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Merge pull request #1222 from lammps/doc-adjust3 

Some adjustments to the documentation for the per style listing pages
This commit is contained in:
Axel Kohlmeyer 2018-11-26 15:20:29 -05:00 committed by GitHub
parent 4004b8f161 4434481c91
commit 6745c37741
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GPG Key ID: 4AEE18F83AFDEB23
92 changed files with 671 additions and 713 deletions
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4
doc/src/Build_basics.txt
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@ -49,7 +49,7 @@ make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre
Serial build (see src/MAKE/Makefile.serial):
MPI_INC = -I../STUBS
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs :pre
@ -172,7 +172,7 @@ want.
Parallel build (see src/MAKE/Makefile.mpi):
CC = mpicxx
CCFLAGS = -g -O3
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O :pre

2
doc/src/Build_cmake.txt
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@ -27,7 +27,7 @@ make command to build LAMMPS, which uses the created
Makefile(s). Example:
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
mkdir build; cd build # create a new directory (folder) for build
cmake ../cmake \[options ...\] # configuration with (command-line) cmake
make # compilation :pre

34
doc/src/Build_extras.txt
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@ -64,7 +64,7 @@ available on your system.
If CMake cannot find the library, you can set these variables:
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre
[Traditional make]:
@ -151,7 +151,7 @@ package uses the library settings from the lib/gpu/Makefile.machine
used to build the GPU library.
:line
KIM package :h4,link(kim)
To build with this package, the KIM library must be downloaded and
@ -178,7 +178,7 @@ package?" page.
[CMake build]:
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
@ -255,7 +255,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables:
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
# archGPU = GPU from list above
-D KOKKOS_ENABLE_CUDA=yes
-D KOKKOS_ENABLE_OPENMP=yes
-D KOKKOS_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre
The wrapper value is the Cuda nvcc compiler wrapper provided in the
@ -297,7 +297,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx :pre
:line
LATTE package :h4,link(latte)
To build with this package, you must download and build the LATTE
@ -325,7 +325,7 @@ args:
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
:pre
@ -336,7 +336,7 @@ also check that the Makefile.lammps file you create is appropriate for
the compiler you use on your system to build LATTE.
:line
MEAM package :h4,link(meam)
NOTE: the use of the MEAM package is discouraged, as it has been
@ -379,7 +379,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
file.
:line
MESSAGE package :h4,link(message)
This package can optionally include support for messaging via sockets,
@ -408,7 +408,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ
library if requested in the build.
:line
MSCG package :h4,link(mscg)
To build with this package, you must download and build the MS-CG
@ -420,7 +420,7 @@ lib/mscg/README and MSCG/Install files for more details.
[CMake build]:
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre
If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
@ -465,7 +465,7 @@ line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
an example.
:line
POEMS package :h4,link(poems)
[CMake build]:
@ -494,7 +494,7 @@ for your system, which should define an EXTRAMAKE variable to specify
a corresponding Makefile.lammps.machine file.
:line
PYTHON package :h4,link(python)
Building with the PYTHON package requires you have a Python shared
@ -521,7 +521,7 @@ Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
build fails.
:line
REAX package :h4,link(reax)
NOTE: the use of the REAX package and its "pair_style
@ -571,7 +571,7 @@ library"_voro-home.
[CMake build]:
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre
If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
@ -791,7 +791,7 @@ settings suitable for LAMMPS to compile and link PLUMED in the desired
linkage mode. After this step is completed, you can install the
USER-PLUMED package and compile LAMMPS in the usual manner:
make yes-user-plumed
make yes-user-plumed
make machine :pre
Once this compilation completes you should be able to run LAMMPS in the
@ -967,7 +967,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version
[CMake build]:
The CMake build system currently does not support building the full
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
You must use the traditional make build for this package.
[Traditional make]:
@ -1037,7 +1037,7 @@ Coulomb solver library"_scafacos-home
[CMake build]:
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre
If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded

22
doc/src/Build_settings.txt
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@ -22,7 +22,7 @@ explain how to do this for building both with CMake and make.
"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
:line
FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the
@ -73,7 +73,7 @@ FFT_LIB with the appropriate FFT libraries to include in the link.
The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the
size of the FFTs and the number of processors used, the other
libraries listed here can be faster.
libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
@ -92,7 +92,7 @@ Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
various options.
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT_LIB setting above).
@ -143,12 +143,12 @@ LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
[CMake and make info]:
The default "smallbig" setting allows for simulations with:
total atom count = 2^63 atoms (about 9e18)
total timesteps = 2^63 (about 9e18)
atom IDs = 2^31 (about 2 billion)
image flags = roll over at 512 :ul
The "bigbig" setting increases the latter two limits. It allows for:
total atom count = 2^63 atoms (about 9e18)
@ -209,12 +209,12 @@ Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre
[Makefile.machine settings]:

6
doc/src/Build_windows.txt
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@ -53,14 +53,14 @@ are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. The CMake build system is untested
for this; you will have to request that makefiles are generated and
manually set the compiler.
manually set the compiler.
When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
this up automatically, but is untested.
this up automatically, but is untested.
In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems

2
doc/src/Errors.txt
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@ -32,7 +32,7 @@ END_RST -->
"Common problems"_Errors_common.html
"Reporting bugs"_Errors_bugs.html
"Error messages"_Errors_messages.html
"Error messages"_Errors_messages.html
"Warning messages"_Errors_warnings.html :all(b)
<!-- END_HTML_ONLY -->

6
doc/src/Howto_bash.txt
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@ -40,7 +40,7 @@ Install Windows Subsystem for Linux :h5
Next you must ensure that the Window Subsystem for Linux is installed. Again,
search for "enable windows features" in the Settings dialog. This opens a
dialog with a list of features you can install. Add a checkmark to Windows
Subsystem for Linux (Beta) and press OK.
Subsystem for Linux (Beta) and press OK.
:image(JPG/bow_tutorial_04_small.png,JPG/bow_tutorial_04.png)
:image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
@ -54,12 +54,12 @@ enter. This will then download Ubuntu for Windows.
:image(JPG/bow_tutorial_06.png)
:image(JPG/bow_tutorial_07.png)
During installation, you will be asked for a new password. This will be used
for installing new software and running commands with sudo.
:image(JPG/bow_tutorial_08.png)
Type exit to close the command-line window.
Go to the Start menu and type "bash" again. This time you will see a "Bash on

4
doc/src/Howto_body.txt
View File

@ -132,7 +132,7 @@ x1 y1 z1
xN yN zN :pre
where M = 6 + 3*N, and N is the number of sub-particles in the body
particle.
particle.
The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
@ -315,7 +315,7 @@ x1 y1 z1
...
xN yN zN
0 1
1 2
1 2
2 3
...
0 1 2 -1

8
doc/src/Howto_client_server.txt
View File

@ -75,7 +75,7 @@ examples/COUPLE/lammps_mc
examples/COUPLE/lammps_vasp :ul
The examples/message dir couples a client instance of LAMMPS to a
server instance of LAMMPS.
server instance of LAMMPS.
The lammps_mc dir shows how to couple LAMMPS as a server to a simple
Monte Carlo client code as the driver.
@ -106,13 +106,13 @@ together to exchange MPI messages between them.
For message exchange in {file}, {zmq}, or {mpi/two} modes:
% mpirun -np 1 lmp_mpi -log log.client < in.client &
% mpirun -np 1 lmp_mpi -log log.client < in.client &
% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
% mpirun -np 4 lmp_mpi -log log.client < in.client &
% mpirun -np 4 lmp_mpi -log log.client < in.client &
% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
% mpirun -np 2 lmp_mpi -log log.client < in.client &
% mpirun -np 2 lmp_mpi -log log.client < in.client &
% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
For message exchange in {mpi/one} mode:

2
doc/src/Howto_library.txt
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@ -185,7 +185,7 @@ by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
If the count is specified as 1, they are returned
If the count is specified as 1, they are returned
in a packed format with all three image flags stored in a single integer.
If the count is specified as 3, the values are unpacked into xyz flags
by the library before returning them.

54
doc/src/Howto_spins.txt
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@ -12,48 +12,48 @@ Magnetic spins :h3
The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
materials.
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
materials.
The magnetic spins are interacting with each others and with the
lattice via pair interactions. Typically, the magnetic exchange
interaction can be defined using the
The magnetic spins are interacting with each others and with the
lattice via pair interactions. Typically, the magnetic exchange
interaction can be defined using the
"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
applies a magnetic torque to a given spin, considering the orientation
of its neighboring spins and their relative distances.
It also applies a force on the atoms as a function of the spin
orientations and their associated inter-atomic distances.
of its neighboring spins and their relative distances.
It also applies a force on the atoms as a function of the spin
orientations and their associated inter-atomic distances.
The command "fix precession/spin"_fix_precession_spin.html allows to
apply a constant magnetic torque on all the spins in the system. This
torque can be an external magnetic field (Zeeman interaction), or an
uniaxial magnetic anisotropy.
uniaxial magnetic anisotropy.
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.
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.
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
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.
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
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
magnetization of the system along x, y, or z, the spin temperature, or
the magnetic energy. The second command is "compute
the magnetic energy. The second command is "compute
property/atom"_compute_property_atom.html. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
:line
:link(Tranchida7)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
arXiv preprint arXiv:1801.10233, (2018).

2
doc/src/Install_linux.txt
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@ -89,7 +89,7 @@ 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
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.
The same mechanism applies when loading the LAMMPS python module.

2
doc/src/Install_patch.txt
View File

@ -17,7 +17,7 @@ how to stay current are on the "Install git"_Install_git.html and
If you prefer to download a tarball, as described on the "Install
git"_Install_tarball.html doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the "bug and feature
a patch file is posted on the "bug and feature
page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local

2
doc/src/Intro_authors.txt
View File

@ -58,7 +58,7 @@ page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)

6
doc/src/Intro_features.txt
View File

@ -110,7 +110,7 @@ Atom creation :h4,link(create)
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4,link(ensemble)
("fix"_fix.html command)
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
@ -128,7 +128,7 @@ Ensembles, constraints, and boundary conditions :h4,link(ensemble)
variety of additional boundary conditions and constraints :ul
Integrators :h4,link(integrate)
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
Brownian dynamics
@ -142,7 +142,7 @@ Diagnostics :h4,link(diag)
see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4,link(output)
("dump"_dump.html, "restart"_restart.html commands)
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities

2
doc/src/Manual_build.txt
View File

@ -61,7 +61,7 @@ make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
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

56
doc/src/Packages_details.txt
View File

@ -205,7 +205,7 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -286,7 +286,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -354,7 +354,7 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -400,7 +400,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -548,7 +548,7 @@ and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -681,7 +681,7 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -713,7 +713,7 @@ have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -770,7 +770,7 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -802,7 +802,7 @@ shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
lib/python/README for more details.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -850,7 +850,7 @@ as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1023,7 +1023,7 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1050,7 +1050,7 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1077,7 +1077,7 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1100,7 +1100,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
of "fix npt"_fix_nh.html which includes the pressure correction to
the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
@ -1185,7 +1185,7 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#user-colvars on the "Build
@ -1395,7 +1395,7 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1433,7 +1433,7 @@ NOTE: the USER-INTEL package contains styles that require using the
[Author:] Mike Brown (Intel).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1603,17 +1603,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
Pair, angle and improper styles needed to employ the MOF-FF
force field by Schmid and coworkers with LAMMPS.
force field by Schmid and coworkers with LAMMPS.
MOF-FF is a first principles derived force field with the primary aim
to simulate MOFs and related porous framework materials, using spherical
to simulate MOFs and related porous framework materials, using spherical
Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
2013, 250, 1128-1141.
For the usage of MOF-FF see the example in the example directory as
For the usage of MOF-FF see the example in the example directory as
well as the "MOF+"_MOFplus website.
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
[Author:] Hendrik Heenen (Technical U of Munich),
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
[Supporting info:]
@ -1654,7 +1654,7 @@ at
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1694,7 +1694,7 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1738,7 +1738,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1817,7 +1817,7 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1875,7 +1875,7 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1994,7 +1994,7 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -2120,7 +2120,7 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build

53
doc/src/Run_options.txt
View File

@ -354,29 +354,31 @@ the LAMMPS simulation domain.
:line
[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
[-restart2data restartfile \[remap\] datafile keyword value ...]
:link(restart2data)
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
read_restart restartfile \[remap\]
write_data datafile keyword value ... :pre
Note that the specified restartfile and/or datafile can have the
wild-card character "*". The restartfile can also have the wild-card
The specified restartfile and/or datafile name may contain the wild-card
character "*". The restartfile name may also contain the wild-card
character "%". The meaning of these characters is explained on the
"read_restart"_read_restart.html and "write_data"_write_data.html doc
pages. The use of "%" means that a parallel restart file can be read.
Note that a filename such as file.* will need to be enclosed in quotes
to avoid shell expansion of the "*" character.
Note that a filename such as file.* may need to be enclosed in quotes or
the "*" character prefixed with a backslash ("\") to avoid shell
expansion of the "*" character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect of adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the data file to still be produced.
Following restartfile argument, the optional word "remap" may be used.
This has the same effect like adding it to a
"read_restart"_read_restart.html command, and operates as explained on
its doc page. This is useful if reading the restart file triggers an
error that atoms have been lost. In that case, use of the remap flag
should allow the data file to still be produced.
The syntax following restartfile (or remap), namely
@ -388,29 +390,30 @@ optional keyword/value settings.
:line
[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
read_restart restartfile \[remap\]
write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
Note that the specified restartfile and dumpfile can have wild-card
characters ("*","%") as explained on the
Note that the specified restartfile and dumpfile names may contain
wild-card characters ("*","%") as explained on the
"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
pages. The use of "%" means that a parallel restart file and/or
parallel dump file can be read and/or written. Note that a filename
such as file.* will need to be enclosed in quotes to avoid shell
expansion of the "*" character.
such as file.* may need to be enclosed in quotes or the "*" character
prefixed with a backslash ("\") to avoid shell expansion of the "*"
character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the dump file to still be produced.
Note that following the restartfile argument, the optional word "remap"
can be used. This has the effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc page.
This is useful if reading the restart file triggers an error that atoms
have been lost. In that case, use of the remap flag should allow the
dump file to still be produced.
The syntax following restartfile (or remap), namely
@ -524,7 +527,7 @@ option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined.
re-defined.
See the "variable"_variable.html command for more info on defining
index and other kinds of variables and the "Commands

14
doc/src/Speed_intel.txt
View File

@ -27,9 +27,9 @@ Bond Styles: fene, fourier, harmonic :l
Dihedral Styles: charmm, harmonic, opls :l
Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
Improper Styles: cvff, harmonic :l
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
rebo, sw, tersoff :l
K-Space Styles: pppm, pppm/disp :l
:ule
@ -233,12 +233,12 @@ However, if you do not have co-processors on your system, building
without offload support will produce a smaller binary.
The general requirements for Makefiles with the USER-INTEL package
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
(unless Intel Math Kernel Library (MKL) is not available in the build
environment). For Intel compilers, LIB should include "-ltbbmalloc"
environment). For Intel compilers, LIB should include "-ltbbmalloc"
or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
@ -399,7 +399,7 @@ the "suffix hybrid intel omp"_suffix.html command can also be used
within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html to the beginning of the input script for
better scalability.

8
doc/src/Speed_kokkos.txt
View File

@ -106,10 +106,10 @@ modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.
NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both

2
doc/src/Tools.txt
View File

@ -263,7 +263,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
emacs tool :h4,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
with various highlighting options set up.

24
doc/src/angle_coeff.txt
View File

@ -60,26 +60,14 @@ doc page for details.
:line
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The full list of all
angle styles is on the "Commands bond"_Commands_bond.html#angle doc
The list of all angle styles defined in LAMMPS is given on the
"angle_style"_angle_style.html doc page. They are also listed in more
compact form on the "Commands angle"_Commands_bond.html#angle doc
page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle
"angle_style table"_angle_table.html - tabulated by angle :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
angle_coeff command.
:line

12
doc/src/angle_cosine_buck6d.txt
View File

@ -23,19 +23,19 @@ The {cosine/buck6d} angle style uses the potential
:c,image(Eqs/angle_cosine_buck6d.jpg)
where K is the energy constant, n is the periodic multiplicity and
where K is the energy constant, n is the periodic multiplicity and
Theta0 is the equilibrium angle.
The coefficients must be defined for each angle type via the
The coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands in the following order:
K (energy)
n
n
Theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
Additional to the cosine term the {cosine/buck6d} angle style computes
@ -51,8 +51,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
[Restrictions:]
{cosine/buck6d} can only be used in combination with the
"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the
USER-MOFFF package. See the "Build package"_Build_package.html doc

2
doc/src/angle_cosine_shift.txt
View File

@ -63,7 +63,7 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER-MISC package.
USER-MISC package.
[Related commands:]

13
doc/src/angle_style.txt
View File

@ -57,10 +57,15 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The full list of all
angle styles are is on the "Commands bond"_Commands_bond.html#angle
doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the angle_style command, and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
angle"_Commands_bond.html#angle doc page are followed by one or more
of (g,i,k,o,t) to indicate which accelerated styles exist.
"none"_angle_none.html - turn off angle interactions
"zero"_angle_zero.html - topology but no interactions

8
doc/src/atom_style.txt
View File

@ -39,7 +39,7 @@ atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style spin
atom_style template myMols
atom_style template myMols
atom_style tdpd 2 :pre
[Description:]
@ -309,9 +309,9 @@ force fields"_pair_eff.html.
The {dpd} style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The {meso} style is part of the USER-SPH package for smoothed particle

24
doc/src/bond_coeff.txt
View File

@ -56,25 +56,13 @@ corresponds to the 1st example above would be listed as
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
The list of all bond styles defined in LAMMPS is given on the
"bond_style"_bond_style.html doc page. They are also listed in more
compact form on the "Commands bond"_Commands_bond.html doc page.
Note that here are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond
"bond_style table"_bond_table.html - tabulated by bond length :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
bond_coeff command.
:line

14
doc/src/bond_style.txt
View File

@ -65,9 +65,15 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that there are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the bond_style command, and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands bond"_Commands_bond.html
doc page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"none"_bond_none.html - turn off bonded interactions
"zero"_bond_zero.html - topology but no interactions
@ -83,7 +89,7 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page.
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"quartic"_bond_quartic.html - breakable quartic bond
"table"_bond_table.html - tabulated by bond length :ul

127
doc/src/compute.txt
View File

@ -164,25 +164,20 @@ and what it does. Here is an alphabetic list of compute styles
available in LAMMPS. They are also listed in more compact form on the
"Commands compute"_Commands_compute.html doc page.
There are also additional compute styles (not listed here) submitted
by users which are included in the LAMMPS distribution. The full list
of all compute styles is on the "Commands
compute"_Commands_compute.html doc page.
There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
(g,i,k,o,t) to indicate which accelerated styles exist.
"ackland/atom"_compute_ackland_atom.html -
"adf"_compute_adf.html - angular distribution function
"ackland/atom"_compute_ackland_atom.html -
"adf"_compute_adf.html - angular distribution function of triples of atoms
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle/local"_compute_bond_local.html - theta and energy of each angle
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
"basal/atom"_compute_basal_atom.html -
"basal/atom"_compute_basal_atom.html -
"body/local"_compute_body_local.html - attributes of body sub-particles
"bond"_compute_bond.html - values computed by a bond style
"bond/local"_compute_bond_local.html - distance and energy of each bond
@ -191,48 +186,48 @@ compute"_Commands_compute.html doc page are followed by one or more of
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"cnp/atom"_compute_cnp_atom.html -
"cnp/atom"_compute_cnp_atom.html -
"com"_compute_com.html - center-of-mass of group of atoms
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
"dihedral"_compute_dihedral.html -
"dihedral"_compute_dihedral.html -
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
"dipole/chunk"_compute_dipole_chunk.html -
"dipole/chunk"_compute_dipole_chunk.html -
"displace/atom"_compute_displace_atom.html - displacement of each atom
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"event/displace"_compute_event_displace.html - detect event on atom displacement
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
"global/atom"_compute_global_atom.html -
"global/atom"_compute_global_atom.html -
"group/group"_compute_group_group.html - energy/force between two groups of atoms
"gyration"_compute_gyration.html - radius of gyration of group of atoms
"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"heat/flux/tally"_compute_tally.html -
"heat/flux/tally"_compute_tally.html -
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
"improper"_compute_improper.html -
"improper"_compute_improper.html -
"improper/local"_compute_improper_local.html - angle of each improper
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
"ke"_compute_ke.html - translational kinetic energy
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@ -242,71 +237,71 @@ compute"_Commands_compute.html doc page are followed by one or more of
"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
"pe"_compute_pe.html - potential energy
"pe/atom"_compute_pe_atom.html - potential energy for each atom
"pe/mol/tally"_compute_tally.html -
"pe/tally"_compute_tally.html -
"pe/mol/tally"_compute_tally.html -
"pe/tally"_compute_tally.html -
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"ptm/atom"_compute_ptm_atom.html -
"ptm/atom"_compute_ptm_atom.html -
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"saed"_compute_saed.html -
"saed"_compute_saed.html -
"slice"_compute_slice.html - extract values from global vector or array
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"spin"_compute_spin.html -
"spin"_compute_spin.html -
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/body"_compute_temp_body.html - temperature of body particles
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/cs"_compute_temp_cs.html -
"temp/cs"_compute_temp_cs.html -
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
"temp/uef"_compute_temp_uef.html -
"temp/uef"_compute_temp_uef.html -
"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms

2
doc/src/compute_angle_local.txt
View File

@ -29,7 +29,7 @@ keyword = {set} :l
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local eng theta
compute 1 all angle/local eng theta
compute 1 all angle/local theta v_cos set theta t :pre
[Description:]

22
doc/src/compute_chunk_spread_atom.txt
View File

@ -74,7 +74,7 @@ produces a global vector or array.
:line
Each listed input is operated on independently.
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
@ -134,16 +134,16 @@ compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
thermo_style custom step etotal press v_ave :pre
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362 :pre
:line

2
doc/src/compute_edpd_temp_atom.txt
View File

@ -24,7 +24,7 @@ compute 1 all edpd/temp/atom :pre
Define a computation that calculates the per-atom temperature
for each eDPD particle in a group.
The temperature is a local temperature derived from the internal energy
The temperature is a local temperature derived from the internal energy
of each eDPD particle based on the local equilibrium hypothesis.
For more details please see "(Espanol1997)"_#Espanol1997 and
"(Li2014)"_#Li2014a.

34
doc/src/compute_entropy_atom.txt
View File

@ -35,11 +35,11 @@ compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
Define a computation that calculates the pair entropy fingerprint for
each atom in the group. The fingerprint is useful to distinguish between
ordered and disordered environments, for instance liquid and solid-like
environments, or glassy and crystalline-like environments. Some
applications could be the identification of grain boundaries, a
melt-solid interface, or a solid cluster emerging from the melt.
The advantage of this parameter over others is that no a priori
ordered and disordered environments, for instance liquid and solid-like
environments, or glassy and crystalline-like environments. Some
applications could be the identification of grain boundaries, a
melt-solid interface, or a solid cluster emerging from the melt.
The advantage of this parameter over others is that no a priori
information about the solid structure is required.
This parameter for atom i is computed using the following formula from
@ -47,8 +47,8 @@ This parameter for atom i is computed using the following formula from
:c,image(Eqs/pair_entropy.jpg)
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
atom i can be noisy and therefore it is smoothed using:
:c,image(Eqs/pair_entropy2.jpg)
@ -57,7 +57,7 @@ where the sum in j goes through the neighbors of atom i, and sigma is a
parameter to control the smoothing.
The input parameters are {sigma} the smoothing parameter, and the
{cutoff} for the calculation of g(r).
{cutoff} for the calculation of g(r).
If the keyword {avg} has the setting {yes}, then this compute also
averages the parameter over the neighbors of atom i according to:
@ -66,25 +66,25 @@ averages the parameter over the neighbors of atom i according to:
where the sum j goes over the neighbors of atom i and N is the number
of neighbors. This procedure provides a sharper distinction between
order and disorder environments. In this case the input parameter
{cutoff2} is the cutoff for the averaging over the neighbors and
order and disorder environments. In this case the input parameter
{cutoff2} is the cutoff for the averaging over the neighbors and
must also be specified.
If the {avg yes} option is used, the effective cutoff of the neighbor
list should be {cutoff}+{cutoff2} and therefore it might be necessary
list should be {cutoff}+{cutoff2} and therefore it might be necessary
to increase the skin of the neighbor list with:
neighbor skin bin :pre
See "neighbor"_neighbor.html for details.
If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
Here are typical input parameters for fcc aluminum (lattice
constant 4.05 Angstroms),
compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
@ -102,7 +102,7 @@ uses per-atom values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The pair entropy values have units of the Boltzmann constant. They are
The pair entropy values have units of the Boltzmann constant. They are
always negative, and lower values (lower entropy) correspond to more
ordered environments.

6
doc/src/compute_pressure_cylinder.txt
View File

@ -42,14 +42,14 @@ output in pressure units.
[Output info:]
This compute calculates a global array with 5 columns and Rmax/bin_width
rows. The output columns are: R (distance units), number density (inverse
volume units), configurational radial pressure (pressure units),
rows. The output columns are: R (distance units), number density (inverse
volume units), configurational radial pressure (pressure units),
configurational azimuthal pressure (pressure units), and configurational
axial pressure (pressure units).
The values calculated by this compute are
"intensive". The pressure values will be in pressure
"units"_units.html. The number density values will be in
"units"_units.html. The number density values will be in
inverse volume "units"_units.html.
[Restrictions:]

2
doc/src/compute_property_atom.txt
View File

@ -86,7 +86,7 @@ input = one or more atom attributes :l
compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type
compute 1 all property/atom ix iy iz
compute 1 all property/atom ix iy iz
compute 3 all property/atom sp spx spy spz :pre
[Description:]

2
doc/src/compute_sna_atom.txt
View File

@ -161,7 +161,7 @@ function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
the calculated bispectrum components. This optional keyword
the calculated bispectrum components. This optional keyword
normally only affects compute {sna/atom}. However, when
{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.

16
doc/src/compute_spin.txt
View File

@ -21,7 +21,7 @@ compute out_mag all spin :pre
[Description:]
Define a computation that calculates magnetic quantities for a system
Define a computation that calculates magnetic quantities for a system
of atoms having spins.
This compute calculates 6 magnetic quantities.
@ -31,11 +31,11 @@ magnetization.
The fourth quantity is the norm of the total magnetization.
The fifth quantity is the magnetic energy.
The fifth quantity is the magnetic energy.
The sixth one is referred to as the spin temperature, according
to the work of "(Nurdin)"_#Nurdin1.
to the work of "(Nurdin)"_#Nurdin1.
The simplest way to output the results of the compute spin calculation
is to define some of the quantities as variables, and to use the thermo and
thermo_style commands, for example:
@ -49,9 +49,9 @@ variable temp_mag equal c_out_mag\[6\] :pre
thermo 10
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
This series of commands evaluates the total magnetization along z, the norm of
the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
This series of commands evaluates the total magnetization along z, the norm of
the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
[Output info:]
@ -59,7 +59,7 @@ every 10 timesteps.
The array values are "intensive". The array values will be in
metal units ("units"_units.html).
[Restrictions:]
[Restrictions:]
The {spin} compute is part of the SPIN package. This compute is only
enabled if LAMMPS was built with this package. See the "Build

8
doc/src/compute_stress_mop.txt
View File

@ -60,7 +60,7 @@ Between one and three keywords can be used to indicate which
contributions to the stress must be computed: kinetic stress (kin),
configurational stress (conf), and/or total stress (total).
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the pressure added by the "pair_modify tail
@ -80,11 +80,11 @@ keywords have been declared). For each keyword, the profiles of stress
tensor components are ordered as follows: stress_dir,x; stress_dir,y;
and stress_dir,z.
The values are in pressure "units"_units.html.
The values are in pressure "units"_units.html.
The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
[Restrictions:]
[Restrictions:]
These styles are part of the USER-MISC package. They are only enabled if
LAMMPS is built with that package. See the "Build package"_Build_package.html
@ -107,5 +107,5 @@ intra-molecular interactions, and long range (kspace) interactions.
:line
:link(mop-todd)
[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
Phys. Rev. E 52, 1627 (1995).

4
doc/src/compute_tdpd_cc_atom.txt
View File

@ -13,7 +13,7 @@ compute tdpd/cc/atom command :h3
compute ID group-ID tdpd/cc/atom index :pre
ID, group-ID are documented in "compute"_compute.html command
tdpd/cc/atom = style name of this compute command
tdpd/cc/atom = style name of this compute command
index = index of chemical species (1 to Nspecies) :ul
[Examples:]
@ -37,7 +37,7 @@ any command that uses per-atom values from a compute as input. See the
"Howto output"_Howto_output.html doc page for an overview of LAMMPS
output options.
The per-atom vector values will be in the units of chemical species
The per-atom vector values will be in the units of chemical species
per unit mass.
[Restrictions:]

8
doc/src/compute_temp_uef.txt
View File

@ -17,17 +17,17 @@ temp/uef = style name of this compute command :ul
[Examples:]
compute 1 all temp/uef
compute 1 all temp/uef
compute 2 sel temp/uef :pre
[Description:]
This command is used to compute the kinetic energy tensor in
This command is used to compute the kinetic energy tensor in
the reference frame of the applied flow field when
"fix nvt/uef"_fix_nh_uef.html or
"fix npt/uef"_fix_nh_uef.html is used.
It is not necessary to use this command to compute the scalar
value of the temperature. A "compute temp"_compute_temp.html
value of the temperature. A "compute temp"_compute_temp.html
may be used for that purpose.
Output information for this command can be found in the
@ -39,7 +39,7 @@ This fix is part of the USER-UEF 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 command can only be used when "fix nvt/uef"_fix_nh_uef.html
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
[Related commands:]

2
doc/src/create_bonds.txt
View File

@ -90,7 +90,7 @@ The {many} style will create bonds between pairs of atoms I,J where I
is in one of the two specified groups, and J is in the other. The two
groups can be the same, e.g. group "all". The created bonds will be
of bond type {btype}, where {btype} must be a value between 1 and the
number of bond types defined.
number of bond types defined.
For a bond to be created, an I,J pair of atoms must be a distance D
apart such that {rmin} <= D <= {rmax}.

24
doc/src/dihedral_coeff.txt
View File

@ -69,24 +69,14 @@ necessary.
:line
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
The list of all dihedral styles defined in LAMMPS is given on the
"dihedral_style"_dihedral_style.html doc page. They are also listed
in more compact form on the "Commands
dihedral"_Commands_bond.html#dihedral doc page.
Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The full list of all
dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
dihedral_coeff command.
:line

14
doc/src/dihedral_style.txt
View File

@ -80,10 +80,16 @@ Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The full list of all
dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the dihedral_style command, and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html
command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
dihedral"_Commands_bond.html#dihedral doc page are followed by one or
more of (g,i,k,o,t) to indicate which accelerated styles exist.
"none"_dihedral_none.html - turn off dihedral interactions
"zero"_dihedral_zero.html - topology but no interactions

2
doc/src/dihedral_table_cut.txt
View File

@ -59,7 +59,7 @@ cutoff angle2
filename
keyword :ul
The cutoff dihedral style uses a tabulated dihedral interaction with a
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
:c,image(Eqs/dihedral_table_cut.jpg)

6
doc/src/dump_cfg_uef.txt
View File

@ -28,10 +28,10 @@ dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre
[Description:]
This command is used to dump atomic coordinates in the
reference frame of the applied flow field when
reference frame of the applied flow field when
"fix nvt/uef"_fix_nh_uef.html or
"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic
coordinates and frame-invariant scalar quantities
"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic
coordinates and frame-invariant scalar quantities
will be in the flow frame. If velocities are selected
as output, for example, they will not be in the same
reference frame as the atomic positions.

194
doc/src/fix.txt
View File

@ -156,10 +156,6 @@ what it does, as listed below. Here is an alphabetic list of fix
styles available in LAMMPS. They are also listed in more compact form
on the "Commands fix"_Commands_fix.html doc page.
There are also additional fix styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The full list of
all fix styles is on the "Commands fix"_Commands_fix.html doc page.
There are also additional accelerated fix styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands fix"_Commands_fix.html doc
@ -167,188 +163,188 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"adapt/fep"_fix_adapt_fep.html -
"adapt/fep"_fix_adapt_fep.html -
"addforce"_fix_addforce.html - add a force to each atom
"addtorque"_fix_addtorque.html -
"addtorque"_fix_addtorque.html -
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"atc"_fix_atc.html -
"atc"_fix_atc.html -
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/correlate/long"_fix_ave_correlate_long.html -
"ave/correlate/long"_fix_ave_correlate_long.html -
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/histo/weight"_fix_ave_histo.html -
"ave/histo/weight"_fix_ave_histo.html -
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"balance"_fix_balance.html - perform dynamic load-balancing
"bocs"_fix_bocs.html -
"bocs"_fix_bocs.html -
"bond/break"_fix_bond_break.html - break bonds on the fly
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/react"_fix_bond_react.html -
"bond/react"_fix_bond_react.html -
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"client/md"_fix_client_md.html -
"cmap"_fix_cmap.html -
"colvars"_fix_colvars.html -
"controller"_fix_controller.html -
"client/md"_fix_client_md.html -
"cmap"_fix_cmap.html -
"colvars"_fix_colvars.html -
"controller"_fix_controller.html -
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"dpd/energy"_fix_dpd_energy.html -
"dpd/energy"_fix_dpd_energy.html -
"drag"_fix_drag.html - drag atoms towards a defined coordinate
"drude"_fix_drude.html -
"drude/transform/direct"_fix_drude_transform.html -
"drude/transform/inverse"_fix_drude_transform.html -
"drude"_fix_drude.html -
"drude/transform/direct"_fix_drude_transform.html -
"drude/transform/inverse"_fix_drude_transform.html -
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"edpd/source"_fix_dpd_source.html -
"edpd/source"_fix_dpd_source.html -
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -
"eos/table/rx"_fix_eos_table_rx.html -
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -
"eos/table/rx"_fix_eos_table_rx.html -
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
"external"_fix_external.html - callback to an external driver program
"ffl"_fix_ffl.html -
"filter/corotate"_fix_filter_corotate.html -
"flow/gauss"_fix_flow_gauss.html -
"ffl"_fix_ffl.html -
"filter/corotate"_fix_filter_corotate.html -
"flow/gauss"_fix_flow_gauss.html -
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
"gld"_fix_gld.html -
"gle"_fix_gle.html -
"gld"_fix_gld.html -
"gle"_fix_gle.html -
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"grem"_fix_grem.html -
"grem"_fix_grem.html -
"halt"_fix_halt.html - terminate a dynamics run or minimization
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"hyper/global"_fix_hyper_global.html - global hyperdynamics
"hyper/local"_fix_hyper_local.html - local hyperdynamics
"imd"_fix_imd.html -
"imd"_fix_imd.html -
"indent"_fix_indent.html - impose force due to an indenter
"ipi"_fix_ipi.html -
"ipi"_fix_ipi.html -
"langevin"_fix_langevin.html - Langevin temperature control
"langevin/drude"_fix_langevin_drude.html -
"langevin/eff"_fix_langevin_eff.html -
"langevin/spin"_fix_langevin_spin.html -
"langevin/drude"_fix_langevin_drude.html -
"langevin/eff"_fix_langevin_eff.html -
"langevin/spin"_fix_langevin_spin.html -
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
"lb/fluid"_fix_lb_fluid.html -
"lb/momentum"_fix_lb_momentum.html -
"lb/pc"_fix_lb_pc.html -
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
"lb/viscous"_fix_lb_viscous.html -
"lb/fluid"_fix_lb_fluid.html -
"lb/momentum"_fix_lb_momentum.html -
"lb/pc"_fix_lb_pc.html -
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
"lb/viscous"_fix_lb_viscous.html -
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"manifoldforce"_fix_manifoldforce.html -
"meso"_fix_meso.html -
"manifoldforce"_fix_manifoldforce.html -
"meso"_fix_meso.html -
"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
"meso/move"_fix_meso_move.html -
"meso/stationary"_fix_meso_stationary.html -
"meso/move"_fix_meso_move.html -
"meso/stationary"_fix_meso_stationary.html -
"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
"move"_fix_move.html - move atoms in a prescribed fashion
"mscg"_fix_mscg.html -
"mscg"_fix_mscg.html -
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
"mvv/dpd"_fix_mvv_dpd.html -
"mvv/edpd"_fix_mvv_dpd.html -
"mvv/tdpd"_fix_mvv_dpd.html -
"mvv/dpd"_fix_mvv_dpd.html -
"mvv/edpd"_fix_mvv_dpd.html -
"mvv/tdpd"_fix_mvv_dpd.html -
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/body"_fix_nph_body.html -
"nph/body"_fix_nph_body.html -
"nph/body"_fix_nve_body.html - NPH for body particles
"nph/eff"_fix_nh_eff.html -
"nph/eff"_fix_nh_eff.html -
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/body"_fix_npt_body.html -
"npt/body"_fix_npt_body.html -
"npt/body"_fix_nve_body.html - NPT for body particles
"npt/eff"_fix_nh_eff.html -
"npt/eff"_fix_nh_eff.html -
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
"npt/uef"_fix_nh_uef.html -
"npt/uef"_fix_nh_uef.html -
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
"nve/awpmd"_fix_nve_awpmd.html -
"nve/awpmd"_fix_nve_awpmd.html -
"nve/body"_fix_nve_body.html - NVE for body particles
"nve/dot"_fix_nve_dot.html -
"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
"nve/eff"_fix_nve_eff.html -
"nve/dot"_fix_nve_dot.html -
"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
"nve/eff"_fix_nve_eff.html -
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
"nve/spin"_fix_nve_spin.html -
"nve/spin"_fix_nve_spin.html -
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvk"_fix_nvk.html -
"nvk"_fix_nvk.html -
"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/body"_fix_nve_body.html - NVT for body particles
"nvt/body"_fix_nvt_body.html -
"nvt/eff"_fix_nh_eff.html -
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
"nvt/body"_fix_nvt_body.html -
"nvt/eff"_fix_nh_eff.html -
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"nvt/uef"_fix_nh_uef.html -
"nvt/uef"_fix_nh_uef.html -
"oneway"_fix_oneway.html - constrain particles on move in one direction
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
"phonon"_fix_phonon.html -
"pimd"_fix_pimd.html -
"phonon"_fix_phonon.html -
"pimd"_fix_pimd.html -
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
"precession/spin"_fix_precession_spin.html -
"precession/spin"_fix_precession_spin.html -
"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"property/atom"_fix_property_atom.html - add customized per-atom values
"python/invoke"_fix_python_invoke.html -
"python/move"_fix_python_move.html -
"qbmsst"_fix_qbmsst.html -
"python/invoke"_fix_python_invoke.html -
"python/move"_fix_python_move.html -
"qbmsst"_fix_qbmsst.html -
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
"qeq/point"_fix_qeq.html - charge equilibration via point method
"qeq/reax"_fix_qeq_reax.html -
"qeq/reax"_fix_qeq_reax.html -
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
"qmmm"_fix_qmmm.html -
"qtb"_fix_qtb.html -
"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_reax_bonds.html -
"reax/c/species"_fix_reaxc_species.html -
"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 -
"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/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/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/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/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
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
"shardlow"_fix_shardlow.html -
"smd"_fix_smd.html -
"smd/adjust_dt"_fix_smd_adjust_dt.html -
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
"smd/setvel"_fix_smd_setvel.html -
"smd/wall_surface"_fix_smd_wall_surface.html -
"shardlow"_fix_shardlow.html -
"smd"_fix_smd.html -
"smd/adjust_dt"_fix_smd_adjust_dt.html -
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
"smd/setvel"_fix_smd_setvel.html -
"smd/wall_surface"_fix_smd_wall_surface.html -
"spring"_fix_spring.html - apply harmonic spring force to group of atoms
"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
@ -356,28 +352,28 @@ accelerated styles exist.
"srd"_fix_srd.html - stochastic rotation dynamics (SRD)
"store/force"_fix_store_force.html - store force on each atom
"store/state"_fix_store_state.html - store attributes for each atom
"tdpd/source"_fix_dpd_source.html -
"tdpd/source"_fix_dpd_source.html -
"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
"temp/rescale/eff"_fix_temp_rescale_eff.html -
"temp/rescale/eff"_fix_temp_rescale_eff.html -
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
"ti/spring"_fix_ti_spring.html -
"ti/spring"_fix_ti_spring.html -
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
"ttm/mod"_fix_ttm.html -
"ttm/mod"_fix_ttm.html -
"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
"vector"_fix_vector.html - accumulate a global vector every N timesteps
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
"viscous"_fix_viscous.html - viscous damping for granular simulations
"wall/body/polygon"_fix_wall_body_polygon.html -
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
"wall/body/polygon"_fix_wall_body_polygon.html -
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
"wall/ees"_fix_wall_ees.html -
"wall/ees"_fix_wall_ees.html -
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
"wall/gran/region"_fix_wall_gran_region.html -
"wall/gran/region"_fix_wall_gran_region.html -
"wall/harmonic"_fix_wall.html - harmonic spring wall
"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
@ -385,7 +381,7 @@ accelerated styles exist.
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
"wall/region"_fix_wall_region.html - use region surface as wall
"wall/region/ees"_fix_wall_ees.html -
"wall/region/ees"_fix_wall_ees.html -
"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
[Restrictions:]

48
doc/src/fix_bocs.txt
View File

@ -24,7 +24,7 @@ keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
[Examples:]
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
thermo_modify press 1_press :pre
@ -32,55 +32,55 @@ thermo_modify press 1_press :pre
[Description:]
These commands incorporate a pressure correction as described by
These commands incorporate a pressure correction as described by
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
The first half of the command mimics a standard fix npt command:
fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
The two differences are replacing {npt} with {bocs}, and replacing
The two differences are replacing {npt} with {bocs}, and replacing
{iso}/{aniso}/{etc} with {cgiso}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:
Volume_i, PressureCorrection_i :pre
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
With the {analytic} option, the arguments are as follows:
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.
[Restrictions:]
As this is computing a (modified) pressure, group-ID should be {all}.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
By default, LAMMPS will still report the normal value for the pressure
if the pressure is printed via a {thermo} command, or if the pressures
are written to a file every so often. In order to have LAMMPS report the
modified pressure, you must include the {thermo_modify} command given in
the examples. For the last argument in the command, you should put
modified pressure, you must include the {thermo_modify} command given in
the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
@ -90,8 +90,8 @@ package"_Build_package.html doc page for more info.
[Related:]
For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on GitHub"_bocsgithub and read the release
For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on GitHub"_bocsgithub and read the release
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .

2
doc/src/fix_client_md.txt
View File

@ -68,7 +68,7 @@ LAMMPS and another code in tandem to perform a coupled simulation.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential energy computed by the server application to

2
doc/src/fix_deform.txt
View File

@ -86,7 +86,7 @@ Change the volume and/or shape of the simulation box during a dynamics
run. Orthogonal simulation boxes have 3 adjustable parameters
(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously by this command.
adjusted independently and simultaneously by this command.
This fix can be used to perform non-equilibrium MD (NEMD) simulations
of a continuously strained system. See the "fix

2
doc/src/fix_dt_reset.txt
View File

@ -55,7 +55,7 @@ current velocity and force. Since performing this calculation exactly
would require the solution to a quartic equation, a cheaper estimate
is generated. The estimate is conservative in that the atom's
displacement is guaranteed not to exceed {Xmax}, though it may be
smaller.
smaller.
In addition if the {emax} keyword is used, the specified {Emax} value
is enforced as a limit on how much an atom's kinetic energy can

4
doc/src/fix_gcmc.txt
View File

@ -74,7 +74,7 @@ materials, or computing vapor-liquid coexistence curves.
Every N timesteps the fix attempts both GCMC exchanges
(insertions or deletions) and MC moves of gas atoms or molecules.
On those timesteps, the average number of attempted GCMC exchanges is X,
while the average number of attempted MC moves is M.
while the average number of attempted MC moves is M.
For GCMC exchanges of either molecular or atomic gasses,
these exchanges can be either deletions or insertions,
with equal probability.
@ -203,7 +203,7 @@ atom translations, molecule translations, and molecule rotations,
respectively. The values must be non-negative integers or real
numbers, with at least one non-zero value. For example, (10,30,0)
would result in 25% of the MC moves being atomic translations, 75%
molecular translations, and no molecular rotations.
molecular translations, and no molecular rotations.
Optionally, users may specify the maximum rotation angle for molecular
rotations using the {maxangle} keyword and specifying the angle in

24
doc/src/fix_langevin_spin.txt
View File

@ -25,35 +25,35 @@ fix 2 all langevin/spin 300.0 0.01 21 :pre
[Description:]
Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the
magnetic spins associated to the atoms.
Used with "fix nve/spin"_fix_nve_spin.html, this command performs
Brownian dynamics (BD).
Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the
magnetic spins associated to the atoms.
Used with "fix nve/spin"_fix_nve_spin.html, this command performs
Brownian dynamics (BD).
A random torque and a transverse dissipation are applied to each spin i according to
the following stochastic differential equation:
:c,image(Eqs/fix_langevin_spin_sLLG.jpg)
with lambda the transverse damping, and eta a random vector.
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
equation.
The components of eta are drawn from a Gaussian probability law. Their amplitude
is defined as a proportion of the temperature of the external thermostat T (in K
The components of eta are drawn from a Gaussian probability law. Their amplitude
is defined as a proportion of the temperature of the external thermostat T (in K
in metal units).
More details about this implementation are reported in "(Tranchida)"_#Tranchida2.
Note: due to the form of the sLLG equation, this fix has to be defined just
before the nve/spin fix (and after all other magnetic fixes).
before the nve/spin fix (and after all other magnetic fixes).
As an example:
fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
fix 2 all langevin/spin 300.0 0.01 21
fix 2 all langevin/spin 300.0 0.01 21
fix 3 all nve/spin lattice yes :pre
is correct, but defining a force/spin command after the langevin/spin command
would give an error message.
would give an error message.
Note: The random # {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
@ -81,10 +81,10 @@ only enabled if LAMMPS was built with this package. See the "Build
package"_Build_package.html doc page for more info.
The numerical integration has to be performed with {fix nve/spin}
when {fix langevin/spin} is enabled.
when {fix langevin/spin} is enabled.
This fix has to be the last defined magnetic fix before the time
integration fix (e.g. {fix nve/spin}).
integration fix (e.g. {fix nve/spin}).
[Related commands:]

4
doc/src/fix_latte.txt
View File

@ -58,7 +58,7 @@ LATTE is a code for performing self-consistent charge transfer
tight-binding (SC-TB) calculations of total energies and the forces
acting on atoms in molecules and solids. This tight-binding method is
becoming more and more popular and widely used in chemistry,
biochemistry, material science, etc.
biochemistry, material science, etc.
The SC-TB formalism is derived from an expansion of the Kohn-Sham
density functional to second order in charge fluctuations about a
@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
integrals are parameterized using a Slater-Koster tight-binding
approach. This procedure, which usually is referred to as the DFTB
method has been described in detail by ("Elstner"_#Elstner) and
("Finnis"_#Finnis2) and coworkers.
("Finnis"_#Finnis2) and coworkers.
The work of the LATTE developers follows that of Elstner closely with
respect to the physical model. However, the development of LATTE is

2
doc/src/fix_modify.txt
View File

@ -78,7 +78,7 @@ virial is included in the calculation performed by the "compute
pressure"_compute_pressure.html or
"compute stress/atom"_compute_stress_atom.html
commands. See the "thermo_style"_thermo_style.html command for info
on how pressure is output.
on how pressure is output.
NOTE: You must specify the {virial yes} setting for a fix if you
are doing "box relaxation"_fix_box_relax.html and

2
doc/src/fix_msst.txt
View File

@ -23,7 +23,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
{p0} value = initial pressure in the shock equations (pressure units)
{v0} value = initial simulation cell volume in the shock equations (distance^3 units)
{e0} value = initial total energy (energy units)
{tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
{tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
{dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
{beta} value = scale factor for improved energy conservation :pre
:ule

2
doc/src/fix_nve_dot.txt
View File

@ -36,7 +36,7 @@ The command is equivalent to the "fix nve"_fix_nve.html.
The particles are always considered to have a finite size.
An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line

14
doc/src/fix_nve_dotc_langevin.txt
View File

@ -24,7 +24,7 @@ keyword = {angmom} :l
[Examples:]
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
[Description:]
@ -79,9 +79,9 @@ a Gaussian random number) for speed.
:line
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
be variables. If used together with the oxDNA force field for
be variables. If used together with the oxDNA force field for
coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
corresponds to T = 300 K.
corresponds to T = 300 K.
The {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 0.03
@ -92,10 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the "fix
viscous"_fix_viscous.html command for more details.
Note that the value 78.9375 in the second example above corresponds
to a diffusion constant, which is about an order of magnitude larger
Note that the value 78.9375 in the second example above corresponds
to a diffusion constant, which is about an order of magnitude larger
than realistic ones. This has been used to sample configurations faster
in Brownian dynamics simulations.
in Brownian dynamics simulations.
The random # {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
@ -114,7 +114,7 @@ The scale factor after the {angmom} keyword gives the ratio of the rotational to
the translational friction coefficient.
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line

12
doc/src/fix_nve_spin.txt
View File

@ -27,20 +27,20 @@ fix 1 all nve/spin lattice no :pre
Perform a symplectic integration for the spin or spin-lattice system.
The {lattice} keyword defines if the spins are integrated on a lattice
The {lattice} keyword defines if the spins are integrated on a lattice
of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
By default (lattice = yes), a spin-lattice integration is performed.
The {nve/spin} fix applies a Suzuki-Trotter decomposition to
The {nve/spin} fix applies a Suzuki-Trotter decomposition to
the equations of motion of the spin lattice system, following the scheme:
:c,image(Eqs/fix_integration_spin_stdecomposition.jpg)
according to the implementation reported in "(Omelyan)"_#Omelyan1.
A sectoring method enables this scheme for parallel calculations.
The implementation of this sectoring algorithm is reported
A sectoring method enables this scheme for parallel calculations.
The implementation of this sectoring algorithm is reported
in "(Tranchida)"_#Tranchida1.
:line
@ -51,7 +51,7 @@ This fix style can only be used if LAMMPS was built with the SPIN
package. See the "Build package"_Build_package.html doc page for more
info.
To use the spin algorithm, it is necessary to define a map with
To use the spin algorithm, it is necessary to define a map with
the atom_modify command. Typically, by adding the command:
atom_modify map array :pre
@ -68,7 +68,7 @@ instead of "array" is also valid.
:line
:link(Omelyan1)
[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett.
[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett.
86(5), 898. (2001).
:link(Tranchida1)

2
doc/src/fix_poems.txt
View File

@ -106,7 +106,7 @@ off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
files"_restart.html.
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
this fix style to set whether per-body forces and torques are computed

32
doc/src/fix_precession_spin.txt
View File

@ -15,7 +15,7 @@ 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
{zeeman} args = H x y z
{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
@ -26,43 +26,43 @@ style = {zeeman} or {anisotropy} :l
[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 all precession/spin anisotropy 0.001 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.
Style {zeeman} is used for the simulation of the interaction
between the magnetic spins in the defined group and an external
Style {zeeman} is used for the simulation of the interaction
between the magnetic spins in the defined group and an external
magnetic field:
:c,image(Eqs/force_spin_zeeman.jpg)
with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
in metal units).
with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
in metal units).
Style {anisotropy} is used to simulate an easy axis or an easy plane
for the magnetic spins in the defined group:
Style {anisotropy} is used to simulate an easy axis or an easy plane
for the magnetic spins in the defined group:
:c,image(Eqs/force_spin_aniso.jpg)
with n defining the direction of the anisotropy, and K (in eV) its intensity.
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.
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.
Both styles can be combined within one single command line.
Both styles can be combined within one single command line.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
By default, the energy associated to this fix is not added to the potential
energy of the system.
The "fix_modify"_fix_modify.html {energy} option is supported by this fix
to add this magnetic potential energy to the potential energy of the system,
By default, the energy associated to this fix is not added to the potential
energy of the system.
The "fix_modify"_fix_modify.html {energy} option is supported by this fix
to add this magnetic potential energy to the potential energy of the system,
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes :pre

2
doc/src/fix_rigid_meso.txt
View File

@ -345,5 +345,5 @@ torque. Also reinit = yes.
:line
:link(Miller)
[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
J Chem Phys, 116, 8649 (2002).

22
doc/src/improper_coeff.txt
View File

@ -62,22 +62,14 @@ page for details.
:line
Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command.
The list of all improper styles defined in LAMMPS is given on the
"improper_style"_improper_style.html doc page. They are also listed
in more compact form on the "Commands
improper"_Commands_bond.html#improper doc page.
Note that there are also additional improper styles submitted by users
which are included in the LAMMPS distribution. The full list of all
improper styles is on the "Commands bond"_Commands_bond.html#improper
doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper
"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
improper_coeff command.
:line

12
doc/src/improper_inversion_harmonic.txt
View File

@ -15,7 +15,7 @@ improper_style inversion/harmonic :pre
[Examples:]
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 :pre
improper_coeff 1 18.776340 0.000000 :pre
[Description:]
@ -24,15 +24,15 @@ out-of-plane angle definition and uses an harmonic potential:
:c,image(Eqs/improper_inversion_harmonic.jpg)
where K is the force constant and omega is the angle evaluated for
where K is the force constant and omega is the angle evaluated for
all three axis-plane combinations centered around the atom I. For
the IL axis and the IJK plane omega looks as follows:
:c,image(Eqs/umbrella.jpg)
Note that the {inversion/harmonic} angle term evaluation differs to
the "improper_umbrella"_improper_umbrella.html due to the cyclic
evaluation of all possible angles omega.
Note that the {inversion/harmonic} angle term evaluation differs to
the "improper_umbrella"_improper_umbrella.html due to the cyclic
evaluation of all possible angles omega.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
@ -45,7 +45,7 @@ omega0 (degrees) :ul
If omega0 = 0 the potential term has a minimum for the planar
structure. Otherwise it has two minima at +/- omega0, with a barrier
in between.
in between.
:line

14
doc/src/improper_style.txt
View File

@ -59,10 +59,16 @@ Click on the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html
command.
Note that there are also additional improper styles submitted by users
which are included in the LAMMPS distribution. The full list of all
improper styles is on the "Commands bond"_Commands_bond.html#improper
doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the improper_style command, and coefficients
specified by the associated "improper_coeff"_improper_coeff.html
command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
improper"_Commands_bond.html#improper doc page are followed by one or
more of (g,i,k,o,t) to indicate which accelerated styles exist.
"none"_improper_none.html - turn off improper interactions
"zero"_improper_zero.html - topology but no interactions

6
doc/src/kspace_modify.txt
View File

@ -58,7 +58,7 @@ keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto}
[Examples:]
kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0
kspace_modify slab 3.0
kspace_modify scafacos tolerance energy :pre
[Description:]
@ -328,8 +328,8 @@ The values with suffix _rel indicate the tolerance is a relative
tolerance; the other values impose an absolute tolerance on the given
quantity. Absolute tolerance in this case means, that for a given
quantity q and a given absolute tolerance of t_a the result should
be between q-t_a and q+t_a. For a relative tolerance t_r the relative
error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r.
be between q-t_a and q+t_a. For a relative tolerance t_r the relative
error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r.
As a consequence of this, the tolerance type should be checked, when
performing computations with a high absolute field / energy. E.g.
if the total energy in the system is 1000000.0 an absolute tolerance

2
doc/src/kspace_style.txt
View File

@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{scafacos} values = method accuracy
method = fmm or p2nfft or ewald or direct
method = fmm or p2nfft or ewald or direct
accuracy = desired relative error in forces :pre
:ule

2
doc/src/message.txt
View File

@ -26,7 +26,7 @@ mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
:ule
[Examples:]
message client md file tmp.couple
message server md file tmp.couple :pre

2
doc/src/package.txt
View File

@ -488,7 +488,7 @@ packing/unpacking operation.
The optimal choice for these keywords depends on the input script and
the hardware used. The {no} value is useful for verifying that the
Kokkos-based {host} and {device} values are working correctly.
Kokkos-based {host} and {device} values are working correctly.
It may also be the fastest choice when using Kokkos styles in
MPI-only mode (i.e. with a thread count of 1).

2
doc/src/pair_airebo.txt
View File

@ -103,7 +103,7 @@ would be 10.2 Angstroms.
By default, the longer-ranged interaction is smoothly switched off
between 2.16 and 3.0 sigma. By specifying {cutoff_min} in addition
to {cutoff}, the switching can be configured to take place between
to {cutoff}, the switching can be configured to take place between
{cutoff_min} and {cutoff}. {cutoff_min} can only be specified if all
optional arguments are given.

58
doc/src/pair_buck6d_coul_gauss.txt
View File

@ -37,55 +37,55 @@ pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 :pre
The {buck6d/coul/gauss} styles evaluate vdW and Coulomb
interactions following the MOF-FF force field after
"(Schmid)"_#Schmid. The vdW term of the {buck6d} styles
"(Schmid)"_#Schmid. The vdW term of the {buck6d} styles
computes a dispersion damped Buckingham potential:
:c,image(Eqs/pair_buck6d.jpg)
where A and C are a force constant, kappa is an ionic-pair dependent
reciprocal length parameter, D is a dispersion correction parameter,
where A and C are a force constant, kappa is an ionic-pair dependent
reciprocal length parameter, D is a dispersion correction parameter,
and the cutoff Rc truncates the interaction distance.
The first term in the potential corresponds to the Buckingham
repulsion term and the second term to the dispersion attraction with
a damping correction analog to the Grimme correction used in DFT.
The latter corrects for artifacts occurring at short distances which
become an issue for soft vdW potentials.
The first term in the potential corresponds to the Buckingham
repulsion term and the second term to the dispersion attraction with
a damping correction analog to the Grimme correction used in DFT.
The latter corrects for artifacts occurring at short distances which
become an issue for soft vdW potentials.
The {buck6d} styles include a smoothing function which is invoked
according to the global smoothing parameter within the specified
cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing
The {buck6d} styles include a smoothing function which is invoked
according to the global smoothing parameter within the specified
cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing
within 90% of the cutoff. No smoothing is applied at a value
of 1.0. For the {gauss/dsf} style this smoothing is only applicable
of 1.0. For the {gauss/dsf} style this smoothing is only applicable
for the dispersion damped Buckingham potential. For the {gauss/long}
styles the smoothing function can also be invoked for the real
space coulomb interactions which enforce continuous energies and
space coulomb interactions which enforce continuous energies and
forces at the cutoff.
Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long}
evaluate a Coulomb potential using spherical Gaussian type charge
distributions which effectively dampen electrostatic interactions
Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long}
evaluate a Coulomb potential using spherical Gaussian type charge
distributions which effectively dampen electrostatic interactions
for high charges at close distances. The electrostatic potential
is thus evaluated as:
:c,image(Eqs/pair_coul_gauss.jpg)
where C is an energy-conversion constant, Qi and Qj are the
charges on the 2 atoms, epsilon is the dielectric constant which
can be set by the "dielectric"_dielectric.html command, alpha is
ion pair dependent damping parameter and erf() is the error-function.
where C is an energy-conversion constant, Qi and Qj are the
charges on the 2 atoms, epsilon is the dielectric constant which
can be set by the "dielectric"_dielectric.html command, alpha is
ion pair dependent damping parameter and erf() is the error-function.
The cutoff Rc truncates the interaction distance.
The style {buck6d/coul/gauss/dsf} computes the Coulomb interaction
via the damped shifted force model described in "(Fennell)"_#Fennell
via the damped shifted force model described in "(Fennell)"_#Fennell
approximating an Ewald sum similar to the "pair coul/dsf"_pair_coul.html
styles. In {buck6d/coul/gauss/long} an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
options. The Coulombic cutoff in this case separates the real and
styles. In {buck6d/coul/gauss/long} an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
options. The Coulombic cutoff in this case separates the real and
reciprocal space evaluation of the Ewald sum.
If one cutoff is specified it is used for both the vdW and Coulomb
terms. If two cutoffs are specified, the first is used as the cutoff
terms. If two cutoffs are specified, the first is used as the cutoff
for the vdW terms, and the second is the cutoff for the Coulombic term.
The following coefficients must be defined for each pair of atoms
@ -101,9 +101,9 @@ D (distance^14 units)
alpha (distance^-1 units)
cutoff (distance units) :ul
The second coefficient, rho, must be greater than zero. The latter
coefficient is optional. If not specified, the global vdW cutoff
is used.
The second coefficient, rho, must be greater than zero. The latter
coefficient is optional. If not specified, the global vdW cutoff
is used.
:line

17
doc/src/pair_coeff.txt
View File

@ -114,21 +114,8 @@ The alphabetic list of pair styles defined in LAMMPS is given on the
"pair_style"_pair_style.html doc page. They are also listed in more
compact form on the "Commands pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated "pair_coeff"_pair_coeff.html command.
Note that there are also additional pair styles (not listed on the
"pair_style"_pair_style.html doc page) submitted by users which are
included in the LAMMPS distribution. The full list of all pair styles
is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed on the
"pair_style"_pair_style.html doc page) included in the LAMMPS
distribution for faster performance on CPUs, GPUs, and KNLs. The
individual style names on the "Commands pair"_Commands_pair.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
Click on the style to display the formula it computes and its
coefficients as specified by the associated pair_coeff command.
:line

2
doc/src/pair_cs.txt
View File

@ -95,7 +95,7 @@ the "/cs" in the name:
except that they correctly treat the special case where the distance
between two charged core and shell atoms in the same core/shell pair
approach r = 0.0.
approach r = 0.0.
Styles with a "/long" in the name are used with a long-range solver
for Coulombic interactions via the "kspace_style"_kspace_style.html

4
doc/src/pair_extep.txt
View File

@ -35,6 +35,6 @@ interactions as described in "(Los2017)"_#Los2017.
:line
:link(Los2017)
[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride:
Energetics and elastic properties of pristine and defective h-BN",
[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride:
Energetics and elastic properties of pristine and defective h-BN",
Phys. Rev. B 96 (184108), 2017.

2
doc/src/pair_ilp_graphene_hbn.txt
View File

@ -13,7 +13,7 @@ pair_style ilp/graphene/hbn command :h3
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
tap_flag = 0/1 to turn off/on the taper function
[Examples:]

2
doc/src/pair_kolmogorov_crespi_full.txt
View File

@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function
[Examples:]

2
doc/src/pair_meam.txt
View File

@ -179,7 +179,7 @@ selected starting from 1. Thus for the example given below
pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
an index of 1 would refer to Si and an index of 2 to C.
an index of 1 would refer to Si and an index of 2 to C.
The recognized keywords for the parameter file are as follows:

16
doc/src/pair_meso.txt
View File

@ -24,7 +24,7 @@ args = list of arguments for a particular style :l
T = temperature (temperature units)
cutoff = global cutoff for mDPD interactions (distance units)
seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed)
{mdpd/rhosum} args =
{mdpd/rhosum} args =
{tdpd} args = T cutoff seed
T = temperature (temperature units)
cutoff = global cutoff for tDPD interactions (distance units)
@ -43,7 +43,7 @@ pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre
pair_style tdpd 1.0 1.58 935662
pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre
[Description:]
@ -73,7 +73,7 @@ heat flux <font size="4">q<sup>V</sup></font>, and random heat flux
:c,image(Eqs/pair_edpd_heat.jpg)
where the mesoscopic heat friction <font size="4">&kappa;</font> is given by
where the mesoscopic heat friction <font size="4">&kappa;</font> is given by
:c,image(Eqs/pair_edpd_kappa.jpg)
@ -84,7 +84,7 @@ The following coefficients must be defined in eDPD system for each
pair of atom types via the "pair_coeff"_pair_coeff.html command as in
the examples above.
A (force units)
A (force units)
gamma (force/velocity units)
power_f (positive real)
cutoff (distance units)
@ -172,7 +172,7 @@ size="4"><i>m</i><sub>s</sub></font> is much smaller than the mass of
a tDPD particle <font size="4"><i>m</i></font>. For more details, see
"(Li2015_JCP)"_#Li2015_JCP.
The following coefficients must be defined for each pair of atom types via the
The following coefficients must be defined for each pair of atom types via the
"pair_coeff"_pair_coeff.html command as in the examples above.
A (force units)
@ -250,10 +250,10 @@ more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html,
"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html,
"fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html,
"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html,
"compute edpd/temp/atom"_compute_edpd_temp_atom.html,
"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html,
"compute edpd/temp/atom"_compute_edpd_temp_atom.html,
"compute tdpd/cc/atom"_compute_tdpd_cc_atom.html
[Default:] none

8
doc/src/pair_oxdna.txt
View File

@ -25,10 +25,10 @@ args = list of arguments for these particular styles :ul
{oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
T = temperature (oxDNA units, 0.1 = 300 K)
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
[Examples:]
@ -72,8 +72,8 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.

6
doc/src/pair_oxdna2.txt
View File

@ -69,7 +69,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
the temperature coefficients have to be matched to the one used in the fix.
@ -78,8 +78,8 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.

30
doc/src/pair_spin_dmi.txt
View File

@ -25,44 +25,44 @@ pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
[Description:]
Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
between pairs of magnetic spins.
between pairs of magnetic spins.
According to the expression reported in "(Rohart)"_#Rohart, one has
the following DM energy:
:c,image(Eqs/pair_spin_dmi_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
where si and sj are two neighboring magnetic spins of two particles,
eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j,
and D is the DM vector defining the intensity (in eV) and the direction
and D is the DM vector defining the intensity (in eV) and the direction
of the interaction.
In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented
In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented
from the high spin-orbit layer to the magnetic ultra-thin film.
The application of a spin-lattice Poisson bracket to this energy (as described
in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a
mechanical force F (for spin-lattice calculations only) for each magnetic
particle i:
mechanical force F (for spin-lattice calculations only) for each magnetic
particle i:
:c,image(Eqs/pair_spin_dmi_forces.jpg)
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida5.
For the {spin/dmi} pair style, the following coefficients must be defined for
each pair of atoms types via the "pair_coeff"_pair_coeff.html 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"_read_restart.html commands, and
set in the following order:
For the {spin/dmi} pair style, the following coefficients must be defined for
each pair of atoms types via the "pair_coeff"_pair_coeff.html 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"_read_restart.html commands, and
set in the following order:
rc (distance units)
|D| (energy units)
Dx, Dy, Dz (direction of D) :ul
Note that rc is the radius cutoff of the considered DM interaction, |D| is
the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction.
Note that rc is the radius cutoff of the considered DM interaction, |D| is
the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction.
None of those coefficients is optional. If not specified, the {spin/dmi}
None of those coefficients is optional. If not specified, the {spin/dmi}
pair style cannot be used.
:line
@ -76,7 +76,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"pair_eam"_pair_eam.html,
[Default:] none

26
doc/src/pair_spin_exchange.txt
View File

@ -24,14 +24,14 @@ pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
[Description:]
Style {spin/exchange} computes the exchange interaction between
Style {spin/exchange} computes the exchange interaction between
pairs of magnetic spins:
:c,image(Eqs/pair_spin_exchange_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
and J(rij) is a function defining the intensity and the sign of the exchange
and J(rij) is a function defining the intensity and the sign of the exchange
interaction for different neighboring shells. This function is defined as:
:c,image(Eqs/pair_spin_exchange_function.jpg)
@ -44,35 +44,35 @@ the value of the exchange interaction for the N neighbor shells taken into accou
Examples and more explanations about this function and its parameterization are reported
in "(Tranchida)"_#Tranchida3.
From this exchange interaction, each spin i will be submitted
From this exchange interaction, each spin i will be submitted
to a magnetic torque omega, and its associated atom can be submitted to a
force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
such as:
:c,image(Eqs/pair_spin_exchange_forces.jpg)
with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
vector between sites i and j.
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida3.
For the {spin/exchange} pair style, the following coefficients must be defined
for each pair of atoms types via the "pair_coeff"_pair_coeff.html 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"_read_restart.html commands, and
set in the following order:
For the {spin/exchange} pair style, the following coefficients must be defined
for each pair of atoms types via the "pair_coeff"_pair_coeff.html 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"_read_restart.html commands, and
set in the following order:
rc (distance units)
a (energy units)
b (adim parameter)
b (adim parameter)
d (distance units) :ul
Note that rc is the radius cutoff of the considered exchange interaction,
and a, b and d are the three coefficients performing the parameterization
of the function J(rij) defined above.
None of those coefficients is optional. If not specified, the
None of those coefficients is optional. If not specified, the
{spin/exchange} pair style cannot be used.
:line
@ -86,7 +86,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"pair_eam"_pair_eam.html,
[Default:] none

4
doc/src/pair_spin_magelec.txt
View File

@ -25,7 +25,7 @@ pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre
Style {spin/me} computes a magneto-electric interaction between
pairs of magnetic spins. According to the derivation reported in
"(Katsura)"_#Katsura1, this interaction is defined as:
"(Katsura)"_#Katsura1, this interaction is defined as:
:c,image(Eqs/pair_spin_me_interaction.jpg)
@ -69,5 +69,5 @@ package"_Build_package.html doc page for more info.
[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
:link(Tranchida4)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
Journal of Computational Physics, (2018).

6
doc/src/pair_spin_neel.txt
View File

@ -24,8 +24,8 @@ pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
[Description:]
Style {spin/neel} computes the Neel pair anisotropy model
between pairs of magnetic spins:
Style {spin/neel} computes the Neel pair anisotropy model
between pairs of magnetic spins:
:c,image(Eqs/pair_spin_neel_interaction.jpg)
@ -71,7 +71,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"pair_eam"_pair_eam.html,
[Default:] none

92
doc/src/pair_style.txt
View File

@ -81,19 +81,15 @@ Here is an alphabetic list of pair styles defined in LAMMPS. They are
also listed in more compact form on the "Commands
pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated "pair_coeff"_pair_coeff.html command.
Click on the style to display the formula it computes, any additional
arguments specified in the pair_style command, and coefficients
specified by the associated "pair_coeff"_pair_coeff.html command.
There are also additional pair styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The full list of
all pair styles is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs,
GPUs, and KNLs. The individual style names on the "Commands
pair"_Commands_pair.html doc page are followed by one or more of
(g,i,k,o,t) to indicate which accelerated styles exist.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands pair"_Commands_pair.html
doc page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"none"_pair_none.html - turn off pairwise interactions
"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
@ -236,7 +232,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
"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
"mie/cut"_pair_mie.html - Mie potential
"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
"morse"_pair_morse.html - Morse potential
"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
"morse/soft"_pair_morse.html - Morse potential with a soft core
@ -246,64 +242,64 @@ pair"_Commands_pair.html doc page are followed by one or more of
"nm/cut"_pair_nm.html - N-M potential
"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
"oxdna/coaxstk"_pair_oxdna.html -
"oxdna/excv"_pair_oxdna.html -
"oxdna/hbond"_pair_oxdna.html -
"oxdna/stk"_pair_oxdna.html -
"oxdna/xstk"_pair_oxdna.html -
"oxdna2/coaxstk"_pair_oxdna2.html -
"oxdna2/dh"_pair_oxdna2.html -
"oxdna2/excv"_pair_oxdna2.html -
"oxdna2/hbond"_pair_oxdna2.html -
"oxdna2/stk"_pair_oxdna2.html -
"oxdna2/xstk"_pair_oxdna2.html -
"oxdna/coaxstk"_pair_oxdna.html -
"oxdna/excv"_pair_oxdna.html -
"oxdna/hbond"_pair_oxdna.html -
"oxdna/stk"_pair_oxdna.html -
"oxdna/xstk"_pair_oxdna.html -
"oxdna2/coaxstk"_pair_oxdna2.html -
"oxdna2/dh"_pair_oxdna2.html -
"oxdna2/excv"_pair_oxdna2.html -
"oxdna2/hbond"_pair_oxdna2.html -
"oxdna2/stk"_pair_oxdna2.html -
"oxdna2/xstk"_pair_oxdna2.html -
"peri/eps"_pair_peri.html - peridynamic EPS potential
"peri/lps"_pair_peri.html - peridynamic LPS potential
"peri/pmb"_pair_peri.html - peridynamic PMB potential
"peri/ves"_pair_peri.html - peridynamic VES potential
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
"python"_pair_python.html -
"quip"_pair_quip.html -
"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
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
"smd/hertz"_pair_smd_hertz.html -
"smd/tlsph"_pair_smd_tlsph.html -
"smd/tri_surface"_pair_smd_triangulated_surface.html -
"smd/ulsph"_pair_smd_ulsph.html -
"smtbq"_pair_smtbq.html -
"smd/hertz"_pair_smd_hertz.html -
"smd/tlsph"_pair_smd_tlsph.html -
"smd/tri_surface"_pair_smd_triangulated_surface.html -
"smd/ulsph"_pair_smd_ulsph.html -
"smtbq"_pair_smtbq.html -
"snap"_pair_snap.html - SNAP quantum-accurate potential
"soft"_pair_soft.html - Soft (cosine) potential
"sph/heatconduction"_pair_sph_heatconduction.html -
"sph/idealgas"_pair_sph_idealgas.html -
"sph/lj"_pair_sph_lj.html -
"sph/rhosum"_pair_sph_rhosum.html -
"sph/taitwater"_pair_sph_taitwater.html -
"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
"spin/dmi"_pair_spin_dmi.html -
"spin/exchange"_pair_spin_exchange.html -
"spin/magelec"_pair_spin_magelec.html -
"spin/neel"_pair_spin_neel.html -
"srp"_pair_srp.html -
"sph/heatconduction"_pair_sph_heatconduction.html -
"sph/idealgas"_pair_sph_idealgas.html -
"sph/lj"_pair_sph_lj.html -
"sph/rhosum"_pair_sph_rhosum.html -
"sph/taitwater"_pair_sph_taitwater.html -
"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
"spin/dmi"_pair_spin_dmi.html -
"spin/exchange"_pair_spin_exchange.html -
"spin/magelec"_pair_spin_magelec.html -
"spin/neel"_pair_spin_neel.html -
"srp"_pair_srp.html -
"sw"_pair_sw.html - Stillinger-Weber 3-body potential
"table"_pair_table.html - tabulated pair potential
"table/rx"_pair_table_rx.html -
"table/rx"_pair_table_rx.html -
"tdpd"_pair_meso.html - tDPD particle interactions
"tersoff"_pair_tersoff.html - Tersoff 3-body potential
"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
"tersoff/mod/c"_pair_tersoff_mod.html -
"tersoff/table"_pair_tersoff.html -
"tersoff/mod/c"_pair_tersoff_mod.html -
"tersoff/table"_pair_tersoff.html -
"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
"thole"_pair_thole.html - Coulomb interactions with thole damping
"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
"tip4p/long/soft"_pair_lj_soft.html -
"tip4p/long/soft"_pair_lj_soft.html -
"tri/lj"_pair_tri_lj.html - LJ potential between triangles
"ufm"_pair_ufm.html -
"ufm"_pair_ufm.html -
"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
"vashishta/table"_pair_vashishta.html -
"vashishta/table"_pair_vashishta.html -
"yukawa"_pair_yukawa.html - Yukawa potential
"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul

2
doc/src/pair_ufm.txt
View File

@ -37,7 +37,7 @@ Style {ufm} computes pairwise interactions using the Uhlenbeck-Ford model (UFM)
where rc is the cutoff, sigma is a distance-scale and epsilon is an energy-scale, i.e., a product of Boltzmann constant kB, temperature T and the Uhlenbeck-Ford p-parameter which is responsible
to control the softness of the interactions "(Paula Leite2017)"_#PL1.
This model is useful as a reference system for fluid-phase free-energy calculations "(Paula Leite2016)"_#PL2.
This model is useful as a reference system for fluid-phase free-energy calculations "(Paula Leite2016)"_#PL2.
The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the examples above,

2
doc/src/read_data.txt
View File

@ -553,7 +553,7 @@ bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
dpd: atom-ID atom-type theta x y z
edpd: atom-ID atom-type edpd_temp edpd_cv x y z
edpd: atom-ID atom-type edpd_temp edpd_cv x y z
mdpd: atom-ID atom-type rho x y z
tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies
electron: atom-ID atom-type q spin eradius x y z

2
doc/src/server.txt
View File

@ -15,7 +15,7 @@ server protocol :pre
protocol = {md} or {mc} :ul
[Examples:]
server md :pre
[Description:]

6
doc/src/server_mc.txt
View File

@ -15,7 +15,7 @@ server mc :pre
mc = the protocol argument to the "server"_server.html command
[Examples:]
server mc :pre
[Description:]
@ -46,7 +46,7 @@ examples/COUPLE/lammps_mc/in.server.
When using this command, LAMMPS (as the server code) receives
instructions from a Monte Carlo (MC) driver to displace random atoms,
compute the energy before and after displacement, and run dynamics to
equilibrate the system.
equilibrate the system.
The MC driver performs the random displacements on random atoms,
accepts or rejects the move in an MC sense, and orchestrates the MD
@ -83,7 +83,7 @@ cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
[Server replies]:
cs->send(NATOMS,1) # msgID = 1 with 1 field
cs->send(NATOMS,1) # msgID = 1 with 1 field
cs->pack_int(1,natoms) # 1st field = number of atoms :pre
cs->send(EINIT,2) # msgID = 2 with 2 fields

2
doc/src/server_md.txt
View File

@ -15,7 +15,7 @@ server md :pre
md = the protocol argument to the "server"_server.html command
[Examples:]
server md :pre
[Description:]

10
doc/src/set.txt
View File

@ -245,13 +245,13 @@ many processors are being used. This keyword does not allow use of an
atom-style variable.
Keyword {spin} uses the specified g value to set the magnitude of the
magnetic spin vectors, and the x,y,z values as components of a vector
to set as the orientation of the magnetic spin vectors of the selected
atoms.
magnetic spin vectors, and the x,y,z values as components of a vector
to set as the orientation of the magnetic spin vectors of the selected
atoms.
Keyword {spin/random} randomizes the orientation of the magnetic spin
vectors for the selected atoms and sets the magnitude of each to the
specified {Dlen} value.
vectors for the selected atoms and sets the magnitude of each to the
specified {Dlen} value.
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The

4
doc/src/temper_npt.txt
View File

@ -23,7 +23,7 @@ index = which temperature (0 to N-1) I am simulating (optional) :ul
[Examples:]
temper/npt 100000 100 $t nptfix 0 58728 1
temper/npt 2500000 1000 300 nptfix 0 32285 $p
temper/npt 2500000 1000 300 nptfix 0 32285 $p
temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre
[Description:]
@ -43,7 +43,7 @@ of pressure, this command works much like the "temper"_temper.html
command. See the documentation on "temper"_temper.html for information
on how the parallel tempering is handled in general.
:line
:line
[Restrictions:]

2
doc/src/write_data.txt
View File

@ -87,7 +87,7 @@ are read in separately anyway, e.g. from an include file.
The {nofix} keyword requests that no extra sections read by fixes
should be written to the data file (see the {fix} option of the
"read_data"_read_data.html command for details). For example, this
option excludes sections for user-created per-atom properties
option excludes sections for user-created per-atom properties
from "fix property/atom"_fix_property_atom.html.
The {pair} keyword lets you specify in what format the pair