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78 lines
3.6 KiB
Plaintext
78 lines
3.6 KiB
Plaintext
"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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Drude induced dipoles :h3
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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 "Howto polarizable"_Howto_polarizable.html 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 ("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. :ulb,l
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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. :l
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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). :l,ule
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A detailed tutorial covering the usage of Drude induced dipoles in
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LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page.
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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 "fix drude"_fix_drude.html 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 "read_data"_read_data.html command. If using "fix
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shake"_fix_shake.html, make sure no Drude particle is in this fix
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group.
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There are two ways to thermostat the Drude particles at a low
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temperature: use either "fix langevin/drude"_fix_langevin_drude.html
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for a Langevin thermostat, or "fix
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drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
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thermostat. The former requires use of the command "comm_modify vel
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yes"_comm_modify.html. The latter 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 "compute
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temp/drude"_compute_temp_drude.html. 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 "pair style
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thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
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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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:line
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:link(howto-Lamoureux)
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[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
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