def test_plot_grid(self):
matplotlib_bands_density(self.grid,
pyplot.gca(),
100,
energy_range=(-3, 3),
show_fermi=False)
matplotlib_bands_density(self.grid,
pyplot.gca(),
100,
energy_range=(-3, 3),
method='gaussian',
show_fermi=False)
l = list(i for i in pyplot.gca().get_children()
if isinstance(i, Line2D))
assert len(l) == 2
yy = []
for ll in l:
x, y = ll.get_data()
yy.append(y)
testing.assert_equal(x, numpy.linspace(-3, 3, 100))
assert numpy.all(y < 10) and numpy.all(y >= 0)
assert numpy.any(y > 0.1)
assert (numpy.abs(yy[0] - yy[1])**2).sum()**.5 / 100 < 1e-2
def test_plot_fill_weights(self):
w1 = 0.3 * numpy.ones(self.cell.values.shape)
w2 = 0.7 * numpy.ones(self.cell.values.shape)
rpc1 = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
weights=w1,
use_fill=True)
rpc2 = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
weights=w2,
on_top_of=w1,
use_fill=True)
for rpc in (rpc1, rpc2):
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert xmin >= -3.31
assert ymin >= 0
assert xmax <= 3.31
assert ymax < 10
def test_unknown_orientation(self):
with self.assertRaises(ValueError):
matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
energy_range=(-3, 3),
orientation="unknown")
def test_unknown_units_portrait(self):
matplotlib_bands_density(self.grid,
pyplot.gca(),
100,
units=2 * Ry,
orientation='portrait')
assert pyplot.gca().get_yaxis().get_label().get_text() == 'Energy'
assert pyplot.gca().get_xaxis().get_label().get_text() == 'Density'
def test_custom_units_portrait(self):
matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
units=2 * Ry,
units_name="Hartree",
orientation='portrait')
assert pyplot.gca().get_xaxis().get_label().get_text().endswith(
"(electrons per unit cell per Hartree)")
assert pyplot.gca().get_yaxis().get_label().get_text().endswith(
"(Hartree)")
def test_plot_weights(self):
w1 = 0.3*numpy.ones(self.cell.values.shape)
w2 = 0.7*numpy.ones(self.cell.values.shape)
rl1 = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, weights = w1)[0]
rl2 = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, weights = w2, on_top_of = w1)[0]
x1,y1 = rl1.get_data()
x2,y2 = rl2.get_data()
testing.assert_allclose(x1, numpy.linspace(-3,3,100))
testing.assert_allclose(x2, numpy.linspace(-3,3,100))
testing.assert_allclose(y1, 0.3*y2)
def test_plot_fill_weights(self):
w1 = 0.3*numpy.ones(self.cell.values.shape)
w2 = 0.7*numpy.ones(self.cell.values.shape)
rpc1 = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, weights = w1, use_fill = True)
rpc2 = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, weights = w2, on_top_of = w1, use_fill = True)
for rpc in (rpc1,rpc2):
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert xmin>=-3.01
assert ymin>=0
assert xmax<=3.01
assert ymax< 10
def test_plot_fill_portrait(self):
rpc = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, use_fill = True, orientation = "portrait")
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert ymin>=-3.01
assert xmin>=0
assert ymax<=3.01
assert xmax< 10
def test_plot_grid(self):
matplotlib_bands_density(self.grid, pyplot.gca(), 100, energy_range = (-3,3), show_fermi = False)
matplotlib_bands_density(self.grid, pyplot.gca(), 100, energy_range = (-3,3), force_gaussian = True, show_fermi = False)
l = list(i for i in pyplot.gca().get_children() if isinstance(i, Line2D))
assert len(l) == 2
yy = []
for ll in l:
x,y = ll.get_data()
yy.append(y)
testing.assert_equal(x, numpy.linspace(-3,3,100))
assert numpy.all(y<10) and numpy.all(y>=0)
assert numpy.any(y>0.1)
assert (numpy.abs(yy[0]-yy[1])**2).sum()**.5/100 < 1e-2
def test_portrait(self):
rl = matplotlib_bands_density(self.cell, pyplot.gca(), 100, energy_range = (-3, 3), orientation = "portrait")[0]
l = list(i for i in pyplot.gca().get_children() if isinstance(i, Line2D))
assert len(l) == 2
x,y = rl.get_data()
testing.assert_equal(y, numpy.linspace(-3,3,100))
assert numpy.all(x<10) and numpy.all(x>0)
assert numpy.any(x>0.1)
def test_gaussian(self):
rl1 = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
method="gaussian",
gaussian_spread=0.1,
units="eV")[0]
a = -0.5 / (0.1 * numericalunits.eV)**2
b = 1 / (2 * math.pi)**0.5 / (0.1 * numericalunits.eV)
rl2 = matplotlib_bands_density(
self.cell,
pyplot.gca(),
100,
method=lambda x: b * numpy.exp(a * x**2))[0]
x1, y1 = rl1.get_data()
x2, y2 = rl2.get_data()
testing.assert_equal(x1, x2)
testing.assert_equal(y1, y2)
def test_plot_weights(self):
w1 = 0.3 * numpy.ones(self.cell.values.shape)
w2 = 0.7 * numpy.ones(self.cell.values.shape)
rl1 = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
weights=w1)[0]
rl2 = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
weights=w2,
on_top_of=w1)[0]
x1, y1 = rl1.get_data()
x2, y2 = rl2.get_data()
testing.assert_allclose(x1, numpy.linspace(-3.3, 3.3, 100))
testing.assert_allclose(x2, numpy.linspace(-3.3, 3.3, 100))
testing.assert_allclose(y1, 0.3 * y2)
def test_plot_fill_portrait(self):
rpc = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
use_fill=True,
orientation="portrait")
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert ymin >= -3.31
assert xmin >= 0
assert ymax <= 3.31
assert xmax < 10
def test_portrait(self):
rl = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
energy_range=(-3, 3),
orientation="portrait")[0]
l = list(i for i in pyplot.gca().get_children()
if isinstance(i, Line2D))
assert len(l) == 2
x, y = rl.get_data()
testing.assert_equal(y, numpy.linspace(-3, 3, 100))
assert numpy.all(x < 10) and numpy.all(x > 0)
assert numpy.any(x > 0.1)
def test_plot_fill(self):
rpc = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False, use_fill = True)
axes = pyplot.gcf().axes
assert len(axes) == 1
axes = axes[0]
pc = list(i for i in axes.get_children() if isinstance(i, PolyCollection))
assert len(pc) == 1
pc = pc[0]
assert pc == rpc
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert xmin>=-3.01
assert ymin>=0
assert xmax<=3.01
assert ymax< 10
def test_plot(self):
rl = matplotlib_bands_density(self.cell, pyplot.gca(), 100, show_fermi = False)
assert len(rl) == 1
rl = rl[0]
axes = pyplot.gcf().axes
assert len(axes) == 1
axes = axes[0]
testing.assert_allclose(axes.get_xlim(), (-3,3))
l = list(i for i in axes.get_children() if isinstance(i, Line2D))
assert len(l) == 1
l = l[0]
assert l == rl
x,y = l.get_data()
testing.assert_allclose(x, numpy.linspace(-3,3,100))
assert numpy.all(y<10) and numpy.all(y>0)
assert numpy.any(y>0.1)
def test_plot_fill(self):
rpc = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False,
use_fill=True)
axes = pyplot.gcf().axes
assert len(axes) == 1
axes = axes[0]
pc = list(i for i in axes.get_children()
if isinstance(i, PolyCollection))
assert len(pc) == 1
pc = pc[0]
assert pc == rpc
for p in rpc.get_paths():
(xmin, ymin), (xmax, ymax) = p.get_extents().get_points()
assert xmin >= -3.31
assert ymin >= 0
assert xmax <= 3.31
assert ymax < 10
def test_plot(self):
rl = matplotlib_bands_density(self.cell,
pyplot.gca(),
100,
show_fermi=False)
assert len(rl) == 1
rl = rl[0]
axes = pyplot.gcf().axes
assert len(axes) == 1
axes = axes[0]
testing.assert_allclose(axes.get_xlim(), (-3.3, 3.3))
l = list(i for i in axes.get_children() if isinstance(i, Line2D))
assert len(l) == 1
l = l[0]
assert l == rl
x, y = l.get_data()
testing.assert_allclose(x, numpy.linspace(-3.3, 3.3, 100))
assert numpy.all(y < 10) and numpy.all(y > 0)
assert numpy.any(y > 0.1)
from dfttools.simple import parse
from dfttools import presentation
from matplotlib import pyplot
with open("plot.py.data",'r') as f:
# Retrieve the last band structure from the file
bands = parse(f, "band-structure")[-1]
# Convert to a grid
grid = bands.as_grid()
# Plot both
presentation.matplotlib_bands_density(bands, pyplot.gca(), 200, energy_range = (-2, 2), label = "bands")
presentation.matplotlib_bands_density(grid, pyplot.gca(), 200, energy_range = (-2, 2), label = "grid")
pyplot.legend()
pyplot.show()
from dfttools.simple import parse
from dfttools import presentation
from matplotlib import pyplot
with open("plot.py.data",'r') as f:
# Read bands data
bands = parse(f, "band-structure")[0]
# Prepare axes
ax_left = pyplot.subplot2grid((1,3), (0, 0), colspan=2)
ax_right = pyplot.subplot2grid((1,3), (0, 2))
# Plot bands
presentation.matplotlib_bands(bands,ax_left)
presentation.matplotlib_bands_density(bands, ax_right, 100, orientation = 'portrait')
ax_right.set_ylabel('')
pyplot.show()
# Set the band values
bands.values[..., 0] = -e
bands.values[..., 1] = e
# Assign some weights
weights = bands.values.copy()
weights -= weights.min()
weights /= weights.max()
# Prepare axes
ax_left = pyplot.subplot2grid((1, 3), (0, 0), colspan=2)
ax_right = pyplot.subplot2grid((1, 3), (0, 2))
# Plot bands
p = presentation.matplotlib_bands(bands, ax_left, weights=weights)
presentation.matplotlib_bands_density(bands,
ax_right,
100,
orientation='portrait')
presentation.matplotlib_bands_density(bands,
ax_right,
100,
orientation='portrait',
weights=weights,
use_fill=True,
color="#AAAAFF")
ax_right.set_ylabel('')
pyplot.colorbar(p)
pyplot.show()
from numericalunits import eV
import numpy
# A reciprocal basis
basis = Basis((1, 1, 1, 0, 0, -0.5), kind='triclinic', meta={"Fermi": 0})
# Grid shape
shape = (50, 50, 1)
# A dummy grid with correct grid coordinates and empty grid values
grid = Grid(
basis,
tuple(numpy.linspace(0, 1, x, endpoint=False) + .5 / x for x in shape),
numpy.zeros(shape + (2, ), dtype=numpy.float64),
)
# Calculate graphene band
k = grid.cartesian() * numpy.pi / 3.**.5 * 2
e = (1 + 4 * numpy.cos(k[..., 1])**2 +
4 * numpy.cos(k[..., 1]) * numpy.cos(k[..., 0] * 3.**.5))**.5 * eV
# Set the band values
grid.values[..., 0] = -e
grid.values[..., 1] = e
presentation.matplotlib_bands_density(grid,
pyplot.gca(),
200,
energy_range=(-1, 1))
pyplot.show()
from dfttools.simple import parse
from dfttools import presentation
from matplotlib import pyplot
with open("plot.py.data", 'r') as f:
# Retrieve the last band structure from the file
bands = parse(f, "band-structure")
# Convert to a grid
grid = bands.as_grid()
# Plot both
presentation.matplotlib_bands_density(bands,
pyplot.gca(),
200,
energy_range=(-2, 2),
label="bands")
presentation.matplotlib_bands_density(grid,
pyplot.gca(),
200,
energy_range=(-2, 2),
label="grid")
pyplot.legend()
pyplot.show()
def test_units(self):
matplotlib_bands_density(self.cell, pyplot.gca(), 100, units = "eV")
assert pyplot.gca().get_xaxis().get_label().get_text().endswith("eV")
assert pyplot.gca().get_yaxis().get_label().get_text().endswith("eV")
def test_custom_units(self):
matplotlib_bands_density(self.cell, pyplot.gca(), 100, units = 2*Ry, units_name = "Hartree")
assert pyplot.gca().get_xaxis().get_label().get_text().endswith("Hartree")
assert pyplot.gca().get_yaxis().get_label().get_text().endswith("Hartree")
def test_unknown_units_portrait(self):
matplotlib_bands_density(self.grid, pyplot.gca(), 100, units = 2*Ry, orientation = 'portrait')
assert pyplot.gca().get_yaxis().get_label().get_text() == 'Energy'
assert pyplot.gca().get_xaxis().get_label().get_text() == 'Density'
def test_unknown_orientation(self):
with self.assertRaises(ValueError):
matplotlib_bands_density(self.cell, pyplot.gca(), 100, energy_range = (-3, 3), orientation = "unknown")
from dfttools.simple import parse
from dfttools import presentation
from matplotlib import pyplot
with open("plot.py.data",'r') as f:
# Read bands data
bands = parse(f, "band-structure")
# Prepare axes
ax_left = pyplot.subplot2grid((1,3), (0, 0), colspan=2)
ax_right = pyplot.subplot2grid((1,3), (0, 2))
# Plot bands
presentation.matplotlib_bands(bands,ax_left)
presentation.matplotlib_bands_density(bands, ax_right, 100, orientation = 'portrait')
ax_right.set_ylabel('')
pyplot.show()
basis,
kp,
numpy.zeros((100,2), dtype = numpy.float64),
)
# Calculate graphene band
k = bands.cartesian()*numpy.pi/3.**.5*2
e = (1+4*numpy.cos(k[...,1])**2 + 4*numpy.cos(k[...,1])*numpy.cos(k[...,0]*3.**.5))**.5*eV
# Set the band values
bands.values[...,0] = -e
bands.values[...,1] = e
# Assign some weights
weights = bands.values.copy()
weights -= weights.min()
weights /= weights.max()
# Prepare axes
ax_left = pyplot.subplot2grid((1,3), (0, 0), colspan=2)
ax_right = pyplot.subplot2grid((1,3), (0, 2))
# Plot bands
p = presentation.matplotlib_bands(bands,ax_left,weights = weights)
presentation.matplotlib_bands_density(bands, ax_right, 100, orientation = 'portrait')
presentation.matplotlib_bands_density(bands, ax_right, 100, orientation = 'portrait', weights = weights, use_fill = True, color = "#AAAAFF")
ax_right.set_ylabel('')
pyplot.colorbar(p)
pyplot.show()
def test_units(self):
matplotlib_bands_density(self.cell, pyplot.gca(), 100, units="eV")
assert pyplot.gca().get_xaxis().get_label().get_text().endswith("(eV)")
assert pyplot.gca().get_yaxis().get_label().get_text().endswith(
"(states per unit cell per eV)")
from dfttools.types import Basis, Grid
from dfttools import presentation
from matplotlib import pyplot
from numericalunits import eV
import numpy
# A reciprocal basis
basis = Basis((1,1,1,0,0,-0.5), kind = 'triclinic', meta = {"Fermi": 0})
# Grid shape
shape = (50,50,1)
# A dummy grid with correct grid coordinates and empty grid values
grid = Grid(
basis,
tuple(numpy.linspace(0,1,x, endpoint = False)+.5/x for x in shape),
numpy.zeros(shape+(2,), dtype = numpy.float64),
)
# Calculate graphene band
k = grid.cartesian()*numpy.pi/3.**.5*2
e = (1+4*numpy.cos(k[...,1])**2 + 4*numpy.cos(k[...,1])*numpy.cos(k[...,0]*3.**.5))**.5*eV
# Set the band values
grid.values[...,0] = -e
grid.values[...,1] = e
presentation.matplotlib_bands_density(grid, pyplot.gca(), 200, energy_range = (-1, 1))
pyplot.show()