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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11809 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-04-17 16:48:47 +00:00
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commit 478db5b99d
2 changed files with 10 additions and 10 deletions
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10
doc/fix_bond_swap.html
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@ -53,9 +53,9 @@ respectively within their own chains. The bond swap operation will
attempt to delete the A1-A2 and B1-B2 bonds and replace them with
A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
<A HREF = "#Sides">(Sides)</A>.
undergone a dramatic conformational change. This reference,
<A HREF = "#Sides">(Sides)</A> provides more details on how the algorithm works and
its application:
</P>
<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,
@ -102,8 +102,8 @@ where all monomers on a single chain are assigned the same ID
(different for each chain), then swaps will only occur within the same
chain. If you assign the same molecule ID to all monomers in all
chains then inter-chain swaps will occur, but they will not conserve
chain length. Neither of these scenarios is probably not what you
want for this fix.
chain length. Neither of these scenarios is probably what you want
for this fix.
</P>
<P>IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in
the new polymer chains can become inconsistent. See the

10
doc/fix_bond_swap.txt
View File

@ -49,9 +49,9 @@ respectively within their own chains. The bond swap operation will
attempt to delete the A1-A2 and B1-B2 bonds and replace them with
A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
"(Sides)"_#Sides.
undergone a dramatic conformational change. This reference,
"(Sides)"_#Sides provides more details on how the algorithm works and
its application:
The bond swapping operation is invoked every {Nevery} timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered,
@ -98,8 +98,8 @@ where all monomers on a single chain are assigned the same ID
(different for each chain), then swaps will only occur within the same
chain. If you assign the same molecule ID to all monomers in all
chains then inter-chain swaps will occur, but they will not conserve
chain length. Neither of these scenarios is probably not what you
want for this fix.
chain length. Neither of these scenarios is probably what you want
for this fix.
IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in
the new polymer chains can become inconsistent. See the