import pybinding as pb
from pybinding.repository import graphene
import matplotlib.pyplot as plt
from math import pi
pb.pltutils.use_style()
model = pb.Model(
graphene.monolayer(),
pb.rectangle(x=2, y=1.2)
)
model.plot()
plt.show()
model = pb.Model(
graphene.monolayer(),
pb.regular_polygon(num_sides=6, radius=1.4, angle=pi/6)
)
model.plot()
plt.show()
# A graphene-specific shape which guaranties armchair edges on all sides
model = pb.Model(
graphene.bilayer(),
graphene.hexagon_ac(side_width=1)
)
model.plot()
plt.show()
ux = 2*c * x*y
uy = c * (x**2 - y**2)
return x + ux, y + uy, z
@pb.hopping_energy_modifier
def strained_hopping(energy, x1, y1, z1, x2, y2, z2):
l = np.sqrt((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)
w = l / graphene.a_cc - 1
return energy * np.exp(-3.37 * w)
return displacement, strained_hopping
model = pb.Model(
graphene.monolayer(),
pb.regular_polygon(num_sides=3, radius=2, angle=pi),
triaxial_strain(c=0.1)
)
model.system.plot()
plt.show()
plt.figure(figsize=(7, 2.5))
grid = plt.GridSpec(nrows=1, ncols=2)
for block, energy in zip(grid, [0, 0.25]):
plt.subplot(block)
plt.title("E = {} eV".format(energy))
solver = pb.solver.arpack(model, k=30, sigma=energy)
ldos_map = solver.calc_spatial_ldos(energy=energy, broadening=0.03)
ldos_map.plot_structure()
import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, group6_tmd
models = {
'graphene-monolayer': [graphene.monolayer(), graphene.hexagon_ac(1)],
'graphene-monolayer-alt': [graphene.monolayer_alt(), pb.rectangle(1.6, 1.4)],
'graphene-monolayer-4atom': [graphene.monolayer_4atom()],
'graphene-monolayer-nn': [graphene.monolayer(2), pb.regular_polygon(6, 0.9)],
'graphene-monolayer-periodic-1d': [graphene.monolayer(), pb.primitive(5, 5),
pb.translational_symmetry(a1=True, a2=False)],
'graphene-monolayer-periodic-1d-alt': [graphene.monolayer_4atom(), pb.rectangle(1),
pb.translational_symmetry(a1=False, a2=0.6)],
'graphene-monolayer-periodic-2d': [graphene.monolayer(), pb.primitive(a1=5, a2=5),
pb.translational_symmetry(a1=1, a2=1)],
'graphene-monolayer-4atom-periodic-2d': [graphene.monolayer_4atom(), pb.rectangle(1),
pb.translational_symmetry(a1=0.6, a2=0.6)],
'graphene-bilayer': [graphene.bilayer(), graphene.hexagon_ac(0.6)],
}
@pytest.fixture(scope='module', ids=list(models.keys()), params=models.values())
def model(request):
return pb.Model(*request.param)
def test_pickle_round_trip(model):
import pickle
unpickled = pickle.loads(pickle.dumps(model.system))
import pytest
import math
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, examples
polygons = {
'triangle': pb.regular_polygon(3, radius=1.1),
'triangle90': pb.regular_polygon(3, radius=1.1, angle=math.pi / 2),
'diamond': pb.regular_polygon(4, radius=1),
'square': pb.regular_polygon(4, radius=1, angle=math.pi / 4),
'pentagon': pb.regular_polygon(5, radius=1),
}
@pytest.fixture(scope='module',
ids=list(polygons.keys()),
params=polygons.values())
def polygon(request):
return request.param
def test_polygon_expected(polygon, baseline, plot_if_fails):
model = pb.Model(graphene.monolayer(), polygon)
expected = baseline(model.system)
plot_if_fails(model.system, expected, "plot")
plot_if_fails(polygon, polygon, "plot")
assert pytest.fuzzy_equal(model.system, expected, 1.e-4, 1.e-6)
#!/usr/bin python # -*- encoding: utf-8 -*- ''' @Author : Celeste Young @File : 石墨烯单层.py @Time : 2021/9/18 16:25 @E-mail : [email protected] @Tips : ''' """Several finite-sized systems created using builtin lattices and shapes""" import pybinding as pb from pybinding.repository import graphene import matplotlib.pyplot as plt from math import pi pb.pltutils.use_style() model_1 = pb.Model( graphene.monolayer(), # pb.rectangle(x=2, y=1.2) pb.regular_polygon(num_sides=6, radius=1.4)) model_2 = pb.Model(graphene.bilayer(), graphene.hexagon_ac(side_width=1)) model_3 = pb.Model( graphene.monolayer(), # pb.rectangle(x=2, y=1.2) pb.regular_polygon(num_sides=6, radius=1.4, angle=0)) model_2.plot() # model_2.plot() plt.show()
import pytest
import pybinding as pb
from pybinding.repository import graphene
models = {
'graphene-monolayer': [graphene.monolayer(), graphene.hexagon_ac(1)],
'graphene-monolayer-alt': [graphene.monolayer_alt(), pb.rectangle(1.6, 1.4)],
'graphene-monolayer-4atom': [graphene.monolayer_4atom()],
'graphene-monolayer-nn': [graphene.monolayer(2), pb.regular_polygon(6, 0.9)],
'graphene-monolayer-periodic-1d': [graphene.monolayer(), pb.primitive(5, 5),
pb.translational_symmetry(a1=True, a2=False)],
'graphene-monolayer-periodic-1d-alt': [graphene.monolayer_4atom(), pb.rectangle(1),
pb.translational_symmetry(a1=False, a2=0.6)],
'graphene-monolayer-periodic-2d': [graphene.monolayer(), pb.primitive(a1=5, a2=5),
pb.translational_symmetry(a1=1, a2=1)],
'graphene-monolayer-4atom-periodic-2d': [graphene.monolayer_4atom(), pb.rectangle(1),
pb.translational_symmetry(a1=0.6, a2=0.6)],
'graphene-bilayer': [graphene.bilayer(), graphene.hexagon_ac(0.6)],
}
@pytest.fixture(scope='module', ids=list(models.keys()), params=models.values())
def model(request):
return pb.Model(*request.param)
def test_api():
model = pb.Model(graphene.monolayer(), pb.primitive(2, 2))
system = model.system
import pytest
import math
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
polygons = {
'triangle': pb.regular_polygon(3, radius=1.1),
'triangle90': pb.regular_polygon(3, radius=1.1, angle=math.pi/2),
'diamond': pb.regular_polygon(4, radius=1),
'square': pb.regular_polygon(4, radius=1, angle=math.pi/4),
'pentagon': pb.regular_polygon(5, radius=1),
}
@pytest.fixture(scope='module', ids=list(polygons.keys()), params=polygons.values())
def polygon(request):
return request.param
def test_polygon_api():
with pytest.raises(RuntimeError) as excinfo:
pb.Polygon([0, 0], [0, 1])
assert "at least 3 sides" in str(excinfo.value)
def test_polygon(polygon, baseline, plot_if_fails):
model = pb.Model(graphene.monolayer(), polygon)
expected = baseline(model.system)
def ring(inner_radius, outer_radius):
def contains(x, y, z):
r = np.sqrt(x**2 + y**2)
return np.logical_and(inner_radius < r, r < outer_radius)
return pb.FreeformShape(contains,
width=[2 * outer_radius, 2 * outer_radius])
#
# shape = ring(inner_radius=1.4, outer_radius=2)
# shape.plot()
rec = pb.rectangle(x=6, y=1)
hexa = pb.regular_polygon(num_sides=6, radius=1.92, angle=np.pi / 6)
cir = pb.circle(radius=0.6)
shape = rec + hexa - cir
model = pb.Model(
graphene.monolayer(),
# trapezoid(a=3.2, b=1.4, h=1.5)
# circle(radius=2.5)
shape)
model.plot()
# model.shape.plot()
# model = pb.Model(
# graphene.monolayer(),
# pb.primitive(a1=6, a2=6) # 在a1 a2方向上扩胞
# )
# model.plot()
plt.show()