Merge remote-tracking branch 'lammps/master' into kim-v2-update
This commit is contained in:
Ryan S. Elliott
@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
|
||||
"OPT"_#opt,
|
||||
"POEMS"_#poems,
|
||||
"PYTHON"_#python,
|
||||
"REAX"_#reax,
|
||||
"VORONOI"_#voronoi,
|
||||
"USER-ATC"_#user-atc,
|
||||
"USER-AWPMD"_#user-awpmd,
|
||||
@ -532,45 +531,6 @@ build fails.
|
||||
|
||||
:line
|
||||
|
||||
REAX package :h4,link(reax)
|
||||
|
||||
NOTE: the use of the REAX package and its "pair_style
|
||||
reax"_pair_reax.html command is discouraged, as it is no longer
|
||||
maintained. Please use the USER-REAXC package and its "pair_style
|
||||
reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
|
||||
enabled variant (pair_style reax/c/kk), which has a more robust memory
|
||||
management. See the "pair_style reax/c"_pair_reaxc.html doc page for
|
||||
details.
|
||||
|
||||
[CMake build]:
|
||||
|
||||
No additional settings are needed besides "-D PKG_REAX=yes".
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
Before building LAMMPS, you must build the REAX library in lib/reax.
|
||||
You can do this manually if you prefer; follow the instructions in
|
||||
lib/reax/README. You can also do it in one step from the lammps/src
|
||||
dir, using a command like these, which simply invoke the
|
||||
lib/reax/Install.py script with the specified args:
|
||||
|
||||
make lib-reax # print help message
|
||||
make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
|
||||
make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
|
||||
make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
|
||||
|
||||
The build should produce two files: lib/reax/libreax.a and
|
||||
lib/reax/Makefile.lammps. The latter is copied from an existing
|
||||
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
|
||||
Fortran (REAX library). Typically the two compilers used for LAMMPS
|
||||
and the REAX library need to be consistent (e.g. both Intel or both
|
||||
GNU compilers). If necessary, you can edit/create a new
|
||||
lib/reax/Makefile.machine file for your system, which should define an
|
||||
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
|
||||
file.
|
||||
|
||||
:line
|
||||
|
||||
VORONOI package :h4,link(voronoi)
|
||||
|
||||
To build with this package, you must download and build the "Voro++
|
||||
|
||||
@ -47,7 +47,6 @@ packages:
|
||||
"OPT"_Build_extras.html#opt,
|
||||
"POEMS"_Build_extras.html#poems,
|
||||
"PYTHON"_Build_extras.html#python,
|
||||
"REAX"_Build_extras.html#reax,
|
||||
"VORONOI"_Build_extras.html#voronoi,
|
||||
"USER-ATC"_Build_extras.html#user-atc,
|
||||
"USER-AWPMD"_Build_extras.html#user-awpmd,
|
||||
|
||||
@ -169,8 +169,7 @@ OPT.
|
||||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"rattle"_fix_shake.html,
|
||||
"reax/bonds"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
|
||||
"reax/c/species (k)"_fix_reaxc_species.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
"restrain"_fix_restrain.html,
|
||||
|
||||
@ -107,6 +107,7 @@ OPT.
|
||||
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
|
||||
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"lcbop"_pair_lcbop.html,
|
||||
"lebedeva/z"_pair_lebedeva_z.html,
|
||||
"lennard/mdf"_pair_mdf.html,
|
||||
"line/lj"_pair_line_lj.html,
|
||||
"list"_pair_list.html,
|
||||
@ -160,8 +161,7 @@ OPT.
|
||||
"lubricateU/poly"_pair_lubricateU.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam"_pair_meam.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/c"_pair_meamc.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
"mgpt"_pair_mgpt.html,
|
||||
@ -194,7 +194,6 @@ OPT.
|
||||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax"_pair_reax.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"rebo (io)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
|
||||
BIN
doc/src/Eqs/pair_lebedeva.png
Normal file
BIN
doc/src/Eqs/pair_lebedeva.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 30 KiB |
@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
|
||||
input with an error message (for instance, when an integer is required,
|
||||
but a floating-point number 1.0 is provided):
|
||||
|
||||
ERROR: Expected integer parameter in input script or data file :pre
|
||||
ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
|
||||
|
||||
Some commands allow for using variable references in place of numeric
|
||||
constants so that the value can be evaluated and may change over the
|
||||
@ -85,6 +85,9 @@ reading the input and before parsing commands,
|
||||
|
||||
NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
|
||||
the documentation of the corresponding command explicitly says it is.
|
||||
Otherwise, you will receive an error message of this kind:
|
||||
|
||||
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
|
||||
|
||||
Generally, LAMMPS will print a message to the screen and logfile and
|
||||
exit gracefully when it encounters a fatal error. Sometimes it will
|
||||
|
||||
@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
|
||||
"Pre-built Fedora Linux executables"_#fedora
|
||||
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
|
||||
"Pre-built OpenSuse Linux executables"_#opensuse
|
||||
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
|
||||
"Gentoo Linux executable"_#gentoo :all(b)
|
||||
|
||||
:line
|
||||
|
||||
@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
|
||||
lammps-openmpi-devel), the header for compiling programs using
|
||||
the C library interface (lammps-headers), and the LAMMPS python
|
||||
module for Python 3. All packages can be installed at the same
|
||||
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
|
||||
By default, {lmp} will refer to the serial executable, unless
|
||||
one of the MPI environment modules is loaded
|
||||
time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
|
||||
or {lmp_mpich} respectively. By default, {lmp} will refer to the
|
||||
serial executable, unless one of the MPI environment modules is loaded
|
||||
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
|
||||
Then the corresponding parallel LAMMPS executable is used.
|
||||
Then the corresponding parallel LAMMPS executable can be used.
|
||||
The same mechanism applies when loading the LAMMPS python module.
|
||||
|
||||
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
|
||||
@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
|
||||
|
||||
:line
|
||||
|
||||
Pre-built Gentoo Linux executable :h4,link(gentoo)
|
||||
Gentoo Linux executable :h4,link(gentoo)
|
||||
|
||||
LAMMPS is part of Gentoo's main package tree and can be installed by
|
||||
typing:
|
||||
|
||||
@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
|
||||
needed to run in parallel.
|
||||
|
||||
The LAMMPS binaries contain all optional packages included in the
|
||||
source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
|
||||
and USER-QMMM. The serial version also does not include the MPIIO and
|
||||
source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
|
||||
The serial version also does not include the MPIIO and
|
||||
USER-LB packages. GPU support is provided for OpenCL.
|
||||
|
||||
The installer site also has instructions on how to run LAMMPS under
|
||||
|
||||
@ -16,7 +16,7 @@ functionality for setting up simulations and analyzing their output.
|
||||
Specifically, LAMMPS was not conceived and designed for:
|
||||
|
||||
being run thru a GUI
|
||||
build molecular systems, or building molecular topologies
|
||||
building molecular systems, or building molecular topologies
|
||||
assign force-field coefficients automagically
|
||||
perform sophisticated analysis of your MD simulation
|
||||
visualize your MD simulation interactively
|
||||
@ -24,18 +24,18 @@ plot your output data :ul
|
||||
|
||||
Although over the years these limitations have been somewhat
|
||||
reduced through features added to LAMMPS or external tools
|
||||
that either interface with LAMMPS or extend LAMMPS.
|
||||
that either closely interface with LAMMPS or extend LAMMPS.
|
||||
|
||||
Here are suggestions on how to perform these tasks:
|
||||
|
||||
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
|
||||
[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
|
||||
the library interface is provided. Thus, GUI interfaces can be
|
||||
written in Python (or C or C++ if desired) that run LAMMPS and
|
||||
visualize or plot its output. Examples of this are provided in the
|
||||
python directory and described on the "Python"_Python_head.html doc
|
||||
page. Also, there are several external wrappers or GUI front ends.:ulb,l
|
||||
page. Also, there are several external wrappers or GUI front ends. :ulb,l
|
||||
|
||||
Builder: Several pre-processing tools are packaged with LAMMPS. Some
|
||||
[Builder:] Several pre-processing tools are packaged with LAMMPS. Some
|
||||
of them convert input files in formats produced by other MD codes such
|
||||
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
|
||||
are simple programs that will build simple molecular systems, such as
|
||||
@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
|
||||
LAMMPS. The "Pre/post processing
|
||||
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
|
||||
describes a variety of 3rd party tools for this task. Furthermore,
|
||||
some LAMMPS internal commands to reconstruct topology, as well as
|
||||
the option to insert molecule templates instead of atoms.:l
|
||||
some LAMMPS internal commands allow to reconstruct, or selectively add
|
||||
topology information, as well as provide the option to insert molecule
|
||||
templates instead of atoms for building bulk molecular systems. :l
|
||||
|
||||
Force-field assignment: The conversion tools described in the previous
|
||||
[Force-field assignment:] The conversion tools described in the previous
|
||||
bullet for CHARMM, AMBER, and Insight will also assign force field
|
||||
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
|
||||
or BIOVIA (formerly Accelrys) force field files. :l
|
||||
or BIOVIA (formerly Accelrys) force field files. The tools
|
||||
"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
|
||||
"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
|
||||
powerful and flexible in converting force field and topology data
|
||||
between various MD simulation programs. :l
|
||||
|
||||
Simulation analysis: If you want to perform analysis on-the-fly as
|
||||
[Simulation analysis:] If you want to perform analysis on-the-fly as
|
||||
your simulation runs, see the "compute"_compute.html and
|
||||
"fix"_fix.html doc pages, which list commands that can be used in a
|
||||
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
|
||||
@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
|
||||
make it easier to import into other programs. See the
|
||||
"Tools"_Tools.html doc page for details on these various options. :l
|
||||
|
||||
Visualization: LAMMPS can produce JPG or PNG snapshot images
|
||||
[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
|
||||
on-the-fly via its "dump image"_dump_image.html command and pass
|
||||
them to an external program FFmpeg to generate movies from them. For
|
||||
high-quality, interactive visualization there are many excellent and
|
||||
free tools available. See the "Other Codes
|
||||
them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
|
||||
movies from them. For high-quality, interactive visualization there are
|
||||
many excellent and free tools available. See the "Other Codes
|
||||
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
|
||||
visualization packages that can use LAMMPS output data. :l
|
||||
|
||||
Plotting: See the next bullet about Pizza.py as well as the
|
||||
[Plotting:] See the next bullet about Pizza.py as well as the
|
||||
"Python"_Python_head.html doc page for examples of plotting LAMMPS
|
||||
output. Scripts provided with the {python} tool in the tools
|
||||
directory will extract and massage data in log and dump files to make
|
||||
it easier to analyze and plot. See the "Tools"_Tools.html doc page
|
||||
for more discussion of the various tools. :l
|
||||
|
||||
Pizza.py: Our group has also written a separate toolkit called
|
||||
[Pizza.py:] Our group has also written a separate toolkit called
|
||||
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
|
||||
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
|
||||
simulations. It thus provides some functionality for several of the
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="12 Dec 2018 version">
|
||||
<META NAME="docnumber" CONTENT="4 Jan 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
|
||||
12 Dec 2018 version :c,h2
|
||||
4 Jan 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
||||
@ -65,6 +65,8 @@ make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data :pre
|
||||
make anchor_check # check for duplicate anchor labels
|
||||
make spelling # spell-check the manual
|
||||
|
||||
:line
|
||||
|
||||
@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
|
||||
|
||||
Installing prerequisites for PDF build
|
||||
|
||||
[TBA]
|
||||
Building the PDF manual requires a working C++ compiler (to
|
||||
compile the txt2html tool and a working installation of
|
||||
"HTMLDOC"_https://www.msweet.org/htmldoc/
|
||||
HTMLDOC has its own list of prerequisites, but in most cases
|
||||
you can install a binary package of it either through your
|
||||
Linux package manager or MacOS (dmg) and Windows installer
|
||||
(msi) packages from its
|
||||
"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its
|
||||
standard packages, it needs to be written in a style compatible with
|
||||
other LAMMPS source files. This means: 2-character indentation per
|
||||
level, [no tabs], no lines over 80 characters. I/O is done via
|
||||
the C-style stdio library, class header files should not import any
|
||||
system headers outside <stdio.h>, STL containers should be avoided
|
||||
in headers, and forward declarations used where possible or needed.
|
||||
the C-style stdio library (mixing of stdio and iostreams is generally
|
||||
discouraged), class header files should not import any system headers
|
||||
outside of <cstdio>, STL containers should be avoided in headers,
|
||||
system header from the C library should use the C++-style names
|
||||
(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
|
||||
<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
|
||||
used where possible or needed to avoid including headers.
|
||||
All added code should be placed into the LAMMPS_NS namespace or a
|
||||
sub-namespace; global or static variables should be avoided, as they
|
||||
conflict with the modular nature of LAMMPS and the C++ class structure.
|
||||
|
||||
@ -45,7 +45,6 @@ as contained in the file name.
|
||||
"LATTE"_#PKG-LATTE,
|
||||
"MANYBODY"_#PKG-MANYBODY,
|
||||
"MC"_#PKG-MC,
|
||||
"MEAM"_#PKG-MEAM,
|
||||
"MESSAGE"_#PKG-MESSAGE,
|
||||
"MISC"_#PKG-MISC,
|
||||
"MOLECULE"_#PKG-MOLECULE,
|
||||
@ -56,7 +55,6 @@ as contained in the file name.
|
||||
"POEMS"_#PKG-POEMS,
|
||||
"PYTHON"_#PKG-PYTHON,
|
||||
"QEQ"_#PKG-QEQ,
|
||||
"REAX"_#PKG-REAX,
|
||||
"REPLICA"_#PKG-REPLICA2,
|
||||
"RIGID"_#PKG-RIGID,
|
||||
"SHOCK"_#PKG-SHOCK,
|
||||
@ -532,37 +530,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
|
||||
|
||||
:line
|
||||
|
||||
MEAM package :link(PKG-MEAM),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential.
|
||||
|
||||
Please note that the use of the MEAM package is discouraged as
|
||||
it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
|
||||
which is a direct translation of the MEAM package to C++.
|
||||
USER-MEAMC contains additional optimizations making it run faster
|
||||
than MEAM on most machines, while providing the identical features
|
||||
and user interface.
|
||||
|
||||
[Author:] Greg Wagner (Northwestern U) while at Sandia.
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MEAM: filenames -> commands
|
||||
src/meam/README
|
||||
lib/meam/README
|
||||
"pair_style meam"_pair_meam.html
|
||||
examples/meam :ul
|
||||
|
||||
:line
|
||||
|
||||
MESSAGE package :link(PKG-MESSAGE),h4
|
||||
|
||||
[Contents:]
|
||||
@ -833,38 +800,6 @@ examples/streitz :ul
|
||||
|
||||
:line
|
||||
|
||||
REAX package :link(PKG-REAX),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
NOTE: the use of the REAX package is discouraged, as it is no longer
|
||||
maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
|
||||
and possibly the KOKKOS enabled variant of that, which has a more robust
|
||||
memory management.
|
||||
|
||||
A pair style which wraps a Fortran library which implements the ReaxFF
|
||||
potential, which is a universal reactive force field. Also included is
|
||||
a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
|
||||
as bonds are created and destroyed.
|
||||
|
||||
[Author:] Aidan Thompson (Sandia).
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/REAX: filenames -> commands
|
||||
lib/reax/README
|
||||
"pair_style reax"_pair_reax.html
|
||||
"fix reax/bonds"_fix_reax_bonds.html
|
||||
examples/reax :ul
|
||||
|
||||
:line
|
||||
|
||||
REPLICA package :link(PKG-REPLICA2),h4
|
||||
|
||||
[Contents:]
|
||||
@ -1551,10 +1486,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
|
||||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential
|
||||
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
|
||||
to plain C++. In contrast to the MEAM package, no library
|
||||
needs to be compiled and the pair style can be instantiated
|
||||
multiple times.
|
||||
translated from the Fortran version in the (obsolete) "MEAM" package
|
||||
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
|
||||
has been removed from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
|
||||
based on the Fortran version of Greg Wagner (Northwestern U) while at
|
||||
@ -1564,8 +1498,8 @@ Sandia.
|
||||
|
||||
src/USER-MEAMC: filenames -> commands
|
||||
src/USER-MEAMC/README
|
||||
"pair_style meam/c"_pair_meam.html
|
||||
examples/meam :ul
|
||||
"pair_style meam/c"_pair_meamc.html
|
||||
examples/meamc :ul
|
||||
|
||||
:line
|
||||
|
||||
@ -1893,9 +1827,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
A pair style which implements the ReaxFF potential in C/C++ (in
|
||||
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
|
||||
is universal reactive force field. See the src/USER-REAXC/README file
|
||||
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
|
||||
is a universal reactive force field. See the src/USER-REAXC/README file
|
||||
for more info on differences between the two packages. Also two fixes
|
||||
for monitoring molecules as bonds are created and destroyed.
|
||||
|
||||
@ -1906,7 +1839,7 @@ for monitoring molecules as bonds are created and destroyed.
|
||||
src/USER-REAXC: filenames -> commands
|
||||
src/USER-REAXC/README
|
||||
"pair_style reax/c"_pair_reaxc.html
|
||||
"fix reax/c/bonds"_fix_reax_bonds.html
|
||||
"fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
"fix reax/c/species"_fix_reaxc_species.html
|
||||
examples/reax :ul
|
||||
|
||||
|
||||
@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
|
||||
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
|
||||
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
|
||||
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
|
||||
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
|
||||
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
|
||||
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
|
||||
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
|
||||
@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
|
||||
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
|
||||
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
|
||||
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
|
||||
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
|
||||
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
|
||||
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
|
||||
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
|
||||
|
||||
@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
|
||||
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
|
||||
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
|
||||
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
|
||||
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
|
||||
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
|
||||
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
|
||||
|
||||
@ -486,8 +486,8 @@ README for more info on Pizza.py and how to use these scripts.
|
||||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alone codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
|
||||
post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
|
||||
the README.txt file for more info.
|
||||
|
||||
These tools were written by Aidan Thompson at Sandia.
|
||||
|
||||
@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
|
||||
compute 1 all pair gauss
|
||||
compute 1 all pair lj/cut/coul/cut ecoul
|
||||
compute 1 all pair tersoff 2 epair
|
||||
compute 1 all pair reax :pre
|
||||
compute 1 all pair reax/c :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -60,8 +60,8 @@ corrections, even if they are enabled via the
|
||||
"pair_modify"_pair_modify.html command.
|
||||
|
||||
Some pair styles tally additional quantities, e.g. a breakdown of
|
||||
potential energy into a dozen or so components is tallied by the
|
||||
"pair_style reax"_pair_reax.html command. These values (1 or more)
|
||||
potential energy into 14 components is tallied by the "pair_style
|
||||
reax/c"_pair_reaxc.html command. These values (1 or more)
|
||||
are stored as a global vector by this compute. See the doc page for
|
||||
"individual pair styles"_pair_style.html for info on these values.
|
||||
|
||||
|
||||
@ -312,9 +312,8 @@ accelerated styles exist.
|
||||
"qmmm"_fix_qmmm.html -
|
||||
"qtb"_fix_qtb.html -
|
||||
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
|
||||
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/bonds"_fix_reax_bonds.html -
|
||||
"reax/c/species"_fix_reaxc_species.html -
|
||||
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
|
||||
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
|
||||
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
|
||||
"rhok"_fix_rhok.html -
|
||||
|
||||
@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
|
||||
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
|
||||
map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
|
||||
zero or more individual keyword/value pairs may be appended to each react argument :l
|
||||
individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
|
||||
individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
|
||||
{prob} values = fraction seed
|
||||
fraction = initiate reaction with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
{max_rxn} value = N
|
||||
N = maximum number of reactions allowed to occur
|
||||
{stabilize_steps} value = timesteps
|
||||
timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
|
||||
{update_edges} value = {none} or {charges} or {custom}
|
||||
@ -69,8 +71,9 @@ Initiate complex covalent bonding (topology) changes. These topology
|
||||
changes will be referred to as 'reactions' throughout this
|
||||
documentation. Topology changes are defined in pre- and post-reaction
|
||||
molecule templates and can include creation and deletion of bonds,
|
||||
angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
|
||||
atom-types, or atomic charges.
|
||||
angles, dihedrals, impropers, bond types, angle types, dihedral types,
|
||||
atom types, or atomic charges. In addition, reaction by-products or
|
||||
other molecules can be identified and deleted.
|
||||
|
||||
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
|
||||
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
|
||||
@ -203,15 +206,16 @@ A discussion of correctly handling this is also provided on the
|
||||
The map file is a text document with the following format:
|
||||
|
||||
A map file has a header and a body. The header of map file the
|
||||
contains one mandatory keyword and two optional keywords. The
|
||||
contains one mandatory keyword and three optional keywords. The
|
||||
mandatory keyword is 'equivalences' and the optional keywords are
|
||||
'edgeIDs' and 'customIDs':
|
||||
'edgeIDs' and 'deleteIDs' and 'customIDs':
|
||||
|
||||
N {equivalences} = # of atoms N in the reaction molecule templates
|
||||
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
|
||||
N {deleteIDs} = # of atoms N that are specified for deletion
|
||||
N {customIDs} = # of atoms N that are specified for a custom update :pre
|
||||
|
||||
The body of the map file contains two mandatory sections and two
|
||||
The body of the map file contains two mandatory sections and three
|
||||
optional sections. The first mandatory section begins with the keyword
|
||||
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
|
||||
pre-reacted molecule template. The second mandatory section begins
|
||||
@ -222,10 +226,12 @@ second column is the corresponding atom ID of the post-reacted
|
||||
molecule template. The first optional section begins with the keyword
|
||||
'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
|
||||
molecule template. The second optional section begins with the keyword
|
||||
'Custom Edges' and allows for forcing the update of a specific atom's
|
||||
atomic charge. The first column is the ID of an atom near the edge of
|
||||
the pre-reacted molecule template, and the value of the second column
|
||||
is either 'none' or 'charges.' Further details are provided in the
|
||||
'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
|
||||
delete. The third optional section begins with the keyword 'Custom
|
||||
Edges' and allows for forcing the update of a specific atom's atomic
|
||||
charge. The first column is the ID of an atom near the edge of the
|
||||
pre-reacted molecule template, and the value of the second column is
|
||||
either 'none' or 'charges.' Further details are provided in the
|
||||
discussion of the 'update_edges' keyword.
|
||||
|
||||
A sample map file is given below:
|
||||
@ -281,7 +287,8 @@ The {prob} keyword can affect whether an eligible reaction actually
|
||||
occurs. The fraction setting must be a value between 0.0 and 1.0. A
|
||||
uniform random number between 0.0 and 1.0 is generated and the
|
||||
eligible reaction only occurs if the random number is less than the
|
||||
fraction.
|
||||
fraction. Up to N reactions are permitted to occur, as optionally
|
||||
specified by the {max_rxn} keyword.
|
||||
|
||||
The {stabilize_steps} keyword allows for the specification of how many
|
||||
timesteps a reaction site is stabilized before being returned to the
|
||||
@ -309,7 +316,16 @@ edge are unaffected by this setting.
|
||||
|
||||
A few other considerations:
|
||||
|
||||
It may be beneficial to ensure reacting atoms are at a certain
|
||||
Many reactions result in one or more atoms that are considered
|
||||
unwanted by-products. Therefore, bond/react provides the option to
|
||||
delete a user-specified set of atoms. These pre-reaction atoms are
|
||||
identified in the map file. A deleted atom must still be included in
|
||||
the post-reaction molecule template, in which it cannot be bonded to
|
||||
an atom that is not deleted. In addition to deleting unwanted reaction
|
||||
by-products, this feature can be used to remove specific topologies,
|
||||
such as small rings, that may be otherwise indistinguishable.
|
||||
|
||||
Also, it may be beneficial to ensure reacting atoms are at a certain
|
||||
temperature before being released to the overall thermostat. For this,
|
||||
you can use the internally-created dynamic group named
|
||||
"bond_react_MASTER_group." For example, adding the following command
|
||||
|
||||
@ -626,10 +626,10 @@ over time or the atom count becomes very small.
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
|
||||
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
|
||||
not coupled to barostat, otherwise no.
|
||||
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
|
||||
dimension and not coupled to barostat, otherwise no.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -6,13 +6,12 @@
|
||||
|
||||
:line
|
||||
|
||||
fix reax/bonds command :h3
|
||||
fix reax/c/bonds command :h3
|
||||
fix reax/c/bonds/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID reax/bonds Nevery filename :pre
|
||||
fix ID group-ID reaxc/bonds Nevery filename :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
reax/bonds = style name of this fix command
|
||||
@ -21,16 +20,14 @@ filename = name of output file :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all reax/bonds 100 bonds.tatb
|
||||
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Write out the bond information computed by the ReaxFF potential
|
||||
specified by "pair_style reax"_pair_reax.html or "pair_style
|
||||
reax/c"_pair_reaxc.html in the exact same format as the original
|
||||
stand-alone ReaxFF code of Adri van Duin. The bond information is
|
||||
written to {filename} on timesteps that are multiples of {Nevery},
|
||||
Write out the bond information computed by the ReaxFF potential specified
|
||||
by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
|
||||
original stand-alone ReaxFF code of Adri van Duin. The bond information
|
||||
is written to {filename} on timesteps that are multiples of {Nevery},
|
||||
including timestep 0. For time-averaged chemical species analysis,
|
||||
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
|
||||
|
||||
@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The fix reax/bonds command requires that the "pair_style
|
||||
reax"_pair_reax.html be invoked. This fix is part of the REAX
|
||||
package. It is only enabled if LAMMPS was built with that package,
|
||||
which also requires the REAX library be built and linked with LAMMPS.
|
||||
The fix reax/c/bonds command requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
reax/c"_pair_reaxc.html is invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax"_pair_reax.html, "pair_style
|
||||
reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:] none
|
||||
@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The fix species currently only works with "pair_style
|
||||
The "fix reax/c/species" currently only works with "pair_style
|
||||
reax/c"_pair_reaxc.html and it requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix
|
||||
reax/bonds"_fix_reax_bonds.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
@ -135,7 +135,7 @@ Fixes :h1
|
||||
fix_qeq_reax
|
||||
fix_qmmm
|
||||
fix_qtb
|
||||
fix_reax_bonds
|
||||
fix_reaxc_bonds
|
||||
fix_reaxc_species
|
||||
fix_recenter
|
||||
fix_restrain
|
||||
|
||||
@ -356,7 +356,7 @@ fix_qeq_comb.html
|
||||
fix_qeq_reax.html
|
||||
fix_qmmm.html
|
||||
fix_qtb.html
|
||||
fix_reax_bonds.html
|
||||
fix_reaxc_bonds.html
|
||||
fix_reaxc_species.html
|
||||
fix_recenter.html
|
||||
fix_restrain.html
|
||||
@ -585,6 +585,7 @@ pair_kim.html
|
||||
pair_kolmogorov_crespi_full.html
|
||||
pair_kolmogorov_crespi_z.html
|
||||
pair_lcbop.html
|
||||
pair_lebedeva_z.html
|
||||
pair_line_lj.html
|
||||
pair_list.html
|
||||
pair_lj.html
|
||||
@ -598,7 +599,7 @@ pair_lj_soft.html
|
||||
pair_lubricate.html
|
||||
pair_lubricateU.html
|
||||
pair_mdf.html
|
||||
pair_meam.html
|
||||
pair_meamc.html
|
||||
pair_meam_spline.html
|
||||
pair_meam_sw_spline.html
|
||||
pair_meso.html
|
||||
@ -617,7 +618,6 @@ pair_peri.html
|
||||
pair_polymorphic.html
|
||||
pair_python.html
|
||||
pair_quip.html
|
||||
pair_reax.html
|
||||
pair_reaxc.html
|
||||
pair_resquared.html
|
||||
pair_sdk.html
|
||||
|
||||
@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
|
||||
model, then you should just list the sub-style once and use the
|
||||
pair_coeff command to assign parameters for the different type pairs.
|
||||
|
||||
NOTE: There are two exceptions to this option to list an individual
|
||||
pair style multiple times. The first is for pair styles implemented
|
||||
as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
|
||||
reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
|
||||
This is because unlike a C++ class, they can not be instantiated
|
||||
multiple times, due to the manner in which they were coded in Fortran.
|
||||
The second is for GPU-enabled pair styles in the GPU package. This is
|
||||
b/c the GPU package also currently assumes that only one instance of a
|
||||
pair style is being used.
|
||||
NOTE: There is one exception to this option to list an individual
|
||||
pair style multiple times: GPU-enabled pair styles in the GPU package.
|
||||
This is because the GPU package currently assumes that only one
|
||||
instance of a pair style is being used.
|
||||
|
||||
In the pair_coeff commands, the name of a pair style must be added
|
||||
after the I,J type specification, with the remaining coefficients
|
||||
|
||||
@ -10,7 +10,7 @@ pair_style ilp/graphene/hbn command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
|
||||
pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
|
||||
|
||||
cutoff = global cutoff (distance units)
|
||||
tap_flag = 0/1 to turn off/on the taper function
|
||||
@ -110,6 +110,7 @@ units, if your simulation does not use {metal} units.
|
||||
"pair_style hybrid/overlay"_pair_hybrid.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,
|
||||
"pair_style pair_coul_shield"_pair_coul_shield.html.
|
||||
|
||||
[Default:] tap_flag = 1
|
||||
|
||||
@ -100,6 +100,7 @@ units.
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.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.
|
||||
|
||||
|
||||
@ -10,7 +10,7 @@ pair_style kolmogorov/crespi/z command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre
|
||||
pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
@ -56,9 +56,12 @@ package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_none"_pair_none.html
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.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
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
66
doc/src/pair_lebedeva_z.txt
Normal file
66
doc/src/pair_lebedeva_z.txt
Normal file
@ -0,0 +1,66 @@
|
||||
"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 lebedeva/z command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style hybrid/overlay lebedeva/z 20.0
|
||||
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
|
||||
|
||||
[Description:]
|
||||
|
||||
The {lebedeva/z} style computes the Lebedeva interaction
|
||||
potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
|
||||
:c,image(Eqs/pair_lebedeva.png)
|
||||
|
||||
It is important to have a sufficiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continuously to zero at the cutoff assuming
|
||||
that the exponential part of {Vij} (first term) decays sufficiently fast.
|
||||
This shift is achieved by the last term in the equation for {Vij} above.
|
||||
|
||||
The parameter file (e.g. CC.Lebedeva), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
Other interactions can be set to zero using pair_style {none}.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix 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.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_style none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.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.
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Leb01)
|
||||
[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
|
||||
|
||||
@ -152,7 +152,7 @@ info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
@ -116,7 +116,7 @@ info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
|
||||
"pair_style meam/spline"_pair_meam_spline.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -6,18 +6,17 @@
|
||||
|
||||
:line
|
||||
|
||||
pair_style meam command :h3
|
||||
pair_style meam/c command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style :pre
|
||||
|
||||
style = {meam} or {meam/c}
|
||||
style = {meam/c}
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style meam
|
||||
pair_style meam/c
|
||||
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
|
||||
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
|
||||
|
||||
@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed
|
||||
as of November 2010; see description below of the mixture_ref_t
|
||||
parameter
|
||||
|
||||
Style {meam} computes pairwise interactions for a variety of materials
|
||||
Style {meam/c} computes pairwise interactions for a variety of materials
|
||||
using modified embedded-atom method (MEAM) potentials
|
||||
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
|
||||
"EAM potentials"_pair_eam.html which adds angular forces. It is
|
||||
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
|
||||
diamond cubic structures, as well as covalently bonded materials like
|
||||
silicon and carbon. Style {meam/c} is a translation of the {meam} code
|
||||
from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
|
||||
silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
|
||||
{meam} code from Fortran to C++. It is functionally equivalent to {meam}
|
||||
but more efficient, and thus {meam} has been removed from LAMMPS after
|
||||
the 12 December 2018 release.
|
||||
|
||||
In the MEAM formulation, the total energy E of a system of atoms is
|
||||
given by:
|
||||
@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {meam} style is part of the MEAM package. It is only enabled if
|
||||
LAMMPS was built with that package, which also requires the MEAM
|
||||
library be built and linked with LAMMPS. The {meam/c} style is
|
||||
provided in the USER-MEAMC package. It is only enabled if LAMMPS was
|
||||
built with that package. In contrast to the {meam} style, {meam/c}
|
||||
does not require a separate library to be compiled and it can be
|
||||
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
|
||||
The {meam/c} style is provided in the USER-MEAMC package. It is
|
||||
only enabled if LAMMPS was built with that package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
@ -1,216 +0,0 @@
|
||||
"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 reax command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style reax hbcut hbnewflag tripflag precision :pre
|
||||
|
||||
hbcut = hydrogen-bond cutoff (optional) (distance units)
|
||||
hbnewflag = use old or new hbond function style (0 or 1) (optional)
|
||||
tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
|
||||
precision = precision for charge equilibration (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style reax
|
||||
pair_style reax 10.0 0 1 1.0e-5
|
||||
pair_coeff * * ffield.reax 3 1 2 2
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {reax} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper:
|
||||
"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.
|
||||
|
||||
WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
|
||||
differs from the {reax/c} style in the lo-level implementation details.
|
||||
The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
|
||||
LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
the ReaxFF parameters for each atom type, bond type, etc. The format
|
||||
is identical to the ffield file used by van Duin and co-workers. The
|
||||
filename is required as an argument in the pair_coeff command. Any
|
||||
value other than "ffield.reax" will be rejected (see below).
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
documented in potentials/README.reax. The default ffield.reax
|
||||
contains parameterizations for the following elements: C, H, O, N.
|
||||
|
||||
NOTE: We do not distribute a wide variety of ReaxFF force field files
|
||||
with LAMMPS. Adri van Duin's group at PSU is the central repository
|
||||
for this kind of data as they are continuously deriving and updating
|
||||
parameterizations for different classes of materials. You can submit
|
||||
a contact request at the Materials Computation Center (MCC) website
|
||||
"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
|
||||
describing the material(s) you are interested in modeling with ReaxFF.
|
||||
They can tell
|
||||
you what is currently available or what it would take to create a
|
||||
suitable ReaxFF parameterization.
|
||||
|
||||
The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of {pair_style reax} potential
|
||||
against the original ReaxFF code for the systems mentioned above. You
|
||||
can use other ffield files for specific chemical systems that may be
|
||||
available elsewhere (but note that their accuracy may not have been
|
||||
tested).
|
||||
|
||||
The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
|
||||
optional arguments. If none are provided, default settings are used:
|
||||
{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
|
||||
new hbond function style), {tripflag} = 1 (apply stabilization to all
|
||||
triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you
|
||||
wish to override any of these defaults, then all of the settings must
|
||||
be specified.
|
||||
|
||||
Two examples using {pair_style reax} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
|
||||
calculated by both of these pair styles match very closely, the
|
||||
contributions due to the valence angles differ slightly due to
|
||||
the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
|
||||
is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom since the {reax} pair style performs a charge equilibration (QEq)
|
||||
calculation. See the "atom_style"_atom_style.html and
|
||||
"read_data"_read_data.html commands for details on how to specify
|
||||
charges.
|
||||
|
||||
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
|
||||
energy contributions, with the exception of the Coulombic and charge
|
||||
equilibration contributions which are stored in the thermo variable
|
||||
{ecoul}. The output of these quantities is controlled by the
|
||||
"thermo"_thermo.html command.
|
||||
|
||||
This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the "compute
|
||||
pair"_compute_pair.html command as a vector of values of length 14.
|
||||
The 14 values correspond to the following sub-categories (the variable
|
||||
names in italics match those used in the ReaxFF FORTRAN library):
|
||||
|
||||
{eb} = bond energy
|
||||
{ea} = atom energy
|
||||
{elp} = lone-pair energy
|
||||
{emol} = molecule energy (always 0.0)
|
||||
{ev} = valence angle energy
|
||||
{epen} = double-bond valence angle penalty
|
||||
{ecoa} = valence angle conjugation energy
|
||||
{ehb} = hydrogen bond energy
|
||||
{et} = torsion energy
|
||||
{eco} = conjugation energy
|
||||
{ew} = van der Waals energy
|
||||
{ep} = Coulomb energy
|
||||
{efi} = electric field energy (always 0.0)
|
||||
{eqeq} = charge equilibration energy :ol
|
||||
|
||||
To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
|
||||
compute reax all pair reax
|
||||
variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
...
|
||||
variable eqeq equal c_reax\[14\]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
|
||||
|
||||
Only a single pair_coeff command is used with the {reax} style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
elements. 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 indices = mapping of ReaxFF elements to atom types :ul
|
||||
|
||||
The specification of the filename and the mapping of LAMMPS atom types
|
||||
recognized by the ReaxFF is done differently than for other LAMMPS
|
||||
potentials, due to the non-portable difficulty of passing character
|
||||
strings (e.g. filename, element names) between C++ and Fortran.
|
||||
|
||||
The filename has to be "ffield.reax" and it has to exist in the
|
||||
directory you are running LAMMPS in. This means you cannot prepend a
|
||||
path to the file in the potentials dir. Rather, you should copy that
|
||||
file into the directory you are running from. If you wish to use
|
||||
another ReaxFF potential file, then name it "ffield.reax" and put it
|
||||
in the directory you run from.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
names, each with a couple dozen numeric parameters. If there are M
|
||||
elements specified in the {ffield} file, think of these as numbered 1
|
||||
to M. Each of the N indices you specify for the N atom types of LAMMPS
|
||||
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
|
||||
be mapped to whatever element you specify as the first index value,
|
||||
etc. If a mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a ReaxFF potential is used as part
|
||||
of the {hybrid} pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
|
||||
NOTE: Currently the reax pair style cannot be used as part of the
|
||||
{hybrid} pair style. Some additional changes still need to be made to
|
||||
enable this.
|
||||
|
||||
As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the {ffield} file. If you want
|
||||
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
||||
H, you would use the following pair_coeff command:
|
||||
|
||||
pair_coeff * * ffield.reax 1 1 4 2 :pre
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, 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 can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real "units"_units.html. You can use
|
||||
the ReaxFF potential with any LAMMPS units, but you would need to
|
||||
create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "real" units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
|
||||
"fix_reax_bonds"_fix_reax_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
|
||||
{precision} = 1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Chenoweth_20081)
|
||||
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
|
||||
@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
|
||||
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper: "(Chenoweth et al.,
|
||||
2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches
|
||||
@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
|
||||
half or full neighbor lists. This setting can be changed using the
|
||||
Kokkos "package"_package.html command.
|
||||
|
||||
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
|
||||
command in the lo-level implementation details. The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
The {reax/c} style differs from the (obsolete) "pair_style reax"
|
||||
command in the implementation details. The {reax} style was a
|
||||
Fortran library, linked to LAMMPS. The {reax} style has been removed
|
||||
from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial
|
||||
code. If these are changed by setting control variables in the control
|
||||
file, the results from LAMMPS and the serial code will not agree.
|
||||
|
||||
Two examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax"_pair_reax.html.
|
||||
Examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom. See the "atom_style"_atom_style.html and
|
||||
@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types:
|
||||
filename
|
||||
N indices = ReaxFF elements :ul
|
||||
|
||||
The filename is the ReaxFF potential file. Unlike for the {reax}
|
||||
pair style, any filename can be used.
|
||||
The filename is the ReaxFF potential file.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units.
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
|
||||
reax/c/bonds"_fix_reax_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html, "pair_style
|
||||
reax"_pair_reax.html
|
||||
reax/c/bonds"_fix_reaxc_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
@ -16,7 +16,7 @@ pair_style snap :pre
|
||||
[Examples:]
|
||||
|
||||
pair_style snap
|
||||
pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
|
||||
pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
|
||||
the SNAP potential files themselves.
|
||||
|
||||
Only a single pair_coeff command is used with the {snap} style which
|
||||
specifies two SNAP files and the list SNAP element(s) to be
|
||||
extracted.
|
||||
The SNAP elements are mapped to LAMMPS atom types by specifying
|
||||
N additional arguments after the 2nd filename in the pair_coeff
|
||||
command, where N is the number of LAMMPS atom types:
|
||||
specifies a SNAP coefficient file followed by a SNAP parameter file
|
||||
and then N additional arguments specifying the mapping of SNAP
|
||||
elements to LAMMPS atom types, where N is the number of
|
||||
LAMMPS atom types:
|
||||
|
||||
SNAP element file
|
||||
Elem1, Elem2, ...
|
||||
SNAP coefficient file
|
||||
SNAP parameter file
|
||||
N element names = mapping of SNAP elements to atom types :ul
|
||||
|
||||
@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
|
||||
types, with the first two being indium and the 3rd and 4th being
|
||||
phophorous, the pair_coeff command would look like this:
|
||||
|
||||
pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
|
||||
pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
|
||||
|
||||
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The two filenames are for the element and parameter files, respectively.
|
||||
The 'In' and 'P' arguments (between the file names) are the two elements
|
||||
which will be extracted from the element file. The
|
||||
two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
||||
The two filenames are for the coefficient and parameter files, respectively.
|
||||
The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
||||
SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
|
||||
3 and 4 to the SNAP 'P' element.
|
||||
|
||||
@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
|
||||
{hybrid} pair style. The NULL values are placeholders for atom types
|
||||
that will be used with other potentials.
|
||||
|
||||
The name of the SNAP element file usually ends in the
|
||||
The name of the SNAP coefficient file usually ends in the
|
||||
".snapcoeff" extension. It may contain coefficients
|
||||
for many SNAP elements.
|
||||
Only those elements listed in the pair_coeff command are extracted.
|
||||
for many SNAP elements. The only requirement is that it
|
||||
contain at least those element names appearing in the
|
||||
LAMMPS mapping list.
|
||||
The name of the SNAP parameter file usually ends in the ".snapparam"
|
||||
extension. It contains a small number
|
||||
of parameters that define the overall form of the SNAP potential.
|
||||
@ -103,15 +100,13 @@ by the following commands:
|
||||
zbl $\{zblcutinner\} $\{zblcutouter\} snap
|
||||
pair_coeff * * zbl 0.0
|
||||
pair_coeff 1 1 zbl $\{zblz\}
|
||||
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
|
||||
../potentials/Ta06A.snapparam Ta :pre
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta :pre
|
||||
|
||||
It is convenient to keep these commands in a separate file that can
|
||||
be inserted in any LAMMPS input script using the "include"_include.html
|
||||
command.
|
||||
|
||||
The top of the SNAP element file can contain any number of blank and comment
|
||||
lines (start with #), but follows a strict
|
||||
The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
|
||||
format after that. The first non-blank non-comment
|
||||
line must contain two integers:
|
||||
|
||||
|
||||
@ -174,6 +174,7 @@ 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
|
||||
"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
|
||||
@ -226,8 +227,7 @@ accelerated styles exist.
|
||||
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
"mdpd"_pair_meso.html - mDPD particle interactions
|
||||
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
|
||||
"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
|
||||
"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
|
||||
"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
|
||||
"meam/spline"_pair_meam_spline.html - splined version of MEAM
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
|
||||
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
@ -260,7 +260,6 @@ accelerated styles exist.
|
||||
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
|
||||
"python"_pair_python.html -
|
||||
"quip"_pair_quip.html -
|
||||
"reax"_pair_reax.html - ReaxFF potential in Fortran
|
||||
"reax/c"_pair_reaxc.html - ReaxFF potential in C
|
||||
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
|
||||
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
|
||||
@ -50,6 +50,7 @@ Pair Styles :h1
|
||||
pair_kolmogorov_crespi_full
|
||||
pair_kolmogorov_crespi_z
|
||||
pair_lcbop
|
||||
pair_lebedeva_z
|
||||
pair_line_lj
|
||||
pair_list
|
||||
pair_lj
|
||||
@ -63,7 +64,7 @@ Pair Styles :h1
|
||||
pair_lubricate
|
||||
pair_lubricateU
|
||||
pair_mdf
|
||||
pair_meam
|
||||
pair_meamc
|
||||
pair_meam_spline
|
||||
pair_meam_sw_spline
|
||||
pair_meso
|
||||
@ -82,7 +83,6 @@ Pair Styles :h1
|
||||
pair_polymorphic
|
||||
pair_python
|
||||
pair_quip
|
||||
pair_reax
|
||||
pair_reaxc
|
||||
pair_resquared
|
||||
pair_sdk
|
||||
|
||||
@ -22,7 +22,8 @@ field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
|
||||
{ix},{iy},{iz} = image flags in each dimension
|
||||
{fx},{fy},{fz} = force components :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
|
||||
keyword = {nfile} or {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
|
||||
{nfile} value = Nfiles = how many parallel dump files exist
|
||||
{box} value = {yes} or {no} = replace simulation box with dump box
|
||||
{replace} value = {yes} or {no} = overwrite atoms with dump atoms
|
||||
{purge} value = {yes} or {no} = delete all atoms before adding dump atoms
|
||||
@ -85,9 +86,18 @@ command, after the dump snapshot is read.
|
||||
|
||||
If the dump filename specified as {file} ends with ".gz", the dump
|
||||
file is read in gzipped format. You cannot (yet) read a dump file
|
||||
that was written in binary format with a ".bin" suffix, or to multiple
|
||||
files via the "%" option in the dump file name. See the
|
||||
"dump"_dump.html command for details.
|
||||
that was written in binary format with a ".bin" suffix.
|
||||
|
||||
You can read dump files that were written (in parallel) to multiple
|
||||
files via the "%" wild-card character in the dump file name. If any
|
||||
specified dump file name contains a "%", they must all contain it.
|
||||
See the "dump"_dump.html command for details.
|
||||
The "%" wild-card character is only supported by the {native} format
|
||||
for dump files, described next.
|
||||
|
||||
If reading parallel dump files, you must also use the {nfile} keyword
|
||||
to tell LAMMPS how many parallel files exist, via its specified
|
||||
{Nfiles} value.
|
||||
|
||||
The format of the dump file is selected through the {format} keyword.
|
||||
If specified, it must be the last keyword used, since all remaining
|
||||
|
||||
@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
|
||||
dim = {x} or {y} or {z} = axis of cylinder
|
||||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
radius = cylinder radius (distance units)
|
||||
radius can be a variable (see below)
|
||||
c1,c2, and radius can be a variable (see below)
|
||||
lo,hi = bounds of cylinder in dim (distance units)
|
||||
{plane} args = px py pz nx ny nz
|
||||
px,py,pz = point on the plane (distance units)
|
||||
@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
|
||||
{sphere} args = x y z radius
|
||||
x,y,z = center of sphere (distance units)
|
||||
radius = radius of sphere (distance units)
|
||||
radius can be a variable (see below)
|
||||
x,y,z, and radius can be a variable (see below)
|
||||
{union} args = N reg-ID1 reg-ID2 ...
|
||||
N = # of regions to follow, must be 2 or greater
|
||||
reg-ID1,reg-ID2, ... = IDs of regions to join together
|
||||
@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
|
||||
as an equal-style "variable"_variable.html. If the value is a
|
||||
variable, it should be specified as v_name, where name is the variable
|
||||
name. In this case, the variable will be evaluated each timestep, and
|
||||
its value used to determine the radius of the region.
|
||||
its value used to determine the radius of the region. For style {sphere}
|
||||
also the x-, y-, and z- coordinate of the center of the sphere and for
|
||||
style {cylinder} the two center positions c1 and c2 for the location of
|
||||
the cylinder axes can be a variable with the same kind of effect and
|
||||
requirements than for the radius.
|
||||
|
||||
Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include "thermo_style"_thermo_style.html command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent radius.
|
||||
time. Thus it is easy to specify a time-dependent radius or have
|
||||
a time dependent position of the sphere or cylinder region.
|
||||
|
||||
See the "Howto tricilinc"_Howto_triclinic.html doc page for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
|
||||
@ -89,12 +89,31 @@ this auxiliary information should be defined in the usual way, e.g. in
|
||||
a data file read in by a "read_data"_read_data.html command, before
|
||||
using the rerun command.
|
||||
|
||||
Also note that the frequency of thermodynamic or dump output from the
|
||||
rerun simulation will depend on settings made in the rerun script, the
|
||||
same as for output from any LAMMPS simulation. See further info below
|
||||
as to what that means if the timesteps for snapshots read from dump
|
||||
files do not match the specified output frequency.
|
||||
|
||||
:line
|
||||
|
||||
If more than one dump file is specified, the dump files are read one
|
||||
after the other. It is assumed that snapshot timesteps will be in
|
||||
ascending order. If a snapshot is encountered that is not in
|
||||
ascending order, it will cause the rerun command to complete.
|
||||
ascending order, it will skip the snapshot until it reads one that is.
|
||||
This allows skipping of a duplicate snapshot (same timestep),
|
||||
e.g. that appeared at the end of one file and beginning of the next.
|
||||
However if you specify a series of dump files in an incorrect order
|
||||
(with respect to the timesteps they contain), you may skip large
|
||||
numbers of snapshots
|
||||
|
||||
Note that the dump files specified as part of the {dump} keyword can
|
||||
be parallel files, i.e. written as multiple files either per processor
|
||||
and/or per snapshot. If that is the case they will also be read in
|
||||
parallel which can make the rerun command operate dramatically faster
|
||||
for large systems. See the doc page for the "read_dump"_read_dump and
|
||||
"dump"_dump.html commands which describe how to read and write
|
||||
parallel dump files.
|
||||
|
||||
The {first}, {last}, {every}, {skip} keywords determine which
|
||||
snapshots are read from the dump file(s). Snapshots are skipped until
|
||||
@ -177,12 +196,12 @@ a timestep it expects to be, LAMMPS will flag an error.
|
||||
|
||||
The various forms of LAMMPS output, as defined by the
|
||||
"thermo_style"_thermo_style.html, "thermo"_thermo.html,
|
||||
"dump"_dump.html, and "restart"_restart.html commands occur on
|
||||
specific timesteps. If successive dump snapshots skip those
|
||||
timesteps, then no output will be produced. E.g. if you request
|
||||
thermodynamic output every 100 steps, but the dump file snapshots are
|
||||
every 1000 steps, then you will only see thermodynamic output every
|
||||
1000 steps.
|
||||
"dump"_dump.html, and "restart"_restart.html commands occur with
|
||||
specified frequency, e.g. every N steps. If the timestep for a dump
|
||||
snapshot is not a multiple of N, then it will be read and processed,
|
||||
but no output will be produced. If you want output for every dump
|
||||
snapshot, you can simply use N=1 for an output frequency, e.g. for
|
||||
thermodynamic output or new dump file output.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
Reference in New Issue
Block a user