diff --git a/doc/src/pair_mesocnt.txt b/doc/src/pair_mesocnt.txt new file mode 100644 index 0000000000..29c1ff2b1c --- /dev/null +++ b/doc/src/pair_mesocnt.txt @@ -0,0 +1,132 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style mesocnt command :h3 + +[Syntax:] + +pair_style mesocnt :pre + +[Examples:] + +pair_style mesocnt +pair_coeff * * 10_10.cnt :pre + +[Description:] + +Style {mesocnt} implements a mesoscopic potential +for the interaction of carbon nanotubes (CNTs). In this potential, +CNTs are modelled as chains of cylindrical segments in which +each infinitesimal surface element interacts with all other +CNT surface elements with the Lennard-Jones (LJ) term adopted from +the "airebo"_pair_airebo.html style. The interation energy +is then computed by integrating over the surfaces of all interacting +CNTs. + +The potential is based on interactions between one cylindrical +segment and infinitely or semi-infinitely long CNTs as described +in "(Volkov1)"_#Volkov1. Chains of segments are +converted to these (semi-)infinite CNTs bases on an approximate +chain approach outlined in "(Volkov2)"_#Volkov2. +This allows to simplify the computation of the interactions +significantly and reduces the computational times to the +same order of magnitude as for regular bead spring models +where beads interact with the standard "pair_lj/cut"_pair_lj.html +potential. + +In LAMMPS, cylindrical segments are represented by bonds. Each +segment is defined by its two end points ("nodes") which correspond +to atoms in LAMMPS. For the exact functional form of the potential +and implementation details, the reader is referred to the +original papers "(Volkov1)"_#Volkov1 and +"(Volkov2)"_#Volkov2. + +The potential requires tabulated data provided in a single ASCII +text file specified in the "pair_coeff"_pair_coeff.html command. +The first line of the file provides a time stamp and +general information. The second line lists four integers giving +the number of data points provided in the subsequent four +data tables. The third line lists four floating point numbers: +the CNT radius R, the LJ parameter sigma and two numerical +parameters delta1 and delta2. These four parameters are given +in Angstroms. This is followed by four data tables each separated +by a single empty line. The first two tables have two columns +and list the parameters uInfParallel and Gamma respectively. +The last two tables have three columns giving data on a quadratic +array and list the parameters Phi and uSemiParallel respectively. +uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is +given in eV and Gamma is unitless. + +Potential files for CNTs can be readily generated using the freely +available code provided on + +https://github.com/phankl/cntpot + +Using the same approach, it should also be possible to +generate potential files for other 1D systems such as +boron nitride nanotubes. + +NOTE: LAMMPS comes with one {mesocnt} style potential file +where the default number of data points per table is 1001. +This is sufficient for NVT simulations. For proper energy +conservation, we recommend using a potential file where +the resolution for Phi is at least 2001 data points. + +NOTE: The {mesocnt} style requires CNTs to be represented +as a chain of atoms connected by bonds. Atoms need +to be numbered consecutively within one chain. +Atoms belonging to different CNTs need to be assigned +different molecule IDs. + +A full summary of the method and LAMMPS implementation details +are expected to soon become available in Computer Physics +Communications. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support mixing. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +The mesocnt pair style do not write their information to "binary restart +files"_restart.html, since it is stored in tabulated potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in +an input script that reads a restart file. + +These pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. They do not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +The mesocnt style is part of the USER-MESOCNT package. It is only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This pair potential requires the "newton"_newton.html setting to be +"on" for pair interactions. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Volkov1) +[(Volkov1)] Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010). + +:link(Volkov2) +[(Volkov2)] Volkov, Simov and Zhigilei, APS Meeting Abstracts, +Q31.013 (2008). diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 2f63f18bad..eeba837855 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -72,6 +72,7 @@ Pair Styles :h1 pair_meam_spline pair_meam_sw_spline pair_meso + pair_mesocnt pair_mgpt pair_mie pair_mm3_switch3_coulgauss diff --git a/src/USER-MESOCNT/pair_mesocnt.cpp b/src/USER-MESOCNT/pair_mesocnt.cpp index 3bb8c48f28..92beac0186 100644 --- a/src/USER-MESOCNT/pair_mesocnt.cpp +++ b/src/USER-MESOCNT/pair_mesocnt.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing author: Philipp Kloza (University of Cambridge) + pak37@cam.ac.uk ------------------------------------------------------------------------- */ #include