This commit is contained in:
Axel Kohlmeyer
2022-08-30 14:42:54 -04:00
parent 46fa86a1e0
commit 85965f01ce
6 changed files with 26 additions and 23 deletions

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@ -1556,9 +1556,9 @@ MESONT package
**Contents:** **Contents:**
MESONT is a LAMMPS package for simulation of nanomechanics of MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
nanotubes (NTs). The model is based on a coarse-grained representation (NTs). The model is based on a coarse-grained representation of NTs as
of NTs as "flexible cylinders" consisting of a variable number of "flexible cylinders" consisting of a variable number of
segments. Internal interactions within a NT and the van der Waals segments. Internal interactions within a NT and the van der Waals
interaction between the tubes are described by a mesoscopic force field interaction between the tubes are described by a mesoscopic force field
designed and parameterized based on the results of atomic-level designed and parameterized based on the results of atomic-level
@ -1566,26 +1566,28 @@ molecular dynamics simulations. The description of the force field is
provided in the papers listed below. provided in the papers listed below.
This package contains two independent implementations of this model: This package contains two independent implementations of this model:
:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original implemention :doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
of the model based on a Fortran library in the ``lib/mesont`` folder. The implementation of the model based on a Fortran library in the
second implementation is given by the mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`, ``lib/mesont`` folder. The second implementation is provided by the
:doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt <pair_mesocnt>`). mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`,
The mesocnt implemenation has the same features as the original implementation with the :doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt
addition of friction, <pair_mesocnt>`). The mesocnt implementation has the same features as
but is directly implemented in C++, interfaces more cleanly with general LAMMPS the original implementation with the addition of friction, but is
functionality and is typically faster. It also doesn't require its own atom style directly implemented in C++, interfaces more cleanly with general LAMMPS
and can be installed without any external libraries. functionality, and is typically faster. It also does not require its own
atom style and can be installed without any external libraries.
**Download of potential files:** **Download of potential files:**
The potential files for these pair styles are *very* large and thus The potential files for these pair styles are *very* large and thus are
are not included in the regular downloaded packages of LAMMPS or the not included in the regular downloaded packages of LAMMPS or the git
git repositories. Instead, they will be automatically downloaded repositories. Instead, they will be automatically downloaded from a web
from a web server when the package is installed for the first time. server when the package is installed for the first time.
**Authors of the *mesont* styles:** **Authors of the *mesont* styles:**
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia) Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* styles:** **Author of the *mesocnt* styles:**
Philipp Kloza (U Cambridge) Philipp Kloza (U Cambridge)

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@ -40,7 +40,7 @@ the harmonic and linear regime respectively and :math:`\Delta
\theta_\text{B}` is the buckling angle. Note that the usual 1/2 factor \theta_\text{B}` is the buckling angle. Note that the usual 1/2 factor
for the harmonic potential is included in :math:`K_\text{H}`. for the harmonic potential is included in :math:`K_\text{H}`.
The style implements parametrisation presets of :math:`K_\text{H}`, The style implements parameterization presets of :math:`K_\text{H}`,
:math:`K_\text{B}` and :math:`\Delta \theta_\text{B}` for mesoscopic :math:`K_\text{B}` and :math:`\Delta \theta_\text{B}` for mesoscopic
simulations of carbon nanotubes based on the atomistic simulations of simulations of carbon nanotubes based on the atomistic simulations of
:ref:`(Srivastava) <Srivastava_2>` and buckling considerations of :ref:`(Srivastava) <Srivastava_2>` and buckling considerations of
@ -68,14 +68,14 @@ Preset *C* is for carbon nanotubes, and the additional parameters are:
Here, :math:`r_0` is the equilibrium distance of the bonds included in Here, :math:`r_0` is the equilibrium distance of the bonds included in
the angle, see :doc:`bond_style mesocnt <bond_mesocnt>`. the angle, see :doc:`bond_style mesocnt <bond_mesocnt>`.
In harmonic mode with preset *custom*, the additional paramter is: In harmonic mode with preset *custom*, the additional parameter is:
* :math:`K_\text{H}` (energy) * :math:`K_\text{H}` (energy)
Hence, this setting is simply a wrapper for :doc:`bond_style harmonic Hence, this setting is simply a wrapper for :doc:`bond_style harmonic
<bond_harmonic>` with an equilibrium angle of 180 degrees. <bond_harmonic>` with an equilibrium angle of 180 degrees.
In harmonic mode with preset *custom*, the additional paramters are: In harmonic mode with preset *custom*, the additional parameters are:
* :math:`K_\text{H}` (energy) * :math:`K_\text{H}` (energy)
* :math:`K_\text{B}` (energy) * :math:`K_\text{B}` (energy)

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@ -31,7 +31,7 @@ The *mesocnt* bond style is a wrapper for the :doc:`harmonic
where :math:`r_0` is the equilibrium bond distance. Note that the where :math:`r_0` is the equilibrium bond distance. Note that the
usual 1/2 factor is included in :math:`K`. The style implements usual 1/2 factor is included in :math:`K`. The style implements
parametrisation presets of :math:`K` for mesoscopic simulations of parameterization presets of :math:`K` for mesoscopic simulations of
carbon nanotubes based on the atomistic simulations of carbon nanotubes based on the atomistic simulations of
:ref:`(Srivastava) <Srivastava_1>`. :ref:`(Srivastava) <Srivastava_1>`.

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@ -95,7 +95,7 @@ accelerated styles exist.
* :doc:`harmonic <bond_harmonic>` - harmonic bond * :doc:`harmonic <bond_harmonic>` - harmonic bond
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff * :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
* :doc:`mesocnt <bond_mesocnt>` - Harmonic bond wrapper with parametrisation presets for nanotubes * :doc:`mesocnt <bond_mesocnt>` - Harmonic bond wrapper with parameterization presets for nanotubes
* :doc:`mm3 <bond_mm3>` - MM3 anharmonic bond * :doc:`mm3 <bond_mm3>` - MM3 anharmonic bond
* :doc:`morse <bond_morse>` - Morse bond * :doc:`morse <bond_morse>` - Morse bond
* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond * :doc:`nonlinear <bond_nonlinear>` - nonlinear bond

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@ -97,7 +97,7 @@ shifted logistic function:
---------- ----------
In the pair_style command, the modes described above can be toggeled In the pair_style command, the modes described above can be toggled
using the *segment* or *chain* keywords. The neighbor list cutoff using the *segment* or *chain* keywords. The neighbor list cutoff
defines the cutoff within which atoms are included in the neighbor defines the cutoff within which atoms are included in the neighbor
list for constructing neighboring CNT chains. This is different from list for constructing neighboring CNT chains. This is different from

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@ -2249,6 +2249,7 @@ nanoparticles
nanotube nanotube
Nanotube Nanotube
nanotubes nanotubes
nanowires
Narulkar Narulkar
nasa nasa
nasr nasr