Atomistic Manipulation Toolkit


Keywords
atom, atomic, atomistic, molecular dynamics
License
Other
Install
pip install atomman==1.2.8

Documentation

AtomMan

Atomistic Manipulation Toolkit

AtomMan: the Atomistic Manipulation Toolkit is a Python library for creating, representing, manipulating, and analyzing large-scale atomic systems of atoms. The focus of the package is to facilitate the rapid design and development of simulations that are fully documented and easily adaptable to new potentials, configurations, etc. The code has no requirements that limit which systems it can be used on, i.e. it should work on Linux, Mac and Windows computers.

Features:

  1. Allows for efficient and fast calculations on millions of atoms, each with many freely defined per-atom properties.
  2. Built-in tools for generating and analyzing crystalline defects, such as point defects, stacking faults, and dislocations.
  1. Call LAMMPS directly from Python and instantly retrieve the resulting data or LAMMPS error statement.
  2. Easily convert systems to/from the other Python atomic representations, such as ase.Atoms and pymatgen.Structure.
  3. Can read and dump crystal structure information from a number of formats, such as LAMMPS data and dump files, and POSCAR.
  4. Built-in unit conversions.

Installation

As of version 1.2, the atomman package is Python 2/3 compatible.

The latest release can be installed using pip:

pip install atomman

For Windows users, it is recommended to use an Anaconda distribution and use conda to install numpy, scipy, matplotlib, pandas and cython prior to installing atomman.

Alternatively, all code and documentation can be downloaded from GitHub.

Documentation

Web-based documentation for the atomman package is available at https://www.ctcms.nist.gov/potentials/atomman.

Source code for the documentation can be found in the github doc directory. The doc directory contains the information both as the source RestructuredText files and as unformatted HTML. If you download a copy, you can view the HTML version offline by

cd {atomman_path}/doc/html python -m http.server (for python 3) python -m SimpleHttpServer (for python 2)

Then, opening localhost:8000 in a web browser.

The documentation consists of two main components:

  1. Tutorial Jupyter Notebooks: Online html version, Downloadable Notebook version. The tutorials starting with ##. provide a general overview/example of the various capabilities. The tutorials starting with ##.#. give more detailed descriptions and list options available to the tools mentioned in the overview tutorials.
  2. Code Documentation: Online html version. This provides a rendering of the Python docstrings for the included functions and classes.

Required packages

This is a list of the required Python packages

Optional packages

This is a list of additional Python packages that can add functionality

  • diffpy.Structure: CIF reader. Required for loading systems from CIF files.
  • ase: The Atomic Simulation Environment for interacting with small systems and DFT calculations. Required for converting to/from ase.Atoms objects.
  • pymatgen: The Python Materials Genomics package used by the Materials Project for DFT calculations. Required for converting to/from pymatgen.Structure objects.
  • spglib: A Python interface to the spglib spacegroup analysis code. spglib can be used to analyze and determine the spacegroup for an atomic system. Required for converting to/from spglib.cell objects.
  • lammps: The Python library interface for the LAMMPS molecular dynamics simulation code that allows for a LAMMPS session to be controlled directly from Python. Required for direct loading/dumping of a system to/from a LAMMPS session.