forked from lijiext/lammps
update documentation to rst format and integrate into lists/tables
This commit is contained in:
Axel Kohlmeyer
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2f1e3d8490
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97bcce77d3
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@ -174,6 +174,7 @@ OPT.
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* :doc:`meam/c <pair_meamc>`
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* :doc:`meam/spline (o) <pair_meam_spline>`
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* :doc:`meam/sw/spline <pair_meam_sw_spline>`
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* :doc:`mesocnt <pair_mesocnt>`
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* :doc:`mgpt <pair_mgpt>`
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* :doc:`mie/cut (g) <pair_mie>`
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
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@ -257,4 +258,3 @@ OPT.
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* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
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* :doc:`zbl (gko) <pair_zbl>`
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*
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*
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@ -1,132 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS 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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pair_style mesocnt command :h3
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[Syntax:]
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pair_style mesocnt :pre
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[Examples:]
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pair_style mesocnt
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pair_coeff * * 10_10.cnt :pre
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[Description:]
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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 "airebo"_pair_airebo.html 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 "(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 "(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 "pair_lj/cut"_pair_lj.html
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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 "(Volkov1)"_#Volkov1 and
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"(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 "pair_coeff"_pair_coeff.html 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: 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: 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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:line
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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 "pair_modify"_pair_modify.html
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shift, table, and tail options.
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The mesocnt pair style do not write their information to "binary restart
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files"_restart.html, 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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"run_style respa"_run_style.html command. They do not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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The mesocnt style is part of the USER-MESOCNT package. It is only
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enabled if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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This pair potential requires the "newton"_newton.html setting to be
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"on" for pair interactions.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Volkov1)
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[(Volkov1)] Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
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:link(Volkov2)
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[(Volkov2)] Volkov, Simov and Zhigilei, APS Meeting Abstracts,
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Q31.013 (2008).
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@ -244,6 +244,7 @@ accelerated styles exist.
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* :doc:`meam/c <pair_meamc>` - modified embedded atom method (MEAM) in C
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* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
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* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
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* :doc:`mesocnt <pair_mesocnt>` - mesoscale model for (carbon) nanotubes
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* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
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* :doc:`mie/cut <pair_mie>` - Mie potential
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
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