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48
doc/special_bonds.html
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@ -48,32 +48,38 @@ special_bonds lj/coul 0 1 1 extra 2
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Set weighting coefficients for pairwise energy and force contributions <P>Set weighting coefficients for pairwise energy and force contributions
from atom pairs that are permanently bonded to each other. These between pairs of atoms that are also permanently bonded to each other,
weighting factors are used by all <A HREF = "pair_style.html">pair styles</A> in either directly or via one or two intermediate bonds. These weighting
LAMMPS that compute simple pairwise interactions. The Coulomb factors factors are used by nearly all <A HREF = "pair_style.html">pair styles</A> in LAMMPS
are applied to any Coulomb (charge interaction) term that the that compute simple pairwise interactions. Permanent bonds between
potential calculates. The LJ factors are applied to the remaining atoms are specified by defining the bond topology in the data file
terms that the potential calculates, whether they represent LJ read by the <A HREF = "read_data.html">read_data</A> command. Typically a
interactions or not. The weighting factors are a scaling pre-factor <A HREF = "bond_style.html">bond_style</A> command is also used to define a bond
on the energy and force between the pair of atoms. Permanent bonds potential. The rationale for using these weighting factors is that
between atoms are specified by defining the bond topology in the data the interaction between a pair of bonded atoms is all (or mostly)
file read by the <A HREF = "read_data.html">read_data</A> command and by using the specified by the bond, angle, dihedral potentials, and thus the
<A HREF = "bond_style.html">bond_style</A> command to define the bond potential. non-bonded Lennard-Jones or Coulombic interaction between the pair of
atoms should be excluded (or reduced by a weighting factor).
</P> </P>
<P>IMPORTANT NOTE: These weighting factors are NOT used by <A HREF = "pair_style.html">pair <P>IMPORTANT NOTE: These weighting factors are NOT used by <A HREF = "pair_style.html">pair
styles</A> that compute many-body interactions, since the styles</A> that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but are "bonds" that result from such interactions are not permanent, but are
created and broken dynamically as atom conformations change. Examples created and broken dynamically as atom conformations change. Examples
of pair styles and potentials in this category are EAM, MEAM, of pair styles in this category are EAM, MEAM, Stillinger-Weber,
Stillinger-Weber, Tersoff, COMB, AIREBO, and ReaxFF. In fact, when Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
using these pair styles, it makes no sense to define permanent bonds sense to define permanent bonds between atoms that interact via these
and to specify special_bonds weighting factors (unless they are potentials, though such bonds may exist elsewhere in your system,
applied to a different part of the system via the <A HREF = "pair_hybrid.html">pair_style e.g. when using the <A HREF = "pair_hybrid.html">pair_style hybrid</A> command.
hybrid</A> command). Though LAMMPS does not check for Thus LAMMPS ignores special_bonds settings when manybody potentials
this, using special_bonds with these potentials will result in errors are calculated.
and possibly crash the code, because the definition of weighting </P>
factors changes the format of the neighor list used by the pair <P>The Coulomb factors are applied to any Coulomb (charge interaction)
styles. term that the potential calculates. The LJ factors are applied to the
remaining terms that the potential calculates, whether they represent
LJ interactions or not. The weighting factors are a scaling
pre-factor on the energy and force between the pair of atoms. A value
of 1.0 means include the full interaction; a value of 0.0 means
exclude it completely.
</P> </P>
<P>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting <P>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to factor on 1-2 atom pairs, which are pairs of atoms directly bonded to

48
doc/special_bonds.txt
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@ -42,32 +42,38 @@ special_bonds lj/coul 0 1 1 extra 2 :pre
[Description:] [Description:]
Set weighting coefficients for pairwise energy and force contributions Set weighting coefficients for pairwise energy and force contributions
from atom pairs that are permanently bonded to each other. These between pairs of atoms that are also permanently bonded to each other,
weighting factors are used by all "pair styles"_pair_style.html in either directly or via one or two intermediate bonds. These weighting
LAMMPS that compute simple pairwise interactions. The Coulomb factors factors are used by nearly all "pair styles"_pair_style.html in LAMMPS
are applied to any Coulomb (charge interaction) term that the that compute simple pairwise interactions. Permanent bonds between
potential calculates. The LJ factors are applied to the remaining atoms are specified by defining the bond topology in the data file
terms that the potential calculates, whether they represent LJ read by the "read_data"_read_data.html command. Typically a
interactions or not. The weighting factors are a scaling pre-factor "bond_style"_bond_style.html command is also used to define a bond
on the energy and force between the pair of atoms. Permanent bonds potential. The rationale for using these weighting factors is that
between atoms are specified by defining the bond topology in the data the interaction between a pair of bonded atoms is all (or mostly)
file read by the "read_data"_read_data.html command and by using the specified by the bond, angle, dihedral potentials, and thus the
"bond_style"_bond_style.html command to define the bond potential. non-bonded Lennard-Jones or Coulombic interaction between the pair of
atoms should be excluded (or reduced by a weighting factor).
IMPORTANT NOTE: These weighting factors are NOT used by "pair IMPORTANT NOTE: These weighting factors are NOT used by "pair
styles"_pair_style.html that compute many-body interactions, since the styles"_pair_style.html that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but are "bonds" that result from such interactions are not permanent, but are
created and broken dynamically as atom conformations change. Examples created and broken dynamically as atom conformations change. Examples
of pair styles and potentials in this category are EAM, MEAM, of pair styles in this category are EAM, MEAM, Stillinger-Weber,
Stillinger-Weber, Tersoff, COMB, AIREBO, and ReaxFF. In fact, when Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
using these pair styles, it makes no sense to define permanent bonds sense to define permanent bonds between atoms that interact via these
and to specify special_bonds weighting factors (unless they are potentials, though such bonds may exist elsewhere in your system,
applied to a different part of the system via the "pair_style e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
hybrid"_pair_hybrid.html command). Though LAMMPS does not check for Thus LAMMPS ignores special_bonds settings when manybody potentials
this, using special_bonds with these potentials will result in errors are calculated.
and possibly crash the code, because the definition of weighting
factors changes the format of the neighor list used by the pair The Coulomb factors are applied to any Coulomb (charge interaction)
styles. term that the potential calculates. The LJ factors are applied to the
remaining terms that the potential calculates, whether they represent
LJ interactions or not. The weighting factors are a scaling
pre-factor on the energy and force between the pair of atoms. A value
of 1.0 means include the full interaction; a value of 0.0 means
exclude it completely.
The 1st of the 3 coefficients (LJ or Coulombic) is the weighting The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to factor on 1-2 atom pairs, which are pairs of atoms directly bonded to