forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@383 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
537846b830
|
|
@ -43,57 +43,36 @@ to edit for your platform) which will build several of the tools which
|
|||
reside in that directory. Some of them are larger packages in their
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own sub-directories with their own Makefiles.
|
||||
</P>
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<UL><LI><A HREF = "#replicate">replicate</A>
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<LI><A HREF = "#restart">restart2data</A>
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<UL><LI><A HREF = "#amber">amber2lammps</A>
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<LI><A HREF = "#binary">binary2txt</A>
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<LI><A HREF = "#data">data2xmovie</A>
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<LI><A HREF = "#chain">chain</A>
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<LI><A HREF = "#micelle">micelle2d</A>
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<LI><A HREF = "#xmovie">xmovie</A>
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<LI><A HREF = "#charmm">ch2lmp</A>
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<LI><A HREF = "#msi">msi2lmp</A>
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<LI><A HREF = "#amber">amber2lammps</A>
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<LI><A HREF = "#chain">chain</A>
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<LI><A HREF = "#data">data2xmovie</A>
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<LI><A HREF = "#arc">lmp2arc</A>
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<LI><A HREF = "#cfg">lmp2cfg</A>
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<LI><A HREF = "#traj">lmp2traj</A>
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<LI><A HREF = "#thermo_extract">thermo_extract</A>
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<LI><A HREF = "#matlab">matlab</A>
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<LI><A HREF = "#micelle">micelle2d</A>
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<LI><A HREF = "#msi">msi2lmp</A>
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<LI><A HREF = "#replicate">replicate</A>
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<LI><A HREF = "#restart">restart2data</A>
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<LI><A HREF = "#thermo_extract">thermo_extract</A>
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<LI><A HREF = "#xmovie">xmovie</A>
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</UL>
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<HR>
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<H4><A NAME = "replicate"></A>replicate tool
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<H4><A NAME = "amber"></A>amber2lmp tool
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</H4>
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<P>The file replicate.c takes a LAMMPS data file and replicates it into a
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larger system. The syntax for running the tool is
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<P>The amber2lmp sub-directory contain two Python scripts for converting
|
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files back-and-forth between the AMBER MD code and LAMMPS. See the
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README file in amber2lmp for more information.
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</P>
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<PRE>replicate <B>options</B> < infile > outfile
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</PRE>
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<P>See the top of the replicate.c file for a discussion of the options.
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This tool is used by some of the <A HREF = "Section_perf.html">LAMMPS benchmarks</A>
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for creating larger systems to run scaled-size problems on multiple
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processors.
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</P>
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<HR>
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<H4><A NAME = "restart"></A>restart2data tool
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</H4>
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<P>The file restart2data.cpp converts a binary LAMMPS restart file into
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an ASCII data file. The syntax for running the tool is
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</P>
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<PRE>restart2data restart-file data-file
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</PRE>
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<P>This tool must be compiled on a platform that can read the binary file
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created by a LAMMPS run, since binary files are not compatible across
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all platforms.
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</P>
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<P>Note that a text data file has less precision than a binary restart
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file. Hence, continuing a run from a converted data file will
|
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typically not conform as closely to a previous run as will restarting
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from a binary restart file.
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</P>
|
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<P>If a "%" appears in the specified restart-file, the tool expects a set
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of multiple files to exist. See the <A HREF = "restart.html">restart</A> and
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<A HREF = "write_restart.html">write_restart</A> commands for info on how such sets
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of files are written by LAMMPS, and how the files are named.
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<P>These tools were written by Keir Novik while he was at Queen Mary
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University of London. Keir is no longer there and cannot support
|
||||
these tools which are out-of-date with respect to the current LAMMPS
|
||||
version (and maybe with respect to AMBER as well). Since we don't use
|
||||
these tools at Sandia, you'll need to experiment with them and make
|
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necessary modifications yourself.
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</P>
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<HR>
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@ -110,83 +89,6 @@ since binary files are not compatible across all platforms.
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</P>
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<HR>
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<H4><A NAME = "data"></A>data2xmovie tool
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</H4>
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<P>The file data2xmovie.c converts a LAMMPS data file into a snapshot
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suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it had
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been output with a dump command from LAMMPS itself. The syntax for
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running the tool is
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</P>
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<PRE>data2xmovie <B>options</B> < infile > outfile
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</PRE>
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<P>See the top of the data2xmovie.c file for a discussion of the options.
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</P>
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<HR>
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<H4><A NAME = "chain"></A>chain tool
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</H4>
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<P>The file chain.f creates a LAMMPS data file containing bead-spring
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polymer chains and/or monomer solvent atoms. It uses a text file
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containing chain definition parameters as an input. The created
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chains and solvent atoms can strongly overlap, so LAMMPS needs to run
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the system initially with a "soft" pair potential to un-overlap it.
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The syntax for running the tool is
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</P>
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<PRE>chain < def.chain > data.file
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</PRE>
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<P>See the def.chain or def.chain.ab files in the tools directory for
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examples of definition files. This tool was used to create the
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system for the <A HREF = "Section_perf.html">chain benchmark</A>.
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</P>
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<HR>
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<H4><A NAME = "micelle"></A>micelle2d tool
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</H4>
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<P>The file micelle2d.f creates a LAMMPS data file containing short lipid
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chains in a monomer solution. It uses a text file containing lipid
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definition parameters as an input. The created molecules and solvent
|
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atoms can strongly overlap, so LAMMPS needs to run the system
|
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initially with a "soft" pair potential to un-overlap it. The syntax
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for running the tool is
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</P>
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<PRE>micelle2d < def.micelle2d > data.file
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</PRE>
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<P>See the def.micelle2d file in the tools directory for an example of a
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definition file. This tool was used to create the system for the
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<A HREF = "Section_example.html">micelle example</A>.
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</P>
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<HR>
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<H4><A NAME = "xmovie"></A>xmovie tool
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</H4>
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<P>The xmovie tool is an X-based visualization package that can read
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LAMMPS dump files and animate them. It is in its own sub-directory
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with the tools directory. You may need to modify its Makefile so that
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it can find the appropriate X libraries to link against.
|
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</P>
|
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<P>The syntax for running xmovie is
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</P>
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<PRE>xmovie <B>options</B> dump.file1 dump.file2 ...
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</PRE>
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<P>If you just type "xmovie" you will see a list of options. Note that
|
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by default, LAMMPS dump files are in scaled coordinates, so you
|
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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.
|
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</P>
|
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<P>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 <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A> were created with xmovie.
|
||||
</P>
|
||||
<P>I've lost contact with Mike, so I hope he's comfortable with us
|
||||
distributing his great tool!
|
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</P>
|
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<HR>
|
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|
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<H4><A NAME = "charmm"></A>ch2lmp tool
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</H4>
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<P>The ch2lmp sub-directory contains tools for converting files
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|
@ -204,34 +106,33 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.
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</P>
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<HR>
|
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<H4><A NAME = "msi"></A>msi2lmp tool
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<H4><A NAME = "chain"></A>chain tool
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</H4>
|
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<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
|
||||
its Discover MD code). See the README file for more information.
|
||||
<P>The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
containing chain definition parameters as an input. The created
|
||||
chains and solvent atoms can strongly overlap, so LAMMPS needs to run
|
||||
the system initially with a "soft" pair potential to un-overlap it.
|
||||
The syntax for running the tool is
|
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</P>
|
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<P>This tool was written by John Carpenter (Cray), Michael Peachey
|
||||
(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
|
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(jec at mayo.edu), but still fields questions about the tool.
|
||||
</P>
|
||||
<P>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.
|
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<PRE>chain < def.chain > data.file
|
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</PRE>
|
||||
<P>See the def.chain or def.chain.ab files in the tools directory for
|
||||
examples of definition files. This tool was used to create the
|
||||
system for the <A HREF = "Section_perf.html">chain benchmark</A>.
|
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</P>
|
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<HR>
|
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|
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<H4><A NAME = "amber"></A>amber2lmp tool
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<H4><A NAME = "data"></A>data2xmovie tool
|
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</H4>
|
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<P>The amber2lmp sub-directory contain two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
README file in amber2lmp for more information.
|
||||
<P>The file data2xmovie.c converts a LAMMPS data file into a snapshot
|
||||
suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it had
|
||||
been output with a dump command from LAMMPS itself. The syntax for
|
||||
running the tool is
|
||||
</P>
|
||||
<P>These tools were written by Keir Novik while he was at Queen Mary
|
||||
University of London. Keir is no longer there and cannot support
|
||||
these tools which are out-of-date with respect to the current LAMMPS
|
||||
version (and maybe with respect to AMBER as well). Since we don't use
|
||||
these tools at Sandia, you'll need to experiment with them and make
|
||||
necessary modifications yourself.
|
||||
<PRE>data2xmovie <B>options</B> < infile > outfile
|
||||
</PRE>
|
||||
<P>See the top of the data2xmovie.c file for a discussion of the options.
|
||||
</P>
|
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<HR>
|
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|
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|
|
@ -274,6 +175,95 @@ README file for more information.
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</P>
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<HR>
|
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|
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<H4><A NAME = "matlab"></A>matlab tool
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</H4>
|
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<P>The matlab sub-directory contains several <A HREF = "http://www.mathworks.com">MATLAB</A> scripts for
|
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post-processing LAMMPS output. The scripts include readers for log
|
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and dump files, a reader for radial distribution output from the <A HREF = "fix_rdf.html">fix
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rdf</A> command, a reader for EAM potential files, and a
|
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converter that reads LAMMPS dump files and produces CFG files that can
|
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be visualized with the
|
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<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
|
||||
</P>
|
||||
<P>See the README.pdf file for more information.
|
||||
</P>
|
||||
<P>These scripts were written by Arun Subramaniyan at Purdue Univ
|
||||
(asubrama at purdue.edu).
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||||
</P>
|
||||
|
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|
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<HR>
|
||||
|
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<H4><A NAME = "micelle"></A>micelle2d tool
|
||||
</H4>
|
||||
<P>The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
definition parameters as an input. The created molecules and solvent
|
||||
atoms can strongly overlap, so LAMMPS needs to run the system
|
||||
initially with a "soft" pair potential to un-overlap it. The syntax
|
||||
for running the tool is
|
||||
</P>
|
||||
<PRE>micelle2d < def.micelle2d > data.file
|
||||
</PRE>
|
||||
<P>See the def.micelle2d file in the tools directory for an example of a
|
||||
definition file. This tool was used to create the system for the
|
||||
<A HREF = "Section_example.html">micelle example</A>.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "msi"></A>msi2lmp tool
|
||||
</H4>
|
||||
<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
|
||||
data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
|
||||
its Discover MD code). See the README file for more information.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "replicate"></A>replicate tool
|
||||
</H4>
|
||||
<P>The file replicate.c takes a LAMMPS data file and replicates it into a
|
||||
larger system. The syntax for running the tool is
|
||||
</P>
|
||||
<PRE>replicate <B>options</B> < infile > outfile
|
||||
</PRE>
|
||||
<P>See the top of the replicate.c file for a discussion of the options.
|
||||
This tool is used by some of the <A HREF = "Section_perf.html">LAMMPS benchmarks</A>
|
||||
for creating larger systems to run scaled-size problems on multiple
|
||||
processors.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "restart"></A>restart2data tool
|
||||
</H4>
|
||||
<P>The file restart2data.cpp converts a binary LAMMPS restart file into
|
||||
an ASCII data file. The syntax for running the tool is
|
||||
</P>
|
||||
<PRE>restart2data restart-file data-file
|
||||
</PRE>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>If a "%" appears in the specified restart-file, the tool expects a set
|
||||
of multiple files to exist. See the <A HREF = "restart.html">restart</A> and
|
||||
<A HREF = "write_restart.html">write_restart</A> commands for info on how such sets
|
||||
of files are written by LAMMPS, and how the files are named.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "thermo_extract"></A>thermo_extract tool
|
||||
</H4>
|
||||
<P>The thermo_extract tool reads one of more LAMMPS log files and
|
||||
|
|
@ -286,4 +276,34 @@ details.
|
|||
<P>This tool was written by Vikas Varshney at Wright Patterson AFB
|
||||
(vikas.varshney at gmail.com).
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "xmovie"></A>xmovie tool
|
||||
</H4>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>The syntax for running xmovie is
|
||||
</P>
|
||||
<PRE>xmovie <B>options</B> dump.file1 dump.file2 ...
|
||||
</PRE>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>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 <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A> were created with xmovie.
|
||||
</P>
|
||||
<P>I've lost contact with Mike, so I hope he's comfortable with us
|
||||
distributing his great tool!
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -39,57 +39,36 @@ to edit for your platform) which will build several of the tools which
|
|||
reside in that directory. Some of them are larger packages in their
|
||||
own sub-directories with their own Makefiles.
|
||||
|
||||
"replicate"_#replicate
|
||||
"restart2data"_#restart
|
||||
"binary2txt"_#binary
|
||||
"data2xmovie"_#data
|
||||
"chain"_#chain
|
||||
"micelle2d"_#micelle
|
||||
"xmovie"_#xmovie
|
||||
"ch2lmp"_#charmm
|
||||
"msi2lmp"_#msi
|
||||
"amber2lammps"_#amber
|
||||
"binary2txt"_#binary
|
||||
"ch2lmp"_#charmm
|
||||
"chain"_#chain
|
||||
"data2xmovie"_#data
|
||||
"lmp2arc"_#arc
|
||||
"lmp2cfg"_#cfg
|
||||
"lmp2traj"_#traj
|
||||
"thermo_extract"_#thermo_extract :ul
|
||||
"matlab"_#matlab
|
||||
"micelle2d"_#micelle
|
||||
"msi2lmp"_#msi
|
||||
"replicate"_#replicate
|
||||
"restart2data"_#restart
|
||||
"thermo_extract"_#thermo_extract
|
||||
"xmovie"_#xmovie :ul
|
||||
|
||||
:line
|
||||
|
||||
replicate tool :h4,link(replicate)
|
||||
amber2lmp tool :h4,link(amber)
|
||||
|
||||
The file replicate.c takes a LAMMPS data file and replicates it into a
|
||||
larger system. The syntax for running the tool is
|
||||
The amber2lmp sub-directory contain two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
README file in amber2lmp for more information.
|
||||
|
||||
replicate [options] < infile > outfile :pre
|
||||
|
||||
See the top of the replicate.c file for a discussion of the options.
|
||||
This tool is used by some of the "LAMMPS benchmarks"_Section_perf.html
|
||||
for creating larger systems to run scaled-size problems on multiple
|
||||
processors.
|
||||
|
||||
:line
|
||||
|
||||
restart2data tool :h4,link(restart)
|
||||
|
||||
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 :pre
|
||||
|
||||
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.
|
||||
These tools were written by Keir Novik while he was at Queen Mary
|
||||
University of London. Keir is no longer there and cannot support
|
||||
these tools which are out-of-date with respect to the current LAMMPS
|
||||
version (and maybe with respect to AMBER as well). Since we don't use
|
||||
these tools at Sandia, you'll need to experiment with them and make
|
||||
necessary modifications yourself.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -106,83 +85,6 @@ since binary files are not compatible across all platforms.
|
|||
|
||||
: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
|
||||
|
||||
chain tool :h4,link(chain)
|
||||
|
||||
The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
containing chain definition parameters as an input. The created
|
||||
chains and solvent atoms can strongly overlap, so LAMMPS needs to run
|
||||
the system initially with a "soft" pair potential to un-overlap it.
|
||||
The syntax for running the tool is
|
||||
|
||||
chain < def.chain > data.file :pre
|
||||
|
||||
See the def.chain or def.chain.ab files in the tools directory for
|
||||
examples of definition files. This tool was used to create the
|
||||
system for the "chain benchmark"_Section_perf.html.
|
||||
|
||||
:line
|
||||
|
||||
micelle2d tool :h4,link(micelle)
|
||||
|
||||
The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
definition parameters as an input. The created molecules and solvent
|
||||
atoms can strongly overlap, so LAMMPS needs to run the system
|
||||
initially with a "soft" pair potential to un-overlap it. The syntax
|
||||
for running the tool is
|
||||
|
||||
micelle2d < def.micelle2d > data.file :pre
|
||||
|
||||
See the def.micelle2d file in the tools directory for an example of a
|
||||
definition file. This tool was used to create the system for the
|
||||
"micelle example"_Section_example.html.
|
||||
|
||||
: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!
|
||||
|
||||
:line
|
||||
|
||||
ch2lmp tool :h4,link(charmm)
|
||||
|
||||
The ch2lmp sub-directory contains tools for converting files
|
||||
|
|
@ -200,34 +102,33 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.
|
|||
|
||||
:line
|
||||
|
||||
msi2lmp tool :h4,link(msi)
|
||||
chain tool :h4,link(chain)
|
||||
|
||||
The msi2lmp sub-directory contains a tool for creating LAMMPS input
|
||||
data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
|
||||
its Discover MD code). See the README file for more information.
|
||||
The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
containing chain definition parameters as an input. The created
|
||||
chains and solvent atoms can strongly overlap, so LAMMPS needs to run
|
||||
the system initially with a "soft" pair potential to un-overlap it.
|
||||
The syntax for running the tool is
|
||||
|
||||
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.
|
||||
chain < def.chain > data.file :pre
|
||||
|
||||
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 def.chain or def.chain.ab files in the tools directory for
|
||||
examples of definition files. This tool was used to create the
|
||||
system for the "chain benchmark"_Section_perf.html.
|
||||
|
||||
:line
|
||||
|
||||
amber2lmp tool :h4,link(amber)
|
||||
data2xmovie tool :h4,link(data)
|
||||
|
||||
The amber2lmp sub-directory contain two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
README file in amber2lmp for more information.
|
||||
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
|
||||
|
||||
These tools were written by Keir Novik while he was at Queen Mary
|
||||
University of London. Keir is no longer there and cannot support
|
||||
these tools which are out-of-date with respect to the current LAMMPS
|
||||
version (and maybe with respect to AMBER as well). Since we don't use
|
||||
these tools at Sandia, you'll need to experiment with them and make
|
||||
necessary modifications yourself.
|
||||
data2xmovie [options] < infile > outfile :pre
|
||||
|
||||
See the top of the data2xmovie.c file for a discussion of the options.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -270,6 +171,95 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
|
|||
|
||||
:line
|
||||
|
||||
matlab tool :h4,link(matlab)
|
||||
|
||||
The matlab sub-directory contains several "MATLAB"_matlab scripts for
|
||||
post-processing LAMMPS output. The scripts include readers for log
|
||||
and dump files, a reader for radial distribution output from the "fix
|
||||
rdf"_fix_rdf.html command, a reader for EAM potential files, and a
|
||||
converter that reads LAMMPS dump files and produces CFG files that can
|
||||
be visualized with the
|
||||
"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer.
|
||||
|
||||
See the README.pdf file for more information.
|
||||
|
||||
These scripts were written by Arun Subramaniyan at Purdue Univ
|
||||
(asubrama at purdue.edu).
|
||||
|
||||
:link(matlab,http://www.mathworks.com)
|
||||
|
||||
:line
|
||||
|
||||
micelle2d tool :h4,link(micelle)
|
||||
|
||||
The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
definition parameters as an input. The created molecules and solvent
|
||||
atoms can strongly overlap, so LAMMPS needs to run the system
|
||||
initially with a "soft" pair potential to un-overlap it. The syntax
|
||||
for running the tool is
|
||||
|
||||
micelle2d < def.micelle2d > data.file :pre
|
||||
|
||||
See the def.micelle2d file in the tools directory for an example of a
|
||||
definition file. This tool was used to create the system for the
|
||||
"micelle example"_Section_example.html.
|
||||
|
||||
:line
|
||||
|
||||
msi2lmp tool :h4,link(msi)
|
||||
|
||||
The msi2lmp sub-directory contains a tool for creating LAMMPS input
|
||||
data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
|
||||
its Discover MD code). See the README file for more information.
|
||||
|
||||
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.
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
replicate tool :h4,link(replicate)
|
||||
|
||||
The file replicate.c takes a LAMMPS data file and replicates it into a
|
||||
larger system. The syntax for running the tool is
|
||||
|
||||
replicate [options] < infile > outfile :pre
|
||||
|
||||
See the top of the replicate.c file for a discussion of the options.
|
||||
This tool is used by some of the "LAMMPS benchmarks"_Section_perf.html
|
||||
for creating larger systems to run scaled-size problems on multiple
|
||||
processors.
|
||||
|
||||
:line
|
||||
|
||||
restart2data tool :h4,link(restart)
|
||||
|
||||
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 :pre
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
thermo_extract tool :h4,link(thermo_extract)
|
||||
|
||||
The thermo_extract tool reads one of more LAMMPS log files and
|
||||
|
|
@ -281,3 +271,33 @@ details.
|
|||
|
||||
This tool was written by Vikas Varshney at Wright Patterson AFB
|
||||
(vikas.varshney 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!
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@
|
|||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>origin</I> or <I>orient</I> or <I>spacings</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I>
|
||||
<LI>keyword = <I>origin</I> or <I>orient</I> or <I>spacing</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I>
|
||||
|
||||
<PRE> <I>origin</I> values = x y z
|
||||
x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
|
||||
|
|
@ -161,9 +161,9 @@ the Z direction.
|
|||
<HR>
|
||||
|
||||
<P>Several LAMMPS commands have the option to use distance units that are
|
||||
inferred from "lattice spacings" in the x,y,z box directions.
|
||||
E.g. the <A HREF = "region.html">region</A> command can create a block of size
|
||||
10x20x20, where 10 means 10 lattice spacings in the x direction.
|
||||
inferred from "lattice spacing" in the x,y,z box directions. E.g. the
|
||||
<A HREF = "region.html">region</A> command can create a block of size 10x20x20,
|
||||
where 10 means 10 lattice spacings in the x direction.
|
||||
</P>
|
||||
<P>The <I>spacing</I> option sets the 3 lattice spacings directly. All must
|
||||
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@ scale = scale factor between lattice and simulation box :l
|
|||
scale = reduced density rho* (for LJ units)
|
||||
scale = lattice constant in Angstroms (for real or metal units) :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {origin} or {orient} or {spacings} or {a1} or {a2} or {a3} or {basis} :l
|
||||
keyword = {origin} or {orient} or {spacing} or {a1} or {a2} or {a3} or {basis} :l
|
||||
{origin} values = x y z
|
||||
x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
|
||||
{orient} values = dim i j k
|
||||
|
|
@ -153,9 +153,9 @@ the Z direction.
|
|||
:line
|
||||
|
||||
Several LAMMPS commands have the option to use distance units that are
|
||||
inferred from "lattice spacings" in the x,y,z box directions.
|
||||
E.g. the "region"_region.html command can create a block of size
|
||||
10x20x20, where 10 means 10 lattice spacings in the x direction.
|
||||
inferred from "lattice spacing" in the x,y,z box directions. E.g. the
|
||||
"region"_region.html command can create a block of size 10x20x20,
|
||||
where 10 means 10 lattice spacings in the x direction.
|
||||
|
||||
The {spacing} option sets the 3 lattice spacings directly. All must
|
||||
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
|
||||
|
|
|
|||
|
|
@ -121,7 +121,7 @@ as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for u
|
|||
lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
|
||||
previously used to define the lattice spacing.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
|
||||
thickness for 2d simulations. For 2d simulations, the xz and yz
|
||||
|
|
|
|||
|
|
@ -112,7 +112,7 @@ as defined by the "units"_units.html command, e.g. Angstroms for units
|
|||
lattice spacings. The "lattice"_lattice.html command must have been
|
||||
previously used to define the lattice spacing.
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
A prism cannot be of 0.0 thickness in any dimension; use a small z
|
||||
thickness for 2d simulations. For 2d simulations, the xz and yz
|
||||
|
|
|
|||
Loading…
Reference in New Issue