forked from lijiext/lammps
169 lines
4.4 KiB
Plaintext
169 lines
4.4 KiB
Plaintext
.. index:: pair_style list
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pair_style list 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 list listfile cutoff keyword
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* listfile = name of file with list of pairwise interactions
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* cutoff = global cutoff (distance units)
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* keyword = optional flag *nocheck* or *check* (default is *check*\ )
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Examples
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""""""""
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.. parsed-literal::
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pair_style list restraints.txt 200.0
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pair_coeff * *
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.. parsed-literal::
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pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff 3* 3* list
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Description
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"""""""""""
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Style *list* computes interactions between explicitly listed pairs of
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atoms with the option to select functional form and parameters for
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each individual pair. Because the parameters are set in the list
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file, the pair_coeff command has no parameters (but still needs to be
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provided). The *check* and *nocheck* keywords enable/disable a test
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that checks whether all listed bonds were present and computed.
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This pair style can be thought of as a hybrid between bonded,
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non-bonded, and restraint interactions. It will typically be used as
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an additional interaction within the *hybrid/overlay* pair style. It
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currently supports three interaction styles: a 12-6 Lennard-Jones, a
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Morse and a harmonic potential.
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The format of the list file is as follows:
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* one line per pair of atoms
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* empty lines will be ignored
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* comment text starts with a '#' character
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* line syntax: *ID1 ID2 style coeffs cutoff*
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.. parsed-literal::
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ID1 = atom ID of first atom
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ID2 = atom ID of second atom
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style = style of interaction
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coeffs = list of coeffs
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cutoff = cutoff for interaction (optional)
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The cutoff parameter is optional. If not specified, the global cutoff
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is used.
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Here is an example file:
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.. parsed-literal::
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# this is a comment
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.. parsed-literal::
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15 259 lj126 1.0 1.0 50.0
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15 603 morse 10.0 1.2 2.0 10.0 # and another comment
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18 470 harmonic 50.0 1.2 5.0
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The style *lj126* computes pairwise interactions with the formula
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.. image:: Eqs/pair_lj.jpg
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:align: center
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and the coefficients:
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* epsilon (energy units)
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* sigma (distance units)
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The style *morse* computes pairwise interactions with the formula
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.. image:: Eqs/pair_morse.jpg
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:align: center
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and the coefficients:
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* D0 (energy units)
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* alpha (1/distance units)
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* r0 (distance units)
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The style *harmonic* computes pairwise interactions with the formula
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.. image:: Eqs/bond_harmonic.jpg
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:align: center
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and the coefficients:
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* K (energy units)
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* r0 (distance units)
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Note that the usual 1/2 factor is included in K.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support mixing since all parameters are
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explicit for each pair.
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The :doc:`pair_modify <pair_modify>` shift option is supported by this
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pair style.
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The :doc:`pair_modify <pair_modify>` table and tail options are not
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relevant for this pair style.
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This pair style does not write its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
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to be specified in an input script that reads a restart file.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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This pair style does not use a neighbor list and instead identifies
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atoms by their IDs. This has two consequences: 1) The cutoff has to be
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chosen sufficiently large, so that the second atom of a pair has to be
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a ghost atom on the same node on which the first atom is local;
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otherwise the interaction will be skipped. You can use the *check*
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option to detect, if interactions are missing. 2) Unlike other pair
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styles in LAMMPS, an atom I will not interact with multiple images of
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atom J (assuming the images are within the cutoff distance), but only
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with the nearest image.
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This style is part of the USER-MISC package. It is only enabled if
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LAMMPS is build with that package. See the :ref:`Making of 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>`,
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:doc:`pair_style hybrid/overlay <pair_hybrid>`,
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:doc:`pair_style lj/cut <pair_lj>`,
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:doc:`pair_style morse <pair_morse>`,
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:doc:`bond_style harmonic <bond_harmonic>`
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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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