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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11769 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-04-10 23:08:00 +00:00
parent 7e30710d5d
commit 1e2c5374d9
2 changed files with 24 additions and 19 deletions
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25
doc/fix_bond_swap.html
View File

@ -15,15 +15,17 @@
</P>
<PRE>fix ID group-ID bond/swap fraction cutoff seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>bond/swap = style name of this fix command
<LI>fraction = fraction of group atoms to consider for swapping
<LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
bond/swap = style name of this fix command
Nevery = attempt bond swapping every this many steps
<UL><LI>fraction = fraction of group atoms to consider for swapping
<LI>cutoff = distance at which swapping will be considered (distance units)
<LI>seed = random # seed (positive integer)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all bond/swap 0.5 1.3 598934
<PRE>fix 1 all bond/swap 50 0.5 1.3 598934
</PRE>
<P><B>Description:</B>
</P>
@ -55,13 +57,14 @@ undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
<A HREF = "#Sides">(Sides)</A>.
</P>
<P>The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
<I>fraction</I> of its atoms as potential swapping monomers for this
timestep. Choosing a small <I>fraction</I> value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
<P>The bond swapping operation is invoked every <I>Nevery</I> timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered,
since a swap alters the list of which neighbors are considered for
pairwise interaction. At each invocation, each processor considers a
random specified <I>fraction</I> of its atoms as potential swapping
monomers for this timestep. Choosing a small <I>fraction</I> value can
reduce the likelihood of a reverse swap occurring soon after an
initial swap.
</P>
<P>For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation

18
doc/fix_bond_swap.txt
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@ -14,13 +14,14 @@ fix ID group-ID bond/swap fraction cutoff seed :pre
ID, group-ID are documented in "fix"_fix.html command
bond/swap = style name of this fix command
Nevery = attempt bond swapping every this many steps :l
fraction = fraction of group atoms to consider for swapping
cutoff = distance at which swapping will be considered (distance units)
seed = random # seed (positive integer) :ul
[Examples:]
fix 1 all bond/swap 0.5 1.3 598934 :pre
fix 1 all bond/swap 50 0.5 1.3 598934 :pre
[Description:]
@ -52,13 +53,14 @@ undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
"(Sides)"_#Sides.
The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
{fraction} of its atoms as potential swapping monomers for this
timestep. Choosing a small {fraction} value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
The bond swapping operation is invoked every {Nevery} timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered,
since a swap alters the list of which neighbors are considered for
pairwise interaction. At each invocation, each processor considers a
random specified {fraction} of its atoms as potential swapping
monomers for this timestep. Choosing a small {fraction} value can
reduce the likelihood of a reverse swap occurring soon after an
initial swap.
For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation