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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
parent 16fb80ec48
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 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 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 two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides undergone a dramatic conformational change. This reference,
more details on how the algorithm works and its application: <A HREF = "#Sides">(Sides)</A> provides more details on how the algorithm works and
<A HREF = "#Sides">(Sides)</A>. its application:
</P> </P>
<P>The bond swapping operation is invoked every <I>Nevery</I> timesteps. If <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, 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 (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 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 chains then inter-chain swaps will occur, but they will not conserve
chain length. Neither of these scenarios is probably not what you chain length. Neither of these scenarios is probably what you want
want for this fix. for this fix.
</P> </P>
<P>IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in <P>IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in
the new polymer chains can become inconsistent. See the the new polymer chains can become inconsistent. See the

10
doc/fix_bond_swap.txt
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@ -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 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 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 two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides undergone a dramatic conformational change. This reference,
more details on how the algorithm works and its application: "(Sides)"_#Sides provides more details on how the algorithm works and
"(Sides)"_#Sides. its application:
The bond swapping operation is invoked every {Nevery} timesteps. If The bond swapping operation is invoked every {Nevery} timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered, 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 (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 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 chains then inter-chain swaps will occur, but they will not conserve
chain length. Neither of these scenarios is probably not what you chain length. Neither of these scenarios is probably what you want
want for this fix. for this fix.
IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in
the new polymer chains can become inconsistent. See the the new polymer chains can become inconsistent. See the