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# creates: transport_setup.png
import numpy as np
from ase import Atoms
from ase.build import molecule
from ase.io import write
a = 3.92 # Experimental lattice constant
sqrt = np.sqrt
cell = np.array(
[
[a / sqrt(3), 0.0, 0.0],
[0.0, a / sqrt(2), 0.0],
[0.0, a / sqrt(8), a * sqrt(3 / 8.0)],
]
)
repeat = (1, 3, 3)
A = Atoms('Pt', pbc=True, positions=[(0.0, 0.0, 0.0)], cell=[1, 1, 1])
B = Atoms('Pt', pbc=True, positions=[(0.0, 1 / 3.0, 1 / 3.0)], cell=[1, 1, 1])
C = Atoms('Pt', pbc=True, positions=[(0.0, 2 / 3.0, 2 / 3.0)], cell=[1, 1, 1])
A *= repeat
B *= repeat
C *= repeat
pyramid_BC = Atoms(
'Pt4',
pbc=True,
tags=[1, 1, 1, 2],
positions=[
(0.0, 1 / 3.0, 1 / 3.0), # B
(0.0, 4 / 3.0, 1 / 3.0), # B
(0.0, 1 / 3.0, 4 / 3.0), # B
(1.0, 2 / 3.0, 2 / 3.0),
], # C
cell=[1, 1, 1],
)
inv_pyramid_BC = pyramid_BC.copy()
inv_pyramid_BC.positions[:, 0] *= -1
def pos(atoms, x):
atoms2 = atoms.copy()
atoms2.translate([x, 0, 0])
return atoms2
princ = pos(A, 0) + pos(B, 1) + pos(C, 2)
large = (
pos(princ, -8)
+ pos(princ, -4)
+ pos(princ, 0)
+ pos(A, 3)
+ pos(pyramid_BC, 4)
+ pos(inv_pyramid_BC, 3)
+ pos(princ, 4)
+ pos(princ, 8)
)
large.set_cell(cell * repeat, scale_atoms=True)
large.cell[0, 0] = 7 * large.cell[0, 0]
dist = 18.0
large.cell[0, 0] += dist - cell[0, 0]
large.positions[-(9 * 6 + 4) :, 0] += dist - cell[0, 0]
tipL, tipR = large.positions[large.get_tags() == 2]
tipdist = np.linalg.norm(tipL - tipR)
mol = molecule('C6H6', pbc=True, tags=[3] * 6 + [4] * 6)
mol.rotate('y', 'x')
mol.rotate('z', 'y')
large += mol
large.positions[-len(mol) :] += tipL
large.positions[-len(mol) :, 0] += tipdist / 2
old = large.cell.copy()
large *= (1, 1, 3)
large.set_cell(old)
# view(large)
colors = np.zeros((len(large), 3))
colors[:] = [1.0, 1.0, 0.75]
pr = [0.7, 0.1, 0.1]
H = [1, 1, 1]
C = [0.3, 0.3, 0.3]
Pt = [0.7, 0.7, 0.9]
colors[164:218] = pr # principal layer
colors[289:316] = pr # principal layer
colors[218:289] = Pt # Central region Pt
colors[316:322] = C # Molecule C
colors[322:328] = H # Molecule H
# write('test.png', large, rotation='-90x,-13y', radii=.9,
# show_unit_cell=0, colors=colors)
write(
'transport_setup.pov',
large,
rotation='-90x,-13y',
radii=1.06,
show_unit_cell=0,
povray_settings=dict(colors=colors, transparent=False),
).render()
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