221 lines
7.5 KiB
Plaintext
221 lines
7.5 KiB
Plaintext
.. index:: pair_style thole
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pair_style thole command
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========================
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pair_style lj/cut/thole/long command
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====================================
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pair_style lj/cut/thole/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 = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*thole* args = damp cutoff
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damp = global damping parameter
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cutoff = global cutoff (distance units)
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*lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
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damp = global damping parameter
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cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
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cutoff2 = global cutoff for Thole (optional) (distance units)
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Examples
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""""""""
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.. parsed-literal::
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pair_style hybrid/overlay ... thole 2.6 12.0
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pair_coeff 1 1 thole 1.0
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pair_coeff 1 2 thole 1.0 2.6 10.0
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pair_coeff * 2 thole 1.0 2.6
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.. parsed-literal::
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pair_style lj/cut/thole/long 2.6 12.0
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Description
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"""""""""""
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The *thole* pair styles are meant to be used with force fields that
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include explicit polarization through Drude dipoles. This link
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describes how to use the :doc:`thermalized Drude oscillator model <tutorial_drude>` in LAMMPS and polarizable models in LAMMPS
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are discussed in :ref:`this Section <howto_25>`.
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The *thole* pair style should be used as a sub-style within in the
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:doc:`pair_hybrid/overlay <pair_hybrid>` command, in conjunction with a
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main pair style including Coulomb interactions, i.e. any pair style
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containing *coul/cut* or *coul/long* in its style name.
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The *lj/cut/thole/long* pair style is equivalent to, but more convenient that
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the frequent combination *hybrid/overlay lj/cut/coul/long cutoff thole damp
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cutoff2*\ . It is not only a shorthand for this pair_style combination, but
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it also allows for mixing pair coefficients instead of listing them all.
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The *lj/cut/thole/long* pair style is also a bit faster because it avoids an
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overlay and can benefit from OMP acceleration. Moreover, it uses a more
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precise approximation of the direct Coulomb interaction at short range similar
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to :doc:`coul/long/cs <pair_coul_long_cs>`, which stabilizes the temperature of
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Drude particles.
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The *thole* pair styles compute the Coulomb interaction damped at
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short distances by a function
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.. math::
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\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
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\frac{s_{ij} r_{ij} }{2} \right)
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\exp \left( - s_{ij} r_{ij} \right) \end{equation}
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This function results from an adaptation to point charges
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:ref:`(Noskov) <Noskov>` of the dipole screening scheme originally proposed
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by :ref:`Thole <Thole>`. The scaling coefficient :math:`s_{ij}` is determined
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by the polarizability of the atoms, :math:`\alpha_i`, and by a Thole
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damping parameter :math:`a`. This Thole damping parameter usually takes
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a value of 2.6, but in certain force fields the value can depend upon
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the atom types. The mixing rule for Thole damping parameters is the
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arithmetic average, and for polarizabilities the geometric average
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between the atom-specific values.
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.. math::
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\begin{equation} s_{ij} = \frac{ a_{ij} }{
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(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
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[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}
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The damping function is only applied to the interactions between the
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point charges representing the induced dipoles on polarizable sites,
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that is, charges on Drude particles, :math:`q_{D,i}`, and opposite
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charges, :math:`-q_{D,i}`, located on the respective core particles
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(to which each Drude particle is bonded). Therefore, Thole screening
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is not applied to the full charge of the core particle :math:`q_i`, but
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only to the :math:`-q_{D,i}` part of it.
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The interactions between core charges are subject to the weighting
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factors set by the :doc:`special_bonds <special_bonds>` command. The
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interactions between Drude particles and core charges or
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non-polarizable atoms are also subject to these weighting factors. The
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Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
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their respective cores.
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For pair_style *thole*\ , the following coefficients must be defined for
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each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
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as in the example above.
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* alpha (distance units^3)
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* damp
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* cutoff (distance units)
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The last two coefficients are optional. If not specified the global
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Thole damping parameter or global cutoff specified in the pair_style
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command are used. In order to specify a cutoff (third argument) a damp
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parameter (second argument) must also be specified.
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For pair style *lj/cut/thole/long*\ , the following coefficients must be
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defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
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command.
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* epsilon (energy units)
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* sigma (length units)
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* alpha (distance units^3)
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* damps
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* LJ cutoff (distance units)
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The last two coefficients are optional and default to the global values from
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the *pair_style* command line.
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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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**Mixing**\ :
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The *thole* pair style does not support mixing. Thus, coefficients
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for all I,J pairs must be specified explicitly.
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The *lj/cut/thole/long* pair style does support mixing. Mixed coefficients
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are defined using
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.. math::
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\begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}
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.. math::
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\begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}
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Restrictions
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""""""""""""
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These pair styles are part of the USER-DRUDE package. They are only
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enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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This pair_style should currently not be used with the :doc:`charmm dihedral style <dihedral_charmm>` if the latter has non-zero 1-4 weighting
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factors. This is because the *thole* pair style does not know which
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pairs are 1-4 partners of which dihedrals.
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The *lj/cut/thole/long* pair style should be used with a :doc:`Kspace solver <kspace_style>`
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like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
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package.
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Related commands
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""""""""""""""""
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:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
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`pair_style lj/cut/coul/long <pair_lj_cut_coul_long>`_
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**Default:** none
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----------
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.. _Noskov:
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**(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
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.. _Thole:
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**(Thole)** Chem Phys, 59, 341 (1981).
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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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