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80 lines
2.7 KiB
80 lines
2.7 KiB
2 years ago
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import numpy as np
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from cmmde_atoms import Atoms
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from cmmde_clusterutil import get_element_info
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def Decahedron(symbol, p, q, r, latticeconstant=None):
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"""
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Return a decahedral cluster.
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Parameters
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----------
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symbol: Chemical symbol (or atomic number) of the element.
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p: Number of atoms on the (100) facets perpendicular to the five
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fold axis.
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q: Number of atoms on the (100) facets parallel to the five fold
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axis. q = 1 corresponds to no visible (100) facets.
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r: Depth of the Marks re-entrence at the pentagon corners. r = 0
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corresponds to no re-entrence.
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latticeconstant (optional): The lattice constant. If not given,
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then it is extracted form ase.data.
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"""
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symbol, atomic_number, latticeconstant = get_element_info(
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symbol, latticeconstant)
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# Check values of p, q, r
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if p < 1 or q < 1:
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raise ValueError("p and q must be greater than 0.")
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if r < 0:
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raise ValueError("r must be greater than or equal to 0.")
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# Defining constants
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t = 2.0 * np.pi / 5.0
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b = latticeconstant / np.sqrt(2.0)
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a = b * np.sqrt(3.0) / 2.0
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verticies = a * np.array([[np.cos(np.pi / 2.), np.sin(np.pi / 2.), 0.],
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[np.cos(t * 1. + np.pi / 2.),
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np.sin(t * 1. + np.pi / 2.), 0.],
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[np.cos(t * 2. + np.pi / 2.),
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np.sin(t * 2. + np.pi / 2.), 0.],
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[np.cos(t * 3. + np.pi / 2.),
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np.sin(t * 3. + np.pi / 2.), 0.],
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[np.cos(t * 4. + np.pi / 2.), np.sin(t * 4. + np.pi / 2.), 0.]])
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# Number of atoms on the five fold axis and a nice constant
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h = p + q + 2 * r - 1
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g = h - q + 1 # p + 2*r
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positions = []
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# Make the five fold axis
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for j in range(h):
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pos = np.array([0.0, 0.0, j * b - (h - 1) * b / 2.0])
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positions.append(pos)
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# Make pentagon rings around the five fold axis
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for n in range(1, h):
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# Condition for (100)-planes
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if n < g:
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for m in range(5):
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v1 = verticies[m - 1]
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v2 = verticies[m]
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for i in range(n):
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# Condition for marks re-entrence
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if n - i < g - r and i < g - r:
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for j in range(h - n):
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pos = (n - i) * v1 + i * v2
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pos += np.array([0.0, 0.0, j * b -
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(h - n - 1) * b / 2.0])
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positions.append(pos)
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symbols = [atomic_number] * len(positions)
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return Atoms(symbols=symbols, positions=positions)
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