diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index c50af2ca78..51c3fd871d 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -40,14 +40,14 @@ is below. -D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc # no default value -The executable created by CMake (after running make) is named *lmp* unless -the LAMMPS\_MACHINE option is set. When setting `LAMMPS_MACHINE=name` -the executable will be named *lmp\_name*\. Using `BUILD\_MPI=no` will +The executable created by CMake (after running make) is named ``lmp`` unless +the LAMMPS_MACHINE option is set. When setting ``LAMMPS_MACHINE=name`` +the executable will be called ``lmp_name``. Using ``BUILD_MPI=no`` will enforce building a serial executable using the MPI STUBS library. **Traditional make**\ : -The build with traditional makefiles has to be done inside the source folder `src`. +The build with traditional makefiles has to be done inside the source folder ``src``. .. code-block:: bash @@ -56,17 +56,17 @@ The build with traditional makefiles has to be done inside the source folder `sr make mybox # uses Makefile.mybox to produce lmp_mybox Any "make machine" command will look up the make settings from a file -Makefile.machine, create a folder Obj\_machine with all objects and -generated files and an executable called *lmp\_machine*\ . The standard -parallel build with `make mpi` assumes a standard MPI installation with +Makefile.machine, create a folder Obj_machine with all objects and +generated files and an executable called ``lmp_machine``\ . The standard +parallel build with ``make mpi`` assumes a standard MPI installation with MPI compiler wrappers where all necessary compiler and linker flags to get access and link with the suitable MPI headers and libraries are set by the wrapper programs. For other cases or the serial build, you have -to adjust the make file variables MPI\_INC, MPI\_PATH, MPI\_LIB as well -as CC and LINK. To enable OpenMP threading usually a compiler specific -flag needs to be added to the compile and link commands. For the GNU -compilers, this is *-fopenmp*\ , which can be added to the CC and LINK -makefile variables. +to adjust the make file variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB`` +as well as ``CC`` and ``LINK``\ . To enable OpenMP threading usually +a compiler specific flag needs to be added to the compile and link +commands. For the GNU compilers, this is ``-fopenmp``\ , which can be +added to the ``CC`` and ``LINK`` makefile variables. For the serial build the following make variables are set (see src/MAKE/Makefile.serial): @@ -79,8 +79,8 @@ For the serial build the following make variables are set (see src/MAKE/Makefile MPI_LIB = -lmpi_stubs You also need to build the STUBS library for your platform before making -LAMMPS itself. A "make serial" build does this for you automatically, -otherwise, type "make mpi-stubs" from the src directory, or "make" from +LAMMPS itself. A ``make serial`` build does this for you automatically, +otherwise, type ``make mpi-stubs`` from the src directory, or ``make`` from the src/STUBS dir. If the build fails, you will need to edit the STUBS/Makefile for your platform. The stubs library does not provide MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB, @@ -88,8 +88,8 @@ and thus is not compatible with those packages. .. note:: - The file STUBS/mpi.c provides a CPU timer function called - MPI\_Wtime() that calls gettimeofday() . If your operating system + The file ``src/STUBS/mpi.c`` provides a CPU timer function called + MPI_Wtime() that calls gettimeofday() . If your operating system does not support gettimeofday() , you will need to insert code to call another timer. Note that the ANSI-standard function clock() rolls over after an hour or so, and is therefore insufficient for @@ -126,29 +126,29 @@ to: e.g. LATTE and USER-COLVARS. See the :doc:`Packages details ` doc page for more info on these packages and the doc pages for their respective commands for OpenMP threading info. -For CMake, if you use BUILD\_OMP=yes, you can use these packages and -turn on their native OpenMP support and turn on their native OpenMP -support at run time, by setting the OMP\_NUM\_THREADS environment +For CMake, if you use ``BUILD_OMP=yes``, you can use these packages +and turn on their native OpenMP support and turn on their native OpenMP +support at run time, by setting the ``OMP_NUM_THREADS`` environment variable before you launch LAMMPS. -For building via conventional make, the CCFLAGS and LINKFLAGS +For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS`` variables in Makefile.machine need to include the compiler flag that -enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel -compilers it is -qopenmp. If you are using a different compiler, +enables OpenMP. For GNU compilers it is ``-fopenmp``\ . For (recent) Intel +compilers it is ``-qopenmp``\ . If you are using a different compiler, please refer to its documentation. .. _default-none-issues: **OpenMP Compiler compatibility info**\ : -Some compilers do not fully support the 'default(none)' directive +Some compilers do not fully support the ``default(none)`` directive and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 -semantics, which are incompatible with the OpenMP 3.1 directives used +semantics, which are incompatible with the OpenMP 3.1 semantics used in LAMMPS (for maximal compatibility with compiler versions in use). -In those case, all 'default(none)' directives (which aid in detecting -incorrect and unwanted sharing) can be replaced with 'default(shared)' -while dropping all 'shared()' directives. The script -'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate +In those case, all ``default(none)`` directives (which aid in detecting +incorrect and unwanted sharing) can be replaced with ``default(shared)`` +while dropping all ``shared()`` directives. The script +'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate this conversion. ---------- @@ -183,11 +183,11 @@ optimization flags appropriate to that compiler and any build. You can tell CMake to look for a specific compiler with these variable -settings. Likewise you can specify the FLAGS variables if you want to -experiment with alternate optimization flags. You should specify all -3 compilers, so that the small number of LAMMPS source files written -in C or Fortran are built with a compiler consistent with the one used -for all the C++ files: +settings. Likewise you can specify the corresponding ``CMAKE_*_FLAGS`` +variables if you want to experiment with alternate optimization flags. +You should specify all 3 compilers, so that the small number of LAMMPS +source files written in C or Fortran are built with a compiler consistent +with the one used for all the C++ files: .. code-block:: bash @@ -300,19 +300,18 @@ are set, defaults are applied. -D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc # no default value -Setting BUILD\_EXE=no will not produce an executable. Setting -BUILD\_LIB=yes will produce a static library named *liblammps.a*\ . -Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a -shared library named *liblammps.so* instead. If LAMMPS\_LIB\_SUFFIX is -set to *name* in addition, the name of the generated libraries will be -changed to either *liblammps\_name.a* or *liblammps\_name.so*\ , -respectively. +Setting ``BUILD_EXE=no`` will not produce an executable. Setting +``BUILD_LIB=yes`` will produce a static library named ``liblammps.a``\ . +Setting both ``BUILD_LIB=yes`` and ``BUILD_SHARED_LIBS=yes`` will produce a +shared library named ``liblammps.so`` instead. If ``LAMMPS_LIB_SUFFIX=name`` +is set in addition, the name of the generated libraries will be changed to +either ``liblammps_name.a`` or ``liblammps_name.so``\ , respectively. **Traditional make**\ : With the traditional makefile based build process, the choice of the generated executable or library depends on the "mode" setting. -Several options are available and "mode=exe" is the default. +Several options are available and ``mode=exe`` is the default. .. code-block:: bash @@ -322,11 +321,11 @@ Several options are available and "mode=exe" is the default. make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so make mode=shexe machine # same as "mode=exe" but uses objects from "mode=shlib" -The two "exe" builds will generate and executable *lmp\_machine*\ , -while the two library builds will create a file *liblammps\_machine.a* -or *liblammps\_machine.so*\ . They will also create generic soft links, -named *liblammps.a* and *liblammps.so*\ , which point to the specific -*liblammps\_machine.a/so* files. +The two "exe" builds will generate and executable ``lmp_machine``\ , +while the two library builds will create a file ``liblammps_machine.a`` +or ``liblammps_machine.so``\ . They will also create generic soft links, +named ``liblammps.a`` and ``liblammps.so``\ , which point to the specific +``liblammps_machine.a/so`` files. **CMake and make info**\ : @@ -335,7 +334,7 @@ the auxiliary libraries it depends on must also exist as shared libraries. This will be the case for libraries included with LAMMPS, such as the dummy MPI library in src/STUBS or any package libraries in the lib/packages directory, since they are always built in a shared -library compatible way using the -fPIC switch. However, if a library +library compatible way using the ``-fPIC`` switch. However, if a library like MPI or FFTW does not exist as a shared library, the shared library build may generate an error. This means you will need to install a shared library version of the auxiliary library. The build instructions @@ -353,10 +352,10 @@ in the default /usr/local/lib location: make make install -You may need to use "sudo make install" in place of the last line if you -do not have write privileges for /usr/local/lib. The end result should -be the file /usr/local/lib/libmpich.so. On many Linux installations the -folder "${HOME}/.local" is an alternative to using /usr/local and does +You may need to use ``sudo make install`` in place of the last line if you +do not have write privileges for ``/usr/local/lib``. The end result should +be the file ``/usr/local/lib/libmpich.so``. On many Linux installations the +folder ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does not require superuser or sudo access. In that case the configuration step becomes: @@ -420,7 +419,7 @@ It is also possible to create the HTML version of the manual within the :doc:`CMake build directory `. The reason for this option is to include the installation of the HTML manual pages into the "install" step when installing LAMMPS after the CMake build via -"make install". +``make install``. .. code-block:: bash @@ -479,6 +478,6 @@ you want to copy files to is protected. **Traditional make**\ : -There is no "install" option in the src/Makefile for LAMMPS. If you -wish to do this you will need to first build LAMMPS, then manually +There is no "install" option in the ``src/Makefile`` for LAMMPS. If +you wish to do this you will need to first build LAMMPS, then manually copy the desired LAMMPS files to the appropriate system directories. diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index a0b33c792c..c41136c0a5 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -13,8 +13,8 @@ good place to start. Building LAMMPS with CMake is a two-step process. First you use CMake to create a build environment in a new directory. On Linux systems, -this will be based on makefiles for use with make. Then you use the -make command to build LAMMPS, which uses the created +this will be by default based on Unix-style makefiles for use with make. +Then you use the *make* command to build LAMMPS, which uses the created Makefile(s). Example: .. code-block:: bash @@ -28,8 +28,8 @@ The cmake command will detect available features, enable selected packages and options, and will generate the build environment. By default this build environment will be created for "Unix Makefiles" on most platforms and particularly on Linux. However, alternate build tools -(e.g. Ninja) and support files for Integrated Development Environments -(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is +(e.g. Ninja) and project files for Integrated Development Environments +(IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is selected via the "-G" command line flag. For the rest of the documentation we will assume that the build environment is generated for makefiles and thus the make command will be used to compile and link LAMMPS as @@ -55,16 +55,17 @@ your system with: This will install the lammps executable and library (if requested), some tools (if configured) and additional files like library API headers, manpages, potential and force field files. The location of the installation -tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults +tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults to ${HOME}/.local ---------- -There are 3 variants of CMake: a command-line version (cmake), a text mode -UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use -any of them interchangeably to configure and create the LAMMPS build -environment. On Linux all the versions produce a Makefile as their -output. See more details on each below. +There are 3 variants of the CMake command itself: a command-line version +(*cmake* or *cmake3*), a text mode UI version (*ccmake* or *ccmake3*), +and a graphical GUI version (*cmake-gui*). You can use any of them +interchangeably to configure and create the LAMMPS build environment. +On Linux all the versions produce a Makefile as their output by default. +See more details on each below. You can specify a variety of options with any of the 3 versions, which affect how the build is performed and what is included in the LAMMPS @@ -82,12 +83,13 @@ this directory or sub-directories within it that CMake creates. .. note:: - To perform a CMake build, no packages can be installed or a - build been previously attempted in the LAMMPS src directory by using - "make" commands to :doc:`perform a conventional LAMMPS build `. CMake detects if this is the case and - generates an error, telling you to type "make no-all purge" in the src - directory to un-install all packages. The purge removes all the \*.h - files auto-generated by make. + To perform a CMake build, no packages can be installed or a build + been previously attempted in the LAMMPS src directory by using "make" + commands to :doc:`perform a conventional LAMMPS build `. + CMake detects if this is the case and generates an error, telling you + to type "make no-all purge" in the src directory to un-install all + packages. The purge removes all the \*.h files auto-generated by + make. You must have CMake version 3.10 or later on your system to build LAMMPS. Installation instructions for CMake are below. @@ -106,8 +108,9 @@ folder, recreate the directory and start over. .. code-block:: bash - cmake [options ...] /path/to/lammps/cmake # build from any dir - cmake [options ...] ../cmake # build from lammps/build + cmake [options ...] /path/to/lammps/cmake # build from any dir + cmake [options ...] ../cmake # build from lammps/build + cmake3 [options ...] ../cmake # build from lammps/build The cmake command takes one required argument, which is the LAMMPS cmake directory which contains the CMakeLists.txt file. @@ -119,7 +122,8 @@ command-line options. Several useful ones are: -D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired -D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug - -G output # style of output CMake generates + -G output # style of output CMake generates (e.g. "Unix Makefiles" or "Ninja") + -D CMAKE_MAKE_PROGRAM=builder # name of the builder executable (e.g. set to "gmake" instead of "make") -DVARIABLE=value # setting for a LAMMPS feature to enable -D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir -C path/to/preset/file # load some CMake settings before configuring @@ -127,7 +131,7 @@ command-line options. Several useful ones are: All the LAMMPS-specific -D variables that a LAMMPS build supports are described on the pages linked to from the :doc:`Build ` doc page. All of these variable names are upper-case and their values are -lower-case, e.g. -D LAMMPS\_SIZES=smallbig. For boolean values, any of +lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of these forms can be used: yes/no, on/off, 1/0. On Unix/Linux machines, CMake generates a Makefile by default to diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 32e1bbb2c8..4589015e35 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -14,7 +14,7 @@ or $ make yes-name -as described on the :doc:`Build\_package ` doc page. +as described on the :doc:`Build_package ` doc page. For a CMake build there may be additional optional or required variables to set. For a build with make, a provided library under the @@ -107,37 +107,37 @@ which GPU hardware to build for. -D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon # value = yes or no (default) -GPU\_ARCH settings for different GPU hardware is as follows: +GPU_ARCH settings for different GPU hardware is as follows: -* sm\_12 or sm\_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) -* sm\_20 or sm\_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) -* sm\_30 or sm\_35 or sm\_37 for Kepler (supported since CUDA 5) -* sm\_50 or sm\_52 for Maxwell (supported since CUDA 6) -* sm\_60 or sm\_61 for Pascal (supported since CUDA 8) -* sm\_70 for Volta (supported since CUDA 9) -* sm\_75 for Turing (supported since CUDA 10) +* sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) +* sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) +* sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5) +* sm_50 or sm_52 for Maxwell (supported since CUDA 6) +* sm_60 or sm_61 for Pascal (supported since CUDA 8) +* sm_70 for Volta (supported since CUDA 9) +* sm_75 for Turing (supported since CUDA 10) A more detailed list can be found, for example, at `Wikipedia's CUDA article `_ CMake can detect which version of the CUDA toolkit is used and thus can include support for **all** major GPU architectures supported by this toolkit. -Thus the GPU\_ARCH setting is merely an optimization, to have code for +Thus the GPU_ARCH setting is merely an optimization, to have code for the preferred GPU architecture directly included rather than having to wait for the JIT compiler of the CUDA driver to translate it. **Traditional make**\ : -Before building LAMMPS, you must build the GPU library in lib/gpu. +Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ . You can do this manually if you prefer; follow the instructions in -lib/gpu/README. Note that the GPU library uses MPI calls, so you must +``lib/gpu/README``. Note that the GPU library uses MPI calls, so you must use the same MPI library (or the STUBS library) settings as the main -LAMMPS code. This also applies to the -DLAMMPS\_BIGBIG, --DLAMMPS\_SMALLBIG, or -DLAMMPS\_SMALLSMALL settings in whichever +LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ , +``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever Makefile you use. -You can also build the library in one step from the lammps/src dir, -using a command like these, which simply invoke the lib/gpu/Install.py +You can also build the library in one step from the ``lammps/src`` dir, +using a command like these, which simply invoke the ``lib/gpu/Install.py`` script with the specified args: .. code-block:: bash @@ -156,22 +156,22 @@ Makefile.machine you start from via the corresponding -c, -a, -p, -e switches (as in the examples above), and also save a copy of the new Makefile if desired: -* CUDA\_HOME = where NVIDIA CUDA software is installed on your system -* CUDA\_ARCH = sm\_XX, what GPU hardware you have, same as CMake GPU\_ARCH above -* CUDA\_PRECISION = precision (double, mixed, single) -* EXTRAMAKE = which Makefile.lammps.\* file to copy to Makefile.lammps +* ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system +* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above +* ``CUDA_PRECISION`` = precision (double, mixed, single) +* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps -The file Makefile.linux\_multi is set up to include support for multiple +The file Makefile.linux_multi is set up to include support for multiple GPU architectures as supported by the CUDA toolkit in use. This is done through using the "--gencode " flag, which can be used multiple times and thus support all GPU architectures supported by your CUDA compiler. If the library build is successful, 3 files should be created: -lib/gpu/libgpu.a, lib/gpu/nvc\_get\_devices, and -lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS -to link with CUDA libraries. If the settings in Makefile.lammps for +``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and +``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS +to link with CUDA libraries. If the settings in ``Makefile.lammps`` for your machine are not correct, the LAMMPS build will fail, and -lib/gpu/Makefile.lammps may need to be edited. +``lib/gpu/Makefile.lammps`` may need to be edited. .. note:: @@ -211,35 +211,36 @@ minutes to hours) to build. Of course you only need to do that once.) -D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on -D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes -If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built +If ``DOWNLOAD_KIM`` is set, the KIM library will be downloaded and built inside the CMake build directory. If the KIM library is already on -your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH +your system (in a location CMake cannot find it), set the ``PKG_CONFIG_PATH`` environment variable so that libkim-api can be found. *For using OpenKIM web queries in LAMMPS*\ : -If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any -libcurl calls within the KIM web query display a lot of information about -libcurl operations. You hardly ever want this set in production use, you will -almost always want this when you debug/report problems. +If the ``LMP_DEBUG_CURL`` environment variable is set, the libcurl verbose +mode will be on, and any libcurl calls within the KIM web query display a +lot of information about libcurl operations. You hardly ever want this +set in production use, you will almost always want this when you debug or +report problems. The libcurl performs peer SSL certificate verification by default. This verification is done using a CA certificate store that the SSL library can use to make sure the peer's server certificate is valid. If SSL reports an error ("certificate verify failed") during the handshake and thus refuses -further communication with that server, you can set LMP\_NO\_SSL\_CHECK. -If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection +further communication with that server, you can set ``LMP_NO_SSL_CHECK``\ . +If ``LMP_NO_SSL_CHECK`` is set, libcurl does not verify the peer and connection succeeds regardless of the names in the certificate. This option is insecure. As an alternative, you can specify your own CA cert path by setting the -environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the -KIM web query would get this value from the environmental variable. +environment variable ``CURL_CA_BUNDLE`` to the path of your choice. A call +to the KIM web query would get this value from the environmental variable. **Traditional make**\ : You can download and build the KIM library manually if you prefer; -follow the instructions in lib/kim/README. You can also do it in one +follow the instructions in ``lib/kim/README``\ . You can also do it in one step from the lammps/src dir, using a command like these, which simply -invoke the lib/kim/Install.py script with the specified args. +invoke the ``lib/kim/Install.py`` script with the specified args. .. code-block:: bash @@ -252,7 +253,7 @@ invoke the lib/kim/Install.py script with the specified args. $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver Settings for OpenKIM web queries discussed above need to be applied by adding -them to the LMP\_INC variable through editing the Makefile.machine you are +them to the ``LMP_INC`` variable through editing the Makefile.machine you are using. For example: .. code-block:: make @@ -271,7 +272,7 @@ build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP) or GPUs (NVIDIA Cuda). For a CMake or make build, these are the possible choices for the -KOKKOS\_ARCH settings described below. Note that for CMake, these are +``KOKKOS_ARCH`` settings described below. Note that for CMake, these are really Kokkos variables, not LAMMPS variables. Hence you must use case-sensitive values, e.g. BDW, not bdw. @@ -334,7 +335,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables: -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper The wrapper value is the Cuda nvcc compiler wrapper provided in the -Kokkos library: lib/kokkos/bin/nvcc\_wrapper. The setting should +Kokkos library: ``lib/kokkos/bin/nvcc_wrapper``\ . The setting should include the full path name to the wrapper, e.g. .. code-block:: bash @@ -343,9 +344,9 @@ include the full path name to the wrapper, e.g. **Traditional make**\ : -Choose which hardware to support in Makefile.machine via -KOKKOS\_DEVICES and KOKKOS\_ARCH settings. See the -src/MAKE/OPTIONS/Makefile.kokkos\* files for examples. +Choose which hardware to support in ``Makefile.machine`` via +``KOKKOS_DEVICES`` and ``KOKKOS_ARCH`` settings. See the +``src/MAKE/OPTIONS/Makefile.kokkos\*`` files for examples. For multicore CPUs using OpenMP: @@ -400,18 +401,18 @@ library. -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes -D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) -If DOWNLOAD\_LATTE is set, the LATTE library will be downloaded and +If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded and built inside the CMake build directory. If the LATTE library is already on your system (in a location CMake cannot find it), -LATTE\_LIBRARY is the filename (plus path) of the LATTE library file, +``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file, not the directory the library file is in. **Traditional make**\ : You can download and build the LATTE library manually if you prefer; -follow the instructions in lib/latte/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invokes the lib/latte/Install.py script with the specified +follow the instructions in ``lib/latte/README``\ . You can also do it in +one step from the ``lammps/src`` dir, using a command like these, which +simply invokes the ``lib/latte/Install.py`` script with the specified args: .. code-block:: bash @@ -450,10 +451,10 @@ be installed on your system. **Traditional make**\ : Before building LAMMPS, you must build the CSlib library in -lib/message. You can build the CSlib library manually if you prefer; -follow the instructions in lib/message/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/message/Install.py script with the specified args: +``lib/message``\ . You can build the CSlib library manually if you prefer; +follow the instructions in ``lib/message/README``\ . You can also do it in +one step from the ``lammps/src`` dir, using a command like these, which +simply invoke the ``lib/message/Install.py`` script with the specified args: .. code-block:: bash @@ -461,9 +462,9 @@ simply invoke the lib/message/Install.py script with the specified args: $ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support $ make lib-message args="-s" # build as serial lib with no ZMQ support -The build should produce two files: lib/message/cslib/src/libmessage.a -and lib/message/Makefile.lammps. The latter is copied from an -existing Makefile.lammps.\* and has settings to link with the ZeroMQ +The build should produce two files: ``lib/message/cslib/src/libmessage.a`` +and ``lib/message/Makefile.lammps``\ . The latter is copied from an +existing ``Makefile.lammps.\*`` and has settings to link with the ZeroMQ library if requested in the build. ---------- @@ -474,10 +475,10 @@ MSCG package ----------------------- To build with this package, you must download and build the MS-CG -library. Building the MS-CG library and using it from LAMMPS requires -a C++11 compatible compiler and that the GSL (GNU Scientific Library) -headers and libraries are installed on your machine. See the -lib/mscg/README and MSCG/Install files for more details. +library. Building the MS-CG library requires that the GSL +(GNU Scientific Library) headers and libraries are installed on your +machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for +more details. **CMake build**\ : @@ -487,19 +488,19 @@ lib/mscg/README and MSCG/Install files for more details. -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) -If DOWNLOAD\_MSCG is set, the MSCG library will be downloaded and built +If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded and built inside the CMake build directory. If the MSCG library is already on -your system (in a location CMake cannot find it), MSCG\_LIBRARY is the +your system (in a location CMake cannot find it), ``MSCG_LIBRARY`` is the filename (plus path) of the MSCG library file, not the directory the -library file is in. MSCG\_INCLUDE\_DIR is the directory the MSCG +library file is in. ``MSCG_INCLUDE_DIR`` is the directory the MSCG include file is in. **Traditional make**\ : You can download and build the MS-CG library manually if you prefer; -follow the instructions in lib/mscg/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/mscg/Install.py script with the specified args: +follow the instructions in ``lib/mscg/README``\ . You can also do it in one +step from the ``lammps/src`` dir, using a command like these, which simply +invoke the ``lib/mscg/Install.py`` script with the specified args: .. code-block:: bash @@ -511,9 +512,9 @@ invoke the lib/mscg/Install.py script with the specified args: $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release Note that 2 symbolic (soft) links, "includelink" and "liblink", will -be created in lib/mscg to point to the MS-CG src/installation dir. -When LAMMPS is built in src it will use these links. You should not -need to edit the lib/mscg/Makefile.lammps file. +be created in ``lib/mscg`` to point to the MS-CG ``src/installation`` +dir. When LAMMPS is built in src it will use these links. You should +not need to edit the ``lib/mscg/Makefile.lammps`` file. ---------- @@ -524,7 +525,7 @@ OPT package **CMake build**\ : -No additional settings are needed besides "-D PKG\_OPT=yes". +No additional settings are needed besides ``-D PKG_OPT=yes`` **Traditional make**\ : @@ -542,15 +543,15 @@ POEMS package **CMake build**\ : -No additional settings are needed besides "-D PKG\_OPT=yes". +No additional settings are needed besides ``-D PKG_OPT=yes`` **Traditional make**\ : -Before building LAMMPS, you must build the POEMS library in lib/poems. +Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ . You can do this manually if you prefer; follow the instructions in -lib/poems/README. You can also do it in one step from the lammps/src +``lib/poems/README``\ . You can also do it in one step from the ``lammps/src`` dir, using a command like these, which simply invoke the -lib/poems/Install.py script with the specified args: +``lib/poems/Install.py`` script with the specified args: .. code-block:: bash @@ -559,13 +560,13 @@ lib/poems/Install.py script with the specified args: $ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") $ make lib-poems args="-m icc" # build with Intel icc compiler -The build should produce two files: lib/poems/libpoems.a and -lib/poems/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.\* and has settings needed to build LAMMPS with the +The build should produce two files: ``lib/poems/libpoems.a`` and +``lib/poems/Makefile.lammps``\ . The latter is copied from an existing +``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the POEMS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/poems/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. +necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file +for your system, which should define an ``EXTRAMAKE`` variable to specify +a corresponding ``Makefile.lammps.machine`` file. ---------- @@ -575,9 +576,9 @@ PYTHON package --------------------------- Building with the PYTHON package requires you have a Python 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 -lib/python/README for more details. +library available on your system, which needs to be a Python 2.7 +version or a Python 3.x version. See ``lib/python/README`` for more +details. **CMake build**\ : @@ -588,16 +589,16 @@ lib/python/README for more details. Without this setting, CMake will guess the default Python on your system. To use a different Python version, you can either create a virtualenv, activate it and then run cmake. Or you can set the -PYTHON\_EXECUTABLE variable to specify which Python interpreter should +PYTHON_EXECUTABLE variable to specify which Python interpreter should be used. Note note that you will also need to have the development headers installed for this version, e.g. python2-devel. **Traditional make**\ : -The build uses the lib/python/Makefile.lammps file in the compile/link +The build uses the ``lib/python/Makefile.lammps`` file in the compile/link process to find Python. You should only need to create a new -Makefile.lammps.\* file (and copy it to Makefile.lammps) if the LAMMPS -build fails. +``Makefile.lammps.\*`` file (and copy it to ``Makefile.lammps``\ ) if +the LAMMPS build fails. ---------- @@ -618,11 +619,11 @@ To build with this package, you must download and build the `Voro++ library ` doc page explains how to build LAMMPS as either a shared or static library. This results in one of these 2 files: -.. parsed-literal:: +.. code-block:: bash liblammps.so # shared library liblammps.a # static library @@ -25,7 +25,7 @@ these 2 files: then its mpi.h file needs to be included. While it is technically possible to use a full MPI library in the calling code and link to a serial LAMMPS library compiled with MPI STUBS, it is recommended - to use the *same* MPI library for both, and then use MPI\_Comm\_split() + to use the *same* MPI library for both, and then use MPI_Comm_split() in the calling code to pass a suitable communicator with a subset of MPI ranks to the function creating the LAMMPS instance. @@ -43,7 +43,7 @@ executable code from the library is copied into the calling executable. *CMake build*\ : This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes" -and installed with "make install" and the PKG\_CONFIG\_PATH environment +and installed with "make install" and the PKG_CONFIG_PATH environment variable updated to include the *liblammps.pc* file installed into the configured destination folder, if needed. The commands to compile and link the coupled executable are then: @@ -167,7 +167,7 @@ traditional make build using "make mode=shlib serial" becomes: However, now the `liblammps.so` file is required at runtime and needs to be in a folder, where the shared linker program of the operating system can find it. This would be either a folder like "/usr/local/lib64" -or "${HOME}/.local/lib64" or a folder pointed to by the LD\_LIBRARY\_PATH +or "${HOME}/.local/lib64" or a folder pointed to by the LD_LIBRARY_PATH environment variable. You can type .. code-block:: bash @@ -177,7 +177,7 @@ environment variable. You can type to see what directories are in that list. Or you can add the LAMMPS src directory (or the directory you performed -a CMake style build in) to your LD\_LIBRARY\_PATH, so that the current +a CMake style build in) to your LD_LIBRARY_PATH, so that the current version of the shared library is always available to programs that use it. For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you @@ -229,7 +229,7 @@ If a required library is missing, you would get a 'not found' entry: Either flavor of library (static or shared) allows one or more LAMMPS objects to be instantiated from the calling program. When used from a C++ program, most of the symbols and functions in LAMMPS are wrapped -in a LAMMPS\_NS namespace; you can safely use any of its classes and +in a LAMMPS_NS namespace; you can safely use any of its classes and methods from within the calling code, as needed, and you will not incur conflicts with functions and variables in your code that share the name. This, however, does not extend to all additional libraries bundled with diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index 0830171de3..0379a8379a 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -31,7 +31,7 @@ machines, especially workstations, desktops, and laptops, so we suggest you try it first when building LAMMPS in those cases. The commands below perform a default LAMMPS build, producing the LAMMPS -executable lmp\_serial and lmp\_mpi in lammps/src: +executable lmp_serial and lmp_mpi in lammps/src: .. code-block:: bash @@ -73,7 +73,7 @@ in the LAMMPS distribution. Typing "make machine" uses use Makefile.serial and Makefile.mpi, respectively. Other makefiles are in these directories: -.. parsed-literal:: +.. code-block:: bash OPTIONS # Makefiles which enable specific options MACHINES # Makefiles for specific machines diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 23ff460d5c..b3d2d3fc56 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -47,13 +47,13 @@ versus make. **CMake build**\ : -.. code-block:: bash +.. code-block:: csh -D PKG_NAME=value # yes or no (default) Examples: -.. code-block:: bash +.. code-block:: csh -D PKG_MANYBODY=yes -D PKG_USER-INTEL=yes @@ -185,7 +185,7 @@ one of them as a starting point and customize it to your needs. The following commands are useful for managing package source files and their installation when building LAMMPS via traditional make. -Just type "make" in lammps/src to see a one-line summary. +Just type ``make`` in lammps/src to see a one-line summary. These commands install/un-install sets of packages: @@ -202,8 +202,8 @@ These commands install/un-install sets of packages: make yes-ext # install packages that require external libraries make no-ext # uninstall packages that require external libraries -which install/un-install various sets of packages. Typing "make -package" will list all the these commands. +which install/un-install various sets of packages. Typing ``make +package`` will list all the these commands. .. note:: @@ -220,23 +220,23 @@ need to use these commands unless you are editing LAMMPS files or are :doc:`installing a patch ` downloaded from the LAMMPS web site. -Type "make package-status" or "make ps" to show which packages are +Type ``make package-status`` or ``make ps`` to show which packages are currently installed. For those that are installed, it will list any files that are different in the src directory and package sub-directory. -Type "make package-installed" or "make pi" to show which packages are +Type ``make package-installed`` or ``make pi`` to show which packages are currently installed, without listing the status of packages that are not installed. -Type "make package-update" or "make pu" to overwrite src files with +Type ``make package-update`` or ``make pu`` to overwrite src files with files from the package sub-directories if the package is installed. It should be used after a :doc:`patch has been applied `, since patches only update the files in the package sub-directory, but not the src files. -Type "make package-overwrite" to overwrite files in the package +Type ``make package-overwrite`` to overwrite files in the package sub-directories with src files. -Type "make package-diff" to list all differences between pairs of +Type ``make package-diff`` to list all differences between pairs of files in both the source directory and the package directory. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 08c1ab7714..01792507e7 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -85,7 +85,7 @@ to assist: FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY -# default is FFT\_PACK\_ARRAY if not specified +# default is FFT_PACK_ARRAY if not specified .. code-block:: make @@ -100,9 +100,9 @@ to assist: FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs -As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if +As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if the compiler can find the FFT header and library files in its default search path. -You must specify FFT\_LIB with the appropriate FFT libraries to include in the link. +You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link. **CMake and make info**\ : @@ -126,14 +126,15 @@ platform and can be faster than the KISS FFT library. You can download it from `www.fftw.org `_. LAMMPS requires version 3.X; the legacy version 2.1.X is no longer supported. -Building FFTW for your box should be as simple as ./configure; make; -make install. The install command typically requires root privileges +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 +the "--prefix" option of configure. Type ``./configure --help`` to see 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). +can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting +above). Performing 3d FFTs in parallel can be time consuming due to data access and required communication. This cost can be reduced by @@ -142,15 +143,15 @@ precision means the real and imaginary parts of a complex datum are 4-byte floats. Double precision means they are 8-byte doubles. Note that Fourier transform and related PPPM operations are somewhat less sensitive to floating point truncation errors and thus the resulting -error is less than the difference in precision. Using the -DFFT\_SINGLE +error is less than the difference in precision. Using the ``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory use and parallel communication costs for transposing 3d FFT data. -When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW +When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW library a second time with support for single-precision. For FFTW3, do the following, which should produce the additional -library libfftw3f.a or libfftw3f.so. +library ``libfftw3f.a`` or ``libfftw3f.so``\ . .. code-block:: bash @@ -159,7 +160,7 @@ library libfftw3f.a or libfftw3f.so. Performing 3d FFTs requires communication to transpose the 3d FFT grid. The data packing/unpacking for this can be done in one of 3 -modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above. +modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above. Depending on the machine, the size of the FFT grid, the number of processors used, one option may be slightly faster. The default is ARRAY mode. @@ -187,7 +188,8 @@ adequate. LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL -# default is LAMMPS\_SMALLBIG if not specified +The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified + **CMake and make info**\ : The default "smallbig" setting allows for simulations with: @@ -235,7 +237,7 @@ than crashing randomly or corrupting data. Also note that the GPU package requires its lib/gpu library to be compiled with the same size setting, or the link will fail. A CMake build does this automatically. When building with make, the setting -in whichever lib/gpu/Makefile is used must be the same as above. +in whichever ``lib/gpu/Makefile`` is used must be the same as above. ---------- @@ -286,15 +288,16 @@ variables: JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them JPG_LIB = -ljpeg -lpng -lz # library names -As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can -find the graphics header and library files. You must specify JPG\_LIB +As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``, +if make can find the graphics header and library files. You must +specify ``JPG_LIB`` with a list of graphics libraries to include in the link. You must insure ffmpeg is in a directory where LAMMPS can find it at runtime, that is a directory in your PATH environment variable. **CMake and make info**\ : -Using ffmpeg to output movie files requires that your machine +Using ``ffmpeg`` to output movie files requires that your machine supports the "popen" function in the standard runtime library. .. note:: @@ -351,7 +354,7 @@ found by LAMMPS during a run. Memory allocation alignment --------------------------------------- -This setting enables the use of the posix\_memalign() call instead of +This setting enables the use of the posix_memalign() call instead of malloc() when LAMMPS allocates large chunks or memory. This can make vector instructions on CPUs more efficient, if dynamically allocated memory is aligned on larger-than-default byte boundaries. @@ -366,7 +369,7 @@ aligned on 64-byte boundaries. -D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) -Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign() +Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using posix_memalign() and revert to using the malloc() C-library function instead. When compiling LAMMPS for Windows systems, malloc() will always be used and this setting ignored. @@ -377,8 +380,8 @@ and this setting ignored. LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 -Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated -with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot** +Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory allocated +with the malloc() function call instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as it does use different function calls for allocating aligned memory, that are not compatible with how LAMMPS manages its dynamical memory. diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst index 4f20a01559..2b7bd27209 100644 --- a/doc/src/Build_windows.rst +++ b/doc/src/Build_windows.rst @@ -55,8 +55,8 @@ and the corresponding new code. A machine makefile for using cygwin for the old build system is provided. Using CMake for this mode of compilation is untested and not likely to work. -When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define -in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker +When compiling for Windows do **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 both to the linker flags when your resulting LAMMPS Windows executable complains about missing .dll files. The CMake configuration should set diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index 64a7315a5f..f8de98c1a2 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -46,7 +46,7 @@ is to have the desired effect. For example, the :doc:`read_data ` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors ` and -:doc:`boundary ` commands need to be used before read\_data to +:doc:`boundary ` commands need to be used before read_data to tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 86d28bafbd..37283823d7 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -101,7 +101,7 @@ LAMMPS: print "B2 = ${b$a}" Nor can you specify an expression like "$($x-1.0)" for an immediate - variable, but you could use $(v\_x-1.0), since the latter is valid + variable, but you could use $(v_x-1.0), since the latter is valid syntax for an :doc:`equal-style variable `. See the :doc:`variable ` command for more details of how diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index d74d5f7f35..603952a29d 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -69,14 +69,14 @@ but a floating-point number 1.0 is provided): Some commands allow for using variable references in place of numeric constants so that the value can be evaluated and may change over the -course of a run. This is typically done with the syntax *v\_name* for a +course of a run. This is typically done with the syntax *v_name* for a parameter, where name is the name of the variable. On the other hand, immediate variable expansion with the syntax ${name} is performed while reading the input and before parsing commands, .. note:: - Using a variable reference (i.e. *v\_name*) is only allowed if + Using a variable reference (i.e. *v_name*) is only allowed if the documentation of the corresponding command explicitly says it is. Otherwise, you will receive an error message of this kind: diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index da36f18d82..82c9d0bd78 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -39,9 +39,9 @@ Doc page with :doc:`WARNING messages ` *All angle coeffs are not set* All angle coefficients must be set in the data file or by the - angle\_coeff command before running a simulation. + angle_coeff command before running a simulation. -*All atom IDs = 0 but atom\_modify id = yes* +*All atom IDs = 0 but atom_modify id = yes* Self-explanatory. *All atoms of a swapped type must have same charge.* @@ -52,15 +52,15 @@ Doc page with :doc:`WARNING messages ` *All bond coeffs are not set* All bond coefficients must be set in the data file or by the - bond\_coeff command before running a simulation. + bond_coeff command before running a simulation. *All dihedral coeffs are not set* All dihedral coefficients must be set in the data file or by the - dihedral\_coeff command before running a simulation. + dihedral_coeff command before running a simulation. *All improper coeffs are not set* All improper coefficients must be set in the data file or by the - improper\_coeff command before running a simulation. + improper_coeff command before running a simulation. *All masses are not set* For atom styles that define masses for each atom type, all masses must @@ -76,9 +76,9 @@ Doc page with :doc:`WARNING messages ` *All pair coeffs are not set* All pair coefficients must be set in the data file or by the - pair\_coeff command before running a simulation. + pair_coeff command before running a simulation. -*All read\_dump x,y,z fields must be specified for scaled, triclinic coords* +*All read_dump x,y,z fields must be specified for scaled, triclinic coords* For triclinic boxes and scaled coordinates you must specify all 3 of the x,y,z fields, else LAMMPS cannot reconstruct the unscaled coordinates. @@ -89,8 +89,8 @@ Doc page with :doc:`WARNING messages ` *All variables in next command must be same style* Self-explanatory. -*Angle atom missing in delete\_bonds* - The delete\_bonds command cannot find one or more atoms in a particular +*Angle atom missing in delete_bonds* + The delete_bonds command cannot find one or more atoms in a particular angle on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid angle. @@ -113,20 +113,20 @@ Doc page with :doc:`WARNING messages ` *Angle coeff for hybrid has invalid style* Angle style hybrid uses another angle style as one of its - coefficients. The angle style used in the angle\_coeff command or read + coefficients. The angle style used in the angle_coeff command or read from a restart file is not recognized. *Angle coeffs are not set* No angle coefficients have been assigned in the data file or via the - angle\_coeff command. + angle_coeff command. *Angle extent > half of periodic box length* - This error was detected by the neigh\_modify check yes setting. It is + This error was detected by the neigh_modify check yes setting. It is an error because the angle atoms are so far apart it is ambiguous how it should be defined. *Angle potential must be defined for SHAKE* - When shaking angles, an angle\_style potential must be used. + When shaking angles, an angle_style potential must be used. *Angle style hybrid cannot have hybrid as an argument* Self-explanatory. @@ -143,18 +143,18 @@ Doc page with :doc:`WARNING messages ` *Angle table parameters did not set N* List of angle table parameters must include N setting. -*Angle\_coeff command before angle\_style is defined* - Coefficients cannot be set in the data file or via the angle\_coeff - command until an angle\_style has been assigned. +*Angle_coeff command before angle_style is defined* + Coefficients cannot be set in the data file or via the angle_coeff + command until an angle_style has been assigned. -*Angle\_coeff command before simulation box is defined* - The angle\_coeff command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Angle_coeff command before simulation box is defined* + The angle_coeff command cannot be used before a read_data, + read_restart, or create_box command. -*Angle\_coeff command when no angles allowed* +*Angle_coeff command when no angles allowed* The chosen atom style does not allow for angles to be defined. -*Angle\_style command when no angles allowed* +*Angle_style command when no angles allowed* The chosen atom style does not allow for angles to be defined. *Angles assigned incorrectly* @@ -211,7 +211,7 @@ Doc page with :doc:`WARNING messages ` This is probably because you have lost some atoms. *Atom in too many rigid bodies - boost MAXBODY* - Fix poems has a parameter MAXBODY (in fix\_poems.cpp) which determines + Fix poems has a parameter MAXBODY (in fix_poems.cpp) which determines the maximum number of rigid bodies a single atom can belong to (i.e. a multibody joint). The bodies you have defined exceed this limit. @@ -242,25 +242,25 @@ Doc page with :doc:`WARNING messages ` Atom-style variables generate one value per atom which is not allowed in an equal-style variable. -*Atom\_modify id command after simulation box is defined* - The atom\_modify id command cannot be used after a read\_data, - read\_restart, or create\_box command. +*Atom_modify id command after simulation box is defined* + The atom_modify id command cannot be used after a read_data, + read_restart, or create_box command. -*Atom\_modify map command after simulation box is defined* - The atom\_modify map command cannot be used after a read\_data, - read\_restart, or create\_box command. +*Atom_modify map command after simulation box is defined* + The atom_modify map command cannot be used after a read_data, + read_restart, or create_box command. -*Atom\_modify sort and first options cannot be used together* +*Atom_modify sort and first options cannot be used together* Self-explanatory. -*Atom\_style command after simulation box is defined* - The atom\_style command cannot be used after a read\_data, - read\_restart, or create\_box command. +*Atom_style command after simulation box is defined* + The atom_style command cannot be used after a read_data, + read_restart, or create_box command. -*Atom\_style line can only be used in 2d simulations* +*Atom_style line can only be used in 2d simulations* Self-explanatory. -*Atom\_style tri can only be used in 3d simulations* +*Atom_style tri can only be used in 3d simulations* Self-explanatory. *Atomfile variable could not read values* @@ -301,17 +301,17 @@ Doc page with :doc:`WARNING messages ` Specified bond type is not valid. *Bad fix ID in fix append/atoms command* - The value of the fix\_id for keyword spatial must start with 'f\_'. + The value of the fix_id for keyword spatial must start with "f\_". *Bad grid of processors* The 3d grid of processors defined by the processors command does not match the number of processors LAMMPS is being run on. -*Bad kspace\_modify kmax/ewald parameter* - Kspace\_modify values for the kmax/ewald keyword must be integers > 0 +*Bad kspace_modify kmax/ewald parameter* + Kspace_modify values for the kmax/ewald keyword must be integers > 0 -*Bad kspace\_modify slab parameter* - Kspace\_modify value for the slab/volume keyword must be >= 2.0. +*Bad kspace_modify slab parameter* + Kspace_modify value for the slab/volume keyword must be >= 2.0. *Bad matrix inversion in mldivide3* This error should not occur unless the matrix is badly formed. @@ -331,16 +331,16 @@ Doc page with :doc:`WARNING messages ` the Newton-Rhaphson method, but found a non-positive or NaN cutoff *Balance command before simulation box is defined* - The balance command cannot be used before a read\_data, read\_restart, - or create\_box command. + The balance command cannot be used before a read_data, read_restart, + or create_box command. *Balance produced bad splits* This should not occur. It means two or more cutting plane locations are on top of each other or out of order. Report the problem to the developers. -*Balance rcb cannot be used with comm\_style brick* - Comm\_style tiled must be used instead. +*Balance rcb cannot be used with comm_style brick* + Comm_style tiled must be used instead. *Balance shift string is invalid* The string can only contain the characters "x", "y", or "z". @@ -367,10 +367,10 @@ Doc page with :doc:`WARNING messages ` *Bitmapped lookup tables require int/float be same size* Cannot use pair tables on this machine, because of word sizes. Use - the pair\_modify command with table 0 instead. + the pair_modify command with table 0 instead. *Bitmapped table in file does not match requested table* - Setting for bitmapped table in pair\_coeff command must match table + Setting for bitmapped table in pair_coeff command must match table in file exactly. *Bitmapped table is incorrect length in table file* @@ -385,8 +385,8 @@ Doc page with :doc:`WARNING messages ` processor. Typically this is because the pairwise cutoff is set too short or the bond has blown apart and an atom is too far away. -*Bond atom missing in delete\_bonds* - The delete\_bonds command cannot find one or more atoms in a particular +*Bond atom missing in delete_bonds* + The delete_bonds command cannot find one or more atoms in a particular bond on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid bond. @@ -412,15 +412,15 @@ Doc page with :doc:`WARNING messages ` *Bond coeff for hybrid has invalid style* Bond style hybrid uses another bond style as one of its coefficients. - The bond style used in the bond\_coeff command or read from a restart + The bond style used in the bond_coeff command or read from a restart file is not recognized. *Bond coeffs are not set* No bond coefficients have been assigned in the data file or via the - bond\_coeff command. + bond_coeff command. *Bond extent > half of periodic box length* - This error was detected by the neigh\_modify check yes setting. It is + This error was detected by the neigh_modify check yes setting. It is an error because the bond atoms are so far apart it is ambiguous how it should be defined. @@ -444,7 +444,7 @@ Doc page with :doc:`WARNING messages ` This bond style can change the bond topology which is not allowed with this atom style. -*Bond style quartic requires special\_bonds = 1,1,1* +*Bond style quartic requires special_bonds = 1,1,1* This is a restriction of the current bond quartic implementation. *Bond table parameters did not set N* @@ -459,18 +459,18 @@ Doc page with :doc:`WARNING messages ` *BondBond coeff for hybrid angle has invalid format* No "bb" field should appear in data file entry. -*Bond\_coeff command before bond\_style is defined* - Coefficients cannot be set in the data file or via the bond\_coeff - command until an bond\_style has been assigned. +*Bond_coeff command before bond_style is defined* + Coefficients cannot be set in the data file or via the bond_coeff + command until an bond_style has been assigned. -*Bond\_coeff command before simulation box is defined* - The bond\_coeff command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Bond_coeff command before simulation box is defined* + The bond_coeff command cannot be used before a read_data, + read_restart, or create_box command. -*Bond\_coeff command when no bonds allowed* +*Bond_coeff command when no bonds allowed* The chosen atom style does not allow for bonds to be defined. -*Bond\_style command when no bonds allowed* +*Bond_style command when no bonds allowed* The chosen atom style does not allow for bonds to be defined. *Bonds assigned incorrectly* @@ -481,7 +481,7 @@ Doc page with :doc:`WARNING messages ` The data file header lists bonds but no bond types. *Bond/react: Cannot use fix bond/react with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom\_style + Only systems with bonds that can be changed can be used. Atom_style template does not qualify. *Bond/react: Invalid template atom ID in map file* @@ -513,7 +513,7 @@ Doc page with :doc:`WARNING messages ` *Bond/react: Fix bond/react needs ghost atoms from farther away* This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The - comm\_modify cutoff command can be used to extend the communication + comm_modify cutoff command can be used to extend the communication range. *Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* @@ -531,12 +531,12 @@ Doc page with :doc:`WARNING messages ` *Bond/react special bond generation overflow* The number of special bonds per-atom created by a reaction exceeds the - system setting. See the read\_data or create\_box command for how to + system setting. See the read_data or create_box command for how to specify this value. *Bond/react topology/atom exceed system topology/atom* The number of bonds, angles etc per-atom created by a reaction exceeds - the system setting. See the read\_data or create\_box command for how to + the system setting. See the read_data or create_box command for how to specify this value. *Both restart files must use % or neither* @@ -550,16 +550,16 @@ Doc page with :doc:`WARNING messages ` be periodic on both sides. *Boundary command after simulation box is defined* - The boundary command cannot be used after a read\_data, read\_restart, - or create\_box command. + The boundary command cannot be used after a read_data, read_restart, + or create_box command. *Box bounds are invalid* - The box boundaries specified in the read\_data file are invalid. The + The box boundaries specified in the read_data file are invalid. The lo value must be less than the hi value for all 3 dimensions. *Box command after simulation box is defined* - The box command cannot be used after a read\_data, read\_restart, or - create\_box command. + The box command cannot be used after a read_data, read_restart, or + create_box command. *CPU neighbor lists must be used for ellipsoid/sphere mix.* When using Gay-Berne or RE-squared pair styles with both ellipsoidal and @@ -609,7 +609,7 @@ Doc page with :doc:`WARNING messages ` *Cannot (yet) use PPPM with triclinic box and TIP4P* This feature is not yet supported. -*Cannot (yet) use PPPM with triclinic box and kspace\_modify diff ad* +*Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad* This feature is not yet supported. *Cannot (yet) use PPPM with triclinic box and slab correction* @@ -618,10 +618,10 @@ Doc page with :doc:`WARNING messages ` *Cannot (yet) use kspace slab correction with long-range dipoles and non-neutral systems or per-atom energy* This feature is not yet supported. -*Cannot (yet) use kspace\_modify diff ad with compute group/group* +*Cannot (yet) use kspace_modify diff ad with compute group/group* This option is not yet supported. -*Cannot (yet) use kspace\_style pppm/stagger with triclinic systems* +*Cannot (yet) use kspace_style pppm/stagger with triclinic systems* This feature is not yet supported. *Cannot (yet) use molecular templates with Kokkos* @@ -636,7 +636,7 @@ Doc page with :doc:`WARNING messages ` *Cannot (yet) use rigid bodies with fix nh and Kokkos* Self-explanatory. -*Cannot (yet) use single precision with MSM (remove -DFFT\_SINGLE from Makefile and re-compile)* +*Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)* Single precision cannot be used with MSM. *Cannot add atoms to fix move variable* @@ -668,10 +668,10 @@ Doc page with :doc:`WARNING messages ` *Cannot change box z boundary to non-periodic for a 2d simulation* Self-explanatory. -*Cannot change dump\_modify every for dump dcd* +*Cannot change dump_modify every for dump dcd* The frequency of writing dump dcd snapshots cannot be changed. -*Cannot change dump\_modify every for dump xtc* +*Cannot change dump_modify every for dump xtc* The frequency of writing dump xtc snapshots cannot be changed. *Cannot change timestep once fix srd is setup* @@ -682,18 +682,18 @@ Doc page with :doc:`WARNING messages ` This is because fix pour pre-computes the time delay for particles to fall out of the insertion volume due to gravity. -*Cannot change to comm\_style brick from tiled layout* +*Cannot change to comm_style brick from tiled layout* Self-explanatory. -*Cannot change\_box after reading restart file with per-atom info* +*Cannot change_box after reading restart file with per-atom info* This is because the restart file info cannot be migrated with the atoms. You can get around this by performing a 0-timestep run which will assign the restart file info to actual atoms. -*Cannot change\_box in xz or yz for 2d simulation* +*Cannot change_box in xz or yz for 2d simulation* Self-explanatory. -*Cannot change\_box in z dimension for 2d simulation* +*Cannot change_box in z dimension for 2d simulation* Self-explanatory. *Cannot clear group all* @@ -703,8 +703,8 @@ Doc page with :doc:`WARNING messages ` This error was generated by MPI when reading/writing an MPI-IO restart file. -*Cannot compute initial g\_ewald\_disp* - LAMMPS failed to compute an initial guess for the PPPM\_disp g\_ewald\_6 +*Cannot compute initial g_ewald_disp* + LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 factor that partitions the computation between real space and k-space for Dispersion interactions. @@ -713,19 +713,19 @@ Doc page with :doc:`WARNING messages ` but the atoms that have been defined have no IDs. *Cannot create atoms with undefined lattice* - Must use the lattice command before using the create\_atoms + Must use the lattice command before using the create_atoms command. *Cannot create/grow a vector/array of pointers for %s* LAMMPS code is making an illegal call to the templated memory allocaters, to create a vector or array of pointers. -*Cannot create\_atoms after reading restart file with per-atom info* +*Cannot create_atoms after reading restart file with per-atom info* The per-atom info was stored to be used when by a fix that you may re-define. If you add atoms before re-defining the fix, then there will not be a correct amount of per-atom info. -*Cannot create\_box after simulation box is defined* +*Cannot create_box after simulation box is defined* A simulation box can only be defined once. *Cannot currently use pair reax with pair hybrid* @@ -746,24 +746,24 @@ Doc page with :doc:`WARNING messages ` *Cannot delete group currently used by a fix* Self-explanatory. -*Cannot delete group currently used by atom\_modify first* +*Cannot delete group currently used by atom_modify first* Self-explanatory. -*Cannot delete\_atoms bond yes for non-molecular systems* +*Cannot delete_atoms bond yes for non-molecular systems* Self-explanatory. -*Cannot displace\_atoms after reading restart file with per-atom info* +*Cannot displace_atoms after reading restart file with per-atom info* This is because the restart file info cannot be migrated with the atoms. You can get around this by performing a 0-timestep run which will assign the restart file info to actual atoms. -*Cannot do GCMC on atoms in atom\_modify first group* +*Cannot do GCMC on atoms in atom_modify first group* This is a restriction due to the way atoms are organized in a list to - enable the atom\_modify first command. + enable the atom_modify first command. -*Cannot do atom/swap on atoms in atom\_modify first group* +*Cannot do atom/swap on atoms in atom_modify first group* This is a restriction due to the way atoms are organized in a list to - enable the atom\_modify first command. + enable the atom_modify first command. *Cannot dump sort on atom IDs with no atom IDs defined* Self-explanatory. @@ -776,15 +776,15 @@ Doc page with :doc:`WARNING messages ` When running LAMMPS via Python through the LAMMPS library interface you cannot also user the input script python command. -*Cannot evaporate atoms in atom\_modify first group* +*Cannot evaporate atoms in atom_modify first group* This is a restriction due to the way atoms are organized in - a list to enable the atom\_modify first command. + a list to enable the atom_modify first command. -*Cannot find create\_bonds group ID* +*Cannot find create_bonds group ID* Self-explanatory. -*Cannot find delete\_bonds group ID* - Group ID used in the delete\_bonds command does not exist. +*Cannot find delete_bonds group ID* + Group ID used in the delete_bonds command does not exist. *Cannot find specified group ID for core particles* Self-explanatory. @@ -792,7 +792,7 @@ Doc page with :doc:`WARNING messages ` *Cannot find specified group ID for shell particles* Self-explanatory. -*Cannot have both pair\_modify shift and tail set to yes* +*Cannot have both pair_modify shift and tail set to yes* These 2 options are contradictory. *Cannot intersect groups using a dynamic group* @@ -958,7 +958,7 @@ Doc page with :doc:`WARNING messages ` *Cannot open gzipped file* LAMMPS was compiled without support for reading and writing gzipped - files through a pipeline to the gzip program with -DLAMMPS\_GZIP. + files through a pipeline to the gzip program with -DLAMMPS_GZIP. *Cannot open input script %s* Self-explanatory. @@ -989,7 +989,7 @@ Doc page with :doc:`WARNING messages ` The specified potential file cannot be opened. Check that the path and name are correct. -*Cannot open pair\_write file* +*Cannot open pair_write file* The specified output file for pair energies and forces cannot be opened. Check that the path and name are correct. @@ -1036,12 +1036,12 @@ Doc page with :doc:`WARNING messages ` This error was generated by MPI when reading/writing an MPI-IO restart file. -*Cannot read\_data without add keyword after simulation box is defined* +*Cannot read_data without add keyword after simulation box is defined* Self-explanatory. -*Cannot read\_restart after simulation box is defined* - The read\_restart command cannot be used after a read\_data, - read\_restart, or create\_box command. +*Cannot read_restart after simulation box is defined* + The read_restart command cannot be used after a read_data, + read_restart, or create_box command. *Cannot redefine variable as a different style* An equal-style variable can be re-defined but only if it was @@ -1086,7 +1086,7 @@ Doc page with :doc:`WARNING messages ` *Cannot set dpd/theta for this atom style* Self-explanatory. -*Cannot set dump\_modify flush for dump xtc* +*Cannot set dump_modify flush for dump xtc* Self-explanatory. *Cannot set mass for this atom style* @@ -1162,7 +1162,7 @@ Doc page with :doc:`WARNING messages ` *Cannot use Ewald with 2d simulation* The kspace style ewald cannot be used in 2d simulations. You can use - 2d Ewald in a 3d simulation; see the kspace\_modify command. + 2d Ewald in a 3d simulation; see the kspace_modify command. *Cannot use Ewald/disp solver on system with no charge, dipole, or LJ particles* No atoms in system have a non-zero charge or dipole, or are LJ @@ -1176,21 +1176,21 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Cannot use NEB unless atom map exists* - Use the atom\_modify command to create an atom map. + Use the atom_modify command to create an atom map. *Cannot use NEB with a single replica* Self-explanatory. -*Cannot use NEB with atom\_modify sort enabled* +*Cannot use NEB with atom_modify sort enabled* This is current restriction for NEB implemented in LAMMPS. *Cannot use PPPM with 2d simulation* The kspace style pppm cannot be used in 2d simulations. You can use - 2d PPPM in a 3d simulation; see the kspace\_modify command. + 2d PPPM in a 3d simulation; see the kspace_modify command. *Cannot use PPPMDisp with 2d simulation* The kspace style pppm/disp cannot be used in 2d simulations. You can - use 2d pppm/disp in a 3d simulation; see the kspace\_modify command. + use 2d pppm/disp in a 3d simulation; see the kspace_modify command. *Cannot use PRD with a changing box* The current box dimensions are not copied between replicas @@ -1201,20 +1201,20 @@ Doc page with :doc:`WARNING messages ` *Cannot use PRD with a time-dependent region defined* PRD alters the timestep in ways that will mess up these regions. -*Cannot use PRD with atom\_modify sort enabled* +*Cannot use PRD with atom_modify sort enabled* This is a current restriction of PRD. You must turn off sorting, - which is enabled by default, via the atom\_modify command. + which is enabled by default, via the atom_modify command. *Cannot use PRD with multi-processor replicas unless atom map exists* - Use the atom\_modify command to create an atom map. + Use the atom_modify command to create an atom map. *Cannot use TAD unless atom map exists for NEB* - See atom\_modify map command to set this. + See atom_modify map command to set this. *Cannot use TAD with a single replica for NEB* NEB requires multiple replicas. -*Cannot use TAD with atom\_modify sort enabled for NEB* +*Cannot use TAD with atom_modify sort enabled for NEB* This is a current restriction of NEB. *Cannot use a damped dynamics min style with fix box/relax* @@ -1230,7 +1230,7 @@ Doc page with :doc:`WARNING messages ` type p (periodic). *Cannot use atomfile-style variable unless atom map exists* - Self-explanatory. See the atom\_modify command to create a map. + Self-explanatory. See the atom_modify command to create a map. *Cannot use both com and bias with compute temp/chunk* Self-explanatory. @@ -1322,34 +1322,34 @@ Doc page with :doc:`WARNING messages ` *Cannot use compute cluster/atom unless atoms have IDs* Atom IDs are used to identify clusters. -*Cannot use create\_atoms rotate unless single style* +*Cannot use create_atoms rotate unless single style* Self-explanatory. -*Cannot use create\_bonds unless atoms have IDs* +*Cannot use create_bonds unless atoms have IDs* This command requires a mapping from global atom IDs to local atoms, but the atoms that have been defined have no IDs. -*Cannot use create\_bonds with non-molecular system* +*Cannot use create_bonds with non-molecular system* Self-explanatory. *Cannot use cwiggle in variable formula between runs* This is a function of elapsed time. -*Cannot use delete\_atoms bond yes with atom\_style template* +*Cannot use delete_atoms bond yes with atom_style template* This is because the bonds for that atom style are hardwired in the molecule template. -*Cannot use delete\_atoms unless atoms have IDs* - Your atoms do not have IDs, so the delete\_atoms command cannot be +*Cannot use delete_atoms unless atoms have IDs* + Your atoms do not have IDs, so the delete_atoms command cannot be used. -*Cannot use delete\_bonds with non-molecular system* +*Cannot use delete_bonds with non-molecular system* Your choice of atom style does not have bonds. -*Cannot use dump\_modify fileper without % in dump file name* +*Cannot use dump_modify fileper without % in dump file name* Self-explanatory. -*Cannot use dump\_modify nfile without % in dump file name* +*Cannot use dump_modify nfile without % in dump file name* Self-explanatory. *Cannot use dynamic group with fix adapt atom* @@ -1358,19 +1358,19 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix TMD unless atom map exists* Using this fix requires the ability to lookup an atom index, which is provided by an atom map. An atom map does not exist (by default) for - non-molecular problems. Using the atom\_modify map command will force + non-molecular problems. Using the atom_modify map command will force an atom map to be created. *Cannot use fix bond/break with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom\_style + Only systems with bonds that can be changed can be used. Atom_style template does not qualify. *Cannot use fix bond/create with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom\_style + Only systems with bonds that can be changed can be used. Atom_style template does not qualify. *Cannot use fix bond/swap with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom\_style + Only systems with bonds that can be changed can be used. Atom_style template does not qualify. *Cannot use fix box/relax on a 2nd non-periodic dimension* @@ -1477,7 +1477,7 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix press/berendsen with triclinic box* Self-explanatory. -*Cannot use fix reax/bonds without pair\_style reax* +*Cannot use fix reax/bonds without pair_style reax* Self-explanatory. *Cannot use fix rigid npt/nph and fix deform on same component of stress tensor* @@ -1531,10 +1531,10 @@ Doc page with :doc:`WARNING messages ` *Cannot use fix wall/srd zlo/zhi for a 2d simulation* Self-explanatory. -*Cannot use fix\_deposit unless atoms have IDs* +*Cannot use fix_deposit unless atoms have IDs* Self-explanatory. -*Cannot use fix\_pour unless atoms have IDs* +*Cannot use fix_pour unless atoms have IDs* Self-explanatory. *Cannot use include command within an if command* @@ -1555,7 +1555,7 @@ Doc page with :doc:`WARNING messages ` *Cannot use multiple fix wall commands with pair lubricateU* Self-explanatory. -*Cannot use neigh\_modify exclude with GPU neighbor builds* +*Cannot use neigh_modify exclude with GPU neighbor builds* This is a current limitation of the GPU implementation in LAMMPS. @@ -1705,22 +1705,22 @@ Doc page with :doc:`WARNING messages ` *Cannot use non-periodic boundaries with Ewald* For kspace style ewald, all 3 dimensions must have periodic boundaries - unless you use the kspace\_modify command to define a 2d slab with a + unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. *Cannot use non-periodic boundaries with EwaldDisp* For kspace style ewald/disp, all 3 dimensions must have periodic - boundaries unless you use the kspace\_modify command to define a 2d + boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. *Cannot use non-periodic boundaries with PPPM* For kspace style pppm, all 3 dimensions must have periodic boundaries - unless you use the kspace\_modify command to define a 2d slab with a + unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. *Cannot use non-periodic boundaries with PPPMDisp* For kspace style pppm/disp, all 3 dimensions must have periodic - boundaries unless you use the kspace\_modify command to define a 2d + boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. *Cannot use order greater than 8 with pppm/gpu.* @@ -1738,21 +1738,21 @@ Doc page with :doc:`WARNING messages ` *Cannot use ramp in variable formula between runs* This is because the ramp() function is time dependent. -*Cannot use read\_data add before simulation box is defined* +*Cannot use read_data add before simulation box is defined* Self-explanatory. -*Cannot use read\_data extra with add flag* +*Cannot use read_data extra with add flag* Self-explanatory. -*Cannot use read\_data offset without add flag* +*Cannot use read_data offset without add flag* Self-explanatory. -*Cannot use read\_data shift without add flag* +*Cannot use read_data shift without add flag* Self-explanatory. *Cannot use region INF or EDGE when box does not exist* Regions that extend to the box boundaries can only be used after the - create\_box command has been used. + create_box command has been used. *Cannot use set atom with no atom IDs defined* Atom IDs are not defined, so they cannot be used to identify an atom. @@ -1793,10 +1793,10 @@ Doc page with :doc:`WARNING messages ` *Cannot use wall in periodic dimension* Self-explanatory. -*Cannot use write\_restart fileper without % in restart file name* +*Cannot use write_restart fileper without % in restart file name* Self-explanatory. -*Cannot use write\_restart nfile without % in restart file name* +*Cannot use write_restart nfile without % in restart file name* Self-explanatory. *Cannot wiggle and shear fix wall/gran* @@ -1809,10 +1809,10 @@ Doc page with :doc:`WARNING messages ` *Cannot yet use KSpace solver with grid with comm style tiled* This is current restriction in LAMMPS. -*Cannot yet use comm\_style tiled with multi-mode comm* +*Cannot yet use comm_style tiled with multi-mode comm* Self-explanatory. -*Cannot yet use comm\_style tiled with triclinic box* +*Cannot yet use comm_style tiled with triclinic box* Self-explanatory. *Cannot yet use compute tally with Kokkos* @@ -1840,10 +1840,10 @@ Doc page with :doc:`WARNING messages ` *Cannot zero momentum of no atoms* Self-explanatory. -*Change\_box command before simulation box is defined* +*Change_box command before simulation box is defined* Self-explanatory. -*Change\_box volume used incorrectly* +*Change_box volume used incorrectly* The "dim volume" option must be used immediately following one or two settings for "dim1 ..." (and optionally "dim2 ...") and must be for a different dimension, i.e. dim != dim1 and dim != dim2. @@ -1882,23 +1882,23 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Comm tiled invalid index in box drop brick* - Internal error check in comm\_style tiled which should not occur. + Internal error check in comm_style tiled which should not occur. Contact the developers. *Comm tiled mis-match in box drop brick* - Internal error check in comm\_style tiled which should not occur. + Internal error check in comm_style tiled which should not occur. Contact the developers. -*Comm\_modify group != atom\_modify first group* +*Comm_modify group != atom_modify first group* Self-explanatory. -*Communication cutoff for comm\_style tiled cannot exceed periodic box length* +*Communication cutoff for comm_style tiled cannot exceed periodic box length* Self-explanatory. *Communication cutoff too small for SNAP micro load balancing* - This can happen if you change the neighbor skin after your pair\_style + This can happen if you change the neighbor skin after your pair_style command or if your box dimensions grow during a run. You can set the - cutoff explicitly via the comm\_modify cutoff command. + cutoff explicitly via the comm_modify cutoff command. *Compute %s does not allow use of dynamic group* Dynamic groups have not yet been enabled for this compute. @@ -2188,7 +2188,7 @@ Doc page with :doc:`WARNING messages ` Only inputs that generate the same number of datums can be used together. E.g. bond and angle quantities cannot be mixed. -*Compute property/local does not (yet) work with atom\_style template* +*Compute property/local does not (yet) work with atom_style template* Self-explanatory. *Compute property/local for property that isn't allocated* @@ -2306,7 +2306,7 @@ Doc page with :doc:`WARNING messages ` The style of the specified compute is not chunk/atom. *Compute temp/cs requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Compute temp/cs used when bonds are not allowed* This compute only works on pairs of bonded particles. @@ -2368,14 +2368,14 @@ Doc page with :doc:`WARNING messages ` *Core/shell partners were not all found* Could not find or more atoms in the bond pairs. -*Could not adjust g\_ewald\_6* +*Could not adjust g_ewald_6* The Newton-Raphson solver failed to converge to a good value for - g\_ewald. This error should not occur for typical problems. Please + g_ewald. This error should not occur for typical problems. Please send an email to the developers. -*Could not compute g\_ewald* +*Could not compute g_ewald* The Newton-Raphson solver failed to converge to a good value for - g\_ewald. This error should not occur for typical problems. Please + g_ewald. This error should not occur for typical problems. Please send an email to the developers. *Could not compute grid size* @@ -2426,11 +2426,11 @@ Doc page with :doc:`WARNING messages ` The provided Python code was run successfully, but it not define a callable function with the required name. -*Could not find atom\_modify first group ID* +*Could not find atom_modify first group ID* Self-explanatory. -*Could not find change\_box group ID* - Group ID used in the change\_box command does not exist. +*Could not find change_box group ID* + Group ID used in the change_box command does not exist. *Could not find compute ID for PRD* Self-explanatory. @@ -2474,20 +2474,20 @@ Doc page with :doc:`WARNING messages ` *Could not find compute/voronoi surface group ID* Self-explanatory. -*Could not find compute\_modify ID* +*Could not find compute_modify ID* Self-explanatory. *Could not find custom per-atom property ID* Self-explanatory. -*Could not find delete\_atoms group ID* - Group ID used in the delete\_atoms command does not exist. +*Could not find delete_atoms group ID* + Group ID used in the delete_atoms command does not exist. -*Could not find delete\_atoms region ID* - Region ID used in the delete\_atoms command does not exist. +*Could not find delete_atoms region ID* + Region ID used in the delete_atoms command does not exist. -*Could not find displace\_atoms group ID* - Group ID used in the displace\_atoms command does not exist. +*Could not find displace_atoms group ID* + Group ID used in the displace_atoms command does not exist. *Could not find dump custom compute ID* Self-explanatory. @@ -2553,13 +2553,13 @@ Doc page with :doc:`WARNING messages ` *Could not find fix srd group ID* Self-explanatory. -*Could not find fix\_modify ID* - A fix ID used in the fix\_modify command does not exist. +*Could not find fix_modify ID* + A fix ID used in the fix_modify command does not exist. -*Could not find fix\_modify pressure ID* +*Could not find fix_modify pressure ID* The compute ID for computing pressure does not exist. -*Could not find fix\_modify temperature ID* +*Could not find fix_modify temperature ID* The compute ID for computing temperature does not exist. *Could not find group clear group ID* @@ -2579,7 +2579,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Could not find thermo compute ID* - Compute ID specified in thermo\_style command does not exist. + Compute ID specified in thermo_style command does not exist. *Could not find thermo custom compute ID* The compute ID needed by thermo style custom to compute a requested @@ -2593,16 +2593,16 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Could not find thermo fix ID* - Fix ID specified in thermo\_style command does not exist. + Fix ID specified in thermo_style command does not exist. *Could not find thermo variable name* Self-explanatory. -*Could not find thermo\_modify pressure ID* +*Could not find thermo_modify pressure ID* The compute ID needed by thermo style custom to compute pressure does not exist. -*Could not find thermo\_modify temperature ID* +*Could not find thermo_modify temperature ID* The compute ID needed by thermo style custom to compute temperature does not exist. @@ -2646,66 +2646,66 @@ Doc page with :doc:`WARNING messages ` *Coulomb PPPMDisp order has been reduced below minorder* The default minimum order is 2. This can be reset by the - kspace\_modify minorder command. + kspace_modify minorder command. -*Coulombic cutoff not supported in pair\_style buck/long/coul/coul* +*Coulombic cutoff not supported in pair_style buck/long/coul/coul* Must use long-range Coulombic interactions. -*Coulombic cutoff not supported in pair\_style lj/long/coul/long* +*Coulombic cutoff not supported in pair_style lj/long/coul/long* Must use long-range Coulombic interactions. -*Coulombic cutoff not supported in pair\_style lj/long/tip4p/long* +*Coulombic cutoff not supported in pair_style lj/long/tip4p/long* Must use long-range Coulombic interactions. *Coulombic cutoffs of pair hybrid sub-styles do not match* If using a Kspace solver, all Coulombic cutoffs of long pair styles must be the same. -*Coulombic cut not supported in pair\_style lj/long/dipole/long* +*Coulombic cut not supported in pair_style lj/long/dipole/long* Must use long-range Coulombic interactions. -*Cound not find dump\_modify ID* +*Cound not find dump_modify ID* Self-explanatory. -*Create\_atoms command before simulation box is defined* - The create\_atoms command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Create_atoms command before simulation box is defined* + The create_atoms command cannot be used before a read_data, + read_restart, or create_box command. -*Create\_atoms molecule has atom IDs, but system does not* - The atom\_style id command can be used to force atom IDs to be stored. +*Create_atoms molecule has atom IDs, but system does not* + The atom_style id command can be used to force atom IDs to be stored. -*Create\_atoms molecule must have atom types* +*Create_atoms molecule must have atom types* The defined molecule does not specify atom types. -*Create\_atoms molecule must have coordinates* +*Create_atoms molecule must have coordinates* The defined molecule does not specify coordinates. -*Create\_atoms region ID does not exist* - A region ID used in the create\_atoms command does not exist. +*Create_atoms region ID does not exist* + A region ID used in the create_atoms command does not exist. -*Create\_bonds command before simulation box is defined* +*Create_bonds command before simulation box is defined* Self-explanatory. -*Create\_bonds command requires no kspace\_style be defined* +*Create_bonds command requires no kspace_style be defined* This is so that atom pairs that are already bonded to not appear in the neighbor list. -*Create\_bonds command requires special\_bonds 1-2 weights be 0.0* +*Create_bonds command requires special_bonds 1-2 weights be 0.0* This is so that atom pairs that are already bonded to not appear in the neighbor list. -*Create\_bonds max distance > neighbor cutoff* +*Create_bonds max distance > neighbor cutoff* Can only create bonds for atom pairs that will be in neighbor list. -*Create\_bonds requires a pair style be defined* +*Create_bonds requires a pair style be defined* Self-explanatory. -*Create\_box region ID does not exist* +*Create_box region ID does not exist* Self-explanatory. -*Create\_box region does not support a bounding box* +*Create_box region does not support a bounding box* Not all regions represent bounded volumes. You cannot use - such a region with the create\_box command. + such a region with the create_box command. *Custom floating point vector for fix store/state does not exist* The command is accessing a vector added by the fix property/atom @@ -2721,13 +2721,13 @@ Doc page with :doc:`WARNING messages ` *Custom per-atom property ID is not integer* Self-explanatory. -*Cut-offs missing in pair\_style lj/long/dipole/long* +*Cut-offs missing in pair_style lj/long/dipole/long* Self-explanatory. -*Cutoffs missing in pair\_style buck/long/coul/long* +*Cutoffs missing in pair_style buck/long/coul/long* Self-explanatory. -*Cutoffs missing in pair\_style lj/long/coul/long* +*Cutoffs missing in pair_style lj/long/coul/long* Self-explanatory. *Cyclic loop in joint connections* @@ -2740,26 +2740,26 @@ Doc page with :doc:`WARNING messages ` *Delete region ID does not exist* Self-explanatory. -*Delete\_atoms command before simulation box is defined* - The delete\_atoms command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Delete_atoms command before simulation box is defined* + The delete_atoms command cannot be used before a read_data, + read_restart, or create_box command. -*Delete\_atoms cutoff > max neighbor cutoff* +*Delete_atoms cutoff > max neighbor cutoff* Can only delete atoms in atom pairs that will be in neighbor list. -*Delete\_atoms mol yes requires atom attribute molecule* +*Delete_atoms mol yes requires atom attribute molecule* Cannot use this option with a non-molecular system. -*Delete\_atoms requires a pair style be defined* +*Delete_atoms requires a pair style be defined* This is because atom deletion within a cutoff uses a pairwise neighbor list. -*Delete\_bonds command before simulation box is defined* - The delete\_bonds command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Delete_bonds command before simulation box is defined* + The delete_bonds command cannot be used before a read_data, + read_restart, or create_box command. -*Delete\_bonds command with no atoms existing* - No atoms are yet defined so the delete\_bonds command cannot be used. +*Delete_bonds command with no atoms existing* + No atoms are yet defined so the delete_bonds command cannot be used. *Deposition region extends outside simulation box* Self-explanatory. @@ -2773,7 +2773,7 @@ Doc page with :doc:`WARNING messages ` Atoms read in from the restart file were not assigned correctly to processors. This is likely due to some atom coordinates being outside a non-periodic simulation box. Normally this should not happen. You - may wish to use the "remap" option on the read\_restart command to see + may wish to use the "remap" option on the read_restart command to see if this helps. *Did not find all elements in MEAM library file* @@ -2781,12 +2781,12 @@ Doc page with :doc:`WARNING messages ` *Did not find fix shake partner info* Could not find bond partners implied by fix shake command. This error - can be triggered if the delete\_bonds command was used before fix + can be triggered if the delete_bonds command was used before fix shake, and it removed bonds without resetting the 1-2, 1-3, 1-4 weighting list via the special keyword. *Did not find keyword in table file* - Keyword used in pair\_coeff command was not found in table file. + Keyword used in pair_coeff command was not found in table file. *Did not set pressure for fix rigid/nph* The press keyword must be specified. @@ -2803,8 +2803,8 @@ Doc page with :doc:`WARNING messages ` *Did not set temperature or pressure for fix rigid/npt* The temp and press keywords must be specified. -*Dihedral atom missing in delete\_bonds* - The delete\_bonds command cannot find one or more atoms in a particular +*Dihedral atom missing in delete_bonds* + The delete_bonds command cannot find one or more atoms in a particular dihedral on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid dihedral. @@ -2831,12 +2831,12 @@ Doc page with :doc:`WARNING messages ` *Dihedral coeff for hybrid has invalid style* Dihedral style hybrid uses another dihedral style as one of its - coefficients. The dihedral style used in the dihedral\_coeff command + coefficients. The dihedral style used in the dihedral_coeff command or read from a restart file is not recognized. *Dihedral coeffs are not set* No dihedral coefficients have been assigned in the data file or via - the dihedral\_coeff command. + the dihedral_coeff command. *Dihedral style hybrid cannot have hybrid as an argument* Self-explanatory. @@ -2848,22 +2848,22 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Dihedral/improper extent > half of periodic box length* - This error was detected by the neigh\_modify check yes setting. It is + This error was detected by the neigh_modify check yes setting. It is an error because the dihedral atoms are so far apart it is ambiguous how it should be defined. -*Dihedral\_coeff command before dihedral\_style is defined* - Coefficients cannot be set in the data file or via the dihedral\_coeff - command until an dihedral\_style has been assigned. +*Dihedral_coeff command before dihedral_style is defined* + Coefficients cannot be set in the data file or via the dihedral_coeff + command until an dihedral_style has been assigned. -*Dihedral\_coeff command before simulation box is defined* - The dihedral\_coeff command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Dihedral_coeff command before simulation box is defined* + The dihedral_coeff command cannot be used before a read_data, + read_restart, or create_box command. -*Dihedral\_coeff command when no dihedrals allowed* +*Dihedral_coeff command when no dihedrals allowed* The chosen atom style does not allow for dihedrals to be defined. -*Dihedral\_style command when no dihedrals allowed* +*Dihedral_style command when no dihedrals allowed* The chosen atom style does not allow for dihedrals to be defined. *Dihedrals assigned incorrectly* @@ -2875,16 +2875,16 @@ Doc page with :doc:`WARNING messages ` The data file header lists dihedrals but no dihedral types. *Dimension command after simulation box is defined* - The dimension command cannot be used after a read\_data, - read\_restart, or create\_box command. + The dimension command cannot be used after a read_data, + read_restart, or create_box command. *Dispersion PPPMDisp order has been reduced below minorder* The default minimum order is 2. This can be reset by the - kspace\_modify minorder command. + kspace_modify minorder command. -*Displace\_atoms command before simulation box is defined* - The displace\_atoms command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Displace_atoms command before simulation box is defined* + The displace_atoms command cannot be used before a read_data, + read_restart, or create_box command. *Distance must be > 0 for compute event/displace* Self-explanatory. @@ -2963,7 +2963,7 @@ Doc page with :doc:`WARNING messages ` Every snapshot written by dump dcd must contain the same # of atoms. *Dump dcd requires sorting by atom ID* - Use the dump\_modify sort command to enable this. + Use the dump_modify sort command to enable this. *Dump every variable returned a bad timestep* The variable must return a timestep greater than the current timestep. @@ -3076,19 +3076,19 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Dump xtc requires sorting by atom ID* - Use the dump\_modify sort command to enable this. + Use the dump_modify sort command to enable this. *Dump xyz/gz only writes compressed files* The dump xyz/gz output file name must have a .gz suffix. -*Dump\_modify buffer yes not allowed for this style* +*Dump_modify buffer yes not allowed for this style* Self-explanatory. -*Dump\_modify format string is too short* +*Dump_modify format string is too short* There are more fields to be dumped in a line of output than your format string specifies. -*Dump\_modify region ID does not exist* +*Dump_modify region ID does not exist* Self-explanatory. *Dumping an atom property that isn't allocated* @@ -3098,7 +3098,7 @@ Doc page with :doc:`WARNING messages ` *Duplicate atom IDs exist* Self-explanatory. -*Duplicate fields in read\_dump command* +*Duplicate fields in read_dump command* Self-explanatory. *Duplicate particle in PeriDynamic bond - simulation box is too small* @@ -3205,7 +3205,7 @@ Doc page with :doc:`WARNING messages ` *Fix ID for fix vector does not exist* Self-explanatory. -*Fix ID for read\_data does not exist* +*Fix ID for read_data does not exist* Self-explanatory. *Fix ID for velocity does not exist* @@ -3227,7 +3227,7 @@ Doc page with :doc:`WARNING messages ` conservative settings. *Fix SRD: too many big particles in bin* - Reset the ATOMPERBIN parameter at the top of fix\_srd.cpp + Reset the ATOMPERBIN parameter at the top of fix_srd.cpp to a larger value, and re-compile the code. *Fix SRD: too many walls in bin* @@ -3473,15 +3473,15 @@ Doc page with :doc:`WARNING messages ` *Fix ave/time variable is not equal-style variable* Self-explanatory. -*Fix balance rcb cannot be used with comm\_style brick* - Comm\_style tiled must be used instead. +*Fix balance rcb cannot be used with comm_style brick* + Comm_style tiled must be used instead. *Fix balance shift string is invalid* The string can only contain the characters "x", "y", or "z". *Fix bond/break needs ghost atoms from further away* This is because the fix needs to walk bonds to a certain distance to - acquire needed info, The comm\_modify cutoff command can be used to + acquire needed info, The comm_modify cutoff command can be used to extend the communication range. *Fix bond/create angle type is invalid* @@ -3498,13 +3498,13 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Fix bond/create induced too many angles/dihedrals/impropers per atom* - See the read\_data command for info on using the "extra/angle/per/atom", + See the read_data command for info on using the "extra/angle/per/atom", (or dihedral, improper) keywords to allow for additional angles, dihedrals, and impropers to be formed. *Fix bond/create needs ghost atoms from further away* This is because the fix needs to walk bonds to a certain distance to - acquire needed info, The comm\_modify cutoff command can be used to + acquire needed info, The comm_modify cutoff command can be used to extend the communication range. *Fix bond/swap cannot use dihedral or improper styles* @@ -3513,7 +3513,7 @@ Doc page with :doc:`WARNING messages ` *Fix bond/swap requires pair and bond styles* Self-explanatory. -*Fix bond/swap requires special\_bonds = 0,1,1* +*Fix bond/swap requires special_bonds = 0,1,1* Self-explanatory. *Fix box/relax generated negative box length* @@ -3521,8 +3521,8 @@ Doc page with :doc:`WARNING messages ` it incrementally, to build to the high pressure. *Fix command before simulation box is defined* - The fix command cannot be used before a read\_data, read\_restart, or - create\_box command. + The fix command cannot be used before a read_data, read_restart, or + create_box command. *Fix deform cannot use yz variable with xy* The yz setting cannot be a variable if xy deformation is also @@ -3553,8 +3553,8 @@ Doc page with :doc:`WARNING messages ` *Fix deposit molecule must have coordinates* The defined molecule does not specify coordinates. -*Fix deposit molecule template ID must be same as atom\_style template ID* - When using atom\_style template, you cannot deposit molecules that are +*Fix deposit molecule template ID must be same as atom_style template ID* + When using atom_style template, you cannot deposit molecules that are not in that template. *Fix deposit region cannot be dynamic* @@ -3625,7 +3625,7 @@ Doc page with :doc:`WARNING messages ` molecule. The user has specified atomic (non-molecular) gas exchanges, but an atom belonging to a molecule could be deleted. -*Fix gcmc does not (yet) work with atom\_style template* +*Fix gcmc does not (yet) work with atom_style template* Self-explanatory. *Fix gcmc molecule command requires that atoms have molecule attributes* @@ -3642,8 +3642,8 @@ Doc page with :doc:`WARNING messages ` *Fix gcmc molecule must have coordinates* The defined molecule does not specify coordinates. -*Fix gcmc molecule template ID must be same as atom\_style template ID* - When using atom\_style template, you cannot insert molecules that are +*Fix gcmc molecule template ID must be same as atom_style template ID* + When using atom_style template, you cannot insert molecules that are not in that template. *Fix gcmc put atom outside box* @@ -3866,7 +3866,7 @@ Doc page with :doc:`WARNING messages ` The defined molecule does not specify coordinates. *Fix pour molecule template ID must be same as atom style template ID* - When using atom\_style template, you cannot pour molecules that are + When using atom_style template, you cannot pour molecules that are not in that template. *Fix pour polydisperse fractions do not sum to 1.0* @@ -3900,10 +3900,10 @@ Doc page with :doc:`WARNING messages ` *Fix property/atom cannot specify q twice* Self-explanatory. -*Fix property/atom mol when atom\_style already has molecule attribute* +*Fix property/atom mol when atom_style already has molecule attribute* Self-explanatory. -*Fix property/atom q when atom\_style already has charge attribute* +*Fix property/atom q when atom_style already has charge attribute* Self-explanatory. *Fix property/atom vector name already exists* @@ -3935,7 +3935,7 @@ Doc page with :doc:`WARNING messages ` *Fix qeq/point has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much - during a run. Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and + during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. *Fix qeq/point requires atom attribute q* @@ -3946,7 +3946,7 @@ Doc page with :doc:`WARNING messages ` *Fix qeq/shielded has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much - during a run. Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and + during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. *Fix qeq/shielded requires atom attribute q* @@ -3960,20 +3960,20 @@ Doc page with :doc:`WARNING messages ` *Fix qeq/slater has insufficient QEq matrix size* Occurs when number of neighbor atoms for an atom increased too much - during a run. Increase SAFE\_ZONE and MIN\_CAP in fix\_qeq.h and + during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and re-compile. *Fix qeq/slater requires atom attribute q* Self-explanatory. -*Fix reax/bonds numbonds > nsbmax\_most* +*Fix reax/bonds numbonds > nsbmax_most* The limit of the number of bonds expected by the ReaxFF force field was exceeded. *Fix recenter group has no atoms* Self-explanatory. -*Fix restrain requires an atom map, see atom\_modify* +*Fix restrain requires an atom map, see atom_modify* Self-explanatory. *Fix rigid atom has non-zero image flag in a non-periodic dimension* @@ -3997,22 +3997,22 @@ Doc page with :doc:`WARNING messages ` *Fix rigid npt/nph period must be > 0.0* Self-explanatory. -*Fix rigid npt/small t\_chain should not be less than 1* +*Fix rigid npt/small t_chain should not be less than 1* Self-explanatory. -*Fix rigid npt/small t\_order must be 3 or 5* +*Fix rigid npt/small t_order must be 3 or 5* Self-explanatory. *Fix rigid nvt/npt/nph damping parameters must be > 0.0* Self-explanatory. -*Fix rigid nvt/small t\_chain should not be less than 1* +*Fix rigid nvt/small t_chain should not be less than 1* Self-explanatory. -*Fix rigid nvt/small t\_iter should not be less than 1* +*Fix rigid nvt/small t_iter should not be less than 1* Self-explanatory. -*Fix rigid nvt/small t\_order must be 3 or 5* +*Fix rigid nvt/small t_order must be 3 or 5* Self-explanatory. *Fix rigid xy torque cannot be on for 2d simulation* @@ -4060,7 +4060,7 @@ Doc page with :doc:`WARNING messages ` *Fix rigid/small nvt/npt/nph dilate group ID does not exist* Self-explanatory. -*Fix rigid/small requires an atom map, see atom\_modify* +*Fix rigid/small requires an atom map, see atom_modify* Self-explanatory. *Fix rigid/small requires atom attribute molecule* @@ -4080,7 +4080,7 @@ Doc page with :doc:`WARNING messages ` *Fix spring couple group ID does not exist* Self-explanatory. -*Fix srd can only currently be used with comm\_style brick* +*Fix srd can only currently be used with comm_style brick* This is a current restriction in LAMMPS. *Fix srd lamda must be >= 0.6 of SRD grid size* @@ -4094,7 +4094,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Fix srd requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Fix srd requires newton pair on* Self-explanatory. @@ -4169,25 +4169,25 @@ Doc page with :doc:`WARNING messages ` *Fix ttm electron temperatures must be > 0.0* Self-explanatory. -*Fix ttm electronic\_density must be > 0.0* +*Fix ttm electronic_density must be > 0.0* Self-explanatory. -*Fix ttm electronic\_specific\_heat must be > 0.0* +*Fix ttm electronic_specific_heat must be > 0.0* Self-explanatory. -*Fix ttm electronic\_thermal\_conductivity must be >= 0.0* +*Fix ttm electronic_thermal_conductivity must be >= 0.0* Self-explanatory. -*Fix ttm gamma\_p must be > 0.0* +*Fix ttm gamma_p must be > 0.0* Self-explanatory. -*Fix ttm gamma\_s must be >= 0.0* +*Fix ttm gamma_s must be >= 0.0* Self-explanatory. *Fix ttm number of nodes must be > 0* Self-explanatory. -*Fix ttm v\_0 must be >= 0.0* +*Fix ttm v_0 must be >= 0.0* Self-explanatory. *Fix used in compute chunk/atom not computed at compatible time* @@ -4261,10 +4261,10 @@ Doc page with :doc:`WARNING messages ` *Fix wall/region cutoff <= 0.0* Self-explanatory. -*Fix\_modify pressure ID does not compute pressure* +*Fix_modify pressure ID does not compute pressure* The compute ID assigned to the fix must compute pressure. -*Fix\_modify temperature ID does not compute temperature* +*Fix_modify temperature ID does not compute temperature* The compute ID assigned to the fix must compute temperature. *For triclinic deformation, specified target stress must be hydrostatic* @@ -4277,7 +4277,7 @@ Doc page with :doc:`WARNING messages ` *GPU library not compiled for this accelerator* Self-explanatory. -*GPU package does not (yet) work with atom\_style template* +*GPU package does not (yet) work with atom_style template* Self-explanatory. *GPU particle split must be set to 1 for this pair style.* @@ -4315,8 +4315,8 @@ Doc page with :doc:`WARNING messages ` This operation is not allowed. *Group command before simulation box is defined* - The group command cannot be used before a read\_data, read\_restart, or - create\_box command. + The group command cannot be used before a read_data, read_restart, or + create_box command. *Group dynamic cannot reference itself* Self-explanatory. @@ -4330,8 +4330,8 @@ Doc page with :doc:`WARNING messages ` *Group region ID does not exist* A region ID used in the group command does not exist. -*If read\_dump purges it cannot replace or trim* - These operations are not compatible. See the read\_dump doc +*If read_dump purges it cannot replace or trim* + These operations are not compatible. See the read_dump doc page for details. *Illegal ... command* @@ -4366,10 +4366,10 @@ Doc page with :doc:`WARNING messages ` One or more of the coefficients defined in the potential file is invalid. -*Illegal dump\_modify sfactor value (must be > 0.0)* +*Illegal dump_modify sfactor value (must be > 0.0)* Self-explanatory. -*Illegal dump\_modify tfactor value (must be > 0.0)* +*Illegal dump_modify tfactor value (must be > 0.0)* Self-explanatory. *Illegal fix gcmc gas mass <= 0* @@ -4423,8 +4423,8 @@ Doc page with :doc:`WARNING messages ` Format of imageint stored in restart file is not consistent with LAMMPS version you are running. See the settings in src/lmptype.h -*Improper atom missing in delete\_bonds* - The delete\_bonds command cannot find one or more atoms in a particular +*Improper atom missing in delete_bonds* + The delete_bonds command cannot find one or more atoms in a particular improper on a particular processor. The pairwise cutoff is too short or the atoms are too far apart to make a valid improper. @@ -4447,12 +4447,12 @@ Doc page with :doc:`WARNING messages ` *Improper coeff for hybrid has invalid style* Improper style hybrid uses another improper style as one of its - coefficients. The improper style used in the improper\_coeff command + coefficients. The improper style used in the improper_coeff command or read from a restart file is not recognized. *Improper coeffs are not set* No improper coefficients have been assigned in the data file or via - the improper\_coeff command. + the improper_coeff command. *Improper style hybrid cannot have hybrid as an argument* Self-explanatory. @@ -4463,18 +4463,18 @@ Doc page with :doc:`WARNING messages ` *Improper style hybrid cannot use same improper style twice* Self-explanatory. -*Improper\_coeff command before improper\_style is defined* - Coefficients cannot be set in the data file or via the improper\_coeff - command until an improper\_style has been assigned. +*Improper_coeff command before improper_style is defined* + Coefficients cannot be set in the data file or via the improper_coeff + command until an improper_style has been assigned. -*Improper\_coeff command before simulation box is defined* - The improper\_coeff command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Improper_coeff command before simulation box is defined* + The improper_coeff command cannot be used before a read_data, + read_restart, or create_box command. -*Improper\_coeff command when no impropers allowed* +*Improper_coeff command when no impropers allowed* The chosen atom style does not allow for impropers to be defined. -*Improper\_style command when no impropers allowed* +*Improper_style command when no impropers allowed* The chosen atom style does not allow for impropers to be defined. *Impropers assigned incorrectly* @@ -4493,7 +4493,7 @@ Doc page with :doc:`WARNING messages ` The selected unit style is not compatible with the requested KIM Simulator Model. -*Incomplete use of variables in create\_atoms command* +*Incomplete use of variables in create_atoms command* The var and set options must be used together. *Inconsistent iparam/jparam values in fix bond/create command* @@ -4540,7 +4540,7 @@ Doc page with :doc:`WARNING messages ` *Incorrect args for pair coefficients* Self-explanatory. Check the input script or data file. -*Incorrect args in pair\_style command* +*Incorrect args in pair_style command* Self-explanatory. *Incorrect atom format in data file* @@ -4551,7 +4551,7 @@ Doc page with :doc:`WARNING messages ` The number of fields per line is not what expected. *Incorrect bonus data format in data file* - See the read\_data doc page for a description of how various kinds of + See the read_data doc page for a description of how various kinds of bonus data must be formatted for certain atom styles. *Incorrect boundaries with slab Ewald* @@ -4652,7 +4652,7 @@ Doc page with :doc:`WARNING messages ` *Indexed per-atom vector in variable formula without atom map* Accessing a value from an atom vector requires the ability to lookup an atom index, which is provided by an atom map. An atom map does not - exist (by default) for non-molecular problems. Using the atom\_modify + exist (by default) for non-molecular problems. Using the atom_modify map command will force an atom map to be created. *Initial temperatures not all set in fix ttm* @@ -4684,7 +4684,7 @@ Doc page with :doc:`WARNING messages ` There is insufficient memory on one of the devices specified for the gpu package -*Internal error in atom\_style body* +*Internal error in atom_style body* This error should not occur. Contact the developers. *Invalid -reorder N value* @@ -4751,7 +4751,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Invalid args for non-hybrid pair coefficients* - "NULL" is only supported in pair\_coeff calls when using pair hybrid + "NULL" is only supported in pair_coeff calls when using pair hybrid *Invalid argument to factorial %d* N must be >= 0 and <= 167, otherwise the factorial result is too @@ -4822,13 +4822,13 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type in Atoms section of data file* Atom types must range from 1 to specified # of types. -*Invalid atom type in create\_atoms command* - The create\_box command specified the range of valid atom types. +*Invalid atom type in create_atoms command* + The create_box command specified the range of valid atom types. An invalid type is being requested. -*Invalid atom type in create\_atoms mol command* +*Invalid atom type in create_atoms mol command* The atom types in the defined molecule are added to the value - specified in the create\_atoms command, as an offset. The final value + specified in the create_atoms command, as an offset. The final value for each atom must be between 1 to N, where N is the number of atom types. @@ -4843,7 +4843,7 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type in fix deposit mol command* The atom types in the defined molecule are added to the value - specified in the create\_atoms command, as an offset. The final value + specified in the create_atoms command, as an offset. The final value for each atom must be between 1 to N, where N is the number of atom types. @@ -4855,7 +4855,7 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type in fix pour mol command* The atom types in the defined molecule are added to the value - specified in the create\_atoms command, as an offset. The final value + specified in the create_atoms command, as an offset. The final value for each atom must be between 1 to N, where N is the number of atom types. @@ -4868,16 +4868,16 @@ Doc page with :doc:`WARNING messages ` *Invalid atom type index for fix shake* Atom types must range from 1 to Ntypes inclusive. -*Invalid atom types in pair\_write command* +*Invalid atom types in pair_write command* Atom types must range from 1 to Ntypes inclusive. *Invalid atom vector in variable formula* The atom vector is not recognized. -*Invalid atom\_style body command* +*Invalid atom_style body command* No body style argument was provided. -*Invalid atom\_style command* +*Invalid atom_style command* Self-explanatory. *Invalid attribute in dump custom command* @@ -4889,7 +4889,7 @@ Doc page with :doc:`WARNING messages ` *Invalid attribute in dump modify command* Self-explanatory. -*Invalid basis setting in create\_atoms command* +*Invalid basis setting in create_atoms command* The basis index must be between 1 to N where N is the number of basis atoms in the lattice. The type index must be between 1 to N where N is the number of atom types. @@ -4921,7 +4921,7 @@ Doc page with :doc:`WARNING messages ` *Invalid bond type in Bonds section of molecule file* Self-explanatory. -*Invalid bond type in create\_bonds command* +*Invalid bond type in create_bonds command* Self-explanatory. *Invalid bond type in fix bond/break command* @@ -4936,9 +4936,9 @@ Doc page with :doc:`WARNING messages ` *Invalid coeffs for this dihedral style* Cannot set class 2 coeffs in data file for this dihedral style. -*Invalid color in dump\_modify command* +*Invalid color in dump_modify command* The specified color name was not in the list of recognized colors. - See the dump\_modify doc page. + See the dump_modify doc page. *Invalid color map min/max values* The min/max values are not consistent with either each other or @@ -4951,17 +4951,17 @@ Doc page with :doc:`WARNING messages ` *Invalid compute ID in variable formula* The compute is not recognized. -*Invalid create\_atoms rotation vector for 2d model* +*Invalid create_atoms rotation vector for 2d model* The rotation vector can only have a z component. *Invalid custom OpenCL parameter string.* There are not enough or too many parameters in the custom string for package GPU. -*Invalid cutoff in comm\_modify command* +*Invalid cutoff in comm_modify command* Specified cutoff must be >= 0.0. -*Invalid cutoffs in pair\_write command* +*Invalid cutoffs in pair_write command* Inner cutoff must be larger than 0.0 and less than outer cutoff. *Invalid d1 or d2 value for pair colloid coeff* @@ -5027,7 +5027,7 @@ Doc page with :doc:`WARNING messages ` *Invalid data file section: Triangles* Atom style does not allow triangles. -*Invalid delta\_conf in tad command* +*Invalid delta_conf in tad command* The value must be between 0 and 1 inclusive. *Invalid density in Atoms section of data file* @@ -5052,7 +5052,7 @@ Doc page with :doc:`WARNING messages ` *Invalid dipole length in set command* Self-explanatory. -*Invalid displace\_atoms rotate axis for 2d* +*Invalid displace_atoms rotate axis for 2d* Axis must be in z direction. *Invalid dump dcd filename* @@ -5064,7 +5064,7 @@ Doc page with :doc:`WARNING messages ` *Invalid dump image element name* The specified element name was not in the standard list of elements. - See the dump\_modify doc page. + See the dump_modify doc page. *Invalid dump image filename* The file produced by dump image cannot be binary and must @@ -5091,7 +5091,7 @@ Doc page with :doc:`WARNING messages ` Filenames used with the dump xyz style cannot be binary or cause files to be written by each processor. -*Invalid dump\_modify threshold operator* +*Invalid dump_modify threshold operator* Operator keyword used for threshold specification in not recognized. *Invalid entry in -reorder file* @@ -5161,13 +5161,13 @@ Doc page with :doc:`WARNING messages ` *Invalid frequency in temper command* Nevery must be > 0. -*Invalid group ID in neigh\_modify command* - A group ID used in the neigh\_modify command does not exist. +*Invalid group ID in neigh_modify command* + A group ID used in the neigh_modify command does not exist. *Invalid group function in variable formula* Group function is not recognized. -*Invalid group in comm\_modify command* +*Invalid group in comm_modify command* Self-explanatory. *Invalid image up vector* @@ -5192,13 +5192,13 @@ Doc page with :doc:`WARNING messages ` *Invalid index in compute body/local command* Self-explanatory. -*Invalid is\_active() function in variable formula* +*Invalid is_active() function in variable formula* Self-explanatory. -*Invalid is\_available() function in variable formula* +*Invalid is_available() function in variable formula* Self-explanatory. -*Invalid is\_defined() function in variable formula* +*Invalid is_defined() function in variable formula* Self-explanatory. *Invalid keyword in angle table parameters* @@ -5266,7 +5266,7 @@ Doc page with :doc:`WARNING messages ` kspace, etc. *Invalid pair table cutoff* - Cutoffs in pair\_coeff command are not valid with read-in pair table. + Cutoffs in pair_coeff command are not valid with read-in pair table. *Invalid pair table length* Length of read-in pair table is invalid @@ -5354,16 +5354,16 @@ Doc page with :doc:`WARNING messages ` *Invalid special function in variable formula* Self-explanatory. -*Invalid style in pair\_write command* +*Invalid style in pair_write command* Self-explanatory. Check the input script. *Invalid syntax in variable formula* Self-explanatory. -*Invalid t\_event in prd command* +*Invalid t_event in prd command* Self-explanatory. -*Invalid t\_event in tad command* +*Invalid t_event in tad command* The value must be greater than 0. *Invalid template atom in Atoms section of data file* @@ -5377,8 +5377,8 @@ Doc page with :doc:`WARNING messages ` *Invalid thermo keyword in variable formula* The keyword is not recognized. -*Invalid threads\_per\_atom specified.* - For 3-body potentials on the GPU, the threads\_per\_atom setting cannot be +*Invalid threads_per_atom specified.* + For 3-body potentials on the GPU, the threads_per_atom setting cannot be greater than 4 for NVIDIA GPUs. *Invalid timestep reset for fix ave/atom* @@ -5473,10 +5473,10 @@ Doc page with :doc:`WARNING messages ` Model. Please contact the OpenKIM database maintainers to verify and potentially correct this. -*KOKKOS package does not yet support comm\_style tiled* +*KOKKOS package does not yet support comm_style tiled* Self-explanatory. -*KOKKOS package requires a kokkos enabled atom\_style* +*KOKKOS package requires a kokkos enabled atom_style* Self-explanatory. *KSpace accuracy must be > 0* @@ -5484,7 +5484,7 @@ Doc page with :doc:`WARNING messages ` *KSpace accuracy too large to estimate G vector* Reduce the accuracy request or specify gewald explicitly - via the kspace\_modify command. + via the kspace_modify command. *KSpace accuracy too low* Requested accuracy must be less than 1.0. @@ -5497,7 +5497,7 @@ Doc page with :doc:`WARNING messages ` simulation boxes. *KSpace style has not yet been set* - Cannot use kspace\_modify command until a kspace style is set. + Cannot use kspace_modify command until a kspace style is set. *KSpace style is incompatible with Pair style* Setting a kspace style requires that a pair style with matching @@ -5509,11 +5509,11 @@ Doc page with :doc:`WARNING messages ` *Kokkos has been compiled for CUDA but no GPUs are requested* One or more GPUs must be used when Kokkos is compiled for CUDA. -*Kspace\_modify mesh parameter must be all zero or all positive* +*Kspace_modify mesh parameter must be all zero or all positive* Valid kspace mesh parameters are >0. The code will try to auto-detect suitable values when all three mesh sizes are set to zero (the default). -*Kspace\_modify mesh/disp parameter must be all zero or all positive* +*Kspace_modify mesh/disp parameter must be all zero or all positive* Valid kspace mesh/disp parameters are >0. The code will try to auto-detect suitable values when all three mesh sizes are set to zero **and** the required accuracy via *force/disp/real* as well as @@ -5531,17 +5531,17 @@ Doc page with :doc:`WARNING messages ` *Kspace style requires atom attribute q* The atom style defined does not have these attributes. -*Kspace\_modify eigtol must be smaller than one* +*Kspace_modify eigtol must be smaller than one* Self-explanatory. *LAMMPS is not built with Python embedded* This is done by including the PYTHON package before LAMMPS is built. This is required to use python-style variables. -*LAMMPS unit\_style lj not supported by KIM models* +*LAMMPS unit_style lj not supported by KIM models* Self-explanatory. Check the input script or data file. -*LJ6 off not supported in pair\_style buck/long/coul/long* +*LJ6 off not supported in pair_style buck/long/coul/long* Self-explanatory. *Label wasn't found in input script* @@ -5578,7 +5578,7 @@ Doc page with :doc:`WARNING messages ` *Lost atoms: original %ld current %ld* Lost atoms are checked for each time thermo output is done. See the - thermo\_modify lost command for options. Lost atoms usually indicate + thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation box, or moved further than one processor's sub-domain away before reneighboring. @@ -5586,13 +5586,13 @@ Doc page with :doc:`WARNING messages ` *MEAM library error %d* A call to the MEAM Fortran library returned an error. -*MPI\_LMP\_BIGINT and bigint in lmptype.h are not compatible* +*MPI_LMP_BIGINT and bigint in lmptype.h are not compatible* The size of the MPI datatype does not match the size of a bigint. -*MPI\_LMP\_TAGINT and tagint in lmptype.h are not compatible* +*MPI_LMP_TAGINT and tagint in lmptype.h are not compatible* The size of the MPI datatype does not match the size of a tagint. -*MSM can only currently be used with comm\_style brick* +*MSM can only currently be used with comm_style brick* This is a current restriction in LAMMPS. *MSM grid is too large* @@ -5605,23 +5605,23 @@ Doc page with :doc:`WARNING messages ` the MSM order can only be 4, 6, 8, or 10. *Mass command before simulation box is defined* - The mass command cannot be used before a read\_data, read\_restart, or - create\_box command. + The mass command cannot be used before a read_data, read_restart, or + create_box command. *Matrix factorization to split dispersion coefficients failed* This should not normally happen. Contact the developers. -*Min\_style command before simulation box is defined* - The min\_style command cannot be used before a read\_data, read\_restart, - or create\_box command. +*Min_style command before simulation box is defined* + The min_style command cannot be used before a read_data, read_restart, + or create_box command. -*Minimization could not find thermo\_pe compute* +*Minimization could not find thermo_pe compute* This compute is created by the thermo command. It must have been explicitly deleted by a uncompute command. *Minimize command before simulation box is defined* - The minimize command cannot be used before a read\_data, read\_restart, - or create\_box command. + The minimize command cannot be used before a read_data, read_restart, + or create_box command. *Mismatched brackets in variable* Self-explanatory. @@ -5703,10 +5703,10 @@ Doc page with :doc:`WARNING messages ` *Molecule sizescale must be 1.0 for body particle* Self-explanatory. -*Molecule template ID for atom\_style template does not exist* +*Molecule template ID for atom_style template does not exist* Self-explanatory. -*Molecule template ID for create\_atoms does not exist* +*Molecule template ID for create_atoms does not exist* Self-explanatory. *Molecule template ID for fix deposit does not exist* @@ -5729,12 +5729,12 @@ Doc page with :doc:`WARNING messages ` *Molecule topology/atom exceeds system topology/atom* The number of bonds, angles, etc per-atom in the molecule exceeds the - system setting. See the create\_box command for how to specify these + system setting. See the create_box command for how to specify these values. *Molecule topology type exceeds system topology type* The number of bond, angle, etc types in the molecule exceeds the - system setting. See the create\_box command for how to specify these + system setting. See the create_box command for how to specify these values. *More than one fix deform* @@ -5750,60 +5750,60 @@ Doc page with :doc:`WARNING messages ` *Mu not allowed when not using semi-grand in fix atom/swap command* Self-explanatory. -*Must define angle\_style before Angle Coeffs* - Must use an angle\_style command before reading a data file that +*Must define angle_style before Angle Coeffs* + Must use an angle_style command before reading a data file that defines Angle Coeffs. -*Must define angle\_style before BondAngle Coeffs* - Must use an angle\_style command before reading a data file that +*Must define angle_style before BondAngle Coeffs* + Must use an angle_style command before reading a data file that defines Angle Coeffs. -*Must define angle\_style before BondBond Coeffs* - Must use an angle\_style command before reading a data file that +*Must define angle_style before BondBond Coeffs* + Must use an angle_style command before reading a data file that defines Angle Coeffs. -*Must define bond\_style before Bond Coeffs* - Must use a bond\_style command before reading a data file that +*Must define bond_style before Bond Coeffs* + Must use a bond_style command before reading a data file that defines Bond Coeffs. -*Must define dihedral\_style before AngleAngleTorsion Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before AngleAngleTorsion Coeffs* + Must use a dihedral_style command before reading a data file that defines AngleAngleTorsion Coeffs. -*Must define dihedral\_style before AngleTorsion Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before AngleTorsion Coeffs* + Must use a dihedral_style command before reading a data file that defines AngleTorsion Coeffs. -*Must define dihedral\_style before BondBond13 Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before BondBond13 Coeffs* + Must use a dihedral_style command before reading a data file that defines BondBond13 Coeffs. -*Must define dihedral\_style before Dihedral Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before Dihedral Coeffs* + Must use a dihedral_style command before reading a data file that defines Dihedral Coeffs. -*Must define dihedral\_style before EndBondTorsion Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before EndBondTorsion Coeffs* + Must use a dihedral_style command before reading a data file that defines EndBondTorsion Coeffs. -*Must define dihedral\_style before MiddleBondTorsion Coeffs* - Must use a dihedral\_style command before reading a data file that +*Must define dihedral_style before MiddleBondTorsion Coeffs* + Must use a dihedral_style command before reading a data file that defines MiddleBondTorsion Coeffs. -*Must define improper\_style before AngleAngle Coeffs* - Must use an improper\_style command before reading a data file that +*Must define improper_style before AngleAngle Coeffs* + Must use an improper_style command before reading a data file that defines AngleAngle Coeffs. -*Must define improper\_style before Improper Coeffs* - Must use an improper\_style command before reading a data file that +*Must define improper_style before Improper Coeffs* + Must use an improper_style command before reading a data file that defines Improper Coeffs. -*Must define pair\_style before Pair Coeffs* - Must use a pair\_style command before reading a data file that defines +*Must define pair_style before Pair Coeffs* + Must use a pair_style command before reading a data file that defines Pair Coeffs. -*Must define pair\_style before PairIJ Coeffs* - Must use a pair\_style command before reading a data file that defines +*Must define pair_style before PairIJ Coeffs* + Must use a pair_style command before reading a data file that defines PairIJ Coeffs. *Must have more than one processor partition to temper* @@ -5840,9 +5840,9 @@ Doc page with :doc:`WARNING messages ` The Atoms section of a data file must come before a Velocities section. -*Must re-specify non-restarted pair style (xxx) after read\_restart* +*Must re-specify non-restarted pair style (xxx) after read_restart* For pair styles, that do not store their settings in a restart file, - it must be defined with a new 'pair\_style' command after read\_restart. + it must be defined with a new 'pair_style' command after read_restart. *Must set both respa inner and outer* Cannot use just the inner or outer option with respa without using the @@ -5850,7 +5850,7 @@ Doc page with :doc:`WARNING messages ` *Must set number of threads via package omp command* Because you are using the USER-OMP package, set the number of threads - via its settings, not by the pair\_style snap nthreads setting. + via its settings, not by the pair_style snap nthreads setting. *Must shrink-wrap piston boundary* The boundary style of the face where the piston is applied must be of @@ -5865,30 +5865,30 @@ Doc page with :doc:`WARNING messages ` *Must specify at least 2 types in fix atom/swap command* Self-explanatory. -*Must use 'kim\_style init' command before simulation box is defined* +*Must use 'kim_style init' command before simulation box is defined* Self-explanatory. -*Must use 'kim\_style define' command after simulation box is defined* +*Must use 'kim_style define' command after simulation box is defined* Self-explanatory. -*Must use 'kim\_style init' command before 'kim\_style define'* +*Must use 'kim_style init' command before 'kim_style define'* Self-explanatory. -*Must use 'kspace\_modify pressure/scalar no' for rRESPA with kspace\_style MSM* +*Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM* The kspace scalar pressure option cannot (yet) be used with rRESPA. -*Must use 'kspace\_modify pressure/scalar no' for tensor components with kspace\_style msm* - Otherwise MSM will compute only a scalar pressure. See the kspace\_modify +*Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm* + Otherwise MSM will compute only a scalar pressure. See the kspace_modify command for details on this setting. -*Must use 'kspace\_modify pressure/scalar no' to obtain per-atom virial with kspace\_style MSM* +*Must use 'kspace_modify pressure/scalar no' to obtain per-atom virial with kspace_style MSM* The kspace scalar pressure option cannot be used to obtain per-atom virial. -*Must use 'kspace\_modify pressure/scalar no' with GPU MSM Pair styles* +*Must use 'kspace_modify pressure/scalar no' with GPU MSM Pair styles* The kspace scalar pressure option is not (yet) compatible with GPU MSM Pair styles. -*Must use 'kspace\_modify pressure/scalar no' with kspace\_style msm/cg* - The kspace scalar pressure option is not compatible with kspace\_style msm/cg. +*Must use 'kspace_modify pressure/scalar no' with kspace_style msm/cg* + The kspace scalar pressure option is not compatible with kspace_style msm/cg. *Must use -in switch with multiple partitions* A multi-partition simulation cannot read the input script from stdin. @@ -5918,12 +5918,12 @@ Doc page with :doc:`WARNING messages ` command. *Must use atom map style array with Kokkos* - See the atom\_modify map command. + See the atom_modify map command. *Must use atom style with molecule IDs with fix bond/swap* Self-explanatory. -*Must use pair\_style comb or comb3 with fix qeq/comb* +*Must use pair_style comb or comb3 with fix qeq/comb* Self-explanatory. *Must use variable energy with fix addforce* @@ -5950,29 +5950,29 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Needed bonus data not in data file* - Some atom styles require bonus data. See the read\_data doc page for + Some atom styles require bonus data. See the read_data doc page for details. *Needed molecular topology not in data file* The header of the data file indicated bonds, angles, etc would be included, but they are not present. -*Neigh\_modify exclude molecule requires atom attribute molecule* +*Neigh_modify exclude molecule requires atom attribute molecule* Self-explanatory. -*Neigh\_modify include group != atom\_modify first group* +*Neigh_modify include group != atom_modify first group* Self-explanatory. *Neighbor delay must be 0 or multiple of every setting* - The delay and every parameters set via the neigh\_modify command are + The delay and every parameters set via the neigh_modify command are inconsistent. If the delay setting is non-zero, then it must be a multiple of the every setting. *Neighbor include group not allowed with ghost neighbors* This is a current restriction within LAMMPS. -*Neighbor list overflow, boost neigh\_modify one* - There are too many neighbors of a single atom. Use the neigh\_modify +*Neighbor list overflow, boost neigh_modify one* + There are too many neighbors of a single atom. Use the neigh_modify command to increase the max number of neighbors allowed for one atom. You may also want to boost the page size. @@ -5991,23 +5991,23 @@ Doc page with :doc:`WARNING messages ` *New atom IDs exceed maximum allowed ID* See the setting for tagint in the src/lmptype.h file. -*New bond exceeded bonds per atom in create\_bonds* -See the read\_data command for info on using the "extra/bond/per/atom" +*New bond exceeded bonds per atom in create_bonds* +See the read_data command for info on using the "extra/bond/per/atom" keyword to allow for additional bonds to be formed *New bond exceeded bonds per atom in fix bond/create* - See the read\_data command for info on using the "extra/bond/per/atom" + See the read_data command for info on using the "extra/bond/per/atom" keyword to allow for additional bonds to be formed *New bond exceeded special list size in fix bond/create* - See the "read\_data extra/special/per/atom" command - (or the "create\_box extra/special/per/atom" command) + See the "read_data extra/special/per/atom" command + (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. *Newton bond change after simulation box is defined* The newton command cannot be used to change the newton bond value - after a read\_data, read\_restart, or create\_box command. + after a read_data, read_restart, or create_box command. *Next command must list all universe and uloop variables* This is to insure they stay in sync. @@ -6090,7 +6090,7 @@ keyword to allow for additional bonds to be formed The data file cannot specify the number of bonds, angles, etc, because this info if inferred from the molecule templates. -*No overlap of box and region for create\_atoms* +*No overlap of box and region for create_atoms* Self-explanatory. *No pair coul/streitz for fix qeq/slater* @@ -6130,10 +6130,10 @@ keyword to allow for additional bonds to be formed *Non-numeric box dimensions - simulation unstable* The box size has apparently blown up. -*Non-zero atom IDs with atom\_modify id = no* +*Non-zero atom IDs with atom_modify id = no* Self-explanatory. -*Non-zero read\_data shift z value for 2d simulation* +*Non-zero read_data shift z value for 2d simulation* Self-explanatory. *Nprocs not a multiple of N for -reorder* @@ -6239,7 +6239,7 @@ keyword to allow for additional bonds to be formed NPT/NPH fix must be defined in input script after all poems fixes, else the fix contribution to the pressure virial is incorrect. -*PPPM can only currently be used with comm\_style brick* +*PPPM can only currently be used with comm_style brick* This is a current restriction in LAMMPS. *PPPM grid is too large* @@ -6248,11 +6248,11 @@ keyword to allow for additional bonds to be formed requested accuracy. *PPPM grid stencil extends beyond nearest neighbor processor* - This is not allowed if the kspace\_modify overlap setting is no. + This is not allowed if the kspace_modify overlap setting is no. *PPPM order < minimum allowed order* The default minimum order is 2. This can be reset by the - kspace\_modify minorder command. + kspace_modify minorder command. *PPPM order cannot be < 2 or > than %d* This is a limitation of the PPPM implementation in LAMMPS. @@ -6267,28 +6267,28 @@ keyword to allow for additional bonds to be formed OFFSET is currently set to 4096. You likely need to decrease the requested accuracy. -*PPPMDisp can only currently be used with comm\_style brick* +*PPPMDisp can only currently be used with comm_style brick* This is a current restriction in LAMMPS. *PPPMDisp coulomb order cannot be greater than %d* This is a limitation of the PPPM implementation in LAMMPS. *PPPMDisp used but no parameters set, for further information please see the pppm/disp documentation* - An efficient and accurate usage of the pppm/disp requires settings via the kspace\_modify command. Please see the pppm/disp documentation for further instructions. + An efficient and accurate usage of the pppm/disp requires settings via the kspace_modify command. Please see the pppm/disp documentation for further instructions. *PRD command before simulation box is defined* - The prd command cannot be used before a read\_data, - read\_restart, or create\_box command. + The prd command cannot be used before a read_data, + read_restart, or create_box command. -*PRD nsteps must be multiple of t\_event* +*PRD nsteps must be multiple of t_event* Self-explanatory. -*PRD t\_corr must be multiple of t\_event* +*PRD t_corr must be multiple of t_event* Self-explanatory. *Package command after simulation box is defined* - The package command cannot be used after a read\_data, read\_restart, or - create\_box command. + The package command cannot be used after a read_data, read_restart, or + create_box command. *Package gpu command without GPU package installed* The GPU package must be installed via "make yes-gpu" before LAMMPS is @@ -6331,7 +6331,7 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Pair coeff for hybrid has invalid style* - Style in pair coeff must have been listed in pair\_style command. + Style in pair coeff must have been listed in pair_style command. *Pair coul/wolf requires atom attribute q* The atom style defined does not have this attribute. @@ -6359,10 +6359,10 @@ keyword to allow for additional bonds to be formed Two atoms are further apart than the pairwise table allows. *Pair dpd requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair gayberne epsilon a,b,c coeffs are not all set* - Each atom type involved in pair\_style gayberne must + Each atom type involved in pair_style gayberne must have these 3 coefficients set at least once. *Pair gayberne requires atom style ellipsoid* @@ -6381,7 +6381,7 @@ keyword to allow for additional bonds to be formed The atom style defined does not have these attributes. *Pair granular requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair granular with shear history requires newton pair off* This is a current restriction of the implementation of pair @@ -6395,7 +6395,7 @@ keyword to allow for additional bonds to be formed that doesn't support it. *Pair hybrid sub-style is not used* - No pair\_coeff command used a sub-style specified in the pair\_style + No pair_coeff command used a sub-style specified in the pair_style command. *Pair inner cutoff < Respa interior cutoff* @@ -6415,7 +6415,7 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Pair lubricate requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair lubricate requires monodisperse particles* All particles must be the same finite size. @@ -6427,7 +6427,7 @@ keyword to allow for additional bonds to be formed One of the particles has radius 0.0. *Pair lubricate/poly requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair lubricate/poly requires newton pair off* Self-explanatory. @@ -6436,13 +6436,13 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Pair lubricateU requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair lubricateU requires monodisperse particles* All particles must be the same finite size. *Pair lubricateU/poly requires ghost atoms store velocity* - Use the comm\_modify vel yes command to enable this. + Use the comm_modify vel yes command to enable this. *Pair lubricateU/poly requires newton pair off* Self-explanatory. @@ -6453,9 +6453,9 @@ keyword to allow for additional bonds to be formed *Pair peri requires a lattice be defined* Use the lattice command for this purpose. -*Pair peri requires an atom map, see atom\_modify* +*Pair peri requires an atom map, see atom_modify* Even for atomic systems, an atom map is required to find Peridynamic - bonds. Use the atom\_modify command to define one. + bonds. Use the atom_modify command to define one. *Pair resquared epsilon a,b,c coeffs are not all set* Self-explanatory. @@ -6595,12 +6595,12 @@ keyword to allow for additional bonds to be formed The pair style does not support the pN value requested by the compute pair/local command. -*Pair style does not support bond\_style quartic* +*Pair style does not support bond_style quartic* The pair style does not have a single() function, so it can - not be invoked by bond\_style quartic. + not be invoked by bond_style quartic. *Pair style does not support compute group/group* - The pair\_style does not have a single() function, so it cannot be + The pair_style does not have a single() function, so it cannot be invoked by the compute group/group command. *Pair style does not support compute pair/local* @@ -6615,7 +6615,7 @@ keyword to allow for additional bonds to be formed The pair style does not have a single() function, so it can not be invoked by fix bond/swap. -*Pair style does not support pair\_write* +*Pair style does not support pair_write* The pair style does not have a single() function, so it can not be invoked by pair write. @@ -6627,7 +6627,7 @@ keyword to allow for additional bonds to be formed Atoms in the simulation do not have IDs, so history effects cannot be tracked by the granular pair potential. -*Pair style hbond/dreiding requires an atom map, see atom\_modify* +*Pair style hbond/dreiding requires an atom map, see atom_modify* Self-explanatory. *Pair style hbond/dreiding requires atom IDs* @@ -6713,7 +6713,7 @@ keyword to allow for additional bonds to be formed molecule adds forces to atoms owned by other processors. *Pair style lj/gromacs/coul/gromacs requires atom attribute q* - An atom\_style with this attribute is needed. + An atom_style with this attribute is needed. *Pair style lj/long/dipole/long does not currently support respa* This feature is not yet supported. @@ -6766,7 +6766,7 @@ keyword to allow for additional bonds to be formed *Pair style requires a KSpace style* No kspace style is defined. -*Pair style requires use of kspace\_style ewald/disp* +*Pair style requires use of kspace_style ewald/disp* Self-explanatory. *Pair style sw/gpu requires atom IDs* @@ -6836,21 +6836,21 @@ keyword to allow for additional bonds to be formed *PairKIM only works with 3D problems* This is a current limitation. -*Pair\_coeff command before pair\_style is defined* +*Pair_coeff command before pair_style is defined* Self-explanatory. -*Pair\_coeff command before simulation box is defined* - The pair\_coeff command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Pair_coeff command before simulation box is defined* + The pair_coeff command cannot be used before a read_data, + read_restart, or create_box command. -*Pair\_modify command before pair\_style is defined* +*Pair_modify command before pair_style is defined* Self-explanatory. -*Pair\_modify special setting for pair hybrid incompatible with global special\_bonds setting* +*Pair_modify special setting for pair hybrid incompatible with global special_bonds setting* Cannot override a setting of 0.0 or 1.0 or change a setting between 0.0 and 1.0. -*Pair\_write command before pair\_style is defined* +*Pair_write command before pair_style is defined* Self-explanatory. *Particle on or inside fix wall surface* @@ -6971,8 +6971,8 @@ keyword to allow for additional bonds to be formed of processors LAMMPS is running on. *Processors command after simulation box is defined* - The processors command cannot be used after a read\_data, read\_restart, - or create\_box command. + The processors command cannot be used after a read_data, read_restart, + or create_box command. *Processors custom grid file is inconsistent* The vales in the custom file are not consistent with the number of @@ -7045,35 +7045,35 @@ keyword to allow for additional bonds to be formed This is because a % signifies one file per processor and MPI-IO creates one large file for all processors. -*Read\_data shrink wrap did not assign all atoms correctly* +*Read_data shrink wrap did not assign all atoms correctly* This is typically because the box-size specified in the data file is large compared to the actual extent of atoms in a shrink-wrapped dimension. When LAMMPS shrink-wraps the box atoms will be lost if the processor they are re-assigned to is too far away. Choose a box size closer to the actual extent of the atoms. -*Read\_dump command before simulation box is defined* - The read\_dump command cannot be used before a read\_data, read\_restart, - or create\_box command. +*Read_dump command before simulation box is defined* + The read_dump command cannot be used before a read_data, read_restart, + or create_box command. -*Read\_dump field not found in dump file* +*Read_dump field not found in dump file* Self-explanatory. -*Read\_dump triclinic status does not match simulation* +*Read_dump triclinic status does not match simulation* Both the dump snapshot and the current LAMMPS simulation must be using either an orthogonal or triclinic box. -*Read\_dump xyz fields do not have consistent scaling/wrapping* +*Read_dump xyz fields do not have consistent scaling/wrapping* Self-explanatory. *Reading from MPI-IO filename when MPIIO package is not installed* Self-explanatory. -*Reax\_defs.h setting for NATDEF is too small* +*Reax_defs.h setting for NATDEF is too small* Edit the setting in the ReaxFF library and re-compile the library and re-build LAMMPS. -*Reax\_defs.h setting for NNEIGHMAXDEF is too small* +*Reax_defs.h setting for NNEIGHMAXDEF is too small* Edit the setting in the ReaxFF library and re-compile the library and re-build LAMMPS. @@ -7154,8 +7154,8 @@ keyword to allow for additional bonds to be formed when you do not intend to. *Replicate command before simulation box is defined* - The replicate command cannot be used before a read\_data, read\_restart, - or create\_box command. + The replicate command cannot be used before a read_data, read_restart, + or create_box command. *Replicate did not assign all atoms correctly* Atoms replicated by the replicate command were not assigned correctly @@ -7173,8 +7173,8 @@ keyword to allow for additional bonds to be formed by Kokkos. *Rerun command before simulation box is defined* - The rerun command cannot be used before a read\_data, read\_restart, or - create\_box command. + The rerun command cannot be used before a read_data, read_restart, or + create_box command. *Rerun dump file does not contain requested snapshot* Self-explanatory. @@ -7273,8 +7273,8 @@ keyword to allow for additional bonds to be formed Rmask is per-atom operation. *Run command before simulation box is defined* - The run command cannot be used before a read\_data, read\_restart, or - create\_box command. + The run command cannot be used before a read_data, read_restart, or + create_box command. *Run command start value is after start of run* Self-explanatory. @@ -7282,9 +7282,9 @@ keyword to allow for additional bonds to be formed *Run command stop value is before end of run* Self-explanatory. -*Run\_style command before simulation box is defined* - The run\_style command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Run_style command before simulation box is defined* + The run_style command cannot be used before a read_data, + read_restart, or create_box command. *SRD bin size for fix srd differs from user request* Fix SRD had to adjust the bin size to fit the simulation box. See the @@ -7309,8 +7309,8 @@ keyword to allow for additional bonds to be formed Cannot specify a partition to be a sender twice. *Set command before simulation box is defined* - The set command cannot be used before a read\_data, read\_restart, - or create\_box command. + The set command cannot be used before a read_data, read_restart, + or create_box command. *Set command floating point vector does not exist* Self-explanatory. @@ -7360,8 +7360,8 @@ keyword to allow for additional bonds to be formed NPT fix must be defined in input script after SHAKE fix, else the SHAKE fix contribution to the pressure virial is incorrect. -*Shear history overflow, boost neigh\_modify one* - There are too many neighbors of a single atom. Use the neigh\_modify +*Shear history overflow, boost neigh_modify one* + There are too many neighbors of a single atom. Use the neigh_modify command to increase the max number of neighbors allowed for one atom. You may also want to boost the page size. @@ -7378,13 +7378,13 @@ keyword to allow for additional bonds to be formed you are running. *Special list size exceeded in fix bond/create* - See the "read\_data extra/special/per/atom" command - (or the "create\_box extra/special/per/atom" command) + See the "read_data extra/special/per/atom" command + (or the "create_box extra/special/per/atom" command) for info on how to leave space in the special bonds list to allow for additional bonds to be formed. *Species XXX is not supported by this KIM Simulator Model* - The kim\_style define command was referencing a species that is not + The kim_style define command was referencing a species that is not present in the requested KIM Simulator Model. *Specified processors != physical processors* @@ -7398,33 +7398,33 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Subsequent read data induced too many angles per atom* - See the extra/angle/per/atom keyword for the create\_box - or the read\_data command to set this limit larger + See the extra/angle/per/atom keyword for the create_box + or the read_data command to set this limit larger *Subsequent read data induced too many bonds per atom* - See the extra/bond/per/atom keyword for the create\_box - or the read\_data command to set this limit larger + See the extra/bond/per/atom keyword for the create_box + or the read_data command to set this limit larger *Subsequent read data induced too many dihedrals per atom* - See the extra/dihedral/per/atom keyword for the create\_box - or the read\_data command to set this limit larger + See the extra/dihedral/per/atom keyword for the create_box + or the read_data command to set this limit larger *Subsequent read data induced too many impropers per atom* - See the extra/improper/per/atom keyword for the create\_box - or the read\_data command to set this limit larger + See the extra/improper/per/atom keyword for the create_box + or the read_data command to set this limit larger *Substitution for illegal variable* Input script line contained a variable that could not be substituted for. *Support for writing images in JPEG format not included* - LAMMPS was not built with the -DLAMMPS\_JPEG switch in the Makefile. + LAMMPS was not built with the -DLAMMPS_JPEG switch in the Makefile. *Support for writing images in PNG format not included* - LAMMPS was not built with the -DLAMMPS\_PNG switch in the Makefile. + LAMMPS was not built with the -DLAMMPS_PNG switch in the Makefile. *Support for writing movies not included* - LAMMPS was not built with the -DLAMMPS\_FFMPEG switch in the Makefile + LAMMPS was not built with the -DLAMMPS_FFMPEG switch in the Makefile *System in data file is too big* See the setting for bigint in the src/lmptype.h file. @@ -7433,7 +7433,7 @@ keyword to allow for additional bonds to be formed The total charge on all atoms on the system is not 0.0. For some KSpace solvers this is an error. -*TAD nsteps must be multiple of t\_event* +*TAD nsteps must be multiple of t_event* Self-explanatory. *TIP4P hydrogen has incorrect atom type* @@ -7480,8 +7480,8 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Temper command before simulation box is defined* - The temper command cannot be used before a read\_data, read\_restart, or - create\_box command. + The temper command cannot be used before a read_data, read_restart, or + create_box command. *Temperature ID for fix bond/swap does not exist* Self-explanatory. @@ -7562,7 +7562,7 @@ keyword to allow for additional bonds to be formed *Temperature for fix nvt/sllod does not have a bias* The specified compute must compute temperature with a bias. -*Tempering could not find thermo\_pe compute* +*Tempering could not find thermo_pe compute* This compute is created by the thermo command. It must have been explicitly deleted by a uncompute command. @@ -7573,7 +7573,7 @@ keyword to allow for additional bonds to be formed The fix specified by the temper command is not one that controls temperature (nvt or langevin). -*Test\_descriptor\_string already allocated* +*Test_descriptor_string already allocated* This is an internal error. Contact the developers. *The package gpu command is required for gpu styles* @@ -7639,28 +7639,28 @@ keyword to allow for additional bonds to be formed your thermo output. *Thermo style does not use press* - Cannot use thermo\_modify to set this parameter since the thermo\_style + Cannot use thermo_modify to set this parameter since the thermo_style is not computing this quantity. *Thermo style does not use temp* - Cannot use thermo\_modify to set this parameter since the thermo\_style + Cannot use thermo_modify to set this parameter since the thermo_style is not computing this quantity. -*Thermo\_modify every variable returned a bad timestep* +*Thermo_modify every variable returned a bad timestep* The returned timestep is less than or equal to the current timestep. -*Thermo\_modify int format does not contain d character* +*Thermo_modify int format does not contain d character* Self-explanatory. -*Thermo\_modify pressure ID does not compute pressure* +*Thermo_modify pressure ID does not compute pressure* The specified compute ID does not compute pressure. -*Thermo\_modify temperature ID does not compute temperature* +*Thermo_modify temperature ID does not compute temperature* The specified compute ID does not compute temperature. -*Thermo\_style command before simulation box is defined* - The thermo\_style command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Thermo_style command before simulation box is defined* + The thermo_style command cannot be used before a read_data, + read_restart, or create_box command. *This variable thermo keyword cannot be used between runs* Keywords that refer to time (such as cpu, elapsed) do not @@ -7683,7 +7683,7 @@ keyword to allow for additional bonds to be formed The timestep must fit in a 32-bit integer to use this dump style. *Too few bits for lookup table* - Table size specified via pair\_modify command does not work with your + Table size specified via pair_modify command does not work with your machine's floating point representation. *Too few lines in %s section of data file* @@ -7730,19 +7730,19 @@ keyword to allow for additional bonds to be formed Cannot sort when running with more than 2\^31 atoms. *Too many exponent bits for lookup table* - Table size specified via pair\_modify command does not work with your + Table size specified via pair_modify command does not work with your machine's floating point representation. *Too many groups* The maximum number of atom groups (including the "all" group) is - given by MAX\_GROUP in group.cpp and is 32. + given by MAX_GROUP in group.cpp and is 32. *Too many iterations* You must use a number of iterations that fit in a 32-bit integer for minimization. *Too many lines in one body in data file - boost MAXBODY* - MAXBODY is a setting at the top of the src/read\_data.cpp file. + MAXBODY is a setting at the top of the src/read_data.cpp file. Set it larger and re-compile the code. *Too many local+ghost atoms for neighbor list* @@ -7751,7 +7751,7 @@ keyword to allow for additional bonds to be formed removed for masking 1-2, 1-3, 1-4 neighbors. *Too many mantissa bits for lookup table* - Table size specified via pair\_modify command does not work with your + Table size specified via pair_modify command does not work with your machine's floating point representation. *Too many masses for fix shake* @@ -7779,7 +7779,7 @@ keyword to allow for additional bonds to be formed See the setting for bigint in the src/lmptype.h file. *Too many total bits for bitmapped lookup table* - Table size specified via pair\_modify command is too large. Note that + Table size specified via pair_modify command is too large. Note that a value of N generates a 2\^N size table. *Too many values in body lines in data file* @@ -7806,7 +7806,7 @@ keyword to allow for additional bonds to be formed +half of the x box length. This constraint can be relaxed by using the box tilt command. -*Tried to convert a double to int, but input\_double > INT\_MAX* +*Tried to convert a double to int, but input_double > INT_MAX* Self-explanatory. *Trying to build an occasional neighbor list before initialization completed* @@ -7868,8 +7868,8 @@ keyword to allow for additional bonds to be formed A read operation from the file failed. *Units command after simulation box is defined* - The units command cannot be used after a read\_data, read\_restart, or - create\_box command. + The units command cannot be used after a read_data, read_restart, or + create_box command. *Universe/uloop variable count < # of partitions* A universe or uloop style variable must specify a number of values >= to the @@ -7887,13 +7887,13 @@ keyword to allow for additional bonds to be formed *Unrecognized bond style* The choice of bond style is unknown. -*Unknown category for info is\_active()* +*Unknown category for info is_active()* Self-explanatory. -*Unknown category for info is\_available()* +*Unknown category for info is_available()* Self-explanatory. -*Unknown category for info is\_defined()* +*Unknown category for info is_defined()* Self-explanatory. *Unrecognized command: %s* @@ -7923,7 +7923,7 @@ keyword to allow for additional bonds to be formed *Unrecognized improper style* The choice of improper style is unknown. -*Unknown keyword in thermo\_style custom command* +*Unknown keyword in thermo_style custom command* One or more specified keywords are not recognized. *Unrecognized kspace style* @@ -7941,7 +7941,7 @@ keyword to allow for additional bonds to be formed *Unrecognized pair style* The choice of pair style is unknown. -*Unknown pair\_modify hybrid sub-style* +*Unknown pair_modify hybrid sub-style* The choice of sub-style is unknown. *Unrecognized region style* @@ -7956,10 +7956,10 @@ keyword to allow for additional bonds to be formed *Unknown table style in bond style table* Self-explanatory. -*Unknown table style in pair\_style command* - Style of table is invalid for use with pair\_style table command. +*Unknown table style in pair_style command* + Style of table is invalid for use with pair_style table command. -*Unknown unit\_style* +*Unknown unit_style* Self-explanatory. Check the input script or data file. *Unrecognized lattice type in MEAM file 1* @@ -7973,13 +7973,13 @@ keyword to allow for additional bonds to be formed *Unrecognized pair style in compute pair command* Self-explanatory. -*Unsupported mixing rule in kspace\_style ewald/disp* +*Unsupported mixing rule in kspace_style ewald/disp* Only geometric mixing is supported. -*Unsupported order in kspace\_style ewald/disp* +*Unsupported order in kspace_style ewald/disp* Only 1/r\^6 dispersion or dipole terms are supported. -*Unsupported order in kspace\_style pppm/disp, pair\_style %s* +*Unsupported order in kspace_style pppm/disp, pair_style %s* Only pair styles with 1/r and 1/r\^6 dependence are currently supported. *Use cutoff keyword to set cutoff in single mode* @@ -8042,10 +8042,10 @@ keyword to allow for additional bonds to be formed *Variable for compute ti is invalid style* Self-explanatory. -*Variable for create\_atoms is invalid style* +*Variable for create_atoms is invalid style* The variables must be equal-style variables. -*Variable for displace\_atoms is invalid style* +*Variable for displace_atoms is invalid style* It must be an equal-style or atom-style variable. *Variable for dump every is invalid style* @@ -8185,10 +8185,10 @@ keyword to allow for additional bonds to be formed *Variable name for compute ti does not exist* Self-explanatory. -*Variable name for create\_atoms does not exist* +*Variable name for create_atoms does not exist* Self-explanatory. -*Variable name for displace\_atoms does not exist* +*Variable name for displace_atoms does not exist* Self-explanatory. *Variable name for dump every does not exist* @@ -8324,8 +8324,8 @@ keyword to allow for additional bonds to be formed Self-explanatory. *Velocity command before simulation box is defined* - The velocity command cannot be used before a read\_data, read\_restart, - or create\_box command. + The velocity command cannot be used before a read_data, read_restart, + or create_box command. *Velocity command with no atoms existing* A velocity command has been used, but no atoms yet exist. @@ -8343,7 +8343,7 @@ keyword to allow for additional bonds to be formed The compute ID given to the velocity command must compute temperature. -*Verlet/split can only currently be used with comm\_style brick* +*Verlet/split can only currently be used with comm_style brick* This is a current restriction in LAMMPS. *Verlet/split does not yet support TIP4P* @@ -8392,17 +8392,17 @@ keyword to allow for additional bonds to be formed A world-style variable must specify a number of values equal to the number of processor partitions. -*Write\_data command before simulation box is defined* +*Write_data command before simulation box is defined* Self-explanatory. -*Write\_restart command before simulation box is defined* - The write\_restart command cannot be used before a read\_data, - read\_restart, or create\_box command. +*Write_restart command before simulation box is defined* + The write_restart command cannot be used before a read_data, + read_restart, or create_box command. *Writing to MPI-IO filename when MPIIO package is not installed* Self-explanatory. -*Zero length rotation vector with displace\_atoms* +*Zero length rotation vector with displace_atoms* Self-explanatory. *Zero length rotation vector with fix move* diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 76bdad7adb..a4738a811c 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -37,7 +37,7 @@ Doc page with :doc:`ERROR messages ` *Angles are defined but no angle style is set* The topology contains angles, but there are no angle forces computed - since there was no angle\_style command. + since there was no angle_style command. *Atom style in data file differs from currently defined atom style* Self-explanatory. @@ -62,7 +62,7 @@ Doc page with :doc:`ERROR messages ` *Bonds are defined but no bond style is set* The topology contains bonds, but there are no bond forces computed - since there was no bond\_style command. + since there was no bond_style command. *Bond/angle/dihedral extent > half of periodic box length* This is a restriction because LAMMPS can be confused about which image @@ -83,8 +83,8 @@ Doc page with :doc:`ERROR messages ` *Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero* Self-explanatory. -*Calling write\_dump before a full system init.* - The write\_dump command is used before the system has been fully +*Calling write_dump before a full system init.* + The write_dump command is used before the system has been fully initialized as part of a 'run' or 'minimize' command. Not all dump styles and features are fully supported at this point and thus the command may fail or produce incomplete or incorrect output. Insert @@ -131,11 +131,11 @@ Doc page with :doc:`ERROR messages ` degrees-of-freedom for the atoms in those partial rigid bodies will not be accounted for. -*Create\_bonds max distance > minimum neighbor cutoff* +*Create_bonds max distance > minimum neighbor cutoff* This means atom pairs for some atom types may not be in the neighbor list and thus no bond can be created between them. -*Delete\_atoms cutoff > minimum neighbor cutoff* +*Delete_atoms cutoff > minimum neighbor cutoff* This means atom pairs for some atom types may not be in the neighbor list and thus an atom in that pair cannot be deleted. @@ -158,7 +158,7 @@ Doc page with :doc:`ERROR messages ` *Dihedrals are defined but no dihedral style is set* The topology contains dihedrals, but there are no dihedral forces computed - since there was no dihedral\_style command. + since there was no dihedral_style command. *Dump dcd/xtc timestamp may be wrong with fix dt/reset* If the fix changes the timestep, the dump dcd file will not @@ -172,7 +172,7 @@ Doc page with :doc:`ERROR messages ` *Estimated error in splitting of dispersion coeffs is %g* Error is greater than 0.0001 percent. -*Ewald/disp Newton solver failed, using old method to estimate g\_ewald* +*Ewald/disp Newton solver failed, using old method to estimate g_ewald* Self-explanatory. Choosing a different cutoff value may help. *FENE bond too long* @@ -209,8 +209,8 @@ Doc page with :doc:`ERROR messages ` This is probably an error, since you should not delete only one atom of a molecule. -*Fix gcmc using full\_energy option* - Fix gcmc has automatically turned on the full\_energy option since it +*Fix gcmc using full_energy option* + Fix gcmc has automatically turned on the full_energy option since it is required for systems like the one specified by the user. User input included one or more of the following: kspace, triclinic, a hybrid pair style, an eam pair style, or no "single" function for the pair @@ -265,19 +265,19 @@ This will most likely cause errors in kinetic fluctuations. *Fixes cannot send data in Kokkos communication, switching to classic communication* This is current restriction with Kokkos. -*For better accuracy use 'pair\_modify table 0'* +*For better accuracy use 'pair_modify table 0'* The user-specified force accuracy cannot be achieved unless the table - feature is disabled by using 'pair\_modify table 0'. + feature is disabled by using 'pair_modify table 0'. *Geometric mixing assumed for 1/r\^6 coefficients* Self-explanatory. -*Group for fix\_modify temp != fix group* - The fix\_modify command is specifying a temperature computation that +*Group for fix_modify temp != fix group* + The fix_modify command is specifying a temperature computation that computes a temperature on a different group of atoms than the fix itself operates on. This is probably not what you want to do. -*H matrix size has been exceeded: m\_fill=%d H.m=%d\n* +*H matrix size has been exceeded: m_fill=%d H.m=%d\n* This is the size of the matrix. *Ignoring unknown or incorrect info command flag* @@ -299,7 +299,7 @@ This will most likely cause errors in kinetic fluctuations. *Impropers are defined but no improper style is set* The topology contains impropers, but there are no improper forces computed - since there was no improper\_style command. + since there was no improper_style command. *Inconsistent image flags* The image flags for a pair on bonded atoms appear to be inconsistent. @@ -334,22 +334,22 @@ This will most likely cause errors in kinetic fluctuations. *KIM Model does not provide 'particleVirial'; virial per atom will be zero* Self-explanatory. -*Kspace\_modify slab param < 2.0 may cause unphysical behavior* - The kspace\_modify slab parameter should be larger to insure periodic +*Kspace_modify slab param < 2.0 may cause unphysical behavior* + The kspace_modify slab parameter should be larger to insure periodic grids padded with empty space do not overlap. *Less insertions than requested* The fix pour command was unsuccessful at finding open space for as many particles as it tried to insert. -*Library error in lammps\_gather\_atoms* +*Library error in lammps_gather_atoms* This library function cannot be used if atom IDs are not defined or are not consecutively numbered. -*Library error in lammps\_scatter\_atoms* +*Library error in lammps_scatter_atoms* This library function cannot be used if atom IDs are not defined or are not consecutively numbered, or if no atom map is defined. See the - atom\_modify command for details about atom maps. + atom_modify command for details about atom maps. *Likewise 1-2 special neighbor interactions != 1.0* The topology contains bonds, but there is no bond style defined @@ -372,15 +372,15 @@ This will most likely cause errors in kinetic fluctuations. pairs in the neighbor list in expectation of interactions for those pairs being computed from the dihedral style. -*Lost atoms via change\_box: original %ld current %ld* +*Lost atoms via change_box: original %ld current %ld* The command options you have used caused atoms to be lost. -*Lost atoms via displace\_atoms: original %ld current %ld* +*Lost atoms via displace_atoms: original %ld current %ld* The command options you have used caused atoms to be lost. *Lost atoms: original %ld current %ld* Lost atoms are checked for each time thermo output is done. See the - thermo\_modify lost command for options. Lost atoms usually indicate + thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation box, or moved further than one processor's sub-domain away before reneighboring. @@ -403,8 +403,8 @@ This will most likely cause errors in kinetic fluctuations. This means the bonded atoms will not be excluded in pair-wise interactions. -*Molecule template for create\_atoms has multiple molecules* - The create\_atoms command will only create molecules of a single type, +*Molecule template for create_atoms has multiple molecules* + The create_atoms command will only create molecules of a single type, i.e. the first molecule in the template. *Molecule template for fix gcmc has multiple molecules* @@ -469,21 +469,21 @@ This will most likely cause errors in kinetic fluctuations. *Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies* This is because excluding specific pair interactions also excludes them from long-range interactions which may not be the desired effect. - The special\_bonds command handles this consistently by insuring + The special_bonds command handles this consistently by insuring excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated consistently by both the short-range pair style and the long-range solver. This is not done for exclusions of charged atom pairs via the - neigh\_modify exclude command. + neigh_modify exclude command. -*New thermo\_style command, previous thermo\_modify settings will be lost* - If a thermo\_style command is used after a thermo\_modify command, the - settings changed by the thermo\_modify command will be reset to their - default values. This is because the thermo\_modify command acts on - the currently defined thermo style, and a thermo\_style command creates +*New thermo_style command, previous thermo_modify settings will be lost* + If a thermo_style command is used after a thermo_modify command, the + settings changed by the thermo_modify command will be reset to their + default values. This is because the thermo_modify command acts on + the currently defined thermo style, and a thermo_style command creates a new style. *No Kspace calculation with verlet/split* - The 2nd partition performs a kspace calculation so the kspace\_style + The 2nd partition performs a kspace calculation so the kspace_style command must be used. *No automatic unit conversion to XTC file format conventions possible for units lj* @@ -507,7 +507,7 @@ This will most likely cause errors in kinetic fluctuations. of two and the number of grid points in one or more directions have been adjusted to meet this requirement. -*OMP\_NUM\_THREADS environment is not set.* +*OMP_NUM_THREADS environment is not set.* This environment variable must be set appropriately to use the USER-OMP package. @@ -541,10 +541,10 @@ This will most likely cause errors in kinetic fluctuations. *Pair dpd needs newton pair on for momentum conservation* Self-explanatory. -*Pair dsmc: num\_of\_collisions > number\_of\_A* +*Pair dsmc: num_of_collisions > number_of_A* Collision model in DSMC is breaking down. -*Pair dsmc: num\_of\_collisions > number\_of\_B* +*Pair dsmc: num_of_collisions > number_of_B* Collision model in DSMC is breaking down. *Pair style in data file differs from currently defined pair style* @@ -569,15 +569,15 @@ This will most likely cause errors in kinetic fluctuations. sub-domain before reneighboring is triggered. *Reducing PPPM order b/c stencil extends beyond nearest neighbor processor* - This may lead to a larger grid than desired. See the kspace\_modify overlap + This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order. *Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor* - This may lead to a larger grid than desired. See the kspace\_modify overlap + This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order. *Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor* - This may lead to a larger grid than desired. See the kspace\_modify overlap + This may lead to a larger grid than desired. See the kspace_modify overlap command to prevent changing of the PPPM order. *Replacing a fix, but new group != old group* @@ -590,19 +590,19 @@ This will most likely cause errors in kinetic fluctuations. dimension to be replicated; this may cause unwanted behavior. *Resetting reneighboring criteria during PRD* - A PRD simulation requires that neigh\_modify settings be delay = 0, + A PRD simulation requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the PRD simulation. *Resetting reneighboring criteria during TAD* - A TAD simulation requires that neigh\_modify settings be delay = 0, + A TAD simulation requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the PRD simulation. *Resetting reneighboring criteria during minimization* - Minimization requires that neigh\_modify settings be delay = 0, every = + Minimization requires that neigh_modify settings be delay = 0, every = 1, check = yes. Since these settings were not in place, LAMMPS changed them and will restore them to their original values after the minimization. @@ -706,7 +706,7 @@ This will most likely cause errors in kinetic fluctuations. which does operate on group all, so this may be inconsistent. *Temperature for thermo pressure is not for group all* - User-assigned temperature to thermo via the thermo\_modify command does + User-assigned temperature to thermo via the thermo_modify command does not compute temperature for all atoms. Since thermo computes a global pressure, the kinetic energy contribution from the temperature is assumed to also be for all atoms. Thus the pressure printed by thermo @@ -738,12 +738,12 @@ This will most likely cause errors in kinetic fluctuations. LAMMPS simulation may be inefficient as a result. *Use special bonds = 0,1,1 with bond style fene* - Most FENE models need this setting for the special\_bonds command. + Most FENE models need this setting for the special_bonds command. *Use special bonds = 0,1,1 with bond style fene/expand* - Most FENE models need this setting for the special\_bonds command. + Most FENE models need this setting for the special_bonds command. -*Using a many-body potential with bonds/angles/dihedrals and special\_bond exclusions* +*Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions* This is likely not what you want to do. The exclusion settings will eliminate neighbors in the neighbor list, which the many-body potential needs to calculated its terms correctly. @@ -772,13 +772,13 @@ This will most likely cause errors in kinetic fluctuations. *Using largest cutoff for lj/long/coul/long* Self-explanatory. -*Using largest cutoff for pair\_style lj/long/tip4p/long* +*Using largest cutoff for pair_style lj/long/tip4p/long* Self-explanatory. *Using package gpu without any pair style defined* Self-explanatory. -*Using pair potential shift with pair\_modify compute no* +*Using pair potential shift with pair_modify compute no* The shift effects will thus not be computed. *Using pair tail corrections with nonperiodic system* @@ -786,8 +786,8 @@ This will most likely cause errors in kinetic fluctuations. computed by integrating the density of a periodic system out to infinity. -*Using pair tail corrections with pair\_modify compute no* +*Using pair tail corrections with pair_modify compute no* The tail corrections will thus not be computed. -*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c* +*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c* Self-explanatory. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index b45be6bcf0..b94db208d9 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -132,7 +132,7 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | reax | RDX and TATB models using the ReaxFF | +-------------+------------------------------------------------------------------+ -| rerun | use of rerun and read\_dump commands | +| rerun | use of rerun and read_dump commands | +-------------+------------------------------------------------------------------+ | rigid | rigid bodies modeled as independent or coupled | +-------------+------------------------------------------------------------------+ @@ -155,7 +155,7 @@ Lowercase directories Here is how you can run and visualize one of the sample problems: -.. parsed-literal:: +.. code-block:: bash cd indent cp ../../src/lmp_linux . # copy LAMMPS executable to this dir @@ -170,16 +170,16 @@ web site. If you uncomment the :doc:`dump image ` line(s) in the input script a series of JPG images will be produced by the run (assuming you built LAMMPS with JPG support; see the -:doc:`Build\_settings ` doc page for details). These can +:doc:`Build_settings ` doc page for details). These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the :doc:`dump image ` doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. -.. parsed-literal:: +.. code-block:: bash - % convert -loop 1 \*.jpg foo.gif + % convert -loop 1 *.jpg foo.gif ---------- @@ -195,7 +195,7 @@ Uppercase directories +------------+--------------------------------------------------------------------------------------------------+ | ELASTIC | compute elastic constants at zero temperature | +------------+--------------------------------------------------------------------------------------------------+ -| ELASTIC\_T | compute elastic constants at finite temperature | +| ELASTIC_T | compute elastic constants at finite temperature | +------------+--------------------------------------------------------------------------------------------------+ | HEAT | compute thermal conductivity for LJ and water via fix ehex | +------------+--------------------------------------------------------------------------------------------------+ @@ -219,7 +219,7 @@ The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further -instructions. See the :doc:`Packages\_details ` doc +instructions. See the :doc:`Packages_details ` doc page for more info on specific USER packages. .. _openkim: https://openkim.org diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index a516315baf..1b4be32106 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -8,7 +8,7 @@ command. This is the default. If using the :doc:`create box ` command to define a simulation box, set the z dimensions narrow, but finite, so that the -create\_atoms command will tile the 3d simulation box with a single z +create_atoms command will tile the 3d simulation box with a single z plane of atoms - e.g. .. code-block:: LAMMPS @@ -17,7 +17,7 @@ plane of atoms - e.g. If using the :doc:`read data ` command to read in a file of atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create\_box command settings just described. For each +similar to the create_box command settings just described. For each atom in the file, assign a z coordinate so it falls inside the z-boundaries of the box - e.g. 0.0. diff --git a/doc/src/Howto_bash.rst b/doc/src/Howto_bash.rst index 2a182f5040..02322e5e1c 100644 --- a/doc/src/Howto_bash.rst +++ b/doc/src/Howto_bash.rst @@ -147,7 +147,7 @@ Compiling serial version cd src/ make -j 4 serial -This will create an executable called lmp\_serial in the src/ directory +This will create an executable called lmp_serial in the src/ directory Compiling MPI version """"""""""""""""""""" @@ -157,7 +157,7 @@ Compiling MPI version cd src/ make -j 4 mpi -This will create an executable called lmp\_mpi in the src/ directory +This will create an executable called lmp_mpi in the src/ directory ---------- @@ -192,8 +192,8 @@ examples/melt folder cd ../examples/melt -The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mpi -version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either +The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi +version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either version as follows: .. code-block:: bash @@ -206,7 +206,7 @@ or mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt -Note the use of our variable $LAMMPS\_DIR, which expands into the full path of +Note the use of our variable $LAMMPS_DIR, which expands into the full path of the LAMMPS src folder we saved earlier. Adding your executable directory to your PATH @@ -241,7 +241,7 @@ and add this line **Example:** -For an executable lmp\_serial with a full path +For an executable lmp_serial with a full path .. code-block:: bash diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 3cb65aab91..efb5a38a59 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -112,7 +112,7 @@ vanilla, prototypical example of a body particle, although as mentioned above, the :doc:`fix rigid ` command already duplicates its functionality. -The atom\_style body command for this body style takes two additional +The atom_style body command for this body style takes two additional arguments: .. parsed-literal:: @@ -188,14 +188,14 @@ The *bflag2* argument is ignored. The *rounded/polygon* body style represents body particles as a 2d polygon with a variable number of N vertices. This style can only be used for 2d models; see the :doc:`boundary ` command. See the -"pair\_style body/rounded/polygon" doc page for a diagram of two +"pair_style body/rounded/polygon" doc page for a diagram of two squares with rounded circles at the vertices. Special cases for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified. One use of this body style is for 2d discrete element models, as described in :ref:`Fraige `. -Similar to body style *nparticle*\ , the atom\_style body command for +Similar to body style *nparticle*\ , the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: @@ -301,7 +301,7 @@ body particles with a wall. The *rounded/polyhedron* body style represents body particles as a 3d polyhedron with a variable number of N vertices, E edges and F faces. This style can only be used for 3d models; see the -:doc:`boundary ` command. See the "pair\_style +:doc:`boundary ` command. See the "pair_style body/rounded/polygon" doc page for a diagram of a two 2d squares with rounded circles at the vertices. A 3d cube with rounded spheres at the 8 vertices and 12 rounded edges would be similar. Special cases @@ -311,7 +311,7 @@ specified. This body style is for 3d discrete element models, as described in :ref:`Wang `. -Similar to body style *rounded/polygon*\ , the atom\_style body command +Similar to body style *rounded/polygon*\ , the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst index 5f4e863797..c22e1ca3ab 100644 --- a/doc/src/Howto_client_server.rst +++ b/doc/src/Howto_client_server.rst @@ -93,22 +93,22 @@ client or server code: * examples/message * examples/COUPLE/README -* examples/COUPLE/lammps\_mc -* examples/COUPLE/lammps\_nwchem -* examples/COUPLE/lammps\_vasp +* examples/COUPLE/lammps_mc +* examples/COUPLE/lammps_nwchem +* examples/COUPLE/lammps_vasp The examples/message directory couples a client instance of LAMMPS to a server instance of LAMMPS. -The files in the *lammps\_mc* folder show how to couple LAMMPS as +The files in the *lammps_mc* folder show how to couple LAMMPS as a server to a simple Monte Carlo client code as the driver. -The files in the *lammps\_nwchem* folder show how to couple LAMMPS +The files in the *lammps_nwchem* folder show how to couple LAMMPS as a client code running MD timestepping to NWChem acting as a server providing quantum DFT forces, through a Python wrapper script on NWChem. -The files in the *lammps\_vasp* folder show how to couple LAMMPS as +The files in the *lammps_vasp* folder show how to couple LAMMPS as a client code running MD timestepping to VASP acting as a server providing quantum DFT forces, through a Python wrapper script on VASP. diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst index 5bcf026387..c652d4f599 100644 --- a/doc/src/Howto_couple.rst +++ b/doc/src/Howto_couple.rst @@ -64,9 +64,9 @@ examples/COUPLE/README for more details: library * plugin: simple driver program in C which invokes LAMMPS as a plugin from a shared library. -* lammps\_quest: coupling of LAMMPS and `Quest `_, to run classical +* lammps_quest: coupling of LAMMPS and `Quest `_, to run classical MD with quantum forces calculated by a density functional code -* lammps\_spparks: coupling of LAMMPS and `SPPARKS `_, to couple +* lammps_spparks: coupling of LAMMPS and `SPPARKS `_, to couple a kinetic Monte Carlo model for grain growth using MD to calculate strain induced across grain boundaries @@ -89,7 +89,7 @@ The files src/library.cpp and library.h contain the C-style interface to LAMMPS. See the :doc:`Howto library ` doc page for a description of the interface and how to extend it for your needs. -Note that the lammps\_open() function that creates an instance of +Note that the lammps_open() function that creates an instance of LAMMPS takes an MPI communicator as an argument. This means that instance of LAMMPS will run on the set of processors in the communicator. Thus the calling code can run LAMMPS on all or a subset diff --git a/doc/src/Howto_dispersion.rst b/doc/src/Howto_dispersion.rst index f1c818162b..a173e0cfbd 100644 --- a/doc/src/Howto_dispersion.rst +++ b/doc/src/Howto_dispersion.rst @@ -29,7 +29,7 @@ that provide fast and accurate simulations, there are two approaches, which both have their up- and downsides. The first approach is to set desired real-space an kspace accuracies -via the *kspace\_modify force/disp/real* and *kspace\_modify +via the *kspace_modify force/disp/real* and *kspace_modify force/disp/kspace* commands. Note that the accuracies have to be specified in force units and are thus dependent on the chosen unit settings. For real units, 0.0001 and 0.002 seem to provide reasonable @@ -37,14 +37,14 @@ accurate and efficient computations for the real-space and kspace accuracies. 0.002 and 0.05 work well for most systems using lj units. PPPM parameters will be generated based on the desired accuracies. The upside of this approach is that it usually provides a -good set of parameters and will work for both the *kspace\_modify diff -ad* and *kspace\_modify diff ik* options. The downside of the method +good set of parameters and will work for both the *kspace_modify diff +ad* and *kspace_modify diff ik* options. The downside of the method is that setting the PPPM parameters will take some time during the initialization of the simulation. The second approach is to set the parameters for the pppm/disp -explicitly using the *kspace\_modify mesh/disp*, *kspace\_modify -order/disp*, and *kspace\_modify gewald/disp* commands. This approach +explicitly using the *kspace_modify mesh/disp*, *kspace_modify +order/disp*, and *kspace_modify gewald/disp* commands. This approach requires a more experienced user who understands well the impact of the choice of parameters on the simulation accuracy and performance. This approach provides a fast initialization of the @@ -60,12 +60,12 @@ To avoid inaccurate or inefficient simulations, the pppm/disp stops simulations with an error message if no action is taken to control the PPPM parameters. If the automatic parameter generation is desired and real-space and kspace accuracies are desired to be equal, this error -message can be suppressed using the *kspace\_modify disp/auto yes* +message can be suppressed using the *kspace_modify disp/auto yes* command. A reasonable approach that combines the upsides of both methods is to -make the first run using the *kspace\_modify force/disp/real* and -*kspace\_modify force/disp/kspace* commands, write down the PPPM +make the first run using the *kspace_modify force/disp/real* and +*kspace_modify force/disp/kspace* commands, write down the PPPM parameters from the output, and specify these parameters using the second approach in subsequent runs (which have the same composition, force field, and approximately the same volume). @@ -82,8 +82,8 @@ The second is that the mixing rule of the pair style has an impact on the computation time when using the pppm/disp. Fastest computations are achieved when using the geometric mixing rule. Using the arithmetic mixing rule substantially increases the computational cost. -The computational overhead can be reduced using the *kspace\_modify -mix/disp geom* and *kspace\_modify splittol* commands. The first +The computational overhead can be reduced using the *kspace_modify +mix/disp geom* and *kspace_modify splittol* commands. The first command simply enforces geometric mixing of the dispersion coefficients in kspace computations. This introduces some error in the computations but will also significantly speed-up the @@ -94,7 +94,7 @@ command, but will usually also not provide an equally good increase of efficiency. Finally, pppm/disp can also be used when no mixing rules apply. -This can be achieved using the *kspace\_modify mix/disp none* command. +This can be achieved using the *kspace_modify mix/disp none* command. Note that the code does not check automatically whether any mixing rule is fulfilled. If mixing rules do not apply, the user will have to specify this command explicitly. diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index 6efe731ee1..62659711c4 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -48,7 +48,7 @@ for a Langevin thermostat, or :doc:`fix drude/transform/\* thermostat. The former requires use of the command :doc:`comm_modify vel yes `. The latter requires two separate integration fixes like *nvt* or *npt*\ . The correct temperatures of the reduced degrees of freedom can be calculated using the :doc:`compute temp/drude `. This requires also to use the -command *comm\_modify vel yes*. +command *comm_modify vel yes*. Short-range damping of the induced dipole interactions can be achieved using Thole functions through the :doc:`pair style thole ` in :doc:`pair_style hybrid/overlay ` diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 039897a20b..cbdbc2d250 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -76,14 +76,14 @@ important features: **Preparation of the data file** The data file is similar to a standard LAMMPS data file for -*atom\_style full*. The DPs and the *harmonic bonds* connecting them +*atom_style full*. The DPs and the *harmonic bonds* connecting them to their DC should appear in the data file as normal atoms and bonds. You can use the *polarizer* tool (Python script distributed with the USER-DRUDE package) to convert a non-polarizable data file (here *data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ ) -.. parsed-literal:: +.. code-block:: bash polarizer -q -f phenol.dff data.102494.lmp data-p.lmp @@ -159,9 +159,9 @@ Let us assume we want to run a simple NVT simulation at 300 K. Note that Drude oscillators need to be thermalized at a low temperature in order to approximate a self-consistent field (SCF), therefore it is not possible to simulate an NVE ensemble with this package. Since dipoles -are approximated by a charged DC-DP pair, the *pair\_style* must +are approximated by a charged DC-DP pair, the *pair_style* must include Coulomb interactions, for instance *lj/cut/coul/long* with -*kspace\_style pppm*. For example, with a cutoff of 10. and a precision +*kspace_style pppm*. For example, with a cutoff of 10. and a precision 1.e-4: .. code-block:: LAMMPS @@ -169,9 +169,9 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with pair_style lj/cut/coul/long 10.0 kspace_style pppm 1.0e-4 -As compared to the non-polarizable input file, *pair\_coeff* lines need +As compared to the non-polarizable input file, *pair_coeff* lines need to be added for the DPs. Since the DPs have no Lennard-Jones -interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line +interactions, their :math:`\epsilon` is 0. so the only *pair_coeff* line that needs to be added is .. code-block:: LAMMPS @@ -222,7 +222,7 @@ modification of forces but no position/velocity updates), the fix fix NVE all nve Finally, do not forget to update the atom type elements if you use -them in a *dump\_modify ... element ...* command, by adding the element +them in a *dump_modify ... element ...* command, by adding the element type of the DPs. Here for instance .. code-block:: LAMMPS @@ -232,19 +232,19 @@ type of the DPs. Here for instance The input file should now be ready for use! -You will notice that the global temperature *thermo\_temp* computed by +You will notice that the global temperature *thermo_temp* computed by LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as standard atoms in his default compute. If you want to output the temperatures of the DC-DP pair centers of mass and of the DPs relative -to their DCs, you should use the :doc:`compute temp\_drude ` +to their DCs, you should use the :doc:`compute temp_drude ` .. code-block:: LAMMPS compute TDRUDE all temp/drude And then output the correct temperatures of the Drude oscillators -using *thermo\_style custom* with respectively *c\_TDRUDE[1]* and -*c\_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average. +using *thermo_style custom* with respectively *c_TDRUDE[1]* and +*c_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average. .. code-block:: LAMMPS @@ -263,8 +263,8 @@ between nearby dipoles on the same molecule may be exaggerated. Often, special bond relations prevent bonded neighboring atoms to see the charge of each other's DP, so that the problem does not always appear. It is possible to use screened dipole-dipole interactions by using the -:doc:`*pair\_style thole* `. This is implemented as a -correction to the Coulomb pair\_styles, which dampens at short distance +:doc:`*pair_style thole* `. This is implemented as a +correction to the Coulomb pair_styles, which dampens at short distance the interactions between the charges representing the induced dipoles. It is to be used as *hybrid/overlay* with any standard *coul* pair style. In our example, we would use @@ -273,15 +273,15 @@ style. In our example, we would use pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0 -This tells LAMMPS that we are using two pair\_styles. The first one is +This tells LAMMPS that we are using two pair_styles. The first one is as above (\ *lj/cut/coul/long 10.0*\ ). The second one is a *thole* -pair\_style with default screening factor 2.6 (:ref:`Noskov `) and +pair_style with default screening factor 2.6 (:ref:`Noskov `) and cutoff 10.0. Since *hybrid/overlay* does not support mixing rules, the interaction coefficients of all the pairs of atom types with i < j should be explicitly defined. The output of the *polarizer* script can be used -to complete the *pair\_coeff* section of the input file. In our +to complete the *pair_coeff* section of the input file. In our example, this will look like: .. code-block:: LAMMPS @@ -324,17 +324,17 @@ For the *thole* pair style the coefficients are #. the atom polarizability in units of cubic length #. the screening factor of the Thole function (optional, default value - specified by the pair\_style command) -#. the cutoff (optional, default value defined by the pair\_style command) + specified by the pair_style command) +#. the cutoff (optional, default value defined by the pair_style command) The special neighbors have charge-charge and charge-dipole -interactions screened by the *coul* factors of the *special\_bonds* +interactions screened by the *coul* factors of the *special_bonds* command (0.0, 0.0, and 0.5 in the example above). Without using the -pair\_style *thole*\ , dipole-dipole interactions are screened by the -same factor. By using the pair\_style *thole*\ , dipole-dipole +pair_style *thole*\ , dipole-dipole interactions are screened by the +same factor. By using the pair_style *thole*\ , dipole-dipole interactions are screened by Thole's function, whatever their special relationship (except within each DC-DP pair of course). Consider for -example 1-2 neighbors: using the pair\_style *thole*\ , their dipoles +example 1-2 neighbors: using the pair_style *thole*\ , their dipoles will see each other (despite the *coul* factor being 0.) and the interactions between these dipoles will be damped by Thole's function. @@ -375,7 +375,7 @@ For our phenol example, the groups would be defined as group DRUDES type 6 7 8 # DPs Note that with the fixes *drude/transform*\ , it is not required to -specify *comm\_modify vel yes* because the fixes do it anyway (several +specify *comm_modify vel yes* because the fixes do it anyway (several times and for the forces also). To avoid the flying ice cube artifact :ref:`(Lamoureux) `, where the atoms progressively freeze and the center of mass of the whole system drifts faster and faster, the *fix @@ -392,7 +392,7 @@ DPs should be *nvt* (or vice versa). Second, the *fix npt* computes a global pressure and thus a global temperature whatever the fix group. We do want the pressure to correspond to the whole system, but we want the temperature to correspond to the fix group only. We must then use -the *fix\_modify* command for this. In the end, the block of +the *fix_modify* command for this. In the end, the block of instructions for thermostatting and barostatting will look like .. code-block:: LAMMPS diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst index 1d633e6e98..4870942458 100644 --- a/doc/src/Howto_elastic.rst +++ b/doc/src/Howto_elastic.rst @@ -4,14 +4,14 @@ Calculate elastic constants Elastic constants characterize the stiffness of a material. The formal definition is provided by the linear relation that holds between the stress and strain tensors in the limit of infinitesimal deformation. -In tensor notation, this is expressed as s\_ij = C\_ijkl \* e\_kl, where -the repeated indices imply summation. s\_ij are the elements of the -symmetric stress tensor. e\_kl are the elements of the symmetric strain -tensor. C\_ijkl are the elements of the fourth rank tensor of elastic +In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where +the repeated indices imply summation. s_ij are the elements of the +symmetric stress tensor. e_kl are the elements of the symmetric strain +tensor. C_ijkl are the elements of the fourth rank tensor of elastic constants. In three dimensions, this tensor has 3\^4=81 elements. Using -Voigt notation, the tensor can be written as a 6x6 matrix, where C\_ij -is now the derivative of s\_i w.r.t. e\_j. Because s\_i is itself a -derivative w.r.t. e\_i, it follows that C\_ij is also symmetric, with at +Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij +is now the derivative of s_i w.r.t. e_j. Because s_i is itself a +derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at most 7\*6/2 = 21 distinct elements. At zero temperature, it is easy to estimate these derivatives by diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index f51d15d865..55db356589 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -287,10 +287,10 @@ After each push, the automated checks are run again. LAMMPS developers may add labels to your pull request to assign it to categories (mostly for bookkeeping purposes), but a few of them are -important: needs\_work, work\_in\_progress, test-for-regression, and +important: needs_work, work_in_progress, test-for-regression, and full-regression-test. The first two indicate, that your pull request -is not considered to be complete. With "needs\_work" the burden is on -exclusively on you; while "work\_in\_progress" can also mean, that a +is not considered to be complete. With "needs_work" the burden is on +exclusively on you; while "work_in_progress" can also mean, that a LAMMPS developer may want to add changes. Please watch the comments to the pull requests. The two "test" labels are used to trigger extended tests before the code is merged. This is sometimes done by @@ -458,7 +458,7 @@ should be submitted, there is now also an "unstable" and a "stable" branch; these have the same content as "master", but are only updated after a patch release or stable release was made. Furthermore, the naming of the patches now follow the pattern -"patch\_" to simplify comparisons between releases. +"patch_" to simplify comparisons between releases. Finally, all patches and submissions are subject to automatic testing and code checks to make sure they at the very least compile. diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index 25fc9869ea..c696d44249 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -22,7 +22,7 @@ Use one of these 3 pair potentials, which compute forces and torques between interacting pairs of particles: * :doc:`pair_style ` gran/history -* :doc:`pair_style ` gran/no\_history +* :doc:`pair_style ` gran/no_history * :doc:`pair_style ` gran/hertzian These commands implement fix options specific to granular systems: diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst index 6b7fa6b54a..08697ecc84 100644 --- a/doc/src/Howto_kappa.rst +++ b/doc/src/Howto_kappa.rst @@ -56,7 +56,7 @@ two preceding non-equilibrium methods, where energy flows continuously between hot and cold regions of the simulation box. The :doc:`compute heat/flux ` command can calculate -the needed heat flux and describes how to implement the Green\_Kubo +the needed heat flux and describes how to implement the Green_Kubo formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate ` command to calculate the needed auto-correlation. See the doc page for the :doc:`compute heat/flux ` command for an example input script that calculates the thermal conductivity of solid Ar via the GK diff --git a/doc/src/Howto_library.rst b/doc/src/Howto_library.rst index 55216f9ef7..774d9838c1 100644 --- a/doc/src/Howto_library.rst +++ b/doc/src/Howto_library.rst @@ -12,7 +12,7 @@ functions therein have a C-style argument list, but contain C++ code you could write yourself in a C++ application that was invoking LAMMPS directly. The C++ code in the functions illustrates how to invoke internal LAMMPS operations. Note that LAMMPS classes are defined -within a LAMMPS namespace (LAMMPS\_NS) if you use them from another C++ +within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ application. The examples/COUPLE and python/examples directories have example C++ @@ -34,7 +34,7 @@ interface LAMMPS to Fortran libraries, or the code uses static variables Another major issue to deal with is to correctly handle MPI. Creating a LAMMPS instance requires passing an MPI communicator, or it assumes -the MPI\_COMM\_WORLD communicator, which spans all MPI processor ranks. +the MPI_COMM_WORLD communicator, which spans all MPI processor ranks. When creating multiple LAMMPS object instances from different threads, this communicator has to be different for each thread or else collisions can happen, or it has to be guaranteed, that only one thread at a time @@ -70,11 +70,11 @@ details. void lammps_commands_string(void *, char *) void lammps_free(void *) -The lammps\_open() function is used to initialize LAMMPS, passing in a +The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were :doc:`command-line arguments ` when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is created, and which is -used in subsequent library calls. The lammps\_open() function can be +used in subsequent library calls. The lammps_open() function can be called multiple times, to create multiple instances of LAMMPS. LAMMPS will run on the set of processors in the communicator. This @@ -86,14 +86,14 @@ half to the other code and run both codes simultaneously before syncing them up periodically. Or it might instantiate multiple instances of LAMMPS to perform different calculations. -The lammps\_open\_no\_mpi() function is similar except that no MPI -communicator is passed from the caller. Instead, MPI\_COMM\_WORLD is +The lammps_open_no_mpi() function is similar except that no MPI +communicator is passed from the caller. Instead, MPI_COMM_WORLD is used to instantiate LAMMPS, and MPI is initialized if necessary. -The lammps\_close() function is used to shut down an instance of LAMMPS +The lammps_close() function is used to shut down an instance of LAMMPS and free all its memory. -The lammps\_version() function can be used to determined the specific +The lammps_version() function can be used to determined the specific version of the underlying LAMMPS code. This is particularly useful when loading LAMMPS as a shared library via dlopen(). The code using the library interface can than use this information to adapt to @@ -101,8 +101,8 @@ changes to the LAMMPS command syntax between versions. The returned LAMMPS version code is an integer (e.g. 2 Sep 2015 results in 20150902) that grows with every new LAMMPS version. -The lammps\_file(), lammps\_command(), lammps\_commands\_list(), and -lammps\_commands\_string() functions are used to pass one or more +The lammps_file(), lammps_command(), lammps_commands_list(), and +lammps_commands_string() functions are used to pass one or more commands to LAMMPS to execute, the same as if they were coming from an input script. @@ -113,19 +113,19 @@ can interleave the command function calls with operations it performs, calls to extract information from or set information within LAMMPS, or calls to another code's library. -The lammps\_file() function passes the filename of an input script. -The lammps\_command() function passes a single command as a string. -The lammps\_commands\_list() function passes multiple commands in a -char\*\* list. In both lammps\_command() and lammps\_commands\_list(), +The lammps_file() function passes the filename of an input script. +The lammps_command() function passes a single command as a string. +The lammps_commands_list() function passes multiple commands in a +char\*\* list. In both lammps_command() and lammps_commands_list(), individual commands may or may not have a trailing newline. The -lammps\_commands\_string() function passes multiple commands +lammps_commands_string() function passes multiple commands concatenated into one long string, separated by newline characters. -In both lammps\_commands\_list() and lammps\_commands\_string(), a single +In both lammps_commands_list() and lammps_commands_string(), a single command can be spread across multiple lines, if the last printable character of all but the last line is "&", the same as if the lines appeared in an input script. -The lammps\_free() function is a clean-up function to free memory that +The lammps_free() function is a clean-up function to free memory that the library allocated previously via other function calls. See comments in src/library.cpp file for which other functions need this clean-up. @@ -146,15 +146,15 @@ which quantities can be queried by name: void *lammps_extract_fix(void *, char *, int, int, int, int) void *lammps_extract_variable(void *, char *, char *) -The extract\_setting() function returns info on the size +The extract_setting() function returns info on the size of data types (e.g. 32-bit or 64-bit atom IDs) used by the LAMMPS executable (a compile-time choice). The other extract functions return a pointer to various global or per-atom quantities stored in LAMMPS or to values calculated by a compute, fix, or variable. The pointer returned by the -extract\_global() function can be used as a permanent reference to a -value which may change. For the extract\_atom() method, see the +extract_global() function can be used as a permanent reference to a +value which may change. For the extract_atom() method, see the extract() method in the src/atom.cpp file for a list of valid per-atom properties. New names could easily be added if the property you want is not listed. For the other extract functions, the underlying @@ -169,18 +169,18 @@ function to assure a current pointer or returned value(s). int lammps_set_variable(void *, char *, char *) void lammps_reset_box(void *, double *, double *, double, double, double) -The lammps\_get\_thermo() function returns the current value of a thermo +The lammps_get_thermo() function returns the current value of a thermo keyword as a double precision value. -The lammps\_get\_natoms() function returns the total number of atoms in +The lammps_get_natoms() function returns the total number of atoms in the system and can be used by the caller to allocate memory for the -lammps\_gather\_atoms() and lammps\_scatter\_atoms() functions. +lammps_gather_atoms() and lammps_scatter_atoms() functions. -The lammps\_set\_variable() function can set an existing string-style +The lammps_set_variable() function can set an existing string-style variable to a new string value, so that subsequent LAMMPS commands can access the variable. -The lammps\_reset\_box() function resets the size and shape of the +The lammps_reset_box() function resets the size and shape of the simulation box, e.g. as part of restoring a previously extracted and saved state of a simulation. @@ -202,17 +202,17 @@ owned by different processors. .. warning:: These functions are not compatible with the - -DLAMMPS\_BIGBIG setting when compiling LAMMPS. Dummy functions + -DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions that result in an error message and abort will be substituted instead of resulting in random crashes and memory corruption. -The lammps\_gather\_atoms() function does this for all N atoms in the +The lammps_gather_atoms() function does this for all N atoms in the system, ordered by atom ID, from 1 to N. The -lammps\_gather\_atoms\_concat() function does it for all N atoms, but +lammps_gather_atoms_concat() function does it for all N atoms, but simply concatenates the subset of atoms owned by each processor. The resulting vector is not ordered by atom ID. Atom IDs can be requested by the same function if the caller needs to know the ordering. The -lammps\_gather\_subset() function allows the caller to request values +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 @@ -220,10 +220,10 @@ 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. -The lammps\_scatter\_atoms() function takes a list of values for all N +The lammps_scatter_atoms() function takes a list of values for all N atoms in the system, ordered by atom ID, from 1 to N, and assigns those values to each atom in the system. The -lammps\_scatter\_atoms\_subset() function takes a subset of IDs as an +lammps_scatter_atoms_subset() function takes a subset of IDs as an argument and only scatters those values to the owning atoms. .. code-block:: c @@ -231,12 +231,12 @@ argument and only scatters those values to the owning atoms. void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, imageint *, int) -The lammps\_create\_atoms() function takes a list of N atoms as input +The lammps_create_atoms() function takes a list of N atoms as input with atom types and coords (required), an optionally atom IDs and velocities and image flags. It uses the coords of each atom to assign it as a new atom to the processor that owns it. This function is useful to add atoms to a simulation or (in tandem with -lammps\_reset\_box()) to restore a previously extracted and saved state +lammps_reset_box()) to restore a previously extracted and saved state of a simulation. Additional properties for the new atoms can then be -assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom() +assigned via the lammps_scatter_atoms() or lammps_extract_atom() functions. diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index e7d31d79d9..41e1fb6a4c 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -19,17 +19,17 @@ to the relevant fixes. +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | cylinder | R | x\^2 + y\^2 - R\^2 = 0 | Cylinder along z-axis, axis going through (0,0,0) | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ -| cylinder\_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 | +| cylinder_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | dumbbell | a A B c | -( x\^2 + y\^2 ) + (a\^2 - z\^2/c\^2) \* ( 1 + (A\*sin(B\*z\^2))\^4) = 0 | A dumbbell | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | ellipsoid | a b c | (x/a)\^2 + (y/b)\^2 + (z/c)\^2 = 0 | An ellipsoid | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ -| gaussian\_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. | +| gaussian_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | plane | a b c x0 y0 z0 | a\*(x-x0) + b\*(y-y0) + c\*(z-z0) = 0 | A plane with normal (a,b,c) going through point (x0,y0,z0) | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ -| plane\_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. | +| plane_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | sphere | R | x\^2 + y\^2 + z\^2 - R\^2 = 0 | A sphere of radius R | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ @@ -37,7 +37,7 @@ to the relevant fixes. +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | spine | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendritic spine | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ -| spine\_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine | +| spine_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ | thylakoid | wB LB lB | Various, see :ref:`(Paquay) ` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 64a9e01971..04e73c2272 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -68,11 +68,11 @@ notation, where ID in this case is the ID of a compute. The leading "c\_" would be replaced by "f\_" for a fix, or "v\_" for a variable: +-------------+--------------------------------------------+ -| c\_ID | entire scalar, vector, or array | +| c_ID | entire scalar, vector, or array | +-------------+--------------------------------------------+ -| c\_ID[I] | one element of vector, one column of array | +| c_ID[I] | one element of vector, one column of array | +-------------+--------------------------------------------+ -| c\_ID[I][J] | one element of array | +| c_ID[I][J] | one element of array | +-------------+--------------------------------------------+ In other words, using one bracket reduces the dimension of the data @@ -92,7 +92,7 @@ The frequency and format of thermodynamic output is set by the :doc:`thermo_style ` command also specifies what values are calculated and written out. Pre-defined keywords can be specified (e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c\_ID, f\_ID, v\_name), where a :doc:`compute ` +also be specified (c_ID, f_ID, v_name), where a :doc:`compute ` or :doc:`fix ` or :doc:`variable ` provides the value to be output. In each case, the compute, fix, or variable must generate global values for input to the :doc:`thermo_style custom ` @@ -121,7 +121,7 @@ pre-defined formats (dump atom, dump xtc, etc). There is also a :doc:`dump custom ` format where the user specifies what values are output with each atom. Pre-defined atom attributes can be specified (id, x, fx, etc). Three additional kinds -of keywords can also be specified (c\_ID, f\_ID, v\_name), where a +of keywords can also be specified (c_ID, f_ID, v_name), where a :doc:`compute ` or :doc:`fix ` or :doc:`variable ` provides the values to be output. In each case, the compute, fix, or variable must generate per-atom values for input to the :doc:`dump custom ` command. @@ -129,7 +129,7 @@ variable must generate per-atom values for input to the :doc:`dump custom There is also a :doc:`dump local ` format where the user specifies what local values to output. A pre-defined index keyword can be specified to enumerate the local values. Two additional kinds of -keywords can also be specified (c\_ID, f\_ID), where a +keywords can also be specified (c_ID, f_ID), where a :doc:`compute ` or :doc:`fix ` or :doc:`variable ` provides the values to be output. In each case, the compute or fix must generate local values for input to the :doc:`dump local ` diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst index bc7a7502ae..6323ba4158 100644 --- a/doc/src/Howto_restart.rst +++ b/doc/src/Howto_restart.rst @@ -46,8 +46,8 @@ last 50 timesteps: run 50 Note that the following commands do not need to be repeated because -their settings are included in the restart file: *units, atom\_style, -special\_bonds, pair\_style, bond\_style*. However these commands do +their settings are included in the restart file: *units, atom_style, +special_bonds, pair_style, bond_style*. However these commands do need to be used, since their settings are not in the restart file: *neighbor, fix, timestep*\ . @@ -89,7 +89,7 @@ Then, this script could be used to re-run the last 50 steps: run 50 Note that nearly all the settings specified in the original *in.chain* -script must be repeated, except the *pair\_coeff* and *bond\_coeff* +script must be repeated, except the *pair_coeff* and *bond_coeff* commands since the new data file lists the force field coefficients. Also, the :doc:`reset_timestep ` command is used to tell LAMMPS the current timestep. This value is stored in restart files, diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 886156c6cc..7ca8a1b060 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -115,7 +115,7 @@ such interactions. These are the various :doc:`pair styles ` that g * :doc:`pair_style gran/history ` * :doc:`pair_style gran/hertzian ` -* :doc:`pair_style gran/no\_history ` +* :doc:`pair_style gran/no_history ` * :doc:`pair_style dipole/cut ` * :doc:`pair_style gayberne ` * :doc:`pair_style resquared ` diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index ffe71e36f6..632d0364d5 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -221,7 +221,7 @@ calculated from the 9 triclinic box parameters zhi_bound = zhi These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo\_bound - +back into the triclinic box parameters, e.g. xlo = xlo_bound - MIN(0.0,xy,xz,xy+xz). One use of triclinic simulation boxes is to model solid-state crystals diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 8185d65e7c..2f6e8096dc 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -16,7 +16,7 @@ commands explained below to communicate with the git servers on GitHub. For people still using subversion (svn), GitHub also provides `limited support for subversion clients `_. -.. warning:: +.. note:: As of October 2016, the official home of public LAMMPS development is on GitHub. The previously advertised LAMMPS git repositories on diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index 0343ccf4f6..ec4f3fcc8e 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -38,7 +38,7 @@ To install LAMMPS do the following once: $ sudo apt-get install lammps-daily -This downloads an executable named "lmp\_daily" to your box, which +This downloads an executable named "lmp_daily" to your box, which can then be used in the usual way to run input scripts: .. code-block:: bash @@ -103,10 +103,10 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel, lammps-openmpi-devel), the header for compiling programs using the C library interface (lammps-headers), and the LAMMPS python module for Python 3. All packages can be installed at the same -time and the name of the LAMMPS executable is *lmp* and *lmp\_openmpi* -or *lmp\_mpich* respectively. By default, *lmp* will refer to the +time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi* +or *lmp_mpich* respectively. By default, *lmp* will refer to the serial executable, unless one of the MPI environment modules is loaded -("module load mpi/mpich-x86\_64" or "module load mpi/openmpi-x86\_64"). +("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64"). Then the corresponding parallel LAMMPS executable can be used. The same mechanism applies when loading the LAMMPS python module. diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index f1cee0dac5..41b53c0595 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -14,7 +14,7 @@ the following commands: % brew install lammps -This will install the executables "lammps\_serial" and "lammps\_mpi", as well as +This will install the executables "lammps_serial" and "lammps_mpi", as well as the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. Once LAMMPS is installed, you can test the installation with the diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index a3df478311..d80fc14f76 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -26,7 +26,7 @@ command: .. code-block:: bash - $ tar -xzvf lammps\*.tar.gz + $ tar -xzvf lammps*.tar.gz This will create a LAMMPS directory with the version date in its name, e.g. lammps-23Jun18. @@ -40,7 +40,7 @@ a lammps-master dir: .. code-block:: bash - $ unzip lammps\*.zip + $ unzip lammps*.zip This version is the most up-to-date LAMMPS development version. It will have the date of the most recent patch release (see the file diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 32375264db..548f67e484 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -4,7 +4,9 @@ Download an executable for Windows Pre-compiled Windows installers which install LAMMPS executables on a Windows system can be downloaded from this site: -`http://packages.lammps.org/windows.html `_ +.. parsed-literal:: + + `http://packages.lammps.org/windows.html `_ Note that each installer package has a date in its name, which corresponds to the LAMMPS version of the same date. Installers for @@ -26,7 +28,7 @@ When you download the installer package, you run it on your Windows machine. It will then prompt you with a dialog, where you can choose the installation directory, unpack and copy several executables, potential files, documentation pdfs, selected example files, etc. It -will then update a few system settings (e.g. PATH, LAMMPS\_POTENTIALS) +will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS) and add an entry into the Start Menu (with references to the documentation, LAMMPS homepage and more). From that menu, there is also a link to an uninstaller that removes the files and undoes the diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst index dfb133a3e4..5d5b749678 100644 --- a/doc/src/Manual_build.rst +++ b/doc/src/Manual_build.rst @@ -5,7 +5,7 @@ Depending on how you obtained LAMMPS, the doc directory has up to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files plus 2 e-book format files: -.. parsed-literal:: +.. code-block:: bash src # content files for LAMMPS documentation html # HTML version of the LAMMPS manual (see html/Manual.html) @@ -28,8 +28,8 @@ and PDF files are not included. Instead you need to create them, in one of two ways: a. You can "fetch" the current HTML and PDF files from the LAMMPS web - site. Just type "make fetch". This should download a html\_www - directory and Manual\_www.pdf/Developer\_www.pdf files. Note that if + site. Just type "make fetch". This should download a html_www + directory and Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS features have been added more recently than the date of your LAMMPS version, the fetched documentation will include those changes (but your source code will not, unless you update your local diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst index 14bcb08ee2..f863da3157 100644 --- a/doc/src/Modify_atom.rst +++ b/doc/src/Modify_atom.rst @@ -8,78 +8,78 @@ style can be created if one of the existing atom styles does not define all the attributes you need to store and communicate with atoms. -Atom\_vec\_atomic.cpp is a simple example of an atom style. +Atom_vec_atomic.cpp is a simple example of an atom style. Here is a brief description of methods you define in your new derived -class. See atom\_vec.h for details. +class. See atom_vec.h for details. +-------------------------+--------------------------------------------------------------------------------+ | init | one time setup (optional) | +-------------------------+--------------------------------------------------------------------------------+ | grow | re-allocate atom arrays to longer lengths (required) | +-------------------------+--------------------------------------------------------------------------------+ -| grow\_reset | make array pointers in Atom and AtomVec classes consistent (required) | +| grow_reset | make array pointers in Atom and AtomVec classes consistent (required) | +-------------------------+--------------------------------------------------------------------------------+ | copy | copy info for one atom to another atom's array locations (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_comm | store an atom's info in a buffer communicated every timestep (required) | +| pack_comm | store an atom's info in a buffer communicated every timestep (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_comm\_vel | add velocity info to communication buffer (required) | +| pack_comm_vel | add velocity info to communication buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_comm\_hybrid | store extra info unique to this atom style (optional) | +| pack_comm_hybrid | store extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_comm | retrieve an atom's info from the buffer (required) | +| unpack_comm | retrieve an atom's info from the buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_comm\_vel | also retrieve velocity info (required) | +| unpack_comm_vel | also retrieve velocity info (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_comm\_hybrid | retrieve extra info unique to this atom style (optional) | +| unpack_comm_hybrid | retrieve extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_reverse | store an atom's info in a buffer communicating partial forces (required) | +| pack_reverse | store an atom's info in a buffer communicating partial forces (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_reverse\_hybrid | store extra info unique to this atom style (optional) | +| pack_reverse_hybrid | store extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_reverse | retrieve an atom's info from the buffer (required) | +| unpack_reverse | retrieve an atom's info from the buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_reverse\_hybrid | retrieve extra info unique to this atom style (optional) | +| unpack_reverse_hybrid | retrieve extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_border | store an atom's info in a buffer communicated on neighbor re-builds (required) | +| pack_border | store an atom's info in a buffer communicated on neighbor re-builds (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_border\_vel | add velocity info to buffer (required) | +| pack_border_vel | add velocity info to buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_border\_hybrid | store extra info unique to this atom style (optional) | +| pack_border_hybrid | store extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_border | retrieve an atom's info from the buffer (required) | +| unpack_border | retrieve an atom's info from the buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_border\_vel | also retrieve velocity info (required) | +| unpack_border_vel | also retrieve velocity info (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_border\_hybrid | retrieve extra info unique to this atom style (optional) | +| unpack_border_hybrid | retrieve extra info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_exchange | store all an atom's info to migrate to another processor (required) | +| pack_exchange | store all an atom's info to migrate to another processor (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_exchange | retrieve an atom's info from the buffer (required) | +| unpack_exchange | retrieve an atom's info from the buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| size\_restart | number of restart quantities associated with proc's atoms (required) | +| size_restart | number of restart quantities associated with proc's atoms (required) | +-------------------------+--------------------------------------------------------------------------------+ -| pack\_restart | pack atom quantities into a buffer (required) | +| pack_restart | pack atom quantities into a buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| unpack\_restart | unpack atom quantities from a buffer (required) | +| unpack_restart | unpack atom quantities from a buffer (required) | +-------------------------+--------------------------------------------------------------------------------+ -| create\_atom | create an individual atom of this style (required) | +| create_atom | create an individual atom of this style (required) | +-------------------------+--------------------------------------------------------------------------------+ -| data\_atom | parse an atom line from the data file (required) | +| data_atom | parse an atom line from the data file (required) | +-------------------------+--------------------------------------------------------------------------------+ -| data\_atom\_hybrid | parse additional atom info unique to this atom style (optional) | +| data_atom_hybrid | parse additional atom info unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| data\_vel | parse one line of velocity information from data file (optional) | +| data_vel | parse one line of velocity information from data file (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| data\_vel\_hybrid | parse additional velocity data unique to this atom style (optional) | +| data_vel_hybrid | parse additional velocity data unique to this atom style (optional) | +-------------------------+--------------------------------------------------------------------------------+ -| memory\_usage | tally memory allocated by atom arrays (required) | +| memory_usage | tally memory allocated by atom arrays (required) | +-------------------------+--------------------------------------------------------------------------------+ The constructor of the derived class sets values for several variables that you must set when defining a new atom style, which are documented -in atom\_vec.h. New atom arrays are defined in atom.cpp. Search for +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for the word "customize" and you will find locations you will need to modify. @@ -95,12 +95,12 @@ modify. New :doc:`pair styles `, :doc:`fixes `, or :doc:`computes ` can be added to LAMMPS, as discussed below. The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find\_custom() method that is +fix property/atom. The Atom class has a find_custom() method that is useful in this context: -.. parsed-literal:: +.. code-block:: c++ - int index = atom->find_custom(char \*name, int &flag); + int index = atom->find_custom(char *name, int &flag); The "name" of a custom attribute, as specified in the :doc:`fix property/atom ` command, is checked to verify that it exists and its index is returned. The method also sets flag = @@ -108,10 +108,10 @@ that it exists and its index is returned. The method also sets flag = The vector of values associated with the attribute can then be accessed using the returned index as -.. parsed-literal:: +.. code-block:: c++ - int \*ivector = atom->ivector[index]; - double \*dvector = atom->dvector[index]; + int *ivector = atom->ivector[index]; + double *dvector = atom->dvector[index]; Ivector or dvector are vectors of length Nlocal = # of owned atoms, which store the attributes of individual atoms. diff --git a/doc/src/Modify_body.rst b/doc/src/Modify_body.rst index e469b8520f..b923416bdc 100644 --- a/doc/src/Modify_body.rst +++ b/doc/src/Modify_body.rst @@ -10,14 +10,14 @@ See the :doc:`Howto body ` doc page for an overview of using body particles and the various body styles LAMMPS supports. New styles can be created to add new kinds of body particles to LAMMPS. -Body\_nparticle.cpp is an example of a body particle that is treated as +Body_nparticle.cpp is an example of a body particle that is treated as a rigid body containing N sub-particles. Here is a brief description of methods you define in your new derived class. See body.h for details. +----------------------+-----------------------------------------------------------+ -| data\_body | process a line from the Bodies section of a data file | +| data_body | process a line from the Bodies section of a data file | +----------------------+-----------------------------------------------------------+ | noutrow | number of sub-particles output is generated for | +----------------------+-----------------------------------------------------------+ @@ -25,11 +25,11 @@ class. See body.h for details. +----------------------+-----------------------------------------------------------+ | output | output values for the Mth sub-particle | +----------------------+-----------------------------------------------------------+ -| pack\_comm\_body | body attributes to communicate every timestep | +| pack_comm_body | body attributes to communicate every timestep | +----------------------+-----------------------------------------------------------+ -| unpack\_comm\_body | unpacking of those attributes | +| unpack_comm_body | unpacking of those attributes | +----------------------+-----------------------------------------------------------+ -| pack\_border\_body | body attributes to communicate when reneighboring is done | +| pack_border_body | body attributes to communicate when reneighboring is done | +----------------------+-----------------------------------------------------------+ -| unpack\_border\_body | unpacking of those attributes | +| unpack_border_body | unpacking of those attributes | +----------------------+-----------------------------------------------------------+ diff --git a/doc/src/Modify_bond.rst b/doc/src/Modify_bond.rst index 06db272395..c2d220767e 100644 --- a/doc/src/Modify_bond.rst +++ b/doc/src/Modify_bond.rst @@ -5,7 +5,7 @@ Classes that compute molecular interactions are derived from the Bond, Angle, Dihedral, and Improper classes. New styles can be created to add new potentials to LAMMPS. -Bond\_harmonic.cpp is the simplest example of a bond style. Ditto for +Bond_harmonic.cpp is the simplest example of a bond style. Ditto for the harmonic forms of the angle, dihedral, and improper style commands. @@ -14,9 +14,9 @@ new derived class. See bond.h, angle.h, dihedral.h, and improper.h for details and specific additional methods. +-----------------------+---------------------------------------------------------------------------+ -| init | check if all coefficients are set, calls *init\_style* (optional) | +| init | check if all coefficients are set, calls *init_style* (optional) | +-----------------------+---------------------------------------------------------------------------+ -| init\_style | check if style specific conditions are met (optional) | +| init_style | check if style specific conditions are met (optional) | +-----------------------+---------------------------------------------------------------------------+ | compute | compute the molecular interactions (required) | +-----------------------+---------------------------------------------------------------------------+ @@ -24,13 +24,13 @@ for details and specific additional methods. +-----------------------+---------------------------------------------------------------------------+ | coeff | set coefficients for one type (required) | +-----------------------+---------------------------------------------------------------------------+ -| equilibrium\_distance | length of bond, used by SHAKE (required, bond only) | +| equilibrium_distance | length of bond, used by SHAKE (required, bond only) | +-----------------------+---------------------------------------------------------------------------+ -| equilibrium\_angle | opening of angle, used by SHAKE (required, angle only) | +| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) | +-----------------------+---------------------------------------------------------------------------+ -| write & read\_restart | writes/reads coeffs to restart files (required) | +| write & read_restart | writes/reads coeffs to restart files (required) | +-----------------------+---------------------------------------------------------------------------+ | single | force and energy of a single bond or angle (required, bond or angle only) | +-----------------------+---------------------------------------------------------------------------+ -| memory\_usage | tally memory allocated by the style (optional) | +| memory_usage | tally memory allocated by the style (optional) | +-----------------------+---------------------------------------------------------------------------+ diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst index 37e1b2c490..2d0a1d99d9 100644 --- a/doc/src/Modify_command.rst +++ b/doc/src/Modify_command.rst @@ -2,8 +2,8 @@ Input script command style ========================== New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create\_atoms, -read\_data, velocity, and run commands are all implemented in this +classes that have a "command" method. For example, the create_atoms, +read_data, velocity, and run commands are all implemented in this fashion. When such a command is encountered in the LAMMPS input script, LAMMPS simply creates a class with the corresponding name, invokes the "command" method of the class, and passes it the arguments diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst index b32350e048..8fad775b3a 100644 --- a/doc/src/Modify_compute.rst +++ b/doc/src/Modify_compute.rst @@ -7,8 +7,8 @@ quantities like kinetic energy and the centro-symmetry parameter are derived from the Compute class. New styles can be created to add new calculations to LAMMPS. -Compute\_temp.cpp is a simple example of computing a scalar -temperature. Compute\_ke\_atom.cpp is a simple example of computing +Compute_temp.cpp is a simple example of computing a scalar +temperature. Compute_ke_atom.cpp is a simple example of computing per-atom kinetic energy. Here is a brief description of methods you define in your new derived @@ -17,41 +17,41 @@ class. See compute.h for details. +-----------------------+------------------------------------------------------------------+ | init | perform one time setup (required) | +-----------------------+------------------------------------------------------------------+ -| init\_list | neighbor list setup, if needed (optional) | +| init_list | neighbor list setup, if needed (optional) | +-----------------------+------------------------------------------------------------------+ -| compute\_scalar | compute a scalar quantity (optional) | +| compute_scalar | compute a scalar quantity (optional) | +-----------------------+------------------------------------------------------------------+ -| compute\_vector | compute a vector of quantities (optional) | +| compute_vector | compute a vector of quantities (optional) | +-----------------------+------------------------------------------------------------------+ -| compute\_peratom | compute one or more quantities per atom (optional) | +| compute_peratom | compute one or more quantities per atom (optional) | +-----------------------+------------------------------------------------------------------+ -| compute\_local | compute one or more quantities per processor (optional) | +| compute_local | compute one or more quantities per processor (optional) | +-----------------------+------------------------------------------------------------------+ -| pack\_comm | pack a buffer with items to communicate (optional) | +| pack_comm | pack a buffer with items to communicate (optional) | +-----------------------+------------------------------------------------------------------+ -| unpack\_comm | unpack the buffer (optional) | +| unpack_comm | unpack the buffer (optional) | +-----------------------+------------------------------------------------------------------+ -| pack\_reverse | pack a buffer with items to reverse communicate (optional) | +| pack_reverse | pack a buffer with items to reverse communicate (optional) | +-----------------------+------------------------------------------------------------------+ -| unpack\_reverse | unpack the buffer (optional) | +| unpack_reverse | unpack the buffer (optional) | +-----------------------+------------------------------------------------------------------+ -| remove\_bias | remove velocity bias from one atom (optional) | +| remove_bias | remove velocity bias from one atom (optional) | +-----------------------+------------------------------------------------------------------+ -| remove\_bias\_all | remove velocity bias from all atoms in group (optional) | +| remove_bias_all | remove velocity bias from all atoms in group (optional) | +-----------------------+------------------------------------------------------------------+ -| restore\_bias | restore velocity bias for one atom after remove\_bias (optional) | +| restore_bias | restore velocity bias for one atom after remove_bias (optional) | +-----------------------+------------------------------------------------------------------+ -| restore\_bias\_all | same as before, but for all atoms in group (optional) | +| restore_bias_all | same as before, but for all atoms in group (optional) | +-----------------------+------------------------------------------------------------------+ -| pair\_tally\_callback | callback function for *tally*\ -style computes (optional). | +| pair_tally_callback | callback function for *tally*\ -style computes (optional). | +-----------------------+------------------------------------------------------------------+ -| memory\_usage | tally memory usage (optional) | +| memory_usage | tally memory usage (optional) | +-----------------------+------------------------------------------------------------------+ Tally-style computes are a special case, as their computation is done in two stages: the callback function is registered with the pair style -and then called from the Pair::ev\_tally() function, which is called for +and then called from the Pair::ev_tally() function, which is called for each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute\_scalar or -compute\_vector or compute\_peratom methods. The USER-TALLY package -provides *examples*\ \_compute\_tally.html for utilizing this mechanism. +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides *examples*\ _compute_tally.html for utilizing this mechanism. diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 358861c720..ed2ef783f4 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -90,8 +90,8 @@ packages in the src directory for examples. If you are uncertain, please ask. * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you - need to test compiling LAMMPS from scratch with -DLAMMPS\_BIGBIG - set in addition to the default -DLAMMPS\_SMALLBIG setting. Your code + need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG + set in addition to the default -DLAMMPS_SMALLBIG setting. Your code will need to work correctly in serial and in parallel using MPI. * For consistency with the rest of LAMMPS and especially, if you want @@ -106,7 +106,7 @@ packages in the src directory for examples. If you are uncertain, please ask. (, , or ) instead of the C-style names , , or ), and forward declarations used where possible or needed to avoid including headers. - All added code should be placed into the LAMMPS\_NS namespace or a + All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must **not** import namespaces with *using*\ . @@ -164,7 +164,7 @@ packages in the src directory for examples. If you are uncertain, please ask. mathematical expression or figures (see doc/JPG for examples). Additional PDF files with further details (see doc/PDF for examples) may also be included. The doc page should also include literature - citations as appropriate; see the bottom of doc/fix\_nh.rst for + citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. Citation labels must be unique across all .rst files. The "Restrictions" section of the doc page should indicate if your @@ -191,7 +191,7 @@ packages in the src directory for examples. If you are uncertain, please ask. * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the \*.cpp - source file. See src/USER-EFF/atom\_vec\_electron.cpp for an example. + source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from diff --git a/doc/src/Modify_dump.rst b/doc/src/Modify_dump.rst index 8d98f848d2..1379326d1e 100644 --- a/doc/src/Modify_dump.rst +++ b/doc/src/Modify_dump.rst @@ -4,21 +4,21 @@ Dump styles Classes that dump per-atom info to files are derived from the Dump class. To dump new quantities or in a new format, a new derived dump class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump\_custom.cpp file. +DumpCustom class contained in the dump_custom.cpp file. -Dump\_atom.cpp is a simple example of a derived dump class. +Dump_atom.cpp is a simple example of a derived dump class. Here is a brief description of methods you define in your new derived class. See dump.h for details. +---------------+---------------------------------------------------+ -| write\_header | write the header section of a snapshot of atoms | +| write_header | write the header section of a snapshot of atoms | +---------------+---------------------------------------------------+ | count | count the number of lines a processor will output | +---------------+---------------------------------------------------+ | pack | pack a proc's output data into a buffer | +---------------+---------------------------------------------------+ -| write\_data | write a proc's data to a file | +| write_data | write a proc's data to a file | +---------------+---------------------------------------------------+ See the :doc:`dump ` command and its *custom* style for a list of diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index 9e1705e435..9a97e30fbe 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -10,7 +10,7 @@ constraints or boundary conditions (SHAKE or walls), and diagnostics (compute a diffusion coefficient). New styles can be created to add new options to LAMMPS. -Fix\_setforce.cpp is a simple example of setting forces on atoms to +Fix_setforce.cpp is a simple example of setting forces on atoms to prescribed values. There are dozens of fix options already in LAMMPS; choose one as a template that is similar to what you want to implement. @@ -23,105 +23,105 @@ derived class. See fix.h for details. +---------------------------+--------------------------------------------------------------------------------------------+ | init | initialization before a run (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| setup\_pre\_exchange | called before atom exchange in setup (optional) | +| setup_pre_exchange | called before atom exchange in setup (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| setup\_pre\_force | called before force computation in setup (optional) | +| setup_pre_force | called before force computation in setup (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | setup | called immediately before the 1st timestep and after forces are computed (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_setup\_pre\_force | like setup\_pre\_force, but for minimizations instead of MD runs (optional) | +| min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_setup | like setup, but for minimizations instead of MD runs (optional) | +| min_setup | like setup, but for minimizations instead of MD runs (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| initial\_integrate | called at very beginning of each timestep (optional) | +| initial_integrate | called at very beginning of each timestep (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pre\_exchange | called before atom exchange on re-neighboring steps (optional) | +| pre_exchange | called before atom exchange on re-neighboring steps (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pre\_neighbor | called before neighbor list build (optional) | +| pre_neighbor | called before neighbor list build (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pre\_force | called before pair & molecular forces are computed (optional) | +| pre_force | called before pair & molecular forces are computed (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| post\_force | called after pair & molecular forces are computed and communicated (optional) | +| post_force | called after pair & molecular forces are computed and communicated (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| final\_integrate | called at end of each timestep (optional) | +| final_integrate | called at end of each timestep (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| end\_of\_step | called at very end of timestep (optional) | +| end_of_step | called at very end of timestep (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| write\_restart | dumps fix info to restart file (optional) | +| write_restart | dumps fix info to restart file (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | restart | uses info from restart file to re-initialize the fix (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| grow\_arrays | allocate memory for atom-based arrays used by fix (optional) | +| grow_arrays | allocate memory for atom-based arrays used by fix (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| copy\_arrays | copy atom info when an atom migrates to a new processor (optional) | +| copy_arrays | copy atom info when an atom migrates to a new processor (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pack\_exchange | store atom's data in a buffer (optional) | +| pack_exchange | store atom's data in a buffer (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| unpack\_exchange | retrieve atom's data from a buffer (optional) | +| unpack_exchange | retrieve atom's data from a buffer (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pack\_restart | store atom's data for writing to restart file (optional) | +| pack_restart | store atom's data for writing to restart file (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| unpack\_restart | retrieve atom's data from a restart file buffer (optional) | +| unpack_restart | retrieve atom's data from a restart file buffer (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| size\_restart | size of atom's data (optional) | +| size_restart | size of atom's data (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| maxsize\_restart | max size of atom's data (optional) | +| maxsize_restart | max size of atom's data (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| setup\_pre\_force\_respa | same as setup\_pre\_force, but for rRESPA (optional) | +| setup_pre_force_respa | same as setup_pre_force, but for rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| initial\_integrate\_respa | same as initial\_integrate, but for rRESPA (optional) | +| initial_integrate_respa | same as initial_integrate, but for rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| post\_integrate\_respa | called after the first half integration step is done in rRESPA (optional) | +| post_integrate_respa | called after the first half integration step is done in rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pre\_force\_respa | same as pre\_force, but for rRESPA (optional) | +| pre_force_respa | same as pre_force, but for rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| post\_force\_respa | same as post\_force, but for rRESPA (optional) | +| post_force_respa | same as post_force, but for rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| final\_integrate\_respa | same as final\_integrate, but for rRESPA (optional) | +| final_integrate_respa | same as final_integrate, but for rRESPA (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_pre\_force | called after pair & molecular forces are computed in minimizer (optional) | +| min_pre_force | called after pair & molecular forces are computed in minimizer (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_post\_force | called after pair & molecular forces are computed and communicated in minimizer (optional) | +| min_post_force | called after pair & molecular forces are computed and communicated in minimizer (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_store | store extra data for linesearch based minimization on a LIFO stack (optional) | +| min_store | store extra data for linesearch based minimization on a LIFO stack (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_pushstore | push the minimization LIFO stack one element down (optional) | +| min_pushstore | push the minimization LIFO stack one element down (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_popstore | pop the minimization LIFO stack one element up (optional) | +| min_popstore | pop the minimization LIFO stack one element up (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_clearstore | clear minimization LIFO stack (optional) | +| min_clearstore | clear minimization LIFO stack (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_step | reset or move forward on line search minimization (optional) | +| min_step | reset or move forward on line search minimization (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| min\_dof | report number of degrees of freedom *added* by this fix in minimization (optional) | +| min_dof | report number of degrees of freedom *added* by this fix in minimization (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| max\_alpha | report maximum allowed step size during linesearch minimization (optional) | +| max_alpha | report maximum allowed step size during linesearch minimization (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pack\_comm | pack a buffer to communicate a per-atom quantity (optional) | +| pack_comm | pack a buffer to communicate a per-atom quantity (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| unpack\_comm | unpack a buffer to communicate a per-atom quantity (optional) | +| unpack_comm | unpack a buffer to communicate a per-atom quantity (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| pack\_reverse\_comm | pack a buffer to reverse communicate a per-atom quantity (optional) | +| pack_reverse_comm | pack a buffer to reverse communicate a per-atom quantity (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| unpack\_reverse\_comm | unpack a buffer to reverse communicate a per-atom quantity (optional) | +| unpack_reverse_comm | unpack a buffer to reverse communicate a per-atom quantity (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | dof | report number of degrees of freedom *removed* by this fix during MD (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| compute\_scalar | return a global scalar property that the fix computes (optional) | +| compute_scalar | return a global scalar property that the fix computes (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| compute\_vector | return a component of a vector property that the fix computes (optional) | +| compute_vector | return a component of a vector property that the fix computes (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| compute\_array | return a component of an array property that the fix computes (optional) | +| compute_array | return a component of an array property that the fix computes (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | deform | called when the box size is changed (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| reset\_target | called when a change of the target temperature is requested during a run (optional) | +| reset_target | called when a change of the target temperature is requested during a run (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| reset\_dt | is called when a change of the time step is requested during a run (optional) | +| reset_dt | is called when a change of the time step is requested during a run (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| modify\_param | called when a fix\_modify request is executed (optional) | +| modify_param | called when a fix_modify request is executed (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ -| memory\_usage | report memory used by fix (optional) | +| memory_usage | report memory used by fix (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ | thermo | compute quantities for thermodynamic output (optional) | +---------------------------+--------------------------------------------------------------------------------------------+ @@ -129,12 +129,12 @@ derived class. See fix.h for details. Typically, only a small fraction of these methods are defined for a particular fix. Setmask is mandatory, as it determines when the fix will be invoked during the timestep. Fixes that perform time -integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial\_integrate() and -final\_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post\_force(). +integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial_integrate() and +final_integrate() to perform velocity Verlet updates. Fixes that +constrain forces implement post_force(). -Fixes that perform diagnostics typically implement end\_of\_step(). For -an end\_of\_step fix, one of your fix arguments must be the variable +Fixes that perform diagnostics typically implement end_of_step(). For +an end_of_step fix, one of your fix arguments must be the variable "nevery" which is used to determine when to call the fix and you must set this variable in the constructor of your fix. By convention, this is the first argument the fix defines (after the ID, group-ID, style). @@ -142,12 +142,12 @@ is the first argument the fix defines (after the ID, group-ID, style). If the fix needs to store information for each atom that persists from timestep to timestep, it can manage that memory and migrate the info with the atoms as they move from processors to processor by -implementing the grow\_arrays, copy\_arrays, pack\_exchange, and -unpack\_exchange methods. Similarly, the pack\_restart and -unpack\_restart methods can be implemented to store information about +implementing the grow_arrays, copy_arrays, pack_exchange, and +unpack_exchange methods. Similarly, the pack_restart and +unpack_restart methods can be implemented to store information about the fix in restart files. If you wish an integrator or force constraint fix to work with rRESPA (see the :doc:`run_style ` -command), the initial\_integrate, post\_force\_integrate, and -final\_integrate\_respa methods can be implemented. The thermo method +command), the initial_integrate, post_force_integrate, and +final_integrate_respa methods can be implemented. The thermo method enables a fix to contribute values to thermodynamic output, as printed quantities and/or to be summed to the potential energy of the system. diff --git a/doc/src/Modify_kspace.rst b/doc/src/Modify_kspace.rst index c45c8f94a1..e1b10eac8d 100644 --- a/doc/src/Modify_kspace.rst +++ b/doc/src/Modify_kspace.rst @@ -17,5 +17,5 @@ class. See kspace.h for details. +---------------+----------------------------------------------+ | compute | every-timestep computation | +---------------+----------------------------------------------+ -| memory\_usage | tally of memory usage | +| memory_usage | tally of memory usage | +---------------+----------------------------------------------+ diff --git a/doc/src/Modify_min.rst b/doc/src/Modify_min.rst index d8bcd2d3f2..ed7c101a6c 100644 --- a/doc/src/Modify_min.rst +++ b/doc/src/Modify_min.rst @@ -5,7 +5,7 @@ Classes that perform energy minimization derived from the Min class. New styles can be created to add new minimization algorithms to LAMMPS. -Min\_cg.cpp is an example of conjugate gradient minimization. +Min_cg.cpp is an example of conjugate gradient minimization. Here is a brief description of methods you define in your new derived class. See min.h for details. @@ -15,5 +15,5 @@ class. See min.h for details. +---------------+------------------------------------------+ | run | perform the minimization | +---------------+------------------------------------------+ -| memory\_usage | tally of memory usage | +| memory_usage | tally of memory usage | +---------------+------------------------------------------+ diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst index 1bbcf8e120..2deceae7db 100644 --- a/doc/src/Modify_overview.rst +++ b/doc/src/Modify_overview.rst @@ -25,8 +25,8 @@ and variables needed to define the new feature are in the 2 files you write, and thus shouldn't make the rest of LAMMPS more complex or cause side-effect bugs. -Here is a concrete example. Suppose you write 2 files pair\_foo.cpp -and pair\_foo.h that define a new class PairFoo that computes pairwise +Here is a concrete example. Suppose you write 2 files pair_foo.cpp +and pair_foo.h that define a new class PairFoo that computes pairwise potentials described in the classic 1997 :ref:`paper ` by Foo, et al. If you wish to invoke those potentials in a LAMMPS input script with a command like @@ -35,7 +35,7 @@ command like pair_style foo 0.1 3.5 -then your pair\_foo.h file should be structured as follows: +then your pair_foo.h file should be structured as follows: .. code-block:: c++ @@ -47,12 +47,12 @@ then your pair\_foo.h file should be structured as follows: ... #endif -where "foo" is the style keyword in the pair\_style command, and -PairFoo is the class name defined in your pair\_foo.cpp and pair\_foo.h +where "foo" is the style keyword in the pair_style command, and +PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h files. When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair\_style command like the +the executable and can be invoked with a pair_style command like the example above. Arguments like 0.1 and 3.5 can be defined and processed by your new class. @@ -80,7 +80,7 @@ that are not set to 0 are functions you may override or not. Those are usually defined with an empty function body. Additionally, new output options can be added directly to the -thermo.cpp, dump\_custom.cpp, and variable.cpp files. These are also +thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also listed on the :doc:`Modify page `. Here are additional guidelines for modifying LAMMPS and adding new diff --git a/doc/src/Modify_pair.rst b/doc/src/Modify_pair.rst index 78ee144d53..7263b8fd48 100644 --- a/doc/src/Modify_pair.rst +++ b/doc/src/Modify_pair.rst @@ -7,7 +7,7 @@ such as EAM or Tersoff where particles interact without a static bond topology. New styles can be created to add new pair potentials to LAMMPS. -Pair\_lj\_cut.cpp is a simple example of a Pair class, though it +Pair_lj_cut.cpp is a simple example of a Pair class, though it includes some optional methods to enable its use with rRESPA. Here is a brief description of the class methods in pair.h: @@ -19,17 +19,17 @@ Here is a brief description of the class methods in pair.h: +---------------------------------+-------------------------------------------------------------------+ | coeff | set coefficients for one i,j type pair | +---------------------------------+-------------------------------------------------------------------+ -| init\_one | perform initialization for one i,j type pair | +| init_one | perform initialization for one i,j type pair | +---------------------------------+-------------------------------------------------------------------+ -| init\_style | initialization specific to this pair style | +| init_style | initialization specific to this pair style | +---------------------------------+-------------------------------------------------------------------+ -| write & read\_restart | write/read i,j pair coeffs to restart files | +| write & read_restart | write/read i,j pair coeffs to restart files | +---------------------------------+-------------------------------------------------------------------+ -| write & read\_restart\_settings | write/read global settings to restart files | +| write & read_restart_settings | write/read global settings to restart files | +---------------------------------+-------------------------------------------------------------------+ | single | force and energy of a single pairwise interaction between 2 atoms | +---------------------------------+-------------------------------------------------------------------+ -| compute\_inner/middle/outer | versions of compute used by rRESPA | +| compute_inner/middle/outer | versions of compute used by rRESPA | +---------------------------------+-------------------------------------------------------------------+ The inner/middle/outer routines are optional. diff --git a/doc/src/Modify_region.rst b/doc/src/Modify_region.rst index a9e9c734a4..fa97df32c7 100644 --- a/doc/src/Modify_region.rst +++ b/doc/src/Modify_region.rst @@ -6,7 +6,7 @@ class. Regions are used elsewhere in LAMMPS to group atoms, delete atoms to create a void, insert atoms in a specified region, etc. New styles can be created to add new region shapes to LAMMPS. -Region\_sphere.cpp is an example of a spherical region. +Region_sphere.cpp is an example of a spherical region. Here is a brief description of methods you define in your new derived class. See region.h for details. @@ -14,9 +14,9 @@ class. See region.h for details. +-------------------+---------------------------------------------------------------------+ | inside | determine whether a point is in the region | +-------------------+---------------------------------------------------------------------+ -| surface\_interior | determine if a point is within a cutoff distance inside of surface | +| surface_interior | determine if a point is within a cutoff distance inside of surface | +-------------------+---------------------------------------------------------------------+ -| surface\_exterior | determine if a point is within a cutoff distance outside of surface | +| surface_exterior | determine if a point is within a cutoff distance outside of surface | +-------------------+---------------------------------------------------------------------+ -| shape\_update | change region shape if set by time-dependent variable | +| shape_update | change region shape if set by time-dependent variable | +-------------------+---------------------------------------------------------------------+ diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index f60fc1c11b..e20c2886ed 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -10,7 +10,7 @@ scripts, and pictures/movies (if available) that illustrate use of the package. The majority of packages can be included in a LAMMPS build with a -single setting (-D PGK\_NAME for CMake) or command ("make yes-name" for +single setting (-D PGK_NAME for CMake) or command ("make yes-name" for make). See the :doc:`Build package ` doc page for more info. A few packages may require additional steps; this is indicated in the descriptions below. The :doc:`Build extras ` doc @@ -123,8 +123,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * :doc:`Howto spherical ` * :doc:`pair_style gayberne ` * :doc:`pair_style resquared ` -* `doc/PDF/pair\_gayberne\_extra.pdf `_ -* `doc/PDF/pair\_resquared\_extra.pdf `_ +* `doc/PDF/pair_gayberne_extra.pdf `_ +* `doc/PDF/pair_resquared_extra.pdf `_ * examples/ASPHERE * examples/ellipse * https://lammps.sandia.gov/movies.html#line @@ -147,7 +147,7 @@ overview. **Supporting info:** * src/BODY filenames -> commands -* :doc:`Howto\_body ` +* :doc:`Howto_body ` * :doc:`atom_style body ` * :doc:`fix nve/body ` * :doc:`pair_style body/nparticle ` @@ -367,7 +367,7 @@ This package contains a set of commands that serve as a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) `_ repository of interatomic models (IMs) enabling compatible ones to be used in LAMMPS simulations. -This includes :doc:`kim_init and kim\_interactions ` +This includes :doc:`kim_init and kim_interactions ` commands to select, initialize and instantiate the IM, and a :doc:`kim_query ` command to perform web queries for material property predictions of OpenKIM IMs. @@ -377,7 +377,7 @@ is provided by the :doc:`pair_style kim ` command. .. note:: - The command *pair\_style kim* is called by *kim\_interactions* and + The command *pair_style kim* is called by *kim_interactions* and is not recommended to be directly used in input scripts. To use this package you must have the KIM API library available on your @@ -392,7 +392,7 @@ The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) and is funded by the `National Science Foundation `_. **Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM -API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and +API and the *pair_style kim* command. Axel Kohlmeyer (Temple U) and Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands ` interface in close collaboration with Ryan Elliott. @@ -782,9 +782,9 @@ Foster (UTSA). **Supporting info:** * src/PERI: filenames -> commands -* `doc/PDF/PDLammps\_overview.pdf `_ -* `doc/PDF/PDLammps\_EPS.pdf `_ -* `doc/PDF/PDLammps\_VES.pdf `_ +* `doc/PDF/PDLammps_overview.pdf `_ +* `doc/PDF/PDLammps_EPS.pdf `_ +* `doc/PDF/PDLammps_VES.pdf `_ * :doc:`atom_style peri ` * :doc:`pair_style peri/\* ` * :doc:`compute damage/atom ` @@ -1890,7 +1890,7 @@ And a :doc:`dynamical_matrix ` as well as a and third order tensor from finite differences. **Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" +and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" **Supporting info:** @@ -1918,8 +1918,8 @@ Matching methodology. **Supporting info:** -* src/USER-PTM: filenames not starting with ptm\\_ -> commands -* src/USER-PTM: filenames starting with ptm\\_ -> supporting code +* src/USER-PTM: filenames not starting with ptm\_ -> commands +* src/USER-PTM: filenames starting with ptm\_ -> supporting code * src/USER-PTM/LICENSE * :doc:`compute ptm/atom ` @@ -2132,7 +2132,7 @@ is an extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal fluctuations are important (see the :ref:`USER-SPH package `). Also two fixes for moving and rigid body integration of SPH/SDPD particles -(particles of atom\_style meso). +(particles of atom_style meso). **Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic Sciences, Iran). @@ -2180,7 +2180,7 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-SMD: filenames -> commands * src/USER-SMD/README -* doc/PDF/SMD\_LAMMPS\_userguide.pdf +* doc/PDF/SMD_LAMMPS_userguide.pdf * examples/USER/smd * https://lammps.sandia.gov/movies.html#smd @@ -2237,7 +2237,7 @@ Dynamics, Ernst Mach Institute, Germany). * src/USER-SPH: filenames -> commands * src/USER-SPH/README -* doc/PDF/SPH\_LAMMPS\_userguide.pdf +* doc/PDF/SPH_LAMMPS_userguide.pdf * examples/USER/sph * https://lammps.sandia.gov/movies.html#sph diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 33f73933df..e0bcf70b9a 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -59,7 +59,7 @@ new potential. To use any of these commands, you only need to build LAMMPS with the PYTHON package installed: -.. parsed-literal:: +.. code-block:: bash make yes-python make machine diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 0bfee9caf5..976358801e 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -20,16 +20,16 @@ distribution. +----------------------------------------------------------------+--------------------------------------------------+ | GUI go/stop/temperature-slider to control LAMMPS | plot.py | +----------------------------------------------------------------+--------------------------------------------------+ -| real-time temperature plot with GnuPlot via Pizza.py | viz\_tool.py | +| real-time temperature plot with GnuPlot via Pizza.py | viz_tool.py | +----------------------------------------------------------------+--------------------------------------------------+ -| real-time viz via some viz package | vizplotgui\_tool.py | +| real-time viz via some viz package | vizplotgui_tool.py | +----------------------------------------------------------------+--------------------------------------------------+ -| combination of viz\_tool.py and plot.py and gui.py | | +| combination of viz_tool.py and plot.py and gui.py | | +----------------------------------------------------------------+--------------------------------------------------+ ---------- -For the viz\_tool.py and vizplotgui\_tool.py commands, replace "tool" +For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" with "gl" or "atomeye" or "pymol" or "vmd", depending on what visualization package you have installed. @@ -79,7 +79,7 @@ variables that have to match the VMD installation on your system. See the python/README file for instructions on how to run them and the source code for individual scripts for comments about what they do. -Here are screenshots of the vizplotgui\_tool.py script in action for +Here are screenshots of the vizplotgui_tool.py script in action for different visualization package options. Click to see larger images: .. image:: JPG/screenshot_gl_small.jpg diff --git a/doc/src/Python_head.rst b/doc/src/Python_head.rst index 0a58ecdde1..fc808489a5 100644 --- a/doc/src/Python_head.rst +++ b/doc/src/Python_head.rst @@ -27,7 +27,7 @@ its library interface, or to hook multiple pieces of software together, such as a simulation code plus a visualization tool, or to run a coupled multiscale or multiphysics model. -See the :doc:`Howto\_couple ` doc page for more ideas about +See the :doc:`Howto_couple ` doc page for more ideas about coupling LAMMPS to other codes. See the :doc:`Howto library ` doc page for a description of the LAMMPS library interface provided in src/library.h and src/library.h. That interface is exposed to Python either when calling LAMMPS from Python diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 04e3660c52..8b2fe9c367 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -31,12 +31,12 @@ If you set the paths to these files as environment variables, you only have to do it once. For the csh or tcsh shells, add something like this to your ~/.cshrc file, one line for each of the two files: -.. parsed-literal:: +.. code-block:: csh setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src -On MacOSX you may also need to set DYLD\_LIBRARY\_PATH accordingly. +On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly. For Bourne/Korn shells accordingly into the corresponding files using the "export" shell builtin. @@ -58,11 +58,11 @@ you can invoke install.py from the python directory manually as * and the optional -d flag to a custom (legacy) installation folder If you use a legacy installation folder, you will need to set your -PYTHONPATH and LD\_LIBRARY\_PATH (and/or DYLD\_LIBRARY\_PATH) environment +PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment variables accordingly, as described above. Note that if you want Python to be able to load different versions of the LAMMPS shared library (see :doc:`this section `), you will -need to manually copy files like liblammps\_g++.so into the appropriate -system directory. This is not needed if you set the LD\_LIBRARY\_PATH +need to manually copy files like liblammps_g++.so into the appropriate +system directory. This is not needed if you set the LD_LIBRARY_PATH environment variable as described above. diff --git a/doc/src/Python_library.rst b/doc/src/Python_library.rst index 0d3767170f..2100074c4e 100644 --- a/doc/src/Python_library.rst +++ b/doc/src/Python_library.rst @@ -135,21 +135,21 @@ script, and coordinate and run multiple simulations, e.g. lmp1.file("in.file1") lmp2.file("in.file2") -The file(), command(), commands\_list(), commands\_string() methods +The file(), command(), commands_list(), commands_string() methods allow an input script, a single command, or multiple commands to be invoked. -The extract\_setting(), extract\_global(), extract\_box(), -extract\_atom(), extract\_compute(), extract\_fix(), and -extract\_variable() methods return values or pointers to data +The extract_setting(), extract_global(), extract_box(), +extract_atom(), extract_compute(), extract_fix(), and +extract_variable() methods return values or pointers to data structures internal to LAMMPS. -For extract\_global() see the src/library.cpp file for the list of +For extract_global() see the src/library.cpp file for the list of valid names. New names could easily be added. A double or integer is returned. You need to specify the appropriate data type via the type argument. -For extract\_atom(), a pointer to internal LAMMPS atom-based data is +For extract_atom(), a pointer to internal LAMMPS atom-based data is returned, which you can use via normal Python subscripting. See the extract() method in the src/atom.cpp file for a list of valid names. Again, new names could easily be added if the property you want is not @@ -157,7 +157,7 @@ listed. A pointer to a vector of doubles or integers, or a pointer to an array of doubles (double \*\*) or integers (int \*\*) is returned. You need to specify the appropriate data type via the type argument. -For extract\_compute() and extract\_fix(), the global, per-atom, or +For extract_compute() and extract_fix(), the global, per-atom, or local data calculated by the compute or fix can be accessed. What is returned depends on whether the compute or fix calculates a scalar or vector or array. For a scalar, a single double value is returned. If @@ -173,7 +173,7 @@ data types. See the doc pages for individual :doc:`computes ` and :doc:`fixes ` for a description of what they calculate and store. -For extract\_variable(), an :doc:`equal-style or atom-style variable ` is evaluated and its result returned. +For extract_variable(), an :doc:`equal-style or atom-style variable ` is evaluated and its result returned. For equal-style variables a single double value is returned and the group argument is ignored. For atom-style variables, a vector of @@ -181,17 +181,17 @@ doubles is returned, one value per atom, which you can use via normal Python subscripting. The values will be zero for atoms not in the specified group. -The get\_thermo() method returns the current value of a thermo +The get_thermo() method returns the current value of a thermo keyword as a float. -The get\_natoms() method returns the total number of atoms in the +The get_natoms() method returns the total number of atoms in the simulation, as an int. -The set\_variable() method sets an existing string-style variable to a +The set_variable() method sets an existing string-style variable to a new string value, so that subsequent LAMMPS commands can access the variable. -The reset\_box() method resets the size and shape of the simulation +The reset_box() method resets the size and shape of the simulation box, e.g. as part of restoring a previously extracted and saved state of a simulation. @@ -203,19 +203,19 @@ passed by all calling processors, to individual atoms, which may be owned by different processors. Note that the data returned by the gather methods, -e.g. gather\_atoms("x"), is different from the data structure returned -by extract\_atom("x") in four ways. (1) Gather\_atoms() returns a -vector which you index as x[i]; extract\_atom() returns an array -which you index as x[i][j]. (2) Gather\_atoms() orders the atoms -by atom ID while extract\_atom() does not. (3) Gather\_atoms() returns -a list of all atoms in the simulation; extract\_atoms() returns just -the atoms local to each processor. (4) Finally, the gather\_atoms() +e.g. gather_atoms("x"), is different from the data structure returned +by extract_atom("x") in four ways. (1) Gather_atoms() returns a +vector which you index as x[i]; extract_atom() returns an array +which you index as x[i][j]. (2) Gather_atoms() orders the atoms +by atom ID while extract_atom() does not. (3) Gather_atoms() returns +a list of all atoms in the simulation; extract_atoms() returns just +the atoms local to each processor. (4) Finally, the gather_atoms() data structure is a copy of the atom coords stored internally in -LAMMPS, whereas extract\_atom() returns an array that effectively +LAMMPS, whereas extract_atom() returns an array that effectively points directly to the internal data. This means you can change values inside LAMMPS from Python by assigning a new values to the -extract\_atom() array. To do this with the gather\_atoms() vector, you -need to change values in the vector, then invoke the scatter\_atoms() +extract_atom() array. To do this with the gather_atoms() vector, you +need to change values in the vector, then invoke the scatter_atoms() method. For the scatter methods, the array of coordinates passed to must be a diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst index 659d5c57fd..02a62c89d0 100644 --- a/doc/src/Python_mpi.rst +++ b/doc/src/Python_mpi.rst @@ -18,7 +18,7 @@ LAMMPS instances on subsets of the total MPI ranks. To install mpi4py (version mpi4py-3.0.3 as of Nov 2019), unpack it and from its main directory, type -.. parsed-literal:: +.. code-block:: bash python setup.py build sudo python setup.py install @@ -27,27 +27,27 @@ Again, the "sudo" is only needed if required to copy mpi4py files into your Python distribution's site-packages directory. To install with user privilege into the user local directory type -.. parsed-literal:: +.. code-block:: bash python setup.py install --user If you have successfully installed mpi4py, you should be able to run Python and type -.. parsed-literal:: +.. code-block:: python from mpi4py import MPI without error. You should also be able to run python in parallel on a simple test script -.. parsed-literal:: +.. code-block:: bash % mpirun -np 4 python test.py where test.py contains the lines -.. parsed-literal:: +.. code-block:: python from mpi4py import MPI comm = MPI.COMM_WORLD @@ -64,7 +64,7 @@ and see one line of output for each processor you run on. it is using, since you specify the details in your low-level src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find information about the MPI it uses to build against. And it tries to - load "libmpi.so" from the LD\_LIBRARY\_PATH. This may or may not find + load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find the MPI library that LAMMPS is using. If you have problems running both mpi4py and LAMMPS together, this is an issue you may need to address, e.g. by moving other MPI installations so that mpi4py finds diff --git a/doc/src/Python_shlib.rst b/doc/src/Python_shlib.rst index b9d8e50242..bd1d559359 100644 --- a/doc/src/Python_shlib.rst +++ b/doc/src/Python_shlib.rst @@ -5,19 +5,19 @@ Build LAMMPS as a shared library using make ------------------------------------------- Instructions on how to build LAMMPS as a shared library are given on -the :doc:`Build\_basics ` doc page. A shared library is +the :doc:`Build_basics ` doc page. A shared library is one that is dynamically loadable, which is what Python requires to wrap LAMMPS. On Linux this is a library file that ends in ".so", not ".a". From the src directory, type -.. parsed-literal:: +.. code-block:: bash make foo mode=shlib where foo is the machine target name, such as mpi or serial. -This should create the file liblammps\_foo.so in the src directory, as +This should create the file liblammps_foo.so in the src directory, as well as a soft link liblammps.so, which is what the Python wrapper will load by default. Note that if you are building multiple machine versions of the shared library, the soft link is always set to the @@ -29,7 +29,7 @@ most recently built version. auxiliary libraries (used by various packages), then all of these extra libraries must also be shared libraries. If the LAMMPS shared-library build fails with an error complaining about this, see - the :doc:`Build\_basics ` doc page. + the :doc:`Build_basics ` doc page. Build LAMMPS as a shared library using CMake -------------------------------------------- @@ -37,7 +37,7 @@ Build LAMMPS as a shared library using CMake When using CMake the following two options are necessary to generate the LAMMPS shared library: -.. parsed-literal:: +.. code-block:: bash -D BUILD_LIB=on # enable building LAMMPS as a library -D BUILD_SHARED_LIBS=on # enable building of LAMMPS shared library (both options are needed!) @@ -45,12 +45,12 @@ shared library: What this does is create a liblammps.so which contains the majority of LAMMPS code. The generated lmp binary also dynamically links to this library. This means that either this liblammps.so file has to be in the same directory, a system -library path (e.g. /usr/lib64/) or in the LD\_LIBRARY\_PATH. +library path (e.g. /usr/lib64/) or in the LD_LIBRARY_PATH. If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as -CMAKE\_INSTALL\_PREFIX. +CMAKE_INSTALL_PREFIX. -.. parsed-literal:: +.. code-block:: bash # create virtualenv virtualenv --python=$(which python3) myenv3 @@ -66,12 +66,12 @@ CMAKE\_INSTALL\_PREFIX. make install This will also install the Python module into your virtualenv. Since virtualenv -doesn't change your LD\_LIBRARY\_PATH, you still need to add its lib64 folder to +doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to it, which contains the installed liblammps.so. -.. parsed-literal:: +.. code-block:: bash export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH Starting Python outside (!) of your build directory, but with the virtualenv -enabled and with the LD\_LIBRARY\_PATH set gives you access to LAMMPS via Python. +enabled and with the LD_LIBRARY_PATH set gives you access to LAMMPS via Python. diff --git a/doc/src/Python_test.rst b/doc/src/Python_test.rst index 1877a12bca..55a1c0a2d3 100644 --- a/doc/src/Python_test.rst +++ b/doc/src/Python_test.rst @@ -31,8 +31,8 @@ first importing from the lammps.py file: >>> CDLL("liblammps.so") If an error occurs, carefully go through the steps on the -:doc:`Build\_basics ` doc page about building a shared -library and the :doc:`Python\_install ` doc page about +:doc:`Build_basics ` doc page about building a shared +library and the :doc:`Python_install ` doc page about insuring Python can find the necessary two files it needs. Test LAMMPS and Python in serial: @@ -49,7 +49,7 @@ interactively from the bench directory: Or put the same lines in the file test.py and run it as -.. parsed-literal:: +.. code-block:: bash % python test.py @@ -68,7 +68,7 @@ To run LAMMPS in parallel, assuming you have installed the `PyPar `_ package as discussed above, create a test.py file containing these lines: -.. parsed-literal:: +.. code-block:: python import pypar from lammps import lammps @@ -81,7 +81,7 @@ To run LAMMPS in parallel, assuming you have installed the `mpi4py `_ package as discussed above, create a test.py file containing these lines: -.. parsed-literal:: +.. code-block:: python from mpi4py import MPI from lammps import lammps @@ -94,13 +94,13 @@ above, create a test.py file containing these lines: You can either script in parallel as: -.. parsed-literal:: +.. code-block:: bash % mpirun -np 4 python test.py and you should see the same output as if you had typed -.. parsed-literal:: +.. code-block:: bash % mpirun -np 4 lmp_g++ -in in.lj @@ -124,7 +124,7 @@ Running Python scripts: Note that any Python script (not just for LAMMPS) can be invoked in one of several ways: -.. parsed-literal:: +.. code-block:: bash % python foo.script % python -i foo.script @@ -133,7 +133,7 @@ one of several ways: The last command requires that the first line of the script be something like this: -.. parsed-literal:: +.. code-block:: bash #!/usr/local/bin/python #!/usr/local/bin/python -i @@ -141,7 +141,7 @@ something like this: where the path points to where you have Python installed, and that you have made the script file executable: -.. parsed-literal:: +.. code-block:: bash % chmod +x foo.script diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 956f341c80..d02873a8be 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -65,7 +65,7 @@ or "-bind-to core" (MPICH) can be used. If the LAMMPS command(s) you are using support multi-threading, you can set the number of threads per MPI task via the environment -variable OMP\_NUM\_THREADS, before you launch LAMMPS: +variable OMP_NUM_THREADS, before you launch LAMMPS: .. code-block:: bash diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 989408a798..afdae20376 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -23,7 +23,7 @@ letter abbreviation can be used: * :ref:`-sf or -suffix ` * :ref:`-v or -var ` -For example, the lmp\_mpi executable might be launched as follows: +For example, the lmp_mpi executable might be launched as follows: .. code-block:: bash @@ -50,8 +50,8 @@ set by using the :doc:`echo ` command in the input script itself. **-help** Print a brief help summary and a list of options compiled into this -executable for each LAMMPS style (atom\_style, fix, compute, -pair\_style, bond\_style, etc). This can tell you if the command you +executable for each LAMMPS style (atom_style, fix, compute, +pair_style, bond_style, etc). This can tell you if the command you want to use was included via the appropriate package at compile time. LAMMPS will print the info and immediately exit if this switch is used. @@ -65,7 +65,7 @@ used. Specify a file to use as an input script. This is an optional switch when running LAMMPS in one-partition mode. If it is not specified, LAMMPS reads its script from standard input, typically from a script -via I/O redirection; e.g. lmp\_linux < in.run. I/O redirection should +via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should also work in parallel, but if it does not (in the unlikely case that an MPI implementation does not support it), then use the -in flag. Note that this is a required switch when running LAMMPS in @@ -201,8 +201,8 @@ command which also launches another executable(s) at the same time. (The other executable could be LAMMPS as well.) The color is an integer value which should be different for each executable (another application may set this value in a different way). LAMMPS and the -other executable(s) perform an MPI\_Comm\_split() with their own colors -to shrink the MPI\_COMM\_WORLD communication to be the subset of +other executable(s) perform an MPI_Comm_split() with their own colors +to shrink the MPI_COMM_WORLD communication to be the subset of processors they are actually running on. Currently, this is only used in LAMMPS to perform client/server @@ -284,7 +284,7 @@ log files are created. This overrides the filename specified in the -log command-line option. This option is useful when working with large numbers of partitions, allowing the partition log files to be suppressed (-plog none) or placed in a sub-directory (-plog -replica\_files/log.lammps) If this option is not used the log file for +replica_files/log.lammps) If this option is not used the log file for partition N is log.lammps.N or whatever is specified by the -log command-line option. @@ -300,7 +300,7 @@ partition screen files are created. This overrides the filename specified in the -screen command-line option. This option is useful when working with large numbers of partitions, allowing the partition screen files to be suppressed (-pscreen none) or placed in a -sub-directory (-pscreen replica\_files/screen). If this option is not +sub-directory (-pscreen replica_files/screen). If this option is not used the screen file for partition N is screen.N or whatever is specified by the -screen command-line option. @@ -469,7 +469,7 @@ The syntax following restartfile (or remap), namely is identical to the arguments of the :doc:`write_dump ` command. See its doc page for details. This includes what per-atom -fields are written to the dump file and optional dump\_modify settings, +fields are written to the dump file and optional dump_modify settings, including ones that affect how parallel dump files are written, e.g. the *nfile* and *fileper* keywords. See the :doc:`dump_modify ` doc page for details. @@ -520,7 +520,7 @@ having to edit an input script. As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style -can be specified explicitly in your input script, e.g. pair\_style +can be specified explicitly in your input script, e.g. pair_style lj/cut/gpu. If the -suffix switch is used the specified suffix (gpu,intel,kk,omp,opt) is automatically appended whenever your input script command creates a new :doc:`atom `, diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index 4aeaf36707..d7d92dc5ee 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -168,7 +168,7 @@ additional information is printed, e.g. The first line is the time spent doing 3d FFTs (several per timestep) and the fraction it represents of the total KSpace time (listed above). Each 3d FFT requires computation (3 sets of 1d FFTs) and -communication (transposes). The total flops performed is 5Nlog\_2(N), +communication (transposes). The total flops performed is 5Nlog_2(N), where N is the number of points in the 3d grid. The FFTs are timed with and without the communication and a Gflop rate is computed. The 3d rate is with communication; the 1d rate is without (just the 1d diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index 65b299421e..0343e123b9 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -7,14 +7,14 @@ To run a serial (non-MPI) executable, follow these steps: then typing "cmd". * Move to the directory where you have your input script, (e.g. by typing: cd "Documents"). -* At the command prompt, type "lmp\_serial -in in.file", where +* At the command prompt, type "lmp_serial -in in.file", where in.file is the name of your LAMMPS input script. Note that the serial executable includes support for multi-threading parallelization from the styles in the USER-OMP packages. To run with 4 threads, you can type this: -.. parsed-literal:: +.. code-block:: bash lmp_serial -in in.lj -pk omp 4 -sf omp @@ -43,7 +43,7 @@ into the MPICH2 installation directory, then into the sub-directory Then type something like this: -.. parsed-literal:: +.. code-block:: bash mpiexec -localonly 4 lmp_mpi -in in.file mpiexec -np 4 lmp_mpi -in in.file @@ -58,13 +58,13 @@ patient before the output shows up. The parallel executable can also run on a single processor by typing something like this: -.. parsed-literal:: +.. code-block:: bash lmp_mpi -in in.lj Note that the parallel executable also includes OpenMP multi-threading, which can be combined with MPI using something like: -.. parsed-literal:: +.. code-block:: bash mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 8adcce52ef..d3947ec3ef 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -66,7 +66,7 @@ section below for examples where this has been done. acceleration and instead run it - concurrently with a GPU accelerated pair style - on the CPU. This can often be easily achieved with placing a *suffix off* command before and a *suffix on* command after the - *kspace\_style pppm* command. + *kspace_style pppm* command. * The KOKKOS/OpenMP and USER-OMP package have different thread management strategies, which should result in USER-OMP being more efficient for a small number of threads with increasing overhead as the number of threads diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index eb03ff560c..9981b22b03 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -35,9 +35,9 @@ toolkit software on your system (this is primarily tested on Linux and completely unsupported on Windows): * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information -* Go to http://www.nvidia.com/object/cuda\_get.html +* Go to http://www.nvidia.com/object/cuda_get.html * Install a driver and toolkit appropriate for your system (SDK is not necessary) -* Run lammps/lib/gpu/nvc\_get\_devices (after building the GPU library, see below) to +* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties To compile and use this package in OpenCL mode, you currently need @@ -47,7 +47,7 @@ installed. There can be multiple of them for the same or different hardware (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those as 'platforms'. The GPU library will select the **first** suitable platform, but this can be overridden using the device option of the :doc:`package ` -command. run lammps/lib/gpu/ocl\_get\_devices to get a list of available +command. run lammps/lib/gpu/ocl_get_devices to get a list of available platforms and devices with a suitable ICD available. **Building LAMMPS with the GPU package:** @@ -76,7 +76,7 @@ automatically append "gpu" to styles that support it. Use the "-pk gpu Ng" :doc:`command-line switch ` to set Ng = # of GPUs/node to use. -.. parsed-literal:: +.. code-block:: bash lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node @@ -106,7 +106,7 @@ and use of multiple MPI tasks/GPU is the same. Use the :doc:`suffix gpu ` command, or you can explicitly add an "gpu" suffix to individual styles in your input script, e.g. -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/gpu 2.5 diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 1cad9cbeb8..4658fb9584 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -79,7 +79,7 @@ order of operations compared to LAMMPS without acceleration: * The *newton* setting applies to all atoms, not just atoms shared between MPI tasks * Vectorization can change the order for adding pairwise forces -* When using the -DLMP\_USE\_MKL\_RNG define (all included intel optimized +* When using the -DLMP_USE_MKL_RNG define (all included intel optimized makefiles do) at build time, the random number generator for dissipative particle dynamics (pair style dpd/intel) uses the Mersenne Twister generator included in the Intel MKL library (that should be @@ -102,8 +102,8 @@ LAMMPS should be built with the USER-INTEL package installed. Simulations should be run with 1 MPI task per physical *core*\ , not *hardware thread*\ . -* Edit src/MAKE/OPTIONS/Makefile.intel\_cpu\_intelmpi as necessary. -* Set the environment variable KMP\_BLOCKTIME=0 +* Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. +* Set the environment variable KMP_BLOCKTIME=0 * "-pk intel 0 omp $t -sf intel" added to LAMMPS command-line * $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi * For some of the simple 2-body potentials without long-range @@ -111,26 +111,26 @@ not *hardware thread*\ . the "newton off" setting added to the input script * For simulations on higher node counts, add "processors \* \* \* grid numa" to the beginning of the input script for better scalability -* If using *kspace\_style pppm* in the input script, add - "kspace\_modify diff ad" for better performance +* If using *kspace_style pppm* in the input script, add + "kspace_modify diff ad" for better performance For Intel Xeon Phi CPUs: * Runs should be performed using MCDRAM. -For simulations using *kspace\_style pppm* on Intel CPUs supporting +For simulations using *kspace_style pppm* on Intel CPUs supporting AVX-512: -* Add "kspace\_modify diff ad" to the input script +* Add "kspace_modify diff ad" to the input script * The command-line option should be changed to "-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of threads minus 1. -* Do not use thread affinity (set KMP\_AFFINITY=none) +* Do not use thread affinity (set KMP_AFFINITY=none) * The "newton off" setting may provide better scalability For Intel Xeon Phi co-processors (Offload): -* Edit src/MAKE/OPTIONS/Makefile.intel\_co-processor as necessary +* Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary * "-pk intel N omp 1" added to command-line where N is the number of co-processors per node. @@ -205,7 +205,7 @@ For building with make, several example Makefiles for building with the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/ directory: -.. parsed-literal:: +.. code-block:: bash Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload Makefile.knl # Intel Compiler, Intel MPI, No Offload @@ -213,7 +213,7 @@ directory: Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload -Makefile.knl is identical to Makefile.intel\_cpu\_intelmpi except that +Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that it explicitly specifies that vectorization should be for Intel Xeon Phi x200 processors making it easier to cross-compile. For users with recent installations of Intel Parallel Studio, the process can be as @@ -234,12 +234,12 @@ 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. -CCFLAGS should include "-DLMP\_INTEL\_USELRT" (unless POSIX Threads -are not supported in the build environment) and "-DLMP\_USE\_MKL\_RNG" +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" -or if the library is not available, "-DLMP\_INTEL\_NO\_TBB" can be added -to CCFLAGS. For builds supporting offload, "-DLMP\_INTEL\_OFFLOAD" is +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 recommended CCFLAG options for best performance are "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div". @@ -297,9 +297,9 @@ almost all cases. OpenMP threads on the host (CPU) will be set by default on the host *when using offload to a co-processor*\ . In this case, it is unnecessary to use other methods to control affinity (e.g. taskset, numactl, - I\_MPI\_PIN\_DOMAIN, etc.). This can be disabled with the *no\_affinity* + I_MPI_PIN_DOMAIN, etc.). This can be disabled with the *no_affinity* option to the :doc:`package intel ` command or by disabling the - option at build time (by adding -DINTEL\_OFFLOAD\_NOAFFINITY to the + option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile). Disabling this option is not recommended, especially when running on a machine with Intel Hyper-Threading technology disabled. @@ -313,7 +313,7 @@ editing the input script. This switch will automatically append :doc:`package intel 1 `. This package command is used to set options for the USER-INTEL package. The default package command will specify that USER-INTEL calculations are performed in mixed precision, -that the number of OpenMP threads is specified by the OMP\_NUM\_THREADS +that the number of OpenMP threads is specified by the OMP_NUM_THREADS environment variable, and that if co-processors are present and the binary was built with offload support, that 1 co-processor per node will be used with automatic balancing of work between the CPU and the @@ -324,11 +324,11 @@ the "-pk intel Nphi" :doc:`command-line switch ` with keyword/value pairs as specified in the documentation. Here, Nphi = # of Xeon Phi co-processors/node (ignored without offload support). Common options to the USER-INTEL package include *omp* to -override any OMP\_NUM\_THREADS setting and specify the number of OpenMP +override any OMP_NUM_THREADS setting and specify the number of OpenMP threads, *mode* to set the floating-point precision mode, and *lrt* to enable Long-Range Thread mode as described below. See the :doc:`package intel ` command for details, including the default values used for all its options if not specified, and how to set the number -of OpenMP threads via the OMP\_NUM\_THREADS environment variable if +of OpenMP threads via the OMP_NUM_THREADS environment variable if desired. Examples (see documentation for your MPI/Machine for differences in @@ -375,7 +375,7 @@ Long-Range Thread (LRT) mode is an option to the :doc:`package intel ` with SMT. It generates an extra pthread for each MPI task. The thread is dedicated to performing some of the PPPM calculations and MPI communications. This feature requires setting the pre-processor flag --DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS. It is unset +-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but it is set in all makefiles tuned for the USER-INTEL package. On Intel Xeon Phi x200 series CPUs, the LRT feature will likely improve @@ -387,7 +387,7 @@ normally be used for the run and add the "lrt yes" option to the "-pk" command-line suffix or "package intel" command. For example, if a run would normally perform best with "-pk intel 0 omp 4", instead use "-pk intel 0 omp 3 lrt yes". When using LRT, you should set the -environment variable "KMP\_AFFINITY=none". LRT mode is not supported +environment variable "KMP_AFFINITY=none". LRT mode is not supported when using offload. .. note:: @@ -425,7 +425,7 @@ alternative to LRT mode and the two cannot be used together. Currently, when using Intel MPI with Intel Xeon Phi x200 series CPUs, better performance might be obtained by setting the -environment variable "I\_MPI\_SHM\_LMT=shm" for Linux kernels that do +environment variable "I_MPI_SHM_LMT=shm" for Linux kernels that do not yet have full support for AVX-512. Runs on Intel Xeon Phi x200 series processors will always perform better using MCDRAM. Please consult your system documentation for the best approach to specify @@ -513,7 +513,7 @@ When offloading to a co-processor, :doc:`hybrid ` styles that require skip lists for neighbor builds cannot be offloaded. Using :doc:`hybrid/overlay ` is allowed. Only one intel accelerated style may be used with hybrid styles when offloading. -:doc:`Special\_bonds ` exclusion lists are not currently +:doc:`Special_bonds ` exclusion lists are not currently supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of the pair styles in the USER-INTEL package currently support the diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 46b4be571c..6658957006 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -21,7 +21,7 @@ package was developed primarily by Christian Trott (Sandia) and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions -see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos\_PG.pdf. +see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. Kokkos currently provides support for 3 modes of execution (per MPI task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP @@ -108,8 +108,8 @@ 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 + 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:: @@ -134,8 +134,8 @@ small numbers of threads (i.e. 8 or less) but does increase memory footprint and is not scalable to large numbers of threads. An alternative to data duplication is to use thread-level atomic operations which do not require data duplication. The use of atomic operations can -be enforced by compiling LAMMPS with the "-DLMP\_KOKKOS\_USE\_ATOMICS" -pre-processor flag. Most but not all Kokkos-enabled pair\_styles support +be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS" +pre-processor flag. Most but not all Kokkos-enabled pair_styles support data duplication. Alternatively, full neighbor lists avoid the need for duplication or atomic operations but require more compute operations per atom. When using the Kokkos Serial back end or the OpenMP back end with @@ -159,9 +159,9 @@ for your MPI installation), binding can be forced with these flags: For binding threads with KOKKOS OpenMP, use thread affinity environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12 or later) setting the environment variable -OMP\_PROC\_BIND=true should be sufficient. In general, for best -performance with OpenMP 4.0 or better set OMP\_PROC\_BIND=spread and -OMP\_PLACES=threads. For binding threads with the KOKKOS pthreads +OMP_PROC_BIND=true should be sufficient. In general, for best +performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and +OMP_PLACES=threads. For binding threads with the KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option as described below. **Running on Knight's Landing (KNL) Intel Xeon Phi:** @@ -290,7 +290,7 @@ one or more nodes, each with two GPUs: .. note:: To get an accurate timing breakdown between time spend in pair, - kspace, etc., you must set the environment variable CUDA\_LAUNCH\_BLOCKING=1. + kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1. However, this will reduce performance and is not recommended for production runs. **Run with the KOKKOS package by editing an input script:** @@ -320,8 +320,8 @@ wish to change any of its option defaults, as set by the "-k on" With the KOKKOS package, both OpenMP multi-threading and GPUs can be used together in a few special cases. In the Makefile, the -KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is -the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi +KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is +the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi .. code-block:: bash @@ -357,7 +357,7 @@ GPU. First compile with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc. in the input file and the "kk" suffix (equal to "kk/device") on the command line. Also make -sure the environment variable CUDA\_LAUNCH\_BLOCKING is not set to "1" +sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" so CPU/GPU overlap can occur. **Speed-ups to expect:** @@ -394,34 +394,34 @@ Makefile.machine, or they can be specified as CMake variables. Each takes a value shown below. The default value is listed, which is set in the lib/kokkos/Makefile.kokkos file. -* KOKKOS\_DEBUG, values = *yes*\ , *no*\ , default = *no* -* KOKKOS\_USE\_TPLS, values = *hwloc*\ , *librt*\ , *experimental\_memkind*, default = *none* -* KOKKOS\_CXX\_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11* -* KOKKOS\_OPTIONS, values = *aggressive\_vectorization*, *disable\_profiling*, default = *none* -* KOKKOS\_CUDA\_OPTIONS, values = *force\_uvm*, *use\_ldg*, *rdc*\ , *enable\_lambda*, default = *enable\_lambda* +* KOKKOS_DEBUG, values = *yes*\ , *no*\ , default = *no* +* KOKKOS_USE_TPLS, values = *hwloc*\ , *librt*\ , *experimental_memkind*, default = *none* +* KOKKOS_CXX_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11* +* KOKKOS_OPTIONS, values = *aggressive_vectorization*, *disable_profiling*, default = *none* +* KOKKOS_CUDA_OPTIONS, values = *force_uvm*, *use_ldg*, *rdc*\ , *enable_lambda*, default = *enable_lambda* -KOKKOS\_USE\_TPLS=hwloc binds threads to hardware cores, so they do not -migrate during a simulation. KOKKOS\_USE\_TPLS=hwloc should always be -used if running with KOKKOS\_DEVICES=Pthreads for pthreads. It is not -necessary for KOKKOS\_DEVICES=OpenMP for OpenMP, because OpenMP +KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not +migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be +used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not +necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is given on the :doc:`Speed omp ` doc page. -KOKKOS\_USE\_TPLS=librt enables use of a more accurate timer mechanism +KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism on most Unix platforms. This library is not available on all platforms. -KOKKOS\_DEBUG is only useful when developing a Kokkos-enabled style -within LAMMPS. KOKKOS\_DEBUG=yes enables printing of run-time +KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style +within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time debugging information that can be useful. It also enables runtime bounds checking on Kokkos data structures. -KOKKOS\_CXX\_STANDARD and KOKKOS\_OPTIONS are typically not changed when +KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS. -KOKKOS\_CUDA\_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS -package must be compiled with the *enable\_lambda* option when using +KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS +package must be compiled with the *enable_lambda* option when using GPUs. Restrictions diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst index 2f86aa18f2..686fdb6adc 100644 --- a/doc/src/Speed_measure.rst +++ b/doc/src/Speed_measure.rst @@ -14,7 +14,7 @@ timings; you can simply extrapolate from short runs. For the set of runs, look at the timing data printed to the screen and log file at the end of each LAMMPS run. The -:doc:`Run\_output ` doc page gives an overview. +:doc:`Run_output ` doc page gives an overview. Running on one (or a few processors) should give a good estimate of the serial performance and what portions of the timestep are taking @@ -42,5 +42,5 @@ inaccurate relative timing data, because processors have to wait when communication occurs for other processors to catch up. Thus the reported times for "Communication" or "Other" may be higher than they really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI\_Barrier() lines in src/timer.cpp, and re-compile +uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile LAMMPS, to obtain synchronized timings. diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 812d774867..04e4366758 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -23,7 +23,7 @@ instructions. These examples assume one or more 16-core nodes. -.. parsed-literal:: +.. code-block:: bash env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels @@ -43,14 +43,14 @@ node), otherwise performance will suffer. As in the lines above, use the "-sf omp" :doc:`command-line switch `, which will automatically append "omp" to styles that support it. The "-sf omp" switch also issues a default :doc:`package omp 0 ` command, which will set the number of -threads per MPI task via the OMP\_NUM\_THREADS environment variable. +threads per MPI task via the OMP_NUM_THREADS environment variable. You can also use the "-pk omp Nt" :doc:`command-line switch `, to explicitly set Nt = # of OpenMP threads per MPI task to use, as well as additional options. Its syntax is the same as the :doc:`package omp ` command whose doc page gives details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the -OMP\_NUM\_THREADS environment variable. +OMP_NUM_THREADS environment variable. **Or run with the USER-OMP package by editing an input script:** @@ -60,14 +60,14 @@ and threads/MPI task is the same. Use the :doc:`suffix omp ` command, or you can explicitly add an "omp" suffix to individual styles in your input script, e.g. -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/omp 2.5 You must also use the :doc:`package omp ` command to enable the USER-OMP package. When you do this you also specify how many threads per MPI task to use. The command doc page explains other options and -how to set the number of threads via the OMP\_NUM\_THREADS environment +how to set the number of threads via the OMP_NUM_THREADS environment variable. **Speed-ups to expect:** diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index f1c7868644..297177f8d4 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -17,7 +17,7 @@ See the :ref:`Build extras ` doc page for instructions. **Run with the OPT package from the command line:** -.. parsed-literal:: +.. code-block:: bash lmp_mpi -sf opt -in in.script # run in serial mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel @@ -30,7 +30,7 @@ automatically append "opt" to styles that support it. Use the :doc:`suffix opt ` command, or you can explicitly add an "opt" suffix to individual styles in your input script, e.g. -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/opt 2.5 diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index e515a89d19..ab02ba7f48 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -90,13 +90,13 @@ listed above: +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | re-build LAMMPS | make machine | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| prepare and test a regular LAMMPS simulation | lmp\_machine -in in.script; mpirun -np 32 lmp\_machine -in in.script | +| prepare and test a regular LAMMPS simulation | lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | enable specific accelerator support via '-k on' :doc:`command-line switch `, | only needed for KOKKOS package | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | set any needed options for the package via "-pk" :doc:`command-line switch ` or :doc:`package ` command, | only if defaults need to be changed | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| use accelerated styles in your input via "-sf" :doc:`command-line switch ` or :doc:`suffix ` command | lmp\_machine -in in.script -sf gpu | +| use accelerated styles in your input via "-sf" :doc:`command-line switch ` or :doc:`suffix ` command | lmp_machine -in in.script -sf gpu | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ Note that the first 4 steps can be done as a single command with @@ -132,7 +132,7 @@ packages. As an example, here is a command that builds with all the GPU related packages installed (GPU, KOKKOS with Cuda), including settings to build the needed auxiliary GPU libraries for Kepler GPUs: -.. parsed-literal:: +.. code-block:: bash Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index cfe8a17d55..6137b1aa6f 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -99,7 +99,7 @@ binary2txt tool The file binary2txt.cpp converts one or more binary LAMMPS dump file into ASCII text files. The syntax for running the tool is -.. parsed-literal:: +.. code-block:: bash binary2txt file1 file2 ... @@ -149,7 +149,7 @@ chains and solvent atoms can strongly overlap, so LAMMPS needs to run the system initially with a "soft" pair potential to un-overlap it. The syntax for running the tool is -.. parsed-literal:: +.. code-block:: bash chain < def.chain > data.file @@ -171,18 +171,18 @@ To compile the tools, edit the makefile for your system and run "make". Please report problems and issues the colvars library and its tools at: https://github.com/colvars/colvars/issues -abf\_integrate: +abf_integrate: MC-based integration of multidimensional free energy gradient Version 20110511 .. parsed-literal:: - Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >] + ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >] The LAMMPS interface to the colvars collective variable library, as well as these tools, were created by Axel Kohlmeyer (akohlmey at -gmail.com) at ICTP, Italy. +gmail.com) while at ICTP, Italy. ---------- @@ -238,7 +238,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr eam database tool ----------------------------- -The tools/eam\_database directory contains a Fortran program that will +The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, Zr. The files can then be used with the :doc:`pair_style eam/alloy ` command. @@ -256,7 +256,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, eam generate tool ----------------------------- -The tools/eam\_generate directory contains several one-file C programs +The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) ` setfl potential file. The potentials they produce are in the potentials directory, and can be used with the :doc:`pair_style eam/alloy ` command. @@ -427,7 +427,7 @@ atoms can strongly overlap, so LAMMPS needs to run the system initially with a "soft" pair potential to un-overlap it. The syntax for running the tool is -.. parsed-literal:: +.. code-block:: bash micelle2d < def.micelle2d > data.file @@ -512,10 +512,10 @@ This tool was written by Zachary Kraus at Georgia Tech. .. _pymol: -pymol\_asphere tool +pymol_asphere tool ------------------------------- -The pymol\_asphere sub-directory contains a tool for converting a +The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the `PyMol visualization package `_ or its `open source variant `_. @@ -525,7 +525,7 @@ particles into an input file for the `PyMol visualization package `_ Specifically, the tool triangulates the ellipsoids so they can be viewed as true ellipsoidal particles within PyMol. See the README and -examples directory within pymol\_asphere for more information. +examples directory within pymol_asphere for more information. This tool was written by Mike Brown at Sandia. @@ -555,7 +555,7 @@ README for more info on Pizza.py and how to use these scripts. replica tool -------------------------- -The tools/replica directory contains the reorder\_remd\_traj python script which +The tools/replica directory contains the reorder_remd_traj python script which can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. @@ -568,7 +568,7 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) ---------- -.. _reax\_tool: +.. _reax_tool: reax tool -------------------------- @@ -587,7 +587,7 @@ These tools were written by Aidan Thompson at Sandia. smd tool ------------------ -The smd sub-directory contains a C++ file dump2vtk\_tris.cpp and +The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output files created by the Smooth-Mach Dynamics (USER-SMD) package into a VTK-compatible unstructured grid file. It could then be read in and @@ -610,7 +610,7 @@ The spin sub-directory contains a C file interpolate.c which can be compiled and used to perform a cubic polynomial interpolation of the MEP following a GNEB calculation. -See the README file in tools/spin/interpolate\_gneb for more details. +See the README file in tools/spin/interpolate_gneb for more details. This tool was written by the SPIN package author, Julien Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei @@ -618,7 +618,7 @@ Ivanov, at University of Iceland (ali5 at hi.is). ---------- -.. _singularity\_tool: +.. _singularity_tool: singularity tool ---------------------------------------- diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index fc8641d93c..a8c227c765 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -36,7 +36,7 @@ The *charmm* angle style uses the potential E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2 -with an additional Urey\_Bradley term based on the distance :math:`r` between +with an additional Urey_Bradley term based on the distance :math:`r` between the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`, :math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle type. diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 95852acd11..4fa95481ac 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -53,7 +53,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_YAFF package. See the :doc:`Build package ` doc +USER_YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index a47f9e5620..a2008f731c 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -66,7 +66,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index 7b257a6a54..795142ccaa 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -65,7 +65,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index e39c079e0a..c84b351132 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -34,7 +34,7 @@ command or in the data file. In the :doc:`angle_coeff ` commands, the name of an angle style must be added after the angle type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 angle\_coeff +appropriate to that style. In the example above, the 2 angle_coeff commands set angles of angle type 1 to be computed with a *harmonic* potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`. All other angle types :math:`(2 - N)` are computed with a *cosine* potential with coefficient diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 9568bf165c..cc6ee120cd 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_YAFF package. See the :doc:`Build package ` doc +USER_YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index be44854298..4559389a2a 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -72,7 +72,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index cbdb809530..5601e4f245 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -37,7 +37,7 @@ where :math:`\theta_0` is the equilibrium value of the angle and *lj/sdk* pair style between the atoms 1 and 3. This angle potential is intended for coarse grained MD simulations with the CMM parameterization using the :doc:`pair_style lj/sdk `. Relative to the -pair\_style *lj/sdk*\ , however, the energy is shifted by +pair_style *lj/sdk*\ , however, the energy is shifted by :math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. @@ -50,7 +50,7 @@ The following coefficients must be defined for each angle type via the :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K` are in energy/radian\^2. The also required *lj/sdk* parameters will be extracted automatically -from the pair\_style. +from the pair_style. ---------- diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index e43dee2591..91232a6b6c 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -41,7 +41,7 @@ files which means angle_style and :doc:`angle_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the :doc:`read_restart ` command for details on how to do this. The one exception is that -angle\_style *hybrid* only stores the list of sub-styles in the restart +angle_style *hybrid* only stores the list of sub-styles in the restart file; angle coefficients need to be re-specified. .. note:: @@ -61,7 +61,7 @@ the style to display the formula it computes and coefficients specified by the associated :doc:`angle_coeff ` command. Click on the style to display the formula it computes, any additional -arguments specified in the angle\_style command, and coefficients +arguments specified in the angle_style command, and coefficients specified by the associated :doc:`angle_coeff ` command. There are also additional accelerated pair styles included in the @@ -98,7 +98,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist. Restrictions """""""""""" -Angle styles can only be set for atom\_styles that allow angles to be +Angle styles can only be set for atom_styles that allow angles to be defined. Most angle styles are part of the MOLECULE package. They are only diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index 9759e7fcd9..729d890d67 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -87,7 +87,7 @@ keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`angle_style table ` command. Let -Ntable = *N* in the angle\_style command, and Nfile = "N" in the +Ntable = *N* in the angle_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate as needed to generate energy and derivative @@ -148,12 +148,12 @@ instructions on how to use the accelerated styles effectively. **Restart info:** -This angle style writes the settings for the "angle\_style table" -command to :doc:`binary restart files `, so a angle\_style +This angle style writes the settings for the "angle_style table" +command to :doc:`binary restart files `, so a angle_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file, since it is tabulated in the potential files. Thus, -angle\_coeff commands do need to be specified in the restart input +angle_coeff commands do need to be specified in the restart input script. Restrictions diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index c4686c4f21..c94ca65c1c 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -60,8 +60,8 @@ The only reason not to use atom IDs is if you are running an atomic simulation so large that IDs cannot be uniquely assigned. For a default LAMMPS build this limit is 2\^31 or about 2 billion atoms. However, even in this case, you can use 64-bit atom IDs, allowing 2\^63 -or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS\_BIGBIG -switch. This is described on the :doc:`Build\_settings ` +or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG +switch. This is described on the :doc:`Build_settings ` doc page. If atom IDs are not used, they must be specified as 0 for all atoms, e.g. in a data or restart file. @@ -108,7 +108,7 @@ this command. Note that specifying "all" as the group-ID effectively turns off the *first* option. It is OK to use the *first* keyword with a group that has not yet been -defined, e.g. to use the atom\_modify first command at the beginning of +defined, e.g. to use the atom_modify first command at the beginning of your input script. LAMMPS does not use the group until a simulation is run. diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index fcd138c836..df00c65f01 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -119,7 +119,7 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *tri* | corner points, angular momentum | rigid bodies | +--------------+-----------------------------------------------------+--------------------------------------+ -| *wavepacket* | charge, spin, eradius, etag, cs\_re, cs\_im | AWPMD | +| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD | +--------------+-----------------------------------------------------+--------------------------------------+ .. note:: @@ -158,7 +158,7 @@ For the *dipole* style, a point dipole is defined for each point particle. Note that if you wish the particles to be finite-size spheres as in a Stockmayer potential for a dipolar fluid, so that the particles can rotate due to dipole-dipole interactions, then you need -to use atom\_style hybrid sphere dipole, which will assign both a +to use atom_style hybrid sphere dipole, which will assign both a diameter and dipole moment to each particle. For the *electron* style, the particles representing electrons are 3d @@ -171,14 +171,14 @@ per-particle mass and volume. The *dpd* style is for dissipative particle dynamics (DPD) particles. Note that it is part of the USER-DPD package, and is not for use with the :doc:`pair_style dpd or dpd/stat ` commands, which can -simply use atom\_style atomic. Atom\_style dpd extends DPD particle +simply use atom_style atomic. Atom_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal chemical energy (uChem). The *edpd* style is for energy-conserving dissipative particle -dynamics (eDPD) particles which store a temperature (edpd\_temp), and -heat capacity(edpd\_cv). +dynamics (eDPD) particles which store a temperature (edpd_temp), and +heat capacity(edpd_cv). The *mdpd* style is for many-body dissipative particle dynamics (mDPD) particles which store a density (rho) for considering @@ -186,7 +186,7 @@ density-dependent many-body interactions. The *tdpd* style is for transport dissipative particle dynamics (tDPD) particles which store a set of chemical concentration. An integer -"cc\_species" is required to specify the number of chemical species +"cc_species" is required to specify the number of chemical species involved in a tDPD system. The *meso* style is for smoothed particle hydrodynamics (SPH) @@ -205,7 +205,7 @@ Those spins have a norm (their magnetic moment) and a direction. The *wavepacket* style is similar to *electron*\ , but the electrons may consist of several Gaussian wave packets, summed up with coefficients -cs= (cs\_re,cs\_im). Each of the wave packets is treated as a separate +cs= (cs_re,cs_im). Each of the wave packets is treated as a separate particle in LAMMPS, wave packets belonging to the same electron must have identical *etag* values. @@ -232,7 +232,7 @@ can be advantageous for large-scale coarse-grained systems. .. note:: When using the *template* style with a :doc:`molecule template ` that contains multiple molecules, you should - insure the atom types, bond types, angle\_types, etc in all the + insure the atom types, bond types, angle_types, etc in all the molecules are consistent. E.g. if one molecule represents H2O and another CO2, then you probably do not want each molecule file to define 2 atom types and a single bond type, because they will conflict @@ -256,7 +256,7 @@ orientation and position can be time integrated due to forces and torques. Note that there may be additional arguments required along with the -*bstyle* specification, in the atom\_style body command. These +*bstyle* specification, in the atom_style body command. These arguments are described on the :doc:`Howto body ` doc page. ---------- @@ -271,7 +271,7 @@ If some atoms have bonds, but others do not, use the *bond* style. The only scenario where the *hybrid* style is needed is if there is no single style which defines all needed properties of all atoms. For example, as mentioned above, if you want dipolar particles which will -rotate due to torque, you need to use "atom\_style hybrid sphere +rotate due to torque, you need to use "atom_style hybrid sphere dipole". When a hybrid style is used, atoms store and communicate the union of all quantities implied by the individual styles. @@ -351,7 +351,7 @@ Related commands Default """"""" -atom\_style atomic +atom_style atomic ---------- diff --git a/doc/src/balance.rst b/doc/src/balance.rst index f3015127d9..5e631fdd27 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -197,7 +197,7 @@ The "grid" methods can be used with either of the :doc:`comm_style ` command options, *brick* or *tiled*\ . The "tiling" methods can only be used with :doc:`comm_style tiled `. Note that it can be useful to use a "grid" method with :doc:`comm_style tiled ` to return the domain -partitioning to a logical 3d grid of processors so that "comm\_style +partitioning to a logical 3d grid of processors so that "comm_style brick" can afterwords be specified for subsequent :doc:`run ` commands. @@ -228,7 +228,7 @@ that specify the position of the cutting planes. This requires knowing Ps = Px or Py or Pz = the number of processors assigned by LAMMPS to the relevant dimension. This assignment is made (and the Px, Py, Pz values printed out) when the simulation box is created by -the "create\_box" or "read\_data" or "read\_restart" command and is +the "create_box" or "read_data" or "read_restart" command and is influenced by the settings of the :doc:`processors ` command. @@ -333,7 +333,7 @@ particles in that sub-box. ---------- -.. _weighted\_balance: +.. _weighted_balance: This sub-section describes how to perform weighted load balancing using the *weight* keyword. @@ -462,7 +462,7 @@ velocity, the volume of its Voronoi cell, etc. The *store* weight style does not compute a weight factor. Instead it stores the current accumulated weights in a custom per-atom property -specified by *name*\ . This must be a property defined as *d\_name* via +specified by *name*\ . This must be a property defined as *d_name* via the :doc:`fix property/atom ` command. Note that these custom per-atom properties can be output in a :doc:`dump ` file, so this is a way to examine, debug, or visualize the diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 2a45e32534..416190a367 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -40,7 +40,7 @@ leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that using a bond\_coeff command can override a previous setting +Note that using a bond_coeff command can override a previous setting for the same bond type. For example, these commands set the coeffs for all bond types, then overwrite the coeffs for just bond type 2: @@ -50,7 +50,7 @@ for all bond types, then overwrite the coeffs for just bond type 2: bond_coeff 2 200.0 1.2 A line in a data file that specifies bond coefficients uses the exact -same format as the arguments of the bond\_coeff command in an input +same format as the arguments of the bond_coeff command in an input script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Bond Coeffs" section of a data file, the line that @@ -68,7 +68,7 @@ compact form on the :doc:`Commands bond ` doc page. On either of those pages, click on the style to display the formula it computes and its coefficients as specified by the associated -bond\_coeff command. +bond_coeff command. ---------- diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 003790ecd5..74bd39988b 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -32,9 +32,9 @@ be computed with a *harmonic* potential. The assignment of bond type to style is made via the :doc:`bond_coeff ` command or in the data file. -In the bond\_coeff commands, the name of a bond style must be added +In the bond_coeff commands, the name of a bond style must be added after the bond type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 bond\_coeff +appropriate to that style. In the example above, the 2 bond_coeff commands set bonds of bond type 1 to be computed with a *harmonic* potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`. All other bond types (2-N) are computed with a *fene* potential with coefficients 30.0, @@ -54,7 +54,7 @@ line in the "Bond Coeffs" section, e.g. ... A bond style of *none* with no additional coefficients can be used in -place of a bond style, either in a input script bond\_coeff command or +place of a bond style, either in a input script bond_coeff command or in the data file, if you desire to turn off interactions for specific bond types. @@ -69,7 +69,7 @@ info. Unlike other bond styles, the hybrid bond style does not store bond coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when restarting a simulation from a restart -file, you need to re-specify bond\_coeff commands. +file, you need to re-specify bond_coeff commands. Related commands """""""""""""""" diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index d86084e01e..8ea79d9139 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER\_YAFF package. See the :doc:`Build package ` doc +USER_YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index 65d314c039..52cc761da1 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -47,10 +47,10 @@ The coefficients associated with a bond style can be specified in a data or restart file or via the :doc:`bond_coeff ` command. All bond potentials store their coefficient data in binary restart -files which means bond\_style and :doc:`bond_coeff ` commands +files which means bond_style and :doc:`bond_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the :doc:`read_restart ` command for -details on how to do this. The one exception is that bond\_style +details on how to do this. The one exception is that bond_style *hybrid* only stores the list of sub-styles in the restart file; bond coefficients need to be re-specified. @@ -71,7 +71,7 @@ the style to display the formula it computes and coefficients specified by the associated :doc:`bond_coeff ` command. Click on the style to display the formula it computes, any additional -arguments specified in the bond\_style command, and coefficients +arguments specified in the bond_style command, and coefficients specified by the associated :doc:`bond_coeff ` command. There are also additional accelerated pair styles included in the diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index a790db595d..445face231 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -146,12 +146,12 @@ instructions on how to use the accelerated styles effectively. **Restart info:** -This bond style writes the settings for the "bond\_style table" -command to :doc:`binary restart files `, so a bond\_style +This bond style writes the settings for the "bond_style table" +command to :doc:`binary restart files `, so a bond_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file, since it is tabulated in the potential files. Thus, -bond\_coeff commands do need to be specified in the restart input +bond_coeff commands do need to be specified in the restart input script. Restrictions diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 95836a6e1c..42df0472a1 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -33,7 +33,7 @@ atoms listed in the data file read by the :doc:`read_data ` command. If no bond style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with a BondCoeff -section for any bond style. Similarly, any bond\_coeff commands +section for any bond style. Similarly, any bond_coeff commands will only be checked for the bond type number and the rest ignored. Note that the :doc:`bond_coeff ` command must be used for diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index a3a252baa0..2ab70ddec8 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -102,10 +102,10 @@ new owning processors. .. note:: - This means that you cannot use the change\_box command to enlarge + This means that you cannot use the change_box command to enlarge a shrink-wrapped box, e.g. to make room to insert more atoms via the :doc:`create_atoms ` command, because the simulation box - will be re-shrink-wrapped before the change\_box command completes. + will be re-shrink-wrapped before the change_box command completes. Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions: @@ -120,7 +120,7 @@ new owning processors. .. note:: - Unlike the earlier "displace\_box" version of this command, atom + Unlike the earlier "displace_box" version of this command, atom remapping is NOT performed by default. This command allows remapping to be done in a more general way, exactly when you specify it (zero or more times) in the sequence of transformations. Thus if you do not @@ -280,7 +280,7 @@ command. This command allows the boundary conditions to be changed later in your input script. Also note that the :doc:`read_restart ` will change boundary conditions to match what is stored in the restart file. So if you wish to change -them, you should use the change\_box command after the read\_restart +them, you should use the change_box command after the read_restart command. ---------- @@ -308,7 +308,7 @@ useful if you wish to use the *remap* keyword more than once or if you wish it to be applied to an intermediate box size/shape in a sequence of keyword operations. Note that the box size/shape is saved before any of the keywords are processed, i.e. the box size/shape at the time -the create\_box command is encountered in the input script. +the create_box command is encountered in the input script. The *remap* keyword remaps atom coordinates from the last saved box size/shape to the current box state. For example, if you stretch the @@ -343,7 +343,7 @@ the input script when this command is issued, no :doc:`dumps ` can be active, nor can a :doc:`fix deform ` be active. This is because these commands test whether the simulation box is orthogonal when they are first issued. Note that these commands can be used in -your script before a change\_box command is issued, so long as an +your script before a change_box command is issued, so long as an :doc:`undump ` or :doc:`unfix ` command is also used to turn them off. diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 8f745c88b1..9a2ae60f1e 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -49,9 +49,9 @@ processors and stored as properties of ghost atoms. you specify a :doc:`comm_style ` or :doc:`read_restart ` command, all communication settings are restored to their default or stored values, including those - previously reset by a comm\_modify command. Thus if your input script - specifies a comm\_style or read\_restart command, you should use the - comm\_modify command after it. + previously reset by a comm_modify command. Thus if your input script + specifies a comm_style or read_restart command, you should use the + comm_modify command after it. The *mode* keyword determines whether a single or multiple cutoff distances are used to determine which atoms to communicate. @@ -82,7 +82,7 @@ printed. Specifying a cutoff value of 0.0 will reset any previous value to the default. If bonded interactions exist and equilibrium bond length information is available, then also a heuristic based on that bond length is computed. It is used as communication cutoff, if there is no pair -style present and no *comm\_modify cutoff* command used. Otherwise a +style present and no *comm_modify cutoff* command used. Otherwise a warning is printed, if this bond based estimate is larger than the communication cutoff used. A diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 3dd079500f..0726a502bc 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -72,11 +72,11 @@ discussed below, it can be referenced via the following bracket notation, where ID is the ID of the compute: +-------------+--------------------------------------------+ -| c\_ID | entire scalar, vector, or array | +| c_ID | entire scalar, vector, or array | +-------------+--------------------------------------------+ -| c\_ID[I] | one element of vector, one column of array | +| c_ID[I] | one element of vector, one column of array | +-------------+--------------------------------------------+ -| c\_ID[I][J] | one element of array | +| c_ID[I][J] | one element of array | +-------------+--------------------------------------------+ In other words, using one bracket reduces the dimension of the @@ -88,7 +88,7 @@ vector or array. Note that commands and :doc:`variables ` which use compute quantities typically do not allow for all kinds, e.g. a command may require a vector of values, not a scalar. This means there is no -ambiguity about referring to a compute quantity as c\_ID even if it +ambiguity about referring to a compute quantity as c_ID even if it produces, for example, both a scalar and vector. The doc pages for various commands explain the details. @@ -116,7 +116,7 @@ e.g. temperature. Extensive means the value scales with the number of atoms in the simulation, e.g. total rotational kinetic energy. :doc:`Thermodynamic output ` will normalize extensive values by the number of atoms in the system, depending on the -"thermo\_modify norm" setting. It will not normalize intensive values. +"thermo_modify norm" setting. It will not normalize intensive values. If a compute value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an intensive or extensive value. See the doc page for individual @@ -125,8 +125,8 @@ computes for further info. ---------- LAMMPS creates its own computes internally for thermodynamic output. -Three computes are always created, named "thermo\_temp", -"thermo\_press", and "thermo\_pe", as if these commands had been invoked +Three computes are always created, named "thermo_temp", +"thermo_press", and "thermo_pe", as if these commands had been invoked in the input script: .. code-block:: LAMMPS diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 3e1160a43d..c0d754d883 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -64,7 +64,7 @@ neighbor atom in each requested ADF. those pairs will not be included in the ADF. This does not apply when using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get around this would be to set - special\_bond scaling factors to very tiny numbers that are not exactly + special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the ADF for snapshots in the dump file. The rerun script can use a @@ -106,7 +106,7 @@ in the range of types represented by *ktypeN*\ . If no *itypeN*\ , *jtypeN*\ , *ktypeN* settings are specified, then LAMMPS will generate a single ADF for all atoms in the group. The inner cutoff is set to zero and the outer cutoff is set -to the force cutoff. If no pair\_style is specified, there is no +to the force cutoff. If no pair_style is specified, there is no force cutoff and LAMMPS will give an error message. Note that in most cases, generating an ADF for all atoms is not a good thing. Such an ADF is both uninformative and diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 666045466f..60f929197c 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -24,8 +24,8 @@ Description """"""""""" Define a computation that extracts the angle energy calculated by each -of the angle sub-styles used in the "angle\_style -hybrid" angle\_hybrid.html command. These values are made accessible +of the angle sub-styles used in the "angle_style +hybrid" angle_hybrid.html command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. @@ -35,7 +35,7 @@ energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices +number of sub_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 24a0a999fb..fe0af199e2 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * angle/local = style name of this compute command * one or more values may be appended -* value = *theta* or *eng* or *v\_name* +* value = *theta* or *eng* or *v_name* .. parsed-literal:: @@ -51,9 +51,9 @@ The value *theta* is the angle for the 3 atoms in the interaction. The value *eng* is the interaction energy for the angle. -The value *v\_name* can be used together with the *set* keyword to +The value *v_name* can be used together with the *set* keyword to compute a user-specified function of the angle theta. The *name* -specified for the *v\_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a +specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a variable which will store the angle theta. This other variable must be an :doc:`internal-style variable ` defined in the input script; its initial numeric value can be anything. It must be an diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index 08da63aacc..395a8ebf91 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -61,7 +61,7 @@ group. For a body particle, the *integer* keywords refer to fields calculated by the body style for each sub-particle. The body style, as specified by the :doc:`atom_style body `, determines how many fields -exist and what they are. See the :doc:`Howto\_body ` doc +exist and what they are. See the :doc:`Howto_body ` doc page for details of the different styles. Here is an example of how to output body information using the :doc:`dump local ` command with this compute. If fields 1,2,3 for the diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index bf11d0ceda..59ac05630a 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -35,7 +35,7 @@ or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. +number of sub_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 0d4c7efd29..32d756d52a 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * bond/local = style name of this compute command * one or more values may be appended -* value = *dist* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v\_name* +* value = *dist* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* .. parsed-literal:: @@ -106,9 +106,9 @@ two atoms in the bond towards each other. A negative value means the 2 atoms are moving toward each other; a positive value means they are moving apart. -The value *v\_name* can be used together with the *set* keyword to +The value *v_name* can be used together with the *set* keyword to compute a user-specified function of the bond distance. The *name* -specified for the *v\_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a +specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a variable which will store the bond distance. This other variable must be an :doc:`internal-style variable ` defined in the input script; its initial numeric value can be anything. It must be an diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index a00d407d70..d486da4e3e 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -14,7 +14,7 @@ Syntax * chunk/spread/atom = style name of this compute command * chunkID = ID of :doc:`compute chunk/atom ` command * one or more inputs can be listed -* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] +* input = c_ID, c_ID[N], f_ID, f_ID[N] .. parsed-literal:: diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index ff84ed686a..d9742a4a4b 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -82,7 +82,7 @@ multiple compute/dump commands, each of a *cluster/atom* or those pairs will not be included when computing the clusters. This does not apply when using long-range coulomb (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get around this would be to set - special\_bond scaling factors to very tiny numbers that are not exactly + special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the clusters for snapshots in the dump file. The rerun script can use a diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index ff2ee2fa92..c51ea212f0 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -78,10 +78,10 @@ identify crystal-like atoms in a system, as discussed in :ref:`ten Wolde ` command is specified as *orientorderID*\ . The compute must invoke its *components* option to -calculate components of the *Ybar\_lm* vector for each atoms, as +calculate components of the *Ybar_lm* vector for each atoms, as described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the -scalar product (*Ybar\_lm(i)*,*Ybar\_lm(j)*), calculated by the +scalar product (*Ybar_lm(i)*,*Ybar_lm(j)*), calculated by the orientorder/atom compute is larger than the specified *threshold*\ , then I and J are connected, and the coordination value of I is incremented by one. diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 135c2d6365..ed87b727ec 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -34,7 +34,7 @@ total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices +number of sub_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 2f998e1138..6fd1401292 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * dihedral/local = style name of this compute command * one or more values may be appended -* value = *phi* or *v\_name* +* value = *phi* or *v_name* .. parsed-literal:: @@ -49,9 +49,9 @@ by the group parameter as explained below. The value *phi* is the dihedral angle, as defined in the diagram on the :doc:`dihedral_style ` doc page. -The value *v\_name* can be used together with the *set* keyword to +The value *v_name* can be used together with the *set* keyword to compute a user-specified function of the dihedral angle phi. The -*name* specified for the *v\_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a +*name* specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a variable which will store the angle phi. This other variable must be an :doc:`internal-style variable ` defined in the input script; its initial numeric value can be anything. It must be an diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 5d208823d7..9e1488cdf1 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -63,7 +63,7 @@ the compute command was issued. The value of the displacement will be ---------- -The *refresh* option can be used in conjunction with the "dump\_modify +The *refresh* option can be used in conjunction with the "dump_modify refresh" command to generate incremental dump files. The definition and motivation of an incremental dump file is as @@ -95,11 +95,11 @@ something like the following commands: The :doc:`dump_modify thresh ` command will only output atoms that have displaced more than 0.6 Angstroms on each snapshot -(assuming metal units). The dump\_modify *refresh* option triggers a +(assuming metal units). The dump_modify *refresh* option triggers a call to this compute at the end of every dump. The *refresh* argument for this compute is the ID of an :doc:`atom-style variable ` which calculates a Boolean value (0 or 1) -based on the same criterion used by dump\_modify thresh. This compute +based on the same criterion used by dump_modify thresh. This compute evaluates the atom-style variable. For each atom that returns 1 (true), the original (reference) coordinates of the atom (stored by this compute) are updated. @@ -112,7 +112,7 @@ Note that in the first snapshot of a subsequent run, no atoms will be typically be output. That is because the initial displacement for all atoms is 0.0. If an initial dump snapshot is desired, containing the initial reference positions of all atoms, one way to do this is -illustrated above. An initial write\_dump command can be used before +illustrated above. An initial write_dump command can be used before the first run. It will contain the positions of all the atoms, Options in the :doc:`dump_modify ` command above will append new output to that same file and delay the output until a later diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index a7d64caa98..4700817609 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -241,9 +241,9 @@ used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. -The *v\_name* argument for keyword *pair* is the name of an +The *v_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time -this compute is invoked. It should be specified as v\_name, where name +this compute is invoked. It should be specified as v_name, where name is the variable name. ---------- @@ -254,9 +254,9 @@ current list of atom parameters that can be used with this compute: * charge = charge on particle -The *v\_name* argument for keyword *pair* is the name of an +The *v_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time -this compute is invoked. It should be specified as v\_name, where name +this compute is invoked. It should be specified as v_name, where name is the variable name. ---------- @@ -282,10 +282,10 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild **Output info:** This compute calculates a global vector of length 3 which contains the -energy difference ( :math:`U_1-U_0` ) as c\_ID[1], the +energy difference ( :math:`U_1-U_0` ) as c_ID[1], the Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or -:math:`V \exp(-(U_1-U_0)/kT)`, as c\_ID[2] and the -volume of the simulation box :math:`V` as c\_ID[3]. :math:`U_1` is the +:math:`V \exp(-(U_1-U_0)/kT)`, as c_ID[2] and the +volume of the simulation box :math:`V` as c_ID[3]. :math:`U_1` is the pair potential energy obtained with the perturbed parameters and :math:`U_0` is the pair potential energy obtained with the unperturbed parameters. The energies include kspace terms if these diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index ae6ca73a36..e9adb0317b 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * global/atom = style name of this compute command -* index = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* index = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -23,7 +23,7 @@ Syntax v_name = per-atom vector calculated by an atom-style variable with name * one or more inputs can be listed -* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* input = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index f0b65c797a..ba29090d5e 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -109,7 +109,7 @@ frequently. means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get - around this would be to set special\_bond scaling factors to very tiny + around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the group/group interactions for snapshots in the dump file. diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 20807ec0db..e00fdde841 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -58,12 +58,12 @@ summation should work fine, while :doc:`pair_style lj/cut ` will perform poorly unless the potential is shifted (via :doc:`pair_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with this compute is -restricted to those that implement the *single\_hessian* method in Pair. -Implementing *single\_hessian* in additional pair styles is simple. +restricted to those that implement the *single_hessian* method in Pair. +Implementing *single_hessian* in additional pair styles is simple. Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at buffalo.edu) if your desired pair style does not have this method. This is the list of pair styles that currently implement -*single\_hessian*: +*single_hessian*: * :doc:`pair_style lj/smooth/linear ` @@ -179,7 +179,7 @@ Related commands :doc:`compute pe `, :doc:`compute pressure ` :doc:`dynamical matrix ` provides a finite difference -formulation of the hessian provided by Pair's single\_hessian, which is used by +formulation of the hessian provided by Pair's single_hessian, which is used by this compute. **Default:** none diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index bb4b150c6a..0a264a74e7 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -34,7 +34,7 @@ total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices +number of sub_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index dddb5273f8..f1cffebc56 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -43,7 +43,7 @@ energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of the system with :math:`\frac{1}{2} k_B T` of energy for each degree of freedom. For the eFF temperature computation via the :doc:`compute -temp\_eff ` command, these are the same. But +temp_eff ` command, these are the same. But different computes that calculate temperature can subtract out different non-thermal components of velocity and/or include other degrees of freedom. diff --git a/doc/src/compute_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst index 9f5385dd48..e44425a65c 100644 --- a/doc/src/compute_meso_t_atom.rst +++ b/doc/src/compute_meso_t_atom.rst @@ -30,7 +30,9 @@ The internal temperature is the ratio of internal energy over the heat capacity associated with the internal degrees of freedom of a mesoscopic particles, e.g. a Smooth-Particle Hydrodynamics particle. -T\_\ *int* = E\_\ *int* / C\_\ *V, int* +.. math:: + + T_{int} = E_{int} / C_{V,int} See `this PDF guide `_ to using SPH in LAMMPS. diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 05a414a0d5..94ab6a1579 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -112,7 +112,7 @@ Restrictions Related commands """""""""""""""" -:doc:`compute msd/nongauss `, :doc:`compute displace\_atom `, :doc:`fix store/state `, :doc:`compute msd/chunk ` +:doc:`compute msd/nongauss `, :doc:`compute displace_atom `, :doc:`fix store/state `, :doc:`compute msd/chunk ` Default """"""" diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index c651804f0a..7b894b886e 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -100,7 +100,7 @@ can be reproduced with this keyword. The optional keyword *components* will output the components of the normalized complex vector :math:`\bar{Y}_{lm}` of degree *ldegree*\ , which must be explicitly included in the keyword *degrees*\ . This option can be used -in conjunction with :doc:`compute coord\_atom ` to +in conjunction with :doc:`compute coord_atom ` to calculate the ten Wolde's criterion to identify crystal-like particles, as discussed in :ref:`ten Wolde `. diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 2efaf78b01..813b577490 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -54,14 +54,14 @@ potential energy. The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. -A compute of this style with the ID of "thermo\_pe" is created when +A compute of this style with the ID of "thermo_pe" is created when LAMMPS starts up, as if this command were in the input script: .. code-block:: LAMMPS compute thermo_pe all pe -See the "thermo\_style" command for more details. +See the "thermo_style" command for more details. ---------- diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index 9d8dea535d..939017f5e9 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -31,7 +31,7 @@ The plasticity for a Peridynamic particle is the so-called consistency parameter (lambda). For elastic deformation lambda = 0, otherwise lambda > 0 for plastic deformation. For details, see :ref:`(Mitchell) ` and the PDF doc included in the LAMMPS -distribution in `doc/PDF/PDLammps\_EPS.pdf `_. +distribution in `doc/PDF/PDLammps_EPS.pdf `_. This command can be invoked for one of the Peridynamic :doc:`pair styles `: peri/eps. diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 402613d504..7366fa6d3d 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -100,15 +100,15 @@ Also note that the N in the first formula above is really degrees-of-freedom divided by d = dimensionality, where the DOF value is calculated by the temperature compute. See the various :doc:`compute temperature ` styles for details. -A compute of this style with the ID of "thermo\_press" is created when +A compute of this style with the ID of "thermo_press" is created when LAMMPS starts up, as if this command were in the input script: .. code-block:: LAMMPS compute thermo_press all pressure thermo_temp -where "thermo\_temp" is the ID of a similarly defined compute of style -"temp". See the "thermo\_style" command for more details. +where "thermo_temp" is the ID of a similarly defined compute of style +"temp". See the "thermo_style" command for more details. ---------- diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index b3e7accb37..104e68d533 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -15,7 +15,7 @@ Syntax * zlo = minimum z-boundary for cylinder * zhi = maximum z-boundary for cylinder * Rmax = maximum radius to perform calculation to -* bin\_width = width of radial bins to use for calculation +* bin_width = width of radial bins to use for calculation Examples """""""" @@ -31,19 +31,19 @@ Define a computation that calculates the pressure tensor of a system in cylindrical coordinates, as discussed in :ref:`(Addington) `. This is useful for systems with a single axis of rotational symmetry, such as cylindrical micelles or carbon nanotubes. The compute splits the -system into radial, cylindrical-shell-type bins of width bin\_width, -centered at x=0,y=0, and calculates the radial (P\_rhorho), azimuthal -(P\_phiphi), and axial (P\_zz) components of the configurational pressure +system into radial, cylindrical-shell-type bins of width bin_width, +centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal +(P_phiphi), and axial (P_zz) components of the configurational pressure tensor. The local density is also calculated for each bin, so that the -true pressure can be recovered as P\_kin+P\_conf=density\*k\*T+P\_conf. The +true pressure can be recovered as P_kin+P_conf=density\*k\*T+P_conf. The output is a global array with 5 columns; one each for bin radius, local -number density, P\_rhorho, P\_phiphi, and P\_zz. The number of rows is -governed by the values of Rmax and bin\_width. Pressure tensor values are +number density, P_rhorho, P_phiphi, and P_zz. The number of rows is +governed by the values of Rmax and bin_width. Pressure tensor values are output in pressure units. **Output info:** -This compute calculates a global array with 5 columns and Rmax/bin\_width +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), configurational azimuthal pressure (pressure units), and configurational @@ -64,7 +64,7 @@ due to exclusions for special bonds) and requires pair-wise force calculations not available for most many-body pair styles. K-space calculations are also excluded. Note that this pressure compute outputs the configurational terms only; the kinetic contribution is not included -and may be calculated from the number density output by P\_kin=density\*k\*T. +and may be calculated from the number density output by P_kin=density\*k\*T. This compute is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 23dd8806d9..1643be8699 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -147,11 +147,11 @@ two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off ` is set, it will be tallied with both atom I and atom J. -The *i\_name* and *d\_name* attributes refer to custom integer and +The *i_name* and *d_name* attributes refer to custom integer and floating-point properties that have been added to each atom via the :doc:`fix property/atom ` command. When that command is used specific names are given to each attribute which are what is -specified as the "name" portion of *i\_name* or *d\_name*. +specified as the "name" portion of *i_name* or *d_name*. **Output info:** diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index 3fac1d8810..112ed1ea6a 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -105,7 +105,7 @@ The type is a number from -1 to 8. The rmsd is a positive real number. The interatomic distance is computed from the scale factor in the RMSD equation. The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the -orientation is determined) can be found in the *ptm\_constants.h* file in the PTM source directory. +orientation is determined) can be found in the *ptm_constants.h* file in the PTM source directory. For atoms that are not within the compute group-ID, all values are set to zero. Restrictions diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index c977e2ac12..5f426ffb51 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -57,7 +57,7 @@ shell of distances in 3d and a thin ring of distances in 2d. those pairs will not be included in the RDF. This does not apply when using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get around this would be to set - special\_bond scaling factors to very tiny numbers that are not exactly + special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the RDF for snapshots in the dump file. The rerun script can use a @@ -74,7 +74,7 @@ distance specified. Normally, you should only use the *cutoff* keyword if no pair style is defined, e.g. the :doc:`rerun ` command is being used to post-process a dump file of snapshots. Or if you really want the RDF - for distances beyond the pair\_style force cutoff and cannot easily + for distances beyond the pair_style force cutoff and cannot easily post-process a dump file to calculate it. This is because using the *cutoff* keyword incurs extra computation and possibly communication, which may slow down your simulation. If you specify a *Rcut* <= force diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 3772a788e0..7599343d2e 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -24,7 +24,7 @@ Syntax * mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* * one or more inputs can be listed -* input = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 3404613875..34619efd06 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -15,7 +15,7 @@ Syntax * chunkID = ID of :doc:`compute chunk/atom ` command * mode = *sum* or *min* or *max* * one or more inputs can be listed -* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_ID +* input = c_ID, c_ID[N], f_ID, f_ID[N], v_ID .. parsed-literal:: diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index ac596962c0..cad4bc1b93 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -15,7 +15,7 @@ Syntax * lambda = wavelength of incident radiation (length units) * type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) * zero or more keyword/value pairs may be appended -* keyword = *Kmax* or *Zone* or *dR\_Ewald* or *c* or *manual* or *echo* +* keyword = *Kmax* or *Zone* or *dR_Ewald* or *c* or *manual* or *echo* .. parsed-literal:: @@ -90,7 +90,7 @@ unless small spacing parameters <0.05 Angstrom\^(-1) are implemented. Meshes with manual spacing do not require a periodic boundary. The limits of the reciprocal lattice mesh are determined by the use of -the *Kmax*\ , *Zone*\ , and *dR\_Ewald* parameters. The rectilinear mesh +the *Kmax*\ , *Zone*\ , and *dR_Ewald* parameters. The rectilinear mesh created about the origin of reciprocal space is terminated at the boundary of a sphere of radius *Kmax* centered at the origin. If *Zone* parameters z1=z2=z3=0 are used, diffraction intensities are @@ -99,7 +99,7 @@ greatly increase the cost of computation. Otherwise, *Zone* parameters will denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an intersecting Ewald sphere. Diffraction intensities will only be computed at the intersection of the reciprocal lattice -mesh and a *dR\_Ewald* thick surface of the Ewald sphere. See the +mesh and a *dR_Ewald* thick surface of the Ewald sphere. See the example 3D intensity data and the intersection of a [010] zone axis in the below image. @@ -247,17 +247,17 @@ Restrictions This compute is part of the USER-DIFFRACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -The compute\_saed command does not work for triclinic cells. +The compute_saed command does not work for triclinic cells. Related commands """""""""""""""" -:doc:`fix saed\_vtk `, :doc:`compute xrd ` +:doc:`fix saed_vtk `, :doc:`compute xrd ` Default """"""" -The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR\_Ewald = +The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = 0.01. ---------- diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 6667dfd880..c8211269bc 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -15,7 +15,7 @@ Syntax * Nstart = starting index within input vector(s) * Nstop = stopping index within input vector(s) * Nskip = extract every Nskip elements from input vector(s) -* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] +* input = c_ID, c_ID[N], f_ID, f_ID[N] .. parsed-literal:: diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 4f9e36db7d..01c543af38 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -27,7 +27,7 @@ Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by -the contact pair styles, e.g., smd/hertz and smd/tri\_surface. +the contact pair styles, e.g., smd/hertz and smd/tri_surface. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. @@ -53,6 +53,6 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`dump custom ` smd/hertz smd/tri\_surface +:doc:`dump custom ` smd/hertz smd/tri_surface **Default:** none diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index eb39c4e452..3f02ac5c74 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -46,6 +46,6 @@ LAMMPS was built with that package. See the "Build Related commands """""""""""""""" -:doc:`smd/plastic\_strain `, :doc:`smd/tlsph\_stress ` +:doc:`smd/plastic_strain `, :doc:`smd/tlsph_stress ` **Default:** none diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 612d4d0aba..56b8a81c01 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -58,7 +58,7 @@ tlsph pair style. **Related Commands:** -:doc:`smd/tlsph\_defgrad ` +:doc:`smd/tlsph_defgrad ` Default """"""" diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index f510ca4bb0..ad33df3ef8 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -24,7 +24,7 @@ Description """"""""""" Define a computation that returns the coordinates of the vertices -corresponding to the triangle-elements of a mesh created by the :doc:`fix smd/wall\_surface `. +corresponding to the triangle-elements of a mesh created by the :doc:`fix smd/wall_surface `. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. @@ -41,10 +41,10 @@ The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and each triangle. It is only meaningful to use this compute for a group of particles -which is created via the :doc:`fix smd/wall\_surface ` command. +which is created via the :doc:`fix smd/wall_surface ` command. -The output of this compute can be used with the dump2vtk\_tris tool to -generate a VTK representation of the smd/wall\_surface mesh for +The output of this compute can be used with the dump2vtk_tris tool to +generate a VTK representation of the smd/wall_surface mesh for visualization purposes. The values will be given in :doc:`units ` of distance. @@ -59,6 +59,6 @@ Related commands """""""""""""""" :doc:`fix smd/move/tri/surf `, -:doc:`fix smd/wall\_surface ` +:doc:`fix smd/wall_surface ` **Default:** none diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index c6ed12d5a8..83e28b913b 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -27,8 +27,8 @@ Syntax * rcutfac = scale factor applied to all cutoff radii (positive real) * rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1) * twojmax = band limit for bispectrum components (non-negative integer) -* R\_1, R\_2,... = list of cutoff radii, one for each type (distance units) -* w\_1, w\_2,... = list of neighbor weights, one for each type +* R_1, R_2,... = list of cutoff radii, one for each type (distance units) +* w_1, w_2,... = list of neighbor weights, one for each type * zero or more keyword/value pairs may be appended * keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* @@ -62,7 +62,7 @@ Define a computation that calculates a set of quantities related to the bispectrum components of the atoms in a group. These computes are used primarily for calculating the dependence of energy, force, and stress components on the linear coefficients in the -:doc:`snap pair\_style `, which is useful when training a +:doc:`snap pair_style `, which is useful when training a SNAP potential to match target data. Bispectrum components of an atom are order parameters characterizing @@ -71,11 +71,11 @@ mathematical definition is given in the paper by Thompson et al. :ref:`(Thompson) ` The position of a neighbor atom *i'* relative to a central atom *i* is -a point within the 3D ball of radius *R\_ii' = rcutfac\*(R\_i + R\_i')* +a point within the 3D ball of radius *R_ii' = rcutfac\*(R_i + R_i')* Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D ball onto the 3-sphere, the surface of the unit ball in a four-dimensional -space. The radial distance *r* within *R\_ii'* is mapped on to a third +space. The radial distance *r* within *R_ii'* is mapped on to a third polar angle *theta0* defined by, .. math:: @@ -87,8 +87,8 @@ of the 3-sphere. Points south of the latitude *theta0max=rfac0\*Pi* are excluded. The natural basis for functions on the 3-sphere is formed by the 4D -hyperspherical harmonics *U\^j\_m,m'(theta, phi, theta0).* These -functions are better known as *D\^j\_m,m',* the elements of the Wigner +hyperspherical harmonics *U\^j_m,m'(theta, phi, theta0).* These +functions are better known as *D\^j_m,m',* the elements of the Wigner *D*\ -matrices :ref:`(Meremianin `, :ref:`Varshalovich) `. @@ -102,18 +102,18 @@ coefficient as u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} -The *w\_i'* neighbor weights are dimensionless numbers that are chosen +The *w_i'* neighbor weights are dimensionless numbers that are chosen to distinguish atoms of different types, while the central atom is arbitrarily assigned a unit weight. The function *fc(r)* ensures that the contribution of each neighbor atom goes smoothly to zero at -*R\_ii'*: +*R_ii'*: .. math:: f_c(r) = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\ = & 0, r > R_{ii'} -The expansion coefficients *u\^j\_m,m'* are complex-valued and they are +The expansion coefficients *u\^j_m,m'* are complex-valued and they are not directly useful as descriptors, because they are not invariant under rotation of the polar coordinate frame. However, the following scalar triple products of expansion coefficients can be shown to be @@ -128,7 +128,7 @@ real-valued and invariant under rotation :ref:`(Bartok) `. {j_2} {m_2} {m'_2} \end{array}} u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2} -The constants *H\^jmm'\_j1m1m1'\_j2m2m2'* are coupling coefficients, +The constants *H\^jmm'_j1m1m1'_j2m2m2'* are coupling coefficients, analogous to Clebsch-Gordan coefficients for rotations on the 2-sphere. These invariants are the components of the bispectrum and these are the quantities calculated by the compute *sna/atom*\ . They @@ -176,8 +176,8 @@ broken out by type). The element in the last column of each row contains the potential energy, force, or stress, according to the row. These quantities correspond to the user-specified reference potential that must be subtracted from the target data when fitting SNAP. -The potential energy calculation uses the built in compute *thermo\_pe*. -The stress calculation uses a compute called *snap\_press* that is +The potential energy calculation uses the built in compute *thermo_pe*. +The stress calculation uses a compute called *snap_press* that is automatically created behind the scenes, according to the following command: diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst index 60a75d10cf..49243e9650 100644 --- a/doc/src/compute_spin.rst +++ b/doc/src/compute_spin.rst @@ -37,7 +37,7 @@ This compute calculates the following 6 magnetic quantities: 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: +thermo_style commands, for example: .. code-block:: LAMMPS @@ -52,7 +52,7 @@ thermo\_style commands, for example: 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 +assigned to those quantities. The thermo and thermo_style commands print them every 10 timesteps. **Output info:** @@ -64,7 +64,7 @@ Restrictions """""""""""" The *spin* compute is part of the SPIN package. This compute is only -enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. The atom\_style +enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. The atom_style has to be "spin" for this compute to be valid. **Related commands:** diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 487e6bc365..83a8374702 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -72,14 +72,14 @@ corrections to the pressure added by the :doc:`pair_modify tail yes `. diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 5988e7791c..f49c872306 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -102,7 +102,7 @@ The computes in this package are not compatible with dynamic groups. Related commands """""""""""""""" -*compute group/group*\ \_compute\_group\_group.html, *compute -heat/flux*\ \_compute\_heat\_flux.html +*compute group/group*\ _compute_group_group.html, *compute +heat/flux*\ _compute_heat_flux.html **Default:** none diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 5616917572..9232191472 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -54,14 +54,14 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -A compute of this style with the ID of "thermo\_temp" is created when +A compute of this style with the ID of "thermo_temp" is created when LAMMPS starts up, as if this command were in the input script: .. code-block:: LAMMPS compute thermo_temp all temp -See the "thermo\_style" command for more details. +See the "thermo_style" command for more details. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index bd49cb377f..8cb9849a24 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -69,7 +69,7 @@ Restrictions The number of degrees of freedom contributing to the temperature is assumed to be constant for the duration of the run unless the -*fix\_modify* command sets the option *dynamic yes*\ . +*fix_modify* command sets the option *dynamic yes*\ . Related commands """""""""""""""" diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 8fe294a2db..79fc56178c 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -58,7 +58,7 @@ to 1 (or vice versa) over the course of a :doc:`run `. The time-dependent adjustment is what the :doc:`fix adapt ` command does. -Assume that the unscaled energy of a pair\_style or kspace\_style is +Assume that the unscaled energy of a pair_style or kspace_style is given by U. Then the scaled energy is .. parsed-literal:: @@ -85,9 +85,9 @@ leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -You also specify two functions, as :doc:`equal-style variables `. The first is specified as *v\_name1*, where +You also specify two functions, as :doc:`equal-style variables `. The first is specified as *v_name1*, where *name1* is the name of the variable, and is f(lambda) in the notation -above. The second is specified as *v\_name2*, where *name2* is the +above. The second is specified as *v_name2*, where *name2* is the name of the variable, and is df(lambda) / dlambda in the notation above. I.e. it is the analytic derivative of f() with respect to lambda. Note that the *name1* variable is also typically given as an diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 88b65ee8b2..a5d99d5de9 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -13,8 +13,8 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * voronoi/atom = style name of this compute command * zero or more keyword/value pairs may be appended -* keyword = *only\_group* or *surface* or *radius* or *edge\_histo* or *edge\_threshold* - or *face\_threshold* or *neighbors* or *peratom* +* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* + or *face_threshold* or *neighbors* or *peratom* .. parsed-literal:: @@ -65,7 +65,7 @@ but they are not accessible. ---------- -If the *only\_group* keyword is specified the tessellation is performed +If the *only_group* keyword is specified the tessellation is performed only with respect to the atoms contained in the compute group. This is equivalent to deleting all atoms not contained in the group prior to evaluating the tessellation. @@ -80,7 +80,7 @@ In the example above, a precipitate embedded in a matrix, only atoms at the surface of the precipitate will have non-zero surface area, and only the outward facing facets of the Voronoi cells are counted (the hull of the precipitate). The total surface area of the precipitate -can be obtained by running a "reduce sum" compute on c\_2[3] +can be obtained by running a "reduce sum" compute on c_2[3] If the *radius* keyword is specified with an atom style variable as the argument, a poly-disperse Voronoi tessellation is @@ -92,11 +92,11 @@ performed. Examples for radius variables are compute radius all property/atom radius variable r2 atom c_radius -Here v\_r1 specifies a per-type radius of 0.1 units for type 1 atoms -and 0.4 units for type 2 atoms, and v\_r2 accesses the radius property -present in atom\_style sphere for granular models. +Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms +and 0.4 units for type 2 atoms, and v_r2 accesses the radius property +present in atom_style sphere for granular models. -The *edge\_histo* keyword activates the compilation of a histogram of +The *edge_histo* keyword activates the compilation of a histogram of number of edges on the faces of the Voronoi cells in the compute group. The argument *maxedge* of the this keyword is the largest number of edges on a single Voronoi cell face expected to occur in the @@ -106,7 +106,7 @@ faces with more than *maxedge* edges. Since the polygon with the smallest amount of edges is a triangle, entries 1 and 2 of the vector will always be zero. -The *edge\_threshold* and *face\_threshold* keywords allow the +The *edge_threshold* and *face_threshold* keywords allow the suppression of edges below a given minimum length and faces below a given minimum area. Ultra short edges and ultra small faces can occur as artifacts of the Voronoi tessellation. These keywords will affect @@ -144,7 +144,7 @@ containing all the Voronoi neighbors in a system: compute 6 all voronoi/atom neighbors yes dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3] -If the *face\_threshold* keyword is used, then only faces +If the *face_threshold* keyword is used, then only faces with areas greater than the threshold are stored. ---------- @@ -199,7 +199,7 @@ per-atom values from a compute as input. See the :doc:`Howto output ` doc page for more info. -The compute\_xrd command does not work for triclinic cells. +The compute_xrd command does not work for triclinic cells. Related commands """""""""""""""" diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 85eaa86f38..2e0b079e09 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -88,7 +88,7 @@ the specified atom *type*\ . E.g. if *type* = 2, and the file specifies atom types 1,2,3, then each created molecule will have atom types 3,4,5. -For the *box* style, the create\_atoms command fills the entire +For the *box* style, the create_atoms command fills the entire simulation box with particles on the lattice. If your simulation box is periodic, you should insure its size is a multiple of the lattice spacings, to avoid unwanted atom overlaps at the box boundaries. If @@ -136,11 +136,11 @@ outside a geometric boundary. Note that this command adds particles to those that already exist. This means it can be used to add particles to a system previously read -in from a data or restart file. Or the create\_atoms command can be +in from a data or restart file. Or the create_atoms command can be used multiple times, to add multiple sets of particles to the simulation. For example, grain boundaries can be created, by -interleaving create\_atoms with :doc:`lattice ` commands -specifying different orientations. By using the create\_atoms command +interleaving create_atoms with :doc:`lattice ` commands +specifying different orientations. By using the create_atoms command in conjunction with the :doc:`delete_atoms ` command, reasonably complex geometries can be created, or a protein can be solvated with a surrounding box of water molecules. @@ -157,10 +157,10 @@ used to remove overlapping atoms or molecules. LAMMPS. This is true even if you are using shrink-wrapped box boundaries, as specified by the :doc:`boundary ` command. However, you can first use the :doc:`change_box ` command to - temporarily expand the box, then add atoms via create\_atoms, then - finally use change\_box command again if needed to re-shrink-wrap the + temporarily expand the box, then add atoms via create_atoms, then + finally use change_box command again if needed to re-shrink-wrap the new atoms. See the :doc:`change_box ` doc page for an - example of how to do this, using the create\_atoms *single* style to + example of how to do this, using the create_atoms *single* style to insert a new atom outside the current simulation box. ---------- @@ -195,7 +195,7 @@ not overlap, regardless of their relative orientations. .. note:: If the :doc:`create_box ` command is used to create - the simulation box, followed by the create\_atoms command with its + the simulation box, followed by the create_atoms command with its *mol* option for adding molecules, then you typically need to use the optional keywords allowed by the :doc:`create_box ` command for extra bonds (angles,etc) or extra special neighbors. This is @@ -300,7 +300,7 @@ spacings. Atom IDs are assigned to created atoms in the following way. The collection of created atoms are assigned consecutive IDs that start immediately following the largest atom ID existing before the -create\_atoms command was invoked. This is done by the processor's +create_atoms command was invoked. This is done by the processor's communicating the number of atoms they each own, the first processor numbering its atoms from 1 to N1, the second processor from N1+1 to N2, etc. Where N1 = number of atoms owned by the first processor, N2 diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 9ac145679c..b69fd909f0 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -114,7 +114,7 @@ apart such that *rmin* <= D <= *rmax*\ . The following settings must have been made in an input script before this style is used: -* special\_bonds weight for 1-2 interactions must be 0.0 +* special_bonds weight for 1-2 interactions must be 0.0 * a :doc:`pair_style ` must be defined * no :doc:`kspace_style ` defined * minimum :doc:`pair_style ` cutoff + :doc:`neighbor ` skin >= *rmax* diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 99d5befd2d..917a4b3b0a 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -63,7 +63,7 @@ positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -By default, a *prism* region used with the create\_box command must +By default, a *prism* region used with the create_box command must have tilt factors (xy,xz,yz) that do not skew the box more than half the distance of the parallel box length. For example, if xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt factor must be @@ -124,7 +124,7 @@ keywords serve the same purpose as the analogous keywords that can be used in a data file which are recognized by the :doc:`read_data ` command when it sets up a system. -Note that if these keywords are not used, then the create\_box command +Note that if these keywords are not used, then the create_box command creates an atomic (non-molecular) simulation that does not allow bonds between pairs of atoms to be defined, or a :doc:`bond potential ` to be specified, or for molecules with special neighbors to be added to the system by commands such as @@ -133,7 +133,7 @@ or :doc:`fix pour `. As an example, see the examples/deposit/in.deposit.molecule script, which deposits molecules onto a substrate. Initially there are no -molecules in the system, but they are added later by the :doc:`fix deposit ` command. The create\_box command in the +molecules in the system, but they are added later by the :doc:`fix deposit ` command. The create_box command in the script uses the bond/types and extra/bond/per/atom keywords to allow this. If the added molecule contained more than 1 special bond (allowed by default), an extra/special/per/atom keyword would also diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 7381682f6d..9c42b5a2a0 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -86,9 +86,9 @@ of all interactions in the specified group is simply reported. This is useful for diagnostic purposes if bonds have been turned off by a bond-breaking potential during a previous run. -The default behavior of the delete\_bonds command is to turn off +The default behavior of the delete_bonds command is to turn off interactions by toggling their type to a negative value, but not to -permanently remove the interaction. E.g. a bond\_type of 2 is set to +permanently remove the interaction. E.g. a bond_type of 2 is set to -2. The neighbor list creation routines will not include such an interaction in their interaction lists. The default is also to not alter the list of 1-2, 1-3, 1-4 neighbors computed by the @@ -105,7 +105,7 @@ interaction. Instead, if any of the atoms in the interaction are in the specified group, it will be turned off (or on if the *undo* keyword is used). -The *undo* keyword inverts the delete\_bonds command so that the +The *undo* keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently turned off. This means a negative value is toggled to positive. For example, for style *angle*\ , if *type* is specified as 2, then all @@ -113,14 +113,14 @@ angles with current type = -2, are reset to type = 2. Note that the :doc:`fix shake ` command also sets bond and angle types negative, so this option should not be used on those interactions. -The *remove* keyword is invoked at the end of the delete\_bonds +The *remove* keyword is invoked at the end of the delete_bonds operation. It causes turned-off bonds (angles, etc) to be removed from each atom's data structure and then adjusts the global bond (angle, etc) counts accordingly. Removal is a permanent change; removed bonds cannot be turned back on via the *undo* keyword. Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list. -The *special* keyword is invoked at the end of the delete\_bonds +The *special* keyword is invoked at the end of the delete_bonds operation, after (optional) removal. It re-computes the pairwise 1-2, 1-3, 1-4 weighting list. The weighting list computation treats turned-off bonds the same as turned-on. Thus, turned-off bonds must @@ -128,7 +128,7 @@ be removed if you wish to change the weighting list. Note that the choice of *remove* and *special* options affects how 1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that -have been modified by the delete\_bonds command. +have been modified by the delete_bonds command. Restrictions """""""""""" diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 84dc42f08e..38cb18d172 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -90,12 +90,12 @@ the ring in the opposite direction and thus the weighting factor is Note that this dihedral weighting factor is unrelated to the scaling factor specified by the :doc:`special bonds ` command which applies to all 1-4 interactions in the system. For CHARMM force -fields, the special\_bonds 1-4 interaction scaling factor should be set +fields, the special_bonds 1-4 interaction scaling factor should be set to 0.0. Since the corresponding 1-4 non-bonded interactions are computed with the dihedral. This means that if any of the weighting factors defined as dihedral coefficients (4th coeff above) are non-zero, then you must use a pair style with "lj/charmm" and set the -special\_bonds 1-4 scaling factor to 0.0 (which is the +special_bonds 1-4 scaling factor to 0.0 (which is the default). Otherwise 1-4 non-bonded interactions in dihedrals will be computed twice. @@ -110,11 +110,11 @@ i.e. within the outer cutoff specified for the pair style. The :doc:`pair_style lj/charmmfsw/coul/long ` commands. Use the *charmm* style with the older :doc:`pair_style ` commands that have just "charmm" in their style name. See the -discussion on the :doc:`CHARMM pair\_style ` doc page for +discussion on the :doc:`CHARMM pair_style ` doc page for details. Note that for AMBER force fields, which use pair styles with "lj/cut", -the special\_bonds 1-4 scaling factor should be set to the AMBER +the special_bonds 1-4 scaling factor should be set to the AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors (4th coeff above) must be set to 0.0. In this case, you can use any pair style you wish, since the dihedral does not need any Lennard-Jones @@ -148,7 +148,7 @@ instructions on how to use the accelerated styles effectively. Restrictions """""""""""" -When using run\_style :doc:`respa `, these dihedral styles +When using run_style :doc:`respa `, these dihedral styles must be assigned to the same r-RESPA level as *pair* or *outer*\ . When used in combination with CHARMM pair styles, the 1-4 diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index f31c933b7c..d72a299416 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -39,7 +39,7 @@ leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that using a dihedral\_coeff command can override a previous setting +Note that using a dihedral_coeff command can override a previous setting for the same dihedral type. For example, these commands set the coeffs for all dihedral types, then overwrite the coeffs for just dihedral type 2: @@ -49,7 +49,7 @@ for all dihedral types, then overwrite the coeffs for just dihedral type 2: dihedral_coeff 2 200.0 1 3 A line in a data file that specifies dihedral coefficients uses the exact -same format as the arguments of the dihedral\_coeff command in an input +same format as the arguments of the dihedral_coeff command in an input script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Dihedral Coeffs" section of a data file, the line that @@ -83,7 +83,7 @@ in more compact form on the :ref:`Commands dihedral ` doc page. On either of those pages, click on the style to display the formula it computes and its coefficients as specified by the associated -dihedral\_coeff command. +dihedral_coeff command. ---------- diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index eef6172ffd..ad5f1f6586 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -73,7 +73,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index 764077359d..9fe4478f67 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -32,10 +32,10 @@ boundary (of dihedral type 2) could be computed with a *helix* potential. The assignment of dihedral type to style is made via the :doc:`dihedral_coeff ` command or in the data file. -In the dihedral\_coeff commands, the name of a dihedral style must be +In the dihedral_coeff commands, the name of a dihedral style must be added after the dihedral type, with the remaining coefficients being those appropriate to that style. In the example above, the 2 -dihedral\_coeff commands set dihedrals of dihedral type 1 to be +dihedral_coeff commands set dihedrals of dihedral type 1 to be computed with a *harmonic* potential with coefficients 6.0, 1, 3 for K, d, n. All other dihedral types (2-N) are computed with a *helix* potential with coefficients 10, 10, 10 for A, B, C. @@ -74,7 +74,7 @@ input script, since AngleTorsion (or EndBondTorsion, etc) coefficients need not be specified at all for dihedral types that are not *class2*\ . A dihedral style of *none* with no additional coefficients can be used -in place of a dihedral style, either in a input script dihedral\_coeff +in place of a dihedral style, either in a input script dihedral_coeff command or in the data file, if you desire to turn off interactions for specific dihedral types. @@ -89,7 +89,7 @@ for more info. Unlike other dihedral styles, the hybrid dihedral style does not store dihedral coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when restarting a simulation from a -restart file, you need to re-specify dihedral\_coeff commands. +restart file, you need to re-specify dihedral_coeff commands. Related commands """""""""""""""" diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index 87125a4918..9ce464f5f6 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -67,7 +67,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index affa53b0bc..bdc5f79559 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -68,7 +68,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index a156b86a03..67919aa77f 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -89,7 +89,7 @@ Restrictions """""""""""" This dihedral style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index ad9cc11da3..bf3cf4902a 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -38,11 +38,11 @@ a data or restart file or via the :doc:`dihedral_coeff ` command. All dihedral potentials store their coefficient data in binary restart -files which means dihedral\_style and +files which means dihedral_style and :doc:`dihedral_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the :doc:`read_restart ` command for details on how to do -this. The one exception is that dihedral\_style *hybrid* only stores +this. The one exception is that dihedral_style *hybrid* only stores the list of sub-styles in the restart file; dihedral coefficients need to be re-specified. @@ -87,7 +87,7 @@ the style to display the formula it computes and coefficients specified by the associated :doc:`dihedral_coeff ` command. Click on the style to display the formula it computes, any additional -arguments specified in the dihedral\_style command, and coefficients +arguments specified in the dihedral_style command, and coefficients specified by the associated :doc:`dihedral_coeff ` command. @@ -135,4 +135,4 @@ Related commands Default """"""" -dihedral\_style none +dihedral_style none diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index dfa4b1c75d..112716a240 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -127,7 +127,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N specified in the :doc:`dihedral_style table ` command. -Let *Ntable* is the number of table entries requested dihedral\_style +Let *Ntable* is the number of table entries requested dihedral_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does is a preliminary interpolation by creating splines using the *Nfile* @@ -197,12 +197,12 @@ instructions on how to use the accelerated styles effectively. **Restart info:** -This dihedral style writes the settings for the "dihedral\_style table" -command to :doc:`binary restart files `, so a dihedral\_style +This dihedral style writes the settings for the "dihedral_style table" +command to :doc:`binary restart files `, so a dihedral_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file, since it is tabulated in the potential files. Thus, -dihedral\_coeff commands do need to be specified in the restart input +dihedral_coeff commands do need to be specified in the restart input script. Restrictions diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 2015146eaf..ae2fcd1f77 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -148,7 +148,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N specified in the :doc:`dihedral_style table ` command. -Let *Ntable* is the number of table entries requested dihedral\_style +Let *Ntable* is the number of table entries requested dihedral_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does is a preliminary interpolation by creating splines using the *Nfile* @@ -198,12 +198,12 @@ that matches the specified keyword. **Restart info:** -This dihedral style writes the settings for the "dihedral\_style table/cut" -command to :doc:`binary restart files `, so a dihedral\_style +This dihedral style writes the settings for the "dihedral_style table/cut" +command to :doc:`binary restart files `, so a dihedral_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file, since it is tabulated in the potential files. Thus, -dihedral\_coeff commands do need to be specified in the restart input +dihedral_coeff commands do need to be specified in the restart input script. Restrictions diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 0dc1578e5c..7d8dcd496a 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -33,7 +33,7 @@ command. If no dihedral style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with a DihedralCoeff -section for any dihedral style. Similarly, any dihedral\_coeff commands +section for any dihedral style. Similarly, any dihedral_coeff commands will only be checked for the dihedral type number and the rest ignored. Note that the :doc:`dihedral_coeff ` command must be diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 214164d776..efc6f9230b 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -59,7 +59,7 @@ The *move* style displaces the group of atoms by the specified 3d displacement vector. Any of the 3 quantities defining the vector components can be specified as an equal-style or atom-style :doc:`variable `. If the value is a variable, it should be -specified as v\_name, where name is the variable name. In this case, +specified as v_name, where name is the variable name. In this case, the variable will be evaluated, and its value(s) used for the displacement(s). The scale factor implied by the *units* keyword will also be applied to the variable result. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 2f1c58158f..c842d5fafe 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -262,10 +262,10 @@ the 3 tilt factors will be included on each of the 3 following lines. This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. -Note that the first two numbers on each line are now xlo\_bound instead +Note that the first two numbers on each line are now xlo_bound instead of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic ` doc page for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the -6 bounding box extents (xlo\_bound,xhi\_bound,etc) are calculated from +6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the triclinic parameters, and how to transform those parameters to and from other commonly used triclinic representations. @@ -280,7 +280,7 @@ scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom is at a location 1/4 of the distance from xlo to xhi of the box boundaries. The format can be changed to unscaled coords via the :doc:`dump_modify ` settings. Image flags can also be -added for each atom via dump\_modify. +added for each atom via dump_modify. Style *custom* allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are @@ -502,7 +502,7 @@ between processor, there is no guarantee that the same index will be used for the same info (e.g. a particular bond) in successive snapshots. -The *c\_ID* and *c\_ID[I]* attributes allow local vectors or arrays +The *c_ID* and *c_ID[I]* attributes allow local vectors or arrays calculated by a :doc:`compute ` to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the @@ -515,20 +515,20 @@ opposed to local quantities, cannot be output in a dump local command. Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and per-atom quantities can be output by the dump custom command. -If *c\_ID* is used as a attribute, then the local vector calculated by -the compute is printed. If *c\_ID[I]* is used, then I must be in the +If *c_ID* is used as a attribute, then the local vector calculated by +the compute is printed. If *c_ID[I]* is used, then I must be in the range from 1-M, which will print the Ith column of the local array with M columns calculated by the compute. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. -The *f\_ID* and *f\_ID[I]* attributes allow local vectors or arrays +The *f_ID* and *f_ID[I]* attributes allow local vectors or arrays calculated by a :doc:`fix ` to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script. -If *f\_ID* is used as a attribute, then the local vector calculated by -the fix is printed. If *f\_ID[I]* is used, then I must be in the +If *f_ID* is used as a attribute, then the local vector calculated by +the fix is printed. If *f_ID[I]* is used, then I must be in the range from 1-M, which will print the Ith column of the local with M columns calculated by the fix. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple @@ -612,7 +612,7 @@ The *tqx*\ , *tqy*\ , *tqz* attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. -The *c\_ID* and *c\_ID[I]* attributes allow per-atom vectors or arrays +The *c_ID* and *c_ID[I]* attributes allow per-atom vectors or arrays calculated by a :doc:`compute ` to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the @@ -626,14 +626,14 @@ command. Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and local quantities can be output by the dump local command. -If *c\_ID* is used as a attribute, then the per-atom vector calculated -by the compute is printed. If *c\_ID[I]* is used, then I must be in +If *c_ID* is used as a attribute, then the per-atom vector calculated +by the compute is printed. If *c_ID[I]* is used, then I must be in the range from 1-M, which will print the Ith column of the per-atom array with M columns calculated by the compute. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. -The *f\_ID* and *f\_ID[I]* attributes allow vector or array per-atom +The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom quantities calculated by a :doc:`fix ` to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script. The :doc:`fix ave/atom ` command is one that calculates per-atom @@ -642,14 +642,14 @@ any :doc:`compute `, :doc:`fix `, or atom-style :doc:`variable `, this allows those time-averaged results to be written to a dump file. -If *f\_ID* is used as a attribute, then the per-atom vector calculated -by the fix is printed. If *f\_ID[I]* is used, then I must be in the +If *f_ID* is used as a attribute, then the per-atom vector calculated +by the fix is printed. If *f_ID[I]* is used, then I must be in the range from 1-M, which will print the Ith column of the per-atom array with M columns calculated by the fix. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. -The *v\_name* attribute allows per-atom vectors calculated by a +The *v_name* attribute allows per-atom vectors calculated by a :doc:`variable ` to be output. The name in the attribute should be replaced by the actual name of the variable that has been defined previously in the input script. Only an atom-style variable @@ -660,7 +660,7 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file. -The *d\_name* and *i\_name* attributes allow to output custom per atom +The *d_name* and *i_name* attributes allow to output custom per atom floating point or integer properties that are managed by :doc:`fix property/atom `. @@ -674,7 +674,7 @@ Restrictions """""""""""" To write gzipped dump files, you must either compile LAMMPS with the --DLAMMPS\_GZIP option or use the styles from the COMPRESS package. +-DLAMMPS_GZIP option or use the styles from the COMPRESS package. See the :doc:`Build settings ` doc page for details. The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are part of diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index ba09b9e6ed..e1b0fe000a 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -42,11 +42,11 @@ ADIOS-BP files are binary, portable and self-describing. .. _adios: https://github.com/ornladios/ADIOS2 -**Use from write\_dump:** +**Use from write_dump:** It is possible to use these dump styles with the :doc:`write_dump ` command. In this case, the sub-intervals -must not be set at all. The write\_dump command can be used to +must not be set at all. The write_dump command can be used to create a new file at each individual dump. .. code-block:: LAMMPS @@ -61,7 +61,7 @@ Restrictions The number of atoms per snapshot CAN change with the adios style. When using the ADIOS tool 'bpls' to list the content of a .bp file, -bpls will print *\__* for the size of the output table indicating that +bpls will print *__* for the size of the output table indicating that its size is changing every step. The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 6b6b4cf88e..de44572307 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -33,8 +33,8 @@ Note that at least one element must be specified and image may only be present if position is specified first. For the elements *position*\ , *velocity*\ , *force* and *species*\ , a -sub-interval may be specified to write the data only every N\_element -iterations of the dump (i.e. every N\*N\_element time steps). This is +sub-interval may be specified to write the data only every N_element +iterations of the dump (i.e. every N\*N_element time steps). This is specified by this option directly following the element declaration: .. parsed-literal:: @@ -58,15 +58,15 @@ Dump a snapshot of atom coordinates every N timesteps in the HDF5 files are binary, portable and self-describing. This dump style will write only one file, on the root node. -Several dumps may write to the same file, by using file\_from and +Several dumps may write to the same file, by using file_from and referring to a previously defined dump. Several groups may also be stored within the same file by defining several dumps. A dump that -refers (via *file\_from*) to an already open dump ID and that concerns -another particle group must specify *create\_group yes*. +refers (via *file_from*) to an already open dump ID and that concerns +another particle group must specify *create_group yes*. .. _h5md: http://nongnu.org/h5md/ -Each data element is written every N\*N\_element steps. For *image*\ , no +Each data element is written every N\*N_element steps. For *image*\ , no sub-interval is needed as it must be present at the same interval as *position*\ . *image* must be given after *position* in any case. The box information (edges in each dimension) is stored at the same @@ -79,13 +79,13 @@ every N steps. timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. -**Use from write\_dump:** +**Use from write_dump:** It is possible to use this dump style with the :doc:`write_dump ` command. In this case, the sub-intervals -must not be set at all. The write\_dump command can be used either to +must not be set at all. The write_dump command can be used either to create a new file or to add current data to an existing dump file by -using the *file\_from* keyword. +using the *file_from* keyword. Typically, the *species* data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and @@ -124,7 +124,7 @@ Related commands ---------- -.. _h5md\_cpc: +.. _h5md_cpc: **(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index d4efc983eb..0477e5d718 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -140,7 +140,7 @@ created. The JPEG and PNG files are binary; PPM has a text mode header followed by binary data. JPEG images have lossy compression; PNG has lossless compression; and PPM files are uncompressed but can be compressed with gzip, if LAMMPS has been compiled with --DLAMMPS\_GZIP and a ".gz" suffix is used. +-DLAMMPS_GZIP and a ".gz" suffix is used. Similarly, the format of the resulting movie is chosen with the *movie* dump style. This is handled by the underlying FFmpeg converter @@ -151,7 +151,7 @@ framerate can be set using the :doc:`dump_modify ` command. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images -into movies, LAMMPS has to be compiled with the -DLAMMPS\_FFMPEG +into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG flag. See the :doc:`Build settings ` doc page for details. @@ -218,7 +218,7 @@ diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam `_ visualization package. @@ -428,7 +428,7 @@ they control how the simulation box appears in the image. All of the *view*\ , *center*\ , *up*\ , *zoom*\ , and *persp* values can be specified as numeric quantities, whose meaning is explained below. -Any of them can also be specified as an :doc:`equal-style variable `, by using v\_name as the value, where "name" is +Any of them can also be specified as an :doc:`equal-style variable `, by using v_name as the value, where "name" is the variable name. In this case the variable will be evaluated on the timestep each image is created to create a new value. If the equal-style variable is time-dependent, this is a means of changing @@ -541,7 +541,7 @@ A series of JPEG, PNG, or PPM images can be converted into a movie file and then played as a movie using commonly available tools. Using dump style *movie* automates this step and avoids the intermediate step of writing (many) image snapshot file. But LAMMPS has to be -compiled with -DLAMMPS\_FFMPEG and an FFmpeg executable have to be +compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be installed. To manually convert JPEG, PNG or PPM files into an animated GIF or @@ -627,12 +627,12 @@ which could then be output into dump files. Restrictions """""""""""" -To write JPEG images, you must use the -DLAMMPS\_JPEG switch when +To write JPEG images, you must use the -DLAMMPS_JPEG switch when building LAMMPS and link with a JPEG library. To write PNG images, you -must use the -DLAMMPS\_PNG switch when building LAMMPS and link with a +must use the -DLAMMPS_PNG switch when building LAMMPS and link with a PNG library. -To write *movie* dumps, you must use the -DLAMMPS\_FFMPEG switch when +To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when building LAMMPS and have the FFmpeg executable available on the machine where LAMMPS is being run. Typically it's name is lowercase, i.e. ffmpeg. diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index c9582775dc..5f7f42b4be 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -139,7 +139,7 @@ As explained on the :doc:`dump ` doc page, the *atom/mpiio*\ , syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in parallel via the MPI-IO library. Thus if a -dump\_modify option below is valid for the *atom* style, it is also +dump_modify option below is valid for the *atom* style, it is also valid for the *atom/mpiio* style, and similarly for the other styles which allow for use of MPI-IO. @@ -163,7 +163,7 @@ The *at* keyword only applies to the *netcdf* dump style. It can only be used if the *append yes* keyword is also used. The *N* argument is the index of which frame to append to. A negative value can be specified for *N*\ , which means a frame counted from the end of the -file. The *at* keyword can only be used if the dump\_modify command is +file. The *at* keyword can only be used if the dump_modify command is before the first command that causes dump snapshots to be output, e.g. a :doc:`run ` or :doc:`minimize ` command. Once the dump file has been opened, this keyword has no further effect. @@ -221,7 +221,7 @@ The *every* keyword changes the dump frequency originally specified by the :doc:`dump ` command to a new value. The every keyword can be specified in one of two ways. It can be a numeric value in which case it must be > 0. Or it can be an :doc:`equal-style variable `, -which should be specified as v\_name, where name is the variable name. +which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a dump snapshot will be written @@ -270,7 +270,7 @@ in file tmp.times: from the file is not a value greater than the current timestep. Thus if you wanted output on steps 0,15,100 of a 100-timestep run, the file should contain the values 15,100,101 and you should also use the - dump\_modify first command. Any final value > 100 could be used in + dump_modify first command. Any final value > 100 could be used in place of 101. ---------- @@ -332,7 +332,7 @@ settings, reverting all values to their default format. values. However, when specifying the *line* option or *format M string* option for those values, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with "%ld", if - LAMMPS was compiled with the -DLAMMPS\_BIGBIG option for 8-byte IDs. + LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs. .. note:: @@ -350,7 +350,7 @@ settings, reverting all values to their default format. dump_modify 1 format "%d %0.0f %0.0f" will output the two atom IDs for atoms in each bond as integers. If -the dump\_modify command were omitted, they would appear as +the dump_modify command were omitted, they would appear as floating-point values, assuming they were large integers (more than 6 digits). The "index" keyword should use the "%d" format since it is not generated by a compute or fix, and is stored internally as an @@ -461,7 +461,7 @@ The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ , *image*\ , and *movie* styles. It allows an "incremental" dump file to be written, by refreshing a compute that is used as a threshold for determining which atoms are included in a dump snapshot. The -specified *c\_ID* gives the ID of the compute. It is prefixed by "c\_" +specified *c_ID* gives the ID of the compute. It is prefixed by "c\_" to indicate a compute, which is the only current option. At some point, other options may be added, e.g. fixes or variables. @@ -503,7 +503,7 @@ Angstroms to be output on a given snapshot (assuming metal units). However, note that when an atom is output, we also need to update the reference position for that atom to its new coordinates. So that it will not be output in every snapshot thereafter. That reference -position is stored by :doc:`compute displace/atom `. So the dump\_modify +position is stored by :doc:`compute displace/atom `. So the dump_modify *refresh* option triggers a call to compute displace/atom at the end of every dump to perform that update. The *refresh check* option shown as part of the :doc:`compute displace/atom ` command enables the compute @@ -511,17 +511,17 @@ to respond to the call from the dump command, and update the appropriate reference positions. This is done be defining an :doc:`atom-style variable `, *check* in this example, which calculates a Boolean value (0 or 1) for each atom, based on the same -criterion used by dump\_modify thresh. +criterion used by dump_modify thresh. See the :doc:`compute displace/atom ` command for more details, including an example of how to produce output that includes an initial snapshot with the reference position of all atoms. Note that only computes with a *refresh* option will work with -dump\_modify refresh. See individual compute doc pages for details. +dump_modify refresh. See individual compute doc pages for details. Currently, only compute displace/atom supports this option. Others may be added at some point. If you use a compute that doesn't support -refresh operations, LAMMPS will not complain; dump\_modify refresh will +refresh operations, LAMMPS will not complain; dump_modify refresh will simply do nothing. ---------- @@ -720,7 +720,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n The specified *color* can be a single color which is any of the 140 pre-defined colors (see below) or a color name defined by the -dump\_modify color option. Or it can be two or more colors separated +dump_modify color option. Or it can be two or more colors separated by a "/" character, e.g. red/green/blue. In the former case, that color is assigned to all the specified atom types. In the latter case, the list of colors are assigned in a round-robin fashion to each @@ -797,7 +797,7 @@ The *N* setting is how many entries follow. The format of the entries depends on whether the color map style is continuous, discrete or sequential. In all cases the *color* setting can be any of the 140 pre-defined colors (see below) or a color name defined by the -dump\_modify color option. +dump_modify color option. For continuous color maps, each entry has a *value* and a *color*\ . The *value* is either a number within the range of values or *min* or @@ -871,7 +871,7 @@ mapped to one of the colors, even if there are 1000s of molecules. The *backcolor* sets the background color of the images. The color name can be any of the 140 pre-defined colors (see below) or a color -name defined by the dump\_modify color option. +name defined by the dump_modify color option. ---------- @@ -891,7 +891,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n The specified *color* can be a single color which is any of the 140 pre-defined colors (see below) or a color name defined by the -dump\_modify color option. Or it can be two or more colors separated +dump_modify color option. Or it can be two or more colors separated by a "/" character, e.g. red/green/blue. In the former case, that color is assigned to all the specified bond types. In the latter case, the list of colors are assigned in a round-robin fashion to each @@ -931,14 +931,14 @@ sub-domain boundaries. See the "dump image box" command for how to specify that a box be drawn via the *box* keyword, and the sub-domain boundaries via the *subbox* keyword. The color name can be any of the 140 pre-defined colors (see below) or a color name defined by the -dump\_modify color option. +dump_modify color option. ---------- The *color* keyword allows definition of a new color name, in addition to the 140-predefined colors (see below), and associates 3 red/green/blue RGB values with that color name. The color name can -then be used with any other dump\_modify keyword that takes a color +then be used with any other dump_modify keyword that takes a color name as a value. The RGB values should each be floating point values between 0.0 and 1.0 inclusive. @@ -1013,7 +1013,7 @@ The option defaults are ---------- These are the standard 109 element names that LAMMPS pre-defines for -use with the :doc:`dump image ` and dump\_modify commands. +use with the :doc:`dump image ` and dump_modify commands. * 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" * 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" @@ -1030,8 +1030,8 @@ use with the :doc:`dump image ` and dump\_modify commands. ---------- These are the 140 colors that LAMMPS pre-defines for use with the -:doc:`dump image ` and dump\_modify commands. Additional -colors can be defined with the dump\_modify color command. The 3 +:doc:`dump image ` and dump_modify commands. Additional +colors can be defined with the dump_modify color command. The 3 numbers listed for each name are the RGB (red/green/blue) values. Divide each value by 255 to get the equivalent 0.0 to 1.0 value. diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index e5264b783c..4f607c4fdd 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -76,7 +76,7 @@ For the *vtk* style, sorting is off by default. See the The dimensions of the simulation box are written to a separate file for each snapshot (either in legacy VTK or XML format depending on the -format of the main dump file) with the suffix *\_boundingBox* appended +format of the main dump file) with the suffix *_boundingBox* appended to the given dump filename. For an orthogonal simulation box this information is saved as a @@ -134,8 +134,8 @@ in order with some post-processing tools. If a "%" character appears in the filename, then each of P processors writes a portion of the dump file, and the "%" character is replaced with the processor ID from 0 to P-1 preceded by an underscore character. -For example, tmp.dump%.vtp becomes tmp.dump\_0.vtp, tmp.dump\_1.vtp, ... -tmp.dump\_P-1.vtp, etc. This creates smaller files and can be a fast +For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ... +tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast mode of output on parallel machines that support parallel I/O for output. By default, P = the number of processors meaning one file per @@ -150,7 +150,7 @@ processor 0 does write files. Note that using the "\*" and "%" characters together can produce a large number of small dump files! -If *dump\_modify binary* is used, the dump file (or files, if "\*" or +If *dump_modify binary* is used, the dump file (or files, if "\*" or "%" is also used) is written in binary format. A binary dump file will be about the same size as a text version, but will typically write out much faster. diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index d1ebe67694..c4ceed64e6 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -73,7 +73,7 @@ Related commands :doc:`fix phonon ` :doc:`compute hma ` uses an analytic formulation of the -Hessian provided by a pair_style's Pair::single\_hessian() function, +Hessian provided by a pair_style's Pair::single_hessian() function, if implemented. Default diff --git a/doc/src/fix.rst b/doc/src/fix.rst index b6088376bc..2182ce7460 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -103,11 +103,11 @@ discussed below, it can be referenced via the following bracket notation, where ID is the ID of the fix: +-------------+--------------------------------------------+ -| f\_ID | entire scalar, vector, or array | +| f_ID | entire scalar, vector, or array | +-------------+--------------------------------------------+ -| f\_ID[I] | one element of vector, one column of array | +| f_ID[I] | one element of vector, one column of array | +-------------+--------------------------------------------+ -| f\_ID[I][J] | one element of array | +| f_ID[I][J] | one element of array | +-------------+--------------------------------------------+ In other words, using one bracket reduces the dimension of the @@ -119,7 +119,7 @@ or array. Note that commands and :doc:`variables ` which use fix quantities typically do not allow for all kinds, e.g. a command may require a vector of values, not a scalar. This means there is no -ambiguity about referring to a fix quantity as f\_ID even if it +ambiguity about referring to a fix quantity as f_ID even if it produces, for example, both a scalar and vector. The doc pages for various commands explain the details. @@ -146,7 +146,7 @@ e.g. temperature. Extensive means the value scales with the number of atoms in the simulation, e.g. total rotational kinetic energy. :doc:`Thermodynamic output ` will normalize extensive values by the number of atoms in the system, depending on the -"thermo\_modify norm" setting. It will not normalize intensive values. +"thermo_modify norm" setting. It will not normalize intensive values. If a fix value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an intensive or extensive value. See the doc page for individual fixes diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index eafc4710f3..eab8f92639 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -121,11 +121,11 @@ meaning of these parameters: +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`born ` | a,b,c | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`born/coul/long, born/coul/msm ` | coulombic\_cutoff | type global | +| :doc:`born/coul/long, born/coul/msm ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`buck ` | a,c | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`buck/coul/long, buck/coul/msm ` | coulombic\_cutoff | type global | +| :doc:`buck/coul/long, buck/coul/msm ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`buck/mdf ` | a,c | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -135,11 +135,11 @@ meaning of these parameters: +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`coul/debye ` | scale | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/dsf ` | coulombic\_cutoff | type global | +| :doc:`coul/dsf ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/long, coul/msm ` | coulombic\_cutoff, scale | type pairs | +| :doc:`coul/long, coul/msm ` | coulombic_cutoff, scale | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/long/soft ` | scale, lambda, coulombic\_cutoff | type pairs | +| :doc:`coul/long/soft ` | scale, lambda, coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`eam, eam/alloy, eam/fs ` | scale | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -149,17 +149,17 @@ meaning of these parameters: +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/class2 ` | epsilon,sigma | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma,coulombic\_cutoff | type pairs | +| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma,coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/cut ` | epsilon,sigma | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma,coulombic\_cutoff | type pairs | +| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma,coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda,coulombic\_cutoff | type pairs | +| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda,coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/cut/coul/dsf ` | cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/tip4p/cut ` | epsilon,sigma,coulombic\_cutoff | type pairs | +| :doc:`lj/cut/tip4p/cut ` | epsilon,sigma,coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -171,7 +171,7 @@ meaning of these parameters: +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lubricate ` | mu | global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`mie/cut ` | epsilon,sigma,gamma\_repulsive,gamma\_attractive | type pairs | +| :doc:`mie/cut ` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`morse, morse/smooth/linear ` | D0,R0,alpha | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -179,19 +179,19 @@ meaning of these parameters: +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`nm/cut ` | E0,R0,m,n | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic\_cutoff | type pairs | +| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`reax/c ` | chi, eta, gamma | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/dmi ` | coulombic\_cutoff | type global | +| :doc:`spin/dmi ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/exchange ` | coulombic\_cutoff | type global | +| :doc:`spin/exchange ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/magelec ` | coulombic\_cutoff | type global | +| :doc:`spin/magelec ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/neel ` | coulombic\_cutoff | type global | +| :doc:`spin/neel ` | coulombic_cutoff | type global | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`table ` | table\_cutoff | type pairs | +| :doc:`table ` | table_cutoff | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`ufm ` | epsilon,sigma | type pairs | +---------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -247,10 +247,10 @@ be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. -The *v\_name* argument for keyword *pair* is the name of an +The *v_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time this fix is invoked to set the parameter to a new value. It should be -specified as v\_name, where name is the variable name. Equal-style +specified as v_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is @@ -284,9 +284,9 @@ from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Currently *bond* does not support bond\_style hybrid nor bond\_style +Currently *bond* does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are -working with fix\_adapt are +working with fix_adapt are +---------------------------------+-------+------------+ | :doc:`gromos ` | k, r0 | type bonds | @@ -313,10 +313,10 @@ current list of atom parameters that can be varied by this fix: * charge = charge on particle * diameter = diameter of particle -The *v\_name* argument of the *atom* keyword is the name of an +The *v_name* argument of the *atom* keyword is the name of an :doc:`equal-style variable ` which will be evaluated each time this fix is invoked to set the parameter to a new value. It should be -specified as v\_name, where name is the variable name. See the +specified as v_name, where name is the variable name. See the discussion above describing the formulas associated with equal-style variables. The new value is assigned to the corresponding attribute for all atoms in the fix group. @@ -343,7 +343,7 @@ over the course of a 1000-step simulation: ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index a9183123e0..ee44d8904f 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -217,10 +217,10 @@ be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. -The *v\_name* argument for keyword *pair* is the name of an +The *v_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time this fix is invoked to set the parameter to a new value. It should be -specified as v\_name, where name is the variable name. Equal-style +specified as v_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is @@ -262,10 +262,10 @@ The *I* argument indicates which atom types are affected. A wild-card asterisk can be used in place of or in conjunction with the I argument to set the coefficients for multiple atom types. -The *v\_name* argument of the *atom* keyword is the name of an +The *v_name* argument of the *atom* keyword is the name of an :doc:`equal-style variable ` which will be evaluated each time this fix is invoked to set the parameter to a new value. It should be -specified as v\_name, where name is the variable name. See the +specified as v_name, where name is the variable name. See the discussion above describing the formulas associated with equal-style variables. The new value is assigned to the corresponding attribute for all atoms in the fix group. @@ -289,7 +289,7 @@ parameters on the outermost rRESPA level. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index c33e77409e..a7403ef7ab 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -50,7 +50,7 @@ a channel. Any of the 3 quantities defining the force components can be specified as an equal-style or atom-style :doc:`variable `, namely *fx*\ , *fy*\ , *fz*\ . If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the force component. @@ -98,7 +98,7 @@ one or more variables, and you are performing energy minimization via the "minimize" command. The keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each atom as function of its position. Like variables used -for *fx*\ , *fy*\ , *fz*\ , the energy variable is specified as v\_name, +for *fx*\ , *fy*\ , *fz*\ , the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy @@ -131,7 +131,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index ba90008153..2b5a7ce8ce 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -39,7 +39,7 @@ This command can be used to drive a group of atoms into rotation. Any of the 3 quantities defining the torque components can be specified as an equal-style :doc:`variable `, namely *Tx*\ , *Ty*\ , *Tz*\ . If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the torque component. @@ -50,7 +50,7 @@ time. Thus it is easy to specify a time-dependent torque. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 3f746424c6..6246787075 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -86,7 +86,7 @@ define the lattice spacings. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 4c40aa2f09..a87fdadf83 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -141,7 +141,7 @@ you MUST enable the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index e22e6cf7c2..93ff48ce0f 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -16,7 +16,7 @@ Syntax * Nrepeat = # of times to use input values for calculating averages * Nfreq = calculate averages every this many timesteps one or more input values can be listed -* value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[i], f\_ID, f\_ID[i], v\_name +* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name .. parsed-literal:: @@ -149,7 +149,7 @@ per-atom quantities to time average. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector quantities are diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index fe610449cb..b19cce417c 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -17,7 +17,7 @@ Syntax * Nfreq = calculate averages every this many timesteps * chunkID = ID of :doc:`compute chunk/atom ` command * one or more input values can be listed -* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c\_ID, c\_ID[I], f\_ID, f\_ID[I], v\_name +* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name .. parsed-literal:: @@ -426,7 +426,7 @@ By default, these header lines are as follows: In the first line, ID and name are replaced with the fix-ID and group name. The second line describes the two values that are printed at the first of each section of output. In the third line the values are -replaced with the appropriate value names, e.g. fx or c\_myCompute[2]. +replaced with the appropriate value names, e.g. fx or c_myCompute[2]. The words in parenthesis only appear with corresponding columns if the chunk style specified for the :doc:`compute chunk/atom ` command supports them. The OrigID @@ -456,7 +456,7 @@ dimensions. Those values are always in distance :doc:`units `. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index d559efc123..c42159e89b 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -16,7 +16,7 @@ Syntax * Nrepeat = # of correlation time windows to accumulate * Nfreq = calculate time window averages every this many timesteps * one or more input values can be listed -* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -310,7 +310,7 @@ included in the variable formula or via the *prefactor* keyword. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index 9416f42f1c..affa7df127 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -15,7 +15,7 @@ Syntax * Nevery = use input values every this many timesteps * Nfreq = save state of the time correlation functions every this many timesteps * one or more input values can be listed -* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -110,7 +110,7 @@ corresponds to about 10 KB. For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate ` doc page. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Contrary to :doc:`fix ave/correlate ` this fix does **not** provide access to its internal data to various output @@ -118,7 +118,7 @@ options. Since this fix in intended for the calculation of time correlation functions over very long MD simulations, the information about this fix is written automatically to binary restart files, so that the time correlation calculation can continue in subsequent -simulations. None of the fix\_modify options are relevant to this fix. +simulations. None of the fix_modify options are relevant to this fix. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization. diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 3482df3703..158f259695 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -21,7 +21,7 @@ Syntax * lo,hi = lo/hi bounds within which to histogram * Nbin = # of histogram bins * one or more input values can be listed -* value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -329,7 +329,7 @@ the histogram. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 778a04f21c..efa8095d69 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -16,7 +16,7 @@ Syntax * Nrepeat = # of times to use input values for calculating averages * Nfreq = calculate averages every this many timesteps * one or more input values can be listed -* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -304,7 +304,7 @@ appropriate fields from the fix ave/time command. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 69debca1dd..437c5caaa7 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -55,7 +55,7 @@ average value without adding in any additional force. Any of the 3 quantities defining the force components can be specified as an equal-style :doc:`variable `, namely *fx*\ , *fy*\ , *fz*\ . -If the value is a variable, it should be specified as v\_name, where +If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the average force. @@ -91,7 +91,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 052abb2a76..13fdf6b1c7 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -362,7 +362,7 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES". ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index 175c33e4c0..5315aa81a1 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -44,8 +44,8 @@ The first half of the command mimics a standard fix npt command: 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 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 @@ -71,8 +71,8 @@ With the *analytic* option, the arguments are as follows: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N -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 @@ -86,9 +86,9 @@ 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 +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 +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 ). This fix is part of the USER-BOCS package. It is only enabled if diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index c4488574dc..3994b58b12 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -115,7 +115,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 42c94fb9bc..0c48a800c9 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -216,7 +216,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 3d9101d20b..8daa52a73d 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -18,7 +18,7 @@ Syntax * bond/react = style name of this fix command * the common keyword/values may be appended directly after 'bond/react' * this applies to all reaction specifications (below) -* common\_keyword = *stabilization* +* common_keyword = *stabilization* .. parsed-literal:: @@ -36,9 +36,9 @@ Syntax * Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) * template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology -* map\_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates +* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates * zero or more individual keyword/value pairs may be appended to each react argument -* individual\_keyword = *prob* or *max\_rxn* or *stabilize\_steps* or *update\_edges* +* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *update_edges* .. parsed-literal:: @@ -110,7 +110,7 @@ The *stabilization* keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms in an internally-created fix :doc:`nve/limit ` time integrator for a set number of timesteps given by the -*stabilize\_steps* keyword. While reacting atoms are being time +*stabilize_steps* keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being involved in any new reactions. The *xmax* value keyword should typically be set to the maximum distance that non-reacting atoms move @@ -123,7 +123,7 @@ automatically thermostatted by an internally-created :doc:`nve/limit ` integrator. The second group contains all atoms currently not involved in a reaction. This group should be used by a thermostat in order to time integrate the system. The name -of this group of non-reacting atoms is created by appending '\_REACT' +of this group of non-reacting atoms is created by appending '_REACT' to the group-ID argument of the *stabilization* keyword, as shown in the second example above. @@ -139,8 +139,8 @@ command creates a :doc:`dynamic group ` that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is used as the parent group of new, internally-created dynamic group. In both cases, this new dynamic -group is named by appending '\_REACT' to the group-ID, e.g. -nvt\_grp\_REACT. By specifying an existing group, you may thermostat +group is named by appending '_REACT' to the group-ID, e.g. +nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time @@ -285,7 +285,7 @@ Edges' and allows for forcing the update of a specific atom's atomic charge. The first column is the ID of an atom near the edge of the pre-reacted molecule template, and the value of the second column is either 'none' or 'charges.' Further details are provided in the -discussion of the 'update\_edges' keyword. The fifth optional section +discussion of the 'update_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are four types of constraints available, as discussed below. @@ -422,9 +422,9 @@ actually occurs. The fraction setting must be a value between 0.0 and 1.0. A uniform random number between 0.0 and 1.0 is generated and the eligible reaction only occurs if the random number is less than the fraction. Up to N reactions are permitted to occur, as optionally -specified by the *max\_rxn* keyword. +specified by the *max_rxn* keyword. -The *stabilize\_steps* keyword allows for the specification of how many +The *stabilize_steps* keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat. In order to produce the most physical behavior, this 'reaction site equilibration time' should be tuned to @@ -435,7 +435,7 @@ individually tuned for each fix reaction step. Note that in some situations, decreasing rather than increasing this parameter will result in an increase in stability. -The *update\_edges* keyword can increase the number of atoms whose +The *update_edges* keyword can increase the number of atoms whose atomic charges are updated, when the pre-reaction template contains edge atoms. When the value is set to 'charges,' all atoms' atomic charges are updated to those specified by the post-reaction template, @@ -461,7 +461,7 @@ such as small rings, that may be otherwise indistinguishable. Optionally, you can enforce additional behaviors on reacting atoms. For example, it may be beneficial to force reacting atoms to remain at a certain temperature. For this, you can use the internally-created -dynamic group named "bond\_react\_MASTER\_group", which consists of all +dynamic group named "bond_react_MASTER_group", which consists of all atoms currently involved in a reaction. For example, adding the following command would add an additional thermostat to the group of all currently-reacting atoms: @@ -487,7 +487,7 @@ local command. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Cumulative reaction counts for each reaction are written to :doc:`binary restart files `. These values are associated with the reaction name (react-ID). Additionally, internally-created per-atom @@ -528,8 +528,8 @@ Related commands Default """"""" -The option defaults are stabilization = no, prob = 1.0, stabilize\_steps = 60, -update\_edges = none +The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, +update_edges = none ---------- diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index 773bceb6e7..9427b0e780 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -129,17 +129,17 @@ appended and the group for the new compute is "all", so that the temperature of the entire system is used. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. ---------- -**Restart, fix\_modify, thermo output, run start/stop, minimize info:** +**Restart, fix_modify, thermo output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" @@ -174,7 +174,7 @@ This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -The settings of the "special\_bond" command must be 0,1,1 in order to +The settings of the "special_bond" command must be 0,1,1 in order to use this fix, which is typical of bead-spring chains with FENE or harmonic bonds. This means that pairwise interactions between bonded atoms are turned off, but are turned on between atoms two or three diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index b7e5c5bb4c..7786a8faef 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -269,7 +269,7 @@ from a restart file. Because pressure is often a very sensitive function of volume, it can be difficult for the minimizer to equilibrate the system the desired pressure with high precision, particularly for solids. Some - techniques that seem to help are (a) use the "min\_modify line + techniques that seem to help are (a) use the "min_modify line quadratic" option when minimizing with box relaxations, (b) minimize several times in succession if need be, to drive the pressure closer to the target pressure, (c) relax the atom positions before relaxing @@ -292,23 +292,23 @@ as if these commands had been issued: compute fix-ID_press group-ID pressure fix-ID_temp virial See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is the same as the fix group. Also note that the pressure compute does not include a kinetic component. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -323,7 +323,7 @@ minimization, most likely in an undesirable way. .. note:: If both the *temp* and *press* keywords are used in a single - thermo\_modify command (or in two separate commands), then the order in + thermo_modify command (or in two separate commands), then the order in which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as an argument when it is specified. The *temp* keyword will override this (for the pressure compute being used by fix box/relax), but only if the diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 2e7f04f01c..2e0cf84cc5 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -40,7 +40,7 @@ for the interacting particles to LAMMPS, so it can complete the timestep. Note that the server code can be a quantum code, or another classical -MD code which encodes a force field (pair\_style in LAMMPS lingo) which +MD code which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS does not have. In the quantum case, this fix is a mechanism for running *ab initio* MD with quantum forces. @@ -66,7 +66,7 @@ LAMMPS and another code in tandem to perform a coupled simulation. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index b2ce4d79ad..6f68d97c59 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -44,7 +44,7 @@ specified should contain the CMAP parameters for a particular version of the CHARMM force field. Two such files are including in the lammps/potentials directory: charmm22.cmap and charmm36.cmap. -The data file read by the "read\_data" must contain the topology of all +The data file read by the "read_data" must contain the topology of all the CMAP interactions, similar to the topology data for bonds, angles, dihedrals, etc. Specially it should have a line like this in its header section: @@ -71,7 +71,7 @@ interaction; it is an index into the CMAP force field file. The remaining 5 columns are the atom IDs of the atoms in the two 4-atom dihedrals that overlap to create the CMAP 5-body interaction. Note that the "crossterm" and "CMAP" keywords for the header and body -sections match those specified in the read\_data command following the +sections match those specified in the read_data command following the data file name; see the :doc:`read_data ` doc page for more details. @@ -90,7 +90,7 @@ the note below about how to include the CMAP energy when performing an ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the list of CMAP cross-terms to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index af778b2207..20315624d6 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -90,7 +90,7 @@ fix that thermostats all atoms in the fix colvars group. This will be used to provide the colvars module with the current thermostat target temperature. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the current status of the colvars module into :doc:`binary restart files `. This is in addition to the text @@ -101,12 +101,12 @@ The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change from the biasing force added by the fix to the system's potential energy as part of :doc:`thermodynamic output `. -The *fix\_modify configfile * option allows to add settings +The *fix_modify configfile * option allows to add settings from an additional config file to the colvars module. This option can only be used, after the system has been initialized with a :doc:`run ` command. -The *fix\_modify config * option allows to add settings +The *fix_modify config * option allows to add settings from inline strings. Those have to fit on a single line when enclosed in a pair of double quotes ("), or can span multiple lines when bracketed by a pair of triple double quotes (""", like python embedded documentation). diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 3d14bdee08..2fd5f17c95 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -17,7 +17,7 @@ Syntax * Kp = proportional gain in PID equation (unitless) * Ki = integral gain in PID equation (unitless) * Kd = derivative gain in PID equation (unitless) -* pvar = process variable of form c\_ID, c\_ID[I], f\_ID, f\_ID[I], or v\_name +* pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name .. parsed-literal:: @@ -190,7 +190,7 @@ equal-style versus internal-style variable interchangeably. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 7001b2304e..75fc6cc5c9 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -581,7 +581,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix will restore the initial box settings from :doc:`binary restart files `, which allows the fix to be properly continue deformation, when using the start/stop options of the :doc:`run ` diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index c379dcd9b0..31df74ce9b 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -163,7 +163,7 @@ command which also appears in your input script. If you wish the new rigid molecules (and other rigid molecules) to be thermostatted correctly via :doc:`fix rigid/small/nvt ` or :doc:`fix rigid/small/npt `, then you need to use the - "fix\_modify dynamic/dof yes" command for the rigid fix. This is to + "fix_modify dynamic/dof yes" command for the rigid fix. This is to inform that fix that the molecule count will vary dynamically. If you wish to insert molecules via the *mol* keyword, that will have @@ -271,7 +271,7 @@ units of distance or velocity. the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the deposition to :doc:`binary restart files `. This includes information about how many particles have been deposited, the random number generator seed, the diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index f7dc52fbe6..0eeb8f9478 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -41,9 +41,9 @@ This fix must be used with the :doc:`pair_style dpd/fdt/energy ` com Note that numerous variants of DPD can be specified by choosing an appropriate combination of the integrator and :doc:`pair_style dpd/fdt/energy ` command. DPD under isoenergetic conditions -can be specified by using fix *dpd/energy*\ , fix *nve* and pair\_style +can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can -be specified by using fix *dpd/energy*\ , fix *nph* and pair\_style +be specified by using fix *dpd/energy*\ , fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the examples/USER/dpd directory. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 8a2cd885ee..5ea1c85fb4 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -64,7 +64,7 @@ cuboid domain to apply the source flux to. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 74d98d7a40..792d4725cc 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -38,7 +38,7 @@ application. This command can be used to steer one or more atoms to a new location in the simulation. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 7a17ab98cf..607c161572 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -151,9 +151,9 @@ relative coordinates, are calculated using :doc:`compute temp/drude `. diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index e86d11ac94..861134f745 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -80,7 +80,7 @@ Note that the cumulative simulation time (in time units), which accounts for changes in the timestep size as a simulation proceeds, can be accessed by the :doc:`thermo_style time ` keyword. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 9084cbc2d6..0410803c13 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -43,7 +43,7 @@ external electric field. For charges, any of the 3 quantities defining the E-field components can be specified as an equal-style or atom-style :doc:`variable `, namely *ex*\ , *ey*\ , *ez*\ . If the value is a -variable, it should be specified as v\_name, where name is the variable +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the E-field component. @@ -101,7 +101,7 @@ minimize the orientation of dipoles in an applied electric field. The *energy* keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each atom as function of its position. Like variables used for *ex*\ , *ey*\ , -*ez*\ , the energy variable is specified as v\_name, where name is the +*ez*\ , the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy @@ -114,7 +114,7 @@ minimization will not converge properly. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 96eb94db01..4e2ea3a73d 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -99,7 +99,7 @@ velocity of that reservoir. The thermostatting force does not affect the center of mass velocities of the individual reservoirs and the entire simulation box. A derivation of the equations and details on the numerical implementation with velocity Verlet in LAMMPS can be -found in reference "(Wirnsberger)"#\_Wirnsberger. +found in reference "(Wirnsberger)"#_Wirnsberger. .. note:: @@ -163,7 +163,7 @@ constraints will be satisfied. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 5fea8a3d6d..cead9f7a12 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -129,7 +129,7 @@ scientific publications, experimental databases or by using of the impact parameter of the ion; these results can be used to derive the stopping power. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -159,7 +159,7 @@ The default is no limitation by region, and minneigh = 1. .. _elstopping: -**(electronic stopping)** Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping\_power\_%28particle\_radiation%29 +**(electronic stopping)** Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29 .. _Nordlund98: @@ -175,7 +175,7 @@ The default is no limitation by region, and minneigh = 1. .. _CasP: -**(CasP)** CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp\_en.html +**(CasP)** CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html .. _PASS: diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index f775572720..d33dd25a61 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -52,7 +52,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index a21de28b04..3800aa0c53 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -28,8 +28,8 @@ Description """"""""""" Fix *eos/table* applies a tabulated mesoparticle equation of state to -relate the particle internal energy (u\_i) to the particle internal -temperature (dpdTheta\_i). +relate the particle internal energy (u_i) to the particle internal +temperature (dpdTheta_i). Fix *eos/table* creates interpolation tables of length *N* from internal energy values listed in a file as a function of internal diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 8883940002..d6b9c6ae34 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -72,7 +72,7 @@ incur overhead due to the cost of building neighbor lists. :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index 01020d27b2..a77545d294 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -67,13 +67,13 @@ The arguments are as follows: Note that *timestep* is a "bigint" which is defined in src/lmptype.h, typically as a 64-bit integer. And *ids* is a pointer to type "tagint" which is typically a 32-bit integer unless LAMMPS is compiled with --DLAMMPS\_BIGBIG. For more info please see the :ref:`build settings +-DLAMMPS_BIGBIG. For more info please see the :ref:`build settings ` section of the manual. Finally, *fexternal* are the forces returned by the driver program. -The fix has a set\_callback() method which the external driver can call +The fix has a set_callback() method which the external driver can call to pass a pointer to its foo() function. See the -couple/lammps\_quest/lmpqst.cpp file in the LAMMPS distribution for an +couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an example of how this is done. This sample application performs classical MD using quantum forces computed by a density functional code `Quest `_. @@ -125,7 +125,7 @@ insure this energy setting is used appropriately in a minimization. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index 837e1c310c..ac23175875 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -68,11 +68,11 @@ different numbers of processors. The flipping type *flip-type* can be chosen between 4 types described in :ref:`(Hijazi) `. The flipping operation occurs during the thermostatting -step and it flips the momenta of the atoms. If no\_flip is chosen, no flip +step and it flips the momenta of the atoms. If no_flip is chosen, no flip will be executed and the integration will be the same as a standard Langevin thermostat :ref:`(Bussi) `. The other flipping types are : rescale - hard - soft. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** The instantaneous values of the extended variables are written to :doc:`binary restart files `. Because the state of the random diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 162b3c244b..1731ef94a2 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -60,7 +60,7 @@ If the clusters are chosen suitably, the :doc:`run_style respa ` is s ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to these fixes. No global or per-atom quantities are diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 9c1b6711e9..7b9e001bd3 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -68,7 +68,7 @@ other methods, such as the pump method :ref:`(Zhu) `. The pressure correction is discussed and described in :ref:`(Strong) `. For a complete example including the considerations discussed -above, see the examples/USER/flow\_gauss directory. +above, see the examples/USER/flow_gauss directory. .. note:: @@ -91,13 +91,13 @@ expensive than usual, so it is not performed by default. To invoke the work calculation, use the *energy* keyword. The :doc:`fix_modify ` *energy* option also invokes the work calculation, and overrides an *energy no* setting here. If neither -*energy yes* or *fix\_modify energy yes* are set, the global scalar +*energy yes* or *fix_modify energy yes* are set, the global scalar computed by the fix will return zero. .. note:: In order to check energy conservation, any other fixes that do - work on the system must have *fix\_modify energy yes* set as well. This + work on the system must have *fix_modify energy yes* set as well. This includes thermostat fixes and any constraints that hold the positions of wall atoms fixed, such as :doc:`fix spring/self `. @@ -111,12 +111,12 @@ computed at different rRESPA levels, then there must be a separate flow/gauss fix for each level. For example, if the flowing fluid and obstacle interact through pairwise and long-range Coulomb interactions, which are computed at rRESPA levels 3 and 4, respectively, then there must be two separate -flow/gauss fixes, one that specifies *fix\_modify respa 3* and one with -*fix\_modify respa 4*. +flow/gauss fixes, one that specifies *fix_modify respa 3* and one with +*fix_modify respa 4*. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index cec9064aba..d6659dc8f8 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -56,7 +56,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 01954a3639..77a0323000 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -169,7 +169,7 @@ at a random position within the current simulation cell or region, and new atom velocities are randomly chosen from the specified temperature distribution given by T. The effective temperature for new atom velocities can be increased or decreased using the optional keyword -*tfac\_insert* (see below). Relative coordinates for atoms in a +*tfac_insert* (see below). Relative coordinates for atoms in a molecule are taken from the template molecule provided by the user. The center of mass of the molecule is placed at the insertion point. The orientation of the molecule is chosen at random by rotating @@ -200,7 +200,7 @@ which also appears in your input script. If you wish the new rigid molecules (and other rigid molecules) to be thermostatted correctly via :doc:`fix rigid/small/nvt ` or :doc:`fix rigid/small/npt `, then you need to use the - "fix\_modify dynamic/dof yes" command for the rigid fix. This is to + "fix_modify dynamic/dof yes" command for the rigid fix. This is to inform that fix that the molecule count will vary dynamically. If you wish to insert molecules via the *mol* keyword, that will have @@ -247,13 +247,13 @@ as: \mu = \mu^{id} + \mu^{ex} -The second term mu\_ex is the excess chemical potential due to +The second term mu_ex is the excess chemical potential due to energetic interactions and is formally zero for the fictitious gas reservoir but is non-zero for interacting systems. So, while the chemical potential of the reservoir and the simulation cell are equal, -mu\_ex is not, and as a result, the densities of the two are generally -quite different. The first term mu\_id is the ideal gas contribution -to the chemical potential. mu\_id can be related to the density or +mu_ex is not, and as a result, the densities of the two are generally +quite different. The first term mu_id is the ideal gas contribution +to the chemical potential. mu_id can be related to the density or pressure of the fictitious gas reservoir by: .. math:: @@ -283,9 +283,9 @@ As an alternative to specifying mu directly, the ideal gas reservoir can be defined by its pressure *P* using the *pressure* keyword, in which case the user-specified chemical potential is ignored. The user may also specify the fugacity coefficient :math:`\phi` using the -*fugacity\_coeff* keyword, which defaults to unity. +*fugacity_coeff* keyword, which defaults to unity. -The *full\_energy* option means that the fix calculates the total +The *full_energy* option means that the fix calculates the total potential energy of the entire simulated system, instead of just the energy of the part that is changed. The total system energy before and after the proposed GCMC exchange or MC move @@ -296,7 +296,7 @@ in which case only partial energies are computed to determine the energy difference due to the proposed change. -The *full\_energy* option is needed for systems with complicated +The *full_energy* option is needed for systems with complicated potential energy calculations, including the following: * long-range electrostatics (kspace) @@ -306,18 +306,18 @@ potential energy calculations, including the following: * tail corrections * need to include potential energy contributions from other fixes -In these cases, LAMMPS will automatically apply the *full\_energy* +In these cases, LAMMPS will automatically apply the *full_energy* keyword and issue a warning message. -When the *mol* keyword is used, the *full\_energy* option also includes +When the *mol* keyword is used, the *full_energy* option also includes the intramolecular energy of inserted and deleted molecules, whereas -this energy is not included when *full\_energy* is not used. If this -is not desired, the *intra\_energy* keyword can be used to define an +this energy is not included when *full_energy* is not used. If this +is not desired, the *intra_energy* keyword can be used to define an amount of energy that is subtracted from the final energy when a molecule is inserted, and subtracted from the initial energy when a molecule is deleted. For molecules that have a non-zero intramolecular energy, this will ensure roughly the same behavior whether or not the -*full\_energy* option is used. +*full_energy* option is used. Inserted atoms and molecules are assigned random velocities based on the specified temperature *T*. Because the relative velocity of all @@ -325,10 +325,10 @@ atoms in the molecule is zero, this may result in inserted molecules that are systematically too cold. In addition, the intramolecular potential energy of the inserted molecule may cause the kinetic energy of the molecule to quickly increase or decrease after insertion. The -*tfac\_insert* keyword allows the user to counteract these effects by +*tfac_insert* keyword allows the user to counteract these effects by changing the temperature used to assign velocities to inserted atoms and molecules by a constant factor. For a particular application, some -experimentation may be required to find a value of *tfac\_insert* that +experimentation may be required to find a value of *tfac_insert* that results in inserted molecules that equilibrate quickly to the correct temperature. @@ -373,13 +373,13 @@ in the context of NVT dynamics. solution is to start a new simulation after the equilibrium density has been reached. -With some pair\_styles, such as :doc:`Buckingham `, +With some pair_styles, such as :doc:`Buckingham `, :doc:`Born-Mayer-Huggins ` and :doc:`ReaxFF `, two atoms placed close to each other may have an arbitrary large, negative potential energy due to the functional form of the potential. While these unphysical configurations are inaccessible to typical dynamical trajectories, they can be generated by Monte Carlo moves. The -*overlap\_cutoff* keyword suppresses these moves by effectively +*overlap_cutoff* keyword suppresses these moves by effectively assigning an infinite positive energy to all new configurations that place any pair of atoms closer than the specified overlap cutoff distance. @@ -395,7 +395,7 @@ The *group* keyword adds all inserted atoms to the adds all inserted atoms of the specified type to the :doc:`group ` of the group-ID value. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number @@ -438,7 +438,7 @@ This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Do not set "neigh\_modify once yes" or else this fix will never be +Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. Can be run in parallel, but aspects of the GCMC part will not scale @@ -472,11 +472,11 @@ Related commands Default """"""" -The option defaults are mol = no, maxangle = 10, overlap\_cutoff = 0.0, -fugacity\_coeff = 1.0, intra\_energy = 0.0, tfac\_insert = 1.0. +The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0, +fugacity_coeff = 1.0, intra_energy = 0.0, tfac_insert = 1.0. (Patomtrans, Pmoltrans, Pmolrotate) = (1, 0, 0) for mol = no and -(0, 1, 1) for mol = yes. full\_energy = no, -except for the situations where full\_energy is required, as +(0, 1, 1) for mol = yes. full_energy = no, +except for the situations where full_energy is required, as listed above. ---------- diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index d5e4fd6f4a..cb93804b1a 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -13,11 +13,11 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * gld = style name of this fix command * Tstart,Tstop = desired temperature at start/end of run (temperature units) -* N\_k = number of terms in the Prony series representation of the memory kernel +* N_k = number of terms in the Prony series representation of the memory kernel * seed = random number seed to use for white noise (positive integer) * series = *pprony* is presently the only available option -* c\_k = the weight of the kth term in the Prony series (mass per time units) -* tau\_k = the time constant of the kth term in the Prony series (time units) +* c_k = the weight of the kth term in the Prony series (mass per time units) +* tau_k = the time constant of the kth term in the Prony series (time units) * zero or more keyword/value pairs may be appended .. parsed-literal:: diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index d4eecaf903..fb6006d514 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -99,7 +99,7 @@ input matrix for :doc:`fix gle `. While the GLE scheme is more general, the form used by :doc:`fix gld ` can be more directly related to the representation of an implicit solvent environment. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** The instantaneous values of the extended variables are written to :doc:`binary restart files `. Because the state of the random diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 06e9581f56..1d31384911 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -82,7 +82,7 @@ length is ignored. For 2d systems, the *z* component is ignored. Any of the quantities *magnitude*\ , *angle*\ , *phi*\ , *theta*\ , *x*\ , *y*\ , *z* which define the gravitational magnitude and direction, can be specified as an equal-style :doc:`variable `. If the value is -a variable, it should be specified as v\_name, where name is the +a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the quantity. You should insure that the variable calculates a result in the appropriate units, @@ -116,7 +116,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 95a15513d4..eef39c1ffc 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -83,7 +83,7 @@ to large temperature changes. Replicas are easily added where needed. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 25ec154ffb..97e5487adf 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * halt = style name of this fix command * N = check halt condition every N steps -* attribute = *bondmax* or *tlimit* or v\_name +* attribute = *bondmax* or *tlimit* or v_name .. parsed-literal:: @@ -50,7 +50,7 @@ specified by the :doc:`run ` or :doc:`minimize ` command. The specified group-ID is ignored by this fix. The specified *attribute* can be one of the options listed above, -namely *bondmax* or *tlimit*\ , or an :doc:`equal-style variable ` referenced as *v\_name*, where "name" is the +namely *bondmax* or *tlimit*\ , or an :doc:`equal-style variable ` referenced as *v_name*, where "name" is the name of a variable that has been defined previously in the input script. @@ -66,7 +66,7 @@ using this method versus the timer command option. The first is that the clock starts at the beginning of the current run (not when the timer or fix command is specified), so that any setup time for the run is not included in the elapsed time. The second is that the timer -invocation and syncing across all processors (via MPI\_Allreduce) is +invocation and syncing across all processors (via MPI_Allreduce) is not performed once every *N* steps by this command. Instead it is performed (typically) only a small number of times and the elapsed times are used to predict when the end-of-the-run will be. Both of @@ -138,7 +138,7 @@ is printed; the run simply exits. The latter may be desirable for post-processing tools that extract thermodynamic information from log files. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index cf046fe000..3412daf63c 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -72,8 +72,8 @@ time. In this case, each value is an "intensive" quantity, which need not be scaled with the number of atoms in the group. As mentioned above, the *eflux* parameter can be specified as an -equal-style or atom\_style :doc:`variable `. If the value is a -variable, it should be specified as v\_name, where name is the variable +equal-style or atom_style :doc:`variable `. If the value is a +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the flux. @@ -108,7 +108,7 @@ their velocities. Thus you must still use an integration fix not normally be used on atoms that have their temperature controlled by another fix - e.g. :doc:`fix nvt ` or :doc:`fix langevin ` fix. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 8ac25ede9b..c24d405b55 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -129,7 +129,7 @@ timesteps is simply t_{hyper} = \sum_{i=1,N} B-i \cdot dt where *dt* is the timestep size defined by the :doc:`timestep ` -command. The effective time acceleration due to GHD is thus t\_hyper / +command. The effective time acceleration due to GHD is thus t_hyper / N\*dt, where N\*dt is elapsed time for a normal MD run of N timesteps. Note that in GHD, the boost factor varies from timestep to timestep. @@ -176,7 +176,7 @@ time-accurate trajectory of the system. Note that if *Vmax* is set too small, the GHD simulation will run correctly. There will just be fewer events because the hyper time -(t\_hyper equation above) will be shorter. +(t_hyper equation above) will be shorter. .. note:: @@ -197,7 +197,7 @@ algorithm. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 5b837ee275..a8e7483dac 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -245,7 +245,7 @@ well for many solid-state systems. atoms move (between quenched states) to be considered an "event". It is an argument to the "compute event/displace" command used to detect events. By default the ghost communication distance is set by the - pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm_modify cutoff ` command should be used to override the ghost + pair_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm_modify cutoff ` command should be used to override the ghost cutoff explicitly, e.g. .. code-block:: LAMMPS @@ -268,7 +268,7 @@ inverse of the alpha parameter discussed in The *Btarget* argument is the desired time boost factor (a value > 1) that all the atoms in the system will experience. The elapsed time -t\_hyper for an LHD simulation running for *N* timesteps is simply +t_hyper for an LHD simulation running for *N* timesteps is simply .. math:: @@ -293,7 +293,7 @@ is the specified temperature of the system Note that if *Btarget* is set smaller than this, the LHD simulation will run correctly. There will just be fewer events because the hyper -time (t\_hyper equation above) will be shorter. +time (t_hyper equation above) will be shorter. .. note:: @@ -365,7 +365,7 @@ enabled by these keywords. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 1db18e515f..fe54e5bf50 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -44,7 +44,7 @@ IMD protocol, as initially implemented in VMD and NAMD. Specifically it allows LAMMPS to connect an IMD client, for example the `VMD visualization program `_, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms. -If LAMMPS is compiled with the pre-processor flag -DLAMMPS\_ASYNC\_IMD +If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD then fix imd will use POSIX threads to spawn a IMD communication thread on MPI rank 0 in order to offload data reading and writing from the main execution thread and potentially lower the inferred @@ -137,7 +137,7 @@ screen output is active. .. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 945b28efdc..ef62506591 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -100,7 +100,7 @@ be specified as an equal-style :doc:`variable `, namely *x*\ , *y*\ , *z*\ , or *R*\ . Similarly, for a cylindrical indenter, any of *c1*\ , *c2*\ , or *R*\ , can be a variable. For a planar indenter, *pos* can be a variable. If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to define the indenter geometry. @@ -112,7 +112,7 @@ change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the :doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. -For example, if a spherical indenter's x-position is specified as v\_x, +For example, if a spherical indenter's x-position is specified as v_x, then this variable definition will keep it's center at a relative position in the simulation box, 1/4 of the way from the left edge to the right edge, even if the box size changes: @@ -129,7 +129,7 @@ from an initial position at 2.5 at a constant velocity of 5: variable x equal "2.5 + 5*elaplong*dt" variable x equal vdisplace(2.5,5) -If a spherical indenter's radius is specified as v\_r, then these +If a spherical indenter's radius is specified as v_r, then these variable definitions will grow the size of the indenter at a specified rate. @@ -176,7 +176,7 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the variable k equal 100.0/xlat/xlat fix 1 all indent $k sphere ... -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 58049bc4ac..d60b25248d 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -69,7 +69,7 @@ If the cell varies too wildly, it may be advisable to re-initialize these interactions at each call. This behavior can be requested by setting the *reset* switch. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** There is no restart information associated with this fix, since all the dynamical parameters are dealt with by i-PI. diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index f282499bcc..7a45293db9 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -122,7 +122,7 @@ run from *Tstart* to *Tstop*\ . *Tstart* can be specified as an equal-style or atom-style :doc:`variable `. In this case, the *Tstop* setting is ignored. If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. @@ -173,8 +173,8 @@ The keyword *angmom* and *omega* keywords enable thermostatting of rotational degrees of freedom in addition to the usual translational degrees of freedom. This can only be done for finite-size particles. -A simulation using atom\_style sphere defines an omega for finite-size -spheres. A simulation using atom\_style ellipsoid defines a finite +A simulation using atom_style sphere defines an omega for finite-size +spheres. A simulation using atom_style ellipsoid defines a finite size and shape for aspherical particles and an angular momentum. The Langevin formulas for thermostatting the rotational degrees of freedom are the same as those above, where force is replaced by @@ -288,7 +288,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" @@ -323,7 +323,7 @@ Restrictions """""""""""" For *gjf* do not choose damp=dt/2. *gjf* is not compatible -with run\_style respa. +with run_style respa. Related commands """""""""""""""" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index bcfc4878a4..f361a88736 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -13,11 +13,11 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * langevin/drude = style name of this fix command * Tcom = desired temperature of the centers of mass (temperature units) -* damp\_com = damping parameter for the thermostat on centers of mass (time units) -* seed\_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) +* damp_com = damping parameter for the thermostat on centers of mass (time units) +* seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) * Tdrude = desired temperature of the Drude oscillators (temperature units) -* damp\_drude = damping parameter for the thermostat on Drude oscillators (time units) -* seed\_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) +* damp_drude = damping parameter for the thermostat on Drude oscillators (time units) +* seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) * zero or more keyword/value pairs may be appended * keyword = *zero* @@ -76,16 +76,16 @@ The Langevin forces are computed as .. math:: - F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' + F' = - \frac {M'} {\mathtt{damp_com}}\, V' + F_r' .. math:: - f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' + f' = - \frac {m'} {\mathtt{damp_drude}}\, v' + f_r' :math:`F_r'` is a random force proportional to -:math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }`. +:math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp_com} } }`. :math:`f_r'` is a random force proportional to -:math:`\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp\_drude} } }`. +:math:`\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp_drude} } }`. Then the real forces acting on the particles are computed from the inverse transform: @@ -156,7 +156,7 @@ be used to thermostat the non-polarizable atoms. *Tdrude* is the (normally low) target temperature of the core-Drude particle pairs (dipoles). *Tcom* and *Tdrude* can be specified as an equal-style :doc:`variable `. If the value is a variable, it should be -specified as v\_name, where name is the variable name. In this case, +specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. @@ -185,14 +185,14 @@ neighboring atoms. The optimal value probably depends on the temperature of the centers of mass and on the mass of the Drude particles. -*damp\_com* is the characteristic time for reaching thermal equilibrium +*damp_com* is the characteristic time for reaching thermal equilibrium of the centers of mass. For example, a value of 100.0 means to relax the temperature of the centers of mass in a timespan of (roughly) 100 time units (tau or fmsec or psec - see the :doc:`units ` -command). *damp\_drude* is the characteristic time for reaching +command). *damp_drude* is the characteristic time for reaching thermal equilibrium of the dipoles. It is typically a few timesteps. -The number *seed\_com* and *seed\_drude* are positive integers. They set +The number *seed_com* and *seed_drude* are positive integers. They set the seeds of the Marsaglia random number generators used for generating the random forces on centers of mass and on the dipoles. Each processor uses the input seed to generate its own unique @@ -247,16 +247,16 @@ Comments: :doc:`compute temp/drude ` * Contrary to the alternative thermostatting using Nose-Hoover thermostat fix *npt* and :doc:`fix drude/transform `, the - *fix\_modify* command is not required here, because the fix *nph* + *fix_modify* command is not required here, because the fix *nph* computes the global pressure even if its group is *ATOMS*\ . This is what we want. If we thermostatted *ATOMS* using *npt*\ , the pressure should be the global one, but the temperature should be only that of - the cores. That's why the command *fix\_modify* should be called in + the cores. That's why the command *fix_modify* should be called in that case. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 004a82f2aa..36768d25b2 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -65,7 +65,7 @@ The operation of this fix is exactly like that described by the thermostatting is also applied to the radial electron velocity for electron particles. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index 7113f1459c..9a70cc1cd1 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -70,7 +70,7 @@ different numbers of processors. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index beeec5a014..f1469153a7 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -104,7 +104,7 @@ larger system sizes and longer time scales ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index 53fb0219d7..f450fdb8f0 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -18,7 +18,7 @@ Syntax * viscosity = the fluid viscosity (units of mass/(time\*length)). * density = the fluid density. * zero or more keyword/value pairs may be appended -* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read\_restart* or *write\_restart* or *zwall\_velocity* or *bodyforce* or *printfluid* +* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read_restart* or *write_restart* or *zwall_velocity* or *bodyforce* or *printfluid* .. parsed-literal:: @@ -153,9 +153,9 @@ t_{collision}` is a collision time, chosen such that :math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and Denniston ` for full details). In order to calculate :math:`m_u`, the fluid density is interpolated to the MD particle location, and -multiplied by a volume, node\_area * :math:`dx_{LB}`, where node\_area +multiplied by a volume, node_area * :math:`dx_{LB}`, where node_area represents the portion of the surface area of the composite object -associated with a given MD particle. By default, node\_area is set +associated with a given MD particle. By default, node_area is set equal to :math:`dx_{LB}^2`; however specific values for given atom types can be set using the *setArea* keyword. @@ -286,7 +286,7 @@ If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is used by the lattice-Boltzmann algorithm. By default, the 15 velocity (D3Q15) lattice is used. -If the keyword *write\_restart* is used, followed by a positive +If the keyword *write_restart* is used, followed by a positive integer, N, a binary restart file is printed every N LB timesteps. This restart file only contains information about the fluid. Therefore, a LAMMPS restart file should also be written in order to @@ -298,10 +298,10 @@ print out full details of the simulation. files may become quite large. In order to restart the fluid portion of the simulation, the keyword -*read\_restart* is specified, followed by the name of the binary -lb\_fluid restart file to be used. +*read_restart* is specified, followed by the name of the binary +lb_fluid restart file to be used. -If the *zwall\_velocity* keyword is used y-velocities are assigned to +If the *zwall_velocity* keyword is used y-velocities are assigned to the lower and upper walls. This keyword requires the presence of walls in the z-direction. This is set by assigning fixed boundary conditions in the z-direction. If fixed boundary conditions are @@ -319,16 +319,16 @@ screen every N timesteps. For further details, as well as descriptions and results of several test runs, see :ref:`Mackay et al. `. Please include a citation to -this paper if the lb\_fluid fix is used in work contributing to +this paper if the lb_fluid fix is used in work contributing to published research. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Due to the large size of the fluid data, this fix writes it's own binary restart files, if requested, independent of the main LAMMPS -:doc:`binary restart files `; no information about *lb\_fluid* +:doc:`binary restart files `; no information about *lb_fluid* is written to the main LAMMPS :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 8a3ff8fcdf..a595ba2ce5 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -50,7 +50,7 @@ be changed by specifying the keyword *linear*\ , along with a set of three flags set to 0/1 in order to exclude/ include the corresponding dimension. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index a7a3ddbccc..874ff21893 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -29,7 +29,7 @@ forces, using the integration algorithm described in :ref:`Mackay et al. ` has been set; do not use this integration algorithm if the force coupling constant has been set by default. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 9edebde0cc..42fb21ca69 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -82,7 +82,7 @@ the rigid fix (although it includes fewer optional arguments, and assumes the constituent atoms are point particles); see :doc:`fix rigid ` for a complete documentation. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about the *rigid* and *rigid/nve* fixes are written to :doc:`binary restart files `. diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index 9b1402af7a..6d7431c780 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -28,7 +28,7 @@ is to be used in place of that command when a lattice-Boltzmann fluid is present, and the user wishes to integrate the particle motion using one of the built in LAMMPS integrators. -This fix adds a force, F = - Gamma\*(velocity-fluid\_velocity), to each +This fix adds a force, F = - Gamma\*(velocity-fluid_velocity), to each atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid ` command (which applies an equal and opposite force to the fluid). @@ -51,7 +51,7 @@ research. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** As described in the :doc:`fix viscous ` documentation: diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index e15286cbde..b02acfa9f4 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -32,7 +32,7 @@ plane perpendicular to the line. If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 2847e26387..8cb9723277 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -34,7 +34,7 @@ adequately though. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -50,9 +50,9 @@ Restrictions This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Only use this with *min\_style hftn* or *min\_style quickmin*. If not, +Only use this with *min_style hftn* or *min_style quickmin*. If not, the constraints will not be satisfied very well at all. A warning is -generated if the *min\_style* is incompatible but no error. +generated if the *min_style* is incompatible but no error. ---------- diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst index 631061244b..dc9f1cb991 100644 --- a/doc/src/fix_meso.rst +++ b/doc/src/fix_meso.rst @@ -31,7 +31,7 @@ internal variables such as SPH or DPDE. See `this PDF guide `_ to using SPH in LAMMPS. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index a1be27abfe..a976c2de34 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -158,7 +158,7 @@ Rperp is a perpendicular vector from the rotation axis to the particle. The *variable* style allows the position and velocity components of each particle to be set by formulas specified via the :doc:`variable ` command. Each of the 6 variables is -specified as an argument to the fix as v\_name, where name is the +specified as an argument to the fix as v_name, where name is the variable name that is defined elsewhere in the input script. Each variable must be of either the *equal* or *atom* style. @@ -171,10 +171,10 @@ fix stores the original coordinates of each particle (see note below) so that per-atom quantity can be used in an atom-style variable formula. See the :doc:`variable ` command for details. -The first 3 variables (v\_dx,v\_dy,v\_dz) specified for the *variable* +The first 3 variables (v_dx,v_dy,v_dz) specified for the *variable* style are used to calculate a displacement from the particle's original position at the time the fix was specified. The second 3 variables -(v\_vx,v\_vy,v\_vz) specified are used to compute a velocity for each +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each particle. Any of the 6 variables can be specified as NULL. If both the @@ -204,7 +204,7 @@ spacings can be different in x,y,z. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the original coordinates of moving particles to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the diff --git a/doc/src/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst index 4c6b35245c..89c30ece14 100644 --- a/doc/src/fix_meso_stationary.rst +++ b/doc/src/fix_meso_stationary.rst @@ -32,7 +32,7 @@ space. See `this PDF guide `_ to using SPH in LAMMPS. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 658ec5b249..604b63550c 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -41,7 +41,7 @@ Description Modify one or more parameters of a previously defined fix. Only specific fix styles support specific parameters. See the doc pages for individual fix commands for info on which ones support which -fix\_modify parameters. +fix_modify parameters. The *temp* keyword is used to determine how a fix computes temperature. The specified compute ID must have been previously @@ -65,8 +65,8 @@ system. The fix's global and per-atom energy is included in the calculation performed by the :doc:`compute pe ` or :doc:`compute pe/atom ` commands. See the :doc:`thermo_style ` command for info on how potential energy is output. For fixes that tally a global -energy, it can be printed by using the keyword f\_ID in the -thermo\_style custom command, where ID is the fix-ID of the appropriate +energy, it can be printed by using the keyword f_ID in the +thermo_style custom command, where ID is the fix-ID of the appropriate fix. .. note:: @@ -104,7 +104,7 @@ This is a number ranging from 1 to the number of levels. If the RESPA level is larger than the current maximum, the outermost level will be used, which is also the default setting. This default can be restored using a value of *0* for the RESPA level. The affected fix has to be -enabled to support this feature; if not, *fix\_modify* will report an +enabled to support this feature; if not, *fix_modify* will report an error. Active fixes with a custom RESPA level setting are reported with their specified level at the beginning of a r-RESPA run. diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index 6412ba8835..58fc9278a1 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -85,7 +85,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index e5aab1259f..e9ebbd726b 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -157,7 +157,7 @@ atom's motion and rotation over time. The *variable* style allows the position and velocity components of each atom to be set by formulas specified via the :doc:`variable ` command. Each of the 6 variables is -specified as an argument to the fix as v\_name, where name is the +specified as an argument to the fix as v_name, where name is the variable name that is defined elsewhere in the input script. Each variable must be of either the *equal* or *atom* style. @@ -170,10 +170,10 @@ fix stores the original coordinates of each atom (see note below) so that per-atom quantity can be used in an atom-style variable formula. See the :doc:`variable ` command for details. -The first 3 variables (v\_dx,v\_dy,v\_dz) specified for the *variable* +The first 3 variables (v_dx,v_dy,v_dz) specified for the *variable* style are used to calculate a displacement from the atom's original position at the time the fix was specified. The second 3 variables -(v\_vx,v\_vy,v\_vz) specified are used to compute a velocity for each +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each atom. Any of the 6 variables can be specified as NULL. If both the @@ -203,7 +203,7 @@ spacings can be different in x,y,z. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the original coordinates of moving atoms to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 7531ab50de..b76af36bb8 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -105,8 +105,8 @@ timestep. To do this, the fix creates its own computes of style "temp" See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the IDs of the -new computes are the fix-ID + "_MSST\_temp" or "MSST\_press" or -"_MSST\_pe". The group for the new computes is "all". +new computes are the fix-ID + "_MSST_temp" or "MSST_press" or +"_MSST_pe". The group for the new computes is "all". ---------- @@ -122,7 +122,7 @@ timestepping. DFTB+ will communicate its info to LAMMPS via that fix. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of all internal variables to :doc:`binary restart files `. See the :doc:`read_restart ` @@ -143,12 +143,12 @@ equations. See also :doc:`thermo_style ` command. The global vector contains four values in this order: -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian\_speed*, *lagrangian\_position*] +[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). 2. *drayleigh* is the departure from the Rayleigh line (pressure units). -3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. +3. *lagrangian_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). +4. *lagrangian_position* is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested: diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index bdae316a13..77ca08e0c5 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -76,7 +76,7 @@ addition to position and velocity, and must be used with the ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 308f8891c4..3612192d5b 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -75,10 +75,10 @@ roughly in the direction of (Ri+i - Ri-1); see the coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its neighbor replicas. The term (Grad(V) dot T') is used to remove the component of the gradient parallel to the path which would tend to -distribute the replica unevenly along the path. Fnudge\_parallel is an +distribute the replica unevenly along the path. Fnudge_parallel is an artificial nudging force which is applied only in the tangent direction and which maintains the equal spacing between replicas (see -below for more information). Fnudge\_perp is an optional artificial +below for more information). Fnudge_perp is an optional artificial spring which is applied in a direction perpendicular to the tangent direction and which prevent the paths from forming acute kinks (see below for more information). @@ -203,7 +203,7 @@ Finally, note that the last replica may never reach the target energy if it is stuck in a local minima which has a larger energy than the target energy. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index 1f89a4b665..93729ac96f 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -47,7 +47,7 @@ The nudging forces are calculated as explained in :ref:`(BessarabB) `). See this reference for more explanation about their expression. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 214ec9c3e9..6927b47fcb 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -41,7 +41,7 @@ Syntax fix ID group-ID style_name keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style\_name = *nvt* or *npt* or *nph* +* style_name = *nvt* or *npt* or *nph* * one or more keyword/value pairs may be appended .. parsed-literal:: @@ -456,17 +456,17 @@ for the entire system. In the case of fix nph, the temperature compute is not used for thermostatting, but just for a kinetic-energy contribution to the pressure. See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the IDs of the new computes are the -fix-ID + underscore + "temp" or fix\_ID + underscore + "press". +fix-ID + underscore + "temp" or fix_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of these +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of these fix's temperature or pressure via the :doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate -compute-ID. It also means that changing attributes of *thermo\_temp* -or *thermo\_press* will have no effect on this fix. +compute-ID. It also means that changing attributes of *thermo_temp* +or *thermo_press* will have no effect on this fix. Like other fixes that perform thermostatting, fix nvt and fix npt can be used with :doc:`compute commands ` that calculate a @@ -564,7 +564,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** These fixes writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the @@ -584,7 +584,7 @@ compute temperature on a subset of atoms. .. note:: If both the *temp* and *press* keywords are used in a single - thermo\_modify command (or in two separate commands), then the order in + thermo_modify command (or in two separate commands), then the order in which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as an argument when it is specified. The *temp* keyword will override this (for the pressure compute being used by fix npt), but only if the @@ -619,21 +619,21 @@ simulation, otherwise its value is 3. The order of values in the global vector and their meaning is as follows. The notation means there are tchain values for eta, followed -by tchain for eta\_dot, followed by ndof for omega, etc: +by tchain for eta_dot, followed by ndof for omega, etc: * eta[tchain] = particle thermostat displacements (unitless) -* eta\_dot[tchain] = particle thermostat velocities (1/time units) +* eta_dot[tchain] = particle thermostat velocities (1/time units) * omega[ndof] = barostat displacements (unitless) -* omega\_dot[ndof] = barostat velocities (1/time units) +* omega_dot[ndof] = barostat velocities (1/time units) * etap[pchain] = barostat thermostat displacements (unitless) -* etap\_dot[pchain] = barostat thermostat velocities (1/time units) -* PE\_eta[tchain] = potential energy of each particle thermostat displacement (energy units) -* KE\_eta\_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) -* PE\_omega[ndof] = potential energy of each barostat displacement (energy units) -* KE\_omega\_dot[ndof] = kinetic energy of each barostat velocity (energy units) -* PE\_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) -* KE\_etap\_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) -* PE\_strain[1] = scalar strain energy (energy units) +* etap_dot[pchain] = barostat thermostat velocities (1/time units) +* PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units) +* KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) +* PE_omega[ndof] = potential energy of each barostat displacement (energy units) +* KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units) +* PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) +* KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) +* PE_strain[1] = scalar strain energy (energy units) These fixes can ramp their external temperature and pressure over multiple runs, using the *start* and *stop* keywords of the diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 2d6b542edf..b5fecf279f 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -17,7 +17,7 @@ Syntax fix ID group-ID style_name keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style\_name = *nvt/eff* or *npt/eff* or *nph/eff* +* style_name = *nvt/eff* or *npt/eff* or *nph/eff* .. parsed-literal:: @@ -85,7 +85,7 @@ to the temperature or kinetic energy from the electron radial velocity. .. note:: there are two different pressures that can be reported for eFF - when defining the pair\_style (see :doc:`pair eff/cut ` to + when defining the pair_style (see :doc:`pair eff/cut ` to understand these settings), one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial @@ -105,7 +105,7 @@ to the temperature or kinetic energy from the electron radial velocity. the user must allow for these degrees of freedom to equilibrate (i.e. equi-partitioning of energy) through time integration. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** See the doc page for the :doc:`fix nvt, npt, and nph ` commands for details. diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 251b1675b9..27851d89a1 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -14,9 +14,9 @@ Syntax fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style\_name = *nvt/uef* or *npt/uef* +* style_name = *nvt/uef* or *npt/uef* * *Tstart*\ , *Tstop*\ , and *Tdamp* are documented in the :doc:`fix npt ` command -* *edot\_x* and *edot\_y* are the strain rates in the x and y directions (1/(time units)) +* *edot_x* and *edot_y* are the strain rates in the x and y directions (1/(time units)) * one or more keyword/value pairs may be appended .. parsed-literal:: @@ -57,10 +57,10 @@ Note that NEMD simulations of a continuously strained system can be performed using the :doc:`fix deform `, :doc:`fix nvt/sllod `, and :doc:`compute temp/deform ` commands. The applied flow field is set by the *eps* keyword. The values -*edot\_x* and *edot\_y* correspond to the strain rates in the xx and yy +*edot_x* and *edot_y* correspond to the strain rates in the xx and yy directions. It is implicitly assumed that the flow field is traceless, and therefore the strain rate in the zz direction is eqal -to -(*edot\_x* + *edot\_y*). +to -(*edot_x* + *edot_y*). .. note:: @@ -169,9 +169,9 @@ issued: See the :doc:`compute temp/uef ` and :doc:`compute pressure/uef ` commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" -or fix\_ID + underscore + "press". +or fix_ID + underscore + "press". -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** The fix writes the state of all the thermostat and barostat variables, as well as the cumulative strain applied, to :doc:`binary restart files `. See the :doc:`read_restart ` command @@ -221,7 +221,7 @@ Default The default keyword values specific to this fix are exy = xyz, strain = 0 0. The remaining defaults are the same as for *fix -npt*\ \_fix\_nh.html except tchain = 1. The reason for this change is +npt*\ _fix_nh.html except tchain = 1. The reason for this change is given in :doc:`fix nvt/sllod `. ---------- diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index c3f2904301..76670f1c30 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -67,18 +67,18 @@ this, the fix creates its own computes of style "temp/asphere" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/asphere ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. ---------- @@ -100,7 +100,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -146,6 +146,6 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` +:doc:`fix nph `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index d2d7542467..c2f6097fef 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -64,18 +64,18 @@ this, the fix creates its own computes of style "temp/body" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/body ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. ---------- @@ -97,7 +97,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -139,6 +139,6 @@ command. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` +:doc:`fix nph `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix npt_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index d71593e4b1..d1e5bfd701 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -80,18 +80,18 @@ this, the fix creates its own computes of style "temp/sphere" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/sphere ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. ---------- @@ -113,7 +113,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -158,7 +158,7 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_sphere `, +:doc:`fix nph `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index fb64966291..fed73f6315 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -100,7 +100,7 @@ When the system reaches a stable equilibrium, the value of :math:`\Delta` should fluctuate about zero. The values of :math:`E_0`, :math:`V_0`, and :math:`P_0` are the instantaneous values at the start of -the simulation. These can be overridden using the fix\_modify keywords *e0*\ , +the simulation. These can be overridden using the fix_modify keywords *e0*\ , *v0*\ , and *p0* described below. ---------- @@ -129,19 +129,19 @@ as if one of these two sets of commands had been issued: compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press". The group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. ---------- @@ -165,7 +165,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the values of :math:`E_0`, :math:`V_0`, and :math:`P_0`, as well as the state of all the thermostat and barostat variables to diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 644e10ee1e..aac88c551e 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -75,18 +75,18 @@ this, the fix creates its own computes of style "temp/asphere" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/asphere ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that calculate a temperature @@ -122,7 +122,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -171,6 +171,6 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix_modify ` +:doc:`fix npt `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index 1a6caebb79..120437eeab 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -72,18 +72,18 @@ this, the fix creates its own computes of style "temp/body" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/body ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that calculate a temperature @@ -119,7 +119,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -164,6 +164,6 @@ command. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix_modify ` +:doc:`fix npt `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index d548002f0e..5e0188c574 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -11,7 +11,7 @@ Syntax fix ID group-ID style_name keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* style\_name = *npt/cauchy* +* style_name = *npt/cauchy* * one or more keyword/value pairs may be appended * keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update* @@ -389,17 +389,17 @@ as if one of these sets of commands had been issued: The group for both the new temperature and pressure compute is "all" since pressure is computed for the entire system. See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the IDs of the new computes are the -fix-ID + underscore + "temp" or fix\_ID + underscore + "press". +fix-ID + underscore + "temp" or fix_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of these +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of these fix's temperature or pressure via the :doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate -compute-ID. It also means that changing attributes of *thermo\_temp* -or *thermo\_press* will have no effect on this fix. +compute-ID. It also means that changing attributes of *thermo_temp* +or *thermo_press* will have no effect on this fix. Like other fixes that perform thermostatting, fix npt/cauchy can be used with :doc:`compute commands ` that calculate a @@ -467,7 +467,7 @@ of the underlying non-Hamiltonian equations of motion. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the @@ -487,7 +487,7 @@ compute temperature on a subset of atoms. .. note:: If both the *temp* and *press* keywords are used in a single - thermo\_modify command (or in two separate commands), then the order in + thermo_modify command (or in two separate commands), then the order in which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as an argument when it is specified. The *temp* keyword will override this (for the pressure compute being used by fix npt), but only if the @@ -522,21 +522,21 @@ simulation, otherwise its value is 3. The order of values in the global vector and their meaning is as follows. The notation means there are tchain values for eta, followed -by tchain for eta\_dot, followed by ndof for omega, etc: +by tchain for eta_dot, followed by ndof for omega, etc: * eta[tchain] = particle thermostat displacements (unitless) -* eta\_dot[tchain] = particle thermostat velocities (1/time units) +* eta_dot[tchain] = particle thermostat velocities (1/time units) * omega[ndof] = barostat displacements (unitless) -* omega\_dot[ndof] = barostat velocities (1/time units) +* omega_dot[ndof] = barostat velocities (1/time units) * etap[pchain] = barostat thermostat displacements (unitless) -* etap\_dot[pchain] = barostat thermostat velocities (1/time units) -* PE\_eta[tchain] = potential energy of each particle thermostat displacement (energy units) -* KE\_eta\_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) -* PE\_omega[ndof] = potential energy of each barostat displacement (energy units) -* KE\_omega\_dot[ndof] = kinetic energy of each barostat velocity (energy units) -* PE\_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) -* KE\_etap\_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) -* PE\_strain[1] = scalar strain energy (energy units) +* etap_dot[pchain] = barostat thermostat velocities (1/time units) +* PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units) +* KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) +* PE_omega[ndof] = potential energy of each barostat displacement (energy units) +* KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units) +* PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) +* KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) +* PE_strain[1] = scalar strain energy (energy units) This fix can ramp its external temperature and pressure over multiple runs, using the *start* and *stop* keywords of the @@ -581,7 +581,7 @@ the set values and the final true (Cauchy) stresses can be considerable. The *cauchystat* keyword modifies the barostat as per Miller et -al. (Miller)\_"#nc-Miller" so that the Cauchy stress is controlled. +al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled. *alpha* is the non-dimensional parameter, typically set to 0.001 or 0.01 that determines how aggressively the algorithm drives the system towards the set Cauchy stresses. Larger values of *alpha* will modify diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 48fdbd90fb..2def29ae47 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -88,18 +88,18 @@ this, the fix creates its own computes of style "temp/sphere" and compute fix-ID_press all pressure fix-ID_temp See the :doc:`compute temp/sphere ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that calculate a temperature @@ -135,7 +135,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -183,6 +183,6 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` +:doc:`fix npt `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 367cdd5552..8089ad094d 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -59,7 +59,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index deda3ded70..f231330831 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -34,7 +34,7 @@ trajectory consistent with the microcanonical ensemble. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 675e3b6684..b518781d6c 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -35,7 +35,7 @@ Dynamics, since the velocity and angular momentum are updated by the ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index 07f98a6a34..45bb002617 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -33,7 +33,7 @@ the electron wave functions are also updated. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 96134e2974..ad68abb0d4 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -32,7 +32,7 @@ particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 57cfc6cd14..78e6352b6e 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -30,7 +30,7 @@ system trajectory consistent with the microcanonical ensemble. The operation of this fix is exactly like that described by the :doc:`fix nve ` command, except that the radius and radial velocity of electrons are also updated. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index d600eb4e66..98d691d6b9 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -60,7 +60,7 @@ very large for overlapped configurations. that need this fix, then turn fix shake on when doing normal dynamics with a fixed-size timestep. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index 208759116b..d47bf34f61 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -32,7 +32,7 @@ segment particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index 3e8ee059a0..1caedf88e1 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -49,7 +49,7 @@ parameters, see the :doc:`Howto manifold ` doc page. Note that the particles must initially be close to the manifold in question. If not, RATTLE will not be able to iterate until the constraint is satisfied, and an error is generated. For simple -manifolds this can be achieved with *region* and *create\_atoms* +manifolds this can be achieved with *region* and *create_atoms* commands, but for more complex surfaces it might be more useful to write a script. @@ -69,7 +69,7 @@ conserved. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 0bc2624ce2..d45648694a 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -37,7 +37,7 @@ unchanged, and can thus be printed by the :doc:`dump ` command or queried with an equal-style :doc:`variable ` that uses the fcm() group function to compute the total force on the group of atoms. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index c92605aa28..753e40cd15 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -90,7 +90,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 4ba1f945da..143ddb2426 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -62,7 +62,7 @@ package. See the :doc:`Build package ` doc page for more info. To use the spin algorithm, it is necessary to define a map with -the atom\_modify command. Typically, by adding the command: +the atom_modify command. Typically, by adding the command: .. code-block:: LAMMPS diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index 0b0a48249a..f5fdb7cc7d 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -33,7 +33,7 @@ using triangular particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index aafeb1fde7..415e3256b4 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -39,7 +39,7 @@ energy prior to this fix. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 4db500e279..6004de2e60 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -63,12 +63,12 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -105,7 +105,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -147,6 +147,6 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` +:doc:`fix nvt `, :doc:`fix nve_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index 37dc4d1f0b..41d652a32d 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -60,12 +60,12 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -102,7 +102,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -140,6 +140,6 @@ command. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` +:doc:`fix nvt `, :doc:`fix nve_body `, :doc:`fix npt_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index f7a14fa266..198208ca0d 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -49,7 +49,7 @@ parameters, see the :doc:`Howto manifold ` doc page. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index e8f4b840d1..829bf8c634 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -95,12 +95,12 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -137,7 +137,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index f2b3edd366..49ad9f608c 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -38,7 +38,7 @@ page), is performed with a :doc:`compute temp/deform/eff `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index f9d5fd954f..95bb0a20c4 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -77,12 +77,12 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -119,7 +119,7 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -160,6 +160,6 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix_modify ` +:doc:`fix nvt `, :doc:`fix nve_sphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 6444776a6b..04186404e6 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -39,7 +39,7 @@ membrane, or as an implementation of Maxwell's demon. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 30e5f87ee9..8fdcc79ace 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -137,7 +137,7 @@ equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are shown below. A tutorial that can help for writing the orientation files is given in :ref:`(Wicaksono2) ` -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 6a6a8c6b96..4eed4efc5b 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -15,7 +15,7 @@ Syntax * N = measure the Green's function every this many timesteps * Noutput = output the dynamical matrix every this many measurements * Nwait = wait this many timesteps before measuring -* map\_file = *file* or *GAMMA* +* map_file = *file* or *GAMMA* .. parsed-literal:: @@ -131,14 +131,14 @@ provided by keyword *nasr* gives the total number of iterations. For a system whose unit cell has only one atom, *nasr* = 1 is sufficient; for other systems, *nasr* = 10 is typically sufficient. -The *map\_file* contains the mapping information between the lattice +The *map_file* contains the mapping information between the lattice indices and the atom IDs, which tells the code which atom sits at which lattice point; the lattice indices start from 0. An auxiliary code, `latgen `_, can be employed to generate the compatible map file for various crystals. In case one simulates a non-periodic system, where the whole simulation -box is treated as a unit cell, one can set *map\_file* as *GAMMA*\ , so +box is treated as a unit cell, one can set *map_file* as *GAMMA*\ , so that the mapping info will be generated internally and a file is not needed. In this case, the dynamical matrix at only the gamma-point will/can be evaluated. Please keep in mind that fix-phonon is designed @@ -150,12 +150,12 @@ The calculated dynamical matrix elements are written out in points in the log file is in the units of the basis vectors of the corresponding reciprocal lattice. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` *temp* option is supported by this -fix. You can use it to change the temperature compute from thermo\_temp +fix. You can use it to change the temperature compute from thermo_temp to the one that reflects the true temperature of atoms in the group. No global scalar or vector or per-atom quantities are stored by this diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index a3df6bff14..c90a3b6bbe 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -32,7 +32,7 @@ force perpendicular to the plane. If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 00886a95b3..aeef6cff50 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -75,7 +75,7 @@ correctly read and parsed. The names of the files in which the results are stored from the various analysis options performed by PLUMED will be specified by the user in the PLUMED input file. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** When performing a restart of a calculation that involves PLUMED you must include a RESTART command in the PLUMED input file as detailed in the diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index ec1d1335a5..1be7a90419 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -92,7 +92,7 @@ this context means a set of rigid bodies connected by joints. For computational efficiency, you should turn off pairwise and bond interactions within each rigid body, as they no longer contribute to -the motion. The "neigh\_modify exclude" and "delete\_bonds" commands +the motion. The "neigh_modify exclude" and "delete_bonds" commands can be used to do this if each rigid body is a group. For computational efficiency, you should only define one fix poems @@ -105,7 +105,7 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index ce89f6a227..26f1cd0eae 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -126,7 +126,7 @@ command which also appears in your input script. If you wish the new rigid molecules (and other rigid molecules) to be thermostatted correctly via :doc:`fix rigid/small/nvt ` or :doc:`fix rigid/small/npt `, then you need to use the - "fix\_modify dynamic/dof yes" command for the rigid fix. This is to + "fix_modify dynamic/dof yes" command for the rigid fix. This is to inform that fix that the molecule count will vary dynamically. If you wish to insert molecules via the *mol* keyword, that will have @@ -225,7 +225,7 @@ line or triangle particles with the insertion region. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. This means you must be careful when restarting a pouring simulation, when the restart file was written in the middle of diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index f7931c1b26..065f894926 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -130,7 +130,7 @@ Those styles can be combined within one single command line. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**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. @@ -152,7 +152,7 @@ Restrictions The *precession/spin* style is part of the SPIN package. This style is only enabled if LAMMPS was built with this package, and if the -atom\_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index a5dc37965c..215ef81b02 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -177,20 +177,20 @@ as if these commands had been issued: compute fix-ID_press group-ID pressure fix-ID_temp See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press", and the group for the new computes is the same as the fix group. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp* -and *thermo\_press*. This means you can change the attributes of this +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this fix's temperature or pressure via the :doc:`compute_modify ` command or print this temperature or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* or -*thermo\_press* will have no effect on this fix. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index e3d64de8e7..82b26d4ef3 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -44,7 +44,7 @@ If it contains variables it must be enclosed in double quotes to insure they are not evaluated when the input script line is read, but will instead be evaluated each time the string is printed. -Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v\_name, where +Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the **next** timestep at which the string will be written out. On that timestep, the variable will be @@ -89,7 +89,7 @@ keyword was used. By default, the title line is as follows: where ID is replaced with the fix-ID. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index d67fd32deb..b6b5a6051f 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -44,7 +44,7 @@ such as proposed by :ref:`(Erdmann) `. For *mode* = *quat* the force is applied along the axis obtained by rotating the x-axis along the atom's quaternion. In other words, the force is along the x-axis in the atom's body frame. This mode requires -all atoms in the group to have a quaternion, so atom\_style should +all atoms in the group to have a quaternion, so atom_style should either be ellipsoid or body. In combination with Langevin thermostat for translation and rotation in the overdamped regime, the quaternion mode corresponds to the active Brownian particle model introduced by @@ -57,7 +57,7 @@ on through the *types* keyword. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -69,7 +69,7 @@ Restrictions In quat mode, this fix makes use of per-atom quaternions to take into account the fact that the orientation can rotate and hence the direction of the active force can change. The quat mode -of this fix only works with atom\_style ellipsoid. +of this fix only works with atom_style ellipsoid. Related commands """""""""""""""" diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 63cdbd0701..f866ddf7a2 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -15,7 +15,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * property/atom = style name of this fix command -* vec1,vec2,... = *mol* or *q* or *rmass* or *i\_name* or *d\_name* +* vec1,vec2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* .. parsed-literal:: @@ -84,7 +84,7 @@ In the future, we may add additional per-atom properties similar to by some atom styles, so they can be used by atom styles that do not define them. -More generally, the *i\_name* and *d\_name* vectors allow one or more +More generally, the *i_name* and *d_name* vectors allow one or more new custom per-atom properties to be defined. Each name must be unique and can use alphanumeric or underscore characters. These vectors can store whatever values you decide are useful in your @@ -197,7 +197,7 @@ properties in a completely general fashion. ---------- -For new atom properties specified as *i\_name* or *d\_name*, the +For new atom properties specified as *i_name* or *d_name*, the :doc:`compute property/atom ` command can access their values. This means that the values can be output via the :doc:`dump custom ` command, accessed by fixes like :doc:`fix ave/atom `, accessed by other computes like :doc:`compute reduce `, or used in :doc:`atom-style variables `. @@ -284,7 +284,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart ` diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 0144e3c4f7..94bad11f00 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are ignored by this fix * python/invoke = style name of this fix command * N = execute every N steps -* callback = *post\_force* or *end\_of\_step* +* callback = *post_force* or *end_of_step* .. parsed-literal:: diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index af32106806..07f61c2b85 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -82,7 +82,7 @@ Examples for how to do this are in the *examples/python* folder. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 57a2c88fac..b7a4f49300 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -15,7 +15,7 @@ Syntax * dir = *x* or *y* or *z* * shockvel = shock velocity (strictly positive, velocity units) * zero or more keyword/value pairs may be appended -* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f\_max* or *N\_f* or *eta* or *beta* or *T\_init* +* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f_max* or *N_f* or *eta* or *beta* or *T_init* .. parsed-literal:: @@ -95,15 +95,15 @@ Hugoniot that is 40% lower than observed with classical molecular dynamics. It is highly recommended that the system be already in an equilibrium -state with a quantum thermal bath at temperature of *T\_init*. The fix -command :doc:`fix qtb ` at constant temperature *T\_init* could +state with a quantum thermal bath at temperature of *T_init*. The fix +command :doc:`fix qtb ` at constant temperature *T_init* could be used before applying this command to introduce self-consistent quantum nuclear effects into the initial state. The parameters *q*\ , *mu*\ , *e0*\ , *p0*\ , *v0* and *tscale* are described in the command :doc:`fix msst `. The values of *e0*\ , *p0*\ , or *v0* will be calculated on the first step if not specified. The -parameter of *damp*\ , *f\_max*, and *N\_f* are described in the command +parameter of *damp*\ , *f_max*, and *N_f* are described in the command :doc:`fix qtb `. The *fix qbmsst* command couples the shock system to a quantum thermal @@ -135,7 +135,7 @@ of the *damp* parameter. \frac{dT^{qm}}{dt} = \gamma\eta\sum^\beta_{l=1}\frac{E^{tot}(t-l\Delta t) - E^{tot}_0}{3\beta N k_B} -The parameter *T\_init* is the initial temperature of the quantum +The parameter *T_init* is the initial temperature of the quantum thermal bath and the system before shock loading. For all pressure styles, the simulation box stays orthorhombic in @@ -144,29 +144,29 @@ supported by LAMMPS, but are not implemented for QBMSST. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Because the state of the random number generator is not written to :doc:`binary restart files `, this fix cannot be restarted "exactly" in an uninterrupted fashion. However, in a statistical sense, a restarted simulation should produce similar behaviors of the system as if it is not interrupted. To achieve such a restart, one -should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , *f\_max*, -*N\_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system is +should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , *f_max*, +*N_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system is compressed during the first run. The progress of the QBMSST can be monitored by printing the global scalar and global vector quantities computed by the fix. The global vector contains five values in this order: -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian\_speed*, *lagrangian\_position*, -*quantum\_temperature*] +[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*, +*quantum_temperature*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). 2. *drayleigh* is the departure from the Rayleigh line (pressure units). -3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front. -5. *quantum\_temperature* is the temperature of the quantum thermal bath :math:`T^{qm}`. +3. *lagrangian_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). +4. *lagrangian_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front. +5. *quantum_temperature* is the temperature of the quantum thermal bath :math:`T^{qm}`. To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested. Here the @@ -185,7 +185,7 @@ also the :doc:`thermo_style ` command. variable T_qm equal f_fix_id[5] thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id -The global scalar under the entry f\_fix\_id is the quantity of thermo +The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of :math:`E^{tot}`. This global scalar and the vector of 5 quantities can be accessed by various :doc:`output commands `. It is worth noting that the temp keyword @@ -218,8 +218,8 @@ Default """"""" The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed -= 880302, f\_max = 200.0, N\_f = 100, eta = 1.0, beta = 100, and -T\_init=300.0. e0, p0, and v0 are calculated on the first step. += 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and +T_init=300.0. e0, p0, and v0 are calculated on the first step. ---------- diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 418fc383b4..ea53fc2b2e 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -193,7 +193,7 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . arbitrary choices of these parameters. We do not develop these QEq parameters. See the examples/qeq directory for some examples. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 012f524b9e..c815ac7eb3 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -37,7 +37,7 @@ Description Perform charge equilibration (QeQ) in conjunction with the COMB (Charge-Optimized Many-Body) potential as described in -:ref:`(COMB\_1) ` and :ref:`(COMB\_2) `. It performs the charge +:ref:`(COMB_1) ` and :ref:`(COMB_2) `. It performs the charge equilibration portion of the calculation using the so-called QEq method, whereby the charge on each atom is adjusted to minimize the energy of the system. This fix can only be used with the COMB @@ -50,8 +50,8 @@ per-atom electronegativity (effective force on the charges). An electronegativity equalization calculation (or QEq) is performed in an iterative fashion, which in parallel requires communication at each iteration for processors to exchange charge information about nearby -atoms with each other. See :ref:`Rappe\_and\_Goddard ` and -:ref:`Rick\_and\_Stuart ` for details. +atoms with each other. See :ref:`Rappe_and_Goddard ` and +:ref:`Rick_and_Stuart ` for details. During a run, charge equilibration is performed every *Nevery* time steps. Charge equilibration is also always enforced on the first step @@ -85,7 +85,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -121,21 +121,21 @@ No file output is performed. ---------- -.. _COMB\_1: +.. _COMB_1: -**(COMB\_1)** J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), +**(COMB_1)** J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), -.. _COMB\_2: +.. _COMB_2: -**(COMB\_2)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. +**(COMB_2)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 81, 125328 (2010). -.. _Rappe\_and\_Goddard: +.. _Rappe_and_Goddard: -**(Rappe\_and\_Goddard)** A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 +**(Rappe_and_Goddard)** A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 (1991). -.. _Rick\_and\_Stuart: +.. _Rick_and_Stuart: -**(Rick\_and\_Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys +**(Rick_and_Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994). diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 854dc01991..1c722606a7 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -71,7 +71,7 @@ The optional *dual* keyword allows to perform the optimization of the S and T matrices in parallel. This is only supported for the *qeq/reax/omp* style. Otherwise they are processed separately. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. No global scalar or vector or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index 889004b9f8..4eb45e490f 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -42,7 +42,7 @@ to be adapted if necessary before being finalized. Details about how to use this fix are currently documented in the description of the QM/MM interface code itself in lib/qmmm/README. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 6980442c9c..6dfabcbaa7 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * qtb = style name of this fix * zero or more keyword/value pairs may be appended -* keyword = *temp* or *damp* or *seed* or *f\_max* or *N\_f* +* keyword = *temp* or *damp* or *seed* or *f_max* or *N_f* .. parsed-literal:: @@ -109,23 +109,23 @@ to generate its own unique seed and its own stream of random numbers. Thus the dynamics of the system will not be identical on two runs on different numbers of processors. -The *f\_max* parameter truncate the noise frequency domain so that -vibrational modes with frequencies higher than *f\_max* will not be +The *f_max* parameter truncate the noise frequency domain so that +vibrational modes with frequencies higher than *f_max* will not be modulated. If we denote :math:`\Delta t` as the time interval for the -MD integration, *f\_max* is always reset by the code to make -:math:`\alpha = (int)(2` *f\_max* :math:`\Delta t)^{-1}` a +MD integration, *f_max* is always reset by the code to make +:math:`\alpha = (int)(2` *f_max* :math:`\Delta t)^{-1}` a positive integer and print out relative information. An appropriate -value for the cutoff frequency *f\_max* would be around 2~3 :math:`f_D`, +value for the cutoff frequency *f_max* would be around 2~3 :math:`f_D`, where :math:`f_D` is the Debye frequency. -The *N\_f* parameter is the frequency grid size, the number of points -from 0 to *f\_max* in the frequency domain that will be -sampled. 3*2\ *N\_f* per-atom random numbers are required +The *N_f* parameter is the frequency grid size, the number of points +from 0 to *f_max* in the frequency domain that will be +sampled. 3*2\ *N_f* per-atom random numbers are required in the random force generation and there could be as many atoms as in the whole simulation that can migrate into every individual -processor. A larger *N\_f* provides a more accurate sampling of the -spectrum while consumes more memory. With fixed *f\_max* and -:math:`\gamma`, *N\_f* should be big enough to converge the classical +processor. A larger *N_f* provides a more accurate sampling of the +spectrum while consumes more memory. With fixed *f_max* and +:math:`\gamma`, *N_f* should be big enough to converge the classical temperature :math:`T^{cl}` as a function of target quantum bath temperature. Memory usage per processor could be from 10 to 100 Mbytes. @@ -145,7 +145,7 @@ Mbytes. ---------- -**Restart, fix\_modify, output, run start/stop, minimizie info:** +**Restart, fix_modify, output, run start/stop, minimizie info:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not @@ -178,7 +178,7 @@ Default """"""" The keyword defaults are temp = 300, damp = 1, seed = 880302, -f\_max=200.0 and N\_f = 100. +f_max=200.0 and N_f = 100. ---------- diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 01b1a8dadf..8f50473af8 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -43,11 +43,11 @@ The meaning of the column header abbreviations is as follows: * id = atom id * type = atom type * nb = number of bonds -* id\_1 = atom id of first bond -* id\_nb = atom id of Nth bond +* id_1 = atom id of first bond +* id_nb = atom id of Nth bond * mol = molecule id -* bo\_1 = bond order of first bond -* bo\_nb = bond order of Nth bond +* bo_1 = bond order of first bond +* bo_nb = bond order of Nth bond * abo = atom bond order (sum of all bonds) * nlp = number of lone pairs * q = atomic charge @@ -58,7 +58,7 @@ version, but will also take longer to write. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -98,7 +98,7 @@ package. See the :doc:`Build package ` doc page for more info. To write gzipped bond files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. +-DLAMMPS_GZIP option. Related commands """""""""""""""" diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 96ad89d7fe..63beb5520d 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -73,7 +73,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these symbols should be chosen to match the chemical identity of each LAMMPS atom type, as -specified using the :doc:`reax/c pair\_coeff ` command and +specified using the :doc:`reax/c pair_coeff ` command and the ReaxFF force field file. The optional keyword *position* writes center-of-mass positions of @@ -112,7 +112,7 @@ average bond-order for the species analysis output on timestep 100. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -167,9 +167,9 @@ package. See the :doc:`Build package ` doc page for more info. To write gzipped species files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. +-DLAMMPS_GZIP option. -It should be possible to extend it to other reactive pair\_styles (such as +It should be possible to extend it to other reactive pair_styles (such as :doc:`rebo `, :doc:`airebo `, :doc:`comb `, and :doc:`bop `), but this has not yet been done. diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 88cdc8d227..eec224c67d 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -93,7 +93,7 @@ velocities with zero aggregate linear and/or angular momentum. simulation scenario is to use the :doc:`fix spring ` command to tether the molecule in place. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 2a2edcb236..3965cee04d 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -182,7 +182,7 @@ current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 2e70b63ed3..72ed56bab1 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -182,7 +182,7 @@ The *rigid* styles are typically the best choice for a system with a small number of large rigid bodies, each of which can extend across the domain of many processors. It operates by creating a single global list of rigid bodies, which all processors contribute to. -MPI\_Allreduce operations are performed each timestep to sum the +MPI_Allreduce operations are performed each timestep to sum the contributions from each processor to the force and torque on all the bodies. This operation will not scale well in parallel if large numbers of rigid bodies are simulated. @@ -756,7 +756,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about the 4 NVE rigid styles is written to :doc:`binary restart files `. The exception is if the *infile* or *mol* keyword is used, in which case an auxiliary file is written out diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index eec2686be7..c9a709175f 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -286,7 +286,7 @@ cross periodic boundaries during the simulation. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information is written to :doc:`binary restart files `. If the *infile* keyword is used, an auxiliary file is written out diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index ba6dc393d9..0d8af574c1 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -18,7 +18,7 @@ Syntax * file = filename containing the reaction kinetic equations and Arrhenius parameters * localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function * matrix = *sparse, dense* format for the stoichiometric matrix -* solver = *lammps\_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method +* solver = *lammps_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method * minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45) * maxSteps = maximum number of steps for the rkf45 solver (rkf45 only) * relTol = relative tolerance for the rkf45 solver (rkf45 only) @@ -63,10 +63,10 @@ constructed based on the *n* reaction rate equations. The ODE systems are solved over the full DPD timestep *dt* using either a 4th order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified -by the *lammps\_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method +by the *lammps_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep for the rk4 method is optionally specified immediately after the rk4 -keyword. The ODE step-size is set as *dt/num\_steps*. Smaller +keyword. The ODE step-size is set as *dt/num_steps*. Smaller step-sizes tend to yield more accurate results but there is not control on the error. For error control, use the rkf45 ODE solver. @@ -74,13 +74,13 @@ The rkf45 method adjusts the step-size so that the local truncation error is hel within the specified absolute and relative tolerances. The initial step-size *h0* can be specified by the user or estimated internally. It is recommended that the user specify *h0* since this will generally reduced the number of ODE integration steps -required. *h0* is defined as *dt / min\_steps* if min\_steps >= 1. If min\_steps == 0, +required. *h0* is defined as *dt / min_steps* if min_steps >= 1. If min_steps == 0, *h0* is estimated such that an explicit Euler method would likely produce an acceptable solution. This is generally overly conservative for the 4th-order method and users are advised to specify *h0* as some fraction of the DPD timestep. For small DPD timesteps, only one step may be necessary depending upon the tolerances. -Note that more than min\_steps ODE steps may be taken depending upon the ODE stiffness -but no more than max\_steps will be taken. If max\_steps is reached, an error warning +Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness +but no more than max_steps will be taken. If max_steps is reached, an error warning is printed and the simulation is stopped. After each ODE step, the solution error *e* is tested and weighted using the absTol @@ -195,7 +195,7 @@ case, the :doc:`read_data ` command with the fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. fix foo all rx reaction.file ... -read\_data data.dpd fix foo\_SPECIES NULL Species +read_data data.dpd fix foo_SPECIES NULL Species ---------- diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index d0adefee00..818d14cc60 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -15,7 +15,7 @@ Syntax * Nevery = use input values every this many timesteps * Nrepeat = # of times to use input values for calculating averages * Nfreq = calculate averages every this many timesteps -* c\_ID = saed compute ID +* c_ID = saed compute ID .. parsed-literal:: @@ -56,7 +56,7 @@ outside the *Kmax* range assigned in the compute saed. The ghost data is assigned a value of -1 and can be removed setting a minimum isovolume of 0 within the visualization software. SAED images can be created by visualizing a spherical slice of the data that is centered at -R\_Ewald\*[h k l]/norm([h k l]), where R\_Ewald=1/lambda. +R_Ewald\*[h k l]/norm([h k l]), where R_Ewald=1/lambda. The group specified within this command is ignored. However, note that specified values may represent calculations performed by saed computes @@ -94,7 +94,7 @@ averaging is done; values are simply generated on timesteps The output for fix ave/time/saed is a file written with the 3rd generation vtk image data formatting. The filename assigned by the *file* keyword is -appended with \_N.vtk where N is an index (0,1,2...) to account for multiple +appended with _N.vtk where N is an index (0,1,2...) to account for multiple diffraction intensity outputs. By default the header contains the following information (with example data): @@ -157,7 +157,7 @@ running or windowed average. The *file* keyword allows a filename to be specified. Every *Nfreq* steps, the vector of saed intensity data is written to a new file using the 3rd generation vtk format. The base of each file is assigned by -the *file* keyword and this string is appended with \_N.vtk where N is +the *file* keyword and this string is appended with _N.vtk where N is an index (0,1,2...) to account for situations with multiple diffraction intensity outputs. @@ -165,7 +165,7 @@ The *overwrite* keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the *ave running* setting. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -176,7 +176,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -The attributes for fix\_saed\_vtk must match the values assigned in the +The attributes for fix_saed_vtk must match the values assigned in the associated :doc:`compute_saed ` command. Related commands diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 1b53bfe200..59de49fbe0 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -55,7 +55,7 @@ alter the force component in that dimension. Any of the 3 quantities defining the force components can be specified as an equal-style or atom-style :doc:`variable `, namely *fx*\ , *fy*\ , *fz*\ . If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -111,7 +111,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index d687920e97..cd3fbd3865 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -121,7 +121,7 @@ constraint lists atom types. All bonds connected to an atom of the specified type will be constrained. The *m* constraint lists atom masses. All bonds connected to atoms of the specified masses will be constrained (within a fudge factor of MASSDELTA specified in -fix\_shake.cpp). The *a* constraint lists angle types. If both bonds +fix_shake.cpp). The *a* constraint lists angle types. If both bonds in the angle are constrained then the angle will also be constrained if its type is in the list. @@ -195,12 +195,12 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). after fix rattle operates, then fix rattle will not take them into account and the overall time integration will typically not satisfy the RATTLE constraints. You can check whether the constraints work - correctly by setting the value of RATTLE\_DEBUG in src/fix\_rattle.cpp + correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp to 1 and recompiling LAMMPS. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the constraints to the diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index a5ce32c89a..9949d3a51c 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -42,12 +42,12 @@ necessary). Note that numerous variants of DPD can be specified by choosing an appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can -be specified by using fix *shardlow*\ , fix *nve* and pair\_style +be specified by using fix *shardlow*\ , fix *nve* and pair_style *dpd/fdt*\ . DPD under isoenergetic conditions can be specified by -using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ . DPD +using fix *shardlow*\ , fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isobaric conditions can be specified by using fix shardlow, fix -*nph* and pair\_style *dpd/fdt*\ . DPD under isoenthalpic conditions can -be specified by using fix shardlow, fix *nph* and pair\_style +*nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can +be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the examples/USER/dpd directory. diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index ddd6a15505..b303114887 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -99,7 +99,7 @@ can then later be used to compute the potential of mean force (PMF) by averaging over multiple independent trajectories along the same pulling path. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** The fix stores the direction of the spring, current pulling target distance and the running PMF to :doc:`binary restart files `. diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index 3135df2dbf..d91ad1392d 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -11,8 +11,8 @@ Syntax fix ID group-ID smd/adjust_dt arg * ID, group-ID are documented in :doc:`fix ` command -* smd/adjust\_dt = style name of this fix command -* arg = *s\_fact* +* smd/adjust_dt = style name of this fix command +* arg = *s_fact* .. parsed-literal:: @@ -41,12 +41,12 @@ step. This fix inquires the minimum stable time increment across all particles contained in the group for which this fix is defined. An -additional safety factor *s\_fact* is applied to the time increment. +additional safety factor *s_fact* is applied to the time increment. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization. @@ -59,6 +59,6 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`smd/tlsph\_dt ` +:doc:`smd/tlsph_dt ` **Default:** none diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index 7536e1f6e2..ef91414788 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -11,9 +11,9 @@ Syntax fix ID group-ID smd/integrate_tlsph keyword values * ID, group-ID are documented in :doc:`fix ` command -* smd/integrate\_tlsph = style name of this fix command +* smd/integrate_tlsph = style name of this fix command * zero or more keyword/value pairs may be appended -* keyword = *limit\_velocity* +* keyword = *limit_velocity* .. parsed-literal:: @@ -37,11 +37,11 @@ interact according with the Total-Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -The *limit\_velocity* keyword will control the velocity, scaling the -norm of the velocity vector to max\_vel in case it exceeds this +The *limit_velocity* keyword will control the velocity, scaling the +norm of the velocity vector to max_vel in case it exceeds this velocity limit. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -55,6 +55,6 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`smd/integrate\_ulsph ` +:doc:`smd/integrate_ulsph ` **Default:** none diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index 36197bd057..c355abf17b 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -11,16 +11,16 @@ Syntax fix ID group-ID smd/integrate_ulsph keyword * ID, group-ID are documented in :doc:`fix ` command -* smd/integrate\_ulsph = style name of this fix command +* smd/integrate_ulsph = style name of this fix command * zero or more keyword/value pairs may be appended -* keyword = adjust\_radius or limit\_velocity +* keyword = adjust_radius or limit_velocity -adjust\_radius values = adjust\_radius\_factor min\_nn max\_nn - adjust\_radius\_factor = factor which scale the smooth/kernel radius - min\_nn = minimum number of neighbors - max\_nn = maximum number of neighbors -limit\_velocity values = max\_velocity - max\_velocity = maximum allowed velocity. +adjust_radius values = adjust_radius_factor min_nn max_nn + adjust_radius_factor = factor which scale the smooth/kernel radius + min_nn = minimum number of neighbors + max_nn = maximum number of neighbors +limit_velocity values = max_velocity + max_velocity = maximum allowed velocity. Examples """""""" @@ -39,17 +39,17 @@ interact with the updated Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -The *adjust\_radius* keyword activates dynamic adjustment of the +The *adjust_radius* keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of -neighbors per particles remains within the interval *min\_nn* to -*max\_nn*. The parameter *adjust\_radius\_factor* determines the amount -of adjustment per timestep. Typical values are *adjust\_radius\_factor* -=1.02, *min\_nn* =15, and *max\_nn* =20. +neighbors per particles remains within the interval *min_nn* to +*max_nn*. The parameter *adjust_radius_factor* determines the amount +of adjustment per timestep. Typical values are *adjust_radius_factor* +=1.02, *min_nn* =15, and *max_nn* =20. -The *limit\_velocity* keyword will control the velocity, scaling the norm of -the velocity vector to max\_vel in case it exceeds this velocity limit. +The *limit_velocity* keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 7dc3758f30..3aa40a75c2 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -11,7 +11,7 @@ Syntax fix ID group-ID smd/move_tri_surf keyword * ID, group-ID are documented in :doc:`fix ` command -* smd/move\_tri\_surf keyword = style name of this fix command +* smd/move_tri_surf keyword = style name of this fix command * keyword = *\*LINEAR* or *\*WIGGLE* or *\*ROTATE* .. parsed-literal:: @@ -39,7 +39,7 @@ Description """"""""""" This fix applies only to rigid surfaces read from .STL files via fix -:doc:`smd/wall\_surface ` . It updates position +:doc:`smd/wall_surface ` . It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. The rigid surfaces can thus be moved along simple trajectories during the simulation. @@ -50,7 +50,7 @@ to V = (Vx,Vy,Vz). The *\*WIGGLE* style moves particles in an oscillatory fashion. Particles are moved along (vx, vy, vz) with constant velocity until a -displacement of max\_travel is reached. Then, the velocity vector is +displacement of max_travel is reached. Then, the velocity vector is reversed. This process is repeated. The *\*ROTATE* style rotates particles around a rotation axis R = @@ -63,7 +63,7 @@ rotation axis to the particle. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -77,7 +77,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`smd/triangle\_mesh\_vertices `, -:doc:`smd/wall\_surface ` +:doc:`smd/triangle_mesh_vertices `, +:doc:`smd/wall_surface ` **Default:** none diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index bdf97354f5..eb92f435e1 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -44,7 +44,7 @@ This fix is indented to be used together with a time integration fix. Any of the 3 quantities defining the velocity components can be specified as an equal-style or atom-style :doc:`variable `, namely *vx*\ , *vy*\ , *vz*\ . If the value is a variable, it should be specified as -v\_name, where name is the variable name. In this case, the variable +v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -63,7 +63,7 @@ specified geometric :doc:`region ` in order to have its velocity set by ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization None of the :doc:`fix_modify ` options diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index fcb007363b..6bebcdf6c2 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -11,7 +11,7 @@ Syntax fix ID group-ID smd/wall_surface arg type mol-ID * ID, group-ID are documented in :doc:`fix ` command -* smd/wall\_surface = style name of this fix command +* smd/wall_surface = style name of this fix command * arg = *file* .. parsed-literal:: @@ -38,19 +38,19 @@ the new particle is that of the minimum circle which encompasses the triangle vertices. The triangulated surface can be used as a complex rigid wall via the -:doc:`smd/tri\_surface ` pair style. It +:doc:`smd/tri_surface ` pair style. It is possible to move the triangulated surface via the -:doc:`smd/move\_tri\_surf ` fix style. +:doc:`smd/move_tri_surf ` fix style. Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel\_flow" example in the USER-SMD examples +in the system. See the "funnel_flow" example in the USER-SMD examples directory. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -71,8 +71,8 @@ multiple objects in one file. Related commands """""""""""""""" -:doc:`smd/triangle\_mesh\_vertices `, -:doc:`smd/move\_tri\_surf `, -:doc:`smd/tri\_surface ` +:doc:`smd/triangle_mesh_vertices `, +:doc:`smd/move_tri_surf `, +:doc:`smd/tri_surface ` **Default:** none diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index db8608ea99..b337a4e048 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -97,7 +97,7 @@ last example holds the ion a distance 5 away from the pore axis spring connecting two groups or a group and the tether point can cross a periodic boundary and its length be calculated correctly. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index 01def4cabc..d839d9158c 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -48,7 +48,7 @@ chunk. Note that *K* thus represents the spring constant for the total force on each chunk of atoms, not for a spring applied to each atom. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 1d552c4d33..962e780f7f 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -57,7 +57,7 @@ for the aggregate force on the group of atoms, not a per-atom force. If :math:`R_{G0}` is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index 8f8d2fb97e..38da0013b1 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -41,7 +41,7 @@ directions, but it can be limited to the xy-, xz-, yz-plane and the x-, y-, or z-direction, thus restraining the atoms to a line or a plane, respectively. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the same in a restarted simulation. See the diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 96ddcb6329..70f07cc0bf 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -334,13 +334,13 @@ interactions is specified, the :doc:`pair_coeff ` command should be used to turn off big/SRD interactions, e.g. by setting their epsilon or cutoff length to 0.0. -The "delete\_atoms overlap" command may be useful in setting up an SRD +The "delete_atoms overlap" command may be useful in setting up an SRD simulation to insure there are no initial overlaps between big and SRD particles. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index e99d5db964..d9ccd162fd 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -49,7 +49,7 @@ potentially modify the force on each atom. Examples of such fixes are to include certain constraints (e.g. fix shake) in the stored force, then it could be specified after some fixes and before others. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -69,6 +69,6 @@ Restrictions Related commands """""""""""""""" -:doc:`fix store\_state ` +:doc:`fix store_state ` **Default:** none diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 2e2049bbdd..b8fee6b5ea 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -102,7 +102,7 @@ The requested values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart ` diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 33eee84bce..4913efdf53 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -50,7 +50,7 @@ of (roughly) 100 time units (tau or fmsec or psec - see the *Tstart* can be specified as an equal-style :doc:`variable `. In this case, the *Tstop* setting is ignored. If the value is a -variable, it should be specified as v\_name, where name is the variable +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. @@ -93,12 +93,12 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -117,7 +117,7 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 7a528bcfa2..cd4e5dc88f 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -64,7 +64,7 @@ of (roughly) 100 time units (tau or fmsec or psec - see the *Tstart* can be specified as an equal-style :doc:`variable `. In this case, the *Tstop* setting is ignored. If the value is a -variable, it should be specified as v\_name, where name is the variable +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. @@ -101,12 +101,12 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, these fixes can be used @@ -125,7 +125,7 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about these fixes are written to :doc:`binary restart files `. diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index d6a433ae42..d23006c52b 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -56,7 +56,7 @@ beginning and end of the run. *Tstart* can be specified as an equal-style :doc:`variable `. In this case, the *Tstop* setting is ignored. If the value is a -variable, it should be specified as v\_name, where name is the variable +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. @@ -100,12 +100,12 @@ ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command or print this temperature during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo\_temp* will have no +It also means that changing attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used @@ -124,7 +124,7 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 679913ab2d..5173e6addc 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -35,7 +35,7 @@ The operation of this fix is exactly like that described by the :doc:`fix temp/r is also applied to the radial electron velocity for electron particles. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index 952850be59..fe290dfc0c 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -116,7 +116,7 @@ rotational component of the tfMC displacements after every iteration. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 133a091b8a..6b8b670694 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -108,7 +108,7 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper accurately infer a thermal conductivity and should try increasing the Nevery parameter. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 0c764895c5..8bf5439e0d 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -13,8 +13,8 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * ti/spring = style name of this fix command * k = spring constant (force/distance units) -* t\_eq = number of steps for the equilibration procedure -* t\_s = number of steps for the switching procedure +* t_eq = number of steps for the equilibration procedure +* t_s = number of steps for the switching procedure * zero or more keyword/value pairs may be appended to args * keyword = *function* @@ -48,8 +48,8 @@ each atom is given by F = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}} -where F\_solid is the force that acts on an atom due to an interatomic -potential (\ *e.g.* EAM potential), F\_harm is the force due to the +where F_solid is the force that acts on an atom due to an interatomic +potential (\ *e.g.* EAM potential), F_harm is the force due to the Einstein crystal harmonic spring, and lambda is the coupling parameter of the thermodynamic integration. An Einstein crystal is a solid where each atom is attached to its equilibrium position by a harmonic spring @@ -58,15 +58,15 @@ independently to each atom in the group defined by the fix to tether it to its initial position. The initial position of each atom is its position at the time the fix command was issued. -The fix acts as follows: during the first *t\_eq* steps after the fix +The fix acts as follows: during the first *t_eq* steps after the fix is defined the value of lambda is zero. This is the period to equilibrate the system in the lambda = 0 state. After this the value of lambda changes dynamically during the simulation from 0 to 1 according to the function defined using the keyword *function* (described below), this switching from lambda from 0 to 1 is done in -*t\_s* steps. Then comes the second equilibration period of *t\_eq* to +*t_s* steps. Then comes the second equilibration period of *t_eq* to equilibrate the system in the lambda = 1 state. After that, the -switching back to the lambda = 0 state is made using *t\_s* timesteps +switching back to the lambda = 0 state is made using *t_s* timesteps and following the same switching function. After this period the value of lambda is kept equal to zero and the fix has no other effect on the dynamics of the system. @@ -88,7 +88,7 @@ time: \lambda(\tau) = \tau -where tau is the scaled time variable *t/t\_s*. The option *2* performs +where tau is the scaled time variable *t/t_s*. The option *2* performs the lambda switching at a rate defined by the following switching function @@ -116,7 +116,7 @@ increase in computational resources cost. option will *NOT* solve this problem). The Langevin thermostat (:doc:`fix langevin `) correctly thermostats the system and we advise its usage with ti/spring command. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the same in a restarted simulation. See the :doc:`read restart ` command for info on how to re-specify a fix diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 4e9b410490..bbc99d3ba2 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * tmd = style name of this fix command -* rho\_final = desired value of rho at the end of the run (distance units) +* rho_final = desired value of rho at the end of the run (distance units) * file1 = filename to read target structure from * N = dump TMD statistics every this many timesteps, 0 = no dump * file2 = filename to write TMD statistics to (only needed if N > 0) @@ -32,12 +32,12 @@ Perform targeted molecular dynamics (TMD) on a group of atoms. A holonomic constraint is used to force the atoms to move towards (or away from) the target configuration. The parameter "rho" is monotonically decreased (or increased) from its initial value to -rho\_final at the end of the run. +rho_final at the end of the run. Rho has distance units and is a measure of the root-mean-squared distance (RMSD) between the current configuration of the atoms in the group and the target coordinates listed in file1. Thus a value of -rho\_final = 0.0 means move the atoms all the way to the final +rho_final = 0.0 means move the atoms all the way to the final structure during the course of the run. The target file1 can be ASCII text or a gzipped text file (detected by @@ -78,10 +78,10 @@ The atoms in the fix tmd group should be integrated (via a fix nve, nvt, npt) along with other atoms in the system. Restarts can be used with a fix tmd command. For example, imagine a -10000 timestep run with a rho\_initial = 11 and a rho\_final = 1. If a +10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a restart file was written after 2000 time steps, then the configuration in the file would have a rho value of 9. A new 8000 time step run -could be performed with the same rho\_final = 1 to complete the +could be performed with the same rho_final = 1 to complete the conformational change at the same transition rate. Note that for restarted runs, the name of the TMD statistics file should be changed to prevent it being overwritten. @@ -89,7 +89,7 @@ to prevent it being overwritten. For more information about TMD, see :ref:`(Schlitter1) ` and :ref:`(Schlitter2) `. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -114,7 +114,7 @@ are not multiple competing holonomic constraints applied to the same atoms. To read gzipped target files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. See the :doc:`Build settings ` +-DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. **Related commands:** none diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index e70243231e..ae759c1b13 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -15,7 +15,7 @@ Syntax fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile * ID, group-ID are documented in :doc:`fix ` command -* style = *ttm* or *ttm\_mod* +* style = *ttm* or *ttm_mod* * seed = random number seed to use for white noise (positive integer) * remaining arguments for fix ttm: @@ -93,11 +93,11 @@ reservoir, whereas the heat reservoir for fix TTM is finite and represents the local electrons. Third, the TTM fix allows users to specify not just one friction coefficient, but rather two independent friction coefficients: one for the electron-ion interactions -(*gamma\_p*), and one for electron stopping (*gamma\_s*). +(*gamma_p*), and one for electron stopping (*gamma_s*). -When the friction coefficient due to electron stopping, *gamma\_s*, is +When the friction coefficient due to electron stopping, *gamma_s*, is non-zero, electron stopping effects are included for atoms moving -faster than the electron stopping critical velocity, *v\_0*. For +faster than the electron stopping critical velocity, *v_0*. For further details about this algorithm, see :ref:`(Duffy) ` and :ref:`(Rutherford) `. @@ -111,11 +111,11 @@ transfer between the subsystems: \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' -where C\_e is the specific heat, rho\_e is the density, kappa\_e is the +where C_e is the specific heat, rho_e is the density, kappa_e is the thermal conductivity, T is temperature, the "e" and "a" subscripts -represent electronic and atomic subsystems respectively, g\_p is the -coupling constant for the electron-ion interaction, and g\_s is the -electron stopping coupling parameter. C\_e, rho\_e, and kappa\_e are +represent electronic and atomic subsystems respectively, g_p is the +coupling constant for the electron-ion interaction, and g_s is the +electron stopping coupling parameter. C_e, rho_e, and kappa_e are specified as parameters to the fix. The other quantities are derived. The form of the heat diffusion equation used here is almost the same as that in equation 6 of :ref:`(Duffy) `, with the exception that the @@ -135,12 +135,12 @@ approach of :ref:`(Rutherford) ` where the atomic subsystem was embedded within a larger continuum representation of the electronic subsystem. -The initial electronic temperature input file, *T\_infile*, is a text +The initial electronic temperature input file, *T_infile*, is a text file LAMMPS reads in with no header and with four numeric columns (ix,iy,iz,Temp) and with a number of rows equal to the number of user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node indices from 0 to nxnodes-1, etc. For example, the initial electronic -temperatures on a 1 by 2 by 3 grid could be specified in a *T\_infile* +temperatures on a 1 by 2 by 3 grid could be specified in a *T_infile* as follows: .. parsed-literal:: @@ -157,7 +157,7 @@ where the electronic temperatures along the y=0 plane have been set to to 2.0. The order of lines in this file is no important. If all the nodal values are not specified, LAMMPS will generate an error. -The temperature output file, *T\_oufile*, is created and written by +The temperature output file, *T_oufile*, is created and written by this fix. Temperatures for both the electronic and atomic subsystems at every node and every N timesteps are output. If N is specified as zero, no output is generated, and no output filename is needed. The @@ -196,22 +196,22 @@ heat sources (e.g. laser heating in ablation simulations): \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin}) -where theta is the Heaviside step function, I\_0 is the (absorbed) -laser pulse intensity for ablation simulations, l\_skin is the depth +where theta is the Heaviside step function, I_0 is the (absorbed) +laser pulse intensity for ablation simulations, l_skin is the depth of skin-layer, and all other designations have the same meaning as in the former equation. The duration of the pulse is set by the parameter -*tau* in the *init\_file*. +*tau* in the *init_file*. -Fix ttm/mod also allows users to specify the dependencies of C\_e and -kappa\_e on the electronic temperature. The specific heat is expressed +Fix ttm/mod also allows users to specify the dependencies of C_e and +kappa_e on the electronic temperature. The specific heat is expressed as .. math:: C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2) -where *X* = T\_e/1000, and the thermal conductivity is defined as -kappa\_e = D\_e\*rho\_e\*C\_e, where D\_e is the thermal diffusion +where *X* = T_e/1000, and the thermal conductivity is defined as +kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion coefficient. Electronic pressure effects are included in the TTM model to account @@ -223,23 +223,23 @@ acting on an ion is: {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion} -where F\_langevin is a force from Langevin thermostat simulating -electron-phonon coupling, and nabla P\_e/n\_ion is the electron blast +where F_langevin is a force from Langevin thermostat simulating +electron-phonon coupling, and nabla P_e/n_ion is the electron blast force. -The electronic pressure is taken to be P\_e = B\*rho\_e\*C\_e\*T\_e +The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e The current fix ttm/mod implementation allows TTM simulations with a vacuum. The vacuum region is defined as the grid cells with zero electronic temperature. The numerical scheme does not allow energy exchange with such cells. Since the material can expand to previously unoccupied region in some simulations, the vacuum border can be -allowed to move. It is controlled by the *surface\_movement* parameter -in the *init\_file*. If it is set to 1, then "vacuum" cells can be -changed to "electron-filled" cells with the temperature *T\_e_min* if +allowed to move. It is controlled by the *surface_movement* parameter +in the *init_file*. If it is set to 1, then "vacuum" cells can be +changed to "electron-filled" cells with the temperature *T_e_min* if atoms move into them (currently only implemented for the case of 1-dimensional motion of flat surface normal to the X axis). The -initial borders of vacuum can be set in the *init\_file* via *lsurface* +initial borders of vacuum can be set in the *init_file* via *lsurface* and *rsurface* parameters. In this case, electronic pressure gradient is calculated as @@ -250,7 +250,7 @@ is calculated as where lambda is the electron mean free path (see :ref:`(Norman) `, :ref:`(Pisarev) `) -The fix ttm/mod parameter file *init\_file* has the following syntax/ +The fix ttm/mod parameter file *init_file* has the following syntax/ Every line with the odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows: @@ -281,7 +281,7 @@ ignored. The lines with the even numbers are treated as follows: ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** These fixes write the state of the electronic subsystem and the energy exchange between the subsystems to :doc:`binary restart files `. See the :doc:`read_restart ` command diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 1f201799cb..66a3fef024 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -83,7 +83,7 @@ Restrictions This fix is part of the KSPACE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Do not set "neigh\_modify once yes" or else this fix will never be +Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. This fix is not compatible with a hybrid pair style, long-range dispersion, diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 4a6d415a22..81922dea8a 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -14,7 +14,7 @@ Syntax * vector = style name of this fix command * Nevery = use input values every this many timesteps * one or more input values can be listed -* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name .. parsed-literal:: @@ -123,7 +123,7 @@ quantities to be stored by fix vector. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index b3c1b92bd3..e31cbf2e45 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -113,7 +113,7 @@ system using a :doc:`PPPM solver ` since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; thus it does not suffer from this limitation. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 5a6d966822..88d619e56c 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -84,7 +84,7 @@ more easily be used as a thermostat. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index acd97d83c6..a56bca3c45 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -165,7 +165,7 @@ EDGE is used, then the corresponding boundary of the current simulation box is used. If a numeric constant is specified then the wall is placed at that position in the appropriate dimension (x, y, or z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v\_name, +If the wall position is a variable, it should be specified as v_name, where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables @@ -222,7 +222,7 @@ inverse distance units, and :math:`r_0` distance units. For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can be specified as an :doc:`equal-style variable `, in which case it should be -specified as v\_name, where name is the variable name. As with a +specified as v_name, where name is the variable name. As with a variable wall position, the variable is evaluated each timestep and the result becomes the current epsilon or sigma of the wall. Equal-style variables can specify formulas with various mathematical @@ -323,7 +323,7 @@ perturbation on the particles: ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 0371710604..a93d71369f 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -12,9 +12,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * wall/body/polygon = style name of this fix command -* k\_n = normal repulsion strength (force/distance or pressure units) -* c\_n = normal damping coefficient (force/distance or pressure units) -* c\_t = tangential damping coefficient (force/distance or pressure units) +* k_n = normal repulsion strength (force/distance or pressure units) +* c_n = normal damping coefficient (force/distance or pressure units) +* c_t = tangential damping coefficient (force/distance or pressure units) * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style @@ -54,7 +54,7 @@ particles themselves, which is similar to a Hookean potential. See the :doc:`Howto body ` doc page for more details on using body particles. -The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as +The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as those specified with the :doc:`pair_style body/rounded/polygon ` command. The *wallstyle* can be planar or cylindrical. The 2 planar options @@ -87,7 +87,7 @@ the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index a36d8a5fca..4b01234f0f 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -12,9 +12,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * wall/body/polyhedron = style name of this fix command -* k\_n = normal repulsion strength (force/distance units or pressure units - see discussion below) -* c\_n = normal damping coefficient (force/distance units or pressure units - see discussion below) -* c\_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) +* k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) +* c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) +* c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style @@ -54,7 +54,7 @@ particles themselves, which is similar to a Hookean potential. See the :doc:`Howto body ` doc page for more details on using body particles. -The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as +The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as those specified with the :doc:`pair_style body/rounded/polyhedron ` command. The *wallstyle* can be planar or cylindrical. The 3 planar options @@ -86,7 +86,7 @@ the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 98cc251fcc..daf3152c34 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -18,7 +18,7 @@ Syntax possible choices: hooke, hooke/history, hertz/history, granular -* fstyle\_params = parameters associated with force interaction style +* fstyle_params = parameters associated with force interaction style .. parsed-literal:: @@ -82,25 +82,25 @@ The nature of the wall/particle interactions are determined by the :doc:`pair_style granular ` commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated -*pair\_coeff* command for the latter. The equation for the force +*pair_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair_style granular ` doc pages, in the limit of one of the two particles going to infinite radius and mass (flat wall). -Specifically, delta = radius - r = overlap of particle with wall, m\_eff +Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be -used for either *Kt* or *gamma\_t* as described on that page. If a +used for either *Kt* or *gamma_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 -*Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used -where *gamma\_t* = 1/2 *gamma\_n*. +*Kn*\ . If a NULL is used for *gamma_t*, then a default value is used +where *gamma_t* = 1/2 *gamma_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair_coeff* command are also supported for walls. These are discussed in greater detail on the doc page for :doc:`pair_style granular `. @@ -122,10 +122,10 @@ material. appropriately in the current code to reproduce the results of a previous Hertzian monodisperse calculation. For example, for the common case of a monodisperse system with particles of diameter 1, Kn, - Kt, gamma\_n, and gamma\_s should be set sqrt(2.0) larger than they were + Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were previously. -The effective mass *m\_eff* in the formulas listed on the :doc:`pair_style granular ` doc page is the mass of the particle for +The effective mass *m_eff* in the formulas listed on the :doc:`pair_style granular ` doc page is the mass of the particle for particle/wall interactions (mass of wall is infinite). If the particle is part of a rigid body, its mass is replaced by the mass of the rigid body in those formulas. This is determined by searching for @@ -171,7 +171,7 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for *vshear* < 0. In this case, *vshear* is the tangential velocity of the wall at whatever *radius* has been defined. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** This fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 8144769270..620baa0942 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -18,7 +18,7 @@ Syntax possible choices: hooke, hooke/history, hertz/history, granular -* fstyle\_params = parameters associated with force interaction style +* fstyle_params = parameters associated with force interaction style .. parsed-literal:: @@ -153,7 +153,7 @@ The nature of the wall/particle interactions are determined by the :doc:`pair_style granular ` commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated -*pair\_coeff* command for the latter. The equation for the force +*pair_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair_style granular ` doc pages, but the effective @@ -161,24 +161,24 @@ radius is calculated using the radius of the particle and the radius of curvature of the wall at the contact point. Specifically, delta = radius - r = overlap of particle with wall, -m\_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with +m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with Rj replaced by the radius of curvature of the wall at the contact point. The radius of curvature can be negative for a concave wall section, e.g. the interior of cylinder. For a flat wall, delta = -radius - r = overlap of particle with wall, m\_eff = mass of particle, +radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* +The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the :doc:`pair_style gran/\* ` commands. This means a NULL can be -used for either *Kt* or *gamma\_t* as described on that page. If a +used for either *Kt* or *gamma_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 -*Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used -where *gamma\_t* = 1/2 *gamma\_n*. +*Kn*\ . If a NULL is used for *gamma_t*, then a default value is used +where *gamma_t* = 1/2 *gamma_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair_coeff* command are also supported for walls. These are discussed in greater detail on the doc page for :doc:`pair_style granular `. @@ -187,7 +187,7 @@ values for the 6 wall/particle coefficients than for particle/particle interactions. E.g. if you wish to model the wall as a different material. -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** Similar to :doc:`fix wall/gran ` command, this fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can continue diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index fe12bbc13c..626634ec83 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -90,7 +90,7 @@ define the lattice spacings. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 76591bebf0..3960105ab9 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -74,7 +74,7 @@ EDGE is used, then the corresponding boundary of the current simulation box is used. If a numeric constant is specified then the wall is placed at that position in the appropriate dimension (x, y, or z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v\_name, +If the wall position is a variable, it should be specified as v_name, where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables @@ -161,7 +161,7 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 9581966b61..b3f4733c56 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -186,10 +186,10 @@ surface no longer interact. The cutoff is always the last argument. The energy of the wall potential is shifted so that the wall-particle interaction energy is 0.0 at the cutoff distance. -For a full description of these wall styles, see fix\_style +For a full description of these wall styles, see fix_style :doc:`wall ` -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index fbcdca3035..5df7345a4d 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -84,7 +84,7 @@ EDGE is used, then the corresponding boundary of the current simulation box is used. If a numeric constant is specified then the wall is placed at that position in the appropriate dimension (x, y, or z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v\_name, +If the wall position is a variable, it should be specified as v_name, where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables @@ -177,7 +177,7 @@ perturbation on the particles: ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index 6b0ab9ab52..3d2878c517 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -40,7 +40,7 @@ to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that using an improper\_coeff command can override a previous +Note that using an improper_coeff command can override a previous setting for the same improper type. For example, these commands set the coeffs for all improper types, then overwrite the coeffs for just improper type 2: @@ -51,7 +51,7 @@ improper type 2: improper_coeff 2 50.0 0.0 A line in a data file that specifies improper coefficients uses the -exact same format as the arguments of the improper\_coeff command in an +exact same format as the arguments of the improper_coeff command in an input script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Improper Coeffs" section of a data file, the line that @@ -74,7 +74,7 @@ in more compact form on the :ref:`Commands improper ` doc page. On either of those pages, click on the style to display the formula it computes and its coefficients as specified by the associated -improper\_coeff command. +improper_coeff command. ---------- diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 933afe9160..d5f07f9971 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -42,8 +42,8 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the improper\_coeff command as in the example above, or in the data -file or restart files read by the read\_data or read\_restart commands: +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: * :math:`K_2` (energy/distance\^2) * :math:`K_4` (energy/distance\^4) diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index b5b20e47d2..113941bee4 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -32,12 +32,12 @@ by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used -in the improper\_style distance. The distance :math:`d` is oriented and can take +in the improper_style distance. The distance :math:`d` is oriented and can take on negative values. This may lead to unwanted behavior if :math:`d_0` is not equal to zero. The following coefficients must be defined for each improper type via -the improper\_coeff command as in the example above, or in the data -file or restart files read by the read\_data or read\_restart commands: +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: * :math:`K` (energy/distance\^2) * :math:`d_0` (distance) diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index a3500f11e6..7842e866f6 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -76,7 +76,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER\_MISC package. See the :doc:`Build package ` doc +USER_MISC package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 12464fee6a..9d5c4c696d 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -32,9 +32,9 @@ boundary (of improper type 2) could be computed with a *cvff* potential. The assignment of improper type to style is made via the :doc:`improper_coeff ` command or in the data file. -In the improper\_coeff command, the first coefficient sets the improper +In the improper_coeff command, the first coefficient sets the improper style and the remaining coefficients are those appropriate to that -style. In the example above, the 2 improper\_coeff commands would set +style. In the example above, the 2 improper_coeff commands would set impropers of improper type 1 to be computed with a *harmonic* potential with coefficients 120.0, 30 for :math:`K`, :math:`\chi_0`. Improper type 2 would be computed with a *cvff* potential with coefficients @@ -49,7 +49,7 @@ appropriate to that style. The AngleAngle coeffs for that improper type will then be ignored. An improper style of *none* can be specified as the 2nd argument to -the improper\_coeff command, if you desire to turn off certain improper +the improper_coeff command, if you desire to turn off certain improper types. ---------- @@ -64,7 +64,7 @@ for more info. Unlike other improper styles, the hybrid improper style does not store improper coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when restarting a simulation from a -restart file, you need to re-specify improper\_coeff commands. +restart file, you need to re-specify improper_coeff commands. Related commands """""""""""""""" diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index ff62812341..0634405c0e 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -39,9 +39,9 @@ equilibrium value. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command) are ordered i,j,k,l then -theta\_\ *ijl* is the angle between atoms i,j and l, theta\_\ *ijk* is the -angle between atoms i,j and k, theta\_\ *kjl* is the angle between atoms -j,k, and l. +:math:`\theta_{ijl}` is the angle between atoms i,j and l, +:math:`\theta_{ijk}` is the angle between atoms i,j and k, +:math:`\theta_{kjl}` is the angle between atoms j,k, and l. The "ring" improper style implements the improper potential introduced by Destree et al., in Equation (9) of :ref:`(Destree) `. This diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 9f4fde5b91..2f8723a68c 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -32,11 +32,11 @@ by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used -in the improper\_style distance. +in the improper_style distance. The following coefficients must be defined for each improper type via -the improper\_coeff command as in the example above, or in the data -file or restart files read by the read\_data or read\_restart commands: +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: * :math:`K` (energy/distance\^4) * :math:`{d_0}^2` (distance\^2) diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index c4ccdb5a74..0667b8f5b9 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -41,11 +41,11 @@ a data or restart file or via the :doc:`improper_coeff ` command. All improper potentials store their coefficient data in binary restart -files which means improper\_style and +files which means improper_style and :doc:`improper_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the :doc:`read_restart ` command for details on how to do -this. The one exception is that improper\_style *hybrid* only stores +this. The one exception is that improper_style *hybrid* only stores the list of sub-styles in the restart file; improper coefficients need to be re-specified. @@ -64,7 +64,7 @@ specified by the associated :doc:`improper_coeff ` command. Click on the style to display the formula it computes, any additional -arguments specified in the improper\_style command, and coefficients +arguments specified in the improper_style command, and coefficients specified by the associated :doc:`improper_coeff ` command. @@ -95,7 +95,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. Restrictions """""""""""" -Improper styles can only be set for atom\_style choices that allow +Improper styles can only be set for atom_style choices that allow impropers to be defined. Most improper styles are part of the MOLECULE package. They are only diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index 6d28566c66..354c0d486e 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -33,7 +33,7 @@ command. If no improper style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with a ImproperCoeff -section for any improper style. Similarly, any improper\_coeff commands +section for any improper style. Similarly, any improper_coeff commands will only be checked for the improper type number and the rest ignored. Note that the :doc:`improper_coeff ` command must be diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 5a4b5c56ae..c710ddfe5d 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -23,12 +23,12 @@ Syntax kim_param get param_name index_range variables formatarg kim_param set param_name index_range values -.. _formatarg\_options: +.. _formatarg_options: * model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) -* user\_units = the LAMMPS :doc:`units ` style assumed in the LAMMPS input script -* unitarg = *unit\_conversion\_mode* (optional) -* typeargs = atom type to species mapping (one entry per atom type) or *fixed\_types* for models with a preset fixed mapping +* user_units = the LAMMPS :doc:`units ` style assumed in the LAMMPS input script +* unitarg = *unit_conversion_mode* (optional) +* typeargs = atom type to species mapping (one entry per atom type) or *fixed_types* for models with a preset fixed mapping * variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. * formatarg = *list, split, or explicit* (optional): @@ -43,10 +43,10 @@ Syntax *explicit* = returns the values separately in one more more variable names provided as arguments that precede *formatarg*\ . [default for *kim_param*] -* query\_function = name of the OpenKIM web API query function to be used +* query_function = name of the OpenKIM web API query function to be used * queryargs = a series of *keyword=value* pairs that represent the web query; supported keywords depend on the query function -* param\_name = name of a KIM portable model parameter -* index\_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) +* param_name = name of a KIM portable model parameter +* index_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) * values = new value(s) to replace the current value(s) of a KIM portable model parameter Examples @@ -68,14 +68,14 @@ Examples Description """"""""""" -The set of *kim\_commands* provide a high-level wrapper around the +The set of *kim_commands* provide a high-level wrapper around the `Open Knowledgebase of Interatomic Models (OpenKIM) `_ repository of interatomic models (IMs) (potentials and force fields), so that they can be used by LAMMPS scripts. These commands do not implement any computations directly, but rather generate LAMMPS input commands based on the information retrieved from the OpenKIM repository to initialize and activate OpenKIM IMs and query their predictions for use in the LAMMPS script. -All LAMMPS input commands generated and executed by *kim\_commands* are +All LAMMPS input commands generated and executed by *kim_commands* are echoed to the LAMMPS log file. Benefits of Using OpenKIM IMs @@ -99,18 +99,18 @@ Reproducibility Convenience ^^^^^^^^^^^ -* IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the *kim\_init* command documented on this page. -* The *kim\_query* web query tool provides the ability to use the predictions of IMs for supported material properties (computed via `KIM Tests `_) as part of a LAMMPS input script setup and analysis. +* IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the *kim_init* command documented on this page. +* The *kim_query* web query tool provides the ability to use the predictions of IMs for supported material properties (computed via `KIM Tests `_) as part of a LAMMPS input script setup and analysis. * Support is provided for unit conversion between the :doc:`unit style ` used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. -.. _IM\_types: +.. _IM_types: Types of IMs in OpenKIM ----------------------- There are two types of IMs archived in OpenKIM: -.. _PM\_type: +.. _PM_type: 1. The first type is called a *KIM Portable Model* (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface (`KIM API `_) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see `complete list of supported codes `_). 2. The second type is called a *KIM Simulator Model* (SM). A KIM SM is an IM that is implemented natively within a simulation code (\ *simulator*\ ) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. @@ -127,7 +127,7 @@ and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code (\ *MO* for a KIM Portable Model, and *SM* for a KIM Simulator Model) followed by a unique 12-digit code and a 3-digit version identifier. -By convention SM prefixes begin with *Sim\_* to readily identify them. +By convention SM prefixes begin with *Sim_* to readily identify them. .. parsed-literal:: @@ -169,57 +169,57 @@ Using OpenKIM IMs with LAMMPS ----------------------------- Two commands are employed when using OpenKIM IMs, one to select the -IM and perform necessary initialization (*kim\_init*), and the second +IM and perform necessary initialization (*kim_init*), and the second to set up the IM for use by executing any necessary LAMMPS commands -(*kim\_interactions*). Both are required. +(*kim_interactions*). Both are required. See the *examples/kim* directory for example input scripts that use KIM PMs and KIM SMs. -OpenKIM IM Initialization (*kim\_init*) +OpenKIM IM Initialization (*kim_init*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The *kim\_init* mode command must be issued **before** +The *kim_init* mode command must be issued **before** the simulation box is created (normally at the top of the file). This command sets the OpenKIM IM that will be used and may issue additional commands changing LAMMPS default settings that are required for using the selected IM (such as :doc:`units ` or :doc:`atom_style `). If needed, those settings can be overridden, -however, typically a script containing a *kim\_init* command -would not include *units* and *atom\_style* commands. +however, typically a script containing a *kim_init* command +would not include *units* and *atom_style* commands. -The required arguments of *kim\_init* are the *model* name of the +The required arguments of *kim_init* are the *model* name of the IM to be used in the simulation (for an IM archived in OpenKIM this is its `extended KIM ID `_, and -the *user\_units*, which are the LAMMPS :doc:`units style ` used +the *user_units*, which are the LAMMPS :doc:`units style ` used in the input script. (Any dimensioned numerical values in the input script and values read in from files are expected to be in the -*user\_units* system.) +*user_units* system.) The selected IM can be either a :ref:`KIM PM or a KIM SM `. -For a KIM SM, the *kim\_init* command verifies that the SM is designed +For a KIM SM, the *kim_init* command verifies that the SM is designed to work with LAMMPS (and not another simulation code). In addition, the LAMMPS version used for defining the SM and the LAMMPS version being currently run are printed to help diagnose any incompatible changes to input script or command syntax between the two LAMMPS versions. -Based on the selected model *kim\_init* may modify the +Based on the selected model *kim_init* may modify the :doc:`atom_style `. Some SMs have requirements for this setting. If this is the case, then -*atom\_style* will be set to the required style. Otherwise, the value is left -unchanged (which in the absence of an *atom\_style* command in the input script -is the :doc:`default atom\_style value `). +*atom_style* will be set to the required style. Otherwise, the value is left +unchanged (which in the absence of an *atom_style* command in the input script +is the :doc:`default atom_style value `). -Regarding units, the *kim\_init* command behaves in different ways depending +Regarding units, the *kim_init* command behaves in different ways depending on whether or not *unit conversion mode* is activated as indicated by the optional *unitarg* argument. -If unit conversion mode is **not** active, then *user\_units* must +If unit conversion mode is **not** active, then *user_units* must either match the required units of the IM or the IM must be able to adjust its units to match. (The latter is only possible with some KIM PMs; SMs can never adjust their units.) If a match is possible, the LAMMPS :doc:`units ` command is called to set the units to -*user\_units*. If the match fails, the simulation is terminated with +*user_units*. If the match fails, the simulation is terminated with an error. Here is an example of a LAMMPS script to compute the cohesive energy @@ -240,13 +240,13 @@ potential for Al: variable Ec equal (pe/count(all))/${_u_energy} print "Cohesive Energy = ${EcJ} eV" -The above script will end with an error in the *kim\_init* line if the +The above script will end with an error in the *kim_init* line if the IM is changed to another potential for Al that does not work with *metal* -units. To address this *kim\_init* offers the *unit\_conversion\_mode* +units. To address this *kim_init* offers the *unit_conversion_mode* as shown below. -If unit conversion mode *is* active, then *kim\_init* calls the LAMMPS +If unit conversion mode *is* active, then *kim_init* calls the LAMMPS :doc:`units ` command to set the units to the IM's required or -preferred units. Conversion factors between the IM's units and the *user\_units* +preferred units. Conversion factors between the IM's units and the *user_units* are defined for all :doc:`physical quantities ` (mass, distance, etc.). (Note that converting to or from the "lj" unit style is not supported.) These factors are stored as :doc:`internal style variables ` with @@ -293,12 +293,12 @@ Joules regardless of the units of the IM. variable Ec_in_J equal (pe/count(all))/${_u_energy} print "Cohesive Energy = ${Ec_in_J} J" -Note the multiplication by ${\_u_distance} and ${\_u_mass} to convert -from SI units (specified in the *kim\_init* command) to whatever units the -IM uses (metal in this case), and the division by ${\_u_energy} +Note the multiplication by ${_u_distance} and ${_u_mass} to convert +from SI units (specified in the *kim_init* command) to whatever units the +IM uses (metal in this case), and the division by ${_u_energy} to convert from the IM's energy units to SI units (Joule). This script will work correctly for any IM for Al (KIM PM or SM) selected by the -*kim\_init* command. +*kim_init* command. Care must be taken to apply unit conversion to dimensional variables read in from a file. For example, if a configuration of atoms is read in from a @@ -324,17 +324,17 @@ be done to convert the box and all atomic positions to the correct units: all appropriate places in the input script. It is up to the user to do this correctly. -OpenKIM IM Execution (*kim\_interactions*) +OpenKIM IM Execution (*kim_interactions*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The second and final step in using an OpenKIM IM is to execute the -*kim\_interactions* command. This command must be preceded by a *kim\_init* +*kim_interactions* command. This command must be preceded by a *kim_init* command and a command that defines the number of atom types *N* (such as :doc:`create_box `). -The *kim\_interactions* command has one argument *typeargs*\ . This argument +The *kim_interactions* command has one argument *typeargs*\ . This argument contains either a list of *N* chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the -keyword *fixed\_types* for models that have a preset fixed mapping (i.e. +keyword *fixed_types* for models that have a preset fixed mapping (i.e. the mapping between LAMMPS atom types and chemical species is defined by the model and cannot be changed). In the latter case, the user must consult the model documentation to see how many atom types there are and how they @@ -342,7 +342,7 @@ map to the chemical species. For example, consider an OpenKIM IM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, -and the fourth is C, the following *kim\_interactions* command would be used: +and the fourth is C, the following *kim_interactions* command would be used: .. code-block:: LAMMPS @@ -354,11 +354,11 @@ Alternatively, for a model with a fixed mapping the command would be: kim_interactions fixed_types -The *kim\_interactions* command performs all the necessary steps to set up -the OpenKIM IM selected in the *kim\_init* command. The specific actions depend +The *kim_interactions* command performs all the necessary steps to set up +the OpenKIM IM selected in the *kim_init* command. The specific actions depend on whether the IM is a KIM PM or a KIM SM. For a KIM PM, a :doc:`pair_style kim ` command is executed followed by -the appropriate *pair\_coeff* command. For example, for the +the appropriate *pair_coeff* command. For example, for the Ercolessi and Adams (1994) KIM PM for Al set by the following commands: .. code-block:: LAMMPS @@ -369,7 +369,7 @@ Ercolessi and Adams (1994) KIM PM for Al set by the following commands: ... kim_interactions Al -the *kim\_interactions* command executes the following LAMMPS input commands: +the *kim_interactions* command executes the following LAMMPS input commands: .. code-block:: LAMMPS @@ -391,7 +391,7 @@ set by the following commands: ... kim_interactions C H N O -the *kim\_interactions* command executes the following LAMMPS input commands: +the *kim_interactions* command executes the following LAMMPS input commands: .. code-block:: LAMMPS @@ -399,7 +399,7 @@ the *kim\_interactions* command executes the following LAMMPS input commands: pair_coeff * * ffield.reax.rdx C H N O fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq -Note that the files *lmp\_control*, *ffield.reax.rdx* and *param.qeq* +Note that the files *lmp_control*, *ffield.reax.rdx* and *param.qeq* are specific to the Strachan et al. (2003) ReaxFF parameterization and are archived as part of the SM package in OpenKIM. Note also that parameters like cutoff radii and charge tolerances, @@ -408,24 +408,24 @@ SM definition ensuring reproducibility. .. note:: - When using *kim\_init* and *kim\_interactions* to select + When using *kim_init* and *kim_interactions* to select and set up an OpenKIM IM, other LAMMPS commands - for the same functions (such as pair\_style, pair\_coeff, bond\_style, - bond\_coeff, fixes related to charge equilibration, etc.) should normally + for the same functions (such as pair_style, pair_coeff, bond_style, + bond_coeff, fixes related to charge equilibration, etc.) should normally not appear in the input script. -Using OpenKIM Web Queries in LAMMPS (*kim\_query*) +Using OpenKIM Web Queries in LAMMPS (*kim_query*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The *kim\_query* command performs a web query to retrieve the predictions -of an IM set by *kim\_init* for material properties archived in +The *kim_query* command performs a web query to retrieve the predictions +of an IM set by *kim_init* for material properties archived in `OpenKIM `_. .. note:: - The *kim\_query* command must be preceded by a *kim\_init* command. + The *kim_query* command must be preceded by a *kim_init* command. -The syntax for the *kim\_query* command is as follows: +The syntax for the *kim_query* command is as follows: .. code-block:: LAMMPS @@ -438,21 +438,21 @@ For the "list" setting of *formatarg* (or if *formatarg* is not specified), the result is returned as a space-separated list of values in *variable*\ . The *formatarg* keyword "split" separates the result values into -individual variables of the form *prefix\_I*, where *prefix* is set to the -*kim\_query* *variable* argument and *I* ranges from 1 to the number of +individual variables of the form *prefix_I*, where *prefix* is set to the +*kim_query* *variable* argument and *I* ranges from 1 to the number of returned values. The number and order of the returned values is determined by the type of query performed. (Note that the "explicit" setting of -*formatarg* is not supported by *kim\_query*.) +*formatarg* is not supported by *kim_query*.) .. note:: - *kim\_query* only supports queries that return a single result or + *kim_query* only supports queries that return a single result or an array of values. More complex queries that return a JSON structure - are not currently supported. An attempt to use *kim\_query* in such + are not currently supported. An attempt to use *kim_query* in such cases will generate an error. -The second required argument *query\_function* is the name of the -query function to be called (e.g. *get\_lattice\_constant\_cubic*). +The second required argument *query_function* is the name of the +query function to be called (e.g. *get_lattice_constant_cubic*). All following :doc:`arguments ` are parameters handed over to the web query in the format *keyword=value*\ , where *value* is always an array of one or more comma-separated items in brackets. @@ -465,12 +465,12 @@ is available on the OpenKIM webpage at All query functions require the *model* keyword, which identifies the IM whose predictions are being queried. This keyword is automatically - generated by *kim\_query* based on the IM set in *kim\_init* and must not - be specified as an argument to *kim\_query*. + generated by *kim_query* based on the IM set in *kim_init* and must not + be specified as an argument to *kim_query*. .. note:: - Each *query\_function* is associated with a default method (implemented + Each *query_function* is associated with a default method (implemented as a `KIM Test `_) used to compute this property. In cases where there are multiple methods in OpenKIM for computing a property, a *method* keyword can @@ -478,10 +478,10 @@ is available on the OpenKIM webpage at `query documentation `_ to see which methods are available for a given *query function*\ . -*kim\_query* Usage Examples and Further Clarifications +*kim_query* Usage Examples and Further Clarifications ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The data obtained by *kim\_query* commands can be used as part of the setup +The data obtained by *kim_query* commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below. **Define an equilibrium fcc crystal** @@ -494,18 +494,18 @@ or analysis phases of LAMMPS simulations. Some examples are given below. lattice fcc ${a0} ... -The *kim\_query* command retrieves from `OpenKIM `_ +The *kim_query* command retrieves from `OpenKIM `_ the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) potential for the fcc structure and places it in variable *a0*\ . This variable is then used on the next line to set up the -crystal. By using *kim\_query*, the user is saved the trouble and possible +crystal. By using *kim_query*, the user is saved the trouble and possible error of tracking this value down, or of having to perform an energy minimization to find the equilibrium lattice constant. -Note that in *unit\_conversion\_mode* the results obtained from a -*kim\_query* would need to be converted to the appropriate units system. +Note that in *unit_conversion_mode* the results obtained from a +*kim_query* would need to be converted to the appropriate units system. For example, in the above script, the lattice command would need to be -changed to: "lattice fcc ${a0}\*${\_u_distance}". +changed to: "lattice fcc ${a0}\*${_u_distance}". **Define an equilibrium hcp crystal** @@ -521,10 +521,10 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}". basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 ... -In this case the *kim\_query* returns two arguments (since the hexagonal +In this case the *kim_query* returns two arguments (since the hexagonal close packed (hcp) structure has two independent lattice constants). The *formatarg* keyword "split" places the two values into -the variables *latconst\_1* and *latconst\_2*. (These variables are +the variables *latconst_1* and *latconst_2*. (These variables are created if they do not already exist.) For convenience the variables *a0* and *c0* are created in order to make the remainder of the input script more readable. @@ -553,7 +553,7 @@ potential. of the temperature in the above example) it is also possible to pass a tolerance indicating how close to the value is considered a match. If no tolerance is passed a default value is used. If multiple results - are returned (indicating that the tolerance is too large), *kim\_query* + are returned (indicating that the tolerance is too large), *kim_query* will return an error. See the `query documentation `_ to see which numerical arguments and tolerances are available for a @@ -578,7 +578,7 @@ ideal fcc cohesive energy of the atoms in the system obtained from .. note:: - *kim\_query* commands return results archived in + *kim_query* commands return results archived in `OpenKIM `_. These results are obtained using programs for computing material properties (KIM Tests and KIM Test Drivers) that were contributed to OpenKIM. @@ -586,7 +586,7 @@ ideal fcc cohesive energy of the atoms in the system obtained from from these programs are queried is tracked. No other information about the nature of the query or its source is recorded. -Accessing KIM Model Parameters from LAMMPS (*kim\_param*) +Accessing KIM Model Parameters from LAMMPS (*kim_param*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ All IMs are functional forms containing a set of @@ -609,10 +609,10 @@ of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS. Two different mechanisms are provided for accessing IM parameters in these two cases: -* For a KIM PM, the *kim\_param* command can be used to *get* and *set* the values of the PM's parameters as explained below. +* For a KIM PM, the *kim_param* command can be used to *get* and *set* the values of the PM's parameters as explained below. * For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible). -The *kim\_param get* and *kim\_param set* commands provide an interface +The *kim_param get* and *kim_param set* commands provide an interface to access and change the parameters of a KIM PM that "publishes" its parameters and makes them publicly available (see the `KIM API documentation `_ @@ -620,19 +620,19 @@ for details). .. note:: - The *kim\_param get/set* commands must be preceded by *kim\_init*. - The *kim\_param set* command must additionally be preceded by a - *kim\_interactions* command (or alternatively by a *pair\_style kim* - and *pair\_coeff* commands). The *kim\_param set* command may be used wherever a *pair\_coeff* command may occur. + The *kim_param get/set* commands must be preceded by *kim_init*. + The *kim_param set* command must additionally be preceded by a + *kim_interactions* command (or alternatively by a *pair_style kim* + and *pair_coeff* commands). The *kim_param set* command may be used wherever a *pair_coeff* command may occur. -The syntax for the *kim\_param* command is as follows: +The syntax for the *kim_param* command is as follows: .. code-block:: LAMMPS kim_param get param_name index_range variable formatarg kim_param set param_name index_range values -Here, *param\_name* is the name of a KIM PM parameter (which is published +Here, *param_name* is the name of a KIM PM parameter (which is published by the PM and available for access). The specific string used to identify a parameter is defined by the PM. For example, for the `Stillinger--Weber (SW) potential in OpenKIM `_, @@ -641,7 +641,7 @@ the parameter names are *A, B, p, q, sigma, gamma, cutoff, lambda, costheta0*\ . .. note:: The list of all the parameters that a PM exposes for access/mutation are - automatically written to the lammps log file when *kim\_init* is called. + automatically written to the lammps log file when *kim_init* is called. Each published parameter of a KIM PM takes the form of an array of numerical values. The array can contain one element for a single-valued @@ -654,32 +654,32 @@ values used for each pairwise combination of the model's six supported species (this model does not have parameters specific to individual ternary combinations of its supported species). -The *index\_range* argument may either be an integer referring to +The *index_range* argument may either be an integer referring to a specific element within the array associated with the parameter -specified by *param\_name*, or a pair of integers separated by a colon +specified by *param_name*, or a pair of integers separated by a colon that refer to a slice of this array. In both cases, one-based indexing is used to refer to the entries of the array. -The result of a *get* operation for a specific *index\_range* is stored in +The result of a *get* operation for a specific *index_range* is stored in one or more :doc:`LAMMPS string style variables ` as determined by the optional *formatarg* argument :ref:`documented above. ` If not specified, the default for *formatarg* is "explicit" for the -*kim\_param* command. +*kim_param* command. For the case where the result is an array with multiple values -(i.e. *index\_range* contains a range), the optional "split" or "explicit" +(i.e. *index_range* contains a range), the optional "split" or "explicit" *formatarg* keywords can be used to separate the results into multiple variables; see the examples below. -Multiple parameters can be retrieved with a single call to *kim\_param get* +Multiple parameters can be retrieved with a single call to *kim_param get* by repeating the argument list following *get*\ . For a *set* operation, the *values* argument contains the new value(s) -for the element(s) of the parameter specified by *index\_range*. For the case +for the element(s) of the parameter specified by *index_range*. For the case where multiple values are being set, *values* contains a set of values separated by spaces. Multiple parameters can be set with a single call to -*kim\_param set* by repeating the argument list following *set*\ . +*kim_param set* by repeating the argument list following *set*\ . -*kim\_param* Usage Examples and Further Clarifications +*kim_param* Usage Examples and Further Clarifications ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Examples of getting and setting KIM PM parameters with further @@ -722,9 +722,9 @@ determined by the *formatarg* argument. In this case, *formatarg* is not specified and therefore the default "explicit" mode is used. (The behavior would be the same if the word -*explicit* were added after *LAM\_TeSe*.) Elements 7, 8 and 9 of parameter +*explicit* were added after *LAM_TeSe*.) Elements 7, 8 and 9 of parameter lambda retrieved by the *get* operation are placed in the LAMMPS variables -*LAM\_TeTe*, *LAM\_TeZn* and *LAM\_TeSe*, respectively. +*LAM_TeTe*, *LAM_TeZn* and *LAM_TeSe*, respectively. .. note:: @@ -754,7 +754,7 @@ The result of the *get* operation is stored in the LAMMPS variable *LAMS* as a string containing the three retrieved values separated by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an *index* variable to access the values one at a time within a loop -as shown in the example. At each iteration of the loop *LAM\_VALUE* +as shown in the example. At each iteration of the loop *LAM_VALUE* contains the current value of lambda. .. code-block:: LAMMPS @@ -765,7 +765,7 @@ contains the current value of lambda. In this case, the "split" mode of *formatarg* is used. The three values retrieved by the *get* operation are stored in -the three LAMMPS variables *LAM\_15*, *LAM\_16* and *LAM\_17*. +the three LAMMPS variables *LAM_15*, *LAM_16* and *LAM_17*. The provided name "LAM" is used as prefix and the location in the lambda array is appended to create the variable names. @@ -792,8 +792,8 @@ operation will return the new value that was set. For example: ... print "original gamma = ${ORIG_GAMMA}, new gamma = ${NEW_GAMMA}" -Here, *ORIG\_GAMMA* will contain the original gamma value for the SW -potential, while *NEW\_GAMMA* will contain the value 2.6. +Here, *ORIG_GAMMA* will contain the original gamma value for the SW +potential, while *NEW_GAMMA* will contain the value 2.6. **Setting multiple scalar parameters with a single call** @@ -842,7 +842,7 @@ and enables open source efforts like OpenKIM to function. Restrictions """""""""""" -The set of *kim\_commands* is part of the KIM package. It is only enabled if +The set of *kim_commands* is part of the KIM package. It is only enabled if LAMMPS is built with that package. A requirement for the KIM package, is the KIM API library that must be downloaded from the `OpenKIM website `_ and installed before @@ -850,7 +850,7 @@ LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package is a dependency that is automatically downloaded and installed. See the KIM section of the :doc:`Packages details ` for details. -Furthermore, when using *kim\_commands* to run KIM SMs, any packages required +Furthermore, when using *kim_commands* to run KIM SMs, any packages required by the native potential being used or other commands or fixes that it invokes must be installed. diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index ac0b0e8aad..afbe1b0043 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -324,18 +324,18 @@ The *tolerance* option affects how the *accuracy* specified with the The following values may be used: * energy = absolute accuracy in total Coulombic energy -* energy\_rel = relative accuracy in total Coulombic energy +* energy_rel = relative accuracy in total Coulombic energy * potential = absolute accuracy in total Coulombic potential -* potential\_rel = relative accuracy in total Coulombic potential +* potential_rel = relative accuracy in total Coulombic potential * field = absolute accuracy in electric field -* field\_rel = relative accuracy in electric field +* field_rel = relative accuracy in electric field -The values with suffix \_rel indicate the tolerance is a relative +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. +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. 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 @@ -343,10 +343,10 @@ of 1e-3 would mean that the result has to be between 999999.999 and 1000000.001, which would be equivalent to a relative tolerance of 1e-9. -The energy and energy\_rel values, set a tolerance based on the total -Coulombic energy of the system. The potential and potential\_rel set a +The energy and energy_rel values, set a tolerance based on the total +Coulombic energy of the system. The potential and potential_rel set a tolerance based on the per-atom Coulombic energy. The field and -field\_rel tolerance types set a tolerance based on the electric field +field_rel tolerance types set a tolerance based on the electric field values computed by ScaFaCoS. Since per-atom forces are derived from the per-atom electric field, this effectively sets a tolerance on the forces, similar to other LAMMPS KSpace styles, as explained on the @@ -355,7 +355,7 @@ forces, similar to other LAMMPS KSpace styles, as explained on the Note that not all ScaFaCoS solvers support all tolerance types. These are the allowed values for each method: -* fmm = energy and energy\_rel +* fmm = energy and energy_rel * p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) * p3m = field * ewald = field @@ -365,7 +365,7 @@ If the tolerance type is not changed, the default values for the tolerance type are the first values in the above list, e.g. energy is the default tolerance type for the fmm solver. -The *fmm\_tuning* option is only relevant when using the FMM method. +The *fmm_tuning* option is only relevant when using the FMM method. It activates (value=1) or deactivates (value=0) an internal tuning mechanism for the FMM solver. The tuning operation runs sequentially and can be very time-consuming. Usually it is not needed for systems @@ -452,7 +452,7 @@ ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order = order/disp = 7. For scafacos settings, the scafacos tolerance option depends on the method chosen, as documented above. The -scafacos fmm\_tuning default = 0. +scafacos fmm_tuning default = 0. ---------- diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 786b048b04..57cd51d549 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -216,13 +216,13 @@ parameters and how to choose them is described in .. note:: All of the PPPM styles can be used with single-precision FFTs by - using the compiler switch -DFFT\_SINGLE for the FFT\_INC setting in your + using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your low-level Makefile. This setting also changes some of the PPPM operations (e.g. mapping charge to mesh and interpolating electric fields to particles) to be performed in single precision. This option can speed-up long-range calculations, particularly in parallel or on - GPUs. The use of the -DFFT\_SINGLE flag is discussed on the :doc:`Build settings ` doc page. MSM does not currently support - the -DFFT\_SINGLE compiler switch. + GPUs. The use of the -DFFT_SINGLE flag is discussed on the :doc:`Build settings ` doc page. MSM does not currently support + the -DFFT_SINGLE compiler switch. ---------- @@ -274,7 +274,7 @@ See details on :ref:`this page `. Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all Coulombic interactions, both short- and long-range. Thus you should - NOT use a Coulombic pair style when using kspace\_style scafacos. This + NOT use a Coulombic pair style when using kspace_style scafacos. This also means the total Coulombic energy (short- and long-range) will be tallied for :doc:`thermodynamic output ` command as part of the *elong* keyword; the *ecoul* keyword will be zero. @@ -377,7 +377,7 @@ produce the same results, except for round-off and precision issues. More specifically, the *pppm/gpu* style performs charge assignment and force interpolation calculations on the GPU. These processes are performed either in single or double precision, depending on whether -the -DFFT\_SINGLE setting was specified in your low-level Makefile, as +the -DFFT_SINGLE setting was specified in your low-level Makefile, as discussed above. The FFTs themselves are still calculated on the CPU. If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM calculation can be performed concurrently on the GPU while other @@ -406,8 +406,8 @@ interactions. Vacuum boundary conditions are not currently supported. The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support non-orthogonal (triclinic symmetry) simulation boxes. However, -triclinic simulation cells may not yet be supported by suffix versions -of these styles. +triclinic simulation cells may not yet be supported by all suffix +versions of these styles. All of the kspace styles are part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index c5452e21f4..a01aab173d 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -108,25 +108,25 @@ all atoms in the system: For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. -Keywords *alpha\_damp* and *discrete\_factor* only make sense when +Keywords *alpha_damp* and *discrete_factor* only make sense when a :doc:`min_spin ` command is declared. -Keyword *alpha\_damp* defines an analog of a magnetic Gilbert +Keyword *alpha_damp* defines an analog of a magnetic Gilbert damping. It defines a relaxation rate toward an equilibrium for a given magnetic system. -Keyword *discrete\_factor* defines a discretization factor for the +Keyword *discrete_factor* defines a discretization factor for the adaptive timestep used in the *spin* minimization. See :doc:`min_spin ` for more information about those quantities. The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs* styles can be specified via the *line* keyword. The -*spin\_cubic* and *spin\_none* keywords only make sense when one of those two -minimization styles is declared. The *spin\_cubic* performs the line +*spin_cubic* and *spin_none* keywords only make sense when one of those two +minimization styles is declared. The *spin_cubic* performs the line search based on a cubic interpolation of the energy along the search -direction. The *spin\_none* keyword deactivates the line search -procedure. The *spin\_none* is a default value for *line* keyword for +direction. The *spin_none* keyword deactivates the line search +procedure. The *spin_none* is a default value for *line* keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of *spin/lbfgs* can be -more robust if *spin\_cubic* line search is used. +more robust if *spin_cubic* line search is used. The Newton *integrator* used for *fire* minimization can be selected to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity @@ -163,7 +163,7 @@ to the *fire/old* style by using the following set of parameters: Restrictions """""""""""" -For magnetic GNEB calculations, only *spin\_none* value for *line* +For magnetic GNEB calculations, only *spin_none* value for *line* keyword can be used when minimization styles *spin/cg* and *spin/lbfgs* are employed. See :doc:`neb/spin ` for more explanation. @@ -178,8 +178,8 @@ Default The option defaults are dmax = 0.1, line = quadratic and norm = two. For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option -defaults are alpha\_damp = 1.0, discrete\_factor = 10.0, line = -spin\_none, and norm = euclidean. +defaults are alpha_damp = 1.0, discrete_factor = 10.0, line = +spin_none, and norm = euclidean. For the *fire* style, the option defaults are integrator = eulerimplicit, tmax = 10.0, tmin = 0.02, delaystep = 20, dtgrow = 1.1, diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 2474493fe8..46fd08b838 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -41,7 +41,7 @@ timestep, according to: with :math:`\lambda` a damping coefficient (similar to a Gilbert damping). :math:`\lambda` can be defined by setting the -*alpha\_damp* keyword with the :doc:`min_modify ` command. +*alpha_damp* keyword with the :doc:`min_modify ` command. The minimization procedure solves this equation using an adaptive timestep. The value of this timestep is defined @@ -56,15 +56,15 @@ with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precess frequency in the system (across all processes, and across all replicas if a spin/neb calculation is performed). -:math:`\kappa` defines a discretization factor *discrete\_factor* for -the definition of this timestep. *discrete\_factor* can be defined with +:math:`\kappa` defines a discretization factor *discrete_factor* for +the definition of this timestep. *discrete_factor* can be defined with the :doc:`min_modify ` command. Style *spin/cg* defines an orthogonal spin optimization (OSO) combined to a conjugate gradient (CG) algorithm. The :doc:`min_modify ` command can be used to couple the *spin/cg* to a line search procedure, and to modify the -discretization factor *discrete\_factor*. +discretization factor *discrete_factor*. By default, style *spin/cg* does not employ the line search procedure and uses the adaptive time-step technique in the same way as style *spin*\ . @@ -74,12 +74,12 @@ algorithm. By default, style *spin/lbfgs* does not employ line search procedure. If the line search procedure is not used then the discrete factor defines the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*. The default value for Kappa is 10. The -*spin\_cubic* line search option can improve the convergence of the +*spin_cubic* line search option can improve the convergence of the *spin/lbfgs* algorithm. The :doc:`min_modify ` command can be used to activate the line search procedure, and to modify the -discretization factor *discrete\_factor*. +discretization factor *discrete_factor*. For more information about styles *spin/cg* and *spin/lbfgs*\ , see their implementation reported in :ref:`(Ivanov) `. @@ -110,8 +110,8 @@ Related commands Default """"""" -The option defaults are *alpha\_damp* = 1.0, *discrete\_factor* = -10.0, *line* = spin\_none and *norm* = euclidean. +The option defaults are *alpha_damp* = 1.0, *discrete_factor* = +10.0, *line* = spin_none and *norm* = euclidean. ---------- diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index f6839c57df..32e6d846ae 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -242,7 +242,7 @@ on each atom in the molecule is 0.0. * diam = diameter of atom This section is only allowed for :doc:`atom styles ` that -support finite-size spherical particles, e.g. atom\_style sphere. If +support finite-size spherical particles, e.g. atom_style sphere. If not listed, the default diameter of each atom in the molecule is 1.0. ---------- diff --git a/doc/src/neb.rst b/doc/src/neb.rst index bd08ae3d1d..acb157e2ec 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -374,24 +374,24 @@ restart the calculation from an intermediate point with altered parameters. There are 2 Python scripts provided in the tools/python directory, -neb\_combine.py and neb\_final.py, which are useful in analyzing output +neb_combine.py and neb_final.py, which are useful in analyzing output from a NEB calculation. Assume a NEB simulation with M replicas, and the NEB atoms labeled with a specific atom type. -The neb\_combine.py script extracts atom coords for the NEB atoms from +The neb_combine.py script extracts atom coords for the NEB atoms from all M dump files and creates a single dump file where each snapshot contains the NEB atoms from all the replicas and one copy of non-NEB atoms from the first replica (presumed to be identical in other replicas). This can be visualized/animated to see how the NEB atoms relax as the NEB calculation proceeds. -The neb\_final.py script extracts the final snapshot from each of the M +The neb_final.py script extracts the final snapshot from each of the M dump files to create a single dump file with M snapshots. This can be visualized to watch the system make its transition over the energy barrier. To illustrate, here are images from the final snapshot produced by the -neb\_combine.py script run on the dump files produced by the two +neb_combine.py script run on the dump files produced by the two example input scripts in examples/neb. Click on them to see a larger image. diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index cbeca25327..10b08f674b 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -369,7 +369,7 @@ calculation fails to converge properly to the MEP, and you wish to restart the calculation from an intermediate point with altered parameters. -A c file script in provided in the tool/spin/interpolate\_gneb +A c file script in provided in the tool/spin/interpolate_gneb directory, that interpolates the MEP given the information provided by the *verbose* output option (as detailed in Appendix D of :ref:`(BessarabA) `). @@ -383,7 +383,7 @@ This command can only be used if LAMMPS was built with the SPIN package. See the :doc:`Build package ` doc page for more info. -For magnetic GNEB calculations, only the *spin\_none* value for the +For magnetic GNEB calculations, only the *spin_none* value for the *line* keyword can be used when minimization styles *spin/cg* and *spin/lbfgs* are employed. diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index fea38e5e50..74b4572b95 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -159,7 +159,7 @@ turning off bond interactions. long-range solver treats the interaction. This is done correctly for pairwise interactions that are excluded (or weighted) via the :doc:`special_bonds ` command. But it is not done for - interactions that are excluded via these neigh\_modify exclude options. + interactions that are excluded via these neigh_modify exclude options. The *page* and *one* options affect how memory is allocated for the neighbor lists. For most simulations the default settings for these diff --git a/doc/src/package.rst b/doc/src/package.rst index 059dfba957..609216206d 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -264,11 +264,11 @@ GPUs from different vendors or for CPU based accelerator support). In LAMMPS only one platform can be active at a time and by default the first platform with an accelerator is selected. This is equivalent to using a platform ID of -1. The platform ID is a number corresponding -to the output of the ocl\_get\_devices tool. The platform ID is passed +to the output of the ocl_get_devices tool. The platform ID is passed to the GPU library, by prefixing the *device* keyword with that number separated by a colon. For CUDA, the *device* keyword is ignored. Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA -Fermi, AMD Cypress, Intel x86\_64 CPU, Intel Xeon Phi, or a generic device. +Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device. More devices may be added later. The default device type can be specified when building LAMMPS with the GPU library, via setting a variable in the lib/gpu/Makefile that is used. @@ -278,19 +278,19 @@ In addition, a device type *custom* is available, which is followed by from the package command. It can be combined with the (colon separated) platform id. The individual settings are: -* MEM\_THREADS -* THREADS\_PER\_ATOM -* THREADS\_PER\_CHARGE -* BLOCK\_PAIR -* MAX\_SHARED\_TYPES -* BLOCK\_NBOR\_BUILD -* BLOCK\_BIO\_PAIR -* BLOCK\_ELLIPSE -* WARP\_SIZE -* PPPM\_BLOCK\_1D -* BLOCK\_CELL\_2D -* BLOCK\_CELL\_ID -* MAX\_BIO\_SHARED\_TYPES +* MEM_THREADS +* THREADS_PER_ATOM +* THREADS_PER_CHARGE +* BLOCK_PAIR +* MAX_SHARED_TYPES +* BLOCK_NBOR_BUILD +* BLOCK_BIO_PAIR +* BLOCK_ELLIPSE +* WARP_SIZE +* PPPM_BLOCK_1D +* BLOCK_CELL_2D +* BLOCK_CELL_ID +* MAX_BIO_SHARED_TYPES The *blocksize* keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) @@ -333,10 +333,10 @@ The *Nthread* value for the *omp* keyword sets the number of OpenMP threads allocated for each MPI task. Setting *Nthread* = 0 (the default) instructs LAMMPS to use whatever value is the default for the given OpenMP environment. This is usually determined via the -*OMP\_NUM\_THREADS* environment variable or the compiler runtime, which +*OMP_NUM_THREADS* environment variable or the compiler runtime, which is usually a value of 1. -For more details, including examples of how to set the OMP\_NUM\_THREADS +For more details, including examples of how to set the OMP_NUM_THREADS environment variable, see the discussion of the *Nthreads* setting on this doc page for the "package omp" command. Nthreads is a required argument for the USER-OMP package. Its meaning is exactly the same @@ -368,7 +368,7 @@ force calculation. The *lrt* keyword can be used to enable "Long Range Thread (LRT)" mode. It can take a value of *yes* to enable and *no* to disable. LRT mode generates an extra thread (in addition to any OpenMP threads -specified with the OMP\_NUM\_THREADS environment variable or the *omp* +specified with the OMP_NUM_THREADS environment variable or the *omp* keyword). The extra thread is dedicated for performing part of the :doc:`PPPM solver ` computations and communications. This can improve parallel performance on processors supporting @@ -381,7 +381,7 @@ ignored and no extra threads are generated. Enabling LRT will replace the :doc:`run_style ` with the *verlet/lrt/intel* style that is identical to the default *verlet* style aside from supporting the LRT feature. This feature requires setting the pre-processor flag --DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS. +-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. The *balance* keyword sets the fraction of :doc:`pair style ` work offloaded to the co-processor for split values between 0.0 and 1.0 inclusive. While this fraction of work is @@ -421,7 +421,7 @@ with 16 threads, for a total of 128. Note that the default settings for *tpc* and *tptask* are fine for most problems, regardless of how many MPI tasks you assign to a Phi. -The *no\_affinity* keyword will turn off automatic setting of core +The *no_affinity* keyword will turn off automatic setting of core affinity for MPI tasks and OpenMP threads on the host when using offload to a co-processor. Affinity settings are used when possible to prevent MPI tasks and OpenMP threads from being on separate NUMA @@ -538,7 +538,7 @@ keywords are set to *device*\ , the value for these *comm* keywords will be automatically changed to *host*\ . This setting has no effect if not running on GPUs or if using only one MPI rank. CUDA-aware MPI is available for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the -"MV2\_USE\_CUDA" environment variable is set to "1", CrayMPI, and IBM +"MV2_USE_CUDA" environment variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu" flag is used. ---------- @@ -557,10 +557,10 @@ tasks \* threads/task should not exceed the physical number of cores Setting *Nthread* = 0 instructs LAMMPS to use whatever value is the default for the given OpenMP environment. This is usually determined -via the *OMP\_NUM\_THREADS* environment variable or the compiler +via the *OMP_NUM_THREADS* environment variable or the compiler runtime. Note that in most cases the default for OpenMP capable compilers is to use one thread for each available CPU core when -*OMP\_NUM\_THREADS* is not explicitly set, which can lead to poor +*OMP_NUM_THREADS* is not explicitly set, which can lead to poor performance. Here are examples of how to set the environment variable when @@ -576,7 +576,7 @@ or you can set it permanently in your shell's start-up script. All three of these examples use a total of 4 CPU cores. Note that different MPI implementations have different ways of passing -the OMP\_NUM\_THREADS environment variable to all MPI processes. The +the OMP_NUM_THREADS environment variable to all MPI processes. The 2nd example line above is for MPICH; the 3rd example line with -x is for OpenMPI. Check your MPI documentation for additional details. diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index fb8394a31b..6c4796fb85 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -46,7 +46,7 @@ and quadruple distortions of the local atomic environment which extend the original EAM framework by introducing angular forces. Note that unlike for other potentials, cutoffs for ADP potentials are -not set in the pair\_style or pair\_coeff command; they are specified in +not set in the pair_style or pair_coeff command; they are specified in the ADP potential files themselves. Likewise, the ADP potential files list atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. @@ -61,10 +61,10 @@ command to specify them. ---------- -Only a single pair\_coeff command is used with the *adp* style which +Only a single pair_coeff command is used with the *adp* style which specifies an extended DYNAMO *setfl* file, which contains information for :math:`M` elements. These are mapped to LAMMPS atom types by specifying :math:`N` -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where :math:`N` is the number of LAMMPS atom types: * filename @@ -78,7 +78,7 @@ potentials directory of the LAMMPS distribution, is an extended *setfl* file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use -the following pair\_coeff command: +the following pair_coeff command: .. code-block:: LAMMPS @@ -105,13 +105,13 @@ command for further details on the *setfl* format. * lines 1,2,3 = comments (ignored) * line 4: :math:`N_{\text{elements}}` Element1 Element2 ... ElementN -* line 5: :math:`N_\rho`, :math:`d_\rho`, :math:`N_r`, :math:`d_r`, cutoff +* line 5: :math:`N_{\rho}`, :math:`d_{\rho}`, :math:`N_r`, :math:`d_r`, cutoff Following the 5 header lines are :math:`N_{\text{elements}}` sections, one for each element, each with the following format: * line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -* embedding function :math:`F(\rho)` (:math:`N_\rho` values) +* embedding function :math:`F(\rho)` (:math:`N_{\rho}` values) * density function :math:`\rho(r)` (:math:`N_r` values) Following the :math:`N_{\text{elements}}` sections, :math:`N_r` values for each pair potential @@ -164,7 +164,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair\_style and pair\_coeff commands in +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index c0453d9130..2023e655f4 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -48,11 +48,11 @@ of the method is to map the atomic environment numerically into a fingerprint, and use machine learning methods to create a mapping to the vectorial atomic forces. -Only a single pair\_coeff command is used with the *agni* style which +Only a single pair_coeff command is used with the *agni* style which specifies an AGNI potential file containing the parameters of the force field for the needed elements. These are mapped to LAMMPS atom types by specifying :math:`N` additional arguments after the filename in the -pair\_coeff command, where :math:`N` is the number of LAMMPS atom types: +pair_coeff command, where :math:`N` is the number of LAMMPS atom types: * filename * :math:`N` element names = mapping of AGNI elements to atom types @@ -91,7 +91,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index dd113b8f4b..d7fc9a9c07 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -36,9 +36,9 @@ Syntax * style = *airebo* or *airebo/morse* or *rebo* * cutoff = LJ or Morse cutoff (:math:`\sigma` scale factor) (AIREBO and AIREBO-M only) -* LJ\_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional) -* TORSION\_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) -* cutoff\_min = Start of the transition region of cutoff (:math:`\sigma` scale factor) (AIREBO and AIREBO-M only, optional) +* LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional) +* TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) +* cutoff_min = Start of the transition region of cutoff (:math:`\sigma` scale factor) (AIREBO and AIREBO-M only, optional) Examples """""""" @@ -87,7 +87,7 @@ The AIREBO potential consists of three terms: \sum_{k \neq i,j} \sum_{l \neq i,j,k} E^{\text{TORSION}}_{kijl} \right] \\ By default, all three terms are included. For the *airebo* style, if -the first two optional flag arguments to the pair\_style command are +the first two optional flag arguments to the pair_style command are included, the LJ and torsional terms can be turned off. Note that both or neither of the flags must be included. If both of the LJ an torsional terms are turned off, it becomes the 2nd-generation REBO @@ -125,9 +125,9 @@ factor of 3.0 (the argument in pair_style), the resulting :math:`E^{\text{LJ}}` would be 10.2 Angstroms. By default, the longer-ranged interaction is smoothly switched off -between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff\_min* in addition +between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff_min* in addition to *cutoff*\ , the switching can be configured to take place between -*cutoff\_min* and *cutoff*\ . *cutoff\_min* can only be specified if all +*cutoff_min* and *cutoff*\ . *cutoff_min* can only be specified if all optional arguments are given. The :math:`E^{\text{TORSION}}` term is an explicit 4-body potential that describes diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index edb6444c24..902e07a80d 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -11,7 +11,7 @@ Syntax pair_style atm cutoff cutoff_triple * cutoff = cutoff for each pair in 3-body interaction (distance units) -* cutoff\_triple = additional cutoff applied to product of 3 pairwise distances (distance units) +* cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) Examples """""""" diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 5ff884e790..701c45849e 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -12,7 +12,7 @@ Syntax * Rc = global cutoff, -1 means cutoff of half the shortest box length * zero or more keyword/value pairs may be appended -* keyword = *hartree* or *dproduct* or *uhf* or *free* or *pbc* or *fix* or *harm* or *ermscale* or *flex\_press* +* keyword = *hartree* or *dproduct* or *uhf* or *free* or *pbc* or *fix* or *harm* or *ermscale* or *flex_press* .. parsed-literal:: @@ -49,7 +49,7 @@ basic formulas here. Could be links to other documents. Rc is the cutoff. -The pair\_style command allows for several optional keywords +The pair_style command allows for several optional keywords to be specified. The *hartree*\ , *dproduct*\ , and *uhf* keywords specify the form of the @@ -77,7 +77,7 @@ The *ermscale* keyword specifies a unitless scaling factor between the electron masses and the width variable mass. More details needed. -If the *flex\_press* keyword is used, then a contribution from the +If the *flex_press* keyword is used, then a contribution from the electrons is added to the total virial and pressure of the system. This potential is designed to be used with :doc:`atom_style wavepacket ` definitions, in order to handle the @@ -93,7 +93,7 @@ commands, or by mixing as described below: For *awpmd/cut*\ , the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value -specified in the pair\_style command is used. +specified in the pair_style command is used. ---------- @@ -102,7 +102,7 @@ specified in the pair\_style command is used. The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for this pair style. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -123,5 +123,5 @@ Related commands Default """"""" -These are the defaults for the pair\_style keywords: *hartree* for the +These are the defaults for the pair_style keywords: *hartree* for the initial wave function, *free* for the wave packet width. diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index b71661ea78..f234366eae 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -90,7 +90,7 @@ for this pair style. This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 152dd9a996..baba67bf7f 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -54,7 +54,7 @@ between two particles are defined with respect to the separation of their respective rounded surfaces, not by the separation of the vertices and edges themselves. -This means that the specified cutoff in the pair\_style command is the +This means that the specified cutoff in the pair_style command is the cutoff distance, :math:`r_c`, for the surface separation, :math:`\delta_n` (see figure below). This is the distance at which two particles no longer interact. If :math:`r_c` is specified as 0.0, then it is a contact-only @@ -121,8 +121,8 @@ above for force versus surface separation, for :math:`\delta_n < 0` and This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index ac4d578c30..72e94db8c9 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -54,7 +54,7 @@ and energies between two particles are defined with respect to the separation of their respective rounded surfaces, not by the separation of the vertices, edges, and faces themselves. -This means that the specified cutoff in the pair\_style command is the +This means that the specified cutoff in the pair_style command is the cutoff distance, :math:`r_c`, for the surface separation, :math:`\delta_n` (see figure below). This is the distance at which two particles no longer interact. If :math:`r_c` is specified as 0.0, then it is a contact-only @@ -116,7 +116,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. -Thus, you need to re-specify the pair\_style and pair\_coeff +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 31a5a369d7..ce7b69f41f 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -36,15 +36,15 @@ quantum mechanical theory incorporating both :math:`\sigma` and :math:`\pi` bond By analytically deriving the BOP from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is similar to the original BOP -developed by Pettifor (:ref:`Pettifor\_1 `, -:ref:`Pettifor\_2 `, :ref:`Pettifor\_3 `) and later updated +developed by Pettifor (:ref:`Pettifor_1 `, +:ref:`Pettifor_2 `, :ref:`Pettifor_3 `) and later updated by Murdick, Zhou, and Ward (:ref:`Murdick `, :ref:`Ward `). Currently, BOP potential files for these systems are provided with LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with only a subset of these elements, including a single element (e.g. C or Cu or Al or Ga or Zn or CdZn), can also be modeled by using the appropriate alloy file and assigning all atom types to the -single element or subset of elements via the pair\_coeff command, as +single element or subset of elements via the pair_coeff command, as discussed below. The BOP potential consists of three terms: @@ -58,7 +58,7 @@ representing the repulsion between a pair of ion cores, :math:`\beta_{\sigma,ij}(r_{ij})` and :math:`\beta_{\sigma,ij}(r_{ij})` are respectively sigma and :math:`\pi` bond integrals, :math:`\Theta_{\sigma,ij}` and :math:`\Theta_{\pi,ij}` are :math:`\sigma` and :math:`\pi` -bond-orders, and U\_prom is the promotion energy for sp-valent systems. +bond-orders, and U_prom is the promotion energy for sp-valent systems. The detailed formulas for this potential are given in Ward (:ref:`Ward `); here we provide only a brief description. @@ -84,7 +84,7 @@ efficient potential formulation suitable for MD simulations, the derived BOP only takes (and retains) the first two levels of the recursive representations for both the :math:`\sigma` and the :math:`\pi` bond-orders. Bond-order terms can be understood in terms of molecular orbital hopping paths -based upon the Cyrot-Lackmann theorem (:ref:`Pettifor\_1 `). +based upon the Cyrot-Lackmann theorem (:ref:`Pettifor_1 `). The :math:`\sigma` bond-order with a half-full valence shell is used to interpolate the bond-order expression that incorporated explicit valance band filling. This :math:`\pi` bond-order expression also contains also contains @@ -96,7 +96,7 @@ length 4. This enables the incorporation of dihedral angles effects. .. note:: Note that unlike for other potentials, cutoffs for BOP - potentials are not set in the pair\_style or pair\_coeff command; they + potentials are not set in the pair_style or pair_coeff command; they are specified in the BOP potential files themselves. Likewise, the BOP potential files list atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. Note that for BOP @@ -106,7 +106,7 @@ length 4. This enables the incorporation of dihedral angles effects. :doc:`pair_coeff ` command to read the BOP potential file. -One option can be specified as a keyword with the pair\_style command. +One option can be specified as a keyword with the pair_style command. The *save* keyword gives you the option to calculate in advance and store a set of distances, angles, and derivatives of angles. The @@ -118,10 +118,10 @@ system configuration. ---------- -Only a single pair\_coeff command is used with the *bop* style which +Only a single pair_coeff command is used with the *bop* style which specifies a BOP potential file, with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -130,7 +130,7 @@ where N is the number of LAMMPS atom types: As an example, imagine the CdTe.bop file has BOP values for Cd and Te. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Cd, and the 4th to be Te, you would use the following -pair\_coeff command: +pair_coeff command: .. parsed-literal:: @@ -143,8 +143,8 @@ element in the BOP file. The final Te argument maps LAMMPS atom type BOP files in the *potentials* directory of the LAMMPS distribution have a ".bop" suffix. The potentials are in tabulated form containing -pre-tabulated pair functions for phi\_ij(r\_ij), beta\_(sigma,ij)(r\_ij), -and beta\_pi,ij)(r\_ij). +pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij), +and beta_pi,ij)(r_ij). The parameters/coefficients format for the different kinds of BOP files are given below with variables matching the formulation of Ward @@ -170,89 +170,89 @@ the tabulated functions are given. * Line 1: nr, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; nBOt is the number - of divisions for the tabulated values of THETA\_(S,ij) -* Line 2: delta\_1-delta\_7 (if all are not used in the particular + of divisions for the tabulated values of THETA_(S,ij) +* Line 2: delta_1-delta_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e\_1-e\_N containing p\_pi. +Following this N lines for e_1-e_N containing p_pi. -* Line 3: p\_pi (for e\_1) -* Line 4: p\_pi (for e\_2 and continues to e\_N) +* Line 3: p_pi (for e_1) +* Line 4: p_pi (for e_2 and continues to e_N) The next section contains several pair constants for the number of -interaction types e\_i-e\_j, with i=1->N, j=i->N +interaction types e_i-e_j, with i=1->N, j=i->N -* Line 1: r\_cut (for e\_1-e\_1 interactions) -* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi -* Line 3: delta\_sigma, delta\_pi -* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of +* Line 1: r_cut (for e_1-e_1 interactions) +* Line 2: c_sigma, a_sigma, c_pi, a_pi +* Line 3: delta_sigma, delta_pi +* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N +e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -* Line 1: g\_(sigma0), g\_(sigma1), g\_(sigma2) (These are coefficients for - g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction. :ref:`Ward ` +* Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for + g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. :ref:`Ward ` contains the full expressions for the constants as functions of - b\_(sigma,ijk), p\_(sigma,ijk), u\_(sigma,ijk)) -* Line 2: g\_(sigma0), g\_(sigma1), g\_(sigma2) (for e\_1-e\_1-e\_2) + b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) +* Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) The next section contains a block for each interaction type for the -phi\_ij(r\_ij). Each block has nr entries with 5 entries per line. +phi_ij(r_ij). Each block has nr entries with 5 entries per line. -* Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e\_1-e\_1 +* Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1 interaction type) * Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues until nr) * ... -* Line nr/5\_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the - e\_1-e\_1 interaction type) +* Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the + e_1-e_1 interaction type) The next section contains a block for each interaction type for the -beta\_(sigma,ij)(r\_ij). Each block has nr entries with 5 entries per +beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per line. -* Line 1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3), beta\_sigma(r4), - beta\_sigma(r5) (for the e\_1-e\_1 interaction type) -* Line 2: beta\_sigma(r6), beta\_sigma(r7), beta\_sigma(r8), beta\_sigma(r9), - beta\_sigma(r10) (this continues until nr) +* Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4), + beta_sigma(r5) (for the e_1-e_1 interaction type) +* Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9), + beta_sigma(r10) (this continues until nr) * ... -* Line nr/5+1: beta\_sigma(r1), beta\_sigma(r2), beta\_sigma(r3), - beta\_sigma(r4), beta\_sigma(r5) (for the e\_1-e\_2 interaction type) +* Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), + beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) The next section contains a block for each interaction type for -beta\_(pi,ij)(r\_ij). Each block has nr entries with 5 entries per line. +beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. -* Line 1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4), beta\_pi(r5) - (for the e\_1-e\_1 interaction type) -* Line 2: beta\_pi(r6), beta\_pi(r7), beta\_pi(r8), beta\_pi(r9), - beta\_pi(r10) (this continues until nr) +* Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5) + (for the e_1-e_1 interaction type) +* Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9), + beta_pi(r10) (this continues until nr) * ... -* Line nr/5+1: beta\_pi(r1), beta\_pi(r2), beta\_pi(r3), beta\_pi(r4), - beta\_pi(r5) (for the e\_1-e\_2 interaction type) +* Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), + beta_pi(r5) (for the e_1-e_2 interaction type) The next section contains a block for each interaction type for the -THETA\_(S,ij)((THETA\_(sigma,ij))\^(1/2), f\_(sigma,ij)). Each block has +THETA_(S,ij)((THETA_(sigma,ij))\^(1/2), f_(sigma,ij)). Each block has nBOt entries with 5 entries per line. -* Line 1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3), - THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type) -* Line 2: THETA\_(S,ij)(r6), THETA\_(S,ij)(r7), THETA\_(S,ij)(r8), - THETA\_(S,ij)(r9), THETA\_(S,ij)(r10) (this continues until nBOt) +* Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), + THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) +* Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8), + THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) * ... -* Line nBOt/5+1: THETA\_(S,ij)(r1), THETA\_(S,ij)(r2), THETA\_(S,ij)(r3), - THETA\_(S,ij)(r4), THETA\_(S,ij)(r5) (for the e\_1-e\_2 interaction type) +* Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), + THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) -The next section contains a block of N lines for e\_1-e\_N +The next section contains a block of N lines for e_1-e_N -* Line 1: delta\^mu (for e\_1) -* Line 2: delta\^mu (for e\_2 and repeats to e\_N) +* Line 1: delta\^mu (for e_1) +* Line 2: delta\^mu (for e_2 and repeats to e_N) -The last section contains more constants for e\_i-e\_j interactions with +The last section contains more constants for e_i-e_j interactions with i=0->N, j=i->N -* Line 1: (A\_ij)\^(mu\*nu) (for e1-e1) -* Line 2: (A\_ij)\^(mu\*nu) (for e1-e2 and repeats as above) +* Line 1: (A_ij)\^(mu\*nu) (for e1-e1) +* Line 2: (A_ij)\^(mu\*nu) (for e1-e2 and repeats as above) ---------- @@ -274,34 +274,34 @@ the tabulated functions are given. * Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; ntheta is the power of the power of the spline used to fit the angular function; nBOt is the number - of divisions for the tabulated values of THETA\_(S,ij) -* Line 2: delta\_1-delta\_7 (if all are not used in the particular + of divisions for the tabulated values of THETA_(S,ij) +* Line 2: delta_1-delta_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e\_1-e\_N containing p\_pi. +Following this N lines for e_1-e_N containing p_pi. -* Line 3: p\_pi (for e\_1) -* Line 4: p\_pi (for e\_2 and continues to e\_N) +* Line 3: p_pi (for e_1) +* Line 4: p_pi (for e_2 and continues to e_N) The next section contains several pair constants for the number of -interaction types e\_i-e\_j, with i=1->N, j=i->N +interaction types e_i-e_j, with i=1->N, j=i->N -* Line 1: r\_cut (for e\_1-e\_1 interactions) -* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi -* Line 3: delta\_sigma, delta\_pi -* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of +* Line 1: r_cut (for e_1-e_1 interactions) +* Line 2: c_sigma, a_sigma, c_pi, a_pi +* Line 3: delta_sigma, delta_pi +* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N +e_j-e_i-e_k with i=0->N, j=0->N, k=j->N * Line 1: g0, g1, g2... (These are coefficients for the angular spline - of the g\_(sigma,jik)(THETA\_ijk) for e\_1-e\_1-e\_1 interaction. The + of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The function can contain up to 10 term thus 10 constants. The first line can contain up to five constants. If the spline has more than five terms the second line will contain the remaining constants The following lines will then contain the constants for the remaining g0, - g1, g2... (for e\_1-e\_1-e\_2) and the other three body + g1, g2... (for e_1-e_1-e_2) and the other three body interactions The rest of the table has the same structure as the previous section @@ -327,34 +327,34 @@ the tabulated functions are given. * Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; ntheta is the number of divisions for the tabulated values of the g angular function; nBOt is the number - of divisions for the tabulated values of THETA\_(S,ij) -* Line 2: delta\_1-delta\_7 (if all are not used in the particular + of divisions for the tabulated values of THETA_(S,ij) +* Line 2: delta_1-delta_7 (if all are not used in the particular * formulation, set unused values to 0.0) -Following this N lines for e\_1-e\_N containing p\_pi. +Following this N lines for e_1-e_N containing p_pi. -* Line 3: p\_pi (for e\_1) -* Line 4: p\_pi (for e\_2 and continues to e\_N) +* Line 3: p_pi (for e_1) +* Line 4: p_pi (for e_2 and continues to e_N) The next section contains several pair constants for the number of -interaction types e\_i-e\_j, with i=1->N, j=i->N +interaction types e_i-e_j, with i=1->N, j=i->N -* Line 1: r\_cut (for e\_1-e\_1 interactions) -* Line 2: c\_sigma, a\_sigma, c\_pi, a\_pi -* Line 3: delta\_sigma, delta\_pi -* Line 4: f\_sigma, k\_sigma, delta\_3 (This delta\_3 is similar to that of +* Line 1: r_cut (for e_1-e_1 interactions) +* Line 2: c_sigma, a_sigma, c_pi, a_pi +* Line 3: delta_sigma, delta_pi +* Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of the previous section but is interaction type dependent) The next section contains a line for each three body interaction type -e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N +e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -* Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e\_1-e\_1-e\_1 +* Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1 interaction type) * Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues until ntheta) * ... * Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the - e\_1-e\_1-e\_2 interaction type) + e_1-e_1-e_2 interaction type) The rest of the table has the same structure as the previous section (see above). @@ -366,7 +366,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -398,23 +398,23 @@ Related commands Default """"""" -non-tabulated potential file, a\_0 is non-zero. +non-tabulated potential file, a_0 is non-zero. ---------- -.. _Pettifor\_1: +.. _Pettifor_1: -**(Pettifor\_1)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 +**(Pettifor_1)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 (1999). -.. _Pettifor\_2: +.. _Pettifor_2: -**(Pettifor\_2)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, +**(Pettifor_2)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, 4124 (2000). -.. _Pettifor\_3: +.. _Pettifor_3: -**(Pettifor\_3)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 +**(Pettifor_3)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002). .. _Murdick: diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index c517e4c301..2fa5785132 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -147,12 +147,12 @@ commands, or by mixing as described below: The second coefficient, rho, must be greater than zero. The last coefficient is optional. If not specified, the global A,C,D -cutoff specified in the pair\_style command is used. +cutoff specified in the pair_style command is used. For *born/coul/long*\ , *born/coul/wolf* and *born/coul/dsf* no Coulombic cutoff can be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the -pair\_style command. +pair_style command. ---------- @@ -189,11 +189,11 @@ The *born/coul/long* pair style supports the :doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. -These styles support the pair\_modify tail option for adding long-range +These styles support the pair_modify tail option for adding long-range tail corrections to energy and pressure. Thess styles writes thei information to binary :doc:`restart ` -files, so pair\_style and pair\_coeff commands do not need to be +files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index db4e1345ec..12566a2993 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -25,7 +25,7 @@ Syntax * flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects * cutinner = inner cutoff distance (distance units) * cutoff = outer cutoff for interactions (distance units) -* t\_target = target temp of the system (temperature units) +* t_target = target temp of the system (temperature units) * seed = seed for the random number generator (positive integer) * flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions * flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms @@ -53,7 +53,7 @@ when dissipative lubrication forces are acting. Thus the parameters specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles. -The *t\_target* setting is used to specify the target temperature of +The *t_target* setting is used to specify the target temperature of the system. The random number *seed* is used to generate random numbers for the thermostatting procedure. @@ -72,7 +72,7 @@ commands, or by mixing as described below: * cutoff (distance units) The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair\_style command are used. Otherwise both +cutoffs specified in the pair_style command are used. Otherwise both must be specified. ---------- @@ -101,7 +101,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See -the "pair\_modify" command for details. +the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -113,7 +113,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -128,10 +128,10 @@ Restrictions These styles are part of the COLLOID package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Only spherical monodisperse particles are allowed for pair\_style +Only spherical monodisperse particles are allowed for pair_style brownian. -Only spherical particles are allowed for pair\_style brownian/poly. +Only spherical particles are allowed for pair_style brownian/poly. Related commands """""""""""""""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 512b751dd0..c0eb0ee282 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -164,7 +164,7 @@ the A,C and Coulombic cutoffs for this type pair. You cannot specify For *buck/coul/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the -pair\_style command. +pair_style command. ---------- @@ -200,11 +200,11 @@ The *buck/coul/long* pair style supports the :doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. -These styles support the pair\_modify tail option for adding long-range +These styles support the pair_modify tail option for adding long-range tail corrections to energy and pressure for the A,C terms in the pair interaction. -These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index f7f190a322..f8c5a29a32 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -127,7 +127,7 @@ These styles do not support the :doc:`pair_modify ` shift option for the energy. Instead the smoothing function should be applied by setting the global smoothing parameter to a value < 1.0. -These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. Restrictions diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 7e4e0f8200..6f1e2d83ef 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -13,14 +13,14 @@ Syntax pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) -* flag\_buck = *long* or *cut* +* flag_buck = *long* or *cut* .. parsed-literal:: *long* = use Kspace long-range summation for the dispersion term 1/r\^6 *cut* = use a cutoff -* flag\_coul = *long* or *off* +* flag_coul = *long* or *off* .. parsed-literal:: @@ -52,34 +52,34 @@ instead of Lennard-Jones 12/6) and Coulombic potential, given by E = & A e^{-r / \rho} - \frac{C}{r^6} \qquad r < r_c \\ E = & \frac{C q_i q_j}{\epsilon r} \qquad r < r_c -:math:`r_c` is the cutoff. If one cutoff is specified in the pair\_style +:math:`r_c` is the cutoff. If one cutoff is specified in the pair_style command, it is used for both the Buckingham and Coulombic terms. If two cutoffs are specified, they are used as cutoffs for the Buckingham and Coulombic terms respectively. The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r\^6 Buckingham and Coulombic 1/r -interactions. This is done by use of the *flag\_buck* and *flag\_coul* +interactions. This is done by use of the *flag_buck* and *flag_coul* settings. The :ref:`Ismail ` paper has more details on when it is appropriate to include long-range 1/r\^6 interactions, using this potential. -If *flag\_buck* is set to *long*\ , no cutoff is used on the Buckingham +If *flag_buck* is set to *long*\ , no cutoff is used on the Buckingham 1/r\^6 dispersion term. The long-range portion can be calculated by using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified Buckingham cutoff then determines which portion of the Buckingham interactions are computed directly by the pair potential versus which part is computed in reciprocal space via -the Kspace style. If *flag\_buck* is set to *cut*\ , the Buckingham +the Kspace style. If *flag_buck* is set to *cut*\ , the Buckingham interactions are simply cutoff, as with :doc:`pair_style buck `. -If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic +If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of several :doc:`kspace_style ` command options such as -*pppm* or *ewald*\ . Note that if *flag\_buck* is also set to long, then +*pppm* or *ewald*\ . Note that if *flag_buck* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the Buckingham and -Coulombic interactions. If *flag\_coul* is set to *off*\ , Coulombic +Coulombic interactions. If *flag_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms @@ -97,14 +97,14 @@ commands: The second coefficient, rho, must be greater than zero. The latter 2 coefficients are optional. If not specified, the global -Buckingham and Coulombic cutoffs specified in the pair\_style command +Buckingham and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both Buckingham and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the Buckingham and Coulombic cutoffs for this type pair. Note that if you are using -*flag\_buck* set to *long*\ , you cannot specify a Buckingham cutoff for +*flag_buck* set to *long*\ , you cannot specify a Buckingham cutoff for an atom type pair, since only one global Buckingham cutoff is allowed. -Similarly, if you are using *flag\_coul* set to *long*\ , you cannot +Similarly, if you are using *flag_coul* set to *long*\ , you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. @@ -137,7 +137,7 @@ I,J pairs must be specified explicitly. This pair style supports the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair -interaction, assuming *flag\_buck* is *cut*\ . +interaction, assuming *flag_buck* is *cut*\ . This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Buckingham portion of the pair @@ -147,7 +147,7 @@ This pair style supports the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of the long-range Coulombic and dispersion interactions. -This pair style write its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style write its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index c9746a58d0..031e6e6717 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -180,7 +180,7 @@ used in the *charmmfsw* and *charmmfsh* styles. When using the *lj/charmm/coul/charmm styles*\ , both the LJ and Coulombic terms require an inner and outer cutoff. They can be the same for both formulas or different depending on whether 2 or 4 -arguments are used in the pair\_style command. For the +arguments are used in the pair_style command. For the *lj/charmmfsw/coul/charmmfsh* style, the LJ term requires both an inner and outer cutoff, while the Coulombic term requires only one cutoff. If the Coulombic cutoff is not specified (2 instead of 3 @@ -206,7 +206,7 @@ factor is applied to the Coulombic term, so it can be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. Only one Coulombic cutoff is specified for these styles; if only 2 arguments are used in the -pair\_style command, then the outer LJ cutoff is used as the single +pair_style command, then the outer LJ cutoff is used as the single Coulombic cutoff. The Coulombic cutoff specified for these styles means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in @@ -231,7 +231,7 @@ are used in the LJ formula between 2 atoms of these types which are also first and fourth atoms in any dihedral. No cutoffs are specified because the CHARMM force field does not allow varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in -the pair\_style command. +the pair_style command. ---------- @@ -257,10 +257,10 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -For atom type pairs I,J and I != J, the epsilon, sigma, epsilon\_14, -and sigma\_14 coefficients for all of the lj/charmm pair styles can be +For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, +and sigma_14 coefficients for all of the lj/charmm pair styles can be mixed. The default mix value is *arithmetic* to coincide with the -usual settings for the CHARMM force field. See the "pair\_modify" +usual settings for the CHARMM force field. See the "pair_modify" command for details. None of the *lj/charmm* or *lj/charmmfsw* pair styles support the @@ -278,8 +278,8 @@ corrections to energy and pressure, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. All of the *lj/charmm* and *lj/charmmfsw* pair styles write their -information to :doc:`binary restart files `, so pair\_style and -pair\_coeff commands do not need to be specified in an input script +information to :doc:`binary restart files `, so pair_style and +pair_coeff commands do not need to be specified in an input script that reads a restart file. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* pair styles @@ -287,7 +287,7 @@ support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of -run\_style respa. See the :doc:`run_style ` command for +run_style respa. See the :doc:`run_style ` command for details. ---------- diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index d279370791..d1c673ab97 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -114,11 +114,11 @@ Coulombic terms. For *lj/class2/coul/long* only the class 2 cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff -specified in the pair\_style command. +specified in the pair_style command. ---------- -If the pair\_coeff command is not used to define coefficients for a +If the pair_coeff command is not used to define coefficients for a particular I != J type pair, the mixing rule for :math:`\epsilon` and :math:`\sigma` for all class2 potentials is to use the *sixthpower* formulas documented by the :doc:`pair_modify ` command. @@ -160,8 +160,8 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/class2 pair styles can be mixed. Epsilon and sigma are always mixed with the value *sixthpower*\ . The -cutoff distance is mixed by whatever option is set by the pair\_modify -command (default = geometric). See the "pair\_modify" command for +cutoff distance is mixed by whatever option is set by the pair_modify +command (default = geometric). See the "pair_modify" command for details. All of the lj/class2 pair styles support the @@ -177,13 +177,13 @@ All of the lj/class2 pair styles support the tail correction to the energy and pressure of the Lennard-Jones portion of the pair interaction. -All of the lj/class2 pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do +All of the lj/class2 pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. Only the *lj/class2* and *lj/class2/coul/long* pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the *pair* keyword of run\_style respa. +The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. Restrictions diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 8ebb15b173..26910c1746 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -49,7 +49,7 @@ types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -Note that a pair\_coeff command can override a previous setting for the +Note that a pair_coeff command can override a previous setting for the same I,J pair. For example, these commands set the coeffs for all I,J pairs, then overwrite the coeffs for just the I,J = 2,3 pair: @@ -59,7 +59,7 @@ pairs, then overwrite the coeffs for just the I,J = 2,3 pair: pair_coeff 2 3 2.0 1.0 1.12 A line in a data file that specifies pair coefficients uses the exact -same format as the arguments of the pair\_coeff command in an input +same format as the arguments of the pair_coeff command in an input script, with the exception of the I,J type arguments. In each line of the "Pair Coeffs" section of a data file, only a single type I is specified, which sets the coefficients for type I interacting with @@ -74,28 +74,28 @@ as 2 1.0 1.0 2.5 For many potentials, if coefficients for type pairs with I != J are -not set explicitly by a pair\_coeff command, the values are inferred +not set explicitly by a pair_coeff command, the values are inferred from the I,I and J,J settings by mixing rules; see the :doc:`pair_modify ` command for a discussion. Details on this option as it pertains to individual potentials are described on the doc page for the potential. Many pair styles, typically for many-body potentials, use tabulated -potential files as input, when specifying the pair\_coeff command. +potential files as input, when specifying the pair_coeff command. Potential files provided with LAMMPS are in the potentials directory of the distribution. For some potentials, such as EAM, other archives of suitable files can be found on the Web. They can be used with LAMMPS so long as they are in the format LAMMPS expects, as discussed on the individual doc pages. -When a pair\_coeff command using a potential file is specified, LAMMPS +When a pair_coeff command using a potential file is specified, LAMMPS looks for the potential file in 2 places. First it looks in the location specified. E.g. if the file is specified as "niu3.eam", it is looked for in the current working directory. If it is specified as "../potentials/niu3.eam", then it is looked for in the potentials directory, assuming it is a sister directory of the current working directory. If the file is not found, it is then looked for in the -directory specified by the LAMMPS\_POTENTIALS environment variable. +directory specified by the LAMMPS_POTENTIALS environment variable. Thus if this is set to the potentials directory in the LAMMPS distribution, then you can use those files from anywhere on your system, without copying them into your working directory. Environment variables are @@ -127,7 +127,7 @@ The alphabetic list of pair styles defined in LAMMPS is given on the compact form on the :doc:`Commands pair ` doc page. Click on the style to display the formula it computes and its -coefficients as specified by the associated pair\_coeff command. +coefficients as specified by the associated pair_coeff command. ---------- diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 453a42a974..d9f086059d 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -137,12 +137,12 @@ particle of size :math:`\sigma`. If either d1 = 0 or d2 = 0 and the other is larger, then the pair interacts via the colloid-solvent formula. Note that the diameter of a particular particle type may appear in -multiple pair\_coeff commands, as it interacts with other particle +multiple pair_coeff commands, as it interacts with other particle types. You should insure the particle diameter is specified consistently each time it appears. The last coefficient is optional. If not specified, the global cutoff -specified in the pair\_style command is used. However, you typically +specified in the pair_style command is used. However, you typically want different cutoffs for interactions between different particle sizes. E.g. if colloidal particles of diameter 10 are used with solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5 @@ -153,7 +153,7 @@ colloid-solvent cutoff in this case. .. note:: - When using pair\_style colloid for a mixture with 2 (or more) + When using pair_style colloid for a mixture with 2 (or more) widely different particles sizes (e.g. sigma=10 colloids in a background sigma=1 LJ fluid), you will likely want to use these commands for efficiency: :doc:`neighbor multi ` and @@ -187,7 +187,7 @@ For atom type pairs I,J and I != J, the A, sigma, d1, and d2 coefficients and cutoff distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is -*geometric*\ . See the "pair\_modify" command for details. +*geometric*\ . See the "pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -199,7 +199,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -216,14 +216,14 @@ LAMMPS was built with that package. See the :doc:`Build package Normally, this pair style should be used with finite-size particles which have a diameter, e.g. see the :doc:`atom_style sphere ` command. However, this is not a requirement, -since the only definition of particle size is via the pair\_coeff +since the only definition of particle size is via the pair_coeff parameters for each type. In other words, the physical radius of the particle is ignored. Thus you should insure that the d1,d2 parameters you specify are consistent with the physical size of the particles of that type. Per-particle polydispersity is not yet supported by this pair style; -only per-type polydispersity is enabled via the pair\_coeff parameters. +only per-type polydispersity is enabled via the pair_coeff parameters. Related commands """""""""""""""" diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index faddf42e70..a03bc3fffe 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -67,16 +67,16 @@ that determine how often charge equilibration is performed, its convergence criterion, and which atoms are included in the calculation. -Only a single pair\_coeff command is used with the *comb* and *comb3* +Only a single pair_coeff command is used with the *comb* and *comb3* styles which specifies the COMB potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the potential file in the pair\_coeff +N additional arguments after the potential file in the pair_coeff command, where N is the number of LAMMPS atom types. For example, if your LAMMPS simulation of a Si/SiO2/ HfO2 interface has 4 atom types, and you want the 1st and last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would -use the following pair\_coeff command: +use the following pair_coeff command: .. code-block:: LAMMPS @@ -129,12 +129,12 @@ For style *comb3*\ , in addition to ffield.comb3, a special parameter file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the -directory pointed to by the environment variable LAMMPS\_POTENTIALS, as +directory pointed to by the environment variable LAMMPS_POTENTIALS, as described on the :doc:`pair_coeff ` command doc page. Keyword *polar* indicates whether the force field includes the atomic polarization. Since the equilibration of the polarization -has not yet been implemented, it can only set polar\_off at present. +has not yet been implemented, it can only set polar_off at present. .. note:: @@ -173,7 +173,7 @@ These pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. These pair styles do not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style, pair\_coeff, and :doc:`fix qeq/comb ` commands in an input script that reads a +need to re-specify the pair_style, pair_coeff, and :doc:`fix qeq/comb ` commands in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index 4669985db9..4f19ddd1e4 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -54,7 +54,7 @@ between two point particles, where (:math:`\sigma, -\epsilon`) is the location of the (rightmost) minimum of the potential, as explained in the syntax section above. -This potential was first used in (Cooke)\_#CKD for a coarse-grained lipid +This potential was first used in (Cooke)_#CKD for a coarse-grained lipid membrane model. It is generally very useful as a non-specific interaction potential because it is fully adjustable in depth and width while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0) @@ -63,7 +63,7 @@ energy calculations etc. This evidently requires *cutoff* to be larger than *sigma*\ . If the *wca* option is used then a Weeks-Chandler-Andersen potential -(Weeks)\_#WCA is added to the above specified cosine-squared potential, +(Weeks)_#WCA is added to the above specified cosine-squared potential, specifically the following: .. math:: @@ -94,7 +94,7 @@ Mixing is not supported for this style. The *shift*\ , *table* and *tail* options are not relevant for this style. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 55a6b9b057..8f77a622d6 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -269,7 +269,7 @@ a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, and the distance to the massless charge site are specified as -pair\_style arguments. Style *tip4p/cut* uses a global cutoff for +pair_style arguments. Style *tip4p/cut* uses a global cutoff for Coulomb interactions; style *tip4p/long* is for use with a long-range Coulombic solver (Ewald or PPPM). @@ -311,11 +311,11 @@ commands, or by mixing as described below: For *coul/cut* and *coul/debye*\ , the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default -global value specified in the pair\_style command is used. +global value specified in the pair_style command is used. For *coul/long* and *coul/msm* no cutoff can be specified for an -individual I,J type pair via the pair\_coeff command. All type pairs -use the same global Coulomb cutoff specified in the pair\_style +individual I,J type pair via the pair_coeff command. All type pairs +use the same global Coulomb cutoff specified in the pair_style command. ---------- @@ -344,7 +344,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the cutoff distance for the *coul/cut* style can be mixed. The default mix value is *geometric*\ . -See the "pair\_modify" command for details. +See the "pair_modify" command for details. The :doc:`pair_modify ` shift option is not relevant for these pair styles. @@ -357,7 +357,7 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 8011137199..02ad620327 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -28,7 +28,7 @@ Description Style *coul/diel* computes a Coulomb correction for implicit solvent ion interactions in which the dielectric permittivity is distance dependent. -The dielectric permittivity epsilon\_D(r) connects to limiting regimes: +The dielectric permittivity epsilon_D(r) connects to limiting regimes: One limit is defined by a small dielectric permittivity (close to vacuum) at or close to contact separation between the ions. At larger separations the dielectric permittivity reaches a bulk value used in the regular Coulomb @@ -43,9 +43,9 @@ in the Coulomb correction term for small ion separations as follows where :math:`r_{me}` is the inflection point of :math:`\epsilon_D(r)` and :math:`\sigma_e` is a slope defining length scale. C is the same Coulomb conversion factor as in the -pair\_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb +pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb interaction between ions is corrected at small distances r. The lower -limit of epsilon\_D(r->0)=5.2 due to dielectric saturation :ref:`(Stiles) ` +limit of epsilon_D(r->0)=5.2 due to dielectric saturation :ref:`(Stiles) ` while the Coulomb interaction reaches its bulk limit by setting :math:`\epsilon_D(r \to \infty) = \epsilon`, the bulk value of the solvent which is 78 for water at 298K. @@ -67,7 +67,7 @@ commands: * :math:`r_{me}` (distance units) * :math:`\sigma_e` (distance units) -The global cutoff (:math:`r_c`) specified in the pair\_style command is used. +The global cutoff (:math:`r_c`) specified in the pair_style command is used. ---------- diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 14de8c773f..c9acbf40ef 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -11,7 +11,7 @@ Syntax pair_style coul/shield cutoff tap_flag * 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 """""""" @@ -58,7 +58,7 @@ each pair of atom types via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: -The global cutoff (:math:`r_c`) specified in the pair\_style command is used. +The global cutoff (:math:`r_c`) specified in the pair_style command is used. ---------- @@ -90,7 +90,7 @@ Related commands :doc:`pair_coeff ` :doc:`pair_style ilp/graphene/hbn ` -**Default:** tap\_flag = 1 +**Default:** tap_flag = 1 ---------- diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index c1aeef745e..72332a87b2 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -132,7 +132,7 @@ to 0.0, which works because the core and shell atoms are bonded to each other. This induces a long-range correction approximation which fails at small distances (~< 10e-8). Therefore, the Coulomb term which is used to calculate the correction factor is extended by a minimal -distance (r\_min = 1.0-6) when the interaction between a core/shell +distance (r_min = 1.0-6) when the interaction between a core/shell pair is treated, as follows .. math:: diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 8cbc949e13..38731dcb6d 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -39,7 +39,7 @@ Syntax * cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) * cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) -* flag\_lj = *long* or *cut* or *off* +* flag_lj = *long* or *cut* or *off* .. parsed-literal:: @@ -47,7 +47,7 @@ Syntax *cut* = use a cutoff on dispersion 1/r\^6 term *off* = omit disperion 1/r\^6 term entirely -* flag\_coul = *long* or *off* +* flag_coul = *long* or *off* .. parsed-literal:: @@ -137,7 +137,7 @@ potential containing extra terms that make both the energy and its derivative go to zero at the cutoff distance; this removes (cutoff-related) problems in energy conservation and any numerical instability in the equations of motion :ref:`(Allen) `. Shifted-force -interactions for the Lennard-Jones (E\_LJ), charge-charge (Eqq), +interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) potentials are computed by these formulas for the energy (E), force (F), and torque (T) between particles I and J: @@ -221,11 +221,11 @@ been obtained by applying equation 5.13 of :ref:`(Allen) `. The formulas for the corresponding forces and torques have been obtained by applying the 'chain rule' as in appendix C.3 of :ref:`(Allen) `. -If one cutoff is specified in the pair\_style command, it is used for +If one cutoff is specified in the pair_style command, it is used for both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, they are used as cutoffs for the LJ and Coulombic (q,p) terms respectively. This pair style also supports an optional *scale* keyword -as part of a pair\_coeff statement, where the interactions can be +as part of a pair_coeff statement, where the interactions can be scaled according to this factor. This scale factor is also made available for use with fix adapt. @@ -243,19 +243,19 @@ dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions. LJ interactions can be cutoff or long-ranged. -For style *lj/long/dipole/long*\ , if *flag\_lj* is set to *long*\ , no +For style *lj/long/dipole/long*\ , if *flag_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range -portion is calculated by using the :doc:`kspace_style ewald\_disp ` command. The specified LJ cutoff then +portion is calculated by using the :doc:`kspace_style ewald_disp ` command. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal -space via the Kspace style. If *flag\_lj* is set to *cut*\ , the LJ -interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag\_lj* is set to *off*\ , LJ interactions +space via the Kspace style. If *flag_lj* is set to *cut*\ , the LJ +interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag_lj* is set to *off*\ , LJ interactions are not computed at all. -If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic or +If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic or dipole interactions. The long-range portion is calculated by using -*ewald\_disp* of the :doc:`kspace_style ` command. If -*flag\_coul* is set to *off*\ , Coulombic and dipole interactions are not +*ewald_disp* of the :doc:`kspace_style ` command. If +*flag_coul* is set to *off*\ , Coulombic and dipole interactions are not computed at all. Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole ` or the :doc:`fix nvt/sphere update dipole ` command to rotate the @@ -280,7 +280,7 @@ commands, or by mixing as described below: * cutoff2 (distance units) The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair\_style command are used. +LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this @@ -312,13 +312,13 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distances for this pair style can be mixed. The default -mix value is *geometric*\ . See the "pair\_modify" command for details. +mix value is *geometric*\ . See the "pair_modify" command for details. For atom type pairs I,J and I != J, the A, sigma, d1, and d2 coefficients and cutoff distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is -*geometric*\ . See the "pair\_modify" command for details. +*geometric*\ . See the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair @@ -331,7 +331,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 560c6f0a03..0a078585c6 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -81,7 +81,7 @@ difference in velocities of the two atoms :math:`= \vec{v}_i - unit variance, dt is the timestep size, and w(r) is a weighting factor that varies between 0 and 1. :math:`r_c` is the cutoff. :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T \gamma}`, where :math:`k_B` is the -Boltzmann constant and T is the temperature parameter in the pair\_style +Boltzmann constant and T is the temperature parameter in the pair_style command. For style *dpd/tstat*\ , the force on atom I due to atom J is the same @@ -174,7 +174,7 @@ These pair style do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles writes their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles writes their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. Note that the user-specified random number seed is stored in the restart file, so when a simulation is restarted, each processor will diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index 5628aa6d66..1fa193777a 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -76,7 +76,7 @@ The :doc:`pair_coeff ` command for DRIP takes *4+N* arguments, where to be *\* \* drip*, the fourth argument is the path to the DRIP parameter file, and the remaining N arguments specifying the mapping between element in the parameter file and atom types. For example, if your LAMMPS simulation has 3 atom -types and you want all of them to be C, you would use the following pair\_coeff +types and you want all of them to be C, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -99,19 +99,19 @@ model H atoms: The potential parameters developed in :ref:`(Wen) ` are provided with LAMMPS (see the "potentials" directory). Besides those in :ref:`Wen `, an - additional parameter "normal\_cutoff", specific to the LAMMPS implementation, is + additional parameter "normal_cutoff", specific to the LAMMPS implementation, is used to find the three nearest neighbors of an atom to construct the normal. ---------- **Mixing, shift, table, tail correction, and restart info**\ : -This pair style does not support the pair\_modify mix, shift, table, +This pair style does not support the pair_modify mix, shift, table, and tail options. This pair style does not write their information to binary restart files, since -it is stored in potential files. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +it is stored in potential files. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. Restrictions """""""""""" @@ -132,7 +132,7 @@ simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair_style lebedeva\_z `, +:doc:`pair_style lebedeva_z `, :doc:`pair_style kolmogorov/crespi/z `, :doc:`pair_style kolmogorov/crespi/full `, :doc:`pair_style ilp/graphene/hbn `. diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index daf63a3752..03f6505d47 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -10,12 +10,12 @@ Syntax pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample -* max\_cell\_size = global maximum cell size for DSMC interactions (distance units) +* max_cell_size = global maximum cell size for DSMC interactions (distance units) * seed = random # seed (positive integer) * weighting = macroparticle weighting * Tref = reference temperature (temperature units) -* Nrecompute = re-compute v\*sigma\_max every this many timesteps (timesteps) -* Nsample = sample this many times in recomputing v\*sigma\_max +* Nrecompute = re-compute v\*sigma_max every this many timesteps (timesteps) +* Nsample = sample this many times in recomputing v\*sigma_max Examples """""""" @@ -34,13 +34,13 @@ direct simulation Monte Carlo (DSMC) model following the exposition in :ref:`(Bird) `. Each collision resets the velocities of the two particles involved. The number of pairwise collisions for each pair or particle types and the length scale within which they occur are -determined by the parameters of the pair\_style and pair\_coeff +determined by the parameters of the pair_style and pair_coeff commands. Stochastic collisions are performed using the variable hard sphere -(VHS) approach, with the user-defined *max\_cell\_size* value used as +(VHS) approach, with the user-defined *max_cell_size* value used as the maximum DSMC cell size, and reference cross-sections for -collisions given using the pair\_coeff command. +collisions given using the pair_coeff command. There is no pairwise energy or virial contributions associated with this pair style. @@ -53,7 +53,7 @@ commands: * sigma (area units, i.e. distance-squared) -The global DSMC *max\_cell\_size* determines the maximum cell length +The global DSMC *max_cell_size* determines the maximum cell length used in the DSMC calculation. A structured mesh is overlayed on the simulation box such that an integer number of cells are created in each direction for each processor's sub-domain. Cell lengths are @@ -119,7 +119,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. Note that the user-specified random number seed is stored in the restart file, so when a simulation is restarted, each processor will diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 08fd7bc56f..68f8708b27 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -69,7 +69,7 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r \end{cases} This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly. -To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair\_style hybrid/overlay*. +To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*. The three body interactions are split into three types: A, B, and C. Type A corresponds to anti-cooperative double hydrogen bond donor interactions. Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond. @@ -79,9 +79,9 @@ The two-body interactions are designed to correct for the effective many-body in The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2. See :ref:`(Kumar 2008) ` for more details. -Only a single *pair\_coeff* command is used with the *e3b* style. +Only a single *pair_coeff* command is used with the *e3b* style. The 1st two arguments must be \* \*. -The oxygen atom type for the pair style is passed as the only argument to the *pair\_style* command, not in the *pair\_coeff* command. +The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command. The hydrogen atom type is inferred by the ordering of the atoms. .. note:: @@ -90,14 +90,14 @@ The hydrogen atom type is inferred by the ordering of the atoms. Each water molecule must have consecutive IDs with the oxygen first. This pair style does not test that this criteria is met. -The *pair\_coeff* command must have at least one keyword/value pair, as described above. +The *pair_coeff* command must have at least one keyword/value pair, as described above. The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) ` or :ref:`(Tainter 2015) `. -To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair\_style hybrid/overlay*, as demonstrated in the second example above. +To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above. The *preset 2011* option should be used with the :doc:`TIP4P water model `. The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model `. If the *preset* keyword is used, no other keyword is needed. Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ . -Note that the other keywords must come after *preset* in the pair\_style command. +Note that the other keywords must come after *preset* in the pair_style command. The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*\ , *Eb*\ , *Ec*\ , *E2*\ , *K3*\ , *K2*\ , *Rc3*\ , *Rc2*\ , *Rs*\ , and *bondL*\ . The keyword *bondL* specifies the intramolecular OH bond length of the water model being used. This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not. @@ -121,7 +121,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style is incompatible with :doc:`respa `. @@ -138,7 +138,7 @@ This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like :doc:`fix deposit `. -If the number of atoms changes between runs, this pair style must be re-initialized by calling the *pair\_style* and *pair\_coeffs* commands. +If the number of atoms changes between runs, this pair style must be re-initialized by calling the *pair_style* and *pair_coeffs* commands. This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms. The *preset* keyword currently only works with real, metal, si, and cgs :doc:`units `. diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 8c3db11687..4710f8a9a1 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -136,7 +136,7 @@ are parameterized in terms of LAMMPS :doc:`metal units `. .. note:: Note that unlike for other potentials, cutoffs for EAM - potentials are not set in the pair\_style or pair\_coeff command; they + potentials are not set in the pair_style or pair_coeff command; they are specified in the EAM potential files themselves. Likewise, the EAM potential files list atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. @@ -164,11 +164,11 @@ by a Fortran program, it cannot have "D" values in it for exponents. C only recognizes "e" or "E" for scientific notation. Note that unlike for other potentials, cutoffs for EAM potentials are -not set in the pair\_style or pair\_coeff command; they are specified in +not set in the pair_style or pair_coeff command; they are specified in the EAM potential files themselves. For style *eam* a potential file must be assigned to each I,I pair of -atom types by using one or more pair\_coeff commands, each with a +atom types by using one or more pair_coeff commands, each with a single argument: * filename @@ -249,21 +249,21 @@ DYNAMO file was created by a Fortran program, it cannot have "D" values in it for exponents. C only recognizes "e" or "E" for scientific notation. -Only a single pair\_coeff command is used with the *eam/alloy* style +Only a single pair_coeff command is used with the *eam/alloy* style which specifies a DYNAMO *setfl* file, which contains information for M elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of *setfl* elements to atom types -As an example, the potentials/NiAlH\_jea.eam.alloy file is a *setfl* +As an example, the potentials/NiAlH_jea.eam.alloy file is a *setfl* file which has tabulated EAM values for 3 elements and their alloy interactions: Ni, Al, and H. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to -be Ni, and the 4th to be Al, you would use the following pair\_coeff +be Ni, and the 4th to be Al, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -332,7 +332,7 @@ of mixing of alloys over the full composition range, as described in :ref:`(Stukowski) `. Style *eam/cd/old* is an older, slightly different and slower two-site formulation of the model :ref:`(Caro) `. -The pair\_coeff command is specified the same as for the *eam/alloy* +The pair_coeff command is specified the same as for the *eam/alloy* style. However the DYNAMO *setfl* file must has two lines added to it, at the end of the file: @@ -373,7 +373,7 @@ element at that atomic site. The associated :doc:`pair_coeff ` command for style *eam/fs* reads a DYNAMO *setfl* file that has been extended to include -additional rho\_alpha\_beta arrays of tabulated values. A discussion of +additional rho_alpha_beta arrays of tabulated values. A discussion of how FS EAM differs from conventional EAM alloy potentials is given in :ref:`(Ackland1) `. An example of such a potential is the same author's Fe-P FS potential :ref:`(Ackland2) `. Note that while FS @@ -382,7 +382,7 @@ dependence on the total density, the implementation in LAMMPS does not require that; the user can tabulate any functional form desired in the FS potential files. -For style *eam/fs*\ , the form of the pair\_coeff command is exactly the +For style *eam/fs*\ , the form of the pair_coeff command is exactly the same as for style *eam/alloy*\ , e.g. .. code-block:: LAMMPS @@ -461,13 +461,13 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above with the individual styles. You never need to specify -a pair\_coeff command with I != J arguments for the eam styles. +a pair_coeff command with I != J arguments for the eam styles. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The eam pair styles do not write their information to :doc:`binary restart files `, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair\_style and pair\_coeff commands in +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. The eam pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 0e8a4aab59..02f779bebf 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -59,10 +59,10 @@ local environment of atom I through its effective coordination number defined by Z, which is unity for a cutoff distance < c and gently goes to 0 at distance = a. -Only a single pair\_coeff command is used with the *edip* style which +Only a single pair_coeff command is used with the *edip* style which specifies a EDIP potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -106,7 +106,7 @@ for three-body interactions. The alpha and cutoffC parameters are used for the coordination environment function only. The EDIP potential file must contain entries for all the -elements listed in the pair\_coeff command. It can also contain +elements listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. @@ -151,7 +151,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index 6726dee2f9..f163e5afaa 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -89,9 +89,9 @@ electronically excited and ionized states of matter can occur and coexist. Furthermore, the interactions between particles -nuclei and electrons- reduce to the sum of a set of effective pairwise potentials in the eFF formulation. The *eff/cut* style computes the pairwise -Coulomb interactions between nuclei and electrons (E\_NN,E\_Ne,E\_ee), -and the quantum-derived Pauli (E\_PR) and Kinetic energy interactions -potentials between electrons (E\_KE) for a total energy expression +Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee), +and the quantum-derived Pauli (E_PR) and Kinetic energy interactions +potentials between electrons (E_KE) for a total energy expression given as, .. math:: @@ -108,10 +108,10 @@ The individual terms are defined as follows: E_{ee} = & \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{1}{{r_{ij} }}Erf\left( {\frac{{\sqrt 2 r_{ij} }}{{\sqrt {s_i^2 + s_j^2 } }}} \right)} \\ E_{Pauli} = & \sum\limits_{\sigma _i = \sigma _j } {E\left( { \uparrow \uparrow } \right)_{ij}} + \sum\limits_{\sigma _i \ne \sigma _j } {E\left( { \uparrow \downarrow } \right)_{ij}} \\ -where, s\_i correspond to the electron sizes, the sigmas i's to the -fixed spins of the electrons, Z\_i to the charges on the nuclei, R\_ij +where, s_i correspond to the electron sizes, the sigmas i's to the +fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij to the distances between the nuclei or the nuclei and electrons, and -r\_ij to the distances between electrons. For additional details see +r_ij to the distances between electrons. For additional details see :ref:`(Jaramillo-Botero) `. The overall electrostatics energy is given in Hartree units of energy @@ -143,11 +143,11 @@ commands, or by mixing as described below: For *eff/cut*\ , the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified -in the pair\_style command is used. +in the pair_style command is used. For *eff/long* (not yet available) no cutoff will be specified for an individual I,J type pair via the :doc:`pair_coeff ` command. -All type pairs use the same global cutoff specified in the pair\_style +All type pairs use the same global cutoff specified in the pair_style command. ---------- @@ -160,7 +160,7 @@ becoming excessively diffuse at very high temperatures were the Gaussian wave packet representation breaks down, and from expanding as free particles to infinite size. If unset, electron radius is free to increase without bounds. If set, a restraining harmonic potential of -the form E = 1/2k\_ss\^2 for s > L\_box/2, where k\_s = 1 Hartrees/Bohr\^2, +the form E = 1/2k_ss\^2 for s > L_box/2, where k_s = 1 Hartrees/Bohr\^2, is applied on the electron radius. The *pressure/evirials* keyword is used to control between two types @@ -179,7 +179,7 @@ representations, after the "ecp" keyword. .. note:: Default ECP parameters are provided for C, N, O, Al, and Si. - Users can modify these using the pair\_coeff command as exemplified + Users can modify these using the pair_coeff command as exemplified above. For this, the User must distinguish between two different functional forms supported, one that captures the orbital overlap assuming the s-type core interacts with an s-like valence electron @@ -191,7 +191,7 @@ representations, after the "ecp" keyword. .. note:: there are two different pressures that can be reported for eFF - when defining this pair\_style, one (default) that considers electrons + when defining this pair_style, one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial electronic contributions to the virials are only tallied if the @@ -264,7 +264,7 @@ dihydride. For atom type pairs I,J and I != J, the cutoff distance for the *eff/cut* style can be mixed. The default mix value is *geometric*\ . -See the "pair\_modify" command for details. +See the "pair_modify" command for details. The :doc:`pair_modify ` shift option is not relevant for these pair styles. @@ -277,7 +277,7 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the @@ -310,7 +310,7 @@ Related commands Default """"""" -If not specified, limit\_eradius = 0 and pressure\_with\_evirials = 0. +If not specified, limit_eradius = 0 and pressure_with_evirials = 0. ---------- diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 7eb850c5ac..bb09e10ed2 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -38,8 +38,8 @@ energy of the system E is given by The first term is a double pairwise sum over the J neighbors of all I atoms, where :math:`\phi_{ij}` is a pair potential. The second term sums over -the embedding energy E\_i of atom I, which is a function of its charge -q\_i and the electrical potential :math:`\sigma_i` at its location. E\_i, q\_i, +the embedding energy E_i of atom I, which is a function of its charge +q_i and the electrical potential :math:`\sigma_i` at its location. E_i, q_i, and :math:`sigma_i` are calculated as .. math:: @@ -77,7 +77,7 @@ atoms in the atomic pair. charge on each atom and thus requires you to assign a charge to each atom, e.g. the *charge* or *full* atom styles. This is because the EIM potential infers the charge on an atom from the equation above for - q\_i; you do not assign charges explicitly. + q_i; you do not assign charges explicitly. ---------- @@ -90,15 +90,15 @@ A system with any combination of these elements can be modeled. This file is parameterized in terms of LAMMPS :doc:`metal units `. Note that unlike other potentials, cutoffs for EIM potentials are not -set in the pair\_style or pair\_coeff command; they are specified in the +set in the pair_style or pair_coeff command; they are specified in the EIM potential file itself. Likewise, the EIM potential file lists atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. -Only a single pair\_coeff command is used with the *eim* style which +Only a single pair_coeff command is used with the *eim* style which specifies an EIM potential file and the element(s) to extract information for. The EIM elements are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair\_coeff +specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * Elem1, Elem2, ... @@ -111,7 +111,7 @@ to specify the path for the potential file. As an example like one of those above, suppose you want to model a system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Na, and the 4th to be Cl, you would -use the following pair\_coeff command: +use the following pair_coeff command: .. code-block:: LAMMPS @@ -147,9 +147,9 @@ radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive energy (LAMMPS ignores it), and q0 (must be 0). Lines starting with "pair:" are entered as: element 1, element 2, -r\_(c,phi), r\_(c,phi) (redundant for historical reasons), E\_b, r\_e, -alpha, beta, r\_(c,eta), A\_(eta), r\_(s,eta), r\_(c,psi), A\_(psi), zeta, -r\_(s,psi), and p. +r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e, +alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta, +r_(s,psi), and p. The lines in the file can be in any order; LAMMPS extracts the info it needs. diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index 823da19ccc..7f2be1817a 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -164,7 +164,7 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction. -This style does not support the pair\_modify tail option for adding long-range +This style does not support the pair_modify tail option for adding long-range tail corrections to energy and pressure for the A,C terms in the pair interaction. diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst index ab15d56d9f..8e5bc3ac9f 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -33,7 +33,7 @@ none Related commands """""""""""""""" -"pair\_tersoff" pair\_tersoff.html +"pair_tersoff" pair_tersoff.html **Default:** none diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index e8cef41eda..c8f7d0d7ab 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -242,7 +242,7 @@ or by mixing as described below: * cutoff2 (distance units) The latter two coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair\_style command are used. +LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this @@ -406,7 +406,7 @@ The *morse/soft* pair style does not support the :doc:`pair_modify pressure. All of these pair styles write information to :doc:`binary restart files -`, so pair\_style and pair\_coeff commands do not need to be specified +`, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. ---------- diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index b1bab752df..1f183c00b9 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -117,22 +117,22 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -For atom type pairs I,J and I != J, the A, B, H, sigma\_h, r\_mh +For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh parameters, and the cutoff distance for these pair styles can be mixed: A (energy units) sqrt(1/B) (distance units, see below) H (energy units) -sigma\_h (distance units) -r\_mh (distance units) +sigma_h (distance units) +r_mh (distance units) cutoff (distance units):ul The default mix value is *geometric*\ . Only *arithmetic* and *geometric* mix values are supported. -See the "pair\_modify" command for details. +See the "pair_modify" command for details. The A and H parameters are mixed using the same rules normally used to mix the "epsilon" parameter in a Lennard Jones interaction. -The sigma\_h, r\_mh, and the cutoff distance are mixed using the same +The sigma_h, r_mh, and the cutoff distance are mixed using the same rules used to mix the "sigma" parameter in a Lennard Jones interaction. The B parameter is converted to a distance (sigma), before mixing (using sigma=B\^-0.5), and converted back to a coefficient @@ -154,7 +154,7 @@ interaction. The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. -These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 1d73c6ef8b..e6cf480852 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -98,7 +98,7 @@ commands, or by mixing as described below: * cutoff (distance units) The last coefficient is optional. If not specified, the global -cutoff specified in the pair\_style command is used. +cutoff specified in the pair_style command is used. It is typical with the Gay-Berne potential to define :math:`\sigma` as the minimum of the 3 shape diameters of the particles involved in an I,I @@ -108,7 +108,7 @@ meaning for :math:`\sigma` than the :doc:`pair_style resquared The :math:`\epsilon_i` and :math:`\epsilon_j` coefficients are actually defined for atom types, not for pairs of atom types. Thus, in a series -of pair\_coeff commands, they only need to be specified once for each +of pair_coeff commands, they only need to be specified once for each atom type. Specifically, if any of :math:`\epsilon_{i,a}`, :math:`\epsilon_{i,b}`, @@ -116,20 +116,20 @@ Specifically, if any of :math:`\epsilon_{i,a}`, :math:`\epsilon_{i,b}`, atom type I. If all the :math:`\epsilon_i` values are zero, they are ignored. If any of :math:`\epsilon_{j,a}`, :math:`\epsilon_{j,b}`, :math:`\epsilon_{j,c}` are non-zero, the three values are assigned to -atom type J. If all three epsilon\_j values are zero, they are ignored. +atom type J. If all three epsilon_j values are zero, they are ignored. Thus the typical way to define the :math:`\epsilon_i` and -:math:`\epsilon_j` coefficients is to list their values in "pair\_coeff +:math:`\epsilon_j` coefficients is to list their values in "pair_coeff I J" commands when I = J, but set them to 0.0 when I != J. If you do list them when I != J, you should insure they are consistent with their -values in other pair\_coeff commands, since only the last setting will +values in other pair_coeff commands, since only the last setting will be in effect. Note that if this potential is being used as a sub-style of -:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair_coeff I I" setting made for Gay-Berne for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the :math:`\epsilon` a,b,c coefficients are assigned to -that type. e.g. in a "pair\_coeff I J" command. +that type. e.g. in a "pair_coeff I J" command. .. note:: @@ -142,13 +142,13 @@ that type. e.g. in a "pair\_coeff I J" command. as the standard LJ parameters. This is much cheaper to compute than the full Gay-Berne formula. To treat the particle as a LJ sphere with sigma = D, you should normally set :math:`\epsilon` a = b = c = - 1.0, set the pair\_coeff :math:`\sigma = D`, and also set the 3 shape + 1.0, set the pair_coeff :math:`\sigma = D`, and also set the 3 shape parameters for the particle to D. The one exception is that if the 3 shape parameters are set to 0.0, which is a valid way in LAMMPS to specify a point particle, then the Gay-Berne potential will treat that as shape parameters of 1.0 (i.e. a LJ particle with :math:`\sigma = 1`), since it requires finite-size particles. In - this case you should still set the pair\_coeff :math:`\sigma` to 1.0 + this case you should still set the pair_coeff :math:`\sigma` to 1.0 as well. ---------- @@ -177,7 +177,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for this pair style can be mixed. The default mix -value is *geometric*\ . See the "pair\_modify" command for details. +value is *geometric*\ . See the "pair_modify" command for details. This pair styles supports the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair @@ -192,7 +192,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 6327f09f35..3cfe946e41 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -31,8 +31,8 @@ Syntax * style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history* * Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) * Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) -* gamma\_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) -* gamma\_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) +* gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) +* gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) * xmu = static yield criterion (unitless value between 0.0 and 1.0e4) * dampflag = 0 or 1 if tangential damping force is excluded or included @@ -41,8 +41,8 @@ Syntax Versions of LAMMPS before 9Jan09 had different style names for granular force fields. This is to emphasize the fact that the Hertzian equation has changed to model polydispersity more accurately. - A side effect of the change is that the Kn, Kt, gamma\_n, and gamma\_t - coefficients in the pair\_style command must be specified with + A side effect of the change is that the Kn, Kt, gamma_n, and gamma_t + coefficients in the pair_style command must be specified with different values in order to reproduce calculations made with earlier versions of LAMMPS, even for monodisperse systems. See the NOTE below for details. @@ -104,14 +104,14 @@ The other quantities in the equations are as follows: * :math:`K_t` = elastic constant for tangential contact * :math:`\gamma_n` = viscoelastic damping constant for normal contact * :math:`\gamma_t` = viscoelastic damping constant for tangential contact -* :math:`m_{eff} = M_i M_j / (M_i + M_j) =` effective mass of 2 particles of mass M\_i and M\_j +* :math:`m_{eff} = M_i M_j / (M_i + M_j) =` effective mass of 2 particles of mass M_i and M_j * :math:`\mathbf{\Delta s}_t =` tangential displacement vector between 2 particles which is truncated to satisfy a frictional yield criterion * :math:`n_{ij} =` unit vector along the line connecting the centers of the 2 particles * :math:`V_n =` normal component of the relative velocity of the 2 particles * :math:`V_t =` tangential component of the relative velocity of the 2 particles The :math:`K_n`, :math:`K_t`, :math:`\gamma_n`, and :math:`\gamma_t` -coefficients are specified as parameters to the pair\_style command. If +coefficients are specified as parameters to the pair_style command. If a NULL is used for :math:`K_t`, then a default value is used where :math:`K_t = 2/7 K_n`. If a NULL is used for :math:`\gamma_t`, then a default value is used where :math:`\gamma_t = 1/2 \gamma_n`. @@ -170,7 +170,7 @@ Hookean styles may not be a suitable model for polydisperse systems. of diameter 1, all 4 of these coefficients should now be set 2x larger than they were previously. -Xmu is also specified in the pair\_style command and is the upper limit +Xmu is also specified in the pair_style command and is the upper limit of the tangential force through the Coulomb criterion Ft = xmu\*Fn, where Ft and Fn are the total tangential and normal force components in the formulas above. Thus in the Hookean case, the tangential force @@ -186,7 +186,7 @@ holds, though the spring is no longer linear. for modeling of systems which can sustain very large tangential forces. -The effective mass *m\_eff* is given by the formula above for two +The effective mass *m_eff* is given by the formula above for two isolated particles. If either particle is part of a rigid body, its mass is replaced by the mass of the rigid body in the formula above. This is determined by searching for a :doc:`fix rigid ` @@ -194,7 +194,7 @@ command (or its variants). For granular styles there are no additional coefficients to set for each pair of atom types via the :doc:`pair_coeff ` command. -All settings are global and are made via the pair\_style command. +All settings are global and are made via the pair_style command. However you must still use the :doc:`pair_coeff ` for all pairs of granular atom types. For example the command @@ -205,7 +205,7 @@ pairs of granular atom types. For example the command should be used if all atoms in the simulation interact via a granular potential (i.e. one of the pair styles above is used). If a granular potential is used as a sub-style of :doc:`pair_style hybrid `, then specific atom types can be used in the -pair\_coeff command to determine which atoms interact via a granular +pair_coeff command to determine which atoms interact via a granular potential. ---------- @@ -235,7 +235,7 @@ instructions on how to use the accelerated styles effectively. The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for granular pair styles. -These pair styles write their information to :doc:`binary restart files `, so a pair\_style command does not need to be +These pair styles write their information to :doc:`binary restart files `, so a pair_style command does not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index d8dc7b3b3e..73b1ec85ec 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -65,12 +65,12 @@ on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions are based on a DMT cohesive model (see below). In that example, 1-1 and 2-2 interactions have different model forms, in which case mixing of coefficients cannot be determined, so 1-2 interactions must be -explicitly defined via the *pair\_coeff 1 \** command, otherwise an +explicitly defined via the *pair_coeff 1 \** command, otherwise an error would result. ---------- -The first required keyword for the *pair\_coeff* command is the normal +The first required keyword for the *pair_coeff* command is the normal contact model. Currently supported options for normal contact models and their required arguments are: @@ -170,7 +170,7 @@ following general form: Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot \mathbf{n} \mathbf{n}` is the component of relative velocity along :math:`\mathbf{n}`. -The optional *damping* keyword to the *pair\_coeff* command followed by +The optional *damping* keyword to the *pair_coeff* command followed by a keyword determines the model form of the damping factor :math:`\eta_n`, and the interpretation of the :math:`\eta_{n0}` or :math:`e` coefficients specified as part of the normal contact model settings. The *damping* @@ -181,7 +181,7 @@ other settings, potentially also the twisting damping). The options for the damping model currently supported are: 1. *velocity* -2. *mass\_velocity* +2. *mass_velocity* 3. *viscoelastic* 4. *tsuji* @@ -198,7 +198,7 @@ user-specified damping coefficient in the *normal* model: Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal contact model, in units of *mass*\ /\ *time*\ . -For *damping mass\_velocity*, the normal damping is given by: +For *damping mass_velocity*, the normal damping is given by: .. math:: @@ -207,7 +207,7 @@ For *damping mass\_velocity*, the normal damping is given by: Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal contact model, in units of *mass*\ /\ *time* and :math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass. -Use *damping mass\_velocity* to reproduce the damping behavior of +Use *damping mass_velocity* to reproduce the damping behavior of *pair gran/hooke/\**. The *damping viscoelastic* model is based on the viscoelastic @@ -251,24 +251,24 @@ damping components: ---------- -The *pair\_coeff* command also requires specification of the tangential +The *pair_coeff* command also requires specification of the tangential contact model. The required keyword *tangential* is expected, followed by the model choice and associated parameters. Currently supported tangential model choices and their expected parameters are as follows: -1. *linear\_nohistory* : :math:`x_{\gamma,t}`, :math:`\mu_s` -2. *linear\_history* : :math:`k_t`, :math:`x_{\gamma,t}`, :math:`\mu_s` +1. *linear_nohistory* : :math:`x_{\gamma,t}`, :math:`\mu_s` +2. *linear_history* : :math:`k_t`, :math:`x_{\gamma,t}`, :math:`\mu_s` 3. *mindlin* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s` -4. *mindlin\_rescale* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s` +4. *mindlin_rescale* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s` Here, :math:`x_{\gamma,t}` is a dimensionless multiplier for the normal damping :math:`\eta_n` that determines the magnitude of the tangential damping, :math:`\mu_t` is the tangential (or sliding) friction coefficient, and :math:`k_t` is the tangential stiffness coefficient. -For *tangential linear\_nohistory*, a simple velocity-dependent Coulomb +For *tangential linear_nohistory*, a simple velocity-dependent Coulomb friction criterion is used, which mimics the behavior of the *pair -gran/hooke* style. The tangential force (\mathbf{F}\_t\) is given by: +gran/hooke* style. The tangential force (\mathbf{F}_t\) is given by: .. math:: @@ -321,10 +321,10 @@ Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and The remaining tangential options all use accumulated tangential displacement (i.e. contact history). This is discussed below in the -context of the *linear\_history* option, but the same treatment of the +context of the *linear_history* option, but the same treatment of the accumulated displacement applies to the other options as well. -For *tangential linear\_history*, the tangential force is given by: +For *tangential linear_history*, the tangential force is given by: .. math:: @@ -387,7 +387,7 @@ overlap region) to induce a torque on each particle according to: \mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t -For *tangential mindlin*\ , the :ref:`Mindlin ` no-slip solution is used, which differs from the *linear\_history* +For *tangential mindlin*\ , the :ref:`Mindlin ` no-slip solution is used, which differs from the *linear_history* option by an additional factor of *a*\ , the radius of the contact region. The tangential force is given by: .. math:: @@ -409,7 +409,7 @@ case, mixing of the shear modulus for different particle types *i* and 1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j -The *mindlin\_rescale* option uses the same form as *mindlin*\ , but the +The *mindlin_rescale* option uses the same form as *mindlin*\ , but the magnitude of the tangential displacement is re-scaled as the contact unloads, i.e. if :math:`a < a_{t_{n-1}}`: @@ -524,9 +524,9 @@ if the twisting torque exceeds this critical value: For *twisting sds*\ , the coefficients :math:`k_{twist}, \gamma_{twist}` and :math:`\mu_{twist}` are simply the user input parameters that follow -the *twisting sds* keywords in the *pair\_coeff* command. +the *twisting sds* keywords in the *pair_coeff* command. -For *twisting\_marshall*, the coefficients are expressed in terms of +For *twisting_marshall*, the coefficients are expressed in terms of sliding friction coefficients, as discussed in :ref:`Marshall ` (see equations 32 and 33 of that work): @@ -568,22 +568,22 @@ The third example is equivalent to ---------- -LAMMPS automatically sets pairwise cutoff values for *pair\_style +LAMMPS automatically sets pairwise cutoff values for *pair_style granular* based on particle radii (and in the case of *jkr* pull-off distances). In the vast majority of situations, this is adequate. -However, a cutoff value can optionally be appended to the *pair\_style +However, a cutoff value can optionally be appended to the *pair_style granular* command to specify a global cutoff (i.e. a cutoff for all atom types). Additionally, the optional *cutoff* keyword can be passed -to the *pair\_coeff* command, followed by a cutoff value. This will -set a pairwise cutoff for the atom types in the *pair\_coeff* command. +to the *pair_coeff* command, followed by a cutoff value. This will +set a pairwise cutoff for the atom types in the *pair_coeff* command. These options may be useful in some rare cases where the automatic cutoff determination is not sufficient, e.g. if particle diameters are being modified via the *fix adapt* command. In that case, the -global cutoff specified as part of the *pair\_style granular* command +global cutoff specified as part of the *pair_style granular* command is applied to all atom types, unless it is overridden for a given atom type combination by the *cutoff* value specified in the *pair coeff* command. If *cutoff* is only specified in the *pair coeff* command -and no global cutoff is appended to the *pair\_style granular* command, +and no global cutoff is appended to the *pair_style granular* command, then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. @@ -620,7 +620,7 @@ most quantities, e.g. if friction coefficient for type 1-type 1 interactions is set to :math:`\mu_1`, and friction coefficient for type 2-type 2 interactions is set to :math:`\mu_2`, the friction coefficient for type1-type2 interactions is computed as :math:`\sqrt{\mu_1\mu_2}` -(unless explicitly specified to a different value by a *pair\_coeff 1 2 +(unless explicitly specified to a different value by a *pair_coeff 1 2 ...* command). The exception to this is elastic modulus, only applicable to *hertz/material*\ , *dmt* and *jkr* normal contact models. In that case, the effective elastic modulus is computed as: @@ -642,7 +642,7 @@ or E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})} -These pair styles write their information to :doc:`binary restart files `, so a pair\_style command does not need to be +These pair styles write their information to :doc:`binary restart files `, so a pair_style command does not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the @@ -661,7 +661,7 @@ particle I. The next entry (8) is the magnitude of the rolling torque. The next entry (9) is the magnitude of the twisting torque acting about the vector connecting the two particle centers. The last 3 (10-12) are the components of the vector connecting -the centers of the two particles (x\_I - x\_J). +the centers of the two particles (x_I - x_J). These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., *p12*\ . @@ -697,7 +697,7 @@ Related commands Default """"""" -For the *pair\_coeff* settings: *damping viscoelastic*\ , *rolling none*\ , +For the *pair_coeff* settings: *damping viscoelastic*\ , *rolling none*\ , *twisting none*\ . **References:** diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 234e7c6894..121181a90d 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -77,7 +77,7 @@ the coarse-grained models of :ref:`(Marrink) `. coefficients A, B, and C are computed by LAMMPS to perform the shifting and smoothing. The function S(r) is actually applied once to each term of the LJ formula and once to the Coulombic formula, so there are 2 or 3 -sets of A,B,C coefficients depending on which pair\_style is used. The +sets of A,B,C coefficients depending on which pair_style is used. The boundary conditions applied to the smoothing function are as follows: :math:`S'(r_1) = S''(r_1) = 0, S(r_c) = -E(r_c), S'(r_c) = -E'(r_c)`, and :math:`S''(r_c) = -E''(r_c)`, where E(r) is the corresponding term @@ -87,7 +87,7 @@ respectively. The inner and outer cutoff for the LJ and Coulombic terms can be the same or different depending on whether 2 or 4 arguments are used in -the pair\_style command. The inner LJ cutoff must be > 0, but the +the pair_style command. The inner LJ cutoff must be > 0, but the inner Coulombic cutoff can be >= 0. The following coefficients must be defined for each pair of atoms @@ -111,7 +111,7 @@ are used. The last 2 coefficients cannot be used with style *lj/gromacs/coul/gromacs* because this force field does not allow varying cutoffs for individual atom pairs; all pairs use the global -cutoff(s) specified in the pair\_style command. +cutoff(s) specified in the pair_style command. ---------- @@ -139,7 +139,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is *geometric*\ . See the "pair\_modify" command +The default mix value is *geometric*\ . See the "pair_modify" command for details. None of the GROMACS pair styles support the @@ -155,7 +155,7 @@ None of the GROMACS pair styles support the corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. -All of the GROMACS pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do +All of the GROMACS pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. All of the GROMACS pair styles can only be used via the *pair* diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 33ddaf2a10..d2d1283618 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -41,10 +41,10 @@ to release the code anyway with only the technical explanations. For details of the model and the parameters, please refer to the linked publication. -Only a single pair\_coeff command is used with the *gw* and *gw/zbl* +Only a single pair_coeff command is used with the *gw* and *gw/zbl* styles which specifies a Gao-Weber potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair\_coeff +specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -55,7 +55,7 @@ to specify the path for the potential file. As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the first 3 to -be Si, and the 4th to be C, you would use the following pair\_coeff command: +be Si, and the 4th to be C, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -89,7 +89,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 9c02311008..0f5470d5f9 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -21,9 +21,9 @@ Syntax * style = *hbond/dreiding/lj* or *hbond/dreiding/morse* * n = cosine angle periodicity -* inner\_distance\_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units) -* outer\_distance\_cutoff = global cutoff for Donor-Acceptor interactions (distance units) -* angle\_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor +* inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units) +* outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units) +* angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor * interactions (degrees) Examples @@ -112,7 +112,7 @@ on the DREIDING force field. In the original Dreiding force field paper 1-4 non-bonded interactions ARE allowed. If this is desired for your model, use the - special\_bonds command (e.g. "special\_bonds lj 0.0 0.0 1.0") to turn + special_bonds command (e.g. "special_bonds lj 0.0 0.0 1.0") to turn these interactions on. ---------- @@ -125,7 +125,7 @@ in the examples above. Unlike other pair styles and their associated :doc:`pair_coeff ` commands, you do not need to specify - pair\_coeff settings for all possible I,J type pairs. Only I,J type + pair_coeff settings for all possible I,J type pairs. Only I,J type pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. @@ -134,11 +134,11 @@ in the examples above. A :doc:`pair_coeff ` command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. - For other pair\_styles, if the pair\_coeff command is re-used for the + For other pair_styles, if the pair_coeff command is re-used for the same I.J type pair, the settings for that type pair are overwritten. For the hydrogen bond potentials this is not the case; the settings are cumulative. This means the only way to turn off a previous - setting, is to re-use the pair\_style command and start over. + setting, is to re-use the pair_style command and start over. For the *hbond/dreiding/lj* style the list of coefficients is as follows: @@ -171,9 +171,9 @@ select multiple types as hydrogen atoms. This takes the form "\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair_coeff ` command doc page for details. -If the donor flag is *i*\ , then the atom of type I in the pair\_coeff +If the donor flag is *i*\ , then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor -flag is *j*\ , then the atom of type J in the pair\_coeff command is +flag is *j*\ , then the atom of type J in the pair_coeff command is treated as the donor and I is the donor. This option is required because the :doc:`pair_coeff ` command requires that I <= J. @@ -187,7 +187,7 @@ hydrogen bond potential based on a Morse functional form. The last 3 coefficients for both styles are optional. If not specified, the global n, distance cutoff, and angle cutoff specified -in the pair\_style command are used. If you wish to only override the +in the pair_style command are used. If you wish to only override the 2nd or 3rd optional parameter, you must also specify the preceding optional parameters. @@ -228,7 +228,7 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles do not write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands need to be +These pair styles do not write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands need to be re-specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 9a3c1af423..8e40466faf 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -58,7 +58,7 @@ using *lj/cut* and *coul/long* together gives the same result as if the *lj/cut/coul/long* potential were used by itself. In this case, it would be more efficient to use the single combined potential, but in general any combination of pair potentials can be used together in -to produce an interaction that is not encoded in any single pair\_style +to produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles. All pair styles that will be used are listed as "sub-styles" following @@ -76,7 +76,7 @@ a Tersoff potential for pure C for the other set (presumably with some could be listed twice. But if you just want to use a Lennard-Jones or other pairwise potential for several different atom type pairs in your model, then you should just list the sub-style once and use the -pair\_coeff command to assign parameters for the different type pairs. +pair_coeff command to assign parameters for the different type pairs. .. note:: @@ -85,10 +85,10 @@ pair\_coeff command to assign parameters for the different type pairs. This is because the GPU package currently assumes that only one instance of a pair style is being used. -In the pair\_coeff commands, the name of a pair style must be added +In the pair_coeff commands, the name of a pair style must be added after the I,J type specification, with the remaining coefficients being those appropriate to that style. If the pair style is used -multiple times in the pair\_style command, then an additional numeric +multiple times in the pair_style command, then an additional numeric argument must also be specified which is a number from 1 to M where M is the number of times the sub-style was listed in the pair style command. The extra number indicates which instance of the sub-style @@ -129,7 +129,7 @@ each line in the "Pair Coeffs" section, e.g. 1 lj/cut/coul/cut 1.0 1.0 ... -Note that the pair\_coeff command for some potentials such as +Note that the pair_coeff command for some potentials such as :doc:`pair_style eam/alloy ` includes a mapping specification of elements to all atom types, which in the hybrid case, can include atom types not assigned to the *eam/alloy* potential. The NULL @@ -139,18 +139,18 @@ sub-style. For the *hybrid* style, each atom type pair I,J is assigned to exactly one sub-style. Just as with a simulation using a single pair style, -if you specify the same atom type pair in a second pair\_coeff command, +if you specify the same atom type pair in a second pair_coeff command, the previous assignment will be overwritten. For the *hybrid/overlay* style, each atom type pair I,J can be assigned to one or more sub-styles. If you specify the same atom type -pair in a second pair\_coeff command with a new sub-style, then the +pair in a second pair_coeff command with a new sub-style, then the second sub-style is added to the list of potentials that will be calculated for two interacting atoms of those types. If you specify -the same atom type pair in a second pair\_coeff command with a +the same atom type pair in a second pair_coeff command with a sub-style that has already been defined for that pair of atoms, then the new pair coefficients simply override the previous ones, as in the -normal usage of the pair\_coeff command. E.g. these two sets of +normal usage of the pair_coeff command. E.g. these two sets of commands are the same: .. code-block:: LAMMPS @@ -181,7 +181,7 @@ sub-style and use the :doc:`neigh_modify exclude type ` command. You can assign it to some sub-style and set the coefficients so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you -can use this form of the pair\_coeff command in your input script: +can use this form of the pair_coeff command in your input script: .. code-block:: LAMMPS @@ -265,7 +265,7 @@ individual sub-style can be accessed and output via the :doc:`compute pair ` command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body @@ -373,12 +373,12 @@ sub-styles of the hybrid potential. For atom type pairs I,J and I != J, if the sub-style assigned to I,I and J,J is the same, and if the sub-style allows for mixing, then the coefficients for I,J can be mixed. This means you do not have to -specify a pair\_coeff command for I,J since the I,J type pair will be +specify a pair_coeff command for I,J since the I,J type pair will be assigned automatically to the sub-style defined for both I,I and J,J and its coefficients generated by the mixing rule used by that sub-style. For the *hybrid/overlay* style, there is an additional requirement that both the I,I and J,J pairs are assigned to a single -sub-style. See the "pair\_modify" command for details of mixing rules. +sub-style. See the "pair_modify" command for details of mixing rules. See the See the doc page for the sub-style to see if allows for mixing. @@ -390,7 +390,7 @@ For the hybrid pair styles, the list of sub-styles and their respective settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart -file. Thus, pair\_coeff commands need to be re-specified in the +file. Thus, pair_coeff commands need to be re-specified in the restart input script. These pair styles support the use of the *inner*\ , *middle*\ , and @@ -401,7 +401,7 @@ Restrictions """""""""""" When using a long-range Coulombic solver (via the -:doc:`kspace_style ` command) with a hybrid pair\_style, +:doc:`kspace_style ` command) with a hybrid pair_style, one or more sub-styles will be of the "long" variety, e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the short-range Coulombic cutoff used by each of these long pair styles is diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 03ac896f1f..22f4a37380 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -11,7 +11,7 @@ Syntax pair_style [hybrid/overlay ...] ilp/graphene/hbn cutoff tap_flag * 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 """""""" @@ -104,14 +104,14 @@ list for calculating the normals for each atom pair. be found in :ref:`(Ouyang1) ` and :ref:`(Ouyang2) `. This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair\_style *none*\ . +Other interactions can be set to zero using pair_style *none*\ . This pair style tallies a breakdown of the total interlayer potential energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 2. The 2 values correspond to the following sub-categories: -1. *E\_vdW* = vdW (attractive) energy -2. *E\_Rep* = Repulsive energy +1. *E_vdW* = vdW (attractive) energy +2. *E_Rep* = Repulsive energy To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: @@ -127,12 +127,12 @@ headings) the following commands could be included in an input script: **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the pair\_modify mix, shift, table, and +This pair style does not support the pair_modify mix, shift, table, and tail options. This pair style does not write their information to binary restart files, since it is stored in potential files. Thus, you need to -re-specify the pair\_style and pair\_coeff commands in an input script +re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. Restrictions @@ -157,12 +157,12 @@ Related commands :doc:`pair_none `, :doc:`pair_style hybrid/overlay `, :doc:`pair_style drip `, -:doc:`pair_style pair\_kolmogorov\_crespi\_z `, -:doc:`pair_style pair\_kolmogorov\_crespi\_full `, -:doc:`pair_style pair\_lebedeva\_z `, -:doc:`pair_style pair\_coul\_shield `. +:doc:`pair_style pair_kolmogorov_crespi_z `, +:doc:`pair_style pair_kolmogorov_crespi_full `, +:doc:`pair_style pair_lebedeva_z `, +:doc:`pair_style pair_coul_shield `. -**Default:** tap\_flag = 1 +**Default:** tap_flag = 1 ---------- diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 4a134f7037..7717545f21 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -33,12 +33,12 @@ KIM API Portable Model Interface (PMI) and can be used by any simulation code that conforms to the KIM API/PMI, and "KIM Simulator Models" that are natively implemented within a single simulation code (like LAMMPS) and can only be used with it. -The *pair\_style kim* command is limited to KIM PMs. It is +The *pair_style kim* command is limited to KIM PMs. It is used by the :doc:`kim_commands interface ` as needed. .. note:: - Since *pair\_style kim* is called by *kim\_interactions* as needed, + Since *pair_style kim* is called by *kim_interactions* as needed, is not recommended to be directly used in input scripts. ---------- @@ -51,17 +51,17 @@ be incompatibilities (for example due to unit matching issues). In the event of an incompatibility, the code will terminate with an error message. Check both the LAMMPS and KIM log files for details. -Only a single *pair\_coeff* command is used with the *kim* style, which +Only a single *pair_coeff* command is used with the *kim* style, which specifies the mapping of LAMMPS atom types to the species supported by the KIM PM. This is done by specifying *N* additional arguments -after the \* \* in the *pair\_coeff* command, where *N* is the number of +after the \* \* in the *pair_coeff* command, where *N* is the number of LAMMPS atom types: * N element names = mapping of KIM elements to atom types For example, consider a KIM PM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, -and the fourth is C, the following *pair\_coeff* command would be used: +and the fourth is C, the following *pair_coeff* command would be used: .. code-block:: LAMMPS @@ -92,7 +92,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since KIM stores the potential parameters. -Thus, you need to re-specify the pair\_style and pair\_coeff commands in +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -107,7 +107,7 @@ Restrictions This pair style is part of the KIM package. See details on restrictions in :doc:`kim_commands `. -This current version of pair\_style kim is compatible with the +This current version of pair_style kim is compatible with the kim-api package version 2.0.0 and higher. Related commands diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index f1a647f7a0..8d9adf0341 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -11,7 +11,7 @@ Syntax pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag * 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 """""""" @@ -72,10 +72,10 @@ list for calculating the normals for each atom pair. .. note:: Two new sets of parameters of KC potential for hydrocarbons, CH.KC - (without the taper function) and CH\_taper.KC (with the taper function) + (without the taper function) and CH_taper.KC (with the taper function) are presented in :ref:`(Ouyang1) `. The energy for the KC potential with the taper function goes continuously to zero at the cutoff. The - parameters in both CH.KC and CH\_taper.KC provide a good description in + parameters in both CH.KC and CH_taper.KC provide a good description in both short- and long-range interaction regimes. While the original parameters (CC.KC) published in :ref:`(Kolmogorov) ` are only suitable for long-range interaction regime. This feature is essential @@ -84,14 +84,14 @@ list for calculating the normals for each atom pair. comparison of these parameters can be found in :ref:`(Ouyang1) ` and :ref:`(Ouyang2) `. This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair\_style *none*\ . +Other interactions can be set to zero using pair_style *none*\ . This pair style tallies a breakdown of the total interlayer potential energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 2. The 2 values correspond to the following sub-categories: -1. *E\_vdW* = vdW (attractive) energy -2. *E\_Rep* = Repulsive energy +1. *E_vdW* = vdW (attractive) energy +2. *E_Rep* = Repulsive energy To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: @@ -107,12 +107,12 @@ headings) the following commands could be included in an input script: **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the pair\_modify mix, shift, table, +This pair style does not support the pair_modify mix, shift, table, and tail options. This pair style does not write their information to binary restart files, since it is stored in potential files. Thus, you need to -re-specify the pair\_style and pair\_coeff commands in an input script +re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. Restrictions @@ -137,11 +137,11 @@ Related commands :doc:`pair_none `, :doc:`pair_style hybrid/overlay `, :doc:`pair_style drip `, -:doc:`pair_style pair\_lebedeva\_z `, +:doc:`pair_style pair_lebedeva_z `, :doc:`pair_style kolmogorov/crespi/z `, :doc:`pair_style ilp/graphene/hbn `. -**Default:** tap\_flag = 0 +**Default:** tap_flag = 0 ---------- diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index 0ed073d5af..8b961773a3 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -53,7 +53,7 @@ is available to facilitate scaling of energies in accordance with :ref:`(vanWijk) `. This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair\_style *none*\ . +Other interactions can be set to zero using pair_style *none*\ . Restrictions """""""""""" diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index b39b149a73..4eb7a345ee 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -25,10 +25,10 @@ The *lcbop* pair style computes the long-range bond-order potential for carbon (LCBOP) of :ref:`(Los and Fasolino) `. See section II in that paper for the analytic equations associated with the potential. -Only a single pair\_coeff command is used with the *lcbop* style which +Only a single pair_coeff command is used with the *lcbop* style which specifies an LCBOP potential file with parameters for specific elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -38,7 +38,7 @@ See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want -the 1st 3 to be C you would use the following pair\_coeff command: +the 1st 3 to be C you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -64,7 +64,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index b8217ccdcc..df81d83999 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -48,7 +48,7 @@ The parameter file (e.g. CC.Lebedeva), is intended for use with metal is available to facilitate scaling of energies. This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair\_style *none*\ . +Other interactions can be set to zero using pair_style *none*\ . Restrictions """""""""""" diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index 908b912aea..70077c61f8 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -49,7 +49,7 @@ each pair of points. The LJ interaction between 2 spheres on different line segments (or a sphere on a line segment and a point particles) is computed with sub-particle :math:`\epsilon`, :math:`\sigma`, and *cutoff* values that -are set by the pair\_coeff command, as described below. If the distance +are set by the pair_coeff command, as described below. If the distance between the 2 spheres is greater than the sub-particle cutoff, there is no interaction. This means that some pairs of sub-particles on 2 line segments may interact, but others may not. @@ -57,8 +57,8 @@ segments may interact, but others may not. For purposes of creating the neighbor list for pairs of interacting line segments or lines/point particles, a regular particle-particle cutoff is used, as defined by the *cutoff* setting above in the -pair\_style command or overridden with an optional argument in the -pair\_coeff command for a type pair as discussed below. The distance +pair_style command or overridden with an optional argument in the +pair_coeff command for a type pair as discussed below. The distance between the centers of 2 line segments, or the center of a line segment and a point particle, must be less than this distance (plus the neighbor skin; see the :doc:`neighbor ` command), for @@ -69,7 +69,7 @@ the pair of particles to be included in the neighbor list. This means that a too-short value for the *cutoff* setting can exclude a pair of particles from the neighbor list even if pairs of their sub-particle spheres would interact, based on the sub-particle - cutoff specified in the pair\_coeff command. E.g. sub-particles at the + cutoff specified in the pair_coeff command. E.g. sub-particles at the ends of the line segments that are close to each other. Which may not be what you want, since it means the ends of 2 line segments could pass through each other. It is up to you to specify a *cutoff* @@ -93,7 +93,7 @@ The *sizeI* and *sizeJ* coefficients are the sub-particle sizes for line particles of type I and type J. They are used to define the N sub-particles per segment as described above. These coefficients are actually stored on a per-type basis. Thus if there are multiple -pair\_coeff commands that involve type I, as either the first or +pair_coeff commands that involve type I, as either the first or second atom type, you should use consistent values for sizeI or sizeJ in all of them. If you do not do this, the last value specified for sizeI will apply to all segments of type I. If typeI or typeJ refers diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index e3fc4ac682..93485b3471 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -32,7 +32,7 @@ Description Style *list* computes interactions between explicitly listed pairs of atoms with the option to select functional form and parameters for each individual pair. Because the parameters are set in the list -file, the pair\_coeff command has no parameters (but still needs to be +file, the pair_coeff command has no parameters (but still needs to be provided). The *check* and *nocheck* keywords enable/disable a test that checks whether all listed bonds were present and computed. @@ -119,7 +119,7 @@ pair style. The :doc:`pair_modify ` table and tail options are not relevant for this pair style. -This pair style does not write its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands need +This pair style does not write its information to :doc:`binary restart files `, so pair_style and pair_coeff commands need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index a0b49ee577..21357ab45f 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -225,7 +225,7 @@ Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by where C is an energy-conversion constant, :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric constant which can be set by the :doc:`dielectric ` command. -If one cutoff is specified in the pair\_style command, it is used for +If one cutoff is specified in the pair_style command, it is used for both the LJ and Coulombic terms. If two cutoffs are specified, they are used as cutoffs for the LJ and Coulombic terms respectively. @@ -298,7 +298,7 @@ site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, and the distance to the massless charge site are specified as -pair\_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for +pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for Coulomb interactions; style *lj/cut/tip4p/long* is for use with a long-range Coulombic solver (Ewald or PPPM). @@ -337,7 +337,7 @@ Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`. The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair\_style command are used. +LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this @@ -348,7 +348,7 @@ For *lj/cut/coul/long* and *lj/cut/coul/msm* and *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the -pair\_style command. +pair_style command. ---------- @@ -385,7 +385,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is *geometric*\ . See the "pair\_modify" command +The default mix value is *geometric*\ . See the "pair_modify" command for details. All of the *lj/cut* pair styles support the @@ -401,13 +401,13 @@ All of the *lj/cut* pair styles support the tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction. -All of the *lj/cut* pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do +All of the *lj/cut* pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the *pair* keyword of run\_style respa. +The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. ---------- diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 7c81803e34..3799020a05 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -52,7 +52,7 @@ commands, or by mixing as described below: * cutoff (distance units) The last coefficient is optional. If not specified, the global LJ -cutoff specified in the pair\_style command is used. +cutoff specified in the pair_style command is used. ---------- @@ -80,7 +80,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is *geometric*\ . See the "pair\_modify" command +The default mix value is *geometric*\ . See the "pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift @@ -93,7 +93,7 @@ This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 52f42e5e13..5bf5d873e4 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -94,7 +94,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is *geometric*\ . See the "pair\_modify" command +The default mix value is *geometric*\ . See the "pair_modify" command for details. The lj/cubic pair style does not support the @@ -110,7 +110,7 @@ The lj/cubic pair style does not support the corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. -The lj/cubic pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do +The lj/cubic pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. The lj/cubic pair style can only be used via the *pair* diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index f27eb83631..1478188bbb 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -78,7 +78,7 @@ used. For *lj/expand/coul/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the -pair\_style command. +pair_style command. ---------- @@ -107,8 +107,8 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon, sigma, and shift coefficients and cutoff distance for this pair style can be mixed. Shift is always mixed via an *arithmetic* rule. The other -coefficients are mixed according to the pair\_modify mix value. The -default mix value is *geometric*\ . See the "pair\_modify" command for +coefficients are mixed according to the pair_modify mix value. The +default mix value is *geometric*\ . See the "pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift @@ -121,7 +121,7 @@ This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 7a256256fc..682f11b95b 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -90,13 +90,13 @@ potential parameters, plus the Coulomb potential, given by: where C is an energy-conversion constant, :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, :math:`\epsilon` is the dielectric constant which can be set by the :doc:`dielectric ` command, and :math:`r_c` is the cutoff. If -one cutoff is specified in the pair\_style command, it is used for both +one cutoff is specified in the pair_style command, it is used for both the LJ and Coulombic terms. If two cutoffs are specified, they are used as cutoffs for the LJ and Coulombic terms respectively. The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r\^6 Lennard-Jones and Coulombic 1/r -interactions. This is done by use of the *flag\_lj* and *flag\_coul* +interactions. This is done by use of the *flag_lj* and *flag_coul* settings. The :ref:`In 't Veld ` paper has more details on when it is appropriate to include long-range 1/r\^6 interactions, using this potential. @@ -106,7 +106,7 @@ Style *lj/long/tip4p/long* implements the TIP4P water model of short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, and the distance to the -massless charge site are specified as pair\_style arguments. +massless charge site are specified as pair_style arguments. .. note:: @@ -126,22 +126,22 @@ LJ cutoff >= Coulombic cutoff + 2\*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. -If *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 +If *flag_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range portion can be calculated by using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If -*flag\_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as +*flag_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as with :doc:`pair_style lj/cut `. -If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic +If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of several :doc:`kspace_style ` command options such as -*pppm* or *ewald*\ . Note that if *flag\_lj* is also set to long, then +*pppm* or *ewald*\ . Note that if *flag_lj* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the LJ and Coulombic -interactions. If *flag\_coul* is set to *off*\ , Coulombic interactions +interactions. If *flag_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms @@ -160,22 +160,22 @@ distance for the potential, not as the energy minimum at 2\^(1/6) sigma. The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair\_style command are used. +LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. -Note that if you are using *flag\_lj* set to *long*\ , you +Note that if you are using *flag_lj* set to *long*\ , you cannot specify a LJ cutoff for an atom type pair, since only one -global LJ cutoff is allowed. Similarly, if you are using *flag\_coul* +global LJ cutoff is allowed. Similarly, if you are using *flag_coul* set to *long*\ , you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. For *lj/long/tip4p/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff -specified in the pair\_style command. +specified in the pair_style command. ---------- @@ -210,12 +210,12 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/long pair styles can be mixed. -The default mix value is *geometric*\ . See the "pair\_modify" command +The default mix value is *geometric*\ . See the "pair_modify" command for details. These pair styles support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair -interaction, assuming *flag\_lj* is *cut*\ . +interaction, assuming *flag_lj* is *cut*\ . These pair styles support the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of @@ -225,7 +225,7 @@ Thes pair styles do not support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the Lennard-Jones portion of the energy and pressure. -These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. The pair lj/long/coul/long styles support the use of the *inner*\ , diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 182de5b40c..b2cf6f7493 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -96,8 +96,8 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon, sigma, Rin coefficients and the cutoff distance for this pair style can be mixed. Rin is a cutoff value and is mixed like the cutoff. The other -coefficients are mixed according to the pair\_modify mix option. The -default mix value is *geometric*\ . See the "pair\_modify" command for +coefficients are mixed according to the pair_modify mix option. The +default mix value is *geometric*\ . See the "pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift @@ -111,7 +111,7 @@ tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 41f980d75f..bb93eddd33 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -50,7 +50,7 @@ commands, or by mixing as described below: * cutoff (distance units) The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair\_style command is used. +LJ cutoff specified in the pair_style command is used. ---------- @@ -78,7 +78,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance can be mixed. The default mix value is geometric. -See the "pair\_modify" command for details. +See the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction, since it goes @@ -92,7 +92,7 @@ tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 9f7ab4cf22..24374658e3 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -41,7 +41,7 @@ vdW potential E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right] -, which goes smoothly to zero at the cutoff r\_c as defined +, which goes smoothly to zero at the cutoff r_c as defined by the switching function .. math:: diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index 4b7564266e..f2510686a9 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -47,8 +47,8 @@ upon initialization. .. note:: Thus when used as the only interaction in the system, there is no - corresponding pair\_coeff command and when used with other pair styles using the - hybrid/overlay option, the corresponding pair\_coeff command must be supplied + corresponding pair_coeff command and when used with other pair styles using the + hybrid/overlay option, the corresponding pair_coeff command must be supplied \* \* as placeholders for the atom types. ---------- @@ -139,14 +139,14 @@ which atom types to use in the calculation of the LD; :math:`b_{\beta} = Of course, a system with many atom types may have many different possible LD potentials, each with their own atom type filters, cutoffs, and embedding functions. The most general form of this potential as implemented in the -pair\_style local/density is: +pair_style local/density is: .. math:: U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] where, *k* is an index that spans the (arbitrary) number of applied LD -potentials N\_LD. Each LD is calculated as before with: +potentials N_LD. Each LD is calculated as before with: .. math:: @@ -154,12 +154,12 @@ potentials N\_LD. Each LD is calculated as before with: The superscript on the indicator function phi simply indicates that it is associated with specific values of the cutoff distances R1(k) and R2(k). In -summary, there may be N\_LD distinct LD potentials. With each potential type (k), +summary, there may be N_LD distinct LD potentials. With each potential type (k), one must specify: * the inner and outer cutoffs as R1 and R2 -* the central type filter a(k), where k = 1,2,...N\_LD -* the neighbor type filter b(k), where k = 1,2,...N\_LD +* the central type filter a(k), where k = 1,2,...N_LD +* the neighbor type filter b(k), where k = 1,2,...N_LD * the LD potential function F(k)(rho), typically as a table that is later spline-interpolated ---------- @@ -189,8 +189,8 @@ one must specify: Block N_LD -Lines 5 to 9+N\_rho constitute the first block. Thus the input file is separated -(by blank lines) into N\_LD blocks each representing a separate LD potential and +Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated +(by blank lines) into N_LD blocks each representing a separate LD potential and each specifying its own upper and lower cutoffs, central and neighbor atoms, and potential. In general, blank lines anywhere are ignored. @@ -211,7 +211,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The local/density pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair\_style and pair\_coeff commands in +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. ---------- diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 602d40de6b..563b88920e 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -96,7 +96,7 @@ particles, :math:`U^{\infty}` represents the velocity and the angular velocity of the undisturbed fluid, and :math:`E^{\infty}` represents the rate of strain tensor of the undisturbed fluid with viscosity *mu*\ . Again, note that this is dynamic viscosity which has units of mass/distance/time, not -kinematic viscosity. Volume fraction corrections to R\_FU are included +kinematic viscosity. Volume fraction corrections to R_FU are included as long as *flagVF* is set to 1 (default). .. note:: @@ -110,7 +110,7 @@ Style *lubricate* requires monodisperse spherical particles; style *lubricate/poly* allows for polydisperse spherical particles. The viscosity *mu* can be varied in a time-dependent manner over the -course of a simulation, in which case in which case the pair\_style +course of a simulation, in which case in which case the pair_style setting for *mu* will be overridden. See the :doc:`fix adapt ` command for details. @@ -118,9 +118,9 @@ If the suspension is sheared via the :doc:`fix deform ` command then the pair style uses the shear rate to adjust the hydrodynamic interactions accordingly. Volume changes due to fix deform are accounted for when computing the volume fraction -corrections to R\_FU. +corrections to R_FU. -When computing the volume fraction corrections to R\_FU, the presence +When computing the volume fraction corrections to R_FU, the presence of walls (whether moving or stationary) will affect the volume fraction available to colloidal particles. This is currently accounted for with the following types of walls: :doc:`wall/lj93 `, @@ -151,7 +151,7 @@ commands, or by mixing as described below: * cutoff (distance units) The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair\_style command are used. Otherwise both +cutoffs specified in the pair_style command are used. Otherwise both must be specified. ---------- @@ -180,7 +180,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See -the "pair\_modify" command for details. +the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -192,7 +192,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -207,10 +207,10 @@ Restrictions These styles are part of the COLLOID package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Only spherical monodisperse particles are allowed for pair\_style +Only spherical monodisperse particles are allowed for pair_style lubricate. -Only spherical particles are allowed for pair\_style lubricate/poly. +Only spherical particles are allowed for pair_style lubricate/poly. These pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index eaf71ac79e..5b485746c8 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -90,7 +90,7 @@ velocities of the undisturbed fluid, and :math:`E^{\infty}` represents the rate of strain tensor of the undisturbed fluid flow with viscosity *mu*\ . Again, note that this is dynamic viscosity which has units of mass/distance/time, not kinematic viscosity. Volume fraction -corrections to R\_FU are included if *flagVF* is set to 1 (default). +corrections to R_FU are included if *flagVF* is set to 1 (default). F\ *rest* represents the forces and torques due to all other types of interactions, e.g. Brownian, electrostatic etc. Note that this @@ -123,9 +123,9 @@ If the suspension is sheared via the :doc:`fix deform ` command then the pair style uses the shear rate to adjust the hydrodynamic interactions accordingly. Volume changes due to fix deform are accounted for when computing the volume fraction -corrections to R\_FU. +corrections to R_FU. -When computing the volume fraction corrections to R\_FU, the presence +When computing the volume fraction corrections to R_FU, the presence of walls (whether moving or stationary) will affect the volume fraction available to colloidal particles. This is currently accounted for with the following types of walls: :doc:`wall/lj93 `, @@ -133,7 +133,7 @@ for with the following types of walls: :doc:`wall/lj93 `, :doc:`wall/harmonic `. For these wall styles, the correct volume fraction will be used when walls do not coincide with the box boundary, as well as when walls move and thereby cause a change in the -volume fraction. To use these wall styles with pair\_style *lubricateU* +volume fraction. To use these wall styles with pair_style *lubricateU* or *lubricateU/poly*\ , the *fld yes* option must be specified in the fix wall command. @@ -156,7 +156,7 @@ commands, or by mixing as described below: * cutoff (distance units) The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair\_style command are used. Otherwise both +cutoffs specified in the pair_style command are used. Otherwise both must be specified. ---------- @@ -165,7 +165,7 @@ must be specified. For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See -the "pair\_modify" command for details. +the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -177,7 +177,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -199,10 +199,10 @@ the pair styles, and that no fixes apply additional constraint forces. One exception is the :doc:`fix wall/colloid ` commands, which has an "fld" option to apply their wall forces correctly. -Only spherical monodisperse particles are allowed for pair\_style +Only spherical monodisperse particles are allowed for pair_style lubricateU. -Only spherical particles are allowed for pair\_style lubricateU/poly. +Only spherical particles are allowed for pair_style lubricateU/poly. For sheared suspensions, it is assumed that the shearing is done in the xy plane, with x being the velocity direction and y being the diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 52120eab61..983e817f1d 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -80,7 +80,7 @@ outer cutoff radius. ---------- -For the *lj/mdf* pair\_style, the potential energy, *E(r)*\ , is the +For the *lj/mdf* pair_style, the potential energy, *E(r)*\ , is the standard 12-6 Lennard-Jones written in the epsilon/sigma form: .. math:: @@ -88,7 +88,7 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form: E(r) = 4\epsilon\biggl[\bigl(\frac{\sigma}{r}\bigr)^{12} - \bigl(\frac{\sigma}{r}\bigr)^6\biggr] Either the first two or all of the following coefficients must be -defined for each pair of atoms types via the pair\_coeff command as in +defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file read by the :doc:`read_data `. The two cutoffs default to the global values and :math:`\epsilon` and :math:`\sigma` can also be determined by mixing as @@ -101,7 +101,7 @@ described below: ---------- -For the *buck/mdf* pair\_style, the potential energy, *E(r)*\ , is the +For the *buck/mdf* pair_style, the potential energy, *E(r)*\ , is the standard Buckingham potential with three required coefficients. The two cutoffs can be omitted and default to the corresponding global values: @@ -118,7 +118,7 @@ global values: ---------- -For the *lennard/mdf* pair\_style, the potential energy, *E(r)*\ , is the +For the *lennard/mdf* pair_style, the potential energy, *E(r)*\ , is the standard 12-6 Lennard-Jones written in the A/B form: .. math:: @@ -126,8 +126,8 @@ standard 12-6 Lennard-Jones written in the A/B form: E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}} The following coefficients must be defined for each pair of atoms -types via the pair\_coeff command as in the examples above, or in the -data file read by the read\_data commands, or by mixing as described below. +types via the pair_coeff command as in the examples above, or in the +data file read by the read_data commands, or by mixing as described below. The two cutoffs default to their global values and must be either both given or both left out: @@ -143,7 +143,7 @@ given or both left out: For atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`sigma` coefficients and cutoff distances for the lj/mdf pair style can be mixed. The default mix value is *geometric*\ . See the -"pair\_modify" command for details. The other two pair styles buck/mdf +"pair_modify" command for details. The other two pair styles buck/mdf and lennard/mdf do not support mixing, so all I,J pairs of coefficients must be specified explicitly. @@ -151,7 +151,7 @@ None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports the :doc:`pair_modify ` shift option or long-range tail corrections to pressure and energy. -These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 7bf82da846..6c4da24625 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -64,7 +64,7 @@ distribution and have a ".meam.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. Note that unlike for other potentials, cutoffs for spline-based MEAM -potentials are not set in the pair\_style or pair\_coeff command; they +potentials are not set in the pair_style or pair_coeff command; they are specified in the potential files themselves. Unlike the EAM pair style, which retrieves the atomic mass from the @@ -72,10 +72,10 @@ potential file, the spline-based MEAM potentials do not include mass information; thus you need to use the :doc:`mass ` command to specify it. -Only a single pair\_coeff command is used with the *meam/spline* style +Only a single pair_coeff command is used with the *meam/spline* style which specifies a potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -86,7 +86,7 @@ to specify the path for the potential file. As an example, imagine the Ti.meam.spline file has values for Ti (old style). If your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potentials, you would use the following pair\_coeff +treated with this potentials, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -143,8 +143,8 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *meam/spline* pair style does not write its information to :doc:`binary restart files `, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair\_style -and pair\_coeff commands in an input script that reads a restart file. +potential parameter file. Thus, you need to re-specify the pair_style +and pair_coeff commands in an input script that reads a restart file. The *meam/spline* pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index c61ae0a54f..ebb51795c2 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -50,7 +50,7 @@ distribution and have a ".meam.sw.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. Note that unlike for other potentials, cutoffs for spline-based -MEAM+SW potentials are not set in the pair\_style or pair\_coeff +MEAM+SW potentials are not set in the pair_style or pair_coeff command; they are specified in the potential files themselves. Unlike the EAM pair style, which retrieves the atomic mass from the @@ -58,10 +58,10 @@ potential file, the spline-based MEAM+SW potentials do not include mass information; thus you need to use the :doc:`mass ` command to specify it. -Only a single pair\_coeff command is used with the meam/sw/spline style +Only a single pair_coeff command is used with the meam/sw/spline style which specifies a potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -72,10 +72,10 @@ to specify the path for the potential file. As an example, imagine the Ti.meam.sw.spline file has values for Ti. If your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potential, you would use the following pair\_coeff +treated with this potential, you would use the following pair_coeff command: -pair\_coeff \* \* Ti.meam.sw.spline Ti Ti Ti +pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element @@ -92,7 +92,7 @@ potentials. systems in the future. Example input scripts that use this pair style are provided -in the examples/USER/misc/meam\_sw\_spline directory. +in the examples/USER/misc/meam_sw_spline directory. ---------- @@ -106,8 +106,8 @@ shift, table, and tail options. The *meam/sw/spline* pair style does not write its information to :doc:`binary restart files `, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair\_style -and pair\_coeff commands in an input script that reads a restart file. +potential parameter file. Thus, you need to re-specify the pair_style +and pair_coeff commands in an input script that reads a restart file. The *meam/sw/spline* pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 098c3cb601..850be5b583 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -25,7 +25,7 @@ Description .. note:: The behavior of the MEAM potential for alloy systems has changed - as of November 2010; see description below of the mixture\_ref\_t + as of November 2010; see description below of the mixture_ref_t parameter Style *meam/c* computes pairwise interactions for a variety of materials @@ -65,13 +65,13 @@ distribution with a ".meam" suffix. All of these are parameterized in terms of LAMMPS :doc:`metal units `. Note that unlike for other potentials, cutoffs for MEAM potentials are -not set in the pair\_style or pair\_coeff command; they are specified in +not set in the pair_style or pair_coeff command; they are specified in the MEAM potential files themselves. -Only a single pair\_coeff command is used with the *meam* style which +Only a single pair_coeff command is used with the *meam* style which specifies two MEAM files and the element(s) to extract information for. The MEAM elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair\_coeff +N additional arguments after the 2nd filename in the pair_coeff command, where N is the number of LAMMPS atom types: * MEAM library file @@ -86,7 +86,7 @@ As an example, the potentials/library.meam file has generic MEAM settings for a variety of elements. The potentials/SiC.meam file has specific parameter settings for a Si and C alloy system. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair\_coeff command: +and the 4th to be C, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -138,7 +138,7 @@ Cu and lat = dia or fcc. Because the library file is used by Fortran MD codes, these strings may be enclosed in single quotes, but this is not required. The other numeric parameters match values in the formulas above. The value of the "elt" string is what is used in the -pair\_coeff command to identify which settings from the library file +pair_coeff command to identify which settings from the library file you wish to read in. There can be multiple entries in the library file with the same "elt" value; LAMMPS reads the 1st matching entry it finds and ignores the rest. @@ -203,7 +203,7 @@ 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: Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr, -augt1, gsmooth\_factor, re +augt1, gsmooth_factor, re where @@ -320,20 +320,20 @@ automatically. When parameter values are fit using the modified density function, as in more recent literature, augt1 should be set to 0. -The mixture\_ref\_t parameter is available to match results with those +The mixture_ref_t parameter is available to match results with those of previous versions of lammps (before January 2011). Newer versions of lammps, by default, use the single-element values of the t parameters to compute the background reference density. This is the proper way to compute these parameters. Earlier versions of lammps used an alloy mixture averaged value of t to compute the background -reference density. Setting mixture\_ref\_t=1 gives the old behavior. -WARNING: using mixture\_ref\_t=1 will give results that are demonstrably +reference density. Setting mixture_ref_t=1 gives the old behavior. +WARNING: using mixture_ref_t=1 will give results that are demonstrably incorrect for second-neighbor MEAM, and non-standard for first-neighbor MEAM; this option is included only for matching with previous versions of lammps and should be avoided if possible. The parameters attrac and repuls, along with the integer selection -parameter erose\_form, can be used to modify the Rose energy function +parameter erose_form, can be used to modify the Rose energy function used to compute the pair potential. This function gives the energy of the reference state as a function of interatomic spacing. The form of this function is: @@ -357,9 +357,9 @@ recent published MEAM parameter sets, such as :ref:`(Valone) ` in March 2009. The current version is correct, but may show different behavior compared with earlier versions of lammps with the attrac and/or repuls parameters are non-zero. To obtain the previous default - form, use erose\_form = 1 (this form does not seem to appear in the + form, use erose_form = 1 (this form does not seem to appear in the literature). An alternative form (see e.g. :ref:`(Lee2) `) is - available using erose\_form = 2. + available using erose_form = 2. ---------- @@ -368,13 +368,13 @@ recent published MEAM parameter sets, such as :ref:`(Valone) ` For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to -specify a pair\_coeff command with I != J arguments for this style. +specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -416,7 +416,7 @@ Related commands **(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). This report may be accessed on-line via `this link `_. -.. _sandreport: http://infoserve.sandia.gov/sand\_doc/2003/038782.pdf +.. _sandreport: http://infoserve.sandia.gov/sand_doc/2003/038782.pdf .. _Lee: diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index c7c9059704..6d9ba79a31 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -106,7 +106,7 @@ shift, table, and tail options. The *mesocnt* pair style do not write their information to :doc:`binary restart files `, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair\_style and pair\_coeff commands in +Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 72c2a02a72..b2e8507d61 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -60,7 +60,7 @@ Description The *edpd* style computes the pairwise interactions and heat fluxes for eDPD particles following the formulations in -:ref:`(Li2014\_JCP) ` and :ref:`Li2015\_CC `. The time +:ref:`(Li2014_JCP) ` and :ref:`Li2015_CC `. The time evolution of an eDPD particle is governed by the conservation of momentum and energy given by @@ -106,7 +106,7 @@ where the mesoscopic heat friction :math:`\kappa` is given by \kappa = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr}, with :math:`\upsilon` being the kinematic viscosity. For more details, -see Eq.(15) in :ref:`(Li2014\_JCP) `. +see Eq.(15) in :ref:`(Li2014_JCP) `. The following coefficients must be defined in eDPD system for each pair of atom types via the :doc:`pair_coeff ` command as in @@ -114,11 +114,11 @@ the examples above. * A (force units) * :math:`\gamma` (force/velocity units) -* power\_f (positive real) +* power_f (positive real) * cutoff (distance units) * kappa (thermal conductivity units) -* power\_T (positive real) -* cutoff\_T (distance units) +* power_T (positive real) +* cutoff_T (distance units) * optional keyword = power or kappa The keyword *power* or *kappa* is optional. Both "power" and "kappa" @@ -127,7 +127,7 @@ dependence of the exponent :math:`s(T) = \mathrm{power}_f ( 1+c_1 (T-1) + c_2 (T-1)^2 + c_3 (T-1)^3 + c_4 (T-1)^4 )` and of the mesoscopic heat friction :math:`s_T(T) = \kappa (1 + c_1 (T-1) + c_2 (T-1)^2 + c_3 (T-1)^3 + c_4 (T-1)^4)`. If the keyword *power* or *kappa* is not -specified, the eDPD system will use constant power\_f and +specified, the eDPD system will use constant power_f and :math:`\kappa`, which is independent to temperature changes. ---------- @@ -144,7 +144,7 @@ via the :doc:`pair_coeff ` command as in the examples above. The *mdpd* style computes the many-body interactions between mDPD particles following the formulations in -:ref:`(Li2013\_POF) `. The dissipative and random forces are in +:ref:`(Li2013_POF) `. The dissipative and random forces are in the form same as the classical DPD, but the conservative force is local density dependent, which are given by @@ -166,14 +166,14 @@ The following coefficients must be defined for each pair of atom types via the * A (force units) * B (force units) * :math:`\gamma` (force/velocity units) -* cutoff\_c (distance units) -* cutoff\_d (distance units) +* cutoff_c (distance units) +* cutoff_d (distance units) ---------- The *tdpd* style computes the pairwise interactions and chemical concentration fluxes for tDPD particles following the formulations in -:ref:`(Li2015\_JCP) `. The time evolution of a tDPD particle is +:ref:`(Li2015_JCP) `. The time evolution of a tDPD particle is governed by the conservation of momentum and concentration given by .. math:: @@ -191,7 +191,7 @@ force :math:`F_{ij}^C` are expressed as \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij} \\ \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\ \omega_{C}(r) & = 1 - r/r_c \\ - \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f} \\ + \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\ \sigma^2 = 2\gamma k_B T The concentration flux between two tDPD particles includes the Fickian @@ -202,13 +202,13 @@ by Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\ Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\ - w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}} \\ + w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\ \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho where the parameters kappa and epsilon determine the strength of the Fickian and random fluxes. :math:`m_s` is the mass of a single solute molecule. In general, :math:`m_s` is much smaller than the mass of a -tDPD particle *m*\ . For more details, see :ref:`(Li2015\_JCP) +tDPD particle *m*\ . For more details, see :ref:`(Li2015_JCP) `. The following coefficients must be defined for each pair of atom types via the @@ -216,16 +216,16 @@ The following coefficients must be defined for each pair of atom types via the * A (force units) * :math:`\gamma` (force/velocity units) -* power\_f (positive real) +* power_f (positive real) * cutoff (distance units) -* cutoff\_CC (distance units) +* cutoff_CC (distance units) * :math:`\kappa_i` (diffusivity units) * :math:`\epsilon_i` (diffusivity units) -* power\_cc\_i (positive real) +* power_cc_i (positive real) The last 3 values must be repeated Nspecies times, so that values for each of the Nspecies chemical species are specified, as indicated by -the "I" suffix. In the first pair\_coeff example above for pair\_style +the "I" suffix. In the first pair_coeff example above for pair_style tdpd, Nspecies = 1. In the second example, Nspecies = 2, so 3 additional coeffs are specified (for species 2). @@ -236,7 +236,7 @@ additional coeffs are specified (for species 2). There are example scripts for using all these pair styles in examples/USER/meso. The example for an eDPD simulation models heat conduction with source terms analog of periodic Poiseuille flow -problem. The setup follows Fig.12 in :ref:`(Li2014\_JCP) `. The +problem. The setup follows Fig.12 in :ref:`(Li2014_JCP) `. The output of the short eDPD simulation (about 2 minutes on a single core) gives a temperature and density profiles as @@ -245,7 +245,7 @@ gives a temperature and density profiles as The example for a mDPD simulation models the oscillations of a liquid droplet started from a liquid film. The mDPD parameters are adopted -from :ref:`(Li2013\_POF) `. The short mDPD run (about 2 minutes +from :ref:`(Li2013_POF) `. The short mDPD run (about 2 minutes on a single core) generates a particle trajectory which can be visualized as follows. @@ -264,7 +264,7 @@ The example for a tDPD simulation computes the effective diffusion coefficient of a tDPD system using a method analogous to the periodic Poiseuille flow. The tDPD system is specified with two chemical species, and the setup follows Fig.1 in -:ref:`(Li2015\_JCP) `. The output of the short tDPD simulation +:ref:`(Li2015_JCP) `. The output of the short tDPD simulation (about one and a half minutes on a single core) gives the concentration profiles of the two chemical species as @@ -283,7 +283,7 @@ the :doc:`pair_modify ` shift, table, and tail options. The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write information to :doc:`binary restart files `. Thus, you need -to re-specify the pair\_style and pair\_coeff commands in an input script +to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. Restrictions @@ -307,22 +307,22 @@ Related commands ---------- -.. _Li2014\_JCP: +.. _Li2014_JCP: -**(Li2014\_JCP)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, +**(Li2014_JCP)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. -.. _Li2015\_CC: +.. _Li2015_CC: -**(Li2015\_CC)** Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 +**(Li2015_CC)** Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI: 10.1039/C5CC01684C. -.. _Li2013\_POF: +.. _Li2013_POF: -**(Li2013\_POF)** Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). +**(Li2013_POF)** Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366. -.. _Li2015\_JCP: +.. _Li2015_JCP: -**(Li2015\_JCP)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, +**(Li2015_JCP)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254. diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 562f1f5802..57fec82a7b 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -40,16 +40,16 @@ elemental bulk material in the form where the prime on each summation sign indicates the exclusion of all self-interaction terms from the summation. The leading volume term -E\_vol as well as the two-ion central-force pair potential v\_2 and the -three- and four-ion angular-force potentials, v\_3 and v\_4, depend +E_vol as well as the two-ion central-force pair potential v_2 and the +three- and four-ion angular-force potentials, v_3 and v_4, depend explicitly on the atomic volume Omega, but are structure independent and transferable to all bulk ion configurations, either ordered or disordered, and with of without the presence of point and line defects. The simplified model GPT or MGPT (:ref:`Moriarty2 `, -:ref:`Moriarty3 `), which retains the form of E\_tot and permits +:ref:`Moriarty3 `), which retains the form of E_tot and permits more efficient large-scale atomistic simulations, derives from the GPT -through a series of systematic approximations applied to E\_vol and the -potentials v\_n that are valid for mid-period transition metals with +through a series of systematic approximations applied to E_vol and the +potentials v_n that are valid for mid-period transition metals with nearly half-filled d bands. Both analytic (:ref:`Moriarty2 `) and matrix @@ -64,12 +64,12 @@ algorithms have been developed independently by Glosli (:ref:`Oppelstrup `) The *mgpt* pair style calculates forces, energies, and the total -energy per atom, E\_tot/N, using the Oppelstrup matrix-MGPT algorithm. +energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. Input potential and control data are entered through the :doc:`pair_coeff ` command. Each material treated requires input parmin and potin potential files, as shown in the above examples, as well as specification by the user of the initial atomic -volume Omega through pair\_coeff. At the beginning of a time step in +volume Omega through pair_coeff. At the beginning of a time step in any simulation, the total volume of the simulation cell V should always be equal to Omega\*N, where N is the number of metal ions present, taking into account the presence of any vacancies and/or @@ -79,25 +79,25 @@ style, Omega, V and N all remain constant throughout the simulation and thus are equal to their initial values. In a constant-stress simulation, the cell volume V will change (slowly) as the simulation proceeds. After each time step, the atomic volume should be updated -by the code as Omega = V/N. In addition, the volume term E\_vol and -the potentials v\_2, v\_3 and v\_4 have to be removed at the end of the +by the code as Omega = V/N. In addition, the volume term E_vol and +the potentials v_2, v_3 and v_4 have to be removed at the end of the time step, and then respecified at the new value of Omega. In all simulations, Omega must remain within the defined volume range for -E\_vol and the potentials for the given material. +E_vol and the potentials for the given material. The default option volpress yes in the :doc:`pair_coeff ` -command includes all volume derivatives of E\_tot required to calculate +command includes all volume derivatives of E_tot required to calculate the stress tensor and pressure correctly. The option volpress no disregards the pressure contribution resulting from the volume term -E\_vol, and can be used for testing and analysis purposes. The +E_vol, and can be used for testing and analysis purposes. The additional optional variable nbody controls the specific terms in -E\_tot that are calculated. The default option and the normal option +E_tot that are calculated. The default option and the normal option for mid-period transition and actinide metals is nbody 1234 for which -all four terms in E\_tot are retained. The option nbody 12, for +all four terms in E_tot are retained. The option nbody 12, for example, retains only the volume term and the two-ion pair potential term and can be used for GPT series-end transition metals that can be -well described without v\_3 and v\_4. The nbody option can also be used -to test or analyze the contribution of any of the four terms in E\_tot +well described without v_3 and v_4. The nbody option can also be used +to test or analyze the contribution of any of the four terms in E_tot to a given calculated property. The *mgpt* pair style makes extensive use of matrix algebra and @@ -155,7 +155,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -needs to re-specify the pair\_style and pair\_coeff commands in an input +needs to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -179,7 +179,7 @@ energies in Rydbergs and distances in Bohr radii. The *mgpt* pair style converts Rydbergs to Hartrees to make the potential files compatible with LAMMPS electron :doc:`units `. -The form of E\_tot used in the *mgpt* pair style is only appropriate +The form of E_tot used in the *mgpt* pair style is only appropriate for elemental bulk solids and liquids. This includes solids with point and extended defects such as vacancies, interstitials, grain boundaries and dislocations. Alloys and free surfaces, however, diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index 165ad7a787..527a568728 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -58,7 +58,7 @@ commands, or by mixing as described below: * cutoff (distance units) The last coefficient is optional. If not specified, the global -cutoff specified in the pair\_style command is used. +cutoff specified in the pair_style command is used. ---------- @@ -69,7 +69,7 @@ and cutoff distance for all of the mie/cut pair styles can be mixed. If not explicitly defined, both the repulsive and attractive gamma exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is -*geometric*\ . See the "pair\_modify" command for details. +*geometric*\ . See the "pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -78,7 +78,7 @@ This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 537cdde457..1338682b95 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -43,7 +43,7 @@ vdW potential :ref:`(Allinger) ` r_{v,ij} & = r_{v,i} + r_{v,j} \\ \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} -, which goes smoothly to zero at the cutoff r\_c as defined +, which goes smoothly to zero at the cutoff r_c as defined by the switching function .. math:: diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index c248a3fcd0..b8969c0131 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -74,7 +74,7 @@ must be set explicitly, either in the input script via the :doc:`pair_coeff ` command or in the "Pair Coeffs" section of the :doc:`data file `. For some pair styles it is not necessary to specify coefficients when I != J, since a "mixing" rule -will create them from the I,I and J,J settings. The pair\_modify +will create them from the I,I and J,J settings. The pair_modify *mix* value determines what formulas are used to compute the mixed coefficients. In each case, the cutoff distance is mixed the same way as sigma. diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 83fb897cdb..d031c70cd2 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -85,7 +85,7 @@ so that both, potential energy and force, go to zero at the cut-off: \phi\left(r\right) & = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\ E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c -The syntax of the pair\_style and pair\_coeff commands are the same for +The syntax of the pair_style and pair_coeff commands are the same for the *morse* and *morse/smooth/linear* styles. ---------- @@ -134,7 +134,7 @@ None of these pair styles support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -All of these pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +All of these pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 4a412ca460..37da1ab965 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -110,7 +110,7 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair\_coeff +initial text must match the argument specified in the pair_coeff command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -118,7 +118,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`pair_style multi/lucy ` command. -Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the +Let Ntable = *N* in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate the density-dependent energy and force at @@ -176,11 +176,11 @@ I,J pairs must be specified explicitly. The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. -This pair style writes the settings for the "pair\_style multi/lucy" command -to :doc:`binary restart files `, so a pair\_style command does +This pair style writes the settings for the "pair_style multi/lucy" command +to :doc:`binary restart files `, so a pair_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair\_coeff +file, since it is tabulated in the potential files. Thus, pair_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 6d9b00f1a1..3824ca96cf 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -138,7 +138,7 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair\_coeff +initial text must match the argument specified in the pair_coeff command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -146,7 +146,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`pair_style multi/lucy/rx ` -command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" +command. Let Ntable = *N* in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate the density-dependent @@ -204,11 +204,11 @@ I,J pairs must be specified explicitly. The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. -This pair style writes the settings for the "pair\_style multi/lucy/rx" command -to :doc:`binary restart files `, so a pair\_style command does +This pair style writes the settings for the "pair_style multi/lucy/rx" command +to :doc:`binary restart files `, so a pair_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair\_coeff +file, since it is tabulated in the potential files. Thus, pair_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index e039accd1a..c4f3f3c3e8 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -30,13 +30,13 @@ energy E of a system of atoms as where :math:`\theta_0` is the equilibrium value of the angle and *K* is a prefactor. Note that the usual 1/2 factor is included in *K*\ . The form -of the potential is identical to that used in angle\_style *harmonic*\ , +of the potential is identical to that used in angle_style *harmonic*\ , but in this case, the atoms do not need to be explicitly bonded. -Only a single pair\_coeff command is used with this style which +Only a single pair_coeff command is used with this style which specifies a potential file with parameters for specified elements. These are mapped to LAMMPS atom types by specifying N additional -arguments after the filename in the pair\_coeff command, where N is the +arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -48,7 +48,7 @@ to specify the path for the potential file. As an example, imagine a file SiC.nb3b.harmonic has potential values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair\_coeff command: +following pair_coeff command: .. code-block:: LAMMPS @@ -61,10 +61,10 @@ type 4 to the C element in the potential file. If a mapping value is specified as NULL, the mapping is not performed. This can be used when the potential is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with -other potentials. An example of a pair\_coeff command for use with the +other potentials. An example of a pair_coeff command for use with the *hybrid* pair style is: -pair\_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H +pair_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H Three-body non-bonded harmonic files in the *potentials* directory of the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that @@ -86,7 +86,7 @@ the entry is for the *K* and :math:`\theta_0` parameters (the cutoff in this case is irrelevant). It is required that the potential file contains entries for *all* -permutations of the elements listed in the pair\_coeff command. +permutations of the elements listed in the pair_coeff command. If certain combinations are not parameterized the corresponding parameters should be set to zero. The potential file can also contain entries for additional elements which are not used in diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index c600432a06..196747b291 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -80,7 +80,7 @@ Style *nm/cut/coul/cut* adds a Coulombic pairwise interaction given by where :math:`C` is an energy-conversion constant, :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, and epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command. If one cutoff is -specified in the pair\_style command, it is used for both the N-M and Coulombic +specified in the pair_style command, it is used for both the N-M and Coulombic terms. If two cutoffs are specified, they are used as cutoffs for the N-M and Coulombic terms respectively. @@ -108,7 +108,7 @@ commands. * cutoff2 (distance units) The latter 2 coefficients are optional. If not specified, the global -N-M and Coulombic cutoffs specified in the pair\_style command are used. +N-M and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both N-M and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the N-M and Coulombic cutoffs for this @@ -118,7 +118,7 @@ has no Coulombic terms. For *nm/cut/coul/long* only the N-M cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the -pair\_style command. +pair_style command. ---------- @@ -139,7 +139,7 @@ All of the *nm* pair styles support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the N-M portion of the pair interaction. -All of the *nm* pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +All of the *nm* pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. All of the *nm* pair styles can only be used via the *pair* keyword of diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 2d95785fff..2b3d3e9b99 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -73,8 +73,8 @@ R. Rahman and J. T. Foster at University of Texas at San Antonio. The original VES formulation is described in "(Mitchell2011)" and the original EPS formulation is in "(Mitchell2011a)". Additional PDF docs that describe the VES and EPS implementations are include in the -LAMMPS distribution in `doc/PDF/PDLammps\_VES.pdf `_ and -`doc/PDF/PDLammps\_EPS.pdf `_. For questions +LAMMPS distribution in `doc/PDF/PDLammps_VES.pdf `_ and +`doc/PDF/PDLammps_EPS.pdf `_. For questions regarding the VES and EPS models in LAMMPS you can contact R. Rahman (rezwanur.rahman at utsa.edu). @@ -118,15 +118,15 @@ For the *peri/ves* style: * horizon (distance units) * s00 (unitless) * :math:`\alpha` (unitless) -* m\_lambdai (unitless) -* m\_taubi (unitless) +* m_lambdai (unitless) +* m_taubi (unitless) K is the bulk modulus and G is the shear modulus. The horizon is a cutoff distance for truncating interactions, and s00 and :math:`\alpha` are -used as a bond breaking criteria. m\_lambdai and m\_taubi are the +used as a bond breaking criteria. m_lambdai and m_taubi are the viscoelastic relaxation parameter and time constant, -respectively. m\_lambdai varies within zero to one. For very small -values of m\_lambdai the viscoelastic model responds very similar to a +respectively. m_lambdai varies within zero to one. For very small +values of m_lambdai the viscoelastic model responds very similar to a linear elastic model. For details please see the description in "(Mtchell2011)". @@ -137,11 +137,11 @@ For the *peri/eps* style: * horizon (distance units) * s00 (unitless) * :math:`\alpha` (unitless) -* m\_yield\_stress (force/area units) +* m_yield_stress (force/area units) K is the bulk modulus and G is the shear modulus. The horizon is a cutoff distance and s00 and :math:`\alpha` are used as a bond breaking -criteria. m\_yield\_stress is the yield stress of the material. For +criteria. m_yield_stress is the yield stress of the material. For details please see the description in "(Mtchell2011a)". ---------- @@ -177,7 +177,7 @@ shift option. The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. -These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +These pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 93de3fe65f..e06e9e7855 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -161,24 +161,24 @@ pair style is different from the sw pair style in this case. It just means that the definitions of the atom energies and atom stresses are different. -Only a single pair\_coeff command is used with the polymorphic style +Only a single pair_coeff command is used with the polymorphic style which specifies an potential file for all needed elements. These are mapped to LAMMPS atom types by specifying N additional arguments after -the filename in the pair\_coeff command, where N is the number of +the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff elements to atom types -See the pair\_coeff doc page for alternate ways to specify the path for +See the pair_coeff doc page for alternate ways to specify the path for the potential file. Several files for polymorphic potentials are included in the potentials directory of the LAMMPS distribution. They have a "poly" suffix. -As an example, imagine the SiC\_tersoff.poly file has tabulated +As an example, imagine the SiC_tersoff.poly file has tabulated functions for Si-C tersoff potential. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you -would use the following pair\_coeff command: +would use the following pair_coeff command: .. parsed-literal:: @@ -204,7 +204,7 @@ and are ignored by LAMMPS. The next line lists two numbers: Here ntypes represent total number of species defined in the potential file, and :math:`\eta = 0` or 1. The number ntypes must equal the total -number of different species defined in the pair\_coeff command. When +number of different species defined in the pair_coeff command. When :math:`\eta = 1`, :math:\eta_{ij}` defined in the potential functions above is set to :math:`1 - \delta_{ij}`, otherwise :math:`\eta_{ij}` is set to :math:`\delta_{ij}`. The next ntypes lines each lists two numbers @@ -254,7 +254,7 @@ Tabulated functions are specified by spline n x1 x2, where n=number of point, (x1,x2)=range and then followed by n values evaluated uniformly over these argument ranges. The valid argument ranges of the functions are between 0 <= r <= cut for the U(r), V(r), W(r) -functions, -cutmax <= delta\_r <= cutmax for the P(delta\_r) functions, +functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions, -1 <= :math:`\cos\theta` <= 1 for the G(:math:`\cos\theta`) functions, and 0 <= X <= maxX for the F(X) functions. @@ -264,7 +264,7 @@ This pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. ---------- @@ -272,8 +272,8 @@ script that reads a restart file. Restrictions """""""""""" -If using create\_atoms command, atomic masses must be defined in the -input script. If using read\_data, atomic masses must be defined in the +If using create_atoms command, atomic masses must be defined in the +input script. If using read_data, atomic masses must be defined in the atomic structure data file. This pair style is part of the MANYBODY package. It is only enabled if diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 886c9c2b53..fa76d4c16c 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -38,10 +38,10 @@ corresponding compiled code. This penalty can be significantly reduced through generating tabulations from the python code through the :doc:`pair_write ` command, which is supported by this style. -Only a single pair\_coeff command is used with the *python* pair style +Only a single pair_coeff command is used with the *python* pair style which specifies a python class inside a python module or file that LAMMPS will look up in the current directory, the folder pointed to by -the LAMMPS\_POTENTIALS environment variable or somewhere in your python +the LAMMPS_POTENTIALS environment variable or somewhere in your python path. A single python module can hold multiple python pair class definitions. The class definitions itself have to follow specific rules that are explained below. @@ -49,15 +49,15 @@ rules that are explained below. Atom types in the python class are specified through symbolic constants, typically strings. These are mapped to LAMMPS atom types by specifying N additional arguments after the class name in the -pair\_coeff command, where N must be the number of currently defined +pair_coeff command, where N must be the number of currently defined atom types: -As an example, imagine a file *py\_pot.py* has a python potential class +As an example, imagine a file *py_pot.py* has a python potential class names *LJCutMelt* with parameters and potential functions for a two Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS input and you would have defined 3 atom types, out of which the first two are supposed to be using the 'LJ1' parameters and the third the -'LJ2' parameters, then you would use the following pair\_coeff command: +'LJ2' parameters, then you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -65,7 +65,7 @@ two are supposed to be using the 'LJ1' parameters and the third the The first two arguments **must** be \* \* so as to span all LAMMPS atom types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to -the LJ1 atom type in the LJCutMelt class of the py\_pot.py file. The +the LJ1 atom type in the LJCutMelt class of the py_pot.py file. The final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the python file. If a mapping value is specified as NULL, the mapping is not performed, any pair interaction with this atom type will be @@ -119,8 +119,8 @@ which the parameters epsilon and sigma are both 1.0: self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}} The class also has to provide two methods for the computation of the -potential energy and forces, which have be named *compute\_force*, -and *compute\_energy*, which both take 3 numerical arguments: +potential energy and forces, which have be named *compute_force*, +and *compute_energy*, which both take 3 numerical arguments: * rsq = the square of the distance between a pair of atoms (float) * itype = the (numerical) type of the first atom @@ -153,7 +153,7 @@ the *LJCutMelt* example, here are the two functions: .. note:: for consistency with the C++ pair styles in LAMMPS, the - *compute\_force* function follows the conventions of the Pair::single() + *compute_force* function follows the conventions of the Pair::single() methods and does not return the full force, but the force scaled by the distance between the two atoms, so this value only needs to be multiplied by delta x, delta y, and delta z to conveniently obtain the @@ -178,7 +178,7 @@ the *LJCutMelt* example, here are the two functions: pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj Note that it is strongly recommended to try to **delete** the potential -table file before generating it. Since the *pair\_write* command will +table file before generating it. Since the *pair_write* command will always **append** to a table file, while pair style table will use the **first match**\ . Thus when changing the potential function in the python class, the table pair style will still read the old variant unless the @@ -209,7 +209,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 032519e4b6..7781f3a9fb 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -31,7 +31,7 @@ interface is chiefly intended to be used to run Gaussian Approximation Potentials (GAP), which are described in the following publications: :ref:`(Bartok et al) ` and :ref:`(PhD thesis of Bartok) `. -Only a single pair\_coeff command is used with the *quip* style that +Only a single pair_coeff command is used with the *quip* style that specifies a QUIP potential file containing the parameters of the potential for all needed elements in XML format. This is followed by a QUIP initialization string. Finally, the QUIP elements are mapped to @@ -64,7 +64,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -83,7 +83,7 @@ therefore should be used with LAMMPS metal :doc:`units `. QUIP potentials are generally not designed to work with the scaling factors set by the :doc:`special_bonds ` command. The recommended setting in molecular systems is to include all -interactions, i.e. to use *special\_bonds lj/coul 1.0 1.0 1.0*. Scaling +interactions, i.e. to use *special_bonds lj/coul 1.0 1.0 1.0*. Scaling factors > 0.0 will be ignored and treated as 1.0. The only exception to this rule is if you know that your QUIP potential needs to exclude bonded, 1-3, or 1-4 interactions and does not already do this exclusion @@ -99,12 +99,12 @@ Related commands ---------- -.. _Bartok\_2010: +.. _Bartok_2010: -**(Bartok\_2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical +**(Bartok_2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010). -.. _Bartok\_PhD: +.. _Bartok_PhD: -**(Bartok\_PhD)** A Bartok-Partay, PhD Thesis, University of Cambridge, +**(Bartok_PhD)** A Bartok-Partay, PhD Thesis, University of Cambridge, (2010). diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index acaac5fce1..e40fbe60c1 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -63,7 +63,7 @@ consideration when using the *reax/c/kk* style is the choice of either half or full neighbor lists. This setting can be changed using the Kokkos :doc:`package ` command. -The *reax/c* style differs from the (obsolete) "pair\_style reax" +The *reax/c* style differs from the (obsolete) "pair_style reax" command in the implementation details. The *reax* style was a Fortran library, linked to LAMMPS. The *reax* style has been removed from LAMMPS after the 12 December 2018 version. @@ -74,7 +74,7 @@ documented in potentials/README.reax. The default ffield.reax contains parameterizations for the following elements: C, H, O, N. The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of *pair\_style reax/c* potential +Duin. We have tested the accuracy of *pair_style reax/c* potential against the original ReaxFF code for the systems mentioned above. You can use other ffield files for specific chemical systems that may be available elsewhere (but note that their accuracy may not have been @@ -108,7 +108,7 @@ below. code. If these are changed by setting control variables in the control file, the results from LAMMPS and the serial code will not agree. -Examples using *pair\_style reax/c* are provided in the examples/reax +Examples using *pair_style reax/c* are provided in the examples/reax sub-directory. Use of this pair style requires that a charge be defined for every @@ -118,7 +118,7 @@ charges. The ReaxFF parameter files provided were created using a charge equilibration (QEq) model for handling the electrostatic interactions. -Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax ` command be used with *pair\_style reax/c* +Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax ` command be used with *pair_style reax/c* when simulating a ReaxFF model, to equilibrate charge each timestep. Using the keyword *checkqeq* with the value *no* turns off the check for *fix qeq/reax*\ , @@ -193,10 +193,10 @@ headings) the following commands could be included in an input script: variable eqeq equal c_reax[14] thermo_style custom step temp epair v_eb v_ea [...] v_eqeq -Only a single pair\_coeff command is used with the *reax/c* style which +Only a single pair_coeff command is used with the *reax/c* style which specifies a ReaxFF potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -219,7 +219,7 @@ types that will be used with other potentials. As an example, say your LAMMPS simulation has 4 atom types and the elements are ordered as C, H, O, N in the *ffield* file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair\_coeff command: +H, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -239,16 +239,16 @@ If the value of a control variable is not specified, then default values are used. What follows is the list of variables along with a brief description of their use and default values. -simulation\_name: Output files produced by *pair\_style reax/c* carry +simulation_name: Output files produced by *pair_style reax/c* carry this name + extensions specific to their contents. Partial energies are reported with a ".pot" extension, while the trajectory file has ".trj" extension. -tabulate\_long\_range: To improve performance, long range interactions +tabulate_long_range: To improve performance, long range interactions can optionally be tabulated (0 means no tabulation). Value of this variable denotes the size of the long range interaction table. The range from 0 to long range cutoff (defined in the *ffield* file) is -divided into *tabulate\_long\_range* points. Then at the start of +divided into *tabulate_long_range* points. Then at the start of simulation, we fill in the entries of the long range interaction table by computing the energies and forces resulting from van der Waals and Coulomb interactions between every possible atom type pairs present in @@ -257,42 +257,42 @@ interaction table to estimate the energy and forces between a pair of atoms. Linear interpolation is used for estimation. (default value = 0) -energy\_update\_freq: Denotes the frequency (in number of steps) of +energy_update_freq: Denotes the frequency (in number of steps) of writes into the partial energies file. (default value = 0) -nbrhood\_cutoff: Denotes the near neighbors cutoff (in Angstroms) +nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms) regarding the bonded interactions. (default value = 5.0) -hbond\_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen +hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen bond interactions.(default value = 7.5. A value of 0.0 turns off hydrogen bonds) -bond\_graph\_cutoff: is the threshold used in determining what is a +bond_graph_cutoff: is the threshold used in determining what is a physical bond, what is not. Bonds and angles reported in the trajectory file rely on this cutoff. (default value = 0.3) -thb\_cutoff: cutoff value for the strength of bonds to be considered in +thb_cutoff: cutoff value for the strength of bonds to be considered in three body interactions. (default value = 0.001) -thb\_cutoff\_sq: cutoff value for the strength of bond order products +thb_cutoff_sq: cutoff value for the strength of bond order products to be considered in three body interactions. (default value = 0.00001) -write\_freq: Frequency of writes into the trajectory file. (default +write_freq: Frequency of writes into the trajectory file. (default value = 0) -traj\_title: Title of the trajectory - not the name of the trajectory +traj_title: Title of the trajectory - not the name of the trajectory file. -atom\_info: 1 means print only atomic positions + charge (default = 0) +atom_info: 1 means print only atomic positions + charge (default = 0) -atom\_forces: 1 adds net forces to atom lines in the trajectory file +atom_forces: 1 adds net forces to atom lines in the trajectory file (default = 0) -atom\_velocities: 1 adds atomic velocities to atoms line (default = 0) +atom_velocities: 1 adds atomic velocities to atoms line (default = 0) -bond\_info: 1 prints bonds in the trajectory file (default = 0) +bond_info: 1 prints bonds in the trajectory file (default = 0) -angle\_info: 1 prints angles in the trajectory file (default = 0) +angle_info: 1 prints angles in the trajectory file (default = 0) ---------- @@ -302,7 +302,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -356,9 +356,9 @@ safezone = 1.2, mincap = 50. ---------- -.. _Chenoweth\_20082: +.. _Chenoweth_20082: -**(Chenoweth\_2008)** Chenoweth, van Duin and Goddard, +**(Chenoweth_2008)** Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008). .. _Aktulga: @@ -366,7 +366,7 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008). (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). -.. _Liu\_2011: +.. _Liu_2011: **(Liu)** L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011). diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index d133274fa4..5bb4de7cb2 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -119,7 +119,7 @@ than the :doc:`pair_style gayberne ` potential uses. The :math:`\epsilon_i` and :math:`\epsilon_j` coefficients are defined for atom types, not for pairs of atom types. Thus, in a series of -pair\_coeff commands, they only need to be specified once for each atom +pair_coeff commands, they only need to be specified once for each atom type. Specifically, if any of :math:`\epsilon_{i,a}`, :math:`\epsilon_{i,b}`, @@ -129,19 +129,19 @@ ignored. If any of :math:`\epsilon_{j,a}`, :math:`\epsilon_{j,b}`, :math:`\epsilon_{j,c}` are non-zero, the three values are assigned to atom type J. If all three :math:`\epsilon_i` values are zero, they are ignored. Thus the typical way to define the :math:`\epsilon_i` and -:math:`\epsilon_j` coefficients is to list their values in "pair\_coeff +:math:`\epsilon_j` coefficients is to list their values in "pair_coeff I J" commands when I = J, but set them to 0.0 when I != J. If you do list them when I != J, you should insure they are consistent with their -values in other pair\_coeff commands. +values in other pair_coeff commands. Note that if this potential is being used as a sub-style of -:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair_coeff I I" setting made for RE-squared for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the epsilon a,b,c coefficients are assigned to -that type in a "pair\_coeff I J" command. +that type in a "pair_coeff I J" command. -For large uniform molecules it has been shown that the epsilon\_\*\_\* +For large uniform molecules it has been shown that the :math:`\epsilon_{*,*}` energy parameters are approximately representable in terms of local contact curvatures :ref:`(Everaers) `: @@ -154,7 +154,7 @@ contact curvatures :ref:`(Everaers) `: where a, b, and c give the particle diameters. The last coefficient is optional. If not specified, the global cutoff -specified in the pair\_style command is used. +specified in the pair_style command is used. ---------- @@ -182,7 +182,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance can be mixed, but only for sphere pairs. The -default mix value is *geometric*\ . See the "pair\_modify" command for +default mix value is *geometric*\ . See the "pair_modify" command for details. Other type pairs cannot be mixed, due to the different meanings of the energy prefactors used to calculate the interactions and the implicit dependence of the ellipsoid-sphere interaction on the @@ -203,7 +203,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 734759477c..2a5167030b 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -96,7 +96,7 @@ above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: -* cg\_type (lj9\_6, lj12\_4, or lj12\_6) +* cg_type (lj9_6, lj12_4, or lj12_6) * epsilon (energy units) * sigma (distance units) * cutoff1 (distance units) @@ -106,7 +106,7 @@ distance for the potential, not as the energy minimum. The prefactors are chosen so that the potential minimum is at -epsilon. The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair\_style command are used. +LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this @@ -115,7 +115,7 @@ type pair. For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global -Coulombic cutoff specified in the pair\_style command. +Coulombic cutoff specified in the pair_style command. ---------- @@ -144,7 +144,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed, since different pairs may have different exponents. So all parameters -for all pairs have to be specified explicitly through the "pair\_coeff" +for all pairs have to be specified explicitly through the "pair_coeff" command. Defining then in a data file is also not supported, due to limitations of that file format. @@ -156,7 +156,7 @@ The *lj/sdk/coul/long* pair styles support the :doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. -All of the lj/sdk pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do +All of the lj/sdk pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. The lj/sdk and lj/cut/coul/long pair styles do not support diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index aeca957071..05e7bbfac0 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -87,8 +87,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -112,6 +112,6 @@ The default seed is 0 (before mixing). ---------- -.. _Espanol\_Revenga: +.. _Espanol_Revenga: **(Espanol and Revenga)** Espanol, Revenga, Physical Review E, 67, 026705 (2003). diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index 53253da3d6..fd7f9c3e01 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -27,14 +27,14 @@ belonging to different physical bodies. The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles (whose spatial extents are defined via its contact radius). The effect is that a particles -cannot penetrate into each other. The parameter +cannot penetrate into each other. The parameter has units of pressure and should equal roughly one half of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles. -The parameter *scale\_factor* can be used to scale the particles' +The parameter *scale_factor* can be used to scale the particles' contact radii. This can be useful to control how close particles can -approach each other. Usually, *scale\_factor* =1.0. +approach each other. Usually, *scale_factor* =1.0. ---------- diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index cf271a0393..d1177b2577 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -1,6 +1,6 @@ .. index:: pair_style smd/tri_surface -pair_style smd/tri\_surface command +pair_style smd/tri_surface command =================================== Syntax @@ -21,21 +21,21 @@ Examples Description """"""""""" -The *smd/tri\_surface* style calculates contact forces between SPH +The *smd/tri_surface* style calculates contact forces between SPH particles and a rigid wall boundary defined via the -:doc:`smd/wall\_surface ` fix. +:doc:`smd/wall_surface ` fix. The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle (whose spatial extents are defined via its contact radius) and the triangle. The effect is that a particle cannot penetrate into the triangular surface. The -parameter has units of pressure and should equal +parameter has units of pressure and should equal roughly one half of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle -The parameter *scale\_factor* can be used to scale the particles' +The parameter *scale_factor* can be used to scale the particles' contact radii. This can be useful to control how close particles can -approach the triangulated surface. Usually, *scale\_factor* =1.0. +approach the triangulated surface. Usually, *scale_factor* =1.0. ---------- diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 81bcc6364c..6210de2423 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -41,7 +41,7 @@ This pair style is invoked similar to the following command: Here, *i* and *j* denote the *LAMMPS* particle types for which this pair style is defined. Note that *i* and *j* can be different, i.e., *ulsph* cross interactions between different particle types are -allowed. However, *i*\ --\ *i* respectively *j*\ --\ *j* pair\_coeff lines have +allowed. However, *i*\ --\ *i* respectively *j*\ --\ *j* pair_coeff lines have to precede a cross interaction. In contrast to the usual *LAMMPS* *pair coeff* definitions, which are given solely a number of floats and integers, the *ulsph* *pair coeff* definition is organized using @@ -55,8 +55,8 @@ diagonal components of the stress tensor), and a material model to compute shear stresses (the off-diagonal components of the stress tensor). -Note that the use of \*GRADIENT\_CORRECTION can lead to severe numerical -instabilities. For a general fluid simulation, \*NO\_GRADIENT\_CORRECTION +Note that the use of \*GRADIENT_CORRECTION can lead to severe numerical +instabilities. For a general fluid simulation, \*NO_GRADIENT_CORRECTION is recommended. Please see the `SMD user guide `_ for a diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index d0d5c1e031..492820124e 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -22,8 +22,8 @@ Description """"""""""" This pair style computes a variable charge SMTB-Q (Second-Moment -tight-Binding QEq) potential as described in :ref:`SMTB-Q\_1 ` and -:ref:`SMTB-Q\_2 `. Briefly, the energy of metallic-oxygen systems +tight-Binding QEq) potential as described in :ref:`SMTB-Q_1 ` and +:ref:`SMTB-Q_2 `. Briefly, the energy of metallic-oxygen systems is given by three contributions: .. math:: @@ -45,14 +45,14 @@ smooth convergence to zero interaction. The parameters appearing in the upper expressions are set in the ffield.SMTBQ.Syst file where Syst corresponds to the selected system (e.g. field.SMTBQ.Al2O3). Examples for :math:`\mathrm{TiO_2}`, -:math:`\mathrm{Al_2O_3}` are provided. A single pair\_coeff command +:math:`\mathrm{Al_2O_3}` are provided. A single pair_coeff command is used with the SMTBQ styles which provides the path to the potential file with parameters for needed elements. These are mapped to LAMMPS atom types by specifying additional arguments after the potential -filename in the pair\_coeff command. Note that atom type 1 must always +filename in the pair_coeff command. Note that atom type 1 must always correspond to oxygen atoms. As an example, to simulate a :math:`\mathrm{TiO_2}` system, atom type 1 has to be oxygen and atom type 2 Ti. The following -pair\_coeff command should then be used: +pair_coeff command should then be used: .. code-block:: LAMMPS @@ -72,7 +72,7 @@ Interaction between oxygen, :math:`E_{OO}`, consists of two parts, an attractive and a repulsive part. The attractive part is effective only at short range (< :math:`r_2^{OO}`). The attractive contribution was optimized to study surfaces reconstruction -(e.g. :ref:`SMTB-Q\_2 ` in :math:`\mathrm{TiO_2}`) and is not necessary +(e.g. :ref:`SMTB-Q_2 ` in :math:`\mathrm{TiO_2}`) and is not necessary for oxide bulk modeling. The repulsive part is the Pauli interaction between the electron clouds of oxygen. The Pauli repulsion and the coulombic electrostatic interaction have same cut off value. In the @@ -84,7 +84,7 @@ The short-range interaction between metal-oxygen, :math:`E_{MO}` is based on the second moment approximation of the density of states with a N-body potential for the band energy term, :math:`E^i_{cov}`, and a Born-Mayer type repulsive terms -as indicated by the keyword *'second\_moment'* in the +as indicated by the keyword *'second_moment'* in the ffield.SMTBQ.Syst. The energy band term is given by: .. math:: @@ -110,7 +110,7 @@ anion. In the literature we find many ways to write the hopping integral depending on whether one takes the point of view of the anion or cation. These are equivalent vision. The correspondence between the two visions is explained in appendix A of the article in the -SrTiO3 :ref:`SMTB-Q\_3 ` (parameter :math:`\beta` shown in +SrTiO3 :ref:`SMTB-Q_3 ` (parameter :math:`\beta` shown in this article is in fact the :math:`\beta_O`). To summarize the relationship between the hopping integral :math:`\xi^O` and the others, we have in an oxide :math:`\mathrm{C_n O_m}` the following @@ -128,7 +128,7 @@ the electron clouds of oxygen by changing the slater radius of the charge density around the oxygen atoms through the parameters *rBB, rB and rS* in the ffield.SMTBQ.Syst. This change in radius is performed according to the method developed by E. Maras -:ref:`SMTB-Q\_2 `. This method needs to determine the number of +:ref:`SMTB-Q_2 `. This method needs to determine the number of nearest neighbors around the oxygen. This calculation is based on first (:math:`r_{1n}`) and second (:math:`r_{2n}`) distances neighbors. @@ -176,12 +176,12 @@ For each cations (metal): 3) Potential parameters: * Keyword for element1, element2 and interaction potential - ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1 - and 2. If the potential is 'second\_moment', specify 'oxide' or + ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 + and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively. * Potential parameter: - - If type of potential is 'second\_moment' : A (eV), *p*, + - If type of potential is 'second_moment' : A (eV), *p*, :math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\mathrm{\mathring{A}})`, :math:`r_{c2} (\mathrm{\mathring{A}})` and :math:`r_0 (\mathrm{\mathring{A}})` - If type of potential is 'buck' : *C* (eV) and :math:`\rho (\mathrm{\mathring{A}})` @@ -237,7 +237,7 @@ For each cations (metal): 9) Verbose * If you want the code to work in verbose mode or not : 'true' or 'false' -* If you want to print or not in the file 'Energy\_component.txt' the +* If you want to print or not in the file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and :math:`N_{Energy}`. This option writes to the file every @@ -247,7 +247,7 @@ For each cations (metal): in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the interaction between oxygen, :math:`E_{OO}`, and short range metal-oxygen interaction, :math:`E_{MO}`. -* If you want to print to the file 'Electroneg\_component.txt' the +* If you want to print to the file 'Electroneg_component.txt' the electronegativity component (:math:`\frac{\partial E_{tot}}{\partial Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This option writes to the file every :math:`N_{Electroneg}` time steps. If @@ -271,7 +271,7 @@ This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -needs to re-specify the pair\_style and pair\_coeff commands in an input +needs to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -303,19 +303,19 @@ and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 ---------- -.. _SMTB-Q\_1: +.. _SMTB-Q_1: -**(SMTB-Q\_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot, +**(SMTB-Q_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 -.. _SMTB-Q\_2: +.. _SMTB-Q_2: -**(SMTB-Q\_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, +**(SMTB-Q_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 -.. _SMTB-Q\_3: +.. _SMTB-Q_3: -**(SMTB-Q\_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface +**(SMTB-Q_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface Science 616, 19-8722 28 (2013) .. _Wolf2: diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 246a461070..06ed748a07 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -50,10 +50,10 @@ The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. Note that unlike for other potentials, cutoffs for SNAP potentials are -not set in the pair\_style or pair\_coeff command; they are specified in +not set in the pair_style or pair_coeff command; they are specified in the SNAP potential files themselves. -Only a single pair\_coeff command is used with the *snap* style which +Only a single pair_coeff command is used with the *snap* style which specifies a SNAP coefficient file followed by a SNAP parameter file and then N additional arguments specifying the mapping of SNAP elements to LAMMPS atom types, where N is the number of @@ -65,7 +65,7 @@ LAMMPS atom types: As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the 3rd and 4th being -phophorous, the pair\_coeff command would look like this: +phophorous, the pair_coeff command would look like this: .. code-block:: LAMMPS @@ -175,13 +175,13 @@ for each element, the upper-triangular elements of alpha. For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to -specify a pair\_coeff command with I != J arguments for this style. +specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 460f97194e..3339009052 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -74,7 +74,7 @@ cutoff is used. The :doc:`fix adapt ` command can be used to vary A for one or more pair types over the course of a simulation, in which case -pair\_coeff settings for A must still be specified, but will be +pair_coeff settings for A must still be specified, but will be overridden. For example these commands will vary the prefactor A for all pairwise interactions from 0.0 at the beginning to 30.0 at the end of a run: @@ -115,9 +115,9 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the A coefficient and cutoff distance for this pair style can be mixed. A is always mixed via a -*geometric* rule. The cutoff is mixed according to the pair\_modify +*geometric* rule. The cutoff is mixed according to the pair_modify mix value. The default mix value is *geometric*\ . See the -"pair\_modify" command for details. +"pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option, since the pair interaction goes to 0.0 at the cutoff. @@ -125,7 +125,7 @@ shift option, since the pair interaction goes to 0.0 at the cutoff. The :doc:`pair_modify ` table and tail options are not relevant for this pair style. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index cc265ac8c5..45d064fdf5 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -44,8 +44,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -59,6 +59,6 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 5d99576aad..fe874797eb 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -53,8 +53,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -68,7 +68,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index defb1bb6fe..bdfe530cfb 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -48,8 +48,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -66,7 +66,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index ff749eac78..b3148bcd6a 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -45,8 +45,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -60,6 +60,6 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/taitwater +:doc:`pair_coeff `, pair_sph/taitwater **Default:** none diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index 498faccdd1..3431a20319 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -57,8 +57,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -72,7 +72,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index b56be5fa67..9c65fd91ec 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -56,8 +56,8 @@ I,J pairs must be specified explicitly. This style does not support the :doc:`pair_modify ` shift, table, and tail options. -This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and -pair\_coeff commands in an input script that reads a restart file. +This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -71,7 +71,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair_sph/rhosum **Default:** none diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index 1b6bade399..fae22d5e8a 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -88,7 +88,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. Restrictions diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 023de43475..dc2d22b30a 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -81,7 +81,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom\_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index cd3d9a202e..14eefaccec 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -42,7 +42,7 @@ interaction for different neighboring shells. This function is defined as: {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij}) where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated -"pair\_coeff" command, and :math:`R_c` is the radius cutoff associated to +"pair_coeff" command, and :math:`R_c` is the radius cutoff associated to the pair interaction (see below for more explanations). The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with @@ -93,7 +93,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom\_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 7caa98d96d..a220299b07 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -60,7 +60,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom\_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index 49adce9ed5..4e6eba1f34 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -56,7 +56,7 @@ the same Bethe-Slater function used to fit the exchange interaction: {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij}) where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the -associated "pair\_coeff" command. +associated "pair_coeff" command. The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with the values of the magneto-elastic constant of the @@ -80,7 +80,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom\_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index cb60a0285d..01517df434 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -137,7 +137,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair_style hybrid `, thus the pair\_coeff commands need to be +This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair_style hybrid `, thus the pair_coeff commands need to be specified in the input script when reading a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 5533e6440b..0433dfa861 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -63,19 +63,19 @@ pairwise interaction between two atoms separated by a distance *r*\ . The force between the atoms is the negative derivative of this expression. -If the pair\_style command has a cutoff argument, it sets global +If the pair_style command has a cutoff argument, it sets global cutoffs for all pairs of atom types. The distance(s) can be smaller or larger than the dimensions of the simulation box. Typically, the global cutoff value can be overridden for a specific pair of atom types by the :doc:`pair_coeff ` command. The pair style settings (including global cutoffs) can be changed by a -subsequent pair\_style command using the same style. This will reset +subsequent pair_style command using the same style. This will reset the cutoffs for all atom type pairs, including those previously set explicitly by a :doc:`pair_coeff ` command. The exceptions -to this are that pair\_style *table* and *hybrid* settings cannot be -reset. A new pair\_style command for these styles will wipe out all -previously specified pair\_coeff values. +to this are that pair_style *table* and *hybrid* settings cannot be +reset. A new pair_style command for these styles will wipe out all +previously specified pair_coeff values. ---------- @@ -83,7 +83,7 @@ Here is an alphabetic list of pair styles defined in LAMMPS. They are also listed in more compact form on the :doc:`Commands pair ` doc page. Click on the style to display the formula it computes, any additional -arguments specified in the pair\_style command, and coefficients +arguments specified in the pair_style command, and coefficients specified by the associated :doc:`pair_coeff ` command. There are also additional accelerated pair styles included in the diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 3cf425536a..f7999c720a 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -54,10 +54,10 @@ where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a three-body term. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`a `\sigma`. -Only a single pair\_coeff command is used with the *sw* style which +Only a single pair_coeff command is used with the *sw* style which specifies a Stillinger-Weber potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -69,7 +69,7 @@ to specify the path for the potential file. As an example, imagine a file SiC.sw has Stillinger-Weber values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following -pair\_coeff command: +pair_coeff command: .. code-block:: LAMMPS @@ -126,7 +126,7 @@ can be separately controlled. If tol = 0.0, then the standard Stillinger-Weber cutoff is used. The Stillinger-Weber potential file must contain entries for all the -elements listed in the pair\_coeff command. It can also contain +elements listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. @@ -200,7 +200,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 6062329fbe..9d1a21f1dc 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -94,7 +94,7 @@ table. The format of this file is described below. If your tabulated potential(s) are designed to be used as the short-range part of one of the long-range solvers specified by the :doc:`kspace_style ` command, then you must use one or -more of the optional keywords listed above for the pair\_style command. +more of the optional keywords listed above for the pair_style command. These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This is so LAMMPS can insure the short-range potential and long-range solver are compatible with each other, as it does for other @@ -104,7 +104,7 @@ functional form to be compatible with the matching long-range solver. ---------- -Here are some guidelines for using the pair\_style table command to +Here are some guidelines for using the pair_style table command to best effect: * Vary the number of table points; you may need to use more than you think @@ -113,7 +113,7 @@ best effect: of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. -* Use *N* in the pair\_style command equal to the "N" in the tabulation +* Use *N* in the pair_style command equal to the "N" in the tabulation file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation is not needed. See discussion below. * Make sure that your tabulated forces and tabulated energies are @@ -143,7 +143,7 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair\_coeff +initial text must match the argument specified in the pair_coeff command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -151,7 +151,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`pair_style table ` command. Let -Ntable = *N* in the pair\_style command, and Nfile = "N" in the +Ntable = *N* in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate energy and force values at Ntable different @@ -195,8 +195,8 @@ This ordering is complex, so it is not documented here, since this file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value -specified in the pair\_style command. Also, a cutoff parameter cannot -be used as an optional 3rd argument in the pair\_coeff command; the +specified in the pair_style command. Also, a cutoff parameter cannot +be used as an optional 3rd argument in the pair_coeff command; the entire table extent as specified in the file must be used. If used, the parameter "FPRIME" is followed by 2 values *fplo* and @@ -247,11 +247,11 @@ I,J pairs must be specified explicitly. The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. -This pair style writes the settings for the "pair\_style table" command -to :doc:`binary restart files `, so a pair\_style command does +This pair style writes the settings for the "pair_style table" command +to :doc:`binary restart files `, so a pair_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair\_coeff +file, since it is tabulated in the potential files. Thus, pair_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 79e8a8475f..32863cbd29 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -99,7 +99,7 @@ the difference is defined to be the internal chemical energy (uChem). ---------- -Here are some guidelines for using the pair\_style table/rx command to +Here are some guidelines for using the pair_style table/rx command to best effect: * Vary the number of table points; you may need to use more than you think @@ -108,7 +108,7 @@ best effect: of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. -* Use *N* in the pair\_style command equal to the "N" in the tabulation +* Use *N* in the pair_style command equal to the "N" in the tabulation file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation is not needed. See discussion below. * Make sure that your tabulated forces and tabulated energies are consistent @@ -137,7 +137,7 @@ A section begins with a non-blank line whose 1st character is not a "#"; blank lines or lines starting with "#" can be used as comments between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair\_coeff +initial text must match the argument specified in the pair_coeff command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -145,7 +145,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`pair_style table/rx ` command. Let -Ntable = *N* in the pair\_style command, and Nfile = "N" in the +Ntable = *N* in the pair_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate as needed to generate energy and force @@ -179,8 +179,8 @@ This ordering is complex, so it is not documented here, since this file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value -specified in the pair\_style command. Also, a cutoff parameter cannot -be used as an optional 3rd argument in the pair\_coeff command; the +specified in the pair_style command. Also, a cutoff parameter cannot +be used as an optional 3rd argument in the pair_coeff command; the entire table extent as specified in the file must be used. If used, the parameter "FPRIME" is followed by 2 values *fplo* and @@ -211,11 +211,11 @@ I,J pairs must be specified explicitly. The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. -This pair style writes the settings for the "pair\_style table/rx" command -to :doc:`binary restart files `, so a pair\_style command does +This pair style writes the settings for the "pair_style table/rx" command +to :doc:`binary restart files `, so a pair_style command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair\_coeff +file, since it is tabulated in the potential files. Thus, pair_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index a289c01ccf..7881c8ee70 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -46,7 +46,7 @@ Description """"""""""" The *tersoff* style computes a 3-body Tersoff potential -:ref:`(Tersoff\_1) ` for the energy E of a system of atoms as +:ref:`(Tersoff_1) ` for the energy E of a system of atoms as .. math:: @@ -76,10 +76,10 @@ between adjacent table entries. The table length is chosen to be accurate within 10\^-6 with respect to the *tersoff* style energy. The *tersoff/table* should give better performance in terms of speed. -Only a single pair\_coeff command is used with the *tersoff* style +Only a single pair_coeff command is used with the *tersoff* style which specifies a Tersoff potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -91,7 +91,7 @@ to specify the path for the potential file. As an example, imagine the SiC.tersoff file has Tersoff values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following -pair\_coeff command: +pair_coeff command: .. code-block:: LAMMPS @@ -139,7 +139,7 @@ parameters are used for both two-body and three-body interactions. The non-annotated parameters are unitless. The value of m must be 3 or 1. The Tersoff potential file must contain entries for all the elements -listed in the pair\_coeff command. It can also contain entries for +listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. @@ -171,7 +171,7 @@ be set to 0.0 if desired. Note that the twobody parameters in entries such as SiCC and CSiSi are often the same, due to the common use of symmetric mixing rules, but this is not always the case. For example, the beta and n parameters in -Tersoff\_2 :ref:`(Tersoff\_2) ` are not symmetric. +Tersoff_2 :ref:`(Tersoff_2) ` are not symmetric. We chose the above form so as to enable users to define all commonly used variants of the Tersoff potential. In particular, our form @@ -179,15 +179,15 @@ reduces to the original Tersoff form when m = 3 and gamma = 1, while it reduces to the form of :ref:`Albe et al. ` when beta = 1 and m = 1. Note that in the current Tersoff implementation in LAMMPS, m must be specified as either 3 or 1. Tersoff used a slightly different but -equivalent form for alloys, which we will refer to as Tersoff\_2 -potential :ref:`(Tersoff\_2) `. +equivalent form for alloys, which we will refer to as Tersoff_2 +potential :ref:`(Tersoff_2) `. The *tersoff/table* style implements -Tersoff\_2 parameterization only. +Tersoff_2 parameterization only. -LAMMPS parameter values for Tersoff\_2 can be obtained as follows: +LAMMPS parameter values for Tersoff_2 can be obtained as follows: :math:`\gamma_{ijk} = \omega_{ik}`, :math:`\lambda_3 = 0` and the value of m has no effect. The parameters for species i and j can be calculated -using the Tersoff\_2 mixing rules: +using the Tersoff_2 mixing rules: .. math:: @@ -198,10 +198,10 @@ using the Tersoff\_2 mixing rules: R_{i,j} & = (R_{i}R_{j})^{1/2}\\ S_{i,j} & = (S_{i}S_{j})^{1/2} -Tersoff\_2 parameters R and S must be converted to the LAMMPS +Tersoff_2 parameters R and S must be converted to the LAMMPS parameters R and D (R is different in both forms), using the following relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff\_2 parameters. +Tersoff_2 parameters. In the potentials directory, the file SiCGe.tersoff provides the LAMMPS parameters for Tersoff's various versions of Si, as well as his @@ -249,7 +249,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -282,15 +282,15 @@ Related commands ---------- -.. _Tersoff\_11: +.. _Tersoff_11: -**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). +**(Tersoff_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). .. _Albe: **(Albe)** J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). -.. _Tersoff\_21: +.. _Tersoff_21: -**(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) +**(Tersoff_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index e3f26a31b8..3d5bdbdaee 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -43,7 +43,7 @@ Description The *tersoff/mod* and *tersoff/mod/c* styles computes a bond-order type interatomic potential :ref:`(Kumagai) ` based on a 3-body Tersoff -potential :ref:`(Tersoff\_1) `, :ref:`(Tersoff\_2) ` with +potential :ref:`(Tersoff_1) `, :ref:`(Tersoff_2) ` with modified cutoff function and angular-dependent term, giving the energy E of a system of atoms as @@ -70,7 +70,7 @@ where :math:`f_R` is a two-body term and :math:`f_A` includes three-body interac The summations in the formula are over all neighbors J and K of atom I within a cutoff distance = R + D. The *tersoff/mod/c* style differs from *tersoff/mod* only in the -formulation of the V\_ij term, where it contains an additional c0 term. +formulation of the V_ij term, where it contains an additional c0 term. .. math:: @@ -87,18 +87,18 @@ form in which the angular-dependent term is improved. The model performs extremely well in describing the crystalline, liquid, and amorphous phases :ref:`(Schelling) `. -Only a single pair\_coeff command is used with the *tersoff/mod* style +Only a single pair_coeff command is used with the *tersoff/mod* style which specifies a Tersoff/MOD potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff/MOD elements to atom types -As an example, imagine the Si.tersoff\_mod file has Tersoff values for Si. +As an example, imagine the Si.tersoff_mod file has Tersoff values for Si. If your LAMMPS simulation has 3 Si atoms types, you would use the following -pair\_coeff command: +pair_coeff command: .. code-block:: LAMMPS @@ -149,7 +149,7 @@ The c0 term applies to *tersoff/mod/c* only. The non-annotated parameters are unitless. The Tersoff/MOD potential file must contain entries for all the elements -listed in the pair\_coeff command. It can also contain entries for +listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. @@ -187,7 +187,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -225,13 +225,13 @@ Related commands **(Kumagai)** T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007). -.. _Tersoff\_12: +.. _Tersoff_12: -**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). +**(Tersoff_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). -.. _Tersoff\_22: +.. _Tersoff_22: -**(Tersoff\_2)** J. Tersoff, Phys Rev B, 38, 9902 (1988). +**(Tersoff_2)** J. Tersoff, Phys Rev B, 38, 9902 (1988). .. _Murty: diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index 854f2630a4..fe86ef2cbb 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -31,7 +31,7 @@ Description """"""""""" The *tersoff/zbl* style computes a 3-body Tersoff potential -:ref:`(Tersoff\_1) ` with a close-separation pairwise modification +:ref:`(Tersoff_1) ` with a close-separation pairwise modification based on a Coulomb potential and the Ziegler-Biersack-Littmark universal screening function :ref:`(ZBL) `, giving the energy E of a system of atoms as @@ -85,10 +85,10 @@ includes three-body interactions. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance = R + D. -Only a single pair\_coeff command is used with the *tersoff/zbl* style +Only a single pair_coeff command is used with the *tersoff/zbl* style which specifies a Tersoff/ZBL potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair\_coeff command, +N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -100,7 +100,7 @@ to specify the path for the potential file. As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair\_coeff command: +following pair_coeff command: .. code-block:: LAMMPS @@ -155,7 +155,7 @@ portion of the potential and in the Fermi-like function. The non-annotated parameters are unitless. The value of m must be 3 or 1. The Tersoff/ZBL potential file must contain entries for all the -elements listed in the pair\_coeff command. It can also contain +elements listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. @@ -187,7 +187,7 @@ be set to 0.0 if desired. Note that the twobody parameters in entries such as SiCC and CSiSi are often the same, due to the common use of symmetric mixing rules, but this is not always the case. For example, the beta and n parameters in -Tersoff\_2 :ref:`(Tersoff\_2) ` are not symmetric. +Tersoff_2 :ref:`(Tersoff_2) ` are not symmetric. We chose the above form so as to enable users to define all commonly used variants of the Tersoff portion of the potential. In particular, @@ -196,12 +196,12 @@ our form reduces to the original Tersoff form when m = 3 and gamma = and m = 1. Note that in the current Tersoff implementation in LAMMPS, m must be specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as -Tersoff\_2 potential :ref:`(Tersoff\_2) `. +Tersoff_2 potential :ref:`(Tersoff_2) `. -LAMMPS parameter values for Tersoff\_2 can be obtained as follows: +LAMMPS parameter values for Tersoff_2 can be obtained as follows: :math:`\gamma = \omega_{ijk}`, :math:`\lambda_3 = 0` and the value of m has no effect. The parameters for species i and j can be calculated -using the Tersoff\_2 mixing rules: +using the Tersoff_2 mixing rules: .. math:: @@ -212,10 +212,10 @@ using the Tersoff\_2 mixing rules: R_{i,j} & = (R_{i}R_{j})^{1/2}\\ S_{i,j} & = (S_{i}S_{j})^{1/2}\\ -Tersoff\_2 parameters R and S must be converted to the LAMMPS +Tersoff_2 parameters R and S must be converted to the LAMMPS parameters R and D (R is different in both forms), using the following relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff\_2 parameters. +Tersoff_2 parameters. In the potentials directory, the file SiCGe.tersoff provides the LAMMPS parameters for Tersoff's various versions of Si, as well as his @@ -264,7 +264,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the @@ -298,9 +298,9 @@ Related commands ---------- -.. _zbl-Tersoff\_1: +.. _zbl-Tersoff_1: -**(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). +**(Tersoff_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). .. _zbl-ZBL: @@ -312,6 +312,6 @@ of Ions in Matter' Vol 1, 1985, Pergamon Press. **(Albe)** J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). -.. _zbl-Tersoff\_2: +.. _zbl-Tersoff_2: -**(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) +**(Tersoff_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 4e0ce8844a..7adf267469 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -56,7 +56,7 @@ containing *coul/cut* or *coul/long* in its style name. The *lj/cut/thole/long* pair style is equivalent to, but more convenient that the frequent combination *hybrid/overlay lj/cut/coul/long cutoff thole damp -cutoff2*\ . It is not only a shorthand for this pair\_style combination, but +cutoff2*\ . It is not only a shorthand for this pair_style combination, but it also allows for mixing pair coefficients instead of listing them all. The *lj/cut/thole/long* pair style is also a bit faster because it avoids an overlay and can benefit from OMP acceleration. Moreover, it uses a more @@ -104,7 +104,7 @@ non-polarizable atoms are also subject to these weighting factors. The Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from their respective cores. -For pair\_style *thole*\ , the following coefficients must be defined for +For pair_style *thole*\ , the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. @@ -113,7 +113,7 @@ as in the example above. * cutoff (distance units) The last two coefficients are optional. If not specified the global -Thole damping parameter or global cutoff specified in the pair\_style +Thole damping parameter or global cutoff specified in the pair_style command are used. In order to specify a cutoff (third argument) a damp parameter (second argument) must also be specified. @@ -128,7 +128,7 @@ command. * LJ cutoff (distance units) The last two coefficients are optional and default to the global values from -the *pair\_style* command line. +the *pair_style* command line. ---------- @@ -170,7 +170,7 @@ Restrictions These pair styles are part of the USER-DRUDE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This pair\_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting +This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting factors. This is because the *thole* pair style does not know which pairs are 1-4 partners of which dihedrals. diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 1546d954d5..1dd69778ed 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -41,16 +41,16 @@ its entirety or not at all. The set of non-overlapping spherical particles that represent a triangle, for purposes of this pair style, are generated in the -following manner. Assume the triangle is of type I, and sigma\_II has +following manner. Assume the triangle is of type I, and sigma_II has been specified. We want a set of spheres with centers in the plane of -the triangle, none of them larger in diameter than sigma\_II, which +the triangle, none of them larger in diameter than sigma_II, which completely cover the triangle's area, but with minimal overlap and a minimal total number of spheres. This is done in a recursive manner. Place a sphere at the centroid of the original triangle. Calculate what diameter it must have to just cover all 3 corner points of the -triangle. If that diameter is equal to or smaller than sigma\_II, then +triangle. If that diameter is equal to or smaller than sigma_II, then include a sphere of the calculated diameter in the set of covering -spheres. It the diameter is larger than sigma\_II, then split the +spheres. It the diameter is larger than sigma_II, then split the triangle into 2 triangles by bisecting its longest side. Repeat the process on each sub-triangle, recursing as far as needed to generate a set of covering spheres. When finished, the original criteria are @@ -62,8 +62,8 @@ The LJ interaction between 2 spheres on different triangles of types I,J is computed with an arithmetic mixing of the sigma values of the 2 spheres and using the specified epsilon value for I,J atom types. Note that because the sigma values for triangles spheres is computed -using only sigma\_II values, specific to the triangles's type, this -means that any specified sigma\_IJ values (for I != J) are effectively +using only sigma_II values, specific to the triangles's type, this +means that any specified sigma_IJ values (for I != J) are effectively ignored. For style *tri/lj*\ , the following coefficients must be defined for @@ -85,7 +85,7 @@ is used. For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of this pair style can be mixed. The -default mix value is *geometric*\ . See the "pair\_modify" command for +default mix value is *geometric*\ . See the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index a26dd582be..2562b2fc2f 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -66,7 +66,7 @@ The last coefficient is optional. If not specified, the global *ufm* cutoff is used. The :doc:`fix adapt ` command can be used to vary epsilon and sigma for this pair style over the course of a simulation, in which case -pair\_coeff settings for epsilon and sigma must still be specified, but will be +pair_coeff settings for epsilon and sigma must still be specified, but will be overridden. For example these commands will vary the prefactor epsilon for all pairwise interactions from 10.0 at the beginning to 100.0 at the end of a run: @@ -112,9 +112,9 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the A coefficient and cutoff distance for this pair style can be mixed. A is always mixed via a -*geometric* rule. The cutoff is mixed according to the pair\_modify +*geometric* rule. The cutoff is mixed according to the pair_modify mix value. The default mix value is *geometric*\ . See the -"pair\_modify" command for details. +"pair_modify" command for details. This pair style support the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -123,7 +123,7 @@ pair style. This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index ca4751d07f..044709d65d 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -87,10 +87,10 @@ with moderate to little loss of accuracy for Ntable values between 10000 and 1000000. It is not recommended to use less than 5000 tabulation points. -Only a single pair\_coeff command is used with either style which +Only a single pair_coeff command is used with either style which specifies a Vashishta potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair\_coeff command, +additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: * filename @@ -102,7 +102,7 @@ to specify the path for the potential file. As an example, imagine a file SiC.vashishta has parameters for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following -pair\_coeff command: +pair_coeff command: .. code-block:: LAMMPS @@ -143,7 +143,7 @@ and three-body coefficients in the formulae above: The non-annotated parameters are unitless. The Vashishta potential file must contain entries for all the elements listed in the -pair\_coeff command. It can also contain entries for additional +pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries. For a single-element simulation, only a single entry is required (e.g. SiSiSi). For a two-element simulation, the file @@ -223,7 +223,7 @@ This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair\_style and pair\_coeff commands in an input +need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index e11b631853..acb6de4f13 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -71,7 +71,7 @@ must be set before this command can be invoked. Due to how the pairwise force is computed, an inner value > 0.0 must be specified even if the potential has a finite value at r = 0.0. -For EAM potentials, the pair\_write command only tabulates the +For EAM potentials, the pair_write command only tabulates the pairwise portion of the potential, not the embedding portion. Related commands diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 4170b32275..fad035ed4b 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -81,7 +81,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the A coefficient and cutoff distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the -"pair\_modify" command for details. +"pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -93,7 +93,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 83e834d7f4..f775f37703 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -44,7 +44,7 @@ In contrast to :doc:`pair_style yukawa `, this functional form arises from the Coulombic interaction between two colloid particles, screened due to the presence of an electrolyte, see the book by :ref:`Safran ` for a derivation in the context of DLVO -theory. :doc:`Pair\_style yukawa ` is a screened Coulombic +theory. :doc:`Pair_style yukawa ` is a screened Coulombic potential between two point-charges and uses no such approximation. This potential applies to nearby particle pairs for which the Derjagin @@ -112,7 +112,7 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, the A coefficient and cutoff distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the -"pair\_modify" command for details. +"pair_modify" command for details. This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. @@ -124,7 +124,7 @@ This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 59b9b52702..26960f71b3 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -39,7 +39,7 @@ repulsion for describing high-energy collisions between atoms. :ref:`(Ziegler) `. It includes an additional switching function that ramps the energy, force, and curvature smoothly to zero between an inner and outer cutoff. The potential -energy due to a pair of atoms at a distance r\_ij is given by: +energy due to a pair of atoms at a distance r_ij is given by: .. math:: @@ -71,7 +71,7 @@ When used with :doc:`hybrid/overlay ` and pairs are assigned to more than one sub-style, the mixing rule is not used and each pair of types interacting with the ZBL sub-style must -be included in a pair\_coeff command. +be included in a pair_coeff command. .. note:: @@ -115,7 +115,7 @@ specified for with :doc:`hybrid/overlay ` and pairs are assigned to more than one sub-style, the mixing rule is not used and each pair of types interacting with the ZBL sub-style -must be included in a pair\_coeff command. +must be included in a pair_coeff command. The :doc:`pair_modify ` mix option has no effect on the mixing behavior @@ -131,7 +131,7 @@ tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. -This pair style does not write information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands must be +This pair style does not write information to :doc:`binary restart files `, so pair_style and pair_coeff commands must be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 86b3fa64fb..a704cf92f2 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -12,7 +12,7 @@ Syntax * zero = style name of this pair style * cutoff = global cutoff (distance units) -* nocoeff = ignore all pair\_coeff parameters (optional) +* nocoeff = ignore all pair_coeff parameters (optional) Examples """""""" @@ -41,7 +41,7 @@ used to insure communication of ghost atoms even when a pair style is not defined, but it will not trigger neighbor list generation. The optional *nocoeff* flag allows to read data files with a PairCoeff -section for any pair style. Similarly, any pair\_coeff commands +section for any pair style. Similarly, any pair_coeff commands will only be checked for the atom type numbers and the rest ignored. In this case, only the global cutoff will be used. @@ -54,7 +54,7 @@ commands, or by mixing as described below: * cutoff (distance units) This coefficient is optional. If not specified, the global cutoff -specified in the pair\_style command is used. If the pair\_style has +specified in the pair_style command is used. If the pair_style has been specified with the optional *nocoeff* flag, then a cutoff pair coefficient is ignored. @@ -63,12 +63,12 @@ pair coefficient is ignored. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The cutoff distance for this pair style can be mixed. The default mix -value is *geometric*\ . See the "pair\_modify" command for details. +value is *geometric*\ . See the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need +This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , diff --git a/doc/src/partition.rst b/doc/src/partition.rst index be333ba581..be0e1152f5 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -59,7 +59,7 @@ from 1 to n (inclusive). A trailing asterisk means all partitions from n to Np (inclusive). A middle asterisk means all partitions from m to n (inclusive). -This command can be useful for the "run\_style verlet/split" command +This command can be useful for the "run_style verlet/split" command which imposed requirements on how the :doc:`processors ` command lays out a 3d grid of processors in each of 2 partitions. diff --git a/doc/src/prd.rst b/doc/src/prd.rst index d849c8f5a8..c3bd1ad1d3 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -11,12 +11,12 @@ Syntax prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ... * N = # of timesteps to run (not including dephasing/quenching) -* t\_event = timestep interval between event checks -* n\_dephase = number of velocity randomizations to perform in each dephase run -* t\_dephase = number of timesteps to run dynamics after each velocity randomization during dephase -* t\_correlate = number of timesteps within which 2 consecutive events are considered to be correlated +* t_event = timestep interval between event checks +* n_dephase = number of velocity randomizations to perform in each dephase run +* t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase +* t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated * compute-ID = ID of the compute used for event detection -* random\_seed = random # seed (positive integer) +* random_seed = random # seed (positive integer) * zero or more keyword/value pairs may be appended * keyword = *min* or *temp* or *vel* @@ -119,9 +119,9 @@ storing the resulting coordinates for reference. In the first stage, dephasing is performed by each replica independently to eliminate correlations between replicas. This is done by choosing a random set of velocities, based on the -*random\_seed* that is specified, and running *t\_dephase* timesteps of -dynamics. This is repeated *n\_dephase* times. At each of the -*n\_dephase* stages, if an event occurs during the *t\_dephase* steps of +*random_seed* that is specified, and running *t_dephase* timesteps of +dynamics. This is repeated *n_dephase* times. At each of the +*n_dephase* stages, if an event occurs during the *t_dephase* steps of dynamics for a particular replica, the replica repeats the stage until no event occurs. @@ -133,7 +133,7 @@ The style of velocity randomization is controlled using the keyword in the :doc:`velocity ` command. In the second stage, each replica runs dynamics continuously, stopping -every *t\_event* steps to check if a transition event has occurred. +every *t_event* steps to check if a transition event has occurred. This check is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. The first time through the PRD loop, the "previous basin" is the set @@ -158,8 +158,8 @@ distance. If so, an "event" has occurred. In the third stage, the replica on which the event occurred (event replica) continues to run dynamics to search for correlated events. -This is done by running dynamics for *t\_correlate* steps, quenching -every *t\_event* steps, and checking if another event has occurred. +This is done by running dynamics for *t_correlate* steps, quenching +every *t_event* steps, and checking if another event has occurred. The first time no correlated event occurs, the final state of the event replica is shared with all replicas, the new basin reference @@ -230,11 +230,11 @@ when a correlated event occurs during the third stage of the loop listed above, i.e. when only one replica is running dynamics. When more than one replica detects an event at the end of the same -event check (every *t\_event* steps) during the second stage, then +event check (every *t_event* steps) during the second stage, then one of them is chosen at random. The number of coincident events is the number of replicas that detected an event. Normally, this value should be 1. If it is often greater than 1, then either the number of -replicas is too large, or *t\_event* is too large. +replicas is too large, or *t_event* is too large. The replica number is the ID of the replica (from 0 to M-1) in which the event occurred. @@ -277,9 +277,9 @@ continued by a new input script in the usual manner. The restart file is generated at the end of the loop listed above. If no correlated events are found, this means it contains a snapshot of -the system at time T + *t\_correlate*, where T is the time at which the +the system at time T + *t_correlate*, where T is the time at which the uncorrelated event occurred. If correlated events were found, then it -contains a snapshot of the system at time T + *t\_correlate*, where T +contains a snapshot of the system at time T + *t_correlate*, where T is the time of the last correlated event. The restart frequency specified in the :doc:`restart ` command @@ -292,7 +292,7 @@ event. When an input script reads a restart file from a previous PRD run, the new script can be run on a different number of replicas or processors. -However, it is assumed that *t\_correlate* in the new PRD command is +However, it is assumed that *t_correlate* in the new PRD command is the same as it was previously. If not, the calculation of the "clock" value for the first event in the new run will be slightly off. @@ -305,8 +305,8 @@ This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. -The *N* and *t\_correlate* settings must be integer multiples of -*t\_event*. +The *N* and *t_correlate* settings must be integer multiples of +*t_event*. Runs restarted from restart file written during a PRD run will not produce identical results due to changes in the random numbers used diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 8fe13f69eb..899c87f4b0 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -213,9 +213,9 @@ mapped to the 3d grid of processors. It is only used by the *onelevel* and *twolevel* grid settings. The *cart* style uses the family of MPI Cartesian functions to perform -the mapping, namely MPI\_Cart\_create(), MPI\_Cart\_get(), -MPI\_Cart\_shift(), and MPI\_Cart\_rank(). It invokes the -MPI\_Cart\_create() function with its reorder flag = 0, so that MPI is +the mapping, namely MPI_Cart_create(), MPI_Cart_get(), +MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the +MPI_Cart_create() function with its reorder flag = 0, so that MPI is not free to reorder the processors. The *cart/reorder* style does the same thing as the *cart* style @@ -244,7 +244,7 @@ of the 8 octants of the simulation domain will be: Note that, in principle, an MPI implementation on a particular machine should be aware of both the machine's network topology and the specific subset of processors and nodes that were assigned to your -simulation. Thus its MPI\_Cart calls can optimize the assignment of +simulation. Thus its MPI_Cart calls can optimize the assignment of MPI processes to the 3d grid to minimize communication costs. In practice, however, few if any MPI implementations actually do this. So it is likely that the *cart* and *cart/reorder* styles simply give @@ -328,7 +328,7 @@ I,J,K are the indices of the processor in the regular 3d grid, each from 1 to Nd, where Nd is the number of processors in that dimension of the grid. -The *name* is what is returned by a call to MPI\_Get\_processor\_name() +The *name* is what is returned by a call to MPI_Get_processor_name() and should represent an identifier relevant to the physical processors in your machine. Note that depending on the MPI implementation, multiple cores can have the same *name*\ . diff --git a/doc/src/python.rst b/doc/src/python.rst index 6c54fb8872..70dfbb70ba 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -139,14 +139,14 @@ itself. This enables the function to call back to LAMMPS through its library interface as explained below. This allows the Python function to query or set values internal to LAMMPS which can affect the subsequent execution of the input script. A LAMMPS variable can also -be used as an argument, specified as v\_name, where "name" is the name +be used as an argument, specified as v_name, where "name" is the name of the variable. Any style of LAMMPS variable can be used, as defined by the :doc:`variable ` command. Each time the Python function is invoked, the LAMMPS variable is evaluated and its value is passed to the Python function. The *return* keyword is only needed if the Python function returns a -value. The specified *varReturn* must be of the form v\_name, where +value. The specified *varReturn* must be of the form v_name, where "name" is the name of a python-style LAMMPS variable, defined by the :doc:`variable ` command. The Python function can return a numeric or string value, as specified by the *format* keyword. @@ -231,7 +231,7 @@ conflict with the triple-quote parsing that the LAMMPS input script performs. All the Python code you specify via one or more python commands is -loaded into the Python "main" module, i.e. \__main\__. The code can +loaded into the Python "main" module, i.e. __main__. The code can define global variables or statements that are outside of function definitions. It can contain multiple functions, only one of which matches the *func* setting in the python command. This means you can @@ -301,7 +301,7 @@ LAMMPS with that library. Third, if your Python code calls back to LAMMPS (discussed in the next section) and causes LAMMPS to perform an MPI operation requires -global communication (e.g. via MPI\_Allreduce), such as computing the +global communication (e.g. via MPI_Allreduce), such as computing the global temperature of the system, then you must insure all your Python functions (running independently on different processors) call back to LAMMPS. Otherwise the code may hang. @@ -384,15 +384,15 @@ with complex logic, much more so than can be created using the LAMMPS :doc:`jump ` and :doc:`if ` commands. Several LAMMPS library functions are called from the loop function. -Get\_natoms() returns the number of atoms in the simulation, so that it +Get_natoms() returns the number of atoms in the simulation, so that it can be used to normalize the potential energy that is returned by -extract\_compute() for the "thermo\_pe" compute that is defined by -default for LAMMPS thermodynamic output. Set\_variable() sets the +extract_compute() for the "thermo_pe" compute that is defined by +default for LAMMPS thermodynamic output. Set_variable() sets the value of a string variable defined in LAMMPS. This library function is a useful way for a Python function to return multiple values to LAMMPS, more than the single value that can be passed back via a return statement. This cutoff value in the "cut" variable is then -substituted (by LAMMPS) in the pair\_style command that is executed +substituted (by LAMMPS) in the pair_style command that is executed next. Alternatively, the "LAMMPS command option" line could be used in place of the 2 preceding lines, to have Python insert the value into the LAMMPS command string. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 02e47e9c0e..2714cee4c1 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -83,7 +83,7 @@ the :doc:`displace_atoms ` command. Note that atoms read from the data file are also always added to the "all" group. The :doc:`group ` command discusses atom groups, as used in LAMMPS. -The *nocoeff* keyword tells read\_data to ignore force field parameters. +The *nocoeff* keyword tells read_data to ignore force field parameters. The various Coeff sections are still read and have to have the correct number of lines, but they are not applied. This also allows to read a data file without having any pair, bond, angle, dihedral or improper @@ -95,22 +95,22 @@ The use of the *fix* keyword is discussed below. **Reading multiple data files** -The read\_data command can be used multiple times with the same or +The read_data command can be used multiple times with the same or different data files to build up a complex system from components contained in individual data files. For example one data file could contain fluid in a confined domain; a second could contain wall atoms, and the second file could be read a third time to create a wall on the other side of the fluid. The third set of atoms could be rotated to an opposing direction using the :doc:`displace_atoms ` -command, after the third read\_data command is used. +command, after the third read_data command is used. The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are useful in this context. If a simulation box does not yet exist, the *add* keyword -cannot be used; the read\_data command is being used for the first +cannot be used; the read_data command is being used for the first time. If a simulation box does exist, due to using the -:doc:`create_box ` command, or a previous read\_data command, +:doc:`create_box ` command, or a previous read_data command, then the *add* keyword must be used. .. note:: @@ -174,12 +174,12 @@ to move a subset of atoms after they have been read from a data file. Likewise, the :doc:`delete_atoms ` command can be used to remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are also added to the simulation box information (xlo, xhi, ylo, yhi, zlo, -zhi) in the data file to shift its boundaries. E.g. xlo\_new = xlo + -Sx, xhi\_new = xhi + Sx. +zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo + +Sx, xhi_new = xhi + Sx. -The *extra* keywords can only be used the first time the read\_data +The *extra* keywords can only be used the first time the read_data command is used. They are useful if you intend to add new atom, bond, -angle, etc types later with additional read\_data commands. This is +angle, etc types later with additional read_data commands. This is because the maximum number of allowed atom, bond, angle, etc types is set by LAMMPS when the system is first initialized. If you do not use the *extra* keywords, then the number of these types will be limited @@ -205,10 +205,10 @@ you would still need to specify coefficients for H/Si and O/Si interactions in your input script to have a complete pairwise interaction model. -An alternative to using the *extra* keywords with the read\_data +An alternative to using the *extra* keywords with the read_data command, is to use the :doc:`create_box ` command to initialize the simulation box and all the various type limits you need -via its *extra* keywords. Then use the read\_data command one or more +via its *extra* keywords. Then use the read_data command one or more times to populate the system with atoms, bonds, angles, etc, using the *offset* keyword if desired to alter types used in the various data files you read. @@ -379,13 +379,13 @@ data file. "shrink-wrap" boundary conditions (see the :doc:`boundary ` command), a huge (mostly empty) box may cause a parallel simulation to lose atoms when LAMMPS shrink-wraps the box around the atoms. The - read\_data command will generate an error in this case. + read_data command will generate an error in this case. The "extra bond per atom" setting (angle, dihedral, improper) is only needed if new bonds (angles, dihedrals, impropers) will be added to the system when a simulation runs, e.g. by using the :doc:`fix bond/create ` command. Using this header flag is deprecated; please use the *extra/bond/per/atom* keyword (and -correspondingly for angles, dihedrals and impropers) in the read\_data +correspondingly for angles, dihedrals and impropers) in the read_data command instead. Either will pre-allocate space in LAMMPS data structures for storing the new bonds (angles, dihedrals, impropers). @@ -405,7 +405,7 @@ pages for more discussion of 1-2,1-3,1-4 neighbors. All of the "extra" settings are only applied in the first data file read and when no simulation box has yet been created; as soon as - the simulation box is created (and read\_data implies that), these + the simulation box is created (and read_data implies that), these settings are *locked* and cannot be changed anymore. Please see the description of the *add* keyword above for reading multiple data files. If they appear in later data files, they are ignored. @@ -586,7 +586,7 @@ of analysis. +------------+---------------------------------------------------------------------------+ | 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 | +------------+---------------------------------------------------------------------------+ @@ -616,7 +616,7 @@ of analysis. +------------+---------------------------------------------------------------------------+ | tri | atom-ID molecule-ID atom-type triangleflag density x y z | +------------+---------------------------------------------------------------------------+ -| wavepacket | atom-ID atom-type charge spin eradius etag cs\_re cs\_im x y z | +| wavepacket | atom-ID atom-type charge spin eradius etag cs_re cs_im x y z | +------------+---------------------------------------------------------------------------+ | hybrid | atom-ID atom-type x y z sub-style1 sub-style2 ... | +------------+---------------------------------------------------------------------------+ @@ -628,13 +628,13 @@ The per-atom values have these meanings and units, listed alphabetically: * bodyflag = 1 for body particles, 0 for point particles * cc = chemical concentration for tDPD particles for each species (mole/volume units) * contact-radius = ??? (distance units) -* cs\_re,cs\_im = real/imaginary parts of wave packet coefficients +* cs_re,cs_im = real/imaginary parts of wave packet coefficients * cv = heat capacity (need units) for SPH particles * density = density of particle (mass/distance\^3 or mass/distance\^2 or mass/distance units, depending on dimensionality of particle) * diameter = diameter of spherical atom (distance units) * e = energy (need units) for SPH particles -* edpd\_temp = temperature for eDPD particles (temperature units) -* edpd\_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) +* edpd_temp = temperature for eDPD particles (temperature units) +* edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) * ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles * eradius = electron radius (or fixed-core radius) * etag = integer ID of electron that each wave packet belongs to @@ -713,12 +713,12 @@ body is unknown. Note that for 2d simulations of spheres, this command will treat them as spheres when converting density to mass. However, they can also be modeled as 2d discs (circles) if the :doc:`set density/disc ` -command is used to reset their mass after the read\_data command is +command is used to reset their mass after the read_data command is used. A *disc* keyword can also be used with time integration fixes, such as :doc:`fix nve/sphere ` and :doc:`fix nvt/sphere ` to time integrate their motion as 2d discs (not 3d spheres), by changing their moment of inertia. -For atom\_style hybrid, following the 5 initial values (ID,type,x,y,z), +For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the :doc:`atom_style ` command. The sub-style specific values @@ -739,7 +739,7 @@ were used in the input script, each atom line would have these fields: Note that if a non-standard value is defined by multiple sub-styles, it must appear multiple times in the atom line. E.g. the atom line -for atom\_style hybrid dipole full would list "q" twice: +for atom_style hybrid dipole full would list "q" twice: .. parsed-literal:: @@ -1176,7 +1176,7 @@ pair style. See the :doc:`pair_style ` and :doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are not specified, these will be generated automatically by the pair style's mixing rule. See the -individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +individual pair_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also be set via the :doc:`pair_coeff ` command in the input script. @@ -1206,7 +1206,7 @@ pair style. See the :doc:`pair_style ` and :doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are all specified, these values will turn off the default mixing rule defined by the pair style. See the -individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +individual pair_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also be set via the :doc:`pair_coeff ` command in the input script. @@ -1277,7 +1277,7 @@ Vx, vy, vz, and ervel are in :doc:`units ` of velocity. Lx, ly, lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, Wz are in units of angular velocity (radians/time). -For atom\_style hybrid, following the 4 initial values (ID,vx,vy,vz), +For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the :doc:`atom_style ` command. The sub-style specific values @@ -1306,7 +1306,7 @@ Restrictions """""""""""" To read gzipped data files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. See the :doc:`Build settings ` +-DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. Related commands diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 3023f719e3..c46c12c951 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -80,9 +80,9 @@ commands for alternative methods to do this. Also see the from a dump file. Note that a simulation box must already be defined before using the -read\_dump command. This can be done by the +read_dump command. This can be done by the :doc:`create_box `, :doc:`read_data `, or -:doc:`read_restart ` commands. The read\_dump command can +:doc:`read_restart ` commands. The read_dump command can reset the simulation box dimensions, as explained below. Also note that reading per-atom information from a dump snapshot is @@ -92,7 +92,7 @@ a valid simulation, such as atom charge, or bond topology information for a molecular system, are not read from (or even contained in) dump files. Thus this auxiliary information should be defined in the usual way, e.g. in a data file read in by a :doc:`read_data ` -command, before using the read\_dump command, or by the :doc:`set ` +command, before using the read_dump command, or by the :doc:`set ` command, after the dump snapshot is read. ---------- @@ -196,7 +196,7 @@ always work perfectly. Per-atom information from the dump file snapshot is then read from the dump file snapshot. This corresponds to the specified *fields* listed -in the read\_dump command. It is an error to specify a z-dimension +in the read_dump command. It is an error to specify a z-dimension field, namely *z*\ , *vz*\ , or *iz*\ , for a 2d simulation. For dump files in *native* format, each column of per-atom data has a @@ -371,7 +371,7 @@ Restrictions """""""""""" To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. See the :doc:`Build settings ` +-DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. The *molfile* dump file formats are part of the USER-MOLFILE package. diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 58f6c113fc..ef77cef1af 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -44,11 +44,11 @@ changed by the :doc:`balance ` or :doc:`fix balance ` comm Normally, restart files are written by the :doc:`restart ` or :doc:`write_restart ` commands so that all atoms in the restart file are inside the simulation box. - If this is not the case, the read\_restart command will print an error + If this is not the case, the read_restart command will print an error that atoms were "lost" when the file is read. This error should be reported to the LAMMPS developers so the invalid writing of the restart file can be fixed. If you still wish to use the restart file, - the optional *remap* flag can be appended to the read\_restart command. + the optional *remap* flag can be appended to the read_restart command. This should avoid the error, by explicitly remapping each atom back into the simulation box, updating image flags for the atom appropriately. @@ -97,11 +97,11 @@ the run command so it doesn't need to be changed either. If a "%" character appears in the restart filename, LAMMPS expects a set of multiple files to exist. The :doc:`restart ` and :doc:`write_restart ` commands explain how such sets are -created. Read\_restart will first read a filename where "%" is +created. Read_restart will first read a filename where "%" is replaced by "base". This file tells LAMMPS how many processors -created the set and how many files are in it. Read\_restart then reads +created the set and how many files are in it. Read_restart then reads the additional files. For example, if the restart file was specified -as save.% when it was written, then read\_restart reads the files +as save.% when it was written, then read_restart reads the files save.base, save.0, save.1, ... save.P-1, where P is the number of processors that created the restart file. @@ -169,7 +169,7 @@ reading the restart file. The :doc:`newton ` command has two settings, one for pairwise interactions, the other for bonded. Both settings are stored in the restart file. For the bond setting, the value in the file will -overwrite the current value (at the time the read\_restart command is +overwrite the current value (at the time the read_restart command is issued) and warn if the two values are not the same and the current value is not the default. For the pair setting, the value in the file will not overwrite the current value (so that you can override the @@ -224,7 +224,7 @@ its calculations in a consistent manner. There are a handful of commands which can be used before or between runs which may require a system initialization. Examples - include the "balance", "displace\_atoms", "delete\_atoms", "set" (some + include the "balance", "displace_atoms", "delete_atoms", "set" (some options), and "velocity" (some options) commands. This is because they can migrate atoms to new processors. Thus they will also discard unused "state" information from fixes. You will know the discard has diff --git a/doc/src/region.rst b/doc/src/region.rst index f080992311..9f2d996b20 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -186,7 +186,7 @@ geometrically equivalent. The *radius* value for style *sphere* and *cylinder* can be specified as an equal-style :doc:`variable `. If the value is a -variable, it should be specified as v\_name, where name is the variable +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the radius of the region. For style *sphere* also the x-, y-, and z- coordinate of the center of the sphere and for @@ -273,7 +273,7 @@ point), though this is not a requirement. The *move* keyword allows one or more :doc:`equal-style variables ` to be used to specify the x,y,z displacement of the region, typically as a function of time. A variable is -specified as v\_name, where name is the variable name. Any of the +specified as v_name, where name is the variable name. Any of the three variables can be specified as NULL, in which case no displacement is calculated in that dimension. @@ -308,7 +308,7 @@ the y direction: The *rotate* keyword rotates the region around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The rotation angle is calculated, presumably as a function of time, by a variable -specified as v\_theta, where theta is the variable name. The variable +specified as v_theta, where theta is the variable name. The variable should generate its result in radians. The direction of rotation for the region around the rotation axis is consistent with the right-hand rule: if your right-hand thumb points along *R*\ , then your fingers diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index c92947ac6d..8463fd774b 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -206,7 +206,7 @@ Restrictions """""""""""" To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS\_GZIP option. See the :doc:`Build settings ` +-DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. Related commands diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 42b4047c79..13a374fc29 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -25,8 +25,8 @@ for bond, angle, dihedral, improper topology data. This will create a set of IDs that are numbered contiguously from 1 to N for a N atoms system. -This can be useful to do after performing a "delete\_atoms" command for -a molecular system. The delete\_atoms compress yes option will not +This can be useful to do after performing a "delete_atoms" command for +a molecular system. The delete_atoms compress yes option will not perform this operation due to the existence of bond topology. It can also be useful to do after any simulation which has lost atoms, e.g. due to atoms moving outside a simulation box with fixed @@ -47,8 +47,8 @@ as the :doc:`create_atoms ` command explains. communication was not sufficient to find atoms in bonds, angles, etc that are owned by other processors. The :doc:`comm_modify cutoff ` command can be used to correct this issue. Or you can define a pair style before using this command. If you do - the former, you should unset the comm\_modify cutoff after using - reset\_ids so that subsequent communication is not inefficient. + the former, you should unset the comm_modify cutoff after using + reset_ids so that subsequent communication is not inefficient. Restrictions """""""""""" diff --git a/doc/src/restart.rst b/doc/src/restart.rst index fbbcdd27b4..fd4c1e9e24 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -103,7 +103,7 @@ timestep of a run unless it is a multiple of N. A restart file is written on the last timestep of a minimization if N > 0 and the minimization converges. -Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v\_name, where +Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a restart file will be written out. On that timestep, the variable will diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 5d72f00eaf..474eab2b85 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -83,7 +83,7 @@ partition. This include the :doc:`pair style `, :doc:`bond style ` portion of the calculation is performed on the 2nd partition. -This is most useful for the PPPM kspace\_style when its performance on +This is most useful for the PPPM kspace_style when its performance on a large number of processors degrades due to the cost of communication in its 3d FFTs. In this scenario, splitting your P total processors into 2 subsets of processors, P1 in the 1st partition and P2 in the @@ -196,7 +196,7 @@ levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The *hybrid* keyword requires as many level assignments as there are hybrid sub-styles, which assigns each sub-style to a rRESPA level, following their order -of definition in the pair\_style command. Since the *hybrid* keyword +of definition in the pair_style command. Since the *hybrid* keyword operates on pair style computations, it is mutually exclusive with either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords. @@ -326,7 +326,7 @@ Default run_style verlet -For run\_style respa, the default assignment of interactions +For run_style respa, the default assignment of interactions to rRESPA levels is as follows: * bond forces = level 1 (innermost loop) diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst index bf02da8e95..e4846a7a33 100644 --- a/doc/src/server_mc.rst +++ b/doc/src/server_mc.rst @@ -41,7 +41,7 @@ processed. The :doc:`server ` doc page gives other options for using LAMMPS See an example of how this command is used in -examples/COUPLE/lammps\_mc/in.server. +examples/COUPLE/lammps_mc/in.server. ---------- @@ -61,8 +61,8 @@ the two codes. See the `CSlib website `_ doc pages for more details on the actual library syntax. The "cs" object in this pseudo code is a pointer to an instance of the CSlib. -See the src/MESSAGE/server\_mc.cpp file for details on how LAMMPS uses -these messages. See the examples/COUPLE/lammps\_mc/mc.cpp file for an +See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses +these messages. See the examples/COUPLE/lammps_mc/mc.cpp file for an example of how an MC driver code can use these messages. Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst index 11b0db6554..8304c808b2 100644 --- a/doc/src/server_md.rst +++ b/doc/src/server_md.rst @@ -64,10 +64,10 @@ the two codes. See the `CSlib website `_ doc pages for more details on the actual library syntax. The "cs" object in this pseudo code is a pointer to an instance of the CSlib. -See the src/MESSAGE/server\_md.cpp and src/MESSAGE/fix\_client\_md.cpp +See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp files for details on how LAMMPS uses these messages. See the -examples/COUPLE/lammps\_vasp/vasp\_wrap.py or -examples/COUPLE/lammps\_nwchem/nwchem\_wrap.py files for examples of how +examples/COUPLE/lammps_vasp/vasp_wrap.py or +examples/COUPLE/lammps_nwchem/nwchem_wrap.py files for examples of how a quantum code (VASP or NWChem) can use these messages. The following pseudo-code uses these values, defined as enums. diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt deleted file mode 100644 index daa6ab57ce..0000000000 --- a/doc/src/server_md.txt +++ /dev/null @@ -1,150 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -server md command :h3 - -[Syntax:] - -server md :pre - -md = the protocol argument to the "server"_server.html command - -[Examples:] - -server md :pre - -[Description:] - -This command starts LAMMPS running in "server" mode, where it will -expect messages from a separate "client" code that match the {md} -protocol for format and content explained below. For each message -LAMMPS receives it will send a message back to the client. - -The "Howto client/server"_Howto_client_server.html doc page gives an -overview of client/server coupling of LAMMPS with another code where -one code is the "client" and sends request messages to a "server" -code. The server responds to each request with a reply message. This -enables the two codes to work in tandem to perform a simulation. - -When this command is invoked, LAMMPS will run in server mode in an -endless loop, waiting for messages from the client code. The client -signals when it is done sending messages to LAMMPS, at which point the -loop will exit, and the remainder of the LAMMPS script will be -processed. - -The "server"_server.html doc page gives other options for using LAMMPS -in server mode. See an example of how this command is used in -examples/message/in.message.server. - -:line - -When using this command, LAMMPS (as the server code) receives the -current coordinates of all particles from the client code each -timestep, computes their interaction, and returns the energy, forces, -and pressure for the interacting particles to the client code, so it -can complete the timestep. This command could also be used with a -client code that performs energy minimization, using the server to -compute forces and energy each iteration of its minimizer. - -When using the "fix client/md"_fix_client_md.html command, LAMMPS (as -the client code) does the timestepping and receives needed energy, -forces, and pressure values from the server code. - -The format and content of the exchanged messages are explained here in -a conceptual sense. Python-style pseudo code for the library calls to -the CSlib is shown, which performs the actual message exchange between -the two codes. See the "CSlib website"_http://cslib.sandia.gov doc -pages for more details on the actual library syntax. The "cs" object -in this pseudo code is a pointer to an instance of the CSlib. - -See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp -files for details on how LAMMPS uses these messages. See the -examples/COUPLE/lammps_vasp/vasp_wrap.py or -examples/COUPLE/lammps_nwchem/nwchem_wrap.py files for examples of how -a quantum code (VASP or NWChem) can use these messages. - -The following pseudo-code uses these values, defined as enums. - -Define: - -SETUP=1, STEP=2 -DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10 -FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre - -[Client sends 2 kinds of messages]: - -# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS -# optional fields: UNITS, CHARGE :pre - -cs->send(SETUP,nfields) # msgID with nfields :pre - -cs->pack_int(DIM,dim) # dimension (2,3) of simulation -cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims -cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box -cs->pack(BOX,9,box) # 3 edge vectors of simulation box -cs->pack_int(NATOMS,natoms) # total number of atoms -cs->pack_int(NTYPES,ntypes) # number of atom types -cs->pack(TYPES,natoms,type) # vector of per-atom types -cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords -cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc -cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre - -# required fields: COORDS -# optional fields: ORIGIN, BOX :pre - -cs->send(STEP,nfields) # msgID with nfields :pre - -cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords -cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box -cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre - -[Server replies to either kind of message]: - -# required fields: FORCES, ENERGY, PRESSURE -# optional fields: ERROR :pre - -cs->send(msgID,nfields) # msgID with nfields -cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms -cs->pack(ENERGY,1,poteng) # total potential energy of system -cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector) -cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre - -:line - -The units for various quantities that are sent and received iva -messages are defined for atomic-scale simulations in the table below. -The client and server codes (including LAMMPS) can use internal units -different than these (e.g. "real units"_units.html in LAMMPS), so long -as they convert to these units for messaging. - -COORDS, ORIGIN, BOX = Angstroms -CHARGE = multiple of electron charge (1.0 is a proton) -ENERGY = eV -FORCES = eV/Angstrom -PRESSURE = bars :ul - -Note that these are "metal units"_units.html in LAMMPS. - -If you wish to run LAMMPS in another its non-atomic units, e.g. "lj -units"_units.html, then the client and server should exchange a UNITS -message as indicated above, and both the client and server should -agree on the units for the data they exchange. - -:line - -[Restrictions:] - -This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"message"_message.html, "fix client/md"_fix_client_md.html - -[Default:] none diff --git a/doc/src/set.rst b/doc/src/set.rst index 6d81eb1936..84792d1a58 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -13,7 +13,7 @@ Syntax * style = *atom* or *type* or *mol* or *group* or *region* * ID = atom ID range or type range or mol ID range or group ID or region ID * one or more keyword/value pairs may be appended -* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *density/disc* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc* or *i\_name* or *d\_name* +* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *density/disc* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name* .. parsed-literal:: @@ -186,7 +186,7 @@ change, for the selected atoms. Note that except where explicitly prohibited below, all of the keywords allow an :doc:`atom-style or atomfile-style variable ` to be used as the specified value(s). If the value is a -variable, it should be specified as v\_name, where name is the +variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated, and its resulting per-atom value used to determine the value assigned to each selected atom. Note that the per-atom value from the variable will be @@ -463,14 +463,14 @@ Keyword *cc* sets the chemical concentration of a tDPD particle for a specified species as defined by the USER-MESODPD package. Currently, only :doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to -Nspecies) where Nspecies is set by the atom\_style command. The value +Nspecies) where Nspecies is set by the atom_style command. The value for the chemical concentration must be >= 0.0. -Keywords *i\_name* and *d\_name* refer to custom integer and +Keywords *i_name* and *d_name* refer to custom integer and floating-point properties that have been added to each atom via the :doc:`fix property/atom ` command. When that command is used specific names are given to each attribute which are what is -specified as the "name" portion of *i\_name* or *d\_name*. +specified as the "name" portion of *i_name* or *d_name*. Restrictions """""""""""" diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 08c6a8b635..a7646a74d2 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -101,7 +101,7 @@ would be the same as invoking % my_setup file1 10 file2 -from a command-line prompt. The executable program "my\_setup" is run +from a command-line prompt. The executable program "my_setup" is run with 3 arguments: file1 10 file2. Restrictions diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index da5a6279f1..d00467b3e8 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -65,7 +65,7 @@ atoms should be excluded (or reduced by a weighting factor). sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, e.g. when using the :doc:`pair_style hybrid ` command. - Thus LAMMPS ignores special\_bonds settings when many-body potentials + Thus LAMMPS ignores special_bonds settings when many-body potentials are calculated. Please note, that the existence of explicit bonds for atoms that are described by a many-body potential will alter the neighbor list and thus can render the computation of those interactions @@ -234,7 +234,7 @@ while only in the second case, you get the desired settings of: This happens because the LJ (and Coul) settings are reset to their default values before modifying them, each time the -*special\_bonds* command is issued. +*special_bonds* command is issued. Restrictions """""""""""" diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 68cbf5d25a..ba94214a9b 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -42,7 +42,7 @@ package. These are the variants these packages provide: -* GPU = a handful of pair styles and the PPPM kspace\_style, optimized to +* GPU = a handful of pair styles and the PPPM kspace_style, optimized to run on one or more GPUs or multicore CPU/GPU nodes * USER-INTEL = a collection of pair styles and neighbor routines optimized to run in single, mixed, or double precision on CPUs and @@ -59,7 +59,7 @@ These are the variants these packages provide: As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, lj/cut/gpu, lj/cut/intel, or lj/cut/kk. A variant styles -can be specified explicitly in your input script, e.g. pair\_style +can be specified explicitly in your input script, e.g. pair_style lj/cut/gpu. If the suffix command is used with the appropriate style, you do not need to modify your input script. The specified suffix (opt,omp,gpu,intel,kk) is automatically appended whenever your @@ -92,9 +92,9 @@ commands in your input script. The default :doc:`run_style ` verlet is invoked prior to reading the input script and is therefore not affected by a suffix command - in the input script. The KOKKOS package requires "run\_style verlet/kk", + in the input script. The KOKKOS package requires "run_style verlet/kk", so when using the KOKKOS package it is necessary to either use the command - line "-sf kk" command or add an explicit "run\_style verlet" command to the + line "-sf kk" command or add an explicit "run_style verlet" command to the input script. Restrictions diff --git a/doc/src/tad.rst b/doc/src/tad.rst index b8de42a7eb..7f4845dc3c 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -11,14 +11,14 @@ Syntax tad N t_event T_lo T_hi delta tmax compute-ID keyword value ... * N = # of timesteps to run (not including dephasing/quenching) -* t\_event = timestep interval between event checks -* T\_lo = temperature at which event times are desired -* T\_hi = temperature at which MD simulation is performed +* t_event = timestep interval between event checks +* T_lo = temperature at which event times are desired +* T_hi = temperature at which MD simulation is performed * delta = desired confidence level for stopping criterion * tmax = reciprocal of lowest expected pre-exponential factor (time units) * compute-ID = ID of the compute used for event detection * zero or more keyword/value pairs may be appended -* keyword = *min* or *neb* or *min\_style* or *neb\_style* or *neb\_log* +* keyword = *min* or *neb* or *min_style* or *neb_style* or *neb_log* .. parsed-literal:: @@ -119,7 +119,7 @@ initial state and storing the resulting coordinates for reference. Inside the inner loop, dynamics is run continuously according to whatever integrator has been specified by the user, stopping every -*t\_event* steps to check if a transition event has occurred. This +*t_event* steps to check if a transition event has occurred. This check is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. @@ -140,13 +140,13 @@ distance. If so, an "event" has occurred. The NEB calculation is similar to that invoked by the :doc:`neb ` command, except that the final state is generated internally, instead of being read in from a file. The style of minimization performed by -NEB is determined by the *neb\_style* keyword and must be a damped +NEB is determined by the *neb_style* keyword and must be a damped dynamics minimizer. The tolerances and limits for each NEB calculation can be set by the *neb* keyword. As discussed on the :doc:`neb `, it is often advantageous to use a larger timestep for NEB than for normal dynamics. Since the size of the timestep set by the :doc:`timestep ` command is used by TAD for performing -dynamics, there is a *neb\_step* keyword which can be used to set a +dynamics, there is a *neb_step* keyword which can be used to set a larger timestep for each NEB calculation if desired. ---------- @@ -164,11 +164,11 @@ are not well characterized (the most common case), it will be necessary to experiment with the values of *delta* and *tmax* to get a good trade-off between accuracy and performance. -A second key aspect is the choice of *t\_hi*. A larger value greatly +A second key aspect is the choice of *t_hi*. A larger value greatly increases the rate at which new events are generated. However, too large a value introduces errors due to anharmonicity (not accounted for within hTST). Once again, for any given system, experimentation is -necessary to determine the best value of *t\_hi*. +necessary to determine the best value of *t_hi*. ---------- @@ -179,7 +179,7 @@ files, and restart files. Event statistics are printed to the screen and master log.lammps file each time an event is executed. The quantities are the timestep, CPU time, global event number *N*\ , local event number *M*\ , event status, -energy barrier, time margin, *t\_lo* and *delt\_lo*. The timestep is +energy barrier, time margin, *t_lo* and *delt_lo*. The timestep is the usual LAMMPS timestep, which corresponds to the high-temperature time at which the event was detected, in units of timestep. The CPU time is the total processor time since the start of the TAD run. The @@ -194,9 +194,9 @@ The time margin is the ratio of the high temperature time in the current basin to the stopping time. This last number can be used to judge whether the stopping time is too short or too long (see above). -*t\_lo* is the low-temperature event time when the current basin was -entered, in units of timestep. del*t\_lo* is the time of each detected -event, measured relative to *t\_lo*. *delt\_lo* is equal to the +*t_lo* is the low-temperature event time when the current basin was +entered, in units of timestep. del*t_lo* is the time of each detected +event, measured relative to *t_lo*. *delt_lo* is equal to the high-temperature time since entering the current basin, scaled by an exponential factor that depends on the hi/lo temperature ratio and the energy barrier for that event. @@ -205,11 +205,11 @@ On lines for executed events, with status *E*\ , the global event number is incremented by one, the local event number and time margin are reset to zero, while the global event number, energy barrier, and -*delt\_lo* match the last event with status *DF* +*delt_lo* match the last event with status *DF* in the immediately preceding block of detected events. -The low-temperature event time *t\_lo* is incremented by *delt\_lo*. +The low-temperature event time *t_lo* is incremented by *delt_lo*. -NEB statistics are written to the file specified by the *neb\_log* +NEB statistics are written to the file specified by the *neb_log* keyword. If the keyword value is "none", then no NEB statistics are printed out. The statistics are written every *Nevery* timesteps. See the :doc:`neb ` command for a full description of the NEB @@ -276,7 +276,7 @@ This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. -*N* setting must be integer multiple of *t\_event*. +*N* setting must be integer multiple of *t_event*. Runs restarted from restart files written during a TAD run will only produce identical results if the user-specified integrator supports @@ -301,8 +301,8 @@ Default """"""" The option defaults are *min* = 0.1 0.1 40 50, *neb* = 0.01 100 100 -10, *neb\_style* = *quickmin*\ , *neb\_step* = the same timestep set by -the :doc:`timestep ` command, and *neb\_log* = "none". +10, *neb_style* = *quickmin*\ , *neb_step* = the same timestep set by +the :doc:`timestep ` command, and *neb_log* = "none". ---------- diff --git a/doc/src/temper.rst b/doc/src/temper.rst index 3ac6481ff1..bb470f0cc0 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -119,7 +119,7 @@ manner: snapshots at 310K, etc. Note that these new dump files will not contain "continuous trajectories" for individual atoms, because two successive snapshots (in time) may be from different replicas. The - reorder\_remd\_traj python script can do the reordering for you + reorder_remd_traj python script can do the reordering for you (and additionally also calculated configurational log-weights of trajectory snapshots in the canonical ensemble). The script can be found in the tools/replica directory while instructions on how to use it is diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index 3ab789457e..154fd59431 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -32,7 +32,7 @@ The content and format of what is printed is controlled by the :doc:`thermo_style ` and :doc:`thermo_modify ` commands. -Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v\_name, where +Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which thermodynamic info will be written out. On that timestep, the diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index b2d4b877fe..3cec230189 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -47,9 +47,9 @@ by LAMMPS. These options apply to the currently defined thermo style. When you specify a :doc:`thermo_style ` command, all thermodynamic settings are restored to their default values, including - those previously reset by a thermo\_modify command. Thus if your input - script specifies a thermo\_style command, you should use the - thermo\_modify command after it. + those previously reset by a thermo_modify command. Thus if your input + script specifies a thermo_style command, you should use the + thermo_modify command after it. The *lost* keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are @@ -104,7 +104,7 @@ The *line* keyword determines whether thermodynamics will be output as a series of numeric values on one line or in a multi-line format with 3 quantities with text strings per line and a dashed-line header containing the timestep and CPU time. This modify option overrides -the *one* and *multi* thermo\_style settings. +the *one* and *multi* thermo_style settings. The *format* keyword can be used to change the default numeric format of any of quantities the :doc:`thermo_style ` command @@ -144,7 +144,7 @@ The specified compute ID must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a temperature. As described in the :doc:`thermo_style ` command, thermo output uses a default -compute for temperature with ID = *thermo\_temp*. This option allows +compute for temperature with ID = *thermo_temp*. This option allows the user to override the default. The *press* keyword is used to determine how thermodynamic pressure is @@ -154,13 +154,13 @@ must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a pressure. As described in the :doc:`thermo_style ` command, thermo output uses a default -compute for pressure with ID = *thermo\_press*. This option allows the +compute for pressure with ID = *thermo_press*. This option allows the user to override the default. .. note:: If both the *temp* and *press* keywords are used in a single - thermo\_modify command (or in two separate commands), then the order in + thermo_modify command (or in two separate commands), then the order in which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as an argument when it is specified. The *temp* keyword will override this (for the pressure compute being used by thermodynamics), but only @@ -183,7 +183,7 @@ Default The option defaults are lost = error, norm = yes for unit style of *lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no, -and temp/press = compute IDs defined by thermo\_style. +and temp/press = compute IDs defined by thermo_style. The defaults for the line and format options depend on the thermo style. For styles "one" and "custom", the line and format defaults diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index a51d9aaf5e..dbb634a2b0 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -100,17 +100,17 @@ Set the style and content for printing thermodynamic data to the screen and log file. Style *one* prints a one-line summary of thermodynamic info that is -the equivalent of "thermo\_style custom step temp epair emol etotal +the equivalent of "thermo_style custom step temp epair emol etotal press". The line contains only numeric values. Style *multi* prints a multiple-line listing of thermodynamic info -that is the equivalent of "thermo\_style custom etotal ke temp pe ebond +that is the equivalent of "thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press". The listing contains numeric values and a string ID for each quantity. Style *custom* is the most general setting and allows you to specify which of the keywords listed above you want printed on each -thermodynamic timestep. Note that the keywords c\_ID, f\_ID, v\_name are +thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to :doc:`computes `, :doc:`fixes `, and equal-style :doc:`variables ` that have been defined elsewhere in the input script or can even be new styles which users have added @@ -124,7 +124,7 @@ outputs if the simulation box volume changes during the simulation. The values printed by the various keywords are instantaneous values, calculated on the current timestep. Time-averaged quantities, which include values from previous timesteps, can be output by using the -f\_ID keyword and accessing a fix that does time-averaging such as the +f_ID keyword and accessing a fix that does time-averaging such as the :doc:`fix ave/time ` command. Options invoked by the :doc:`thermo_modify ` command can @@ -135,11 +135,11 @@ atoms in the system), and the numeric precision of each printed value. .. note:: - When you use a "thermo\_style" command, all thermodynamic + When you use a "thermo_style" command, all thermodynamic settings are restored to their default values, including those previously set by a :doc:`thermo_modify ` command. Thus - if your input script specifies a thermo\_style command, you should use - the thermo\_modify command after it. + if your input script specifies a thermo_style command, you should use + the thermo_modify command after it. ---------- @@ -153,7 +153,7 @@ when LAMMPS starts up, as if this command had been issued: compute thermo_temp all temp See the :doc:`compute temp ` command for details. Note -that the ID of this compute is *thermo\_temp* and the group is *all*\ . +that the ID of this compute is *thermo_temp* and the group is *all*\ . You can change the attributes of this temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that @@ -171,7 +171,7 @@ if this command had been issued: compute thermo_press all pressure thermo_temp See the :doc:`compute pressure ` command for details. -Note that the ID of this compute is *thermo\_press* and the group is +Note that the ID of this compute is *thermo_press* and the group is *all*\ . You can change the attributes of this pressure via the :doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that calculates pressure) which you @@ -189,7 +189,7 @@ command had been issued: compute thermo_pe all pe See the :doc:`compute pe ` command for details. Note that -the ID of this compute is *thermo\_pe* and the group is *all*\ . You can +the ID of this compute is *thermo_pe* and the group is *all*\ . You can change the attributes of this potential energy via the :doc:`compute_modify ` command. @@ -233,7 +233,7 @@ The *dt* keyword is the current timestep size in time simulation time, also in time :doc:`units `, which is simply (step\*dt) if the timestep size has not changed and the timestep has not been reset. If the timestep has changed (e.g. via :doc:`fix dt/reset `) or the timestep has been reset (e.g. via -the "reset\_timestep" command), then the simulation time is effectively +the "reset_timestep" command), then the simulation time is effectively a cumulative value up to the current point. The *cpu* keyword is elapsed CPU seconds since the beginning of this @@ -305,7 +305,7 @@ quantities in terms of the internal LAMMPS cell dimensions *lx*\ , *ly*\ , ---------- For output values from a compute or fix, the bracketed index I used to -index a vector, as in *c\_ID[I]* or *f\_ID[I]*, can be specified +index a vector, as in *c_ID[I]* or *f_ID[I]*, can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = scalar) or the number of @@ -316,7 +316,7 @@ all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the -vector had been listed one by one. E.g. these 2 thermo\_style commands +vector had been listed one by one. E.g. these 2 thermo_style commands are equivalent, since the :doc:`compute temp ` command creates a global vector with 6 values. @@ -330,14 +330,14 @@ creates a global vector with 6 values. ---------- -The *c\_ID* and *c\_ID[I]* and *c\_ID[I][J]* keywords allow global +The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global values calculated by a compute to be output. As discussed on the :doc:`compute ` doc page, computes can calculate global, per-atom, or local values. Only global values can be referenced by this command. However, per-atom compute values for an individual atom can be referenced in a :doc:`variable ` and the variable -referenced by thermo\_style custom, as discussed below. See the -discussion above for how the I in *c\_ID[I]* can be specified with a +referenced by thermo_style custom, as discussed below. See the +discussion above for how the I in *c_ID[I]* can be specified with a wildcard asterisk to effectively specify multiple values from a global compute vector. @@ -351,18 +351,18 @@ Note that some computes calculate "intensive" global quantities like temperature; others calculate "extensive" global quantities like kinetic energy that are summed over all atoms in the compute group. Intensive quantities are printed directly without normalization by -thermo\_style custom. Extensive quantities may be normalized by the +thermo_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the compute group) when output, depending on the :doc:`thermo_modify norm ` option being used. -The *f\_ID* and *f\_ID[I]* and *f\_ID[I][J]* keywords allow global +The *f_ID* and *f_ID[I]* and *f_ID[I][J]* keywords allow global values calculated by a fix to be output. As discussed on the :doc:`fix ` doc page, fixes can calculate global, per-atom, or local values. Only global values can be referenced by this command. However, per-atom fix values can be referenced for an individual atom in a :doc:`variable ` and the variable referenced by -thermo\_style custom, as discussed below. See the discussion above for -how the I in *f\_ID[I]* can be specified with a wildcard asterisk to +thermo_style custom, as discussed below. See the discussion above for +how the I in *f_ID[I]* can be specified with a wildcard asterisk to effectively specify multiple values from a global fix vector. The ID in the keyword should be replaced by the actual ID of a fix @@ -374,13 +374,13 @@ brackets will reference a scalar value from the fix. Note that some fixes calculate "intensive" global quantities like timestep size; others calculate "extensive" global quantities like energy that are summed over all atoms in the fix group. Intensive -quantities are printed directly without normalization by thermo\_style +quantities are printed directly without normalization by thermo_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the fix group) when output, depending on the :doc:`thermo_modify norm ` option being used. -The *v\_name* keyword allow the current value of a variable to be +The *v_name* keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the variable name that has been defined elsewhere in the input script. Only equal-style and vector-style variables can be referenced; the latter @@ -396,7 +396,7 @@ output. Note that equal-style and vector-style variables are assumed to produce "intensive" global quantities, which are thus printed as-is, -without normalization by thermo\_style custom. You can include a +without normalization by thermo_style custom. You can include a division by "natoms" in the variable formula if this is not the case. ---------- diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 63b236148e..2a6de933e0 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -46,7 +46,7 @@ three elements correspond to the three gamma elements for a specific i/alpha/j/b The initial five numbers are i, alpha, j, beta, and k respectively. If the style eskm is selected, the tensor will be using energy units of 10 J/mol. -These units conform to eskm style from the dynamical\_matrix command, which +These units conform to eskm style from the dynamical_matrix command, which will simplify operations using dynamical matrices with third order tensors. Restrictions @@ -66,4 +66,4 @@ Related commands Default """"""" -The default settings are file = "third\_order.dat", binary = no +The default settings are file = "third_order.dat", binary = no diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 354af1ff20..0e30efc0ab 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -194,7 +194,7 @@ There are two exceptions to this rule. First, variables of style allows these style of variables to be redefined multiple times in an input script. In a loop, this means the formula associated with an *equal* or *atom* style variable can change if it contains a -substitution for another variable, e.g. $x or v\_x. +substitution for another variable, e.g. $x or v_x. Second, as described below, if a variable is iterated on to the end of its list of strings via the :doc:`next ` command, it is removed @@ -485,11 +485,11 @@ references, and references to other variables. +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q | +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Compute references | c\_ID, c\_ID[i], c\_ID[i][j], C\_ID, C\_ID[i] | +| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] | +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Fix references | f\_ID, f\_ID[i], f\_ID[i][j], F\_ID, F\_ID[i] | +| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] | +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Other variables | v\_name, v\_name[i] | +| Other variables | v_name, v_name[i] | +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ Most of the formula elements produce a scalar value. Some produce a @@ -545,7 +545,7 @@ require a :doc:`compute ` to calculate their values such as "temp" or "press", use computes stored and invoked by the :doc:`thermo_style ` command. This means that you can only use those keywords in a variable if the style you are using with -the thermo\_style command (and the thermo keywords associated with that +the thermo_style command (and the thermo keywords associated with that style) also define and use the needed compute. Note that some thermo keywords use a compute indirectly to calculate their value (e.g. the enthalpy keyword uses temp, pe, and pressure). If a variable is @@ -822,15 +822,15 @@ Special functions take specific kinds of arguments, meaning their arguments cannot be formulas themselves. The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions -each take 1 argument which is of the form "c\_ID" or "c\_ID[N]" or -"f\_ID" or "f\_ID[N]" or "v\_name". The first two are computes and the +each take 1 argument which is of the form "c_ID" or "c_ID[N]" or +"f_ID" or "f_ID[N]" or "v_name". The first two are computes and the second two are fixes; the ID in the reference should be replaced by the ID of a compute or fix defined elsewhere in the input script. The compute or fix must produce either a global vector or array. If it produces a global vector, then the notation without "[N]" should be used. If it produces a global array, then the notation with "[N]" should be used, when N is an integer, to specify which column of the -global array is being referenced. The last form of argument "v\_name" +global array is being referenced. The last form of argument "v_name" is for a vector-style variable where "name" is replaced by the name of the variable. @@ -875,7 +875,7 @@ variables. It returns a 1 for atoms that are in both the group and region, and a 0 for atoms that are not in both. The next(x) function takes 1 argument which is a variable ID (not -"v\_foo", just "foo"). It must be for a file-style or atomfile-style +"v_foo", just "foo"). It must be for a file-style or atomfile-style variable. Each time the next() function is invoked (i.e. each time the equal-style or atom-style variable is evaluated), the following steps occur. @@ -912,23 +912,23 @@ themselves (only $-style immediate variable expansion is possible). Return value is either 1.0 or 0.0 depending on whether the function evaluates to true or false, respectively. -The *is\_active()* function allows to query for active settings which +The *is_active()* function allows to query for active settings which are grouped by categories. Currently supported categories and arguments are: * *package* (argument = *gpu* or *intel* or *kokkos* or *omp*\ ) * *newton* (argument = *pair* or *bond* or *any*\ ) * *pair* (argument = *single* or *respa* or *manybody* or *tail* or *shift*\ ) -* *comm\_style* (argument = *brick* or *tiled*\ ) -* *min\_style* (argument = any of the compiled in minimizer styles) -* *run\_style* (argument = any of the compiled in run styles) -* *atom\_style* (argument = any of the compiled in atom styles) -* *pair\_style* (argument = any of the compiled in pair styles) -* *bond\_style* (argument = any of the compiled in bond styles) -* *angle\_style* (argument = any of the compiled in angle styles) -* *dihedral\_style* (argument = any of the compiled in dihedral styles) -* *improper\_style* (argument = any of the compiled in improper styles) -* *kspace\_style* (argument = any of the compiled in kspace styles) +* *comm_style* (argument = *brick* or *tiled*\ ) +* *min_style* (argument = any of the compiled in minimizer styles) +* *run_style* (argument = any of the compiled in run styles) +* *atom_style* (argument = any of the compiled in atom styles) +* *pair_style* (argument = any of the compiled in pair styles) +* *bond_style* (argument = any of the compiled in bond styles) +* *angle_style* (argument = any of the compiled in angle styles) +* *dihedral_style* (argument = any of the compiled in dihedral styles) +* *improper_style* (argument = any of the compiled in improper styles) +* *kspace_style* (argument = any of the compiled in kspace styles) Most of the settings are self-explanatory, the *single* argument in the *pair* category allows to check whether a pair style supports a @@ -952,14 +952,14 @@ Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, othe timestep $(2.0*(1.0+2.0*is_active(pair,respa)) if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" -The *is\_defined()* function allows to query categories like *compute*\ , +The *is_defined()* function allows to query categories like *compute*\ , *dump*\ , *fix*\ , *group*\ , *region*\ , and *variable* whether an entry with the provided name or id is defined. -The *is\_available(category,name)* function allows to query whether +The *is_available(category,name)* function allows to query whether a specific optional feature is available, i.e. compiled in. This currently works for the following categories: *command*\ , -*compute*\ , *fix*\ , *pair\_style* and *feature*\ . For all categories +*compute*\ , *fix*\ , *pair_style* and *feature*\ . For all categories except *command* and *feature* also appending active suffixes is tried before reporting failure. @@ -984,14 +984,14 @@ Atom Values and Vectors Atom values take an integer argument I from 1 to N, where I is the atom-ID, e.g. x[243], which means use the x coordinate of the atom -with ID = 243. Or they can take a variable name, specified as v\_name, -where name is the name of the variable, like x[v\_myIndex]. The +with ID = 243. Or they can take a variable name, specified as v_name, +where name is the name of the variable, like x[v_myIndex]. The variable can be of any style except *vector* or *atom* or *atomfile* variables. The variable is evaluated and the result is expected to be numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an index, which must be a value from 1 to N. Note that a "formula" cannot be used as the argument between the brackets, e.g. x[243+10] -or x[v\_myIndex+1] are not allowed. To do this a single variable can +or x[v_myIndex+1] are not allowed. To do this a single variable can be defined that contains the needed formula. Note that the 0 < atom-ID <= N, where N is the largest atom ID @@ -1038,15 +1038,15 @@ reference means, since computes only produce either global or per-atom quantities, never both. +-------------+-------------------------------------------------------------------------------------------------------+ -| c\_ID | global scalar, or per-atom vector | +| c_ID | global scalar, or per-atom vector | +-------------+-------------------------------------------------------------------------------------------------------+ -| c\_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array | +| c_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array | +-------------+-------------------------------------------------------------------------------------------------------+ -| c\_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array | +| c_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array | +-------------+-------------------------------------------------------------------------------------------------------+ For I and J indices, integers can be specified or a variable name, -specified as v\_name, where name is the name of the variable. The +specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for the "Atom Values and Vectors" discussion above. @@ -1060,12 +1060,12 @@ vector-style variable: variable a vector c_foo*v_myVec -The reference "c\_foo" could refer to either the global scalar or -global vector produced by compute "foo". In this case, "c\_foo" will -always refer to the global scalar, and "C\_foo" can be used to +The reference "c_foo" could refer to either the global scalar or +global vector produced by compute "foo". In this case, "c_foo" will +always refer to the global scalar, and "C_foo" can be used to reference the global vector. Similarly if the compute produces both a -global vector and global array, then "c\_foo[I]" will always refer to -an element of the global vector, and "C\_foo[I]" can be used to +global vector and global array, then "c_foo[I]" will always refer to +an element of the global vector, and "C_foo[I]" can be used to reference the Ith column of the global array. Note that if a variable containing a compute is evaluated directly in @@ -1098,15 +1098,15 @@ as to what a reference means, since fixes only produce either global or per-atom quantities, never both. +-------------+-------------------------------------------------------------------------------------------------------+ -| f\_ID | global scalar, or per-atom vector | +| f_ID | global scalar, or per-atom vector | +-------------+-------------------------------------------------------------------------------------------------------+ -| f\_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array | +| f_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array | +-------------+-------------------------------------------------------------------------------------------------------+ -| f\_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array | +| f_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array | +-------------+-------------------------------------------------------------------------------------------------------+ For I and J indices, integers can be specified or a variable name, -specified as v\_name, where name is the name of the variable. The +specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for the "Atom Values and Vectors" discussion above. @@ -1114,10 +1114,10 @@ One source of ambiguity for fix references is the same ambiguity discussed for compute references above. Namely when a vector-style variable refers to a fix that produces both a global scalar and a global vector. The solution is the same as for compute references. -For a fix with ID "foo", "f\_foo" will always refer to the global -scalar, and "F\_foo" can be used to reference the global vector. And +For a fix with ID "foo", "f_foo" will always refer to the global +scalar, and "F_foo" can be used to reference the global vector. And similarly for distinguishing between a fix's global vector versus -global array with "f\_foo[I]" versus "F\_foo[I]". +global array with "f_foo[I]" versus "F_foo[I]". Note that if a variable containing a fix is evaluated directly in an input script (not during a run), then the values accessed by the fix @@ -1147,7 +1147,7 @@ generate a per-atom vector of numeric values. All other variables store one or more strings. The formula for an equal-style variable can use any style of variable -including a vector\_style or atom-style or atomfile-style. For these +including a vector_style or atom-style or atomfile-style. For these 3 styles, a subscript must be used to access a single value from the vector-, atom-, or atomfile-style variable. If a string-storing variable is used, the string is converted to a numeric value. Note @@ -1169,19 +1169,19 @@ There is no ambiguity as to what a reference means, since variables produce only a global scalar or global vector or per-atom vector. +------------+----------------------------------------------------------------------+ -| v\_name | global scalar from equal-style variable | +| v_name | global scalar from equal-style variable | +------------+----------------------------------------------------------------------+ -| v\_name | global vector from vector-style variable | +| v_name | global vector from vector-style variable | +------------+----------------------------------------------------------------------+ -| v\_name | per-atom vector from atom-style or atomfile-style variable | +| v_name | per-atom vector from atom-style or atomfile-style variable | +------------+----------------------------------------------------------------------+ -| v\_name[I] | Ith element of a global vector from vector-style variable | +| v_name[I] | Ith element of a global vector from vector-style variable | +------------+----------------------------------------------------------------------+ -| v\_name[I] | value of atom with ID = I from atom-style or atomfile-style variable | +| v_name[I] | value of atom with ID = I from atom-style or atomfile-style variable | +------------+----------------------------------------------------------------------+ For the I index, an integer can be specified or a variable name, -specified as v\_name, where name is the name of the variable. The +specified as v_name, where name is the name of the variable. The rules for this syntax are the same as for the "Atom Values and Vectors" discussion above. @@ -1200,12 +1200,12 @@ named variable. More generally, there is a difference between referencing a variable with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v\_" -(e.g. v\_x or v\_abc). The former can be used in any input script +(e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value into the command. As explained on the :doc:`Commands parse ` doc page, you can also use un-named "immediate" variables for this purpose. For example, a string like -this $((xlo+xhi)/2+sqrt(v\_area)) in an input script command evaluates +this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v\_" is an optional or required @@ -1226,7 +1226,7 @@ define the variable "v" as before a run where the simulation box size changes. You might think this will assign the initial volume to the variable "v". That is not the case. Rather it assigns a formula which evaluates the volume -(using the thermo\_style keyword "vol") to the variable "v". If you +(using the thermo_style keyword "vol") to the variable "v". If you use the variable "v" in some other command like :doc:`fix ave/time ` then the current volume of the box will be evaluated continuously during the run. diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index 7b34f80f86..59ce0a19f6 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -74,7 +74,7 @@ The *set* style sets the velocities of all atoms in the group to the specified values. If any component is specified as NULL, then it is not set. Any of the vx,vy,vz velocity components can be specified as an equal-style or atom-style :doc:`variable `. If the value -is a variable, it should be specified as v\_name, where name is the +is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated, and its value used to determine the velocity component. Note that if a variable is used, the velocity it calculates must be in box units, not diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst index e2aa7bcc62..71cfe9cb02 100644 --- a/doc/src/write_coeff.rst +++ b/doc/src/write_coeff.rst @@ -30,7 +30,7 @@ the Coeffs sections from a data file into a separate file. .. note:: - The write\_coeff command is not yet fully implemented as + The write_coeff command is not yet fully implemented as some pair styles do not output their coefficient information. This means you will need to add/copy this information manually. diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index c157dff546..13a6476ac4 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -51,7 +51,7 @@ value. the :doc:`pair_coeff ` command. Second, a few of the :doc:`atom styles ` (body, ellipsoid, line, tri) that store auxiliary "bonus" information about aspherical particles, do not yet write the bonus info into the data file. Both these functionalities - will be added to the write\_data command later. + will be added to the write_data command later. Because a data file is in text format, if you use a data file written out by this command to restart a simulation, the initial state of the diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index d0daa73052..f0f57bd674 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -49,14 +49,14 @@ added. The latter is so that the full range of :doc:`dump_modify ` options can be specified for the single snapshot, just as they can be for multiple snapshots. The *modify* keyword separates the arguments that would normally be passed to the -*dump* command from those that would be given the *dump\_modify*. Both +*dump* command from those that would be given the *dump_modify*. Both support optional arguments and thus LAMMPS needs to be able to cleanly separate the two sets of args. Note that if the specified filename uses wildcard characters "\*" or "%", as supported by the :doc:`dump ` command, they will operate in the same fashion to create the new filename(s). Normally, :doc:`dump image ` files require a filename with a "\*" character -for the timestep. That is not the case for the write\_dump command; no +for the timestep. That is not the case for the write_dump command; no wildcard "\*" character is necessary. ---------- diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index 41193d05b7..bdb77dd4b4 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -37,7 +37,7 @@ Write a binary restart file of the current state of the simulation. During a long simulation, the :doc:`restart ` command is typically used to output restart files periodically. The -write\_restart command is useful after a minimization or whenever you +write_restart command is useful after a minimization or whenever you wish to write out a single current restart file. Similar to :doc:`dump ` files, the restart filename can contain diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index 3ff23439de..72536d494f 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -1,31 +1,53 @@ -from pygments.lexer import RegexLexer, words +from pygments.lexer import RegexLexer, words, include, default from pygments.token import * LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style", "balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box", -"change_box", "clear", "comm_modify", "comm_style", "compute", +"clear", "comm_modify", "comm_style", "compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms", "delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension", -"displace_atoms", "dump", "dump_modify", "dynamical_matrix", "echo", "fix", -"fix_modify", "group", "group2ndx", "hyper", "if", "improper_coeff", +"displace_atoms", "dump_modify", "dynamical_matrix", "echo", +"fix_modify", "group2ndx", "hyper", "if", "improper_coeff", "improper_style", "include", "info", "jump", "kim_init", "kim_interactions", "kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice", "log", "mass", "message", "minimize", "min_modify", "min_style", "molecule", "ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next", "package", "pair_coeff", "pair_modify", "pair_style", "pair_write", "partition", "prd", "print", "processors", "python", "quit", "read_data", -"read_dump", "read_restart", "region", "replicate", "rerun", "reset_ids", +"read_dump", "read_restart", "replicate", "rerun", "reset_ids", "reset_timestep", "restart", "run", "run_style", "server", "set", "shell", "special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep", -"uncompute", "undump", "unfix", "units", "variable", "velocity", "write_coeff", -"write_data", "write_dump", "write_restart") +"units", "velocity", "write_coeff", +"write_data", "write_restart") + +#fix ID group-ID style args +#compute ID group-ID style args +#dump ID group-ID style N file args +#region ID style args keyword arg ... +#variable name style args ... +#group ID style args +#uncompute compute-ID +#undump dump-ID +#unfix fix-ID +#write_dump group-ID style file dump-args modify dump_modify-args class LAMMPSLexer(RegexLexer): name = 'LAMMPS' tokens = { 'root': [ - (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword), + (r'fix\s+', Keyword, 'fix'), + (r'compute\s+', Keyword, 'compute'), + (r'dump\s+', Keyword, 'dump'), + (r'region\s+', Keyword, 'region'), + (r'variable\s+', Keyword, 'variable'), + (r'group\s+', Keyword, 'group'), + (r'change_box\s+', Keyword, 'change_box'), + (r'uncompute\s+', Keyword, 'uncompute'), + (r'unfix\s+', Keyword, 'unfix'), + (r'undump\s+', Keyword, 'undump'), + (r'write_dump\s+', Keyword, 'write_dump'), + include('keywords'), (r'#.*?\n', Comment), ('"', String, 'string'), ('\'', String, 'single_quote_string'), @@ -37,6 +59,10 @@ class LAMMPSLexer(RegexLexer): (r'\s+', Whitespace), (r'[\+\-\*\^\|\/\!%&=<>]', Operator), ], + 'keywords' : [ + (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword) + ] + , 'variable' : [ ('[^\}]+', Name.Variable), ('\}', Name.Variable, '#pop'), @@ -53,5 +79,56 @@ class LAMMPSLexer(RegexLexer): ('[^\(\)]+', Name.Variable), ('\(', Name.Variable, 'expression'), ('\)', Name.Variable, '#pop'), + ], + 'fix' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + (r'\s+', Whitespace, 'group_id'), + default('#pop') + ], + 'compute' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + (r'\s+', Whitespace, 'group_id'), + default('#pop') + ], + 'dump' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + (r'\s+', Whitespace, 'group_id'), + default('#pop') + ], + 'region' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'variable' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'group' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'change_box' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'unfix' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'undump' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'uncompute' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'write_dump' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop') + ], + 'group_id' : [ + (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), + default('#pop:2') ] } diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index a9f9cb952a..ffb43e7bff 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -334,3 +334,6 @@ from sphinx.highlighting import lexers lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True) sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python')) + +# avoid syntax highlighting in blocks that don't specify language +highlight_language = 'none' diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 62c404212b..7d06896215 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -69,7 +69,7 @@ CommandStyle(kim_init,KimInit) #include // Forward declaration. -class KIM_Model; +typedef struct KIM_Model KIM_Model; namespace LAMMPS_NS { diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index 1a9437ebe2..1cbce3a7f9 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -45,7 +45,7 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) : if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map"); if (sizeof(tagint) != 4) - error->all(FLERR,"Fix client/md requires 4-byte atom IDs"); + error->all(FLERR,"Fix client/md only supports 32-bit atom IDs"); if (strcmp(update->unit_style,"real") == 0) units = REAL; else if (strcmp(update->unit_style,"metal") == 0) units = METAL; diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp index 8152b1f772..af7850a0e9 100644 --- a/src/MESSAGE/server_mc.cpp +++ b/src/MESSAGE/server_mc.cpp @@ -13,6 +13,7 @@ #include "server_mc.h" #include "atom.h" +#include "domain.h" #include "update.h" #include "integrate.h" #include "input.h" @@ -43,17 +44,17 @@ void ServerMC::loop() CSlib *cs = (CSlib *) lmp->cslib; - // require atom map + if (domain->box_exist == 0) + error->all(FLERR,"Server command before simulation box is defined"); - if (!atom->map_style) error->all(FLERR,"Server mode requires atom map"); + if (!atom->map_style) error->all(FLERR,"Server mc requires atom map"); + if (atom->tag_enable == 0) error->all(FLERR,"Server mc requires atom IDs"); + if (sizeof(tagint) != 4) error->all(FLERR,"Server mc requires 32-bit atom IDs"); // initialize LAMMPS for dynamics input->one("run 0"); - //update->whichflag = 1; - //lmp->init(); - // loop on messages // receive a message, process it, send return message if necessary @@ -123,8 +124,6 @@ void ServerMC::loop() int nsteps = cs->unpack_int(1); - //input->one("run 100"); - update->nsteps = nsteps; update->firststep = update->ntimestep; update->laststep = update->ntimestep + nsteps; diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index e16095ad4c..418162e5d9 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -48,7 +48,7 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp) if (!atom->map_style) error->all(FLERR,"Server md requires atom map"); if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs"); - if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs"); + if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 32-bit atom IDs"); if (strcmp(update->unit_style,"real") == 0) units = REAL; else if (strcmp(update->unit_style,"metal") == 0) units = METAL; diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 9d075c78a1..985be3aa48 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -62,6 +62,7 @@ enum{FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM, PPPMDispIntel::PPPMDispIntel(LAMMPS *lmp) : PPPMDisp(lmp) { suffix_flag |= Suffix::INTEL; + triclinic_support = 0; order = 7; order_6 = 7; //sets default stencil sizes to 7 diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index e3d1e7d4aa..e3bf779cc1 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -208,16 +208,23 @@ void PPPMIntel::compute_first(int eflag, int vflag) // find grid points for all my particles // map my particle charge onto my local 3d density grid + // optimized versions can only be used for orthogonal boxes - if (fix->precision() == FixIntel::PREC_MODE_MIXED) { - particle_map(fix->get_mixed_buffers()); - make_rho(fix->get_mixed_buffers()); - } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) { - particle_map(fix->get_double_buffers()); - make_rho(fix->get_double_buffers()); + if (triclinic) { + PPPM::particle_map(); + PPPM::make_rho(); } else { - particle_map(fix->get_single_buffers()); - make_rho(fix->get_single_buffers()); + + if (fix->precision() == FixIntel::PREC_MODE_MIXED) { + particle_map(fix->get_mixed_buffers()); + make_rho(fix->get_mixed_buffers()); + } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) { + particle_map(fix->get_double_buffers()); + make_rho(fix->get_double_buffers()); + } else { + particle_map(fix->get_single_buffers()); + make_rho(fix->get_single_buffers()); + } } // all procs communicate density values from their ghost cells @@ -258,21 +265,26 @@ void PPPMIntel::compute_second(int /*eflag*/, int /*vflag*/) int i,j; // calculate the force on my particles + // optimized versions can only be used for orthogonal boxes - if (differentiation_flag == 1) { - if (fix->precision() == FixIntel::PREC_MODE_MIXED) - fieldforce_ad(fix->get_mixed_buffers()); - else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) - fieldforce_ad(fix->get_double_buffers()); - else - fieldforce_ad(fix->get_single_buffers()); + if (triclinic) { + PPPM::fieldforce(); } else { - if (fix->precision() == FixIntel::PREC_MODE_MIXED) - fieldforce_ik(fix->get_mixed_buffers()); - else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) - fieldforce_ik(fix->get_double_buffers()); - else - fieldforce_ik(fix->get_single_buffers()); + if (differentiation_flag == 1) { + if (fix->precision() == FixIntel::PREC_MODE_MIXED) + fieldforce_ad(fix->get_mixed_buffers()); + else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) + fieldforce_ad(fix->get_double_buffers()); + else + fieldforce_ad(fix->get_single_buffers()); + } else { + if (fix->precision() == FixIntel::PREC_MODE_MIXED) + fieldforce_ik(fix->get_mixed_buffers()); + else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) + fieldforce_ik(fix->get_double_buffers()); + else + fieldforce_ik(fix->get_single_buffers()); + } } // extra per-atom energy/virial communication diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 0b0a9d801b..53bedfbb6c 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -314,7 +314,7 @@ int MinFire::iterate(int maxiter) for (int i = 0; i < nlocal; i++) v[i][0] = v[i][1] = v[i][2] = 0.0; } - + // min dtv over replicas, if necessary // this communicator would be invalid for multiprocess replicas diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index fe319da9e9..4d8d6f6902 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -742,7 +742,7 @@ void PairHybrid::read_restart(FILE *fp) keywords[m] = new char[n]; if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); - styles[m] = force->new_pair(keywords[m],0,dummy); + styles[m] = force->new_pair(keywords[m],1,dummy); styles[m]->read_restart_settings(fp); // read back per style special settings, if present special_lj[m] = special_coul[m] = NULL;