Merge pull request #427 from akohlmey/small-updates-and-corrections

the first page of the manual (this page).

If you browse the HTML doc pages on the LAMMPS WWW site, they always

describe the most current version of LAMMPS. :ulb,l

describe the most current [development] version of LAMMPS. :ulb,l

If you browse the HTML doc pages included in your tarball, they

describe the version you have. :l

"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l

Aidan Thompson, athomps at sandia.gov :l

Stan Moore, stamoore at sandia.gov :l

Stan Moore, stamoor at sandia.gov :l

"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l

:ule

LAMMPS is designed to be a computational kernel for performing

molecular dynamics computations.  Additional pre- and post-processing

steps are often necessary to setup and analyze a simulation.  A few

additional tools are provided with the LAMMPS distribution and are

described in this section.

steps are often necessary to setup and analyze a simulation. A

list of such tools can be found on the LAMMPS home page

at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html

A few additional tools are provided with the LAMMPS distribution

and are described in this section.

Our group has also written and released a separate toolkit called

"Pizza.py"_pizza which provides tools for doing setup, analysis,

"chain"_#chain

"colvars"_#colvars

"createatoms"_#create

"data2xmovie"_#data

"eam database"_#eamdb

"eam generate"_#eamgn

"eff"_#eff

"kate"_#kate

"lmp2arc"_#arc

"lmp2cfg"_#cfg

"lmp2vmd"_#vmd

"matlab"_#matlab

"micelle2d"_#micelle

"moltemplate"_#moltemplate

"restart2data"_#restart

"vim"_#vim

"xmgrace"_#xmgrace

"xmovie"_#xmovie :ul

:line

:line

data2xmovie tool :h4,link(data)

The file data2xmovie.c converts a LAMMPS data file into a snapshot

suitable for visualizing with the "xmovie"_#xmovie tool, as if it had

been output with a dump command from LAMMPS itself.  The syntax for

running the tool is

data2xmovie \[options\] < infile > outfile :pre

See the top of the data2xmovie.c file for a discussion of the options.

:line

eam database tool :h4,link(eamdb)

The tools/eam_database directory contains a Fortran program that will

:line

lmp2vmd tool :h4,link(vmd)

The lmp2vmd sub-directory contains a README.txt file that describes

details of scripts and plugin support within the "VMD

package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS

dump files.

The VMD plugins and other supporting scripts were written by Axel

Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.

:line

matlab tool :h4,link(matlab)

The matlab sub-directory contains several "MATLAB"_matlabhome scripts for

msi2lmp tool :h4,link(msi)

The msi2lmp sub-directory contains a tool for creating LAMMPS input

data files from Accelrys' Insight MD code (formerly MSI/Biosym and

its Discover MD code).  See the README file for more information.

data files from BIOVIA's Materias Studio files (formerly Accelrys'

Insight MD code, formerly MSI/Biosym and its Discover MD code).

This tool was written by John Carpenter (Cray), Michael Peachey

(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic

(jec at mayo.edu), but still fields questions about the tool.

(Cray), and Steve Lustig (Dupont). Several people contributed changes

to remove bugs and adapt its output to changes in LAMMPS.

This tool may be out-of-date with respect to the current LAMMPS and

Insight versions.  Since we don't use it at Sandia, you'll need to

experiment with it yourself.

See the README file for more information.

:line

write_data datafile

which will produce the same data file that the restart2data tool used

to create.  The following information is included in case you have an

older version of LAMMPS which still includes the restart2data tool.

to create.

The file restart2data.cpp converts a binary LAMMPS restart file into

an ASCII data file.  The syntax for running the tool is

restart2data restart-file data-file (input-file) :pre

Input-file is optional and if specified will contain LAMMPS input

commands for the masses and force field parameters, instead of putting

those in the data-file.  Only a few force field styles currently

support this option.

This tool must be compiled on a platform that can read the binary file

created by a LAMMPS run, since binary files are not compatible across

all platforms.

Note that a text data file has less precision than a binary restart

file.  Hence, continuing a run from a converted data file will

typically not conform as closely to a previous run as will restarting

from a binary restart file.

If a "%" appears in the specified restart-file, the tool expects a set

of multiple files to exist.  See the "restart"_restart.html and

"write_restart"_write_restart.html commands for info on how such sets

of files are written by LAMMPS, and how the files are named.

IMPORTANT NOTE: LAMMPS' binary restart files are generally not portable

between platforms, compiler settings and LAMMPS versions. Changes in

the format itself are rare, but no effort is made to maintain backward

compatibility. Data files are mostly backward and forward portable,

if no features are used that exist in only one LAMMPS version.

:line

These files were provided by Vikas Varshney (vv0210 at gmail.com)

:line

xmovie tool :h4,link(xmovie)

The xmovie tool is an X-based visualization package that can read

LAMMPS dump files and animate them.  It is in its own sub-directory

with the tools directory.  You may need to modify its Makefile so that

it can find the appropriate X libraries to link against.

The syntax for running xmovie is

xmovie \[options\] dump.file1 dump.file2 ... :pre

If you just type "xmovie" you will see a list of options.  Note that

by default, LAMMPS dump files are in scaled coordinates, so you

typically need to use the -scale option with xmovie.  When xmovie runs

it opens a visualization window and a control window.  The control

options are straightforward to use.

Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he

spent a summer at Sandia.  It displays 2d projections of a 3d domain.

While simple in design, it is an amazingly fast program that can

render large numbers of atoms very quickly.  It's a useful tool for

debugging LAMMPS input and output and making sure your simulation is

doing what you think it should.  The animations on the Examples page

of the "LAMMPS WWW site"_lws were created with xmovie.

I've lost contact with Mike, so I hope he's comfortable with us

distributing his great tool!

[References:]

Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., “Optimizing Classical Molecular Dynamics in LAMMPS,” in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l

Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l

Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l

the momentum at infrequent intervals using the

"fix momentum"_fix_momentum.html command.

NOTE: This implementation has been shown to conserve linear momentum

up to machine precision under NVT dynamics. Under NPT dynamics,

for a system with zero initial total linear momentum, the total

momentum fluctuates close to zero. It may occasionally undergo brief

excursions to non-negligible values, before returning close to zero.

Over long simulations, this has the effect of causing the center-of-mass

to undergo a slow random walk. This can be mitigated by resetting

the momentum at infrequent intervals using the

"fix momentum"_fix_momentum.html command.

:line

The fix npt and fix nph commands can be used with rigid bodies or

[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

:link(vanWijk)

[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, 

[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,

Physical Review Letters, 113, 135504 (2014)