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
References
FAQ
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.
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 COVID19," 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, "Compressioninduced polycrystalglass 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
shortrange 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 hardsphere glasses," Nature Communications, 1, 5, 4435 (2014)

M. N. Bannerman, S. Strobl, A. Formella, and T. Poschel, "Stable algorithm for event detection in eventdriven particle dynamics," Comp. Part. Mech., 1, 191198 (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 Glassforming 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, 811814
(2013)

S. Mandal, V. Chikkadi, B. Nienhuis, D. Raabe, P. Schall, and
F. Varnik, "Singleparticle fluctuations and directional correlations in driven hardsphere 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
eventrate formulae for squarewell and squareshoulder
systems," J. Chem. Phys., 133, 124506 (2010)

M. N. Bannerman, L. Lue,
L. V. Woodcock "Thermodynamic
pressures for hard spheres and closedvirial
equationofstate,"
J. Chem. Phys., 132, 084507 (2010)

Wm. G. Hoover, C. G. Hoover,
M. N. Bannerman, "SingleSpeed
Molecular Dynamics of Hard Parallel Squares and Cubes,"
J. Stat. Phys., 136, 715732 (2009)

M. N. Bannerman, J. E. Magee,
L. Lue, "Structure
and stability of helices in squarewell
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 CommandLine
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 eventdriven 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