forked from lijiext/lammps
110 lines
4.0 KiB
HTML
110 lines
4.0 KiB
HTML
<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 evaporate command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>fix ID group-ID evaporate N M region-ID seed
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>evaporate = style name of this fix command
|
|
|
|
<LI>N = delete atoms every this many timesteps
|
|
|
|
<LI>M = number of atoms to delete each time
|
|
|
|
<LI>region-ID = ID of region within which to perform deletions
|
|
|
|
<LI>seed = random number seed to use for choosing atoms to delete
|
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
<PRE>keyword = <I>molecule</I>
|
|
<I>molecule</I> value = <I>no</I> or <I>yes</I>
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 1 solvent evaporate 1000 10 surface 49892
|
|
fix 1 solvent evaporate 1000 10 surface 38277 molecule yes
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Remove M atoms from the simulation every N steps. This can be used,
|
|
for example, to model evaporation of solvent particles or moleclues
|
|
(i.e. drying) of a system. Every N steps, the number of atoms in the
|
|
fix group and within the specifed region are counted. M of these are
|
|
chosen at random and deleted. If there are less than M eligible
|
|
particles, then all of them are deleted.
|
|
</P>
|
|
<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
|
|
atoms are deleted. In this case, you should insure you do not delete
|
|
only a portion of a molecule (only some of its atoms), or LAMMPS will
|
|
soon generate an error when it tries to find those atoms. LAMMPS will
|
|
warn you if any of the atoms eligible for deletion have a non-zero
|
|
molecule ID, but does not check for this at the time of deletion.
|
|
</P>
|
|
<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, then when an atom
|
|
is chosen for deletion, the entire molecule it is part of is deleted.
|
|
The count of deleted atoms is incremented by the number of atoms in
|
|
the molecule, which may make it exceed <I>M</I>. If the molecule ID of the
|
|
chosen atom is 0, then it is assumed to not be part of a molecule, and
|
|
just the single atom is deleted.
|
|
</P>
|
|
<P>As an example, if you wish to delete 10 water molecules every <I>N</I>
|
|
steps, you should set <I>M</I> to 30. If only the water's oxygen atoms
|
|
were in the fix group, then two hydrogen atoms would be deleted when
|
|
an oxygen atom is selected for deletion, whether the hydrogens are
|
|
inside the evaporation region or not.
|
|
</P>
|
|
<P>Note that neighbor lists are re-built on timesteps that atoms are
|
|
removed. Thus you should not remove atoms too frequently or you will
|
|
incur overhead due to the cost of building neighbor lists.
|
|
</P>
|
|
<P>IMPORTANT NOTE: If you are monitoring the temperature of a system
|
|
where the atom count is changing due to evaporation, you typically
|
|
should use the <A HREF = "compute_modify.html">compute_modify dynamic yes</A>
|
|
command for the temperature compute you are using.
|
|
</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 computes a global scalar, which can be accessed by various
|
|
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
|
|
cummulative number of deleted atoms. The scalar value calculated by
|
|
this fix is "intensive".
|
|
</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 is part of the MISC package. It is only enabled if LAMMPS
|
|
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_deposit.html">fix deposit</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are molecule = no.
|
|
</P>
|
|
</HTML>
|