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<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>
-<P>General features: h4
-</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 needed: MPI and single-processor FFT
<LI> easy to extend with new features and functionality
<LI> in parallel, run one or multiple simulations simultaneously
<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 a series of simluations from one script
</UL>
-<H4>Kinds of systems LAMMPS can simulate:
+<H4>Kinds of systems LAMMPS can simulate
</H4>
<P>(<A HREF = "atom_style.html">atom style</A> command)
</P>
<UL><LI> atomic (e.g. box of Lennard-Jonesium)
<LI> 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> ellipsoidal particles
<LI> point dipolar particles
<LI> hybrid combinations of these
</UL>
-<H4>Force fields:
+<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
<LI> coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
<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> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
<LI> overlaid potentials: superposition of multiple pair potentials
<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> CHARMM, AMBER, OPLS, GROMACS, force-field compatibility
+<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
</UL>
-<H4>Creation of atoms:
+<H4>Creation of atoms
</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> 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> displace atoms
</UL>
-<H4>Ensembles, constraints, and boundary conditions:
+<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> independent or coupled rigid body integration
<LI> SHAKE bond and angle constraints
<LI> bond breaking, formation, swapping
<LI> walls of various kinds
<LI> targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
<LI> non-equilibrium molecular dynamics (NEMD)
<LI> variety of additional boundary conditions and constraints
</UL>
-<H4>Integrators:
+<H4>Integrators
</H4>
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "temper.html">temper</A> commands)
</P>
<UL><LI> velocity-Verlet integrator
<LI> Brownian dynamics
<LI> energy minimization via conjugate gradient or steepest descent relaxation
<LI> rRESPA hierarchical timestepping
<LI> parallel tempering (replica exchange)
</UL>
-<H4>Output:
+<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, 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 formats
</UL>
-<H4>Pre- and post-processing:
+<H4>Pre- and post-processing
</H4>
<P>Our group has also written and released a separate toolkit called
<A HREF = "http://www.cs.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.cs.sandia.gov/~sjplimp/pizza.html">the
Pizza.py WWW site</A>.
</P>
<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.cs.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.cs.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://164.107.79.177/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.cs.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 >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>
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index 982399b30..bb9afb0e5 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -1,552 +1,552 @@
"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
1. Introduction :h3
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.
1.1 "What is LAMMPS"_#1_1
1.2 "LAMMPS features"_#1_2
1.3 "LAMMPS non-features"_#1_3
1.4 "Open source distribution"_#1_4
1.5 "Acknowledgments and citations"_#1_5 :all(b)
:line
1.1 What is LAMMPS :link(1_1),h4
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.
For examples of LAMMPS simulations, see the Publications page of the
"LAMMPS WWW Site"_lws.
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 "MPI"_mpi
message-passing library. This includes distributed- or shared-memory
parallel machines and Beowulf-style clusters.
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
LAMMPS can model systems with only a few particles up to millions or
billions. See "this section"_Section_perf.html for information on LAMMPS
performance and scalability, or the Benchmarks section of the "LAMMPS
WWW Site"_lws.
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish. See "this section"_#1_4 for a brief
discussion of the open-source philosophy.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
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 "this section"_Section_modify.html for
more details.
The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See "this section"_Section_history.html
for more information on different versions. All versions can be
downloaded from the "LAMMPS WWW Site"_lws.
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 "Sandia National Labs"_snl.
See "this section"_#1_5 for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
:link(snl,http://www.sandia.gov)
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 "this section"_#1_5.
:line
1.2 LAMMPS features :link(1_2),h4
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
"this section"_Section_modify.html, which describes how you can add it to
LAMMPS.
-General features: h4
+General features :h4
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
spatial-decomposition of simulation domain for parallelism
open-source distribution
highly portable C++
optional libraries needed: MPI and single-processor FFT
easy to extend with new features and functionality
in parallel, run one or multiple simulations simultaneously
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run a series of simluations from one script :ul
-Kinds of systems LAMMPS can simulate: :h4
+Kinds of systems LAMMPS can simulate :h4
("atom style"_atom_style.html command)
atomic (e.g. box of Lennard-Jonesium)
bead-spring polymers
united-atom polymers or organic molecules
all-atom polymers, organic molecules, proteins, DNA
metals
granular materials
coarse-grained mesoscale models
ellipsoidal particles
point dipolar particles
hybrid combinations of these :ul
-Force fields: :h4
+Force fields :h4
("pair style"_pair_style.html, "bond style"_bond_style.html,
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
"improper style"_improper_style.html, "kspace style"_kspace_style.html
commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, \
Yukawa, soft, class 2 (COMPASS), tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
Stillinger-Weber, Tersoff, AI-REBO
coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
mesoscopic potentials: granular, Peridynamics
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
long-range Coulombics and dispersion: Ewald, \
PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
- CHARMM, AMBER, OPLS, GROMACS, force-field compatibility :ul
+ force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options :ul
-Creation of atoms: :h4
+Creation of atoms :h4
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html commands)
read in atom coords from files
create atoms on one or more lattices (e.g. grain boundaries)
delete geometric or logical groups of atoms (e.g. voids)
displace atoms :ul
-Ensembles, constraints, and boundary conditions: :h4
+Ensembles, constraints, and boundary conditions :h4
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
independent or coupled rigid body integration
SHAKE bond and angle constraints
bond breaking, formation, swapping
walls of various kinds
targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
-Integrators: :h4
+Integrators :h4
("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands)
velocity-Verlet integrator
Brownian dynamics
energy minimization via conjugate gradient or steepest descent relaxation
rRESPA hierarchical timestepping
parallel tempering (replica exchange) :ul
-Output: :h4
+Output :h4
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities
binary restart files
per-atom quantities (energy, stress, centro-symmetry parameter, etc)
user-defined system-wide (log file) or per-atom (dump file) calculations
spatial and time averaging of per-atom quantities
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD formats :ul
-Pre- and post-processing: :h4
+Pre- and post-processing :h4
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
:line
1.3 LAMMPS non-features :link(1_3),h4
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:
the desire to keep LAMMPS simple
they are not parallel operations
other codes already do them
limited development resources :ul
Specifically, LAMMPS itself does not:
run thru a GUI
build molecular systems
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
visualize your MD simulation
plot your output data :ul
A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described in "this
section"_Section_tools.html. However, many people use other codes or
write their own tools for these tasks.
As noted above, our group has also written and released a separate
toolkit called "Pizza.py"_pizza 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
"Python"_python and is available for download from "the Pizza.py WWW
site"_pizza.
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.
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
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 "pair coeff"_pair_coeff.html, "bond
coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, 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.
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
"CHARMM"_charmm or "AMBER"_amber 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 "this
section"_Section_tools.html can assist in this process.
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 "this section"_Section_modify.html for a discussion
of how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html 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.
A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
section"_Section_tools.html. 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:
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://164.107.79.177/Archive/Graphics/A
"PyMol"_http://pymol.sourceforge.net
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "this section"_Section_history.html.
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.
"CHARMM"_charmm
"AMBER"_amber
"NAMD"_namd
"NWCHEM"_nwchem
"DL_POLY"_dlpoly
"Tinker"_tinker :ul
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
:link(namd,http://www.ks.uiuc.edu/Research/namd/)
:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
:link(tinker,http://dasher.wustl.edu/tinker)
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.
:line
1.4 Open source distribution :link(1_4),h4
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 "GNU Public License"_gnu (GPL). This
is often referred to as open-source distribution - see
"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
details. The legal text of the GPL is in the LICENSE file that is
included in the LAMMPS distribution.
:link(gnuorg,http://www.gnu.org)
:link(opensource,http://www.opensource.org)
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(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.
(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.
(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.
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
"developers"_http://lammps.sandia.gov/authors.html on any of these
items.
Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
talks or link to it from your WWW site. :ulb,l
If you find an error or omission in this manual or on the "LAMMPS WWW
Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "this section"_Section_errors.html#9_2 describes
how to report it. :l
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 "LAMMPS WWW Site"_lws, with links
and attributions back to you. :l
Create a new Makefile.machine that can be added to the src/MAKE
directory. :l
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 "this section"_Section_tools.html. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
"This section"_Section_modify.html gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution. :l
The Benchmark page of the "LAMMPS WWW Site"_lws 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. :l
You can send feedback for the User Comments page of the "LAMMPS WWW
Site"_lws. It might be added to the page. No promises. :l
Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged. :ule,l
:line
1.5 Acknowledgments and citations :h4,link(1_5)
LAMMPS development has been funded by the "US Department of
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its "OASCR"_oascr and "OBER"_ober offices.
Specifically, work on the latest version was funded in part by the US
Department of Energy's Genomics:GTL program
("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling".
:link(doe,http://www.doe.gov)
:link(gtl,http://www.doegenomestolife.org)
:link(ourgtl,http://www.genomes2life.org)
:link(oascr,http://www.sc.doe.gov/ascr/home.html)
:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
The following papers describe the parallel algorithms used in LAMMPS.
S. J. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
Dynamics], J Comp Phys, 117, 1-19 (1995).
S. J. Plimpton, R. Pollock, M. Stevens, [Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations], in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov).
If you send is information about your publication, we'll be pleased to
add it to the Publications page of the "LAMMPS WWW Site"_lws. Ditto
for a picture or movie for the Pictures or Movies pages.
The core group of LAMMPS developers is at Sandia National Labs. They
include "Steve Plimpton"_sjp, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
Tersoff/ZBL potential : Dave Farrell (Northwestern U)
peridynamics : Mike Parks (Sandia)
fix smd for steered MD : Axel Kohlmeyer (U Penn)
GROMACS pair potentials : Mark Stevens (Sandia)
lmp2vmd tool : Axel Kohlmeyer (U Penn)
compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
CG-CMM user package for coarse-graining : Axel Kohlmeyer (U Penn)
cosine/delta angle potential : Axel Kohlmeyer (U Penn)
VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
pair lubricate : Randy Schunk (Sandia)
compute ackland/atom : Gerolf Zeigenhain
kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
Pieter in 't Veld (Sandia)
AI-REBO bond-order potential : Ase Henry (MIT)
making LAMMPS a true "object" that can be instantiated multiple times, \
e.g. as a library : Ben FrantzDale (RPI)
pymol_asphere viz tool : Mike Brown (Sandia)
NEMD SLLOD integration : Pieter in 't Veld (Sandia)
tensile and shear deformations : Pieter in 't Veld (Sandia)
GayBerne potential : Mike Brown (Sandia)
ellipsoidal particles : Mike Brown (Sandia)
colloid potentials : Pieter in 't Veld (Sandia)
fix heat : Paul Crozier and Ed Webb (Sandia)
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
MEAM potential : Greg Wagner (Sandia)
optimized pair potentials for lj/cut, charmm/long, eam, morse : \
James Fischer (High Performance Technologies), \
David Richie and Vincent Natoli (Stone Ridge Technologies)
fix wall/lj126 : Mark Stevens (Sandia)
Stillinger-Weber and Tersoff potentials : Aidan Thompson and Xiaowang Zhou (Sandia)
region prism : Pieter in 't Veld (Sandia)
LJ tail corrections for energy/pressure : Paul Crozier (Sandia)
fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
OPLS dihedral potential: Mark Stevens (Sandia)
POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
faster pair hybrid potential: James Fischer \
(High Performance Technologies, Inc), Vincent Natoli and \
David Richie (Stone Ridge Technology)
breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
grain boundary orientation fix : Koenraad Janssens and David Olmsted (Sandia)
lj/smooth pair potential : Craig Maloney (UCSB)
radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Paul Crozier (Sandia)
self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Mark Stevens (Sandia)
Finnis/Sinclair EAM: Tim Lau (MIT)
dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
Frank van Swol (Sandia)
TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia)
uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia)
compressed dump files: Erik Luijten (U Illinois)
cylindrical indenter fix: Ravi Agrawal (Northwestern U)
electric field fix: Christina Payne (Vanderbilt U)
AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
Vikas Varshney (U Akron)
CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
Morse bond potential: Jeff Greathouse (Sandia)
radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
force tables for long-range Coulombics: Paul Crozier (Sandia)
targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany)
FFT support for SGI SCSL (Altix): Jim Shepherd (Ga Tech)
lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia)
parallel tempering: Mark Sears (Sandia)
embedded atom method (EAM) potential: Stephen Foiles (Sandia)
multi-harmonic dihedral potential: Mathias Puetz (Sandia)
granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
2d Ewald/PPPM: Paul Crozier (Sandia)
CHARMM force fields: Paul Crozier (Sandia)
msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
HTFN energy minimizer: Todd Plantenga (Sandia)
class 2 force fields: Eric Simon (Cray)
NVT/NPT integrators: Mark Stevens (Sandia)
rRESPA: Mark Stevens & Paul Crozier (Sandia)
Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:)
Other CRADA partners involved in the design and testing of LAMMPS were
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak (LLNL) :ul
diff --git a/doc/bond_fene.html b/doc/bond_fene.html
index 49fe2823c..4dcc2447f 100644
--- a/doc/bond_fene.html
+++ b/doc/bond_fene.html
@@ -1,67 +1,67 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>bond_style fene command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages.
</P>
-<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
-to use this bond style. LAMMPS will issue a warning it that's not the
-case.
+<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
+or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
+style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
</HTML>
diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt
index 78f399e8f..8d0ab6c25 100644
--- a/doc/bond_fene.txt
+++ b/doc/bond_fene.txt
@@ -1,61 +1,61 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style fene command :h3
[Syntax:]
bond_style fene :pre
[Examples:]
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0 :pre
[Description:]
The {fene} bond style uses the potential
:c,image(Eqs/bond_fene.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
-You typically should specify "special_bonds 0 1 1"_special_bonds.html
-to use this bond style. LAMMPS will issue a warning it that's not the
-case.
+You typically should specify "special_bonds fene"_special_bonds.html"
+or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
+style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html
index 586f9b91e..190e14ca3 100644
--- a/doc/bond_fene_expand.html
+++ b/doc/bond_fene_expand.html
@@ -1,72 +1,72 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>bond_style fene/expand command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene/expand
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene/expand</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene_expand.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
</P>
<P>The <I>fene/expand</I> bond style is similar to <I>fene</I> except that an extra
shift factor of delta (positive or negative) is added to <I>r</I> to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
<LI>delta (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info on packages.
</P>
-<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
-to use this bond style. LAMMPS will issue a warning it that's not the
-case.
+<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
+or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
+style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
</HTML>
diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt
index 142766ff8..b12bb6de0 100644
--- a/doc/bond_fene_expand.txt
+++ b/doc/bond_fene_expand.txt
@@ -1,66 +1,66 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style fene/expand command :h3
[Syntax:]
bond_style fene/expand :pre
[Examples:]
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
[Description:]
The {fene/expand} bond style uses the potential
:c,image(Eqs/bond_fene_expand.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The {fene/expand} bond style is similar to {fene} except that an extra
shift factor of delta (positive or negative) is added to {r} to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance)
delta (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
-You typically should specify "special_bonds 0 1 1"_special_bonds.html
-to use this bond style. LAMMPS will issue a warning it that's not the
-case.
+You typically should specify "special_bonds fene"_special_bonds.html"
+or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
+style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 1fb8315ca..c079ae01e 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -1,394 +1,396 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>pair_style eam command
</H3>
<H3>pair_style eam/opt command
</H3>
<H3>pair_style eam/alloy command
</H3>
<H3>pair_style eam/alloy/opt command
</H3>
<H3>pair_style eam/fs command
</H3>
<H3>pair_style eam/fs/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/fs</I> or <I>eam/opt</I> or <I>eam/alloy/opt</I> or <I>eam/fs/opt</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eam
pair_style eam/opt
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
</PRE>
<PRE>pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni
</PRE>
<PRE>pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>eam</I> computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials <A HREF = "#Daw">(Daw)</A>. The total
energy Ei of an atom I is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_eam.jpg">
</CENTER>
<P>where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
</P>
<P>Style <I>eam/opt</I> is an optimized version of style <I>eam</I> that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
</P>
<P>The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
"potentials" directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
</P>
<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>. For the
alloy case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/fs</I> styles
as described below. These files require no mixing since they specify
alloy interactions explicitly.
</P>
<P>There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:
</P>
<PRE>http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
</PRE>
<P>These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
-and described on this page.
+and described on this page. The NIST site is maintained by Chandler
+Becker (cbecker at nist.gov) who is good resource for info on
+interatomic potentials and file formats.
</P>
<HR>
<P>For style <I>eam</I>, potential values are read from a file that is in the
DYNAMO single-element <I>funcfl</I> format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
</P>
<P>Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.
</P>
<P>For style <I>eam</I> a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
</P>
<UL><LI>filename
</UL>
<P>Thus the following command
</P>
<PRE>pair_coeff *2 1*2 cuu3.eam
</PRE>
<P>will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). In effect, this makes atom types 1 and 2 in
LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs.
</P>
<P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
distribution have an ".eam" suffix. A DYNAMO single-element <I>funcfl</I>
file is formatted as follows:
</P>
<UL><LI>line 1: comment (ignored)
<LI>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>line 3: Nrho, drho, Nr, dr, cutoff
</UL>
<P>On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass <A HREF = "units.html">units</A> (e.g. mass number or grams/mole for metal
units). The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
</P>
<P>Following the three header lines are three arrays of tabulated values:
</P>
<UL><LI>embedding function F(rho) (Nrho values)
<LI>effective charge function Z(r) (Nr values)
<LI>density function rho(r) (Nr values)
</UL>
<P>The values for each array can be listed as multiple values per line,
so long as each array starts on a new line. For example, the
individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
</P>
<P>The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula
</P>
<PRE>r*phi = 27.2 * 0.529 * Zi * Zj
</PRE>
<P>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
</P>
<HR>
<P>Style <I>eam/alloy</I> computes pairwise interactions using the same
formula as style <I>eam</I>. However the associated
<A HREF = "pair_coeff.html">pair_coeff</A> command reads a DYNAMO <I>setfl</I> file
instead of a <I>funcfl</I> file. <I>Setfl</I> files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, <I>setfl</I> files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than <I>funcfl</I> files for
modeling alloys.
</P>
<P>Style <I>eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>
that should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
</P>
<P>For style <I>eam/alloy</I>, potential values are read from a file that is
in the DYNAMO multi-element <I>setfl</I> format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have "D"
values in it for exponents. C only recognizes "e" or "E" for
scientific notation.
</P>
<P>Only a single pair_coeff command is used with the <I>eam/alloy</I> style
which specifies a DYNAMO <I>setfl</I> file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of <I>setfl</I> elements to atom types
</UL>
<P>As an example, the potentials/nialhjea <I>setfl</I> file has tabulated EAM
values for 3 elements and their alloy interactions: Ni, Al, and H. If
your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be
Ni, and the 4th to be Al, you would use the following pair_coeff
command:
</P>
<PRE>pair_coeff * * nialhjea.eam.alloy Ni Ni Ni Al
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the <I>setfl</I> file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the <I>setfl</I> file. Note that there is no
requirement that your simulation use all the elements specified by the
<I>setfl</I> file.
</P>
<P>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <I>eam/alloy</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P><I>Setfl</I> files in the <I>potentials</I> directory of the LAMMPS distribution
have an ".eam.alloy" suffix. A DYNAMO multi-element <I>setfl</I> file is
formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements Element1 Element2 ... ElementN
<LI>line 5: Nrho, drho, Nr, dr, cutoff
</UL>
<P>In a DYNAMO <I>setfl</I> file, line 4 only lists Nelements = the # of
elements in the <I>setfl</I> file. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to the line, in the order the
elements appear in the file.
</P>
<P>The meaning and units of the values in line 5 is the same as for the
<I>funcfl</I> file described above. Note that the cutoff (in Angstroms) is
a global value, valid for all pairwise interactions for all element
pairings.
</P>
<P>Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
</P>
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>embedding function F(rho) (Nrho values)
<LI>density function rho(r) (Nr values)
</UL>
<P>As with the <I>funcfl</I> files, only the mass (g/cm^3) is used by LAMMPS
from the 1st line. The cubic lattice constant is in Angstroms. The F
and rho arrays are unique to a single element and have the same format
and units as in a <I>funcfl</I> file.
</P>
<P>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). Unlike the effective charge array Z(r) in <I>funcfl</I> files,
the tabulated values for each phi function are listed in <I>setfl</I> files
directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.
</P>
<HR>
<P>Style <I>eam/fs</I> computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair <A HREF = "#Finnis">(Finnis)</A>. The total energy Ei of an atom I is
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_eam_fs.jpg">
</CENTER>
<P>This has the same form as the EAM formula above, except that rho is
now a functional specific to the atomic types of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
</P>
<P>Style <I>eam/fs/opt</I> is an optimized version of style <I>eam/fs</I> that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
</P>
<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
reads a DYNAMO <I>setfl</I> file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
<A HREF = "#Ackland1">(Ackland1)</A>. An example of such a potential is the same
author's Fe-P FS potential <A HREF = "#Ackland2">(Ackland2)</A>. Note that while FS
potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
</P>
<P>For style <I>eam/fs</I>, the form of the pair_coeff command is exactly the
same as for style <I>eam/alloy</I>, e.g.
</P>
<PRE>pair_coeff * * nialhjea.eam.fs Ni Ni Ni Al
</PRE>
<P>where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described above
for style <I>eam/alloy</I>. As with <I>eam/alloy</I>, if a mapping value is
NULL, the mapping is not performed. This can be used when an <I>eam/fs</I>
potential is used as part of the <I>hybrid</I> pair style. The NULL values
are used as placeholders for atom types that will be used with other
potentials.
</P>
<P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
files read by <I>eam/alloy</I>, in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
</P>
<P>FS EAM files in the <I>potentials</I> directory of the LAMMPS distribution
have an ".eam.fs" suffix. They are formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements Element1 Element2 ... ElementN
<LI>line 5: Nrho, drho, Nr, dr, cutoff
</UL>
<P>The 5-line header section is identical to an EAM <I>setfl</I> file.
</P>
<P>Following the header are Nelements sections, one for each element I,
each with the following format:
</P>
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>embedding function F(rho) (Nrho values)
<LI>density function rho(r) for element I at element 1 (Nr values)
<LI>density function rho(r) for element I at element 2
<LI>...
<LI>density function rho(r) for element I at element Nelement
</UL>
<P>The units of these quantities in line 1 are the same as for <I>setfl</I>
files. Note that the rho(r) arrays in Finnis/Sinclair can be
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
file.
</P>
<P>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed in the same manner (r*phi, units of
eV-Angstroms) as in EAM <I>setfl</I> files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
are listed.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>The eam pair styles do not write their information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
</P>
<P>The eam pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>All of these styles except those ending in <I>opt</I> are part of the
"manybody" package. They are only enabled if LAMMPS was built with
that package (which it is by default). The styles ending in <I>opt</I> are
part of the "opt" package and also require the "manybody" package.
They are only enabled if LAMMPS was built with those packages. See
the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ackland1"></A>
<P><B>(Ackland1)</B> Ackland, Condensed Matter (2005).
</P>
<A NAME = "Ackland2"></A>
<P><B>(Ackland2)</B> Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).
</P>
<A NAME = "Daw"></A>
<P><B>(Daw)</B> Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
</P>
<A NAME = "Finnis"></A>
<P><B>(Finnis)</B> Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
</P>
</HTML>
diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt
index d7d3553fd..46f0ce150 100644
--- a/doc/pair_eam.txt
+++ b/doc/pair_eam.txt
@@ -1,380 +1,382 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style eam command :h3
pair_style eam/opt command :h3
pair_style eam/alloy command :h3
pair_style eam/alloy/opt command :h3
pair_style eam/fs command :h3
pair_style eam/fs/opt command :h3
[Syntax:]
pair_style style :pre
style = {eam} or {eam/alloy} or {eam/fs} or {eam/opt} or {eam/alloy/opt} or {eam/fs/opt} :ul
[Examples:]
pair_style eam
pair_style eam/opt
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam :pre
pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni :pre
pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni :pre
[Description:]
Style {eam} computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials "(Daw)"_#Daw. The total
energy Ei of an atom I is given by
:c,image(Eqs/pair_eam.jpg)
where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
Style {eam/opt} is an optimized version of style {eam} that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the "pair_coeff"_pair_coeff.html command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
"potentials" directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS "metal units"_units.html.
IMPORTANT NOTE: The {eam} style reads single-element EAM potentials in
the DYNAMO {funcfl} format. Either single element or alloy systems
can be modeled using multiple {funcfl} files and style {eam}. For the
alloy case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO {setfl} file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the {eam/alloy} or {eam/fs} styles
as described below. These files require no mixing since they specify
alloy interactions explicitly.
There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:
http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm :pre
These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
-and described on this page.
+and described on this page. The NIST site is maintained by Chandler
+Becker (cbecker at nist.gov) who is good resource for info on
+interatomic potentials and file formats.
:line
For style {eam}, potential values are read from a file that is in the
DYNAMO single-element {funcfl} format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.
For style {eam} a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
filename :ul
Thus the following command
pair_coeff *2 1*2 cuu3.eam :pre
will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). In effect, this makes atom types 1 and 2 in
LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs.
{Funcfl} files in the {potentials} directory of the LAMMPS
distribution have an ".eam" suffix. A DYNAMO single-element {funcfl}
file is formatted as follows:
line 1: comment (ignored)
line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
line 3: Nrho, drho, Nr, dr, cutoff :ul
On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass "units"_units.html (e.g. mass number or grams/mole for metal
units). The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
Following the three header lines are three arrays of tabulated values:
embedding function F(rho) (Nrho values)
effective charge function Z(r) (Nr values)
density function rho(r) (Nr values) :ul
The values for each array can be listed as multiple values per line,
so long as each array starts on a new line. For example, the
individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula
r*phi = 27.2 * 0.529 * Zi * Zj :pre
where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
:line
Style {eam/alloy} computes pairwise interactions using the same
formula as style {eam}. However the associated
"pair_coeff"_pair_coeff.html command reads a DYNAMO {setfl} file
instead of a {funcfl} file. {Setfl} files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, {setfl} files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than {funcfl} files for
modeling alloys.
Style {eam/alloy/opt} is an optimized version of style {eam/alloy}
that should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
For style {eam/alloy}, potential values are read from a file that is
in the DYNAMO multi-element {setfl} format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have "D"
values in it for exponents. C only recognizes "e" or "E" for
scientific notation.
Only a single pair_coeff command is used with the {eam/alloy} style
which specifies a DYNAMO {setfl} file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of {setfl} elements to atom types :ul
As an example, the potentials/nialhjea {setfl} file has tabulated EAM
values for 3 elements and their alloy interactions: Ni, Al, and H. If
your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be
Ni, and the 4th to be Al, you would use the following pair_coeff
command:
pair_coeff * * nialhjea.eam.alloy Ni Ni Ni Al :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the {setfl} file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the {setfl} file. Note that there is no
requirement that your simulation use all the elements specified by the
{setfl} file.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an {eam/alloy} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
{Setfl} files in the {potentials} directory of the LAMMPS distribution
have an ".eam.alloy" suffix. A DYNAMO multi-element {setfl} file is
formatted as follows:
lines 1,2,3 = comments (ignored)
line 4: Nelements Element1 Element2 ... ElementN
line 5: Nrho, drho, Nr, dr, cutoff :ul
In a DYNAMO {setfl} file, line 4 only lists Nelements = the # of
elements in the {setfl} file. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to the line, in the order the
elements appear in the file.
The meaning and units of the values in line 5 is the same as for the
{funcfl} file described above. Note that the cutoff (in Angstroms) is
a global value, valid for all pairwise interactions for all element
pairings.
Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
embedding function F(rho) (Nrho values)
density function rho(r) (Nr values) :ul
As with the {funcfl} files, only the mass (g/cm^3) is used by LAMMPS
from the 1st line. The cubic lattice constant is in Angstroms. The F
and rho arrays are unique to a single element and have the same format
and units as in a {funcfl} file.
Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). Unlike the effective charge array Z(r) in {funcfl} files,
the tabulated values for each phi function are listed in {setfl} files
directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.
:line
Style {eam/fs} computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair "(Finnis)"_#Finnis. The total energy Ei of an atom I is
given by
:c,image(Eqs/pair_eam_fs.jpg)
This has the same form as the EAM formula above, except that rho is
now a functional specific to the atomic types of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
Style {eam/fs/opt} is an optimized version of style {eam/fs} that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
reads a DYNAMO {setfl} file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
"(Ackland1)"_#Ackland1. An example of such a potential is the same
author's Fe-P FS potential "(Ackland2)"_#Ackland2. Note that while FS
potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
For style {eam/fs}, the form of the pair_coeff command is exactly the
same as for style {eam/alloy}, e.g.
pair_coeff * * nialhjea.eam.fs Ni Ni Ni Al :pre
where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described above
for style {eam/alloy}. As with {eam/alloy}, if a mapping value is
NULL, the mapping is not performed. This can be used when an {eam/fs}
potential is used as part of the {hybrid} pair style. The NULL values
are used as placeholders for atom types that will be used with other
potentials.
FS EAM files include more information than the DYNAMO {setfl} format
files read by {eam/alloy}, in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
FS EAM files in the {potentials} directory of the LAMMPS distribution
have an ".eam.fs" suffix. They are formatted as follows:
lines 1,2,3 = comments (ignored)
line 4: Nelements Element1 Element2 ... ElementN
line 5: Nrho, drho, Nr, dr, cutoff :ul
The 5-line header section is identical to an EAM {setfl} file.
Following the header are Nelements sections, one for each element I,
each with the following format:
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
embedding function F(rho) (Nrho values)
density function rho(r) for element I at element 1 (Nr values)
density function rho(r) for element I at element 2
...
density function rho(r) for element I at element Nelement :ul
The units of these quantities in line 1 are the same as for {setfl}
files. Note that the rho(r) arrays in Finnis/Sinclair can be
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
file.
Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed in the same manner (r*phi, units of
eV-Angstroms) as in EAM {setfl} files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
are listed.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
The eam pair styles do not write their information to "binary restart
files"_restart.html, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
The eam pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
All of these styles except those ending in {opt} are part of the
"manybody" package. They are only enabled if LAMMPS was built with
that package (which it is by default). The styles ending in {opt} are
part of the "opt" package and also require the "manybody" package.
They are only enabled if LAMMPS was built with those packages. See
the "Making LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Ackland1)
[(Ackland1)] Ackland, Condensed Matter (2005).
:link(Ackland2)
[(Ackland2)] Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).
:link(Daw)
[(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Finnis)
[(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).