def test_hex():
from javelin.unitcell import UnitCell
positions = [[0, 1, 0], [1, 1, 0], [1, 0, 0], [0, -1, 0], [-1, -1, 0],
[-1, 0, 0]]
symbols = ['C'] * 6
unitcell = (1.4, 1.4, 1, 90, 90, 120)
hex_cell = Structure(unitcell=UnitCell(unitcell),
symbols=symbols,
positions=positions)
assert hex_cell.number_of_atoms == 6
assert_array_equal(hex_cell.element, ['C', 'C', 'C', 'C', 'C', 'C'])
assert_array_equal(hex_cell.get_atom_symbols(), ['C'])
assert_array_equal(hex_cell.get_atom_count(), 6)
assert_array_equal(hex_cell.get_chemical_symbols(),
['C', 'C', 'C', 'C', 'C', 'C'])
assert_array_equal(hex_cell.get_atom_Zs(), [6])
assert_array_equal(hex_cell.get_atomic_numbers(), [6, 6, 6, 6, 6, 6])
assert_array_equal(hex_cell.x, [0, 1, 1, 0, -1, -1])
assert_array_equal(hex_cell.y, [1, 1, 0, -1, -1, 0])
assert_array_equal(hex_cell.z, [0, 0, 0, 0, 0, 0])
assert_array_equal(hex_cell.xyz, positions)
assert_array_equal(hex_cell.get_scaled_positions(), positions)
real_positions = [[0, 1.4, 0], [1.21243557, 0.7, 0], [1.21243557, -0.7, 0],
[0, -1.4, 0], [-1.21243557, -0.7, 0],
[-1.21243557, 0.7, 0]]
assert_array_almost_equal(hex_cell.xyz_cartn, real_positions)
assert_array_almost_equal(hex_cell.get_positions(), real_positions)
assert_array_almost_equal(hex_cell.unitcell.cell, unitcell)
def test_hex():
from javelin.unitcell import UnitCell
positions = [[0, 1, 0], [1, 1, 0], [1, 0, 0], [0, -1, 0], [-1, -1, 0], [-1, 0, 0]]
symbols = ['C']*6
unitcell = (1.4, 1.4, 1, 90, 90, 120)
hex_cell = Structure(unitcell=UnitCell(unitcell),
symbols=symbols,
positions=positions)
assert hex_cell.number_of_atoms == 6
assert_array_equal(hex_cell.element, ['C', 'C', 'C', 'C', 'C', 'C'])
assert_array_equal(hex_cell.get_atom_symbols(), ['C'])
assert_array_equal(hex_cell.get_atom_count(), 6)
assert_array_equal(hex_cell.get_chemical_symbols(), ['C', 'C', 'C', 'C', 'C', 'C'])
assert_array_equal(hex_cell.get_atom_Zs(), [6])
assert_array_equal(hex_cell.get_atomic_numbers(), [6, 6, 6, 6, 6, 6])
assert_array_equal(hex_cell.x, [0, 1, 1, 0, -1, -1])
assert_array_equal(hex_cell.y, [1, 1, 0, -1, -1, 0])
assert_array_equal(hex_cell.z, [0, 0, 0, 0, 0, 0])
assert_array_equal(hex_cell.xyz, positions)
assert_array_equal(hex_cell.get_scaled_positions(), positions)
real_positions = [[0, 1.4, 0],
[1.21243557, 0.7, 0],
[1.21243557, -0.7, 0],
[0, -1.4, 0],
[-1.21243557, -0.7, 0],
[-1.21243557, 0.7, 0]]
assert_array_almost_equal(hex_cell.xyz_cartn, real_positions)
assert_array_almost_equal(hex_cell.get_positions(), real_positions)
assert_array_almost_equal(hex_cell.unitcell.cell, unitcell)
def test_empty():
structure = Structure()
assert structure.number_of_atoms == 0
assert_array_equal(structure.element, np.empty(0))
assert_array_equal(structure.get_atom_symbols(), np.empty(0))
assert_array_equal(structure.get_atom_count(), 0)
assert_array_equal(structure.get_chemical_symbols(), np.empty(0))
assert_array_equal(structure.get_atom_Zs(), np.empty(0))
assert_array_equal(structure.get_atomic_numbers(), np.empty(0))
assert_array_equal(structure.x, np.empty(0))
assert_array_equal(structure.y, np.empty(0))
assert_array_equal(structure.z, np.empty(0))
assert_array_equal(structure.xyz, np.empty((0, 3)))
assert_array_equal(structure.get_scaled_positions(), np.empty((0, 3)))
assert_array_equal(structure.xyz_cartn, np.empty((0, 3)))
assert_array_equal(structure.get_positions(), np.empty((0, 3)))
assert_array_equal(structure.unitcell.cell, (1.0, 1.0, 1.0, 90.0, 90.0, 90.0))
def test_one_atom_init():
structure = Structure(symbols=['Au'], positions=[[0.5, 0, 0.25]], unitcell=(3, 4, 5))
assert structure.number_of_atoms == 1
assert_array_equal(structure.element, ['Au'])
assert_array_equal(structure.get_atom_symbols(), ['Au'])
assert_array_equal(structure.get_atom_count(), 1)
assert_array_equal(structure.get_chemical_symbols(), ['Au'])
assert_array_equal(structure.get_atom_Zs(), [79])
assert_array_equal(structure.get_atomic_numbers(), [79])
assert_array_equal(structure.x, [0.5])
assert_array_equal(structure.y, [0])
assert_array_equal(structure.z, [0.25])
assert_array_equal(structure.xyz, [[0.5, 0, 0.25]])
assert_array_equal(structure.get_scaled_positions(), [[0.5, 0, 0.25]])
assert_array_almost_equal(structure.xyz_cartn, [[1.5, 0, 1.25]])
assert_array_almost_equal(structure.get_positions(), [[1.5, 0, 1.25]])
assert_array_equal(structure.unitcell.cell, (3.0, 4.0, 5.0, 90.0, 90.0, 90.0))
def test_empty():
structure = Structure()
assert structure.number_of_atoms == 0
assert_array_equal(structure.element, np.empty(0))
assert_array_equal(structure.get_atom_symbols(), np.empty(0))
assert_array_equal(structure.get_atom_count(), 0)
assert_array_equal(structure.get_chemical_symbols(), np.empty(0))
assert_array_equal(structure.get_atom_Zs(), np.empty(0))
assert_array_equal(structure.get_atomic_numbers(), np.empty(0))
assert_array_equal(structure.x, np.empty(0))
assert_array_equal(structure.y, np.empty(0))
assert_array_equal(structure.z, np.empty(0))
assert_array_equal(structure.xyz, np.empty((0, 3)))
assert_array_equal(structure.get_scaled_positions(), np.empty((0, 3)))
assert_array_equal(structure.xyz_cartn, np.empty((0, 3)))
assert_array_equal(structure.get_positions(), np.empty((0, 3)))
assert_array_equal(structure.unitcell.cell,
(1.0, 1.0, 1.0, 90.0, 90.0, 90.0))
def test_one_atom_add():
structure = Structure()
structure.unitcell.cell = (3.0, 4.0, 5.0, 90.0, 90.0, 90.0)
structure.add_atom(symbol='Au', position=[0.5, 0, 0.25])
assert structure.number_of_atoms == 1
assert_array_equal(structure.element, ['Au'])
assert_array_equal(structure.get_atom_symbols(), ['Au'])
assert_array_equal(structure.get_atom_count(), 1)
assert_array_equal(structure.get_chemical_symbols(), ['Au'])
assert_array_equal(structure.get_atom_Zs(), [79])
assert_array_equal(structure.get_atomic_numbers(), [79])
assert_array_equal(structure.x, [0.5])
assert_array_equal(structure.y, [0])
assert_array_equal(structure.z, [0.25])
assert_array_equal(structure.xyz, [[0.5, 0, 0.25]])
assert_array_equal(structure.get_scaled_positions(), [[0.5, 0, 0.25]])
assert_array_almost_equal(structure.xyz_cartn, [[1.5, 0, 1.25]])
assert_array_almost_equal(structure.get_positions(), [[1.5, 0, 1.25]])
assert_array_equal(structure.unitcell.cell,
(3.0, 4.0, 5.0, 90.0, 90.0, 90.0))
def test_repeat():
structure = Structure(unitcell=5, symbols=['Au', 'Ag'], positions=[[0, 0, 0], [0.5, 0.5, 0.5]])
assert structure.number_of_atoms == 2
assert_array_equal(structure.get_atom_count(), [1, 1])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(structure.get_atomic_numbers(), [79, 47])
assert_array_equal(structure.element, ['Au', 'Ag'])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.xyz, [[0., 0., 0.],
[0.5, 0.5, 0.5]])
assert_array_almost_equal(structure.xyz_cartn, [[0., 0., 0.],
[2.5, 2.5, 2.5]])
structure.repeat((2, 3, 1))
assert structure.number_of_atoms == 12
assert_array_equal(structure.get_atom_count(), [6, 6])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(structure.get_atomic_numbers(), [79, 47, 79, 47, 79, 47,
79, 47, 79, 47, 79, 47])
assert_array_equal(structure.element, ['Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag'])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), ['Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag'])
assert_array_equal(structure.xyz, np.tile([[0., 0., 0.],
[0.5, 0.5, 0.5]], (6, 1)))
assert_array_almost_equal(structure.xyz_cartn, [[0.0, 0.0, 0.0],
[2.5, 2.5, 2.5],
[0.0, 5.0, 0.0],
[2.5, 7.5, 2.5],
[0.0, 10.0, 0.0],
[2.5, 12.5, 2.5],
[5.0, 0.0, 0.0],
[7.5, 2.5, 2.5],
[5.0, 5.0, 0.0],
[7.5, 7.5, 2.5],
[5.0, 10.0, 0.0],
[7.5, 12.5, 2.5]])
structure = Structure(unitcell=5, symbols=['Au', 'Ag'], positions=[[0, 0, 0], [0.5, 0.5, 0.5]])
structure.repeat(2)
assert structure.number_of_atoms == 16
assert_array_equal(structure.get_atom_count(), [8, 8])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(structure.get_atomic_numbers(), [79, 47, 79, 47, 79, 47, 79, 47,
79, 47, 79, 47, 79, 47, 79, 47])
assert_array_equal(structure.element, ['Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag'])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), ['Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag'])
assert_array_equal(structure.xyz, np.tile([[0., 0., 0.],
[0.5, 0.5, 0.5]], (8, 1)))
assert_array_almost_equal(structure.xyz_cartn, [[0.0, 0.0, 0.0],
[2.5, 2.5, 2.5],
[0.0, 0.0, 5.0],
[2.5, 2.5, 7.5],
[0.0, 5.0, 0.0],
[2.5, 7.5, 2.5],
[0.0, 5.0, 5.0],
[2.5, 7.5, 7.5],
[5.0, 0.0, 0.0],
[7.5, 2.5, 2.5],
[5.0, 0.0, 5.0],
[7.5, 2.5, 7.5],
[5.0, 5.0, 0.0],
[7.5, 7.5, 2.5],
[5.0, 5.0, 5.0],
[7.5, 7.5, 7.5]])
def test_repeat():
structure = Structure(unitcell=5,
symbols=['Au', 'Ag'],
positions=[[0, 0, 0], [0.5, 0.5, 0.5]])
assert structure.number_of_atoms == 2
assert_array_equal(structure.get_atom_count(), [1, 1])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(structure.get_atomic_numbers(), [79, 47])
assert_array_equal(structure.element, ['Au', 'Ag'])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.xyz, [[0., 0., 0.], [0.5, 0.5, 0.5]])
assert_array_almost_equal(structure.xyz_cartn,
[[0., 0., 0.], [2.5, 2.5, 2.5]])
structure.repeat((2, 3, 1))
assert structure.number_of_atoms == 12
assert_array_equal(structure.get_atom_count(), [6, 6])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(structure.get_atomic_numbers(),
[79, 47, 79, 47, 79, 47, 79, 47, 79, 47, 79, 47])
assert_array_equal(structure.element, [
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag'
])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), [
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag'
])
assert_array_equal(structure.xyz,
np.tile([[0., 0., 0.], [0.5, 0.5, 0.5]], (6, 1)))
assert_array_almost_equal(
structure.xyz_cartn,
[[0.0, 0.0, 0.0], [2.5, 2.5, 2.5], [0.0, 5.0, 0.0], [2.5, 7.5, 2.5],
[0.0, 10.0, 0.0], [2.5, 12.5, 2.5], [5.0, 0.0, 0.0], [7.5, 2.5, 2.5],
[5.0, 5.0, 0.0], [7.5, 7.5, 2.5], [5.0, 10.0, 0.0], [7.5, 12.5, 2.5]])
structure = Structure(unitcell=5,
symbols=['Au', 'Ag'],
positions=[[0, 0, 0], [0.5, 0.5, 0.5]])
structure.repeat(2)
assert structure.number_of_atoms == 16
assert_array_equal(structure.get_atom_count(), [8, 8])
assert_array_equal(structure.get_atom_Zs(), [79, 47])
assert_array_equal(
structure.get_atomic_numbers(),
[79, 47, 79, 47, 79, 47, 79, 47, 79, 47, 79, 47, 79, 47, 79, 47])
assert_array_equal(structure.element, [
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag'
])
assert_array_equal(structure.get_atom_symbols(), ['Au', 'Ag'])
assert_array_equal(structure.get_chemical_symbols(), [
'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag', 'Au', 'Ag',
'Au', 'Ag', 'Au', 'Ag'
])
assert_array_equal(structure.xyz,
np.tile([[0., 0., 0.], [0.5, 0.5, 0.5]], (8, 1)))
assert_array_almost_equal(
structure.xyz_cartn,
[[0.0, 0.0, 0.0], [2.5, 2.5, 2.5], [0.0, 0.0, 5.0], [2.5, 2.5, 7.5],
[0.0, 5.0, 0.0], [2.5, 7.5, 2.5], [0.0, 5.0, 5.0], [2.5, 7.5, 7.5],
[5.0, 0.0, 0.0], [7.5, 2.5, 2.5], [5.0, 0.0, 5.0], [7.5, 2.5, 7.5],
[5.0, 5.0, 0.0], [7.5, 7.5, 2.5], [5.0, 5.0, 5.0], [7.5, 7.5, 7.5]])
def read_stru(filename, starting_cell=(1, 1, 1)):
"""Read in a .stru file saved from DISCUS into a javelin Structure
If the line ncell is not present in the file all the atoms will be
read into a single cell."""
from javelin.structure import Structure
import numpy as np
with open(filename) as f:
lines = f.readlines()
a = b = c = alpha = beta = gamma = 0
reading_atom_list = False
ncell = None
symbols = []
x = []
y = []
z = []
for l in lines:
line = l.replace(',', ' ').split()
if not reading_atom_list: # Wait for 'atoms' line before reading atoms
if line[0] == 'cell':
a, b, c, alpha, beta, gamma = [
float(word) for word in line[1:7]
]
elif line[0] == 'ncell':
ncell = [int(word) for word in line[1:5]]
elif line[0] == 'atoms':
if a == 0:
print("Cell not found")
a = b = c = 1
alpha = beta = gamma = 90
reading_atom_list = True
else:
symbol, xx, yy, zz = line[:4]
symbols.append(symbol)
x.append(xx)
y.append(yy)
z.append(zz)
print("Found a = {}, b = {}, c = {}, alpha = {}, beta = {}, gamma = {}".
format(a, b, c, alpha, beta, gamma))
x = np.array(x, dtype=np.float64)
y = np.array(y, dtype=np.float64)
z = np.array(z, dtype=np.float64)
symbols = np.array(symbols)
if ncell is not None:
x -= np.tile(np.repeat(np.array(range(ncell[0])), ncell[3]),
ncell[1] * ncell[2]) + starting_cell[0]
y -= np.tile(np.repeat(np.array(range(ncell[1])), ncell[0] * ncell[3]),
ncell[2]) + starting_cell[1]
z -= np.repeat(np.array(range(ncell[2])),
ncell[0] * ncell[1] * ncell[3]) + starting_cell[2]
# reorder atom arrays, discus stru files have x increment fastest
# and z slowest, javelin is the opposite
x = x.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
y = y.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
z = z.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
symbols = symbols.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
xyz = np.array((x, y, z)).T
structure = Structure(unitcell=(a, b, c, alpha, beta, gamma),
symbols=symbols,
positions=xyz,
ncells=ncell)
print("Read in these atoms:")
print(structure.get_atom_count())
return structure
def read_stru(filename, starting_cell=(1, 1, 1)):
"""Read in a .stru file saved from DISCUS into a javelin Structure
If the line ncell is not present in the file all the atoms will be
read into a single cell."""
from javelin.structure import Structure
import numpy as np
with open(filename) as f:
lines = f.readlines()
a = b = c = alpha = beta = gamma = 0
reading_atom_list = False
ncell = None
symbols = []
x = []
y = []
z = []
for l in lines:
line = l.replace(',', ' ').split()
if not reading_atom_list: # Wait for 'atoms' line before reading atoms
if line[0] == 'cell':
a, b, c, alpha, beta, gamma = [float(word) for word in line[1:7]]
elif line[0] == 'ncell':
ncell = [int(word) for word in line[1:5]]
elif line[0] == 'atoms':
if a == 0:
print("Cell not found")
a = b = c = 1
alpha = beta = gamma = 90
reading_atom_list = True
else:
symbol, xx, yy, zz = line[:4]
symbols.append(symbol)
x.append(xx)
y.append(yy)
z.append(zz)
print("Found a = {}, b = {}, c = {}, alpha = {}, beta = {}, gamma = {}"
.format(a, b, c, alpha, beta, gamma))
x = np.array(x, dtype=np.float64)
y = np.array(y, dtype=np.float64)
z = np.array(z, dtype=np.float64)
symbols = np.array(symbols)
if ncell is not None:
x -= np.tile(np.repeat(np.array(range(ncell[0])),
ncell[3]), ncell[1]*ncell[2]) + starting_cell[0]
y -= np.tile(np.repeat(np.array(range(ncell[1])),
ncell[0]*ncell[3]), ncell[2]) + starting_cell[1]
z -= np.repeat(np.array(range(ncell[2])),
ncell[0]*ncell[1]*ncell[3]) + starting_cell[2]
# reorder atom arrays, discus stru files have x increment fastest
# and z slowest, javelin is the opposite
x = x.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
y = y.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
z = z.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
symbols = symbols.reshape(ncell).transpose((2, 1, 0, 3)).flatten()
xyz = np.array((x, y, z)).T
structure = Structure(unitcell=(a, b, c, alpha, beta, gamma),
symbols=symbols,
positions=xyz,
ncells=ncell)
print("Read in these atoms:")
print(structure.get_atom_count())
return structure
