/// Sets the temperature of system.
///
/// Selects atom velocities randomly from a boltzmann (equilibrium)
/// distribution that corresponds to the specified temperature. This
/// random process will typically result in a small, but non zero center
/// of mass velocity and a small difference from the specified
/// temperature. For typical MD runs these small differences are
/// unimportant, However, to avoid possible confusion, we set the center
/// of mass velocity to zero and scale the velocities to exactly match
/// the input temperature.
void setTemperature(SimFlat* s, real_t temperature)
{
// set initial velocities for the distribution
printf("CnC: Inside setTemperature %f, %d\n",temperature, s->boxes->nLocalBoxes);
for (int iBox=0; iBox<s->boxes->nLocalBoxes; ++iBox)
{
for (int iOff=MAXATOMS*iBox, ii=0; ii<s->boxes->nAtoms[iBox]; ++ii, ++iOff)
{
int iType = s->atoms->iSpecies[iOff];
real_t mass = s->species[iType].mass;
real_t sigma = sqrt(kB_eV * temperature/mass);
uint64_t seed = mkSeed(s->atoms->gid[iOff], 123);
#ifndef CNCOCR_TG // Manu: gasdev not working with TG
s->atoms->p[iOff][0] = mass * sigma * gasdev(&seed);
s->atoms->p[iOff][1] = mass * sigma * gasdev(&seed);
s->atoms->p[iOff][2] = mass * sigma * gasdev(&seed);
#else
s->atoms->p[iOff][0] = mass * sigma;
s->atoms->p[iOff][1] = mass * sigma;
s->atoms->p[iOff][2] = mass * sigma;
#endif
}
}
// compute the resulting temperature
// kinetic energy = 3/2 kB * Temperature
if (temperature == 0.0) return;
real_t vZero[3] = {0., 0., 0.};
setVcm(s, vZero);
kineticEnergy(s);
real_t temp = (s->eKinetic/s->atoms->nGlobal)/kB_eV/1.5;
// scale the velocities to achieve the target temperature
real_t scaleFactor = sqrt(temperature/temp);
// real_t scaleFactor =1;
for (int iBox=0; iBox<s->boxes->nLocalBoxes; ++iBox)
{
for (int iOff=MAXATOMS*iBox, ii=0; ii<s->boxes->nAtoms[iBox]; ++ii, ++iOff)
{
s->atoms->p[iOff][0] *= scaleFactor;
s->atoms->p[iOff][1] *= scaleFactor;
s->atoms->p[iOff][2] *= scaleFactor;
}
}
kineticEnergy(s);
temp = s->eKinetic/s->atoms->nGlobal/kB_eV/1.5;
}
/// Add a random displacement to the atom positions.
/// Atoms are displaced by a random distance in the range
/// [-delta, +delta] along each axis.
/// \param [in] delta The maximum displacement (along each axis).
void randomDisplacements(SimFlat* s, real_t delta)
{
for (int iBox=0; iBox<s->boxes->nLocalBoxes; ++iBox)
{
for (int iOff=MAXATOMS*iBox, ii=0; ii<s->boxes->nAtoms[iBox]; ++ii, ++iOff)
{
uint64_t seed = mkSeed(s->atoms->gid[iOff], 457);
s->atoms->r[iOff][0] += (2.0*lcg61(&seed)-1.0) * delta;
s->atoms->r[iOff][1] += (2.0*lcg61(&seed)-1.0) * delta;
s->atoms->r[iOff][2] += (2.0*lcg61(&seed)-1.0) * delta;
}
}
}