65 lines
3.6 KiB
ReStructuredText
65 lines
3.6 KiB
ReStructuredText
Drude induced dipoles
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=====================
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The thermalized Drude model represents induced dipoles by a pair of
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charges (the core atom and the Drude particle) connected by a harmonic
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spring. See the :doc:`Howto polarizable <Howto_polarizable>` doc page
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for a discussion of all the polarizable models available in LAMMPS.
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The Drude model has a number of features aimed at its use in
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molecular systems (:ref:`Lamoureux and Roux <howto-Lamoureux>`):
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* Thermostatting of the additional degrees of freedom associated with the
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induced dipoles at very low temperature, in terms of the reduced
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coordinates of the Drude particles with respect to their cores. This
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makes the trajectory close to that of relaxed induced dipoles.
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* Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
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pair represents a single (polarizable) atom, so the special screening
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factors in a covalent structure should be the same for the core and
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the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
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special neighbor relations from their respective cores.
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* Stabilization of the interactions between induced dipoles. Drude
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dipoles on covalently bonded atoms interact too strongly due to the
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short distances, so an atom may capture the Drude particle of a
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neighbor, or the induced dipoles within the same molecule may align
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too much. To avoid this, damping at short range can be done by Thole
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functions (for which there are physical grounds). This Thole damping
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is applied to the point charges composing the induced dipole (the
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charge of the Drude particle and the opposite charge on the core, not
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to the total charge of the core atom).
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A detailed tutorial covering the usage of Drude induced dipoles in
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LAMMPS is on the :doc:`here <Howto_drude2>`.
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As with the core-shell model, the cores and Drude particles should
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appear in the data file as standard atoms. The same holds for the
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springs between them, which are described by standard harmonic bonds.
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The nature of the atoms (core, Drude particle or non-polarizable) is
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specified via the :doc:`fix drude <fix_drude>` command. The special
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list of neighbors is automatically refactored to account for the
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equivalence of core and Drude particles as regards special 1-2 to 1-4
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screening. It may be necessary to use the *extra/special/per/atom*
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keyword of the :doc:`read_data <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
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group.
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There are three ways to thermostat the Drude particles at a low
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temperature: use either :doc:`fix langevin/drude <fix_langevin_drude>`
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for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
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thermostat, or :doc:`fix tgnvt/drude <fix_tgnh_drude>` for a temperature-grouped Nose-Hoover thermostat.
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The first and third require use of the command :doc:`comm_modify vel yes <comm_modify>`. The second requires two separate integration
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fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
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degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
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command *comm_modify vel yes*.
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Short-range damping of the induced dipole interactions can be achieved
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using Thole functions through the :doc:`pair style thole <pair_thole>` in :doc:`pair_style hybrid/overlay <pair_hybrid>`
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with a Coulomb pair style. It may be useful to use *coul/long/cs* or
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similar from the CORESHELL package if the core and Drude particle come
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too close, which can cause numerical issues.
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----------
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.. _howto-Lamoureux:
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**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
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