def collectGlobalEnergy(self):
eLocal = np.zeros(2)
eSum = np.zeros(2)
eLocal[0] = self.eKineticLocal
eLocal[1] = self.ePotLocal
parallel.addParallel(eLocal, eSum)
self._eKinetic = eSum[0]
self._ePot = eSum[1]
self.globalEnergyGood = True
def computeVcm(sim):
vcm = np.zeros(3)
vcmGlobal = np.zeros(3)
totalMass = 0.0
# for i in range(sim.atoms.nAtoms):
for iBox in range(sim.boxes.nLocalBoxes):
iOff = sim.boxes.MAXATOMS * iBox
for ii in range(sim.boxes.nAtoms[iBox]):
vcm += sim.atoms.p[iOff, :]
iSpecies = sim.atoms.species[iOff]
totalMass += sim.species[iSpecies].mass
iOff += 1
parallel.addParallel(vcm, vcmGlobal)
vcm = vcmGlobal / totalMass
return vcm
def createFccLattice(nx, ny, nz, lat, atoms, boxes, domain):
"""Create atom positions on a face centered cubic (FCC) lattice
with nx * ny * nz unit cells and lattice constance 'lat'
"""
nb = 4 # number of atoms in this basis
basis = [(0.25, 0.25, 0.25), (0.25, 0.75, 0.75), (0.75, 0.25, 0.75), (0.75, 0.75, 0.25)]
begin = [int(x) for x in np.floor(domain.localMin / lat)]
end = [int(x) for x in np.ceil(domain.localMax / lat)]
idx = 0
for ix in range(begin[0], end[0]):
for iy in range(begin[1], end[1]):
for iz in range(begin[2], end[2]):
for ib in range(nb):
rx = (ix + basis[ib][0]) * lat
ry = (iy + basis[ib][1]) * lat
rz = (iz + basis[ib][2]) * lat
if rx < domain.localMin[0] or rx >= domain.localMax[0]:
continue
if ry < domain.localMin[1] or ry >= domain.localMax[1]:
continue
if rz < domain.localMin[2] or rz >= domain.localMax[2]:
continue
gid = ib + nb * (iz + nz * (iy + ny * ix))
boxes.putAtomInBox(atoms, gid, 0, rx, ry, rz)
idx += 1
nlocal = np.zeros(1, dtype=np.int)
nglobal = np.zeros(1, dtype=np.int)
nlocal[0] = idx
parallel.addParallel(nlocal, nglobal)
atoms.nGlobal = nglobal[0]
if atoms.nGlobal != nb * nx * ny * nz:
print "nGlobal = ", atoms.nGlobal
print "nb,nx,ny,nz,product", nb, nx, ny, nz, nb * nx * ny * nz
assert atoms.nGlobal == nb * nx * ny * nz