forked from lijiext/lammps
113 lines
4.1 KiB
Plaintext
113 lines
4.1 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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bond_style quartic command :h3
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bond_style quartic/omp command :h3
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[Syntax:]
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bond_style quartic :pre
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[Examples:]
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bond_style quartic
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bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
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[Description:]
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The {quartic} bond style uses the potential
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:c,image(Eqs/bond_quartic.jpg)
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to define a bond that can be broken as the simulation proceeds (e.g.
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due to a polymer being stretched). The sigma and epsilon used in the
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LJ portion of the formula are both set equal to 1.0 by LAMMPS.
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The following coefficients must be defined for each bond type via the
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"bond_coeff"_bond_coeff.html command as in the example above, or in
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the data file or restart files read by the "read_data"_read_data.html
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or "read_restart"_read_restart.html commands:
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K (energy/distance^4)
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B1 (distance)
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B2 (distance)
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Rc (distance)
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U0 (energy) :ul
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This potential was constructed to mimic the FENE bond potential for
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coarse-grained polymer chains. When monomers with sigma = epsilon =
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1.0 are used, the following choice of parameters gives a quartic
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potential that looks nearly like the FENE potential: K = 1200, B1 =
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-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
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can be specified using the "bond_coeff"_bond_coeff.html command, but
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you will need to choose them carefully so they form a suitable bond
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potential.
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Rc is the cutoff length at which the bond potential goes smoothly to a
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local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
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the bond, which means two things. First, the bond potential is turned
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off by setting its type to 0, and is no longer computed. Second, a
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pairwise interaction between the two atoms is turned on, since they
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are no longer bonded.
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LAMMPS does the second task via a computational sleight-of-hand. It
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subtracts the pairwise interaction as part of the bond computation.
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When the bond breaks, the subtraction stops. For this to work, the
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pairwise interaction must always be computed by the
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"pair_style"_pair_style.html command, whether the bond is broken or
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not. This means that "special_bonds"_special_bonds.html must be set
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to 1,1,1, as indicated as a restriction below.
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Note that when bonds are dumped to a file via the "dump
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local"_dump.html command, bonds with type 0 are not included. The
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"delete_bonds"_delete_bonds.html command can also be used to query the
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status of broken bonds or permanently delete them, e.g.:
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delete_bonds all stats
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delete_bonds all bond 0 remove :pre
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This bond style can only be used if LAMMPS was built with the
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MOLECULAR package (which it is by default). See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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The {quartic} style requires that "special_bonds"_special_bonds.html
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parameters be set to 1,1,1. Three- and four-body interactions (angle,
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dihedral, etc) cannot be used with {quartic} bonds.
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[Related commands:]
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"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
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[Default:] none
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