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

<table> <tr> <td align="center" width="25%"> <a href="Manual/displacement_list.md"> <img src="Manual/assets/highlights/mobile_particles.png" alt="Identification of highly mobile particles" width="100%"> </a><br/> <sub>Identification of highly mobile particles<br/>(image: Pierre Kawak)</sub> </td> <td align="center" width="25%"> <a href="Manual/displacement_list.md"> <img src="Manual/assets/highlights/displacements_2d.png" alt="Particle displacements in binary 2D LJ" width="100%"> </a><br/> <sub>Particle displacements (binary 2D LJ)<br/>(image: Pierre Kawak)</sub> </td> <td align="center" width="25%"> <a href="Manual/create_bin_list.md"> <img src="Manual/assets/highlights/color_by_distance.png" alt="Sorting by distance from nanoparticle/interface" width="100%"> </a><br/> <sub>Sorting by distance from a nanoparticle/interface<br/>(image: Pierre Kawak)</sub> </td> <td align="center" width="25%"> <a href="Manual/n_fold.md"> <img src="Manual/assets/highlights/2d_hexatic.png" alt="6-fold orientational order parameter in binary 2D LJ" width="100%"> </a><br/> <sub>6-fold orientational order parameter (binary 2D LJ)<br/>(image: Daniel Hunsicker)</sub> </td> </tr> </table> <table> <tr> <td align="center" width="50%"> <a href="Manual/msd.md"> <img src="Manual/assets/highlights/msd.jpg" alt="Mean-squre displacments for a bead-spring polymer (image by Sean Hung, adapted from Hung, Patra, Meenakshisundaram, Mangalara, Simmons, Soft Matter, 15 (2019) 1223-1242. doi: 10.1039/C8SM02051E." width="100%"> </a><br/> <sub> Mean-square displacement for bead-spring polymer<br/> doi: <a href="https://doi.org/10.1039/C8SM02051E">10.1039/C8SM02051E</a><br/> (image: Sean Hung) </sub> </td> <td align="center" width="50%"> <a href="Manual/isfs.md"> <img src="Manual/assets/highlights/isfs.gif" alt="Intermediate scattering functions for a bead-spring polymer (image by Sean Hung, adapted from Hung, Patra, Meenakshisundaram, Mangalara, Simmons, Soft Matter, 15 (2019) 1223-1242. doi: 10.1039/C8SM02051E." width="100%"> </a><br/> <sub> Time-resolved structure factor peak for bead-spring polymer<br/> doi: <a href="https://doi.org/10.1039/C8SM02051E">10.1039/C8SM02051E</a><br/> (image: Sean Hung) </sub> </td> </tr> </table> <table> <tr> <td align="center" width="100%"> <a href="Manual/overview.md"> <img src="Manual/assets/highlights/cg_map.png" alt="AMDAT-based post-simulation mapping of atomistic polystyrene repeat units to segmental center of mass calculations (left), and identificiation of string-like cooperative rearrangements (a la doi.org/10.1103/PhysRevLett.80.2338) (middle two), visualized across two timesteps (red and blue in right image). Images by Sean Hung. Computed for simulations reported in Jui Hsiang Hung, David S Simmons, Do String-like Cooperative Motions Predict Relaxation Times in Glass-Forming Liquids?, Journal of Physical Chemistry B, 124, 1 (2020) 266-276. doi: 10.1021/acs.jpcb.9b09468." width="100%"> </a><br/> <sub> Coarse-graining of atomistic polystyrene and identification of string-like cooperative rearrangements<br/> doi: <a href="https://doi.org/10.1021/acs.jpcb.9b09468">10.1021/acs.jpcb.9b09468</a> </sub> </td> </tr> </table> <table> <tr> <td align="center" width="100%"> <a href="Manual/overview.md"> <img src="Manual/assets/highlights/string_rdf.jpeg" alt="Radial distribution functions for (a) bead−spring polymer; (b) OTP; (c,f,i) binary LJ glass former; (d,g,j) Cu4Ag6; (e,h,k) SiO2. Reproduced from Jui Hsiang Hung, David S Simmons, Do String-like Cooperative Motions Predict Relaxation Times in Glass-Forming Liquids?, Journal of Physical Chemistry B, 124, 1 (2020) 266-276. doi:10.1021/acs.jpcb.9b09468." width="100%"> </a><br/> <sub> 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)<br/> doi: <a href="https://doi.org/10.1021/acs.jpcb.9b09468">10.1021/acs.jpcb.9b09468</a> </sub> </td> </tr> </table> <table> <tr> <td align="center" width="100%"> <a href="Manual/overview.md"> <img src="Manual/assets/highlights/struct.png" alt="Clockwise from top left, structure factors for Bead-spring polymer, binary Lennard Jones glass-former, binary copper-silver alloy, OTP (atomistic structure factor in red and ring-center-of mass structure factor in blue, see inset), and SiO2. Computed for simulations reported in Jui Hsiang Hung, David S Simmons, Do String-like Cooperative Motions Predict Relaxation Times in Glass-Forming Liquids?, Journal of Physical Chemistry B, 124, 1 (2020) 266-276. doi:10.1021/acs.jpcb.9b09468." width="100%"> </a><br/> <sub> Structure factors for (clockwise from top left) bead-spring polymer, binary LJ glass former, binary copper-silver allow, OTP, and SiO2<br/> doi: <a href="https://doi.org/10.1021/acs.jpcb.9b09468">10.1021/acs.jpcb.9b09468</a> </sub> </td> </tr> </table>

Citation

If you use AMDAT, please cite:

Simmons, Kawak, Drayer and Mackura, "Amorphous Molecular Dynamics Analysis Toolkit (AMDAT)". Zenodo, 2025. DOI: 10.5281/zenodo.17417166.

Kawak, Drayer, and Simmons, "AMDAT: An Open-Source Molecular Dynamics Analysis Toolkit for Supercooled Liquids, Glass-Forming Materials, and Complex Fluids". arXiv, 2026. DOI: 10.48550/arXiv.2602.05865

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.

AMDAT

Install / Use

README