diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 47801890c4..90a91db60f 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -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 diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index f8b52056fc..1406d290f5 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -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 diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 4377981662..bc03b5c8ce 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -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 diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index c871d4ab42..f1db9f0130 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -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]: diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index 6ac6f52d54..bf1ec265a1 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -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 diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt index 10f84874a3..0489d228bd 100644 --- a/doc/src/Errors.txt +++ b/doc/src/Errors.txt @@ -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) diff --git a/doc/src/Howto_bash.txt b/doc/src/Howto_bash.txt index f1438418e7..b6e1a65b01 100755 --- a/doc/src/Howto_bash.txt +++ b/doc/src/Howto_bash.txt @@ -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 diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt index 3e7db9bc8e..7cbdf95315 100644 --- a/doc/src/Howto_body.txt +++ b/doc/src/Howto_body.txt @@ -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 diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 5875a48744..61d99f7572 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -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: diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt index 9a9656784c..796c5b2e2d 100644 --- a/doc/src/Howto_library.txt +++ b/doc/src/Howto_library.txt @@ -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. diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index 88a5fbd86f..7f16883487 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -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). diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt index bd22de057c..f1da9de66e 100644 --- a/doc/src/Install_linux.txt +++ b/doc/src/Install_linux.txt @@ -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. diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt index ff9b14c12c..40c272d1c8 100644 --- a/doc/src/Install_patch.txt +++ b/doc/src/Install_patch.txt @@ -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 diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt index dc41727c05..8f025df96d 100644 --- a/doc/src/Intro_authors.txt +++ b/doc/src/Intro_authors.txt @@ -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) diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt index d5e5b7f8b5..66874e79e0 100644 --- a/doc/src/Intro_features.txt +++ b/doc/src/Intro_features.txt @@ -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 diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt index ac12dd7b2e..42c77c4500 100644 --- a/doc/src/Manual_build.txt +++ b/doc/src/Manual_build.txt @@ -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 diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index d6a3e17866..364ff3fe30 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -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 diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index 7ff8d73ae9..da772f29fd 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -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. diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 0a24753a9f..ef193d7401 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -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 diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index 1ec4969620..d2e53d8b77 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -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. diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 686e123ca0..1ce3556ea6 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -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 diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 3a4efad218..65dc0924e5 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -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:] diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index ff714e31d9..ff96fedab9 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -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 diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index d603bc28fd..ae19f2369d 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -89,7 +89,7 @@ accelerated styles exist. "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 diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 8c3c5d5dde..4886e73ab6 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -170,14 +170,14 @@ 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 - +"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 @@ -186,48 +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 @@ -237,71 +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 diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 8acaec94d5..332a7a07af 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -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:] diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt index f84ef67974..5f65900a49 100644 --- a/doc/src/compute_chunk_spread_atom.txt +++ b/doc/src/compute_chunk_spread_atom.txt @@ -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 diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt index f3c1418d44..ac3fb5e277 100644 --- a/doc/src/compute_edpd_temp_atom.txt +++ b/doc/src/compute_edpd_temp_atom.txt @@ -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. diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt index 04f0fd0b82..cd90a9b590 100644 --- a/doc/src/compute_entropy_atom.txt +++ b/doc/src/compute_entropy_atom.txt @@ -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. diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt index f4312e67bc..5cca9ea3a5 100644 --- a/doc/src/compute_pressure_cylinder.txt +++ b/doc/src/compute_pressure_cylinder.txt @@ -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:] diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index 3c55c88d10..a0c8579283 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -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:] diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 95d183937f..ab652daf83 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -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}. diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index 4edecc2408..d27e402972 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -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 diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt index 1006463179..d97581afd5 100644 --- a/doc/src/compute_stress_mop.txt +++ b/doc/src/compute_stress_mop.txt @@ -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). diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt index a385bef10b..d1f9c38319 100644 --- a/doc/src/compute_tdpd_cc_atom.txt +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -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:] diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index 97e1d6e1ae..b9e6187533 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -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:] diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index fbf741d914..abd1959e81 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -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}. diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index b8e0ec64c8..6f3f6edbcc 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -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) diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index 16e4aba4c0..ca43b0b6ea 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -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. diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 92d0725828..916e9887f9 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -163,188 +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 @@ -352,28 +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 @@ -381,7 +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:] diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index cbcd1138d3..db9c35069c 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -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 . diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt index 6828731021..5fee8511fe 100644 --- a/doc/src/fix_client_md.txt +++ b/doc/src/fix_client_md.txt @@ -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 diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index d35c3065a2..3259f79497 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -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 diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 0c5a4493ae..adca2c3072 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -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 diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 6b9a02eeca..8a66a007a3 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -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 diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index d4836706e2..ddd3a0319b 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -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:] diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index c97095bcfc..e6edf6ac8a 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -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 diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index f50747948a..f7882c58f7 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -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 diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index 64195abb37..a46e79c5b0 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -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 diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 3112b586d1..fcd8926c13 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -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 diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index bb59a8423c..898ca5132b 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -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 diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt index 08f0eab61d..af435dc730 100644 --- a/doc/src/fix_nve_spin.txt +++ b/doc/src/fix_nve_spin.txt @@ -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) diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 8fe793ce7f..027a15a5ff 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -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 diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt index d58cd622b0..f16522c7b6 100644 --- a/doc/src/fix_precession_spin.txt +++ b/doc/src/fix_precession_spin.txt @@ -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 diff --git a/doc/src/fix_rigid_meso.txt b/doc/src/fix_rigid_meso.txt index b0a7e3cf9e..d86d359f1d 100644 --- a/doc/src/fix_rigid_meso.txt +++ b/doc/src/fix_rigid_meso.txt @@ -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). diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt index 43ffdeb8e9..857eaecc5f 100644 --- a/doc/src/improper_inversion_harmonic.txt +++ b/doc/src/improper_inversion_harmonic.txt @@ -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 diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index c4bd4db3ee..65b2174334 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -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 diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index fdf78ce4ec..d676beff16 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -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 diff --git a/doc/src/message.txt b/doc/src/message.txt index d258cfbd08..0c10af4ac6 100644 --- a/doc/src/message.txt +++ b/doc/src/message.txt @@ -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 diff --git a/doc/src/package.txt b/doc/src/package.txt index f9ed0734c9..c226d7942f 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -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). diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index c090a39af7..3708fb287d 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -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. diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 21de3330f4..1f013e91ef 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -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 diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 830e0586d2..5fce65d6f7 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -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 diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt index 3acad1132d..5d69df69e9 100644 --- a/doc/src/pair_extep.txt +++ b/doc/src/pair_extep.txt @@ -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. diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index f9b500d066..a8d74dca0f 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -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:] diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index df9a9696be..a13825abe5 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -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:] diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index 0b1c1ac767..b4893d1db1 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -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: diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt index 005498d8bf..54186a0e75 100644 --- a/doc/src/pair_meso.txt +++ b/doc/src/pair_meso.txt @@ -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 qV, and random heat flux :c,image(Eqs/pair_edpd_heat.jpg) -where the mesoscopic heat friction κ is given by +where the mesoscopic heat friction κ 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">ms is much smaller than the mass of a tDPD particle m. 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 diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 153fc50189..b63b5371cf 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -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. diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index a928bdf886..f2963f7b17 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -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. diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index a040f27d68..bc67e43ecd 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -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 diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt index fdbac9df3e..10d65a55a1 100644 --- a/doc/src/pair_spin_exchange.txt +++ b/doc/src/pair_spin_exchange.txt @@ -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 diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt index 360f440792..151ecdec3d 100644 --- a/doc/src/pair_spin_magelec.txt +++ b/doc/src/pair_spin_magelec.txt @@ -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). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 4458a0767b..8e2242f013 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -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 diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 00cbbb04c0..46a4f31dd4 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -232,7 +232,7 @@ accelerated styles exist. "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 @@ -242,64 +242,64 @@ accelerated styles exist. "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 diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 787c60a1bd..f0efcfbf19 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -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, diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 7669b78f85..30ee1201d9 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -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 diff --git a/doc/src/server.txt b/doc/src/server.txt index 86fb68d012..8f87b5c76b 100644 --- a/doc/src/server.txt +++ b/doc/src/server.txt @@ -15,7 +15,7 @@ server protocol :pre protocol = {md} or {mc} :ul [Examples:] - + server md :pre [Description:] diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt index 638d3dadfb..ef3c56f886 100644 --- a/doc/src/server_mc.txt +++ b/doc/src/server_mc.txt @@ -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 diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt index fc9ae5d53a..03f3db7e19 100644 --- a/doc/src/server_md.txt +++ b/doc/src/server_md.txt @@ -15,7 +15,7 @@ server md :pre md = the protocol argument to the "server"_server.html command [Examples:] - + server md :pre [Description:] diff --git a/doc/src/set.txt b/doc/src/set.txt index b83ad54f4e..15c96071ae 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -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 diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index 50ac5615f6..00a3e35ec3 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -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:] diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index b6002b5252..a8168b70a0 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -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