forked from lijiext/lammps
129 lines
4.2 KiB
Plaintext
129 lines
4.2 KiB
Plaintext
.. index:: bond_style quartic
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bond_style quartic command
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==========================
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bond_style quartic/omp command
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==============================
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Syntax
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""""""
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.. parsed-literal::
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bond_style quartic
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Examples
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""""""""
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.. parsed-literal::
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bond_style quartic
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bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
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Description
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"""""""""""
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The *quartic* bond style uses the potential
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.. image:: Eqs/bond_quartic.jpg
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:align: center
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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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:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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or :doc:`read_restart <read_restart>` 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)
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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 :doc:`bond_coeff <bond_coeff>` 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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:doc:`pair_style <pair_style>` command, whether the bond is broken or
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not. This means that :doc:`special_bonds <special_bonds>` 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 :doc:`dump local <dump>` command, bonds with type 0 are not included. The
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:doc:`delete_bonds <delete_bonds>` 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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.. parsed-literal::
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delete_bonds all stats
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delete_bonds all bond 0 remove
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----------
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Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` 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 :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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----------
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Restrictions
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""""""""""""
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This bond style can only be used if LAMMPS was built with the
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MOLECULE package (which it is by default). See the :ref:`Making LAMMPS <start_3>` section for more info on packages.
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The *quartic* style requires that :doc:`special_bonds <special_bonds>`
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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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""""""""""""""""
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:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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