# This section imports the Python packages required during this exercise.
from MorseCalculator import MorsePotential
from ase.io import write, read
from ase import units
from ase.md.nvtberendsen import NVTBerendsen
import numpy as np
# Parameters for the Morse potential for Cu
D = 0.3429
r0 = 2.866
alpha = 1.3588
atoms = read('hexagonal_lattice.xyz')
atoms.set_calculator(MorsePotential(D=D, alpha=alpha, r0=r0))
vel = np.zeros((len(atoms), 3))
# initialize velocities with uniform random numbers between [-0.005, 0.005]
# gives random initial velocity
vel[:, 0] = (np.random.rand(len(atoms)) - 0.5) * 1e-2
vel[:, 1] = (np.random.rand(len(atoms)) - 0.5) * 1e-2
atoms.set_velocities(vel)
open('berendsen.log', 'w').close()
dyn = NVTBerendsen(atoms,
timestep=1 * units.fs,
temperature=600,
taut=100 * units.fs,
# -*- coding: utf-8 -*-
"""
Exercise 05
"""
import ase
from MorseCalculator import MorsePotential # imports the MorsePotential from MorseCalculator.py
# Parameters for the Morse potential
D = 1.0
r0 = 1.0
alpha = 1.0
structure = ase.Atoms('H2', positions=[[0, 0, 0], [
0, 0, 0.5
]]) # creates the particle system for the specific distance
structure.set_calculator(
MorsePotential(D=D, alpha=alpha, r0=r0)
) # determines how the interaction is calculated between the particles
print(structure.get_forces()) # calculates and prints the forces