/usr/share/pyshared/ase/dft/stm.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 | from math import exp, sqrt
import numpy as np
from ase.atoms import Atoms
class STM:
def __init__(self, atoms, symmetries=None):
if isinstance(atoms, Atoms):
calc = atoms.get_calculator()
else:
calc = atoms
atoms = calc.get_atoms()
self.nbands = calc.get_number_of_bands()
self.weights = calc.get_k_point_weights()
self.nkpts = len(self.weights)
self.nspins = calc.get_number_of_spins()
self.eigs = np.array([[calc.get_eigenvalues(k, s)
for k in range(self.nkpts)]
for s in range(self.nspins)])
self.eigs -= calc.get_fermi_level()
self.calc = calc
self.cell = atoms.get_cell()
assert not self.cell[2, :2].any() and not self.cell[:2, 2].any()
self.ldos = None
self.symmetries = symmetries or []
def calculate_ldos(self, width=None):
if self.ldos is not None and width == self.width:
return
if width is None:
width = 0.1
ldos = None
for s in range(self.nspins):
for k in range(self.nkpts):
for n in range(self.nbands):
psi = self.calc.get_pseudo_wave_function(n, k, s)
if ldos is None:
ldos = np.zeros(psi.shape)
f = (exp(-(self.eigs[s, k, n] / width)**2) *
self.weights[k])
ldos += f * (psi * np.conj(psi)).real
if 0 in self.symmetries:
# (x,y) -> (-x,y)
ldos[1:] += ldos[:0:-1].copy()
ldos[1:] *= 0.5
if 1 in self.symmetries:
# (x,y) -> (x,-y)
ldos[:, 1:] += ldos[:, :0:-1].copy()
ldos[:, 1:] *= 0.5
if 2 in self.symmetries:
# (x,y) -> (y,x)
ldos += ldos.transpose((1, 0, 2)).copy()
ldos *= 0.5
self.ldos = ldos
self.width = width
#def save_ldos(self, filename='ldos.pckl'):
def get_averaged_current(self, z, width=None):
self.calculate_ldos(width)
nz = self.ldos.shape[2]
# Find grid point:
n = z / self.cell[2, 2] * nz
dn = n - np.floor(n)
n = int(n) % nz
print n,dn
# Average and do linear interpolation:
return ((1 - dn) * self.ldos[:, :, n].mean() +
dn * self.ldos[:, :, (n + 1) % nz].mean())
def scan(self, current, z=None, width=None):
self.calculate_ldos(width)
L = self.cell[2, 2]
if z is None:
z = L / 2
nz = self.ldos.shape[2]
n = int(round(z / L * nz)) % nz
h = L / nz
ldos = self.ldos.reshape((-1, nz))
heights = np.empty(ldos.shape[0])
for i, a in enumerate(ldos):
heights[i], z, n = find_height(a, current, z, n, nz, h)
heights.shape = self.ldos.shape[:2]
return heights
def linescan(self, current, p1, p2, npoints=None, z=None, width=None):
self.calculate_ldos(width)
L = self.cell[2, 2]
if z is None:
z = L / 2
nz = self.ldos.shape[2]
n = int(round(z / L * nz)) % nz
h = L / nz
ldos = self.ldos.reshape((-1, nz))
p1 = np.asarray(p1)
p2 = np.asarray(p2)
d = p2 - p1
s = sqrt(np.dot(d, d))
if npints == None:
npoints = int(3 * s / h + 2)
cell = self.cell[:2, :2]
shape = np.array(self.ldos.shape[:2], float)
M = cell.I
heights = np.empty(npoints)
for i in range(npoints):
p = p1 + i * d / (npoints - 1)
q = np.dot(M, p) * shape
qi = q.astype(int)
n0, n1 = qi
f = q - qi
g = 1 - f
a = (g[0] * g[0] * ldos[n0, n1 ] +
f[0] * g[0] * ldos[n0 + 1, n1 ] +
g[0] * f[0] * ldos[n0, n1 + 1] +
f[0] * f[0] * ldos[n0 + 1, n1 + 1])
heights[i], z, n = find_height(a, current, z, n, nz, h)
return np.linspace(0, s, npoints), heights
def cube(self, filename, atoms=None):
pass
def find_height(array, current, z, n, nz, h):
c1 = array[n]
sign = cmp(c1, current)
m = 0
while m < nz:
n = (n + sign) % nz
z += sign * h
c2 = array[n]
if cmp(c2, current) != sign:
break
c1 = c2
m += 1
if m == nz:
print z, n, nz, h, current, array
raise RuntimeError('Tip crash!')
return z - sign * h * (current - c2) / (c1 - c2), z, n
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