def test_random():
from numpy import dot, all, abs
from numpy.random import randint
from random import choice
from pylada.ce import Cluster
from pylada.crystal import binary, supercell
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# now try random clusters with cell and their supercells
for i in xrange(10):
# random cluster
a = Cluster(lattice)
site = choice([0, 1])
a.add_spin(lattice[site].pos)
for j in xrange(4):
site = choice([0, 1])
pos = lattice[site].pos + dot(lattice.cell, randint(4, size=(3,))-2)
try: a.add_spin(pos)
except ValueError: pass
# random structure
structure = supercell(lattice, dot(lattice.cell, get_cell(3)))
for atom in structure: atom.type = choice(lattice[atom.site].type)
# random supercell
for j in xrange(5):
sp = supercell(structure, dot(structure.cell, get_cell(3)))
for atom in sp: atom.site = structure[atom.site].site
assert all(abs(a(sp) - len(sp) / len(structure) * a(structure)) < 1e-8)
def test_occmap(): from numpy import cos, sin, pi, abs, all from pylada.crystal import binary from pylada.ce import Cluster lattice = binary.zinc_blende() for atom in lattice: atom.type = ['Si', 'Ge'] a = Cluster(lattice) mapping = a.occupation_mapping() assert len(mapping) == len(lattice) assert len(mapping[0]) == 2 assert len(mapping[1]) == 2 assert abs(mapping[0]['Si'] - cos(2e0*pi*0e0/2.0)) < 1e-8 assert abs(mapping[0]['Ge'] - cos(2e0*pi*1e0/2.0)) < 1e-8 assert abs(mapping[1]['Si'] - cos(2e0*pi*0e0/2.0)) < 1e-8 assert abs(mapping[1]['Ge'] - cos(2e0*pi*1e0/2.0)) < 1e-8 lattice = binary.zinc_blende() lattice[1].type = ['Si', 'Ge', 'C'] a = Cluster(lattice) mapping = a.occupation_mapping() assert len(mapping) == len(lattice) assert mapping[0] is None assert len(mapping[1]) == len(lattice[1].type) assert all(abs(mapping[1]['C'] - [cos(2e0*pi*0e0/3.0), sin(2e0*pi*2e0/3.0)])) assert all(abs(mapping[1]['Si'] - [cos(2e0*pi*1e0/3.0), sin(2e0*pi*1e0/3.0)])) assert all(abs(mapping[1]['Ge'] - [cos(2e0*pi*2e0/3.0), sin(2e0*pi*2e0/3.0)]))
def test_cmp():
""" Test Cluster._contains function """
from numpy import all, any
from pylada.crystal import binary
from pylada.ce import Cluster
from pylada.ce.cluster import spin
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
def cmp(a,b):
if len(a) != len(b): return False
return all([any([all(v == s) for s in a]) for v in b])
a = Cluster(lattice)
a.add_spin(lattice[0].pos)
assert cmp(a.spins, [spin([0, 0, 0], 0)])
assert not cmp(a.spins, [spin([0.5, 0.5, 0.5], 0)])
assert not cmp(a.spins, [spin([0, 0, 0], 1)])
a = Cluster(lattice)
a.add_spin(lattice[1].pos)
assert cmp(a.spins, [spin([0, 0, 0], 1)])
assert not cmp(a.spins, [spin([0.5, 0.5, 0.5], 1)])
assert not cmp(a.spins, [spin([0, 0, 0], 0)])
a.add_spin(lattice[0].pos)
assert cmp(a.spins, [spin([0, 0, 0], 1), spin([0, 0, 0])])
assert cmp(a.spins, [spin([0, 0, 0]), spin([0, 0, 0], 1)])
assert not cmp(a.spins, [spin([0, 0, 0], 1), spin([0, 0, 0]), spin([1, 0, 0])])
assert not cmp(a.spins, [spin([1, 0, 0]), spin([0, 0, 0], 1)])
def test_onsite():
""" Tests J0 PI calculation.
This uses the same algorithmic pathway as more complex figures, but can
be easily computed as the sum of particular specie-dependent terms on
each site.
"""
from numpy import dot, abs, all
from random import choice
from pylada.crystal import binary, supercell
from pylada.ce import Cluster
lattice = binary.zinc_blende()
for atom in lattice: atom.type = ['Si', 'Ge', 'C']
structure = binary.zinc_blende()
for atom in structure: atom.type = 'Si'
a = Cluster(lattice)
# Empty cluster first
assert abs(a(structure) - len(structure)) < 1e-8
for i in xrange(10):
superstructure = supercell(lattice, dot(lattice.cell, get_cell()))
for atom in superstructure: atom.type = choice(atom.type)
assert abs(a(superstructure) - len(superstructure)) < 1e-8
# Try on-site cluster.
# loop over random supercells.
# PI should be number of proportional to number of each atomic type on each
# site, or thereabouts
mapping = a.occupation_mapping()
for i in xrange(10):
# create random superstructure
superstructure = supercell(lattice, dot(lattice.cell, get_cell()))
for atom in superstructure: atom.type = choice(atom.type)
# now first and second site clusters
for i, site in enumerate(lattice):
# loop over flavors.
types = [u.type for u in superstructure]
a.spins = None
a.add_spin(site.pos)
s = mapping[i].itervalues().next().copy()
s[:] = 0e0
for t in site.type:
s += float(types.count(t)) * mapping[i][t]
assert all(abs(a(superstructure) - s) < 1e-8)
def test_spins_are_sorted():
""" Check spin sorting when using add_spins. """
from numpy import all, dot
from numpy.random import randint
from random import choice
from itertools import permutations
from pylada.ce.cluster import spin
from pylada.ce import Cluster
from pylada.crystal import binary
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# Trial with known result.
a = Cluster(lattice)
a.add_spin(lattice[1].pos)
a.add_spin(lattice[0].pos + [0.5, 0, 0.5])
a.add_spin(lattice[1].pos + [-0.5, 0, 0.5])
a.add_spin(lattice[0].pos + [-2.5, -1.0, 0.5])
assert all(a.spins[0] == spin([0, 0, 0], 1))
assert all(a.spins[1] == spin([0.5, 0, 0.5]))
assert all(a.spins[2] == spin([-0.5, 0, 0.5], 1))
assert all(a.spins[3] == spin([-2.5, -1.0, 0.5], 0))
spins = a.spins.copy()
for p in permutations(range(len(spins))):
a = Cluster(lattice)
for i in p:
a.add_spin(spins[i]['position'] + lattice[spins[i]['sublattice']].pos)
assert all(a.spins == spins)
# Trial with unknown result.
for i in xrange(20):
a = Cluster(lattice)
for j in xrange(5):
site = choice([0, 1])
pos = lattice[site].pos + dot(lattice.cell, randint(4, size=(3,))-2)
try: a.add_spin(pos)
except ValueError: pass
if a.order < 1: continue
spins = a.spins.copy()
for p in permutations(range(len(spins))):
a = Cluster(lattice)
for i in p:
a.add_spin(spins[i]['position'] + lattice[spins[i]['sublattice']].pos)
assert all(a.spins == spins)
def test_addspins():
""" Test adding spins to cluster.
Check failure modes.
"""
from numpy import all
from pylada.crystal import binary
from pylada.ce import Cluster
from pylada.ce.cluster import spin
from pylada.error import ValueError
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
a = Cluster(lattice)
# Wrong position
try: a.add_spin(lattice[0].pos+0.1)
except ValueError: pass
else: raise Exception()
# now add first spin
a.add_spin(lattice[0].pos)
assert len(a.spins) == 1
assert all(a.spins[0] == spin([0, 0, 0], 0))
# try adding it again
try: a.add_spin(lattice[0].pos)
except ValueError: pass
else: raise Exception()
# Wrong position
try: a.add_spin(lattice[1].pos+[1.1, -0.5, -2.5])
except ValueError: pass
else: raise Exception()
# Then add a different spin
a.add_spin(lattice[1].pos + [1.0, -0.5, -2.5])
assert len(a.spins) == 2
assert all(a.spins[0] == spin([0, 0, 0], 0))
assert all(a.spins[1] == spin([1.0, -0.5, -2.5], 1))
def test_symmetrized():
""" Tests that symmetrized clusters are determined correctly. """
from numpy import all, any
from pylada.ce import Cluster
from pylada.crystal import binary, neighbors
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge']
a = Cluster(lattice)
a.add_spin(lattice[0].pos)
a.add_spin(lattice[0].pos + [0.0, -0.5, -0.5])
a._create_symmetrized()
assert len(a._symmetrized) == 2 * 12
for i, (atom, vec, d) in enumerate(neighbors(lattice, 16, lattice[0].pos)):
if i < 4: continue
b = Cluster(lattice)
b.add_spin(lattice[0].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
for i, (atom, vec, d) in enumerate(neighbors(lattice, 16, lattice[1].pos)):
if i < 4: continue
b = Cluster(lattice)
b.add_spin(lattice[1].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
a = Cluster(lattice)
a.add_spin(lattice[1].pos)
a.add_spin(lattice[1].pos + [1.0, 0, 0])
a._create_symmetrized()
assert len(a._symmetrized) == 6
for i, (atom, vec, d) in enumerate(neighbors(lattice, 24, lattice[0].pos)):
if i < 16: continue
b = Cluster(lattice)
b.add_spin(lattice[1].pos)
b.add_spin(vec)
assert any(all(b.spins == u) for u in a._symmetrized)
