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 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 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 command. +
Note that even if your simulation starts with no bonds, you must define a bond_style and use the bond_coeff command to specify coefficients for the diff --git a/doc/fix_bond_create.txt b/doc/fix_bond_create.txt index ea65e54932..284028eea6 100755 --- a/doc/fix_bond_create.txt +++ b/doc/fix_bond_create.txt @@ -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