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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4540 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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115
doc/fix_qeq.html
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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix qeq/comb command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID qeq/comb Nevery precision keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>qeq/comb = style name of this fix command
<LI>Nevery = perform charge equilibration every this many steps
<LI>precision = convergence criterion for charge equilibration
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>file</I>
<PRE> <I>file</I> value = filename
filename = name of file to write QEQ equilibration info to
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 surface qeq/comb 10 0.0001
</PRE>
<P><B>Description:</B>
</P>
<P>This fix is designed for use with the pair_style comb command which
implements the COMB COMB (Charge-Optimized Many-Body) potential as
described in <A HREF = "#COMB_1">(COMB_1)</A> and <A HREF = "#COMB_2">(COMB_2)</A>. It performs
the charge equilibration portion of the calculation using the
so-called QEq method, whereby the charge on each atom is adjusted to
minimize the energy of the system.
</P>
<P>Only charges on the atoms in the specified group are equilibrated.
The fix relies on the pair style (COMB in this case) to calculate the
per-atom electronegativity (effective force on the charges). An
electronegativity equalization calculation (or QEq) is performed in an
interative fashion, which in parallel requires communication at each
iteration for processors to exchange charge information about nearby
atoms with each other. See <A HREF = "#Rappe_and_Goddard">Rappe_and_Goddard</A> and
<A HREF = "#Rick_and_Stuart">Rick_and_Stuart</A> for details.
</P>
<P>During a run, charge equilibration is peformed every <I>Nevery</I> time
steps. Charge equilibration is also always enforced on the first step
of each run. The <I>precision</I> argument controls the tolerance for the
difference in electronegativity for all atoms during charge
equilibration. <I>Precision</I> is a trade-off between the cost of
performing charge equilibration (more iterations) and accuracy.
</P>
<P>If the <I>file</I> keyword is used, then information about each
equilibration calculation is written to the specifed file.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix produces a per-atom vector which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The vector stores the
gradient of the charge on each atom. The per-atom values be accessed
on any timestep.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix command currently only supports <A HREF = "pair_comb.html">pair style <I>comb</I></A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_comb.html">pair_style comb</A>
</P>
<P><B>Default:</B>
</P>
<P>No file output is performed.
</P>
<HR>
<A NAME = "COMB_1"></A>
<P><B>(COMB_1)</B> J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
</P>
<A NAME = "COMB_2"></A>
<P><B>(COMB_2)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
Phillpot, Phys Rev B, 81, 125328 (2010).
</P>
<A NAME = "Rappe_and_Goddard"></A>
<P><B>(Rappe_and_Goddard)</B> A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358
(1991).
</P>
<A NAME = "Rick_and_Stuart"></A>
<P><B>(Rick_and_Stuart)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys
101, 16141 (1994).
</P>
</HTML>

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@ -176,8 +176,9 @@ shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff and fix_qeq commands in
an input script that reads a restart file.
need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
qeq/comb</A> commands in an input script that reads a
restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
@ -204,7 +205,7 @@ doesn't use "metal" units.
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "fix_qeq.html">fix_qeq</A>
<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
</P>
<P><B>Default:</B> none
</P>

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doc/pair_comb.txt
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@ -173,8 +173,9 @@ shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff and fix_qeq commands in
an input script that reads a restart file.
need to re-specify the pair_style, pair_coeff, and "fix
qeq/comb"_fix_qeq_comb.html commands in an input script that reads a
restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
@ -201,7 +202,7 @@ doesn't use "metal" units.
[Related commands:]
"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
"fix_qeq"_fix_qeq.html
"fix_qeq/comb"_fix_qeq_comb.html
[Default:] none