forked from lijiext/lammps
260 lines
9.8 KiB
Plaintext
260 lines
9.8 KiB
Plaintext
.. index:: pair_style resquared
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pair_style resquared command
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============================
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pair_style resquared/gpu command
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================================
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pair_style resquared/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 resquared cutoff
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* cutoff = global cutoff for interactions (distance units)
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Examples
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""""""""
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.. parsed-literal::
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pair_style resquared 10.0
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pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
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Description
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"""""""""""
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Style *resquared* computes the RE-squared anisotropic interaction
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:ref:`(Everaers) <Everaers>`, :ref:`(Babadi) <Babadi>` between pairs of
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ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
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interactions, the potential considers the ellipsoid as being comprised
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of small spheres of size sigma. LJ particles are a single sphere of
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size sigma. The distinction is made to allow the pair style to make
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efficient calculations of ellipsoid/solvent interactions.
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Details for the equations used are given in the references below and
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in `this supplementary document <PDF/pair_resquared_extra.pdf>`_.
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Use of this pair style requires the NVE, NVT, or NPT fixes with the
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*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
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order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid <atom_style>` should be used since it defines the
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rotational state and the size and shape of each ellipsoidal particle.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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above, or in the data file or restart files read by the
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands:
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* A12 = Energy Prefactor/Hamaker constant (energy units)
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* sigma = atomic interaction diameter (distance units)
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* epsilon_i_a = relative well depth of type I for side-to-side interactions
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* epsilon_i_b = relative well depth of type I for face-to-face interactions
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* epsilon_i_c = relative well depth of type I for end-to-end interactions
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* epsilon_j_a = relative well depth of type J for side-to-side interactions
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* epsilon_j_b = relative well depth of type J for face-to-face interactions
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* epsilon_j_c = relative well depth of type J for end-to-end interactions
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* cutoff (distance units)
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The parameters used depend on the type of the interacting particles,
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i.e. ellipsoids or LJ spheres. The type of a particle is determined
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by the diameters specified for its 3 shape paramters. If all 3 shape
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parameters = 0.0, then the particle is treated as an LJ sphere. The
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epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
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the 3 shape paraemters are > 0.0, then the particle is treated as an
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ellipsoid (even if the 3 parameters are equal to each other).
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A12 specifies the energy prefactor which depends on the types of the
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two interacting particles.
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For ellipsoid/ellipsoid interactions, the interaction is computed by
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the formulas in the supplementary docuement referenced above. A12 is
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the Hamaker constant as described in :ref:`(Everaers) <Everaers>`. In LJ
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units:
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.. image:: Eqs/pair_resquared.jpg
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:align: center
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where rho gives the number density of the spherical particles
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composing the ellipsoids and epsilon_LJ determines the interaction
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strength of the spherical particles.
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For ellipsoid/LJ sphere interactions, the interaction is also computed
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by the formulas in the supplementary docuement referenced above. A12
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has a modifed form (see `here <PDF/pair_resquared_extra.pdf>`_ for
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details):
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.. image:: Eqs/pair_resquared2.jpg
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:align: center
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For ellipsoid/LJ sphere interactions, a correction to the distance-
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of-closest approach equation has been implemented to reduce the error
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from two particles of disparate sizes; see `this supplementary document <PDF/pair_resquared_extra.pdf>`_.
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For LJ sphere/LJ sphere interactions, the interaction is computed
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using the standard Lennard-Jones formula, which is much cheaper to
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compute than the ellipsoidal formulas. A12 is used as epsilon in the
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standard LJ formula:
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.. image:: Eqs/pair_resquared3.jpg
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:align: center
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and the specified *sigma* is used as the sigma in the standard LJ
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formula.
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When one of both of the interacting particles are ellipsoids, then
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*sigma* specifies the diameter of the continuous distribution of
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constituent particles within each ellipsoid used to model the
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RE-squared potential. Note that this is a different meaning for
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*sigma* than the :doc:`pair_style gayberne <pair_gayberne>` potential
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uses.
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The epsilon_i and epsilon_j coefficients are defined for atom types,
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not for pairs of atom types. Thus, in a series of pair_coeff
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commands, they only need to be specified once for each atom type.
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Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
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non-zero, the three values are assigned to atom type I. If all the
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epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
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epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
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to atom type J. If all three epsilon_i values are zero, they are
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ignored. Thus the typical way to define the epsilon_i and epsilon_j
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coefficients is to list their values in "pair_coeff I J" commands when
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I = J, but set them to 0.0 when I != J. If you do list them when I !=
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J, you should insure they are consistent with their values in other
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pair_coeff commands.
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Note that if this potential is being used as a sub-style of
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:doc:`pair_style hybrid <pair_hybrid>`, and there is no "pair_coeff I I"
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setting made for RE-squared for a particular type I (because I-I
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interactions are computed by another hybrid pair potential), then you
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still need to insure the epsilon a,b,c coefficients are assigned to
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that type in a "pair_coeff I J" command.
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For large uniform molecules it has been shown that the epsilon_*_*
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energy parameters are approximately representable in terms of local
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contact curvatures :ref:`(Everaers) <Everaers>`:
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.. image:: Eqs/pair_resquared4.jpg
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:align: center
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where a, b, and c give the particle diameters.
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The last coefficient is optional. If not specified, the global cutoff
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specified in the pair_style command is used.
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----------
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Styles with a *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 GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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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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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance can be mixed, but only for sphere pairs. The
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default mix value is *geometric*\ . See the "pair_modify" command for
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details. Other type pairs cannot be mixed, due to the different
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meanings of the energy prefactors used to calculate the interactions
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and the implicit dependence of the ellipsoid-sphere interaction on the
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equation for the Hamaker constant presented here. Mixing of sigma and
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epsilon followed by calculation of the energy prefactors using the
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equations above is recommended.
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This pair styles supports the :doc:`pair_modify <pair_modify>` shift
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option for the energy of the Lennard-Jones portion of the pair
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interaction, but only for sphere-sphere interactions. There is no
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shifting performed for ellipsoidal interactions due to the anisotropic
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dependence of the interaction.
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The :doc:`pair_modify <pair_modify>` table option is not relevant
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for this pair style.
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This pair style does not support the :doc:`pair_modify <pair_modify>`
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tail option for adding long-range tail corrections to energy and
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pressure.
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This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not 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 of the :doc:`run_style command <run_style>`.
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----------
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Restrictions
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""""""""""""
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This style is part of the ASPHERE package. It is only enabled if
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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This pair style requires that atoms be ellipsoids as defined by the
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:doc:`atom_style ellipsoid <atom_style>` command.
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Particles acted on by the potential can be finite-size aspherical or
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spherical particles, or point particles. Spherical particles have all
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3 of their shape parameters equal to each other. Point particles have
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all 3 of their shape parameters equal to 0.0.
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The distance-of-closest-approach approximation used by LAMMPS becomes
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less accurate when high-aspect ratio ellipsoids are used.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
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:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair_style gayberne <pair_gayberne>`
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**Default:** none
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----------
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.. _Everaers:
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**(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
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.. _Babadi:
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**(Berardi)** Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
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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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