/usr/share/pyshared/ase/cluster/decahedron.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | import numpy as np
from ase import Atoms
from ase.data import atomic_numbers, reference_states
def Decahedron(symbol, p, q, r, latticeconstant=None):
"""
Returns a cluster in the decahedra class.
Prameters
---------
symbol: Chemical symbol (or atomic number) of the element.
p: Number of atoms on the (100) facets perpendicular to the five
fold axis.
q: Number of atoms on the (100) facets parallel to the five fold
axis. q = 1 corresponds to no visible (100) facets.
r: Depth of the Marks re-entrence at the pentagon corners. r = 0
corresponds to no re-entrence.
latticeconstant (optional): The lattice constant. If not given,
then it is extracted form ase.data.
"""
# Interpret symbol
if isinstance(symbol, str):
atomic_number = atomic_numbers[symbol]
else:
atomic_number = symbol
# Interpret lattice constant
if latticeconstant is None:
if reference_states[atomic_number]['symmetry'] in ['fcc', 'bcc', 'sc']:
lattice_constant = reference_states[atomic_number]['a']
else:
raise NotImplementedError(("Cannot guess lattice constant of a %s element." %
(reference_states[atomic_number]['symmetry'],)))
else:
if isinstance(latticeconstant, (int, float)):
lattice_constant = latticeconstant
else:
raise ValueError("Lattice constant must be of type int or float.")
# Check values of p, q, r
if p < 1 or q < 1:
raise ValueError("p and q must be greater than 0.")
if r < 0:
raise ValueError("r must be greater than or equal to 0.")
# Defining constants
t = 2.0*np.pi/5.0
b = lattice_constant/np.sqrt(2.0)
a = b*np.sqrt(3.0)/2.0
verticies = a * np.array([[np.cos(np.pi/2.), np.sin(np.pi/2.), 0.],
[np.cos(t*1. + np.pi/2.), np.sin(t*1. + np.pi/2.), 0.],
[np.cos(t*2. + np.pi/2.), np.sin(t*2. + np.pi/2.), 0.],
[np.cos(t*3. + np.pi/2.), np.sin(t*3. + np.pi/2.), 0.],
[np.cos(t*4. + np.pi/2.), np.sin(t*4. + np.pi/2.), 0.]])
# Number of atoms on the five fold axis and a nice constant
h = p + q + 2*r - 1
g = h - q + 1 # p + 2*r
positions = []
# Make the five fold axis
for j in range(h):
pos = np.array([0.0, 0.0, j*b - (h-1)*b/2.0])
positions.append(pos)
# Make pentagon rings around the five fold axis
for n in range(1, h):
# Condition for (100)-planes
if n < g:
for m in range(5):
v1 = verticies[m-1]
v2 = verticies[m]
for i in range(n):
# Condition for marks re-entrence
if n - i < g - r and i < g - r:
for j in range(h-n):
pos = (n-i)*v1 + i*v2
pos += np.array([0.0, 0.0, j*b - (h-n-1)*b/2.0])
positions.append(pos)
# Fit the cell, so it only just consist the atoms
min = np.zeros(3)
max = np.zeros(3)
axes = np.array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
for i in range(3):
r = np.dot(positions, axes[i])
min[i] = r.min()
max[i] = r.max()
cell = max - min
positions = np.array(positions) - min
symbols = [atomic_number] * len(positions)
return Atoms(symbols=symbols, positions=positions, cell=cell)
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