forked from lijiext/lammps
603 lines
31 KiB
HTML
603 lines
31 KiB
HTML
<HTML>
|
|
<CENTER><A HREF = "Manual.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_start.html">Next Section</A>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>1. Introduction
|
|
</H3>
|
|
<P>These sections provide an overview of what LAMMPS can and can't do,
|
|
describe what it means for LAMMPS to be an open-source code, and
|
|
acknowledge the funding and people who have contributed to LAMMPS over
|
|
the years.
|
|
</P>
|
|
1.1 <A HREF = "#1_1">What is LAMMPS</A><BR>
|
|
1.2 <A HREF = "#1_2">LAMMPS features</A><BR>
|
|
1.3 <A HREF = "#1_3">LAMMPS non-features</A><BR>
|
|
1.4 <A HREF = "#1_4">Open source distribution</A><BR>
|
|
1.5 <A HREF = "#1_5">Acknowledgments and citations</A> <BR>
|
|
|
|
<HR>
|
|
|
|
<A NAME = "1_1"></A><H4>1.1 What is LAMMPS
|
|
</H4>
|
|
<P>LAMMPS is a classical molecular dynamics code that models an ensemble
|
|
of particles in a liquid, solid, or gaseous state. It can model
|
|
atomic, polymeric, biological, metallic, granular, and coarse-grained
|
|
systems using a variety of force fields and boundary conditions.
|
|
</P>
|
|
<P>For examples of LAMMPS simulations, see the Publications page of the
|
|
<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
|
|
</P>
|
|
<P>LAMMPS runs efficiently on single-processor desktop or laptop
|
|
machines, but is designed for parallel computers. It will run on any
|
|
parallel machine that compiles C++ and supports the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPI</A>
|
|
message-passing library. This includes distributed- or shared-memory
|
|
parallel machines and Beowulf-style clusters.
|
|
</P>
|
|
|
|
|
|
<P>LAMMPS can model systems with only a few particles up to millions or
|
|
billions. See <A HREF = "Section_perf.html">this section</A> for information on LAMMPS
|
|
performance and scalability, or the Benchmarks section of the <A HREF = "http://lammps.sandia.gov">LAMMPS
|
|
WWW Site</A>.
|
|
</P>
|
|
<P>LAMMPS is a freely-available open-source code, distributed under the
|
|
terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
|
|
modify the code however you wish. See <A HREF = "#1_4">this section</A> for a brief
|
|
discussion of the open-source philosophy.
|
|
</P>
|
|
|
|
|
|
<P>LAMMPS is designed to be easy to modify or extend with new
|
|
capabilities, such as new force fields, atom types, boundary
|
|
conditions, or diagnostics. See <A HREF = "Section_modify.html">this section</A> for
|
|
more details.
|
|
</P>
|
|
<P>The current version of LAMMPS is written in C++. Earlier versions
|
|
were written in F77 and F90. See <A HREF = "Section_history.html">this section</A>
|
|
for more information on different versions. All versions can be
|
|
downloaded from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
|
|
</P>
|
|
<P>LAMMPS was originally developed under a US Department of Energy CRADA
|
|
(Cooperative Research and Development Agreement) between two DOE labs
|
|
and 3 companies. It is distributed by <A HREF = "http://www.sandia.gov">Sandia National Labs</A>.
|
|
See <A HREF = "#1_5">this section</A> for more information on LAMMPS funding and
|
|
individuals who have contributed to LAMMPS.
|
|
</P>
|
|
|
|
|
|
<P>In the most general sense, LAMMPS integrates Newton's equations of
|
|
motion for collections of atoms, molecules, or macroscopic particles
|
|
that interact via short- or long-range forces with a variety of
|
|
initial and/or boundary conditions. For computational efficiency
|
|
LAMMPS uses neighbor lists to keep track of nearby particles. The
|
|
lists are optimized for systems with particles that are repulsive at
|
|
short distances, so that the local density of particles never becomes
|
|
too large. On parallel machines, LAMMPS uses spatial-decomposition
|
|
techniques to partition the simulation domain into small 3d
|
|
sub-domains, one of which is assigned to each processor. Processors
|
|
communicate and store "ghost" atom information for atoms that border
|
|
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
|
|
systems whose particles fill a 3d rectangular box with roughly uniform
|
|
density. Papers with technical details of the algorithms used in
|
|
LAMMPS are listed in <A HREF = "#1_5">this section</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "1_2"></A><H4>1.2 LAMMPS features
|
|
</H4>
|
|
<P>This section highlights LAMMPS features, with pointers to specific
|
|
commands which give more details. If LAMMPS doesn't have your
|
|
favorite interatomic potential, boundary condition, or atom type, see
|
|
<A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
|
|
LAMMPS.
|
|
</P>
|
|
<H4>General features
|
|
</H4>
|
|
<UL><LI> runs on a single processor or in parallel
|
|
<LI> distributed-memory message-passing parallelism (MPI)
|
|
<LI> spatial-decomposition of simulation domain for parallelism
|
|
<LI> open-source distribution
|
|
<LI> highly portable C++
|
|
<LI> optional libraries used: MPI and single-processor FFT
|
|
<LI> easy to extend with new features and functionality
|
|
<LI> runs from an input script
|
|
<LI> syntax for defining and using variables and formulas
|
|
<LI> syntax for looping over runs and breaking out of loops
|
|
<LI> run one or multiple simulations simultaneously (in parallel) from one script
|
|
</UL>
|
|
<H4>Particle and model types
|
|
</H4>
|
|
<P>(<A HREF = "atom_style.html">atom style</A> command)
|
|
</P>
|
|
<UL><LI> atoms
|
|
<LI> coarse-grained particles (e.g. bead-spring polymers)
|
|
<LI> united-atom polymers or organic molecules
|
|
<LI> all-atom polymers, organic molecules, proteins, DNA
|
|
<LI> metals
|
|
<LI> granular materials
|
|
<LI> coarse-grained mesoscale models
|
|
<LI> extended spherical and ellipsoidal particles
|
|
<LI> point dipolar particles
|
|
<LI> rigid collections of particles
|
|
<LI> hybrid combinations of these
|
|
</UL>
|
|
<H4>Force fields
|
|
</H4>
|
|
<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
|
|
<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
|
|
<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
|
|
commands)
|
|
</P>
|
|
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, soft, class 2 (COMPASS), tabulated
|
|
<LI> charged pairwise potentials: Coulombic, point-dipole
|
|
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), Stillinger-Weber, Tersoff, AI-REBO, ReaxFF
|
|
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
|
|
<LI> mesoscopic potentials: granular, Peridynamics
|
|
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
|
|
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
|
|
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
|
|
<LI> improper potentials: harmonic, cvff, class 2 (COMPASS)
|
|
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
|
|
<LI> water potentials: TIP3P, TIP4P, SPC
|
|
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
|
|
<LI> long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
|
|
<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
|
|
<LI> handful of GPU-enabled pair styles
|
|
</UL>
|
|
<P> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
|
|
overlaid potentials: superposition of multiple pair potentials
|
|
</P>
|
|
<H4>Atom creation
|
|
</H4>
|
|
<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
|
|
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
|
|
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
|
|
</P>
|
|
<UL><LI> read in atom coords from files
|
|
<LI> create atoms on one or more lattices (e.g. grain boundaries)
|
|
<LI> delete geometric or logical groups of atoms (e.g. voids)
|
|
<LI> replicate existing atoms multiple times
|
|
<LI> displace atoms
|
|
</UL>
|
|
<H4>Ensembles, constraints, and boundary conditions
|
|
</H4>
|
|
<P>(<A HREF = "fix.html">fix</A> command)
|
|
</P>
|
|
<UL><LI> 2d or 3d systems
|
|
<LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains
|
|
<LI> constant NVE, NVT, NPT, NPH integrators
|
|
<LI> thermostatting options for groups and geometric regions of atoms
|
|
<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
|
|
<LI> simulation box deformation (tensile and shear)
|
|
<LI> harmonic (umbrella) constraint forces
|
|
<LI> rigid body constraints
|
|
<LI> SHAKE bond and angle constraints
|
|
<LI> bond breaking, formation, swapping
|
|
<LI> walls of various kinds
|
|
<LI> non-equilibrium molecular dynamics (NEMD)
|
|
<LI> variety of additional boundary conditions and constraints
|
|
</UL>
|
|
<H4>Integrators
|
|
</H4>
|
|
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
|
|
</P>
|
|
<UL><LI> velocity-Verlet integrator
|
|
<LI> Brownian dynamics
|
|
<LI> rigid body integration
|
|
<LI> energy minimization via conjugate gradient or steepest descent relaxation
|
|
<LI> rRESPA hierarchical timestepping
|
|
</UL>
|
|
<H4>Diagnostics
|
|
</H4>
|
|
<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
|
|
</UL>
|
|
<H4>Output
|
|
</H4>
|
|
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
|
|
</P>
|
|
<UL><LI> log file of thermodynamic info
|
|
<LI> text dump files of atom coords, velocities, other per-atom quantities
|
|
<LI> binary restart files
|
|
<LI> per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
|
|
<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
|
|
<LI> spatial and time averaging of per-atom quantities
|
|
<LI> time averaging of system-wide quantities
|
|
<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
|
|
</UL>
|
|
<H4>Pre- and post-processing
|
|
</H4>
|
|
<UL><LI>Various pre- and post-processing serial tools are packaged
|
|
with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
|
|
|
|
<LI>Our group has also written and released a separate toolkit called
|
|
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
|
|
plotting, and visualization for LAMMPS simulations. Pizza.py is
|
|
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
|
|
Pizza.py WWW site</A>.
|
|
</UL>
|
|
|
|
|
|
|
|
|
|
<H4>Specialized features
|
|
</H4>
|
|
<P>These are LAMMPS capabilities which you may not think of as typical
|
|
molecular dynamics options:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
|
|
<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
|
|
<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
|
|
<LI><A HREF = "temper.html">parallel tempering</A>
|
|
<LI><A HREF = "prd.html">parallel replica dynamics</A>
|
|
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
|
|
<LI><A HREF = "pair_peri_pmb.html">Peridynamics mesoscale modeling</A>
|
|
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
|
|
<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
|
|
</UL>
|
|
<HR>
|
|
|
|
<A NAME = "1_3"></A><H4>1.3 LAMMPS non-features
|
|
</H4>
|
|
<P>LAMMPS is designed to efficiently compute Newton's equations of motion
|
|
for a system of interacting particles. Many of the tools needed to
|
|
pre- and post-process the data for such simulations are not included
|
|
in the LAMMPS kernel for several reasons:
|
|
</P>
|
|
<UL><LI>the desire to keep LAMMPS simple
|
|
<LI>they are not parallel operations
|
|
<LI>other codes already do them
|
|
<LI>limited development resources
|
|
</UL>
|
|
<P>Specifically, LAMMPS itself does not:
|
|
</P>
|
|
<UL><LI>run thru a GUI
|
|
<LI>build molecular systems
|
|
<LI>assign force-field coefficients automagically
|
|
<LI>perform sophisticated analyses of your MD simulation
|
|
<LI>visualize your MD simulation
|
|
<LI>plot your output data
|
|
</UL>
|
|
<P>A few tools for pre- and post-processing tasks are provided as part of
|
|
the LAMMPS package; they are described in <A HREF = "Section_tools.html">this
|
|
section</A>. However, many people use other codes or
|
|
write their own tools for these tasks.
|
|
</P>
|
|
<P>As noted above, our group has also written and released a separate
|
|
toolkit called <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
|
|
bullets. It provides tools for doing setup, analysis, plotting, and
|
|
visualization for LAMMPS simulations. Pizza.py is written in
|
|
<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
|
|
site</A>.
|
|
</P>
|
|
<P>LAMMPS requires as input a list of initial atom coordinates and types,
|
|
molecular topology information, and force-field coefficients assigned
|
|
to all atoms and bonds. LAMMPS will not build molecular systems and
|
|
assign force-field parameters for you.
|
|
</P>
|
|
<P>For atomic systems LAMMPS provides a <A HREF = "create_atoms.html">create_atoms</A>
|
|
command which places atoms on solid-state lattices (fcc, bcc,
|
|
user-defined, etc). Assigning small numbers of force field
|
|
coefficients can be done via the <A HREF = "pair_coeff.html">pair coeff</A>, <A HREF = "bond_coeff.html">bond
|
|
coeff</A>, <A HREF = "angle_coeff.html">angle coeff</A>, etc commands.
|
|
For molecular systems or more complicated simulation geometries, users
|
|
typically use another code as a builder and convert its output to
|
|
LAMMPS input format, or write their own code to generate atom
|
|
coordinate and molecular topology for LAMMPS to read in.
|
|
</P>
|
|
<P>For complicated molecular systems (e.g. a protein), a multitude of
|
|
topology information and hundreds of force-field coefficients must
|
|
typically be specified. We suggest you use a program like
|
|
<A HREF = "http://www.scripps.edu/brooks">CHARMM</A> or <A HREF = "http://amber.scripps.edu">AMBER</A> or other molecular builders to setup
|
|
such problems and dump its information to a file. You can then
|
|
reformat the file as LAMMPS input. Some of the tools in <A HREF = "Section_tools.html">this
|
|
section</A> can assist in this process.
|
|
</P>
|
|
<P>Similarly, LAMMPS creates output files in a simple format. Most users
|
|
post-process these files with their own analysis tools or re-format
|
|
them for input into other programs, including visualization packages.
|
|
If you are convinced you need to compute something on-the-fly as
|
|
LAMMPS runs, see <A HREF = "Section_modify.html">this section</A> for a discussion
|
|
of how you can use the <A HREF = "dump.html">dump</A> and <A HREF = "compute.html">compute</A> and
|
|
<A HREF = "fix.html">fix</A> commands to print out data of your choosing. Keep in
|
|
mind that complicated computations can slow down the molecular
|
|
dynamics timestepping, particularly if the computations are not
|
|
parallel, so it is often better to leave such analysis to
|
|
post-processing codes.
|
|
</P>
|
|
<P>A very simple (yet fast) visualizer is provided with the LAMMPS
|
|
package - see the <A HREF = "Section_tools.html#xmovie">xmovie</A> tool in <A HREF = "Section_tools.html">this
|
|
section</A>. It creates xyz projection views of
|
|
atomic coordinates and animates them. We find it very useful for
|
|
debugging purposes. For high-quality visualization we recommend the
|
|
following packages:
|
|
</P>
|
|
<UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
|
|
<LI><A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
|
|
<LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
|
|
<LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
|
|
<LI><A HREF = "http://www.openrasmol.org">RasMol</A>
|
|
</UL>
|
|
<P>Other features that LAMMPS does not yet (and may never) support are
|
|
discussed in <A HREF = "Section_history.html">this section</A>.
|
|
</P>
|
|
<P>Finally, these are freely-available molecular dynamics codes, most of
|
|
them parallel, which may be well-suited to the problems you want to
|
|
model. They can also be used in conjunction with LAMMPS to perform
|
|
complementary modeling tasks.
|
|
</P>
|
|
<UL><LI><A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
|
|
<LI><A HREF = "http://amber.scripps.edu">AMBER</A>
|
|
<LI><A HREF = "http://www.ks.uiuc.edu/Research/namd/">NAMD</A>
|
|
<LI><A HREF = "http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</A>
|
|
<LI><A HREF = "http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</A>
|
|
<LI><A HREF = "http://dasher.wustl.edu/tinker">Tinker</A>
|
|
</UL>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<P>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
|
|
modeling biological molecules. CHARMM and AMBER use
|
|
atom-decomposition (replicated-data) strategies for parallelism; NAMD
|
|
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
|
|
Tinker is a serial code. DL_POLY includes potentials for a variety of
|
|
biological and non-biological materials; both a replicated-data and
|
|
spatial-decomposition version exist.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "1_4"></A><H4>1.4 Open source distribution
|
|
</H4>
|
|
<P>LAMMPS comes with no warranty of any kind. As each source file states
|
|
in its header, it is a copyrighted code that is distributed free-of-
|
|
charge, under the terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A> (GPL). This
|
|
is often referred to as open-source distribution - see
|
|
<A HREF = "http://www.gnu.org">www.gnu.org</A> or <A HREF = "http://www.opensource.org">www.opensource.org</A> for more
|
|
details. The legal text of the GPL is in the LICENSE file that is
|
|
included in the LAMMPS distribution.
|
|
</P>
|
|
|
|
|
|
|
|
|
|
<P>Here is a summary of what the GPL means for LAMMPS users:
|
|
</P>
|
|
<P>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
|
|
choose, including for commercial purposes.
|
|
</P>
|
|
<P>(2) If you distribute a modified version of LAMMPS, it must remain
|
|
open-source, meaning you distribute it under the terms of the GPL.
|
|
You should clearly annotate such a code as a derivative version of
|
|
LAMMPS.
|
|
</P>
|
|
<P>(3) If you release any code that includes LAMMPS source code, then it
|
|
must also be open-sourced, meaning you distribute it under the terms
|
|
of the GPL.
|
|
</P>
|
|
<P>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
|
|
source file headers (including the copyright and GPL notices) should
|
|
remain part of the code.
|
|
</P>
|
|
<P>In the spirit of an open-source code, these are various ways you can
|
|
contribute to making LAMMPS better. You can send email to the
|
|
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A> on any of these
|
|
items.
|
|
</P>
|
|
<UL><LI>Point prospective users to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Mention it in
|
|
talks or link to it from your WWW site.
|
|
|
|
<LI>If you find an error or omission in this manual or on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
|
|
Site</A>, or have a suggestion for something to clarify or include,
|
|
send an email to the
|
|
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
|
|
|
|
<LI>If you find a bug, <A HREF = "Section_errors.html#9_2">this section</A> describes
|
|
how to report it.
|
|
|
|
<LI>If you publish a paper using LAMMPS results, send the citation (and
|
|
any cool pictures or movies if you like) to add to the Publications,
|
|
Pictures, and Movies pages of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>, with links
|
|
and attributions back to you.
|
|
|
|
<LI>Create a new Makefile.machine that can be added to the src/MAKE
|
|
directory.
|
|
|
|
<LI>The tools sub-directory of the LAMMPS distribution has various
|
|
stand-alone codes for pre- and post-processing of LAMMPS data. More
|
|
details are given in <A HREF = "Section_tools.html">this section</A>. If you write
|
|
a new tool that users will find useful, it can be added to the LAMMPS
|
|
distribution.
|
|
|
|
<LI>LAMMPS is designed to be easy to extend with new code for features
|
|
like potentials, boundary conditions, diagnostic computations, etc.
|
|
<A HREF = "Section_modify.html">This section</A> gives details. If you add a
|
|
feature of general interest, it can be added to the LAMMPS
|
|
distribution.
|
|
|
|
<LI>The Benchmark page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> lists LAMMPS
|
|
performance on various platforms. The files needed to run the
|
|
benchmarks are part of the LAMMPS distribution. If your machine is
|
|
sufficiently different from those listed, your timing data can be
|
|
added to the page.
|
|
|
|
<LI>You can send feedback for the User Comments page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
|
|
Site</A>. It might be added to the page. No promises.
|
|
|
|
<LI>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
|
|
Leave on desk. VISA also accepted. Chocolate chip cookies
|
|
encouraged.
|
|
</UL>
|
|
<HR>
|
|
|
|
<H4><A NAME = "1_5"></A>1.5 Acknowledgments and citations
|
|
</H4>
|
|
<P>LAMMPS development has been funded by the <A HREF = "http://www.doe.gov">US Department of
|
|
Energy</A> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
|
|
programs and its <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and <A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices.
|
|
</P>
|
|
<P>Specifically, work on the latest version was funded in part by the US
|
|
Department of Energy's Genomics:GTL program
|
|
(<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the <A HREF = "http://www.genomes2life.org">project</A>, "Carbon
|
|
Sequestration in Synechococcus Sp.: From Molecular Machines to
|
|
Hierarchical Modeling".
|
|
</P>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<P>The following papers describe the parallel algorithms used in LAMMPS.
|
|
</P>
|
|
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
|
|
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
|
|
</P>
|
|
<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
|
|
rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
|
|
Eighth SIAM Conference on Parallel Processing for Scientific
|
|
Computing, Minneapolis, MN (March 1997).
|
|
</P>
|
|
<P>If you use LAMMPS results in your published work, please cite the J
|
|
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
|
|
(http://lammps.sandia.gov).
|
|
</P>
|
|
<P>If you send is information about your publication, we'll be pleased to
|
|
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
|
|
for a picture or movie for the Pictures or Movies pages.
|
|
</P>
|
|
<P>The core group of LAMMPS developers is at Sandia National Labs. They
|
|
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
|
|
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
|
|
</P>
|
|
<P>Here are various folks who have made significant contributions to
|
|
features in LAMMPS. The most recent contributions are at the top of
|
|
the list.
|
|
</P>
|
|
|
|
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
|
|
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
|
|
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
|
|
<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
|
|
<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
|
|
<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
|
|
<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
|
|
<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
|
|
<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
|
|
<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
|
|
<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
|
|
<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
|
|
<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
|
|
<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
|
|
<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
|
|
<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
|
|
<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
|
|
<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
|
|
<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
|
|
<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
|
|
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
|
|
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
|
|
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
|
<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
|
<TR><TD >compute group/group </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >CG-CMM user package for coarse-graining </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
|
<TR><TD >cosine/delta angle potential </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
|
<TR><TD >VIM editor add-ons for LAMMPS input scripts </TD><TD > Gerolf Ziegenhain</TD></TR>
|
|
<TR><TD >pair lubricate </TD><TD > Randy Schunk (Sandia)</TD></TR>
|
|
<TR><TD >compute ackland/atom </TD><TD > Gerolf Zeigenhain</TD></TR>
|
|
<TR><TD >kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >AI-REBO bond-order potential </TD><TD > Ase Henry (MIT)</TD></TR>
|
|
<TR><TD >making LAMMPS a true "object" that can be instantiated multiple times, e.g. as a library </TD><TD > Ben FrantzDale (RPI)</TD></TR>
|
|
<TR><TD >pymol_asphere viz tool </TD><TD > Mike Brown (Sandia)</TD></TR>
|
|
<TR><TD >NEMD SLLOD integration </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >tensile and shear deformations </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >GayBerne potential </TD><TD > Mike Brown (Sandia)</TD></TR>
|
|
<TR><TD >ellipsoidal particles </TD><TD > Mike Brown (Sandia)</TD></TR>
|
|
<TR><TD >colloid potentials </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >fix heat </TD><TD > Paul Crozier and Ed Webb (Sandia)</TD></TR>
|
|
<TR><TD >neighbor multi and communicate multi </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >MATLAB post-processing scripts </TD><TD > Arun Subramaniyan (Purdue)</TD></TR>
|
|
<TR><TD >triclinic (non-orthogonal) simulation domains </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >thermo_extract tool</TD><TD > Vikas Varshney (Wright Patterson AFB)</TD></TR>
|
|
<TR><TD >fix ave/time and fix ave/spatial </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >MEAM potential </TD><TD > Greg Wagner (Sandia)</TD></TR>
|
|
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)</TD></TR>
|
|
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson and Xiaowang Zhou (Sandia)</TD></TR>
|
|
<TR><TD >region prism </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
|
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >fix momentum and recenter </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >multi-letter variable names </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
|
|
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
|
|
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >DCD and XTC dump styles</TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >grain boundary orientation fix </TD><TD > Koenraad Janssens and David Olmsted (Sandia)</TD></TR>
|
|
<TR><TD >lj/smooth pair potential </TD><TD > Craig Maloney (UCSB) </TD></TR>
|
|
<TR><TD >radius-of-gyration spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >self spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >EAM CoAl and AlCu potentials </TD><TD > Kwang-Reoul Lee (KIST, Korea)</TD></TR>
|
|
<TR><TD >cosine/squared angle potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
|
<TR><TD >helix dihedral potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >Finnis/Sinclair EAM</TD><TD > Tim Lau (MIT)</TD></TR>
|
|
<TR><TD >dissipative particle dynamics (DPD) potentials</TD><TD > Kurt Smith (U Pitt) and Frank van Swol (Sandia)</TD></TR>
|
|
<TR><TD >TIP4P potential (4-site water)</TD><TD > Ahmed Ismail and Amalie Frischknecht (Sandia)</TD></TR>
|
|
<TR><TD >uniaxial strain fix</TD><TD > Carsten Svaneborg (Max Planck Institute)</TD></TR>
|
|
<TR><TD >thermodynamics enhanced by fix quantities</TD><TD > Aidan Thompson (Sandia)</TD></TR>
|
|
<TR><TD >compressed dump files</TD><TD > Erik Luijten (U Illinois)</TD></TR>
|
|
<TR><TD >cylindrical indenter fix</TD><TD > Ravi Agrawal (Northwestern U)</TD></TR>
|
|
<TR><TD >electric field fix</TD><TD > Christina Payne (Vanderbilt U)</TD></TR>
|
|
<TR><TD >AMBER <-> LAMMPS tool</TD><TD > Keir Novik (Univ College London) and Vikas Varshney (U Akron)</TD></TR>
|
|
<TR><TD >CHARMM <-> LAMMPS tool</TD><TD > Pieter in 't Veld and Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >Morse bond potential</TD><TD > Jeff Greathouse (Sandia)</TD></TR>
|
|
<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
|
|
<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR>
|
|
<TR><TD >FFT support for SGI SCSL (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
|
|
<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
|
|
<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
|
|
<TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR>
|
|
<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Puetz (Sandia)</TD></TR>
|
|
<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
|
|
<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >msi2lmp tool</TD><TD > Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)</TD></TR>
|
|
<TR><TD >HTFN energy minimizer</TD><TD > Todd Plantenga (Sandia)</TD></TR>
|
|
<TR><TD >class 2 force fields</TD><TD > Eric Simon (Cray)</TD></TR>
|
|
<TR><TD >NVT/NPT integrators</TD><TD > Mark Stevens (Sandia)</TD></TR>
|
|
<TR><TD >rRESPA</TD><TD > Mark Stevens & Paul Crozier (Sandia)</TD></TR>
|
|
<TR><TD >Ewald and PPPM solvers</TD><TD > Roy Pollock (LLNL) </TD><TD >
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Other CRADA partners involved in the design and testing of LAMMPS were
|
|
</P>
|
|
<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
|
|
<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
|
|
<LI>Steve Lustig (Dupont)
|
|
<LI>Jim Belak (LLNL)
|
|
</UL>
|
|
</HTML>
|