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@ -901,11 +901,24 @@ interface and how to extend it for your needs.
<H4><A NAME = "start_6"></A>2.6 Running LAMMPS
</H4>
<P>By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
containing the desired commands. <A HREF = "Section_commands.html">This section</A>
describes how input scripts are structured and what commands they
contain.
<P>By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.
</P>
<PRE>lmp_linux
</PRE>
<P>it will simply wait, expecting commands from the keyboard. Typically
you should put commands in an input script and use I/O redirection,
e.g.
</P>
<PRE>lmp_linux < in.file
</PRE>
<P>For parallel environments this should also work. If it does not, use
the '-in' command-line switch, e.g.
</P>
<PRE>lmp_linux -in in.file
</PRE>
<P><A HREF = "Section_commands.html">This section</A> describes how input scripts are
structured and what commands they contain.
</P>
<P>You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
@ -921,8 +934,9 @@ cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux < in.lj
</PRE>
<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks
on various platforms.
<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require
LAMMPS to be built with one or more of its optional packages.
</P>
@ -951,12 +965,13 @@ with the name of your LAMMPS input script.
<P>For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:
</P>
<UL><LI>Download and install
<UL><LI>Download and install
<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
for Windows.
<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in
same directory (or path) as the LAMMPS Windows executable.
<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
package. Put them in same directory (or path) as the LAMMPS Windows
executable.
<LI>Get a command prompt by going to Start->Run... ,
then typing "cmd".
@ -964,18 +979,17 @@ then typing "cmd".
<LI>Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd "Documents").
<LI>Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj",
replacing in.lj with the name of your LAMMPS input script.
<LI>Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
in.lj", replacing in.lj with the name of your LAMMPS input script.
<LI>Note that you may need to provide smpd with a passphrase --- it doesn't matter what you
type.
<LI>Note that you may need to provide smpd with a passphrase (it doesn't
matter what you type).
<LI>In this mode, output may not immediately show up on the screen, so
if your input script takes a long time to execute, you may need to be
patient before the output shows up.
<LI>Alternatively, you can still use this executable to run on a single processor by
typing something like: "lmp_win_mpi -in in.lj".
<LI>In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something
like: "lmp_win_mpi -in in.lj".
</UL>
<HR>
@ -1062,17 +1076,22 @@ set by using the <A HREF = "echo.html">echo</A> command in the input script itse
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
LAMMPS reads its script from standard input, typically from a script
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
also work in parallel, but if it does not (in the unlikely case that
an MPI implementation does not support it), then use the -in flag.
Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
</P>
<PRE>-help
</PRE>
<P>Print a list of options compiled into this executable for each LAMMPS
style (atom_style, fix, compute, pair_style, bond_style, etc). This
can help you know if the command you want to use was included via the
appropriate package. LAMMPS will print the info and immediately exit
if this switch is used.
<P>Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
</P>
<PRE>-log file
</PRE>