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<HTML>
<CENTER><A HREF = "main.html">Return to Steve Plimpton's home page</A>
</CENTER>
<HR>
<H3>Molecular Dynamics - Parallel Algorithms
</H3>
<P>I work in the area of classical molecular dynamics (MD). It's an
atomistic simulation method where:
</P>
<UL><LI>each atom is treated as a point mass,
<LI>simple force rules describe the interactions between atoms
<LI>Newton's equations are integrated to advance the atomic positions & velocities, and
<LI>thermodynamic statistics are extracted from the motion of the atoms.
</UL>
<P>I've worked on several parallel algorithms that are useful for MD
simulations. They are described in the next section.
</P>
<P>I've also written several parallel MD codes that I distribute freely.
They are available from <A HREF = "download.html">this page</A>.
</P>
<P>Performance of these parallel codes for a variety of systems (atomic,
polymer, biomolecular, metal, granular) on several parallel platforms
are discussed on the <A HREF = "https://www.lammps.org/bench.html">Benchmark
page</A> of the <A HREF = "https://www.lammps.org">LAMMPS
website</A>.
</P>
<P>Simulation efforts that I've been involved in are discussed on <A HREF = "mdsim.html">this
page</A>. Work of others using these codes is listed on the
<A HREF = "https://www.lammps.org/bench.html">Publications page</A> of the <A HREF = "lammmps">LAMMPS
website</A>, along with
<A HREF = "https://www.lammps.org/pictures.html">pictures</A> and
<A HREF = "https://www.lammps.org/movies.html">movies</A>.
</P>
<HR>
<HR>
<P>This paper gives an overview of the LAMMPS MD code, including its
algorithms, code design, and applications:
</P>
<P><B>LAMMPS - A flexible simulation tool for particle-based materials
modeling at the atomic, meso, and continuum scales</B>, A. P. Thompson,
H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown,
P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D.
Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott,
S. J. Plimpton, Comp Phys Comm, 271, 108171 (2022).
(<A HREF = "abstracts/cpc22.html">abstract</A>)
</P>
<HR>
<P>This paper describes 3 classes of parallel algorithms suitable for
short-range MD force fields: so-called atom-, force-, and
spatial-decomposition algorithms. All 3 are implemented and compared
in the paper, but the only one I "invented" was force-decomposition
which was work with Bruce Hendrickson at Sandia.
</P>
<P>In a nutshell, atom-decomposition methods assign a subset of atoms
permanently to each processor, force-decomposition methods assign a
subset of pairwise force computations to each proc, and
spatial-decomposition methods assign a sub-region of the simulation
box to each proc.
</P>
<P><B>Fast Parallel Algorithms for Short-Range Molecular Dynamics</B>,
S. J. Plimpton, J Comp Phys, 117, 1-19
(1995). (<A HREF = "abstracts/jcompphys95.html">abstract</A>)
</P>
<P>The Lennard-Jones codes discussed in the paper that implement the
various parallel algorithms are available for download
<A HREF = "download.html">here</A>.
</P>
<HR>
<P>These two papers describe how MD kernels like force calcluation and
neighbor list formation can be formulated to run efficiently Intel
CPUs and Xeon Phis:
</P>
<P><B>Increasing Molecular Dynamics Simulation Rates with an 8-Fold
Increase in Electrical Power Efficiency</B>, W. M. Brown, A. Semin,
M. Hebenstreit, S. Khvostov, K. Raman, S. J. Plimpton, SC16
Conference, SLC, Utah, Nov 2016. (<A HREF = "abstracts/sc16.html">abstract</A>)
</P>
<P><B>Optimizing legacy molecular dynamics software with directive-based
offload</B>, W. M. Brown, J.-M. Y. Carrillo, N. Gavhane, F. M. Thakkar,
S. J. Plimpton, Comp Phys Comm, 195, 95-101 (2015).
(<A HREF = "abstracts/cpc15.html">abstract</A>)
</P>
<P>This paper discusses how LAMMPS was designed to make it
flexible and extensible in an open-source context:
</P>
<P><B>Developing community codes for materials modeling</B>, S. J. Plimpton
and J. D. Gale, Current Opinion in Solid State and Materials Science
17, 271-276 (2013).
(<A HREF = "abstracts/cossms13.html">abstract</A>)
</P>
<P>This paper discusses computational attributes of many-body
potentials and their performance as implemented in LAMMPS:
</P>
<P><B>Computational Aspects of Many-body Potentials</B>, S. J. Plimpton and
A. P. Thompson, MRS Bulletin, 37, 513-521 (2012).
(<A HREF = "abstracts/mrs12.html">abstract</A>)
</P>
<P>These papers describe how MD kernels like force calcluation and
neighbor list formation and PPPM can be formulated to run efficiently
on hybrid processors, meaning ones that have both a multicore CPU and
a GPU:
</P>
<P><B>Implementing Molecular Dynamics on Hybrid High Performance Computers
- Short Range Forces</B>, W. M. Brown, P. Wang, S. J. Plimpton,
A. N. Tharrington, Comp Phys Comm, 182, 898-911, (2011).
(<A HREF = "abstracts/cpc11.html">abstract</A>)
</P>
<P><B>Implementing Molecular Dynamics on Hybrid High Performance Computers
- Particle-Particle Particle-Mesh</B>, W. M. Brown, A. Kohlmeyer,
S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 183, 449-459
(2012). (<A HREF = "abstracts/cpc12.html">abstract</A>)
</P>
<P>This paper describes how our parallel MD code LAMMPS is structured at
the outer level to enable it to be used as one tool in conjunction
with others, e.g. as part of a coupled multiscale calculation:
</P>
<P><B>Software components for parallel multiscale simulation: an example
with LAMMPS</B>, B. Frantzdale, S. J. Plimpton, M. S. Shephard,
Engineering with Computers, 26, 205-211
(2010). (<A HREF = "abstracts/ec10.html">abstract</A>)
</P>
<P>This paper describes how the virial/pressure tensor is computed
in LAMMPS for many-body potentials, both in serial and parallel:
</P>
<P><B>General formulation of pressure and stress tensor for arbitrary
many-body interaction potentials under periodic boundary conditions</B>,
A. P. Thompson, S. J. Plimpton, W. Mattson, J Chem Phys, 131, 154107
(2009). (<A HREF = "abstracts/jcp09a.html">abstract</A>)
</P>
<P>This paper describes the coupling of our LAMMPS MD code to the POEMS
multi-body dynamics solver:
</P>
<P><B>Substructured molecular dynamics using multibody dynamics
algorithms</B>, R. M. Mukherjee, P. S. Crozier, S. J. Plimpton,
K. S. Anderson, Intl J of Non-Linear Mechanics, 43, 1045-1055 (2008).
(<A HREF = "abstracts/ijnlm08.html">abstract</A>)
</P>
<P>This paper discusses a perdynamic model we added to our LAMMPS MD code
to enable mesoscale/continuum modeling of material properties:
</P>
<P><B>Implementing peridynamics within a molecular dynamics code</B>,
M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling, Comp Phys
Comm, 179, 777-783 (2008). (<A HREF = "abstracts/cpc08a.html">abstract</A>)
</P>
<P>This paper discusses algorithms we added to our LAMMPS MD code to
enable efficient modeling of mixtures with widely disparate particles
sizes:
</P>
<P><B>Accurate and Efficient Methods for Modeling Colloidal Mixtures in an
Explicit Solvent using Molecular Dynamics</B>, P. J. in 't Veld,
S. J. Plimpton, G. S. Grest, Comp Phys Comm, 179, 320-329
(2008). (<A HREF = "abstracts/cpc08.html">abstract</A>)
</P>
<HR>
<P>This paper describes the pros and cons of the 3 parallel algorithms
mentioned above in the context of molecular systems, where one must
also compute intra-molecular forces - e.g. bond, angle, torsional
terms within each molecule's topology.
</P>
<P><B>Parallel Molecular Dynamics Algorithms for Simulation of Molecular
Systems</B>, S. J. Plimpton and B. A. Hendrickson, chapter in Parallel
Computing in Computational Chemistry, edited by T. G. Mattson,
published by the American Chemical Society, Symposium Series 592,
114-132 (1995). (<A HREF = "abstracts/acs95.html">abstract</A>)
</P>
<HR>
<P>This paper describes how to use the force-decomposition algorithm
with embedded atom method (EAM) potentials which are commonly used for
metals and alloy systems. We implemented the idea in a code called
ParaDyn, which is a parallelization of the serial DYNAMO EAM code of
Stephen Foiles and Murray Daw, and which is available for download
<A HREF = "download.html">here</A>.
</P>
<P><B>Parallel Molecular Dynamics With the Embedded Atom Method</B>,
S. J. Plimpton and B. A. Hendrickson, in Materials Theory and
Modelling, edited by J. Broughton, P. Bristowe, and J. Newsam, MRS
Proceedings 291, Pittsburgh, PA, 1993, p 37. (<A HREF = "abstracts/mrs92.html">abstract</A>)
</P>
<HR>
<P>The extension of the force-decomposition idea to molecular MD is
described in this paper. We used these ideas in a Sandia code called
ParBond; it has since been superceded by our LAMMPS MD code.
</P>
<P><B>A New Parallel Method for Molecular-Dynamics Simulation of
Macromolecular Systems</B>, S. J. Plimpton and B. A. Hendrickson, J Comp
Chem, 17, 326-337 (1996). (<A HREF = "abstracts/jcc96.html">abstract</A>)
</P>
<HR>
<P>LAMMPS is our current production-scale MD code (suitable for molecular
or atomic systems). Two of its parallel algorithms are discussed in
this paper.
</P>
<P><B>Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics
Simulations</B>, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN, March 1997. (<A HREF = "abstracts/siam97.html">abstract</A>)
</P>
<HR>
<P>This paper discusses projections of what will be possible with
classical MD using current techniques on high-end computers of the
future.
</P>
<P><B>Computational Limits of Classical Molecular-Dynamics Simulations</B>,
S. J. Plimpton, Computational Materials Science, 4, 361-364
(1995). (<A HREF = "abstracts/cms95.html">abstract</A>)
</P>
</HTML>