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62
doc/fix_evaporate.html
View File

@ -15,29 +15,59 @@
</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
<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
<UL><LI>keyword = <I>molecule</I>
</UL>
<PRE> <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
<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 (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.
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>Note that you cannot currently delete solvent molecules with this
command, only individual atoms. If you delete only one atom in a
molecule, an error will result.
<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. 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
@ -64,6 +94,8 @@ minimization</A>.
</P>
<P><A HREF = "fix_deposit.html">fix deposit</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The option defaults are molecule = no.
</P>
</HTML>

55
doc/fix_evaporate.txt
View File

@ -12,29 +12,50 @@ fix evaporate command :h3
fix ID group-ID evaporate N M region-ID seed :pre
ID, group-ID are documented in "fix"_fix.html command
evaporate = style name of this fix command
N = delete atoms every this many timesteps
M = number of atoms to delete each time
region-ID = ID of region within which to perform deletions
seed = random number seed to use for choosing atoms to delete :ul
ID, group-ID are documented in "fix"_fix.html command :ulb,l
evaporate = style name of this fix command :l
N = delete atoms every this many timesteps :l
M = number of atoms to delete each time :l
region-ID = ID of region within which to perform deletions :l
seed = random number seed to use for choosing atoms to delete :l
zero or more keyword/value pairs may be appended :l
keyword = {molecule} :ul
{molecule} value = {no} or {yes} :pre
:ule
[Examples:]
fix 1 solvent evaporate 1000 10 surface 49892 :pre
fix 1 solvent evaporate 1000 10 surface 49892
fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
[Description:]
Remove M atoms from the simulation every N steps. This can be used,
for example, to model evaporation of solvent particles (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.
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.
Note that you cannot currently delete solvent molecules with this
command, only individual atoms. If you delete only one atom in a
molecule, an error will result.
If the setting for the {molecule} keyword is {no}, 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.
If the setting for the {molecule} keyword is {yes}, 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. 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.
As an example, if you wish to delete 10 water molecules every {N}
steps, you should set {M} 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.
Note that neighbor lists are re-built on timesteps that atoms are
removed. Thus you should not remove atoms too frequently or you will
@ -61,4 +82,6 @@ minimization"_minimize.html.
"fix deposit"_fix_deposit.html
[Default:] none
[Default:]
The option defaults are molecule = no.