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/// \file
/// Initialize the atom configuration.
#include "initAtoms.h"
#include <math.h>
#include <assert.h>
#include "constants.h"
#include "decomposition.h"
#include "parallel.h"
#include "random.h"
#include "linkCells.h"
#include "timestep.h"
#include "memUtils.h"
#include "performanceTimers.h"
static void computeVcm(SimFlat* s, real_t vcm[3]);
/// \details
/// Call functions such as createFccLattice and setTemperature to set up
/// initial atom positions and momenta.
Atoms* initAtoms(LinkCell* boxes)
{
Atoms* atoms = comdMalloc(sizeof(Atoms));
int maxTotalAtoms = MAXATOMS*boxes->nTotalBoxes;
atoms->gid = (int*) comdMalloc(maxTotalAtoms*sizeof(int));
atoms->iSpecies = (int*) comdMalloc(maxTotalAtoms*sizeof(int));
atoms->r = (real3*) comdMalloc(maxTotalAtoms*sizeof(real3));
atoms->p = (real3*) comdMalloc(maxTotalAtoms*sizeof(real3));
atoms->f = (real3*) comdMalloc(maxTotalAtoms*sizeof(real3));
atoms->U = (real_t*)comdMalloc(maxTotalAtoms*sizeof(real_t));
atoms->nLocal = 0;
atoms->nGlobal = 0;
for (int iOff = 0; iOff < maxTotalAtoms; iOff++)
{
atoms->gid[iOff] = 0;
atoms->iSpecies[iOff] = 0;
zeroReal3(atoms->r[iOff]);
zeroReal3(atoms->p[iOff]);
zeroReal3(atoms->f[iOff]);
atoms->U[iOff] = 0.;
}
return atoms;
}
void destroyAtoms(Atoms *atoms)
{
freeMe(atoms,gid);
freeMe(atoms,iSpecies);
freeMe(atoms,r);
freeMe(atoms,p);
freeMe(atoms,f);
freeMe(atoms,U);
comdFree(atoms);
}
/// Creates atom positions on a face centered cubic (FCC) lattice with
/// nx * ny * nz unit cells and lattice constant lat.
/// Set momenta to zero.
void createFccLattice(int nx, int ny, int nz, real_t lat, SimFlat* s)
{
const real_t* localMin = s->domain->localMin; // alias
const real_t* localMax = s->domain->localMax; // alias
int nb = 4; // number of atoms in the basis
real3 basis[4] = { {0.25, 0.25, 0.25},
{0.25, 0.75, 0.75},
{0.75, 0.25, 0.75},
{0.75, 0.75, 0.25} };
// create and place atoms
int begin[3];
int end[3];
for (int ii=0; ii<3; ++ii)
{
begin[ii] = floor(localMin[ii]/lat);
end[ii] = ceil (localMax[ii]/lat);
}
real_t px,py,pz;
px=py=pz=0.0;
for (int ix=begin[0]; ix<end[0]; ++ix)
for (int iy=begin[1]; iy<end[1]; ++iy)
for (int iz=begin[2]; iz<end[2]; ++iz)
for (int ib=0; ib<nb; ++ib)
{
real_t rx = (ix+basis[ib][0]) * lat;
real_t ry = (iy+basis[ib][1]) * lat;
real_t rz = (iz+basis[ib][2]) * lat;
if (rx < localMin[0] || rx >= localMax[0]) continue;
if (ry < localMin[1] || ry >= localMax[1]) continue;
if (rz < localMin[2] || rz >= localMax[2]) continue;
int id = ib+nb*(iz+nz*(iy+ny*(ix)));
putAtomInBox(s->boxes, s->atoms, id, 0, rx, ry, rz, px, py, pz);
}
// set total atoms in simulation
startTimer(commReduceTimer);
addIntParallel(&s->atoms->nLocal, &s->atoms->nGlobal, 1);
stopTimer(commReduceTimer);
assert(s->atoms->nGlobal == nb*nx*ny*nz);
}
/// Sets the center of mass velocity of the system.
/// \param [in] newVcm The desired center of mass velocity.
void setVcm(SimFlat* s, real_t newVcm[3])
{
real_t oldVcm[3];
computeVcm(s, oldVcm);
real_t vShift[3];
vShift[0] = (newVcm[0] - oldVcm[0]);
vShift[1] = (newVcm[1] - oldVcm[1]);
vShift[2] = (newVcm[2] - oldVcm[2]);
for (int iBox=0; iBox<s->boxes->nLocalBoxes; ++iBox)
{
for (int iOff=MAXATOMS*iBox, ii=0; ii<s->boxes->nAtoms[iBox]; ++ii, ++iOff)
{
int iSpecies = s->atoms->iSpecies[iOff];
real_t mass = s->species[iSpecies].mass;
s->atoms->p[iOff][0] += mass * vShift[0];
s->atoms->p[iOff][1] += mass * vShift[1];
s->atoms->p[iOff][2] += mass * vShift[2];
}
}
}
/// 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
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);
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);
}
}
// 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);
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;
}
}
}
/// Computes the center of mass velocity of the system.
void computeVcm(SimFlat* s, real_t vcm[3])
{
real_t vcmLocal[4] = {0., 0., 0., 0.};
real_t vcmSum[4] = {0., 0., 0., 0.};
// sum the momenta and particle masses
for (int iBox=0; iBox<s->boxes->nLocalBoxes; ++iBox)
{
for (int iOff=MAXATOMS*iBox, ii=0; ii<s->boxes->nAtoms[iBox]; ++ii, ++iOff)
{
vcmLocal[0] += s->atoms->p[iOff][0];
vcmLocal[1] += s->atoms->p[iOff][1];
vcmLocal[2] += s->atoms->p[iOff][2];
int iSpecies = s->atoms->iSpecies[iOff];
vcmLocal[3] += s->species[iSpecies].mass;
}
}
startTimer(commReduceTimer);
addRealParallel(vcmLocal, vcmSum, 4);
stopTimer(commReduceTimer);
real_t totalMass = vcmSum[3];
vcm[0] = vcmSum[0]/totalMass;
vcm[1] = vcmSum[1]/totalMass;
vcm[2] = vcmSum[2]/totalMass;
}
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