def test_B2(): from numpy import all from pylada.ce import cluster_factory from pylada.crystal import binary # test multi-lattice with different occupations. lattice = binary.zinc_blende() lattice[0].type = ['Si', 'Ge'] lattice[1].type = ['Si', 'Ge', 'C'] a = cluster_factory(lattice, B2=1) assert len(a) == 2 assert all(a[0].spins['sublattice'] == [0, 1]) assert all(abs(a[0].spins['position'][0]) < 1e-8) vector = a[0].spins[1] assert abs(sum((lattice[vector[1]].pos + vector[0])**2) - 3*0.25*0.25) < 1e-8 assert all(a[1].spins['sublattice'] == [1, 0]) assert all(abs(a[1].spins['position'][0]) < 1e-8) assert all(abs(a[1].spins['position'][1]) < 1e-8) a = cluster_factory(lattice, B2=2) assert len(a) == 4 a = cluster_factory(lattice, B2=3) assert len(a) == 6 # test multi-lattice with same occupations. lattice = binary.zinc_blende() lattice[0].type = ['Si', 'Ge'] lattice[1].type = ['Si', 'Ge'] a = cluster_factory(lattice, B2=1) assert len(a) == 1 a = cluster_factory(lattice, B2=2) assert len(a) == 2 a = cluster_factory(lattice, B2=3) assert len(a) == 3
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_J1(): from numpy import all from pylada.ce import cluster_factory from pylada.crystal import binary # test multi-lattice with different occupations. lattice = binary.zinc_blende() lattice[0].type = ['Si', 'Ge'] lattice[1].type = ['Si', 'Ge', 'C'] a = cluster_factory(lattice, J1=True) assert len(a) == 2 assert all(all(abs(u.spins['position']) < 1e-8) for u in a) assert a[0].spins['sublattice'] == 0 assert a[1].spins['sublattice'] == 1 # test multi-lattice with same occupations. lattice = binary.zinc_blende() lattice[0].type = ['Si', 'Ge'] lattice[1].type = ['Si', 'Ge'] a = cluster_factory(lattice, J1=True) assert len(a) == 1 assert all(all(abs(u.spins['position']) < 1e-8) for u in a) assert a[0].spins['sublattice'] == 0
def test_B3():
from numpy import all
from pylada.ce import cluster_factory
from pylada.crystal import binary
def topos(s):
return lattice[s[1]].pos + s[0]
# test multi-lattice with different occupations.
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
a = cluster_factory(lattice, B3=1)
assert len(a) == 2
for cluster in a:
assert all(abs(abs(topos(cluster.spins[1]) - topos(cluster.spins[0])) - 0.25) < 1e-8)
assert all(abs(abs(topos(cluster.spins[2]) - topos(cluster.spins[0])) - 0.25) < 1e-8)
# test multi-lattice with same occupations.
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge']
a = cluster_factory(lattice, B3=1)
assert len(a) == 1
for cluster in a:
assert all(abs(abs(topos(cluster.spins[1]) - topos(cluster.spins[0])) - 0.25) < 1e-8)
assert all(abs(abs(topos(cluster.spins[2]) - topos(cluster.spins[0])) - 0.25) < 1e-8)
def test_single_counting():
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[4, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
n = 0
for center in b:
for endpoint, vector in center.sc_bond_iter():
n += 1
for other, v in endpoint.sc_bond_iter(): assert other is not center
assert id(center) in [id(c) for c, v in endpoint]
assert n == 2 * len(a)
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_disorder(lim=8):
from numpy import all, array, dot
from numpy.random import random, randint
from numpy.linalg import det
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
lattice = binary.zinc_blende()
for i in xrange(10):
cell = randint(-lim, lim, (3,3))
while det(cell) == 0: cell = randint(-lim, lim, (3,3))
a = supercell(lattice, dot(lattice.cell, cell))
b = build_tree(a, overlap=0.8)
ids = [id(node.center) for node in b]
connections = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
epsilon = random((3,3)) * 0.1
epsilon = epsilon + epsilon.T
a.cell += dot(epsilon, a.cell)
for atom in a: atom.pos += dot(epsilon, atom.pos)
b = build_tree(a, overlap=0.8)
c = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
assert all(connections == c)
b = build_tree(a, overlap=0.8)
for atom in a: atom.pos += random(3) * 0.05 - 0.025
c = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
assert all(connections == c)
return a
def test_tree():
from numpy import all, array, dot, sum, any
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[2, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
for center in b:
positions = []
for i, (bond, vector) in enumerate(center):
position = bond.pos + dot(a.cell, vector)
assert abs(sum((position - center.pos)**2) - 0.25*0.25*3) < 1e-8
assert all( [any(abs(array(p) - position[None, :]) > 1e-8) for p in positions] )
positions.append(position)
assert i == 3
def test_translations(cell):
from numpy import abs, all
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
translations = Transforms(lattice).translations(hft)
assert translations.shape == (len(structure) // len(lattice) - 1,
len(structure))
# compute each translation and gets decorations
for atom in structure:
if atom.site != 0:
continue
# create translation
trans = atom.pos - lattice[0].pos
if all(abs(trans) < 1e-8):
continue
# figure out its index
index = hft.index(trans) - 1
for site in structure:
pos = site.pos - lattice[site.site].pos
i = hft.index(pos, site.site)
j = hft.index(pos + trans, site.site)
assert translations[index, i] == j
def test_inas():
from numpy import identity, abs, all, dot, array
from pylada.crystal.binary import zinc_blende
from quantities import eV, angstrom
vff = functional()
structure = zinc_blende()
structure[0].type = 'In'
structure[1].type = 'As'
structure.scale = 6.5 #2.62332 * 2 / sqrt(3) / 0.529177
out = vff._pyeval(structure)
assert abs(out.energy - 0.34958768908 * eV) < 1e-8
assert abs(out.energy - vff.energy(structure)) < 1e-8
assert all(abs(out.stress - vff.jacobian(structure)[0]) < 1e-8)
assert all(abs(out.stress - identity(3) * -0.04096678 * eV/angstrom**3) < 1e-8)
assert all(abs(out[0].gradient) < 1e-8)
assert all(abs(out[1].gradient) < 1e-8)
epsilon = array([[1e0, 0.1, 0], [0.1, 1e0, 0], [0, 0, 1e0]])
structure.cell = dot(epsilon, structure.cell)
for atom in structure: atom.pos = dot(epsilon, atom.pos)
out = vff._pyeval(structure)
assert abs(out.energy - 0.527010806043 * eV) < 1e-8
assert abs(out.energy - vff.energy(structure)) < 1e-8
assert all(abs(out.stress - [[ -2.50890474e-02, -2.95278697e-02, 0],
[ -2.95278697e-02, -2.50890474e-02, 0],
[ 0, 0, -1.85427515e-02]] * eV / angstrom**3) < 1e-6)
assert all(abs(out.stress - vff.jacobian(structure)[0]) < 1e-8)
assert all(abs(out[0].gradient - [0, 0, 1.09205526] * eV / angstrom) < 1e-6)
assert all(abs(out[1].gradient - [0, 0, -1.09205526] * eV / angstrom) < 1e-6)
assert all(abs([u.gradient for u in out] - vff.jacobian(structure)[1].magnitude) < 1e-8)
def test_toarray():
""" Tests label exchange """
from random import choice
from numpy import all, zeros
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
for u in range(11):
structure = supercell(lattice, get_cell())
for atom in structure:
atom.type = choice(atom.type)
hft = HFTransform(lattice, structure)
a = transforms.toarray(hft, structure)
b = zeros(len(structure), dtype='int')
for atom in structure:
site = lattice[atom.site]
b[hft.index(atom.pos - site.pos,
atom.site)] = site.type.index(atom.type) + 1
assert all(a == b)
def test_zb():
from numpy import all, abs, dot
from pylada.crystal import space_group, transform, binary
from pylada.crystal.cppwrappers import equivalent
structure = binary.zinc_blende()
ops = space_group(structure)
assert len(ops) == 24
for op in ops:
assert op.shape == (4, 3)
other = transform(structure, op)
assert all(abs(dot(op[:3], structure.cell)-other.cell) < 1e-8)
for a, atom in zip(structure, other):
assert all(abs(dot(op[:3], a.pos) + op[3] - atom.pos) < 1e-8)
assert a.type == atom.type
assert equivalent(structure, other, cartesian=False)
assert equivalent(other, structure, cartesian=False)
for atom in structure: atom.type = ['A', 'B']
ops = space_group(structure)
assert len(ops) == 48
for op in ops:
assert op.shape == (4, 3)
other = transform(structure, op)
assert all(abs(dot(op[:3], structure.cell)-other.cell) < 1e-8)
for a, atom in zip(structure, other):
assert all(abs(dot(op[:3], a.pos) + op[3] - atom.pos) < 1e-8)
assert a.type == atom.type
assert equivalent(structure, other, cartesian=False)
assert equivalent(other, structure, cartesian=False)
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_translations(cell):
from numpy import abs, all
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
translations = Transforms(lattice).translations(hft)
assert translations.shape == (len(structure) // len(lattice) - 1, len(structure))
# compute each translation and gets decorations
for atom in structure:
if atom.site != 0:
continue
# create translation
trans = atom.pos - lattice[0].pos
if all(abs(trans) < 1e-8):
continue
# figure out its index
index = hft.index(trans) - 1
for site in structure:
pos = site.pos - lattice[site.site].pos
i = hft.index(pos, site.site)
j = hft.index(pos + trans, site.site)
assert translations[index, i] == j
def test_zb():
from numpy import all, abs, dot
from pylada.crystal import space_group, transform, binary
structure = binary.zinc_blende()
ops = space_group(structure)
assert len(ops) == 24
for op in ops:
assert op.shape == (4, 3)
other = transform(structure, op)
assert all(abs(dot(op[:3], structure.cell) - other.cell) < 1e-8)
for a, atom in zip(structure, other):
assert all(abs(dot(op[:3], a.pos) + op[3] - atom.pos) < 1e-8)
assert a.type == atom.type
for atom in structure:
atom.type = ['A', 'B']
ops = space_group(structure)
assert len(ops) == 48
for op in ops:
assert op.shape == (4, 3)
other = transform(structure, op)
assert all(abs(dot(op[:3], structure.cell) - other.cell) < 1e-8)
for a, atom in zip(structure, other):
assert all(abs(dot(op[:3], a.pos) + op[3] - atom.pos) < 1e-8)
assert a.type == atom.type
def test_angle():
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[4, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
for center in b:
ids = [id(u.center) for u, d in center]
angles = set([(id(u.center), id(v.center)) for (u, d), (v, d) in center.angle_iter()])
for i, ida in enumerate(ids[:-1]):
for idb in ids[i+1:]:
if (ida, idb) in angles: assert (idb, ida) not in angles
else: assert (idb, ida) in angles
assert len(angles) == 6
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_labelexchange():
""" Tests label exchange """
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
structure = supercell(lattice, [[8, 0, 0], [0, 0.5, 0.5], [0, -0.5, 0.5]])
species = ['Ge', 'C', 'Si', 'C', 'Si', 'C', 'Si', 'Si', 'Ge', 'Si', 'Ge',
'Si', 'Ge', 'Si', 'Ge', 'Ge', 'Ge', 'C', 'Ge', 'Si', 'Si', 'Si',
'Si', 'Ge', 'Si', 'Ge', 'Si', 'Si', 'Si', 'C', 'Ge', 'Si']
for atom, s in zip(structure, species):
atom.type = s
hft = HFTransform(lattice, structure)
x = transforms.toarray(hft, structure)
results = [21112222221111123331111231122131, # <- this is x
21112222221111122221111321133121,
21112222221111123332222132211232,
21112222221111121112222312233212,
21112222221111122223333123311323,
21112222221111121113333213322313,
12221111112222213331111231122131,
12221111112222212221111321133121,
12221111112222213332222132211232,
12221111112222211112222312233212,
12221111112222212223333123311323,
12221111112222211113333213322313]
permutations = transforms.label_exchange(hft)
for a, b in zip(permutations(x), results[1:]):
assert int(str(a)[1:-1].replace(' ', '')) == b
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)
def test_write_gulp_zinc_blende(): """ Tries and writes a gulp file. """ from numpy import array, abs, all from pylada.crystal.binary import zinc_blende from pylada.crystal.write import gulp a = zinc_blende() string = [u.rstrip().lstrip() for u in gulp(a).splitlines()] string = [u for u in string if len(u) > 0] assert string[0] == 'name' assert string[1] == 'Zinc-Blende' assert string[2] == 'vectors' assert all(abs(array(string[3].split(), dtype='float64') - [0, 0.5, 0.5]) < 1e-8) assert all(abs(array(string[4].split(), dtype='float64') - [0.5, 0, 0.5]) < 1e-8) assert all(abs(array(string[5].split(), dtype='float64') - [0.5, 0.5, 0]) < 1e-8) assert string[6] == 'cartesian' assert string[7].split()[:2] == ['A', 'core'] assert all(abs(array(string[7].split()[2:], dtype='float64')) < 1e-8) assert string[8].split()[:2] == ['B', 'core'] assert all(abs(array(string[8].split()[2:], dtype='float64') - [0.25, 0.25, 0.25]) < 1e-8) string2 = gulp(a, symmgroup=216).splitlines() string2 = [u.rstrip().lstrip() for u in string2] string2 = [u for u in string2 if len(u) > 0] assert string2[:6] == string[:6] assert string2[6] == 'spacegroup' assert string2[7] == '216' assert string2[8:] == string[6:] a.symmgroup = 216 string = gulp(a).splitlines() string = [u.rstrip().lstrip() for u in string] string = [u for u in string if len(u) > 0] assert string2 == string a[0].asymmetric = True a[1].asymmetric = False string = gulp(a).splitlines() string = [u.rstrip().lstrip() for u in string] string = [u for u in string if len(u) > 0] assert string2[:-1] == string del a[0].asymmetric string = gulp(a).splitlines() string = [u.rstrip().lstrip() for u in string] string = [u for u in string if len(u) > 0] assert string2 == string del a[1].asymmetric a[1].type = 'A' a.symmgroup = 227 string = gulp(a).splitlines() string = [u.rstrip().lstrip() for u in string] string = [u for u in string if len(u) > 0] assert string2[:7] == string[:7] assert string[7] == '227' assert string2[8:-1] == string[8:]
def testzb():
""" Tries and writes a gulp file. """
from numpy import array, abs, all
from pylada.crystal.binary import zinc_blende
from pylada.crystal.write import gulp
a = zinc_blende()
string = [u.rstrip().lstrip() for u in gulp(a).splitlines()]
string = [u for u in string if len(u) > 0]
assert string[0] == "name"
assert string[1] == "Zinc-Blende"
assert string[2] == "vectors"
assert all(abs(array(string[3].split(), dtype="float64") - [0, 0.5, 0.5]) < 1e-8)
assert all(abs(array(string[4].split(), dtype="float64") - [0.5, 0, 0.5]) < 1e-8)
assert all(abs(array(string[5].split(), dtype="float64") - [0.5, 0.5, 0]) < 1e-8)
assert string[6] == "cartesian"
assert string[7].split()[:2] == ["A", "core"]
assert all(abs(array(string[7].split()[2:], dtype="float64")) < 1e-8)
assert string[8].split()[:2] == ["B", "core"]
assert all(abs(array(string[8].split()[2:], dtype="float64") - [0.25, 0.25, 0.25]) < 1e-8)
string2 = gulp(a, symmgroup=216).splitlines()
string2 = [u.rstrip().lstrip() for u in string2]
string2 = [u for u in string2 if len(u) > 0]
assert string2[:6] == string[:6]
assert string2[6] == "spacegroup"
assert string2[7] == "216"
assert string2[8:] == string[6:]
a.symmgroup = 216
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2 == string
a[0].asymmetric = True
a[1].asymmetric = False
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2[:-1] == string
del a[0].asymmetric
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2 == string
del a[1].asymmetric
a[1].type = "A"
a.symmgroup = 227
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2[:7] == string[:7]
assert string[7] == "227"
assert string2[8:-1] == string[8:]
def test(): import gc from numpy import all, abs, ones from sys import getrefcount from pylada.crystal.binary import zinc_blende from pylada.error import ValueError, AttributeError from pylada.vff import Node structure = zinc_blende() assert getrefcount(structure[0]) == 2 # structure, getrefcount arg. nodeA = Node(structure[0], 0)
def test_J0(): from pylada.ce import cluster_factory from pylada.crystal import binary lattice = binary.zinc_blende() lattice[0].type = ['Si', 'Ge'] lattice[1].type = ['Si', 'Ge', 'C'] a = cluster_factory(lattice, J0=True) assert len(a) == 1 assert a[0].order == 0
def test_zincblende():
from pylada.crystal import binary
from pylada.enum import generate_bitstrings
from zincblendesets import zincblendesets
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Ga']
for n in xrange(2, 8):
result = []
for x, hft, hermite in generate_bitstrings(lattice, [n]):
result.append( ''.join(str(i) for i in hermite.flatten()[[0, 3, 4, 6, 7, 8]])
+ ' ' + ''.join(str(i-1) for i in x) )
assert len(result) == len(zincblendesets[n])
assert set(result) == zincblendesets[n]
def test_firstisid(cell):
""" Assumption is made in Transforms.transformations """
from numpy import abs, all, identity
from pylada.crystal import binary, supercell, space_group
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# create random structure
structure = supercell(lattice, cell)
while len(structure) > 1:
structure.pop(-1)
assert len(structure) == 1
sg = space_group(structure)[0]
assert all(abs(sg[:3] - identity(3, dtype='float64')) < 1e-8)
assert all(abs(sg[3]) < 1e-8)
def create_jobs():
""" Simple job-folders. """
from pylada.jobfolder import JobFolder
from pylada.crystal.binary import zinc_blende
root = JobFolder()
for name, value, species in zip( ['diamond', 'diamond/alloy', 'GaAs'],
[0, 1, 2],
[('Si', 'Si'), ('Si', 'Ge'), ('Ga', 'As')] ):
job = root / name
job.functional = functional
job.params['value'] = value
job.params['structure'] = zinc_blende()
for atom, specie in zip(job.structure, species): atom.type = specie
return root
def test_firstisid(cell):
""" Assumption is made in Transforms.transformations """
from numpy import abs, all, identity
from pylada.crystal import binary, supercell, space_group
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# create random structure
structure = supercell(lattice, cell)
while len(structure) > 1:
structure.pop(-1)
assert len(structure) == 1
sg = space_group(structure)[0]
assert all(abs(sg[:3] - identity(3, dtype='float64')) < 1e-8)
assert all(abs(sg[3]) < 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_rotations():
from numpy import all, dot, zeros
from numpy.linalg import inv
from pylada.crystal import binary, supercell, HFTransform, space_group, \
which_site
from pylada.enum import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
sg = space_group(lattice)
invcell = inv(lattice.cell)
def get_cells(n):
for i in xrange(1, n):
yield [[i, 0, 0], [0, 0.5, 0.5], [0, -0.5, 0.5]]
for i in xrange(1, n):
yield [[i, 0, 0], [0, i, 0], [0, 0, 1]]
for i in xrange(1, n):
yield [[i, 0, 0], [0, i, 0], [0, 0, i]]
yield dot(lattice.cell, [[1, 0, 0], [0, 1, 0], [0, 0, 2]])
for cell in get_cells(8):
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
transforms = Transforms(lattice)
permutations = transforms.transformations(hft)
assert permutations.shape == (len(sg) - 1, len(structure))
operations = transforms.invariant_ops(structure)
assert any(operations)
# compute each translation and gets decorations
for index, (op, isgood) in enumerate(zip(sg[1:], operations)):
if not isgood: continue
# Create rotation and figure out its index
permutation = zeros(len(structure), dtype='int') - 1
for atom in structure:
pos = dot(op[:3], atom.pos) + op[3]
newsite = which_site(pos, lattice, invcell)
i = hft.index(atom.pos - lattice[atom.site].pos, atom.site)
j = hft.index(pos - lattice[newsite].pos, newsite)
permutation[i] = j
assert all(permutation == permutations[index])
def create_jobs():
""" Simple job-folders. """
from pylada.jobfolder import JobFolder
from pylada.crystal.binary import zinc_blende
root = JobFolder()
for name, value, species in zip(['diamond', 'diamond/alloy', 'GaAs'],
[0, 1, 2], [('Si', 'Si'), ('Si', 'Ge'),
('Ga', 'As')]):
job = root / name
job.functional = functional
job.params['value'] = value
job.params['structure'] = zinc_blende()
for atom, specie in zip(job.structure, species):
atom.type = specie
return root
def test_zinc_blende_lattice_diff_occupations():
from numpy import all
from pylada.crystal import binary
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 2
assert transforms.lattice[0].asymmetric
assert transforms.lattice[0].equivto == 0
assert transforms.lattice[0].nbflavors == 2
assert transforms.lattice[0].index == 0
assert transforms.lattice[0].asymmetric
assert transforms.lattice[1].equivto == 1
assert transforms.lattice[1].nbflavors == 3
assert transforms.lattice[1].index == 1
assert all(all(a == b) for a, b in zip(transforms.flavors, (list(range(1)), list(range(2)))))
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_zinc_blende_lattice_diff_occupations():
from numpy import all
from pylada.crystal import binary
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 2
assert transforms.lattice[0].asymmetric
assert transforms.lattice[0].equivto == 0
assert transforms.lattice[0].nbflavors == 2
assert transforms.lattice[0].index == 0
assert transforms.lattice[0].asymmetric
assert transforms.lattice[1].equivto == 1
assert transforms.lattice[1].nbflavors == 3
assert transforms.lattice[1].index == 1
assert all(
all(a == b)
for a, b in zip(transforms.flavors, (list(range(1)), list(range(2)))))
def test_manysupercell():
from numpy import dot
from numpy.linalg import inv, det
from pylada.crystal import supercell, binary, are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in range(10):
cell = get_cell()
struc = supercell(lattice, dot(lattice.cell, cell))
assert len(struc) == len(lattice) * int(abs(det(cell)) + 0.01)
invcell = inv(struc.cell)
for i, atom in enumerate(struc):
# compare to lattice
tolat = [api(atom.pos, site.pos, invlat) for site in lattice]
assert tolat.count(True) == 1
assert tolat.index(True) == atom.site
assert lattice[tolat.index(True)].type == atom.type
# compare to self
tolat = [api(atom.pos, site.pos, invcell) for site in struc]
assert tolat.count(True) == 1
assert i == tolat.index(True)
def test_manysupercell():
from numpy import dot
from numpy.linalg import inv, det
from pylada.crystal import supercell, binary, are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in range(10):
cell = get_cell()
struc = supercell(lattice, dot(lattice.cell, cell))
assert len(struc) == len(lattice) * int(abs(det(cell)) + 0.01)
invcell = inv(struc.cell)
for i, atom in enumerate(struc):
# compare to lattice
tolat = [api(atom.pos, site.pos, invlat) for site in lattice]
assert tolat.count(True) == 1
assert tolat.index(True) == atom.site
assert lattice[tolat.index(True)].type == atom.type
# compare to self
tolat = [api(atom.pos, site.pos, invcell) for site in struc]
assert tolat.count(True) == 1
assert i == tolat.index(True)
def test_gradients(epsilon = 1e-4):
from numpy import abs, dot, array, sqrt
from pylada.crystal.binary import zinc_blende
vff = functional()
structure = zinc_blende()
structure[0].type = 'In'
structure[1].type = 'As'
structure.scale = 6.5 #2.62332 * 2 / sqrt(3) / 0.529177
out = vff(structure)
for atom, check in zip(structure, out):
oldpos = atom.pos.copy()
for dir in [[1, 0, 0], [0, 1, 0], [0, 0, 1]]:
dir = array(dir) / sqrt(dot(dir, dir))
atom.pos = epsilon * dir + oldpos
xplus = vff(structure).energy
atom.pos = -epsilon * dir + oldpos
xminus = vff(structure).energy
assert abs(xplus - xminus) < 1e-8
strain = array([[1e0, 0.1, 0], [0.1, 1e0, 0], [0, 0, 1e0]])
structure.cell = dot(strain, structure.cell)
for atom in structure: atom.pos = dot(strain, atom.pos)
out = vff(structure)
for atom, check in zip(structure, out):
oldpos = atom.pos.copy()
for dir in [[1, 0, 0], [0, 1, 0], [0, 0, 1]]:
dir = array(dir) / sqrt(dot(dir, dir))
atom.pos = epsilon * dir + oldpos
xplus = vff(structure).energy
atom.pos = -epsilon * dir + oldpos
xminus = vff(structure).energy
deriv = (xplus - xminus).magnitude / (2e0*structure.scale * epsilon)
assert abs(deriv.magnitude - dot(check.gradient, dir)) < 1e2*epsilon
def test_labelexchange():
""" Tests label exchange """
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
structure = supercell(lattice, [[8, 0, 0], [0, 0.5, 0.5], [0, -0.5, 0.5]])
species = [
'Ge', 'C', 'Si', 'C', 'Si', 'C', 'Si', 'Si', 'Ge', 'Si', 'Ge', 'Si',
'Ge', 'Si', 'Ge', 'Ge', 'Ge', 'C', 'Ge', 'Si', 'Si', 'Si', 'Si', 'Ge',
'Si', 'Ge', 'Si', 'Si', 'Si', 'C', 'Ge', 'Si'
]
for atom, s in zip(structure, species):
atom.type = s
hft = HFTransform(lattice, structure)
x = transforms.toarray(hft, structure)
results = [
21112222221111123331111231122131, # <- this is x
21112222221111122221111321133121,
21112222221111123332222132211232,
21112222221111121112222312233212,
21112222221111122223333123311323,
21112222221111121113333213322313,
12221111112222213331111231122131,
12221111112222212221111321133121,
12221111112222213332222132211232,
12221111112222211112222312233212,
12221111112222212223333123311323,
12221111112222211113333213322313
]
permutations = transforms.label_exchange(hft)
for a, b in zip(permutations(x), results[1:]):
assert int(str(a)[1:-1].replace(' ', '')) == b
def test_rotations(cell):
from numpy import all, dot, zeros
from numpy.linalg import inv
from pylada.crystal import binary, supercell, HFTransform, space_group, \
which_site
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
sg = space_group(lattice)
invcell = inv(lattice.cell)
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
transforms = Transforms(lattice)
permutations = transforms.transformations(hft)
assert permutations.shape == (len(sg) - 1, len(structure))
operations = transforms.invariant_ops(structure)
assert any(operations)
# compute each translation and gets decorations
for index, (op, isgood) in enumerate(zip(sg[1:], operations)):
if not isgood:
continue
# Create rotation and figure out its index
permutation = zeros(len(structure), dtype='int') - 1
for atom in structure:
pos = dot(op[:3], atom.pos) + op[3]
newsite = which_site(pos, lattice, invcell)
i = hft.index(atom.pos - lattice[atom.site].pos, atom.site)
j = hft.index(pos - lattice[newsite].pos, newsite)
permutation[i] = j
assert all(permutation == permutations[index])
def test_toarray():
""" Tests label exchange """
from random import choice
from numpy import all, zeros
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
for u in range(11):
structure = supercell(lattice, get_cell())
for atom in structure:
atom.type = choice(atom.type)
hft = HFTransform(lattice, structure)
a = transforms.toarray(hft, structure)
b = zeros(len(structure), dtype='int')
for atom in structure:
site = lattice[atom.site]
b[hft.index(atom.pos - site.pos, atom.site)] = site.type.index(atom.type) + 1
assert all(a == b)
# crystal structures, as well as to a number of DFT (VASP, CRYSTAL) and atomic potential programs. It
# is able to organise and launch computational jobs on PBS and SLURM.
#
# PyLaDa is free software: you can redistribute it and/or modify it under the terms of the GNU General
# Public License as published by the Free Software Foundation, either version 3 of the License, or (at
# your option) any later version.
#
# PyLaDa is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
# the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along with PyLaDa. If not, see
# <http://www.gnu.org/licenses/>.
###############################
from pylada.crystal import binary
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Ga']
dummy = r""" 1 0 1 0 0 1 02
1 0 1 0 0 1 12
1 0 1 0 0 2 0122
1 0 1 0 1 2 0122
1 0 1 0 0 3 001222
1 0 1 0 0 3 011222
1 0 1 0 1 3 001222
1 0 1 0 1 3 011222
1 0 1 0 2 3 001222
1 0 1 0 2 3 011222
1 0 1 0 0 4 00012222
1 0 1 0 2 4 00012222
def test_write_gulp_zinc_blende():
""" Tries and writes a gulp file. """
from numpy import array, abs, all
from pylada.crystal.binary import zinc_blende
from pylada.crystal.write import gulp
a = zinc_blende()
string = [u.rstrip().lstrip() for u in gulp(a).splitlines()]
string = [u for u in string if len(u) > 0]
assert string[0] == 'name'
assert string[1] == 'Zinc-Blende'
assert string[2] == 'vectors'
assert all(
abs(array(string[3].split(), dtype='float64') - [0, 0.5, 0.5]) < 1e-8)
assert all(
abs(array(string[4].split(), dtype='float64') - [0.5, 0, 0.5]) < 1e-8)
assert all(
abs(array(string[5].split(), dtype='float64') - [0.5, 0.5, 0]) < 1e-8)
assert string[6] == 'cartesian'
assert string[7].split()[:2] == ['A', 'core']
assert all(abs(array(string[7].split()[2:], dtype='float64')) < 1e-8)
assert string[8].split()[:2] == ['B', 'core']
assert all(
abs(
array(string[8].split()[2:], dtype='float64') -
[0.25, 0.25, 0.25]) < 1e-8)
string2 = gulp(a, symmgroup=216).splitlines()
string2 = [u.rstrip().lstrip() for u in string2]
string2 = [u for u in string2 if len(u) > 0]
assert string2[:6] == string[:6]
assert string2[6] == 'spacegroup'
assert string2[7] == '216'
assert string2[8:] == string[6:]
a.symmgroup = 216
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2 == string
a[0].asymmetric = True
a[1].asymmetric = False
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2[:-1] == string
del a[0].asymmetric
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2 == string
del a[1].asymmetric
a[1].type = 'A'
a.symmgroup = 227
string = gulp(a).splitlines()
string = [u.rstrip().lstrip() for u in string]
string = [u for u in string if len(u) > 0]
assert string2[:7] == string[:7]
assert string[7] == '227'
assert string2[8:-1] == string[8:]
