add missing rst format doc file
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Axel Kohlmeyer
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doc/src/pair_mesocnt.rst
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doc/src/pair_mesocnt.rst
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.. index:: pair\_style mesocnt
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pair\_style mesocnt 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 mesocnt
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Examples
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""""""""
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.. parsed-literal::
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pair_style mesocnt
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pair_coeff \* \* 10_10.cnt
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Description
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"""""""""""
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Style *mesocnt* implements a mesoscopic potential
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for the interaction of carbon nanotubes (CNTs). In this potential,
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CNTs are modelled as chains of cylindrical segments in which
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each infinitesimal surface element interacts with all other
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CNT surface elements with the Lennard-Jones (LJ) term adopted from
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the :doc:`airebo <pair_airebo>` style. The interaction energy
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is then computed by integrating over the surfaces of all interacting
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CNTs.
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The potential is based on interactions between one cylindrical
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segment and infinitely or semi-infinitely long CNTs as described
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in :ref:`(Volkov1) <Volkov1>`. Chains of segments are
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converted to these (semi-)infinite CNTs bases on an approximate
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chain approach outlined in :ref:`(Volkov2) <Volkov2>`.
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This allows to simplify the computation of the interactions
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significantly and reduces the computational times to the
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same order of magnitude as for regular bead spring models
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where beads interact with the standard :doc:`pair\_lj/cut <pair_lj>`
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potential.
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In LAMMPS, cylindrical segments are represented by bonds. Each
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segment is defined by its two end points ("nodes") which correspond
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to atoms in LAMMPS. For the exact functional form of the potential
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and implementation details, the reader is referred to the
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original papers :ref:`(Volkov1) <Volkov1>` and
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:ref:`(Volkov2) <Volkov2>`.
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The potential requires tabulated data provided in a single ASCII
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text file specified in the :doc:`pair\_coeff <pair_coeff>` command.
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The first line of the file provides a time stamp and
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general information. The second line lists four integers giving
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the number of data points provided in the subsequent four
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data tables. The third line lists four floating point numbers:
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the CNT radius R, the LJ parameter sigma and two numerical
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parameters delta1 and delta2. These four parameters are given
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in Angstroms. This is followed by four data tables each separated
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by a single empty line. The first two tables have two columns
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and list the parameters uInfParallel and Gamma respectively.
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The last two tables have three columns giving data on a quadratic
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array and list the parameters Phi and uSemiParallel respectively.
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uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is
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given in eV and Gamma is unitless.
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Potential files for CNTs can be readily generated using the freely
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available code provided on
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https://github.com/phankl/cntpot
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Using the same approach, it should also be possible to
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generate potential files for other 1D systems such as
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boron nitride nanotubes.
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.. note::
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LAMMPS comes with one *mesocnt* style potential file
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where the default number of data points per table is 1001.
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This is sufficient for NVT simulations. For proper energy
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conservation, we recommend using a potential file where
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the resolution for Phi is at least 2001 data points.
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.. note::
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The *mesocnt* style requires CNTs to be represented
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as a chain of atoms connected by bonds. Atoms need
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to be numbered consecutively within one chain.
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Atoms belonging to different CNTs need to be assigned
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different molecule IDs.
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A full summary of the method and LAMMPS implementation details
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is expected to soon become available in Computer Physics
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Communications.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support mixing.
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This pair style does not support the :doc:`pair\_modify <pair_modify>`
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shift, table, and tail options.
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The mesocnt pair style do not write their information to :doc:`binary restart files <restart>`, since it is stored in tabulated potential files.
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Thus, you need to re-specify the pair\_style and pair\_coeff commands in
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an input script that reads a restart file.
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These pair style can only be used via the *pair* keyword of the
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:doc:`run\_style respa <run_style>` command. They do not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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The mesocnt pair style is part of the USER-MISC package. It is only
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enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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This pair potential requires the :doc:`newton <newton>` setting to be
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"on" for pair interactions.
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Related commands
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""""""""""""""""
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:doc:`pair\_coeff <pair_coeff>`
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**Default:** none
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----------
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.. _Volkov1:
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**(Volkov1)** Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
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.. _Volkov2:
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**(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts,
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Q31.013 (2008).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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