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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11810 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-04-17 17:04:23 +00:00
parent 478db5b99d
commit df2f44c23e
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15
doc/fix_bond_create.html
View File

@ -159,6 +159,21 @@ it. There are 3 ways to do this. See the <A HREF = "read_data.html">read_data<
or <A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
details.
</P>
<P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or
<I>itype</I> keywords, the list of topological neighbors is updated for
atoms affected by the new bond. This in turn affects which neighbors
are considered for pairwise interactions, using the weighting rules
set by the <A HREF = "special_bonds.html">special_bonds</A> command. Consider a new
bond created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the <I>atype</I> keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
by the <A HREF = "special_bonds.html">special_bonds</A> command. This is the case
even if the "angle yes" option was used with that command. The same
is true for 3rd neighbors (1-4 interactions), the <I>dtype</I> keyword, and
the "dihedral yes" option used with the
<A HREF = "special_bonds.html">special_bonds</A> command.
</P>
<P>Note that even if your simulation starts with no bonds, you must
define a <A HREF = "bond_style.html">bond_style</A> and use the
<A HREF = "bond_coeff.html">bond_coeff</A> command to specify coefficients for the

15
doc/fix_bond_create.txt
View File

@ -147,6 +147,21 @@ it. There are 3 ways to do this. See the "read_data"_read_data.html
or "create_box"_create_box.html or "special_bonds extra" commands for
details.
IMPORTANT NOTE: Even if you do not use the {atype}, {dtype}, or
{itype} keywords, the list of topological neighbors is updated for
atoms affected by the new bond. This in turn affects which neighbors
are considered for pairwise interactions, using the weighting rules
set by the "special_bonds"_special_bonds.html command. Consider a new
bond created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the {atype} keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
by the "special_bonds"_special_bonds.html command. This is the case
even if the "angle yes" option was used with that command. The same
is true for 3rd neighbors (1-4 interactions), the {dtype} keyword, and
the "dihedral yes" option used with the
"special_bonds"_special_bonds.html command.
Note that even if your simulation starts with no bonds, you must
define a "bond_style"_bond_style.html and use the
"bond_coeff"_bond_coeff.html command to specify coefficients for the