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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4794 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-09-15 22:15:54 +00:00
parent cf897522fd
commit 1d3b37782f
4 changed files with 96 additions and 74 deletions
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doc/dump_modify.html
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@ -36,7 +36,10 @@
<I>precision</I> arg = power-of-10 value from 10 to 1000000
<I>region</I> arg = region-ID or "none"
<I>scale</I> arg = <I>yes</I> or <I>no</I>
<I>sort</I> arg = <I>yes</I> or <I>no</I>
<I>sort</I> arg = <I>off</I> or 0 or N
off = no sorting of per-atom lines within a snapshot
0 = sort per-atom lines by atom ID
N = sort per-atom lines by the Nth column
<I>thresh</I> args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
@ -169,11 +172,21 @@ value of <I>yes</I> means atom coords are written in normalized units from
value of <I>no</I> means they are written in absolute distance units
(e.g. Angstroms or sigma).
</P>
<P>The <I>sort</I> keyword applies only to the dump <I>cfg</I> style. A sort value
of <I>yes</I> means atoms will be written into the CFG file in sorted
order, sorted by the atom ID. A value of <I>no</I> means a sort will not
be performed and that atoms may be in an indeterminate order,
depending on which processor owns which atoms.
<P>The <I>sort</I> keyword determines whether lines of per-atom output in a
snapshot are sorted or not. A sort value of <I>off</I> means they will
typically be written in indeterminate order, either in serial or
parallel. This is the case even in serial if the <A HREF = "atom_modify.html">atom_modify
sort</A> option is turned on, which it is by default, to
improve performance. A sort value of 0 means sort the output by atom
ID. A sort value of N means sort the output by the value in the Nth
column of per-atom info. The dump <I>local</I> style cannot be sorted by
atom ID, since there are typically multiple lines of output per atom.
Some dump styles, such as <I>dcd</I> and <I>xtc</I>, require sorting by atom
ID to format the output file correctly.
</P>
<P>IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
file output requires extra overhead in terms of CPU and communication
cost, as well as memory.
</P>
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
styles. Multiple thresholds can be specified. Specifying "none"
@ -215,7 +228,8 @@ box size stored with the snapshot.
<LI>precision = 1000
<LI>region = none
<LI>scale = yes
<LI>sort = no
<LI>sort = off for dump styles <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I>
<LI>sort = 0 for dump styles <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> meaning sort by atom ID
<LI>thresh = none
<LI>unwrap = no
</UL>