def aluminum():
from quantities import bohr_radius
from pylada.crystal.bravais import fcc
result = fcc()
result.scale = 7.5 * bohr_radius
result[0].type = 'Al'
return result
def aluminum_structure():
from quantities import bohr_radius
from pylada.crystal.bravais import fcc
result = fcc()
result.scale = 7.5 * bohr_radius
result[0].type = 'Al'
return result
def test_supercells():
from pylada.crystal.bravais import fcc
from pylada.enum import supercells
# First, a lattice without symmetry
lattice = fcc()
lattice.cell = [[1.0, 0.2, 0], [0, 0.9, -0.1], [0, 0, 0.8]]
scs = supercells(lattice, range(17))
results = [1, 7, 13, 35, 31, 91, 57, 155, 130, 217, 133, 455, 183, 399, 403, 651]
for r, s in zip(results, scs.itervalues()):
assert r == len(s)
# Then, an fcc lattice.
lattice = fcc()
scs = supercells(lattice, range(11))
results = [1, 2, 3, 7, 5, 10, 7, 20, 14, 18]
for r, s in zip(results, scs.itervalues()):
assert r, len(s)
def diamond_structure():
from quantities import bohr_radius
from pylada.crystal.bravais import fcc
result = fcc()
result.scale = 10.2 * bohr_radius
result[0].type = 'Si'
result.add_atom(0.25, 0.25, 0.25, 'Si')
return result
def test_fcc_supercells():
from pylada.crystal.bravais import fcc
from pylada.decorations import supercells
lattice = fcc()
scs = supercells(lattice, list(range(11)))
results = [1, 2, 3, 7, 5, 10, 7, 20, 14, 18]
for r, s in zip(results, scs.values()):
assert r, len(s)
def test_fcc_supercells():
from pylada.crystal.bravais import fcc
from pylada.decorations import supercells
lattice = fcc()
scs = supercells(lattice, list(range(11)))
results = [1, 2, 3, 7, 5, 10, 7, 20, 14, 18]
for r, s in zip(results, scs.values()):
assert r, len(s)
def test_3b(): """ Tests triplet generation. """ from pylada.ce._single_site_factory import factory from pylada.crystal import bravais lattice = bravais.fcc() lattice[0].type = ['A', 'B'] results = factory(lattice, B3=1) assert len(results) == 4 results = factory(lattice, B3=2) assert len(results) == 9
def test_defects():
from pylada.crystal.bravais import fcc
from pylada.decorations.defects import defects
lattice = fcc()
lattice[0].type = 'Zr', 'Ti'
lattice.add_atom(0.25, 0.25, 0.25, 'O', 'A')
lattice.add_atom(0.75, 0.75, 0.75, 'O', 'A')
i = 0
for i, (x, hft, hermite) in enumerate(defects(lattice, 32, {'A': 2, 'Ti': 2})):
print(x)
print(i)
def test_hfgroups():
from pylada.crystal.bravais import fcc
from pylada.decorations import hf_groups
# First, a lattice without symmetry
lattice = fcc()
lattice.cell = [[1.0, 0.2, 0], [0, 0.9, -0.1], [0, 0, 0.8]]
a = [1, 1, 1, 2, 1, 1, 1, 3, 2, 1, 1, 2, 1, 1, 1, 4]
b = [1, 7, 13, 35, 31, 91, 57, 155, 130, 217, 133, 455, 183, 399, 403, 651]
results = [u for u in zip(a, b)]
for r, s in zip(results, hf_groups(lattice, list(range(17)))):
assert len(s) == r[0]
assert sum(len(u) for u in s) == r[1]
def test_hfgroups():
from pylada.crystal.bravais import fcc
from pylada.enum import hf_groups
# First, a lattice without symmetry
lattice = fcc()
lattice.cell = [[1.0, 0.2, 0], [0, 0.9, -0.1], [0, 0, 0.8]]
a = [1, 1, 1, 2, 1, 1, 1, 3, 2, 1, 1, 2, 1, 1, 1, 4]
b = [1, 7, 13, 35, 31, 91, 57, 155, 130, 217, 133, 455, 183, 399, 403, 651]
results = [u for u in zip(a, b)]
for r, s in zip(results, hf_groups(lattice, range(17))):
assert len(s) == r[0]
assert sum(len(u) for u in s) == r[1]
def test_ternary():
from pylada.crystal import bravais
from pylada.enum import generate_bitstrings
from ternarysets import ternarysets
lattice = bravais.fcc()
lattice[0].type = ['Si', 'Ge', 'C']
for n in xrange(1, 9):
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(ternarysets[n])
assert set(result) == ternarysets[n]
def test_defects():
from pylada.crystal.bravais import fcc
from pylada.decorations.defects import defects
lattice = fcc()
lattice[0].type = 'Zr', 'Ti'
lattice.add_atom(0.25, 0.25, 0.25, 'O', 'A')
lattice.add_atom(0.75, 0.75, 0.75, 'O', 'A')
i = 0
for i, (x, hft,
hermite) in enumerate(defects(lattice, 32, {
'A': 2,
'Ti': 2
})):
print(x)
print(i)
def test_pairs(): """ Tests pair generation. """ from numpy import all, sum from pylada.ce._single_site_factory import factory from pylada.crystal import bravais from pylada.error import ValueError lattice = bravais.fcc() try: results = factory(lattice, B2=1) except ValueError: pass else: raise Exception() lattice[0].type = ['A', 'B'] results = factory(lattice, B2=1) assert len(results) == 1 assert all(results[0].spins['position'][0] == [0,0,0]) assert abs(sum(results[0].spins['position'][1]**2) - 2*0.5*0.5) < 1e-8 assert len(results[0]._symmetrized) == 12 results = factory(lattice, B2=2) assert len(results) == 2 assert all(results[0].spins['position'][0] == [0,0,0]) assert sum(results[0].spins['position'][1]**2) == 2*0.5*0.5 assert len(results[0]._symmetrized) == 12 assert all(results[1].spins['position'][0] == [0,0,0]) assert abs(sum(results[1].spins['position'][1]**2) - 1e0) < 1e-8 assert len(results[1]._symmetrized) == 6 results = factory(lattice, B2=3) assert len(results) == 3 assert all(results[0].spins['position'][0] == [0,0,0]) assert sum(results[0].spins['position'][1]**2) == 2*0.5*0.5 assert len(results[0]._symmetrized) == 12 assert all(results[1].spins['position'][0] == [0,0,0]) assert abs(sum(results[1].spins['position'][1]**2) - 1e0) < 1e-8 assert len(results[1]._symmetrized) == 6 assert all(results[2].spins['position'][0] == [0,0,0]) assert abs(sum(results[2].spins['position'][1]**2) - 1-2*0.25) < 1e-8 assert len(results[2]._symmetrized) == 24
def main():
from pylada import ce
import boost.mpi as mpi
from numpy import array
from pylada.crystal.bravais import fcc
functional = ce.Cubic()
functional.set_mpi(mpi.world)
functional.load( "input.xml" )
lattice = fcc(); lattice.sites[0].type = "Au", "Pd"
structure = lattice.to_structure( array([[0,1.0,1.5],[1,0,1.5],[1.0,1.0,0]]))
# print structure.lattice.space_group
mlclasses = ce.MLClusterClasses("input.xml", False)
# mlclasses[0]
# print mlclasses
classes = convert(mlclasses)
# print classes
# print
# print functional.clusters
# mlclusters = convert_clusters_to_mlclusters
tests = [ ("000011100000", -74.377010),
("111000000101", -83.064845),
("101000000011", -80.889828),
("000111111000", -84.277151),
("000111111001", -71.156430),
("110000000111", -83.064845),
("110000000101", -80.889828),
("111000000111", -84.277151),
("000111101000", -83.064845),
("000110111000", -83.064845),
("101000000111", -83.064845),
("000110011000", -80.889828),
("000011101000", -80.889828),
("000111011000", -83.064845),
("000011111000", -83.064845),
("110000000011", -80.889828),
("111000100111", -71.156430),
("001000000000", -27.375282),
("011000000111", -83.064845),
("000010000000", -27.375282),
("000000100000", -27.375282),
("000000000001", -27.375282),
("000100001000", -55.269849),
("111010000111", -71.156430),
("000000000100", -27.375282),
("010000000000", -27.375282),
("000111111100", -71.156430),
("000001100000", -55.269849),
("000011110000", -80.889828),
("111001100111", -58.030174),
("100000000010", -55.269849),
("010000000100", -55.269849),
("000001110000", -74.377010),
("010000000001", -55.269849) ]
for test in tests:
for i, atom in enumerate(structure.atoms):
if test[0][i] == "0": atom.type = "Au"
else: atom.type = "Pd"
e = mlclasses(structure)
c = functional.chemical(structure)
if not e == 0e0:
print "check %f, test %f, diff %f " \
% ( c, e, c-e )