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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7921 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-03-07 14:57:25 +00:00
parent 2c65b2923c
commit fd73d2de7d
2 changed files with 24 additions and 24 deletions
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24
doc/fix_bond_swap.html
View File

@ -83,24 +83,24 @@ by this processor on this timestep.
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the <A HREF = "read_data.html">read_data</A> comand.
Consider a system of 6-mer chains. You have 3 choices. If the
Consider a system of 6-mer chains. You have 2 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve length. For a particular momoner there will be
only one other monomer on another chain which is a potential swap
swaps will conserve chain length. For a particular momoner there will
be only one other monomer on another chain which is a potential swap
partner. If the molecule IDs for monomers on each chain are set to
1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
occur at either end of a chain. Thus for a particular monomer there
will be 2 possible swap partners on another chain. In this scenario,
swaps can also occur within a single chain, i.e. the two ends of a
chain swap with each other. The third choice is to give all monomers
on all chains the same molecule ID, e.g. 0. This will allow a wide
variety of swaps to occur, but will NOT conserve chain lengths.
1,2,3,3,2,1 then swaps will conserve chain length but swaps will be
able to occur at either end of a chain. Thus for a particular monomer
there will be 2 possible swap partners on another chain. In this
scenario, swaps can also occur within a single chain, i.e. the two
ends of a chain swap with each other.
</P>
<P>IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
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 and will NOT conserve chain length. This is probably not what
you want for this fix.
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.
</P>
<HR>

24
doc/fix_bond_swap.txt
View File

@ -80,24 +80,24 @@ The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the "read_data"_read_data.html comand.
Consider a system of 6-mer chains. You have 3 choices. If the
Consider a system of 6-mer chains. You have 2 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve length. For a particular momoner there will be
only one other monomer on another chain which is a potential swap
swaps will conserve chain length. For a particular momoner there will
be only one other monomer on another chain which is a potential swap
partner. If the molecule IDs for monomers on each chain are set to
1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
occur at either end of a chain. Thus for a particular monomer there
will be 2 possible swap partners on another chain. In this scenario,
swaps can also occur within a single chain, i.e. the two ends of a
chain swap with each other. The third choice is to give all monomers
on all chains the same molecule ID, e.g. 0. This will allow a wide
variety of swaps to occur, but will NOT conserve chain lengths.
1,2,3,3,2,1 then swaps will conserve chain length but swaps will be
able to occur at either end of a chain. Thus for a particular monomer
there will be 2 possible swap partners on another chain. In this
scenario, swaps can also occur within a single chain, i.e. the two
ends of a chain swap with each other.
IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
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 and will NOT conserve chain length. This is probably not what
you want for this fix.
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.
:line