def grapheneHex(x, y, z):
"""
Create a hexagonal cell of graphene
x -> x-dimension
y -> 0.5*x+0.5*sqrt(3)*y-dimension
z -> interlayer distance
"""
mol = Molecule(name="({:},{:})-hex graphene".format(x, y))
mol.setCellDim(Agraph)
mol.setVec([vecX, vecYh, z * vecZ])
mol.newAtom('C', [1. / 3., 2. / 3., 0])
mol.newAtom('C', [2. / 3., 1. / 3., 0])
# mol.scaleAtoms("crystal")
# mol.setFmt("crystal")
mol.setFmt("crystal", scale=True)
mol.mult(x, y, 1)
return mol
def grapheneOrtho(x, y, z):
"""
Create an orthogonal cell of graphene
x -> x-dimension
y -> sqrt(3)*y-dimension
z -> interlayer distance
"""
mol = Molecule(name="({:},{:})-ortho graphene".format(x, y))
mol.setCellDim(Agraph)
mol.setVec([vecX, sq3 * vecY, z * vecZ])
mol.newAtom('C', [0, 0, 0])
mol.newAtom('C', [0, 1. / 3., 0])
mol.newAtom('C', [0.5, 0.5, 0])
mol.newAtom('C', [0.5, 5. / 6., 0])
# mol.scaleAtoms("crystal")
# mol.setFmt("crystal")
mol.setFmt("crystal", scale=True)
mol.mult(x, y, 1)
return mol
def test_modify():
Mol = Molecule()
assert Mol.getUndo() == None
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('C', (0.5, 0.5, 0.5), fmt='crystal')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 1
Mol.mult(2, 1, 1)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 2
Mol.mult(1, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.crop()
assert Mol.nat == 1
Mol.mult(2, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((7, 0, 0), (0, 7, 0), (0, 0, 7)))
Mol.wrap()
assert Mol.nat == 8
assert list(map(len, Mol.getBonds(1.1))) == [24, 0, 0, 0, 0, 0, 0, 0]
assert Mol.getUndo() == 'wrap atoms'
Mol.undo()
assert list(map(len, Mol.getBonds(1.1))) == [0, 4, 4, 4, 4, 4, 4, 0]
Mol.wrap()
Mol.reshape(((14, 7, 0), (0, 7, 0), (0, 0, 7)))
assert list(map(len, Mol.getBonds(1.1))) == [38, 0, 10, 0, 0, 0, 0, 0]
assert vec_equal(Mol.getVec(), ((14, 7, 0), (0, 7, 0), (0, 0, 7)))
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert atom_equal(Mol.getAtom(1, fmt="crystal"), ('C', (0.1, 0.5, 0.5)))
Mol.align(1, 'x')
assert vec_equal(Mol.getVec(), ((0, -5, 0), (5, 0, 0), (0, 0, 5)))
Mol.undo()
Mol.align(1, 'y')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.align(1, 'z')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 0, 5), (0, -5, 0)))
Mol.undo()
try:
Mol.align(0, 1)
except ValueError:
assert True
except:
assert False, "Wrong error"
else:
assert False, "Error missing"
