 267 |
+ |
jy = vbar * entry_plug->gaussStream->getGaussian(); |
| 268 |
+ |
|
| 269 |
+ |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 270 |
+ |
jz = vbar * entry_plug->gaussStream->getGaussian(); |
| 271 |
+ |
#endif |
| 272 |
|
|
| 273 |
|
dAtom->setJx( jx ); |
| 274 |
|
dAtom->setJy( jy ); |
