initAtoms.c

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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);
}

/// 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;
}