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Tweaked multireplica docs

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5490 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
2011-01-05 18:03:37 +00:00
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13
doc/Section_howto.html
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@ -345,14 +345,19 @@ periodically.
</P>
<UL><LI><A HREF = "neb.html">neb</A> for nudged elastic band calculations
<LI><A HREF = "prd.html">prd</A> for parallel replica dynamics
<LI><A HREF = "tad.html">tad</A> for temperature accelerated dynamics
<LI><A HREF = "temper.html">temper</A> for parallel tempering
</UL>
<P>NEB is a method for finding transition states and barrier energies.
PRD is a method for performing accelerated dynamics to find and
perform infrequent events. Parallel tempering or replica exchange
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.
</P>
<P>These command can only be used if LAMMPS was built with the "replica"
package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
more info on packages.
</P>
<P>In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the <A HREF = "Section_start.html#2_6">-partition command-line
@ -1149,7 +1154,7 @@ discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
@ -1343,7 +1348,7 @@ data and scalar/vector/array data.
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>