forked from lijiext/lammps
146 lines
6.7 KiB
Plaintext
146 lines
6.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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special_bonds command :h3
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[Syntax:]
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special_bonds keyword values ... :pre
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one or more keyword/value pairs may be appended :ulb,l
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keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
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{amber} values = none
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{charmm} values = none
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{fene} values = none
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{lj/coul} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
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{lj} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
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{coul} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
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{angle} value = {yes} or {no}
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{dihedral} value = {yes} or {no}
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{extra} value = N
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N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
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:ule
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Examples:
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special_bonds amber
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special_bonds charmm
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special_bonds fene dihedral no
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special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
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special_bonds lj/coul 0 1 1 extra 2 :pre
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[Description:]
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Set weighting coefficients for pairwise energy and force contributions
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from atom pairs that are also bonded to each other directly or
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indirectly. For Lennard-Jones (LJ) and Coulombic pairwise
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interactions, these coefficients come in sets of three. The 1st
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coefficient is the weighting factor on 1-2 atom pairs, which are those
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directly bonded to each other. The 2nd coefficient is the weighting
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factor on 1-3 atom pairs which are those separated by 2 bonds
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(e.g. the two H atoms in a water molecule). The 3rd coefficient is
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the weighting factor on 1-4 atom pairs which are those separated by 3
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bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if
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the 1-2 coefficient is set to 0.0, then the pairwise interaction is
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effectively turned off for all pairs of atoms bonded to each other.
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IMPORTANT NOTE: For purposes of computing weighted pairwise
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interactions, 1-3 and 1-4 interactions are not defined from the list
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of angles or dihedrals used by the simulation. Rather, they are
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inferred topologically from the set of bonds defined when the
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simulation is defined from a data or restart file (see
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
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apply to is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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The two exceptions to this rule are (a) if the {angle} or {dihedral}
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keywords are set to {yes} (see below), or (b) if the
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"delete_bonds"_delete_bonds.html command is used with the {special}
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the "delete_bonds"_delete_bonds.html command for more
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details.
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The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
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interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
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is the default for a commonly used version of the AMBER force field,
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where the last value is really 5/6.
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The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
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LJ and Coulombic interactions, which is the default for a commonly
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used version of the CHARMM force field. Note that in pair styles
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{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
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are defined explicitly, and these pairwise contributions are computed
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as part of the charmm dihedral style - see the
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"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
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commands for more information.
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The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
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LJ and Coulombic interactions, which is consistent with a
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coarse-grained polymer model with "FENE bonds"_bond_fene.html.
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The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
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be set explicitly. The {lj/coul} keyword sets both the LJ and
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Coulombic coefficients to the same 3 values. The {lj} and {coul}
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keywords only set either the LJ or Coulombic coefficients. Use both
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of them if you wish to set the LJ coefficients to different values
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than the Coulombic coefficients.
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The {angle} keyword allows the 1-3 weighting factor to be ignored for
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individual atom pairs if they are not listed as the first and last
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atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
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any dihedral defined in the simulation. For example, imagine the 1-3
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weighting factor is set to 0.5 and you have a linear molecule with 4
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atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
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as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
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dihedral, then the pairwise interaction between atoms 1 and 3 will
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always be weighted by 0.5, but different force fields use different
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rules for weighting the pairwise interaction between atoms 2 and 4.
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If the {angle} keyword is specified as {yes}, then the pairwise
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interaction between atoms 2 and 4 will be unaffected (full weighting
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of 1.0). If the {angle} keyword is specified as {no} which is the
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default, then the 2,4 interaction will also be weighted by 0.5.
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The {dihedral} keyword allows the 1-4 weighting factor to be ignored
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for individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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the 1-4 weighting factor is set to 0.5 and you have a linear molecule
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with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
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defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
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dihedral, then the pairwise interaction between atoms 1 and 4 will
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always be weighted by 0.5, but different force fields use different
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rules for weighting the pairwise interaction between atoms 2 and 5.
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If the {dihedral} keyword is specified as {yes}, then the pairwise
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interaction between atoms 2 and 5 will be unaffected (full weighting
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of 1.0). If the {dihedral} keyword is specified as {no} which is the
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default, then the 2,5 interaction will also be weighted by 0.5.
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The {extra} keyword is used when additional bonds will be created
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during a simulation run, e.g. by the "fix
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bond/create"_fix_bond_create.html command. A list of 1-2,1-3,1-4
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neighbors for each atom is calculated and stored by LAMMPS. If new
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bonds are created, the list needs to grow. Using the {extra} keyword
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leaves empty space in the list for N additional bonds to be added. If
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you do not do this, you may get an error when bonds are added.
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[Restrictions:] none
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[Related commands:]
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"delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html
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[Default:]
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All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
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angle = no, dihedral = no, and extra = 0.
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