Here are the tutorials and reference documentation for DynamO.

All of the documentation of DynamO assumes the reader has some experience with both Linux and Molecular Dynamics simulation. There are some recommended resources listed below which will introduce the basics of these topics if you are at all unfamiliar with them.

Tutorials

1: Compiling DynamO from source

2: Introduction to DynamO

3: The configuration file

4: Thermostats and transport properties

5: Multiple species/interactions, compression dynamics, and ticker output plugins

6: Polydispersity, walls, granular dynamics, and a bit of python

A: Automatically processing output and config files

References

Configuration File Format Reference

Output Plugin Reference

FAQ

Frequently Asked Questions

DynamO Publications

If you find the DynamO useful and publish a paper using results obtained from DynamO, please help support it's development by citing the following paper.

M. N. Bannerman, R. Sargant, L. Lue, "DynamO: A free O(N) general event-driven simulator," J. Comp. Chem., 32, 3329-3338 (2011)

Below is an incomplete list of publications which have used DynamO:

C. Alexandrou, V. Harmandaris, A. Irakleous, G. Koutsou,and N. Savva, "Modeling the evolution of COVID-19," Arxiv, 2008.03165 (2020)
S. Pieprzyk, M. N. Bannerman, A. C. Brańka, M. Chudakc, and D. M. Heyes, "Thermodynamic and dynamical properties of the hard sphere system revisited by molecular dynamics simulation," Phys. Chem. Chem. Phys., 21, 6886–6899 (2019)
H. Zhang and Y. Han, "Compression-induced polycrystal-glass transition in binary crystals," Phys. Rev. X, 8, 041023 (2018)
A. J. Dunleavy, K. Wiesner, R. Yamamoto, and C. P. Royall "Mutual information reveals multiple structural relaxation mechanisms in a model glass former," Nature Communications, 6, 6089 (2015)
J. Wei, L. Xu, and F. Song "Range effect on percolation threshold and structural properties for short-range attractive spheres," J. Chem. Phys, 142, 034504 (2015)
S. Mandal, S. Lang, M. Gross, M. Oettel, D. Raabe, T. Franosch, and F. Varnik, "Multiple reentrant glass transitions in confined hard-sphere glasses," Nature Communications, 1, 5, 4435 (2014)
M. N. Bannerman, S. Strobl, A. Formella, and T. Poschel, "Stable algorithm for event detection in event-driven particle dynamics," Comp. Part. Mech., 1, 191-198 (2014)
C. Thomson, L. Lue, and M. N. Bannerman, "Mapping continuous potentials to discrete forms," J. Chem. Phys., 140, 034105 (2014)
P. C. Royall, A. Malins, A. J. Dunleavy, and R. Pinney, "Geometric Frustration is Strong in Model Fragile Glassformers," In Fragility of Glass-forming Liquids, TRiPS 13, Ed. A. L. Greer, K. F. Kelton, S. Sastry (2014)
J. E. Kollmer, A. Sack, M. Heckel, F. Zimber, P. Mueller, M. N. Campbell Bannerman and T. Poeschel, "Collective Granular Dynamics in a Shaken Container at Low Gravity Conditions," AIP Conf. Proc., 1542, 811-814 (2013)
S. Mandal, V. Chikkadi, B. Nienhuis, D. Raabe, P. Schall, and F. Varnik, "Single-particle fluctuations and directional correlations in driven hard-sphere glasses," Phys. Rev. E, 88, 022129 (2013)
K. B. Hollingshead, A. Jain, and T. M. Truskett, "Communication: Fine discretization of pair interactions and an approximate analytical strategy for predicting equilibrium behavior of complex fluids," J. Chem. Phys., 139, 161102 (2013)
S. Mandal, M. Gross, D. Raabe, and F. Varnik, "Heterogeneous Shear in Hard Sphere Glasses," Phys. Rev. Lett., 108, 098301 (2012)
M. N. Bannerman, J. E. Kollmer, A. Sack, M. Heckel, P. Müller, and T. Pöschel, "Movers and shakers: Granular damping in microgravity," Phys. Rev. E, 84, 011301 (2011)
M. N. Bannerman and L. Lue, "Exact event-rate formulae for square-well and square-shoulder systems," J. Chem. Phys., 133, 124506 (2010)
M. N. Bannerman, L. Lue, L. V. Woodcock "Thermodynamic pressures for hard spheres and closed-virial equation-of-state," J. Chem. Phys., 132, 084507 (2010)
Wm. G. Hoover, C. G. Hoover, M. N. Bannerman, "Single-Speed Molecular Dynamics of Hard Parallel Squares and Cubes," J. Stat. Phys., 136, 715-732 (2009)
M. N. Bannerman, J. E. Magee, L. Lue, "Structure and stability of helices in square-well homopolymers," Phys. Rev. E, 80, 021801 (2009)
M. N. Bannerman, L. Lue, "Transport properties of highly asymmetric hard sphere mixtures," J. Chem. Phys., 130, 164507 (2009)
M. N. Bannerman, T. E. Green, P. Grassia, L. Lue, "Collision statistics in sheared inelastic hard spheres," Phys. Rev. E, 79, 041308 (2009)

If you have any publications you want to be listed here please contact the developers.

Recommended Resources

DynamO, like many Linux programs, is driven through a Command-Line Interface (CLI). To be able to use DynamO, you will need to be familiar with the Linux terminal. Take a look at this link to learn more about the terminal and how it works if you are at all unsure what this means.

If you're looking for general documentation on Molecular Dynamics, there are a few good introductory textbooks available. The definitive text by Allen and Tildesley has always been very popular with students and veterans alike.

"Computer Simulation of Liquids," M. P. Allen, and D. J. Tildesley, 1989, Oxford Science Pub.

A short summary of the basics, also written by Allen, is also available online if you cannot find a copy of the book.

Although the fundamentals of Molecular Dynamics are always the same, the event-driven techniques used in DynamO differ in implementation from the techniques described in the resources above. These differences are best described in the excellent book by Haile.

"Molecular Dynamics Simulation: Elementary Methods," J. M. Haile, 1992, Wiley

Page last modified: Sunday 9th June 2024