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@ -15,15 +15,17 @@
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</P>
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<PRE>fix ID group-ID bond/swap fraction cutoff seed
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>bond/swap = style name of this fix command
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<LI>fraction = fraction of group atoms to consider for swapping
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<LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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bond/swap = style name of this fix command
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Nevery = attempt bond swapping every this many steps
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<UL><LI>fraction = fraction of group atoms to consider for swapping
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<LI>cutoff = distance at which swapping will be considered (distance units)
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<LI>seed = random # seed (positive integer)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all bond/swap 0.5 1.3 598934
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<PRE>fix 1 all bond/swap 50 0.5 1.3 598934
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -55,13 +57,14 @@ undergone a dramatic conformational change. This reference provides
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more details on how the algorithm works and its application:
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<A HREF = "#Sides">(Sides)</A>.
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</P>
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<P>The bond swapping operation is invoked each time neighbor lists are
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built during a simulation, since it potentially alters the list of
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which neighbors are considered for pairwise interaction. At each
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reneighboring step, each processor considers a random specified
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<I>fraction</I> of its atoms as potential swapping monomers for this
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timestep. Choosing a small <I>fraction</I> value can reduce the likelihood
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of a reverse swap occurring soon after an initial swap.
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<P>The bond swapping operation is invoked every <I>Nevery</I> timesteps. If
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any bond is swapped, a re-build of the neighbor lists is triggered,
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since a swap alters the list of which neighbors are considered for
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pairwise interaction. At each invocation, each processor considers a
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random specified <I>fraction</I> of its atoms as potential swapping
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monomers for this timestep. Choosing a small <I>fraction</I> value can
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reduce the likelihood of a reverse swap occurring soon after an
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initial swap.
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</P>
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<P>For each monomer A1, its neighbors are examined to find a possible B1
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monomer. Both A1 and B1 must be in the fix group, their separation
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@ -14,13 +14,14 @@ fix ID group-ID bond/swap fraction cutoff seed :pre
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ID, group-ID are documented in "fix"_fix.html command
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bond/swap = style name of this fix command
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Nevery = attempt bond swapping every this many steps :l
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fraction = fraction of group atoms to consider for swapping
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cutoff = distance at which swapping will be considered (distance units)
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seed = random # seed (positive integer) :ul
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[Examples:]
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fix 1 all bond/swap 0.5 1.3 598934 :pre
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fix 1 all bond/swap 50 0.5 1.3 598934 :pre
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[Description:]
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@ -52,13 +53,14 @@ undergone a dramatic conformational change. This reference provides
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more details on how the algorithm works and its application:
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"(Sides)"_#Sides.
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The bond swapping operation is invoked each time neighbor lists are
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built during a simulation, since it potentially alters the list of
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which neighbors are considered for pairwise interaction. At each
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reneighboring step, each processor considers a random specified
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{fraction} of its atoms as potential swapping monomers for this
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timestep. Choosing a small {fraction} value can reduce the likelihood
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of a reverse swap occurring soon after an initial swap.
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The bond swapping operation is invoked every {Nevery} timesteps. If
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any bond is swapped, a re-build of the neighbor lists is triggered,
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since a swap alters the list of which neighbors are considered for
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pairwise interaction. At each invocation, each processor considers a
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random specified {fraction} of its atoms as potential swapping
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monomers for this timestep. Choosing a small {fraction} value can
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reduce the likelihood of a reverse swap occurring soon after an
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initial swap.
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For each monomer A1, its neighbors are examined to find a possible B1
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monomer. Both A1 and B1 must be in the fix group, their separation
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