mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6904 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
a434d6fd00
commit
d43381d50c
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@ -24,56 +24,46 @@ molecular dynamics codes I've distributed.
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<H4><A NAME = "hist_1"></A>13.1 Coming attractions
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</H4>
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<P>The current version of LAMMPS incorporates nearly all the features
|
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from previous parallel MD codes developed at Sandia. These include
|
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earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
|
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GranFlow for granular materials.
|
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<P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the
|
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LAMMPS WWW page gives a list of features we are hoping to add to
|
||||
LAMMPS in the future, including contact names of individuals you can
|
||||
email if you are interested in contributing to the developement or
|
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would be a future user of that feature.
|
||||
</P>
|
||||
<P>These are new features we'd like to eventually add to LAMMPS. Some
|
||||
are being worked on; some haven't been implemented because of lack of
|
||||
time or interest; others are just a lot of work! See <A HREF = "http://lammps.sandia.gov/future.html">this
|
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page</A> on the LAMMPS WWW site for more details.
|
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<P>You can also send <A HREF = "http://lammps.sandia.gov/authors.html">email to the
|
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developers</A> if you want to add
|
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your wish to the list.
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||||
</P>
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<UL><LI>Coupling to finite elements for streess-strain
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<LI>New ReaxFF implementation
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<LI>Nudged elastic band
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<LI>Temperature accelerated dynamics
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<LI>Triangulated particles
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<LI>Stochastic rotation dynamics
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<LI>Stokesian dynamics via fast lubrication dynamics
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<LI>Long-range point-dipole solver
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<LI>Per-atom energy and stress for long-range Coulombics
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<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes
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<LI>Metadynamics
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<LI>Direct Simulation Monte Carlo - DSMC
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</UL>
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<HR>
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<H4><A NAME = "hist_2"></A>13.2 Past versions
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</H4>
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<P>LAMMPS development began in the mid 1990s under a cooperative research
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& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
|
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and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after
|
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the CRADA ended, a final F77 version of the code, LAMMPS 99, was
|
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released. As development of LAMMPS continued at Sandia, the memory
|
||||
management in the code was converted to F90; a final F90 version was
|
||||
released as LAMMPS 2001.
|
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and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
|
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to develop a large-scale parallel classical MD code; the coding effort
|
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was led by Steve Plimpton at Sandia.
|
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</P>
|
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<P>After the CRADA ended, a final F77 version, LAMMPS 99, was
|
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released. As development of LAMMPS continued at Sandia, its memory
|
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management was converted to F90; a final F90 version was released as
|
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LAMMPS 2001.
|
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</P>
|
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<P>The current LAMMPS is a rewrite in C++ and was first publicly released
|
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in 2004. It includes many new features, including features from other
|
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parallel molecular dynamics codes written at Sandia, namely ParaDyn,
|
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Warp, and GranFlow. ParaDyn is a parallel implementation of the
|
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popular serial DYNAMO code developed by Stephen Foiles and Murray Daw
|
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for their embedded atom method (EAM) metal potentials. ParaDyn uses
|
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atom- and force-decomposition algorithms to run in parallel. Warp is
|
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also a parallel implementation of the EAM potentials designed for
|
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large problems, with boundary conditions specific to shearing solids
|
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in varying geometries. GranFlow is a granular materials code with
|
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potentials and boundary conditions peculiar to granular systems. All
|
||||
of these codes (except ParaDyn) use spatial-decomposition techniques
|
||||
for their parallelism.
|
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as an open source code in 2004. It includes many new features beyond
|
||||
those in LAMMPS 99 or 2001. It also includes features from older
|
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parallel MD codes written at Sandia, namely ParaDyn, Warp, and
|
||||
GranFlow (see below).
|
||||
</P>
|
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<P>In late 2006 we began merging new capabilities into LAMMPS that were
|
||||
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
|
||||
a parallel framework similar to LAMMPS. Most notably, these have
|
||||
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
|
||||
and the associated charge-equilibration routines needed for ReaxFF.
|
||||
</P>
|
||||
<P>The <A HREF = "http://lammps.sandia.gov/history.html">History link</A> on the
|
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LAMMPS WWW page gives a timeline of features added to the
|
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C++ open-source version of LAMMPS over the last several years.
|
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</P>
|
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<P>These older codes are available for download from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
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site</A>, except for Warp & GranFlow which were primarily used
|
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|
|
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|||
|
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@ -21,30 +21,15 @@ molecular dynamics codes I've distributed.
|
|||
|
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13.1 Coming attractions :h4,link(hist_1)
|
||||
|
||||
The current version of LAMMPS incorporates nearly all the features
|
||||
from previous parallel MD codes developed at Sandia. These include
|
||||
earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
|
||||
GranFlow for granular materials.
|
||||
The "Wish list link"_http://lammps.sandia.gov/future.html on the
|
||||
LAMMPS WWW page gives a list of features we are hoping to add to
|
||||
LAMMPS in the future, including contact names of individuals you can
|
||||
email if you are interested in contributing to the developement or
|
||||
would be a future user of that feature.
|
||||
|
||||
These are new features we'd like to eventually add to LAMMPS. Some
|
||||
are being worked on; some haven't been implemented because of lack of
|
||||
time or interest; others are just a lot of work! See "this
|
||||
page"_lwsfuture on the LAMMPS WWW site for more details.
|
||||
|
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:link(lwsfuture,http://lammps.sandia.gov/future.html)
|
||||
|
||||
Coupling to finite elements for streess-strain
|
||||
New ReaxFF implementation
|
||||
Nudged elastic band
|
||||
Temperature accelerated dynamics
|
||||
Triangulated particles
|
||||
Stochastic rotation dynamics
|
||||
Stokesian dynamics via fast lubrication dynamics
|
||||
Long-range point-dipole solver
|
||||
Per-atom energy and stress for long-range Coulombics
|
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Long-range Coulombics via Ewald and PPPM for triclinic boxes
|
||||
Metadynamics
|
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Direct Simulation Monte Carlo - DSMC :ul
|
||||
You can also send "email to the
|
||||
developers"_http://lammps.sandia.gov/authors.html if you want to add
|
||||
your wish to the list.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -52,25 +37,30 @@ Direct Simulation Monte Carlo - DSMC :ul
|
|||
|
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LAMMPS development began in the mid 1990s under a cooperative research
|
||||
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
|
||||
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). Soon after
|
||||
the CRADA ended, a final F77 version of the code, LAMMPS 99, was
|
||||
released. As development of LAMMPS continued at Sandia, the memory
|
||||
management in the code was converted to F90; a final F90 version was
|
||||
released as LAMMPS 2001.
|
||||
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
|
||||
to develop a large-scale parallel classical MD code; the coding effort
|
||||
was led by Steve Plimpton at Sandia.
|
||||
|
||||
After the CRADA ended, a final F77 version, LAMMPS 99, was
|
||||
released. As development of LAMMPS continued at Sandia, its memory
|
||||
management was converted to F90; a final F90 version was released as
|
||||
LAMMPS 2001.
|
||||
|
||||
The current LAMMPS is a rewrite in C++ and was first publicly released
|
||||
in 2004. It includes many new features, including features from other
|
||||
parallel molecular dynamics codes written at Sandia, namely ParaDyn,
|
||||
Warp, and GranFlow. ParaDyn is a parallel implementation of the
|
||||
popular serial DYNAMO code developed by Stephen Foiles and Murray Daw
|
||||
for their embedded atom method (EAM) metal potentials. ParaDyn uses
|
||||
atom- and force-decomposition algorithms to run in parallel. Warp is
|
||||
also a parallel implementation of the EAM potentials designed for
|
||||
large problems, with boundary conditions specific to shearing solids
|
||||
in varying geometries. GranFlow is a granular materials code with
|
||||
potentials and boundary conditions peculiar to granular systems. All
|
||||
of these codes (except ParaDyn) use spatial-decomposition techniques
|
||||
for their parallelism.
|
||||
as an open source code in 2004. It includes many new features beyond
|
||||
those in LAMMPS 99 or 2001. It also includes features from older
|
||||
parallel MD codes written at Sandia, namely ParaDyn, Warp, and
|
||||
GranFlow (see below).
|
||||
|
||||
In late 2006 we began merging new capabilities into LAMMPS that were
|
||||
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
|
||||
a parallel framework similar to LAMMPS. Most notably, these have
|
||||
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
|
||||
and the associated charge-equilibration routines needed for ReaxFF.
|
||||
|
||||
The "History link"_http://lammps.sandia.gov/history.html on the
|
||||
LAMMPS WWW page gives a timeline of features added to the
|
||||
C++ open-source version of LAMMPS over the last several years.
|
||||
|
||||
These older codes are available for download from the "LAMMPS WWW
|
||||
site"_lws, except for Warp & GranFlow which were primarily used
|
||||
|
|
|
|||
|
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@ -477,154 +477,58 @@ Hierarchical Modeling".
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|
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<P>The following papers describe the parallel algorithms used in LAMMPS.
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<P>The following paper describe the basic parallel algorithms used in
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LAMMPS. If you use LAMMPS results in your published work, please cite
|
||||
this paper and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
|
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(http://lammps.sandia.gov):
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</P>
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<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
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Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
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</P>
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<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
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rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
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Eighth SIAM Conference on Parallel Processing for Scientific
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Computing, Minneapolis, MN (March 1997).
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<P>Other papers describing specific algorithms used in LAMMPS are listed
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under the <A HREF = "http://lammps.sandia.gov/cite.html">Citing LAMMPS link</A> of
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the LAMMPS WWW page.
|
||||
</P>
|
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<P>If you use LAMMPS results in your published work, please cite the J
|
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Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
|
||||
(http://lammps.sandia.gov).
|
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<P>The <A HREF = "http://lammps.sandia.gov/papers.html">Publications link</A> on the
|
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LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
|
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not listed there for some reason, feel free to send us the info. If
|
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the simulations in your paper produced cool pictures or animations,
|
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we'll be pleased to add them to the
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<A HREF = "http://lammps.sandia.gov/pictures.html">Pictures</A> or
|
||||
<A HREF = "http://lammps.sandia.gov/movies.html">Movies</A> pages of the LAMMPS WWW
|
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site.
|
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</P>
|
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<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
|
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for a picture or movie for the Pictures or Movies pages.
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<P>The core group of LAMMPS developers is at Sandia National Labs:
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</P>
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<P>The core group of LAMMPS developers is at Sandia National Labs. They
|
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include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
|
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be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
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<UL><LI>Steve Plimpton, sjplimp at sandia.gov
|
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<LI>Aidan Thompson, athomps at sandia.gov
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<LI>Paul Crozier, pscrozi at sandia.gov
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</UL>
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<P>The following folks are responsible for significant contributions to
|
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the code, or other aspects of the LAMMPS development effort. Many of
|
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the packages they have written are somewhat unique to LAMMPS and the
|
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code would not be as general-purpose as it is without their expertise
|
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and efforts.
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</P>
|
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<P>Here are various folks who have made significant contributions to
|
||||
features in LAMMPS. The most recent contributions are at the top of
|
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the list.
|
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >pppm GPU single and double </TD><TD > Mike Brown (ORNL)</TD></TR>
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<TR><TD >pair_style lj/cut/expand </TD><TD > Inderaj Bains (NVIDIA)</TD></TR>
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<TR><TD >temperature accelerated dynamics (TAD) </TD><TD > Aidan Thompson (Sandia)</TD></TR>
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<TR><TD >pair reax/c and fix qeq/reax </TD><TD > Metin Aktulga (Purdue, now LBNL)</TD></TR>
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<TR><TD >DREIDING force field, pair_style hbond/dreiding, etc </TD><TD > Tod Pascal (CalTech)</TD></TR>
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<TR><TD >fix adapt and compute ti for thermodynamic integreation for free energies </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
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<TR><TD >pair born and pair gauss </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
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<TR><TD >stochastic rotation dynamics (SRD) via fix srd </TD><TD > Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)</TD></TR>
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<TR><TD >ipp Perl script tool </TD><TD > Reese Jones (Sandia)</TD></TR>
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<TR><TD >eam_database and createatoms tools </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
|
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<TR><TD >electron force field (eFF) </TD><TD > Andres Jaramillo-Botero and Julius Su (Caltech)</TD></TR>
|
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<TR><TD >embedded ion method (EIM) potential </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
|
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<TR><TD >COMB potential with charge equilibration </TD><TD > Tzu-Ray Shan (U Florida)</TD></TR>
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<TR><TD >fix ave/correlate </TD><TD > Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)</TD></TR>
|
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<TR><TD >pair_style peri/lps </TD><TD > Mike Parks (Sandia)</TD></TR>
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<TR><TD >fix msst </TD><TD > Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)</TD></TR>
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<TR><TD >thermo_style custom tpcpu & spcpu keywords </TD><TD > Axel Kohlmeyer (Temple U) </TD></TR>
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<TR><TD >fix rigid/nve, fix rigid/nvt </TD><TD > Tony Sheh and Trung Dac Nguyen (U Michigan)</TD></TR>
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<TR><TD >public SVN & Git repositories for LAMMPS </TD><TD > Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)</TD></TR>
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<TR><TD >fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax </TD><TD > Aidan Thompson (Sandia)</TD></TR>
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<TR><TD >compute heat/flux </TD><TD > German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)</TD></TR>
|
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<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
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<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
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<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
|
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<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
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<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
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<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
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<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
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<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
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<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
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<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
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<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
|
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<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
|
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<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
|
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<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
|
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<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
|
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<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
|
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<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
|
||||
<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
|
||||
<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
|
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<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
|
||||
<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
|
||||
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
|
||||
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
|
||||
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
||||
<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
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<TR><TD >compute group/group </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
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<TR><TD >USER-CG-CMM 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>
|
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<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 >AIREBO bond-order potential </TD><TD > Ase Henry (MIT)</TD></TR>
|
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<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>
|
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<TR><TD >pymol_asphere viz tool </TD><TD > Mike Brown (Sandia)</TD></TR>
|
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<TR><TD >NEMD SLLOD integration </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
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<TR><TD >tensile and shear deformations </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
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<TR><TD >GayBerne potential </TD><TD > Mike Brown (Sandia)</TD></TR>
|
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<TR><TD >ellipsoidal particles </TD><TD > Mike Brown (Sandia)</TD></TR>
|
||||
<TR><TD >colloid potentials </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
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<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>
|
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<TR><TD >MEAM potential </TD><TD > Greg Wagner (Sandia)</TD></TR>
|
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<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
|
||||
<UL><LI>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
|
||||
<LI>Roy Pollock (LLNL), Ewald and PPPM solvers
|
||||
<LI>Mike Brown (ORNL), brownw at ornl.gov, GPU package
|
||||
<LI>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
|
||||
<LI>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
|
||||
<LI>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
|
||||
<LI>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
|
||||
<LI>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
|
||||
<LI>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
|
||||
<LI>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
|
||||
<LI>Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
|
||||
<LI>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
|
||||
<LI>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
|
||||
<LI>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package
|
||||
</UL>
|
||||
<P>As discussed in <A HREF = "Section_history.html">this section</A>, LAMMPS originated
|
||||
as a cooperative project between DOE labs and industrial
|
||||
partners. Folks involved in the design and testing of the original
|
||||
version of LAMMPS were the following:
|
||||
</P>
|
||||
<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
|
||||
<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
|
||||
|
|
|
|||
|
|
@ -463,165 +463,59 @@ Hierarchical Modeling".
|
|||
: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.
|
||||
The following paper describe the basic parallel algorithms used in
|
||||
LAMMPS. If you use LAMMPS results in your published work, please cite
|
||||
this paper and include a pointer to the "LAMMPS WWW Site"_lws
|
||||
(http://lammps.sandia.gov):
|
||||
|
||||
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).
|
||||
Other papers describing specific algorithms used in LAMMPS are listed
|
||||
under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
|
||||
the LAMMPS WWW page.
|
||||
|
||||
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).
|
||||
The "Publications link"_http://lammps.sandia.gov/papers.html on the
|
||||
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
|
||||
not listed there for some reason, feel free to send us the info. If
|
||||
the simulations in your paper produced cool pictures or animations,
|
||||
we'll be pleased to add them to the
|
||||
"Pictures"_http://lammps.sandia.gov/pictures.html or
|
||||
"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
|
||||
site.
|
||||
|
||||
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:
|
||||
|
||||
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.
|
||||
Steve Plimpton, sjplimp at sandia.gov
|
||||
Aidan Thompson, athomps at sandia.gov
|
||||
Paul Crozier, pscrozi at sandia.gov :ul
|
||||
|
||||
Here are various folks who have made significant contributions to
|
||||
features in LAMMPS. The most recent contributions are at the top of
|
||||
the list.
|
||||
The following folks are responsible for significant contributions to
|
||||
the code, or other aspects of the LAMMPS development effort. Many of
|
||||
the packages they have written are somewhat unique to LAMMPS and the
|
||||
code would not be as general-purpose as it is without their expertise
|
||||
and efforts.
|
||||
|
||||
:link(sjp,http://www.sandia.gov/~sjplimp)
|
||||
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
|
||||
Roy Pollock (LLNL), Ewald and PPPM solvers
|
||||
Mike Brown (ORNL), brownw at ornl.gov, GPU package
|
||||
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
|
||||
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
|
||||
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
|
||||
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
|
||||
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
|
||||
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
|
||||
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
|
||||
Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
|
||||
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
|
||||
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
|
||||
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
|
||||
|
||||
pppm GPU single and double : Mike Brown (ORNL)
|
||||
pair_style lj/cut/expand : Inderaj Bains (NVIDIA)
|
||||
temperature accelerated dynamics (TAD) : Aidan Thompson (Sandia)
|
||||
pair reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
|
||||
DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (CalTech)
|
||||
fix adapt and compute ti for thermodynamic integreation for free energies : Sai Jayaraman (Sandia)
|
||||
pair born and pair gauss : Sai Jayaraman (Sandia)
|
||||
stochastic rotation dynamics (SRD) via fix srd : Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)
|
||||
ipp Perl script tool : Reese Jones (Sandia)
|
||||
eam_database and createatoms tools : Xiaowang Zhou (Sandia)
|
||||
electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
|
||||
embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
|
||||
COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
|
||||
fix ave/correlate : Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)
|
||||
pair_style peri/lps : Mike Parks (Sandia)
|
||||
fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
|
||||
thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
|
||||
fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
|
||||
public SVN & Git repositories for LAMMPS : Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
|
||||
fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax : Aidan Thompson (Sandia)
|
||||
compute heat/flux : German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
|
||||
pair yukawa/colloid : Randy Schunk (Sandia)
|
||||
fix wall/colloid : Jeremy Lechman (Sandia)
|
||||
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia)
|
||||
fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
|
||||
concentration-dependent EAM potential : Alexander Stukowski (Technical University of Darmstadt)
|
||||
parallel replica dymamics (PRD) : Mike Brown (Sandia)
|
||||
min_style hftn : Todd Plantenga (Sandia)
|
||||
fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
|
||||
dump cfg : Liang Wan (Chinese Academy of Sciences)
|
||||
fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
|
||||
pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
|
||||
pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
|
||||
fix langevin tally : Carolyn Phillips (U Michigan)
|
||||
compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
|
||||
region cone : Pim Schravendijk
|
||||
fix reax/bonds : Aidan Thompson (Sandia)
|
||||
pair born/coul/long : Ahmed Ismail (Sandia)
|
||||
fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
|
||||
fix box/relax : Aidan Thompson and David Olmsted (Sandia)
|
||||
ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
|
||||
compute cna/atom : Wan Liang (Chinese Academy of Sciences)
|
||||
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)
|
||||
USER-CG-CMM 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)
|
||||
AIREBO 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=:)
|
||||
As discussed in "this section"_Section_history.html, LAMMPS originated
|
||||
as a cooperative project between DOE labs and industrial
|
||||
partners. Folks involved in the design and testing of the original
|
||||
version of LAMMPS were the following:
|
||||
|
||||
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)
|
||||
|
|
|
|||
Loading…
Reference in New Issue