from __future__ import print_function import numpy as np from ase import Atoms from ase.units import eV, Ang, GPa d = 2.5*Ang a = Atoms('2Cu', positions=[(0., 0., 0.), (0., 0., d)])

import sys sys.path.append(r'files') import Morse calc = Morse.MorsePotential() a.set_calculator(calc) a.get_potential_energy()

p = a.get_positions() p

p[1,2] = 2.8 p

a.set_positions(p) a.get_potential_energy()

a.positions[1,2] = 2.9 a.get_positions()

f = a.get_forces() f

from ase.build import bulk cu = bulk("Cu", "fcc", a=3.6, cubic=True)

cu.cell

np.array(cu.cell)

cu.get_positions()

cu.set_calculator(calc) print("Number of atoms: ", cu.get_global_number_of_atoms()) print("Potential energy per atom: ", cu.get_potential_energy()/cu.get_global_number_of_atoms())

cu222 = cu.copy() # creating a copy of an Atoms object cu222.set_calculator(calc) # copying DOES NOT bring the attached calculator, so we need to set it again cu222 *= (2,2,2) # replicating the unit cell is accomplished by the multiplying operator print("Number of atoms: ", cu222.get_global_number_of_atoms()) print("Potential energy per atom: ", cu222.get_potential_energy()/cu222.get_global_number_of_atoms())

cell = cu.get_cell() cell *= 0.99 cu.set_cell(cell, scale_atoms=True) # To apply strain, the atomic positions need to be scaled together with the unit cell cu.get_cell()

cu.get_potential_energy()/cu.get_number_of_atoms()

cu.get_stress(voigt=False)

# Those who browse the documentation of ASE can discover that it has functionality to fit the equation of state # and extract parameters using more accurate methods. Compare your result above to those computed by ASE. # The call below takes two arrays: the variable V is an array of volumes/atom and E # is an array of corresponding potential energy values, again per atom. If you want to execute this # notebook cell, you will need to substitute your own arrays for V and E. from ase.eos import EquationOfState from ase.units import kJ eos = EquationOfState(V, E, eos="birchmurnaghan") # Birch-Murnaghan is a particular functional form fitted to the equation of state v0, e0, B = eos.fit() print('Bulk modulus: ', B / kJ * 1.0e24, 'GPa') eos.plot()