forked from lijiext/lammps
193 lines
6.0 KiB
Plaintext
193 lines
6.0 KiB
Plaintext
.. index:: pair_style lj/sdk
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pair_style lj/sdk command
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=========================
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pair_style lj/sdk/gpu command
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=============================
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pair_style lj/sdk/kk command
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============================
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pair_style lj/sdk/omp command
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=============================
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pair_style lj/sdk/coul/long command
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===================================
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pair_style lj/sdk/coul/long/gpu command
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=======================================
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pair_style lj/sdk/coul/long/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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pair_style style args
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* style = *lj/sdk* or *lj/sdk/coul/long*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*lj/sdk* args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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*lj/sdk/coul/long* args = cutoff (cutoff2)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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Examples
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""""""""
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.. parsed-literal::
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pair_style lj/sdk 2.5
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pair_coeff 1 1 lj12_6 1 1.1 2.8
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.. parsed-literal::
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pair_style lj/sdk/coul/long 10.0
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pair_style lj/sdk/coul/long 10.0 12.0
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pair_coeff 1 1 lj9_6 100.0 3.5 12.0
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Description
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"""""""""""
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The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
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given by
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.. image:: Eqs/pair_cmm.jpg
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:align: center
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as required for the SDK Coarse-grained MD parametrization discussed in
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:ref:`(Shinoda) <Shinoda>` and :ref:`(DeVane) <DeVane>`. Rc is the cutoff.
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Style *lj/sdk/coul/long* computes the adds Coulombic interactions
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with an additional damping factor applied so it can be used in
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conjunction with the :doc:`kspace_style <kspace_style>` command and
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its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff
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specified for this style means that pairwise interactions within
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this distance are computed directly; interactions outside that
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distance are computed in reciprocal space.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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above, or in the data file or restart files read by the
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands, or by mixing as described below:
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* cg_type (lj9_6, lj12_4, or lj12_6)
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* epsilon (energy units)
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* sigma (distance units)
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* cutoff1 (distance units)
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum. The prefactors
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are chosen so that the potential minimum is at -epsilon.
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The latter 2 coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair.
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For *lj/sdk/coul/long* only the LJ cutoff can be specified since a
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Coulombic cutoff cannot be specified for an individual I,J type pair.
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All type pairs use the same global Coulombic cutoff specified in the
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pair_style command.
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----------
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Styles with a *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 GPU, USER-INTEL, KOKKOS,
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USER-OMP, and OPT packages respectively. They are only enabled if
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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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**Mixing, shift, table, tail correction, restart, and rRESPA info**\ :
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
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since different pairs may have different exponents. So all parameters
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for all pairs have to be specified explicitly through the "pair_coeff"
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command. Defining then in a data file is also not supported, due to
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limitations of that file format.
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All of the lj/sdk pair styles support the
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:doc:`pair_modify <pair_modify>` shift option for the energy of the
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Lennard-Jones portion of the pair interaction.
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The *lj/sdk/coul/long* pair styles support the
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:doc:`pair_modify <pair_modify>` table option since they can tabulate
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the short-range portion of the long-range Coulombic interaction.
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All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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The lj/sdk and lj/cut/coul/long pair styles do not support
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the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command.
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----------
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Restrictions
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""""""""""""
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All of the lj/sdk pair styles are part of the USER-CG-CMM package.
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The *lj/sdk/coul/long* style also requires the KSPACE package to be
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built (which is enabled by default). They are only enabled if LAMMPS
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was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
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**Default:** none
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----------
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.. _Shinoda:
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**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
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.. _DeVane:
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**(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
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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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