AACSD: An atomistic analyzer for crystal structure and defects

ZR Liu and RF Zhang, COMPUTER PHYSICS COMMUNICATIONS, 222, 229-239 (2018).

DOI: 10.1016/j.cpc.2017.07.026

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post- analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality. Program summary Program title: AACSD Program Files doi: http://dx.doi.org/10.17632/3hrmbbgp6s.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C++ Nature of problem: Post-analysis of atomic configurations for LAMMPS 1 dump files, including crystals structure, defect and grain's orientation. Solution method: Reading a LAMMPS custom dump file or LAMMPS data file from hard disk, get them analyzed and dumped to a new LAMMPS custom dump file together with the generated results, which can be visualized by OVITO 2. References: 1 S. Plimpton, J. Comput. Phys. 117 (1995) 1-19. Link: http://lammps.sandia.gov/ 2 A. Stukowski, Modell. Simul. Mater. Sci. Eng. 18 (2010) 015012. Link: http://www.ovito.org/ (C) 2017 Elsevier B.V. All rights reserved.

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