def test_inverse_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
lattice[0], lattice[-1] = lattice[-1], lattice[0]
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 1, 4]])
assert all([not transforms.lattice[i].asymmetric for i in list(range(2, 4)) + list(range(5, 14))])
assert all([transforms.lattice[i].equivto == 0 for i in [0] + list(range(6, 13))])
assert all([transforms.lattice[i].equivto == 1 for i in list(range(1, 4)) + [13]])
assert all([transforms.lattice[i].equivto == 4 for i in [4, 5]])
assert all([transforms.lattice[i].nbflavors == 1 for i in [0] + list(range(6, 13))])
assert all([transforms.lattice[i].nbflavors == 2 for i in list(range(1, 4)) + [13]])
assert all([transforms.lattice[i].nbflavors == 2 for i in [4, 5]])
index = 0
for i, atom in enumerate(transforms.lattice):
if atom.nbflavors == 1:
assert not hasattr(atom, 'index')
else:
assert atom.index == index
index += 1
def test_inverse_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
lattice[0], lattice[-1] = lattice[-1], lattice[0]
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 1, 4]])
assert all([
not transforms.lattice[i].asymmetric
for i in list(range(2, 4)) + list(range(5, 14))
])
assert all(
[transforms.lattice[i].equivto == 0 for i in [0] + list(range(6, 13))])
assert all(
[transforms.lattice[i].equivto == 1 for i in list(range(1, 4)) + [13]])
assert all([transforms.lattice[i].equivto == 4 for i in [4, 5]])
assert all([
transforms.lattice[i].nbflavors == 1 for i in [0] + list(range(6, 13))
])
assert all([
transforms.lattice[i].nbflavors == 2 for i in list(range(1, 4)) + [13]
])
assert all([transforms.lattice[i].nbflavors == 2 for i in [4, 5]])
index = 0
for i, atom in enumerate(transforms.lattice):
if atom.nbflavors == 1:
assert not hasattr(atom, 'index')
else:
assert atom.index == index
index += 1
def test_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 4, 6]])
assert all([not transforms.lattice[i].asymmetric for i in list(range(1, 4)) + [5] + list(range(7, 14))])
assert all([transforms.lattice[i].equivto == 0 for i in range(4)])
assert all([transforms.lattice[i].equivto == 4 for i in range(4, 6)])
assert all([transforms.lattice[i].equivto == 6 for i in range(6, 14)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4, 6)])
assert all([transforms.lattice[i].nbflavors == 1 for i in range(6, 14)])
assert all([transforms.lattice[i].index == i for i in range(6)])
assert all([not hasattr(transforms.lattice[i], 'index') for i in range(6, 14)])
def test_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 4, 6]])
assert all([
not transforms.lattice[i].asymmetric
for i in list(range(1, 4)) + [5] + list(range(7, 14))
])
assert all([transforms.lattice[i].equivto == 0 for i in range(4)])
assert all([transforms.lattice[i].equivto == 4 for i in range(4, 6)])
assert all([transforms.lattice[i].equivto == 6 for i in range(6, 14)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4, 6)])
assert all([transforms.lattice[i].nbflavors == 1 for i in range(6, 14)])
assert all([transforms.lattice[i].index == i for i in range(6)])
assert all(
[not hasattr(transforms.lattice[i], 'index') for i in range(6, 14)])
j = which_site(op(site.pos), lattice)
if j != i and j in result:
result.remove(j)
return result
from numpy.linalg import norm
from pylada.crystal import A2BX4
from pylada.ce import create_clusters
from math import exp
# input
shell = 35
# create spinel lattice.
lattice = A2BX4.b5()
# occupations.
for site in lattice.sites:
if "X" in site.type:
continue
site.type = ["A", "B"]
# recomputes space group for safety.
lattice.find_space_group()
lattice.set_as_crystal_lattice()
# creates random structure.
structure = A2BX4.b5I().to_structure()
normal = A2BX4.b5().to_structure()
# for atom in structure.atoms:
# atom.type = choice(lattice.sites[atom.site].type)
nfu = float(len(structure)/7)*0.5 # 0.5 because 2 f.u. in spinel unit-cell.
vol = det(structure.cell)
return (nfu * spvol / vol)**(1e0/3e0)
#problem with Rh2TiO4 for some reason
""" Materials to compute. """
materials = [ "Al2MgO4"]
""" Number of random anti-ferro trials. """
nbantiferro = 8
nbrandom = 3
do_ferro = False
do_antiferro = False
lattices = [A2BX4.b5(), A2BX4.b21()]
mlen = len( materials)
llen = len( lattices)
matLatPairs = (mlen * llen) * [None]
print " test/hi/inputFixed: mlen: ", mlen
print " test/hi/inputFixed: llen: ", llen
print " test/hi/inputFixed: pairs len: ", len(matLatPairs)
kk = 0
for mat in materials:
print " test/hi/inputFixed: mat: ", mat
for lat in lattices:
print " test/hi/inputFixed: lat: ", lat
matLatPairs[kk] = (mat, lat,)
kk += 1
def test_lattice():
""" Tests lattice enhancements. """
from numpy import all
from pylada.crystal import binary, A2BX4
from pylada.enum import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge']
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 1
assert transforms.lattice[0].asymmetric
assert transforms.lattice[0].equivto == 0
assert transforms.lattice[0].nbflavors == 2
assert transforms.lattice[0].index == 0
assert not transforms.lattice[1].asymmetric
assert transforms.lattice[1].equivto == 0
assert transforms.lattice[1].nbflavors == 2
assert transforms.lattice[1].index == 1
assert all(all(a == b) for a, b in zip(transforms.flavors, (range(1), range(1))))
assert all(not hasattr(atom, 'nbflavors') for atom in lattice)
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, (range(1), range(2))))
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']: atom.type = 'A', 'B'
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 4, 6]])
assert all([not transforms.lattice[i].asymmetric for i in range(1, 4) + [5] + range(7, 14)])
assert all([transforms.lattice[i].equivto == 0 for i in range(4)])
assert all([transforms.lattice[i].equivto == 4 for i in range(4, 6)])
assert all([transforms.lattice[i].equivto == 6 for i in range(6, 14)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4, 6)])
assert all([transforms.lattice[i].nbflavors == 1 for i in range(6, 14)])
assert all([transforms.lattice[i].index == i for i in range(6)])
assert all([not hasattr(transforms.lattice[i], 'index') for i in range(6, 14)])
lattice[0], lattice[-1] = lattice[-1], lattice[0]
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 1, 4]])
assert all([not transforms.lattice[i].asymmetric for i in range(2, 4) + range(5, 14)])
assert all([transforms.lattice[i].equivto == 0 for i in [0] + range(6, 13)])
assert all([transforms.lattice[i].equivto == 1 for i in range(1, 4) + [13]])
assert all([transforms.lattice[i].equivto == 4 for i in [4, 5]])
assert all([transforms.lattice[i].nbflavors == 1 for i in [0] + range(6, 13)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(1, 4) + [13]])
assert all([transforms.lattice[i].nbflavors == 2 for i in [4, 5]])
index = 0
for i, atom in enumerate(transforms.lattice):
if atom.nbflavors == 1: assert not hasattr(atom, 'index')
else:
assert atom.index == index
index += 1
# 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/>.
###############################
""" Input script for the calculation of Point Defects. """
from pylada.crystal import A2BX4
lattice = A2BX4.b5()
""" Back-bone lattice. """
# changes species in lattice.
for site in lattice.sites:
site.type = {"A": "Rh", "B": "Zn", "X": "O"}[site.type[0]]
lattice.scale = 8.506
supercell = array([[-1, 1, 1],\
[ 1, -1, 1],\
[ 1, 1, -1]], dtype="float64" )
""" Supercell of defect structures. """
vasp = Vasp()
""" VASP functional """
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"