Amorphous Molecular Dynamics Analysis Toolkit
Amorphous Molecular Dynamics Analysis Toolkit
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The Simmons group develops and maintains the Amorphous Molecular Dynamics Analysis Toolkit - a comprehensive open source package for analysis of structure and dynamics in soft materials simulations, with a focus on amorphous and glass-forming systems. The source code for AMDAT can be found here: https://github.com/dssimmons-codes/AMDAT. Please cite use of AMDAT via the following doi: https://doi.org/10.5281/zenodo.17417167. AMDAT provides a robust environment for atom selection and analysis, including many analysis tools. It is designed to work smoothly with simulation trajectory outputs from LAMMPS and other software that produces equivalently formated trajectory files. Selected examples of analysis outputs from AMDAT are provided below (trajectory renderings are performed in OVITO or VMD based on output from AMDAT).
AMDAT development is led by David S. Simmons, with major ongoing development contributions by Pierre Kawak and William Drayer. Other significant contributors to AMDAT development have included Michael Marvin, Mark Mackura, and Daniel Hunsicker.
Identification of highly mobile particles (image by Pierre Kawak)
Sorting of beads by distance from a nanoparticle or other interface (image by Pierre Kawak)
6-fold orientational order parameter for a 2-D binary Lennard Jones liquid (image by Daniel Hunsicker)
Particle displacements in a 2-D binary Lennard-Jones liquid (image by Pierre Kawak)
Mean-squre displacments for a bead-spring polymer (image by Sean Hung, adapted from Jui-Hsiang Hung, Tarak K Patra, Venkatesh Meenakshisundaram, Jayachandra Hari Mangalara, David S Simmons , Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids, Soft Matter, 15 (2019) 1223-1242. doi: 10.1039/C8SM02051E. (Inside cover article, In Special Issue on Soft Matter Emerging Investigators)
Intermediate scattering functions for a bead-spring polymer (image by Sean Hung, adapted from Jui-Hsiang Hung, Tarak K Patra, Venkatesh Meenakshisundaram, Jayachandra Hari Mangalara, David S Simmons , Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids, Soft Matter, 15 (2019) 1223-1242. doi: 10.1039/C8SM02051E. (Inside cover article, In Special Issue on Soft Matter Emerging Investigators)
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.
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.
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.
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