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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5527 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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50
doc/special_bonds.html
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@ -48,22 +48,48 @@ 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 also bonded to each other directly or from atom pairs that are permanently bonded to each other. These
indirectly. For Lennard-Jones (LJ) and Coulombic pairwise weighting factors are used by all <A HREF = "pair_style.html">pair styles</A> in
interactions, these coefficients come in sets of three. The 1st LAMMPS that compute simple pairwise interactions. The Coulomb factors
coefficient is the weighting factor on 1-2 atom pairs, which are those are applied to any Coulomb (charge interaction) term that the
directly bonded to each other. The 2nd coefficient is the weighting potential calculates. The LJ factors are applied to the remaining
factor on 1-3 atom pairs which are those separated by 2 bonds terms that the potential calculates, whether they represent LJ
(e.g. the two H atoms in a water molecule). The 3rd coefficient is interactions or not. The weighting factors are a scaling pre-factor
the weighting factor on 1-4 atom pairs which are those separated by 3 on the energy and force between the pair of atoms. Permanent bonds
bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if between atoms are specified by defining the bond topology in the data
the 1-2 coefficient is set to 0.0, then the pairwise interaction is file read by the <A HREF = "read_data.html">read_data</A> command and by using the
effectively turned off for all pairs of atoms bonded to each other. <A HREF = "bond_style.html">bond_style</A> command to define the bond potential.
</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.
</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
each other. The 2nd coefficient is the weighting factor on 1-3 atom
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
water molecule). The 3rd coefficient is the weighting factor on 1-4
atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
to 0.0, then the pairwise interaction is effectively turned off for
all pairs of atoms bonded to each other. If it is set to 1.0, then
that interaction will be at full strength.
</P> </P>
<P>IMPORTANT NOTE: For purposes of computing weighted pairwise <P>IMPORTANT NOTE: For purposes of computing weighted pairwise
interactions, 1-3 and 1-4 interactions are not defined from the list interactions, 1-3 and 1-4 interactions are not defined from the list
of angles or dihedrals used by the simulation. Rather, they are of angles or dihedrals used by the simulation. Rather, they are
inferred topologically from the set of bonds defined when the inferred topologically from the set of bonds specified when the
simulation is defined from a data or restart file (see simulation is defined from a data or restart file (see
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands). Thus the set of 1-2,1-3,1-4 interactions that the weights commands). Thus the set of 1-2,1-3,1-4 interactions that the weights

50
doc/special_bonds.txt
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@ -42,22 +42,48 @@ 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 also bonded to each other directly or from atom pairs that are permanently bonded to each other. These
indirectly. For Lennard-Jones (LJ) and Coulombic pairwise weighting factors are used by all "pair styles"_pair_style.html in
interactions, these coefficients come in sets of three. The 1st LAMMPS that compute simple pairwise interactions. The Coulomb factors
coefficient is the weighting factor on 1-2 atom pairs, which are those are applied to any Coulomb (charge interaction) term that the
directly bonded to each other. The 2nd coefficient is the weighting potential calculates. The LJ factors are applied to the remaining
factor on 1-3 atom pairs which are those separated by 2 bonds terms that the potential calculates, whether they represent LJ
(e.g. the two H atoms in a water molecule). The 3rd coefficient is interactions or not. The weighting factors are a scaling pre-factor
the weighting factor on 1-4 atom pairs which are those separated by 3 on the energy and force between the pair of atoms. Permanent bonds
bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if between atoms are specified by defining the bond topology in the data
the 1-2 coefficient is set to 0.0, then the pairwise interaction is file read by the "read_data"_read_data.html command and by using the
effectively turned off for all pairs of atoms bonded to each other. "bond_style"_bond_style.html command to define the bond potential.
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.
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
each other. The 2nd coefficient is the weighting factor on 1-3 atom
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
water molecule). The 3rd coefficient is the weighting factor on 1-4
atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
to 0.0, then the pairwise interaction is effectively turned off for
all pairs of atoms bonded to each other. If it is set to 1.0, then
that interaction will be at full strength.
IMPORTANT NOTE: For purposes of computing weighted pairwise IMPORTANT NOTE: For purposes of computing weighted pairwise
interactions, 1-3 and 1-4 interactions are not defined from the list interactions, 1-3 and 1-4 interactions are not defined from the list
of angles or dihedrals used by the simulation. Rather, they are of angles or dihedrals used by the simulation. Rather, they are
inferred topologically from the set of bonds defined when the inferred topologically from the set of bonds specified when the
simulation is defined from a data or restart file (see simulation is defined from a data or restart file (see
"read_data"_read_data.html or "read_restart"_read_restart.html "read_data"_read_data.html or "read_restart"_read_restart.html
commands). Thus the set of 1-2,1-3,1-4 interactions that the weights commands). Thus the set of 1-2,1-3,1-4 interactions that the weights