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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11299 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-22 18:32:56 +00:00
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doc/dump.html
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@ -25,7 +25,7 @@
<LI>group-ID = ID of the group of atoms to be dumped
<LI>style = <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>image</I> or <I>molfile</I> or <I>local</I> or <I>custom</I>
<LI>style = <I>atom</I> or <I>aotm\mpiio</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
<LI>N = dump every this many timesteps
@ -34,11 +34,14 @@
<LI>args = list of arguments for a particular style
<PRE> <I>atom</I> args = none
<I>atom/mpiio</I> args = none
<I>cfg</I> args = same as <I>custom</I> args, see below
<I>dcd</I> args = none
<I>xtc</I> args = none
<I>xyz</I> args = none
</PRE>
<PRE> <I>xyz/mpiio</I> args = none
</PRE>
<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
</PRE>
<PRE> <I>molfile</I> args = discussed on <A HREF = "dump_molfile.html">dump molfile</A> doc page
@ -52,6 +55,7 @@
f_ID[N] = Nth column of local array calculated by a fix with ID
</PRE>
<PRE> <I>custom</I> args = list of atom attributes
<I>custom/mpiio</I> args = list of atom attributes
possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
@ -96,7 +100,9 @@
<P><B>Examples:</B>
</P>
<PRE>dump myDump all atom 100 dump.atom
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
@ -143,6 +149,15 @@ default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles,
atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
page for details.
</P>
<P>As explained below, the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I>
styles are identical in command syntax and in the format of the dump
files they create, to the corresponding styles without "mpiio", except
the single dump file they produce is written in parallel via the
MPI-IO library. For the remainder of this doc page, you should thus
consider the <I>atom</I> and <I>atom/mpiio</I> styles (etc) to be
inter-changeable. The one exception is how the filename is specified
for the MPI-IO styles, as explained below.
</P>
<HR>
<P>The <I>style</I> keyword determines what atom quantities are written to the
@ -352,6 +367,31 @@ when running on large numbers of processors.
<P>Note that using the "*" and "%" characters together can produce a
large number of small dump files!
</P>
<P>For the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles, a single
dump file is written in parallel via the MPI-IO library, which is part
of the MPI standard for versions 2.0 and above. Using MPI-IO requires
two steps. First, build LAMMPS with its MPIIO package installed, e.g.
</P>
<PRE>make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform
</PRE>
<P>Second, use a dump filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO restart files, which must be both written and read using
MPI-IO, the dump files produced by these MPI-IO styles are identical
in format to the files produced by their non-MPI-IO style
counterparts. This means you can write a dump file using MPI-IO and
use the <A HREF = "read_dump.html">read_dump</A> command or perform other
post-processing, just as if the dump file was not written using
MPI-IO.
</P>
<P>Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple
files. You can use the ".bin" suffix described below in an MPI-IO
dump file; again this file will be written in parallel and have the
same binary format as if it were written without MPI-IO.
</P>
<P>If the filename ends with ".bin", the dump file (or files, if "*" or
"%" is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically