def test_stm():
atoms = make_test_dft_calculation()
stm = STM(atoms, [0, 1, 2])
c = stm.get_averaged_current(-1.0, 4.5)
x, y, h = stm.scan(-1.0, c)
stm.write('stm.pckl')
x, y, h2 = STM('stm.pckl').scan(-1, c)
assert abs(h - h2).max() == 0
stm = STM(atoms, use_density=True)
c = stm.get_averaged_current(-1, 4.5)
x, y, I = stm.scan2(-1.0, 1.0)
stm.write('stm2.pckl')
x, y, I2 = STM('stm2.pckl').scan2(-1, 1)
assert abs(I - I2).max() == 0
stm = STM(atoms, use_density=True)
c = stm.get_averaged_current(42, 4.5)
x, y = stm.linescan(42, c, [0, 0], [2, 2])
assert abs(x[-1] - 2 * 2**0.5) < 1e-13
assert abs(y[-1] - y[0]) < 1e-13
def linescan(self, bias, current, p1, p2, npoints=50, z0=None):
"""Line scan for a given current [nA]"""
return STM.linescan(self, bias, self.current_to_density(current), p1,
p2, npoints, z0)
# plot1
import matplotlib.pyplot as plt
plt.gca(aspect='equal')
plt.contourf(x, y, h, 40)
plt.colorbar()
plt.savefig('2d.png')
# plot2
plt.figure()
plt.gca(aspect='equal')
x, y, I = stm.scan2(bias, z, repeat=(3, 5))
plt.contourf(x, y, I, 40)
plt.colorbar()
plt.savefig('2d_I.png')
# plot3
plt.figure()
a = atoms.cell[0, 0]
x, y = stm.linescan(bias, c, [0, 0], [2 * a, 0])
plt.plot(x, y)
plt.savefig('line.png')
# plot4
plt.figure()
biasstart = -2.0
biasend = 2.0
biasstep = 0.05
bias, I, dIdV = stm.sts(0, 0, z, biasstart, biasend, biasstep)
plt.plot(bias, I, label='I')
plt.plot(bias, dIdV, label='dIdV')
plt.xlim(biasstart, biasend)
plt.legend()
plt.savefig('dIdV.png')
from ase.dft.stm import STM
from gpaw import GPAW
calc = GPAW('al111.gpw')
atoms = calc.get_atoms()
stm = STM(atoms)
z = 8.0
bias = 1.0
c = stm.get_averaged_current(bias, z)
x, y, h = stm.scan(bias, c, repeat=(3, 5))
import matplotlib.pyplot as plt
import numpy as np
plt.gca(aspect='equal')
plt.contourf(x, y, h, 40)
plt.hot()
plt.colorbar()
plt.savefig('2d.png')
plt.figure()
a = atoms.cell[0, 0]
x, y = stm.linescan(bias, c, [0, 0], [2 * a, 0])
plt.plot(x, y)
plt.savefig('line.png')
from ase.calculators.test import make_test_dft_calculation
from ase.dft.stm import STM
atoms = make_test_dft_calculation()
stm = STM(atoms, [0, 1, 2])
c = stm.get_averaged_current(-1.0, 4.5)
x, y, h = stm.scan(-1.0, c)
stm.write('stm.pckl')
x, y, h2 = STM('stm.pckl').scan(-1, c)
assert abs(h - h2).max() == 0
stm = STM(atoms, use_density=True)
c = stm.get_averaged_current(42, 4.5)
x, y = stm.linescan(42, c, [0, 0], [2, 2])
assert abs(x[-1] - 2 * 2**0.5) < 1e-13
assert abs(y[-1] - y[0]) < 1e-13
from ase.calculators.test import make_test_dft_calculation
from ase.dft.stm import STM
atoms = make_test_dft_calculation()
stm = STM(atoms, [0, 1, 2])
c = stm.get_averaged_current(-1.0, 4.5)
x, y, h = stm.scan(-1.0, c)
stm.write('stm.pckl')
x, y, h2 = STM('stm.pckl').scan(-1, c)
assert abs(h - h2).max() == 0
stm = STM(atoms, use_density=True)
c = stm.get_averaged_current(-1, 4.5)
x, y, I = stm.scan2(-1.0, 1.0)
stm.write('stm2.pckl')
x, y, I2 = STM('stm2.pckl').scan2(-1, 1)
assert abs(I - I2).max() == 0
stm = STM(atoms, use_density=True)
c = stm.get_averaged_current(42, 4.5)
x, y = stm.linescan(42, c, [0, 0], [2, 2])
assert abs(x[-1] - 2 * 2**0.5) < 1e-13
assert abs(y[-1] - y[0]) < 1e-13