Description:
Set weighting coefficients for pairwise energy and force contributions -from atom pairs that are also bonded to each other directly or -indirectly. For Lennard-Jones (LJ) and Coulombic pairwise -interactions, these coefficients come in sets of three. The 1st -coefficient is the weighting factor on 1-2 atom pairs, which are those -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. +from atom pairs that are permanently bonded to each other. These +weighting factors are used by all pair styles 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 command and by using the +bond_style command to define the bond potential. +
+IMPORTANT NOTE: These weighting factors are NOT used by pair +styles 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 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 interactions, 1-3 and 1-4 interactions are not defined from the list 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 read_data or read_restart commands). Thus the set of 1-2,1-3,1-4 interactions that the weights diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt index 5988115dcb..f5be9da5fb 100644 --- a/doc/special_bonds.txt +++ b/doc/special_bonds.txt @@ -42,22 +42,48 @@ 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 also bonded to each other directly or -indirectly. For Lennard-Jones (LJ) and Coulombic pairwise -interactions, these coefficients come in sets of three. The 1st -coefficient is the weighting factor on 1-2 atom pairs, which are those -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. +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. + +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 interactions, 1-3 and 1-4 interactions are not defined from the list 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 "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