The atomic simulation environment—a Python library for working with atoms

Abstract

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Dynamic breaking of a single gold bond

“…Langevin MD simulations were performed in the atomistic simulation environment1920. The energy and force were calculated using EMT2122.…”

Oxygen Functionalization of Hexagonal Boron Nitride on Ni(111)

“…E BN/Ni is the total energy of the pristine h-BN/ Ni(111). [67] First, ac limbing-image nudged-elastic band (NEB) [40] search was performed with reduced optimization parameters, the k-point set was reduced to the G point.…”

Key findings and recommendations

“…These digesters may be considered pools for the discovery of new biomass-converting microbes and enzymes for bioenergy production. Wilkens and co-workers brought the understanding of anaerobic digestion one step further by ranking the types of organisms present in relation to the different types of biomass-converting groups of enzymes (cellulolytic, xylanolytic and amylolytic [34]; see Figure 5). …”

“…At present, NOMAD contains >50 million DFT calculations for different materials and thus constitutes a rich resource for testing and validating intelligent materials discovery methods [33]. DTU researchers are also very active in developing generally applicable software such as ASE (Atomic Simulation Environment) for setting up, manipulating, running, visualizing and analyzing atomistic simulations [34]. Local infrastructure for storing and sharing computed materials data is also available through the open Computational Materials Repository (CMR) [https://cmr.fysik.dtu.dk/], for example, a comprehensive 2D computational materials database containing calculated structural and electronic properties of a range of 2D materials (see Figure 5) [35].…”