AMDAT

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 nanoparticle/interface

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

6-fold orientational order parameter in binary 2D LJ

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

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.

_{Mean-square displacement for bead-spring polymer

doi: 10.1039/C8SM02051E

(image: Sean Hung)}

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.

_{Time-resolved structure factor peak for bead-spring polymer

doi: 10.1039/C8SM02051E

(image: Sean Hung)}

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.

_{Coarse-graining of atomistic polystyrene and identification of string-like cooperative rearrangements

doi: 10.1021/acs.jpcb.9b09468}

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.

_{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}

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.

_{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.

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