Example: Ase calculator¶

This example illustrates the usage of atomicrex as a calculator in the Atomic Simulation Environment (ASE). A bcc-Fe structure is created and the forces, stress and total energy are calculated using an ABOP [MulErhAlb07a]

Location¶

examples/python_ase_calculator

Input files¶

• calculate_energy.py: main input file

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 from atomicrex.ase_calculator import Atomicrex from ase.lattice.cubic import BodyCenteredCubic __doc__ = """ This script demonstrates the usage of the Atomicrex ase calculator. """ atoms = BodyCenteredCubic(size=(2, 2, 2), symbol='Fe', latticeconstant=2.86) calc = Atomicrex(file_name="main.xml") atoms.set_calculator(calc) f = atoms.get_forces() print("Forces: {}".format(f)) e = atoms.get_potential_energy() print("Total energy: {}".format(e)) p = atoms.get_stress() print("Stress: {}".format(p)) 
• main.xml: file with definition of potential

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  ase calculator Fe Fe.tersoff 
• Fe.tersoff: definition of potential parameters in Lammps/Tersoff format

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 # Values taken from: # Michael Mueller et al # J. Phys.: Condens. Matter 19 (2007) 326220 # Potential file was prepared by A. Stukowski (TU Darmstadt) # Parameters converted from K. Albe's analytical bond-order formalism to LAMMPS Tersoff format: # gamma = gamma # lambda3 = 2*mu # c = c # d = d # R = Rc # D = Dc # costheta0 = -h # lambda1 = beta*sqrt(2*S) # lambda2 = beta*sqrt(2/S) # A = D0/(S-1)*exp(lambda1*r0) # B = S*D0/(S-1)*exp(lambda2*r0) Fe Fe Fe 1.0 0.0115751 0 1.2898716 0.3413219 0.26 1.0 1.0 1.37635404 67.8647723 3.15 0.2 2.84810441 953.948593 

Output (files)¶

• log.calculate_energy: stdout from run calculating the energy

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Forces: [[ 1.25940924e-15 1.70523318e-15 3.91180144e-15] [ 1.36522738e-15 1.25420507e-15 1.49533164e-15] [ 1.25940924e-15 1.48145385e-15 1.77375475e-16] [ -2.65412692e-15 1.65048097e-15 6.85974715e-16] [ 2.10508694e-15 2.58690638e-15 -7.86697096e-16] [ 1.67487552e-15 -3.68021585e-15 -1.69742692e-15] [ -2.21409993e-16 4.46458545e-16 -1.64822005e-15] [ -1.97758476e-15 -2.64371858e-15 0.00000000e+00] [ 1.03216047e-16 7.70217223e-16 -1.87697080e-15] [ 1.21343907e-15 6.57460197e-16 -3.11469600e-15] [ -4.66640615e-16 -5.74193471e-16 -3.43995665e-15] [ -4.17808149e-15 1.88737914e-15 -4.78393367e-15] [ 2.89698820e-16 8.91647867e-16 -2.60208521e-15] [ 1.44328993e-15 -4.43568793e-15 -5.62267247e-15] [ 7.97105437e-16 1.68268177e-15 -4.16333634e-17] [ -2.98892855e-15 -4.32100636e-15 -3.89618893e-15]] Total energy: -68.48002450272035 Stress: [ 3.47784417e+02 3.47784417e+02 3.47784417e+02 6.13341821e-12 1.36628202e-12 -2.32045181e-11]