アルゴンの結晶構造作成 | 24/11/28(木)

アルゴンの結晶構造について

WebElements Periodic Table » Argon » crystal structures

This WebElements periodic table page contains crystal structures for the element argon

www.webelements.com

アルゴンの結晶構造作成プログラム

cat make_crystal_structure.py

stdout:

import sys


class Atom:
    def __init__(self, x, y, z):
        self.x = x
        self.y = y
        self.z = z
        self.type = 1


def add_ball(r):
    atoms = []
    r = r
    s = 5.256 # lattice constant (Å)
    h = 0.5 * s
    for ix in range(-r, r+1):
        for iy in range(-r, r+1):
            for iz in range(-r, r+1):
                x = ix * s
                y = iy * s
                z = iz * s
                atoms.append(Atom(x, y, z))
                atoms.append(Atom(x, y+h, z+h))
                atoms.append(Atom(x+h, y, z+h))
                atoms.append(Atom(x+h, y+h, z))
    print(f"{len(atoms)} atoms")
    return atoms


def save_file(filename, atoms, r):
    with open(filename, "w") as f:
        f.write("Position Data\n\n")
        f.write("{} atoms\n".format(len(atoms)))
        f.write("1 atom types\n\n")
        s = 5.256
        f.write(f"{-r*s} {r*s} xlo xhi\n")
        f.write(f"{-r*s} {r*s} ylo yhi\n")
        f.write(f"{-r*s} {r*s} zlo zhi\n")
        f.write("\n")
        f.write("Atoms\n\n")
        for i, a in enumerate(atoms):
            f.write("{} {} {} {} {}\n".format(i+1, a.type, a.x, a.y, a.z))
    print("Generated {}".format(filename))


args = sys.argv
r = int(args[1])

save_file(f"config.atoms", add_ball(r=r), r=r)

アルゴンの結晶構造作成

コマンド:

python3 make_crystal_structure.py <number of grid iterations>

実行ログ:

python3 make_crystal_structure.py 2

stdout:

500 atoms
Generated config.atoms

可視化して検証

OVITOをインストール

OVITO ??? Scientific data visualization and analysis software

???? Scientific data visualization and analysis software for particle-based simulation models

www.ovito.org

OVITOを用いて可視化

config.atomsをOVITOで開く．

アルゴンの結晶構造が作成できたようだ．