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Stan Moore
2019-05-16 12:31:26 -06:00
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doc/src/Commands_all.txt
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@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neb/spin"_neb_spin.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,

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doc/src/Commands_category.txt
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@ -116,6 +116,7 @@ Actions:
"minimize"_minimize.html,
"neb"_neb.html,
"neb_spin"_neb_spin.html,
"prd"_prd.html,
"rerun"_rerun.html,
"run"_run.html,

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doc/src/Commands_fix.txt
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@ -107,6 +107,7 @@ OPT.
"mvv/edpd"_fix_mvv_dpd.html,
"mvv/tdpd"_fix_mvv_dpd.html,
"neb"_fix_neb.html,
"neb_spin"_fix_neb_spin.html,
"nph (ko)"_fix_nh.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/body"_fix_nph_body.html,

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doc/src/Commands_pair.txt
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@ -80,6 +80,8 @@ OPT.
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
"dpd/tstat (go)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"e3b"_pair_e3b.html,
"drip"_pair_drip.html,
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,

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@ -0,0 +1,15 @@
\documentclass[12pt]{article}
\usepackage{amsmath}
\begin{document}
\begin{align*}
E =& E_2 \sum_{i,j}e^{-k_2 r_{ij}} + E_A \sum_{\substack{i,j,k,\ell \\\in \textrm{type A}}} f(r_{ij})f(r_{k\ell}) + E_B \sum_{\substack{i,j,k,\ell \\\in \textrm{type B}}} f(r_{ij})f(r_{k\ell}) + E_C \sum_{\substack{i,j,k,\ell \\\in \textrm{type C}}} f(r_{ij})f(r_{k\ell}) \\
f(r) =& e^{-k_3 r}s(r) \\
s(r) =& \begin{cases}
1 & r<R_s \\
\displaystyle\frac{(R_f-r)^2(R_f-3R_s+2r)}{(R_f-R_s)^3} & R_s\leq r\leq R_f \\
0 & r>R_f\\
\end{cases}
\end{align*}
\end{document}

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\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath,amssymb,amsthm,bm}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
\Big[
\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
+K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/neb_spin_angle.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\omega_i^{\nu} =
(\nu - 1) \Delta \omega_i
{\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/neb_spin_k.tex Normal file
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@ -0,0 +1,16 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\vec{k}_i =
\frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I
\times \vec{m}_i^F\right|}
%&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

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@ -0,0 +1,16 @@
\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
+ (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
+ (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
\vec{m}_i^{I})
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

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@ -0,0 +1,14 @@
\documentclass[12pt]{article}
\usepackage{amsmath}
\usepackage{bm}
\begin{document}
\begin{eqnarray*}
E &=& \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} \phi_{ij} \\\phi_{ij} &=& f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] \\
\end{eqnarray*}
\end{document}

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doc/src/Eqs/pair_mdf-6.tex
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@ -1,9 +1,9 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}}
E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}}
$$
\end{document}

2
doc/src/Examples.txt
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@ -11,7 +11,7 @@ Section"_Tools.html :c
Example scripts :h3
The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
sample problems. Many are 2d models that run quickly and are
straightforward to visualize, requiring at most a couple of minutes to
run on a desktop machine. Each problem has an input script (in.*) and
produces a log file (log.*) when it runs. Some use a data file

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doc/src/Howto_bioFF.txt
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@ -56,7 +56,7 @@ COMPASS is a general force field for atomistic simulation of common
organic molecules, inorganic small molecules, and polymers which was
developed using ab initio and empirical parameterization techniques.
See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA’s Materials Studio
LAMMPS template input and data files from BIOVIA's Materials Studio
files. Please note that the msi2lmp tool is very old and largely
unmaintained, so it does not support all features of Materials Studio
provided force field files, especially additions during the last decade.
@ -129,7 +129,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(howto-Sun)
[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998).
[(Sun)] Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909

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doc/src/Howto_diffusion.txt
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@ -29,3 +29,5 @@ diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the "fix vector"_fix_vector.html command,
and time integrated via the "variable trap"_variable.html function,
and thus extract D.
:line

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doc/src/Howto_drude2.txt
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@ -274,7 +274,7 @@ crash. Even without reaching this extreme case, the correlation
between nearby dipoles on the same molecule may be exaggerated. Often,
special bond relations prevent bonded neighboring atoms to see the
charge of each other's DP, so that the problem does not always appear.
It is possible to use screened dipole dipole interactions by using the
It is possible to use screened dipole-dipole interactions by using the
"{pair_style thole}"_pair_thole.html. This is implemented as a
correction to the Coulomb pair_styles, which dampens at short distance
the interactions between the charges representing the induced dipoles.

1
doc/src/Howto_replica.txt
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@ -17,6 +17,7 @@ periodically.
These are the relevant commands:
"neb"_neb.html for nudged elastic band calculations
"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
"prd"_prd.html for parallel replica dynamics
"tad"_tad.html for temperature accelerated dynamics
"temper"_temper.html for parallel tempering

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doc/src/Howto_spins.txt
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@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Magnetic spins :h3
The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
implementation is detailed in "Tranchida"_#Tranchida.
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
@ -36,13 +36,28 @@ A Langevin thermostat can be applied to those magnetic spins using
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
can be coupled to another Langevin thermostat applied to the atoms
using "fix langevin"_fix_langevin.html in order to simulate
thermostatted spin-lattice system.
thermostatted spin-lattice systems.
The magnetic Gilbert damping can also be applied using "fix
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
The command "fix setforce/spin"_fix_setforce.html allows to set the
components of the magnetic precession vectors (while erasing and
replacing the previously computed magnetic precession vectors on
the atom).
This command can be used to freeze the magnetic moment of certain
atoms in the simulation by zeroing their precession vector.
The command "fix nve/spin"_fix_nve_spin.html can be used to
perform a symplectic integration of the combined dynamics of spins
and atomic motions.
The minimization style "min/spin"_min_spin.html can be applied
to the spins to perform a minimization of the spin configuration.
All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
@ -54,6 +69,6 @@ magnetic spin, or the magnetic force acting on this spin.
:line
:link(Tranchida7)
:link(Tranchida)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
arXiv preprint arXiv:1801.10233, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

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doc/src/Install_git.txt
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@ -52,7 +52,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
typing "make html" from the doc directory.
After initial cloning, as bug fixes and new features are added to
LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

2
doc/src/Install_svn.txt
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@ -40,7 +40,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
typing "make html" from the doc directory.
After initial checkout, as bug fixes and new features are added to
LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="29 Mar 2019 version">
<META NAME="docnumber" CONTENT="15 May 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
29 Mar 2019 version :c,h2
15 May 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

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doc/src/Packages_details.txt
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@ -706,7 +706,7 @@ PERI package :link(PKG-PERI),h4
An atom style, several pair styles which implement different
Peridynamics materials models, and several computes which calculate
diagnostics. Peridynamics is a a particle-based meshless continuum
diagnostics. Peridynamics is a particle-based meshless continuum
model.
[Authors:] The original package was created by Mike Parks (Sandia).
@ -905,7 +905,7 @@ SPIN package :link(PKG-SPIN),h4
Model atomic magnetic spins classically, coupled to atoms moving in
the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
[Author:] Julien Tranchida (Sandia).
[Supporting info:]
@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
"fix nve/spin"_fix_nve_spin.html
"fix precession/spin"_fix_precession_spin.html
"compute spin"_compute_spin.html
"neb/spin"_neb_spin.html
examples/SPIN :ul
:line
@ -1228,7 +1229,7 @@ isothermal, isoenergetic, isobaric and isenthalpic conditions are
included. These enable long timesteps via the Shardlow splitting
algorithm.
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
Brennan (ARL).
[Supporting info:]
@ -1536,7 +1537,7 @@ USER-MESO package :link(PKG-USER-MESO),h4
[Contents:]
Several extensions of the the dissipative particle dynamics (DPD)
Several extensions of the dissipative particle dynamics (DPD)
method. Specifically, energy-conserving DPD (eDPD) that can model
non-isothermal processes, many-body DPD (mDPD) for simulating
vapor-liquid coexistence, and transport DPD (tDPD) for modeling

2
doc/src/Python_library.txt
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@ -180,7 +180,7 @@ doubles is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
The get_thermo() method returns returns the current value of a thermo
The get_thermo() method returns the current value of a thermo
keyword as a float.
The get_natoms() method returns the total number of atoms in the

2
doc/src/Run_options.txt
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@ -242,7 +242,7 @@ processors.
Running with multiple partitions can be useful for running
"multi-replica simulations"_Howto_replica.html, where each replica
runs on on one or a few processors. Note that with MPI installed on a
runs on one or a few processors. Note that with MPI installed on a
machine (e.g. your desktop), you can run on more (virtual) processors
than you have physical processors.

2
doc/src/Run_output.txt
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@ -93,7 +93,7 @@ monitor thread utilization and load balance is provided. A new {Thread
timings} section is also added, which lists the time spent in reducing
the per-thread data elements to the storage for non-threaded
computation. These thread timings are measured for the first MPI rank
only and and thus, because the breakdown for MPI tasks can change from
only and thus, because the breakdown for MPI tasks can change from
MPI rank to MPI rank, this breakdown can be very different for
individual ranks. Here is an example output for this section:

15
doc/src/Tools.txt
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@ -77,6 +77,7 @@ Post-processing tools :h3
"python"_#pythontools,
"reax"_#reax_tool,
"smd"_#smd,
"spin"_#spin,
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
Miscellaneous tools :h3
@ -511,6 +512,20 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
spin tool :h4,link(spin)
The spin sub-directory contains a C file interpolate.c which can
be compiled and used to perform a cubic polynomial interpolation of
the MEP following a GNEB calculation.
See the README file in tools/spin/interpolate_gneb for more details.
This tool was written by the SPIN package author, Julien
Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
Ivanov, at University of Iceland (ali5 at hi.is).
:line
vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor

1
doc/src/commands_list.txt
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@ -67,6 +67,7 @@ Commands :h1
minimize
molecule
neb
neb_spin
neigh_modify
neighbor
newton

2
doc/src/compute_chunk_atom.txt
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@ -468,7 +468,7 @@ property/chunk"_compute_property_chunk.html command.
NOTE: The compression operation requires global communication across
all processors to share their chunk ID values. It can require large
memory on every processor to store them, even after they are
compressed, if there are are a large number of unique chunk IDs with
compressed, if there are a large number of unique chunk IDs with
atoms assigned to them. It uses a STL map to find unique chunk IDs
and store them in sorted order. Each time an atom is assigned a
compressed chunk ID, it must access the STL map. All of this means

2
doc/src/compute_chunk_spread_atom.txt
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@ -49,7 +49,7 @@ For inputs that are computes, they must be a compute that calculates
per-chunk values. These are computes whose style names end in
"/chunk".
For inputs that are fixes, they should be a a fix that calculates
For inputs that are fixes, they should be a fix that calculates
per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or
"fix ave/time"_fix_ave_time.html (assuming it is time-averaging
per-chunk data).

2
doc/src/compute_voronoi_atom.txt
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@ -96,7 +96,7 @@ group. The argument {maxedge} of the this keyword is the largest number
of edges on a single Voronoi cell face expected to occur in the
sample. This keyword adds the generation of a global vector with
{maxedge}+1 entries. The last entry in the vector contains the number of
faces with with more than {maxedge} edges. Since the polygon with the
faces with more than {maxedge} edges. Since the polygon with the
smallest amount of edges is a triangle, entries 1 and 2 of the vector
will always be zero.

2
doc/src/dihedral_spherical.txt
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@ -47,7 +47,7 @@ division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the Dihedral Coeffs section of a data file file read by the
the Dihedral Coeffs section of a data file read by the
"read_data"_read_data.html command:
n (integer >= 1)

2
doc/src/dihedral_table_cut.txt
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@ -174,7 +174,7 @@ radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the the {Ntable} different entries in the
the user to save all of the {Ntable} different entries in the
interpolated energy table to a file to make sure that the interpolated
function agrees with the user's expectations. (Note: You can
temporarily increase the {Ntable} parameter to a high value for this

6
doc/src/dump.txt
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@ -21,7 +21,7 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
@ -196,7 +196,7 @@ For post-processing purposes the {atom}, {local}, and {custom} text
files are self-describing in the following sense.
The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:
For an orthogonal simulation box this information is formatted as:
ITEM: BOX BOUNDS xx yy zz
xlo xhi
@ -619,7 +619,7 @@ should be replaced by the actual name of the variable that has been
defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
values. Variables of style {atom} can reference individual atom
attributes, per-atom atom attributes, thermodynamic keywords, or
attributes, per-atom attributes, thermodynamic keywords, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.

2
doc/src/dump_modify.txt
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@ -310,7 +310,7 @@ NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte
signed integers, depending on how LAMMPS was compiled. When
specifying the {format int} option you can use a "%d"-style format
identifier in the format string and LAMMPS will convert this to the
corresponding 8-byte form it it is needed when outputting those
corresponding 8-byte form if it is needed when outputting those
values. However, when specifying the {line} option or {format M
string} option for those values, you should specify a format string
appropriate for an 8-byte signed integer, e.g. one with "%ld", if

22
doc/src/fix.txt
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@ -321,20 +321,16 @@ accelerated styles exist.
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
"rhok"_fix_rhok.html -
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
"rigid/nph/small"_fix_rigid.html -
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
"rigid/npt/small"_fix_rigid.html -
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nve/small"_fix_rigid.html -
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
"rigid/nvt/small"_fix_rigid.html -
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom

2
doc/src/fix_ave_chunk.txt
View File

@ -361,7 +361,7 @@ computes that calculate a temperature to see which ones implement a
bias.
The {adof} and {cdof} keywords define the values used in the degree of
freedom (DOF) formula described above for for temperature calculation
freedom (DOF) formula described above for temperature calculation
for each chunk. They are only used when the {temp} value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples:

10
doc/src/fix_colvars.txt
View File

@ -98,6 +98,16 @@ fix to add the energy change from the biasing force added by the fix
to the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The {fix_modify configfile <config file>} option allows to add settings
from an additional config file to the colvars module. This option can
only be used, after the system has been initialized with a "run"_run.html
command.
The {fix_modify config <quoted string>} option allows to add settings
from inline strings. Those have to fit on a single line when enclosed
in a pair of double quotes ("), or can span multiple lines when bracketed
by a pair of triple double quotes (""", like python embedded documentation).
This fix computes a global scalar which can be accessed by various
"output commands"_Howto_output.html. The scalar is the cumulative
energy change due to this fix. The scalar value calculated by this

11
doc/src/fix_halt.txt
View File

@ -113,12 +113,11 @@ state of the system, e.g. via a "write_dump"_write_dump.html or
"write_restart"_write_restart.html command.
If its value is {continue}, the behavior is the same as for {soft},
except subsequent subsequent "run"_run.html or
"minimize"_minimize.html commands are executed. This allows your
script to remedy the condition that triggered the halt, if necessary.
Note that you may wish use the "unfix"_unfix.html command on the fix
halt ID, so that the same condition is not immediately triggered in a
subsequent run.
except subsequent "run"_run.html or "minimize"_minimize.html commands
are executed. This allows your script to remedy the condition that
triggered the halt, if necessary. Note that you may wish use the
"unfix"_unfix.html command on the fix halt ID, so that the same
condition is not immediately triggered in a subsequent run.
The optional {message} keyword determines whether a message is printed
to the screen and logfile when the halt condition is triggered. If

2
doc/src/fix_hyper_global.txt
View File

@ -188,7 +188,7 @@ No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of the bias potential to the the system's
fix to add the energy of the bias potential to the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and global vector of length 12, which

6
doc/src/fix_hyper_local.txt
View File

@ -301,7 +301,7 @@ No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of the bias potential to the the system's
fix to add the energy of the bias potential to the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and global vector of length 21,
@ -322,13 +322,13 @@ vector stores the following quantities:
9 = fraction of biased bonds with negative strain during this run
10 = average bias coeff for all bonds during this run (unitless)
11 = min bias coeff for any bond during this run (unitless)
12 = max bias coeff for any bond during this run (unitless)
12 = max bias coeff for any bond during this run (unitless) :ul
13 = max drift distance of any bond atom during this run (distance units)
14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
16 = count of ghost atoms that could not be found on reneighbor steps during this run
17 = count of bias overlaps (< Dcut) found during this run
17 = count of bias overlaps (< Dcut) found during this run :ul
18 = cumulative hyper time since fix created (time units)
19 = cumulative count of event timesteps since fix created

2
doc/src/fix_langevin_spin.txt
View File

@ -99,4 +99,4 @@ integration fix (e.g. {fix nve/spin}).
:link(Tranchida2)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

6
doc/src/fix_neb.txt
View File

@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
units.
With a value of {ideal}, the spring force is computed as suggested in
"(WeinenE)"_#WeinenE :
"(WeinanE)"_#WeinanE :
Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
:link(WeinenE)
[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
:link(WeinanE)
[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
:link(Jonsson)
[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

76
doc/src/fix_neb_spin.txt Normal file
View File

@ -0,0 +1,76 @@
"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
fix neb/spin command :h3
[Syntax:]
fix ID group-ID neb/spin Kspring :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
neb/spin = style name of this fix command :l
Kspring = spring constant for parallel nudging force
(force/distance units or force units, see parallel keyword) :pre,ule
[Examples:]
fix 1 active neb/spin 1.0
[Description:]
Add nudging forces to spins in the group for a multi-replica
simulation run via the "neb/spin"_neb_spin.html command to perform a
geodesic nudged elastic band (GNEB) calculation for finding the
transition state.
Hi-level explanations of GNEB are given with the
"neb/spin"_neb_spin.html command and on the
"Howto replica"_Howto_replica.html doc page.
The fix neb/spin command must be used with the "neb/spin" command and
defines how inter-replica nudging forces are computed. A GNEB
calculation is divided in two stages. In the first stage n replicas
are relaxed toward a MEP until convergence. In the second stage, the
climbing image scheme is enabled, so that the replica having the highest
energy relaxes toward the saddle point (i.e. the point of highest energy
along the MEP), and a second relaxation is performed.
The nudging forces are calculated as explained in
"(BessarabB)"_#BessarabB).
See this reference for more explanation about their expression.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
as invoked by the "minimize"_minimize.html command via the
"neb/spin"_neb_spin.html command.
[Restrictions:]
This command can only be used if LAMMPS was built with the SPIN
package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"neb_spin"_neb_spin.html
[Default:]
none
:line
:link(BessarabB)
[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
335-347 (2015).

2
doc/src/fix_nve_spin.txt
View File

@ -73,4 +73,4 @@ instead of "array" is also valid.
:link(Tranchida1)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

41
doc/src/fix_precession_spin.txt
View File

@ -14,24 +14,28 @@ fix ID group precession/spin style args :pre
ID, group are documented in "fix"_fix.html command :ulb,l
precession/spin = style name of this fix command :l
style = {zeeman} or {anisotropy} :l
style = {zeeman} or {anisotropy} or {cubic} :l
{zeeman} args = H x y z
H = intensity of the magnetic field (in Tesla)
x y z = vector direction of the field
{anisotropy} args = K x y z
K = intensity of the magnetic anisotropy (in eV)
x y z = vector direction of the anisotropy :pre
{cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
K1 and K2c = intensity of the magnetic anisotropy (in eV)
n1x to n3z = three direction vectors of the cubic anisotropy :pre
:ule
[Examples:]
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0
fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
[Description:]
Impose a force torque to each magnetic spin in the group.
This fix applies a precession torque to each magnetic spin in the group.
Style {zeeman} is used for the simulation of the interaction
between the magnetic spins in the defined group and an external
@ -50,10 +54,29 @@ for the magnetic spins in the defined group:
with n defining the direction of the anisotropy, and K (in eV) its intensity.
If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
In both cases, the choice of (x y z) imposes the vector direction for the force.
Only the direction of the vector is important; it's length is ignored.
Style {cubic} is used to simulate a cubic anisotropy, with three
possible easy axis for the magnetic spins in the defined group:
Both styles can be combined within one single command line.
:c,image(Eqs/fix_spin_cubic.jpg)
with K1 and K2c (in eV) the intensity coefficients and
n1, n2 and n3 defining the three anisotropic directions
defined by the command (from n1x to n3z).
For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
iron type anisotropy (easy axis along the (001)-type cube
edges), and K1 > 0 defines a nickel type anisotropy (easy axis
along the (111)-type cube diagonals).
K2^c > 0 also defines easy axis along the (111)-type cube
diagonals.
See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
anisotropies.
In all cases, the choice of (x y z) only imposes the vector
directions for the forces. Only the direction of the vector is
important; it's length is ignored (the entered vectors are
normalized).
Those styles can be combined within one single command line.
:line
@ -85,3 +108,9 @@ package"_Build_package.html doc page for more info.
"atom_style spin"_atom_style.html
[Default:] none
:line
:link(Skomski1)
[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
Oxford University Press.

17
doc/src/fix_print.txt
View File

@ -14,7 +14,7 @@ fix ID group-ID print N string keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
print = style name of this fix command :l
N = print every N steps :l
N = print every N steps; N can be a variable (see below) :l
string = text string to print with optional variable names :l
zero or more keyword/value pairs may be appended :l
keyword = {file} or {append} or {screen} or {title} :l
@ -40,6 +40,21 @@ If it contains variables it must be enclosed in double quotes to
insure they are not evaluated when the input script line is read, but
will instead be evaluated each time the string is printed.
Instead of a numeric value, N can be specified as an "equal-style
variable"_variable.html, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the [next] timestep at which the
string will be written out. On that timestep, the variable will be
evaluated again to determine the next timestep, etc.
Thus the variable should return timestep values. See the stagger()
and logfreq() and stride() math functions for "equal-style
variables"_variable.html, as examples of useful functions to use in
this context. For example, the following commands will print output at
timesteps 10,20,30,100,200,300,1000,2000,etc:
variable s equal logfreq(10,3,10)
fix extra all print v_s "Coords of marker atom = $x $y $z" :pre
The specified group-ID is ignored by this fix.
See the "variable"_variable.html command for a description of {equal}

20
doc/src/fix_setforce.txt
View File

@ -8,6 +8,7 @@
fix setforce command :h3
fix setforce/kk command :h3
fix setforce/spin command :h3
[Syntax:]
@ -27,6 +28,7 @@ keyword = {region} :l
fix freeze indenter setforce 0.0 0.0 0.0
fix 2 edge setforce NULL 0.0 0.0
fix 1 edge setforce/spin 0.0 0.0 0.0
fix 2 edge setforce NULL 0.0 v_oscillate :pre
[Description:]
@ -65,6 +67,19 @@ to it.
:line
Style {spin} suffix sets the components of the magnetic precession
vectors instead of the mechanical forces. This also erases all
previously computed magnetic precession vectors on the atom, though
additional magnetic fixes could add new forces.
This command can be used to freeze the magnetic moment of certain
atoms in the simulation by zeroing their precession vector.
All options defined above remain valid, they just apply to the magnetic
precession vectors instead of the forces.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -117,7 +132,10 @@ forces to any value besides zero when performing a minimization. Use
the "fix addforce"_fix_addforce.html command if you want to apply a
non-zero force to atoms during a minimization.
[Restrictions:] none
[Restrictions:]
The fix {setforce/spin} only makes sense when LAMMPS was built with the
SPIN package.
[Related commands:]

22
doc/src/fix_wall_gran.txt
View File

@ -17,13 +17,13 @@ wall/gran = style name of this fix command :l
fstyle = style of force interactions between particles and wall :l
possible choices: hooke, hooke/history, hertz/history, granular :pre
fstyle_params = parameters associated with force interaction style :l
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
args = list of arguments for a particular style :l
@ -46,10 +46,10 @@ keyword = {wiggle} or {shear} :l
fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
[Description:]

22
doc/src/fix_wall_gran_region.txt
View File

@ -17,23 +17,23 @@ wall/region = style name of this fix command :l
fstyle = style of force interactions between particles and wall :l
possible choices: hooke, hooke/history, hertz/history, granular :pre
fstyle_params = parameters associated with force interaction style :l
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
dampflag = 0 or 1 if tangential damping force is excluded or included :pre
For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
region-ID = region whose boundary will act as wall :l,ule
[Examples:]
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
[Description:]

1
doc/src/fixes.txt
View File

@ -84,6 +84,7 @@ Fixes :h1
fix_msst
fix_mvv_dpd
fix_neb
fix_neb_spin
fix_nh
fix_nh_eff
fix_nh_uef

4
doc/src/lammps.book
View File

@ -179,6 +179,7 @@ min_spin.html
minimize.html
molecule.html
neb.html
neb_spin.html
neigh_modify.html
neighbor.html
newton.html
@ -309,6 +310,7 @@ fix_mscg.html
fix_msst.html
fix_mvv_dpd.html
fix_neb.html
fix_neb_spin.html
fix_nh.html
fix_nh_eff.html
fix_nph_asphere.html
@ -572,6 +574,8 @@ pair_dipole.html
pair_dpd.html
pair_dpd_fdt.html
pair_dsmc.html
pair_e3b.html
pair_drip.html
pair_eam.html
pair_edip.html
pair_eff.html

2
doc/src/lattice.txt
View File

@ -124,7 +124,7 @@ so that they describe a tilted parallelepiped. Via the {basis}
keyword you add atoms, one at a time, to the unit cell. Its arguments
are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector
x of a basis atom within the unit cell is thus a linear combination of
the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
where bx,by,bz are the 3 values specified for the {basis} keyword.
:line

2
doc/src/molecule.txt
View File

@ -396,7 +396,7 @@ If flag = 0, no a,b,c,d values are listed on the line, just the
If flag = 1, a,b,c are listed, where a = ID of central atom in the
angle, and b,c the other two atoms in the angle.
If flag = 2, a,b are listed, where a = ID of atom in bond with the the
If flag = 2, a,b are listed, where a = ID of atom in bond with the
lowest ID, and b = ID of atom in bond with the highest ID.
If flag = 3, a,b,c are listed, where a = ID of central atom,

375
doc/src/neb_spin.txt Normal file
View File

@ -0,0 +1,375 @@
"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
neb/spin command :h3
[Syntax:]
neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
etol = stopping tolerance for energy (energy units) :ulb,l
ttol = stopping tolerance for torque ( units) :l
N1 = max # of iterations (timesteps) to run initial NEB :l
N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
Nevery = print replica energies and reaction coordinates every this many timesteps :l
file-style = {final} or {each} or {none} :l
{final} arg = filename
filename = file with initial coords for final replica
coords for intermediate replicas are linearly interpolated
between first and last replica
{each} arg = filename
filename = unique filename for each replica (except first)
with its initial coords
{none} arg = no argument all replicas assumed to already have
their initial coords :pre
keyword = {verbose}
:ule
[Examples:]
neb/spin 0.1 0.0 1000 500 50 final coords.final
neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
neb/spin 0.0 0.001 1000 500 50 none verbose :pre
[Description:]
Perform a geodesic nudged elastic band (GNEB) calculation using multiple
replicas of a system. Two or more replicas must be used; the first
and last are the end points of the transition path.
GNEB is a method for finding both the spin configurations and height
of the energy barrier associated with a transition state, e.g.
spins to perform a collective rotation from one energy basin to
another.
The implementation in LAMMPS follows the discussion in the
following paper: "(BessarabA)"_#BessarabA.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the "-partition command-line
switch"_Run_options.html. Note that if you have MPI installed, you
can run a multi-replica simulation with more replicas (partitions)
than you have physical processors, e.g you can run a 10-replica
simulation on just one or two processors. You will simply not get the
performance speed-up you would see with one or more physical
processors per replica. See the "Howto replica"_Howto_replica.html
doc page for further discussion.
NOTE: As explained below, a GNEB calculation performs a damped dynamics
minimization across all the replicas. The "spin"_min_spin.html
style minimizer has to be defined in your input script.
When a GNEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this.
I.e. the simulation domain, the number of magnetic atoms, the
interaction potentials, and the starting configuration when the neb
command is issued should be the same for every replica.
In a GNEB calculation each replica is connected to other replicas by
inter-replica nudging forces. These forces are imposed by the "fix
neb/spin"_fix_neb_spin.html command, which must be used in conjunction
with the neb command.
The group used to define the fix neb/spin command defines the
GNEB magnetic atoms which are the only ones that inter-replica springs
are applied to.
If the group does not include all magnetic atoms, then non-GNEB
magnetic atoms have no inter-replica springs and the torques they feel
and their precession motion is computed in the usual way due only
to other magnetic atoms within their replica.
Conceptually, the non-GNEB atoms provide a background force field for
the GNEB atoms.
Their magnetic spins can be allowed to evolve during the GNEB
minimization procedure.
The initial spin configuration for each of the replicas can be
specified in different manners via the {file-style} setting, as
discussed below. Only atomic spins whose initial coordinates should
differ from the current configuration need to be specified.
Conceptually, the initial and final configurations for the first
replica should be states on either side of an energy barrier.
As explained below, the initial configurations of intermediate
replicas can be spin coordinates interpolated in a linear fashion
between the first and last replicas. This is often adequate for
simple transitions. For more complex transitions, it may lead to slow
convergence or even bad results if the minimum energy path (MEP, see
below) of states over the barrier cannot be correctly converged to
from such an initial path. In this case, you will want to generate
initial states for the intermediate replicas that are geometrically
closer to the MEP and read them in.
:line
For a {file-style} setting of {final}, a filename is specified which
contains atomic and spin coordinates for zero or more atoms, in the
format described below.
For each atom that appears in the file, the new coordinates are
assigned to that atom in the final replica. Each intermediate replica
also assigns a new spin to that atom in an interpolated manner.
This is done by using the current direction of the spin at the starting
point and the read-in direction as the final point.
The "angular distance" between them is calculated, and the new direction
is assigned to be a fraction of the angular distance.
NOTE: The "angular distance" between the starting and final point is
evaluated in the geodesic sense, as described in
"(BessarabA)"_#BessarabA.
NOTE: The angular interpolation between the starting and final point
is achieved using Rodrigues formula:
:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
where m_i^I is the initial spin configuration for the spin i,
omega_i^nu is a rotation angle defined as:
:c,image(Eqs/neb_spin_angle.jpg)
with nu the image number, Q the total number of images, and
omega_i the total rotation between the initial and final spins.
k_i defines a rotation axis such as:
:c,image(Eqs/neb_spin_k.jpg)
if the initial and final spins are not aligned.
If the initial and final spins are aligned, then their cross
product is null, and the expression above does not apply.
If they point toward the same direction, the intermediate images
conserve the same orientation.
If the initial and final spins are aligned, but point toward
opposite directions, an arbitrary rotation vector belonging to
the plane perpendicular to initial and final spins is chosen.
In this case, a warning message is displayed.
For a {file-style} setting of {each}, a filename is specified which is
assumed to be unique to each replica.
See the "neb"_neb.html documentation page for more information about this
option.
For a {file-style} setting of {none}, no filename is specified. Each
replica is assumed to already be in its initial configuration at the
time the neb command is issued. This allows each replica to define
its own configuration by reading a replica-specific data or restart or
dump file, via the "read_data"_read_data.html,
"read_restart"_read_restart.html, or "read_dump"_read_dump.html
commands. The replica-specific names of these files can be specified
as in the discussion above for the {each} file-style. Also see the
section below for how a NEB calculation can produce restart files, so
that a long calculation can be restarted if needed.
NOTE: None of the {file-style} settings change the initial
configuration of any atom in the first replica. The first replica
must thus be in the correct initial configuration at the time the neb
command is issued.
:line
A NEB calculation proceeds in two stages, each of which is a
minimization procedure, performed via damped dynamics. To enable
this, you must first define a damped spin dynamics
"min_style"_min_style.html, using the {spin} style (see
"min_spin"_min_spin.html for more information).
The other styles cannot be used, since they relax the lattice
degrees of freedom instead of the spins.
The minimizer tolerances for energy and force are set by {etol} and
{ttol}, the same as for the "minimize"_minimize.html command.
A non-zero {etol} means that the GNEB calculation will terminate if the
energy criterion is met by every replica. The energies being compared
to {etol} do not include any contribution from the inter-replica
nudging forces, since these are non-conservative. A non-zero {ttol}
means that the GNEB calculation will terminate if the torque criterion
is met by every replica. The torques being compared to {ttol} include
the inter-replica nudging forces.
The maximum number of iterations in each stage is set by {N1} and
{N2}. These are effectively timestep counts since each iteration of
damped dynamics is like a single timestep in a dynamics
"run"_run.html. During both stages, the potential energy of each
replica and its normalized distance along the reaction path (reaction
coordinate RD) will be printed to the screen and log file every
{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
For intermediate replicas, it is the cumulative angular distance
(normalized by the total cumulative angular distance) between adjacent
replicas, where "distance" is defined as the length of the 3N-vector of
the geodesic distances in spin coordinates, with N the number of
GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
These outputs allow you to monitor NEB's progress in
finding a good energy barrier. {N1} and {N2} must both be multiples
of {Nevery}.
In the first stage of GNEB, the set of replicas should converge toward
a minimum energy path (MEP) of conformational states that transition
over a barrier. The MEP for a transition is defined as a sequence of
3N-dimensional spin states, each of which has a potential energy
gradient parallel to the MEP itself.
The configuration of highest energy along a MEP corresponds to a saddle
point. The replica states will also be roughly equally spaced along
the MEP due to the inter-replica nudging force added by the
"fix neb"_fix_neb.html command.
In the second stage of GNEB, the replica with the highest energy is
selected and the inter-replica forces on it are converted to a force
that drives its spin coordinates to the top or saddle point of the
barrier, via the barrier-climbing calculation described in
"(BessarabA)"_#BessarabA. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.
When both stages are complete, if the GNEB calculation was successful,
the configurations of the replicas should be along (close to) the MEP
and the replica with the highest energy should be a spin
configuration at (close to) the saddle point of the transition. The
potential energies for the set of replicas represents the energy
profile of the transition along the MEP.
:line
An atom map must be defined which it is not by default for "atom_style
atomic"_atom_style.html problems. The "atom_modify
map"_atom_modify.html command can be used to do this.
An initial value can be defined for the timestep. Although, the {spin}
minimization algorithm is an adaptive timestep methodology, so that
this timestep is likely to evolve during the calculation.
The minimizers in LAMMPS operate on all spins in your system, even
non-GNEB atoms, as defined above.
:line
Each file read by the neb/spin command containing spin coordinates used
to initialize one or more replicas must be formatted as follows.
The file can be ASCII text or a gzipped text file (detected by a .gz
suffix). The file can contain initial blank lines or comment lines
starting with "#" which are ignored. The first non-blank, non-comment
line should list N = the number of lines to follow. The N successive
lines contain the following information:
ID1 g1 x1 y1 z1 sx1 sy1 sz1
ID2 g2 x2 y2 z2 sx2 sy2 sz2
...
IDN gN yN zN sxN syN szN :pre
The fields are the atom ID, the norm of the associated magnetic spin,
followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
The lines can be listed in any order. Additional trailing information on
the line is OK, such as a comment.
Note that for a typical GNEB calculation you do not need to specify
initial spin coordinates for very many atoms to produce differing starting
and final replicas whose intermediate replicas will converge to the
energy barrier. Typically only new spin coordinates for atoms
geometrically near the barrier need be specified.
Also note there is no requirement that the atoms in the file
correspond to the GNEB atoms in the group defined by the "fix
neb"_fix_neb.html command. Not every GNEB atom need be in the file,
and non-GNEB atoms can be listed in the file.
:line
Four kinds of output can be generated during a GNEB calculation: energy
barrier statistics, thermodynamic output by each replica, dump files,
and restart files.
When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file
contains a line of output, printed once every {Nevery} timesteps. It
contains the timestep, the maximum torque per replica, the maximum
torque per atom (in any replica), potential gradients in the initial,
final, and climbing replicas, the forward and backward energy
barriers, the total reaction coordinate (RDT), and the normalized
reaction coordinate and potential energy of each replica.
The "maximum torque per replica" is the two-norm of the
3N-length vector given by the cross product of a spin by its
precession vector omega, in each replica, maximized across replicas,
which is what the {ttol} setting is checking against. In this case, N is
all the atoms in each replica. The "maximum torque per atom" is the
maximum torque component of any atom in any replica. The potential
gradients are the two-norm of the 3N-length magnetic precession vector
solely due to the interaction potential i.e. without adding in
inter-replica forces, and projected along the path tangent (as detailed
in Appendix D of "(BessarabA)"_#BessarabA).
The "reaction coordinate" (RD) for each replica is the two-norm of the
3N-length vector of geodesic distances between its spins and the preceding
replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to
the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
the RD of the final replica RDN = RDT, the total reaction coordinate.
The normalized RDs are divided by RDT, so that they form a monotonically
increasing sequence from zero to one. When computing RD, N only includes
the spins being operated on by the fix neb/spin command.
The forward (reverse) energy barrier is the potential energy of the
highest replica minus the energy of the first (last) replica.
Supplementary information for all replicas can be printed out to the
screen and master log.lammps file by adding the verbose keyword. This
information include the following.
The "GradVidottan" are the projections of the potential gradient for
the replica i on its tangent vector (as detailed in Appendix D of
"(BessarabA)"_#BessarabA).
The "DNi" are the non normalized geodesic distances (see equation (13)
of "(BessarabA)"_#BessarabA), between a replica i and the next replica
i+1. For the last replica, this distance is not defined and a "NAN"
value is the corresponding output.
When a NEB calculation does not converge properly, the supplementary
information can help understanding what is going wrong.
When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
GNEB calculation, these contain the thermodynamic output for each
replica.
If "dump"_dump.html commands in the input script define a filename
that includes a {universe} or {uloop} style "variable"_variable.html,
then one dump file (per dump command) will be created for each
replica. At the end of the GNEB calculation, the final snapshot in
each file will contain the sequence of snapshots that transition the
system over the energy barrier. Earlier snapshots will show the
convergence of the replicas to the MEP.
Likewise, "restart"_restart.html filenames can be specified with a
{universe} or {uloop} style "variable"_variable.html, to generate
restart files for each replica. These may be useful if the GNEB
calculation fails to converge properly to the MEP, and you wish to
restart the calculation from an intermediate point with altered
parameters.
A c file script in provided in the tool/spin/interpolate_gneb
directory, that interpolates the MEP given the information provided
by the verbose output option (as detailed in Appendix D of
"(BessarabA)"_#BessarabA).
:line
[Restrictions:]
This command can only be used if LAMMPS was built with the SPIN
package. See the "Build package"_Build_package.html doc
page for more info.
:line
[Related commands:]
"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html
[Default:]
none
:line
:link(BessarabA)
[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
335-347 (2015).

6
doc/src/neigh_modify.txt
View File

@ -187,9 +187,9 @@ used in neighbor list construction to sort and find neighboring atoms.
By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins
that are 1/2 the size of the maximum pair cutoff. For "neighbor style
multi"_neighbor.html, the bins are 1/2 the size of the minimum pair
cutoff. Typically these are good values values for minimizing the
time for neighbor list construction. This setting overrides the
default. If you make it too big, there is little overhead due to
cutoff. Typically these are good values for minimizing the time for
neighbor list construction. This setting overrides the default.
If you make it too big, there is little overhead due to
looping over bins, but more atoms are checked. If you make it too
small, the optimal number of atoms is checked, but bin overhead goes
up. If you set the binsize to 0.0, LAMMPS will use the default

2
doc/src/neighbor.txt
View File

@ -56,7 +56,7 @@ bin size is set to 1/2 of the shortest cutoff distance and multiple
sets of bins are defined to search over for different atom types.
This imposes some extra setup overhead, but the searches themselves
may be much faster for the short-cutoff cases. See the "comm_modify
mode multi"_comm_modify.html command for a communication option option
mode multi"_comm_modify.html command for a communication option
that may also be beneficial for simulations of this kind.
The "neigh_modify"_neigh_modify.html command has additional options

2
doc/src/package.txt
View File

@ -638,7 +638,7 @@ except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
Phi co-processor support. These settings are made automatically if the
"-sf intel" "command-line switch"_Run_options.html is used. If it is
not used, you must invoke the package intel command in your input
script or or via the "-pk intel" "command-line
script or via the "-pk intel" "command-line
switch"_Run_options.html.
For the KOKKOS package, the option defaults for GPUs are neigh = full,

17
doc/src/pair_airebo.txt
View File

@ -36,7 +36,7 @@ pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C :pre
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C :pre
pair_coeff * * ../potentials/CH.rebo H C :pre
[Description:]
@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
initial AIREBO; it is just a subset of the potential energy terms.
initial AIREBO; it is just a subset of the potential energy terms
with a few slightly different parameters
The AIREBO potential consists of three terms:
@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations.
:line
Only a single pair_coeff command is used with the {airebo}, {airebo}
or {rebo} style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the {rebo} style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N additional arguments after the
filename in the pair_coeff command, where N is the number of LAMMPS
atom types:
or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential
file with parameters for C and H. Note that as of LAMMPS version
15 May 2019 the {rebo} style in LAMMPS uses its own potential
file (CH.rebo). These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of AIREBO elements to atom types :ul

141
doc/src/pair_drip.txt Normal file
View File

@ -0,0 +1,141 @@
"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 drip command :h3
[Syntax:]
pair_style hybrid/overlay drip \[styles ...\] :pre
styles = other styles to be overlayed with drip (optional) :ul
[Examples:]
pair_style hybrid/overlay drip
pair_coeff * * none
pair_coeff * * drip C.drip C :pre
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.airebo C :pre
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H :pre
[Description:]
Style {drip} computes the interlayer interactions of layered materials using
the dihedral-angle-corrected registry-dependent (DRIP) potential as described
in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005
potential and provides an improved prediction for forces.
The total potential energy of a system is
:c,image(Eqs/pair_drip.jpg)
where the {r^-6} term models the attractive London dispersion,
the exponential term is designed to capture the registry effect due to
overlapping {pi} bonds, and {fc} is a cutoff function.
This potential (DRIP) only provides the interlayer interactions between
graphene layers. So, to perform a realistic simulation, it should be used in
combination with an intralayer potential such as "REBO"_pair_airebo.html and
"Tersoff"_pair_tersoff.html.
To keep the intralayer interactions unaffected, we should avoid applying DRIP
to contribute energy to intralayer interactions. This can be achieved by
assigning different molecular IDs to atoms in different layers, and DRIP is
implemented such that only atoms with different molecular ID can interact with
each other. For this purpose, "atom style"_atom_style.html "molecular" or
"full" has to be used.
On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html
or any other potential used to provide the intralayer interactions) should not
interfere with the interlayer interactions described by DRIP. This is typically
automatically achieved using the commands provided in the {Examples} section
above, since the cutoff distance for carbon-carbon interaction in the intralayer
potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than
the equilibrium layer distance of graphene layers (about 3.4 Angstrom).
If you want, you can enforce this by assigning different atom types to atoms in
different layers, and apply an intralayer potential to one atom type.
See "pair_hybrid"_pair_hybrid.html for details.
:line
The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where
{N} is the number of LAMMPS atom types. The fist three arguments must be fixed
to be {* * drip}, the fourth argument is the path to the DRIP parameter file,
and the remaining N arguments specifying the mapping between element in the
parameter file and atom types. For example, if your LAMMPS simulation has 3 atom
types and you want all of them to be C, you would use the following pair_coeff
command:
pair_coeff * * drip C.drip C C C :pre
If a mapping value is specified as NULL, the mapping is not performed. This
could be useful when DRIP is used to model part of the system where other
element exists. Suppose you have a hydrocarbon system, with C of atom type 1
and H of atom type 2, you can use the following command to inform DRIP not to
model H atoms:
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H :pre
NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with
LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an
additional parameter "normal_cutoff", specific to the LAMMPS implementation, is
used to find the three nearest neighbors of an atom to construct the normal.
:line
[Mixing, shift, table, tail correction, and restart info]:
This pair style does not support the pair_modify mix, shift, table,
and tail options.
This pair style does not write their information to binary restart files, since
it is stored in potential files. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.
[Restrictions:]
This pair style is part of the USER-MISC 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.
The {C.drip} parameter file provided with LAMMPS (see the "potentials"
directory) is parameterized for metal "units"_units.html. You can use the DRIP
potential with any LAMMPS units, but you would need to create your own custom
parameter file with coefficients listed in the appropriate units, if your
simulation doesn't use "metal" units.
[Related commands:]
"pair_style lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
:line
:link(Wen2018)
[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
98, 235404 (2018)
:link(Kolmogorov2005)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

140
doc/src/pair_e3b.txt Normal file
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@ -0,0 +1,140 @@
"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 e3b command :h3
[Syntax:]
pair_style e3b Otype :pre
Otype = atom type for oxygen :l
pair_coeff * * keyword :pre
one or more keyword/value pairs must be appended. :l
keyword = {preset} or {Ea} or {Eb} or {Ec} or {E2} or {K3} or {K2} or {Rs} or {Rc3} or {Rc2} or {bondL} or {neigh} :l
If the {preset} keyword is given, no others are needed.
Otherwise, all are mandatory except for {neigh}.
The {neigh} keyword is always optional. :l
{preset} arg = {2011} or {2015} = which set of predefined parameters to use
2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
{Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units)
{Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units)
{Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units)
{E2} arg = two-body energy correction (energy units)
{K3} arg = three-body exponential constant (inverse distance units)
{K2} arg = two-body exponential constant (inverse distance units)
{Rc3} arg = three-body cutoff (distance units)
{Rc2} arg = two-body cutoff (distance units)
{Rs} arg = three-body switching function cutoff (distance units)
{bondL} arg = intramolecular OH bond length (distance units)
{neigh} arg = approximate integer number of molecules within Rc3 of an oxygen atom :pre
[Examples:]
pair_style e3b 1
pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 :pre
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
pair_coeff * * e3b preset 2011 :pre
[Description:]
The {e3b} style computes an \"explicit three-body\" (E3B) potential for water "(Kumar 2008)"_#Kumar.
:c,image(Eqs/e3b.jpg)
This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
To use it in this way, it must be applied in conjunction with a conventional two-body water model, through {pair_style hybrid/overlay}.
The three body interactions are split into three types: A, B, and C.
Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
See "(Kumar 2008)"_#Kumar for more details.
Only a single {pair_coeff} command is used with the {e3b} style.
The 1st two arguments must be * *.
The oxygen atom type for the pair style is passed as the only argument to the {pair_style} command, not in the {pair_coeff} command.
The hydrogen atom type is inferred by the ordering of the atoms.
NOTE: Every atom of type Otype must be part of a water molecule.
Each water molecule must have consecutive IDs with the oxygen first.
This pair style does not test that this criteria is met.
The {pair_coeff} command must have at least one keyword/value pair, as described above.
The {preset} keyword sets the potential parameters to the values used in "(Tainter 2011)"_#Tainter2011 or "(Tainter 2015)"_#Tainter2015.
To use the water models defined in those references, the {e3b} style should always be used in conjunction with an {lj/cut/tip4p/long} style through {pair_style hybrid/overlay}, as demonstrated in the second example above.
The {preset 2011} option should be used with the "TIP4P water model"_Howto_tip4p.html.
The {preset 2015} option should be used with the "TIP4P/2005 water model"_Howto_tip4p.html.
If the {preset} keyword is used, no other keyword is needed.
Changes to the preset parameters can be made by specifying the {preset} keyword followed by the specific parameter to change, like {Ea}.
Note that the other keywords must come after {preset} in the pair_style command.
The {e3b} style can also be used to implement any three-body potential of the same form by specifying all the keywords except {neigh}: {Ea}, {Eb}, {Ec}, {E2}, {K3}, {K2}, {Rc3}, {Rc2}, {Rs}, and {bondL}.
The keyword {bondL} specifies the intramolecular OH bond length of the water model being used.
This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
This estimate defaults to 10 and can be changed using the {neigh} keyword, which takes an integer as an argument.
If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
If the neigh setting is too large, the pair style will use more memory than necessary.
This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the "compute pair"_compute_pair.html command as a vector of values of length 4.
The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
See the examples/USER/e3b directory for a complete example script.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style is incompatible with "respa"_run_style.html.
:line
[Restrictions:]
This pair style is part of the USER-MISC 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 style requires the "newton"_newton.html setting to be "on"
for pair interactions.
This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like "fix deposit"_fix_deposit.html.
If the number of atoms changes between runs, this pair style must be re-initialized by calling the {pair_style} and {pair_coeffs} commands.
This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms.
The {preset} keyword currently only works with real, metal, si, and cgs "units"_units.html.
[Related commands:]
"pair_coeff"_pair_coeff.html, "compute pair"_compute_pair.html
[Default:]
The option default for the {neigh} keyword is 10.
:line
:link(Kumar)
[(Kumar)] Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
:link(Tainter2011)
[(Tainter 2011)] Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011)
:link(Tainter2015)
[(Tainter 2015)] Tainter, Shi, and Skinner, 11, 2268 (2015)

4
doc/src/pair_fep_soft.txt
View File

@ -201,7 +201,7 @@ model. The usage of the TIP4P pair style is documented in the
"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ
and alpha_C are set in the "pair_style"_pair_style.html command, after the
specific parameters of the TIP4P water model and before the cutoffs. The
activation parameter lambda is supplied as an argument of the the
activation parameter lambda is supplied as an argument of the
"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the
optional cutoffs.
@ -210,7 +210,7 @@ Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified
"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,
alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before
the global cutoffs. The activation parameter lambda is introduced as an argument
of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
before the optional eps14 and sigma14.
Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in

78
doc/src/pair_granular.txt
View File

@ -24,22 +24,24 @@ cutoff = global cutoff (optional). See discussion below. :ul
[Examples:]
pair_style granular
pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre
pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity :pre
pair_style granular
pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity :pre
pair_style granular
pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 :pre
pair_style granular
pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
pair_style granular
pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall
pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre
pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
pair_style granular
pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall :pre
[Description:]
@ -57,18 +59,18 @@ global, but can be set to different values for different combinations
of particle types, as determined by the "pair_coeff"_pair_coeff.html
command. If the contact model choice is the same for two particle
types, the mixing for the cross-coefficients can be carried out
automatically. This is shown in the second example, where model
automatically. This is shown in the last example, where model
choices are the same for type 1 - type 1 as for type 2 - type2
interactions, but coefficients are different. In this case, the
coefficients for type 2 - type interactions can be determined from
mixed coefficients for type 1 - type 2 interactions can be determined from
mixing rules discussed below. For additional flexibility,
coefficients as well as model forms can vary between particle types,
as shown in the third example: type 1- type 1 interactions are based
on a Hertzian normal contact model and 2-2 interactions are based on a
DMT cohesive model (see below). In that example, 1-1 and 2-2
interactions have different model forms, in which case mixing of
as shown in the fourth example: type 1 - type 1 interactions are based
on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions
are based on a DMT cohesive model (see below). In that example, 1-1
and 2-2 interactions have different model forms, in which case mixing of
coefficients cannot be determined, so 1-2 interactions must be
explicitly defined via the {pair_coeff 1 2} command, otherwise an
explicitly defined via the {pair_coeff 1 *} command, otherwise an
error would result.
:line
@ -189,6 +191,7 @@ other settings, potentially also the twisting damping). The options
for the damping model currently supported are:
{velocity}
{mass_velocity}
{viscoelastic}
{tsuji} :ol
@ -199,11 +202,23 @@ For {damping velocity}, the normal damping is simply equal to the
user-specified damping coefficient in the {normal} model:
\begin\{equation\}
\eta_n = \eta_\{n0\}\
\eta_n = \eta_\{n0\}
\end\{equation\}
Here, \(\gamma_n\) is the damping coefficient specified for the normal
contact model, in units of {mass}/{time},
Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
contact model, in units of {mass}/{time}.
For {damping mass_velocity}, the normal damping is given by:
\begin\{equation\}
\eta_n = \eta_\{n0\} m_\{eff\}
\end\{equation\}
Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
contact model, in units of {mass}/{time} and
\(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass.
Use {damping mass_velocity} to reproduce the damping behavior of
{pair gran/hooke/*}.
The {damping viscoelastic} model is based on the viscoelastic
treatment of "(Brilliantov et al)"_#Brill1996, where the normal
@ -213,11 +228,10 @@ damping is given by:
\eta_n = \eta_\{n0\}\ a m_\{eff\}
\end\{equation\}
Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a}
is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models
except {jkr}, for which it is given implicitly according to \(delta =
a^2/R - 2\sqrt\{\pi \gamma a/E\}\). In this case, \eta_\{n0\}\ is in
units of 1/({time}*{distance}).
Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\)
for all models except {jkr}, for which it is given implicitly according
to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\). For {damping viscoelastic},
\(\eta_\{n0\}\) is in units of 1/({time}*{distance}).
The {tsuji} model is based on the work of "(Tsuji et
al)"_#Tsuji1992. Here, the damping coefficient specified as part of
@ -564,6 +578,20 @@ Finally, the twisting torque on each particle is given by:
:line
The {granular} pair style can reproduce the behavior of the
{pair gran/*} styles with the appropriate settings (some very
minor differences can be expected due to corrections in
displacement history frame-of-reference, and the application
of the torque at the center of the contact rather than
at each particle). The first example above
is equivalent to {pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1}.
The second example is equivalent to
{pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1}.
The third example is equivalent to
{pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1}.
:line
LAMMPS automatically sets pairwise cutoff values for {pair_style
granular} based on particle radii (and in the case of {jkr} pull-off
distances). In the vast majority of situations, this is adequate.
@ -619,7 +647,7 @@ interactions is set to \(\mu_1\), and friction coefficient for type
2-type 2 interactions is set to \(\mu_2\), the friction coefficient
for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\)
(unless explicitly specified to a different value by a {pair_coeff 1 2
...} command. The exception to this is elastic modulus, only
...} command). The exception to this is elastic modulus, only
applicable to {hertz/material}, {dmt} and {jkr} normal contact
models. In that case, the effective elastic modulus is computed as:
@ -706,7 +734,7 @@ For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
J. M., & Poschel, T. (1996). Model for collisions in granular
gases. Physical review E, 53(5), 5382.
:link(Tsuji1992)
:link(Tsuji1992)
[(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
T. (1992). Lagrangian numerical simulation of plug flow of
cohesionless particles in a horizontal pipe. Powder technology, 71(3),

9
doc/src/pair_ilp_graphene_hbn.txt
View File

@ -21,7 +21,7 @@ pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
pair_coeff * * rebo CH.airebo NULL NULL C
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
@ -50,11 +50,11 @@ calculating the normals.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
To perform a realistic simulation, this potential must be used in combination with
intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
@ -117,6 +117,7 @@ units, if your simulation does not use {metal} units.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,

9
doc/src/pair_kolmogorov_crespi_full.txt
View File

@ -22,7 +22,7 @@ pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff * * rebo CH.airebo C H
pair_coeff * * rebo CH.rebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
[Description:]
@ -44,12 +44,12 @@ can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene. To perform a realistic simulation, this potential
must be used in combination with intra-layer potential, such as
must be used in combination with intralayer potential, such as
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
@ -106,6 +106,7 @@ units.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

3
doc/src/pair_kolmogorov_crespi_z.txt
View File

@ -19,7 +19,7 @@ pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
pair_coeff * * rebo CH.airebo C C
pair_coeff * * rebo CH.rebo C C
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
[Description:]
@ -59,6 +59,7 @@ package"_Build_package.html doc page for more info.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"pair_style lebedeva/z"_pair_lebedeva_z.html

5
doc/src/pair_lebedeva_z.txt
View File

@ -19,8 +19,8 @@ pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
pair_style hybrid/overlay rebo lebedeva/z 14.0
pair_coeff * * rebo CH.airebo C C
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
pair_coeff * * rebo CH.rebo C C
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
[Description:]
@ -53,6 +53,7 @@ package"_Build_package.html doc page for more info.
"pair_coeff"_pair_coeff.html,
"pair_style none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.

2
doc/src/pair_lj_long.txt
View File

@ -91,7 +91,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the the "Howto tip4p"_Howto_tip4p.html doc page for more
See the "Howto tip4p"_Howto_tip4p.html doc page for more
information on how to use the TIP4P pair style. Note that the
neighbor list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for

68
doc/src/pair_mdf.txt
View File

@ -30,16 +30,16 @@ args = list of arguments for a particular style :l
[Examples:]
pair_style lj/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre
pair_style buck 2.5 3.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre
pair_style lennard/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre
[Description:]
@ -69,11 +69,12 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
:c,image(Eqs/pair_mdf-4.jpg)
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the "read_data"_read_data.html or
"read_restart commands"_read_restart.html, or by mixing as described
below:
Either the first two or all of the following coefficients must be
defined for each pair of atoms types via the pair_coeff command as
in the examples above, or in the data file read by the
"read_data"_read_data.html. The two cutoffs default to the global
values and epsilon and sigma can also be determined by mixing as
described below:
epsilon (energy units)
sigma (distance units)
@ -83,7 +84,9 @@ r_{cut} (distance units) :ul
:line
For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the
standard Buckingham potential:
standard Buckingham potential with three required coefficients.
The two cutoffs can be omitted and default to the corresponding
global values:
:c,image(Eqs/pair_mdf-5.jpg)
@ -91,19 +94,20 @@ A (energy units)
\rho (distance units)
C (energy-distance^6 units)
r_m (distance units)
r_{cut}$ (distance units) :ul
r_{cut} (distance units) :ul
:line
For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the
standard 12-6 Lennard-Jones written in the $A/B$ form:
standard 12-6 Lennard-Jones written in the A/B form:
:c,image(Eqs/pair_mdf-6.jpg)
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the read_data or read_restart
commands, or by mixing as described below:
data file read by the read_data commands, or by mixing as described below.
The two cutoffs default to their global values and must be either both
given or both left out:
A (energy-distance^12 units)
B (energy-distance^6 units)
@ -115,33 +119,23 @@ r_{cut} (distance units) :ul
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
and cutoff distances for the lj/mdf pair style can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
for details. The other two pair styles buck/mdf and lennard/mdf do not
support mixing, so all I,J pairs of coefficients must be specified
explicitly.
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports
the "pair_modify"_pair_modify.html shift option or long-range
tail corrections to pressure and energy.
The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
"pair_modify"_pair_modify.html table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
These styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the {lj/cut} pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the {pair} keyword of run_style respa.
See the "run_style"_run_style.html command for details.
These styles 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

2
doc/src/pair_spin_dmi.txt
View File

@ -88,4 +88,4 @@ package"_Build_package.html doc page for more info.
Physical Review B, 88(18), 184422. (2013).
:link(Tranchida5)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

2
doc/src/pair_spin_exchange.txt
View File

@ -95,4 +95,4 @@ package"_Build_package.html doc page for more info.
:link(Tranchida3)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

2
doc/src/pair_spin_magelec.txt
View File

@ -70,4 +70,4 @@ package"_Build_package.html doc page for more info.
:link(Tranchida4)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

2
doc/src/pair_spin_neel.txt
View File

@ -80,4 +80,4 @@ package"_Build_package.html doc page for more info.
:link(Tranchida6)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
Journal of Computational Physics, 372, 406-425, (2018).

4
doc/src/pair_style.txt
View File

@ -147,6 +147,8 @@ accelerated styles exist.
"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
"e3b"_pair_e3b.html - Explicit-three body (E3B) water model
"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
"eam"_pair_eam.html - embedded atom method (EAM)
"eam/alloy"_pair_eam.html - alloy EAM
"eam/cd"_pair_eam.html - concentration-dependent EAM
@ -174,7 +176,7 @@ accelerated styles exist.
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
"line/lj"_pair_line_lj.html - LJ potential between line segments
"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file

2
doc/src/pair_vashishta.txt
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@ -63,7 +63,7 @@ equally spaced in R^2 space from cutinner^2 to cutoff^2. For the
two-body term in the above equation, a linear interpolation for each
pairwise distance between adjacent points in the table. In practice
the tabulated version can run 3-5x faster than the analytic version
with with moderate to little loss of accuracy for Ntable values
with moderate to little loss of accuracy for Ntable values
between 10000 and 1000000. It is not recommended to use less than
5000 tabulation points.

2
doc/src/pairs.txt
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@ -31,7 +31,9 @@ Pair Styles :h1
pair_dipole
pair_dpd
pair_dpd_fdt
pair_drip
pair_dsmc
pair_e3b
pair_eam
pair_edip
pair_eff

2
doc/src/python.txt
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@ -480,7 +480,7 @@ information on those settings.
If you use Python code which calls back to LAMMPS, via the SELF input
argument explained above, there is an extra step required when
building LAMMPS. LAMMPS must also be built as a shared library and
your Python function must be able to to load the Python module in
your Python function must be able to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
Details on these steps are explained on the "Python"_Python_head.html

2
doc/src/read_data.txt
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@ -701,7 +701,7 @@ of 0 means the atom is still inside the box when unwrapped. A value
of 2 means add 2 box lengths to get the unwrapped coordinate. A value
of -1 means subtract 1 box length to get the unwrapped coordinate.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The "dump"_dump.html command can output atom atom
the simulation. The "dump"_dump.html command can output atom
coordinates in wrapped or unwrapped form, as well as the 3 image
flags.

2
doc/src/server_md.txt
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@ -65,7 +65,7 @@ in this pseudo code is a pointer to an instance of the CSlib.
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
files for details on how LAMMPS uses these messages. See the
examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
a quantum code (VASP) can use use these messages.
a quantum code (VASP) can use these messages.
The following pseudo-code uses these values, defined as enums.

2
doc/src/tad.txt
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@ -62,7 +62,7 @@ results at a specified lower temperature. A good overview of
accelerated dynamics methods for such systems is given in "this review
paper"_#Voter2002 from the same group. In general, these methods assume
that the long-time dynamics is dominated by infrequent events i.e. the
system is is confined to low energy basins for long periods,
system is confined to low energy basins for long periods,
punctuated by brief, randomly-occurring transitions to adjacent
basins. TAD is suitable for infrequent-event systems, where in
addition, the transition kinetics are well-approximated by harmonic

6
doc/src/variable.txt
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@ -293,7 +293,7 @@ list of runs (e.g. 1000) without having to list N strings in the input
script.
For the {string} style, a single string is assigned to the variable.
Two differences between this this and using the {index} style exist:
Two differences between this style and using the {index} style exist:
a variable with {string} style can be redefined, e.g. by another command later
in the input script, or if the script is read again in a loop. The other
difference is that {string} performs variable substitution even if the
@ -359,7 +359,7 @@ per-atom values is read, a non-blank line is searched for in the file.
A comment character "#" can be used anywhere on a line; text starting
with the comment character is stripped. Blank lines are skipped. The
first "word" of a non-blank line, delimited by white-space, is read as
the count N of per-atom lines to immediately follow. N can be be the
the count N of per-atom lines to immediately follow. N can be the
total number of atoms in the system, or only a subset. The next N
lines have the following format
@ -931,7 +931,7 @@ with ID = 243. Or they can take a variable name, specified as v_name,
where name is the name of the variable, like x\[v_myIndex\]. The
variable can be of any style except {vector} or {atom} or {atomfile}
variables. The variable is evaluated and the result is expected to be
numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an an
numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an
index, which must be a value from 1 to N. Note that a "formula"
cannot be used as the argument between the brackets, e.g. x\[243+10\]
or x\[v_myIndex+1\] are not allowed. To do this a single variable can

2
doc/src/velocity.txt
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@ -157,7 +157,7 @@ is issued.
The {bias} keyword with a {yes} setting is used by {create} and
{scale}, but only if the {temp} keyword is also used to specify a
"compute"_compute.html that calculates temperature in a desired way.
If the temperature compute also calculates a velocity bias, the the
If the temperature compute also calculates a velocity bias, the
bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is
added back to the atom velocities. See the "Howto

8
doc/src/write_coeff.txt
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@ -26,11 +26,9 @@ coefficients in a way, that it can be read by LAMMPS with the
option of "write_data"_write_data.html this can be used to move
the Coeffs sections from a data file into a separate file.
NOTE: The write_coeff command is not yet fully implemented in two
respects. First, some pair styles do not yet write their coefficient
information into the coeff file. This means you will need to specify
that information in your input script that reads the data file, via
the "pair_coeff"_pair_coeff.html command.
NOTE: The write_coeff command is not yet fully implemented as
some pair styles do not output their coefficient information.
This means you will need to add/copy this information manually.
:line

2
doc/src/write_data.txt
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@ -106,7 +106,7 @@ written for all I,J pairs where I <= J. These coefficients will
include any specific settings made in the input script up to that
point. The presence of these I != J coefficients in the data file
will effectively turn off the default mixing rule for the pair style.
Again, the coefficient values in the data file can can be overridden
Again, the coefficient values in the data file can be overridden
in the input script after reading the data file, by specifying
additional "pair_coeff"_pair_coeff.html commands for any desired I,J
pairs.