107 lines
3.7 KiB
ReStructuredText
107 lines
3.7 KiB
ReStructuredText
.. index:: bond_style special
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bond_style special command
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=================================
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Syntax
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""""""
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.. code-block:: LAMMPS
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bond_style special
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Examples
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""""""""
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.. code-block:: LAMMPS
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bond_style special
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bond_coeff 0.5 0.5
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Description
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"""""""""""
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The *special* bond style can be used to create conceptual bonds which
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effectively impose weightings on the pairwise Lennard Jones and/or
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Coulombic interactions between selected pairs of particles in the
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system. The form of the pairwise interaction will be whatever is
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computed by the :doc:`pair_style <pair_style>` command defined for the
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system; this command defines the weightings for its two terms.
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This command can thus be useful to apply weightings that cannot be
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handled by the :doc:`special_bonds <special_bonds>` command, such as
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on 1-5 or 1-6 interactions. Or it can be used to add pairwise forces
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between one or more pairs of atoms that otherwise would not be include
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in the :doc:`pair_style <pair_style>` computation.
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The potential for this bond style has the form
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.. math::
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E = w_{LJ} E_{LJ} + w_{Coul} E_{Coul}
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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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* :math:`w_{LJ}` weight (0.0 to 1.0) on pairwise Lennard-Jones interactions
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* :math:`w_{Coul}` weight (0.0 to 1.0) on pairwise Coulombic interactions
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----------
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Normally this bond style should be used in conjunction with one (or
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more) other bond styles which compute forces between atoms directly
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bonded to each other in a molecule. This means the :doc:`bond_style
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hybrid <bond_hybrid>` command should be used with bond_style special
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as one of its sub-styles.
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Note that the same as for any other bond style, pairs of bonded atoms
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must be enumerated in the data file read by the :doc:`read_data
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<read_data>` command. Thus if this command is used to weight all 1-5
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interactions in the system, all the 1-5 pairs of atoms must be listed
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in the "Bonds" section of the data file.
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This bond style imposes strict requirements on settings made with the
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:doc:`special_bonds <special_bonds>` command. These requirements
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ensure that the new bonds created by this style do not create spurious
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1-2, 1-3, or 1-4 interactions within the molecular topology.
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Specifically 1-2 interactions must have weights of zero, 1-3
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interactions must either have weights of unity or :doc:`special_bonds
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angle yes <special_bonds>` must be used, and 1-4 interactions must
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have weights of unity or :doc:`special_bonds dihedral yes <special_bonds>`
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must be used.
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If this command is used to create bonded interactions between
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particles that are further apart than usual (e.g. 1-5 or 1-6
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interactions), this style may require an increase in the communication
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cutoff via the :doc:`comm_modify cutoff <comm_modify>` command. If
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LAMMPS cannot find a partner atom in a bond, an error will be issued.
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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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USER-MISC package. See the :doc:`Build package <Build_package>` doc
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page for more info.
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This bond style requires the use of a :doc:`pair_style <pair_style>` which
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computes a pairwise additive interaction and provides the ability to
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compute interactions for individual pairs of atoms. Manybody potentials
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are not compatible in general, but also some other pair styles are missing
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the required functionality and thus will cause an error.
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This command is not compatible with long-range Coulombic interactions. If a
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`kspace_style <kspace_style>` is declared, an error will be issued.
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Related commands
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""""""""""""""""
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:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
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**Default:** none
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