def test_crystal():
'''Building a crystal by using spacegroup module'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0],[0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[13,13,13])
def test_crystal():
'''Building a crystal by using spacegroup module'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[13, 13, 13])
def test_sort():
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0],[0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3,3,3])
tsys.sort()
assert np.all(tsys.type_array[:tsys.n_mol/2] == 'Cl')
def test_sort():
na = Molecule([Atom("Na", [0.0, 0.0, 0.0])])
cl = Molecule([Atom("Cl", [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3, 3, 3])
tsys.sort()
assert_npequal(tsys.type_array[: tsys.n_mol / 2], ["Cl"] * (tsys.n_mol / 2))
def test_crystal():
"""Building a crystal by using spacegroup module"""
na = Molecule([Atom("Na", [0.0, 0.0, 0.0])])
cl = Molecule([Atom("Cl", [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[13, 13, 13])
eq_(tsys.r_array.min(), 0.0)
eq_(tsys.r_array.max(), 12.5)
def test_sort():
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
tsys.sort()
assert np.all(tsys.type_array[:tsys.n_mol / 2] == 'Cl')
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0],[0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3,3,3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
def test_serialization():
cl = Molecule([Atom.from_fields(type="Cl", r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom("Na", [0.0, 0.0, 0.0])])
cl = Molecule([Atom("Cl", [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
eq_(System.from_json(jsonstr).to_json(), jsonstr)
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
npeq_(System.from_json(jsonstr).r_array, tsys.r_array)
from chemlab.core import Atom, Molecule, crystal
from chemlab.graphics.qt import display_system
# Molecule templates
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
s = crystal(
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], # Fractional Positions
[na, cl], # Molecules
225, # Space Group
cellpar=[.54, .54, .54, 90, 90, 90], # unit cell parameters
repetitions=[5, 5, 5]) # unit cell repetitions in each direction
display_system(s)
#thr_a2 = thr_a * thr_a
thr_b2 = thr_b * thr_b
dr2 = ((r_array[i] - r_array[j])**2).sum()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
# END_PATCH ---
Si = Molecule([Atom('Si', [0.0, 0.0, 0.0])])
la = 0.5431
s = crystal([[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], # Fractional Positions
[Si, Si], # Molecules
225, # Space Group
cellpar = [la,la,la, 90, 90, 90], # unit cell parameters
repetitions = [2, 2, 2]) # unit cell repetitions in each direction
bonds = guess_bonds(s.r_array, s.type_array, threshold=0.02)
#s.bonds = [[0,1], [1, 2]]
v = QtViewer()
v.add_renderer(BallAndStickRenderer, s.r_array, s.type_array,
bonds,shading='phong')
v.run()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
# END_PATCH ---
Si = Molecule([Atom('Si', [0.0, 0.0, 0.0])])
la = 0.5431
s = crystal(
[[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], # Fractional Positions
[Si, Si], # Molecules
225, # Space Group
cellpar=[la, la, la, 90, 90, 90], # unit cell parameters
repetitions=[2, 2, 2]) # unit cell repetitions in each direction
bonds = guess_bonds(s.r_array, s.type_array, threshold=0.02)
#s.bonds = [[0,1], [1, 2]]
v = QtViewer()
v.add_renderer(BallAndStickRenderer,
s.r_array,
s.type_array,
bonds,
shading='phong')
v.run()
