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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5898 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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48
doc/special_bonds.html
View File

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

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