AMDAT — Amorphous Molecular Dynamics Analysis Toolkit

High-performance analysis of molecular dynamics (MD) trajectories for amorphous, glass-forming, and polymer systems.

AMDAT is a C++ toolkit that loads trajectories into memory for rapid analysis, with robust atom selection, time-resolved statistics, and modular data objects. It reads common LAMMPS trajectory formats and GROMACS .xtc. It provides a wide variety of high-performance analyses integral to molecular modeling studies, such as clustering, spatial decomposition, and calculating time-resolved structure factors, mean-square displacements, radial distribution functions, etc.

Why AMDAT (at a glance)

• Fast, in-memory engine – load once, analyze many time delays without re-reading files.
• Blocked exponential time spacing – efficient long-timescale dynamics across orders of magnitude.
• Modular data abstractions – trajectory / neighbor / multibody / value lists compose into rich workflows.
• Validated analyses –
  • static and time-resolved structure factors,
  • radial distribution functions,
  • mean-square displacements,
  • neighbor correlations,
  • clustering, and more.
• Plain-text outputs – easy post-processing in Python/Matlab/Excel/VMD/OVITO.

More details in the Overview.

Quick start (Linux, Conda)

Clone the repo from GitHub

Prereqs:

• Conda
• Set up GitHub ssh keys on your machine

git clone git@github.com:dssimmons-codes/AMDAT.git
cd AMDAT/

Build with conda environment (Recommended)

make conda-setup
conda activate amdat
make

Run

./AMDAT -i path/to/input.in

More details in Build/Install.

Highlights

Identification of highly mobile particles (image: Pierre Kawak)

Particle displacements (binary 2D LJ) (image: Pierre Kawak)

Sorting by distance from a nanoparticle/interface (image: Pierre Kawak)

6-fold orientational order parameter (binary 2D LJ) (image: Daniel Hunsicker)

Mean-square displacement for bead-spring polymer doi: 10.1039/C8SM02051E (image: Sean Hung)

Time-resolved structure factor peak for bead-spring polymer doi: 10.1039/C8SM02051E (image: Sean Hung)

Coarse-graining of atomistic polystyrene and identification of string-like cooperative rearrangements doi: 10.1021/acs.jpcb.9b09468

Radial distribution functions for bead-spring polymer (top left), OTP (top right), binary LJ glass former (left column), Cu4Ag6 (middle column), and SiO2 (right column) doi: 10.1021/acs.jpcb.9b09468

Structure factors for (clockwise from top left) bead-spring polymer, binary LJ glass former, binary copper-silver allow, OTP, and SiO2 doi: 10.1021/acs.jpcb.9b09468

Citation

If you use AMDAT, please cite:

AMDAT — Amorphous Molecular Dynamics Analysis Toolkit DOI: 10.5281/zenodo.17417166

Also see CITATION.cff.

Authors & Maintainers

• Lead: David S. Simmons
• Maintainers: Pierre Kawak · William Drayer
• Contributors: Michael Marvin · Mark Mackura · Daniel Hunsicker

License

GNU GPLv3.0 (see LICENSE). It bundles:

• Voro++ (see Voro++ LICENSE)
• xdrfile (LGPL-3.0, see xdrfile LICENSE)

Contributing

We welcome issues, discussions, and pull requests. Please skim CONTRIBUTING.md first.