def initSimulation(cmd):
sim = SimFlat(cmd.nSteps, cmd.printRate, cmd.dt)
latticeConstant = cmd.lat
if cmd.lat < 0.0:
latticeConstant = sim.pot.lat
box_size = np.zeros(3)
box_size[0] = cmd.nx*latticeConstant
box_size[1] = cmd.ny*latticeConstant
box_size[2] = cmd.nz*latticeConstant
sim.domain = domain.Domain(cmd.xproc, cmd.yproc, cmd.zproc, box_size)
sim.boxes = linkcell.initLinkCells(sim, sim.domain)
sim.atoms = initatoms.initAtoms(sim.boxes.nTotalBoxes * sim.boxes.MAXATOMS)
sim.atoms.setBounds(cmd.nx, cmd.ny, cmd.nz, latticeConstant)
initatoms.createFccLattice(cmd.nx, cmd.ny, cmd.nz, latticeConstant, sim.atoms, sim.boxes, sim.domain)
initatoms.setTemperature(sim, cmd.temp)
sim.atomHalo = halo.Halo(sim.boxes, sim.domain)
redistributeAtoms(sim, sim.atoms)
return sim
import numpy as np
sim = simflat.SimFlat(10, 10, 0.1)
lat = 3.615
nx = 4
ny = 4
nz = 4
box_size = np.zeros(3)
box_size[0] = nx * lat
box_size[1] = ny * lat
box_size[2] = nz * lat
boxes = linkcell.initLinkCells(sim, box_size)
sim.atoms = initatoms.atoms(boxes.nTotalBoxes * boxes.MAXATOMS)
sim.atoms.setBounds(nx, ny, nz, lat)
sim.boxes = boxes
initatoms.createFccLattice(nx, ny, nz, lat, sim.atoms, sim.boxes)
def test_tuple(boxes):
"""
Test the conversion from 3-D indices to a linear index and back
"""
ix = 0
iy = 0
iz = 0
for ix in range(-1, boxes.gridSize[0] + 1):