diff --git a/doc/src/Build.rst b/doc/src/Build.rst index bd218c8165..c96fb0b5b9 100644 --- a/doc/src/Build.rst +++ b/doc/src/Build.rst @@ -8,7 +8,6 @@ for use with GNU make or gmake, or a build environment generated by CMake alternative you can download a package with pre-built executables as described on the :doc:`Install ` doc page. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 800b82645d..a03f101d79 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -10,10 +10,8 @@ CMake and make: * :ref:`Build the LAMMPS documentation ` * :ref:`Install LAMMPS after a build ` - ---------- - .. _serial: Serial vs parallel build @@ -57,7 +55,6 @@ The build with traditional makefiles has to be done inside the source folder `sr make serial # serial build, produces lmp_serial using Makefile/serial 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 @@ -154,10 +151,8 @@ while dropping all 'shared()' directives. The script 'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate this conversion. - ---------- - .. _compile: Choice of compiler and compile/link options @@ -204,7 +199,6 @@ for all the C++ files: -D CMAKE_C_FLAGS=string # flags to use with C compiler -D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler - A few example command lines are: .. code-block:: bash @@ -347,7 +341,6 @@ build may generate an error. This means you will need to install a shared library version of the auxiliary library. The build instructions for the library should tell you how to do this. - As an example, here is how to build and install the `MPICH library `_, a popular open-source version of MPI, as a shared library in the default /usr/local/lib location: @@ -377,7 +370,6 @@ recommended to ensure the integrity of the system software installation. ---------- - .. _doc: Build the LAMMPS documentation @@ -412,7 +404,6 @@ LAMMPS source distribution. make package_check # check for complete and consistent package lists make spelling # spell-check the manual - Thus "make html" will create a "doc/html" directory with the HTML format manual pages so that you can browse them with a web browser locally on your system. @@ -423,7 +414,6 @@ your system. current LAMMPS version (HTML and PDF files), from the website `download page `_. - **CMake build option**\ : It is also possible to create the HTML version of the manual within @@ -436,10 +426,8 @@ the "install" step when installing LAMMPS after the CMake build via -D BUILD_DOC=value # yes or no (default) - ---------- - .. _tools: Build LAMMPS tools @@ -450,7 +438,6 @@ using CMake or Make. **CMake build3**\ : - .. code-block:: bash -D BUILD_TOOLS=value # yes or no (default) @@ -460,7 +447,6 @@ The generated binaries will also become part of the LAMMPS installation **Traditional make**\ : - .. code-block:: bash cd lammps/tools @@ -470,10 +456,8 @@ The generated binaries will also become part of the LAMMPS installation make micelle2d # build only micelle2d tool make thermo_extract # build only thermo_extract tool - ---------- - .. _install: Install LAMMPS after a build @@ -487,7 +471,6 @@ you want to copy files to is protected. **CMake build**\ : - .. code-block:: bash cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 939431c6b3..1f7c335d65 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -9,17 +9,14 @@ Richard Berger (Temple U) has also written a `more comprehensive guide `_ for more information. - ---------- - **GUI version of CMake**\ : - .. code-block:: bash cmake-gui ../cmake @@ -205,15 +189,12 @@ edit some of the entries of CMake configuration variables in between. Please see the `cmake-gui manual `_ for more information. - ---------- - **Installing CMake** Check if your machine already has CMake installed: - .. code-block:: bash which cmake # do you have it? @@ -223,7 +204,6 @@ Check if your machine already has CMake installed: On clusters or supercomputers which use environment modules to manage software packages, do this: - .. code-block:: bash module list # is a module for cmake already loaded? diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index f8eee73197..722f436063 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -4,10 +4,8 @@ Development build options (CMake only) The CMake build of LAMMPS has a few extra options which are useful during development, testing or debugging. - ---------- - .. _compilation: Verify compilation flags @@ -17,22 +15,18 @@ Sometimes it is necessary to verify the complete sequence of compilation flags generated by the CMake build. To enable a more verbose output during compilation you can use the following option. - .. code-block:: bash -D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1: - .. code-block:: bash make VERBOSE=1 - ---------- - .. _sanitizer: Address, Undefined Behavior, and Thread Sanitizer Support @@ -47,17 +41,14 @@ The following settings allow you enable these features if your compiler supports it. Please note that they come with a performance hit. However, they are usually faster than using tools like Valgrind. - .. code-block:: bash -D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes -D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes -D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes - ---------- - .. _testing: Code Coverage and Testing @@ -71,7 +62,6 @@ developers can run the tests directly on their workstation. this is incomplete and only represents a small subset of tests that we run - .. code-block:: bash -D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes @@ -80,7 +70,6 @@ developers can run the tests directly on their workstation. If you enable testing in the CMake build it will create an additional target called "test". You can run them with: - .. code-block:: bash make test @@ -92,14 +81,12 @@ faster. You can also collect code coverage metrics while running the tests by enabling coverage support during building. - .. code-block:: bash -D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes This will also add the following targets to generate coverage reports after running the LAMMPS executable: - .. code-block:: bash make test # run tests first! @@ -108,7 +95,6 @@ This will also add the following targets to generate coverage reports after runn These reports require GCOVR to be installed. The easiest way to do this to install it via pip: - .. code-block:: bash pip install git+https://github.com/gcovr/gcovr.git diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 07adb67a3a..e0ef938e62 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -4,7 +4,6 @@ Packages with extra build options When building with some packages, additional steps may be required, in addition to: - .. code-block:: bash $ cmake -D PKG_NAME=yes @@ -57,7 +56,6 @@ This is the list of packages that may require additional steps. ---------- - .. _compress: COMPRESS package @@ -70,7 +68,6 @@ available on your system. If CMake cannot find the library, you can set these variables: - .. code-block:: bash -D ZLIB_INCLUDE_DIR=path # path to zlib.h header file @@ -82,10 +79,8 @@ If make cannot find the library, you can edit the file lib/compress/Makefile.lammps to specify the paths and library name. - ---------- - .. _gpu: GPU package @@ -96,7 +91,6 @@ which GPU hardware to build for. **CMake build**\ : - .. code-block:: bash -D GPU_API=value # value = opencl (default) or cuda @@ -146,7 +140,6 @@ 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 $ make lib-gpu # print help message @@ -188,10 +181,8 @@ lib/gpu/Makefile.lammps may need to be edited. package uses the library settings from the lib/gpu/Makefile.machine used to build the GPU library. - ---------- - .. _kim: KIM package @@ -214,7 +205,6 @@ minutes to hours) to build. Of course you only need to do that once.) **CMake build**\ : - .. code-block:: bash -D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes @@ -251,7 +241,6 @@ 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. - .. code-block:: bash $ make lib-kim # print help message @@ -272,7 +261,6 @@ using. For example: ---------- - .. _kokkos: KOKKOS package @@ -323,7 +311,6 @@ case-sensitive values, e.g. BDW, not bdw. For multicore CPUs using OpenMP, set these 2 variables. - .. code-block:: bash -D KOKKOS_ARCH=archCPU # archCPU = CPU from list above @@ -331,7 +318,6 @@ For multicore CPUs using OpenMP, set these 2 variables. For Intel KNLs using OpenMP, set these 2 variables: - .. code-block:: bash -D KOKKOS_ARCH=KNL @@ -339,7 +325,6 @@ For Intel KNLs using OpenMP, set these 2 variables: For NVIDIA GPUs using CUDA, set these 4 variables: - .. code-block:: bash -D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU @@ -352,7 +337,6 @@ The wrapper value is the Cuda nvcc compiler wrapper provided in the Kokkos library: lib/kokkos/bin/nvcc\_wrapper. The setting should include the full path name to the wrapper, e.g. - .. code-block:: bash -D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper @@ -365,7 +349,6 @@ src/MAKE/OPTIONS/Makefile.kokkos\* files for examples. For multicore CPUs using OpenMP: - .. code-block:: make KOKKOS_DEVICES = OpenMP @@ -373,7 +356,6 @@ For multicore CPUs using OpenMP: For Intel KNLs using OpenMP: - .. code-block:: make KOKKOS_DEVICES = OpenMP @@ -381,7 +363,6 @@ For Intel KNLs using OpenMP: For NVIDIA GPUs using CUDA: - .. code-block:: make KOKKOS_DEVICES = Cuda @@ -396,17 +377,14 @@ The 2 lines define a nvcc wrapper compiler, which will use nvcc for compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA files. - .. code-block:: make KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper CC = mpicxx - ---------- - .. _latte: LATTE package @@ -417,7 +395,6 @@ library. **CMake build**\ : - .. code-block:: bash -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes @@ -437,7 +414,6 @@ 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 $ make lib-latte # print help message @@ -452,10 +428,8 @@ dir. When LAMMPS itself is built it will use these links. You should also check that the Makefile.lammps file you create is appropriate for the compiler you use on your system to build LATTE. - ---------- - .. _message: MESSAGE package @@ -467,7 +441,6 @@ be installed on your system. **CMake build**\ : - .. code-block:: bash -D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes @@ -482,7 +455,6 @@ 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 $ make lib-message # print help message @@ -494,10 +466,8 @@ 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. - ---------- - .. _mscg: MSCG package @@ -511,7 +481,6 @@ lib/mscg/README and MSCG/Install files for more details. **CMake build**\ : - .. code-block:: bash -D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes @@ -532,7 +501,6 @@ 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 $ make lib-mscg # print help message @@ -547,10 +515,8 @@ 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. - ---------- - .. _opt: OPT package @@ -567,10 +533,8 @@ package when using Intel compilers. It should be added to the CCFLAGS line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for an example. - ---------- - .. _poems: POEMS package @@ -588,7 +552,6 @@ 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: - .. code-block:: bash $ make lib-poems # print help message @@ -604,10 +567,8 @@ 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. - ---------- - .. _python: PYTHON package @@ -620,7 +581,6 @@ lib/python/README for more details. **CMake build**\ : - .. code-block:: bash -D PYTHON_EXECUTABLE=path # path to Python executable to use @@ -639,10 +599,8 @@ 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. - ---------- - .. _voronoi: VORONOI package @@ -652,11 +610,8 @@ To build with this package, you must download and build the `Voro++ library ` doc page. **CMake build**\ : - .. code-block:: bash -D INTEL_ARCH=value # value = cpu (default) or knl @@ -1120,7 +1046,6 @@ additional information. For CPUs: - .. code-block:: make OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high @@ -1130,7 +1055,6 @@ For CPUs: For KNLs: - .. code-block:: make OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits @@ -1138,10 +1062,8 @@ For KNLs: LINKFLAGS = -g -qopenmp $(OPTFLAGS) LIB = -ltbbmalloc - ---------- - .. _user-molfile: USER-MOLFILE package @@ -1149,7 +1071,6 @@ USER-MOLFILE package **CMake build**\ : - .. code-block:: bash -D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed @@ -1176,10 +1097,8 @@ default headers, but these are not compatible with all VMD versions, so it is often best to change this setting to the location of the same include files of the local VMD installation in use. - ---------- - .. _user-netcdf: USER-NETCDF package @@ -1205,10 +1124,8 @@ and library files which LAMMPS needs to build with this package. If the settings are not valid for your system, you will need to edit the Makefile.lammps file. See lib/netcdf/README for details. - ---------- - .. _user-omp: USER-OMP package @@ -1227,7 +1144,6 @@ styles supporting OpenMP) the following compile and link flags must be added to your Makefile.machine file. See src/MAKE/OPTIONS/Makefile.omp for an example. - .. parsed-literal:: CCFLAGS: -fopenmp # for GNU and Clang Compilers @@ -1239,10 +1155,8 @@ For other platforms and compilers, please consult the documentation about OpenMP support for your compiler. Please see the note about how to address compatibility :ref:`issues with the 'default(none)' directive ` of some compilers. - ---------- - .. _user-qmmm: USER-QMMM package @@ -1282,7 +1196,6 @@ go back to the lib/qmmm folder and follow the instructions on the README file to build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder. You need to make certain, that - **Traditional make**\ : Before building LAMMPS, you must build the QMMM library in lib/qmmm. @@ -1291,7 +1204,6 @@ explained in lib/qmmm/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/qmmm/Install.py script with the specified args: - .. code-block:: bash $ make lib-qmmm # print help message @@ -1316,7 +1228,6 @@ lib/qmmm folder. ---------- - .. _user-quip: USER-QUIP package @@ -1330,7 +1241,6 @@ lib/quip/README file for details on how to do this. **CMake build**\ : - .. code-block:: bash -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) @@ -1349,10 +1259,8 @@ LAMMPS with this package. You should only need to edit Makefile.lammps if the LAMMPS build can not use its settings to successfully build on your system. - ---------- - .. _user-scafacos: USER-SCAFACOS package @@ -1362,11 +1270,8 @@ To build with this package, you must download and build the `ScaFaCoS Coulomb so .. _scafacos-home: http://www.scafacos.de - - **CMake build**\ : - .. code-block:: bash -D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes @@ -1397,10 +1302,8 @@ created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS builds in src it will use these links. You should not need to edit the lib/scafacos/Makefile.lammps file. - ---------- - .. _user-smd: USER-SMD package @@ -1411,7 +1314,6 @@ Eigen3 is a template library, so you do not need to build it. **CMake build**\ : - .. code-block:: bash -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes @@ -1429,7 +1331,6 @@ instructions in lib/smd/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/smd/Install.py script with the specified args: - .. code-block:: bash $ make lib-smd # print help message @@ -1441,10 +1342,8 @@ lib/smd to point to the Eigen dir. When LAMMPS builds it will use this link. You should not need to edit the lib/smd/Makefile.lammps file. - ---------- - .. _user-vtk: USER-VTK package diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index fdb98d3785..eee61ba552 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -31,7 +31,6 @@ these 2 files: ---------- - **Link with LAMMPS as a static library**\ : The calling application can link to LAMMPS as a static library with @@ -54,7 +53,6 @@ link the coupled executable are then: mpicc -c -O $(pkgconf liblammps --cflags) caller.c mpicxx -o caller caller.o -$(pkgconf liblammps --libs) - *Traditional make*\ : This assumes that LAMMPS has been compiled in the folder @@ -193,7 +191,6 @@ would add something like this to your ~/.profile file: For the csh or tcsh shells, you would equivalently add something like this to your ~/.cshrc file: - .. code-block:: csh setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src @@ -212,7 +209,6 @@ You can verify whether all required shared libraries are found with the libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000) /lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000) - If a required library is missing, you would get a 'not found' entry: .. code-block:: bash @@ -226,10 +222,8 @@ If a required library is missing, you would get a 'not found' entry: libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000) /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000) - ---------- - **Calling the LAMMPS library**\ : Either flavor of library (static or shared) allows one or more LAMMPS diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index ebd1790e11..0830171de3 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -73,7 +73,6 @@ in the LAMMPS distribution. Typing "make machine" uses use Makefile.serial and Makefile.mpi, respectively. Other makefiles are in these directories: - .. parsed-literal:: OPTIONS # Makefiles which enable specific options @@ -93,7 +92,6 @@ customized machine Makefile are contributed by users. Since both compilers, OS configurations, and LAMMPS itself keep changing, their settings may become outdated: - .. code-block:: bash make mac # build serial LAMMPS on a Mac diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f3c98f9bcb..23ff460d5c 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -47,14 +47,12 @@ versus make. **CMake build**\ : - .. code-block:: bash -D PKG_NAME=value # yes or no (default) Examples: - .. code-block:: bash -D PKG_MANYBODY=yes @@ -76,7 +74,6 @@ once with CMake. **Traditional make**\ : - .. code-block:: bash cd lammps/src @@ -87,7 +84,6 @@ once with CMake. Examples: - .. code-block:: bash make no-rigid @@ -132,10 +128,8 @@ src directory. That is no longer the case, so that CMake will build as-is without the need to un-install those packages. - ---------- - **CMake shortcuts for installing many packages**\ : Instead of specifying all the CMake options via the command-line, @@ -169,7 +163,6 @@ one of them as a starting point and customize it to your needs. **Example:** - .. code-block:: bash # build LAMMPS with most commonly used packages, but then remove @@ -186,10 +179,8 @@ one of them as a starting point and customize it to your needs. # but leaving all other settings untouched. You can run: cmake -C ../cmake/presets/no_all.cmake . - ---------- - **Make shortcuts for installing many packages**\ : The following commands are useful for managing package source files diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index dca5f0f37f..476ddb7732 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -14,10 +14,8 @@ explain how to do this for building both with CMake and make. * :ref:`Workaround for long long integers ` * :ref:`Error handling exceptions ` when using LAMMPS as a library - ---------- - .. _cxx11: C++11 standard compliance @@ -35,7 +33,6 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x: ---------- - .. _fft: FFT library @@ -49,7 +46,6 @@ LAMMPS can use them if they are available on your system. **CMake variables**\ : - .. code-block:: bash -D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS @@ -69,7 +65,6 @@ OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is used. If CMake cannot detect the FFT library, you can set these variables to assist: - .. code-block:: bash -D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files @@ -81,7 +76,6 @@ to assist: **Makefile.machine settings**\ : - .. code-block:: make FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS @@ -93,7 +87,6 @@ to assist: # default is FFT\_PACK\_ARRAY if not specified - .. code-block:: make FFT_INC = -I/usr/local/include @@ -159,7 +152,6 @@ 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. - .. code-block:: bash make clean @@ -172,10 +164,8 @@ 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. - ---------- - .. _size: Size of LAMMPS data types @@ -187,14 +177,12 @@ adequate. **CMake variable**\ : - .. code-block:: bash -D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall **Makefile.machine setting**\ : - .. code-block:: make LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL @@ -249,10 +237,8 @@ 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. - ---------- - .. _graphics: Output of JPG, PNG, and movie files @@ -265,7 +251,6 @@ following settings: **CMake variables**\ : - .. code-block:: bash -D WITH_JPEG=value # yes or no @@ -279,7 +264,6 @@ Usually these settings are all that is needed. If CMake cannot find the graphics header, library, executable files, you can set these variables: - .. code-block:: bash -D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file @@ -292,7 +276,6 @@ variables: **Makefile.machine settings**\ : - .. code-block:: make LMP_INC = -DLAMMPS_JPEG @@ -321,10 +304,8 @@ supports the "popen" function in the standard runtime library. communication library and lead to simulations using ffmpeg to hang or crash. - ---------- - .. _gzip: Read or write compressed files @@ -336,7 +317,6 @@ gzip compression by several LAMMPS commands, including **CMake variables**\ : - .. code-block:: bash -D WITH_GZIP=value # yes or no @@ -345,7 +325,6 @@ gzip compression by several LAMMPS commands, including **Makefile.machine setting**\ : - .. code-block:: make LMP_INC = -DLAMMPS_GZIP @@ -365,10 +344,8 @@ found by LAMMPS during a run. I/O is also available using a compression library instead, which is what the :ref:`COMPRESS package ` enables. - ---------- - .. _align: Memory allocation alignment @@ -385,7 +362,6 @@ aligned on 64-byte boundaries. **CMake variable**\ : - .. code-block:: bash -D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) @@ -397,7 +373,6 @@ and this setting ignored. **Makefile.machine setting**\ : - .. code-block:: make LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 @@ -408,10 +383,8 @@ 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. - ---------- - .. _longlong: Workaround for long long integers @@ -424,22 +397,18 @@ those systems: **CMake variable**\ : - .. code-block:: bash -D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) **Makefile.machine setting**\ : - .. code-block:: make LMP_INC = -DLAMMPS_LONGLONG_TO_LONG - ---------- - .. _exceptions: Exception handling when using LAMMPS as a library @@ -453,14 +422,12 @@ e.g. to Python. Of course the calling code has to be set up to **CMake variable**\ : - .. code-block:: bash -D LAMMPS_EXCEPTIONS=value # yes or no (default) **Makefile.machine setting**\ : - .. code-block:: make LMP_INC = -DLAMMPS_EXCEPTIONS diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst index 264e4bf44f..4f20a01559 100644 --- a/doc/src/Build_windows.rst +++ b/doc/src/Build_windows.rst @@ -6,10 +6,8 @@ Notes for building LAMMPS on Windows * :ref:`Using GNU GCC ported to Windows ` * :ref:`Using a cross-compiler ` - ---------- - .. _generic: General remarks diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst index f192d6a59d..72a98159ff 100644 --- a/doc/src/Commands.rst +++ b/doc/src/Commands.rst @@ -4,7 +4,6 @@ Commands These pages describe how a LAMMPS input script is formatted and the commands in it are used to define a LAMMPS simulation. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 19be6d8cbc..0cb1b723b8 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -99,7 +99,6 @@ have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. - .. table_from_list:: :columns: 4 diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index 69d3393d08..64a7315a5f 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -16,7 +16,6 @@ simulation with all the settings. Rather, the input script is read one line at a time and each command takes effect when it is read. Thus this sequence of commands: - .. code-block:: LAMMPS timestep 0.5 @@ -25,7 +24,6 @@ Thus this sequence of commands: does something different than this sequence: - .. code-block:: LAMMPS run 100 diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 750369d118..86d28bafbd 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -86,7 +86,6 @@ LAMMPS: This can be useful for formatting print output to a desired precision: - .. code-block:: LAMMPS print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" diff --git a/doc/src/Errors.rst b/doc/src/Errors.rst index 9c53467719..896dfbcbef 100644 --- a/doc/src/Errors.rst +++ b/doc/src/Errors.rst @@ -7,7 +7,6 @@ and warnings doc pages give complete lists of all the messages the code may generate (except those generated by USER packages), with additional details for many of them. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index b8832d8f34..133890c961 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -63,7 +63,6 @@ is an integer or floating-point number, respectively, and reject the input with an error message (for instance, when an integer is required, but a floating-point number 1.0 is provided): - .. parsed-literal:: ERROR: Expected integer parameter instead of '1.0' in input script or data file @@ -81,7 +80,6 @@ reading the input and before parsing commands, the documentation of the corresponding command explicitly says it is. Otherwise, you will receive an error message of this kind: - .. parsed-literal:: ERROR: Expected floating point parameter instead of 'v_name' in input script or data file diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 4866de31c6..4955af773b 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -7,7 +7,6 @@ documentation for the offending command may help. Error messages also list the source file and line number where the error was generated. For example, a message like this: - .. parsed-literal:: ERROR: Illegal velocity command (velocity.cpp:78) @@ -21,12 +20,8 @@ code or contact the author of the package. Doc page with :doc:`WARNING messages ` - ---------- - - - *1-3 bond count is inconsistent* An inconsistency was detected when computing the number of 1-3 neighbors for each atom. This likely means something is wrong with diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index cb4bdf3e3f..76bdad7adb 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -7,7 +7,6 @@ documentation for the offending command may help. Warning messages also list the source file and line number where the warning was generated. For example, a message like this: - .. parsed-literal:: WARNING: Bond atom missing in box size check (domain.cpp:187) @@ -21,12 +20,8 @@ code or contact the author of the package. Doc page with :doc:`ERROR messages ` - ---------- - - - *Adjusting Coulombic cutoff for MSM, new cutoff = %g* The adjust/cutoff command is turned on and the Coulombic cutoff has been adjusted to match the user-specified accuracy. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 243ffdfd93..365ff21db5 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -38,10 +38,8 @@ particular quantity. Lists of both kinds of directories are given below. - ---------- - Lowercase directories --------------------- @@ -157,7 +155,6 @@ Lowercase directories Here is how you can run and visualize one of the sample problems: - .. parsed-literal:: cd indent @@ -180,15 +177,12 @@ like ImageMagick or QuickTime or various Windows-based tools. See the Imagemagick command would create a GIF file suitable for viewing in a browser. - .. parsed-literal:: % convert -loop 1 \*.jpg foo.gif - ---------- - Uppercase directories --------------------- diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 05af2ffafc..b9109d921f 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -12,7 +12,6 @@ also show how to setup and run various kinds of simulations. Tutorials howto =============== - .. toctree:: :name: tutorials :maxdepth: 1 @@ -24,7 +23,6 @@ Tutorials howto General howto ============= - .. toctree:: :name: general_howto :maxdepth: 1 @@ -40,7 +38,6 @@ General howto Settings howto ============== - .. toctree:: :name: settings_howto :maxdepth: 1 @@ -56,7 +53,6 @@ Settings howto Analysis howto ============== - .. toctree:: :name: analysis_howto :maxdepth: 1 @@ -72,7 +68,6 @@ Analysis howto Force fields howto ================== - .. toctree:: :name: force_howto :maxdepth: 1 @@ -85,7 +80,6 @@ Force fields howto Packages howto ============== - .. toctree:: :name: packages_howto :maxdepth: 1 diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index 59060fbe1e..a516315baf 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -11,7 +11,6 @@ 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 plane of atoms - e.g. - .. code-block:: LAMMPS :doc:`create box ` 1 -10 10 -10 10 -0.25 0.25 diff --git a/doc/src/Howto_bash.rst b/doc/src/Howto_bash.rst index f8a5130b33..4a84da2f85 100644 --- a/doc/src/Howto_bash.rst +++ b/doc/src/Howto_bash.rst @@ -3,10 +3,8 @@ Using LAMMPS with Bash on Windows **written by Richard Berger** - ---------- - Starting with Windows 10 you can install Linux tools directly in Windows. This allows you to compile LAMMPS following the same procedure as on a real Ubuntu Linux installation. Software can be easily installed using the package manager @@ -82,10 +80,8 @@ Congratulations, you have installed **Bash on Ubuntu on Windows**\ . .. image:: JPG/bow_tutorial_10.png - ---------- - Compiling LAMMPS in Bash on Windows ----------------------------------- @@ -97,7 +93,6 @@ Installing prerequisite packages First upgrade all existing packages using - .. code-block:: bash sudo apt update @@ -106,7 +101,6 @@ First upgrade all existing packages using Next install the following packages, which include compilers and libraries needed for various LAMMPS features: - .. code-block:: bash sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools @@ -126,7 +120,6 @@ Obtain a copy of the LAMMPS code and go into it using "cd" Option 1: Downloading LAMMPS tarball using wget """"""""""""""""""""""""""""""""""""""""""""""" - .. code-block:: bash wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz @@ -136,7 +129,6 @@ Option 1: Downloading LAMMPS tarball using wget Option 2: Obtaining LAMMPS code from GitHub """"""""""""""""""""""""""""""""""""""""""" - .. code-block:: bash git clone https://github.com/lammps/lammps.git @@ -150,7 +142,6 @@ At this point you can compile LAMMPS like on Ubuntu Linux. Compiling serial version """""""""""""""""""""""" - .. code-block:: bash cd src/ @@ -161,7 +152,6 @@ This will create an executable called lmp\_serial in the src/ directory Compiling MPI version """"""""""""""""""""" - .. code-block:: bash cd src/ @@ -169,20 +159,16 @@ Compiling MPI version This will create an executable called lmp\_mpi in the src/ directory - ---------- - Finally, please note the absolute path of your src folder. You can get this using - .. code-block:: bash pwd or - .. code-block:: bash echo $PWD @@ -190,22 +176,18 @@ or To run any examples you need the location of the executable. For now, let us save this location in a temporary variable - .. code-block:: bash LAMMPS_DIR=$PWD - ---------- - Running an example script ^^^^^^^^^^^^^^^^^^^^^^^^^ Once compiled you can execute some of the LAMMPS examples. Switch into the examples/melt folder - .. code-block:: bash cd ../examples/melt @@ -214,14 +196,12 @@ The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mp version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either version as follows: - .. code-block:: bash $LAMMPS_DIR/lmp_serial -in in.melt or - .. code-block:: bash mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt @@ -235,21 +215,18 @@ Adding your executable directory to your PATH You can avoid having to type the full path of your LAMMPS binary by adding its parent folder to the PATH environment variable as follows: - .. code-block:: bash export PATH=$LAMMPS_DIR:$PATH Input scripts can then be run like this: - .. code-block:: bash lmp_serial -in in.melt or - .. code-block:: bash mpirun -np 4 lmp_mpi -in in.melt @@ -258,7 +235,6 @@ However, this PATH variable will not persist if you close your bash window. To persist this setting edit the $HOME/.bashrc file using your favorite editor and add this line - .. code-block:: bash export PATH=/full/path/to/your/lammps/src:$PATH @@ -267,14 +243,12 @@ and add this line For an executable lmp\_serial with a full path - .. code-block:: bash /home/richard/lammps/src/lmp_serial the PATH variable should be - .. code-block:: bash export PATH=/home/richard/lammps/src:$PATH diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 4d31d1ee47..e7bfcdfdb2 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -20,12 +20,8 @@ force field. .. _charmm: http://www.scripps.edu/brooks - - .. _amber: http://amber.scripps.edu - - The interaction styles listed below compute force field formulas that are consistent with common options in CHARMM or AMBER. See each command's documentation for the formula it computes. @@ -114,33 +110,23 @@ documentation for the formula it computes. * :doc:`special_bonds ` dreiding - ---------- - .. _howto-MacKerell: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). .. _howto-Cornell: - - **(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). .. _howto-Sun: - - **(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998). .. _howto-Mayo: - - **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index f60a608eae..3cb65aab91 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -33,10 +33,8 @@ style are described below. More styles may be added in the future. See the :doc:`Modify body ` doc page for details on how to add a new body style to the code. - ---------- - **When to use body particles:** You should not use body particles to model a rigid body made of @@ -104,10 +102,8 @@ particles of different styles The pair styles defined for use with specific body styles are listed in the sections below. - ---------- - **Specifics of body style nparticle:** The *nparticle* body style represents body particles as a rigid body @@ -119,7 +115,6 @@ duplicates its functionality. The atom\_style body command for this body style takes two additional arguments: - .. parsed-literal:: atom_style body nparticle Nmin Nmax @@ -133,7 +128,6 @@ When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: - .. parsed-literal:: atom-ID 1 M @@ -170,7 +164,6 @@ For output purposes via the :doc:`compute body/local ` and : commands, this body style produces one datum for each of the N sub-particles in a body particle. The datum has 3 values: - .. parsed-literal:: 1 = x position of sub-particle @@ -188,10 +181,8 @@ collection of spheres, one for each sub-particle. The size of each sphere is determined by the *bflag1* parameter for the *body* keyword. The *bflag2* argument is ignored. - ---------- - **Specifics of body style rounded/polygon:** The *rounded/polygon* body style represents body particles as a 2d @@ -207,7 +198,6 @@ described in :ref:`Fraige `. Similar to body style *nparticle*\ , the atom\_style body command for this body style takes two additional arguments: - .. parsed-literal:: atom_style body rounded/polygon Nmin Nmax @@ -221,7 +211,6 @@ When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: - .. parsed-literal:: atom-ID 1 M @@ -262,7 +251,6 @@ orientation of the square is aligned with the xy coordinate axes which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = 1 1 4 0 0 0. Note that only Izz matters in 2D simulations. - .. parsed-literal:: 3 1 27 @@ -281,7 +269,6 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends by circles of diameter 0.5, is specified as follows: - .. parsed-literal:: 1 1 13 @@ -293,7 +280,6 @@ by circles of diameter 0.5, is specified as follows: A disk, whose diameter is 3.0, mass 1.0, is specified as follows: - .. parsed-literal:: 1 1 10 @@ -308,10 +294,8 @@ interactions. The :doc:`fix wall/body/polygon ` command can be used with this body style to compute the interaction of body particles with a wall. - ---------- - **Specifics of body style rounded/polyhedron:** The *rounded/polyhedron* body style represents body particles as a 3d @@ -330,7 +314,6 @@ This body style is for 3d discrete element models, as described in Similar to body style *rounded/polygon*\ , the atom\_style body command for this body style takes two additional arguments: - .. parsed-literal:: atom_style body rounded/polyhedron Nmin Nmax @@ -344,7 +327,6 @@ When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: - .. parsed-literal:: atom-ID 3 M @@ -401,7 +383,6 @@ The orientation of the cube is aligned with the xyz coordinate axes which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = 0.667 0.667 0.667 0 0 0. - .. parsed-literal:: 1 3 79 @@ -438,7 +419,6 @@ iyz = 0.667 0.667 0.667 0 0 0. A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends by circles of diameter 0.5, is specified as follows: - .. parsed-literal:: 1 1 13 @@ -450,7 +430,6 @@ by circles of diameter 0.5, is specified as follows: A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: - .. parsed-literal:: 1 1 10 @@ -465,15 +444,12 @@ be used with this body style to compute body/body interactions. The used with this body style to compute the interaction of body particles with a wall. - ---------- - For output purposes via the :doc:`compute body/local ` and :doc:`dump local ` commands, this body style produces one datum for each of the N sub-particles in a body particle. The datum has 3 values: - .. parsed-literal:: 1 = x position of vertex @@ -495,20 +471,14 @@ tangent to the spheres). The drawn diameter of each line segment is determined by the *bflag1* parameter for the *body* keyword. The *bflag2* argument is ignored. - ---------- - .. _body-Fraige: - - **(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). .. _body-Wang: - - **(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011). diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index cedc05d9f4..4bbbf7e368 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -150,7 +150,6 @@ properties: (1) Average velocity in each of 1000 2d spatial bins: - .. code-block:: LAMMPS compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced @@ -159,7 +158,6 @@ properties: (2) Temperature in each spatial bin, after subtracting a flow velocity: - .. code-block:: LAMMPS compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced @@ -168,7 +166,6 @@ velocity: (3) Center of mass of each molecule: - .. code-block:: LAMMPS compute cc1 all chunk/atom molecule @@ -177,7 +174,6 @@ velocity: (4) Total force on each molecule and ave/max across all molecules: - .. code-block:: LAMMPS compute cc1 all chunk/atom molecule @@ -189,7 +185,6 @@ velocity: (5) Histogram of cluster sizes: - .. code-block:: LAMMPS compute cluster all cluster/atom 1.0 diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst index e98a3c9a98..160d3ae092 100644 --- a/doc/src/Howto_client_server.rst +++ b/doc/src/Howto_client_server.rst @@ -134,7 +134,6 @@ together to exchange MPI messages between them. For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes: - .. code-block:: bash % mpirun -np 1 lmp_mpi -log log.client < in.client & @@ -150,7 +149,6 @@ For message exchange in *mpi/one* mode: Launch both codes in a single mpirun command: - .. code-block:: bash mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index bf600583c1..94fb5b7b42 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -24,7 +24,6 @@ shell of a core/shell pair should be bonded to each other with a harmonic bond that provides the spring force. For example, a data file for NaCl, as found in examples/coreshell, has this format: - .. parsed-literal:: 432 atoms # core and shell atoms @@ -87,7 +86,6 @@ Ewald solvers can be used. For the NaCL example problem, these pair style and bond style settings are used: - .. code-block:: LAMMPS pair_style born/coul/long/cs 20.0 20.0 @@ -131,7 +129,6 @@ this temperature be output for the overall system. For the NaCl example, this can be done as follows: - .. code-block:: LAMMPS group cores type 1 2 @@ -150,7 +147,6 @@ the default :doc:`temperature ` and specifying it as a second argument in :doc:`fix modify ` and :doc:`thermo_modify ` resulting in: - .. code-block:: LAMMPS (...) @@ -174,7 +170,6 @@ the pairs. This can be done by using the *bias* keyword of the :doc:`velocity create ` command and assigning the :doc:`compute temp/cs ` command to the *temp* keyword of the :doc:`velocity ` command, e.g. - .. code-block:: LAMMPS velocity all create 1427 134 bias yes temp CSequ @@ -211,7 +206,6 @@ pairs as chunks. For example if core/shell pairs are the only molecules: - .. code-block:: LAMMPS read_data NaCl_CS_x0.1_prop.data @@ -222,7 +216,6 @@ For example if core/shell pairs are the only molecules: For example if core/shell pairs and other molecules are present: - .. code-block:: LAMMPS fix csinfo all property/atom i_CSID # property/atom command @@ -232,7 +225,6 @@ For example if core/shell pairs and other molecules are present: The additional section in the date file would be formatted like this: - .. parsed-literal:: CS-Info # header of additional section @@ -247,20 +239,14 @@ The additional section in the date file would be formatted like this: 8 4 (...) - ---------- - .. _MitchellFincham: - - **(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993). .. _MitchellFincham2: - - **(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994). diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst index 55c7d813d6..5bcf026387 100644 --- a/doc/src/Howto_couple.rst +++ b/doc/src/Howto_couple.rst @@ -12,10 +12,8 @@ LAMMPS can be coupled to other codes in at least 4 ways. Each has advantages and disadvantages, which you will have to think about in the context of your application. - ---------- - (1) Define a new :doc:`fix ` command that calls the other code. In this scenario, LAMMPS is the driver code. During its timestepping, the fix is invoked, and can make library calls to the other code, @@ -27,12 +25,8 @@ LAMMPS. .. _poems: http://www.rpi.edu/~anderk5/lab - - - ---------- - (2) Define a new LAMMPS command that calls the other code. This is conceptually similar to method (1), but in this case LAMMPS and the other code are on a more equal footing. Note that now the other code @@ -53,10 +47,8 @@ command writes and reads. See the :doc:`Modify command ` doc page for info on how to add a new command to LAMMPS. - ---------- - (3) Use LAMMPS as a library called by another code. In this case the other code is the driver and calls LAMMPS as needed. Or a wrapper code could link and call both LAMMPS and another code as libraries. @@ -78,15 +70,10 @@ examples/COUPLE/README for more details: a kinetic Monte Carlo model for grain growth using MD to calculate strain induced across grain boundaries - .. _quest: http://dft.sandia.gov/Quest - - .. _spparks: http://www.sandia.gov/~sjplimp/spparks.html - - The :doc:`Build basics ` doc page describes how to build LAMMPS as a library. Once this is done, you can interface with LAMMPS either via C++, C, Fortran, or Python (or any other language that @@ -113,10 +100,8 @@ LAMMPS and 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. - ---------- - (4) Couple LAMMPS with another code in a client/server mode. This is described on the :doc:`Howto client/server ` doc page. diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index b6292ca622..6efe731ee1 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -56,12 +56,8 @@ with a Coulomb pair style. It may be useful to use *coul/long/cs* or similar from the CORESHELL package if the core and Drude particle come too close, which can cause numerical issues. - ---------- - .. _howto-Lamoureux: - - **(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index fb99077137..039897a20b 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -30,7 +30,6 @@ zero. The (half-)stiffness of the :doc:`harmonic bond ` :math:`K_D = k_D/2` and the Drude charge :math:`q_D` are related to the atom polarizability :math:`\alpha` by - .. math:: K_D = \frac 1 2\, \frac {q_D^2} \alpha @@ -46,7 +45,6 @@ fields: * Alternately :ref:`Schroeder and Steinhauser ` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K. * In both these force fields hydrogen atoms are treated as non-polarizable. - The motion of of the Drude particles can be calculated by minimizing the energy of the induced dipoles at each timestep, by an iterative, self-consistent procedure. The Drude particles can be massless and @@ -85,7 +83,6 @@ 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:: polarizer -q -f phenol.dff data.102494.lmp data-p.lmp @@ -96,7 +93,6 @@ from *phenol.dff*\ , as well as the DC-DP bond constants. The file *phenol.dff* contains the polarizabilities of the atom types and the mass of the Drude particles, for instance: - .. parsed-literal:: # units: kJ/mol, A, deg @@ -113,7 +109,6 @@ have to be specified as comments at the end of lines of the *Masses* section. You probably need to edit it to add these names. It should look like - .. parsed-literal:: Masses @@ -124,10 +119,8 @@ look like 4 1.008 # HA 5 1.008 # HO - ---------- - **Basic input file** The atom style should be set to (or derive from) *full*\ , so that you @@ -138,7 +131,6 @@ script (the use of these lines will be explained below). In order for LAMMPS to recognize that you are using Drude oscillators, you should use the fix *drude*\ . The command is - .. code-block:: LAMMPS fix DRUDE all drude C C C N N D D D @@ -159,7 +151,6 @@ command. With our phenol, there is 1 more special neighbor for which space is required. Otherwise LAMMPS crashes and gives the required value. - .. code-block:: LAMMPS read_data data-p.lmp extra/special/per/atom 1 @@ -173,7 +164,6 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with *kspace\_style pppm*. For example, with a cutoff of 10. and a precision 1.e-4: - .. code-block:: LAMMPS pair_style lj/cut/coul/long 10.0 @@ -184,14 +174,12 @@ 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 that needs to be added is - .. code-block:: LAMMPS pair_coeff * 6* 0.0 0.0 # All-DPs Now for the thermalization, the simplest choice is to use the :doc:`fix langevin/drude `. - .. code-block:: LAMMPS fix LANG all langevin/drude 300. 100 12435 1. 20 13977 @@ -205,7 +193,6 @@ atoms need to be in this fix's group. LAMMPS will thermostat the DPs together with their DC. For this, ghost atoms need to know their velocities. Thus you need to add the following command: - .. code-block:: LAMMPS comm_modify vel yes @@ -217,7 +204,6 @@ can add the *zero yes* option at the end of the fix line. If the fix *shake* is used to constrain the C-H bonds, it should be invoked after the fix *langevin/drude* for more accuracy. - .. code-block:: LAMMPS fix SHAKE ATOMS shake 0.0001 20 0 t 4 5 @@ -231,7 +217,6 @@ Since the fix *langevin/drude* does not perform time integration (just modification of forces but no position/velocity updates), the fix *nve* should be used in conjunction. - .. code-block:: LAMMPS fix NVE all nve @@ -240,7 +225,6 @@ Finally, do not forget to update the atom type elements if you use them in a *dump\_modify ... element ...* command, by adding the element type of the DPs. Here for instance - .. code-block:: LAMMPS dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz @@ -254,7 +238,6 @@ 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 ` - .. code-block:: LAMMPS compute TDRUDE all temp/drude @@ -263,15 +246,12 @@ 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. - .. code-block:: LAMMPS thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2] - ---------- - **Thole screening** Dipolar interactions represented by point charges on springs may not @@ -289,7 +269,6 @@ 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 - .. code-block:: LAMMPS pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0 @@ -305,7 +284,6 @@ explicitly defined. The output of the *polarizer* script can be used to complete the *pair\_coeff* section of the input file. In our example, this will look like: - .. code-block:: LAMMPS pair_coeff 1 1 lj/cut/coul/long 0.0700 3.550 @@ -349,7 +327,6 @@ For the *thole* pair style the coefficients are 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* command (0.0, 0.0, and 0.5 in the example above). Without using the @@ -361,16 +338,13 @@ 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. - ---------- - **Thermostats and barostats** Using a Nose-Hoover barostat with the *langevin/drude* thermostat is straightforward using fix *nph* instead of *nve*\ . For example: - .. code-block:: LAMMPS fix NPH all nph iso 1. 1. 500 @@ -385,7 +359,6 @@ with respect to their DC. The *fix drude/transform/inverse* performs the reverse transformation. For a NVT simulation, with the DCs and atoms at 300 K and the DPs at 1 K relative to their DC one would use - .. code-block:: LAMMPS fix DIRECT all drude/transform/direct @@ -395,7 +368,6 @@ atoms at 300 K and the DPs at 1 K relative to their DC one would use For our phenol example, the groups would be defined as - .. code-block:: LAMMPS group ATOMS type 1 2 3 4 5 # DCs and non-polarizable atoms @@ -409,7 +381,6 @@ times and for the forces also). To avoid the flying ice cube artifact center of mass of the whole system drifts faster and faster, the *fix momentum* can be used. For instance: - .. code-block:: LAMMPS fix MOMENTUM all momentum 100 linear 1 1 1 @@ -424,7 +395,6 @@ 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 instructions for thermostatting and barostatting will look like - .. code-block:: LAMMPS compute TATOMS ATOMS temp @@ -434,10 +404,8 @@ instructions for thermostatting and barostatting will look like fix NVT DRUDES nvt temp 1. 1. 20 fix INVERSE all drude/transform/inverse - ---------- - **Rigid bodies** You may want to simulate molecules as rigid bodies (but polarizable). @@ -448,7 +416,6 @@ review the different thermostats and ensemble combinations. NVT ensemble using Langevin thermostat: - .. code-block:: LAMMPS comm_modify vel yes @@ -458,7 +425,6 @@ NVT ensemble using Langevin thermostat: NVT ensemble using Nose-Hoover thermostat: - .. code-block:: LAMMPS fix DIRECT all drude/transform/direct @@ -468,7 +434,6 @@ NVT ensemble using Nose-Hoover thermostat: NPT ensemble with Langevin thermostat: - .. code-block:: LAMMPS comm_modify vel yes @@ -478,7 +443,6 @@ NPT ensemble with Langevin thermostat: NPT ensemble using Nose-Hoover thermostat: - .. code-block:: LAMMPS compute TATOM ATOMS temp @@ -488,45 +452,31 @@ NPT ensemble using Nose-Hoover thermostat: fix NVT DRUDES nvt temp 1. 1. 20 fix INVERSE all drude/transform/inverse - ---------- - .. _Lamoureux2: - - **(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) .. _Schroeder: - - **(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010). .. _Jiang2: - - **(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). .. _Thole2: - - **(Thole)** Chem Phys, 59, 341 (1981). .. _Noskov2: - - **(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). .. _SWM4-NDP: - - **(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys Let, 418, 245-249 (2006) diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst index 001eb4886b..1d633e6e98 100644 --- a/doc/src/Howto_elastic.rst +++ b/doc/src/Howto_elastic.rst @@ -33,12 +33,8 @@ tensor. Another approach is to sample the triclinic cell fluctuations that occur in an NPT simulation. This method can also be slow to converge and requires careful post-processing :ref:`(Shinoda) ` - ---------- - .. _Shinoda1: - - **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 6e1bc5bb60..f51d15d865 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -22,10 +22,8 @@ and will reduce the time until the integration is complete. For more information on the requirements to have your code included into LAMMPS please see the :doc:`Modify contribute ` doc page. - ---------- - **Making an account** First of all, you need a GitHub account. This is fairly simple, just @@ -34,10 +32,8 @@ the "Sign up for GitHub" button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. - ---------- - **Forking the repository** To get changes into LAMMPS, you need to first fork the `lammps/lammps` @@ -63,10 +59,8 @@ At the same time, you can set things up, so you can include changes from upstream into your repository and thus keep it in sync with the ongoing LAMMPS development. - ---------- - **Adding changes to your own fork** Additions to the upstream version of LAMMPS are handled using *feature @@ -81,14 +75,12 @@ explained in more detail here: `feature branch workflow /lammps.git or, if you have set up your GitHub account for using SSH keys, via SSH: - .. code-block:: bash $ git clone git@github.com:/lammps.git @@ -108,7 +100,6 @@ test them without interfering with the repository on GitHub. To pull changes from upstream into this copy, you can go to the directory and use git pull: - .. code-block:: bash $ cd mylammps @@ -117,7 +108,6 @@ and use git pull: You can also add this URL as a remote: - .. code-block:: bash $ git remote add lammps_upstream https://www.github.com/lammps/lammps @@ -127,7 +117,6 @@ branch for the feature you want to work on. This tutorial contains the workflow that updated this tutorial, and hence we will call the branch "github-tutorial-update": - .. code-block:: bash $ git checkout -b github-tutorial-update master @@ -140,7 +129,6 @@ unrelated feature, you should switch branches! After everything is done, add the files to the branch and commit them: - .. code-block:: bash $ git add doc/src/Howto_github.txt @@ -165,14 +153,12 @@ After everything is done, add the files to the branch and commit them: After adding all files, the change set can be committed with some useful message that explains the change. - .. code-block:: bash $ git commit -m 'Finally updated the github tutorial' After the commit, the changes can be pushed to the same branch on GitHub: - .. code-block:: bash $ git push @@ -181,7 +167,6 @@ Git will ask you for your user name and password on GitHub if you have not configured anything. If your local branch is not present on GitHub yet, it will ask you to add it by running - .. code-block:: bash $ git push --set-upstream origin github-tutorial-update @@ -192,22 +177,18 @@ password, the feature branch should be added to your fork on GitHub. If you want to make really sure you push to the right repository (which is good practice), you can provide it explicitly: - .. code-block:: bash $ git push origin or using an explicit URL: - .. code-block:: bash $ git push git@github.com:Pakketeretet2/lammps.git - ---------- - **Filing a pull request** Up to this point in the tutorial, all changes were to *your* clones of @@ -255,10 +236,8 @@ Now just write some nice comments and click on "Create pull request". .. image:: JPG/tutorial_create_new_pull_request2.png :align: center - ---------- - **After filing a pull request** .. note:: @@ -408,7 +387,6 @@ Because the changes are OK with us, we are going to merge by clicking on Now, since in the meantime our local text for the tutorial also changed, we need to pull Axel's change back into our branch, and merge them: - .. code-block:: bash $ git add Howto_github.txt @@ -425,7 +403,6 @@ With Axel's changes merged in and some final text updates, our feature branch is now perfect as far as we are concerned, so we are going to commit and push again: - .. code-block:: bash $ git add Howto_github.txt @@ -438,10 +415,8 @@ This merge also shows up on the lammps GitHub page: .. image:: JPG/tutorial_reverse_pull_request7.png :align: center - ---------- - **After a merge** When everything is fine, the feature branch is merged into the master branch: @@ -456,7 +431,6 @@ It is in principle safe to delete them from your own fork. This helps keep it a bit more tidy. Note that you first have to switch to another branch! - .. code-block:: bash $ git checkout master @@ -472,7 +446,6 @@ first delete and then pull, everything should still be fine. Finally, if you delete the branch locally, you might want to push this to your remote(s) as well: - .. code-block:: bash $ git push origin :github-tutorial-update diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst index b737f8317d..6b7fa6b54a 100644 --- a/doc/src/Howto_kappa.rst +++ b/doc/src/Howto_kappa.rst @@ -62,20 +62,14 @@ auto-correlation. See the doc page for the :doc:`compute heat/flux `_. diff --git a/doc/src/Howto_multiple.rst b/doc/src/Howto_multiple.rst index 42b58c041c..ec2729acf0 100644 --- a/doc/src/Howto_multiple.rst +++ b/doc/src/Howto_multiple.rst @@ -8,7 +8,6 @@ If "multiple simulations" means continue a previous simulation for more timesteps, then you simply use the :doc:`run ` command multiple times. For example, this script - .. code-block:: LAMMPS units lj @@ -27,7 +26,6 @@ If you wish to run totally different simulations, one after the other, the :doc:`clear ` command can be used in between them to re-initialize LAMMPS. For example, this script - .. code-block:: LAMMPS units lj @@ -48,7 +46,6 @@ For large numbers of independent simulations, you can use multiple times with different settings. For example, this script, named in.polymer - .. code-block:: LAMMPS variable d index run1 run2 run3 run4 run5 run6 run7 run8 @@ -65,7 +62,6 @@ file in each directory. The same concept could be used to run the same system at 8 different temperatures, using a temperature variable and storing the output in different log and dump files, for example - .. code-block:: LAMMPS variable a loop 8 diff --git a/doc/src/Howto_nemd.rst b/doc/src/Howto_nemd.rst index 1138315c1e..f2be8ca444 100644 --- a/doc/src/Howto_nemd.rst +++ b/doc/src/Howto_nemd.rst @@ -43,13 +43,9 @@ NEMD simulations can also be used to measure transport properties of a fluid through a pore or channel. Simulations of steady-state flow can be performed using the :doc:`fix flow/gauss ` command. - ---------- - .. _Daivis-nemd: - - **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 9030e6edf8..64a9e01971 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -12,7 +12,6 @@ There are four basic kinds of LAMMPS output: screen. * :doc:`Restart files `. - A simulation prints one set of thermodynamic output and (optionally) restart files. It can generate any number of dump files and fix output files, depending on what :doc:`dump ` and :doc:`fix ` diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index 5ee9892db9..e1694e2062 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -56,7 +56,6 @@ output support enabled. Step 1a: For the CMake based build system, the steps are: - .. code-block:: bash mkdir $LAMMPS_DIR/build-shared @@ -68,7 +67,6 @@ Step 1a: For the CMake based build system, the steps are: Step 1b: For the legacy, make based build system, the steps are: - .. code-block:: bash cd $LAMMPS_DIR/src @@ -85,7 +83,6 @@ Step 2: Installing the LAMMPS Python package PyLammps is part of the lammps Python package. To install it simply install that package into your current Python installation with: - .. code-block:: bash make install-python @@ -110,7 +107,6 @@ Benefits of using a virtualenv **Prerequisite (e.g. on Ubuntu)** - .. code-block:: bash apt-get install python-virtualenv @@ -118,7 +114,6 @@ Benefits of using a virtualenv Creating a virtualenv with lammps installed """"""""""""""""""""""""""""""""""""""""""" - .. code-block:: bash # create virtualenv named 'testing' @@ -132,7 +127,6 @@ When using CMake and the shared library has already been build, you need to re-run CMake to update the location of the python executable to the location in the virtual environment with: - .. code-block:: bash cmake . -DPYTHON_EXECUTABLE=$(which python) @@ -154,7 +148,6 @@ Creating a new instance of PyLammps To create a PyLammps object you need to first import the class from the lammps module. By using the default constructor, a new *lammps* instance is created. - .. code-block:: Python from lammps import PyLammps @@ -162,7 +155,6 @@ module. By using the default constructor, a new *lammps* instance is created. You can also initialize PyLammps on top of this existing *lammps* object: - .. code-block:: Python from lammps import lammps, PyLammps @@ -177,7 +169,6 @@ the command method of the lammps object instance. For instance, let's take the following LAMMPS command: - .. code-block:: LAMMPS region box block 0 10 0 5 -0.5 0.5 @@ -185,7 +176,6 @@ For instance, let's take the following LAMMPS command: In the original interface this command can be executed with the following Python code if *L* was a lammps instance: - .. code-block:: Python L.command("region box block 0 10 0 5 -0.5 0.5") @@ -193,7 +183,6 @@ Python code if *L* was a lammps instance: With the PyLammps interface, any command can be split up into arbitrary parts separated by white-space, passed as individual arguments to a region method. - .. code-block:: Python L.region("box block", 0, 10, 0, 5, -0.5, 0.5) @@ -206,7 +195,6 @@ The benefit of this approach is avoiding redundant command calls and easier parameterization. In the original interface parameterization needed to be done manually by creating formatted strings. - .. code-block:: Python L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) @@ -214,7 +202,6 @@ manually by creating formatted strings. In contrast, methods of PyLammps accept parameters directly and will convert them automatically to a final command string. - .. code-block:: Python L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) @@ -225,8 +212,6 @@ System state In addition to dispatching commands directly through the PyLammps object, it also provides several properties which allow you to query the system state. - - L.system Is a dictionary describing the system such as the bounding box or number of atoms @@ -260,8 +245,6 @@ L.dump L.groups List of groups present in the current system - - Working with LAMMPS variables ----------------------------- @@ -269,7 +252,6 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface. To define a variable you can use the :doc:`variable ` command: - .. code-block:: Python L.variable("a index 2") @@ -279,7 +261,6 @@ A dictionary of all variables is returned by L.variables you can access an individual variable by retrieving a variable object from the L.variables dictionary by name - .. code-block:: Python a = L.variables['a'] @@ -287,7 +268,6 @@ L.variables dictionary by name The variable value can then be easily read and written by accessing the value property of this object. - .. code-block:: Python print(a.value) @@ -300,7 +280,6 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The passed string parameter can be any expression containing global thermo values, variables, compute or fix data. - .. code-block:: Python result = L.eval("ke") # kinetic energy @@ -315,7 +294,6 @@ All atoms in the current simulation can be accessed by using the L.atoms list. Each element of this list is an object which exposes its properties (id, type, position, velocity, force, etc.). - .. code-block:: Python # access first atom @@ -329,7 +307,6 @@ position, velocity, force, etc.). Some properties can also be used to set: - .. code-block:: Python # set position in 2D simulation @@ -347,7 +324,6 @@ after a run via the L.runs list. This list contains a growing list of run data. The first element is the output of the first run, the second element that of the second run. - .. code-block:: Python L.run(1000) @@ -359,7 +335,6 @@ the second run. Each run contains a dictionary of all trajectories. Each trajectory is accessible through its thermo name: - .. code-block:: Python L.runs[0].thermo.Step # list of time steps in first run @@ -367,7 +342,6 @@ accessible through its thermo name: Together with matplotlib plotting data out of LAMMPS becomes simple: - .. code-block:: Python import matplotlib.plot as plt @@ -406,7 +380,6 @@ tutorials and showcasing your latest research. To launch an instance of Jupyter simply run the following command inside your Python environment (this assumes you followed the Quick Start instructions): - .. code-block:: bash jupyter notebook @@ -429,7 +402,6 @@ Four atoms are placed in the simulation and the dihedral potential is applied on them using a datafile. Then one of the atoms is rotated along the central axis by setting its position from Python, which changes the dihedral angle. - .. code-block:: Python phi = [d \* math.pi / 180 for d in range(360)] @@ -463,7 +435,6 @@ Initially, a 2D system is created in a state with minimal energy. It is then disordered by moving each atom by a random delta. - .. code-block:: Python random.seed(27848) @@ -483,7 +454,6 @@ It is then disordered by moving each atom by a random delta. Finally, the Monte Carlo algorithm is implemented in Python. It continuously moves random atoms by a random delta and only accepts certain moves. - .. code-block:: Python estart = L.eval("pe") @@ -536,7 +506,6 @@ Using PyLammps and mpi4py (Experimental) PyLammps can be run in parallel using mpi4py. This python package can be installed using - .. code-block:: bash pip install mpi4py @@ -544,7 +513,6 @@ PyLammps can be run in parallel using mpi4py. This python package can be install The following is a short example which reads in an existing LAMMPS input file and executes it in parallel. You can find in.melt in the examples/melt folder. - .. code-block:: Python from mpi4py import MPI @@ -561,7 +529,6 @@ executes it in parallel. You can find in.melt in the examples/melt folder. To run this script (melt.py) in parallel using 4 MPI processes we invoke the following mpirun command: - .. code-block:: bash mpirun -np 4 python melt.py diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index f9aca02dcd..e9fba37dcd 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -37,7 +37,6 @@ replica. The processors assigned to each replica are determined at run-time by using the :doc:`-partition command-line switch ` to launch LAMMPS on multiple partitions, which in this context are the same as replicas. E.g. these commands: - .. code-block:: bash mpirun -np 16 lmp_linux -partition 8x2 -in in.temper diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst index 484f09775b..bc7a7502ae 100644 --- a/doc/src/Howto_restart.rst +++ b/doc/src/Howto_restart.rst @@ -21,7 +21,6 @@ Look at the *in.chain* input script provided in the *bench* directory of the LAMMPS distribution to see the original script that these 2 scripts are based on. If that script had the line - .. code-block:: LAMMPS restart 50 tmp.restart @@ -32,7 +31,6 @@ and tmp.restart.100) as it ran. This script could be used to read the 1st restart file and re-run the last 50 timesteps: - .. code-block:: LAMMPS read_restart tmp.restart.50 @@ -62,14 +60,12 @@ uses random numbers in a way that does not allow for perfect restarts. As an alternate approach, the restart file could be converted to a data file as follows: - .. code-block:: LAMMPS lmp_g++ -r tmp.restart.50 tmp.restart.data Then, this script could be used to re-run the last 50 steps: - .. code-block:: LAMMPS units lj diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index e7ff0bef89..5431376924 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -40,13 +40,9 @@ the SPC and SPC/E models. Wikipedia also has a nice article on `water models `_. - ---------- - .. _howto-Berendsen: - - **(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987). diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 066329a985..886156c6cc 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -38,7 +38,6 @@ The dipole style does not actually define finite-size particles, but is often used in conjunction with spherical particles, via a command like - .. code-block:: LAMMPS atom_style hybrid sphere dipole diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst index 08939576e3..0afcc12c91 100644 --- a/doc/src/Howto_spins.rst +++ b/doc/src/Howto_spins.rst @@ -56,13 +56,9 @@ the magnetic energy. The second command is :doc:`compute property/atom ` comman :doc:`thermo_modify ` command to re-define what temperature compute is used for default thermodynamic output. - ---------- - .. _Daivis-thermostat: - - **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 7b36f7f742..1178aa8b67 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -51,26 +51,18 @@ details: Wikipedia also has a nice article on `water models `_. - ---------- - .. _howto-tip3p: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). .. _Jorgensen1: - - **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). .. _Price1: - - **(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004). diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index f814496128..f96fd15a17 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -99,13 +99,9 @@ and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long `_. - ---------- - .. _Jorgensen5: - - **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index ce3792a622..ffe71e36f6 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -200,7 +200,6 @@ an orthogonal bounding box which encloses the triclinic simulation box is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic box, formatted as follows: - .. parsed-literal:: ITEM: BOX BOUNDS xy xz yz @@ -212,7 +211,6 @@ This bounding box is convenient for many visualization programs and is calculated from the 9 triclinic box parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: - .. parsed-literal:: xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index 9e00c18732..dff414ce9d 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -62,7 +62,6 @@ simulation box. Here is an example input script that calculates the viscosity of liquid Ar via the GK formalism: - .. code-block:: LAMMPS # Sample LAMMPS input script for viscosity of liquid Ar @@ -131,13 +130,9 @@ time-integrated momentum fluxes play the role of Cartesian coordinates, whose mean-square displacement increases linearly with time at sufficiently long times. - ---------- - .. _Daivis-viscosity: - - **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index a5e83ce2c3..573aa13232 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -27,10 +27,6 @@ snapshots. .. _pizza: http://www.sandia.gov/~sjplimp/pizza.html - - .. _ensight: http://www.ensight.com - - .. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A diff --git a/doc/src/Install.rst b/doc/src/Install.rst index b2d72d61c8..03a1551686 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -8,7 +8,6 @@ have more flexibility as to what features to include or exclude in the build. If you plan to :doc:`modify or extend LAMMPS `, then you need the source code. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 238f53d5a3..8185d65e7c 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -16,7 +16,6 @@ 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:: As of October 2016, the official home of public LAMMPS development is @@ -35,7 +34,6 @@ You can follow LAMMPS development on 3 different git branches: To access the git repositories on your box, use the clone command to create a local copy of the LAMMPS repository with a command like: - .. code-block:: bash $ git clone -b unstable https://github.com/lammps/lammps.git mylammps @@ -57,7 +55,6 @@ LAMMPS, as listed on :doc:`this page `, you can stay up-to-date by typing the following git commands from within the "mylammps" directory: - .. code-block:: bash $ git checkout unstable # not needed if you always stay in this branch @@ -92,7 +89,6 @@ Once you have updated your local files with a "git pull" (or "git checkout"), you still need to re-build LAMMPS if any source files have changed. To do this, you should cd to the src directory and type: - .. code-block:: bash $ make purge # remove any deprecated src files diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index 03acf55734..0343ccf4f6 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -206,7 +206,6 @@ Gentoo Linux executable LAMMPS is part of Gentoo's main package tree and can be installed by typing: - .. code-block:: bash % emerge --ask lammps @@ -216,7 +215,6 @@ built on the your machine. Certain LAMMPS packages can be enable via USE flags, type - .. code-block:: bash % equery uses lammps diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index 82d77446c8..f1cee0dac5 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -10,7 +10,6 @@ GPU, KOKKOS, LATTE, MSCG, MESSAGE, MPIIO POEMS VORONOI. After installing Homebrew, you can install LAMMPS on your system with the following commands: - .. code-block:: bash % brew install lammps @@ -21,7 +20,6 @@ the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. Once LAMMPS is installed, you can test the installation with the Lennard-Jones benchmark file: - .. code-block:: bash % brew test lammps -v @@ -31,7 +29,6 @@ results in Homebrew also installing the `kim-api` binaries when LAMMPS is installed. In order to use potentials from `openkim.org `_, you can install the `openkim-models` package - .. code-block:: bash % brew install openkim-models @@ -44,5 +41,4 @@ If you have problems with the installation you can post issues to Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting up the Homebrew capability. - .. _openkim: https://openkim.org diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index 1b04d8ac93..79dd9b9f2d 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -52,7 +52,6 @@ the next patch release tarball. ---------- - If you download a current LAMMPS tarball, one way to stay current as new patch tarballs are released, is to download a patch file which you can apply to your local directory to update it for each new patch diff --git a/doc/src/Intro.rst b/doc/src/Intro.rst index cc4ae4c48f..6d388aa87e 100644 --- a/doc/src/Intro.rst +++ b/doc/src/Intro.rst @@ -3,7 +3,6 @@ Introduction These pages provide a brief introduction to LAMMPS. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 0b08dd5d52..c34dafe069 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -13,23 +13,18 @@ University: .. _sjp: http://www.cs.sandia.gov/~sjplimp .. _lws: http://lammps.sandia.gov - Past developers include Paul Crozier and Mark Stevens, both at Sandia, and Ray Shan, now at Materials Design. - ---------- - The `Authors page `_ of the `LAMMPS website `_ has a comprehensive list of all the individuals who have contributed code for a new feature or command or tool to LAMMPS. - ---------- - The following folks deserve special recognition. Many of the packages they have written are unique for an MD code and LAMMPS would not be as general-purpose as it is without their expertise and efforts. @@ -49,10 +44,8 @@ general-purpose as it is without their expertise and efforts. * Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD * Greg Wagner (Northwestern U), MEAM package for MEAM potential - ---------- - As discussed on the `History page `_ of the website, LAMMPS originated as a cooperative project between DOE labs and industrial partners. Folks involved in the design and testing of the original diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 7c25a6f09b..3ea1c88885 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -16,10 +16,8 @@ classes of functionality: 10. :ref:`Pre- and post-processing ` 11. :ref:`Specialized features (beyond MD itself) ` - ---------- - .. _general: General features @@ -191,12 +189,8 @@ Pre- and post-processing .. _pizza: http://www.sandia.gov/~sjplimp/pizza.html - - .. _python: http://www.python.org - - .. _special: Specialized features diff --git a/doc/src/Intro_opensource.rst b/doc/src/Intro_opensource.rst index ea06bd4814..2fd692c304 100644 --- a/doc/src/Intro_opensource.rst +++ b/doc/src/Intro_opensource.rst @@ -15,16 +15,10 @@ distribution. .. _gnu: http://www.gnu.org/copyleft/gpl.html - - .. _gnuorg: http://www.gnu.org - - .. _opensource: http://www.opensource.org - - Here is a summary of what the GPL means for LAMMPS users: (1) Anyone is free to use, modify, or extend LAMMPS in any way they diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst index b401a65ac9..dfb133a3e4 100644 --- a/doc/src/Manual_build.rst +++ b/doc/src/Manual_build.rst @@ -5,7 +5,6 @@ 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:: src # content files for LAMMPS documentation @@ -49,11 +48,9 @@ b. You can build the HTML or PDF files yourself, by typing "make html" ---------- - The generation of all documentation is managed by the Makefile in the doc directory. - .. code-block:: bash Documentation Build Options: @@ -74,7 +71,6 @@ the doc directory. ---------- - Installing prerequisites for HTML build ======================================= @@ -84,7 +80,6 @@ have to be installed. Here are instructions for common setups: Ubuntu ------ - .. code-block:: bash sudo apt-get install python-virtualenv @@ -92,7 +87,6 @@ Ubuntu Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) ------------------------------------------------------------------------------------ - .. code-block:: bash sudo yum install python3-virtualenv @@ -100,7 +94,6 @@ Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version Fedora (since version 22) ------------------------- - .. code-block:: bash sudo dnf install python3-virtualenv @@ -121,17 +114,14 @@ virtualenv Once Python 3 is installed, open a Terminal and type - .. code-block:: bash pip3 install virtualenv This will install virtualenv from the Python Package Index. - ---------- - Installing prerequisites for epub build ======================================= diff --git a/doc/src/Modify.rst b/doc/src/Modify.rst index 677e94b026..531fb6b1f3 100644 --- a/doc/src/Modify.rst +++ b/doc/src/Modify.rst @@ -10,7 +10,6 @@ If you add a new feature to LAMMPS and think it will be of interest to general users, we encourage you to submit it for inclusion in LAMMPS as a pull request on our `GitHub site `_, after reading the :doc:`Modify contribute ` doc page. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst index 5499a6d7be..14bcb08ee2 100644 --- a/doc/src/Modify_atom.rst +++ b/doc/src/Modify_atom.rst @@ -98,7 +98,6 @@ 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 useful in this context: - .. parsed-literal:: int index = atom->find_custom(char \*name, int &flag); @@ -109,7 +108,6 @@ 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:: int \*ivector = atom->ivector[index]; diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 4a1377bcf0..97eac24055 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -203,7 +203,6 @@ packages in the src directory for examples. If you are uncertain, please ask. usage. That kind of citation should just be in the doc page you provide. - Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst index 6b5b07e538..1bbcf8e120 100644 --- a/doc/src/Modify_overview.rst +++ b/doc/src/Modify_overview.rst @@ -31,14 +31,12 @@ 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 - .. code-block:: LAMMPS pair_style foo 0.1 3.5 then your pair\_foo.h file should be structured as follows: - .. code-block:: c++ #ifdef PAIR_CLASS @@ -103,5 +101,4 @@ functionality: .. _Foo: - **(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Modify_variable.rst b/doc/src/Modify_variable.rst index c1fe0440ff..ded76af9da 100644 --- a/doc/src/Modify_variable.rst +++ b/doc/src/Modify_variable.rst @@ -9,7 +9,6 @@ via the :doc:`print `, :doc:`fix print `, or "equal" can compute complex equations that involve the following types of arguments: - .. parsed-literal:: thermo keywords = ke, vol, atoms, ... diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index f8f5febaca..042485eb4b 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -11,7 +11,6 @@ distribution. The :doc:`Build package ` doc page gives general info on how to install and un-install packages as part of the LAMMPS build process. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 00103088a7..5ad6f16681 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -60,7 +60,6 @@ page gives those details. * :ref:`SRD ` * :ref:`VORONOI ` - .. table_from_list:: :columns: 6 @@ -106,10 +105,8 @@ page gives those details. * :ref:`USER-VTK ` * :ref:`USER-YAFF ` - ---------- - .. _PKG-ASPHERE: ASPHERE package @@ -133,10 +130,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * http://lammps.sandia.gov/movies.html#line * http://lammps.sandia.gov/movies.html#tri - ---------- - .. _PKG-BODY: BODY package @@ -158,10 +153,8 @@ overview. * :doc:`pair_style body/nparticle ` * examples/body - ---------- - .. _PKG-CLASS2: CLASS2 package @@ -181,10 +174,8 @@ CLASS2 molecular force field. * :doc:`improper_style class2 ` * :doc:`pair_style lj/class2 ` - ---------- - .. _PKG-COLLOID: COLLOID package @@ -213,10 +204,8 @@ Higdon's group at UIUC. * examples/colloid * examples/srd - ---------- - .. _PKG-COMPRESS: COMPRESS package @@ -246,10 +235,8 @@ This package has :ref:`specific installation instructions ` on the :do * :doc:`dump custom/gz ` * :doc:`dump xyz/gz ` - ---------- - .. _PKG-CORESHELL: CORESHELL package @@ -276,10 +263,8 @@ this package. * :doc:`pair_style lj/cut/coul/long/cs ` * examples/coreshell - ---------- - .. _PKG-DIPOLE: DIPOLE package @@ -299,10 +284,8 @@ short-range or long-range interactions. * :doc:`pair_style lj/long/dipole/long ` * examples/dipole - ---------- - .. _PKG-GPU: GPU package @@ -341,10 +324,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu for styles followed by (g) * `Benchmarks page `_ of web site - ---------- - .. _PKG-GRANULAR: GRANULAR package @@ -373,10 +354,8 @@ potentials. * http://lammps.sandia.gov/movies.html#brazil * http://lammps.sandia.gov/movies.html#granregion - ---------- - .. _PKG-KIM: KIM package @@ -430,10 +409,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * lib/kim/README * examples/kim - ---------- - .. _PKG-KOKKOS: KOKKOS package @@ -486,10 +463,8 @@ This package has :ref:`specific installation instructions ` on the :doc: :doc:`kspace `) for styles followed by (k) * `Benchmarks page `_ of web site - ---------- - .. _PKG-KSPACE: KSPACE package @@ -523,10 +498,8 @@ different FFT options for your LAMPMS build. * examples/peptide * bench/in.rhodo - ---------- - .. _PKG-LATTE: LATTE package @@ -544,8 +517,6 @@ description is given with the :doc:`fix latte ` command. .. _latte-home: https://github.com/lanl/LATTE - - **Authors:** Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre. @@ -563,10 +534,8 @@ This package has :ref:`specific installation instructions ` on the :doc:` * examples/latte * `LAMMPS-LATTE tutorial `_ - ---------- - .. _PKG-MANYBODY: MANYBODY package @@ -589,10 +558,8 @@ A variety of many-body and bond-order potentials. These include * examples/vashishta * bench/in.eam - ---------- - .. _PKG-MC: MC package @@ -616,10 +583,8 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`pair_style dsmc ` * http://lammps.sandia.gov/movies.html#gcmc - ---------- - .. _PKG-MESSAGE: MESSAGE package @@ -644,10 +609,8 @@ This package has :ref:`specific installation instructions ` on the :doc * :doc:`server mc ` * examples/message - ---------- - .. _PKG-MISC: MISC package @@ -678,10 +641,8 @@ listing, "ls src/MISC", to see the list of commands. * http://lammps.sandia.gov/pictures.html#ttm * http://lammps.sandia.gov/movies.html#evaporation - ---------- - .. _PKG-MOLECULE: MOLECULE package @@ -712,10 +673,8 @@ force fields, and a TIP4P water model. * bench/in.chain * bench/in.rhodo - ---------- - .. _PKG-MPIIO: MPIIO package @@ -736,10 +695,8 @@ written and read in parallel. * :doc:`write_restart ` * :doc:`read_restart ` - ---------- - .. _PKG-mscg: MSCG package @@ -752,8 +709,6 @@ Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library ` on the :doc:`B * lib/mscg/README * examples/mscg - ---------- - .. _PKG-OPT: OPT package @@ -808,10 +761,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * Search the :doc:`pair style ` page for styles followed by (t) * `Benchmarks page `_ of web site - ---------- - .. _PKG-PERI: PERI package @@ -841,10 +792,8 @@ Foster (UTSA). * examples/peri * http://lammps.sandia.gov/movies.html#peri - ---------- - .. _PKG-POEMS: POEMS package @@ -872,10 +821,8 @@ This package has :ref:`specific installation instructions ` on the :doc:` * :doc:`fix poems ` * examples/rigid - ---------- - .. _PKG-PYTHON: PYTHON package @@ -907,10 +854,8 @@ This package has :ref:`specific installation instructions ` on the :doc: * lib/python/README * examples/python - ---------- - .. _PKG-QEQ: QEQ package @@ -929,10 +874,8 @@ part of their formulation. * examples/qeq * examples/streitz - ---------- - .. _PKG-REPLICA: REPLICA package @@ -962,10 +905,8 @@ another set. * examples/prd * examples/tad - ---------- - .. _PKG-RIGID: RIGID package @@ -991,10 +932,8 @@ Also several computes which calculate properties of rigid bodies. * http://lammps.sandia.gov/movies.html#box * http://lammps.sandia.gov/movies.html#star - ---------- - .. _PKG-SHOCK: SHOCK package @@ -1015,10 +954,8 @@ a material. * examples/hugoniostat * examples/msst - ---------- - .. _PKG-SNAP: SNAP package @@ -1042,10 +979,8 @@ computes which analyze attributes of the potential. * :doc:`compute snav/atom ` * examples/snap - ---------- - .. _PKG-SPIN: SPIN package @@ -1074,10 +1009,8 @@ the usual manner via MD. Various pair, fix, and compute styles. * :doc:`neb/spin ` * examples/SPIN - ---------- - .. _PKG-SRD: SRD package @@ -1100,10 +1033,8 @@ colloidal particles. * http://lammps.sandia.gov/movies.html#line * http://lammps.sandia.gov/movies.html#poly - ---------- - .. _PKG-VORONOI: VORONOI package @@ -1118,8 +1049,6 @@ neighbors. .. _voro-home: http://math.lbl.gov/voro++ - - To use this package you must have the Voro++ library available on your system. @@ -1139,10 +1068,8 @@ This package has :ref:`specific installation instructions ` on the :doc * :doc:`compute voronoi/atom ` * examples/voronoi - ---------- - .. _PKG-USER-ADIOS: USER-ADIOS package @@ -1171,11 +1098,8 @@ This package has :ref:`specific installation instructions ` on the : * :doc:`dump custom/adios ` * :doc:`read_dump ` - - ---------- - .. _PKG-USER-ATC: USER-ATC package @@ -1201,10 +1125,8 @@ This package has :ref:`specific installation instructions ` on the :do * examples/USER/atc * http://lammps.sandia.gov/pictures.html#atc - ---------- - .. _PKG-USER-AWPMD: USER-AWPMD package @@ -1230,10 +1152,8 @@ This package has :ref:`specific installation instructions ` on the : * :doc:`pair_style awpmd/cut ` * examples/USER/awpmd - ---------- - .. _PKG-USER-BOCS: USER-BOCS package @@ -1265,10 +1185,8 @@ J. Phys. Chem. B. 122, 13, 3363-3377 (2018). Example inputs are in the examples/USER/bocs folder. - ---------- - .. _PKG-USER-CGDNA: USER-CGDNA package @@ -1295,10 +1213,8 @@ rigid-body integrators with improved stability. * :doc:`bond_style oxrna2/\* ` * :doc:`fix nve/dotc/langevin ` - ---------- - .. _PKG-USER-CGSDK: USER-CGSDK package @@ -1322,10 +1238,8 @@ acids. * examples/USER/cgsdk * http://lammps.sandia.gov/pictures.html#cg - ---------- - .. _PKG-USER-COLVARS: USER-COLVARS package @@ -1359,10 +1273,8 @@ This package has :ref:`specific installation instructions ` on the * :doc:`fix colvars ` * examples/USER/colvars - ---------- - .. _PKG-USER-PLUMED: USER-PLUMED package @@ -1381,8 +1293,6 @@ Tribello. .. _PLUMED: http://www.plumed.org - - **Install:** This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` doc page. @@ -1394,10 +1304,8 @@ This package has :ref:`specific installation instructions ` on the * :doc:`fix plumed ` * examples/USER/plumed - ---------- - .. _PKG-USER-DIFFRACTION: USER-DIFFRACTION package @@ -1418,10 +1326,8 @@ intensities based on kinematic diffraction theory. * :doc:`fix saed/vtk ` * examples/USER/diffraction - ---------- - .. _PKG-USER-DPD: USER-DPD package @@ -1461,10 +1367,8 @@ Brennan (ARL). * :doc:`pair_style multi/lucy/rx ` * examples/USER/dpd - ---------- - .. _PKG-USER-DRUDE: USER-DRUDE package @@ -1495,10 +1399,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal). * examples/USER/drude * tools/drude - ---------- - .. _PKG-USER-EFF: USER-EFF package @@ -1533,10 +1435,8 @@ tools/eff; see its README file. * tools/eff * http://lammps.sandia.gov/movies.html#eff - ---------- - .. _PKG-USER-FEP: USER-FEP package @@ -1562,10 +1462,8 @@ for using this package in tools/fep; see its README file. * tools/fep/README * tools/fep - ---------- - .. _PKG-USER-H5MD: USER-H5MD package @@ -1581,8 +1479,6 @@ LAMMPS snapshots in this format. .. _HDF5: http://www.hdfgroup.org/HDF5 - - To use this package you must have the HDF5 library available on your system. @@ -1600,10 +1496,8 @@ This package has :ref:`specific installation instructions ` on the :d * lib/h5md/README * :doc:`dump h5md ` - ---------- - .. _PKG-USER-INTEL: USER-INTEL package @@ -1649,10 +1543,8 @@ This package has :ref:`specific installation instructions ` on the : * src/USER-INTEL/TEST * `Benchmarks page `_ of web site - ---------- - .. _PKG-USER-LB: USER-LB package @@ -1675,10 +1567,8 @@ Ontario). * :doc:`fix lb/viscous ` * examples/USER/lb - ---------- - .. _PKG-USER-MGPT: USER-MGPT package @@ -1704,10 +1594,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. * :doc:`pair_style mgpt ` * examples/USER/mgpt - ---------- - .. _PKG-USER-MISC: USER-MISC package @@ -1729,10 +1617,8 @@ src/USER-MISC/README file. * one doc page per individual command listed in src/USER-MISC/README * examples/USER/misc - ---------- - .. _PKG-USER-MANIFOLD: USER-MANIFOLD package @@ -1762,10 +1648,8 @@ Waltham, MA, USA) * examples/USER/manifold * http://lammps.sandia.gov/movies.html#manifold - ---------- - .. _PKG-USER-MEAMC: USER-MEAMC package @@ -1789,10 +1673,8 @@ Sandia. * :doc:`pair_style meam/c ` * examples/meamc - ---------- - .. _PKG-USER-MESODPD: USER-MESODPD package @@ -1822,10 +1704,8 @@ algorithm. * examples/USER/mesodpd * http://lammps.sandia.gov/movies.html#mesodpd - ---------- - .. _PKG-USER-MOFFF: USER-MOFFF package @@ -1844,8 +1724,6 @@ well as the `MOF+ `_ website. .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF - - **Author:** Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum). @@ -1859,10 +1737,8 @@ Rochus Schmid (Ruhr-University Bochum). * :doc:`improper_style inversion/harmonic ` * examples/USER/mofff - ---------- - .. _PKG-USER-MOLFILE: USER-MOLFILE package @@ -1903,10 +1779,8 @@ This package has :ref:`specific installation instructions ` on the * lib/molfile/README * :doc:`dump molfile ` - ---------- - .. _PKG-USER-NETCDF: USER-NETCDF package @@ -1931,16 +1805,10 @@ tools: .. _ovito: http://www.ovito.org - - .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ - - .. _atomeye: http://www.libatoms.org - - **Author:** Lars Pastewka (Karlsruhe Institute of Technology). **Install:** @@ -1954,10 +1822,8 @@ This package has :ref:`specific installation instructions ` on the * lib/netcdf/README * :doc:`dump netcdf ` - ---------- - .. _PKG-USER-OMP: USER-OMP package @@ -2010,10 +1876,8 @@ This package has :ref:`specific installation instructions ` on the :do :doc:`kspace `) for styles followed by (o) * `Benchmarks page `_ of web site - ---------- - .. _PKG-USER-PHONON: USER-PHONON package @@ -2040,10 +1904,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" * :doc:`third_order ` * examples/USER/phonon - ---------- - .. _PKG-USER-PTM: USER-PTM package @@ -2064,10 +1926,8 @@ Matching methodology. * src/USER-PTM/LICENSE * :doc:`compute ptm/atom ` - ---------- - .. _PKG-USER-QMMM: USER-QMMM package @@ -2097,7 +1957,6 @@ changes to LAMMPS itself. **Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) - **Install:** This package has :ref:`specific installation instructions ` @@ -2112,10 +1971,8 @@ on the :doc:`Build extras ` doc page. * lib/qmmm/example-ec/README * lib/qmmm/example-mc/README - ---------- - .. _PKG-USER-QTB: USER-QTB package @@ -2142,10 +1999,8 @@ simulation. * :doc:`fix qbmsst ` * examples/USER/qtb - ---------- - .. _PKG-USER-QUIP: USER-QUIP package @@ -2159,8 +2014,6 @@ developed by the Cambridge University group. .. _quip: https://github.com/libAtoms/QUIP - - To use this package you must have the QUIP libAtoms library available on your system. @@ -2177,10 +2030,8 @@ This package has :ref:`specific installation instructions ` on the :d * :doc:`pair_style quip ` * examples/USER/quip - ---------- - .. _PKG-USER-REACTION: USER-REACTION package @@ -2210,10 +2061,8 @@ molecules, and chiral-sensitive reactions. * `2019 LAMMPS Workshop `_ * disarmmd.org - ---------- - .. _PKG-USER-REAXC: USER-REAXC package @@ -2237,10 +2086,8 @@ for monitoring molecules as bonds are created and destroyed. * :doc:`fix reax/c/species ` * examples/reax - ---------- - .. _PKG-USER-SCAFACOS: USER-SCAFACOS package @@ -2274,10 +2121,8 @@ This package has :ref:`specific installation instructions ` on th * :doc:`kspace_modify ` * examples/USER/scafacos - ---------- - .. _PKG-USER-SDPD: USER-SDPD package @@ -2304,10 +2149,8 @@ Sciences, Iran). * :doc:`fix rigid/meso ` * examples/USER/sdpd - ---------- - .. _PKG-USER-SMD: USER-SMD package @@ -2344,10 +2187,8 @@ This package has :ref:`specific installation instructions ` on the :do * examples/USER/smd * http://lammps.sandia.gov/movies.html#smd - ---------- - .. _PKG-USER-SMTBQ: USER-SMTBQ package @@ -2369,10 +2210,8 @@ Tetot (LAAS-CNRS, France). * :doc:`pair_style smtbq ` * examples/USER/smtbq - ---------- - .. _PKG-USER-SPH: USER-SPH package @@ -2405,10 +2244,8 @@ Dynamics, Ernst Mach Institute, Germany). * examples/USER/sph * http://lammps.sandia.gov/movies.html#sph - ---------- - .. _PKG-USER-TALLY: USER-TALLY package @@ -2429,10 +2266,8 @@ stress, etc) about individual interactions. * :doc:`compute \*/tally ` * examples/USER/tally - ---------- - .. _PKG-USER-UEF: USER-UEF package @@ -2457,10 +2292,8 @@ supporting compute styles and an output option. * :doc:`dump cfg/uef ` * examples/uef - ---------- - .. _PKG-USER-VTK: USER-VTK package @@ -2474,12 +2307,8 @@ other visualization packages. .. _vtk: http://www.vtk.org - - .. _paraview: http://www.paraview.org - - To use this package you must have VTK library available on your system. @@ -2496,10 +2325,8 @@ This package has :ref:`specific installation instructions ` on the :do * lib/vtk/README * :doc:`dump vtk ` - ---------- - .. _PKG-USER-YAFF: USER-YAFF package diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 155d4e0462..33f73933df 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -59,7 +59,6 @@ new potential. To use any of these commands, you only need to build LAMMPS with the PYTHON package installed: - .. parsed-literal:: make yes-python diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 59525d57be..f26a23dd35 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -27,10 +27,8 @@ distribution. | combination of viz\_tool.py and plot.py and gui.py | | +----------------------------------------------------------------+--------------------------------------------------+ - ---------- - 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. @@ -40,13 +38,10 @@ which is included in the pizza sub-directory. See the `Pizza.py doc pages `_ or `here `_ for more details: - .. parsed-literal:: http://mt.seas.upenn.edu/Archive/Graphics/A @@ -54,12 +49,8 @@ AtomEye WWW pages `here `_ or `here `_ for more details: .. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A - - .. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html - - The latter link is to AtomEye 3 which has the scripting capability needed by these Python scripts. @@ -68,7 +59,6 @@ open-source version of PyMol in your Python, so that you can import it from a Python script. See the PyMol WWW pages `here `_ or `here `_ for more details: - .. parsed-literal:: http://www.pymol.org @@ -76,22 +66,16 @@ from a Python script. See the PyMol WWW pages `here `_ or .. _pymolhome: http://www.pymol.org - - .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 - - The latter link is to the open-source version. Note that for VMD, you need a fairly current version (1.8.7 works for me) and there are some lines in the pizza/vmd.py script for 4 PIZZA 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. diff --git a/doc/src/Python_head.rst b/doc/src/Python_head.rst index ce514629ae..0a58ecdde1 100644 --- a/doc/src/Python_head.rst +++ b/doc/src/Python_head.rst @@ -4,7 +4,6 @@ Use Python with LAMMPS These doc pages describe various ways that LAMMPS and Python can be used together. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 8a03dd7249..04e3660c52 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -31,7 +31,6 @@ 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:: setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python @@ -49,7 +48,6 @@ files are updated with the new version. If the default settings of "make install-python" are not what you want, you can invoke install.py from the python directory manually as - .. parsed-literal:: % python install.py -m \ -l -v [-d \] diff --git a/doc/src/Python_library.rst b/doc/src/Python_library.rst index d4acd07257..0d3767170f 100644 --- a/doc/src/Python_library.rst +++ b/doc/src/Python_library.rst @@ -8,7 +8,6 @@ methods that can be invoked on that object. The sample Python code below assumes you have first imported the "lammps" module in your Python script, as follows: - .. code-block:: Python from lammps import lammps @@ -22,7 +21,6 @@ from a C++ or C or Fortran program, and which are described on the The python/examples directory has Python scripts which show how Python can run LAMMPS, grab data, change it, and put it back into LAMMPS. - .. code-block:: Python lmp = lammps() # create a LAMMPS object using the default liblammps.so library @@ -93,13 +91,10 @@ can run LAMMPS, grab data, change it, and put it back into LAMMPS. lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags - ---------- - The lines - .. code-block:: Python from lammps import lammps @@ -116,7 +111,6 @@ prompt. If the ptr argument is set like this: - .. code-block:: Python lmp = lammps(ptr=lmpptr) @@ -133,7 +127,6 @@ instance "lmp" to make calls to that instance of LAMMPS. See the Note that you can create multiple LAMMPS objects in your Python script, and coordinate and run multiple simulations, e.g. - .. code-block:: Python from lammps import lammps @@ -229,7 +222,6 @@ For the scatter methods, the array of coordinates passed to must be a ctypes vector of ints or doubles, allocated and initialized something like this: - .. code-block:: Python from ctypes import \* @@ -247,10 +239,8 @@ like this: Alternatively, you can just change values in the vector returned by the gather methods, since they are also ctypes vectors. - ---------- - As noted above, these Python class methods correspond one-to-one with the functions in the LAMMPS library interface in src/library.cpp and library.h. This means you can extend the Python wrapper via the @@ -264,7 +254,6 @@ following steps: * You should now be able to invoke the new interface function from a Python script. - ---------- .. autoclass:: lammps.lammps diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst index d1c9ab0ca0..659d5c57fd 100644 --- a/doc/src/Python_mpi.rst +++ b/doc/src/Python_mpi.rst @@ -18,7 +18,6 @@ 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:: python setup.py build @@ -28,7 +27,6 @@ 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:: python setup.py install --user @@ -36,7 +34,6 @@ user privilege into the user local directory type If you have successfully installed mpi4py, you should be able to run Python and type - .. parsed-literal:: from mpi4py import MPI @@ -44,14 +41,12 @@ Python and type without error. You should also be able to run python in parallel on a simple test script - .. parsed-literal:: % mpirun -np 4 python test.py where test.py contains the lines - .. parsed-literal:: from mpi4py import MPI diff --git a/doc/src/Python_shlib.rst b/doc/src/Python_shlib.rst index 0289b7acc4..b9d8e50242 100644 --- a/doc/src/Python_shlib.rst +++ b/doc/src/Python_shlib.rst @@ -12,7 +12,6 @@ wrap LAMMPS. On Linux this is a library file that ends in ".so", not From the src directory, type - .. parsed-literal:: make foo mode=shlib @@ -38,7 +37,6 @@ 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:: -D BUILD_LIB=on # enable building LAMMPS as a library @@ -52,7 +50,6 @@ 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. - .. parsed-literal:: # create virtualenv @@ -72,7 +69,6 @@ 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 it, which contains the installed liblammps.so. - .. parsed-literal:: export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH diff --git a/doc/src/Python_test.rst b/doc/src/Python_test.rst index 13d0a1ab27..1877a12bca 100644 --- a/doc/src/Python_test.rst +++ b/doc/src/Python_test.rst @@ -4,7 +4,6 @@ Test the Python/LAMMPS interface To test if LAMMPS is callable from Python, launch Python interactively and type: - .. parsed-literal:: >>> from lammps import lammps @@ -13,7 +12,6 @@ and type: If you get no errors, you're ready to use LAMMPS from Python. If the 2nd command fails, the most common error to see is - .. parsed-literal:: OSError: Could not load LAMMPS dynamic library @@ -27,7 +25,6 @@ should give you an indication of what went wrong. You can also test the load directly in Python as follows, without first importing from the lammps.py file: - .. parsed-literal:: >>> from ctypes import CDLL @@ -44,7 +41,6 @@ Test LAMMPS and Python in serial: To run a LAMMPS test in serial, type these lines into Python interactively from the bench directory: - .. parsed-literal:: >>> from lammps import lammps @@ -53,7 +49,6 @@ interactively from the bench directory: Or put the same lines in the file test.py and run it as - .. parsed-literal:: % python test.py @@ -62,7 +57,6 @@ Either way, you should see the results of running the in.lj benchmark on a single processor appear on the screen, the same as if you had typed something like: - .. parsed-literal:: lmp_g++ -in in.lj @@ -74,7 +68,6 @@ 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:: import pypar @@ -88,7 +81,6 @@ 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:: from mpi4py import MPI @@ -102,14 +94,12 @@ above, create a test.py file containing these lines: You can either script in parallel as: - .. parsed-literal:: % mpirun -np 4 python test.py and you should see the same output as if you had typed - .. parsed-literal:: % mpirun -np 4 lmp_g++ -in in.lj @@ -134,7 +124,6 @@ Running Python scripts: Note that any Python script (not just for LAMMPS) can be invoked in one of several ways: - .. parsed-literal:: % python foo.script @@ -144,7 +133,6 @@ one of several ways: The last command requires that the first line of the script be something like this: - .. parsed-literal:: #!/usr/local/bin/python @@ -153,7 +141,6 @@ something like this: where the path points to where you have Python installed, and that you have made the script file executable: - .. parsed-literal:: % chmod +x foo.script diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 53acb9096f..e90ccc09f7 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -5,7 +5,6 @@ LAMMPS is run from the command line, reading commands from a file via the -in command line flag, or from standard input. Using the "-in in.file" variant is recommended: - .. code-block:: bash $ lmp_serial -in in.file @@ -68,7 +67,6 @@ 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: - .. code-block:: bash $ export OMP_NUM_THREADS=2 # bash @@ -80,10 +78,8 @@ package command. See the :doc:`package ` command or :doc:`Speed ` doc pages for more details about which accelerator packages and which commands support multi-threading. - ---------- - You can experiment with running LAMMPS using any of the input scripts provided in the examples or bench directory. Input scripts are named in.\* and sample outputs are named log.\*.P where P is the number of diff --git a/doc/src/Run_head.rst b/doc/src/Run_head.rst index bdc122e3f7..5da5942d9b 100644 --- a/doc/src/Run_head.rst +++ b/doc/src/Run_head.rst @@ -6,7 +6,6 @@ and :doc:`built an executable `. The :doc:`Commands ` doc page describes how input scripts are structured and the commands they can contain. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 6c1a2e1ed5..382381d432 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -25,16 +25,13 @@ letter abbreviation can be used: For example, the lmp\_mpi executable might be launched as follows: - .. code-block:: bash $ mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy $ mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy - ---------- - .. _echo: **-echo style** @@ -46,10 +43,8 @@ can be useful to figure out which line of your script is causing an input error. The default value is *log*\ . The echo style can also be set by using the :doc:`echo ` command in the input script itself. - ---------- - .. _help: **-help** @@ -61,10 +56,8 @@ 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. - ---------- - .. _file: **-in file** @@ -79,10 +72,8 @@ Note that this is a required switch when running LAMMPS in multi-partition mode, since multiple processors cannot all read from stdin. - ---------- - .. _run-kokkos: **-kokkos on/off keyword/value ...** @@ -114,7 +105,6 @@ settings to use on different platforms is given on the :doc:`Speed kokkos ` command in the input script will override this setting. Option -plog will override the name of the partition log files file.N. - ---------- - .. _mpicolor: **-mpicolor** color @@ -232,10 +214,8 @@ by the :doc:`message ` command and the CSlib library LAMMPS links with from the lib/message directory. See the :doc:`message ` command for more details. - ---------- - .. _nocite: **-nocite** @@ -245,10 +225,8 @@ references for specific cite-able features used during a LAMMPS run. See the `citation page `_ for more details. - ---------- - .. _package: **-package style args ....** @@ -265,10 +243,8 @@ Along with the "-suffix" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. - ---------- - .. _partition: **-partition 8x2 4 5 ...** @@ -296,10 +272,8 @@ multiple partitions, see the :doc:`Howto multiple ` doc page. World- and universe-style :doc:`variables ` are useful in this context. - ---------- - .. _plog: **-plog file** @@ -314,10 +288,8 @@ 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. - ---------- - .. _pscreen: **-pscreen file** @@ -332,17 +304,14 @@ 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. - ---------- - .. _reorder: **-reorder** This option has 2 forms: - .. parsed-literal:: -reorder nth N @@ -371,21 +340,18 @@ This can boost performance. For example, if you use "-reorder nth 4" and "-partition 9 3" and you are running on 12 processors, the processors will be reordered from - .. parsed-literal:: 0 1 2 3 4 5 6 7 8 9 10 11 to - .. parsed-literal:: 0 1 2 4 5 6 8 9 10 3 7 11 so that the processors in each partition will be - .. parsed-literal:: 0 1 2 4 5 6 8 9 10 @@ -400,7 +366,6 @@ file is as follows. Any number of initial blank or comment lines (starting with a "#" character) can be present. These should be followed by P lines of the form: - .. parsed-literal:: I J @@ -424,20 +389,16 @@ itself. See the :doc:`processors out ` command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. - ---------- - .. _restart2data: **-restart2data restartfile [remap] datafile keyword value ...** - Convert the restart file into a data file and immediately exit. This is the same operation as if the following 2-line input script were run: - .. code-block:: LAMMPS read_restart restartfile [remap] @@ -461,7 +422,6 @@ should allow the data file to still be produced. The syntax following restartfile (or remap), namely - .. parsed-literal:: datafile keyword value ... @@ -470,10 +430,8 @@ is identical to the arguments of the :doc:`write_data ` command. See its doc page for details. This includes its optional keyword/value settings. - ---------- - .. _restart2dump: **-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** @@ -482,7 +440,6 @@ Convert the restart file into a dump file and immediately exit. This is the same operation as if the following 2-line input script were run: - .. code-block:: LAMMPS read_restart restartfile [remap] @@ -517,10 +474,8 @@ 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. - ---------- - .. _screen: **-screen file** @@ -538,10 +493,8 @@ multi-partition mode, if the specified file is "none", then no screen output is performed. Option -pscreen will override the name of the partition screen files file.N. - ---------- - .. _suffix: **-suffix style args** @@ -607,10 +560,8 @@ The :doc:`suffix ` command can also be used within an input script to set a suffix, or to turn off or back on any suffix setting made via the command line. - ---------- - .. _var: **-var name value1 value2 ...** diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index a75513b2c5..4aeaf36707 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -14,7 +14,6 @@ thermodynamic state and a total run time for the simulation. It also appends statistics about the CPU time and storage requirements for the simulation. An example set of statistics is shown here: - .. parsed-literal:: Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms @@ -47,10 +46,8 @@ simulation. An example set of statistics is shown here: Neighbor list builds = 26 Dangerous builds = 0 - ---------- - The first section provides a global loop timing summary. The *loop time* is the total wall-clock time for the simulation to run. The *Performance* line is provided for convenience to help predict how @@ -60,10 +57,8 @@ line provides the CPU utilization per MPI task; it should be close to Lower numbers correspond to delays due to file I/O or insufficient thread utilization. - ---------- - The *MPI task* section gives the breakdown of the CPU run time (in seconds) into major categories: @@ -96,7 +91,6 @@ only and thus, because the breakdown for MPI tasks can change from MPI rank to MPI rank, this breakdown can be very different for individual ranks. Here is an example output for this section: - .. parsed-literal:: Thread timings breakdown (MPI rank 0): @@ -109,20 +103,16 @@ individual ranks. Here is an example output for this section: Neigh \| 0.084778 \| 0.086969 \| 0.089161 \| 0.7 \| 12.70 Reduce \| 0.0036485 \| 0.003737 \| 0.0038254 \| 0.1 \| 0.55 - ---------- - The third section above lists the number of owned atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored per processor. The max and min values give the spread of these values across processors with a 10-bin histogram showing the distribution. The total number of histogram counts is equal to the number of processors. - ---------- - The last section gives aggregate statistics (across all processors) for pair-wise neighbors and special neighbors that LAMMPS keeps track of (see the :doc:`special_bonds ` command). The number @@ -135,15 +125,12 @@ non-zero you may wish to reduce the delay factor to insure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place. - ---------- - If an energy minimization was performed via the :doc:`minimize ` command, additional information is printed, e.g. - .. parsed-literal:: Minimization stats: @@ -167,15 +154,12 @@ Multiple force evaluations are typically done at each iteration to perform a 1d line minimization in the search direction. See the :doc:`minimize ` doc page for more details. - ---------- - If a :doc:`kspace_style ` long-range Coulombics solver that performs FFTs was used during the run (PPPM, Ewald), then additional information is printed, e.g. - .. parsed-literal:: FFT time (% of Kspce) = 0.200313 (8.34477) diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index af7ade1ac7..65b299421e 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -14,15 +14,12 @@ 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:: lmp_serial -in in.lj -pk omp 4 -sf omp - ---------- - For the MPI executable, which allows you to run LAMMPS under Windows in parallel, follow these steps. @@ -46,7 +43,6 @@ into the MPICH2 installation directory, then into the sub-directory Then type something like this: - .. parsed-literal:: mpiexec -localonly 4 lmp_mpi -in in.file @@ -62,7 +58,6 @@ patient before the output shows up. The parallel executable can also run on a single processor by typing something like this: - .. parsed-literal:: lmp_mpi -in in.lj @@ -70,7 +65,6 @@ something like this: Note that the parallel executable also includes OpenMP multi-threading, which can be combined with MPI using something like: - .. parsed-literal:: mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index a5b3d36a25..a409772655 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -19,7 +19,6 @@ page, for several of the standard LAMMPS benchmark problems, as a function of problem size and number of compute nodes, on different hardware platforms. - .. toctree:: :maxdepth: 1 diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index c577bc426a..c67842bcc0 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -26,7 +26,6 @@ The 5 standard problems are as follow: particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT integration - Input files for these 5 problems are provided in the bench directory of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 timesteps. The size of the problem (number of atoms) can be varied @@ -53,10 +52,8 @@ of the Benchmarks web page has performance data for very large benchmark runs of simple Lennard-Jones (LJ) models, which use the bench/in.lj input script. - ---------- - For all the benchmarks, a useful metric is the CPU cost per atom per timestep. Since performance scales roughly linearly with problem size and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index f6795e202a..8adcce52ef 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -77,7 +77,6 @@ section below for examples where this has been done. to unlock this potential, an Intel compiler is required. The package code will compile with GNU gcc, but it will not be as efficient. - **Differences between the GPU and KOKKOS packages:** * The GPU package accelerates only pair force, neighbor list, and (parts diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 9492d1466a..618b135620 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -27,7 +27,6 @@ It has the following general features: NVIDIA support as well as more general OpenCL support, so that the same functionality is supported on a variety of hardware. - **Required hardware/software:** To compile and use this package in CUDA mode, you currently need @@ -77,7 +76,6 @@ 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:: lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU @@ -108,7 +106,6 @@ 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:: pair_style lj/cut/gpu 2.5 @@ -172,9 +169,7 @@ results, since they will typically be faster. This is the maximum memory used at one time on the GPU for data storage by a single MPI process. - Restrictions """""""""""" - None. diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 86afd8d2ed..956e03cb87 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -25,7 +25,6 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously. rebo, sw, tersoff * K-Space Styles: pppm, pppm/disp - .. warning:: None of the styles in the USER-INTEL package currently @@ -58,10 +57,8 @@ Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio *src/USER-INTEL/TEST/README* for the raw simulation rates and instructions to reproduce. - ---------- - **Accuracy and order of operations:** In most molecular dynamics software, parallelization parameters @@ -88,7 +85,6 @@ order of operations compared to LAMMPS without acceleration: Twister generator included in the Intel MKL library (that should be more robust than the default Masaglia random number generator) - The precision mode (described below) used with the USER-INTEL package can change the *accuracy* of the calculations. For the default *mixed* precision option, calculations between pairs or @@ -98,10 +94,8 @@ is performed in double precision to prevent the error from growing with the number of atoms in the simulation. *Single* precision mode should not be used without appropriate validation. - ---------- - **Quick Start for Experienced Users:** LAMMPS should be built with the USER-INTEL package installed. @@ -120,12 +114,10 @@ not *hardware thread*\ . * 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 AVX-512: @@ -136,18 +128,14 @@ AVX-512: * 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 * "-pk intel N omp 1" added to command-line where N is the number of co-processors per node. - - ---------- - **Required hardware/software:** In order to use offload to co-processors, an Intel Xeon Phi @@ -204,7 +192,6 @@ will report every hardware thread as a separate core allowing one to determine the number of hardware threads available. On Linux systems, this information can normally be obtained with: - .. parsed-literal:: cat /proc/cpuinfo @@ -218,7 +205,6 @@ 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:: Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload @@ -233,7 +219,6 @@ Phi x200 processors making it easier to cross-compile. For users with recent installations of Intel Parallel Studio, the process can be as simple as: - .. parsed-literal:: make yes-user-intel @@ -349,7 +334,6 @@ desired. Examples (see documentation for your MPI/Machine for differences in launching MPI applications): - .. parsed-literal:: mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads @@ -362,7 +346,6 @@ can be edited to enable the USER-INTEL package. This requires adding the :doc:`package intel ` command to the top of the input script. For the second example above, this would be: - .. parsed-literal:: package intel 0 omp 2 mode double @@ -370,7 +353,6 @@ script. For the second example above, this would be: To enable the USER-INTEL package only for individual styles, you can add an "intel" suffix to the individual style, e.g.: - .. parsed-literal:: pair_style lj/cut/intel 2.5 @@ -527,7 +509,6 @@ MPI task. Restrictions """""""""""" - 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 diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 700ef91998..2a1e451d28 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -71,7 +71,6 @@ Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and Here is a quick overview of how to use the KOKKOS package for CPU acceleration, assuming one or more 16-core nodes. - .. parsed-literal:: mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading @@ -85,7 +84,6 @@ command. You must use the "-k on" :doc:`command-line switch ` to e additional arguments for hardware settings appropriate to your system. For OpenMP use: - .. parsed-literal:: -k on t Nt @@ -121,7 +119,6 @@ below. page for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: - .. parsed-literal:: mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm @@ -154,7 +151,6 @@ they do not migrate during a simulation. If you are not certain MPI tasks are being bound (check the defaults for your MPI installation), binding can be forced with these flags: - .. parsed-literal:: OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ... @@ -184,7 +180,6 @@ tasks. Examples of mpirun commands that follow these rules are shown below. - .. parsed-literal:: Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): @@ -210,7 +205,6 @@ threads/task as Nt. The product of these two values should be N, i.e. details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: - .. parsed-literal:: mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm @@ -245,7 +239,6 @@ avoided by using :doc:`-pk kokkos cuda/aware no `. As above for multi-core CPUs (and no GPU), if N is the number of physical cores/node, then the number of MPI tasks/node should not exceed N. - .. parsed-literal:: -k on g Ng @@ -253,7 +246,6 @@ then the number of MPI tasks/node should not exceed N. Here are examples of how to use the KOKKOS package for GPUs, assuming one or more nodes, each with two GPUs: - .. parsed-literal:: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node @@ -274,7 +266,6 @@ one or more nodes, each with two GPUs: default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: - .. parsed-literal:: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff @@ -317,7 +308,6 @@ hardware options appropriate to your system, as documented above. You can use the :doc:`suffix kk ` command, or you can explicitly add a "kk" suffix to individual styles in your input script, e.g. - .. parsed-literal:: pair_style lj/cut/kk 2.5 @@ -333,7 +323,6 @@ 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 - .. parsed-literal:: KOKKOS_DEVICES=Cuda,OpenMP @@ -345,14 +334,12 @@ style in the input script, the Kokkos OpenMP (CPU) version of that specific style will be used instead. Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng" - .. parsed-literal:: -k on t Nt g Ng For example, the command to run with 1 GPU and 8 OpenMP threads is then: - .. parsed-literal:: mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk @@ -394,7 +381,6 @@ Generally speaking, the following rules of thumb apply: * When running on Intel hardware, KOKKOS is not as fast as the USER-INTEL package, which is optimized for that hardware. - See the `Benchmark page `_ of the LAMMPS web site for performance of the KOKKOS package on different hardware. @@ -441,6 +427,5 @@ GPUs. Restrictions """""""""""" - Currently, there are no precision options with the KOKKOS package. All compilation and computation is performed in double precision. diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 44233902a7..812d774867 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -23,7 +23,6 @@ instructions. These examples assume one or more 16-core nodes. - .. parsed-literal:: env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS @@ -61,7 +60,6 @@ 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:: pair_style lj/cut/omp 2.5 @@ -140,7 +138,6 @@ circumstances: with the USER-OMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation. - Additional performance tips are as follows: * The best parallel efficiency from *omp* styles is typically achieved @@ -154,9 +151,7 @@ Additional performance tips are as follows: one core and thus is likely to be counterproductive. Instead, binding MPI tasks to a (multi-core) socket, should solve this issue. - Restrictions """""""""""" - None. diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index f684720905..f1c7868644 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -17,7 +17,6 @@ See the :ref:`Build extras ` doc page for instructions. **Run with the OPT package from the command line:** - .. parsed-literal:: lmp_mpi -sf opt -in in.script # run in serial @@ -31,7 +30,6 @@ 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:: pair_style lj/cut/opt 2.5 @@ -49,5 +47,4 @@ Just try out an OPT pair style to see how it performs. Restrictions """""""""""" - None. diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 0526961a81..d606d7497f 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -132,7 +132,6 @@ 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:: 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 @@ -178,7 +177,6 @@ are in the individual accelerator sections. speed-up the pairwise calculations of your simulation by 5-25% on a CPU. - The individual accelerator package doc pages explain: * what hardware and software the accelerated package requires diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 403c244a5e..7b39bcfd28 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -18,8 +18,6 @@ visualization for LAMMPS simulations. .. _pizza: http://pizza.sandia.gov .. _python: http://www.python.org - - Additional tools included in the LAMMPS distribution are described on this page. @@ -37,10 +35,8 @@ to edit for your platform) which will build several of the tools which reside in that directory. Most of them are larger packages in their own sub-directories with their own Makefiles and/or README files. - ---------- - Pre-processing tools ==================== @@ -72,10 +68,8 @@ Miscellaneous tools | :ref:`vim ` | | | | | +--------------------------+----------------------+-------------------+--------------------+---------------------------------------+ - ---------- - Tool descriptions ================= @@ -95,10 +89,8 @@ version (and maybe with respect to AMBER as well). Since we don't use these tools at Sandia, you will need to experiment with them and make necessary modifications yourself. - ---------- - .. _binary: binary2txt tool @@ -107,7 +99,6 @@ 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:: binary2txt file1 file2 ... @@ -116,10 +107,8 @@ which creates file1.txt, file2.txt, etc. This tool must be compiled on a platform that can read the binary file created by a LAMMPS run, since binary files are not compatible across all platforms. - ---------- - .. _charmm: ch2lmp tool @@ -146,10 +135,8 @@ Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and Tigran Abramyan, (Clemson University) and Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. - ---------- - .. _chain: chain tool @@ -162,7 +149,6 @@ 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:: chain < def.chain > data.file @@ -171,10 +157,8 @@ See the def.chain or def.chain.ab files in the tools directory for examples of definition files. This tool was used to create the system for the :doc:`chain benchmark `. - ---------- - .. _colvars: colvars tools @@ -192,7 +176,6 @@ 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 >] @@ -201,10 +184,8 @@ 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. - ---------- - .. _createatoms: createatoms tool @@ -219,10 +200,8 @@ See the included Manual.pdf for details. The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. - ---------- - .. _doxygen: doxygen tool @@ -236,10 +215,8 @@ See the included README file for details. The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. - ---------- - .. _drude: drude tool @@ -254,10 +231,8 @@ See the header of the polarizer.py file for details. The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr - ---------- - .. _eamdb: eam database tool @@ -274,10 +249,8 @@ and is based on his paper: X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, 144113 (2004). - ---------- - .. _eamgn: eam generate tool @@ -291,10 +264,8 @@ produce are in the potentials directory, and can be used with the The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com). - ---------- - .. _eff: eff tool @@ -307,10 +278,8 @@ electron force field (eFF). These tools were provided by Andres Jaramillo-Botero at CalTech (ajaramil at wag.caltech.edu). - ---------- - .. _emacs: emacs tool @@ -323,10 +292,8 @@ with various highlighting options set up. These tools were provided by Aidan Thompson at Sandia (athomps at sandia.gov). - ---------- - .. _fep: fep tool @@ -341,10 +308,8 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. See README file in the tools/fep directory. - ---------- - .. _ipi: i-pi tool @@ -363,10 +328,8 @@ See the tools/i-pi/manual.pdf file for an overview of i-PI, and the :doc:`fix ipi ` doc page for further details on running PIMD calculations with LAMMPS. - ---------- - .. _ipp: ipp tool @@ -382,10 +345,8 @@ sandia.gov. See two examples in the tools/ipp directory. One of them is for the tools/createatoms tool's input file. - ---------- - .. _kate: kate tool @@ -398,10 +359,8 @@ scripts. See the README.txt file for details. The file was provided by Alessandro Luigi Sellerio (alessandro.sellerio at ieni.cnr.it). - ---------- - .. _arc: lmp2arc tool @@ -419,10 +378,8 @@ This tool was written by John Carpenter (Cray), Michael Peachey This tool was updated for the current LAMMPS C++ version by Jeff Greathouse at Sandia (jagreat at sandia.gov). - ---------- - .. _cfg: lmp2cfg tool @@ -435,10 +392,8 @@ the README file for more information. This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). - ---------- - .. _matlab: matlab tool @@ -458,12 +413,8 @@ These scripts were written by Arun Subramaniyan at Purdue Univ .. _matlabhome: http://www.mathworks.com - - - ---------- - .. _micelle: micelle2d tool @@ -476,7 +427,6 @@ 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:: micelle2d < def.micelle2d > data.file @@ -485,10 +435,8 @@ See the def.micelle2d file in the tools directory for an example of a definition file. This tool was used to create the system for the :doc:`micelle example `. - ---------- - .. _moltemplate: moltemplate tool @@ -505,10 +453,8 @@ supports it. It has its own WWW page at `http://moltemplate.org `_. The latest sources can be found `on its GitHub page `_ - ---------- - .. _msi: msi2lmp tool @@ -527,10 +473,8 @@ development, so there are no changes except for the occasional bug fix. See the README file in the tools/msi2lmp folder for more information. - ---------- - .. _phonon: phonon tool @@ -547,10 +491,8 @@ for example problems that can be post-processed with this tool. This tool was written by Ling-Ti Kong at Shanghai Jiao Tong University. - ---------- - .. _polybond: polybond tool @@ -566,10 +508,8 @@ See the Manual.pdf for details and example scripts. This tool was written by Zachary Kraus at Georgia Tech. - ---------- - .. _pymol: pymol\_asphere tool @@ -581,22 +521,16 @@ particles into an input file for the `PyMol visualization package `_ .. _pymolhome: http://www.pymol.org - - .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 - - 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. This tool was written by Mike Brown at Sandia. - ---------- - .. _pythontools: python tool @@ -614,10 +548,8 @@ that perform common LAMMPS post-processing tasks, such as: These are simple scripts built on `Pizza.py `_ modules. See the README for more info on Pizza.py and how to use these scripts. - ---------- - .. _replica: replica tool @@ -634,10 +566,8 @@ the README.md file for further details. Try out the peptide example provided. This tool was written by (and is maintained by) Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) - ---------- - .. _reax\_tool: reax tool @@ -650,10 +580,8 @@ the README.txt file for more info. These tools were written by Aidan Thompson at Sandia. - ---------- - .. _smd: smd tool @@ -671,10 +599,8 @@ This tool was written by the USER-SMD package author, Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). - ---------- - .. _spin: spin tool @@ -690,10 +616,8 @@ This tool was written by the SPIN package author, Julien Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei Ivanov, at University of Iceland (ali5 at hi.is). - ---------- - .. _singularity\_tool: singularity tool @@ -704,10 +628,8 @@ that can be used to build container images for building and testing LAMMPS on specific OS variants using the `Singularity `_ container software. Contributions for additional variants are welcome. - ---------- - .. _vim: vim tool @@ -720,10 +642,8 @@ file for details. These files were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com) - ---------- - .. _xmgrace: xmgrace tool diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 34843fe855..fc8641d93c 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -15,7 +15,6 @@ angle_style charmm/omp command Syntax """""" - .. code-block:: LAMMPS angle_style charmm @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style charmm @@ -38,7 +36,6 @@ 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 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 @@ -60,10 +57,8 @@ or :doc:`read_restart ` commands: :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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -82,14 +77,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -101,13 +93,9 @@ Related commands **Default:** none - ---------- - .. _angle-MacKerell: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index ae5330d964..afacfb7c1d 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -15,7 +15,6 @@ angle_style class2/p6 command Syntax """""" - .. code-block:: LAMMPS angle_style class2 @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style class2 @@ -43,7 +41,6 @@ The *class2* angle style uses the potential E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\ E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) - where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. @@ -94,10 +91,8 @@ the angle type. The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified, since it is the same value from the :math:`E_a` formula. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -116,17 +111,14 @@ 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. - ---------- - The *class2/p6* angle style uses the *class2* potential expanded to sixth order: .. math:: E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 - In this expanded term 6 coefficients for the :math:`E_a` formula need to be set: * :math:`\theta_0` (degrees) @@ -138,14 +130,11 @@ In this expanded term 6 coefficients for the :math:`E_a` formula need to be set: The bond-bond and bond-angle terms remain unchanged. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the CLASS2 package. For the *class2/p6* style LAMMPS needs to be built with the USER-MOFFF package. See the :doc:`Build package ` doc @@ -158,12 +147,8 @@ Related commands **Default:** none - ---------- - .. _angle-Sun: - - **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 5f9a71371a..9066b45462 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -6,7 +6,6 @@ angle_coeff command Syntax """""" - .. code-block:: LAMMPS angle_coeff N args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_coeff 1 300.0 107.0 @@ -45,7 +43,6 @@ Note that using an :doc:`angle_coeff ` command can override a previ for the same angle type. For example, these commands set the coeffs for all angle types, then overwrite the coeffs for just angle type 2: - .. code-block:: LAMMPS angle_coeff * 200.0 107.0 1.2 @@ -58,7 +55,6 @@ coefficients for all N types must be listed in the file. For example, under the "Angle Coeffs" section of a data file, the line that corresponds to the 1st example above would be listed as - .. parsed-literal:: 1 300.0 107.0 @@ -68,10 +64,8 @@ rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. - ---------- - The list of all angle styles defined in LAMMPS is given on the :doc:`angle_style ` doc page. They are also listed in more compact form on the :ref:`Commands angle ` doc @@ -81,14 +75,11 @@ On either of those pages, click on the style to display the formula it computes and its coefficients as specified by the associated :doc:`angle_coeff ` command. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index 583f43bc40..f104771781 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -12,7 +12,6 @@ angle_style cosine/kk command Syntax """""" - .. code-block:: LAMMPS angle_style cosine @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine @@ -35,7 +33,6 @@ The *cosine* angle style uses the potential E = K [1 + \cos(\theta)] - where :math:`K` is defined for each angle type. The following coefficients must be defined for each angle type via the @@ -45,10 +42,8 @@ or :doc:`read_restart ` commands: * :math:`K` (energy) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -67,14 +62,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 86f22b9ec4..228b96abc8 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -6,7 +6,6 @@ angle_style cosine/buck6d command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/buck6d @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/buck6d @@ -52,14 +50,11 @@ with the :doc:`pair_style buck6d ` styles and needs the :doc:`special_bonds ` 1-3 interactions to be weighted 0.0 to prevent double counting. - ---------- - Restrictions """""""""""" - *cosine/buck6d* can only be used in combination with the :doc:`pair_style buck6d ` style and with a :doc:`special_bonds ` 0.0 weighting of 1-3 interactions. diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index f83b03b36d..3d29d134e0 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -9,7 +9,6 @@ angle_style cosine/delta/omp command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/delta @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/delta @@ -32,7 +30,6 @@ The *cosine/delta* angle style uses the potential E = K [1 - \cos(\theta - \theta_0)] - where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. @@ -47,10 +44,8 @@ or :doc:`read_restart ` commands: :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -69,14 +64,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index c8ede7e03d..d0c774e5f6 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -9,7 +9,6 @@ angle_style cosine/periodic/omp command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/periodic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/periodic @@ -36,7 +34,6 @@ center: E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] - where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. See :ref:`(Mayo) ` for a description of the DREIDING force field @@ -55,10 +52,8 @@ constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum f linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -77,14 +72,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -96,13 +88,9 @@ Related commands **Default:** none - ---------- - .. _cosine-Mayo: - - **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index b4c5f9c38d..70198034ed 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -9,7 +9,6 @@ angle_style cosine/shift/omp command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/shift @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/shift @@ -32,7 +30,6 @@ The *cosine/shift* angle style uses the potential E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right] - where :math:`\theta_0` is the equilibrium angle. The potential is bounded between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum :math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence @@ -46,10 +43,8 @@ or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) * :math:`\theta` (angle) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -68,14 +63,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER-MISC package. diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index 40117df221..5193b3abfc 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -9,7 +9,6 @@ angle_style cosine/shift/exp/omp command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/shift/exp @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/shift/exp @@ -56,10 +54,8 @@ or :doc:`read_restart ` commands: * :math:`\theta` (angle) * :math:`A` (real number) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -78,14 +74,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index ee9258dda8..722b098f54 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -9,7 +9,6 @@ angle_style cosine/squared/omp command Syntax """""" - .. code-block:: LAMMPS angle_style cosine/squared @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cosine/squared @@ -32,7 +30,6 @@ The *cosine/squared* angle style uses the potential E = K [\cos(\theta) - \cos(\theta_0)]^2 - where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. @@ -47,10 +44,8 @@ or :doc:`read_restart ` commands: :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -69,14 +64,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index eb5865c060..95852acd11 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -6,7 +6,6 @@ angle_style cross command Syntax """""" - .. code-block:: LAMMPS angle_style cross @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style cross @@ -54,7 +52,6 @@ internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_YAFF package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index cfa4313b30..8cd171c35e 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -9,7 +9,6 @@ angle_style dipole/omp command Syntax """""" - .. code-block:: LAMMPS angle_style dipole @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style dipole @@ -40,14 +38,12 @@ and the reference (bond) vector :math:`\vec{r_{ij}}`: \cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}} - The *dipole* angle style uses the potential: .. math:: E = K (\cos\gamma - \cos\gamma_0)^2 - where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference) angle. @@ -59,7 +55,6 @@ potential using the 'chain rule' as in appendix C.3 of \vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j} - Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by the potential will tend to align the dipole along the reference direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is @@ -74,7 +69,6 @@ couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`: -\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\ \vec{F_j} & = -\vec{F_i} - where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i` and :math:`j`, respectively. @@ -86,10 +80,8 @@ or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\gamma_0` (degrees) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -111,7 +103,6 @@ instructions on how to use the accelerated styles effectively. Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -140,20 +131,14 @@ Related commands **Default:** none - ---------- - .. _Orsi: - - **(Orsi)** Orsi & Essex, The ELBA force field for coarse-grain modeling of lipid membranes, PloS ONE 6(12): e28637, 2011. .. _Allen1: - - **(Allen)** Allen & Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index d290e2d1f7..a47f9e5620 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -9,7 +9,6 @@ angle_style fourier/omp command Syntax """""" - .. code-block:: LAMMPS angle_style fourier @@ -31,7 +30,6 @@ The *fourier* angle style uses the potential E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] - The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -42,10 +40,8 @@ or :doc:`read_restart ` commands: * :math:`C_1` (real) * :math:`C_2` (real) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -64,14 +60,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index d19dd19753..7b257a6a54 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -9,7 +9,6 @@ angle_style fourier/simple/omp command Syntax """""" - .. code-block:: LAMMPS angle_style fourier/simple @@ -31,7 +30,6 @@ The *fourier/simple* angle style uses the potential E = K [ 1.0 + c \cos ( n \theta) ] - The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -41,10 +39,8 @@ or :doc:`read_restart ` commands: * :math:`c` (real) * :math:`n` (real) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -63,14 +59,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 6b9ed776f5..4110f01d9b 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -15,7 +15,6 @@ angle_style harmonic/omp command Syntax """""" - .. code-block:: LAMMPS angle_style harmonic @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style harmonic @@ -38,7 +36,6 @@ The *harmonic* angle style uses the potential E = K (\theta - \theta_0)^2 - where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. @@ -53,10 +50,8 @@ or :doc:`read_restart ` commands: :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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -75,14 +70,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index f685beacc8..e39c079e0a 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -6,7 +6,6 @@ angle_style hybrid command Syntax """""" - .. code-block:: LAMMPS angle_style hybrid style1 style2 ... @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style hybrid harmonic cosine @@ -47,7 +45,6 @@ If angle coefficients are specified in the data file read via the E.g. "harmonic" or "cosine", must be added after the angle type, for each line in the "Angle Coeffs" section, e.g. - .. parsed-literal:: Angle Coeffs @@ -63,7 +60,6 @@ each line after the angle type. For lines in the BondBond (or BondAngle) section of the data file for angle types that are not *class2*\ , you must use an angle style of *skip* as a placeholder, e.g. - .. parsed-literal:: BondBond Coeffs @@ -81,14 +77,11 @@ in place of an angle style, either in a input script :doc:`angle_coeff ` doc page for more info. diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 6d6c6d874c..9568bf165c 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -6,7 +6,6 @@ angle_style mm3 command Syntax """""" - .. code-block:: LAMMPS angle_style mm3 @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style mm3 @@ -30,7 +28,6 @@ as defined in :ref:`(Allinger) ` E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right] - where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... @@ -49,7 +46,6 @@ internally; hence the units of :math:`K` are in energy/radian\^2. Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_YAFF package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_none.rst b/doc/src/angle_none.rst index e848391932..eea4f2f951 100644 --- a/doc/src/angle_none.rst +++ b/doc/src/angle_none.rst @@ -6,7 +6,6 @@ angle_style none command Syntax """""" - .. code-block:: LAMMPS angle_style none @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style none diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index bbf1dd618e..be44854298 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -9,7 +9,6 @@ angle_style quartic/omp command Syntax """""" - .. code-block:: LAMMPS angle_style quartic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style quartic @@ -32,7 +30,6 @@ The *quartic* angle style uses the potential E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 - where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. @@ -49,10 +46,8 @@ or :doc:`read_restart ` commands: :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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -71,14 +66,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 0b0f8087b0..cbdb809530 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -9,7 +9,6 @@ angle_style sdk/omp command Syntax """""" - .. code-block:: LAMMPS angle_style sdk @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style sdk @@ -34,7 +32,6 @@ The *sdk* angle style is a combination of the harmonic angle potential, E = K (\theta - \theta_0)^2 - where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor, with the *repulsive* part of the non-bonded *lj/sdk* pair style between the atoms 1 and 3. This angle potential is @@ -55,10 +52,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -77,14 +72,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER-CGSDK package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 3e22113d85..e43dee2591 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -6,7 +6,6 @@ angle_style command Syntax """""" - .. code-block:: LAMMPS angle_style style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style harmonic @@ -56,10 +54,8 @@ file; angle coefficients need to be re-specified. In the formulas listed for each angle style, *theta* is the angle between the 3 atoms in the angle. - ---------- - Here is an alphabetic list of angle styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated :doc:`angle_coeff ` command. @@ -97,14 +93,11 @@ of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`sdk ` - harmonic angle with repulsive SDK pair style between 1-3 atoms * :doc:`table ` - tabulated by angle - ---------- - Restrictions """""""""""" - Angle styles can only be set for atom\_styles that allow angles to be defined. @@ -120,7 +113,6 @@ Related commands Default """"""" - .. code-block:: LAMMPS angle_style none diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index f63cf167d9..9759e7fcd9 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -9,7 +9,6 @@ angle_style table/omp command Syntax """""" - .. code-block:: LAMMPS angle_style table style N @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style table linear 1000 @@ -59,14 +57,11 @@ The filename specifies a file containing tabulated energy and derivative values. The keyword specifies a section of the file. The format of this file is described below. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # Angle potential for harmonic (one or more comment or blank lines) @@ -129,10 +124,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -151,10 +144,8 @@ 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 info:** This angle style writes the settings for the "angle\_style table" @@ -168,7 +159,6 @@ script. Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst index e5dab4e3a0..22b2e95c04 100644 --- a/doc/src/angle_zero.rst +++ b/doc/src/angle_zero.rst @@ -6,7 +6,6 @@ angle_style zero command Syntax """""" - .. code-block:: LAMMPS angle_style zero *nocoeff* @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS angle_style zero diff --git a/doc/src/angles.rst b/doc/src/angles.rst index 79c52a5525..c940689d4d 100644 --- a/doc/src/angles.rst +++ b/doc/src/angles.rst @@ -1,7 +1,6 @@ Angle Styles ############ - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index 28104d129c..c4686c4f21 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -6,7 +6,6 @@ atom_modify command Syntax """""" - .. code-block:: LAMMPS atom_modify keyword values ... @@ -23,12 +22,9 @@ Syntax Nfreq = sort atoms spatially every this many time steps binsize = bin size for spatial sorting (distance units) - - Examples """""""" - .. code-block:: LAMMPS atom_modify map yes @@ -160,7 +156,6 @@ cache locality will be undermined. Restrictions """""""""""" - The *first* and *sort* options cannot be used together. Since sorting is on by default, it will be turned off if the *first* keyword is used with a group-ID that is not "all". @@ -179,12 +174,8 @@ frequency of 1000 and a binsize of 0.0, which means the neighbor cutoff will be used to set the bin size. If no neighbor cutoff is defined, sorting will be turned off. - ---------- - .. _Meloni: - - **(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index da371ee59c..fcd138c836 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -6,7 +6,6 @@ atom_style command Syntax """""" - .. code-block:: LAMMPS atom_style style args @@ -28,11 +27,9 @@ Syntax * accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* - Examples """""""" - .. code-block:: LAMMPS atom_style atomic @@ -262,10 +259,8 @@ Note that there may be additional arguments required along with the *bstyle* specification, in the atom\_style body command. These arguments are described on the :doc:`Howto body ` doc page. - ---------- - Typically, simulations require only a single (non-hybrid) atom style. If some atoms in the simulation do not have all the properties defined by a particular style, use the simplest style that defines all the @@ -287,10 +282,8 @@ per-atom basis. LAMMPS can be extended with new atom styles as well as new body styles; see the :doc:`Modify ` doc page. - ---------- - Styles with a *kk* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in on @@ -315,7 +308,6 @@ instructions on how to use the accelerated styles effectively. Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. @@ -361,13 +353,9 @@ Default atom\_style atomic - ---------- - .. _Grime: - - **(Grime)** Grime and Voth, to appear in J Chem Theory & Computation (2014). diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 033aa68663..f43fdd6bc8 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -6,7 +6,6 @@ balance command Syntax """""" - .. parsed-literal:: balance thresh style args ... keyword args ... @@ -57,12 +56,9 @@ Syntax *out* arg = filename filename = write each processor's sub-domain to a file - - Examples """""""" - .. parsed-literal:: balance 0.9 x uniform y 0.4 0.5 0.6 @@ -168,10 +164,8 @@ fractions of the box length) are also printed. :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. - ---------- - The method used to perform a load balance is specified by one of the listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are described in detail below. There are 2 kinds of styles. @@ -193,7 +187,6 @@ sub-box for each of 16 processors); the middle diagram is after a .. image:: JPG/balance_rcb_small.jpg :target: JPG/balance_rcb.jpg - The *rcb* style is a "tiling" method which does not produce a logical 3d grid of processors. Rather it tiles the simulation domain with rectangular sub-boxes of varying size and shape in an irregular @@ -220,10 +213,8 @@ When a "tiling" method is specified, the current domain partitioning ("grid" or "tiled") is ignored, and a new partitioning is computed from scratch. - ---------- - The *x*\ , *y*\ , and *z* styles invoke a "grid" method for balancing, as described above. Note that any or all of these 3 styles can be specified together, one after the other, but they cannot be used with @@ -250,10 +241,8 @@ there are 2 processors in the x dimension, you specify a single value such as 0.75, which would make the left processor's sub-domain 3x larger than the right processor's sub-domain. - ---------- - The *shift* style invokes a "grid" method for balancing, as described above. It changes the positions of cutting planes between processors in an iterative fashion, seeking to reduce the imbalance @@ -307,10 +296,8 @@ the balance procedure ends. the same number of iterations to converge even if the cutting plane is initially close to the target value. - ---------- - The *rcb* style invokes a "tiled" method for balancing, as described above. It performs a recursive coordinate bisectioning (RCB) of the simulation domain. The basic idea is as follows. @@ -344,10 +331,8 @@ box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the (weighted) particles in that sub-box. - ---------- - .. _weighted\_balance: This sub-section describes how to perform weighted load balancing @@ -483,10 +468,8 @@ these custom per-atom properties can be output in a :doc:`dump ` file, so this is a way to examine, debug, or visualize the per-particle weights computed during the load-balancing operation. - ---------- - The *out* keyword writes a text file to the specified *filename* with the results of the balancing operation. The file contains the bounds of the sub-domain for each processor after the balancing operation @@ -495,7 +478,6 @@ completes. The format of the file is compatible with the visualizing mesh files. An example is shown here for a balancing by 4 processors for a 2d problem: - .. parsed-literal:: ITEM: TIMESTEP @@ -543,14 +525,11 @@ rectangle for each processor (1 to 4). For a 3d problem, the syntax is similar with 8 vertices listed for each processor, instead of 4, and "SQUARES" replaced by "CUBES". - ---------- - Restrictions """""""""""" - For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 7b07c8a69a..3aee22dbf4 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -12,7 +12,6 @@ bond_style class2/kk command Syntax """""" - .. code-block:: LAMMPS bond_style class2 @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style class2 @@ -35,7 +33,6 @@ The *class2* bond style uses the potential E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 - where :math:`r_0` is the equilibrium bond distance. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. @@ -50,10 +47,8 @@ or :doc:`read_restart ` commands: * :math:`K_3` (energy/distance\^3) * :math:`K_4` (energy/distance\^4) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -72,14 +67,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the CLASS2 package. See the :doc:`Build package ` doc page for more info. @@ -91,12 +83,8 @@ Related commands **Default:** none - ---------- - .. _bond-Sun: - - **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 157403a301..2a45e32534 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -6,7 +6,6 @@ bond_coeff command Syntax """""" - .. code-block:: LAMMPS bond_coeff N args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_coeff 5 80.0 1.2 @@ -46,7 +44,6 @@ 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: - .. code-block:: LAMMPS bond_coeff * 100.0 1.2 @@ -59,15 +56,12 @@ 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 corresponds to the 1st example above would be listed as - .. parsed-literal:: 5 80.0 1.2 - ---------- - The list of all bond styles defined in LAMMPS is given on the :doc:`bond_style ` doc page. They are also listed in more compact form on the :doc:`Commands bond ` doc page. @@ -76,14 +70,11 @@ 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. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index a36db3a170..3ba9672294 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -15,7 +15,6 @@ bond_style fene/omp command Syntax """""" - .. code-block:: LAMMPS bond_style fene @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style fene @@ -38,7 +36,6 @@ The *fene* bond style uses the potential E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon - to define a finite extensible nonlinear elastic (FENE) potential :ref:`(Kremer) `, used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. The @@ -55,10 +52,8 @@ or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) * :math:`\sigma` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -77,14 +72,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -100,12 +92,8 @@ Related commands **Default:** none - ---------- - .. _fene-Kremer: - - **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 8a05e141d7..032b726121 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -9,7 +9,6 @@ bond_style fene/expand/omp command Syntax """""" - .. code-block:: LAMMPS bond_style fene/expand @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style fene/expand @@ -32,7 +30,6 @@ The *fene/expand* bond style uses the potential E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon - to define a finite extensible nonlinear elastic (FENE) potential :ref:`(Kremer) `, used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. @@ -53,10 +50,8 @@ or :doc:`read_restart ` commands: * :math:`\sigma` (distance) * :math:`\Delta` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -75,14 +70,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -98,12 +90,8 @@ Related commands **Default:** none - ---------- - .. _feneexpand-Kremer: - - **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index 3b935568bb..ad1b143a24 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -9,7 +9,6 @@ bond_style gromos/omp command Syntax """""" - .. code-block:: LAMMPS bond_style gromos @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style gromos @@ -32,7 +30,6 @@ The *gromos* bond style uses the potential E = K (r^2 - r_0^2)^2 - where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4 factor is included in :math:`K`. @@ -44,10 +41,8 @@ or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^4) * :math:`r_0` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -66,14 +61,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index 06af4037f6..befab173d6 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -15,7 +15,6 @@ bond_style harmonic/omp command Syntax """""" - .. code-block:: LAMMPS bond_style harmonic @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style harmonic @@ -38,7 +36,6 @@ The *harmonic* bond style uses the potential E = K (r - r_0)^2 - where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2 factor is included in :math:`K`. @@ -50,10 +47,8 @@ or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`r_0` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -72,14 +67,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index 26373790a2..a044797c6f 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -9,7 +9,6 @@ bond_style harmonic/shift/omp command Syntax """""" - .. code-block:: LAMMPS bond_style harmonic/shift @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style harmonic/shift @@ -33,7 +31,6 @@ the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] - where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance. The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. @@ -49,10 +46,8 @@ or :doc:`read_restart ` commands: * :math:`r_c` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -71,14 +66,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index 4a2dcbb4b2..64a7ae2e3d 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -9,7 +9,6 @@ bond_style harmonic/shift/cut/omp command Syntax """""" - .. code-block:: LAMMPS bond_style harmonic/shift/cut @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style harmonic/shift/cut @@ -33,7 +31,6 @@ uses the potential E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] - where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. @@ -47,10 +44,8 @@ or :doc:`read_restart ` commands: * :math:`r_0` (distance) * :math:`r_c` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -69,14 +64,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 6b8175858f..003790ecd5 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -6,7 +6,6 @@ bond_style hybrid command Syntax """""" - .. code-block:: LAMMPS bond_style hybrid style1 style2 ... @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block: LAMMPS bond_style hybrid harmonic fene @@ -47,7 +45,6 @@ If bond coefficients are specified in the data file read via the E.g. "harmonic" or "fene" must be added after the bond type, for each line in the "Bond Coeffs" section, e.g. - .. parsed-literal:: Bond Coeffs @@ -61,14 +58,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index e7baa78ea0..d86084e01e 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -6,7 +6,6 @@ bond_style mm3 command Syntax """""" - .. code-block:: LAMMPS bond_style mm3 @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style mm3 @@ -30,7 +28,6 @@ as defined in :ref:`(Allinger) ` E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] - where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a prefactor. The anharmonic prefactors have units angstrom\^(-n): -2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes @@ -49,7 +46,6 @@ or :doc:`read_restart ` commands: Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the USER\_YAFF package. See the :doc:`Build package ` doc page for more info. @@ -61,13 +57,9 @@ Related commands **Default:** none - ---------- - .. _mm3-allinger1989: - - **(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 (1989), diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 13f24855f3..5cc30bcdf9 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -9,7 +9,6 @@ bond_style morse/omp command Syntax """""" - .. code-block:: LAMMPS bond_style morse @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style morse @@ -32,7 +30,6 @@ The *morse* bond style uses the potential E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 - where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness parameter, and :math:`D` determines the depth of the potential well. @@ -45,10 +42,8 @@ or :doc:`read_restart ` commands: * :math:`\alpha` (inverse distance) * :math:`r_0` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -67,14 +62,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst index ac838581be..3712ef08d5 100644 --- a/doc/src/bond_none.rst +++ b/doc/src/bond_none.rst @@ -6,7 +6,6 @@ bond_style none command Syntax """""" - .. code-block:: LAMMPS bond_style none @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-blocK:: LAMMPS bond_style none diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 4f8a0c881e..05ed28fffe 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -9,7 +9,6 @@ bond_style nonlinear/omp command Syntax """""" - .. code-block:: LAMMPS bond_style nonlinear @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style nonlinear @@ -32,7 +30,6 @@ The *nonlinear* bond style uses the potential E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]} - to define an anharmonic spring :ref:`(Rector) ` of equilibrium length :math:`r_0` and maximum extension lamda. @@ -45,10 +42,8 @@ or :doc:`read_restart ` commands: * :math:`r_0` (distance) * :math:`\lambda` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -67,14 +62,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -86,12 +78,8 @@ Related commands **Default:** none - ---------- - .. _Rector: - - **(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 4284ab2c60..8e69b298bf 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -12,7 +12,6 @@ bond_style oxrna2/fene command Syntax """""" - .. code-block:: LAMMPS bond_style oxdna/fene @@ -24,7 +23,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style oxdna/fene @@ -45,7 +43,6 @@ The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right] - to define a modified finite extensible nonlinear elastic (FENE) potential :ref:`(Ouldridge) ` to model the connectivity of the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained @@ -96,14 +93,11 @@ Please cite also the relevant oxDNA/oxRNA publications. These are and for sequence-specific hydrogen-bonding and stacking interactions :ref:`(Sulc2) `. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -118,7 +112,6 @@ Related commands none - ---------- .. _Henrich0: diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 249f8edea2..1321e01586 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -9,7 +9,6 @@ bond_style quartic/omp command Syntax """""" - .. code-block:: LAMMPS bond_style quartic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style quartic @@ -83,16 +81,13 @@ Note that when bonds are dumped to a file via the :doc:`dump local ` comma :doc:`delete_bonds ` command can also be used to query the status of broken bonds or permanently delete them, e.g.: - .. code-block:: LAMMPS delete_bonds all stats delete_bonds all bond 0 remove - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -111,14 +106,11 @@ 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. - ---------- - Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index a0908606e4..65d314c039 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -6,7 +6,6 @@ bond_style command Syntax """""" - .. code-block:: LAMMPS bond_style style args @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style harmonic @@ -66,10 +64,8 @@ coefficients need to be re-specified. In the formulas listed for each bond style, *r* is the distance between the 2 atoms in the bond. - ---------- - Here is an alphabetic list of bond styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated :doc:`bond_coeff ` command. @@ -104,14 +100,11 @@ accelerated styles exist. * :doc:`quartic ` - breakable quartic bond * :doc:`table ` - tabulated by bond length - ---------- - Restrictions """""""""""" - Bond styles can only be set for atom styles that allow bonds to be defined. diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 79ad429222..a790db595d 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -9,7 +9,6 @@ bond_style table/omp command Syntax """""" - .. code-block:: LAMMPS bond_style table style N @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style table linear 1000 @@ -59,14 +57,11 @@ The filename specifies a file containing tabulated energy and force values. The keyword specifies a section of the file. The format of this file is described below. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # Bond potential for harmonic (one or more comment or blank lines) @@ -127,10 +122,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -149,10 +142,8 @@ 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 info:** This bond style writes the settings for the "bond\_style table" @@ -166,7 +157,6 @@ script. Restrictions """""""""""" - This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index f7055d42aa..5f93e41da0 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -6,7 +6,6 @@ bond_write command Syntax """""" - .. code-block:: LAMMPS bond_write btype N inner outer file keyword itype jtype @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_write 1 500 0.5 3.5 table.txt Harmonic_1 @@ -54,7 +52,6 @@ and a force (in force units). Restrictions """""""""""" - All force field coefficients for bond and other kinds of interactions must be set before this command can be invoked. diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 329cd9d13a..95836a6e1c 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -6,7 +6,6 @@ bond_style zero command Syntax """""" - .. code-block:: LAMMPS bond_style zero [nocoeff] @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS bond_style zero diff --git a/doc/src/bonds.rst b/doc/src/bonds.rst index 3019e0c177..4118e153e9 100644 --- a/doc/src/bonds.rst +++ b/doc/src/bonds.rst @@ -1,7 +1,6 @@ Bond Styles ########### - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 3d3dac4bd2..7784db0bae 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -6,7 +6,6 @@ boundary command Syntax """""" - .. parsed-literal:: boundary x y z @@ -20,12 +19,9 @@ Syntax *s* is non-periodic and shrink-wrapped *m* is non-periodic and shrink-wrapped with a minimum value - - Examples """""""" - .. parsed-literal:: boundary p p f @@ -97,7 +93,6 @@ triclinic representations. Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command or :doc:`read_restart ` command. See the @@ -115,7 +110,6 @@ of lost atoms. Default """"""" - .. parsed-literal:: boundary p p p diff --git a/doc/src/box.rst b/doc/src/box.rst index 77a64bd01e..fe4f6e2f37 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -6,7 +6,6 @@ box command Syntax """""" - .. parsed-literal:: box keyword value ... @@ -18,12 +17,9 @@ Syntax *tilt* value = *small* or *large* - - Examples """""""" - .. parsed-literal:: box tilt large @@ -58,7 +54,6 @@ error. Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command or :doc:`read_restart ` command. diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index 0701953423..a3a252baa0 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -6,7 +6,6 @@ change_box command Syntax """""" - .. code-block:: LAMMPS change_box group-ID parameter args ... keyword args ... @@ -52,12 +51,9 @@ Syntax lattice = distances are defined in lattice units box = distances are defined in simulation box units - - Examples """""""" - .. code-block:: LAMMPS change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box @@ -113,7 +109,6 @@ new owning processors. Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions: - .. code-block:: LAMMPS change_box all x final -10 20 @@ -166,10 +161,8 @@ new owning processors. transformations. For more information on the allowed limits for box skew see the discussion on triclinic boxes on :doc:`Howto triclinic ` doc page. - ---------- - For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their styles and values. @@ -194,7 +187,6 @@ used following a keyword that changed the volume, which is any of the style, then both it and the current keyword apply to the keyword preceding "key". I.e. this sequence of keywords is allowed: - .. code-block:: LAMMPS change_box all x scale 1.1 y volume z volume @@ -206,7 +198,6 @@ preceding keyword was invoked. If the following command is used, then the z box length will shrink by the same 1.1 factor the x box length was increased by: - .. code-block:: LAMMPS change_box all x scale 1.1 z volume @@ -216,7 +207,6 @@ shrink by sqrt(1.1) to keep the volume constant. In this case, the y,z box lengths shrink so as to keep their relative aspect ratio constant: - .. code-block:: LAMMPS change_box all x scale 1.1 y volume z volume @@ -225,7 +215,6 @@ If the following command is used, then the final box will be a factor of 10% larger in x and y, and a factor of 21% smaller in z, so as to keep the volume constant: - .. code-block:: LAMMPS change_box all x scale 1.1 z volume y scale 1.1 z volume @@ -242,10 +231,8 @@ keep the volume constant: For the *scale* and *volume* styles, the box length is expanded or compressed around its mid point. - ---------- - For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. @@ -269,10 +256,8 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent. Any tilt factor specified by this command must be within these limits. - ---------- - The *boundary* keyword takes arguments that have exactly the same meaning as they do for the :doc:`boundary ` command. In each dimension, a single letter assigns the same style to both the lower @@ -298,10 +283,8 @@ 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 command. - ---------- - The *ortho* and *triclinic* keywords convert the simulation box to be orthogonal or triclinic (non-orthogonal). @@ -318,10 +301,8 @@ be toggled to triclinic, and then a :doc:`non-equilibrium MD (NEMD) simulation < If the simulation box is currently triclinic and has non-zero tilt in xy, yz, or xz, then it cannot be converted to an orthogonal box. - ---------- - The *set* keyword saves the current box size/shape. This can be 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 @@ -343,10 +324,8 @@ including this one, have been processed. Only atoms in the specified group are remapped. - ---------- - The *units* keyword determines the meaning of the distance units used to define various arguments. A *box* value selects standard distance units as defined by the :doc:`units ` command, e.g. Angstroms for @@ -354,14 +333,11 @@ units = real or metal. A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacing. - ---------- - Restrictions """""""""""" - If you use the *ortho* or *triclinic* keywords, then at the point in the input script when this command is issued, no :doc:`dumps ` can be active, nor can a :doc:`fix deform ` be active. This is diff --git a/doc/src/clear.rst b/doc/src/clear.rst index b8cb8b7410..6c4ef9a22c 100644 --- a/doc/src/clear.rst +++ b/doc/src/clear.rst @@ -6,7 +6,6 @@ clear command Syntax """""" - .. parsed-literal:: clear @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. parsed-literal:: (commands for 1st simulation) diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 65e0c90fe5..8f745c88b1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -6,7 +6,6 @@ comm_modify command Syntax """""" - .. code-block:: LAMMPS comm_modify keyword value ... @@ -24,12 +23,9 @@ Syntax *group* value = group-ID = only communicate atoms in the group *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms - - Examples """""""" - .. code-block:: LAMMPS comm_modify mode multi @@ -165,7 +161,6 @@ that boundary (e.g. due to dilation or shear). Restrictions """""""""""" - Communication mode *multi* is currently only available for :doc:`comm_style ` *brick*\ . diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index 37184794c1..2137378547 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -6,7 +6,6 @@ comm_style command Syntax """""" - .. code-block:: LAMMPS comm_style style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS comm_style brick @@ -57,7 +55,6 @@ commands. The decomposition can be changed via the Restrictions """""""""""" - Communication style *tiled* cannot be used with *triclinic* simulation cells. diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 1b1691cefd..349d388923 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -1,7 +1,6 @@ Commands ######## - .. toctree:: :maxdepth: 1 diff --git a/doc/src/compute.rst b/doc/src/compute.rst index fd3c08c626..0cd27650b5 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -6,7 +6,6 @@ compute command Syntax """""" - .. parsed-literal:: compute ID group-ID style args @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all temp @@ -43,10 +41,8 @@ various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and underscores. - ---------- - Computes calculate one of three styles of quantities: global, per-atom, or local. A global quantity is one or more system-wide values, e.g. the temperature of the system. A per-atom quantity is @@ -96,10 +92,8 @@ 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. - ---------- - In LAMMPS, the values generated by a compute can be used in several ways: @@ -115,7 +109,6 @@ ways: command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command, or output by the :doc:`dump local ` command. - The results of computes that calculate global quantities can be either "intensive" or "extensive" values. Intensive means the value is independent of the number of atoms in the simulation, @@ -129,16 +122,13 @@ If a compute value is accessed in another way, e.g. by a intensive or extensive value. See the doc page for individual 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 in the input script: - .. parsed-literal:: compute thermo_temp all temp @@ -166,10 +156,8 @@ Code for new computes can be added to LAMMPS; see the :doc:`Modify ` doc page for details. The results of their calculations accessed in the various ways described above. - ---------- - Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also listed in more compact form on the diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index 81cd579008..8ee3a32df1 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -6,7 +6,6 @@ compute ackland/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID ackland/atom keyword/value @@ -20,12 +19,9 @@ Syntax *legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation - - Examples """""""" - .. parsed-literal:: compute 1 all ackland/atom @@ -72,7 +68,6 @@ LAMMPS output options. Restrictions """""""""""" - 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. @@ -88,12 +83,8 @@ Default """"""" The keyword *legacy* defaults to *no*\ . - ---------- - .. _Ackland: - - **(Ackland)** Ackland, Jones, Phys Rev B, 73, 054104 (2006). diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index ea5f7c0175..0a151e9395 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -6,7 +6,6 @@ compute adf command Syntax """""" - .. parsed-literal:: compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ... @@ -29,12 +28,9 @@ Syntax *ordinate* value = *degree* or *radian* or *cosine* Choose the ordinate parameter for the histogram - - Examples """""""" - .. parsed-literal:: compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 & @@ -172,7 +168,6 @@ The simplest way to output the results of the compute adf calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5 @@ -208,7 +203,6 @@ angles per atom satisfying the ADF criteria. Restrictions """""""""""" - The ADF is not computed for neighbors outside the force cutoff, since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an ADF for larger diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 155b387d4e..6c5bda7c39 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -6,7 +6,6 @@ compute angle command Syntax """""" - .. parsed-literal:: compute ID group-ID angle @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all angle diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 115808b024..8485d25702 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -6,7 +6,6 @@ compute angle/local command Syntax """""" - .. parsed-literal:: compute ID group-ID angle/local value1 value2 ... keyword args ... @@ -31,12 +30,9 @@ Syntax theta = only currently allowed arg name = name of variable to set with theta - - Examples """""""" - .. parsed-literal:: compute 1 all angle/local theta @@ -72,7 +68,6 @@ As an example, these commands can be added to the bench/in.rhodo script to compute the cosine and cosine\^2 of every angle in the system and output the statistics in various ways: - .. parsed-literal:: variable t internal 0.0 @@ -96,10 +91,8 @@ with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a file. - ---------- - The local data stored by this command is generated by looping over all the atoms owned on a processor and their angles. An angle will only be included if all 3 atoms in the angle are in the specified compute @@ -120,7 +113,6 @@ command in a consistent way. Here is an example of how to do this: - .. parsed-literal:: compute 1 all property/local atype aatom1 aatom2 aatom3 diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index b800c91303..4b48fa5832 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -6,7 +6,6 @@ compute angmom/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID angmom/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid angmom/chunk molchunk @@ -64,7 +62,6 @@ The simplest way to output the results of the compute angmom/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index ed10a2ffd5..668d12f5dd 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -6,7 +6,6 @@ compute basal/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID basal/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all basal/atom @@ -59,7 +57,6 @@ components of a unit vector. Restrictions """""""""""" - 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. @@ -74,12 +71,8 @@ Related commands **Default:** none - ---------- - .. _Barrett: - - **(Barrett)** Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012). diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index a245030e6e..a007b0831e 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -6,7 +6,6 @@ compute body/local command Syntax """""" - .. parsed-literal:: compute ID group-ID body/local input1 input2 ... @@ -22,12 +21,9 @@ Syntax *type* = atom type of the body particle *integer* = 1,2,3,etc = index of fields defined by body style - - Examples """""""" - .. parsed-literal:: compute 1 all body/local type 1 2 3 @@ -73,7 +69,6 @@ body sub-particles are x,y,z coordinates, then the dump file will be formatted similar to the output of a :doc:`dump atom or custom ` command. - .. parsed-literal:: compute 1 all body/local type 1 2 3 diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index ee95e29de8..30296fd2b3 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -6,7 +6,6 @@ compute bond command Syntax """""" - .. parsed-literal:: compute ID group-ID bond @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all bond diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index cc2f929af9..49b85f6363 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -6,7 +6,6 @@ compute bond/local command Syntax """""" - .. parsed-literal:: compute ID group-ID bond/local value1 value2 ... keyword args ... @@ -39,14 +38,9 @@ Syntax dist = only currently allowed arg name = name of variable to set with distance (dist) - - - - Examples """""""" - .. parsed-literal:: compute 1 all bond/local engpot @@ -126,7 +120,6 @@ As an example, these commands can be added to the bench/in.rhodo script to compute the distance\^2 of every bond in the system and output the statistics in various ways: - .. parsed-literal:: variable d internal 0.0 @@ -148,10 +141,8 @@ those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the distance\^2 values and write them to a file. - ---------- - The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. @@ -172,7 +163,6 @@ command in a consistent way. Here is an example of how to do this: - .. parsed-literal:: compute 1 all property/local btype batom1 batom2 diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index 6e706d9f97..53b06b1ab0 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -6,7 +6,6 @@ compute centro/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID centro/atom lattice keyword value ... @@ -23,12 +22,9 @@ Syntax *no* = do not calculate 3 symmetry axes *yes* = calculate 3 symmetry axes - - Examples """""""" - .. parsed-literal:: compute 1 all centro/atom fcc @@ -56,7 +52,6 @@ This parameter is computed using the following formula from CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2 - where the :math:`N` nearest neighbors of each atom are identified and :math:`\vec{R}_i` and :math:`\vec{R}_{i+N/2}` are vectors from the central atom to a particular pair of nearest neighbors. There are @@ -130,7 +125,6 @@ Here are typical centro-symmetry values, from a nanoindentation simulation into gold (FCC). These were provided by Jon Zimmerman (Sandia): - .. parsed-literal:: Bulk lattice = 0 @@ -141,7 +135,6 @@ simulation into gold (FCC). These were provided by Jon Zimmerman These values are \*not\* normalized by the square of the lattice parameter. If they were, normalized values would be: - .. parsed-literal:: Bulk lattice = 0 @@ -167,12 +160,8 @@ Default The default value for the optional keyword is axes = no. - ---------- - .. _Kelchner: - - **(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index ad03523304..eb40bec01d 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -6,7 +6,6 @@ compute chunk/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID chunk/atom style args keyword values ... @@ -82,12 +81,9 @@ Syntax yes = use periodic distance for bin/sphere and bin/cylinder styles *units* value = *box* or *lattice* or *reduced* - - Examples """""""" - .. parsed-literal:: compute 1 all chunk/atom type @@ -141,19 +137,15 @@ timesteps it specifies, while it accumulates per-chunk averages. The details are described below. - ---------- - The different chunk styles operate as follows. For each style, how it calculates *Nchunk* and assigns chunk IDs to atoms is explained. Note that using the optional keywords can change both of those actions, as described further below where the keywords are discussed. - ---------- - The *binning* styles perform a spatial binning of atoms, and assign an atom the chunk ID corresponding to the bin number it is in. *Nchunk* is set to the number of bins, which can change if the simulation box @@ -241,18 +233,14 @@ have moved outside the bounds of all bins. If an atom is not inside any bin, the *discard* keyword is used to determine how a chunk ID is assigned to the atom. - ---------- - The *type* style uses the atom type as the chunk ID. *Nchunk* is set to the number of atom types defined for the simulation, e.g. via the :doc:`create_box ` or :doc:`read_data ` commands. - ---------- - The *molecule* style uses the molecule ID of each atom as its chunk ID. *Nchunk* is set to the largest chunk ID. Note that this excludes molecule IDs for atoms which are not in the specified group or @@ -269,10 +257,8 @@ solvent atoms, have an out-of-range chunk ID. These atoms are discarded (not assigned to any chunk) or assigned to *Nchunk*\ , depending on the value of the *discard* keyword. - ---------- - The *compute/fix/variable* styles set the chunk ID of each atom based on a quantity calculated and stored by a compute, fix, or variable. In each case, it must be a per-atom quantity. In each case the @@ -308,10 +294,8 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to treat as a chunk ID. - ---------- - Normally, *Nchunk* = the number of chunks, is re-calculated every time this fix is invoked, though the value may or may not change. As explained below, the *nchunk* keyword can be set to *once* which means @@ -335,10 +319,8 @@ the same compute chunk/atom compute. However, the time windows they induce for holding *Nchunk* constant must be identical, else an error will be generated. - ---------- - The various optional keywords operate as follows. Note that some of them function differently or are ignored by different chunk styles. Some of them also have different default values, depending on @@ -348,10 +330,8 @@ The *region* keyword applies to all chunk styles. If used, an atom must be in both the specified group and the specified geometric :doc:`region ` to be assigned to a chunk. - ---------- - The *nchunk* keyword applies to all chunk styles. It specifies how often *Nchunk* is recalculated, which in turn can affect the chunk IDs assigned to individual atoms. @@ -368,10 +348,8 @@ chunk style and other system and keyword settings. They attempt to represent typical use cases for the various chunk styles. The *nchunk* value can always be set explicitly if desired. - ---------- - The *limit* keyword can be used to limit the calculated value of *Nchunk* = the number of chunks. The limit is applied each time *Nchunk* is calculated, which also limits the chunk IDs assigned to @@ -423,10 +401,8 @@ assigned to them. Note that in this case, all atoms will end up with chunk IDs <= *Nc*\ , and their original values (e.g. molecule ID or compute/fix/variable value) will also have been <= *Nc*\ . - ---------- - The *ids* keyword applies to all chunk styles. If the setting is *once* then the chunk IDs assigned to atoms the first time this compute is invoked will be permanent, and never be re-computed. @@ -449,10 +425,8 @@ re-calculated on any timestep this compute is invoked. quantities will also have the same ID, and thus be initialized correctly with chunk IDs from the restart file. - ---------- - The *compress* keyword applies to all chunk styles and affects how *Nchunk* is calculated, which in turn affects the chunk IDs assigned to each atom. It is useful for converting a "sparse" set of chunk IDs @@ -504,10 +478,8 @@ conjunction with the :doc:`compute property/chunk ` comm can affect these costs, depending on which keyword is used first. So use this option with care. - ---------- - The *discard* keyword applies to all chunk styles. It affects what chunk IDs are assigned to atoms that do not match one of the valid chunk IDs from 1 to *Nchunk*\ . Note that it does not apply to atoms @@ -585,10 +557,8 @@ than *rmin*\ , it will be assigned to the first bin. If the distance of the atom from the origin is greater than *rmax*\ , it will be assigned to the last bin. - ---------- - The *bound* keyword only applies to the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles and to the axis dimension of the *bin/cylinder* style; otherwise it is ignored. It can be used one or more times to limit @@ -648,10 +618,8 @@ are scaled by the lattice spacing or reduced value of the 1st dimension perpendicular to the cylinder axis. E.g. y for an x-axis cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. - ---------- - **Output info:** This compute calculates a per-atom vector, which can be accessed by @@ -666,7 +634,6 @@ belonging to a chunk. Restrictions """""""""""" - Even if the *nchunk* keyword is set to *once*\ , the chunk IDs assigned to each atom are not stored in a restart files. This means you cannot expect those assignments to persist in a restarted simulation. diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index c00b7e7478..1cee445f43 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -6,7 +6,6 @@ compute chunk/spread/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID chunk/spread/atom chunkID input1 input2 ... @@ -24,12 +23,9 @@ Syntax f_ID = global vector calculated by a fix with ID f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) - - Examples """""""" - .. parsed-literal:: compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration @@ -85,10 +81,8 @@ or fix. does not check that it is per-chunk data. It only checks that the fix produces a global vector or array. - ---------- - Each listed input is operated on independently. If a bracketed index I is used, it can be specified using a wildcard @@ -105,22 +99,18 @@ had been listed one by one. E.g. these 2 compute chunk/spread/atom commands are equivalent, since the :doc:`compute com/chunk ` command creates a per-atom array with 3 columns: - .. parsed-literal:: compute com all com/chunk mychunk compute 10 all chunk/spread/atom mychunk c_com[*] compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3] - ---------- - Here is an example of writing a dump file the with the center-of-mass (COM) for the chunk each atom is in. The commands below can be added to the bench/in.chain script. - .. parsed-literal:: compute cmol all chunk/atom molecule @@ -134,7 +124,6 @@ forces for the :doc:`fix addforce ` command. In this example the forces act to pull atoms of an extended polymer chain towards its COM in an attractive manner. - .. parsed-literal:: compute prop all property/atom xu yu zu @@ -155,7 +144,6 @@ bench/in.chain script. Thermo output is shown for 1000 steps, where the last column is the average radius of gyration over all 320 chains in the 32000 atom system: - .. parsed-literal:: compute gyr all gyration/chunk cmol @@ -174,10 +162,8 @@ in the 32000 atom system: 900 22.59128 5.0247538 4.5611513 1000 22.586832 4.94697 4.5238362 - ---------- - Here is an example for using one set of chunks, defined for molecules, to compute the dipole moment vector for each chunk. E.g. for water molecules. Then spreading those values to each atom in each chunk. @@ -185,7 +171,6 @@ Then defining a second set of chunks based on spatial bins. And finally, using the :doc:`fix ave/chunk ` command to calculate an average dipole moment vector per spatial bin. - .. parsed-literal:: compute cmol all chunk/atom molecule @@ -201,10 +186,8 @@ If a molecule straddles bin boundaries, each of its atoms contributes in a weighted manner to the average dipole moment of the spatial bin it is in. - ---------- - **Output info:** This compute calculates a per-atom vector or array, which can be diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 908974de38..b83e9e461e 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -12,7 +12,6 @@ compute aggregate/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID cluster/atom cutoff @@ -26,7 +25,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all cluster/atom 3.5 diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index f270891d82..66ef266659 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -6,7 +6,6 @@ compute cna/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID cna/atom cutoff @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all cna/atom 3.08 @@ -57,7 +55,6 @@ obtain a good cutoff distance: r_{c}^{bcc} = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\ r_{c}^{hcp} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a} - where a is the lattice constant for the crystal structure concerned and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a for HCP crystals. @@ -70,7 +67,6 @@ following relation should also be satisfied: r_c + r_s > 2*{\rm cutoff} - where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin distance as specified by the :doc:`neighbor ` command, and @@ -104,18 +100,12 @@ Related commands **Default:** none - ---------- - .. _Faken: - - **(Faken)** Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). .. _Tsuzuki1: - - **(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 42e187ba69..edcaf328a6 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -6,7 +6,6 @@ compute cnp/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID cnp/atom cutoff @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all cnp/atom 3.08 @@ -44,7 +42,6 @@ This parameter is computed using the following formula from Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2 - where the index *j* goes over the :math:`n_i` nearest neighbors of atom *i*\ , and the index *k* goes over the :math:`n_{ij}` common nearest neighbors between atom *i* and atom *j*\ . :math:`\vec{R}_{ik}` and @@ -65,7 +62,6 @@ obtain a good cutoff distance: r_{c}^{bcc} = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\ r_{c}^{hcp} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a} - where a is the lattice constant for the crystal structure concerned and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a for HCP crystals. @@ -78,7 +74,6 @@ following relation should also be satisfied: r_c + r_s > 2*{\rm cutoff} - where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is the skin distance as specified by the :doc:`neighbor ` command, and @@ -101,7 +96,6 @@ LAMMPS output options. The per-atom vector values will be real positive numbers. Some typical CNP values: - .. parsed-literal:: FCC lattice = 0.0 @@ -115,7 +109,6 @@ values: Restrictions """""""""""" - 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. @@ -127,12 +120,8 @@ Related commands **Default:** none - ---------- - .. _Tsuzuki2: - - **(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index a77d00a004..b272f4a933 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -6,7 +6,6 @@ compute com command Syntax """""" - .. parsed-literal:: compute ID group-ID com @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all com diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index 0d210fb113..9ac71bd694 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -6,7 +6,6 @@ compute com/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID com/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid com/chunk molchunk @@ -62,7 +60,6 @@ The simplest way to output the results of the compute com/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index 3c88f66ea5..2adb332154 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -6,7 +6,6 @@ compute contact/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID contact/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all contact/atom @@ -49,7 +47,6 @@ above. Restrictions """""""""""" - This compute requires that atoms store a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index 08b688cf67..d3478307a7 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -6,7 +6,6 @@ compute coord/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID coord/atom cstyle args ... @@ -25,12 +24,9 @@ Syntax orientorderID = ID of an orientorder/atom compute threshold = minimum value of the product of two "connected" atoms - - Examples """""""" - .. parsed-literal:: compute 1 all coord/atom cutoff 2.0 @@ -145,13 +141,9 @@ Default group = all - ---------- - .. _tenWolde1: - - **(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index b39076c17d..471b028b98 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -6,7 +6,6 @@ compute damage/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID damage/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all damage/atom @@ -54,7 +52,6 @@ The per-atom vector values are unitless numbers (damage) >= 0.0. Restrictions """""""""""" - This compute is part of the PERI 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_dihedral.rst b/doc/src/compute_dihedral.rst index c8d4e14d7e..fb913c4d63 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -6,7 +6,6 @@ compute dihedral command Syntax """""" - .. parsed-literal:: compute ID group-ID dihedral @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all dihedral diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 554af6724e..ae67d382d5 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -6,7 +6,6 @@ compute dihedral/local command Syntax """""" - .. parsed-literal:: compute ID group-ID dihedral/local value1 value2 ... keyword args ... @@ -30,12 +29,9 @@ Syntax phi = only currently allowed arg name = name of variable to set with phi - - Examples """""""" - .. parsed-literal:: compute 1 all dihedral/local phi @@ -70,7 +66,6 @@ As an example, these commands can be added to the bench/in.rhodo script to compute the cosine and cosine\^2 of every dihedral angle in the system and output the statistics in various ways: - .. parsed-literal:: variable p internal 0.0 @@ -94,10 +89,8 @@ with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a file. - ---------- - The local data stored by this command is generated by looping over all the atoms owned on a processor and their dihedrals. A dihedral will only be included if all 4 atoms in the dihedral are in the specified @@ -114,7 +107,6 @@ command in a consistent way. Here is an example of how to do this: - .. parsed-literal:: compute 1 all property/local dtype datom1 datom2 datom3 datom4 diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index cc64634397..abd6917395 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -6,7 +6,6 @@ compute dilatation/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID dilatation/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all dilatation/atom @@ -57,7 +55,6 @@ The per-atom vector values are unitless numbers (theta) >= 0.0. Restrictions """""""""""" - This compute is part of the PERI 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_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 44875e48d8..91077d56ae 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -6,7 +6,6 @@ compute dipole/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID dipole/chunk chunkID charge-correction @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid dipole/chunk molchunk @@ -67,7 +65,6 @@ The simplest way to output the results of the compute com/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 08b285a925..62e28e11c1 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -6,7 +6,6 @@ compute displace/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID displace/atom @@ -20,12 +19,9 @@ Syntax *replace* arg = name of per-atom variable - - Examples """""""" - .. parsed-literal:: compute 1 all displace/atom @@ -65,10 +61,8 @@ the compute command was issued. The value of the displacement will be quantities will also have the same ID, and thus be initialized correctly with time=0 atom coordinates from the restart file. - ---------- - The *refresh* option can be used in conjunction with the "dump\_modify refresh" command to generate incremental dump files. @@ -88,7 +82,6 @@ a distance *Dhop*\ . For any snapshot we only want to output atoms that have hopped since the last snapshot. This can be accomplished with something like the following commands: - .. parsed-literal:: write_dump all custom tmp.dump id type x y z # see comment below @@ -126,10 +119,8 @@ append new output to that same file and delay the output until a later timestep. The *delay* setting avoids a second time = 0 snapshot which would be empty. - ---------- - **Output info:** This compute calculates a per-atom array with 4 columns, which can be diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index 1bf7f73d90..f348894d68 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -6,7 +6,6 @@ compute dpd command Syntax """""" - .. parsed-literal:: compute ID group-ID dpd @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all dpd @@ -44,13 +42,10 @@ relations: U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\ \theta_{avg} = & (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\ - where :math:`N` is the number of particles in the system - ---------- - **Output info:** This compute calculates a global vector of length 5 (:math:`U^{cond}`, @@ -64,7 +59,6 @@ The vector values will be in energy and temperature :doc:`units `. Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -79,14 +73,10 @@ Related commands **Default:** none - ---------- - .. _Larentzos1: - - **(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 215e16a9c9..6abac88965 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -6,7 +6,6 @@ compute dpd/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID dpd/atom @@ -48,7 +47,6 @@ and temperature (:math:`theta`) :doc:`units `. Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -62,14 +60,10 @@ Related commands **Default:** none - ---------- - .. _Larentzos2: - - **(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index f71e04a2c2..962daf2709 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -6,7 +6,6 @@ compute edpd/temp/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID edpd/temp/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all edpd/temp/atom @@ -45,7 +43,6 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -56,20 +53,14 @@ Related commands **Default:** none - ---------- - .. _Espanol1997: - - **(Espanol1997)** Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8 .. _Li2014a: - - **(Li2014)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index 9b4bb5f62b..51daee323c 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -6,7 +6,6 @@ compute entropy/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID entropy/atom sigma cutoff keyword value ... @@ -26,12 +25,9 @@ Syntax cutoff2 = cutoff for the averaging over neighbors *local* values = *yes* or *no* = use the local density around each atom to normalize the g(r) - - Examples """""""" - .. parsed-literal:: compute 1 all entropy/atom 0.25 5. @@ -57,7 +53,6 @@ This parameter for atom i is computed using the following formula from s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr - where r is a distance, g(r) is the radial distribution function of atom i and rho is the density of the system. The g(r) computed for each atom i can be noisy and therefore it is smoothed using: @@ -66,7 +61,6 @@ atom i can be noisy and therefore it is smoothed using: g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} - where the sum in j goes through the neighbors of atom i, and :math:`\sigma` is a parameter to control the smoothing. @@ -80,7 +74,6 @@ averages the parameter over the neighbors of atom i according to: \left< s_S^i \right> = \frac{\sum_j s_S^j + s_S^i}{N + 1} - where the sum j goes over the neighbors of atom i and N is the number of neighbors. This procedure provides a sharper distinction between order and disorder environments. In this case the input parameter @@ -91,7 +84,6 @@ If the *avg yes* option is used, the effective cutoff of the neighbor list should be *cutoff*\ +\ *cutoff2* and therefore it might be necessary to increase the skin of the neighbor list with: - .. parsed-literal:: neighbor skin bin @@ -107,14 +99,12 @@ inhomogeneous systems such as those that have surfaces. Here are typical input parameters for fcc aluminum (lattice constant 4.05 Angstroms), - .. parsed-literal:: compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 and for bcc sodium (lattice constant 4.23 Angstroms), - .. parsed-literal:: compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 @@ -133,7 +123,6 @@ ordered environments. Restrictions """""""""""" - 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. @@ -148,18 +137,12 @@ Default The default values for the optional keywords are avg = no and local = no. - ---------- - .. _Piaggi: - - **(Piaggi)** Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). .. _Nettleton: - - **(Nettleton)** Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 9ba2edb1a6..d3db52e437 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -6,7 +6,6 @@ compute erotate/asphere command Syntax """""" - .. parsed-literal:: compute ID group-ID erotate/asphere @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all erotate/asphere @@ -55,7 +53,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute requires that ellipsoidal particles atoms store a shape and quaternion orientation and angular momentum as defined by the :doc:`atom_style ellipsoid ` command. diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index 9fbea18529..42d2715e7e 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -6,7 +6,6 @@ compute erotate/rigid command Syntax """""" - .. parsed-literal:: compute ID group-ID erotate/rigid fix-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all erotate/rigid myRigid @@ -53,7 +51,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the RIGID 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_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 61e3b5c1dc..fadaf61fcc 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -6,7 +6,6 @@ compute erotate/sphere command Syntax """""" - .. parsed-literal:: compute ID group-ID erotate/sphere @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all erotate/sphere @@ -50,7 +48,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute requires that atoms store a radius and angular velocity (omega) as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index 94cc5948e7..8523ed7df6 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -6,7 +6,6 @@ compute erotate/sphere/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID erotate/sphere/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all erotate/sphere/atom diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index a99f77ec52..4ef3a63ac5 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -6,7 +6,6 @@ compute event/displace command Syntax """""" - .. parsed-literal:: compute ID group-ID event/displace threshold @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all event/displace 0.5 @@ -58,7 +56,6 @@ scalar value will be a 0 or 1 as explained above. Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 08600c482c..b95fff8e80 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -6,7 +6,6 @@ compute fep command Syntax """""" - .. parsed-literal:: compute ID group-ID fep temp attribute args ... keyword value ... @@ -41,12 +40,9 @@ Syntax *no* = ignore volume changes (e.g. in *NVE* or *NVT* trajectories) *yes* = include volume changes (e.g. in *NpT* trajectories) - - Examples """""""" - .. parsed-literal:: compute 1 all fep 298 pair lj/cut epsilon 1 \* v_delta pair lj/cut sigma 1 \* v_delta volume yes @@ -151,10 +147,8 @@ the reference and perturbed states, or along the alchemical transformation route. This compute command does not change bond lengths or other internal coordinates :ref:`(Boresch, Karplus) `. - ---------- - The *pair* attribute enables various parameters of potentials defined by the :doc:`pair_style ` and :doc:`pair_coeff ` commands to be changed, if the pair style supports it. @@ -252,10 +246,8 @@ The *v\_name* argument for keyword *pair* is the name of an this compute is invoked. It should be specified as v\_name, where name is the variable name. - ---------- - The *atom* attribute enables atom properties to be changed. The *aparam* argument is the name of the parameter to change. This is the current list of atom parameters that can be used with this compute: @@ -267,10 +259,8 @@ The *v\_name* argument for keyword *pair* is the name of an this compute is invoked. It should be specified as v\_name, where name is the variable name. - ---------- - The *tail* keyword controls the calculation of the tail correction to "van der Waals" pair energies beyond the cutoff, if this has been activated via the :doc:`pair_modify ` command. If the @@ -289,7 +279,6 @@ 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 @@ -311,7 +300,6 @@ The values calculated by this compute are "extensive". Restrictions """""""""""" - This compute is distributed as the USER-FEP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -326,10 +314,8 @@ Default The option defaults are *tail* = *no*\ , *volume* = *no*\ . - ---------- - .. _Pearlman: **(Pearlman)** Pearlman, J Chem Phys, 98, 1487 (1994) diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index c85a6326dc..a6bb0373e9 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -6,7 +6,6 @@ compute global/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID style index input1 input2 ... @@ -34,12 +33,9 @@ Syntax f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) v_name = global vector calculated by a vector-style variable with name - - Examples """""""" - .. parsed-literal:: compute 1 all global/atom c_chunk c_com[1\] c_com[2\] c_com[3\] @@ -84,7 +80,6 @@ of each atom from the center-of-mass of the molecule it is in, and dump those values to a dump file. In this case, each molecule is a chunk. - .. parsed-literal:: compute cc1 all chunk/atom molecule @@ -102,10 +97,8 @@ chunk. You can add these commands to the bench/in.chain script to see how they work. - ---------- - Note that for input values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" @@ -121,7 +114,6 @@ had been listed one by one. E.g. these 2 compute global/atom commands are equivalent, since the :doc:`compute com/chunk ` command creates a global array with 3 columns: - .. parsed-literal:: compute cc1 all chunk/atom molecule @@ -129,10 +121,8 @@ command creates a global array with 3 columns: compute 1 all global/atom c_cc1 c_com[1] c_com[2] c_com[3] compute 1 all global/atom c_cc1 c_com[\*] - ---------- - This section explains the *index* parameter. Note that it must reference per-atom values, as contrasted with the *input* values which must reference global values. @@ -175,10 +165,8 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to use as *index*\ . - ---------- - This section explains the kinds of *input* values that can be used. Note that inputs reference global values, as contrasted with the *index* parameter which must reference per-atom values. @@ -215,10 +203,8 @@ evaluated, so this is a very general means of generating a vector of global quantities which the *index* parameter will reference for assignment of global values to atoms. - ---------- - **Output info:** If a single input is specified this compute produces a per-atom diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 354f19495f..5df21103b6 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -6,7 +6,6 @@ compute group/group command Syntax """""" - .. parsed-literal:: compute ID group-ID group/group group2-ID keyword value ... @@ -24,12 +23,9 @@ Syntax *boundary* value = *yes* or *no* *molecule* value = *off* or *inter* or *intra* - - Examples """""""" - .. parsed-literal:: compute 1 lower group/group upper @@ -93,10 +89,8 @@ that included in the regular Ewald and PPPM routines. This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups. - ---------- - The pairwise contributions to the group-group interactions are calculated by looping over a neighbor list. The Kspace contribution to the group-group interactions require essentially the same amount of @@ -132,10 +126,8 @@ The individual contributions can be summed in a This `document `_ describes how the long-range group-group calculations are performed. - ---------- - **Output info:** This compute calculates a global scalar (the energy) and a global @@ -151,7 +143,6 @@ The vector values will be in force :doc:`units `. Restrictions """""""""""" - Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, such as :doc:`Tersoff ` and @@ -171,12 +162,8 @@ Default The option defaults are pair = yes, kspace = no, boundary = yes, molecule = off. - ---------- - .. _Bogusz: - - Bogusz et al, J Chem Phys, 108, 7070 (1998) diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index fa3b6acbc5..55e55adc40 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -6,7 +6,6 @@ compute gyration command Syntax """""" - .. parsed-literal:: compute ID group-ID gyration @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 molecule gyration @@ -36,7 +34,6 @@ the square root of the Rg\^2 value in this formula {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2 - where :math:`M` is the total mass of the group, :math:`r_{cm}` is the center-of-mass position of the group, and the sum is over all atoms in the group. diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index e40d793980..5de32198e9 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -6,7 +6,6 @@ compute gyration/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID gyration/chunk chunkID keyword value ... @@ -21,12 +20,9 @@ Syntax *tensor* value = none - - Examples """""""" - .. parsed-literal:: compute 1 molecule gyration/chunk molchunk @@ -56,7 +52,6 @@ formula {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2 - where :math:`M` is the total mass of the chunk, :math:`r_{cm}` is the center-of-mass position of the chunk, and the sum is over all atoms in the chunk. @@ -91,7 +86,6 @@ The simplest way to output the results of the compute gyration/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index aca485122f..5aeb599a0f 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -6,7 +6,6 @@ compute gyration/shape command Syntax """""" - .. parsed-literal:: compute ID group-ID gyration/shape compute-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 molecule gyration/shape pe @@ -39,7 +37,6 @@ and the relative shape anisotropy, k: b = & l_y - l_x \\ k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} - where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems can be found in :ref:`(Theodorou) `. @@ -82,7 +79,6 @@ distance\^2 :doc:`units ` while the sixth one is dimensionless. Restrictions """""""""""" - 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. @@ -93,18 +89,12 @@ Related commands **Default:** none - ---------- - .. _Mattice1: - - **(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. .. _Theodorou1: - - **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 80bdbd4200..69fc0d5c31 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -6,7 +6,6 @@ compute gyration/shape/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID gyration/shape/chunk compute-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 molecule gyration/shape/chunk pe @@ -39,7 +37,6 @@ and the relative shape anisotropy, k: b = & l_y - l_x \\ k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} - where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems can be found in :ref:`(Theodorou) `. The asphericity is always non-negative and zero @@ -83,7 +80,6 @@ distance\^2 :doc:`units ` while the sixth one is dimensionless. Restrictions """""""""""" - 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. @@ -95,18 +91,12 @@ Related commands **Default:** none - ---------- - .. _Mattice2: - - **(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. .. _Theodorou2: - - **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 2122c3acd0..aef61a7707 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -6,7 +6,6 @@ compute heat/flux command Syntax """""" - .. parsed-literal:: compute ID group-ID heat/flux ke-ID pe-ID stress-ID @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute myFlux all heat/flux myKE myPE myStress @@ -88,7 +86,6 @@ included in the calculation. or :doc:`compute centroid/stress/atom virial ` so as not to include a kinetic energy term in the heat flux. - .. warning:: The compute *heat/flux* has been reported to produce unphysical @@ -106,10 +103,8 @@ to the thermal conductivity :math:`\kappa`: .. math:: \kappa = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0) J_x(t) \rangle \, \mathrm{d} t = \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot \mathbf{J}(t) \rangle \, \mathrm{d}t - ---------- - The heat flux can be output every so many timesteps (e.g. via the :doc:`thermo_style custom ` command). Then as a post-processing operation, an auto-correlation can be performed, its @@ -122,10 +117,8 @@ the auto-correlation. The trap() function in the An example LAMMPS input script for solid Ar is appended below. The result should be: average conductivity ~0.29 in W/mK. - ---------- - **Output info:** This compute calculates a global vector of length 6. @@ -166,11 +159,8 @@ Related commands **Default:** none - ---------- - - .. parsed-literal:: # Sample LAMMPS input script for thermal conductivity of solid Ar @@ -236,18 +226,12 @@ Related commands variable ndens equal count(all)/vol print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A\^3" - ---------- - .. _Surblys2: - - **(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019). .. _Boone: - - **(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019). diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 98371f247b..a7edca0153 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -6,7 +6,6 @@ compute hexorder/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID hexorder/atom keyword values ... @@ -22,12 +21,9 @@ Syntax *nnn* value = number of nearest neighbors *degree* value = degree *n* of order parameter - - Examples """""""" - .. parsed-literal:: compute 1 all hexorder/atom @@ -46,7 +42,6 @@ is a complex number (stored as two real numbers) defined as follows: q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})} - where the sum is over the *nnn* nearest neighbors of the central atom. The angle :math:`\theta` is formed by the bond vector :math:`r_{ij}` and the *x* axis. @@ -126,12 +121,8 @@ Default The option defaults are *cutoff* = pair style cutoff, *nnn* = 6, *degree* = 6 - ---------- - .. _Nelson: - - **(Nelson)** Nelson, Halperin, Phys Rev B, 19, 2457 (1979). diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index e1b1d3e3a9..3971f328a3 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -6,7 +6,6 @@ compute hma command Syntax """""" - .. parsed-literal:: compute ID group-ID hma temp-ID keyword ... @@ -23,12 +22,9 @@ Syntax *p* = compute will return pressure. the following keyword must be the difference between the harmonic pressure and lattice pressure as described below *cv* = compute will return the heat capacity - - Examples """""""" - .. parsed-literal:: compute 2 all hma 1 u @@ -71,13 +67,11 @@ method. This is the list of pair styles that currently implement * :doc:`pair_style lj/smooth/linear ` - In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination by noise produced by the already-known harmonic behavior. A detailed description of this method can be found in (:ref:`Moustafa `). The potential energy is computed by the formula: - .. math:: \left< U\right>_{HMA} = \frac{d}{2} (N-1) k_B T + \left< U + \frac{1}{2} F\bullet\Delta r \right> @@ -90,7 +84,6 @@ pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. The pressure is computed by the formula: - .. math:: \left< P\right>_{HMA} = \Delta \hat P + \left< P_{vir} + \frac{\beta \Delta \hat P - \rho}{d(N-1)} F\bullet\Delta r \right> @@ -105,7 +98,6 @@ pressure is sensitive to :math:`\Delta \hat P`; the precision tends to be best when :math:`\Delta \hat P` is the actual the difference between the lattice pressure and harmonic pressure. - .. math:: \left_{HMA} = \frac{d}{2} (N-1) k_B + \frac{1}{k_B T^2} \left( \left< @@ -121,7 +113,6 @@ round-off error when computing :math:`C_V`. To address this, the *anharmonic* keyword can be passed and/or the output format can be specified with more digits. - .. parsed-literal:: thermo_modify format float '%22.15e' @@ -145,7 +136,6 @@ should be avoided as its extra forces interfere with the HMA implementation. The following example illustrates the placement of this command in the input script: - .. parsed-literal:: min_style cg @@ -178,7 +168,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-MISC package. It is enabled only if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -195,13 +184,9 @@ this compute. **Default:** none - ---------- - .. _hma-Moustafa: - - **(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) `_ diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index e7fb761958..62671a1cf8 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -6,7 +6,6 @@ compute improper command Syntax """""" - .. parsed-literal:: compute ID group-ID improper @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all improper diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index ef4bab41a8..fbf4c50bd6 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -6,7 +6,6 @@ compute improper/local command Syntax """""" - .. parsed-literal:: compute ID group-ID improper/local value1 value2 ... @@ -20,12 +19,9 @@ Syntax *chi* = tabulate improper angles - - Examples """""""" - .. parsed-literal:: compute 1 all improper/local chi @@ -58,7 +54,6 @@ command in a consistent way. Here is an example of how to do this: - .. parsed-literal:: compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4 diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index b592fe828f..2e0ecb7f7a 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -6,7 +6,6 @@ compute inertia/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID inertia/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid inertia/chunk molchunk @@ -63,7 +61,6 @@ The simplest way to output the results of the compute inertia/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index e93d493b97..0e50c968b3 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -6,7 +6,6 @@ compute ke command Syntax """""" - .. parsed-literal:: compute ID group-ID ke @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all ke diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 37f08e83d8..81d17e6208 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -6,7 +6,6 @@ compute ke/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID ke/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all ke/atom diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index d9cfbf8c94..7aa89d0dfc 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -6,7 +6,6 @@ compute ke/atom/eff command Syntax """""" - .. parsed-literal:: compute ID group-ID ke/atom/eff @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all ke/atom/eff @@ -53,7 +51,6 @@ of freedom in eFF. thermodynamic output by using the :doc:`thermo_modify ` command, as shown in the following example: - .. code-block:: LAMMPS compute effTemp all temp/eff @@ -75,7 +72,6 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-EFF 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_ke_eff.rst b/doc/src/compute_ke_eff.rst index ab3f37ef81..5721472622 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -6,7 +6,6 @@ compute ke/eff command Syntax """""" - .. parsed-literal:: compute ID group-ID ke/eff @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all ke/eff @@ -79,7 +77,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-EFF 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_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index 3edb69f2a1..2a11b6bb44 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -6,7 +6,6 @@ compute ke/rigid command Syntax """""" - .. parsed-literal:: compute ID group-ID ke/rigid fix-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all ke/rigid myRigid @@ -52,7 +50,6 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the RIGID 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_meso_e_atom.rst b/doc/src/compute_meso_e_atom.rst index b805121b20..e61af26d2b 100644 --- a/doc/src/compute_meso_e_atom.rst +++ b/doc/src/compute_meso_e_atom.rst @@ -6,7 +6,6 @@ compute meso/e/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID meso/e/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all meso/e/atom @@ -50,7 +48,6 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SPH 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_meso_rho_atom.rst b/doc/src/compute_meso_rho_atom.rst index 1f525c1d25..0461a5d403 100644 --- a/doc/src/compute_meso_rho_atom.rst +++ b/doc/src/compute_meso_rho_atom.rst @@ -6,7 +6,6 @@ compute meso/rho/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID meso/rho/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all meso/rho/atom @@ -50,7 +48,6 @@ The per-atom vector values will be in mass/volume :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SPH 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_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst index 7969953128..60d9f44b82 100644 --- a/doc/src/compute_meso_t_atom.rst +++ b/doc/src/compute_meso_t_atom.rst @@ -6,7 +6,6 @@ compute meso/t/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID meso/t/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all meso/t/atom @@ -52,7 +50,6 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SPH 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_modify.rst b/doc/src/compute_modify.rst index f81374d394..3b8f613744 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -6,7 +6,6 @@ compute_modify command Syntax """""" - .. code-block:: LAMMPS compute_modify compute-ID keyword value ... @@ -24,12 +23,9 @@ Syntax yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature *dynamic* syntax is identical to *dynamic/dof*\ , will be disabled at some point - - Examples """""""" - .. code-block:: LAMMPS compute_modify myTemp extra/dof 0 diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index 32e325a103..13449d56f8 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -6,7 +6,6 @@ compute momentum command Syntax """""" - .. parsed-literal:: compute ID group-ID momentum @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all momentum @@ -44,7 +42,6 @@ value will be in mass\*velocity :doc:`units `. Restrictions """""""""""" - 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_msd.rst b/doc/src/compute_msd.rst index 9113ce0331..982962ed05 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -6,7 +6,6 @@ compute msd command Syntax """""" - .. parsed-literal:: compute ID group-ID msd keyword values ... @@ -21,12 +20,9 @@ Syntax *com* value = *yes* or *no* *average* value = *yes* or *no* - - Examples """""""" - .. parsed-literal:: compute 1 all msd diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 9cf2b0bc8a..248e602616 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -6,7 +6,6 @@ compute msd/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID msd/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all msd/chunk molchunk @@ -101,7 +99,6 @@ The simplest way to output the results of the compute msd/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 9bcd90098c..2a2cce5abf 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -6,7 +6,6 @@ compute msd/nongauss command Syntax """""" - .. parsed-literal:: compute ID group-ID msd/nongauss keyword values ... @@ -20,12 +19,9 @@ Syntax *com* value = *yes* or *no* - - Examples """""""" - .. parsed-literal:: compute 1 all msd/nongauss @@ -50,7 +46,6 @@ group. The 3rd component is the nonGaussian diffusion parameter NGP = NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1 - The NGP is a commonly used quantity in studies of dynamical heterogeneity. Its minimum theoretical value (-0.4) occurs when all atoms have the same displacement magnitude. NGP=0 for Brownian @@ -78,7 +73,6 @@ the 3rd is dimensionless. Restrictions """""""""""" - This compute is part of the 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_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 66e21a2ae4..e07e64cb05 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -6,7 +6,6 @@ compute omega/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID omega/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid omega/chunk molchunk @@ -64,7 +62,6 @@ The simplest way to output the results of the compute omega/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 5020cd76e4..278d281d32 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -6,7 +6,6 @@ compute orientorder/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID orientorder/atom keyword values ... @@ -25,12 +24,9 @@ Syntax *wl/hat* value = yes or no *components* value = ldegree - - Examples """""""" - .. parsed-literal:: compute 1 all orientorder/atom @@ -171,10 +167,8 @@ The option defaults are *cutoff* = pair style cutoff, *nnn* = 12, *degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`, *wl* = no, *wl/hat* = no, and *components* off - ---------- - .. _Steinhardt: **(Steinhardt)** P. Steinhardt, D. Nelson, and M. Ronchetti, @@ -187,6 +181,5 @@ J. Chem. Phys. 138, 044501 (2013). .. _tenWolde2: - **(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 87ea8bda58..5b0e3d613d 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -6,7 +6,6 @@ compute pair command Syntax """""" - .. parsed-literal:: compute ID group-ID pair pstyle [nstyle] [evalue] @@ -17,11 +16,9 @@ Syntax * nsub = *n*\ -instance of a sub-style, if a pair style is used multiple times in a hybrid style * *evalue* = *epair* or *evdwl* or *ecoul* or blank (optional) - Examples """""""" - .. parsed-literal:: compute 1 all pair gauss diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 1421d4d5da..403b03bf5a 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -6,7 +6,6 @@ compute pair/local command Syntax """""" - .. parsed-literal:: compute ID group-ID pair/local value1 value2 ... keyword args ... @@ -31,12 +30,9 @@ Syntax *cutoff* arg = *type* or *radius* - - Examples """""""" - .. parsed-literal:: compute 1 all pair/local eng @@ -119,7 +115,6 @@ command in a consistent way. Here is an example of how to do this: - .. parsed-literal:: compute 1 all property/local patom1 patom2 diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index e8075a361a..afadb7a8c0 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -6,7 +6,6 @@ compute pe command Syntax """""" - .. parsed-literal:: compute ID group-ID pe keyword ... @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all pe @@ -59,17 +57,14 @@ potential energy. 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: - .. parsed-literal:: compute thermo_pe all pe See the "thermo\_style" command for more details. - ---------- - **Output info:** This compute calculates a global scalar (the potential energy). This diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index abc504a56b..979960b50a 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -6,7 +6,6 @@ compute pe/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID pe/atom keyword ... @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all pe/atom @@ -74,7 +72,6 @@ As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output: - .. parsed-literal:: compute peratom all pe/atom @@ -99,7 +96,6 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" - Related commands """""""""""""""" @@ -107,12 +103,8 @@ Related commands **Default:** none - ---------- - .. _Heyes1: - - **(Heyes)** Heyes, Phys Rev B 49, 755 (1994), diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index 8c9515941f..f561d39045 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -6,7 +6,6 @@ compute plasticity/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID plasticity/atom @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all plasticity/atom @@ -52,7 +50,6 @@ The per-atom vector values are unitless numbers (lambda) >= 0.0. Restrictions """""""""""" - This compute is part of the PERI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -64,14 +61,10 @@ Related commands **Default:** none - ---------- - .. _Mitchell: - - **(Mitchell)** Mitchell, "A non-local, ordinary-state-based viscoelasticity model for peridynamics", Sandia National Lab Report, 8064:1-28 (2011). diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 905fb5eb68..402613d504 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -6,7 +6,6 @@ compute pressure command Syntax """""" - .. parsed-literal:: compute ID group-ID pressure temp-ID keyword ... @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all pressure thermo_temp @@ -41,7 +39,6 @@ The pressure is computed by the formula P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV} - where *N* is the number of atoms in the system (see discussion of DOF below), :math:`k_B` is the Boltzmann constant, *T* is the temperature, d is the dimensionality of the system (2 or 3 for 2d/3d), and *V* is the @@ -69,7 +66,6 @@ second term uses components of the virial tensor: P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V} - If no extra keywords are listed, the entire equations above are calculated. This includes a kinetic energy (temperature) term and the virial as the sum of pair, bond, angle, dihedral, improper, kspace @@ -107,7 +103,6 @@ is calculated by the temperature compute. See the various :doc:`compute tempera 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 @@ -115,10 +110,8 @@ LAMMPS starts up, as if this command were in the input script: where "thermo\_temp" is the ID of a similarly defined compute of style "temp". See the "thermo\_style" command for more details. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -137,10 +130,8 @@ 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. - ---------- - **Output info:** This compute calculates a global scalar (the pressure) and a global @@ -165,12 +156,8 @@ Related commands **Default:** none - ---------- - .. _Thompson1: - - **(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index 9c20e55a39..7407053f01 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -6,7 +6,6 @@ compute pressure/cylinder command Syntax """""" - .. parsed-literal:: compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 @@ -59,7 +57,6 @@ inverse volume :doc:`units `. Restrictions """""""""""" - This compute currently calculates the pressure tensor contributions for pair styles only (i.e. no bond, angle, dihedral, etc. contributions and in the presence of bonded interactions, the result will be incorrect @@ -80,12 +77,8 @@ Related commands **Default:** none - ---------- - .. _Addington1: - - **(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018). diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index e674950c32..02545dfa17 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -6,7 +6,6 @@ compute pressure/uef command Syntax """""" - .. parsed-literal:: compute ID group-ID pressure/uef temp-ID keyword ... @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all pressure/uef my_temp_uef @@ -43,7 +41,6 @@ The keywords and output information are documented in Restrictions """""""""""" - This fix is part of the USER-UEF 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 d9968566e2..e3cffa2c35 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -6,7 +6,6 @@ compute property/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID property/atom input1 input2 ... @@ -36,7 +35,6 @@ Syntax rho, drho, e, de, cv, i_name, d_name - .. parsed-literal:: id = atom ID @@ -66,14 +64,12 @@ Syntax corner123x, corner123y, corner123z = corner points of triangle nbonds = number of bonds assigned to an atom - .. parsed-literal:: PERI package per-atom properties: vfrac = ??? s0 = ??? - .. parsed-literal:: USER-EFF and USER-AWPMD package per-atom properties: @@ -82,7 +78,6 @@ Syntax ervel = electron radial velocity erforce = electron radial force - .. parsed-literal:: USER-SPH package per-atom properties: @@ -92,19 +87,15 @@ Syntax de = ??? cv = ??? - .. parsed-literal:: :doc:`fix property/atom ` per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with name - - Examples """""""" - .. parsed-literal:: compute 1 all property/atom xs vx fx mux diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 699a675055..995a2b5dbf 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -6,7 +6,6 @@ compute property/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID property/chunk chunkID input1 input2 ... @@ -22,12 +21,9 @@ Syntax id = original chunk IDs before compression by :doc:`compute chunk/atom ` coord123 = coordinates for spatial bins calculated by :doc:`compute chunk/atom ` - - Examples """""""" - .. parsed-literal:: compute 1 all property/chunk count @@ -85,7 +81,6 @@ The simplest way to output the results of the compute property/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 79d40fae1f..210bc943f9 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -6,7 +6,6 @@ compute property/local command Syntax """""" - .. parsed-literal:: compute ID group-ID property/local attribute1 attribute2 ... keyword args ... @@ -24,7 +23,6 @@ Syntax datom1 datom2 datom3 datom4 dtype iatom1 iatom2 iatom3 iatom4 itype - .. parsed-literal:: natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) @@ -47,12 +45,9 @@ Syntax *cutoff* arg = *type* or *radius* - - Examples """""""" - .. parsed-literal:: compute 1 all property/local btype batom1 batom2 diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index 503c8df168..a1bf48e40a 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -6,7 +6,6 @@ compute ptm/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID ptm/atom structures threshold group2-ID @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all ptm/atom default 0.1 all @@ -68,7 +66,6 @@ The deviation is calculated as: \text{RMSD}(\mathbf{u}, \mathbf{v}) = \min_{s, \mathbf{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N} {\left|\left| s[\vec{u_i} - \overline{\mathbf{u}}] - \mathbf{Q} \vec{v_i} \right|\right|}^2} - Here, u and v contain the coordinates of the local and ideal structures respectively, s is a scale factor, and Q is a rotation. The best match is identified by the lowest RMSD value, using the optimal scaling, rotation, and correspondence between the @@ -114,7 +111,6 @@ For atoms that are not within the compute group-ID, all values are set to zero. Restrictions """""""""""" - This fix is part of the USER-PTM package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -126,12 +122,8 @@ Related commands **Default:** none - ---------- - .. _Larsen: - - **(Larsen)** Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 3d7392565f..b5c30adbb2 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -6,7 +6,6 @@ compute rdf command Syntax """""" - .. parsed-literal:: compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ... @@ -24,12 +23,9 @@ Syntax *cutoff* value = Rcut Rcut = cutoff distance for RDF computation (distance units) - - Examples """""""" - .. parsed-literal:: compute 1 all rdf 100 @@ -151,7 +147,6 @@ The simplest way to output the results of the compute rdf calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute myRDF all rdf 50 @@ -179,7 +174,6 @@ also numbers >= 0.0. Restrictions """""""""""" - The RDF is not computed for distances longer than the force cutoff, since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an RDF for larger diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 416067e0fc..a91e276199 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -9,7 +9,6 @@ compute reduce/region command Syntax """""" - .. parsed-literal:: compute ID group-ID style arg mode input1 input2 ... keyword args ... @@ -45,12 +44,9 @@ Syntax vec1 = reduced value from this input vector will be replaced vec2 = replace it with vec1[N] where N is index of max/min value from vec2 - - Examples """""""" - .. parsed-literal:: compute 1 all reduce sum c_force @@ -112,7 +108,6 @@ had been listed one by one. E.g. these 2 compute reduce commands are equivalent, since the :doc:`compute stress/atom ` command creates a per-atom array with 6 columns: - .. parsed-literal:: compute myPress all stress/atom NULL @@ -120,10 +115,8 @@ command creates a per-atom array with 6 columns: compute 2 all reduce min c_myPress[1] c_myPress[2] c_myPress[3] & c_myPress[4] c_myPress[5] c_myPress[6] - ---------- - The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying @@ -160,10 +153,8 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce. - ---------- - If the *replace* keyword is used, two indices *vec1* and *vec2* are specified, where each index ranges from 1 to the # of input values. The replace keyword can only be used if the *mode* is *min* or *max*\ . @@ -175,7 +166,6 @@ stored index is used to select the Nth element of the *vec1* vector. Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: - .. parsed-literal:: compute 1 all property/local batom1 batom2 @@ -191,10 +181,8 @@ information in this context, the *replace* keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output. - ---------- - If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of @@ -206,10 +194,8 @@ scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the :doc:`thermo_style custom ` command with :doc:`thermo_modify norm yes ` set as an option. Or it can be accessed by a :doc:`variable ` that divides by the appropriate atom count. - ---------- - **Output info:** This compute calculates a global scalar if a single input value is diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 2053143c56..8b792fa2f0 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -6,7 +6,6 @@ compute reduce/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID reduce/chunk chunkID mode input1 input2 ... @@ -26,12 +25,9 @@ Syntax f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name - - Examples """""""" - .. parsed-literal:: compute 1 all reduce/chunk/atom mychunk min c_cluster @@ -91,17 +87,14 @@ had been listed one by one. E.g. these 2 compute reduce/chunk commands are equivalent, since the :doc:`compute property/chunk ` command creates a per-atom array with 3 columns: - .. parsed-literal:: compute prop all property/atom vx vy vz compute 10 all reduce/chunk mychunk max c_prop[\*] compute 10 all reduce/chunk mychunk max c_prop[1] c_prop[2] c_prop[3] - ---------- - Here is an example of using this compute, in conjunction with the compute chunk/spread/atom command to identify self-assembled micelles. The commands below can be added to the examples/in.micelle script. @@ -118,7 +111,6 @@ attraction induced by the hydrophobicity. The output of the chunk/reduce command will be a cluster ID per chunk (molecule). Molecules with the same cluster ID are in the same micelle. - .. parsed-literal:: group phobic type 4 # specific to in.micelle model @@ -128,7 +120,6 @@ Molecules with the same cluster ID are in the same micelle. This per-chunk info could be output in at least two ways: - .. parsed-literal:: fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector @@ -147,7 +138,6 @@ The result from compute chunk/spread/atom can be used to define a new set of chunks, where all the atoms in all the molecules in the same micelle are assigned to the same chunk, i.e. one chunk per micelle. - .. parsed-literal:: compute micelle all chunk/atom c_spread compress yes @@ -158,7 +148,6 @@ doc page. E.g. count the number of atoms in each micelle, calculate its center or mass, shape (moments of inertia), radius of gyration, etc. - .. parsed-literal:: compute prop all property/chunk micelle count @@ -169,10 +158,8 @@ with its count of atoms, plus a first line for a chunk with all the solvent atoms. By the time 50000 steps have elapsed there are a handful of large micelles. - ---------- - **Output info:** This compute calculates a global vector if a single input value is diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index 825cc3497f..8702a006f3 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -6,7 +6,6 @@ compute rigid/local command Syntax """""" - .. parsed-literal:: compute ID group-ID rigid/local rigidID input1 input2 ... @@ -40,12 +39,9 @@ Syntax tqx,tqy,tqz = torque on body inertiax,inertiay,inertiaz = diagonalized moments of inertia of body - - Examples """""""" - .. parsed-literal:: compute 1 all rigid/local myRigid mol x y z @@ -91,16 +87,13 @@ vector or array from one timestep to the next. Here is an example of how to use this compute to dump rigid body info to a file: - .. parsed-literal:: compute 1 all rigid/local myRigid mol x y z fx fy fz dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7] - ---------- - This section explains the rigid body attributes that can be specified. The *id* attribute is the atom-ID of the atom which owns the rigid body, which is @@ -155,10 +148,8 @@ diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS. - ---------- - **Output info:** This compute calculates a local vector or local array depending on the @@ -188,7 +179,6 @@ corresponding attribute is in: Restrictions """""""""""" - This compute is part of the RIGID 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_saed.rst b/doc/src/compute_saed.rst index 565095daa6..9d2f6cf4aa 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -6,7 +6,6 @@ compute saed command Syntax """""" - .. parsed-literal:: compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... @@ -34,12 +33,9 @@ Syntax based on the values of the *c* parameters *echo* = flag to provide extra output for debugging purposes - - Examples """""""" - .. parsed-literal:: compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 @@ -64,7 +60,6 @@ is computed from the structure factor F using the equations: I = & \frac{F^{*}F}{N} \\ F(\mathbf{k}) = & \sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k} \cdot \mathbf{r}_j) - Here, K is the location of the reciprocal lattice node, :math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering factors. @@ -124,7 +119,6 @@ The analytic approximation is computed using the formula f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5} a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right ) - Coefficients parameterized by :ref:`(Fox) ` are assigned for each atom type designating the chemical symbol and charge of each atom type. Valid chemical symbols for compute saed are: @@ -250,7 +244,6 @@ All array values calculated by this compute are "intensive". 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. @@ -267,27 +260,19 @@ Default The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR\_Ewald = 0.01. - ---------- - .. _saed-Coleman: - - **(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013). .. _Brown: - - **(Brown)** Brown et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 554-95 (2004). .. _Fox: - - **(Fox)** Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 (1989). diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index debae12991..c7ccb35be8 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -6,7 +6,6 @@ compute slice command Syntax """""" - .. parsed-literal:: compute ID group-ID slice Nstart Nstop Nskip input1 input2 ... @@ -26,12 +25,9 @@ Syntax f_ID[I] = Ith column of global array calculated by a fix with ID v_name = vector calculated by an vector-style variable with name - - Examples """""""" - .. parsed-literal:: compute 1 all slice 1 100 10 c_msdmol[4] @@ -91,10 +87,8 @@ even if the length of the vector is 1. If multiple inputs are specified, then a global array of values is produced, with the number of columns equal to the number of inputs specified. - ---------- - **Output info:** This compute calculates a global vector if a single input value is diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 5ac0cc1de7..698c4ec4ac 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -6,7 +6,6 @@ compute smd/contact/radius command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/contact/radius @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/contact/radius @@ -49,7 +47,6 @@ The per-particle vector values will be in distance :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_damage.rst b/doc/src/compute_smd_damage.rst index 235f6f63cc..4d33cec4e7 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -6,7 +6,6 @@ compute smd/damage command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/damage @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/damage @@ -42,7 +40,6 @@ The per-particle values are dimensionless an in the range of zero to one. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the "Build diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index d7c3764088..98ca7b2596 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -6,7 +6,6 @@ compute smd/hourglass/error command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/hourglass/error @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/hourglass/error @@ -52,7 +50,6 @@ The per-particle vector values will are dimensionless. See Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index 5aa618a031..ec36346079 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -6,7 +6,6 @@ compute smd/internal/energy command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/internal/energy @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/internal/energy @@ -43,7 +41,6 @@ The per-particle vector values will be given in :doc:`units ` of energy. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 3330a34dd0..c443162459 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -6,7 +6,6 @@ compute smd/plastic/strain command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/plastic/strain @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/plastic/strain @@ -44,7 +42,6 @@ The per-particle values will be given dimensionless. See :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index b3157bec12..a572f91b9e 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -6,7 +6,6 @@ compute smd/plastic/strain/rate command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/plastic/strain/rate @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/plastic/strain/rate @@ -44,7 +42,6 @@ The per-particle values will be given in :doc:`units ` of one over time. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index f6e4c9b764..7ef76160c5 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -6,7 +6,6 @@ compute smd/rho command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/rho @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/rho @@ -45,7 +43,6 @@ The per-particle values will be in :doc:`units ` of mass over volume. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index 7ef38db492..68c819e190 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -6,7 +6,6 @@ compute smd/tlsph/defgrad command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/defgrad @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/defgrad @@ -48,7 +46,6 @@ entry is the determinant of the deformation gradient. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. TThis compute can only be used for particles which interact via the total Lagrangian SPH diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 4213448101..7a95da63fa 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -6,7 +6,6 @@ compute smd/tlsph/dt command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/dt @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/dt @@ -49,7 +47,6 @@ The per-particle values will be given in :doc:`units ` of time. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index afd398e8a2..5ebe3d3812 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -6,7 +6,6 @@ compute smd/tlsph/num/neighs command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/num/neighs @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/num/neighs @@ -44,7 +42,6 @@ The per-particle values are dimensionless. See :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index 9787d8304c..d968b5e636 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -6,7 +6,6 @@ compute smd/tlsph/shape command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/shape @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/shape @@ -51,7 +49,6 @@ particle relative to its initial state. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index 5382382773..9d615e451a 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -6,7 +6,6 @@ compute smd/tlsph/strain command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/strain @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/strain @@ -47,7 +45,6 @@ zz, xy, xz, yz components of the symmetric strain tensor. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index fd489d4f29..c6f8d4f4fa 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -6,7 +6,6 @@ compute smd/tlsph/strain/rate command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/strain/rate @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/strain/rate @@ -46,7 +44,6 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index 7060144cfd..589ef5785e 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -6,7 +6,6 @@ compute smd/tlsph/stress command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/tlsph/stress @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/tlsph/stress @@ -48,7 +46,6 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index 9b92a896cb..3c9abfaa86 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -6,7 +6,6 @@ compute smd/triangle/vertices command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/triangle/vertices @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/triangle/mesh/vertices @@ -54,7 +52,6 @@ The values will be given in :doc:`units ` of distance. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index baa53f4eda..70824fc517 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -6,7 +6,6 @@ compute smd/ulsph/num/neighs command Syntax """""" - .. code-block:: LAMMPS compute ID group-ID smd/ulsph/num/neighs @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all smd/ulsph/num/neighs @@ -44,7 +42,6 @@ The per-particle values will be given dimensionless, see :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index 9f5a952778..dbf6751bf7 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -6,7 +6,6 @@ compute smd/ulsph/strain command Syntax """""" - .. code-block:: LAMMPS compute ID group-ID smd/ulsph/strain @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all smd/ulsph/strain @@ -47,7 +45,6 @@ The per-particle tensor values will be given dimensionless, see Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 0145e86f7e..7f911e9332 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -6,7 +6,6 @@ compute smd/ulsph/strain/rate command Syntax """""" - .. code-block:: LAMMPS compute ID group-ID smd/ulsph/strain/rate @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all smd/ulsph/strain/rate @@ -47,7 +45,6 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" - This compute is part of the USER-SMD 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_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index 9295112478..c74b37508a 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -6,7 +6,6 @@ compute smd/ulsph/stress command Syntax """""" - .. code-block:: LAMMPS compute ID group-ID smd/ulsph/stress @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute 1 all smd/ulsph/stress @@ -47,7 +45,6 @@ stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" - This compute is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index caae817ff1..ba40ea48ef 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -6,7 +6,6 @@ compute smd/vol command Syntax """""" - .. parsed-literal:: compute ID group-ID smd/vol @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all smd/vol @@ -47,7 +45,6 @@ per-particle volumes of the group for which the fix is defined. Restrictions """""""""""" - This compute is part of the USER-SMD 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_sna_atom.rst b/doc/src/compute_sna_atom.rst index c821477404..8fc2aa9a7a 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -15,7 +15,6 @@ compute snap command Syntax """""" - .. parsed-literal:: compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... @@ -49,7 +48,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0 @@ -84,7 +82,6 @@ polar angle *theta0* defined by, \theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi - In this way, all possible neighbor positions are mapped on to a subset of the 3-sphere. Points south of the latitude *theta0max=rfac0\*Pi* are excluded. @@ -105,7 +102,6 @@ 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 to distinguish atoms of different types, while the central atom is arbitrarily assigned a unit weight. The function *fc(r)* ensures that @@ -117,7 +113,6 @@ the contribution of each neighbor atom goes smoothly to zero at 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 not directly useful as descriptors, because they are not invariant under rotation of the polar coordinate frame. However, the following @@ -133,7 +128,6 @@ 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, analogous to Clebsch-Gordan coefficients for rotations on the 2-sphere. These invariants are the components of the bispectrum and @@ -154,7 +148,6 @@ summed separately for each atom type: -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} - The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*\ , this compute evaluates the above expression for each direction, each atom type, and each bispectrum component. See section below on output @@ -167,7 +160,6 @@ derivatives: -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} - Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom *i*\ , this compute evaluates the above expression for each of the six virial components, each atom type, and each bispectrum component. See @@ -189,7 +181,6 @@ The stress calculation uses a compute called *snap\_press* that is automatically created behind the scenes, according to the following command: - .. parsed-literal:: compute snap_press all pressure NULL virial @@ -259,7 +250,6 @@ of columns and the identity of the bispectrum component contained in each column depend of the value of *twojmax*\ , as described by the following piece of python code: - .. parsed-literal:: for j1 in range(0,twojmax+1): @@ -329,7 +319,6 @@ page for an overview of LAMMPS output options. Restrictions """""""""""" - These computes are part of the SNAP package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -344,32 +333,22 @@ Default The optional keyword defaults are *rmin0* = 0, *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0, - ---------- - .. _Thompson20141: - - **(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint available at `arXiv:1409.3880 `_ .. _Bartok20101: - - **(Bartok)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). .. _Meremianin2006: - - **(Meremianin)** Meremianin, J. Phys. A, 39, 3099 (2006). .. _Varshalovich1987: - - **(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987). diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst index 034d2ab685..60a75d10cf 100644 --- a/doc/src/compute_spin.rst +++ b/doc/src/compute_spin.rst @@ -6,7 +6,6 @@ compute spin command Syntax """""" - .. code-block:: LAMMPS compute ID group-ID spin @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS compute out_mag all spin @@ -37,12 +35,10 @@ This compute calculates the following 6 magnetic quantities: * The sixth one is referred to as the spin temperature, according to the work of :ref:`(Nurdin) `. - 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: - .. code-block:: LAMMPS compute out_mag all spin @@ -67,7 +63,6 @@ metal units (:doc:`units `). 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 has to be "spin" for this compute to be valid. @@ -80,12 +75,8 @@ none none - ---------- - .. _Nurdin1: - - **(Nurdin)** Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000) diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index e87b49428e..7301337111 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -8,7 +8,6 @@ compute centroid/stress/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID style temp-ID keyword ... @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 mobile stress/atom NULL @@ -177,10 +175,8 @@ subtracting a background streaming velocity. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. - ---------- - Note that as defined in the formula, per-atom stress is the negative of the per-atom pressure tensor. It is also really a stress\*volume formulation, meaning the computed quantity is in units of @@ -199,7 +195,6 @@ is the total pressure of the system. These lines in an input script for a 3d system should yield that result. I.e. the last 2 columns of thermo output will be the same: - .. parsed-literal:: compute peratom all stress/atom NULL @@ -245,30 +240,20 @@ Related commands **Default:** none - ---------- - .. _Heyes2: - - **(Heyes)** Heyes, Phys Rev B, 49, 755 (1994). .. _Sirk1: - - **(Sirk)** Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013). .. _Thompson2: - - **(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). .. _Surblys1: - - **(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019). diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 0d721db3fe..487e6bc365 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -9,7 +9,6 @@ compute stress/mop/profile command Syntax """""" - .. parsed-literal:: compute ID group-ID style dir args keywords ... @@ -20,7 +19,6 @@ Syntax * args = argument specific to the compute style * keywords = *kin* or *conf* or *total* (one of more can be specified) - .. parsed-literal:: *stress/mop* args = pos @@ -90,7 +88,6 @@ The values produced by this compute can be accessed by various :doc:`output comm Restrictions """""""""""" - These styles are part of the USER-MISC package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page on for more info. @@ -110,13 +107,9 @@ Related commands **Default:** none - ---------- - .. _mop-todd: - - **(Todd)** B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995). diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index a5973a038a..b311590298 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -18,7 +18,6 @@ compute stress/tally command Syntax """""" - .. parsed-literal:: compute ID group-ID style group2-ID @@ -30,7 +29,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 lower force/tally upper @@ -53,10 +51,8 @@ and intramolecular energies. Something that would otherwise be impossible without integrating this as a core functionality into the based classes of LAMMPS. - ---------- - The pairwise contributions are computing via a callback that the compute registers with the non-bonded pairwise force computation. This limits the use to systems that have no bonds, no Kspace, and no @@ -65,10 +61,8 @@ have to compute forces or energies a second time and thus can be much more efficient. The callback mechanism allows to write more complex pairwise property computations. - ---------- - **Output info:** Compute *pe/tally* calculates a global scalar (the energy) and a per @@ -92,7 +86,6 @@ Both the scalar and vector values calculated by this compute are Restrictions """""""""""" - This compute is part of the USER-TALLY 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_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index ba1a9d5d0f..98840c41b8 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -6,7 +6,6 @@ compute tdpd/cc/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID tdpd/cc/atom index @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all tdpd/cc/atom 2 @@ -47,7 +45,6 @@ per unit mass. Restrictions """""""""""" - This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -58,13 +55,9 @@ Related commands **Default:** none - ---------- - .. _Li2015a: - - **(Li2015)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254 diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index e485b982f2..871ffba2f9 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -9,7 +9,6 @@ compute temp/kk command Syntax """""" - .. parsed-literal:: compute ID group-ID temp @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all temp @@ -59,7 +57,6 @@ needed, the subtracted degrees-of-freedom can be altered using the 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: - .. parsed-literal:: compute thermo_temp all temp @@ -70,10 +67,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -92,10 +87,8 @@ 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. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index f2faf8c2d5..215d310e9b 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -6,7 +6,6 @@ compute temp/asphere command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/asphere keyword value ... @@ -24,12 +23,9 @@ Syntax all = compute temperature of translational and rotational degrees of freedom rotate = compute temperature of just rotational degrees of freedom - - Examples """""""" - .. parsed-literal:: compute 1 all temp/asphere @@ -107,10 +103,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - The keyword/value option pairs are used in the following ways. For the *bias* keyword, *bias-ID* refers to the ID of a temperature @@ -127,10 +121,8 @@ that includes both translational and rotational degrees of freedom. A setting of *rotate* calculates a temperature that includes only rotational degrees of freedom. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global @@ -148,7 +140,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the ASPHERE 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_temp_body.rst b/doc/src/compute_temp_body.rst index ded3701420..4f8198fb1c 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -6,7 +6,6 @@ compute temp/body command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/body keyword value ... @@ -24,12 +23,9 @@ Syntax all = compute temperature of translational and rotational degrees of freedom rotate = compute temperature of just rotational degrees of freedom - - Examples """""""" - .. parsed-literal:: compute 1 all temp/body @@ -87,10 +83,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - The keyword/value option pairs are used in the following ways. For the *bias* keyword, *bias-ID* refers to the ID of a temperature @@ -107,10 +101,8 @@ that includes both translational and rotational degrees of freedom. A setting of *rotate* calculates a temperature that includes only rotational degrees of freedom. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global @@ -128,7 +120,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the BODY 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_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index 24ea9ab558..1c6e260377 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -6,7 +6,6 @@ compute temp/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... @@ -38,12 +37,9 @@ Syntax *cdof* value = dof_per_chunk dof_per_chunk = define this many degrees-of-freedom per chunk - - Examples """""""" - .. parsed-literal:: compute 1 fluid temp/chunk molchunk @@ -116,10 +112,8 @@ chunk. The interal KE is summed over the atoms in the chunk using an internal "thermal" velocity for each atom, which is its velocity minus the center-of-mass velocity of the chunk. - ---------- - Note that currently the global and per-chunk temperatures calculated by this compute only include translational degrees of freedom for each atom. No rotational degrees of freedom are included for finite-size @@ -155,17 +149,14 @@ calculating the temperature; fix ave/chunk does not. The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule compute myChunk all temp/chunk cc1 temp fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector - ---------- - The keyword/value option pairs are used in the following ways. The *com* keyword can be used with a value of *yes* to subtract the @@ -208,10 +199,8 @@ set to the remaining degrees of freedom for the entire molecule (entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid molecule. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global @@ -240,7 +229,6 @@ energy :doc:`units ` for the *kecom* and *internal* values. Restrictions """""""""""" - The *com* and *bias* keywords cannot be used together. Related commands diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index edc7adb3bf..017de2b6fc 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -6,7 +6,6 @@ compute temp/com command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/com @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all temp/com diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index fa4949fa78..253baa26e7 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -6,7 +6,6 @@ compute temp/cs command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/cs group1 group2 @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute oxygen_c-s all temp/cs O_core O_shell @@ -102,7 +100,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - The number of core/shell pairs contributing to the temperature is assumed to be constant for the duration of the run. No fixes should be used which generate new molecules or atoms during a simulation. @@ -114,13 +111,9 @@ Related commands **Default:** none - ---------- - .. _MitchellFinchham1: - - **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index d470b24bdc..cd5f5e56a0 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -6,7 +6,6 @@ compute temp/deform command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/deform @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute myTemp all temp/deform diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 46292fcfc1..a220893919 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -6,7 +6,6 @@ compute temp/deform/eff command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/deform/eff @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute myTemp all temp/deform/eff @@ -62,7 +60,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-EFF 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_temp_drude.rst b/doc/src/compute_temp_drude.rst index 706ee32beb..aa5086caa1 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -6,7 +6,6 @@ compute temp/drude command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/drude @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute TDRUDE all temp/drude @@ -69,7 +67,6 @@ are "extensive". 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*\ . diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 06cdfbb8f0..b1e5a368bd 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -6,7 +6,6 @@ compute temp/eff command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/eff @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all temp/eff @@ -53,7 +51,6 @@ densities two to five times the density of liquid H2 ranges from :doc:`thermo_modify ` command, as shown in the following example: - .. parsed-literal:: compute effTemp all temp/eff @@ -91,7 +88,6 @@ the simulation. Restrictions """""""""""" - This compute is part of the USER-EFF 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_temp_partial.rst b/doc/src/compute_temp_partial.rst index a01abd49a0..c74ed4a02f 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -6,7 +6,6 @@ compute temp/partial command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/partial xflag yflag zflag @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute newT flow temp/partial 1 1 0 @@ -69,10 +67,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -91,10 +87,8 @@ 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. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index d83e1b009c..b75d944c74 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -6,7 +6,6 @@ compute temp/profile command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/profile xflag yflag zflag binstyle args @@ -34,12 +33,9 @@ Syntax *out* value = *tensor* or *bin* - - Examples """""""" - .. parsed-literal:: compute myTemp flow temp/profile 1 1 1 x 10 @@ -169,7 +165,6 @@ temperature :doc:`units `. Restrictions """""""""""" - You should not use too large a velocity-binning grid, especially in 3d. In the current implementation, the binned velocity averages are summed across all processors, so this will be inefficient if the grid @@ -186,12 +181,8 @@ Default The option default is out = tensor. - ---------- - .. _Evans1: - - **(Evans)** Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 1fae6bb419..0f321520e6 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -6,7 +6,6 @@ compute temp/ramp command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... @@ -20,7 +19,6 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - .. parsed-literal:: *units* value = *lattice* or *box* @@ -28,7 +26,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index b896863756..6c6ca29c82 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -6,7 +6,6 @@ compute temp/region command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/region region-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute mine flow temp/region boundary diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 9026d15d67..8bffb2577d 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -6,7 +6,6 @@ compute temp/region/eff command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/region/eff region-ID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute mine flow temp/region/eff boundary @@ -54,7 +52,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the USER-EFF 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_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 697444c6ed..d30211228e 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -6,7 +6,6 @@ compute temp/rotate command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/rotate @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute Tbead bead temp/rotate @@ -85,7 +83,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - 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_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 66cba3f671..323a01e7da 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -6,7 +6,6 @@ compute temp/sphere command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/sphere keyword value ... @@ -24,12 +23,9 @@ Syntax all = compute temperature of translational and rotational degrees of freedom rotate = compute temperature of just rotational degrees of freedom - - Examples """""""" - .. parsed-literal:: compute 1 all temp/sphere @@ -94,10 +90,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - The keyword/value option pairs are used in the following ways. For the *bias* keyword, *bias-ID* refers to the ID of a temperature @@ -114,10 +108,8 @@ that includes both translational and rotational degrees of freedom. A setting of *rotate* calculates a temperature that includes only rotational degrees of freedom. - ---------- - **Output info:** This compute calculates a global scalar (the temperature) and a global @@ -135,7 +127,6 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" - This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index ca554c2314..368774ae4a 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -6,7 +6,6 @@ compute temp/uef command Syntax """""" - .. parsed-literal:: compute ID group-ID temp/uef @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all temp/uef @@ -40,7 +38,6 @@ documentation for :doc:`compute temp `. Restrictions """""""""""" - This fix is part of the USER-UEF 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_ti.rst b/doc/src/compute_ti.rst index de8d10e0b7..9cd78503ef 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -6,7 +6,6 @@ compute ti command Syntax """""" - .. parsed-literal:: compute ID group ti keyword args ... @@ -31,12 +30,9 @@ Syntax v_name1 = variable with name1 that is K-Space scale factor and function of lambda v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda - - Examples """""""" - .. parsed-literal:: compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks @@ -65,14 +61,12 @@ command does. Assume that the unscaled energy of a pair\_style or kspace\_style is given by U. Then the scaled energy is - .. parsed-literal:: Us = f(lambda) U where f() is some function of lambda. What this compute calculates is - .. parsed-literal:: dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda @@ -117,10 +111,8 @@ command. More details about the exact functional forms for the computation of du/dl can be found in the paper by :ref:`Eike `. - ---------- - **Output info:** This compute calculates a global scalar, namely dUs/dlambda. This @@ -135,7 +127,6 @@ The scalar value will be in energy :doc:`units `. Restrictions """""""""""" - This compute is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -146,12 +137,8 @@ Related commands **Default:** none - ---------- - .. _Eike: - - **(Eike)** Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006). diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index ae4d5f120c..5ed4b2cb7d 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -6,7 +6,6 @@ compute torque/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID torque/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid torque/chunk molchunk @@ -63,7 +61,6 @@ The simplest way to output the results of the compute torque/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index a10299d5e1..57dd7996ac 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -6,7 +6,6 @@ compute vacf command Syntax """""" - .. parsed-literal:: compute ID group-ID vacf @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 all vacf @@ -43,7 +41,6 @@ The integral of the VACF versus time is proportional to the diffusion coefficient of the diffusing atoms. This can be computed in the following manner, using the :doc:`variable trap() ` function: - .. parsed-literal:: compute 2 all vacf diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index 338265374b..5ce42e2a2e 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -6,7 +6,6 @@ compute vcm/chunk command Syntax """""" - .. parsed-literal:: compute ID group-ID vcm/chunk chunkID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: compute 1 fluid vcm/chunk molchunk @@ -53,7 +51,6 @@ The simplest way to output the results of the compute vcm/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: - .. parsed-literal:: compute cc1 all chunk/atom molecule diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 58b46fdf39..1d72e739ff 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -6,7 +6,6 @@ compute voronoi/atom command Syntax """""" - .. parsed-literal:: compute ID group-ID voronoi/atom keyword arg ... @@ -35,12 +34,9 @@ Syntax *neighbors* value = *yes* or *no* = store list of all neighbors or no *peratom* value = *yes* or *no* = per-atom quantities accessible or no - - Examples """""""" - .. parsed-literal:: compute 1 all voronoi/atom @@ -67,10 +63,8 @@ plus any exterior faces (see note below). If the *peratom* keyword is set to "no", the per-atom quantities are still calculated, but they are not accessible. - ---------- - 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 @@ -92,7 +86,6 @@ If the *radius* keyword is specified with an atom style variable as the argument, a poly-disperse Voronoi tessellation is performed. Examples for radius variables are - .. parsed-literal:: variable r1 atom (type==1)\*0.1+(type==2)\*0.4 @@ -146,7 +139,6 @@ overview of LAMMPS output options. More specifically, the array can be accessed by a :doc:`dump local ` command to write a file containing all the Voronoi neighbors in a system: - .. parsed-literal:: compute 6 all voronoi/atom neighbors yes @@ -155,10 +147,8 @@ containing all the Voronoi neighbors in a system: If the *face\_threshold* keyword is used, then only faces with areas greater than the threshold are stored. - ---------- - The Voronoi calculation is performed by the freely available `Voro++ package `_, written by Chris Rycroft at UC Berkeley and LBL, which must be installed on your system when building LAMMPS for use with this compute. See instructions on obtaining and installing the @@ -166,8 +156,6 @@ Voro++ software in the src/VORONOI/README file. .. _voronoi: http://math.lbl.gov/voro++/ - - .. note:: The calculation of Voronoi volumes is performed by each @@ -235,7 +223,6 @@ The Voronoi face area will be in distance :doc:`units ` squared. Restrictions """""""""""" - This compute is part of the VORONOI 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_xrd.rst b/doc/src/compute_xrd.rst index 382d48dc38..80f5e9cb2c 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -6,7 +6,6 @@ compute xrd command Syntax """""" - .. parsed-literal:: compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... @@ -32,12 +31,9 @@ Syntax based on the values of the *c* parameters *echo* = flag to provide extra output for debugging purposes - - Examples """""""" - .. parsed-literal:: compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo @@ -226,7 +222,6 @@ All array values calculated by this compute are "intensive". 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. @@ -244,27 +239,19 @@ Default The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, no manual flag, no echo flag. - ---------- - .. _xrd-Coleman: - - **(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013). .. _Colliex: - - **(Colliex)** Colliex et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 249-429 (2004). .. _Peng: - - **(Peng)** Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996). diff --git a/doc/src/computes.rst b/doc/src/computes.rst index 1c1819a444..8d53b6cf06 100644 --- a/doc/src/computes.rst +++ b/doc/src/computes.rst @@ -1,7 +1,6 @@ Computes ######## - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index cb4b24f6e3..85eaa86f38 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -6,7 +6,6 @@ create_atoms command Syntax """""" - .. code-block:: LAMMPS create_atoms type style args keyword values ... @@ -55,12 +54,9 @@ Syntax *lattice* = the geometry is defined in lattice units *box* = the geometry is defined in simulation box units - - Examples """""""" - .. code-block:: LAMMPS create_atoms 1 box @@ -167,10 +163,8 @@ used to remove overlapping atoms or molecules. example of how to do this, using the create\_atoms *single* style to insert a new atom outside the current simulation box. - ---------- - Individual atoms are inserted by this command, unless the *mol* keyword is used. It specifies a *template-ID* previously defined using the :doc:`molecule ` command, which reads a file that @@ -208,10 +202,8 @@ not overlap, regardless of their relative orientations. because by default, the :doc:`create_box ` command sets up a non-molecular system which doesn't allow molecules to be added. - ---------- - This is the meaning of the other allowed keywords. The *basis* keyword is only used when atoms (not molecules) are being @@ -268,7 +260,6 @@ the sinusoid would appear to be "smoother". Also note the use of the converts lattice spacings to distance. Click on the image for a larger version. - .. code-block:: LAMMPS dimension 2 @@ -304,10 +295,8 @@ the :doc:`units ` command, e.g. Angstroms for units = real or metal. A *lattice* value means the distance units are in lattice 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 @@ -358,14 +347,11 @@ and thus also set the mass for the particle to 1.0. The :doc:`set ` command can be used to override many of these default settings. - ---------- - Restrictions """""""""""" - An :doc:`atom_style ` must be previously defined to use this command. diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 04749f0289..9ac145679c 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -6,14 +6,12 @@ create_bonds command Syntax """""" - .. code-block:: LAMMPS create_bonds style args ... keyword value ... * style = *many* or *single/bond* or *single/angle* or *single/dihedral* - .. parsed-literal:: *many* args = group-ID group2-ID btype rmin rmax @@ -42,12 +40,9 @@ Syntax *special* value = *yes* or *no* - - Examples """""""" - .. code-block:: LAMMPS create_bonds many all all 1 1.0 1.2 @@ -105,10 +100,8 @@ data file for a complex system of molecules. "extra/bond/per/atom" arguments. And similarly for angles, dihedrals and impropers. See the doc pages for these 2 commands for details. - ---------- - The *many* style will create bonds between pairs of atoms I,J where I is in one of the two specified groups, and J is in the other. The two groups can be the same, e.g. group "all". The created bonds will be @@ -146,10 +139,8 @@ executes, e.g. if you wish to use long-range Coulombic interactions via the :doc:`kspace_style ` command for your subsequent simulation. - ---------- - The *single/bond* style creates a single bond of type *btype* between two atoms with IDs *batom1* and *batom2*\ . *Btype* must be a value between 1 and the number of bond types defined. @@ -176,10 +167,8 @@ read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the improper. *itype* must be a value between 1 and the number of improper types defined. - ---------- - The keyword *special* controls whether an internal list of special bonds is created after one or more bonds, or a single angle, dihedral or improper is added to the system. @@ -197,7 +186,6 @@ the same time, by using this command repeatedly, it is more efficient to only trigger the internal list to be created once, after the last bond (or angle, or dihedral, or improper) is added: - .. code-block:: LAMMPS create_bonds single/bond 5 52 98 special no @@ -211,14 +199,11 @@ bond (angle, dihedral, improper) is added, before performing a simulation. Otherwise pairwise interactions will not be properly excluded or weighted. LAMMPS does NOT check that you have done this correctly. - ---------- - Restrictions """""""""""" - This command cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and :doc:`atom_style template ` commands. diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index c167f77ac5..99d5befd2d 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -6,7 +6,6 @@ create_box command Syntax """""" - .. code-block:: LAMMPS create_box N region-ID keyword value ... @@ -28,12 +27,9 @@ Syntax *extra/improper/per/atom* value = # of impropers per atom *extra/special/per/atom* value = # of special neighbors per atom - - Examples """""""" - .. code-block:: LAMMPS create_box 2 mybox @@ -119,10 +115,8 @@ using the :doc:`change box ` command with its *ortho* and a parallel simulation to lose atoms the first time that LAMMPS shrink-wraps the box around the atoms. - ---------- - The optional keywords can be used to create a system that allows for bond (angle, dihedral, improper) interactions, or for molecules with special 1-2,1-3,1-4 neighbors to be added later. These optional @@ -145,14 +139,11 @@ this. If the added molecule contained more than 1 special bond (allowed by default), an extra/special/per/atom keyword would also need to be specified. - ---------- - Restrictions """""""""""" - An :doc:`atom_style ` and :doc:`region ` must have been previously defined to use this command. diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index c08bba0d72..d695603ded 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -6,7 +6,6 @@ delete_atoms command Syntax """""" - .. code-block:: LAMMPS delete_atoms style args keyword value ... @@ -35,12 +34,9 @@ Syntax *bond* value = *no* or *yes* *mol* value = *no* or *yes* - - Examples """""""" - .. code-block:: LAMMPS delete_atoms group edge @@ -139,7 +135,6 @@ part of molecules. Restrictions """""""""""" - The *overlap* styles requires inter-processor communication to acquire ghost atoms and build a neighbor list. This means that your system must be ready to perform a simulation before using this command (force diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 6b96db4f92..7381682f6d 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -6,7 +6,6 @@ delete_bonds command Syntax """""" - .. code-block:: LAMMPS delete_bonds group-ID style arg keyword ... @@ -27,11 +26,9 @@ Syntax * zero or more keywords may be appended * keyword = *any* or *undo* or *remove* or *special* - Examples """""""" - .. code-block:: LAMMPS delete_bonds frozen multi remove @@ -136,7 +133,6 @@ have been modified by the delete\_bonds command. Restrictions """""""""""" - This command requires inter-processor communication to acquire ghost atoms, to coordinate the deleting of bonds, angles, etc between atoms shared by multiple processors. This means that your system must be diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index f5cbf56a0f..1b057302e2 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -6,7 +6,6 @@ dielectric command Syntax """""" - .. parsed-literal:: dielectric value @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: dielectric 2.0 @@ -44,7 +42,6 @@ Related commands Default """"""" - .. parsed-literal:: dielectric 1.0 diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 56eba0fe02..84dc42f08e 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -18,7 +18,6 @@ dihedral_style charmmfsw command Syntax """""" - .. code-block:: LAMMPS dihedral_style style @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style charmm @@ -46,7 +44,6 @@ The *charmm* and *charmmfsw* dihedral styles use the potential E = K [ 1 + \cos (n \phi - d) ] - See :ref:`(MacKerell) ` for a description of the CHARMM force field. This dihedral style can also be used for the AMBER force field (see comment on weighting factors below). See @@ -126,10 +123,8 @@ interactions. Likewise the *charmm* or *charmmfsw* styles are identical in this case since no 1-4 non-bonded interactions are computed. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -148,14 +143,11 @@ 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. - ---------- - Restrictions """""""""""" - When using run\_style :doc:`respa `, these dihedral styles must be assigned to the same r-RESPA level as *pair* or *outer*\ . @@ -175,20 +167,14 @@ Related commands **Default:** none - ---------- - .. _dihedral-Cornell: - - **(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). .. _dihedral-MacKerell: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998). diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index f079314129..034020429b 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -12,7 +12,6 @@ dihedral_style class2/kk command Syntax """""" - .. code-block:: LAMMPS dihedral_style class2 @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style class2 @@ -48,7 +46,6 @@ The *class2* dihedral style uses the potential E_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\ E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3) - where :math:`E_d` is the dihedral term, :math:`E_{mbt}` is a middle-bond-torsion term, :math:`E_{ebt}` is an end-bond-torsion term, :math:`E_{at}` is an angle-torsion term, :math:`E_{aat}` is an angle-angle-torsion term, and :math:`E_{bb13}` is a bond-bond-13 term. @@ -155,10 +152,8 @@ listed under a *BondBond13 Coeffs* heading and you must leave out the * :math:`r_1` (distance) * :math:`r_3` (distance) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -177,14 +172,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the CLASS2 package. See the :doc:`Build package ` doc page for more info. @@ -196,12 +188,8 @@ Related commands **Default:** none - ---------- - .. _dihedral-Sun: - - **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index 491546d9e0..f31c933b7c 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -6,7 +6,6 @@ dihedral_coeff command Syntax """""" - .. code-block:: LAMMPS dihedral_coeff N args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_coeff 1 80.0 1 3 @@ -45,7 +43,6 @@ 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: - .. code-block:: LAMMPS dihedral_coeff * 80.0 1 3 @@ -58,7 +55,6 @@ 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 corresponds to the 1st example above would be listed as - .. parsed-literal:: 1 80.0 1 3 @@ -79,10 +75,8 @@ page for details. to define *K* appropriately to account for this difference if necessary. - ---------- - The list of all dihedral styles defined in LAMMPS is given on the :doc:`dihedral_style ` doc page. They are also listed in more compact form on the :ref:`Commands dihedral ` doc page. @@ -91,14 +85,11 @@ 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. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index e866b79170..4ce537409c 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -9,7 +9,6 @@ dihedral_style cosine/shift/exp/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style cosine/shift/exp @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style cosine/shift/exp @@ -32,7 +30,6 @@ The *cosine/shift/exp* dihedral style uses the potential E = -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right) - where :math:`U_{min}`, :math:`\theta`, and :math:`a` are defined for each dihedral type. @@ -57,10 +54,8 @@ commands: * :math:`\theta` (angle) * :math:`a` (real number) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,14 +74,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 58f7ec9cb0..eef6172ffd 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -12,7 +12,6 @@ dihedral_style fourier/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style fourier @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style fourier @@ -35,7 +33,6 @@ The *fourier* dihedral style uses the potential: E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ] - The following coefficients must be defined for each dihedral type via the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -70,14 +67,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index 665d055269..703b96cf95 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -15,7 +15,6 @@ dihedral_style harmonic/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style harmonic @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style harmonic @@ -38,7 +36,6 @@ The *harmonic* dihedral style uses the potential E = K [ 1 + d \cos (n \phi) ] - The following coefficients must be defined for each dihedral type via the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -61,11 +58,8 @@ or :doc:`read_restart ` commands: * Some force fields let :math:`n` be positive or negative which corresponds to :math:`d = 1` or :math:`d = -1` for the harmonic style. - - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -84,14 +78,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 06fd754286..00c0006e98 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -9,7 +9,6 @@ dihedral_style helix/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style helix @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style helix @@ -33,7 +31,6 @@ The *helix* dihedral style uses the potential E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + C [1 + \cos(\theta + \frac{\pi}{4})] - This coarse-grain dihedral potential is described in :ref:`(Guo) `. For dihedral angles in the helical region, the energy function is represented by a standard potential consisting of three minima, one @@ -52,10 +49,8 @@ or :doc:`read_restart ` commands: * :math:`B` (energy) * :math:`C` (energy) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -74,14 +69,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -93,12 +85,8 @@ Related commands **Default:** none - ---------- - .. _Guo: - - **(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index a2c962fab3..764077359d 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -6,7 +6,6 @@ dihedral_style hybrid command Syntax """""" - .. code-block:: LAMMPS dihedral_style hybrid style1 style2 ... @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style hybrid harmonic helix @@ -47,7 +45,6 @@ If dihedral coefficients are specified in the data file read via the E.g. "harmonic" or "helix", must be added after the dihedral type, for each line in the "Dihedral Coeffs" section, e.g. - .. parsed-literal:: Dihedral Coeffs @@ -64,7 +61,6 @@ lines in the AngleTorsion (or EndBondTorsion, etc) section of the data file for dihedral types that are not *class2*\ , you must use an dihedral style of *skip* as a placeholder, e.g. - .. parsed-literal:: AngleTorsion Coeffs @@ -82,14 +78,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index 8edd7bcd26..11d4419202 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -9,7 +9,6 @@ dihedral_style multi/harmonic/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style multi/harmonic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style multi/harmonic @@ -32,7 +30,6 @@ The *multi/harmonic* dihedral style uses the potential E = \sum_{n=1,5} A_n \cos^{n-1}(\phi) - The following coefficients must be defined for each dihedral type via the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -44,10 +41,8 @@ or :doc:`read_restart ` commands: * :math:`A_4` (energy) * :math:`A_5` (energy) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -66,14 +61,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index c34c523368..87125a4918 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -9,7 +9,6 @@ dihedral_style nharmonic/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style nharmonic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style nharmonic @@ -32,7 +30,6 @@ The *nharmonic* dihedral style uses the potential: E = \sum_{n=1,n} A_n \cos^{n-1}(\phi) - The following coefficients must be defined for each dihedral type via the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` @@ -44,10 +41,8 @@ or :doc:`read_restart ` commands: * ... * :math:`A_n` (energy) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -66,14 +61,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index d4520595d4..eda8d1c39e 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -6,7 +6,6 @@ dihedral_style none command Syntax """""" - .. code-block:: LAMMPS dihedral_style none @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style none diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index a22bd8b8ab..b123a1c64b 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -15,7 +15,6 @@ dihedral_style opls/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style opls @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style opls @@ -41,7 +39,6 @@ The *opls* dihedral style uses the potential E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + \\ & \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)] - Note that the usual 1/2 factor is not included in the K values. This dihedral potential is used in the OPLS force field and is @@ -57,10 +54,8 @@ or :doc:`read_restart ` commands: * :math:`K_3` (energy) * :math:`K_4` (energy) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,14 +74,11 @@ 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. - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -98,12 +90,8 @@ Related commands **Default:** none - ---------- - .. _Watkins: - - **(Watkins)** Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001). diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index b329f1a2f6..affa53b0bc 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -9,7 +9,6 @@ dihedral_style quadratic/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style quadratic @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style quadratic @@ -32,7 +30,6 @@ The *quadratic* dihedral style uses the potential: E = K (\phi - \phi_0)^2 - This dihedral potential can be used to keep a dihedral in a predefined value (cis=zero, right-hand convention is used). @@ -45,10 +42,8 @@ commands: * :math:`K` (energy/radian\^2) * :math:`\phi_0` (degrees) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -67,14 +62,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 784a12c65e..a156b86a03 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -6,7 +6,6 @@ dihedral_style spherical command Syntax """""" - .. code-block:: LAMMPS dihedral_style spherical @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 @@ -37,7 +35,6 @@ The *spherical* dihedral style uses the potential: \Theta_{1i}(\theta_1) & = v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\ \Theta_{2i}(\theta_2) & = w_i - \mathrm{cos}((\theta_2-c_i)M_i) - For this dihedral style, the energy can be any function that combines the 4-body dihedral-angle (:math:`\phi`) and the two 3-body bond-angles (:math:`\theta_1`, :math:`\theta_2`). @@ -86,14 +83,11 @@ the Dihedral Coeffs section of a data file read by the * :math:`c_n` (degrees, typically 0.0 or 90.0) * :math:`w_n` (typically 0.0 or 1.0) - ---------- - Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 59a28d034c..ad9cc11da3 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -6,7 +6,6 @@ dihedral_style command Syntax """""" - .. code-block:: LAMMPS dihedral_style style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style harmonic @@ -82,10 +80,8 @@ coefficients you specify. :doc:`dihedral_coeff ` command to account for this difference if necessary. - ---------- - Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated :doc:`dihedral_coeff ` command. @@ -119,14 +115,11 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`table ` - tabulated dihedral * :doc:`table/cut ` - tabulated dihedral with analytic cutoff - ---------- - Restrictions """""""""""" - Dihedral styles can only be set for atom styles that allow dihedrals to be defined. diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index a29e784ef5..dfa4b1c75d 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -9,7 +9,6 @@ dihedral_style table/omp command Syntax """""" - .. code-block:: LAMMPS dihedral_style table style Ntable @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS dihedral_style table spline 400 @@ -64,15 +62,12 @@ The filename specifies a file containing tabulated energy and derivative values. The keyword specifies a section of the file. The format of this file is described below. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments). It can begin with one or more comment or blank lines. - .. parsed-literal:: # Table of the potential and its negative derivative @@ -180,10 +175,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -215,7 +208,6 @@ script. Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 81ebcacaef..2015146eaf 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -6,7 +6,6 @@ dihedral_style table/cut command Syntax """""" - .. code-block:: LAMMPS dihedral_style table/cut style Ntable @@ -70,7 +69,6 @@ cutoff function: f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 - The cutoff specifies an prefactor to the cutoff function. While this value would ordinarily equal 1 there may be situations where the value should change. @@ -85,15 +83,12 @@ The filename specifies a file containing tabulated energy and derivative values. The keyword specifies a section of the file. The format of this file is described below. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments). It can begin with one or more comment or blank lines. - .. parsed-literal:: # Table of the potential and its negative derivative @@ -214,7 +209,6 @@ script. Restrictions """""""""""" - This dihedral style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -228,6 +222,4 @@ Related commands .. _dihedralcut-Salerno: - - **(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index be900ef13d..0dc1578e5c 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -6,7 +6,6 @@ dihedral_style zero command Syntax """""" - .. code-block:: LAMMPS dihedral_style zero [nocoeff] diff --git a/doc/src/dihedrals.rst b/doc/src/dihedrals.rst index bab913f1c2..f56e323427 100644 --- a/doc/src/dihedrals.rst +++ b/doc/src/dihedrals.rst @@ -1,7 +1,6 @@ Dihedral Styles ############### - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index 0f4fc329d6..cb7ca1c437 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -6,7 +6,6 @@ dimension command Syntax """""" - .. parsed-literal:: dimension N @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: dimension 2 @@ -43,7 +41,6 @@ additional instructions on how to run 2d simulations. Restrictions """""""""""" - This command must be used before the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. @@ -55,7 +52,6 @@ Related commands Default """"""" - .. parsed-literal:: dimension 3 diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 555f0a4fdf..214164d776 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -6,7 +6,6 @@ displace_atoms command Syntax """""" - .. code-block:: LAMMPS displace_atoms group-ID style args keyword value ... @@ -39,12 +38,9 @@ Syntax keyword = *units* value = *box* or *lattice* - - Examples """""""" - .. code-block:: LAMMPS displace_atoms top move 0 -5 0 units box @@ -113,10 +109,8 @@ style are determined by the setting of *box* or *lattice* for the :doc:`lattice ` command must have been previously used to define the lattice spacing. - ---------- - .. note:: Care should be taken not to move atoms on top of other atoms. @@ -139,14 +133,11 @@ define the lattice spacing. the simulation box may not end up as optimal as the initial mapping attempted to be. - ---------- - Restrictions """""""""""" - For a 2d simulation, only rotations around the a vector parallel to the z-axis are allowed. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 2e4d281fd2..b0d2dbbf18 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -30,7 +30,6 @@ dump command Syntax """""" - .. parsed-literal:: dump ID group-ID style N file args @@ -81,7 +80,6 @@ Syntax angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name - .. parsed-literal:: id = atom ID @@ -124,12 +122,9 @@ Syntax f_ID = local vector calculated by a fix with ID f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) - - Examples """""""" - .. parsed-literal:: dump myDump all atom 100 dump.atom @@ -216,10 +211,8 @@ The precision of values output to text-based dump files can be controlled by the :doc:`dump_modify format ` command and its options. - ---------- - The *style* keyword determines what atom quantities are written to the file and in what format. Settings made via the :doc:`dump_modify ` command can also alter the format of @@ -237,7 +230,6 @@ files are self-describing in the following sense. The dimensions of the simulation box are included in each snapshot. For an orthogonal simulation box this information is formatted as: - .. parsed-literal:: ITEM: BOX BOUNDS xx yy zz @@ -258,7 +250,6 @@ bounding box which encloses the triclinic simulation box is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic box, formatted as follows: - .. parsed-literal:: ITEM: BOX BOUNDS xy xz yz xx yy zz @@ -378,10 +369,8 @@ Note that *atom*\ , *custom*\ , *dcd*\ , *xtc*\ , and *xyz* style dump files can be read directly by `VMD `_, a popular molecular viewing program. - ---------- - Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be @@ -436,7 +425,6 @@ library, which is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO package installed, e.g. - .. parsed-literal:: make yes-mpiio # installs the MPIIO package @@ -474,10 +462,8 @@ be about 3x smaller than the text version, but will also take longer to write. This option is not available for the *dcd* and *xtc* styles. - ---------- - Note that in the discussion which follows, for styles which can reference values from a compute or fix, like the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can be specified using a @@ -495,7 +481,6 @@ had been listed one by one. E.g. these 2 dump commands are equivalent, since the :doc:`compute stress/atom ` command creates a per-atom array with 6 columns: - .. parsed-literal:: compute myPress all stress/atom NULL @@ -503,10 +488,8 @@ command creates a per-atom array with 6 columns: dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] & myPress[4] myPress[5] myPress[6] - ---------- - This section explains the local attributes that can be specified as part of the *local* style. @@ -554,17 +537,14 @@ values. Here is an example of how to dump bond info for a system, including the distance and energy of each bond: - .. parsed-literal:: compute 1 all property/local batom1 batom2 btype compute 2 all bond/local dist eng dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] - ---------- - This section explains the atom attributes that can be specified as part of the *custom* and *cfg* styles. @@ -688,14 +668,11 @@ See the :doc:`Modify ` doc page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. - ---------- - Restrictions """""""""""" - To write gzipped dump files, you must either compile LAMMPS with the -DLAMMPS\_GZIP option or use the styles from the COMPRESS package. See the :doc:`Build settings ` doc page for details. diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index 950d453eb2..89e1c9836d 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -10,7 +10,6 @@ dump custom/adios command Syntax """""" - .. parsed-literal:: dump ID group-ID atom/adios N file.bp @@ -24,11 +23,9 @@ Syntax * file.bp = name of file/stream to write to * args = same options as in :doc:`\ *dump custom*\ ` command - Examples """""""" - .. parsed-literal:: dump adios1 all atom/adios 100 atoms.bp @@ -45,8 +42,6 @@ ADIOS-BP files are binary, portable and self-describing. .. _adios: https://github.com/ornladios/ADIOS2 - - **Use from write\_dump:** It is possible to use these dump styles with the @@ -54,20 +49,16 @@ It is possible to use these dump styles with the must not be set at all. The write\_dump command can be used to create a new file at each individual dump. - .. parsed-literal:: dump 4 all atom/adios 100 dump.bp write_dump all atom/adios singledump.bp - ---------- - 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 @@ -77,10 +68,8 @@ The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Related commands """""""""""""""" diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index a75476529f..acef1b0bbd 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -6,7 +6,6 @@ dump cfg/uef command Syntax """""" - .. parsed-literal:: dump ID group-ID cfg/uef N file mass type xs ys zs args @@ -20,12 +19,9 @@ Syntax args = same as args for :doc:`dump custom ` - - Examples """""""" - .. parsed-literal:: dump 1 all cfg/uef 10 dump.\*.cfg mass type xs ys zs @@ -46,7 +42,6 @@ reference frame as the atomic positions. Restrictions """""""""""" - This fix is part of the USER-UEF 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/dump_h5md.rst b/doc/src/dump_h5md.rst index ee42cc54a6..53a9b5cf78 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -6,7 +6,6 @@ dump h5md command Syntax """""" - .. parsed-literal:: dump ID group-ID h5md N file.h5 args @@ -30,8 +29,6 @@ Syntax create_group value = *yes* or *no* author value = quoted string - - Note that at least one element must be specified and image may only be present if position is specified first. @@ -40,17 +37,13 @@ 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:: every N_element - - Examples """""""" - .. parsed-literal:: dump h5md1 all h5md 100 dump_h5md.h5 position image @@ -73,8 +66,6 @@ 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 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 @@ -100,20 +91,16 @@ Typically, the *species* data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and store once the species data in the same file. - .. parsed-literal:: dump h5md1 all h5md 100 dump.h5 position image write_dump all h5md dump.h5 file_from h5md1 species - ---------- - Restrictions """""""""""" - The number of atoms per snapshot cannot change with the h5md style. The position data is stored wrapped (box boundaries not enforced, see note above). Only orthogonal domains are currently supported. This is @@ -128,25 +115,17 @@ provided by the HDF5 library. .. _HDF5-ws: http://www.hdfgroup.org/HDF5/ - - - ---------- - Related commands """""""""""""""" :doc:`dump `, :doc:`dump_modify `, :doc:`undump ` - ---------- - .. _h5md\_cpc: - - **(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) - diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index e6fc008693..25d76b7308 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -9,7 +9,6 @@ dump movie command Syntax """""" - .. parsed-literal:: dump ID group-ID style N file color diameter keyword value ... @@ -83,12 +82,9 @@ Syntax seed = random # seed (positive integer) dfactor = strength of shading from 0.0 to 1.0 - - Examples """""""" - .. code-block:: LAMMPS dump d0 all image 100 dump.\*.jpg type type @@ -160,10 +156,8 @@ details. timesteps when neighbor lists are rebuilt, the coordinates of an atom in the image may be slightly outside the simulation box. - ---------- - Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be @@ -187,10 +181,8 @@ Dump *movie* filenames on the other hand, must not have any wildcard character since only one file combining all images into a single movie will be written by the movie encoder. - ---------- - The *color* and *diameter* settings determine the color and size of atoms rendered in the image. They can be any atom attribute defined for the :doc:`dump custom ` command, including *type* and @@ -339,10 +331,8 @@ lines will be drawn as cylinders with that diameter, e.g. 1.0, which is in whatever distance :doc:`units ` the input script defines, e.g. Angstroms. - ---------- - The *tri* keyword can be used when :doc:`atom_style tri ` is used to define particles as triangles, and will draw them as triangles or edges (3 lines) or both, depending on the setting for *tflag*\ . If @@ -363,10 +353,8 @@ default the mapping of types to colors is as follows: and repeats itself for types > 6. There is not yet an option to change this via the :doc:`dump_modify ` command. - ---------- - The *body* keyword can be used when :doc:`atom_style body ` is used to define body particles with internal state (e.g. sub-particles), and will drawn them in a manner specific to the @@ -398,10 +386,8 @@ particle. By default the mapping of types to colors is as follows: and repeats itself for types > 6. There is not yet an option to change this via the :doc:`dump_modify ` command. - ---------- - The *fix* keyword can be used with a :doc:`fix ` that produces objects to be drawn. @@ -424,17 +410,13 @@ the mapping of types to colors is as follows: and repeats itself for types > 6. There is not yet an option to change this via the :doc:`dump_modify ` command. - ---------- - The *size* keyword sets the width and height of the created images, i.e. the number of pixels in each direction. - ---------- - The *view*\ , *center*\ , *up*\ , *zoom*\ , and *persp* values determine how 3d simulation space is mapped to the 2d plane of the image. Basically they control how the simulation box appears in the image. @@ -478,7 +460,6 @@ plane perpendicular to the view vector implied by the *theta* and vector and user-specified up vector. Thus this internal vector is computed from the user-specified *up* vector as - .. parsed-literal:: up_internal = view cross (up cross view) @@ -506,10 +487,8 @@ perspective. The *persp* keyword is not yet supported as an option. - ---------- - The *box* keyword determines if and how the simulation box boundaries are rendered as thin cylinders in the image. If *no* is set, then the box boundaries are not drawn and the *diam* setting is ignored. If @@ -536,10 +515,8 @@ processor sub-domain are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor ` command. - ---------- - The *shiny* keyword determines how shiny the objects rendered in the image will appear. The *sfactor* value must be a value 0.0 <= *sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface @@ -553,10 +530,8 @@ cost of computing the image by roughly 2x. The strength of the effect can be scaled by the *dfactor* parameter. If *no* is set, no depth shading is performed. - ---------- - 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 @@ -574,7 +549,6 @@ MPEG or other movie file you can use: % convert *.jpg foo.gif % convert -loop 1 *.ppm foo.mpg - Animated GIF files from ImageMagick are not optimized. You can use a program like gifsicle to optimize and thus massively shrink them. MPEG files created by ImageMagick are in MPEG-1 format with a rather @@ -596,19 +570,16 @@ MPEG or other movie file you can use: FFmpeg is a command line tool that is available on many platforms and allows extremely flexible encoding and decoding of movies. - .. code-block:: bash cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi - Front ends for FFmpeg exist for multiple platforms. For more information see the `FFmpeg homepage `_ ---------- - Play the movie: * a) Use your browser to view an animated GIF movie. @@ -646,14 +617,11 @@ See the :doc:`Modify ` doc page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. - ---------- - Restrictions """""""""""" - 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 @@ -672,7 +640,6 @@ errors and warnings printed by it. Those warnings and error messages will be printed to the screen only. Due to the way image data is communicated to FFmpeg, it will often print the message - .. parsed-literal:: pipe:: Input/output error @@ -684,7 +651,6 @@ and 2 format streams) have video bandwidth limits that can be crossed when rendering too large of image sizes. Typical warnings look like this: - .. parsed-literal:: [mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 2c672b4cf0..b2c1566894 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -6,7 +6,6 @@ dump_modify command Syntax """""" - .. code-block:: LAMMPS dump_modify dump-ID keyword values ... @@ -115,12 +114,9 @@ Syntax *framerate* arg = fps fps = frames per second for movie - - Examples """""""" - .. code-block:: LAMMPS dump_modify 1 format line "%d %d %20.15g %g %g" scale yes @@ -147,17 +143,13 @@ 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. - ---------- - These keywords apply to various dump styles, including the :doc:`dump image ` and :doc:`dump movie ` styles. The description gives details. - ---------- - The *append* keyword applies to all dump styles except *cfg* and *xtc* and *dcd*\ . It also applies only to text output files, not to binary or gzipped or image/movie files. If specified as *yes*\ , then dump @@ -165,10 +157,8 @@ snapshots are appended to the end of an existing dump file. If specified as *no*\ , then a new dump file will be created which will overwrite an existing file with the same name. - ---------- - 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 @@ -178,10 +168,8 @@ 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. - ---------- - The *buffer* keyword applies only to dump styles *atom*\ , *cfg*\ , *custom*\ , *local*\ , and *xyz*\ . It also applies only to text output files, not to binary or gzipped files. If specified as *yes*\ , which @@ -197,20 +185,16 @@ relatively expensive task of formatting the output for its own atoms. However it requires about twice the memory (per processor) for the extra buffering. - ---------- - The *delay* keyword applies to all dump styles. No snapshots will be output until the specified *Dstep* timestep or later. Specifying *Dstep* < 0 is the same as turning off the delay setting. This is a way to turn off unwanted output early in a simulation, for example, during an equilibration phase. - ---------- - The *element* keyword applies only to the dump *cfg*\ , *xyz*\ , and *image* styles. It associates element names (e.g. H, C, Fe) with LAMMPS atom types. See the list of element names at the bottom of @@ -231,12 +215,8 @@ will be accepted. .. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A - - - ---------- - 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 @@ -264,7 +244,6 @@ to the dump file. The *every* keyword cannot be used with the dump For example, the following commands will write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: - .. code-block:: LAMMPS variable s equal logfreq(10,3,10) @@ -274,7 +253,6 @@ write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: The following commands would write snapshots at the timesteps listed in file tmp.times: - .. code-block:: LAMMPS variable f file tmp.times @@ -295,10 +273,8 @@ in file tmp.times: dump\_modify first command. Any final value > 100 could be used in place of 101. - ---------- - The *first* keyword determines whether a dump snapshot is written on the very first timestep after the dump command is invoked. This will always occur if the current timestep is a multiple of N, the frequency @@ -307,20 +283,16 @@ if this is not the case, a dump snapshot will only be written if the setting of this keyword is *yes*\ . If it is *no*\ , which is the default, then it will not be written. - ---------- - The *flush* keyword determines whether a flush operation is invoked after a dump snapshot is written to the dump file. A flush insures the output in that file is current (no buffering by the OS), even if LAMMPS halts before the simulation completes. Flushes cannot be performed with dump style *xtc*\ . - ---------- - The *format* keyword can be used to change the default numeric format output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and *xyz* styles, and their MPIIO variants. Only the *line* or *none* @@ -371,7 +343,6 @@ settings, reverting all values to their default format. (large) integer, then you need to use an appropriate format. For example, these commands: - .. code-block:: LAMMPS compute 1 all property/local batom1 batom2 @@ -385,16 +356,12 @@ 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 integer. - ---------- - The *fileper* keyword is documented below with the *nfile* keyword. - ---------- - The *image* keyword applies only to the dump *atom* style. If the image value is *yes*\ , 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For @@ -405,16 +372,13 @@ current coordinate. Note that for dump style *custom* these various values can be printed in the dump file by using the appropriate atom attributes in the dump command itself. - ---------- - The *label* keyword applies only to the dump *local* style. When it writes local information, such as bond or angle topology to a dump file, it will use the specified *label* to format the header. By default this includes 2 lines: - .. parsed-literal:: ITEM: NUMBER OF ENTRIES @@ -423,10 +387,8 @@ the header. By default this includes 2 lines: The word "ENTRIES" will be replaced with the string specified, e.g. BONDS or ANGLES. - ---------- - The *maxfiles* keyword can only be used when a '\*' wildcard is included in the dump file name, i.e. when writing a new file(s) for each snapshot. The specified *Fmax* is how many snapshots will be @@ -439,10 +401,8 @@ timestep something bad will happen, e.g. when LAMMPS will exit with an error. You can dump every timestep, and limit the number of dump files produced, even if you run for 1000s of steps. - ---------- - The *nfile* or *fileper* keywords can be used in conjunction with the "%" wildcard character in the specified dump file name, for all dump styles except the *dcd*\ , *image*\ , *movie*\ , *xtc*\ , and *xyz* styles @@ -463,10 +423,8 @@ file for every Np processors. For example, if Np = 4, every 4th processor (0,4,8,12,etc) will collect information from itself and the next 3 processors and write it to a dump file. - ---------- - The *pad* keyword only applies when the dump filename is specified with a wildcard "\*" character which becomes the timestep. If *pad* is 0, which is the default, the timestep is converted into a string of @@ -477,10 +435,8 @@ yield 0000100, 0012000, 2000000. This can be useful so that post-processing programs can easily read the files in ascending timestep order. - ---------- - The *pbc* keyword applies to all the dump styles. As explained on the :doc:`dump ` doc page, atom coordinates in a dump file may be slightly outside the simulation box. This is because periodic @@ -492,19 +448,15 @@ snapshot is written, then restored to their original position. If it is set to *no* they will not be. The *no* setting is the default because it requires no extra computation. - ---------- - The *precision* keyword only applies to the dump *xtc* style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to 1/1000 nanometer accuracy. - ---------- - 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 @@ -534,7 +486,6 @@ any snapshot we only want to output atoms that have hopped since the last snapshot. This can be accomplished with something the following commands: - .. code-block:: LAMMPS variable Dhop equal 0.6 @@ -573,10 +524,8 @@ 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 simply do nothing. - ---------- - The *region* keyword only applies to the dump *custom*\ , *cfg*\ , *image*\ , and *movie* styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only @@ -586,10 +535,8 @@ can be defined as the "inside" or "outside" of a geometric shape, and it can be the "union" or "intersection" of a series of simpler regions. - ---------- - The *scale* keyword applies only to the dump *atom* style. A scale value of *yes* means atom coords are written in normalized units from 0.0 to 1.0 in each box dimension. If the simulation box is triclinic @@ -597,10 +544,8 @@ value of *yes* means atom coords are written in normalized units from value of *no* means they are written in absolute distance units (e.g. Angstroms or sigma). - ---------- - The *sfactor* and *tfactor* keywords only apply to the dump *xtc* style. They allow customization of the unit conversion factors used when writing to XTC files. By default they are initialized for @@ -614,10 +559,8 @@ different units, since the compression algorithm used in XTC files is most effective when the typical magnitude of position data is between 10.0 and 0.1. - ---------- - The *sort* keyword determines whether lines of per-atom output in a snapshot are sorted or not. A sort value of *off* means they will typically be written in indeterminate order, either in serial or @@ -640,19 +583,15 @@ performed. output requires extra overhead in terms of CPU and communication cost, as well as memory, versus unsorted output. - ---------- - The *thermo* keyword only applies the dump *netcdf* style. It triggers writing of :doc:`thermo ` information to the dump file alongside per-atom data. The values included in the dump file are identical to the values specified by :doc:`thermo_style `. - ---------- - The *thresh* keyword only applies to the dump *custom*\ , *cfg*\ , *image*\ , and *movie* styles. Multiple thresholds can be specified. Specifying *none* turns off all threshold criteria. If thresholds are @@ -677,7 +616,6 @@ the dump command was invoked to produce a snapshot. This is a way to only dump atoms whose attribute has changed (or not changed). Three examples follow. - .. code-block:: LAMMPS dump_modify ... thresh ix != LAST @@ -687,7 +625,6 @@ simulation box since the last dump. (Note that atoms that crossed once and then crossed back between the two dump timesteps would not be included.) - .. code-block:: LAMMPS region foo sphere 10 20 10 15 @@ -697,7 +634,6 @@ included.) This will dump atoms which crossed the boundary of the spherical region since the last dump. - .. code-block:: LAMMPS variable charge atom "(q > 0.5) || (q < -0.5)" @@ -714,16 +650,13 @@ In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. - ---------- - The *time* keyword only applies to the dump *atom*\ , *custom*\ , and *local* styles (and their COMPRESS package versions *atom/gz*\ , *custom/gz* and *local/gz*\ ). If set to *yes*\ , each frame will will contain two extra lines before the "ITEM: TIMESTEP" entry: - .. parsed-literal:: ITEM: TIME @@ -735,16 +668,13 @@ This is to simplify post-processing of trajectories using a variable time step, e.g. when using :doc:`fix dt/reset `. The default setting is *no*\ . - ---------- - The *units* keyword only applies to the dump *atom*\ , *custom*\ , and *local* styles (and their COMPRESS package versions *atom/gz*\ , *custom/gz* and *local/gz*\ ). If set to *yes*\ , each individual dump file will contain two extra lines at the very beginning with: - .. parsed-literal:: ITEM: UNITS @@ -755,10 +685,8 @@ to the dump file and thus allows visualization and post-processing tools to determine the choice of units of the data in the dump file. The default setting is *no*\ . - ---------- - The *unwrap* keyword only applies to the dump *dcd* and *xtc* styles. If set to *yes*\ , coordinates will be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through @@ -767,19 +695,15 @@ the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot. - ---------- - These keywords apply only to the :doc:`dump image ` and :doc:`dump movie ` styles. Any keyword that affects an image, also affects a movie, since the movie is simply a collection of images. Some of the keywords only affect the :doc:`dump movie ` style. The descriptions give details. - ---------- - The *acolor* keyword can be used with the :doc:`dump image ` command, when its atom color setting is *type*\ , to set the color that atoms of each type will be drawn in the image. @@ -802,10 +726,8 @@ 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 of the specified atom types. - ---------- - The *adiam* keyword can be used with the :doc:`dump image ` command, when its atom diameter setting is *type*\ , to set the size that atoms of each type will be drawn in the image. The specified @@ -815,10 +737,8 @@ argument to specify a range of atom types. The specified *diam* is the size in whatever distance :doc:`units ` the input script is using, e.g. Angstroms. - ---------- - The *amap* keyword can be used with the :doc:`dump image ` command, with its *atom* keyword, when its atom setting is an atom-attribute, to setup a color map. The color map is used to assign @@ -934,7 +854,6 @@ atoms in individual molecules with a different color. See the examples/pour/in.pour.2d.molecule input script for an example of how this is used. - .. code-block:: LAMMPS variable colors string & @@ -948,18 +867,14 @@ this is used. In this case, 10 colors are defined, and molecule IDs are 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. - ---------- - The *bcolor* keyword can be used with the :doc:`dump image ` command, with its *bond* keyword, when its color setting is *type*\ , to set the color that bonds of each type will be drawn in the image. @@ -982,10 +897,8 @@ 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 of the specified bond types. - ---------- - The *bdiam* keyword can be used with the :doc:`dump image ` command, with its *bond* keyword, when its diam setting is *type*\ , to set the diameter that bonds of each type will be drawn in the image. @@ -995,10 +908,8 @@ the *type* argument to specify a range of bond types. The specified *diam* is the size in whatever distance :doc:`units ` you are using, e.g. Angstroms. - ---------- - The *bitrate* keyword can be used with the :doc:`dump movie ` command to define the size of the resulting movie file and its quality via setting how many kbits per second are to be used for the movie file. Higher bitrates require less @@ -1012,10 +923,8 @@ older compression formats. Not all movie file formats supported by dump movie allow the bitrate to be set. If not, the setting is silently ignored. - ---------- - The *boxcolor* keyword sets the color of the simulation box drawn around the atoms in each image as well as the color of processor sub-domain boundaries. See the "dump image box" command for how to @@ -1024,10 +933,8 @@ 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. - ---------- - 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 @@ -1040,10 +947,8 @@ names are searched first, then the 140 pre-defined color names. This means you can also use the *color* keyword to overwrite one of the pre-defined color names with new RBG values. - ---------- - The *framerate* keyword can be used with the :doc:`dump movie ` command to define the duration of the resulting movie file. Movie files written by the dump *movie* command have a default frame rate of 24 frames per second and the images generated @@ -1055,10 +960,8 @@ frame rate higher than 24 is not recommended, as it will result in simply dropping the rendered images. It is more efficient to dump images less frequently. - ---------- - Restrictions """""""""""" none @@ -1107,10 +1010,8 @@ The option defaults are * color = 140 color names are pre-defined as listed below * framerate = 24 - ---------- - These are the standard 109 element names that LAMMPS pre-defines for use with the :doc:`dump image ` and dump\_modify commands. @@ -1126,10 +1027,8 @@ use with the :doc:`dump image ` and dump\_modify commands. * 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" * 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" - ---------- - 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 diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index fa9eb106c9..099ac25ef5 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -6,7 +6,6 @@ dump molfile command Syntax """""" - .. parsed-literal:: dump ID group-ID molfile N file format path @@ -19,11 +18,9 @@ Syntax * format = file format to be used * path = file path with plugins (optional) - Examples """""""" - .. parsed-literal:: dump mf1 all molfile 10 melt1.xml hoomd @@ -56,10 +53,8 @@ by this dump style: the number of atoms must not change, the atoms must be sorted, outside of the coordinates no change in atom properties (like type, mass, charge) will be recorded. - ---------- - The *format* keyword determines what format is used to write out the dump. For this to work, LAMMPS must be able to find and load a compatible molfile plugin that supports this format. Settings made via @@ -79,10 +74,8 @@ if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot. - ---------- - Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be @@ -94,14 +87,11 @@ an arbitrary timestep. N can be changed between runs by using the :doc:`dump_modify every ` command. The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. - ---------- - Restrictions """""""""""" - The *molfile* dump style is part of the USER-MOLFILE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -125,10 +115,8 @@ application itself. The plugins are installed in the directory: with a set of header files that are compatible with VMD 1.9 and 1.9.1 (June 2012) - ---------- - Related commands """""""""""""""" diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index c03ea4ef1e..3dd8a7c5c5 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -9,7 +9,6 @@ dump netcdf/mpiio command Syntax """""" - .. parsed-literal:: dump ID group-ID netcdf N file args @@ -25,7 +24,6 @@ Syntax Examples """""""" - .. parsed-literal:: dump 1 all netcdf 100 traj.nc type x y z vx vy vz @@ -63,29 +61,20 @@ by :doc:`thermo_style `. .. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/ - - .. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/ - - - ---------- - Restrictions """""""""""" - The *netcdf* and *netcdf/mpiio* dump styles are part of the USER-NETCDF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Related commands """""""""""""""" diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index aab7d7809d..8b5843a86b 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -6,7 +6,6 @@ dump vtk command Syntax """""" - .. parsed-literal:: dump ID group-ID vtk N file args @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: dump dmpvtk all vtk 100 dump\*.myforce.vtk id type vx fx @@ -74,10 +72,8 @@ determine the kind of output. For the *vtk* style, sorting is off by default. See the :doc:`dump_modify ` doc page for details. - ---------- - 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 @@ -109,10 +105,8 @@ a wildcard "\*" must be included in the filename, as discussed below. Otherwise the dump files will get overwritten with the new snapshot each time. - ---------- - Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be @@ -161,14 +155,11 @@ If *dump\_modify binary* is used, the dump file (or files, if "\*" or will be about the same size as a text version, but will typically write out much faster. - ---------- - Restrictions """""""""""" - The *vtk* style does not support writing of gzipped dump files. The *vtk* dump style is part of the USER-VTK package. It is only diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index d3fba63f1d..d1ebe67694 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -6,7 +6,6 @@ dynamical_matrix command Syntax """""" - .. code-block:: LAMMPS dynamical_matrix group-ID style gamma args keyword value ... @@ -22,12 +21,9 @@ Syntax *file* name = name of output file for the dynamical matrix *binary* arg = *yes* or *no* or *gzip* - - Examples """""""" - .. code-block:: LAMMPS dynamical_matrix 1 regular 0.000001 @@ -51,7 +47,6 @@ matrix defined by \Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}} - The output for the dynamical matrix is printed three elements at a time. The three elements are the three :math:`\beta` elements for a respective i/:math:`\alpha`/j combination. Each line is printed in order of j diff --git a/doc/src/echo.rst b/doc/src/echo.rst index 6ed4911b2c..d91571ed0c 100644 --- a/doc/src/echo.rst +++ b/doc/src/echo.rst @@ -6,7 +6,6 @@ echo command Syntax """""" - .. parsed-literal:: echo style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: echo both @@ -42,7 +40,6 @@ Restrictions Default """"""" - .. parsed-literal:: echo log diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 57a1b706b3..42fb071a43 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -6,7 +6,6 @@ fix command Syntax """""" - .. parsed-literal:: fix ID group-ID style args @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve @@ -77,10 +75,8 @@ continue on with its calculations in a restarted simulation. See the a fix in an input script that reads a restart file. See the doc pages for individual fixes for info on which ones can be restarted. - ---------- - Some fixes calculate one of three styles of quantities: global, per-atom, or local, which can be used by other commands or output as described below. A global quantity is one or more system-wide values, @@ -127,10 +123,8 @@ 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. - ---------- - In LAMMPS, the values generated by a fix can be used in several ways: * Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. @@ -142,7 +136,6 @@ In LAMMPS, the values generated by a fix can be used in several ways: command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command. - See the :doc:`Howto output ` doc page for a summary of various LAMMPS output options, many of which involve fixes. @@ -159,10 +152,8 @@ If a fix value is accessed in another way, e.g. by a intensive or extensive value. See the doc page for individual fixes for further info. - ---------- - Each fix style has its own doc page which describes its arguments and what it does, as listed below. Here is an alphabetic list of fix styles available in LAMMPS. They are also listed in more compact form @@ -396,7 +387,6 @@ accelerated styles exist. Restrictions """""""""""" - Some fix styles are part of specific packages. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for individual fixes tell if it is part of a package. diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 102504d3bc..fe4236f790 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -6,7 +6,6 @@ fix adapt command Syntax """""" - .. parsed-literal:: fix ID group-ID adapt N attribute args ... keyword value ... @@ -47,12 +46,9 @@ Syntax *no* = values will remain altered at the end of a run *yes* = reset altered values to their original values at the end of a run - - Examples """""""" - .. parsed-literal:: fix 1 all adapt 1 pair soft a 1 1 v_prefactor @@ -102,10 +98,8 @@ themselves are actually altered by this fix. Make sure you use the *reset yes* option if you want the parameters to be restored to their initial values after the run. - ---------- - The *pair* keyword enables various parameters of potentials defined by the :doc:`pair_style ` command to be changed, if the pair style supports it. Note that the :doc:`pair_style ` and @@ -270,16 +264,13 @@ For example, these commands would change the prefactor coefficient of the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: - .. parsed-literal:: variable prefactor equal ramp(10,30) fix 1 all adapt 1 pair soft a \* \* v_prefactor - ---------- - The *bond* keyword uses the specified variable to change the value of a bond coefficient over time, very similar to how the *pair* keyword operates. The only difference is that now a bond coefficient for a @@ -303,10 +294,8 @@ working with fix\_adapt are | :doc:`harmonic ` | k,r0 | type bonds | +---------------------------------+-------+------------+ - ---------- - The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is defined by the :doc:`kspace_style ` command. If the @@ -315,10 +304,8 @@ variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword is set to *no* or *yes*\ . - ---------- - The *atom* keyword enables various atom properties to be changed. The *aparam* argument is the name of the parameter to change. This is the current list of atom parameters that can be varied by this fix: @@ -349,16 +336,13 @@ For example, these commands would shrink the diameter of all granular particles in the "center" group from 1.0 to 0.1 in a linear fashion over the course of a 1000-step simulation: - .. parsed-literal:: variable size equal ramp(1.0,0.1) fix 1 center adapt 10 atom diameter v_size - ---------- - **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 diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 00b498c178..fac0703fc1 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -6,7 +6,6 @@ fix adapt/fep command Syntax """""" - .. parsed-literal:: fix ID group-ID adapt/fep N attribute args ... keyword value ... @@ -47,12 +46,9 @@ Syntax *no* = parameters are adapted at timestep N *yes* = parameters are adapted one timestep after N - - Examples """""""" - .. parsed-literal:: fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor @@ -74,7 +70,6 @@ with two differences, * There is a new option *after* for better compatibility with "fix ave/time". - This version is suited for free energy calculations using :doc:`compute ti ` or :doc:`compute fep `. @@ -106,10 +101,8 @@ such as "fix ave/time" is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with the same values of the parameters. - ---------- - The *pair* keyword enables various parameters of potentials defined by the :doc:`pair_style ` command to be changed, if the pair style supports it. Note that the :doc:`pair_style ` and @@ -241,16 +234,13 @@ For example, these commands would change the prefactor coefficient of the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: - .. parsed-literal:: variable prefactor equal ramp(10,30) fix 1 all adapt 1 pair soft a \* \* v_prefactor - ---------- - The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is defined by the :doc:`kspace_style ` command. If the @@ -259,10 +249,8 @@ variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword is set to *no* or *yes*\ . - ---------- - The *atom* keyword enables various atom properties to be changed. The *aparam* argument is the name of the parameter to change. This is the current list of atom parameters that can be varied by this fix: @@ -291,7 +279,6 @@ For example, these commands would shrink the diameter of all granular particles in the "center" group from 1.0 to 0.1 in a linear fashion over the course of a 1000-step simulation: - .. parsed-literal:: variable size equal ramp(1.0,0.1) @@ -300,10 +287,8 @@ over the course of a 1000-step simulation: For :doc:`rRESPA time integration `, this fix changes parameters on the outermost rRESPA level. - ---------- - **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 diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 8902a482d9..e48e54a809 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -6,7 +6,6 @@ fix addforce command Syntax """""" - .. parsed-literal:: fix ID group-ID addforce fx fy fz keyword value ... @@ -31,12 +30,9 @@ Syntax *energy* value = v_name v_name = variable with name that calculates the potential energy of each atom in the added force field - - Examples """""""" - .. parsed-literal:: fix kick flow addforce 1.0 0.0 0.0 @@ -76,10 +72,8 @@ If the *region* keyword is used, the atom must also be in the specified geometric :doc:`region ` in order to have force added to it. - ---------- - Adding a force to atoms implies a change in their potential energy as they move due to the applied force field. For dynamics via the "run" command, this energy can be optionally added to the system's potential @@ -115,10 +109,8 @@ were a spring-like F = kx, then the energy formula should be E = -0.5kx\^2. If you don't do this correctly, the minimization will not converge properly. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -137,10 +129,8 @@ 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:** 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 f9a17cc3ef..cb07b7a9dc 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -6,7 +6,6 @@ fix addtorque command Syntax """""" - .. parsed-literal:: fix ID group-ID addtorque Tx Ty Tz @@ -16,11 +15,9 @@ Syntax * Tx,Ty,Tz = torque component values (torque units) * any of Tx,Ty,Tz can be a variable (see below) - Examples """""""" - .. parsed-literal:: fix kick bead addtorque 2.0 3.0 5.0 @@ -37,7 +34,6 @@ the group such that: * the group would move as a rigid body in the absence of other forces. - 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 @@ -52,10 +48,8 @@ functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent torque. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -91,7 +85,6 @@ the iteration count during the minimization. Restrictions """""""""""" - 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_append_atoms.rst b/doc/src/fix_append_atoms.rst index 095be0daaf..269454dc75 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -6,7 +6,6 @@ fix append/atoms command Syntax """""" - .. parsed-literal:: fix ID group-ID append/atoms face ... keyword value ... @@ -38,12 +37,9 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix 1 all append/atoms zhi size 5.0 freq 295 units lattice @@ -88,10 +84,8 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings. - ---------- - **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 @@ -103,7 +97,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix style is part of the SHOCK 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_atc.rst b/doc/src/fix_atc.rst index 48ee5cb243..fa22e9d7b7 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -6,7 +6,6 @@ fix atc command Syntax """""" - .. parsed-literal:: fix atc @@ -24,11 +23,9 @@ Syntax * parameter\_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file - Examples """""""" - .. parsed-literal:: fix AtC internal atc thermal Ar_thermal.dat @@ -44,7 +41,6 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or an on-th .. image:: JPG/atc_nanotube.jpg :align: center - .. parsed-literal:: The following coupling example is typical, but non-exhaustive: @@ -74,7 +70,6 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or an on-th likewise for this post-processing example: - .. parsed-literal:: # ... commands to create and initialize the MD system @@ -107,7 +102,6 @@ likewise for this post-processing example: the mesh's linear interpolation functions can be used as the localization function by using the field option: - .. parsed-literal:: fix AtC internal atc field @@ -116,10 +110,8 @@ by using the field option: Note coupling and post-processing can be combined in the same simulations using separate fixes. - ---------- - **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 ` options @@ -132,7 +124,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - Thermal and two\_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently: * the coupling is restricted to thermal physics @@ -241,52 +232,36 @@ Default """"""" None - ---------- - For detailed exposition of the theory and algorithms please see: .. _Wagner: - - **(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. .. _Zimmeman2004: - - **(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. .. _Zimmerman2010: - - **(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364. .. _Templeton2010: - - **(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. .. _Jones: - - **(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940. .. _Templeton2011: - - **(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736. .. _Mandadapu: - - **(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation. diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 79634c0796..57be2dd24f 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -6,7 +6,6 @@ fix atom/swap command Syntax """""" - .. parsed-literal:: fix ID group-ID atom/swap N X seed T keyword values ... @@ -33,12 +32,9 @@ Syntax *region* value = region-ID region-ID = ID of region to use as an exchange/move volume - - Examples """""""" - .. parsed-literal:: fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2 @@ -178,7 +174,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. @@ -196,13 +191,9 @@ Default The option defaults are ke = yes, semi-grand = no, mu = 0.0 for all atom types. - ---------- - .. _Sadigh: - - **(Sadigh)** B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012). diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 70337e9fa2..bea3963d06 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -6,7 +6,6 @@ fix ave/atom command Syntax """""" - .. parsed-literal:: fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ... @@ -28,12 +27,9 @@ Syntax f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) v_name = per-atom vector calculated by an atom-style variable with name - - Examples """""""" - .. parsed-literal:: fix 1 all ave/atom 1 100 100 vx vy vz @@ -83,7 +79,6 @@ had been listed one by one. E.g. these 2 fix ave/atom commands are equivalent, since the :doc:`compute stress/atom ` command creates a per-atom array with 6 columns: - .. parsed-literal:: compute my_stress all stress/atom NULL @@ -92,10 +87,8 @@ command creates a per-atom array with 6 columns: c_my_stress[3] c_my_stress[4] & c_my_stress[5] c_my_stress[6] - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps @@ -111,10 +104,8 @@ timesteps 90,92,94,96,98,100 will be used to compute the final average on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on timestep 200, etc. - ---------- - The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying @@ -156,10 +147,8 @@ thermodynamic keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to time average. - ---------- - **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 diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index d6d813f4e4..6d31ca9f93 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -6,7 +6,6 @@ fix ave/chunk command Syntax """""" - .. parsed-literal:: fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... @@ -62,12 +61,9 @@ Syntax *title3* arg = string string = text to print as 3rd line of output file - - Examples """""""" - .. parsed-literal:: fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values" @@ -82,14 +78,12 @@ with the newer, more flexible fix ave/chunk and :doc:`compute chunk/atom ` command creates, in this case, a per-atom array with 3 columns: - .. parsed-literal:: compute myAng all property/atom angmomx angmomy angmomz @@ -173,10 +166,8 @@ case, a per-atom array with 3 columns: computational cost (summing across processors), so be careful to define a reasonable number of chunks. - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be accessed and contribute to the average. The final averaged quantities are generated on timesteps @@ -219,10 +210,8 @@ discussed below. the size of each bin can vary at each timestep if the simulation box size changes, e.g. for an NPT simulation. - ---------- - The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. As noted above, any other atom attributes can be used as input values to this fix by using the :doc:`compute property/atom ` command and then specifying @@ -303,10 +292,8 @@ attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to average within chunks. - ---------- - Additional optional keywords also affect the operation of this fix and its outputs. @@ -430,7 +417,6 @@ values for each of these, so they do not need to be specified. By default, these header lines are as follows: - .. parsed-literal:: # Chunk-averaged data for fix ID and group name @@ -468,10 +454,8 @@ be in unitless reduced units (0-1). This is not true for the Coord1 value of style *bin/sphere* or *bin/cylinder* which both represent radial dimensions. Those values are always in distance :doc:`units `. - ---------- - **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 diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 6f2aaedc9f..693f498640 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -6,7 +6,6 @@ fix ave/correlate command Syntax """""" - .. parsed-literal:: fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... @@ -57,12 +56,9 @@ Syntax *title3* arg = string string = text to print as 3rd line of output file - - Examples """""""" - .. parsed-literal:: fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate @@ -124,7 +120,6 @@ vector had been listed one by one. E.g. these 2 fix ave/correlate commands are equivalent, since the :doc:`compute pressure ` command creates a global vector with 6 values. - .. parsed-literal:: compute myPress all pressure NULL @@ -133,10 +128,8 @@ values. c_myPress[1] c_myPress[2] c_myPress[3] & c_myPress[4] c_myPress[5] c_myPress[6] - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be used to calculate correlation data. The input values are sampled every *Nevery* timesteps. The @@ -147,7 +140,6 @@ beginning of the simulation or the last output time; see the *ave* keyword for options. For the set of samples, the correlation value Cij is calculated as: - .. parsed-literal:: Cij(delta) = ave(Vi(t)\*Vj(t+delta)) @@ -160,7 +152,6 @@ time delta. The maximum delta used is of size (\ *Nrepeat*\ -1)\*\ *Nevery*\ . Thus the correlation between a pair of input values yields *Nrepeat* correlation datums: - .. parsed-literal:: Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij((Nrepeat-1)\*Nevery) @@ -176,10 +167,8 @@ Vi(10)\*V j20), Vi(15)\*Vj(25), ..., Vi(85)\*Vj(95), Vi(90)\*Vj(100). non-zero. Also, if the *ave* keyword is set to *one* which is the default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required. - ---------- - If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a @@ -219,10 +208,8 @@ keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to time correlate. - ---------- - Additional optional keywords also affect the operation of this fix. The *type* keyword determines which pairs of input values are @@ -248,7 +235,6 @@ pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time. itself and every other value. I.e. Cij = Vi\*Vj, for i,j = 1,N so Npair = N\^2. - The *ave* keyword determines what happens to the accumulation of correlation samples every *Nfreq* timesteps. If the *ave* setting is *one*\ , then the accumulation is restarted or zeroed every *Nfreq* @@ -292,7 +278,6 @@ values for each of these, so they do not need to be specified. By default, these header lines are as follows: - .. parsed-literal:: # Time-correlated data for fix ID @@ -304,14 +289,11 @@ describes the two values that are printed at the first of each section of output. In the third line the value pairs are replaced with the appropriate fields from the fix ave/correlate command. - ---------- - Let Sij = a set of time correlation data for input values I and J, namely the *Nrepeat* values: - .. parsed-literal:: Sij = Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij(\*Nrepeat-1)\*Nevery) @@ -326,10 +308,8 @@ quantities which can be derived from time correlation data. If a normalization factor is needed for the time integration, it can be included in the variable formula or via the *prefactor* keyword. - ---------- - **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 @@ -362,7 +342,6 @@ as determined by the *type* keyword, as described above. ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, CNN. - The array values calculated by this fix are treated as intensive. If you need to divide them by the number of atoms, you must do this in a later processing step, e.g. when using them in a diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index 2aa33f9040..444ff35a98 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -6,7 +6,6 @@ fix ave/correlate/long command Syntax """""" - .. parsed-literal:: fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... @@ -54,12 +53,9 @@ Syntax *ncount* args = Ncount Ncount = number of values over which succesive correlators are averaged - - Examples """""""" - .. parsed-literal:: fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate @@ -130,7 +126,6 @@ the run command. This fix is not invoked during energy minimization. Restrictions """""""""""" - 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. @@ -148,13 +143,9 @@ the :doc:`fix ave/correlate ` doc page. The option defaults for keywords unique to this command are as follows: ncorr=20, nlen=16, ncount=2. - ---------- - .. _Ramirez: - - **(Ramirez)** J. Ramirez, S.K. Sukumaran, B. Vorselaars and A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index ca8c312527..d2296c1d27 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -9,7 +9,6 @@ fix ave/histo/weight command Syntax """""" - .. parsed-literal:: fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ... @@ -63,12 +62,9 @@ Syntax *title3* arg = string string = text to print as 3rd line of output file, only for vector mode - - Examples """""""" - .. parsed-literal:: fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running @@ -138,7 +134,6 @@ vector or columns of the array had been listed one by one. E.g. these 2 fix ave/histo commands are equivalent, since the :doc:`compute com/chunk ` command creates a global array with 3 columns: - .. parsed-literal:: compute myCOM all com/chunk @@ -155,10 +150,8 @@ corresponding weight is tallied. E.g. The Nth entry (weight) in the second vector is tallied to the bin corresponding to the Nth entry in the first vector. - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the histogram. The final histogram is generated on timesteps that are @@ -176,10 +169,8 @@ histogram on timestep 100. Similarly for timesteps = 100, then no time averaging of the histogram is done; a histogram is simply generated on timesteps 100,200,etc. - ---------- - The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying @@ -237,10 +228,8 @@ thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to histogram. - ---------- - Additional optional keywords also affect the operation of this fix. If the *mode* keyword is set to *scalar*\ , then all input values must @@ -327,7 +316,6 @@ values for each of these, so they do not need to be specified. By default, these header lines are as follows: - .. parsed-literal:: # Histogram for fix ID @@ -339,10 +327,8 @@ describes the six values that are printed at the first of each section of output. The third describes the 4 values printed for each bin in the histogram. - ---------- - **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 diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 9f3f7660c9..159740433e 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -6,7 +6,6 @@ fix ave/time command Syntax """""" - .. parsed-literal:: fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ... @@ -56,12 +55,9 @@ Syntax *title3* arg = string string = text to print as 3rd line of output file, only for vector mode - - Examples """""""" - .. parsed-literal:: fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile @@ -132,17 +128,14 @@ vector or columns of the array had been listed one by one. E.g. these 2 fix ave/time commands are equivalent, since the :doc:`compute rdf ` command creates, in this case, a global array with 3 columns, each of length 50: - .. parsed-literal:: compute myRDF all rdf 50 1 2 fix 1 all ave/time 100 1 100 c_myRDF[\*] file tmp1.rdf mode vector fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps @@ -160,10 +153,8 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. - ---------- - If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If *mode* = scalar, then if no bracketed term is appended, the global scalar calculated by the @@ -212,10 +203,8 @@ keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to time average. - ---------- - Additional optional keywords also affect the operation of this fix. If the *mode* keyword is set to *scalar*\ , then all input values must @@ -290,7 +279,6 @@ default values for each of these, so they do not need to be specified. By default, these header lines are as follows for *mode* = scalar: - .. parsed-literal:: # Time-averaged data for fix ID @@ -303,7 +291,6 @@ so the *title3* setting is ignored when *mode* = scalar. By default, these header lines are as follows for *mode* = vector: - .. parsed-literal:: # Time-averaged data for fix ID @@ -315,10 +302,8 @@ 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 fields from the fix ave/time command. - ---------- - **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 diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index c4bb8e79e4..2b4bcb0257 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -6,7 +6,6 @@ fix aveforce command Syntax """""" - .. parsed-literal:: fix ID group-ID aveforce fx fy fz keyword value ... @@ -27,12 +26,9 @@ Syntax *region* value = region-ID region-ID = ID of region atoms must be in to have added force - - Examples """""""" - .. parsed-literal:: fix pressdown topwall aveforce 0.0 -1.0 0.0 @@ -73,10 +69,8 @@ If the *region* keyword is used, the atom must also be in the specified geometric :doc:`region ` in order to have force added to it. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -95,10 +89,8 @@ 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:** 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 b407921477..85288c9db8 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -6,7 +6,6 @@ fix balance command Syntax """""" - .. parsed-literal:: fix ID group-ID balance Nfreq thresh style args keyword args ... @@ -47,12 +46,9 @@ Syntax *out* arg = filename filename = write each processor's sub-domain to a file, at each re-balancing - - Examples """""""" - .. parsed-literal:: fix 2 all balance 1000 1.05 shift x 10 1.05 @@ -147,10 +143,8 @@ forced even if the current balance is perfect (1.0) be specifying a :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. - ---------- - The method used to perform a load balance is specified by one of the listed styles, which are described in detail below. There are 2 kinds of styles. @@ -172,7 +166,6 @@ applied. .. image:: JPG/balance_rcb_small.jpg :target: JPG/balance_rcb.jpg - The *rcb* style is a "tiling" method which does not produce a logical 3d grid of processors. Rather it tiles the simulation domain with rectangular sub-boxes of varying size and shape in an irregular @@ -195,10 +188,8 @@ When a "tiling" method is specified, the current domain partitioning ("grid" or "tiled") is ignored, and a new partitioning is computed from scratch. - ---------- - The *group-ID* is ignored. However the impact of balancing on different groups of atoms can be affected by using the *group* weight style as described below. @@ -214,10 +205,8 @@ command settings. On re-balance steps, re-balancing will only be attempted if the current imbalance factor, as defined above, exceeds the *thresh* setting. - ---------- - The *shift* style invokes a "grid" method for balancing, as described above. It changes the positions of cutting planes between processors in an iterative fashion, seeking to reduce the imbalance factor. @@ -282,10 +271,8 @@ the normal reneighboring procedure. the threshold accuracy is reached (in a dimension) is less iterations than *Niter* and exit early. - ---------- - The *rcb* style invokes a "tiled" method for balancing, as described above. It performs a recursive coordinate bisectioning (RCB) of the simulation domain. The basic idea is as follows. @@ -311,10 +298,8 @@ the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the atoms in that sub-box. - ---------- - The *out* keyword writes text to the specified *filename* with the results of each re-balancing operation. The file contains the bounds of the sub-domain for each processor after the balancing operation @@ -323,7 +308,6 @@ completes. The format of the file is compatible with the visualizing mesh files. An example is shown here for a balancing by 4 processors for a 2d problem: - .. parsed-literal:: ITEM: TIMESTEP @@ -371,10 +355,8 @@ rectangle for each processor (1 to 4). For a 3d problem, the syntax is similar with 8 vertices listed for each processor, instead of 4, and "SQUARES" replaced by "CUBES". - ---------- - **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 @@ -399,14 +381,11 @@ by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index 5ee6ba2f83..4356bcc9b5 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -6,7 +6,6 @@ fix bocs command Syntax """""" - .. parsed-literal:: fix ID group-ID bocs keyword values ... @@ -19,12 +18,9 @@ Syntax *linear_spline* values = input_filename *cubic_spline* values = input_filename - - Examples """""""" - .. parsed-literal:: fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 @@ -41,7 +37,6 @@ Dunn and Noid in :ref:`(Dunn1) ` to the standard MTTK barostat by Martyna et. al. in :ref:`(Martyna) ` . The first half of the command mimics a standard fix npt command: - .. parsed-literal:: fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp @@ -56,7 +51,6 @@ With either spline method, the only argument that needs to follow it is the name of a file that contains the desired pressure correction as a function of volume. The file must be formatted so each line has: - .. parsed-literal:: Volume_i, PressureCorrection_i @@ -73,7 +67,6 @@ range provided, the simulation will stop. With the *analytic* option, the arguments are as follows: - .. parsed-literal:: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N @@ -85,7 +78,6 @@ coefficients should all be in atmospheres \* cubic angstroms. Restrictions """""""""""" - As this is computing a (modified) pressure, group-ID should be *all*\ . The pressure correction has only been tested for use with an isotropic @@ -110,26 +102,16 @@ paper by Dunn et. al. :ref:`(Dunn2) ` . .. _bocsgithub: https://github.com/noid-group/BOCS - - - ---------- - .. _bocs-Dunn1: - - **(Dunn1)** Dunn and Noid, J Chem Phys, 143, 243148 (2015). .. _bocs-Martyna: - - **(Martyna)** Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994). .. _bocs-Dunn2: - - **(Dunn2)** Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018). diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index fd384cad56..6951cfc806 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -6,7 +6,6 @@ fix bond/break command Syntax """""" - .. parsed-literal:: fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... @@ -25,12 +24,9 @@ Syntax fraction = break a bond with this probability if otherwise eligible seed = random number seed (positive integer) - - Examples """""""" - .. parsed-literal:: fix 5 all bond/break 10 2 1.2 @@ -117,10 +113,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local may need to thermostat your system to compensate for energy changes resulting from broken bonds (and angles, dihedrals, impropers). - ---------- - **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 @@ -141,7 +135,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 62815f5f40..8f09c638ca 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -6,7 +6,6 @@ fix bond/create command Syntax """""" - .. parsed-literal:: fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... @@ -38,12 +37,9 @@ Syntax *itype* value = impropertype impropertype = type of created impropers - - Examples """""""" - .. parsed-literal:: fix 5 all bond/create 10 1 2 0.8 1 @@ -218,10 +214,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local thermostat your system to compensate for energy changes resulting from created bonds (and angles, dihedrals, impropers). - ---------- - **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 @@ -242,7 +236,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 1206177ba1..7f69f1bda7 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -6,7 +6,6 @@ fix bond/react command Syntax """""" - .. parsed-literal:: fix ID group-ID bond/react common_keyword values ... @@ -55,14 +54,11 @@ Syntax charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges - - Examples """""""" For unabridged example scripts and files, see examples/USER/reaction. - .. parsed-literal:: molecule mol1 pre_reacted_topology.txt @@ -255,7 +251,6 @@ A map file has a header and a body. The header of map file the contains one mandatory keyword and five optional keywords. The mandatory keyword is 'equivalences': - .. parsed-literal:: N *equivalences* = # of atoms N in the reaction molecule templates @@ -263,7 +258,6 @@ mandatory keyword is 'equivalences': The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and 'constraints': - .. parsed-literal:: N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template @@ -298,11 +292,8 @@ there are four types of constraints available, as discussed below. A sample map file is given below: - ---------- - - .. parsed-literal:: # this is a map file @@ -330,10 +321,8 @@ A sample map file is given below: 6 6 7 7 - ---------- - The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be bonded to four atoms with mutually different atom types. This feature @@ -347,7 +336,6 @@ Any number of additional constraints may be specified in the Constraints section of the map file. The constraint of type 'distance' has syntax as follows: - .. parsed-literal:: distance *ID1* *ID2* *rmin* *rmax* @@ -358,7 +346,6 @@ distance between *rmin* and *rmax* for the reaction to occur. The constraint of type 'angle' has the following syntax: - .. parsed-literal:: angle *ID1* *ID2* *ID3* *amin* *amax* @@ -372,7 +359,6 @@ reacting molecules. The constraint of type 'dihedral' has the following syntax: - .. parsed-literal:: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* @@ -395,10 +381,8 @@ probability according to the temperature-dependent Arrhenius equation: k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}} - The Arrhenius constraint has the following syntax: - .. parsed-literal:: arrhenius *A* *n* *E_a* *seed* @@ -482,7 +466,6 @@ 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: - .. parsed-literal:: fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 @@ -502,10 +485,8 @@ you should be cautious about invoking this fix too frequently. You can dump out snapshots of the current bond topology via the dump local command. - ---------- - **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 @@ -532,7 +513,6 @@ all other fixes that use any group created by fix bond/react. Restrictions """""""""""" - This fix is part of the USER-REACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -551,12 +531,8 @@ Default The option defaults are stabilization = no, prob = 1.0, stabilize\_steps = 60, update\_edges = none - ---------- - .. _Gissinger: - - **(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017). diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index 296cf986cf..b593c8de1f 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -6,7 +6,6 @@ fix bond/swap command Syntax """""" - .. parsed-literal:: fix ID group-ID bond/swap Nevery fraction cutoff seed @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all bond/swap 50 0.5 1.3 598934 @@ -115,15 +113,12 @@ ends of a chain swap with each other. running dynamics, but can affect calculation of some diagnostic quantities or the printing of unwrapped coordinates to a dump file. - ---------- - This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of style *temp*\ , as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp all temp @@ -142,10 +137,8 @@ during thermodynamic output via the :doc:`thermo_style custom ` co 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:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator @@ -177,7 +170,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. @@ -199,13 +191,9 @@ Related commands **Default:** none - ---------- - .. _Sides: - - **(Sides)** Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004). diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 7d7c326800..a90b301e4b 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -6,7 +6,6 @@ fix box/relax command Syntax """""" - .. parsed-literal:: fix ID group-ID box/relax keyword value ... @@ -30,12 +29,9 @@ Syntax *fixedpoint* values = x y z x,y,z = perform relaxation dilation/contraction around this point (distance units) - - Examples """""""" - .. parsed-literal:: fix 1 all box/relax iso 0.0 vmax 0.001 @@ -54,10 +50,8 @@ close to the specified external tensor. Conceptually, specifying a positive pressure is like squeezing on the simulation box; a negative pressure typically allows the box to expand. - ---------- - The external pressure tensor is specified using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* keywords. These keywords give you the ability to specify all 6 @@ -138,10 +132,8 @@ displaced by the same amount, different on each iteration. new objective function valid for the new box size/shape. Repeat as necessary until the box size/shape has reached its new equilibrium. - ---------- - The *couple* keyword allows two or three of the diagonal components of the pressure tensor to be "coupled" together. The value specified with the keyword determines which are coupled. For example, *xz* @@ -155,10 +147,8 @@ dilated or contracted by the same percentage every timestep. The *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. - ---------- - The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. @@ -167,7 +157,6 @@ pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using "iso Ptarget" is the same as specifying these 4 keywords: - .. parsed-literal:: x Ptarget @@ -181,7 +170,6 @@ stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Ptarget" is the same as specifying these 4 keywords: - .. parsed-literal:: x Ptarget @@ -195,7 +183,6 @@ as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Ptarget" is the same as specifying these 7 keywords: - .. parsed-literal:: x Ptarget @@ -206,10 +193,8 @@ these 7 keywords: xz 0.0 couple none - ---------- - The *vmax* keyword can be used to limit the fractional change in the volume of the simulation box that can occur in one iteration of the minimizer. If the pressure is not settling down during the @@ -220,10 +205,8 @@ percent in one iteration when *couple xyz* has been specified. For any other case it means no linear dimension of the simulation box can change by more than 1/10 of a percent. - ---------- - With this fix, the potential energy used by the minimizer is augmented by an additional energy provided by the fix. The overall objective function then is: @@ -232,7 +215,6 @@ function then is: E = U + P_t \left(V-V_0 \right) + E_{strain} - where *U* is the system potential energy, :math:`P_t` is the desired hydrostatic pressure, :math:`V` and :math:`V_0` are the system and reference volumes, respectively. :math:`E_{strain}` is the strain energy expression @@ -245,7 +227,6 @@ global system stress tensor **P** will satisfy the relation: \mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d} - where **I** is the identity matrix, :math:`\mathbf{h_0}` is the box dimension tensor of the reference cell, and ::math:`\mathbf{h_{0d}}` is the diagonal part of :math:`\mathbf{h_0}`. :math:`\mathbf{S_t}` @@ -297,17 +278,14 @@ from a restart file. systems (e.g. liquids) will not sustain a non-hydrostatic applied pressure, which means the minimizer will not converge. - ---------- - This fix computes a temperature and pressure each timestep. The temperature is used to compute the kinetic contribution to the pressure, even though this is subsequently ignored by default. To do this, the fix creates its own computes of style "temp" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -328,10 +306,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom `. @@ -367,7 +343,6 @@ result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants: - .. parsed-literal:: variable emin equal pe+f_1 @@ -385,7 +360,6 @@ described above. Restrictions """""""""""" - Only dimensions that are available can be adjusted by this fix. Non-periodic dimensions are not available. *z*\ , *xz*\ , and *yz*\ , are not available for 2D simulations. *xy*\ , *xz*\ , and *yz* are only @@ -411,12 +385,8 @@ Default The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0. - ---------- - .. _Parrinello1981: - - **(Parrinello1981)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index f274341a68..93b489023e 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -6,7 +6,6 @@ fix client/md command Syntax """""" - .. parsed-literal:: fix ID group-ID client/md @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all client/md @@ -66,10 +64,8 @@ the "client" and/or "server" code for this kind of client/server MD simulation. The examples/message/README file explains how to launch LAMMPS and another code in tandem to perform a coupled simulation. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -94,7 +90,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the MESSAGE 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_cmap.rst b/doc/src/fix_cmap.rst index 00a1851e88..f2b26ba73a 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -6,7 +6,6 @@ fix cmap command Syntax """""" - .. parsed-literal:: fix ID group-ID cmap filename @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix myCMAP all cmap ../potentials/cmap36.data @@ -51,7 +49,6 @@ 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: - .. parsed-literal:: N crossterms @@ -59,7 +56,6 @@ in its header section: where N is the number of CMAP cross-terms. It should also have a section in the body of the data file like this with N lines: - .. parsed-literal:: CMAP @@ -92,10 +88,8 @@ energy of the system, as output by the the note below about how to include the CMAP energy when performing an :doc:`energy minimization `. - ---------- - **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 @@ -133,7 +127,6 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - To function as expected this fix command must be issued *before* a :doc:`read_data ` command but *after* a :doc:`read_restart ` command. @@ -149,19 +142,13 @@ Related commands **Default:** none - ---------- - .. _Buck: - - **(Buck)** Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006). .. _Brooks2: - - **(Brooks)** Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009). diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 042edbad6b..9b415127f1 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -6,7 +6,6 @@ fix colvars command Syntax """""" - .. parsed-literal:: fix ID group-ID colvars configfile keyword values ... @@ -25,12 +24,9 @@ Syntax use unwrapped coordinates in collective variables (default: yes) *tstat* arg = fix id of a thermostat or NULL (default: NULL) - - Examples """""""" - .. parsed-literal:: fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide @@ -56,10 +52,8 @@ A detailed discussion of its implementation is in :ref:`(Fiorin) `. There are some example scripts for using this package with LAMMPS in the examples/USER/colvars directory. - ---------- - The only mandatory argument to the fix is the filename to the colvars input file that contains the input that is independent from the MD program in which the colvars library has been integrated. @@ -125,7 +119,6 @@ fix is "extensive". Restrictions """""""""""" - This fix is part of the USER-COLVARS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -146,12 +139,8 @@ Default The default options are input = NULL, output = out, seed = 1966, unwrap yes, and tstat = NULL. - ---------- - .. _Fiorin: - - **(Fiorin)** Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 2f7913eb04..1c58516a8a 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -6,7 +6,6 @@ fix controller command Syntax """""" - .. parsed-literal:: fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar @@ -31,11 +30,9 @@ Syntax * setpoint = desired value of process variable (same units as process variable) * cvar = name of control variable - Examples """""""" - .. parsed-literal:: fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol @@ -111,7 +108,6 @@ keywords described above. The discretized version of this equation is: c_n = \hat{E} c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right) - where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time interval between updates, and the subscripted variables indicate the values of *c* and *e* at @@ -149,10 +145,8 @@ fix performs its first update of *cvar* after *Nevery* timesteps. On the first update, the value of the derivative term is set to zero, because the value of :math:`e_n-1` is not yet defined. - ---------- - The process variable *pvar* can be specified as the output of a :doc:`compute ` or :doc:`fix ` or the evaluation of a :doc:`variable `. In each case, the compute, fix, or variable @@ -194,10 +188,8 @@ variable. It must be an internal-style variable, because this fix updates its value directly. Note that other commands can use an equal-style versus internal-style variable interchangeably. - ---------- - **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 diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 308a0cd4d6..70e6140714 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -9,7 +9,6 @@ fix deform/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID deform N parameter args ... keyword value ... @@ -79,12 +78,9 @@ Syntax lattice = distances are defined in lattice units box = distances are defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box @@ -129,10 +125,8 @@ command. Every Nth timestep during the run, the simulation box is expanded, contracted, or tilted to ramped values between the initial and final values. - ---------- - For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their styles and values. @@ -173,7 +167,6 @@ is defined as delta/L0, where L0 is the original box length and delta is the change relative to the original length. The box length L as a function of time will change as - .. parsed-literal:: L(t) = L0 (1 + erate\*dt) @@ -201,7 +194,6 @@ is the change relative to the original length. The box length L as a function of time will change as - .. parsed-literal:: L(t) = L0 exp(trate\*dt) @@ -254,7 +246,6 @@ The *wiggle* style oscillates the specified box length dimension sinusoidally with the specified amplitude and period. I.e. the box length L as a function of time is given by - .. parsed-literal:: L(t) = L0 + A sin(2\*pi t/Tp) @@ -289,7 +280,6 @@ Here is an example of using the *variable* style to perform the same box deformation as the *wiggle* style formula listed above, where we assume that the current timestep = 0. - .. parsed-literal:: variable A equal 5.0 @@ -302,10 +292,8 @@ For the *scale*\ , *vel*\ , *erate*\ , *trate*\ , *volume*\ , *wiggle*\ , and *variable* styles, the box length is expanded or compressed around its mid point. - ---------- - For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. @@ -345,7 +333,6 @@ direction for xy deformation) from the unstrained orientation. The tilt factor T as a function of time will change as - .. parsed-literal:: T(t) = T0 + L0\*erate\*dt @@ -378,7 +365,6 @@ from the unstrained orientation. The tilt factor T as a function of time will change as - .. parsed-literal:: T(t) = T0 exp(trate\*dt) @@ -406,7 +392,6 @@ The *wiggle* style oscillates the specified tilt factor sinusoidally with the specified amplitude and period. I.e. the tilt factor T as a function of time is given by - .. parsed-literal:: T(t) = T0 + A sin(2\*pi t/Tp) @@ -440,7 +425,6 @@ Here is an example of using the *variable* style to perform the same box deformation as the *wiggle* style formula listed above, where we assume that the current timestep = 0. - .. parsed-literal:: variable A equal 5.0 @@ -449,10 +433,8 @@ assume that the current timestep = 0. variable rate equal "2\*PI\*v_A/v_Tp \* cos(2\*PI \* step\*dt/v_Tp)" fix 2 all deform 1 xy variable v_displace v_rate remap v - ---------- - All of the tilt styles change the xy, xz, yz tilt factors during a simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes are normally bounded by half the distance of the parallel box length. @@ -488,10 +470,8 @@ does not change the atom positions due to non-periodicity. In this mode, if you tilt the system to extreme angles, the simulation will simply become inefficient due to the highly skewed simulation box. - ---------- - Each time the box size or shape is changed, the *remap* keyword determines whether atom positions are remapped to the new box. If *remap* is set to *x* (the default), atoms in the fix group are @@ -581,10 +561,8 @@ does not affect the *variable* style. You should use the *xlat*\ , *ylat*\ , *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -620,7 +598,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - You cannot apply x, y, or z deformations to a dimension that is shrink-wrapped via the :doc:`boundary ` command. diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 585106e8f7..cf2b59709e 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -6,7 +6,6 @@ fix deposit command Syntax """""" - .. parsed-literal:: fix ID group-ID deposit N type M seed keyword values ... @@ -63,12 +62,9 @@ Syntax lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box @@ -299,7 +295,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the 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_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index ce370a90f6..436af3c344 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -9,7 +9,6 @@ fix dpd/energy/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID dpd/energy @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all dpd/energy @@ -49,10 +47,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -71,14 +67,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -99,14 +92,10 @@ Related commands **Default:** none - ---------- - .. _Lisal1: - - **(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", @@ -114,8 +103,6 @@ J. Chem. Phys., 135, 204105 (2011). .. _Larentzos3: - - **(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 04ab50dbd8..a13382728d 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -9,7 +9,6 @@ fix tdpd/source command Syntax """""" - .. parsed-literal:: fix ID group-ID edpd/source keyword values ... @@ -31,12 +30,9 @@ Syntax dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units) source = heat source or concentration source (flux units, see below) - - Examples """""""" - .. parsed-literal:: fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01 @@ -66,10 +62,8 @@ spherical domain to apply the source flux to. If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a cuboid domain to apply the source flux to. - ---------- - **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 @@ -81,7 +75,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -96,14 +89,10 @@ Related commands **Default:** none - ---------- - .. _Li2014b: - - **(Li2014)** Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis, "Energy-conserving dissipative particle dynamics with temperature-dependent properties", J. Comput. Phys., 265: 113-127 @@ -111,8 +100,6 @@ temperature-dependent properties", J. Comput. Phys., 265: 113-127 .. _Li2015b: - - **(Li2015)** Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis, "Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101 diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 38f86ff8f8..ed94f0e7fa 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -6,7 +6,6 @@ fix drag command Syntax """""" - .. parsed-literal:: fix ID group-ID drag x y z fmag delta @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0 diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 2bf34ce90f..73b9921fda 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -6,7 +6,6 @@ fix drude command Syntax """""" - .. parsed-literal:: fix ID group-ID drude flag1 flag2 ... flagN @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all drude 1 1 0 1 0 2 2 2 @@ -42,7 +40,6 @@ or capital letter (N,C,D): Restrictions """""""""""" - This fix should be invoked before any other commands that implement the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole `. diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 07db211528..10c4bbfc60 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -9,7 +9,6 @@ fix drude/transform/inverse command Syntax """""" - .. parsed-literal:: fix ID group-ID style keyword value ... @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 3 all drude/transform/direct @@ -56,7 +54,6 @@ Masses: M' = M + m - .. math:: m' = \frac {M\, m } {M'} @@ -67,7 +64,6 @@ Positions: X' = \frac {M\, X + m\, x} {M'} - .. math:: x' = x - X @@ -78,7 +74,6 @@ Velocities: V' = \frac {M\, V + m\, v} {M'} - .. math:: v' = v - V @@ -89,7 +84,6 @@ Forces: F' = F + f - .. math:: f' = \frac { M\, f - m\, F} {M'} @@ -107,10 +101,8 @@ and the virial defined with absolute positions X\, F + x\, f = X'\, F' + x'\, f' - ---------- - This fix requires each atom know whether it is a Drude particle or not. You must therefore use the :doc:`fix drude ` command to specify the Drude status of each atom type. @@ -123,10 +115,8 @@ specify the Drude status of each atom type. electrons or non-polarizable atoms in the group. The non-polarizable atoms will simply not be transformed. - ---------- - This fix does NOT perform time integration. It only transform masses, coordinates, velocities and forces. Thus you must use separate time integration fixes, like :doc:`fix nve ` or :doc:`fix npt ` to actually update the velocities and positions of @@ -142,7 +132,6 @@ acting on two distinct groups. Example: - .. parsed-literal:: fix fDIRECT all drude/transform/direct @@ -168,7 +157,6 @@ pressure *thermo\_press*. Example: - .. parsed-literal:: compute cTEMP_CORE gCORES temp/com @@ -188,15 +176,12 @@ In order to avoid the flying ice cube problem (irreversible transfer of linear momentum to the center of mass of the system), you may need to add a *fix momentum* command: - .. parsed-literal:: fix fMOMENTUM all momentum 100 linear 1 1 1 - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -215,12 +200,8 @@ Related commands **Default:** none - ---------- - .. _Lamoureux1: - - **(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index ca95e576b7..cc0de3dfbc 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -6,7 +6,6 @@ fix dt/reset command Syntax """""" - .. parsed-literal:: fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... @@ -20,7 +19,6 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *emax* or *units* - .. parsed-literal:: *emax* value = Emax @@ -32,7 +30,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 5 all dt/reset 10 1.0e-5 0.01 0.1 diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 03ad47fcee..9f54cd2ad3 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -6,7 +6,6 @@ fix efield command Syntax """""" - .. parsed-literal:: fix ID group-ID efield ex ey ez keyword value ... @@ -25,12 +24,9 @@ Syntax *energy* value = v_name v_name = variable with name that calculates the potential energy of each atom in the added E-field - - Examples """""""" - .. parsed-literal:: fix kick external-field efield 1.0 0.0 0.0 @@ -71,10 +67,8 @@ If the *region* keyword is used, the atom must also be in the specified geometric :doc:`region ` in order to have force added to it. - ---------- - Adding a force or torque to atoms implies a change in their potential energy as they move or rotate due to the applied E-field. @@ -118,10 +112,8 @@ due to the electric field were a spring-like F = kx, then the energy formula should be E = -0.5kx\^2. If you don't do this correctly, the minimization will not converge properly. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -169,7 +161,6 @@ the iteration count during the minimization. Restrictions """""""""""" - This fix is part of the 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_ehex.rst b/doc/src/fix_ehex.rst index e981c63b36..86cb42c8cd 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -6,7 +6,6 @@ fix ehex command Syntax """""" - .. parsed-literal:: fix ID group-ID ehex nevery F keyword value @@ -29,12 +28,9 @@ Syntax *hex* value = none omit the coordinate correction to recover the HEX algorithm - - Examples """""""" - .. parsed-literal:: # Lennard-Jones, from examples/in.ehex.lj @@ -128,10 +124,8 @@ cool continuously. This fix will default to :doc:`fix_heat ` (HEX algorithm) if the keyword *hex* is specified. - ---------- - **Compatibility with SHAKE and RATTLE (rigid molecules)**\ : This fix is compatible with :doc:`fix shake ` and :doc:`fix rattle `. If either of these constraining algorithms is @@ -167,10 +161,8 @@ constraints will be satisfied. temperature gradients. A higher precision can be achieved by decreasing the timestep. - ---------- - **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 @@ -182,7 +174,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -193,19 +184,13 @@ Related commands **Default:** none - ---------- - .. _Ikeshoji: - - **(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994). .. _Wirnsberger: - - **(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015). diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 09be2e34c7..459883ea2f 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -6,7 +6,6 @@ fix electron/stopping command Syntax """""" - .. parsed-literal:: fix ID group-ID electron/stopping Ecut file keyword value ... @@ -25,12 +24,9 @@ Syntax *minneigh* value = minneigh minneigh = minimum number of neighbors an atom to have stopping applied - - Examples """""""" - .. parsed-literal:: fix el all electron/stopping 10.0 elstop-table.txt @@ -52,7 +48,6 @@ considered, the simulated range of the ions can be severely overestimated The electronic stopping is implemented by applying a friction force to each atom as: - .. math:: \vec{F}_i = \vec{F}^0_i - \frac{\vec{v}_i}{\|\vec{v}_i\|} \cdot S_e @@ -97,10 +92,8 @@ geometric :doc:`region ` in order to have electronic stopping applied to it. This is useful if the position of the bulk material is fixed. By default the electronic stopping is applied everywhere in the simulation cell. - ---------- - The energy ranges and stopping powers are read from the file *file*\ . Lines starting with *#* and empty lines are ignored. Otherwise each line must contain exactly **N+1** numbers, where **N** is the number of atom @@ -115,7 +108,6 @@ intermediate energy values are calculated with linear interpolation between For example: - .. parsed-literal:: # This is a comment @@ -154,7 +146,6 @@ on this fix. Restrictions """""""""""" - This pair style 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. @@ -164,42 +155,28 @@ Default 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 .. _Nordlund98: - - **(Nordlund98)** Nordlund, Kai, et al. Physical Review B 57.13 (1998): 7556. .. _Nordlund95: - - **(Nordlund95)** Nordlund, Kai. Computational materials science 3.4 (1995): 448-456. .. _SRIM: - - **(SRIM)** SRIM webpage: http://www.srim.org/ .. _CasP: - - **(CasP)** CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp\_en.html .. _PASS: - - **(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index 7605c3cd5a..3351d59303 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -9,7 +9,6 @@ fix enforce2d/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID enforce2d @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 5 all enforce2d @@ -32,10 +30,8 @@ Zero out the z-dimension velocity and force on each atom in the group. This is useful when running a 2d simulation to insure that atoms do not move from their initial z coordinate. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -54,10 +50,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index da1459970f..5913d0e887 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -6,7 +6,6 @@ fix eos/cv command Syntax """""" - .. parsed-literal:: fix ID group-ID eos/cv cv @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all eos/cv 0.01 @@ -35,20 +33,16 @@ the constant-volume heat capacity, and is defined as follows: u_{i} = u^{mech}_{i} + u^{cond}_{i} = C_{V} \theta_{i} - where :math:`C_V` is the constant-volume heat capacity, :math:`u^{cond}` is the internal conductive energy, and :math:`u^{mech}` is the internal mechanical energy. Note that alternative definitions of the mesoparticle equation of state are possible. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -62,14 +56,10 @@ Related commands **Default:** none - ---------- - .. _Larentzos4: - - **(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index 1f8ec7ba9b..e15bcfa882 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -6,7 +6,6 @@ fix eos/table command Syntax """""" - .. parsed-literal:: fix ID group-ID eos/table style file N keyword @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all eos/table linear eos.table 100000 KEYWORD @@ -51,14 +49,11 @@ The filename specifies a file containing tabulated internal temperature and internal energy values. The keyword specifies a section of the file. The format of this file is described below. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # EOS TABLE (one or more comment or blank lines) @@ -102,14 +97,11 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD 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_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 8f95876bcc..b85df50769 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -9,7 +9,6 @@ fix eos/table/rx/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID eos/table/rx style file1 N keyword ... @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table @@ -49,7 +47,6 @@ computed according to the following relation: U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{b}T}{2} + Nk_{b}T \\ - where *m* is the number of species, :math:`c_{i,j}` is the concentration of species *j* in particle *i*\ , :math:`u_j` is the internal energy of species j, :math:`\Delta H_{f,j} is the heat of @@ -92,14 +89,11 @@ value for the single species. Additionally, the energy correction and temperature correction coefficients may also be specified as fix arguments. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # EOS TABLE (one or more comment or blank lines) @@ -138,14 +132,11 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - The format of a heat of formation file is as follows (without the parenthesized comments): - .. parsed-literal:: # HEAT OF FORMATION TABLE (one or more comment or blank lines) @@ -166,7 +157,6 @@ three additional columns that correspond to the energy correction, the temperature correction coefficient and molecule correction coefficient. In this case, the format of the file is as follows: - .. parsed-literal:: # HEAT OF FORMATION TABLE (one or more comment or blank lines) @@ -178,10 +168,8 @@ coefficient. In this case, the format of the file is as follows: ... no 0.93 0.00 0.000 -1.76 - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -200,14 +188,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD 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_evaporate.rst b/doc/src/fix_evaporate.rst index 628fd3226e..36469dc5c3 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -6,7 +6,6 @@ fix evaporate command Syntax """""" - .. parsed-literal:: fix ID group-ID evaporate N M region-ID seed @@ -24,12 +23,9 @@ Syntax keyword = *molecule* *molecule* value = *no* or *yes* - - Examples """""""" - .. parsed-literal:: fix 1 solvent evaporate 1000 10 surface 49892 @@ -92,7 +88,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the 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_external.rst b/doc/src/fix_external.rst index 756d896e80..78a60ac93a 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -6,7 +6,6 @@ fix external command Syntax """""" - .. parsed-literal:: fix ID group-ID external mode args @@ -23,12 +22,9 @@ Syntax *pf/array* args = Napply Napply = apply array forces every Napply steps - - Examples """""""" - .. parsed-literal:: fix 1 all external pf/callback 1 1 @@ -43,10 +39,8 @@ This fix allows external programs that are running LAMMPS through its properties on specific timesteps, similar to the way other fixes do. The external driver can be a :doc:`C/C++ or Fortran program ` or a :doc:`Python script `. - ---------- - If mode is *pf/callback* then the fix will make a callback every *Ncall* timesteps or minimization iterations to the external program. The external program computes forces on atoms by setting values in an @@ -57,7 +51,6 @@ be used multiple times to update atom forces. The callback function "foo" is invoked by the fix as: - .. parsed-literal:: foo(void \*ptr, bigint timestep, int nlocal, int \*ids, double \*\*x, double \*\*fexternal); @@ -85,12 +78,8 @@ code `Quest `_. .. _quest: http://dft.sandia.gov/Quest - - - ---------- - If mode is *pf/array* then the fix simply stores force values in an array. The fix adds these forces to each atom in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce ` command works. @@ -98,7 +87,6 @@ every *Napply* steps, similar to the way the :doc:`fix addforce ` The name of the public force array provided by the FixExternal class is - .. parsed-literal:: double \*\*fexternal; @@ -114,10 +102,8 @@ between calls to the LAMMPS :doc:`run ` command, it could retrieve atom coordinates from LAMMPS, compute forces, set values in fexternal, etc. - ---------- - To use this fix during energy minimization, the energy corresponding to the added forces must also be set so as to be consistent with the added forces. Otherwise the minimization will not converge correctly. @@ -125,7 +111,6 @@ added forces. Otherwise the minimization will not converge correctly. This can be done from the external driver by calling this public method of the FixExternal class: - .. parsed-literal:: void set_energy(double eng); @@ -136,10 +121,8 @@ atoms. It should also be provided in :doc:`energy units ` consistent with the simulation. See the details below for how to insure this energy setting is used appropriately in a minimization. - ---------- - **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 56093550f7..f6fd3e5c69 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -6,7 +6,6 @@ fix ffl command Syntax """""" - .. parsed-literal:: fix ID id-group ffl tau Tstart Tstop seed [flip-type] @@ -22,12 +21,9 @@ Syntax flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default - - Examples """""""" - .. parsed-literal:: fix 3 boundary ffl 10 300 300 31415 @@ -46,12 +42,10 @@ on the same atom groups. The time-evolution of a single particle undergoing Langevin dynamics is described by the equations - .. math:: \frac {dq}{dt} = \frac{p}{m}, - .. math:: \frac {dp}{dt} = -\gamma p + W + F, @@ -107,7 +101,6 @@ fix is "extensive". Restrictions """""""""""" - In order to perform constant-pressure simulations please use :doc:`fix press/berendsen `, rather than :doc:`fix npt `, to avoid duplicate integration of the @@ -121,17 +114,12 @@ Related commands :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld `, :doc:`fix gle ` - ---------- - .. _Hijazi: - - .. _Bussi3: **(Hijazi)** M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018) - **(Bussi)** G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007) diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index a3dd56d577..95a5a19042 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -6,7 +6,6 @@ fix filter/corotate command Syntax """""" - .. parsed-literal:: fix ID group-ID filter/corotate keyword value ... @@ -22,12 +21,9 @@ Syntax *t* values = one or more atom types *m* value = one or more mass values - - Examples """""""" - .. parsed-literal:: timestep 8 @@ -62,10 +58,8 @@ contain the fastest covalent bonds inside clusters. If the clusters are chosen suitably, the :doc:`run_style respa ` is stable for outer time-steps of at least 8fs. - ---------- - **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 @@ -77,7 +71,6 @@ fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" - 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. @@ -88,12 +81,8 @@ Related commands **Default:** none - ---------- - .. _Fath2017: - - **(Fath)** Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017). diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 510336f4d2..1e1b418bdd 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -6,7 +6,6 @@ fix flow/gauss command Syntax """""" - .. parsed-literal:: fix ID group-ID flow/gauss xflag yflag zflag keyword @@ -29,12 +28,9 @@ Syntax no = do not compute work done by this fix yes = compute work done by this fix - - Examples """""""" - .. parsed-literal:: fix GD fluid flow/gauss 1 0 0 @@ -118,10 +114,8 @@ 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*. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** This fix is part of the USER-MISC package. It is only enabled if @@ -162,24 +156,16 @@ Default The option default for the *energy* keyword is energy = no. - ---------- - .. _Strong: - - **(Strong)** Strong and Eaves, J. Phys. Chem. B 121, 189 (2017). .. _Evans2: - - **(Evans)** Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986). .. _Zhu: - - **(Zhu)** Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index 3aa7512bad..ef74690c21 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -9,7 +9,6 @@ fix freeze/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID freeze @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 2 bottom freeze @@ -36,10 +34,8 @@ particles appropriately, as if the frozen particle has infinite mass. A similar functionality for normal (point) particles can be obtained using :doc:`fix setforce `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -58,10 +54,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options @@ -79,7 +73,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the GRANULAR 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_gcmc.rst b/doc/src/fix_gcmc.rst index ac14b2bcc4..04694704d1 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -6,7 +6,6 @@ fix gcmc command Syntax """""" - .. parsed-literal:: fix ID group-ID gcmc N X M type seed T mu displace keyword values ... @@ -54,12 +53,9 @@ Syntax *max* value = Maximum number of molecules allowed in the system *min* value = Minimum number of molecules allowed in the system - - Examples """""""" - .. parsed-literal:: fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01 @@ -154,7 +150,6 @@ thermal equilibrium with the simulation cell. Also, it is important that the temperature used by fix nvt be dynamic/dof, which can be achieved as follows: - .. parsed-literal:: compute mdtemp mdatoms temp @@ -252,7 +247,6 @@ as: \mu = \mu^{id} + \mu^{ex} - 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 @@ -267,7 +261,6 @@ pressure of the fictitious gas reservoir by: \mu^{id} = & k T \ln{\rho \Lambda^3} \\ = & k T \ln{\frac{\phi P \Lambda^3}{k T}} - where *k* is Boltzman's constant, *T* is the user-specified temperature, :math:`\rho` is the number density, *P* is the pressure, and :math:`\phi` is the fugacity coefficient. The constant @@ -278,7 +271,6 @@ styles except *lj* it is defined as the thermal de Broglie wavelength \Lambda = \sqrt{ \frac{h^2}{2 \pi m k T}} - where *h* is Planck's constant, and *m* is the mass of the exchanged atom or molecule. For unit style *lj*\ , :math:`\Lambda` is simply set to unity. Note that prior to March 2017, :math:`\Lambda` for unit style *lj* @@ -365,7 +357,6 @@ therefore, you will want to use the current number of atoms is used as a normalizing factor each time temperature is computed. A simple example of this is: - .. parsed-literal:: compute_modify thermo_temp dynamic yes @@ -443,7 +434,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. @@ -489,13 +479,9 @@ fugacity\_coeff = 1.0, intra\_energy = 0.0, tfac\_insert = 1.0. except for the situations where full\_energy is required, as listed above. - ---------- - .. _Frenkel: - - **(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002. diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index 9a2538d6be..f06c244364 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -6,7 +6,6 @@ fix gld command Syntax """""" - .. parsed-literal:: fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... @@ -31,12 +30,9 @@ Syntax *no* = do not set total random force to zero *yes* = set total random force to zero - - Examples """""""" - .. parsed-literal:: fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes @@ -68,7 +64,6 @@ With this fix active, the force on the *j*\ th atom is given as \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) - Here, the first term is representative of all conservative (pairwise, bonded, etc) forces external to this fix, the second is the temporally non-local dissipative force given as a Prony series, and the third is @@ -105,10 +100,8 @@ 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 keyword/value option pairs are used in the following ways. The keyword *frozen* can be used to specify how the extended variables @@ -128,10 +121,8 @@ to zero by subtracting off an equal part of it from each atom in the group. As a result, the center-of-mass of a system with zero initial momentum will not drift over time. - ---------- - **Restart, run start/stop, minimize info:** The instantaneous values of the extended variables are written to @@ -154,7 +145,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -169,12 +159,8 @@ Default The option defaults are frozen = no, zero = no. - ---------- - .. _Baczewski: - - **(Baczewski)** A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013). diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index 6f95b6030a..e2f3d130b6 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -6,7 +6,6 @@ fix gle command Syntax """""" - .. parsed-literal:: fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride] @@ -27,12 +26,9 @@ Syntax of the integration of the GLE, but has \*no effect\* on the accuracy of equilibrium sampling. It might change sampling properties when used together with *noneq*\ . - - Examples """""""" - .. parsed-literal:: fix 3 boundary gle 6 300 300 31415 smart.A @@ -55,7 +51,6 @@ Each degree of freedom in the thermostatted group is supplemented with Ns additional degrees of freedom s, and the equations of motion become - .. parsed-literal:: dq/dt=p/m @@ -133,7 +128,6 @@ fix is "extensive". Restrictions """""""""""" - The GLE thermostat in its current implementation should not be used with rigid bodies, SHAKE or RATTLE. It is expected that all the thermostatted degrees of freedom are fully flexible, and the sampled @@ -152,26 +146,18 @@ Related commands :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld ` - ---------- - .. _Ceriotti: - - **(Ceriotti)** Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010) .. _GLE4MD: - - **(GLE4MD)** `http://gle4md.org/ `_ .. _Ceriotti2: - - **(Ceriotti2)** Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, 030603 (2009) diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 3466bb393a..f9e9c10c5e 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -12,7 +12,6 @@ fix gravity/kk command Syntax """""" - .. parsed-literal:: fix ID group gravity magnitude style args @@ -36,12 +35,9 @@ Syntax x y z = vector direction to apply the acceleration x or y or z can be a variable (see below) - - Examples """""""" - .. parsed-literal:: fix 1 all gravity 1.0 chute 24.0 @@ -98,10 +94,8 @@ keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent gravitational field. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -120,10 +114,8 @@ 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:** 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 53b815ec36..cbe13fa634 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -6,7 +6,6 @@ fix grem command Syntax """""" - .. parsed-literal:: fix ID group-ID grem lambda eta H0 thermostat-ID @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix fxgREM all grem 400 -0.01 -30000 fxnpt @@ -42,7 +40,6 @@ dependent effective temperature T_{eff} = \lambda + \eta (H - H_0) - with :math:`\eta` negative and steep enough to only intersect the characteristic microcanonical temperature (Ts) of the system once, ensuring a unimodal enthalpy distribution in that replica. @@ -84,10 +81,8 @@ insight to Ts. Initially using an evenly-spaced :math:`\lambda` distribution identifies regions where small changes in enthalpy lead to large temperature changes. Replicas are easily added where needed. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -99,7 +94,6 @@ by this fix to add the rescaled kinetic pressure as part of Restrictions """""""""""" - 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. @@ -110,19 +104,13 @@ Related commands **Default:** none - ---------- - .. _Kim2010: - - **(Kim)** Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010). .. _Malolepsza: - - **(Malolepsza)** Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015). diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index ab0918a63d..f8a46de8a9 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -6,7 +6,6 @@ fix halt command Syntax """""" - .. parsed-literal:: fix ID group-ID halt N attribute operator avalue keyword value ... @@ -32,12 +31,9 @@ Syntax *error* value = *hard* or *soft* or *continue* *message* value = *yes* or *no* - - Examples """""""" - .. parsed-literal:: fix 10 all halt 1 bondmax > 1.5 @@ -90,7 +86,6 @@ computing some attribute of the current system. For example, the following "bondmax" variable will calculate the same quantity as the hstyle = bondmax option. - .. parsed-literal:: compute bdist all bond/local dist @@ -99,7 +94,6 @@ hstyle = bondmax option. Thus these two versions of a fix halt command will do the same thing: - .. parsed-literal:: fix 10 all halt 1 bondmax > 1.5 @@ -117,10 +111,8 @@ it is "false". The specified *avalue* must be a numeric value. - ---------- - The optional *error* keyword determines how the current run is halted. If its value is *hard*\ , then LAMMPS will stop with an error message. diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 5cc8504ff2..f140c5117d 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -6,7 +6,6 @@ fix heat command Syntax """""" - .. parsed-literal:: fix ID group-ID heat N eflux @@ -24,12 +23,9 @@ Syntax *region* value = region-ID region-ID = ID of region atoms must be in to have added force - - Examples """""""" - .. parsed-literal:: fix 3 qin heat 1 1.0 diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 2d0cda5970..eb45cee17e 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -6,7 +6,6 @@ fix hyper/global command Syntax """""" - .. parsed-literal:: fix ID group-ID hyper/global cutbond qfactor Vmax Tequil @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all hyper/global 1.0 0.3 0.8 300.0 @@ -68,7 +66,6 @@ the specified group. The current strain of bond *ij* (when running dynamics) is defined as - .. math:: E_{ij} = \frac{R_{ij} - R^0_{ij}}{R^0_{ij}} @@ -79,7 +76,6 @@ and :math:`R^0_{ij}` is the equilibrium distance in the quenched state. The bias energy :math:`V_{ij}` of any bond between atoms *i* and *j* is defined as - .. math:: V_{ij} = V^{max} \cdot \left( 1 - \left(\frac{E_{ij}}{q}\right)^2 \right) \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise} @@ -102,7 +98,6 @@ The derivative of :math:`V^{max}_{ij}` with respect to the position of each atom in the :math:`E^{max}` bond gives a bias force :math:`F^{max}_{ij}` acting on the bond as - .. math:: F^{max}_{ij} = - \frac{dV^{max}_{ij}}{dE_{ij}} = \frac{2 V^{max} E-{ij}}{\textrm{qfactor}^2} \textrm{ for } \left|E_{ij}\right| < \textrm{qfactor} \textrm{ or } 0 \textrm{ otherwise} @@ -112,7 +107,6 @@ only the two *ij* atoms in the :math:`E^{max}` bond. The time boost factor for the system is given each timestep I by - .. math:: B_i = e^{\beta V^{max}_{ij}} @@ -130,7 +124,6 @@ and an argument to this fix. Note that :math:`B_i >= 1` at every step. The elapsed time :math:`t_{hyper}` for a GHD simulation running for *N* timesteps is simply - .. math:: t_{hyper} = \sum_{i=1,N} B-i \cdot dt @@ -145,10 +138,8 @@ atoms the bias potential is added to, will also vary from timestep to timestep. This is in contrast to local hyperdynamics (LHD) where the boost factor is an input parameter; see the :doc:`fix hyper/local ` doc page for details. - ---------- - Here is additional information on the input parameters for GHD. The *cutbond* argument is the cutoff distance for defining bonds @@ -204,10 +195,8 @@ In general, the lower the value of *Tequil* and the higher the value of *Vmax*\ , the more time boost will be achievable by the GHD algorithm. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -268,7 +257,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. @@ -280,19 +268,13 @@ Related commands **Default:** None - ---------- - .. _Voter2013ghd: - - **(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013). .. _Mironghd: - - **(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 87bb71e4f0..acea82ecd3 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -6,7 +6,6 @@ fix hyper/local command Syntax """""" - .. parsed-literal:: fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget @@ -32,12 +31,9 @@ Syntax *check/ghost* values = none *check/bias* values = Nevery error/warn/ignore - - Examples """""""" - .. parsed-literal:: fix 1 all hyper/local 1.0 0.3 0.8 300.0 @@ -83,7 +79,6 @@ the same except for a pre-factor :math:`C_{ij}`, explained below. The bias energy :math:`V_{ij}` applied to a bond *ij* with maximum strain is - .. math:: V^{max}_{ij} = C_{ij} \cdot V^{max} \cdot \left(1 - \left(\frac{E_{ij}}{q}\right)^2\right) \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise} @@ -92,7 +87,6 @@ The derivative of :math:`V^{max}_{ij}` with respect to the position of each atom in the *ij* bond gives a bias force :math:`F^{max}_{ij}` acting on the bond as - .. math:: F^{max}_{ij} = - \frac{dV^{max}_{ij}}{dE_{ij}} = 2 C_{ij} V^{max} \frac{E_{ij}}{qfactor^2} \textrm{ for } \left|E_{ij}\right| < qfactor \textrm{ or } 0 \textrm{ otherwise} @@ -128,7 +122,6 @@ is first defined. The specified *Btarget* factor is then used to adjust the An instantaneous boost factor :math:`B_{ij}` is computed each timestep for each bond, as - .. math:: B_{ij} = e^{\beta V^{max}_{kl}} @@ -171,10 +164,8 @@ factor varies each timestep and is computed as a function of :math:`V_{max}`, :math:`E_{max}`, and :math:`T_{equil}`; see the :doc:`fix hyper/global ` doc page for details. - ---------- - Here is additional information on the input parameters for LHD. Note that the *cutbond*\ , *qfactor*\ , and *Tequil* arguments have the @@ -257,7 +248,6 @@ well for many solid-state systems. 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. - .. parsed-literal:: comm_modify cutoff 12.0 @@ -280,7 +270,6 @@ 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 - .. math:: t_{hyper} = B_{target} \cdot N \cdot dt @@ -293,7 +282,6 @@ is the elapsed time for a normal MD run of N timesteps. You cannot choose an arbitrarily large setting for *Btarget*\ . The maximum value you should choose is - .. math:: B_{target} = e^{\beta V_{small}} @@ -315,10 +303,8 @@ time (t\_hyper equation above) will be shorter. simulations with smaller and smaller *Btarget* values, until the event rate does not change (as a function of hyper time). - ---------- - Here is additional information on the optional keywords for this fix. The *bound* keyword turns on min/max bounds for bias coefficients @@ -377,10 +363,8 @@ keyword is not enabled, the output of that statistic will be 0. Note that both of these computations are costly, hence they are only enabled by these keywords. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -544,7 +528,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -561,19 +544,13 @@ The default settings for optimal keywords are bounds = -1 and reset = -1. The check/ghost and check/bias keywords are not enabled by default. - ---------- - .. _Voter2013lhd: - - **(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013). .. _Mironlhd: - - **(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 14246d90e1..4423a95872 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -6,7 +6,6 @@ fix imd command Syntax """""" - .. parsed-literal:: fix ID group-ID imd trate port keyword values ... @@ -28,12 +27,9 @@ Syntax off = LAMMPS waits to be connected to an IMD client before continuing (default) on = LAMMPS listens for an IMD client, but continues with the run - - Examples """""""" - .. parsed-literal:: fix vmd all imd 5678 @@ -108,7 +104,6 @@ with fix imd enabled, one needs to start VMD and load a coordinate or topology file that matches the fix group. When the VMD command prompts appears, one types the command line: - .. parsed-literal:: imd connect localhost 5678 @@ -138,16 +133,10 @@ screen output is active. .. _VMD: http://www.ks.uiuc.edu/Research/vmd - - .. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/ - - .. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms - - **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 @@ -159,7 +148,6 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - 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_indent.rst b/doc/src/fix_indent.rst index 8eabfd4447..337508dfd2 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -6,7 +6,6 @@ fix indent command Syntax """""" - .. parsed-literal:: fix ID group-ID indent K keyword values ... @@ -40,12 +39,9 @@ Syntax lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0 @@ -66,7 +62,6 @@ must set one of those 3 keywords. A spherical indenter exerts a force of magnitude - .. parsed-literal:: F(r) = - K (r - R)\^2 @@ -122,7 +117,6 @@ 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: - .. parsed-literal:: variable x equal "xlo + 0.25\*lx" @@ -130,7 +124,6 @@ the right edge, even if the box size changes: Similarly, either of these variable definitions will move the indenter from an initial position at 2.5 at a constant velocity of 5: - .. parsed-literal:: variable x equal "2.5 + 5\*elaplong\*dt" @@ -140,7 +133,6 @@ 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. - .. parsed-literal:: variable r0 equal 0.0 @@ -179,7 +171,6 @@ lattice spacing, you can define K with a variable whose formula contains *xlat*\ , *ylat*\ , *zlat* keywords of the :doc:`thermo_style ` command, e.g. - .. parsed-literal:: variable k equal 100.0/xlat/xlat diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index d0e1903689..f041bdea94 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -6,7 +6,6 @@ fix ipi command Syntax """""" - .. parsed-literal:: fix ID group-ID ipi address port [unix] [reset] @@ -76,7 +75,6 @@ the dynamical parameters are dealt with by i-PI. Restrictions """""""""""" - Using this fix on anything other than all atoms requires particular care, since i-PI will know nothing on atoms that are not those whose coordinates are transferred. However, one could use this strategy to @@ -93,20 +91,14 @@ Related commands :doc:`fix nve ` - ---------- - .. _IPICPC: - - **(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014). .. _ipihome: - - **(IPI)** `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi `_ diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index b176d39651..f282499bcc 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -9,7 +9,6 @@ fix langevin/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID langevin Tstart Tstop damp seed keyword values ... @@ -45,12 +44,9 @@ Syntax *no* = do not set total random force to zero *yes* = set total random force to zero - - Examples """""""" - .. code-block:: LAMMPS fix 3 boundary langevin 1.0 1.0 1000.0 699483 @@ -66,7 +62,6 @@ implicit solvent. Used with :doc:`fix nve `, this command performs Brownian dynamics (BD), since the total force on each atom will have the form: - .. math:: F = & F_c + F_f + F_r \\ @@ -170,10 +165,8 @@ 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 keyword/value option pairs are used in the following ways. The keyword *angmom* and *omega* keywords enable thermostatting of @@ -273,10 +266,8 @@ Regardless of the choice of output velocity, the sampling of the configurational distribution of atom positions is the same, and linearly consistent with the target temperature. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -295,10 +286,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator @@ -333,7 +322,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - For *gjf* do not choose damp=dt/2. *gjf* is not compatible with run\_style respa. @@ -348,37 +336,25 @@ Default The option defaults are angmom = no, omega = no, scale = 1.0 for all types, tally = no, zero = no, gjf = no. - ---------- - .. _Dunweg1: - - **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). .. _Schneider1: - - **(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978). .. _Gronbech-Jensen: - - **(Gronbech-Jensen)** Gronbech-Jensen and Farago, Mol Phys, 111, 983 (2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014) .. _2Gronbech-Jensen: - - **(Gronbech-Jensen)** Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019) .. _1Gronbech-Jensen: - - **(Gronbech-Jensen)** Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506 diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 56a0861003..0cc2a7e898 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -6,7 +6,6 @@ fix langevin/drude command Syntax """""" - .. parsed-literal:: fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ... @@ -28,12 +27,9 @@ Syntax *no* = do not set total random force on centers of mass to zero *yes* = set total random force on centers of mass to zero - - Examples """""""" - .. parsed-literal:: fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 @@ -62,7 +58,6 @@ Velocities: V' = \frac {M\, V + m\, v} {M'} - .. math:: v' = v - V @@ -73,7 +68,6 @@ Masses: M' = M + m - .. math:: m' = \frac {M\, m } {M'} @@ -84,7 +78,6 @@ The Langevin forces are computed as F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' - .. math:: f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' @@ -100,7 +93,6 @@ transform: F = \frac M {M'}\, F' - f' - .. math:: f = \frac m {M'}\, F' + f' @@ -132,10 +124,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. - ---------- - This fix requires each atom know whether it is a Drude particle or not. You must therefore use the :doc:`fix drude ` command to specify the Drude status of each atom type. @@ -155,15 +145,12 @@ specify the Drude status of each atom type. correctly. You must use the :doc:`comm_modify ` command to enable this, e.g. - .. parsed-literal:: comm_modify vel yes - ---------- - *Tcom* is the target temperature of the centers of mass, which would be used to thermostat the non-polarizable atoms. *Tdrude* is the (normally low) target temperature of the core-Drude particle pairs @@ -229,13 +216,10 @@ center-of-mass and relative coordinates, respectively, can be calculated using the :doc:`compute temp/drude ` command. - ---------- - Usage example for rigid bodies in the NPT ensemble: - .. parsed-literal:: comm_modify vel yes @@ -270,11 +254,8 @@ Comments: the cores. That's why the command *fix\_modify* should be called in that case. - - ---------- - **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 @@ -309,13 +290,9 @@ Default The option defaults are zero = no. - ---------- - .. _Jiang1: - - **(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index cde59b39ab..004a82f2aa 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -6,7 +6,6 @@ fix langevin/eff command Syntax """""" - .. parsed-literal:: fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... @@ -28,19 +27,15 @@ Syntax *no* = do not tally the energy added/subtracted to atoms *yes* = do tally the energy added/subtracted to atoms - .. parsed-literal:: *zero* value = *no* or *yes* *no* = do not set total random force to zero *yes* = set total random force to zero - - Examples """""""" - .. code-block:: LAMMPS fix 3 boundary langevin/eff 1.0 1.0 10.0 699483 @@ -54,14 +49,12 @@ to a group of nuclei and electrons in the :doc:`electron force field ` this command performs Brownian dynamics (BD), since the total force on each atom will have the form: - .. math:: F = & F_c + F_f + F_r \\ F_f = & - \frac{m}{\mathrm{damp}} v \\ F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}} - :math:`F_c` is the conservative force computed via the usual inter-particle interactions (:doc:`pair_style `). The :math:`F_f` and :math:`F_r` terms are added by this fix on a @@ -121,18 +114,12 @@ Default The option defaults are scale = 1.0 for all types and tally = no. - ---------- - .. _Dunweg2: - - **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). .. _Schneider2: - - **(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978). diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index b229a2ae8d..3ed7c3bbab 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -6,7 +6,6 @@ fix langevin/spin command Syntax """""" - .. parsed-literal:: fix ID group-ID langevin/spin T Tdamp seed @@ -17,11 +16,9 @@ Syntax * Tdamp = transverse magnetic damping parameter (adim) * seed = random number seed to use for white noise (positive integer) - Examples """""""" - .. parsed-literal:: fix 2 all langevin/spin 300.0 0.01 21 @@ -56,7 +53,6 @@ Note: due to the form of the sLLG equation, this fix has to be defined just before the nve/spin fix (and after all other magnetic fixes). As an example: - .. parsed-literal:: fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 @@ -72,10 +68,8 @@ 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. - ---------- - **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 @@ -89,7 +83,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - The *langevin/spin* fix is part of the SPIN package. This style is only enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. @@ -106,19 +99,13 @@ Related commands **Default:** none - ---------- - .. _Mayergoyz1: - - **(Mayergoyz)** I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009) .. _Tranchida2: - - **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index ddea5a809f..2482e994af 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -6,7 +6,6 @@ fix latte command Syntax """""" - .. parsed-literal:: fix ID group-ID latte peID @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix dftb all latte NULL @@ -55,10 +53,8 @@ specified as NULL. Eventually it will be used to enable LAMMPS to calculate a Coulomb potential as an alternative to LATTE performing the calculation. - ---------- - LATTE is a code for performing self-consistent charge transfer tight-binding (SC-TB) calculations of total energies and the forces acting on atoms in molecules and solids. This tight-binding method is @@ -106,10 +102,8 @@ areas of chemistry and materials science, as we now can simulate larger system sizes and longer time scales (:ref:`Cawkwell2012 `), (:ref:`Negre2016 `). - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -144,7 +138,6 @@ energy minimization, invoked by the :doc:`minimize ` command. Restrictions """""""""""" - This fix is part of the LATTE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -170,85 +163,61 @@ doing 99% or more of the work to compute quantum-accurate forces. **Default:** none - ---------- - .. _Elstner: - - **(Elstner)** M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). .. _Elstner1: - - **(Elstner)** M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). .. _Finnis2: - - **(Finnis)** M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998). .. _Mniszewski: - - **(Mniszewski)** S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015). .. _Niklasson2002: - - **(Niklasson2002)** A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). .. _Rubensson: - - **(Rubensson)** E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014). .. _Niklasson2008: - - **(Niklasson2008)** A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008). .. _Niklasson2014: - - **(Niklasson2014)** A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014). .. _Niklasson2017: - - **(Niklasson2017)** A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). .. _Cawkwell2012: - - **(Cawkwell2012)** A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012). .. _Negre2016: - - **(Negre2016)** C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016). diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index 09cec05750..d9f783e6a4 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -6,7 +6,6 @@ fix lb/fluid command Syntax """""" - .. parsed-literal:: fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ... @@ -48,12 +47,9 @@ Syntax *bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid. *printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps. - - Examples """""""" - .. parsed-literal:: fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1 @@ -74,14 +70,12 @@ the Navier Stokes equations, \partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= & 0 \\ \partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = & \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right) - with, .. math:: \eta_{\alpha \beta \gamma \nu} = \eta\left[\delta_{\alpha \gamma}\delta_{\beta \nu} + \delta_{\alpha \nu}\delta_{\beta \gamma} - \frac{2}{3}\delta_{\alpha \beta}\delta_{\gamma \nu}\right] + \Lambda \delta_{\alpha \beta}\delta_{\gamma \nu} - where :math:`\rho` is the fluid density, *u* is the local fluid velocity, :math:`\sigma` is the stress tensor, *F* is a local external force, and :math:`\eta` and :math:`\Lambda` are the shear and bulk viscosities @@ -91,7 +85,6 @@ respectively. Here, we have implemented \sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta} - with :math:`a_0` set to :math:`\frac{1}{3} \frac{dx}{dt}^2` by default. The algorithm involves tracking the time evolution of a set of partial @@ -102,7 +95,6 @@ discretized version of the Boltzmann equation, \left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i - where the first term on the right hand side represents a single time relaxation towards the equilibrium distribution function, and :math:`\tau` is a parameter physically related to the viscosity. On a technical note, @@ -134,7 +126,6 @@ calculated as: {\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha} - where :math:`\mathbf{v}_n` is the velocity of the MD particle, :math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle location, and :math:`\gamma` is the force @@ -156,7 +147,6 @@ according to \gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right) - Here, :math:`m_v` is the mass of the MD particle, :math:`m_u` is a representative fluid mass at the particle location, and :math:`\Delta t_{collision}` is a collision time, chosen such that @@ -325,19 +315,15 @@ If the *printfluid* keyword is used, followed by a positive integer, N, the fluid densities and velocities at each lattice site are printed to the 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 published research. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** Due to the large size of the fluid data, this fix writes it's own @@ -354,7 +340,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the USER-LB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -389,7 +374,6 @@ By default, the force coupling constant is set according to \gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right) - and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at the particle node location, is assumed. @@ -401,30 +385,20 @@ The Peskin stencil is used as the default interpolation method. The D3Q15 lattice is used for the lattice-Boltzmann algorithm. If walls are present, they are assumed to be stationary. - ---------- - .. _Ollila: - - **(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902. .. _fluid-Mackay: - - **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. .. _Mackay2: - - **(Mackay and Denniston)** Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298. .. _Adhikari: - - **(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479. diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index d498e06f7d..7e2d1d70d8 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -6,7 +6,6 @@ fix lb/momentum command Syntax """""" - .. parsed-literal:: fix ID group-ID lb/momentum nevery keyword values ... @@ -22,12 +21,9 @@ Syntax *linear* values = xflag yflag zflag xflag,yflag,zflag = 0/1 to exclude/include each dimension. - - Examples """""""" - .. parsed-literal:: fix 1 sphere lb/momentum @@ -65,7 +61,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this command. diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index 44a86047fb..cacc11810b 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -6,7 +6,6 @@ fix lb/pc command Syntax """""" - .. parsed-literal:: fix ID group-ID lb/pc @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all lb/pc @@ -42,7 +40,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-LB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -57,12 +54,8 @@ Related commands **Default:** None. - ---------- - .. _Mackay1: - - **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 90059b5cac..9f4beca41a 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -6,7 +6,6 @@ fix lb/rigid/pc/sphere command Syntax """""" - .. parsed-literal:: fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ... @@ -36,12 +35,9 @@ Syntax *innerNodes* values = innergroup-ID innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid - - Examples """""""" - .. parsed-literal:: fix 1 spheres lb/rigid/pc/sphere @@ -61,10 +57,8 @@ solid, uniform density spheres, with moments of inertia calculated using the combined sum of the masses of all the constituent particles (which are assumed to be point particles). - ---------- - By default, all of the atoms that this fix acts on experience a hydrodynamic force due to the presence of the lattice-Boltzmann fluid. However, the *innerNodes* keyword allows the user to specify atoms @@ -81,10 +75,8 @@ is desirable simply to place an atom at the center of each sphere, which does not contribute to the hydrodynamic force, and have these central atoms interact with one another. - ---------- - Apart from the features described above, this fix is very similar to the rigid fix (although it includes fewer optional arguments, and assumes the constituent atoms are point particles); see @@ -136,7 +128,6 @@ of the :doc:`run ` command. These fixes are not invoked during Restrictions """""""""""" - This fix is part of the USER-LB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -157,12 +148,8 @@ Default The defaults are force \* on on on, and torque \* on on on. - ---------- - .. _Mackay: - - **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index d20e969f80..2cd489d8f6 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -6,7 +6,6 @@ fix lb/viscous command Syntax """""" - .. parsed-literal:: fix ID group-ID lb/viscous @@ -41,19 +40,15 @@ opposite force to the fluid). value is used, then this fix provides the only method for adding the hydrodynamic forces to the particles. - ---------- - 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 this fix is used in work contributing to published research. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** As described in the :doc:`fix viscous ` documentation: @@ -73,7 +68,6 @@ for details." Restrictions """""""""""" - This fix is part of the USER-LB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -92,12 +86,8 @@ Related commands **Default:** none - ---------- - .. _Mackay3: - - **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index b97936fead..748373da93 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -6,7 +6,6 @@ fix lineforce command Syntax """""" - .. parsed-literal:: fix ID group-ID lineforce x y z @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix hold boundary lineforce 0.0 1.0 1.0 diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 63a90c626e..0f6deeb0fa 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -6,7 +6,6 @@ fix manifoldforce command Syntax """""" - .. parsed-literal:: fix ID group-ID manifoldforce manifold manifold-args ... @@ -15,7 +14,6 @@ Syntax * manifold = name of the manifold * manifold-args = parameters for the manifold - Examples """""""" @@ -32,10 +30,8 @@ given manifold, e.g. to set up a run with :doc:`fix nve/manifold/rattle `. None of the :doc:`fix_modify ` options @@ -44,14 +40,11 @@ by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is invoked during :doc:`energy minimization `. - ---------- - 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. @@ -59,10 +52,8 @@ 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. - ---------- - Related commands """""""""""""""" diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst index 8eb6b4831d..f838fe9b5d 100644 --- a/doc/src/fix_meso.rst +++ b/doc/src/fix_meso.rst @@ -6,7 +6,6 @@ fix meso command Syntax """""" - .. parsed-literal:: fix ID group-ID meso @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all meso @@ -44,7 +42,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-SPH 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_meso_move.rst b/doc/src/fix_meso_move.rst index 81074d306a..47a5dbd0e8 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -6,7 +6,6 @@ fix meso/move command Syntax """""" - .. parsed-literal:: fix ID group-ID meso/move style args keyword values ... @@ -37,12 +36,9 @@ Syntax *units* value = *box* or *lattice* - - Examples """""""" - .. parsed-literal:: fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box @@ -88,15 +84,12 @@ internal energy and extrapolated velocity are also updated. (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. - ---------- - The *linear* style moves particles at a constant velocity, so that their position *X* = (x,y,z) as a function of time is given in vector notation as - .. parsed-literal:: X(t) = X0 + V \* delta @@ -114,7 +107,6 @@ Note that the *linear* style is identical to using the *variable* style with an :doc:`equal-style variable ` that uses the vdisplace() function. E.g. - .. parsed-literal:: variable V equal 10.0 @@ -125,7 +117,6 @@ The *wiggle* style moves particles in an oscillatory fashion, so that their position *X* = (x,y,z) as a function of time is given in vector notation as - .. parsed-literal:: X(t) = X0 + A sin(omega\*delta) @@ -144,7 +135,6 @@ Note that the *wiggle* style is identical to using the *variable* style with :doc:`equal-style variables ` that use the swiggle() and cwiggle() functions. E.g. - .. parsed-literal:: variable A equal 10.0 @@ -212,10 +202,8 @@ been previously used to define the lattice spacing. Each of these 3 quantities may be dependent on the x,y,z dimension, since the lattice spacings can be different in x,y,z. - ---------- - **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 @@ -247,7 +235,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the USER-SDPD 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_meso_stationary.rst b/doc/src/fix_meso_stationary.rst index 6d8eebfdd7..2ae11725fc 100644 --- a/doc/src/fix_meso_stationary.rst +++ b/doc/src/fix_meso_stationary.rst @@ -6,7 +6,6 @@ fix meso/stationary command Syntax """""" - .. parsed-literal:: fix ID group-ID meso/stationary @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 boundary meso/stationary @@ -45,7 +43,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-SPH 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_modify.rst b/doc/src/fix_modify.rst index 1a728d6c88..658ec5b249 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -6,7 +6,6 @@ fix_modify command Syntax """""" - .. code-block:: LAMMPS fix_modify fix-ID keyword value ... @@ -27,12 +26,9 @@ Syntax *bodyforces* value = *early* or *late* early/late = compute rigid-body forces/torques early or late in the timestep - - Examples """""""" - .. code-block:: LAMMPS fix_modify 3 temp myTemp press myPress diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index b0e2e2a456..0a28aa0c26 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -9,7 +9,6 @@ fix momentum/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID momentum N keyword values ... @@ -26,17 +25,13 @@ Syntax xflag,yflag,zflag = 0/1 to exclude/include each dimension *angular* values = none - .. parsed-literal:: *rescale* values = none - - Examples """""""" - .. parsed-literal:: fix 1 all momentum 1 linear 1 1 0 @@ -70,10 +65,8 @@ of atoms by rescaling the velocities after the momentum was removed. Note that the :doc:`velocity ` command can be used to create initial velocities with zero aggregate linear and/or angular momentum. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index f4cd1b0231..34e74e2688 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -6,7 +6,6 @@ fix move command Syntax """""" - .. parsed-literal:: fix ID group-ID move style args keyword values ... @@ -37,12 +36,9 @@ Syntax *units* value = *box* or *lattice* - - Examples """""""" - .. parsed-literal:: fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box @@ -83,15 +79,12 @@ whose movement can influence nearby atoms. (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. - ---------- - The *linear* style moves atoms at a constant velocity, so that their position *X* = (x,y,z) as a function of time is given in vector notation as - .. parsed-literal:: X(t) = X0 + V \* delta @@ -109,7 +102,6 @@ Note that the *linear* style is identical to using the *variable* style with an :doc:`equal-style variable ` that uses the vdisplace() function. E.g. - .. parsed-literal:: variable V equal 10.0 @@ -120,7 +112,6 @@ The *wiggle* style moves atoms in an oscillatory fashion, so that their position *X* = (x,y,z) as a function of time is given in vector notation as - .. parsed-literal:: X(t) = X0 + A sin(omega\*delta) @@ -139,7 +130,6 @@ Note that the *wiggle* style is identical to using the *variable* style with :doc:`equal-style variables ` that use the swiggle() and cwiggle() functions. E.g. - .. parsed-literal:: variable A equal 10.0 @@ -211,10 +201,8 @@ been previously used to define the lattice spacing. Each of these 3 quantities may be dependent on the x,y,z dimension, since the lattice spacings can be different in x,y,z. - ---------- - **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 diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index 76819c8598..7f9f3fd046 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -6,7 +6,6 @@ fix mscg command Syntax """""" - .. parsed-literal:: fix ID group-ID mscg N keyword args ... @@ -27,12 +26,9 @@ Syntax *max* args = maxb maxa maxd maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom - - Examples """""""" - .. parsed-literal:: fix 1 all mscg 1 @@ -94,10 +90,8 @@ also be output depending on the parameters in the MS-CG library input script. Again, see the documentation provided with the MS-CG library for more info. - ---------- - The *range* keyword specifies which MS-CG library functionality should be invoked. If *on*\ , the step 4 range finder functionality is invoked. *off*\ , the step 5 force matching functionality is invoked. @@ -112,7 +106,6 @@ dihedrals a bead can have in the coarse-grained model. Restrictions """""""""""" - This fix is part of the MSCG package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -132,19 +125,13 @@ Default The default keyword settings are range off, max 4 12 36. - ---------- - .. _Izvekov: - - **(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005). .. _Noid: - - **(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008). diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 7bbbe95202..7531ab50de 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -6,7 +6,6 @@ fix msst command Syntax """""" - .. parsed-literal:: fix ID group-ID msst dir shockvel keyword value ... @@ -29,12 +28,9 @@ Syntax *dftb* value = *yes* or *no* for whether using MSST in conjunction with DFTB+ *beta* value = scale factor for improved energy conservation - - Examples """""""" - .. code-block:: LAMMPS fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 @@ -100,7 +96,6 @@ This fix computes a temperature and pressure and potential energy each timestep. To do this, the fix creates its own computes of style "temp" "pressure", and "pe", as if these commands had been issued: - .. code-block:: LAMMPS compute fix-ID_MSST_temp all temp @@ -113,10 +108,8 @@ See the :doc:`compute temp ` and :doc:`compute pressure new computes are the fix-ID + "_MSST\_temp" or "MSST\_press" or "_MSST\_pe". The group for the new computes is "all". - ---------- - The *dftb* keyword is to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the keyword *dftb* is used with a value of *yes*\ , then the MSST equations @@ -127,10 +120,8 @@ you must define a :doc:`fix external ` command in your input script, which is used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will communicate its info to LAMMPS via that fix. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** This fix writes the state of all internal variables to :doc:`binary @@ -162,7 +153,6 @@ The global vector contains four values in this order: To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested: - .. code-block:: LAMMPS fix msst all msst z @@ -181,7 +171,6 @@ quantities, which can be accessed by various :doc:`output commands Restrictions """""""""""" - This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -202,26 +191,18 @@ The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no, beta = 0.0. Note that p0, v0, and e0 are calculated on the first timestep. - ---------- - .. _Reed: - - **(Reed)** Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). .. _Reed2: - - **(Reed2)** Reed, J. Phys. Chem. C, 116, 2205 (2012). .. _Goldman2: - - **(Goldman)** Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013). diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index dbe4231616..3fb2fdd3d3 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -12,7 +12,6 @@ fix mvv/tdpd command Syntax """""" - .. parsed-literal:: fix ID group-ID mvv/dpd lambda @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all mvv/dpd @@ -76,10 +74,8 @@ Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition to position and velocity, and must be used with the :doc:`pair_style tdpd ` command. - ---------- - **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 @@ -91,7 +87,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -106,13 +101,9 @@ Default The default value for the optional *lambda* parameter is 0.5. - ---------- - .. _Groot2: - - **(Groot)** Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784 diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 63cdfb4be1..97deca7688 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -6,7 +6,6 @@ fix neb command Syntax """""" - .. parsed-literal:: fix ID group-ID neb Kspring keyword value @@ -35,7 +34,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 active neb 10.0 @@ -66,7 +64,6 @@ interatomic force Fi = -Grad(V) for each replica I is altered. For all intermediate replicas (i.e. for 1 < I < N, except the climbing replica) the force vector becomes: - .. parsed-literal:: Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp @@ -90,23 +87,19 @@ In the second stage of the NEB calculation, the interatomic force Fi for the climbing replica (the replica of highest energy after the first stage) is changed to: - .. parsed-literal:: Fi = -Grad(V) + 2 (Grad(V) dot T') T' and the relaxation procedure is continued to a new converged MEP. - ---------- - The keyword *parallel* specifies how the parallel nudging force is computed. With a value of *neigh*\ , the parallel nudging force is computed as in :ref:`(Henkelman1) ` by connecting each intermediate replica with the previous and the next image: - .. parsed-literal:: Fnudge_parallel = *Kspring* \* (\|Ri+1 - Ri\| - \|Ri - Ri-1\|) @@ -117,7 +110,6 @@ units. With a value of *ideal*\ , the spring force is computed as suggested in ref`(WeinanE) ` - .. parsed-literal:: Fnudge_parallel = -\ *Kspring* \* (RD-RDideal) / (2 \* meanDist) @@ -132,10 +124,8 @@ in force units. Note that the *ideal* form of nudging can often be more effective at keeping the replicas equally spaced. - ---------- - The keyword *perp* specifies if and how a perpendicular nudging force is computed. It adds a spring force perpendicular to the path in order to prevent the path from becoming too strongly kinked. It can @@ -145,7 +135,6 @@ resolution is poor. I.e. when few replicas are used; see The perpendicular spring force is given by - .. parsed-literal:: Fnudge_perp = *Kspring2* \* F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) @@ -158,10 +147,8 @@ acute. F(Ri-1 Ri R+1) is defined in :ref:`(Jonsson) `. If *Kspring2* is set to 0.0 (the default) then no perpendicular spring force is added. - ---------- - By default, no additional forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their respective local minima. By using the key word *end*\ , additional @@ -171,7 +158,6 @@ target energy ETarget. If ETarget>E, the interatomic force Fi for the specified replica becomes: - .. parsed-literal:: Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)\*Kspring3) T', *when* Grad(V) dot T' < 0 @@ -232,7 +218,6 @@ as invoked by the :doc:`minimize ` command via the Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. @@ -248,40 +233,28 @@ Default The option defaults are parallel = neigh, perp = 0.0, ends is not specified (no inter-replica force on the end replicas). - ---------- - .. _Henkelman1: - - **(Henkelman1)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). .. _Henkelman2: - - **(Henkelman2)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). .. _WeinanE: - - **(WeinanE)** E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002). .. _Jonsson: - - **(Jonsson)** Jonsson, Mills and Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker World Scientific, Singapore, 1998, p 385. .. _Maras1: - - **(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016). diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index ffef23873c..6e1978df03 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -6,7 +6,6 @@ fix neb/spin command Syntax """""" - .. parsed-literal:: fix ID group-ID neb/spin Kspring @@ -61,7 +60,6 @@ as invoked by the :doc:`minimize ` command via the Restrictions """""""""""" - This command can only be used if LAMMPS was built with the SPIN package. See the :doc:`Build package ` doc page for more info. @@ -76,13 +74,9 @@ Default none - ---------- - .. _BessarabB: - - **(BessarabB)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015). diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 7d45272ae0..3f3c573e44 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -36,7 +36,6 @@ fix nph/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID style_name keyword value ... @@ -82,12 +81,9 @@ Syntax dipole = update dipole orientation (only for sphere variants) dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) - - Examples """""""" - .. parsed-literal:: fix 1 all nvt temp 300.0 300.0 100.0 @@ -128,10 +124,8 @@ energy proposed by Parrinello and Rahman in follow the time-reversible measure-preserving Verlet and rRESPA integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. - ---------- - The thermostat parameters for fix styles *nvt* and *npt* are specified using the *temp* keyword. Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , which are discussed below. @@ -159,15 +153,12 @@ by the velocity/position update portion of the integration. via using an :doc:`immediate variable ` expression accessing the thermo property 'dt', which is the length of the time step. Example: - .. parsed-literal:: fix 1 all nvt temp 300.0 300.0 $(100.0\*dt) - ---------- - The barostat parameters for fix styles *npt* and *nph* is specified using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* keywords. These keywords give you the @@ -233,10 +224,8 @@ group, a separate time integration fix like :doc:`fix nve ` or :doc:`fix nvt ` can be used on them, independent of whether they are dilated or not. - ---------- - The *couple* keyword allows two or three of the diagonal components of the pressure tensor to be "coupled" together. The value specified with the keyword determines which are coupled. For example, *xz* @@ -250,10 +239,8 @@ dilated or contracted by the same percentage every timestep. The be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. - ---------- - The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. @@ -262,7 +249,6 @@ pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using "iso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -276,7 +262,6 @@ stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -290,7 +275,6 @@ as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as specifying these 7 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -301,10 +285,8 @@ specifying these 7 keywords: xz 0.0 0.0 Pdamp couple none - ---------- - In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional *drag* keyword will @@ -398,10 +380,8 @@ Dullweber-Leimkuhler-McLachlan integration scheme giving better energy conservation and allows slightly longer timesteps at only a small additional computational cost. - ---------- - .. note:: Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can @@ -449,10 +429,8 @@ See the :doc:`Howto thermostat ` and :doc:`Howto barostat `. When using one of the barostat fixes with *respa*\ , LAMMPS uses an integrator constructed @@ -532,7 +507,6 @@ according to the following factorization of the Liouville propagator \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) - This factorization differs somewhat from that of Tuckerman et al, in that the barostat is only updated at the outermost rRESPA level, whereas Tuckerman's factorization requires splitting the pressure into @@ -556,20 +530,16 @@ of the underlying non-Hamiltonian equations of motion. the momentum at infrequent intervals using the :doc:`fix momentum ` command. - ---------- - The fix npt and fix nph commands can be used with rigid bodies or mixtures of rigid bodies and non-rigid particles (e.g. solvent). But there are also :doc:`fix rigid/npt ` and :doc:`fix rigid/nph ` commands, which are typically a more natural choice. See the doc page for those commands for more discussion of the various ways to do this. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -588,10 +558,8 @@ 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:** These fixes writes the state of all the thermostat and barostat @@ -670,14 +638,11 @@ how to do this. These fixes are not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the simulation domain is triclinic and the 2nd dimension in the keyword @@ -720,38 +685,26 @@ ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no. - ---------- - .. _nh-Martyna: - - **(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). .. _nh-Parrinello: - - **(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). .. _nh-Tuckerman: - - **(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006). .. _nh-Shinoda: - - **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). .. _nh-Dullweber: - - **(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 78aae45ad6..1417453706 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -12,7 +12,6 @@ fix nph/eff command Syntax """""" - .. parsed-literal:: fix ID group-ID style_name keyword value ... @@ -43,12 +42,9 @@ Syntax *drag* value = drag factor added to barostat/thermostat (0.0 = no drag) *dilate* value = *all* or *partial* - - Examples """""""" - .. parsed-literal:: fix 1 all nvt/eff temp 300.0 300.0 0.1 @@ -117,7 +113,6 @@ for details. Restrictions """""""""""" - This fix is part of the USER-EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -146,31 +141,21 @@ Default The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none. - ---------- - .. _Martyna1: - - **(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). .. _Parrinello: - - **(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). .. _Tuckerman1: - - **(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006). .. _Shinoda2: - - **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 6724597e13..15dc43dc46 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -9,7 +9,6 @@ fix npt/uef command Syntax """""" - .. parsed-literal:: fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... @@ -30,12 +29,9 @@ Syntax *iso*\ , *x*\ , *y*\ , *z*\ , *tchain*\ , *pchain*\ , *tloop*\ , *ploop*\ , *mtk* keywords documented by the :doc:`fix npt ` command - - Examples """""""" - .. parsed-literal:: fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005 @@ -98,10 +94,8 @@ during all of the output steps, and therefore trajectory files made using the dump command will be in the LAMMPS frame unless the :doc:`dump cfg/uef ` command is used. - ---------- - Temperature control is achieved with the default Nose-Hoover style thermostat documented in :doc:`fix npt `. When this fix is active, only the peculiar velocity of each atom is stored, defined as @@ -122,7 +116,6 @@ pressure (Pxx+Pyy)/2 will be controlled. This example command will control the total hydrostatic pressure under uniaxial tension: - .. parsed-literal:: fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz @@ -131,7 +124,6 @@ This example command will control the average stress in compression directions, which would typically correspond to free surfaces under drawing with uniaxial tension: - .. parsed-literal:: fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy @@ -148,7 +140,6 @@ method. For example, the following commands will work: - .. parsed-literal:: fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5 @@ -156,22 +147,18 @@ For example, the following commands will work: The following commands will not work: - .. parsed-literal:: fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5 fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 - ---------- - These fix computes a temperature and pressure each timestep. To do this, it creates its own computes of style "temp/uef" and "pressure/uef", as if one of these two sets of commands had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp/uef @@ -210,7 +197,6 @@ The fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the USER-UEF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -238,37 +224,25 @@ The default keyword values specific to this fix are exy = xyz, strain npt*\ \_fix\_nh.html except tchain = 1. The reason for this change is given in :doc:`fix nvt/sllod `. - ---------- - .. _Dobson: - - **(Dobson)** Dobson, J Chem Phys, 141, 184103 (2014). .. _Hunt: - - **(Hunt)** Hunt, Mol Simul, 42, 347 (2016). .. _Semaev: - - **(Semaev)** Semaev, Cryptography and Lattices, 181 (2001). .. _Sllod: - - **(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984). .. _Nicholson: - - **(Nicholson and Rutledge)** Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016). diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 8f4a4ad39b..814e8c18aa 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -9,7 +9,6 @@ fix nph/asphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nph/asphere args keyword value ... @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nph/asphere iso 0.0 0.0 1000.0 @@ -57,15 +55,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/asphere" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/asphere @@ -85,10 +80,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom `. Restrictions """""""""""" - This fix is part of the ASPHERE 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_nph_body.rst b/doc/src/fix_nph_body.rst index bae12f2b86..81689d3c30 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -6,7 +6,6 @@ fix nph/body command Syntax """""" - .. parsed-literal:: fix ID group-ID nph/body args keyword value ... @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nph/body iso 0.0 0.0 1000.0 @@ -54,15 +52,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/body" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/body @@ -82,10 +77,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom `. Restrictions """""""""""" - This fix is part of the BODY 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_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index ebda193f51..2a01b1690c 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -9,7 +9,6 @@ fix nph/sphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nph/sphere args keyword value ... @@ -27,7 +26,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nph/sphere iso 0.0 0.0 1000.0 @@ -70,15 +68,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/sphere" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/sphere @@ -98,10 +93,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom `. Restrictions """""""""""" - This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index e47debdfb9..fa5752b41a 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -9,7 +9,6 @@ fix nphug/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nphug keyword value ... @@ -42,12 +41,9 @@ Syntax *scalexz* value = *yes* or *no* = scale xz with lz *scalexy* value = *yes* or *no* = scale xy with ly - - Examples """""""" - .. parsed-literal:: fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 @@ -92,7 +88,6 @@ target temperature Tt obtained from the following equation: T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = \Delta - where *T* and :math:`T_t` are the instantaneous and target temperatures, *P* and :math:`P_0` are the instantaneous and reference pressures or axial stresses, depending on whether hydrostatic or uniaxial compression is being @@ -108,10 +103,8 @@ The values of :math:`E_0`, :math:`V_0`, and :math:`P_0` are the instantaneous va the simulation. These can be overridden using the fix\_modify keywords *e0*\ , *v0*\ , and *p0* described below. - ---------- - .. note:: Unlike the :doc:`fix temp/berendsen ` command @@ -121,15 +114,12 @@ the simulation. These can be overridden using the fix\_modify keywords *e0*\ , this fix should not be used on atoms that have their temperature controlled by another fix - e.g. by :doc:`fix langevin ` or :doc:`fix temp/rescale ` commands. - ---------- - This fix computes a temperature and pressure at each timestep. To do this, the fix creates its own computes of style "temp" and "pressure", as if one of these two sets of commands had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -153,10 +143,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - **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`, @@ -229,7 +215,6 @@ shock calculated from the RH conditions. They have units of distance/time. Restrictions """""""""""" - This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -246,12 +231,8 @@ Default The keyword defaults are the same as those for :doc:`fix npt ` - ---------- - .. _Ravelo1: - - **(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 2b84011cc8..41766a0130 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -9,7 +9,6 @@ fix npt/asphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID npt/asphere keyword value ... @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 @@ -65,15 +63,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/asphere" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/asphere @@ -107,10 +102,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -164,7 +157,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the ASPHERE 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_npt_body.rst b/doc/src/fix_npt_body.rst index 4eecd404ff..aab32f664c 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -6,7 +6,6 @@ fix npt/body command Syntax """""" - .. parsed-literal:: fix ID group-ID npt/body keyword value ... @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 @@ -62,15 +60,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/body" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/body @@ -104,10 +99,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -161,7 +154,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the BODY 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_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index cf1425e6e4..936369195d 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -6,7 +6,6 @@ fix npt/cauchy command Syntax """""" - .. parsed-literal:: fix ID group-ID style_name keyword value ... @@ -52,8 +51,6 @@ Syntax *fixedpoint* values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) - - Examples """""""" @@ -91,10 +88,8 @@ energy proposed by Parrinello and Rahman in follow the time-reversible measure-preserving Verlet and rRESPA integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. - ---------- - The thermostat parameters are specified using the *temp* keyword. Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , which are discussed below. @@ -120,10 +115,8 @@ by the velocity/position update portion of the integration. 100 timesteps. Note that this is NOT the same as 100 time units for most :doc:`units ` settings. - ---------- - The barostat parameters are specified using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* keywords. These keywords give you the ability to specify all 6 components of an @@ -188,10 +181,8 @@ group, a separate time integration fix like :doc:`fix nve ` or :doc:`fix nvt ` can be used on them, independent of whether they are dilated or not. - ---------- - The *couple* keyword allows two or three of the diagonal components of the pressure tensor to be "coupled" together. The value specified with the keyword determines which are coupled. For example, *xz* @@ -205,10 +196,8 @@ dilated or contracted by the same percentage every timestep. The be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. - ---------- - The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. @@ -217,7 +206,6 @@ pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using "iso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -231,7 +219,6 @@ stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -245,7 +232,6 @@ as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as specifying these 7 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -256,10 +242,8 @@ specifying these 7 keywords: xz 0.0 0.0 Pdamp couple none - ---------- - In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional *drag* keyword will @@ -340,10 +324,8 @@ far. In all cases, the particle trajectories are unaffected by the chosen value, except for a time-dependent constant translation of positions. - ---------- - .. note:: Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can @@ -391,15 +373,12 @@ See the :doc:`Howto thermostat ` and :doc:`Howto barostat `. When using this fix with *respa*\ , LAMMPS uses an integrator constructed @@ -486,10 +463,8 @@ of the underlying non-Hamiltonian equations of motion. resetting the momentum at infrequent intervals using the :doc:`fix momentum ` command. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** This fix writes the state of all the thermostat and barostat @@ -568,14 +543,11 @@ how to do this. This fix is not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - 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. @@ -655,38 +627,26 @@ cauchystat = no, scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no. - ---------- - .. _nc-Martyna: - - **(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). .. _nc-Parrinello: - - **(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). .. _nc-Tuckerman: - - **(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006). .. _nc-Shinoda: - - **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). .. _nc-Miller: - - **(Miller)** Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 144, 184107 (2016). diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index d82e4e26cb..3d16e717ca 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -9,7 +9,6 @@ fix npt/sphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID npt/sphere keyword value ... @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 @@ -78,15 +76,12 @@ only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp/sphere" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp all temp/sphere @@ -120,10 +115,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -177,7 +170,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index b3928e6389..9ddac818bc 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -15,7 +15,6 @@ fix nve/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nve @@ -26,7 +25,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve @@ -39,10 +37,8 @@ atoms in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -61,10 +57,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index ea311d3f69..29d9941029 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -9,7 +9,6 @@ fix nve/asphere/intel command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/asphere @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/asphere @@ -44,10 +42,8 @@ by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -66,14 +62,11 @@ 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. - ---------- - Restrictions """""""""""" - This fix is part of the ASPHERE 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_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index ed2897c978..699749a969 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -6,7 +6,6 @@ fix nve/asphere/noforce command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/asphere/noforce @@ -32,10 +31,8 @@ This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the :doc:`pair_style lubricuteU ` command. - ---------- - **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 @@ -47,7 +44,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the ASPHERE 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_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index c29de946d8..a57423282e 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -6,7 +6,6 @@ fix nve/awpmd command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/awpmd @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/awpmd @@ -33,10 +31,8 @@ ensemble. The operation of this fix is exactly like that described by the :doc:`fix nve ` command, except that the width and width-velocity of the electron wave functions are also updated. - ---------- - **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 @@ -48,7 +44,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-AWPMD 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_nve_body.rst b/doc/src/fix_nve_body.rst index 36a9a426ec..2cb4e1097d 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -6,7 +6,6 @@ fix nve/body command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/body @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/body @@ -45,7 +43,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the BODY 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_nve_dot.rst b/doc/src/fix_nve_dot.rst index 5f3ede0386..8960fbe0bf 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -6,7 +6,6 @@ fix nve/dot command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/dot @@ -14,11 +13,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * nve/dot = style name of this fix command - Examples """""""" - .. parsed-literal:: fix 1 all nve/dot @@ -43,14 +40,11 @@ An example input file can be found in /examples/USER/cgdna/examples/duplex1/. Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) `. The preprint version of the article can be found `here `_. - ---------- - Restrictions """""""""""" - These pair styles can only be used if LAMMPS was built with the :ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -62,10 +56,8 @@ Related commands **Default:** none - ---------- - .. _Davidchack4: **(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index bda47d4901..88d15b9e17 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -6,7 +6,6 @@ fix nve/dotc/langevin command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value @@ -23,12 +22,9 @@ Syntax *angmom* value = factor factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below - - Examples """""""" - .. code-block:: LAMMPS fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 @@ -60,7 +56,6 @@ over the standard integrator, permitting slightly larger timestep sizes. The total force on each atom will have the form: - .. math:: F = & F_c + F_f + F_r \\ @@ -89,10 +84,8 @@ and magnitude of this force as described in :ref:`(Dunweg) `, where a uniform random number is used (instead of a Gaussian random number) for speed. - ---------- - *Tstart* and *Tstop* have to be constant values, i.e. they cannot be variables. If used together with the oxDNA force field for coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units @@ -131,14 +124,11 @@ An example input file can be found in examples/USER/cgdna/examples/duplex2/. Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) `. The preprint version of the article can be found `here `_. - ---------- - Restrictions """""""""""" - These pair styles can only be used if LAMMPS was built with the :ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -150,10 +140,8 @@ Related commands **Default:** none - ---------- - .. _Davidchack5: **(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 88bc6a3607..2d21bcc60f 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -6,7 +6,6 @@ fix nve/eff command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/eff @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/eff @@ -43,7 +41,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the USER-EFF 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_nve_limit.rst b/doc/src/fix_nve_limit.rst index 07746e71a2..5b83e1ab63 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -6,7 +6,6 @@ fix nve/limit command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/limit xmax @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/limit 0.1 diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index ec971bc41e..1515899631 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -6,7 +6,6 @@ fix nve/line command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/line @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/line @@ -45,7 +43,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the ASPHERE 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_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index be73bd1abc..df5555efa4 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -6,7 +6,6 @@ fix nve/manifold/rattle command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ... @@ -25,12 +24,9 @@ Syntax *every* values = N N = print info about iteration every N steps. N = 0 means no output - - Examples """""""" - .. parsed-literal:: fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0 @@ -59,7 +55,6 @@ write a script. The manifold args may be equal-style variables, like so: - .. parsed-literal:: variable R equal "ramp(5.0,3.0)" @@ -72,10 +67,8 @@ the particles. Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved. - ---------- - **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 @@ -84,21 +77,16 @@ by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - 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. - ---------- - Related commands """""""""""""""" @@ -106,19 +94,13 @@ Related commands **Default:** every = 0, tchain = 3 - ---------- - .. _Andersen1: - - **(Andersen)** Andersen, J. Comp. Phys. 52, 24, (1983). .. _Paquay2: - - **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 568be83bdc..da5f122df5 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -6,7 +6,6 @@ fix nve/noforce command Syntax """""" - .. parsed-literal:: fix ID group-ID nve @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 3 wall nve/noforce diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 4419a6b8ad..fc34785ae1 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -12,7 +12,6 @@ fix nve/sphere/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/sphere @@ -29,12 +28,9 @@ Syntax dipole/dlm = use DLM integrator to update dipole orientation *disc* value = none = treat particles as 2d discs, not spheres - - Examples """""""" - .. parsed-literal:: fix 1 all nve/sphere @@ -72,10 +68,8 @@ simulations, as defined by the :doc:`dimension ` keyword. The only difference between discs and spheres in this context is their moment of inertia, as used in the time integration. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -94,10 +88,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options @@ -109,7 +101,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the :doc:`atom_style sphere ` command. If the *dipole* keyword is used, then they must also store a @@ -129,13 +120,9 @@ Related commands **Default:** none - ---------- - .. _nve-Dullweber: - - **(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index b583121a2b..8167c408d9 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -6,7 +6,6 @@ fix nve/spin command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/spin keyword values @@ -21,12 +20,9 @@ Syntax moving = integrate both spin and atomic degress of freedom frozen = integrate spins on a fixed lattice - - Examples """""""" - .. parsed-literal:: fix 3 all nve/spin lattice moving @@ -56,14 +52,11 @@ A sectoring method enables this scheme for parallel calculations. The implementation of this sectoring algorithm is reported in :ref:`(Tranchida) `. - ---------- - Restrictions """""""""""" - This fix style can only be used if LAMMPS was built with the SPIN package. See the :doc:`Build package ` doc page for more info. @@ -71,7 +64,6 @@ info. To use the spin algorithm, it is necessary to define a map with the atom\_modify command. Typically, by adding the command: - .. parsed-literal:: atom_modify map array @@ -89,20 +81,14 @@ Default The option default is lattice = moving. - ---------- - .. _Omelyan1: - - **(Omelyan)** Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001). .. _Tranchida1: - - **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index 6c4bb882e6..7fd325f6af 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -6,7 +6,6 @@ fix nve/tri command Syntax """""" - .. parsed-literal:: fix ID group-ID nve/tri @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve/tri @@ -46,7 +44,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the ASPHERE 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_nvk.rst b/doc/src/fix_nvk.rst index 3eb1755411..5b88a3e7c5 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -6,7 +6,6 @@ fix nvk command Syntax """""" - .. parsed-literal:: fix ID group-ID nvk @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvk @@ -39,10 +37,8 @@ nvk is initiated. If a different kinetic energy is desired, the :doc:`velocity ` command should be used to change the kinetic energy prior to this fix. - ---------- - **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 @@ -54,7 +50,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - The Gaussian thermostat only works when it is applied to all atoms in the simulation box. Therefore, the group must be set to all. @@ -67,18 +62,12 @@ LAMMPS was built with that package. See the :doc:`Build package **Default:** none - ---------- - .. _nvk-Minary: - - **(Minary)** Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003). .. _nvk-Zhang: - - **(Zhang)** Zhang, J Chem Phys, 106, 6102 (1997). diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 35a18a205c..46b3354f53 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -9,7 +9,6 @@ fix nvt/asphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/asphere keyword value ... @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvt/asphere temp 300.0 300.0 100.0 @@ -55,7 +53,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp/asphere", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp/asphere @@ -88,10 +85,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -138,7 +133,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the ASPHERE 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_nvt_body.rst b/doc/src/fix_nvt_body.rst index e564092d35..0299d5cbca 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -6,7 +6,6 @@ fix nvt/body command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/body keyword value ... @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvt/body temp 300.0 300.0 100.0 @@ -52,7 +50,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp/body", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp/body @@ -85,10 +82,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -135,7 +130,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the BODY 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_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 8bd7307cbf..1e4200dd0f 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -6,7 +6,6 @@ fix nvt/manifold/rattle command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ... @@ -30,8 +29,6 @@ Syntax *every* value = N N = print info about iteration every N steps. N = 0 means no output - - Examples """""""" @@ -48,10 +45,8 @@ canonical ensemble of particles constrained to a curved surface O(dt). For a list of currently supported manifolds and their parameters, see the :doc:`Howto manifold ` doc page. - ---------- - **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 @@ -60,39 +55,28 @@ by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - 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. - ---------- - Related commands """""""""""""""" :doc:`fix nve/manifold/rattle `, :doc:`fix manifoldforce ` **Default:** every = 0 - ---------- - .. _Andersen2: - - **(Andersen)** Andersen, J. Comp. Phys. 52, 24, (1983). .. _Paquay3: - - **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index e195121c9a..1e61055cfc 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -12,7 +12,6 @@ fix nvt/sllod/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/sllod keyword value ... @@ -24,7 +23,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvt/sllod temp 300.0 300.0 100.0 @@ -87,7 +85,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp/deform", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp/deform @@ -120,10 +117,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -170,7 +165,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix works best without Nose-Hoover chain thermostats, i.e. using tchain = 1. Setting tchain to larger values can result in poor equilibration. @@ -186,25 +180,17 @@ Default Same as :doc:`fix nvt `, except tchain = 1. - ---------- - .. _Evans3: - - **(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984). .. _Daivis: - - **(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006). .. _Daivis-sllod: - - **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 58836f17d6..139b5762d5 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -6,7 +6,6 @@ fix nvt/sllod/eff command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/sllod/eff keyword value ... @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 @@ -68,7 +66,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the USER-EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -86,13 +83,9 @@ Default Same as :doc:`fix nvt/eff `, except tchain = 1. - ---------- - .. _Tuckerman2: - - **(Tuckerman)** Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997). diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index 3d08b5a910..d7c4634228 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -9,7 +9,6 @@ fix nvt/sphere/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID nvt/sphere keyword value ... @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nvt/sphere temp 300.0 300.0 100.0 @@ -69,7 +67,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp/sphere", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp/sphere @@ -102,10 +99,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -152,7 +147,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index d72d750c1b..ade25e39ac 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -6,7 +6,6 @@ fix oneway command Syntax """""" - .. parsed-literal:: fix ID group-ID oneway N region-ID direction @@ -17,11 +16,9 @@ Syntax * region-ID = ID of region where fix is active * direction = *x* or *-x* or *y* or *-y* or *z* or *-z* = coordinate and direction of the oneway constraint - Examples """""""" - .. parsed-literal:: fix ions oneway 10 semi -x @@ -40,10 +37,8 @@ only. This can be used, for example, as a simple model of a semi-permeable membrane, or as an implementation of Maxwell's demon. - ---------- - **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 diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index a23b98fbae..72bdc57bb7 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -6,7 +6,6 @@ fix orient/fcc command fix orient/bcc command ====================== - .. parsed-literal:: fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 @@ -23,7 +22,6 @@ fix orient/bcc command Examples """""""" - .. parsed-literal:: fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec @@ -74,7 +72,6 @@ The potential energy added to atom I is given by these formulas \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \quad \left(6\right) \\ = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i} - which are fully explained in :ref:`(Janssens) `. For fcc crystals this order parameter Xi for atom I in equation (1) is a sum over the 12 nearest neighbors of atom I. For bcc crystals it is the @@ -169,7 +166,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -182,42 +178,31 @@ Related commands **Default:** none - ---------- - .. _Janssens: - - **(Janssens)** Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006). .. _Wicaksono1: - - **(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016). .. _Wicaksono2: - - **(Wicaksono2)** Wicaksono, figshare, https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015). - ---------- - For illustration purposes, here are example files that specify a Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706 Angs. file0: - .. parsed-literal:: 0.798410432046075 1.785300000000000 1.596820864092150 @@ -229,7 +214,6 @@ file0: file1: - .. parsed-literal:: -0.798410432046075 1.785300000000000 1.596820864092150 diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 1e302fa28d..df31c2530e 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -6,7 +6,6 @@ fix phonon command Syntax """""" - .. parsed-literal:: fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ... @@ -22,7 +21,6 @@ Syntax *file* is the file that contains the mapping info between atom ID and the lattice indices. - .. parsed-literal:: *GAMMA* flags to treate the whole simulation box as a unit cell, so that the mapping @@ -40,12 +38,9 @@ Syntax *nasr* value = n n = number of iterations to enforce the acoustic sum rule - - Examples """""""" - .. parsed-literal:: fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1 @@ -68,21 +63,18 @@ Based on fluctuation-dissipation theory, the force constant coefficients of the system in reciprocal space are given by (:ref:`Campana ` , :ref:`Kong `) - .. math:: \mathbf{\Phi}_{k\alpha,k^\prime \beta}(\mathbf{q}) = k_B T \mathbf{G}^{-1}_{k\alpha,k^\prime \beta}(\mathbf{q}) where :math:`\mathbf{G}` is the Green's functions coefficients given by - .. math:: \mathbf{G}_{k\alpha,k^\prime \beta}(\mathbf{q}) = \left< \mathbf{u}_{k\alpha}(\mathbf{q}) \bullet \mathbf{u}_{k^\prime \beta}^*(\mathbf{q}) \right> where :math:`\left< \ldots \right>` denotes the ensemble average, and - .. math:: \mathbf{u}_{k\alpha}(\mathbf{q}) = \sum_l \mathbf{u}_{l k \alpha} \exp{(i\mathbf{qr}_l)} @@ -92,7 +84,6 @@ th atom in the unit cell in reciprocal space at :math:`\mathbf{q}`. In practice, the Green's functions coefficients can also be measured according to the following formula, - .. math:: \mathbf{G}_{k\alpha,k^\prime \beta}(\mathbf{q}) = @@ -107,7 +98,6 @@ easier to implement in an MD code. Once the force constant matrix is known, the dynamical matrix :math:`\mathbf{D}` can then be obtained by - .. math:: \mathbf{D}_{k\alpha, k^\prime\beta}(\mathbf{q}) = @@ -186,7 +176,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix assumes a crystalline system with periodical lattice. The temperature of the system should not exceed the melting temperature to keep the system in its solid state. @@ -208,22 +197,16 @@ Default The option defaults are sysdim = the same dimension as specified by the :doc:`dimension ` command, and nasr = 20. - ---------- - .. _Campana: - - **(Campana)** C. Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ .. _Kong: - - **(Kong)** L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, *Implementation of Green's function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). `_ @@ -234,7 +217,5 @@ method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index dfdb9eb36e..bdf4734dd0 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -6,7 +6,6 @@ fix pimd command Syntax """""" - .. parsed-literal:: fix ID group-ID pimd keyword value ... @@ -24,12 +23,9 @@ Syntax *temp* value = temperature (temperarate units) *nhc* value = Nc = number of chains in Nose-Hoover thermostat - - Examples """""""" - .. parsed-literal:: fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4 @@ -132,7 +128,6 @@ To run a PIMD simulation with M quasi-beads in each ring polymer using N MPI tasks for each partition's domain-decomposition, you would use P = MxN processors (cores) and run the simulation as follows: - .. parsed-literal:: mpirun -np P lmp_mpi -partition MxN -in script @@ -140,7 +135,6 @@ N MPI tasks for each partition's domain-decomposition, you would use P Note that in the LAMMPS input script for a multi-partition simulation, it is often very useful to define a :doc:`uloop-style variable ` such as - .. parsed-literal:: variable ibead uloop M pad @@ -149,7 +143,6 @@ where M is the number of quasi-beads (partitions) used in the calculation. The uloop variable can then be used to manage I/O related tasks for each of the partitions, e.g. - .. parsed-literal:: dump dcd all dcd 10 system_${ibead}.dcd @@ -159,7 +152,6 @@ related tasks for each of the partitions, e.g. Restrictions """""""""""" - 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. @@ -171,7 +163,6 @@ To avoid this, users can simply initialize velocities with different random number seeds assigned to each partition, as defined by the uloop variable, e.g. - .. parsed-literal:: velocity all create 300.0 1234${ibead} rot yes dist gaussian @@ -182,45 +173,31 @@ Default The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, and nhc = 2. - ---------- - .. _Feynman: - - **(Feynman)** R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and Path Integrals, McGraw-Hill, New York (1965). .. _pimd-Tuckerman: - - **(Tuckerman)** M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993). .. _Cao1: - - **(Cao1)** J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993). .. _Cao2: - - **(Cao2)** J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994). .. _Hone: - - **(Hone)** T. Hone, P. Rossky, G. Voth, J Chem Phys, 124, 154103 (2006). .. _Calhoun: - - **(Calhoun)** A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996). diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index ed830e7135..e83cbc84b4 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -6,7 +6,6 @@ fix planeforce command Syntax """""" - .. parsed-literal:: fix ID group-ID planeforce x y z @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix hold boundary planeforce 1.0 0.0 0.0 diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 98c126a421..7f033c3f87 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -6,7 +6,6 @@ fix plumed command Syntax """""" - .. parsed-literal:: fix ID group-ID plumed keyword value ... @@ -20,8 +19,6 @@ Syntax *plumedfile* arg = name of PLUMED input file to use (default: NULL) *outfile* arg = name of file on which to write the PLUMED log (default: NULL) - - Examples """""""" @@ -47,10 +44,8 @@ A detailed discussion of the code can be found in :ref:`(PLUMED) `. There is an example input for using this package with LAMMPS in the examples/USER/plumed directory. - ---------- - The command to make LAMMPS call PLUMED during a run requires two keyword value pairs pointing to the PLUMED input file and an output file for the PLUMED log. The user must specify these arguments every time PLUMED is @@ -101,7 +96,6 @@ however. Restrictions """""""""""" - This fix is part of the USER-PLUMED package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -118,18 +112,12 @@ Default The default options are plumedfile = NULL and outfile = NULL - ---------- - .. _PLUMED: - - **(PLUMED)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) .. _plumeddocs: http://www.plumed.org/doc.html - - .. _plumedhome: http://www.plumed.org/ diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 43bbdd09e7..c1ef3f8a15 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -5,7 +5,6 @@ fix poems command Syntax: - .. parsed-literal:: fix ID group-ID poems keyword values @@ -20,12 +19,9 @@ Syntax: *molecule* values = none *file* values = filename - - Examples """""""" - .. parsed-literal:: fix 3 fluid poems group clump1 clump2 clump3 @@ -53,8 +49,6 @@ documents in the poems directory distributed with LAMMPS. .. _poems: http://www.rpi.edu/~anderk5/lab - - This fix updates the positions and velocities of the rigid atoms with a constant-energy time integration, so you should not update the same atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). @@ -128,7 +122,6 @@ command. This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the POEMS package. It is only enabled if LAMMPS was built with that package, which also requires the POEMS library be built and linked with LAMMPS. See the :doc:`Build package ` doc page for more info. @@ -141,14 +134,10 @@ Related commands **Default:** none - ---------- - .. _Anderson: - - **(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006). (`link to paper `_) diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 2537b836ac..7d9e4c33c9 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -6,7 +6,6 @@ fix pour command Syntax """""" - .. parsed-literal:: fix ID group-ID pour N type seed keyword values ... @@ -61,12 +60,9 @@ Syntax skip any line or triangle particles when detecting possible overlaps with inserted particles - - Examples """""""" - .. parsed-literal:: fix 3 all pour 1000 2 29494 region myblock @@ -157,10 +153,8 @@ many timesteps until the desired # of particles has been inserted. should use the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. - ---------- - All other keywords are optional with defaults as shown below. The *diam* option is only used when inserting atoms and specifies the @@ -229,10 +223,8 @@ causes the overlap check to skip any line or triangle particles. Obviously you should only use it if there is in fact no overlap of the line or triangle particles with the insertion region. - ---------- - **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 @@ -258,7 +250,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the GRANULAR 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_precession_spin.rst b/doc/src/fix_precession_spin.rst index 07bbe40bfb..f7931c1b26 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -6,7 +6,6 @@ fix precession/spin command Syntax """""" - .. code-block:: LAMMPS fix ID group precession/spin style args @@ -24,19 +23,15 @@ Syntax K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy - .. parsed-literal:: *cubic* args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy - - Examples """""""" - .. code-block:: LAMMPS fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 @@ -65,7 +60,6 @@ with: * :math:`\mu_i` the atomic moment of spin :math:`i` given as a multiple of the Bohr magneton :math:`\mu_B` (for example, :math:`\mu_i \approx 2.2` in bulk iron). - The field value in Tesla is multiplied by the gyromagnetic ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`). @@ -134,10 +128,8 @@ normalized). Those styles can be combined within one single command line. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** By default, the energy associated to this fix is not added to the potential @@ -145,7 +137,6 @@ energy of the system. The :doc:`fix_modify ` *energy* option is supported by this fix to add this magnetic potential energy to the potential energy of the system, - .. code-block:: LAMMPS fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 @@ -159,7 +150,6 @@ No information about this fix is written to :doc:`binary restart files 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. @@ -173,13 +163,9 @@ Related commands none - ---------- - .. _Skomski1: - - **(Skomski)** Skomski, R. (2008). Simple models of magnetism. Oxford University Press. diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index 0107302c94..b38db2564d 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -6,7 +6,6 @@ fix press/berendsen command Syntax """""" - .. parsed-literal:: fix ID group-ID press/berendsen keyword value ... @@ -28,12 +27,9 @@ Syntax *modulus* value = bulk modulus of system (pressure units) *dilate* value = *all* or *partial* - - Examples """""""" - .. parsed-literal:: fix 1 all press/berendsen iso 0.0 0.0 1000.0 @@ -68,10 +64,8 @@ unchanged and controlling the pressure of a surrounding fluid. See the :doc:`Howto baroostat ` doc page for a discussion of different ways to perform barostatting. - ---------- - The barostat is specified using one or more of the *iso*\ , *aniso*\ , *x*\ , *y*\ , *z*\ , and *couple* keywords. These keywords give you the ability to specify the 3 diagonal components of an external stress @@ -126,10 +120,8 @@ means to relax the pressure in a timespan of (roughly) 10 time units too small for solids. Thus you should experiment to find appropriate values of *Pdamp* and/or the *modulus* when using this fix. - ---------- - The *couple* keyword allows two or three of the diagonal components of the pressure tensor to be "coupled" together. The value specified with the keyword determines which are coupled. For example, *xz* @@ -143,10 +135,8 @@ dilated or contracted by the same percentage every timestep. The be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. - ---------- - The *iso* and *aniso* keywords are simply shortcuts that are equivalent to specifying several other keywords together. @@ -155,7 +145,6 @@ pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using "iso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -169,7 +158,6 @@ stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -177,15 +165,12 @@ these 4 keywords: z Pstart Pstop Pdamp couple none - ---------- - This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style "temp" and "pressure", as if these commands had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -230,7 +215,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - Any dimension being adjusted by this fix must be periodic. Related commands @@ -245,13 +229,9 @@ Default The keyword defaults are dilate = all, modulus = 10.0 in units of pressure for whatever :doc:`units ` are defined. - ---------- - .. _Berendsen1: - - **(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index ab81edd773..e87eb26f4c 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -6,7 +6,6 @@ fix print command Syntax """""" - .. parsed-literal:: fix ID group-ID print N string keyword value ... @@ -26,12 +25,9 @@ Syntax *title* value = string string = text to print as 1st line of output file - - Examples """""""" - .. parsed-literal:: fix extra all print 100 "Coords of marker atom = $x $y $z" @@ -58,7 +54,6 @@ and logfreq() and stride() math functions for :doc:`equal-style variables `. @@ -69,7 +64,6 @@ This fix is not imposed during minimization. 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 @@ -82,27 +76,19 @@ Related commands .. _Erdmann: - - **(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000. .. _Henkes: - - **(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011. .. _Bialke: - - **(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012. .. _Fily: - - **(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. **Default:** types diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index bddb742aaa..b78eb1c324 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -9,7 +9,6 @@ fix property/atom/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID property/atom vec1 vec2 ... keyword value ... @@ -33,12 +32,9 @@ Syntax *ghost* value = *no* or *yes* for whether ghost atom info in communicated - - Examples """""""" - .. parsed-literal:: fix 1 all property/atom mol @@ -136,10 +132,8 @@ new properties are also defined for the ghost atoms. a 'run 0' command should be issued to properly initialize the storage created by this fix. - ---------- - This fix is one of a small number that can be defined in an input script before the simulation box is created or atoms are defined. This is so it can be used with the :doc:`read_data ` command @@ -154,7 +148,6 @@ passing it the fix-ID of this fix. Thus these commands: - .. parsed-literal:: fix prop all property/atom mol d_flag @@ -162,7 +155,6 @@ Thus these commands: would allow a data file to have a section like this: - .. parsed-literal:: Molecules @@ -185,7 +177,6 @@ Another way of initializing the new properties is via the defined for every set of 10 atoms, based on their atom-IDs, these commands could be used: - .. parsed-literal:: fix prop all property/atom mol @@ -204,10 +195,8 @@ molecule IDs could be read-in from a separate file and assigned by the :doc:`set ` command. This allows you to initialize new per-atom properties in a completely general fashion. - ---------- - 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 `. @@ -215,31 +204,24 @@ their values. This means that the values can be output via the :doc:`dump custo For example, these commands will output two new properties to a custom dump file: - .. parsed-literal:: fix prop all property/atom i_flag1 d_flag2 compute 1 all property/atom i_flag1 d_flag2 dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] - ---------- - If you wish to add new :doc:`pair styles `, :doc:`fixes `, or :doc:`computes ` that use the per-atom properties defined by this fix, see the :doc:`Modify atom ` doc page which has details on how the properties can be accessed from added classes. - ---------- - .. _isotopes: - - Example for using per-atom masses with TIP4P water to study isotope effects. When setting up simulations with the :doc:`TIP4P pair styles ` for water, you have to provide exactly one atom type each to identify the water oxygen and hydrogen @@ -251,7 +233,6 @@ for regular TIP4P water, where water oxygen is atom type 1 and water hydrogen is atom type 2, the following lines of input script convert this to using per-atom masses: - .. parsed-literal:: fix Isotopes all property/atom rmass ghost yes @@ -265,7 +246,6 @@ existing data file and just add this *Isotopes* section with one line per atom containing atom-ID and mass. Either way, the extended data file can be read back with: - .. parsed-literal:: fix Isotopes all property/atom rmass ghost yes @@ -276,17 +256,14 @@ and the second to the name of the section. The following input script code will now change the first 100 water molecules in this example to heavy water: - .. parsed-literal:: group hwat id 2:300:3 group hwat id 3:300:3 set group hwat mass 2.0141018 - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -305,10 +282,8 @@ 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:** This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 600fa4aedc..c6f96ef4d6 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -6,7 +6,6 @@ fix python/invoke command Syntax """""" - .. parsed-literal:: fix ID group-ID python/invoke N callback function_name @@ -21,12 +20,9 @@ Syntax *post_force* = callback after force computations on atoms every N time steps *end_of_step* = callback after every N time steps - - Examples """""""" - .. parsed-literal:: python post_force_callback here """ @@ -73,7 +69,6 @@ gives access to the LAMMPS state from Python. Restrictions """""""""""" - This fix is part of the PYTHON 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_python_move.rst b/doc/src/fix_python_move.rst index 44fd76040a..4ea6f14e94 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -6,7 +6,6 @@ fix python/move command Syntax """""" - .. parsed-literal:: fix python/move pymodule.CLASS @@ -16,7 +15,6 @@ pymodule.CLASS = use class **CLASS** in module/file **pymodule** to compute how Examples """""""" - .. parsed-literal:: fix 1 all python/move py_nve.NVE @@ -37,13 +35,10 @@ however, the performance of this fix can be moderately to significantly slower than the corresponding C++ code. For specific cases, this performance penalty can be limited through effective use of NumPy. - ---------- - The python module file has to start with the following code: - .. parsed-literal:: from __future_\_ import print_function @@ -85,10 +80,8 @@ methods as needed. Examples for how to do this are in the *examples/python* folder. - ---------- - **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 @@ -100,7 +93,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This pair style is part of the PYTHON 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_qbmsst.rst b/doc/src/fix_qbmsst.rst index 5b4e70a5dd..57a2c88fac 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -6,7 +6,6 @@ fix qbmsst command Syntax """""" - .. parsed-literal:: fix ID group-ID qbmsst dir shockvel keyword value ... @@ -34,12 +33,9 @@ Syntax *beta* value = the quantum temperature is updated every beta time steps (positive integer) *T_init* value = quantum temperature for the initial state (temperature units) - - Examples """""""" - .. code-block:: LAMMPS # (liquid methane modeled with the REAX force field, real units) @@ -146,10 +142,8 @@ For all pressure styles, the simulation box stays orthorhombic in shape. Parrinello-Rahman boundary conditions (tilted box) are supported by LAMMPS, but are not implemented for QBMSST. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** Because the state of the random number generator is not written to @@ -180,7 +174,6 @@ headers, the following LAMMPS commands are suggested. Here the the thermo keyword *etotal* to print the quantity :math:`E^{tot}`. See also the :doc:`thermo_style ` command. - .. parsed-literal:: fix fix_id all msst z @@ -200,14 +193,11 @@ under the :doc:`thermo_style ` command print the instantaneous classical temperature :math:`T^{cl}` as described in the command :doc:`fix qtb `. - ---------- - Restrictions """""""""""" - This fix style is part of the USER-QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -215,19 +205,15 @@ All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The QBMSST fix has been tested only for the group-ID all. - ---------- - Related commands """""""""""""""" :doc:`fix qtb `, :doc:`fix msst ` - ---------- - Default """"""" @@ -235,18 +221,12 @@ 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. - ---------- - .. _Goldman1: - - **(Goldman)** Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009) .. _Qi: - - **(Qi)** Qi and Reed, J. Phys. Chem. A 116, 10451 (2012). diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 19b0741e7b..f205d1fe9a 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -18,7 +18,6 @@ fix qeq/fire command Syntax """""" - .. parsed-literal:: fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ... @@ -39,12 +38,9 @@ Syntax *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) - - Examples """""""" - .. parsed-literal:: fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1 @@ -100,7 +96,6 @@ interactions with their neighbors within *cutoff*\ . It requires a few parameters, in *metal* units, for each atom type which provided in a file specified by *qfile*\ . The file has the following format - .. parsed-literal:: 1 chi eta gamma zeta qcore @@ -209,7 +204,6 @@ Thexe fixes are invoked during :doc:`energy minimization `. Restrictions """""""""""" - These fixes are part of the QEQ package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -220,46 +214,32 @@ Related commands **Default:** none - ---------- - .. _Rappe1: - - **(Rappe and Goddard)** A. K. Rappe and W. A. Goddard III, J Physical Chemistry, 95, 3358-3363 (1991). .. _Nakano1: - - **(Nakano)** A. Nakano, Computer Physics Communications, 104, 59-69 (1997). .. _Rick1: - - **(Rick and Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics 101, 16141 (1994). .. _Streitz1: - - **(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50, 16, 11996 (1994) .. _vanDuin: - - **(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J Physical Chemistry, 105, 9396-9049 (2001) .. _Shan: - - **(QEq/Fire)** T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 4947165265..34c40b6184 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -9,7 +9,6 @@ fix qeq/comb/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID qeq/comb Nevery precision keyword value ... @@ -26,12 +25,9 @@ Syntax *file* value = filename filename = name of file to write QEQ equilibration info to - - Examples """""""" - .. parsed-literal:: fix 1 surface qeq/comb 10 0.0001 @@ -67,10 +63,8 @@ performing charge equilibration (more iterations) and accuracy. If the *file* keyword is used, then information about each equilibration calculation is written to the specified file. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -89,10 +83,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. @@ -115,7 +107,6 @@ This fix can be invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix command currently only supports :doc:`pair style *comb*\ `. Related commands @@ -128,33 +119,23 @@ Default No file output is performed. - ---------- - .. _COMB\_1: - - **(COMB\_1)** J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), .. _COMB\_2: - - **(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)** A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 (1991). .. _Rick\_and\_Stuart: - - **(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 ab26c27bde..af3dfeba1b 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -12,7 +12,6 @@ fix qeq/reax/omp command Syntax """""" - .. parsed-literal:: fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c @@ -57,7 +55,6 @@ and the file must contain one line for each atom type. The latter form must be used when performing QeQ with a non-ReaxFF potential. Each line should be formatted as follows: - .. parsed-literal:: itype chi eta gamma @@ -82,10 +79,8 @@ with the *start/stop* keywords of the :doc:`run ` command. This fix is invoked during :doc:`energy minimization `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -104,14 +99,11 @@ 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. - ---------- - Restrictions """""""""""" - This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -126,26 +118,18 @@ Related commands **Default:** none - ---------- - .. _Rappe2: - - **(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95, 3358-3363 (1991). .. _Nakano2: - - **(Nakano)** Nakano, Computer Physics Communications, 104, 59-69 (1997). .. _qeq-Aktulga: - - **(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index d3aaa4b6f3..a7670cee35 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -6,7 +6,6 @@ fix qmmm command Syntax """""" - .. parsed-literal:: fix ID group-ID qmmm @@ -32,8 +31,6 @@ should be possible without changes to LAMMPS itself. .. _espresso: http://www.quantum-espresso.org - - The interface code for this is in the lib/qmmm directory of the LAMMPS distribution and is being made available at this early stage of development in order to encourage contributions for interfaces to @@ -54,7 +51,6 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the USER-QMMM package. It is only enabled if LAMMPS was built with that package. It also requires building a library provided with LAMMPS. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 77b00cdcbc..6980442c9c 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -6,7 +6,6 @@ fix qtb command Syntax """""" - .. parsed-literal:: fix ID group-ID qtb keyword value ... @@ -24,12 +23,9 @@ Syntax *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units) *N_f* value = number of frequency bins (positive integer) - - Examples """""""" - .. code-block:: LAMMPS # (liquid methane modeled with the REAX force field, real units) @@ -71,7 +67,6 @@ temperature-sensitive energy :math:`\theta(\omega,T)` which resembles the energy expectation for a quantum harmonic oscillator with the same natural frequency: - .. math:: \theta(\omega T) = \frac{\hbar}{2} + \hbar\omega \left[\exp(\frac{\hbar\omega}{k_B T})-1 \right]^{-1} @@ -148,10 +143,8 @@ Mbytes. e.g. :doc:`fix nvt ` and :doc:`fix temp/rescale `. - ---------- - **Restart, fix\_modify, output, run start/stop, minimizie info:** No information about this fix is written to :doc:`binary restart files @@ -162,51 +155,38 @@ should produce similar behaviors of the system. This fix is not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - This fix style is part of the USER-QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nph `, :doc:`fix langevin `, :doc:`fix qbmsst ` - ---------- - Default """"""" The keyword defaults are temp = 300, damp = 1, seed = 880302, f\_max=200.0 and N\_f = 100. - ---------- - .. _Dammak: - - **(Dammak)** Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev Lett, 103, 190601 (2009). .. _Barrat: - - **(Barrat)** Barrat and Rodney, J. Stat. Phys, 144, 679 (2011). diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index dd5c9e6634..7dcf8eda8e 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -9,7 +9,6 @@ fix reax/c/bonds/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID reaxc/bonds Nevery filename @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all reax/c/bonds 100 bonds.reaxc @@ -58,10 +56,8 @@ If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. - ---------- - **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 @@ -70,10 +66,8 @@ by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -93,14 +87,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See :doc:`Speed ` of the manual for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" - The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` is invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 1725f2aeef..8d22434a95 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -9,7 +9,6 @@ fix reax/c/species/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... @@ -33,12 +32,9 @@ Syntax posfreq = write position files every this many timestep filepos = name of position output file - - Examples """""""" - .. parsed-literal:: fix 1 all reax/c/species 10 10 100 species.out @@ -97,10 +93,8 @@ character appears in *filepos*\ , then one file per snapshot is written at *posfreq* and the "\*" character is replaced with the timestep value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc. - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the bond-order values are sampled to get the average bond order. The species analysis is performed using the average bond-order @@ -116,10 +110,8 @@ For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on timesteps 90,92,94,96,98,100 will be used to compute the average bond-order for the species analysis output on timestep 100. - ---------- - **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 @@ -143,10 +135,8 @@ any atom in the molecule. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -166,14 +156,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See :doc:`Speed ` of the manual for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" - The "fix reax/c/species" currently only works with :doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 9639890060..4a7572f63e 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -6,7 +6,6 @@ fix recenter command Syntax """""" - .. parsed-literal:: fix ID group-ID recenter x y z keyword value ... @@ -23,12 +22,9 @@ Syntax group-ID = group of atoms whose coords are shifted *units* value = *box* or *lattice* or *fraction* - - Examples """""""" - .. parsed-literal:: fix 1 all recenter 0.0 0.5 0.0 @@ -119,7 +115,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix should not be used with an x,y,z setting that causes a large shift in the system on the 1st timestep, due to the requested COM being very different from the initial COM. This could cause atoms to diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 1eeb632da7..2a2edcb236 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -6,7 +6,6 @@ fix restrain command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID restrain keyword args ... @@ -33,12 +32,9 @@ Syntax keyword/value = optional keyword value pairs. supported keyword/value pairs: *mult* n = dihedral multiplicity n (integer >= 0, default = 1) - - Examples """""""" - .. code-block:: LAMMPS fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 @@ -106,7 +102,6 @@ molecule with particular restraints (e.g. for fitting force field parameters or constructing a potential energy surface), commands such as the following may be useful: - .. code-block:: LAMMPS # minimize molecule energy with restraints @@ -126,10 +121,8 @@ as the following may be useful: unfix REST run 0 - ---------- - The *bond* keyword applies a bond restraint to the specified atoms using the same functional form used by the :doc:`bond_style harmonic ` command. The potential associated with the restraint is @@ -138,7 +131,6 @@ the restraint is E = K (r - r_0)^2 - with the following coefficients: * :math:`K` (energy/distance\^2) @@ -147,10 +139,8 @@ with the following coefficients: :math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor is included in :math:`K`. - ---------- - The *angle* keyword applies an angle restraint to the specified atoms using the same functional form used by the :doc:`angle_style harmonic ` command. The potential associated with the restraint is @@ -167,10 +157,8 @@ with the following coefficients: :math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2 factor is included in :math:`K`. - ---------- - The *dihedral* keyword applies a dihedral restraint to the specified atoms using a simplified form of the function used by the :doc:`dihedral_style charmm ` command. The potential @@ -180,7 +168,6 @@ associated with the restraint is E = K [ 1 + \cos (n \phi - d) ] - with the following coefficients: * :math:`K` (energy) @@ -193,10 +180,8 @@ optional *mult* keyword to set it to a different positive integer. Also note that the energy will be a minimum when the current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. - ---------- - **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_rhok.rst b/doc/src/fix_rhok.rst index 9374f43798..41b6db6e60 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -3,7 +3,6 @@ fix rhok command ================ - .. parsed-literal:: fix ID group-ID rhok nx ny nz K a @@ -16,7 +15,6 @@ fix rhok command Examples """""""" - .. parsed-literal:: fix bias all rhok 16 0 0 4.0 16.0 @@ -35,7 +33,6 @@ The fix applies a force to atoms given by the potential \rho_{\vec{k}} = & \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\ \vec{k} = & (2\pi n_x /L_x , 2\pi n_y /L_y , 2\pi n_z/L_z ) - as described in :ref:`(Pedersen) `. This field, which biases configurations with long-range order, can be @@ -48,7 +45,6 @@ An example of using the interface pinning method is located in the Restrictions """""""""""" - 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. @@ -59,12 +55,8 @@ Related commands **Default:** none - ---------- - .. _Pedersen: - - **(Pedersen)** Pedersen, J. Chem. Phys., 139, 104102 (2013). diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index aad626a66f..2f11f4aa22 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -51,7 +51,6 @@ fix rigid/nph/small command Syntax """""" - .. parsed-literal:: fix ID group-ID style bodystyle args keyword values ... @@ -110,12 +109,9 @@ Syntax *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command - - Examples """""""" - .. parsed-literal:: fix 1 clump rigid single reinit yes @@ -261,10 +257,8 @@ differences may accumulate to produce divergent trajectories. and velocity of individual atoms in the body will be reset when time integration starts again. - ---------- - Each rigid body must have two or more atoms. An atom can belong to at most one rigid body. Which atoms are in which bodies can be defined via several options. @@ -364,10 +358,8 @@ rigid or fix rigid/small command which includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. - ---------- - The constituent particles within a rigid body can be point particles (the default in LAMMPS) or finite-size particles, such as spheres or ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more @@ -385,10 +377,8 @@ commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body. - ---------- - The *rigid*\ , *rigid/nve*\ , *rigid/small*\ , and *rigid/small/nve* styles perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the *rigid* and @@ -478,7 +468,6 @@ pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using "iso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -492,7 +481,6 @@ stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: - .. parsed-literal:: x Pstart Pstop Pdamp @@ -500,10 +488,8 @@ these 4 keywords: z Pstart Pstop Pdamp couple none - ---------- - The keyword/value option pairs are used in the following ways. The *reinit* keyword determines, whether the rigid body properties @@ -579,10 +565,8 @@ freedom. temperature as well without use of the Langevin or Nose/Hoover options associated with the fix rigid commands. - ---------- - The *mol* keyword can only be used with the *rigid/small* styles. It must be used when other commands, such as :doc:`fix deposit ` or :doc:`fix pour `, add rigid bodies on-the-fly during a simulation. You specify a *template-ID* @@ -603,10 +587,8 @@ Also note that when using the *mol* keyword, extra restart information about all rigid bodies is written out whenever a restart file is written out. See the NOTE in the next section for details. - ---------- - The *infile* keyword allows a file of rigid body attributes to be read in from a file, rather then having LAMMPS compute them. There are 5 such attributes: the total mass of the rigid body, its center-of-mass @@ -628,7 +610,6 @@ comment lines starting with "#" which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information: - .. parsed-literal:: ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm @@ -681,10 +662,8 @@ cross periodic boundaries during the simulation. auxiliary file will contain one line for every rigid body, even if the original file only listed a subset of the rigid bodies. - ---------- - If you use a :doc:`temperature compute ` with a group that includes particles in rigid bodies, the degrees-of-freedom removed by each rigid body are accounted for in the temperature (and pressure) @@ -706,10 +685,8 @@ degrees of freedom (2 translational, 1 rotational). The rigid body contribution to the pressure of the system (virial) is also accounted for by this fix. - ---------- - If your simulation is a hybrid model with a mixture of rigid bodies and non-rigid particles (e.g. solvent) there are several ways these rigid fixes can be used in tandem with :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix npt `, and :doc:`fix nph `. @@ -746,7 +723,6 @@ choices: rigid styles for the rigid bodies. Use :doc:`fix nvt ` (or any other thermostat) for the non-rigid particles. - In all case, the rigid bodies and non-rigid particles both contribute to the global pressure and the box is scaled the same by any of the barostatting fixes. @@ -758,10 +734,8 @@ and change the box dimensions, but not time integrate any particles. The integration of the rigid bodies will be performed by fix rigid/nvt. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -780,10 +754,8 @@ 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:** No information about the 4 NVE rigid styles is written to :doc:`binary restart files `. The exception is if the *infile* or @@ -872,14 +844,11 @@ No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These fixes are not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - These fixes are all part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -896,7 +865,6 @@ insures all DOFs are accounted for properly, and then rescale the temperature to the desired value before performing a simulation. For example: - .. parsed-literal:: velocity all create 300.0 12345 @@ -916,38 +884,26 @@ The option defaults are force \* on on on and torque \* on on on, meaning all rigid bodies are acted on by center-of-mass force and torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes. - ---------- - .. _Hoover: - - **(Hoover)** Hoover, Phys Rev A, 31, 1695 (1985). .. _Kamberaj: - - **(Kamberaj)** Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005). .. _Martyna2: - - **(Martyna)** Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. .. _Miller3: - - **(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002). .. _Zhang1: - - **(Zhang)** Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index b0a6629c48..3375c46ff3 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -6,7 +6,6 @@ fix rigid/meso command Syntax """""" - .. parsed-literal:: fix ID group-ID rigid/meso bodystyle args keyword values ... @@ -41,12 +40,9 @@ Syntax *infile* filename filename = file with per-body values of mass, center-of-mass, moments of inertia - - Examples """""""" - .. parsed-literal:: fix 1 ellipsoid rigid/meso single @@ -119,10 +115,8 @@ internal energy and extrapolated velocity are also updated. and velocity of individual particles in the body will be reset when time integration starts again. - ---------- - Each rigid body must have two or more particles. A particle can belong to at most one rigid body. Which particles are in which bodies can be defined via several options. @@ -203,10 +197,8 @@ rigid/meso command which includes all the desired rigid bodies. LAMMPS will allow multiple rigid/meso fixes to be defined, but it is more expensive. - ---------- - The keyword/value option pairs are used in the following ways. The *reinit* keyword determines, whether the rigid body properties @@ -217,10 +209,8 @@ unphysical manipulations between runs or when properties cannot be easily re-computed (e.g. when read from a file). When using the *infile* keyword, the *reinit* option is automatically set to *no*\ . - ---------- - The *infile* keyword allows a file of rigid body attributes to be read in from a file, rather then having LAMMPS compute them. There are 5 such attributes: the total mass of the rigid body, its center-of-mass @@ -242,7 +232,6 @@ comment lines starting with "#" which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information: - .. parsed-literal:: ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm @@ -295,10 +284,8 @@ cross periodic boundaries during the simulation. auxiliary file will contain one line for every rigid body, even if the original file only listed a subset of the rigid bodies. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information is written to :doc:`binary restart files `. @@ -349,14 +336,11 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. - ---------- - Restrictions """""""""""" - This fix is part of the USER-SDPD package and also depends on the RIGID package. It is only enabled if LAMMPS was built with both packages. See the :doc:`Build package ` doc page for more info. @@ -379,13 +363,9 @@ The option defaults are force \* on on on and torque \* on on on, meaning all rigid bodies are acted on by center-of-mass force and torque. Also reinit = yes. - ---------- - .. _Miller: - - **(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002). diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 2f0df1ebd5..3945878d3b 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -9,7 +9,6 @@ fix rx/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID rx file localTemp matrix solver minSteps ... @@ -29,7 +28,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all rx kinetics.rx none dense lammps_rk4 @@ -50,14 +48,12 @@ For a general reaction such that \nu_{A}A + \nu_{B}B \rightarrow \nu_{C}C - the reaction rate equation is defined to be of the form .. math:: r = k(T)[A]^{\nu_{A}}[B]^{\nu_{B}} - In the current implementation, the exponents are defined to be equal to the stoichiometric coefficients. A given reaction set consisting of *n* reaction equations will contain a total of *m* species. A set @@ -107,10 +103,8 @@ statistics per MPI process can be useful to examine any load imbalance caused by adaptive ODE solver. (Some DPD particles can take longer to solve than others. This can lead to an imbalance across the MPI processes.) - ---------- - The filename specifies a file that contains the entire set of reaction kinetic equations and corresponding Arrhenius parameters. The format of this file is described below. @@ -129,7 +123,6 @@ Arrhenius equation: k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}} - where *A* is the Arrhenius factor in time units or concentration/time units, *n* is the unitless exponent of the temperature dependence, and :math:`E_a` is the activation energy in energy units. The temperature @@ -146,14 +139,12 @@ particle internal temperature is defined as: \theta_i^{-1} = \frac{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)\theta_j^{-1}}{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)} - where the Lucy function is expressed as: .. math:: \omega_{Lucy}\left(r_{ij}\right) = \left( 1 + \frac{3r_{ij}}{r_c} \right) \left( 1 - \frac{r_{ij}}{r_c} \right)^3 - The self-particle interaction is included in the above equation. The stoichiometric coefficients for the reaction mechanism are stored @@ -167,14 +158,11 @@ numbers <= 3), a fast exponential function is used. This can save significant computational time so users are encouraged to use integer coefficients where possible. - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # Rxn equations and parameters (one or more comment or blank lines) @@ -209,10 +197,8 @@ should be specified, where the fix-ID will be the "fix rx`ID with a `_ fix foo all rx reaction.file ... read\_data data.dpd fix foo\_SPECIES NULL Species - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -231,14 +217,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD 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_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index e89641363c..1368a80139 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -6,7 +6,6 @@ fix saed/vtk command Syntax """""" - .. parsed-literal:: fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... @@ -31,12 +30,9 @@ Syntax filename = name of file to output time averages to *overwrite* arg = none = overwrite output file with only latest output - - Examples """""""" - .. parsed-literal:: compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 @@ -69,16 +65,13 @@ which store their own "group" definitions. Fix saed/vtk is designed to work only with :doc:`compute saed ` values, e.g. - .. parsed-literal:: compute 3 top saed 0.0251 Al O fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed - ---------- - The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps @@ -97,10 +90,8 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time averaging is done; values are simply generated on timesteps 100,200,etc. - ---------- - 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 @@ -108,7 +99,6 @@ diffraction intensity outputs. By default the header contains the following information (with example data): - .. parsed-literal:: # vtk DataFile Version 3.0 c_SAED @@ -130,10 +120,8 @@ The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are sampled in total. - ---------- - Additional optional keywords also affect the operation of this fix. The *ave* keyword determines how the values produced every *Nfreq* @@ -188,7 +176,6 @@ 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 associated :doc:`compute_saed ` command. @@ -202,13 +189,9 @@ Default The option defaults are ave = one, start = 0, no file output. - ---------- - .. _Coleman: - - **(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013). diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 0257d6dedf..27ddc5bf0d 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -12,7 +12,6 @@ fix setforce/spin command Syntax """""" - .. parsed-literal:: fix ID group-ID setforce fx fy fz keyword value ... @@ -29,12 +28,9 @@ Syntax *region* value = region-ID region-ID = ID of region atoms must be in to have added force - - Examples """""""" - .. parsed-literal:: fix freeze indenter setforce 0.0 0.0 0.0 @@ -77,10 +73,8 @@ If the *region* keyword is used, the atom must also be in the specified geometric :doc:`region ` in order to have force added to it. - ---------- - Style *spin* suffix sets the components of the magnetic precession vectors instead of the mechanical forces. This also erases all previously computed magnetic precession vectors on the atom, though @@ -92,10 +86,8 @@ atoms in the simulation by zeroing their precession vector. All options defined above remain valid, they just apply to the magnetic precession vectors instead of the forces. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -117,10 +109,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. @@ -150,7 +140,6 @@ non-zero force to atoms during a minimization. Restrictions """""""""""" - The fix *setforce/spin* only makes sense when LAMMPS was built with the SPIN package. diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index ce0739900f..2df89918bc 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -9,7 +9,6 @@ fix rattle command Syntax """""" - .. parsed-literal:: fix ID group-ID style tol iter N constraint values ... keyword value ... @@ -37,12 +36,9 @@ Syntax *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command - - Examples """""""" - .. parsed-literal:: fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2 @@ -79,7 +75,6 @@ molecule. The distance vector between sites *i* and *j* is given by \mathbf r^{n+1}_{ij} = \mathbf r^n_j - \mathbf r^n_i - The constraints can then be formulated as .. math:: @@ -87,7 +82,6 @@ The constraints can then be formulated as \mathbf r^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= d^2_{ij} \quad \text{and} \\ \mathbf v^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= 0 - The SHAKE algorithm satisfies the first condition, i.e. the sites at time *n+1* will have the desired separations Dij immediately after the coordinates are integrated. If we also enforce the second condition, @@ -152,10 +146,8 @@ for. defined in your input script after any other fixes which add or change forces (to atoms that fix shake operates on). - ---------- - The *mol* keyword should be used when other commands, such as :doc:`fix deposit ` or :doc:`fix pour `, add molecules on-the-fly during a simulation, and you wish to constrain the new molecules via SHAKE. You specify a *template-ID* previously defined @@ -167,10 +159,8 @@ file. See the :doc:`molecule ` command for details. The only settings required to be in this file (by this command) are the SHAKE info of atoms in the molecule. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -189,10 +179,8 @@ 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. - ---------- - **RATTLE:** The velocity constraints lead to a linear system of equations which @@ -210,10 +198,8 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). 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:** The :doc:`fix_modify ` *virial* option is supported by this @@ -230,7 +216,6 @@ fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" - These fixes are part of the RIGID package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -252,19 +237,13 @@ make a linear molecule rigid. **Default:** none - ---------- - .. _Ryckaert: - - **(Ryckaert)** J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, J of Comp Phys, 23, 327-341 (1977). .. _Andersen3: - - **(Andersen)** H. Andersen, J of Comp Phys, 52, 24-34 (1983). diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 771b6bf7e3..8fd26c8471 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -9,7 +9,6 @@ fix shardlow/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID shardlow @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all shardlow @@ -53,10 +51,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -75,14 +71,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -104,14 +97,10 @@ Related commands **Default:** none - ---------- - .. _Lisal: - - **(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics as isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", @@ -119,8 +108,6 @@ J. Chem. Phys., 135, 204105 (2011). .. _Larentzos1sh: - - **(Larentzos1)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting @@ -128,8 +115,6 @@ Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). .. _Larentzos2sh: - - **(Larentzos2)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 2bd41cfa84..9c269891c1 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -6,7 +6,6 @@ fix smd command Syntax """""" - .. parsed-literal:: fix ID group-ID smd type values keyword values @@ -35,12 +34,9 @@ Syntax x,y,z = direction of spring, automatically computed with 'auto' R0 = distance of end of spring (distance units) - - Examples """""""" - .. parsed-literal:: fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 @@ -139,7 +135,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - 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. @@ -153,14 +148,10 @@ Related commands **Default:** none - ---------- - .. _Izrailev: - - **(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, Wriggers, Schulten. Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and @@ -168,12 +159,8 @@ Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. .. _Park: - - **(Park)** Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) .. _Jarzynski: - - **(Jarzynski)** Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index c6332753ea..3135df2dbf 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -6,7 +6,6 @@ fix smd/adjust_dt command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID smd/adjust_dt arg @@ -19,12 +18,9 @@ Syntax *s_fact* = safety factor - - Examples """""""" - .. code-block:: LAMMPS fix 1 all smd/adjust_dt 0.1 @@ -57,7 +53,6 @@ Currently, no part of USER-SMD supports restarting nor minimization. Restrictions """""""""""" - This fix is part of the USER-SMD 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_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index f2f10121e5..7536e1f6e2 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -6,7 +6,6 @@ fix smd/integrate_tlsph command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID smd/integrate_tlsph keyword values @@ -16,7 +15,6 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *limit\_velocity* - .. parsed-literal:: *limit_velocity* value = max_vel @@ -25,7 +23,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS fix 1 all smd/integrate_tlsph @@ -52,7 +49,6 @@ minimization. This fix has no outputs. Restrictions """""""""""" - This fix is part of the USER-SMD 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_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index 1bea4bfb15..36197bd057 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -6,7 +6,6 @@ fix smd/integrate_ulsph command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID smd/integrate_ulsph keyword @@ -58,7 +57,6 @@ minimization. This fix has no outputs. Restrictions """""""""""" - This fix is part of the USER-SMD 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_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index f3e1417f4b..7dc3758f30 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -6,7 +6,6 @@ fix smd/move_tri_surf command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID smd/move_tri_surf keyword @@ -27,12 +26,9 @@ Syntax Rx,Ry,Rz = axis of rotation vector period = period of rotation (time units) - - Examples """""""" - .. code-block:: LAMMPS fix 1 tool smd/move_tri_surf *LINEAR 20 20 10 @@ -75,7 +71,6 @@ minimization. This fix has no outputs. Restrictions """""""""""" - This fix is part of the USER-SMD 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_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index b98b334a40..bd14ca1765 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -6,7 +6,6 @@ fix smd/setvel command Syntax """""" - .. parsed-literal:: fix ID group-ID smd/setvel vx vy vz keyword value ... @@ -23,12 +22,9 @@ Syntax *region* value = region-ID region-ID = ID of region particles must be in to have their velocities set - - Examples """""""" - .. parsed-literal:: fix top_velocity top_group setvel 1.0 0.0 0.0 @@ -65,10 +61,8 @@ field with optional time-dependence as well. If the *region* keyword is used, the particle must also be in the specified geometric :doc:`region ` in order to have its velocity set by this command. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization @@ -86,7 +80,6 @@ the :doc:`run ` command. Restrictions """""""""""" - This fix is part of the USER-SMD 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_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 60ad5bfd35..fcb007363b 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -6,7 +6,6 @@ fix smd/wall_surface command Syntax """""" - .. code-block:: LAMMPS fix ID group-ID smd/wall_surface arg type mol-ID @@ -25,7 +24,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS fix stl_surf all smd/wall_surface tool.stl 2 65535 @@ -60,7 +58,6 @@ minimization. This fix has no outputs. Restrictions """""""""""" - This fix is part of the USER-SMD 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_spring.rst b/doc/src/fix_spring.rst index 1a3469ccc8..21792be179 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -6,7 +6,6 @@ fix spring command Syntax """""" - .. parsed-literal:: fix ID group-ID spring keyword values @@ -27,12 +26,9 @@ Syntax x,y,z = direction of spring R0 = equilibrium distance of spring (distance units) - - Examples """""""" - .. parsed-literal:: fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0 diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index 8cd05d98aa..b6e1410905 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -6,7 +6,6 @@ fix spring/chunk command Syntax """""" - .. parsed-literal:: fix ID group-ID spring/chunk K chunkID comID @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix restrain all spring/chunk 100 chunkID comID diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index fd3b09754b..8f6edec46e 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -6,7 +6,6 @@ fix spring/rg command Syntax """""" - .. parsed-literal:: fix ID group-ID spring/rg K RG0 @@ -16,7 +15,6 @@ Syntax * K = harmonic force constant (force/distance units) * RG0 = target radius of gyration to constrain to (distance units) - .. parsed-literal:: if RG0 = NULL, use the current RG as the target value @@ -24,7 +22,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 protein spring/rg 5.0 10.0 @@ -52,7 +49,6 @@ than the target value RG0. F_{i} & = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G} \right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right) - The (:math:`x_i` - center-of-mass) term is computed taking into account periodic boundary conditions, :math:`m_i` is the mass of the atom, and *M* is the mass of the entire group. Note that K is thus a force constant diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index e74e515631..63a9893549 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -6,7 +6,6 @@ fix spring/self command Syntax """""" - .. parsed-literal:: fix ID group-ID spring/self K dir @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix tether boundary-atoms spring/self 10.0 diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 0a9f0bd1ab..827dc684e2 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -6,7 +6,6 @@ fix srd command Syntax """""" - .. parsed-literal:: fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... @@ -48,12 +47,9 @@ Syntax *rotate* = rescale during velocity rotation, but not collisions *collide* = rescale during collisions, but not velocity rotation - - Examples """""""" - .. parsed-literal:: fix 1 srd srd 10 big 1.0 0.25 482984 @@ -99,7 +95,6 @@ SRD particles have a mass, temperature, characteristic timestep (:math:`\lambda`). The fundamental equation relating these 4 quantities is - .. math:: \lambda = dt_{SRD} \sqrt{\frac{k_B T_{SRD}}{m}} @@ -155,10 +150,8 @@ SRD velocity is chosen randomly. This collision style imparts torque to a big particle. Thus a time integrator :doc:`fix ` that rotates the big particles appropriately should be used. - ---------- - The *overlap* keyword should be set to *yes* if two (or more) big particles can ever overlap. This depends on the pair potential interaction used for big-big interactions, or could be the case if @@ -204,10 +197,8 @@ bounces between nearby big particles. Note that if the limit is reached, the SRD can be left inside a big particle. A setting of 0 is the same as no limit. - ---------- - There are 2 kinds of bins created and maintained when running an SRD simulation. The first are "SRD bins" which are used to bin SRD particles and reset their velocities, as discussed above. The second @@ -322,10 +313,8 @@ rescaling off during collisions and the per-bin velocity rotation operation. The *collide* and *rotate* values turn it on for one of the operations and off for the other. - ---------- - .. note:: This fix is normally used for simulations with a huge number of @@ -349,10 +338,8 @@ 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:** No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options @@ -388,7 +375,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This command can only be used if LAMMPS was built with the SRD package. See the :doc:`Build package ` doc page for more info. @@ -406,25 +392,17 @@ collision = noslip, overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0, search = hgrid, cubic = error 0.01, shift = no, tstat = no, and rescale = yes. - ---------- - .. _Hecht: - - **(Hecht)** Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). .. _Petersen1: - - **(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J Chem Phys, 132, 174106 (2010). .. _Lechman: - - **(Lechman)** Lechman, et al, in preparation (2010). diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index 1a9dbf5849..32f4540e3d 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -6,7 +6,6 @@ fix store/force command Syntax """""" - .. parsed-literal:: fix ID group-ID store/force @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all store/force diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index d1f61b7c1e..f6d96841d3 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -6,7 +6,6 @@ fix store/state command Syntax """""" - .. parsed-literal:: fix ID group-ID store/state N input1 input2 ... keyword value ... @@ -27,7 +26,6 @@ Syntax c_ID, c_ID[N], f_ID, f_ID[N], v_name, d_name, i_name - .. parsed-literal:: id = atom ID @@ -63,12 +61,9 @@ Syntax *com* value = *yes* or *no* - - Examples """""""" - .. parsed-literal:: fix 1 all store/state 0 x y z diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 5f0b83b63a..400ba2d399 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -6,7 +6,6 @@ fix temp/berendsen command Syntax """""" - .. parsed-literal:: fix ID group-ID temp/berendsen Tstart Tstop Tdamp @@ -21,11 +20,9 @@ Syntax * Tdamp = temperature damping parameter (time units) - Examples """""""" - .. parsed-literal:: fix 1 all temp/berendsen 300.0 300.0 100.0 @@ -87,7 +84,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -119,10 +115,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -151,7 +145,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix can be used with dynamic groups as defined by the :doc:`group ` command. Likewise it can be used with groups to which atoms are added or deleted over time, e.g. a deposition @@ -169,13 +162,9 @@ Related commands **Default:** none - ---------- - .. _Berendsen2: - - **(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 445b5cc676..488eccfb69 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -9,7 +9,6 @@ fix temp/csld command Syntax """""" - .. parsed-literal:: fix ID group-ID temp/csvr Tstart Tstop Tdamp seed @@ -27,11 +26,9 @@ Syntax * Tdamp = temperature damping parameter (time units) * seed = random number seed to use for white noise (positive integer) - Examples """""""" - .. parsed-literal:: fix 1 all temp/csvr 300.0 300.0 100.0 54324 @@ -97,7 +94,6 @@ These fixes compute a temperature each timestep. To do this, the fix creates its own compute of style "temp", as if this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -129,10 +125,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about these fixes are written to :doc:`binary restart files `. @@ -157,7 +151,6 @@ is "extensive". Restrictions """""""""""" - These fixes are not compatible with :doc:`fix shake `. The fix can be used with dynamic groups as defined by the @@ -177,17 +170,12 @@ Related commands **Default:** none - ---------- - .. _Bussi1: - - .. _Bussi2: **(Bussi1)** Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007) - **(Bussi2)** Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007) diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 4b524c2e23..23d6d9f7fc 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -6,7 +6,6 @@ fix temp/rescale command Syntax """""" - .. parsed-literal:: fix ID group-ID temp/rescale N Tstart Tstop window fraction @@ -23,11 +22,9 @@ Syntax * window = only rescale if temperature is outside this window (temperature units) * fraction = rescale to target temperature by this fraction - Examples """""""" - .. parsed-literal:: fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5 @@ -94,7 +91,6 @@ This fix computes a temperature each timestep. To do this, the fix creates its own compute of style "temp", as if one of this command had been issued: - .. parsed-literal:: compute fix-ID_temp group-ID temp @@ -126,10 +122,8 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. - ---------- - **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 6a13b4e922..339c35d631 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -6,7 +6,6 @@ fix temp/rescale/eff command Syntax """""" - .. parsed-literal:: fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 @@ -65,7 +63,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - This fix is part of the USER-EFF 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_tfmc.rst b/doc/src/fix_tfmc.rst index 750207a567..853c094288 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -6,7 +6,6 @@ fix tfmc command Syntax """""" - .. parsed-literal:: fix ID group-ID tfmc Delta Temp seed keyword value @@ -25,12 +24,9 @@ Syntax xflag,yflag,zflag = 0/1 to exclude/include each dimension *rot* args = none - - Examples """""""" - .. parsed-literal:: fix 1 all tfmc 0.1 1000.0 159345 @@ -118,10 +114,8 @@ rotational component of the tfMC displacements after every iteration. external forces, and removing them will lead to a violation of detailed balance. - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -134,7 +128,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - 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. @@ -151,26 +144,18 @@ Default The option default is com = 0 0 0 - ---------- - .. _Bal: - - **(Bal)** K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014). .. _Mees: - - **(Mees)** M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and A. Stesmans, Phys. Rev. B 85, 134301 (2012). .. _Neyts: - - **(Neyts)** E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013). diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index ede20b2ad9..d6a360ec10 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -6,7 +6,6 @@ fix thermal/conductivity command Syntax """""" - .. parsed-literal:: fix ID group-ID thermal/conductivity N edim Nbin keyword value ... @@ -23,12 +22,9 @@ Syntax *swap* value = Nswap = number of swaps to perform every N steps - - Examples """""""" - .. parsed-literal:: fix 1 all thermal/conductivity 100 z 20 @@ -67,7 +63,6 @@ this induces a temperature gradient in the system which can be measured using commands such as the following, which writes the temperature profile (assuming z = edim) to the file tmp.profile: - .. parsed-literal:: compute ke all ke/atom @@ -133,7 +128,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -165,19 +159,13 @@ Default The option defaults are swap = 1. - ---------- - .. _Muller-Plathe1: - - **(Muller-Plathe)** Muller-Plathe, J Chem Phys, 106, 6082 (1997). .. _Zhang2: - - **(Zhang)** Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005). diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 6b7f59fa92..0a5a137e1b 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -6,7 +6,6 @@ fix ti/spring command Syntax """""" - .. parsed-literal:: fix ID group-ID ti/spring k t_s t_eq keyword value ... @@ -24,11 +23,8 @@ Syntax *function* value = function-ID function-ID = ID of the switching function (1 or 2) - - **Example:** - .. parsed-literal:: fix 1 all ti/spring 50.0 2000 1000 function 2 @@ -52,7 +48,6 @@ 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 Einstein crystal harmonic spring, and lambda is the coupling parameter @@ -93,7 +88,6 @@ time: \lambda(\tau) = \tau - 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 @@ -102,7 +96,6 @@ function \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right) - This function has zero slope as lambda approaches its extreme values (0 and 1), according to :ref:`de Koning ` this results in smaller fluctuations on the integral to be computed on the @@ -163,7 +156,6 @@ Related commands Restrictions """""""""""" - 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. @@ -172,19 +164,13 @@ Default The keyword default is function = 1. - ---------- - .. _Freitas1: - - **(Freitas)** Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016). .. _deKoning96: - - **(de Koning)** de Koning and Antonelli, Phys Rev E, 53, 465 (1996). diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 30a927c7e7..81b7013962 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -6,7 +6,6 @@ fix tmd command Syntax """""" - .. parsed-literal:: fix ID group-ID tmd rho_final file1 N file2 @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix 1 all nve @@ -45,7 +43,6 @@ structure during the course of the run. The target file1 can be ASCII text or a gzipped text file (detected by a .gz suffix). The format of the target file1 is as follows: - .. parsed-literal:: 0.0 25.0 xlo xhi @@ -107,7 +104,6 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - All TMD fixes must be listed in the input script after all integrator fixes (nve, nvt, npt) are applied. This ensures that atoms are moved before their positions are corrected to comply with the constraint. @@ -125,22 +121,16 @@ doc page for details. **Default:** none - ---------- - .. _Schlitter1: - - **(Schlitter1)** Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001). .. _Schlitter2: - - **(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction coordinate at multiple constraints: a concise formulation", Molecular Physics, 101, 3439-3443 (2003). diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 1a3fcf2ad9..8d497534fa 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -9,7 +9,6 @@ fix ttm/mod command Syntax """""" - .. parsed-literal:: fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile @@ -47,12 +46,9 @@ Syntax N = dump TTM temperatures every this many timesteps, 0 = no dump T_outfile = filename to write TTM temperatures to (only needed if N > 0) - - Examples """""""" - .. parsed-literal:: fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out @@ -115,7 +111,6 @@ 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 thermal conductivity, T is temperature, the "e" and "a" subscripts represent electronic and atomic subsystems respectively, g\_p is the @@ -148,7 +143,6 @@ 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* as follows: - .. parsed-literal:: 0 0 0 1.0 @@ -189,10 +183,8 @@ temperature controlled by another fix - e.g. :doc:`fix nvt ` or you should insure that this grid is not too large, else your simulation could incur high memory and communication costs. - ---------- - **Additional details for fix ttm/mod** Fix ttm/mod uses the heat diffusion equation with possible external @@ -204,7 +196,6 @@ 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 of skin-layer, and all other designations have the same meaning as in @@ -219,7 +210,6 @@ as 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 coefficient. @@ -233,7 +223,6 @@ 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 force. @@ -258,7 +247,6 @@ is calculated as \nabla_x P_e = \left[\frac{C_e{}T_e(x)\lambda}{(x+\lambda)^2} + \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right] - where lambda is the electron mean free path (see :ref:`(Norman) `, :ref:`(Pisarev) `) @@ -266,7 +254,6 @@ 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: - .. parsed-literal:: a_0, energy/(temperature\*electron) units @@ -292,10 +279,8 @@ ignored. The lines with the even numbers are treated as follows: surface_movement: 0 to disable tracking of surface motion, 1 to enable T_e_min, temperature units - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** These fixes write the state of the electronic subsystem and the energy @@ -335,7 +320,6 @@ of the :doc:`run ` command. The fixes are not invoked during Restrictions """""""""""" - Fix *ttm* is part of the MISC package. It is only enabled if LAMMPS was built with that package. Fix *ttm/mod* is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. @@ -352,41 +336,29 @@ Related commands **Default:** none - ---------- - .. _Duffy: - - **(Duffy)** D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007). .. _Rutherford: - - **(Rutherford)** A M Rutherford and D M Duffy, J. Phys.: Condens. Matter, 19, 496201-496210 (2007). .. _Chen: - - **(Chen)** J Chen, D Tzou and J Beraun, Int. J. Heat Mass Transfer, 49, 307-316 (2006). .. _Norman: - - **(Norman)** G E Norman, S V Starikov, V V Stegailov et al., Contrib. Plasma Phys., 53, 129-139 (2013). .. _Pisarev: - - **(Pisarev)** V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014). diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 42040af013..b9a25778b9 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -6,7 +6,6 @@ fix tune/kspace command Syntax """""" - .. parsed-literal:: fix ID group-ID tune/kspace N @@ -15,11 +14,9 @@ Syntax * tune/kspace = style name of this fix command * N = invoke this fix every N steps - Examples """""""" - .. parsed-literal:: fix 2 all tune/kspace 100 @@ -83,7 +80,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim 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. diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 752d794728..7d16d6c1d0 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -6,7 +6,6 @@ fix vector command Syntax """""" - .. parsed-literal:: fix ID group-ID vector Nevery value1 value2 ... @@ -26,12 +25,9 @@ Syntax v_name = value calculated by an equal-style variable with name v_name[I] = Ith component of vector-style variable with name - - Examples """""""" - .. parsed-literal:: fix 1 all vector 100 c_myTemp @@ -52,7 +48,6 @@ time-integrated using the :doc:`variable trap() ` function. For example the velocity auto-correlation function (VACF) can be time-integrated, to yield a diffusion coefficient, as follows: - .. parsed-literal:: compute 2 all vacf @@ -89,10 +84,8 @@ command with a timestep value that encompasses all the runs. This is so that the vector or array stored by this fix can be allocated to a sufficient size. - ---------- - If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a @@ -128,10 +121,8 @@ keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to be stored by fix vector. - ---------- - **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 diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index db54257df9..919aea0e1d 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -6,7 +6,6 @@ fix viscosity command Syntax """""" - .. parsed-literal:: fix ID group-ID viscosity N vdim pdim Nbin keyword value ... @@ -25,12 +24,9 @@ Syntax *swap* value = Nswap = number of swaps to perform every N steps *vtarget* value = V or INF = target velocity of swap partners (velocity units) - - Examples """""""" - .. parsed-literal:: fix 1 all viscosity 100 x z 20 @@ -66,7 +62,6 @@ directions. Over time, this induces a shear velocity profile in the system which can be measured using commands such as the following, which writes the profile to the file tmp.profile: - .. parsed-literal:: compute layers all chunk/atom bin/1d z lower 0.05 units reduced @@ -138,7 +133,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -168,19 +162,13 @@ Default The option defaults are swap = 1 and vtarget = INF. - ---------- - .. _Muller-Plathe2: - - **(Muller-Plathe)** Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). .. _Maginn: - - **(Maginn)** Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007). diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 5163872e65..ec8e05aa91 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -6,7 +6,6 @@ fix viscous command Syntax """""" - .. parsed-literal:: fix ID group-ID viscous gamma keyword values ... @@ -23,12 +22,9 @@ Syntax type = atom type (1-N) ratio = factor to scale the damping coefficient by - - Examples """""""" - .. parsed-literal:: fix 1 flow viscous 0.1 diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index c44a6cbb81..93bf208919 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -24,7 +24,6 @@ fix wall/morse command Syntax """""" - .. parsed-literal:: fix ID group-ID style face args ... keyword value ... @@ -80,12 +79,9 @@ Syntax *yes* = allow periodic boundary in a wall dimension *no* = require non-perioidic boundaries in any wall dimension - - Examples """""""" - .. parsed-literal:: fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box @@ -110,7 +106,6 @@ For style *wall/lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c - For style *wall/lj126*\ , the energy E is given by the 12/6 potential: .. math:: @@ -119,7 +114,6 @@ For style *wall/lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: .. math:: @@ -129,7 +123,6 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c - For style *wall/colloid*\ , the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: @@ -140,7 +133,6 @@ of the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c - For style *wall/harmonic*\ , the energy E is given by a harmonic spring potential: @@ -148,7 +140,6 @@ potential: E = \epsilon \quad (r - r_c)^2 \qquad r < r_c - For style *wall/morse*\ , the energy E is given by a Morse potential: .. math:: @@ -156,7 +147,6 @@ For style *wall/morse*\ , the energy E is given by a Morse potential: E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c - In all cases, *r* is the distance from the particle to the wall at position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the particle and wall no longer interact. The energy of the wall @@ -288,16 +278,13 @@ then particles may interact with both the wall and with periodic images on the other side of the box, which is probably not what you want. - ---------- - Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style :doc:`variables `. The wall interaction parameters (epsilon, sigma) could be varied with additional variable definitions. - .. parsed-literal:: variable ramp equal ramp(0,10) @@ -321,7 +308,6 @@ The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period: - .. parsed-literal:: position = c0 + A sin(omega\*delta) @@ -331,15 +317,12 @@ oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles: - .. parsed-literal:: position = c0 + A (1 - cos(omega\*delta)) - ---------- - **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. @@ -379,10 +362,8 @@ invoked by the :doc:`minimize ` command. minimized), you MUST enable the :doc:`fix_modify ` *energy* option for this fix. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -401,10 +382,8 @@ 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. - ---------- - Restrictions """""""""""" none @@ -421,13 +400,9 @@ Default The option defaults units = lattice, fld = no, and pbc = no. - ---------- - .. _Magda: - - **(Magda)** Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); erratum in JCP 84, 2901 (1986). diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 4847d58e0f..7bffa0d46f 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -6,7 +6,6 @@ fix wall/body/polygon command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... @@ -36,8 +35,6 @@ Syntax amplitude = size of oscillation (distance units) period = time of oscillation (time units) - - Examples """""""" @@ -79,7 +76,6 @@ the z dimension. Each timestep, the position of a wiggled wall in the appropriate *dim* is set according to this equation: - .. parsed-literal:: position = coord + A - A cos (omega \* delta) @@ -100,7 +96,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the BODY 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_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 13283b0a50..ca6fdf4be5 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -6,7 +6,6 @@ fix wall/body/polyhedron command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... @@ -36,8 +35,6 @@ Syntax amplitude = size of oscillation (distance units) period = time of oscillation (time units) - - Examples """""""" @@ -78,7 +75,6 @@ the z dimension. Each timestep, the position of a wiggled wall in the appropriate *dim* is set according to this equation: - .. parsed-literal:: position = coord + A - A cos (omega \* delta) @@ -99,7 +95,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the BODY 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_wall_ees.rst b/doc/src/fix_wall_ees.rst index d77880f2c4..e915b9d890 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -9,7 +9,6 @@ fix wall/region/ees command Syntax """""" - .. parsed-literal:: fix ID group-ID style args @@ -32,7 +31,6 @@ Syntax sigma can be a variable (see below) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) - .. parsed-literal:: args for style *wall/region/ees*\ : *region-ID* *epsilon* *sigma* *cutoff* @@ -41,12 +39,9 @@ Syntax sigma = size factor for wall-particle interaction (distance units) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) - - Examples """""""" - .. parsed-literal:: fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box @@ -69,7 +64,6 @@ wall-particle interactions E is given by: E = \epsilon \left[ \frac{2 \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c - Introduced by Babadi and Ejtehadi in :ref:`(Babadi) `. Here, *r* is the distance from the particle to the wall at position *coord*\ , and Rc is the *cutoff* distance at which the particle and wall no @@ -92,7 +86,6 @@ pre-factor is 8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon \quad \sigma_a \quad \sigma_b \quad \sigma_c - where :math:`\epsilon` is the LJ energy parameter for the constituent LJ particles and :math:`\sigma_a`, :math:`\sigma_b`, and :math:`\sigma_c` are the radii of the ellipsoidal particles. :math:`\rho_{wall}` and @@ -118,7 +111,6 @@ of using this fix in the examples/USER/misc/ees/ directory. Restrictions """""""""""" - 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. @@ -136,12 +128,8 @@ Default none - ---------- - .. _BabadiEjtehadi: - - **(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002. diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 3a1ed6a2fb..ea8d32686a 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -6,7 +6,6 @@ fix wall/gran command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... @@ -31,7 +30,6 @@ Syntax xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included - .. parsed-literal:: For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` @@ -59,12 +57,9 @@ Syntax dim = *x* or *y* or *z* vshear = magnitude of shear velocity (velocity units) - - Examples """""""" - .. parsed-literal:: fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 @@ -156,7 +151,6 @@ be wiggled in the z dimension. Each timestep, the position of a wiggled wall in the appropriate *dim* is set according to this equation: - .. parsed-literal:: position = coord + A - A cos (omega \* delta) @@ -195,7 +189,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the GRANULAR 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_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index c02179a958..00ad42b639 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -6,7 +6,6 @@ fix wall/gran/region command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID @@ -31,7 +30,6 @@ Syntax xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included - .. parsed-literal:: For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` @@ -42,7 +40,6 @@ Syntax Examples """""""" - .. parsed-literal:: fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone @@ -71,10 +68,8 @@ web site. .. image:: JPG/gran_mixer_small.jpg :target: JPG/gran_mixer.png - ---------- - The distance between a particle and the region boundary is the distance to the nearest point on the region surface. The force the wall exerts on the particle is along the direction between that point @@ -229,7 +224,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" - This fix is part of the GRANULAR 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_wall_piston.rst b/doc/src/fix_wall_piston.rst index 7cc577ca7d..20f7774c0a 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -6,7 +6,6 @@ fix wall/piston command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/piston face ... keyword value ... @@ -33,12 +32,9 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix xwalls all wall/piston zlo @@ -92,10 +88,8 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings. - ---------- - **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 @@ -107,7 +101,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - This fix style is part of the SHOCK 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_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 4d8dbdcd0c..89b7dd21df 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -9,7 +9,6 @@ fix wall/reflect/kk command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/reflect face arg ... keyword value ... @@ -35,12 +34,9 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix xwalls all wall/reflect xlo EDGE xhi EDGE @@ -99,15 +95,12 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings. - ---------- - Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style :doc:`variables `. - .. parsed-literal:: variable ramp equal ramp(0,10) @@ -131,7 +124,6 @@ The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period: - .. parsed-literal:: position = c0 + A sin(omega\*delta) @@ -141,15 +133,12 @@ oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles: - .. parsed-literal:: position = c0 + A (1 - cos(omega\*delta)) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -170,10 +159,8 @@ use the :doc:`suffix ` command in your input script. 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:** No information about this fix is written to :doc:`binary restart files @@ -187,7 +174,6 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - Any dimension (xyz) that has a reflecting wall must be non-periodic. A reflecting wall should not be used with rigid bodies such as those @@ -208,9 +194,6 @@ The default for the units keyword is lattice. ---------- - .. _Bond1: - - **(Bond)** Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index 696d1a465c..96380d7bf1 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/doc/src/fix_wall_reflect_stochastic.rst @@ -6,7 +6,6 @@ fix wall/reflect/stochastic command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/reflect/stochastic rstyle seed face args ... keyword value ... @@ -40,12 +39,9 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix zwalls all wall/reflect/stochastic diffusive 23424 zlo EDGE 300 0.1 0.1 0 zhi EDGE 200 0.1 0.1 0 @@ -99,14 +95,11 @@ as defined by the :doc:`units ` command, e.g. Angstroms for units lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings. - ---------- - Restrictions """""""""""" - This fix has the same limitations as the :doc:`fix wall/reflect ` command. Any dimension (xyz) that has a wall must be non-periodic. It should not be used with rigid bodies such as those defined by the :doc:`fix rigid ` @@ -126,27 +119,19 @@ Default The default for the units keyword is lattice. - ---------- - .. _Maxwell: - - **(Maxwell)** J.C. Maxwell, Philos. Tans. Royal Soc. London, 157: 49-88 (1867). .. _CL: - - **(Cercignani)** C. Cercignani and M. Lampis. Trans. Theory Stat. Phys. 1, 2, 101 (1971). .. _To: - - **(To)** Q.D. To, V.H. Vu, G. Lauriat, and C. Leonard. J. Math. Phys. 56, 103101 (2015). diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 932f82dfde..c56c604a15 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -6,7 +6,6 @@ fix wall/region command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/region region-ID style args ... cutoff @@ -32,11 +31,9 @@ Syntax * cutoff = distance from wall at which wall-particle interaction is cut off (distance units) - Examples """""""" - .. parsed-literal:: fix wall all wall/region mySphere lj93 1.0 1.0 2.5 @@ -138,7 +135,6 @@ For style *lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c - For style *lj126*\ , the energy E is given by the 12/6 potential: .. math:: @@ -147,7 +143,6 @@ For style *lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: .. math:: @@ -157,7 +152,6 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c - For style *colloid*\ , the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: @@ -168,7 +162,6 @@ the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c - For style *wall/harmonic*\ , the energy E is given by a harmonic spring potential (the distance parameter is ignored): @@ -176,7 +169,6 @@ potential (the distance parameter is ignored): E = \epsilon \quad (r - r_c)^2 \qquad r < r_c - For style *wall/morse*\ , the energy E is given by the Morse potential: .. math:: @@ -184,7 +176,6 @@ For style *wall/morse*\ , the energy E is given by the Morse potential: E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c - Unlike other styles, this requires three parameters (:math:`D_0`, :math:`\alpha`, and :math:`r_0` in this order) instead of two like for the other wall styles. diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 1553844875..09434d96ea 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -6,7 +6,6 @@ fix wall/srd command Syntax """""" - .. parsed-literal:: fix ID group-ID wall/srd face arg ... keyword value ... @@ -36,12 +35,9 @@ Syntax *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units - - Examples """""""" - .. parsed-literal:: fix xwalls all wall/srd xlo EDGE xhi EDGE @@ -137,15 +133,12 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings. - ---------- - Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style :doc:`variables `. - .. parsed-literal:: variable ramp equal ramp(0,10) @@ -169,7 +162,6 @@ The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period: - .. parsed-literal:: position = c0 + A sin(omega\*delta) @@ -179,15 +171,12 @@ oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles: - .. parsed-literal:: position = c0 + A (1 - cos(omega\*delta)) - ---------- - **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 @@ -209,7 +198,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - Any dimension (xyz) that has an SRD wall must be non-periodic. Related commands diff --git a/doc/src/fixes.rst b/doc/src/fixes.rst index 5a85738c45..eb0215e310 100644 --- a/doc/src/fixes.rst +++ b/doc/src/fixes.rst @@ -1,7 +1,6 @@ Fixes ##### - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/group.rst b/doc/src/group.rst index bb78921e65..87c76f8ee4 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -6,7 +6,6 @@ group command Syntax """""" - .. parsed-literal:: group ID style args @@ -46,12 +45,9 @@ Syntax *every* value = N = update group every this many timesteps *static* = no args - - Examples """""""" - .. parsed-literal:: group edge region regstrip @@ -159,7 +155,6 @@ For example, these lines define a variable "eatom" that calculates the potential energy of each atom and includes it in the group if its potential energy is above the threshold value -3.0. - .. parsed-literal:: compute 1 all pe/atom @@ -172,7 +167,6 @@ potential energy is above the threshold value -3.0. Note that these lines - .. parsed-literal:: compute 2 all reduce sum c_1 @@ -224,10 +218,8 @@ The *intersect* style takes a list of two or more existing group names as arguments. Atoms that belong to every one of the listed groups are added to the specified group. - ---------- - The *dynamic* style flags an existing or new group as dynamic. This means atoms will be (re)assigned to the group periodically as a simulation runs. This is in contrast to static groups where atoms are @@ -274,7 +266,6 @@ used to model a quench of the system, freezing atoms outside the shrinking sphere, then converting the remaining atoms to a static group and running further. - .. parsed-literal:: variable nsteps equal 5000 @@ -298,14 +289,11 @@ The *static* style removes the setting for a dynamic group, converting it to a static group (the default). The atoms in the static group are those currently in the dynamic group. - ---------- - Restrictions """""""""""" - There can be no more than 32 groups defined at one time, including "all". diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 59528ac7bb..b8b04ff19c 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -9,7 +9,6 @@ ndx2group command Syntax """""" - .. parsed-literal:: group2ndx file group-ID ... @@ -18,11 +17,9 @@ Syntax * file = name of index file to write out or read in * zero or more group IDs may be appended - Examples """""""" - .. parsed-literal:: group2ndx allindex.ndx @@ -52,14 +49,11 @@ recreated. If a group of the same name already exists, it will be completely reset. When specifying group IDs, those groups, if present, will be read from the index file and restored. - ---------- - Restrictions """""""""""" - This command requires that atoms have atom IDs, since this is the information that is written to the index file. diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index 0324e8301e..60e5020ad4 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -6,7 +6,6 @@ hyper command Syntax """""" - .. parsed-literal:: hyper N Nevent fix-ID compute-ID keyword values ... @@ -30,12 +29,9 @@ Syntax *rebond* value = Nrebond Nrebond = frequency at which to reset bonds, even if no event has occurred - - Examples """""""" - .. parsed-literal:: compute event all event/displace 1.0 @@ -83,7 +79,6 @@ occur. See the :doc:`prd ` doc page for more info about PRD. An HD run has several stages, which are repeated each time an event occurs, as explained below. The logic for an HD run is as follows: - .. parsed-literal:: quench @@ -142,10 +137,8 @@ local hyperdynamics, such as the number of events and the elapsed hyper time (accelerated time), And it includes info specific to one or the other, depending on which style of fix was specified by *fix-ID*\ . - ---------- - The optional keywords operate as follows. As explained above, the *min* keyword can be used to specify @@ -173,14 +166,11 @@ if more frequent resets alter event statistics, perhaps because the parameters chosen for defining what is a bond and what is an event are producing bad dynamics in the presence of the bias potential. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. @@ -195,20 +185,14 @@ Default The option defaults are min = 0.1 0.1 40 50 and time = steps. - ---------- - .. _Voter2013: - - **(Voter2013)** S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013). .. _Voter2002hd: - - **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). diff --git a/doc/src/if.rst b/doc/src/if.rst index f7d09c8f50..4b7a4dbcbf 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -6,7 +6,6 @@ if command Syntax """""" - .. parsed-literal:: if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. parsed-literal:: if "${steps} > 1000" then quit @@ -77,7 +75,6 @@ above. Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: - .. parsed-literal:: if "$a < $b" then & @@ -102,7 +99,6 @@ checked, so long as it is current on the timestep when the run completes. As explained on the :doc:`variable ` doc page, this can be insured by including the variable in thermodynamic output. - .. parsed-literal:: variable myTemp equal temp @@ -119,7 +115,6 @@ Here is an example of a double loop which uses the if and :doc:`jump ` commands to break out of the inner loop when a condition is met, then continues iterating through the outer loop. - .. parsed-literal:: label loopa @@ -136,10 +131,8 @@ condition is met, then continues iterating through the outer loop. next a jump SELF loopa - ---------- - The Boolean expressions for the if and elif keywords have a C-like syntax. Note that each expression is a single argument within the if command. Thus if you want to include spaces in the expression for @@ -149,7 +142,6 @@ An expression is built out of numbers (which start with a digit or period or minus sign) or strings (which start with a letter and can contain alphanumeric characters or underscores): - .. parsed-literal:: 0.2, 100, 1.0e20, -15.4, etc @@ -157,7 +149,6 @@ contain alphanumeric characters or underscores): and Boolean operators: - .. parsed-literal:: A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A \|\| B, A \|\^ B, !A @@ -202,10 +193,8 @@ strings. The overall Boolean expression produces a TRUE result if the result is non-zero. If the result is zero, the expression result is FALSE. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index e2bcc3829b..5affc0d4bb 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -12,7 +12,6 @@ improper_style class2/kk command Syntax """""" - .. code-block:: LAMMPS improper_style class2 @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style class2 @@ -40,7 +38,6 @@ The *class2* improper style uses the potential & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\ & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3) - where :math:`E_i` is the improper term and :math:`E_{aa}` is an angle-angle term. The 3 :math:`\chi` terms in :math:`E_i` are an average over 3 out-of-plane angles. @@ -101,10 +98,8 @@ listed under a *AngleAngle Coeffs* heading and you must leave out the The theta values are specified in degrees, but LAMMPS converts them to radians internally; hence the units of M are in energy/radian\^2. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -123,14 +118,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the CLASS2 package. See the :doc:`Build package ` doc page for more info. @@ -142,12 +134,8 @@ Related commands **Default:** none - ---------- - .. _improper-Sun: - - **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index d8974a6494..6b0ab9ab52 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -6,7 +6,6 @@ improper_coeff command Syntax """""" - .. code-block:: LAMMPS improper_coeff N args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_coeff 1 300.0 0.0 @@ -47,7 +45,6 @@ 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: - .. code-block:: LAMMPS improper_coeff * 300.0 0.0 @@ -60,7 +57,6 @@ 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 corresponds to the 1st example above would be listed as - .. parsed-literal:: 1 300.0 0.0 @@ -70,10 +66,8 @@ this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. - ---------- - The list of all improper styles defined in LAMMPS is given on the :doc:`improper_style ` doc page. They are also listed in more compact form on the :ref:`Commands improper ` doc page. @@ -82,14 +76,11 @@ 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. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 39a1c014dc..6e669d3dbe 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -9,7 +9,6 @@ improper_style cossq/omp command Syntax """""" - .. code-block:: LAMMPS improper_style cossq @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style cossq @@ -32,7 +30,6 @@ The *cossq* improper style uses the potential E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)} - where :math:`\chi` is the improper angle, :math:`\chi_0` is its equilibrium value, and :math:`K` is a prefactor. @@ -57,10 +54,8 @@ commands: * :math:`K` (energy) * :math:`\chi_0` (degrees) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,14 +74,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 644caa1a92..a952d9f3b8 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -12,7 +12,6 @@ improper_style cvff/omp command Syntax """""" - .. code-block:: LAMMPS improper_style cvff @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style cvff @@ -35,7 +33,6 @@ The *cvff* improper style uses the potential E = K [1 + d \cos (n \phi) ] - where phi is the improper dihedral angle. If the 4 atoms in an improper quadruplet (listed in the data file read @@ -60,10 +57,8 @@ commands: * :math:`d` (+1 or -1) * :math:`n` (0,1,2,3,4,6) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -82,14 +77,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 8917b6ed22..933afe9160 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -13,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style distance @@ -28,7 +27,6 @@ The *distance* improper style uses the potential E = K_2 d^2 + K_4 d^4 - where :math:`d` is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` @@ -50,14 +48,11 @@ 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) - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index 49c64ae133..b5b20e47d2 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -13,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style distharm @@ -28,7 +27,6 @@ The *distharm* improper style uses the potential E = K (d - d_0)^2 - where :math:`d` is the oriented distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` @@ -44,14 +42,11 @@ file or restart files read by the read\_data or read\_restart commands: * :math:`K` (energy/distance\^2) * :math:`d_0` (distance) - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-YAFF package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index f85eb4784d..a3500f11e6 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -9,7 +9,6 @@ improper_style fourier/omp command Syntax """""" - .. code-block:: LAMMPS improper_style fourier @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style fourier @@ -32,7 +30,6 @@ The *fourier* improper style uses the following potential: E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ] - where K is the force constant, C0, C1, C2 are dimensionless coefficients, and omega is the angle between the IL axis and the IJK plane: @@ -53,10 +50,8 @@ commands: * :math:`C_2` (unitless) * all (0 or 1, optional) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -75,14 +70,11 @@ 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. - ---------- - Restrictions """""""""""" - This angle style can only be used if LAMMPS was built with the USER\_MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 1fcaa181be..0f525ff34b 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -15,7 +15,6 @@ improper_style harmonic/omp command Syntax """""" - .. code-block:: LAMMPS improper_style harmonic @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style harmonic @@ -38,7 +36,6 @@ The *harmonic* improper style uses the potential E = K (\chi - \chi_0)^2 - where :math:`\chi` is the improper angle, :math:`\chi_0` is its equilibrium value, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. @@ -68,10 +65,8 @@ commands: :math:`\chi_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian\^2. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -90,14 +85,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 4696296ff5..12464fee6a 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -6,7 +6,6 @@ improper_style hybrid command Syntax """""" - .. code-block:: LAMMPS improper_style hybrid style1 style2 ... @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style hybrid harmonic helix @@ -54,14 +52,11 @@ 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 types. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index f74ac78e07..4a4ad9e863 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -6,7 +6,6 @@ improper_style inversion/harmonic command Syntax """""" - .. code-block:: LAMMPS improper_style inversion/harmonic @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style inversion/harmonic @@ -30,7 +28,6 @@ out-of-plane angle definition and uses an harmonic potential: E = K \left(\omega - \omega_0\right)^2 - where :math:`K` is the force constant and :math:`\omega` is the angle evaluated for all three axis-plane combinations centered around the atom I. For the IL axis and the IJK plane :math:`\omega` looks as follows: @@ -55,14 +52,11 @@ If :math:`\omega_0 = 0` the potential term has a single minimum for the planar structure. Otherwise it has two minima at +/- :math:`\omega_0`, with a barrier in between. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-MOFFF package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index 9037ba9892..c1c194041a 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -6,7 +6,6 @@ improper_style none command Syntax """""" - .. code-block:: LAMMPS improper_style none @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style none diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index b09e353fd1..ff62812341 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -9,7 +9,6 @@ improper_style ring/omp command Syntax """""" - .. code-block:: LAMMPS improper_style ring @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style ring @@ -35,7 +33,6 @@ The *ring* improper style uses the potential \Delta_{ijk} = & \cos{\theta_{ijk} - \cos{\theta_0}} \\ \Delta_{kjl} = & \cos{\theta_{kjl} - \cos{\theta_0}} - where :math:`K` is a prefactor, :math:`\theta` is the angle formed by the atoms specified by (i,j,k,l) indices and :math:`\theta_0` its equilibrium value. @@ -65,10 +62,8 @@ commands: * :math:`K` (energy) * :math:`\theta_0` (degrees) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -87,14 +82,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -106,7 +98,5 @@ Related commands .. _Destree: - - **(Destree)** M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J Chem Phys, 112, 9632 (2000). diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index b883d5e4f0..9f4fde5b91 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -43,14 +43,11 @@ file or restart files read by the read\_data or read\_restart commands: Note that :math:`{d_0}^2` (in units distance\^2) has be provided and not :math:`d_0`. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 4035f763df..c4ccdb5a74 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -6,7 +6,6 @@ improper_style command Syntax """""" - .. code-block:: LAMMPS improper_style style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style harmonic @@ -58,10 +56,8 @@ to be re-specified. turn off (or weight) the pairwise interaction that would otherwise exist between a group of 4 bonded atoms. - ---------- - Here is an alphabetic list of improper styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated :doc:`improper_coeff ` @@ -94,14 +90,11 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist. :doc:`sqdistharm ` - improper that is harmonic in the square of the out-of-plane distance - ---------- - Restrictions """""""""""" - Improper styles can only be set for atom\_style choices that allow impropers to be defined. @@ -117,7 +110,6 @@ Related commands Default """"""" - .. code-block:: LAMMPS improper_style none diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index cc690dc3b4..ad070319bc 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -9,7 +9,6 @@ improper_style umbrella/omp command Syntax """""" - .. code-block:: LAMMPS improper_style umbrella @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style umbrella @@ -35,7 +33,6 @@ commonly referred to as a classic inversion and used in the E = & \frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o \\ E = & K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o - where :math:`K` is the force constant and :math:`\omega` is the angle between the IL axis and the IJK plane: @@ -57,10 +54,8 @@ commands: * :math:`K` (energy) * :math:`\omega_0` (degrees) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,14 +74,11 @@ 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. - ---------- - Restrictions """""""""""" - This improper style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. @@ -98,13 +90,9 @@ Related commands **Default:** none - ---------- - .. _umbrella-Mayo: - - **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990), diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index d1419f7618..6d28566c66 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -6,7 +6,6 @@ improper_style zero command Syntax """""" - .. code-block:: LAMMPS improper_style zero [nocoeff] @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS improper_style zero diff --git a/doc/src/impropers.rst b/doc/src/impropers.rst index 93b4776d2c..a6653fde7d 100644 --- a/doc/src/impropers.rst +++ b/doc/src/impropers.rst @@ -1,7 +1,6 @@ Improper Styles ############### - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/include.rst b/doc/src/include.rst index 906fe0b16a..3721eabff2 100644 --- a/doc/src/include.rst +++ b/doc/src/include.rst @@ -6,7 +6,6 @@ include command Syntax """""" - .. parsed-literal:: include file @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: include newfile diff --git a/doc/src/info.rst b/doc/src/info.rst index 70f9e9bfed..f83813e637 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -6,7 +6,6 @@ info command Syntax """""" - .. parsed-literal:: info args @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: info system diff --git a/doc/src/jump.rst b/doc/src/jump.rst index e7ece020e3..d067b53832 100644 --- a/doc/src/jump.rst +++ b/doc/src/jump.rst @@ -6,7 +6,6 @@ jump command Syntax """""" - .. parsed-literal:: jump file label @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: jump newfile @@ -41,7 +39,6 @@ script is re-opened and read again. The SELF option is not guaranteed to work when the current input script is being read through stdin (standard input), e.g. - .. parsed-literal:: lmp_g++ < in.script @@ -50,7 +47,6 @@ since the SELF option invokes the C-library rewind() call, which may not be supported for stdin on some systems or by some MPI implementations. This can be worked around by using the :doc:`-in command-line switch `, e.g. - .. parsed-literal:: lmp_g++ -in in.script @@ -60,7 +56,6 @@ the script name as a variable to the input script. In the latter case, a :doc:`variable ` called "fname" could be used in place of SELF, e.g. - .. parsed-literal:: lmp_g++ -var fname in.script < in.script @@ -75,7 +70,6 @@ etc. The :doc:`next ` command is used to exit the loop after 10 iterations. When the "a" variable has been incremented for the tenth time, it will cause the next jump command to be skipped. - .. parsed-literal:: variable a loop 10 @@ -93,7 +87,6 @@ partitions of 10 procs each. An in.file containing the example variable and jump command will cause each partition to run a different simulation. - .. parsed-literal:: mpirun -np 40 lmp_ibm -partition 4x10 -in in.file @@ -108,7 +101,6 @@ checked, so long as it is current on the timestep when the run completes. As explained on the :doc:`variable ` doc page, this can be insured by including the variable in thermodynamic output. - .. parsed-literal:: variable myTemp equal temp @@ -125,7 +117,6 @@ Here is an example of a double loop which uses the if and :doc:`jump ` commands to break out of the inner loop when a condition is met, then continues iterating through the outer loop. - .. parsed-literal:: label loopa @@ -145,7 +136,6 @@ condition is met, then continues iterating through the outer loop. Restrictions """""""""""" - If you jump to a file and it does not contain the specified label, LAMMPS will come to the end of the file and exit. diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 99a4735427..cefae204ce 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -15,7 +15,6 @@ kim_param command Syntax """""" - .. code-block:: LAMMPS kim_init model user_units unitarg @@ -26,8 +25,6 @@ Syntax .. _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) @@ -55,7 +52,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal @@ -109,8 +105,6 @@ Convenience .. _IM\_types: - - Types of IMs in OpenKIM ----------------------- @@ -118,8 +112,6 @@ There are two types of IMs archived in OpenKIM: .. _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. @@ -137,7 +129,6 @@ which begins with an IM code followed by a unique 12-digit code and a 3-digit version identifier. By convention SM prefixes begin with *Sim\_* to readily identify them. - .. parsed-literal:: SW_StillingerWeber_1985_Si__MO_405512056662_005 @@ -151,7 +142,6 @@ access to raw files, and other information. The URL for the Model Page is constructed from the `extended KIM ID `_ of the IM: - .. parsed-literal:: https://openkim.org/id/extended_KIM_ID @@ -159,7 +149,6 @@ The URL for the Model Page is constructed from the For example, for the Stillinger--Weber potential listed above the Model Page is located at: - .. parsed-literal:: `https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 `_ @@ -237,7 +226,6 @@ Here is an example of a LAMMPS script to compute the cohesive energy of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) potential for Al: - .. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal @@ -264,7 +252,6 @@ are defined for all :doc:`physical quantities ` (mass, distance, etc.). These factors are stored as :doc:`internal style variables ` with the following standard names: - .. parsed-literal:: _u_mass @@ -292,7 +279,6 @@ script constructs an fcc lattice with a lattice parameter defined in meters, computes the total energy, and prints the cohesive energy in Joules regardless of the units of the IM. - .. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode @@ -319,7 +305,6 @@ from a file. For example, if a configuration of atoms is read in from a dump file using the :doc:`read_dump ` command, the following can be done to convert the box and all atomic positions to the correct units: - .. code-block:: LAMMPS variable xyfinal equal xy*${_u_distance} @@ -359,14 +344,12 @@ 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: - .. code-block:: LAMMPS kim_interactions Si Si Si C Alternatively, for a model with a fixed mapping the command would be: - .. code-block:: LAMMPS kim_interactions fixed_types @@ -378,7 +361,6 @@ a :doc:`pair_style kim ` command is executed followed by 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 kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal @@ -389,7 +371,6 @@ Ercolessi and Adams (1994) KIM PM for Al set by the following commands: the *kim\_interactions* command executes the following LAMMPS input commands: - .. code-block:: LAMMPS pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 @@ -402,7 +383,6 @@ is defined in the SM specification file, which is part of the SM package. For example, for the Strachan et al. (2003) ReaxFF SM set by the following commands: - .. code-block:: LAMMPS kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real @@ -413,7 +393,6 @@ set by the following commands: the *kim\_interactions* command executes the following LAMMPS input commands: - .. code-block:: LAMMPS pair_style reax/c lmp_control safezone 2.0 mincap 100 @@ -448,7 +427,6 @@ of an IM set by *kim\_init* for material properties archived in The syntax for the *kim\_query* command is as follows: - .. code-block:: LAMMPS kim_query variable formatarg query_function queryargs @@ -508,7 +486,6 @@ or analysis phases of LAMMPS simulations. Some examples are given below. **Define an equilibrium fcc crystal** - .. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal @@ -532,7 +509,6 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}". **Define an equilibrium hcp crystal** - .. code-block:: LAMMPS kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal @@ -555,7 +531,6 @@ input script more readable. **Define a crystal at finite temperature accounting for thermal expansion** - .. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal @@ -586,7 +561,6 @@ potential. **Compute defect formation energy** - .. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal @@ -653,7 +627,6 @@ for details). The syntax for the *kim\_param* command is as follows: - .. code-block:: LAMMPS kim_param get param_name index_range variable formatarg @@ -714,7 +687,6 @@ clarifications are provided below. **Getting a scalar parameter** - .. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal @@ -728,7 +700,6 @@ LAMMPS variable. **Getting multiple scalar parameters with a single call** - .. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal @@ -743,7 +714,6 @@ them in the LAMMPS variables *VARA* and *VARB*\ . There are several options when getting a range of values from a parameter determined by the *formatarg* argument. - .. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal @@ -766,7 +736,6 @@ lambda retrieved by the *get* operation are placed in the LAMMPS variables provided with the driver for the PM being used. A link to the driver is provided at the top of the model page. - .. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal @@ -788,7 +757,6 @@ by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an as shown in the example. At each iteration of the loop *LAM\_VALUE* contains the current value of lambda. - .. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal @@ -803,7 +771,6 @@ the lambda array is appended to create the variable names. **Setting a scalar parameter** - .. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal @@ -815,7 +782,6 @@ Here, the SW potential's gamma parameter is set to 2.6. Note that the *get* and *set* commands work together, so that a *get* following a *set* operation will return the new value that was set. For example: - .. code-block:: LAMMPS ... @@ -831,7 +797,6 @@ potential, while *NEW\_GAMMA* will contain the value 2.6. **Setting multiple scalar parameters with a single call** - .. parsed-literal:: kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal @@ -848,7 +813,6 @@ be used when setting parameters. **Setting a range of values of a parameter** - .. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal @@ -878,7 +842,6 @@ 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 LAMMPS is built with that package. A requirement for the KIM package, is the KIM API library that must be downloaded from the @@ -896,20 +859,14 @@ Related commands :doc:`pair_style kim ` - ---------- - .. _kim-mainpaper: - - **(Tadmor)** Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). doi: `https://doi.org/10.1007/s11837-011-0102-6 `_ .. _kim-api: - - **(Elliott)** Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api `_ (2011) doi: `https://doi.org/10.25950/FF8F563A `_ diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 5d2293fb2c..ac0b0e8aad 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -6,7 +6,6 @@ kspace_modify command Syntax """""" - .. code-block:: LAMMPS kspace_modify keyword value ... @@ -56,12 +55,9 @@ Syntax *splittol* value = tol tol = relative size of two eigenvalues (see discussion below) - - Examples """""""" - .. code-block:: LAMMPS kspace_modify mesh 24 24 30 order 6 @@ -75,10 +71,8 @@ Set parameters used by the kspace solvers defined by the :doc:`kspace_style ` command. Not all parameters are relevant to all kspace styles. - ---------- - The *collective* keyword applies only to PPPM. It is set to *no* by default, except on IBM BlueGene machines. If this option is set to *yes*\ , LAMMPS will use MPI collective operations to remap data for @@ -87,10 +81,8 @@ This is faster on IBM BlueGene machines, and may also be faster on other machines if they have an efficient implementation of MPI collective operations and adequate hardware. - ---------- - The *compute* keyword allows Kspace computations to be turned off, even though a :doc:`kspace_style ` is defined. This is not useful for running a real simulation, but can be useful for @@ -100,10 +92,8 @@ defining a :doc:`kspace_style `, but a Kspace-compatible :doc:`pair_style ` requires a kspace style to be defined. This keyword gives you that option. - ---------- - The *cutoff/adjust* keyword applies only to MSM. If this option is turned on, the Coulombic cutoff will be automatically adjusted at the beginning of the run to give the desired estimated error. Other @@ -113,10 +103,8 @@ grid that minimizes cost using an estimate given by :ref:`(Hardy) `. Note that this cost estimate is not exact, somewhat experimental, and still may not yield the optimal parameters. - ---------- - The *diff* keyword specifies the differentiation scheme used by the PPPM method to compute forces on particles given electrostatic potentials on the PPPM mesh. The *ik* approach is the default for @@ -140,10 +128,8 @@ always used for MSM. Currently, not all PPPM styles support the *ad* option. Support for those PPPM variants will be added later. - ---------- - The *disp/auto* option controls whether the pppm/disp is allowed to generate PPPM parameters automatically. If set to *no*\ , parameters have to be specified using the *gewald/disp*\ , *mesh/disp*\ , @@ -155,29 +141,23 @@ will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good parameters, see the :doc:`How-To ` discussion. - ---------- - The *fftbench* keyword applies only to PPPM. It is off by default. If this option is turned on, LAMMPS will perform a short FFT benchmark computation and report its timings, and will thus finish a some seconds later than it would if this option were off. - ---------- - The *force/disp/real* and *force/disp/kspace* keywords set the force accuracy for the real and space computations for the dispersion part of pppm/disp. As shown in :ref:`(Isele-Holder) `, optimal performance and accuracy in the results is obtained when these values are different. - ---------- - The *force* keyword overrides the relative accuracy parameter set by the :doc:`kspace_style ` command with an absolute accuracy. The accuracy determines the RMS error in per-atom forces @@ -188,10 +168,8 @@ conjunction with the pairwise cutoff to determine the number of K-space vectors for style *ewald*\ , the FFT grid size for style *pppm*\ , or the real space grid size for style *msm*\ . - ---------- - The *gewald* keyword sets the value of the Ewald or PPPM G-ewald parameter for charge as *rinv* in reciprocal distance units. Without this setting, LAMMPS chooses the parameter automatically as a function @@ -203,18 +181,14 @@ and G-ewald parameter automatically. If the value is set to 0.0, LAMMPS will choose the G-ewald parameter automatically. MSM does not use the *gewald* parameter. - ---------- - The *gewald/disp* keyword sets the value of the Ewald or PPPM G-ewald parameter for dispersion as *rinv* in reciprocal distance units. It has the same meaning as the *gewald* setting for Coulombics. - ---------- - The *kmax/ewald* keyword sets the number of kspace vectors in each dimension for kspace style *ewald*\ . The three values must be positive integers, or else (0,0,0), which unsets the option. When this option @@ -223,10 +197,8 @@ consistent with the user-specified accuracy and pairwise cutoff. In any case, if kspace style *ewald* is invoked, the values used are printed to the screen and the log file at the start of the run. - ---------- - The *mesh* keyword sets the grid size for kspace style *pppm* or *msm*\ . In the case of PPPM, this is the FFT mesh, and each dimension must be factorizable into powers of 2, 3, and 5. In the case of MSM, @@ -236,10 +208,8 @@ or MSM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. - ---------- - The *mesh/disp* keyword sets the grid size for kspace style *pppm/disp*\ . This is the FFT mesh for long-range dispersion and ach dimension must be factorizable into powers of 2, 3, and 5. When this @@ -247,10 +217,8 @@ option is not set, the PPPM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. - ---------- - The *minorder* keyword allows LAMMPS to reduce the *order* setting if necessary to keep the communication of ghost grid point limited to exchanges between nearest-neighbor processors. See the discussion of @@ -266,10 +234,8 @@ error if the grid communication is non-nearest-neighbor and *overlap* is set to *no*\ . The *minorder* keyword is not currently supported in MSM. - ---------- - The *mix/disp* keyword selects the mixing rule for the dispersion coefficients. With *pair*\ , the dispersion coefficients of unlike types are computed as indicated with :doc:`pair_modify `. @@ -288,10 +254,8 @@ dispersion coefficients is approximated. This leads to faster computations, but the accuracy in the reciprocal space computations of the dispersion part is decreased. - ---------- - The *order* keyword determines how many grid spacings an atom's charge extends when it is mapped to the grid in kspace style *pppm* or *msm*\ . The default for this parameter is 5 for PPPM and 8 for MSM, which @@ -314,19 +278,15 @@ be generated indicating the order parameter is being reduced to allow LAMMPS to run the problem. Automatic adjustment of the order parameter is not supported in MSM. - ---------- - The *order/disp* keyword determines how many grid spacings an atom's dispersion term extends when it is mapped to the grid in kspace style *pppm/disp*\ . It has the same meaning as the *order* setting for Coulombics. - ---------- - The *overlap* keyword can be used in conjunction with the *minorder* keyword with the PPPM styles to adjust the amount of communication that occurs when values on the FFT grid are exchanged between @@ -342,10 +302,8 @@ communication will be limited to nearest-neighbor processors and the *minorder* keyword discussion. The *overlap* keyword is always set to *yes* in MSM. - ---------- - The *pressure/scalar* keyword applies only to MSM. If this option is turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will be computed, which can be used, for example, to run an isotropic barostat. @@ -356,10 +314,8 @@ instead of using the virial equation. This option cannot be used to access individual components of the pressure tensor, to compute per-atom virial, or with suffix kspace/pair styles of MSM, like OMP or GPU. - ---------- - The *scafacos* keyword is used for settings that are passed to the ScaFaCoS library when using :doc:`kspace_style scafacos `. @@ -417,10 +373,8 @@ with a homogeneous charge distribution. The default for this option is therefore *0*\ . The FMM internal tuning is performed once, when the solver is set up. - ---------- - The *slab* keyword allows an Ewald or PPPM solver to be used for a systems that are periodic in x,y but non-periodic in z - a :doc:`boundary ` setting of "boundary p p f". This is done by @@ -456,10 +410,8 @@ slab correction has also been extended to point dipole interactions dielectric constant due to the Yeh/Berkowitz :ref:`(Yeh) ` correction not being compatible with how :doc:`fix efield ` works. - ---------- - The *force/disp/real* and *force/disp/kspace* keywords set the force accuracy for the real and space computations for the dispersion part of pppm/disp. As shown in :ref:`(Isele-Holder) `, optimal @@ -477,10 +429,8 @@ provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good parameters, see the :doc:`Howto dispersion ` doc page. - ---------- - Restrictions """""""""""" @@ -504,60 +454,42 @@ 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. - ---------- - .. _Hockney1: - - **(Hockney)** Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989). .. _Yeh: - - **(Yeh)** Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). .. _Ballenegger: - - **(Ballenegger)** Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009). .. _Klapp: - - **(Klapp)** Klapp, Schoen, J Chem Phys, 117, 8050 (2002). .. _Hardy1: - - **(Hardy)** David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). .. _Hummer: - - **(Hummer)** Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998) .. _Isele-Holder1: - - **(Isele-Holder)** Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput, 9, 5412 (2013). .. _Wennberg: - - **(Wennberg)** Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013). diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index ce2b988256..786b048b04 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -6,7 +6,6 @@ kspace_style command Syntax """""" - .. code-block:: LAMMPS kspace_style style value @@ -76,12 +75,9 @@ Syntax method = fmm or p2nfft or p3m or ewald or direct accuracy = desired relative error in forces - - Examples """""""" - .. code-block:: LAMMPS kspace_style pppm 1.0e-4 @@ -120,10 +116,8 @@ matching keyword to the name of the KSpace style, as in this table: | tip4p/long | tip4p | +----------------------+-----------------------+ - ---------- - The *ewald* style performs a standard Ewald summation as described in any solid-state physics text. @@ -143,10 +137,8 @@ The *ewald/dipole/spin* style adds long-range standard Ewald summations for magnetic dipole-dipole interactions between magnetic spins. - ---------- - The *pppm* style invokes a particle-particle particle-mesh solver :ref:`(Hockney) ` which maps atom charge to a 3d mesh, uses 3d FFTs to solve Poisson's equation on the mesh, then interpolates electric @@ -201,10 +193,8 @@ page. must be used if energy and/or pressure are quantities of interest, such as when using a barostat. - ---------- - The *pppm/disp* and *pppm/disp/tip4p* styles add a mesh-based long-range dispersion sum option for 1/r\^6 potentials :ref:`(Isele-Holder) `, similar to the *ewald/disp* style. The 1/r\^6 capability means @@ -221,10 +211,8 @@ parameters and how to choose them is described in :ref:`(Isele-Holder) `, :ref:`(Isele-Holder2) ` and the :doc:`Howto dispersion ` doc page. - ---------- - .. note:: All of the PPPM styles can be used with single-precision FFTs by @@ -236,10 +224,8 @@ parameters and how to choose them is described in 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. - ---------- - The *msm* style invokes a multi-level summation method MSM solver, :ref:`(Hardy) ` or :ref:`(Hardy2) `, which maps atom charge to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser @@ -263,10 +249,8 @@ to run an isotropic barostat. If the full pressure tensor is needed, then calculating the pressure at every timestep or using a fixed pressure simulation with MSM will cause the code to run slower. - ---------- - The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library `_ which provides a variety of solver methods which can be used with LAMMPS. The paper by :ref:`(Who) ` gives an overview of ScaFaCoS. @@ -325,10 +309,8 @@ the :doc:`kspace_modify scafacos accuracy ` doc page. The :doc:`kspace_modify scafacos ` command also explains other ScaFaCoS options currently exposed to LAMMPS. - ---------- - The specified *accuracy* determines the relative RMS error in per-atom forces calculated by the long-range solver. It is set as a dimensionless number, relative to the force that two unit point @@ -383,10 +365,8 @@ options of the K-space solvers that can be set, including a *force* option for setting an absolute RMS error in forces, as opposed to a relative RMS error. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -415,14 +395,11 @@ LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" - Note that the long-range electrostatic solvers in LAMMPS assume conducting metal (tinfoil) boundary conditions for both charge and dipole interactions. Vacuum boundary conditions are not currently supported. @@ -465,128 +442,89 @@ Related commands Default """"""" - .. code-block:: LAMMPS kspace_style none - ---------- - .. _Darden: - - **(Darden)** Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993). .. _Deserno: - - **(Deserno)** Deserno and Holm, J Chem Phys, 109, 7694 (1998). .. _Hockney: - - **(Hockney)** Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989). .. _Kolafa: - - **(Kolafa)** Kolafa and Perram, Molecular Simulation, 9, 351 (1992). .. _Petersen: - - **(Petersen)** Petersen, J Chem Phys, 103, 3668 (1995). .. _Wang: - - **(Wang)** Wang and Holm, J Chem Phys, 115, 6277 (2001). .. _Pollock: - - **(Pollock)** Pollock and Glosli, Comp Phys Comm, 95, 93 (1996). .. _Cerutti: - - **(Cerutti)** Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory and Computation 5, 2322 (2009) .. _Neelov: - - **(Neelov)** Neelov, Holm, J Chem Phys 132, 234103 (2010) .. _Veld: - - **(Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007). .. _Toukmaji: - - **(Toukmaji)** Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000). .. _Isele-Holder2012: - - **(Isele-Holder)** Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012). .. _Isele-Holder2013: - - **(Isele-Holder2)** Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput 9, 5412 (2013). .. _Hardy2006: - - **(Hardy)** David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). .. _Hardy2009: - - **(Hardy2)** Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 (2009). .. _Sutmann2013: - - **(Sutmann)** Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) .. _Cerda2008: - - **(Cerda)** Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008) .. _Who2012: - - **(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012). diff --git a/doc/src/label.rst b/doc/src/label.rst index 52387f661f..75c5d2cccc 100644 --- a/doc/src/label.rst +++ b/doc/src/label.rst @@ -6,7 +6,6 @@ label command Syntax """""" - .. parsed-literal:: label ID @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: label xyz diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index a1b643ce14..97d20ca181 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -6,7 +6,6 @@ lattice command Syntax """""" - .. parsed-literal:: lattice style scale keyword values ... @@ -36,12 +35,9 @@ Syntax *basis* values = x y z x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) - - Examples """""""" - .. parsed-literal:: lattice fcc 3.52 @@ -94,10 +90,8 @@ can be repeated multiple times to build a poly-crystalline model with different geometric regions populated with atoms in different lattice orientations. - ---------- - A lattice of style *none* does not define a unit cell and basis set, so it cannot be used with the :doc:`create_atoms ` command. However it does define a lattice spacing via the specified @@ -140,10 +134,8 @@ x of a basis atom within the unit cell is thus a linear combination of the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, where bx,by,bz are the 3 values specified for the *basis* keyword. - ---------- - This sub-section discusses the arguments that determine how the idealized unit cell is transformed into a lattice of points within the simulation box. @@ -199,10 +191,8 @@ the Z direction. applied to a1,a2,a3 to rotate the original unit cell to a new orientation in the simulation box. - ---------- - Several LAMMPS commands have the option to use distance units that are inferred from "lattice spacings" in the x,y,z box directions. E.g. the :doc:`region ` command can create a block of size @@ -259,14 +249,11 @@ Note that whenever the lattice command is used, the values of the lattice spacings LAMMPS calculates are printed out. Thus their effect in commands that use the spacings should be decipherable. - ---------- - Example commands for generating a Wurtzite crystal (courtesy of Aidan Thompson), with its 8 atom unit cell. - .. parsed-literal:: variable a equal 4.340330 @@ -301,14 +288,11 @@ of Aidan Thompson), with its 8 atom unit cell. basis 7 2 & basis 8 2 - ---------- - Restrictions """""""""""" - The *a1,a2,a3,basis* keywords can only be used with style *custom*\ . Related commands @@ -320,7 +304,6 @@ Related commands Default """"""" - .. parsed-literal:: lattice none 1.0 diff --git a/doc/src/log.rst b/doc/src/log.rst index 6c014953f5..ab8f1b73d1 100644 --- a/doc/src/log.rst +++ b/doc/src/log.rst @@ -6,7 +6,6 @@ log command Syntax """""" - .. parsed-literal:: log file keyword @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: log log.equil diff --git a/doc/src/mass.rst b/doc/src/mass.rst index c9c21b5d8d..4185cfbd7d 100644 --- a/doc/src/mass.rst +++ b/doc/src/mass.rst @@ -6,7 +6,6 @@ mass command Syntax """""" - .. parsed-literal:: mass I value @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: mass 1 1.0 @@ -48,7 +46,6 @@ mass command in an input script, except that no wild-card asterisk can be used. For example, under the "Masses" section of a data file, the line that corresponds to the 1st example above would be listed as - .. parsed-literal:: 1 1.0 @@ -75,7 +72,6 @@ per-atom mass will be used by LAMMPS. Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/message.rst b/doc/src/message.rst index 4792c064d8..d1c6423e3d 100644 --- a/doc/src/message.rst +++ b/doc/src/message.rst @@ -6,7 +6,6 @@ message command Syntax """""" - .. parsed-literal:: message which protocol mode arg @@ -26,12 +25,9 @@ Syntax *mpi/two* arg = filename filename = file used to establish communication between 2 MPI jobs - - Examples """""""" - .. parsed-literal:: message client md file tmp.couple @@ -60,20 +56,16 @@ 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. - ---------- - The *which* argument defines LAMMPS to be the client or the server. As explained below the *quit* option should be used when LAMMPS is finished as a client. It sends a message to the server to tell it to shut down. - ---------- - The *protocol* argument defines the format and content of messages that will be exchanged between the two codes. The current options are: @@ -86,10 +78,8 @@ For protocol *md*\ , LAMMPS can be either a client or server. See the For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. - ---------- - The *mode* argument specifies how messages are exchanged between the client and server codes. Both codes must use the same mode and use consistent parameters. @@ -108,7 +98,6 @@ format) or the DNS name of the machine the server code is running on, followed by a 4-digit port ID for the socket, separated by a colon. E.g. - .. parsed-literal:: localhost:5555 # client and server running on same machine @@ -131,7 +120,6 @@ what the client specifies. For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched by the same mpirun command, e.g. with this syntax for OpenMPI: - .. parsed-literal:: mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client @@ -148,10 +136,8 @@ inter-communicator can be established to enable the 2 codes to send MPI messages to each other. Both codes must be able to access the path/file in a common filesystem. - ---------- - Normally, the message client or message server command should be used at the top of a LAMMPS input script. It performs an initial handshake with the other code to setup messaging and to verify that both codes @@ -186,14 +172,11 @@ the client). As an example, this can be performed in a loop to use a quantum code as a server to compute quantum forces for multiple LAMMPS data files or periodic snapshots while running dynamics. - ---------- - Restrictions """""""""""" - This command is part of the MESSAGE 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/min_modify.rst b/doc/src/min_modify.rst index bad1b1366d..c5452e21f4 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -6,7 +6,6 @@ min_modify command Syntax """""" - .. code-block:: LAMMPS min_modify keyword values ... @@ -33,12 +32,9 @@ Syntax *tmax* value = factor factor = maximum adaptive timestep for fire minimization (adim) - - Examples """""""" - .. code-block:: LAMMPS min_modify dmax 0.2 @@ -167,7 +163,6 @@ to the *fire/old* style by using the following set of parameters: Restrictions """""""""""" - 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. diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 2dc29c7544..2474493fe8 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -12,7 +12,6 @@ min_style spin/lbfgs command Syntax """""" - .. code-block:: LAMMPS min_style spin @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS min_style spin/lbfgs @@ -100,7 +98,6 @@ see their implementation reported in :ref:`(Ivanov) `. Restrictions """""""""""" - This minimization procedure is only applied to spin degrees of freedom for a frozen lattice configuration. @@ -116,12 +113,8 @@ Default The option defaults are *alpha\_damp* = 1.0, *discrete\_factor* = 10.0, *line* = spin\_none and *norm* = euclidean. - ---------- - .. _Ivanov1: - - **(Ivanov)** Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019). diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index a7453b5a57..c03015d4d9 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -6,7 +6,6 @@ min_style command Syntax """""" - .. code-block:: LAMMPS min_style style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS min_style cg @@ -70,7 +68,6 @@ in :ref:`(Guenole) ` that include different time integration schemes and defaults parameters. The default parameters can be modified with the command :doc:`min_modify `. - Style *fire/old* is the original implementation of *fire* in Lammps, conserved for backward compatibility. The main differences regarding the current version *fire* are: time integration by Explicit Euler @@ -118,10 +115,8 @@ calculations via the :doc:`neb/spin ` command. or minimizations involving the electron radius in :doc:`eFF ` models. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -142,10 +137,8 @@ use the :doc:`suffix ` command in your input script. See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" @@ -159,15 +152,12 @@ Related commands Default """"""" - .. code-block:: LAMMPS min_style cg - ---------- - .. _Sheppard: **(Sheppard)** Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 1ffb99ebb6..07fef5ca95 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -9,7 +9,6 @@ minimize/kk command Syntax """""" - .. parsed-literal:: minimize etol ftol maxiter maxeval @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. parsed-literal:: minimize 1.0e-4 1.0e-6 100 1000 @@ -81,10 +79,8 @@ they require a :doc:`timestep ` be defined. will converge more quickly if you use a timestep about 10x larger than you would normally use for dynamics simulations. - ---------- - In all cases, the objective function being minimized is the total potential energy of the system as a function of the N atom coordinates: @@ -97,7 +93,6 @@ coordinates: \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) + \sum_i E_{\it fix}(r_i) - where the first term is the sum of all non-bonded :doc:`pairwise interactions ` including :doc:`long-range Coulombic interactions `, the 2nd through 5th terms are :doc:`bond @@ -111,10 +106,8 @@ commands affect minimization. The starting point for the minimization is the current configuration of the atoms. - ---------- - The minimization procedure stops if any of several criteria are met: * the change in energy between outer iterations is less than *etol* @@ -176,7 +169,6 @@ which convergence criterion caused the minimizer to stop, as well as information about the energy, force, final line search, and iteration counts. An example is as follows: - .. parsed-literal:: Minimization stats: @@ -214,10 +206,8 @@ reduced. The iterations and force evaluation values are what is checked by the *maxiter* and *maxeval* parameters. - ---------- - .. note:: There are several force fields in LAMMPS which have @@ -287,10 +277,8 @@ that can be used include: :doc:`fix shake ` or :doc:`fix rigid `. See more info in the Restrictions section below. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -309,14 +297,11 @@ 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. - ---------- - Restrictions """""""""""" - Features that are not yet implemented are listed here, in case someone knows how they could be coded: diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index 36980cd568..e25684d6f4 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -6,7 +6,6 @@ molecule command Syntax """""" - .. parsed-literal:: molecule ID file1 keyword values ... file2 keyword values ... fileN ... @@ -37,12 +36,9 @@ Syntax *scale* value = sfactor sfactor = scale factor to apply to the size and mass of the molecule - - Examples """""""" - .. parsed-literal:: molecule 1 mymol.txt @@ -209,30 +205,24 @@ should be a number from 1 to Nlines for the section, indicating which atom (or bond, etc) the entry applies to. The lines are assumed to be listed in order from 1 to Nlines, but LAMMPS does not check for this. - ---------- - *Coords* section: * one line per atom * line syntax: ID x y z * x,y,z = coordinate of atom - ---------- - *Types* section: * one line per atom * line syntax: ID type * type = atom type of atom - ---------- - *Charges* section: * one line per atom @@ -243,10 +233,8 @@ This section is only allowed for :doc:`atom styles ` that support charge. If this section is not included, the default charge on each atom in the molecule is 0.0. - ---------- - *Diameters* section: * one line per atom @@ -257,10 +245,8 @@ This section is only allowed for :doc:`atom styles ` that 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. - ---------- - *Masses* section: * one line per atom @@ -274,10 +260,8 @@ included, the default mass for each atom is derived from its volume (see Diameters section) and a default density of 1.0, in :doc:`units ` of mass/volume. - ---------- - *Bonds* section: * one line per bond @@ -288,10 +272,8 @@ included, the default mass for each atom is derived from its volume The IDs for the two atoms in each bond should be values from 1 to Natoms, where Natoms = # of atoms in the molecule. - ---------- - *Angles* section: * one line per angle @@ -304,10 +286,8 @@ Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are ordered linearly within the angle. Thus the central atom (around which the angle is computed) is the atom2 in the list. - ---------- - *Dihedrals* section: * one line per dihedral @@ -319,10 +299,8 @@ The IDs for the four atoms in each dihedral should be values from 1 to Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are ordered linearly within the dihedral. - ---------- - *Impropers* section: * one line per improper @@ -336,10 +314,8 @@ the 4 atoms determines the definition of the improper angle used in the formula for the defined :doc:`improper style `. See the doc pages for individual styles for details. - ---------- - *Special Bond Counts* section: * one line per atom @@ -358,10 +334,8 @@ As explained above, LAMMPS will auto-generate this information if this section is not specified. If specified, this section will override what would be auto-generated. - ---------- - *Special Bonds* section: * one line per atom @@ -381,10 +355,8 @@ As explained above, LAMMPS will auto-generate this information if this section is not specified. If specified, this section will override what would be auto-generated. - ---------- - *Shake Flags* section: * one line per atom @@ -404,10 +376,8 @@ clusters. * 3 = part of a 3-atom SHAKE cluster with two bonds * 4 = part of a 4-atom SHAKE cluster with three bonds - ---------- - *Shake Atoms* section: * one line per atom @@ -442,10 +412,8 @@ and b,c,d = IDs of other three atoms bonded to the central atom. See the :doc:`fix shake ` doc page for a further description of SHAKE clusters. - ---------- - *Shake Bond Types* section: * one line per atom @@ -489,14 +457,11 @@ atom (value d in the Shake Atoms section). See the :doc:`fix shake ` doc page for a further description of SHAKE clusters. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is define by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/neb.rst b/doc/src/neb.rst index 0ad7718d78..c7641ed7c2 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -6,7 +6,6 @@ neb command Syntax """""" - .. parsed-literal:: neb etol ftol N1 N2 Nevery file-style arg keyword @@ -35,7 +34,6 @@ keyword = *verbose* Examples """""""" - .. parsed-literal:: neb 0.1 0.0 1000 500 50 final coords.final @@ -114,10 +112,8 @@ from such an initial path. In this case, you will want to generate initial states for the intermediate replicas that are geometrically closer to the MEP and read them in. - ---------- - For a *file-style* setting of *final*\ , a filename is specified which contains atomic coordinates for zero or more atoms, in the format described below. For each atom that appears in the file, the new @@ -151,7 +147,6 @@ For a *file-style* setting of *each*\ , a filename is specified which is assumed to be unique to each replica. This can be done by using a variable in the filename, e.g. - .. parsed-literal:: variable i equal part @@ -185,10 +180,8 @@ that a long calculation can be restarted if needed. must thus be in the correct initial configuration at the time the neb command is issued. - ---------- - A NEB calculation proceeds in two stages, each of which is a minimization procedure, performed via damped dynamics. To enable this, you must first define a damped dynamics @@ -246,10 +239,8 @@ configuration at (close to) the saddle point of the transition. The potential energies for the set of replicas represents the energy profile of the transition along the MEP. - ---------- - A few other settings in your input script are required or advised to perform a NEB calculation. See the NOTE about the choice of timestep at the beginning of this doc page. @@ -271,10 +262,8 @@ Euler integration step. Thus you must define an appropriate will often converge more quickly if you use a timestep about 10x larger than you would normally use for dynamics simulations. - ---------- - Each file read by the neb command containing atomic coordinates used to initialize one or more replicas must be formatted as follows. @@ -284,7 +273,6 @@ starting with "#" which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information: - .. parsed-literal:: ID1 x1 y1 z1 @@ -306,10 +294,8 @@ Also note there is no requirement that the atoms in the file correspond to the NEB atoms in the group defined by the :doc:`fix neb ` command. Not every NEB atom need be in the file, and non-NEB atoms can be listed in the file. - ---------- - Four kinds of output can be generated during a NEB calculation: energy barrier statistics, thermodynamic output by each replica, dump files, and restart files. @@ -415,22 +401,17 @@ image. .. image:: JPG/hop2_small.jpg :target: JPG/hop2.jpg - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. - ---------- - Related commands """""""""""""""" @@ -442,32 +423,22 @@ Default none - ---------- - .. _HenkelmanA: - - **(HenkelmanA)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). .. _HenkelmanB: - - **(HenkelmanB)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). .. _Nakano3: - - **(Nakano)** Nakano, Comp Phys Comm, 178, 280-289 (2008). .. _Maras2: - - **(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016) diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 9a8e538a14..9e9431671a 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -6,7 +6,6 @@ neb/spin command Syntax """""" - .. parsed-literal:: neb/spin etol ttol N1 N2 Nevery file-style arg keyword @@ -39,7 +38,6 @@ Syntax Examples """""""" - .. parsed-literal:: neb/spin 0.1 0.0 1000 500 50 final coords.final @@ -114,10 +112,8 @@ from such an initial path. In this case, you will want to generate initial states for the intermediate replicas that are geometrically closer to the MEP and read them in. - ---------- - For a *file-style* setting of *final*\ , a filename is specified which contains atomic and spin coordinates for zero or more atoms, in the format described below. @@ -195,10 +191,8 @@ that a long calculation can be restarted if needed. must thus be in the correct initial configuration at the time the neb command is issued. - ---------- - A NEB calculation proceeds in two stages, each of which is a minimization procedure. To enable this, you must first define a @@ -259,10 +253,8 @@ configuration at (close to) the saddle point of the transition. The potential energies for the set of replicas represents the energy profile of the transition along the MEP. - ---------- - An atom map must be defined which it is not by default for :doc:`atom_style atomic ` problems. The :doc:`atom_modify map ` command can be used to do this. An initial value can be defined for the timestep. Although, the *spin* @@ -272,10 +264,8 @@ this timestep is likely to evolve during the calculation. The minimizers in LAMMPS operate on all spins in your system, even non-GNEB atoms, as defined above. - ---------- - Each file read by the neb/spin command containing spin coordinates used to initialize one or more replicas must be formatted as follows. @@ -285,7 +275,6 @@ starting with "#" which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information: - .. parsed-literal:: ID1 g1 x1 y1 z1 sx1 sy1 sz1 @@ -308,10 +297,8 @@ Also note there is no requirement that the atoms in the file correspond to the GNEB atoms in the group defined by the :doc:`fix neb ` command. Not every GNEB atom need be in the file, and non-GNEB atoms can be listed in the file. - ---------- - Four kinds of output can be generated during a GNEB calculation: energy barrier statistics, thermodynamic output by each replica, dump files, and restart files. @@ -387,14 +374,11 @@ directory, that interpolates the MEP given the information provided by the *verbose* output option (as detailed in Appendix D of :ref:`(BessarabA) `). - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the SPIN package. See the :doc:`Build package ` doc page for more info. @@ -403,10 +387,8 @@ 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. - ---------- - Related commands """""""""""""""" @@ -417,13 +399,9 @@ Default none - ---------- - .. _BessarabA: - - **(BessarabA)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015). diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 1d36350366..fea38e5e50 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -6,7 +6,6 @@ neigh_modify command Syntax """""" - .. code-block:: LAMMPS neigh_modify keyword values ... @@ -49,12 +48,9 @@ Syntax *binsize* value = size size = bin size for neighbor list construction (distance units) - - Examples """""""" - .. code-block:: LAMMPS neigh_modify every 2 delay 10 check yes page 100000 @@ -132,7 +128,6 @@ sample scenarios where this is useful: * When one or more rigid bodies are specified, interactions within each body can be turned off to save needless computation. See the :doc:`fix rigid ` command for more details. - The *exclude type* option turns off the pairwise interaction if one atom is of type M and the other of type N. M can equal N. The *exclude group* option turns off the interaction if one atom is in the @@ -205,7 +200,6 @@ binsize of 1/2 the cutoff. Restrictions """""""""""" - If the "delay" setting is non-zero, then it must be a multiple of the "every" setting. diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index ba391c0250..aa05146805 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -6,7 +6,6 @@ neighbor command Syntax """""" - .. parsed-literal:: neighbor skin style @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: neighbor 0.3 bin diff --git a/doc/src/newton.rst b/doc/src/newton.rst index 38324e8143..ca981e917a 100644 --- a/doc/src/newton.rst +++ b/doc/src/newton.rst @@ -6,7 +6,6 @@ newton command Syntax """""" - .. parsed-literal:: newton flag @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. parsed-literal:: newton off @@ -54,7 +52,6 @@ communication in the innermost loop. Restrictions """""""""""" - The newton bond setting cannot be changed after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. @@ -67,7 +64,6 @@ Related commands Default """"""" - .. parsed-literal:: newton on diff --git a/doc/src/next.rst b/doc/src/next.rst index 7a1e2264a1..828d6bd0f5 100644 --- a/doc/src/next.rst +++ b/doc/src/next.rst @@ -6,7 +6,6 @@ next command Syntax """""" - .. parsed-literal:: next variables @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: next x @@ -84,7 +82,6 @@ command with an *index*\ -style variable. If this input script is named in.polymer, 8 simulations would be run using data files from directories run1 through run8. - .. parsed-literal:: variable d index run1 run2 run3 run4 run5 run6 run7 run8 @@ -106,7 +103,6 @@ finished. Jump and next commands can also be nested to enable multi-level loops. For example, this script will run 15 simulations in a double loop. - .. parsed-literal:: variable i loop 3 @@ -125,7 +121,6 @@ Here is an example of a double loop which uses the :doc:`if ` and :doc:`jump ` commands to break out of the inner loop when a condition is met, then continues iterating through the outer loop. - .. parsed-literal:: label loopa @@ -146,7 +141,6 @@ condition is met, then continues iterating through the outer loop. Restrictions """""""""""" - As described above. Related commands diff --git a/doc/src/package.rst b/doc/src/package.rst index db40602f81..a4a70ccb59 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -6,7 +6,6 @@ package command Syntax """""" - .. parsed-literal:: package style args @@ -100,12 +99,9 @@ Syntax yes = threaded neighbor list build (default) no = non-threaded neighbor list build - - Examples """""""" - .. parsed-literal:: package gpu 1 @@ -165,10 +161,8 @@ See the :doc:`Speed packages ` doc page for more details about using the various accelerator packages for speeding up LAMMPS simulations. - ---------- - The *gpu* style invokes settings associated with the use of the GPU package. @@ -236,7 +230,6 @@ As an example, if you have two GPUs per node and 8 CPU cores per node, and would like to run on 4 nodes (32 cores) with dynamic balancing of force calculation across CPU and GPU cores, you could specify - .. parsed-literal:: mpirun -np 32 -sf gpu -in in.script # launch command @@ -306,10 +299,8 @@ are 64, 128, or 256. A larger block size increases occupancy of individual GPU cores, but reduces the total number of thread blocks, thus may lead to load imbalance. - ---------- - The *intel* style invokes settings associated with the use of the USER-INTEL package. All of its settings, except the *omp* and *mode* keywords, are ignored if LAMMPS was not built with Xeon Phi @@ -437,10 +428,8 @@ to prevent MPI tasks and OpenMP threads from being on separate NUMA domains and to prevent offload threads from interfering with other processes/threads used for LAMMPS. - ---------- - The *kokkos* style invokes settings associated with the use of the KOKKOS package. @@ -552,10 +541,8 @@ 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 Spectrum MPI when the "-gpu" flag is used. - ---------- - The *omp* style invokes settings associated with the use of the USER-OMP package. @@ -579,7 +566,6 @@ performance. Here are examples of how to set the environment variable when launching LAMMPS: - .. parsed-literal:: env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script @@ -613,14 +599,11 @@ expense of using more memory. Specifically, neighbor list pages are allocated for all threads at the same time and each thread works within its own pages. - ---------- - Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 43a94933ad..fb8394a31b 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -9,7 +9,6 @@ pair_style adp/omp command Syntax """""" - .. code-block:: LAMMPS pair_style adp @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style adp @@ -39,7 +37,6 @@ which is a generalization of the :doc:`embedded atom method (EAM) potential ` doc page for more 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, where types I and J correspond to @@ -180,14 +171,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. @@ -198,19 +186,13 @@ Related commands **Default:** none - ---------- - .. _Mishin: - - **(Mishin)** Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005). .. _Singh: - - **(Singh)** Singh and Warner, Acta Mater, 58, 5797-5805 (2010), diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index bb7408f363..c0453d9130 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -9,7 +9,6 @@ pair_style agni/omp command Syntax """""" - .. code-block:: LAMMPS pair_style agni @@ -35,7 +34,6 @@ an atom as V_i^u(\eta) & = \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\ f_d\left(r_{ij}\right) & = \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right] - :math:`u` labels the individual components, i.e. :math:`x`, :math:`y` or :math:`z`, and :math:`V` is the corresponding atomic fingerprint. :math:`d` is the Euclidean distance between any two atomic fingerprints. A total of :math:`N_t` reference atomic @@ -67,10 +65,8 @@ parameters of the force field, i.e., the reference training environments used to construct the machine learning force field. Example force field and input files are provided in the examples/USER/misc/agni directory. - ---------- - Styles with *omp* suffix is functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated style takes @@ -87,10 +83,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -104,14 +98,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - Currently, only elemental systems are implemented. Also, the method only provides access to the forces and not energies or stresses. The lack of potential energy data makes this pair style incompatible with @@ -137,24 +128,16 @@ Related commands **Default:** none - ---------- - .. _Botu2015adaptive: - - **(Botu1)** V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015). .. _Botu2015learning: - - **(Botu2)** V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015). .. _Botu2016construct: - - **(Botu3)** V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016). diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index 922f213051..dd113b8f4b 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -30,7 +30,6 @@ pair_style rebo/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style cutoff LJ_flag TORSION_flag cutoff_min @@ -44,7 +43,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style airebo 3.0 @@ -135,10 +133,8 @@ optional arguments are given. The :math:`E^{\text{TORSION}}` term is an explicit 4-body potential that describes various dihedral angle preferences in hydrocarbon configurations. - ---------- - Only a single pair_coeff command is used with the *airebo*\ , *airebo* or *rebo* style which specifies an AIREBO, REBO, or AIREBO-M potential file with parameters for C and H. Note that as of LAMMPS version @@ -157,7 +153,6 @@ As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C, and the 4th to be H, you would use the following pair_coeff command: - .. code-block:: LAMMPS pair_coeff * * CH.airebo C C C H @@ -194,7 +189,6 @@ The 3 values correspond to the following sub-categories: To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: - .. code-block:: LAMMPS compute 0 all pair airebo @@ -203,10 +197,8 @@ headings) the following commands could be included in an input script: variable TORSION equal c_0[3] thermo_style custom step temp epair v_REBO v_LJ v_TORSION - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -225,10 +217,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support the :doc:`pair_modify ` @@ -245,7 +235,6 @@ These pair styles can only be used via the *pair* keyword of the Restrictions """""""""""" - These pair styles are part of the MANYBODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -266,26 +255,18 @@ Related commands **Default:** none - ---------- - .. _Stuart: - - **(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 (2000). .. _Brenner: - - **(Brenner)** Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J Physics: Condensed Matter, 14, 783-802 (2002). .. _OConnor: - - **(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015). diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index c8c4edeb54..edb6444c24 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -6,7 +6,6 @@ pair_style atm command Syntax """""" - .. code-block:: LAMMPS pair_style atm cutoff cutoff_triple @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style atm 4.5 2.5 @@ -40,7 +38,6 @@ potential for the energy E of a system of atoms as E & = \nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3} \\ - where :math:`\nu` is the three-body interaction strength. The distances between pairs of atoms :math:`r_{12}`, :math:`r_{23}`, :math:`r_{31}` and the angles :math:`\gamma_1`, :math:`\gamma_2`, :math:`\gamma_3` are as shown in this diagram: @@ -95,7 +92,6 @@ Note that a pair_coeff command can override a previous setting for the same :math:`I,J,K` triplet. For example, these commands set :math:`\nu` for all :math:`I,J.K` triplets, then overwrite nu for just the :math:`I,J,K = 2,3,4` triplet: - .. code-block:: LAMMPS pair_coeff * * * 0.25 @@ -104,7 +100,6 @@ triplets, then overwrite nu for just the :math:`I,J,K = 2,3,4` triplet: Note that for a simulation with a single atom type, only a single entry is required, e.g. - .. code-block:: LAMMPS pair_coeff 1 1 1 0.25 @@ -112,7 +107,6 @@ entry is required, e.g. For a simulation with two atom types, four pair_coeff commands will specify all possible nu values: - .. code-block:: LAMMPS pair_coeff 1 1 1 nu1 @@ -123,7 +117,6 @@ specify all possible nu values: For a simulation with three atom types, ten pair_coeff commands will specify all possible nu values: - .. code-block:: LAMMPS pair_coeff 1 1 1 nu1 @@ -145,10 +138,8 @@ combination and all its permutations. However, as with all pair styles, it is required to specify a pair_coeff command for all :math:`I,J` combinations, else an error will result. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair styles do not support the :doc:`pair_modify ` @@ -165,14 +156,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -183,14 +171,10 @@ Related commands **Default:** none - ---------- - .. _Axilrod: - - **(Axilrod)** Axilrod and Teller, J Chem Phys, 11, 299 (1943); Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943). diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 5626ac37e3..5ff884e790 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -6,7 +6,6 @@ pair_style awpmd/cut command Syntax """""" - .. code-block:: LAMMPS pair_style awpmd/cut Rc keyword value ... @@ -31,12 +30,9 @@ Syntax factor = scaling between electron mass and width variable mass *flex_press* value = none - - Examples """""""" - .. code-block:: LAMMPS pair_style awpmd/cut -1 @@ -99,10 +95,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The :doc:`pair_modify ` mix, shift, table, and tail options @@ -115,10 +109,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 88abfe9798..b71661ea78 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -12,7 +12,6 @@ pair_style beck/omp command Syntax """""" - .. code-block:: LAMMPS pair_style beck Rc @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style beck 8.0 @@ -40,7 +38,6 @@ includes truncation at a cutoff distance Rc. E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\ - The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the @@ -57,10 +54,8 @@ commands. The last coefficient is optional. If not specified, the global cutoff :math:`R_c` is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,10 +74,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, coefficients must be specified. @@ -104,10 +97,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none @@ -119,12 +110,8 @@ Related commands **Default:** none - ---------- - .. _Beck: - - **(Beck)** Beck, Molecular Physics, 14, 311 (1968). diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index edfd4f3ab2..cdb4870cbf 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -6,7 +6,6 @@ pair_style body/nparticle command Syntax """""" - .. code-block:: LAMMPS pair_style body/nparticle cutoff @@ -16,7 +15,6 @@ cutoff = global cutoff for interactions (distance units) Examples """""""" - .. code-block:: LAMMPS pair_style body/nparticle 3.0 @@ -73,7 +71,6 @@ interaction, using the standard formula \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < R_c \\ - where :math:`R_c` is the cutoff. As explained above, an interaction involving one or two body sub-particles may be computed even for :math:`r > R_c`. @@ -90,10 +87,8 @@ commands: The last coefficient is optional. If not specified, the global cutoff is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -110,14 +105,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style is part of the BODY 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/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 652c618d4a..152dd9a996 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -6,12 +6,10 @@ pair_style body/rounded/polygon command Syntax """""" - .. code-block:: LAMMPS pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff - .. parsed-literal:: c_n = normal damping coefficient @@ -23,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5 @@ -149,7 +146,5 @@ Related commands .. _pair-Fraige: - - **(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 20dbbafb13..ac4d578c30 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -6,7 +6,6 @@ pair_style body/rounded/polyhedron command Syntax """""" - .. code-block:: LAMMPS pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 @@ -128,7 +126,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - These pair styles are part of the BODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -144,7 +141,5 @@ Related commands .. _pair-Wang: - - **(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011). diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 5cf3bbb4a8..31a5a369d7 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -6,7 +6,6 @@ pair_style bop command Syntax """""" - .. code-block:: LAMMPS pair_style bop keyword ... @@ -18,12 +17,9 @@ Syntax save = pre-compute and save some values - - Examples """""""" - .. code-block:: LAMMPS pair_style bop @@ -57,7 +53,6 @@ The BOP potential consists of three terms: E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left( r_{ij} \right) - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\sigma,ij} \left( r_{ij} \right) \cdot \Theta_{\sigma,ij} - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\pi,ij} \left( r_{ij} \right) \cdot \Theta_{\pi,ij} + U_{prom} - where :math:`\phi_{ij}(r_{ij})` is a short-range two-body function representing the repulsion between a pair of ion cores, :math:`\beta_{\sigma,ij}(r_{ij})` and :math:`\beta_{\sigma,ij}(r_{ij})` @@ -121,10 +116,8 @@ The latter requires less memory, but may be slower. It is best to test this option to optimize the speed of BOP for your particular system configuration. - ---------- - 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 @@ -139,7 +132,6 @@ 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: - .. parsed-literal:: pair_coeff \* \* CdTe Cd Cd Cd Te @@ -159,10 +151,8 @@ files are given below with variables matching the formulation of Ward (:ref:`Ward `) and Zhou (:ref:`Zhou `). Each header line containing a ":" is preceded by a blank line. - ---------- - **No angular table file format**\ : The parameters/coefficients format for the BOP potentials input file @@ -184,7 +174,6 @@ the tabulated functions are given. * 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. * Line 3: p\_pi (for e\_1) @@ -199,7 +188,6 @@ interaction types e\_i-e\_j, with i=1->N, j=i->N * 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 @@ -209,7 +197,6 @@ e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N 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. @@ -221,7 +208,6 @@ phi\_ij(r\_ij). Each block has nr entries with 5 entries per line. * 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 line. @@ -234,7 +220,6 @@ line. * 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. @@ -246,7 +231,6 @@ beta\_(pi,ij)(r\_ij). Each block has nr entries with 5 entries per line. * 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 nBOt entries with 5 entries per line. @@ -259,7 +243,6 @@ nBOt entries with 5 entries per line. * 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 * Line 1: delta\^mu (for e\_1) @@ -271,10 +254,8 @@ 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) - ---------- - **Angular spline table file format**\ : The parameters/coefficients format for the BOP potentials input file @@ -297,7 +278,6 @@ the tabulated functions are given. * 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. * Line 3: p\_pi (for e\_1) @@ -312,7 +292,6 @@ interaction types e\_i-e\_j, with i=1->N, j=i->N * 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 @@ -325,14 +304,11 @@ e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N 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 (see above). - ---------- - **Angular no-spline table file format**\ : The parameters/coefficients format for the BOP potentials input file @@ -355,7 +331,6 @@ the tabulated functions are given. * 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. * Line 3: p\_pi (for e\_1) @@ -370,7 +345,6 @@ interaction types e\_i-e\_j, with i=1->N, j=i->N * 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 @@ -382,13 +356,10 @@ e\_j-e\_i-e\_k with i=0->N, j=0->N, k=j->N * Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the e\_1-e\_1-e\_2 interaction type) - The rest of the table has the same structure as the previous section (see above). - ---------- - **Mixing, shift, table tail correction, restart**\ : This pair style does not support the :doc:`pair_modify ` @@ -402,14 +373,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - These pair styles are part of the MANYBODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -432,47 +400,33 @@ Default non-tabulated potential file, a\_0 is non-zero. - ---------- - .. _Pettifor\_1: - - **(Pettifor\_1)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 (1999). .. _Pettifor\_2: - - **(Pettifor\_2)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, 4124 (2000). .. _Pettifor\_3: - - **(Pettifor\_3)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002). .. _Murdick: - - **(Murdick)** D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006). .. _Ward: - - **(Ward)** D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. Zimmerman, Phys. Rev. B, 85,115206 (2012). .. _Zhou1: - - **(Zhou)** X.W. Zhou, D.K. Ward, M. Foster (TBP). diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index a5c51c0cb6..c517e4c301 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -39,7 +39,6 @@ pair_style born/coul/dsf command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -47,7 +46,6 @@ Syntax * style = *born* or *born/coul/long* or *born/coul/msm* or *born/coul/wolf* * args = list of arguments for a particular style - .. parsed-literal:: *born* args = cutoff @@ -70,7 +68,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style born 10.0 @@ -107,7 +104,6 @@ potential described in :ref:`(Fumi and Tosi) `, given by E = A \exp \left(\frac{\sigma - r}{\rho} \right) - \frac{C}{r^6} + \frac{D}{r^8} \qquad r < r_c - where :math:`\sigma` is an interaction-dependent length parameter, :math:`\rho` is an ionic-pair dependent length parameter, and :math:`r_c` is the cutoff. @@ -158,10 +154,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -180,10 +174,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -207,14 +199,11 @@ 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*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - The *born/coul/long* style 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. @@ -225,13 +214,9 @@ Related commands **Default:** none - ---------- - .. _FumiTosi: - - Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 24c93551cf..db4e1345ec 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -15,7 +15,6 @@ pair_style brownian/poly/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF @@ -34,7 +33,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) @@ -62,10 +60,8 @@ numbers for the thermostatting procedure. The *flagHI* and *flagVF* settings are optional. Neither should be used, or both must be defined. - ---------- - The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the @@ -79,10 +75,8 @@ The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair\_style command are used. Otherwise both must be specified. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -101,10 +95,8 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See :doc:`this section ` of the manual for more 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 two cutoff distances for this @@ -128,14 +120,11 @@ This pair 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. - ---------- - 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. diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 7c09e7a0ed..512b751dd0 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -54,7 +54,6 @@ pair_style buck/coul/msm/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -62,7 +61,6 @@ Syntax * style = *buck* or *buck/coul/cut* or *buck/coul/long* or *buck/coul/msm* * args = list of arguments for a particular style - .. parsed-literal:: *buck* args = cutoff @@ -80,7 +78,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style buck 2.5 @@ -113,7 +110,6 @@ Lennard-Jones 12/6) given by E = A e^{-r / \rho} - \frac{C}{r^6} \qquad r < r_c - where :math:`\rho` is an ionic-pair dependent length parameter, and :math:`r_c` is the cutoff on both terms. @@ -170,10 +166,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -192,10 +186,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -221,7 +213,6 @@ These styles can only be used via the *pair* keyword of the :doc:`run_style resp Restrictions """""""""""" - The *buck/coul/long* style is 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. @@ -234,6 +225,4 @@ Related commands .. _Khrapak: - - **(Khrapak)** Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011). diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 6b38c7f570..f7f190a322 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -9,7 +9,6 @@ pair_style buck6d/coul/gauss/long command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -17,7 +16,6 @@ Syntax * style = *buck6d/coul/gauss/dsf* or *buck6d/coul/gauss/long* * args = list of arguments for a particular style - .. parsed-literal:: *buck6d/coul/gauss/dsf* args = smooth cutoff (cutoff2) @@ -33,7 +31,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style buck6d/coul/gauss/dsf 0.9000 12.0000 @@ -54,7 +51,6 @@ computes a dispersion damped Buckingham potential: E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\ - where A and C are a force constant, :math:`\kappa` is an ionic-pair dependent reciprocal length parameter, D is a dispersion correction parameter, and the cutoff :math:`r_c` truncates the interaction distance. @@ -84,7 +80,6 @@ is thus evaluated as: E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c - where C is an energy-conversion constant, :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, :math:`\alpha` @@ -121,10 +116,8 @@ The second coefficient, :math:`\rho`, must be greater than zero. The latter coefficient is optional. If not specified, the global vdW cutoff is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -140,7 +133,6 @@ to be specified in an input script that reads a restart file. Restrictions """""""""""" - These styles are part of the USER-MOFFF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -153,11 +145,8 @@ Related commands .. _Schmid: - - .. _Fennell: **(Schmid)** S. Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T.K. Roy and R. Schmid, Phys. Status Solidi B, 6, 1128 (2013). - **(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 711d8b2b82..7e4e0f8200 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -9,7 +9,6 @@ pair_style buck/long/coul/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) @@ -31,11 +30,9 @@ Syntax * cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) * cutoff2 = global cutoff for Coulombic (optional) (distance units) - Examples """""""" - .. code-block:: LAMMPS pair_style buck/long/coul/long cut off 2.5 @@ -111,10 +108,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -133,10 +128,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair styles does not support mixing. Thus, coefficients for all @@ -163,14 +156,11 @@ pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for details. - ---------- - Restrictions """""""""""" - This style 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. @@ -181,13 +171,9 @@ Related commands **Default:** none - ---------- - .. _Ismail: - - **(Ismail)** Ismail, Tsige, In 't Veld, Grest, Molecular Physics (accepted) (2007). diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index a9c18291f8..c9746a58d0 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -54,7 +54,6 @@ pair_style lj/charmmfsw/coul/long command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -62,7 +61,6 @@ Syntax * style = *lj/charmm/coul/charmm* or *lj/charmm/coul/charmm/implicit* or *lj/charmm/coul/long* or *lj/charmm/coul/msm* or *lj/charmmfsw/coul/charmmfsh* or *lj/charmmfsw/coul/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/charmm/coul/charmm* args = inner outer (inner2) (outer2) @@ -87,7 +85,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/charmm/coul/charmm 8.0 10.0 @@ -175,7 +172,6 @@ artifacts. \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } - where S(r) is the energy switching function mentioned above for the *charmm* styles. See the :ref:`(Steinbach) ` paper for the functional forms of the force switching and force shifting functions @@ -237,10 +233,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -259,10 +253,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon, sigma, epsilon\_14, @@ -298,14 +290,11 @@ hierarchy. The other styles only support the *pair* keyword of run\_style respa. See the :doc:`run_style ` command for details. - ---------- - Restrictions """""""""""" - All the styles with *coul/charmm* or *coul/charmmfsh* styles are part of the MOLECULE package. All the styles with *coul/long* style are part of the KSPACE package. They are only enabled if LAMMPS was built @@ -319,25 +308,17 @@ Related commands **Default:** none - ---------- - .. _Brooks1: - - **(Brooks)** Brooks, et al, J Comput Chem, 30, 1545 (2009). .. _pair-MacKerell: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). .. _Steinbach: - - **(Steinbach)** Steinbach, Brooks, J Comput Chem, 15, 667 (1994). diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 33c6487af0..d279370791 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -36,7 +36,6 @@ pair_style lj/class2/coul/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -44,7 +43,6 @@ Syntax * style = *lj/class2* or *lj/class2/coul/cut* or *lj/class2/coul/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/class2* args = cutoff @@ -59,7 +57,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/class2 10.0 @@ -88,7 +85,6 @@ The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by 3 \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - :math:`r_c` is the cutoff. The *lj/class2/coul/cut* and *lj/class2/coul/long* styles add a @@ -120,10 +116,8 @@ 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. - ---------- - 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* @@ -132,19 +126,15 @@ The :doc:`pair_modify mix ` setting is thus ignored for class2 potentials for epsilon and sigma. However it is still followed for mixing the cutoff distance. - ---------- - A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -163,10 +153,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -201,7 +189,6 @@ See the :doc:`run_style ` command for details. Restrictions """""""""""" - These styles are part of the CLASS2 package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -212,12 +199,8 @@ Related commands **Default:** none - ---------- - .. _pair-Sun: - - **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 3b8b93e3ff..8ebb15b173 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -6,7 +6,6 @@ pair_coeff command Syntax """""" - .. code-block:: LAMMPS pair_coeff I J args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_coeff 1 2 1.0 1.0 2.5 @@ -55,7 +53,6 @@ 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: - .. code-block:: LAMMPS pair_coeff \* \* 1.0 1.0 2.5 @@ -72,7 +69,6 @@ should also not be used as part of the I argument. Thus in a data file, the line corresponding to the 1st example above would be listed as - .. parsed-literal:: 2 1.0 1.0 2.5 @@ -108,29 +104,24 @@ for csh, tcsh: - .. parsed-literal:: % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials bash: - .. parsed-literal:: % export LAMMPS_POTENTIALS=/path/to/lammps/potentials Windows: - .. parsed-literal:: % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" - ---------- - The alphabetic list of pair styles defined in LAMMPS is given on the :doc:`pair_style ` doc page. They are also listed in more compact form on the :doc:`Commands pair ` doc page. @@ -138,14 +129,11 @@ 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. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 102c3f0b94..453a42a974 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -12,7 +12,6 @@ pair_style colloid/omp command Syntax """""" - .. code-block:: LAMMPS pair_style colloid cutoff @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style colloid 10.0 @@ -161,10 +159,8 @@ colloid-solvent cutoff in this case. commands for efficiency: :doc:`neighbor multi ` and :doc:`comm_modify multi `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -183,10 +179,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the A, sigma, d1, and d2 @@ -212,14 +206,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -241,12 +232,8 @@ Related commands **Default:** none - ---------- - .. _Everaers1: - - **(Everaers)** Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003). diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 782ef5d5ad..faddf42e70 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -12,24 +12,19 @@ pair_style comb3 command Syntax """""" - .. code-block:: LAMMPS pair_style comb pair_style comb3 keyword - .. parsed-literal:: keyword = *polar* *polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization - - Examples """""""" - .. code-block:: LAMMPS pair_style comb @@ -53,7 +48,6 @@ total energy :math:`E_T` of a system of atoms is given by E_T = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\ & E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] - where :math:`E_i^{self}` is the self-energy of atom *i* (including atomic ionization energies and electron affinities), :math:`E_{ij}^{short}` is the bond-order potential between atoms *i* and @@ -84,7 +78,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * ../potentials/ffield.comb Si Hf O Si @@ -132,7 +125,6 @@ following table: * M = Only optimized for dimer molecule * P = in progress, but have it from mixing rule - 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 @@ -149,10 +141,8 @@ has not yet been implemented, it can only set polar\_off at present. You can not use potential file *ffield.comb* with style *comb3*\ , nor file *ffield.comb3* with style *comb*\ . - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -171,10 +161,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -192,14 +180,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - These pair styles are part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -221,28 +206,20 @@ Related commands **Default:** none - ---------- - .. _COMB: - - **(COMB)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010) .. _COMB3: - - **(COMB3)** T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013). .. _Rick2: - - **(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 (1994). diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index b92d7bb3e4..4669985db9 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -6,14 +6,12 @@ pair_style cosine/squared command Syntax """""" - .. code-block:: LAMMPS pair_style cosine/squared cutoff * cutoff = global cutoff for cosine-squared interactions (distance units) - .. code-block:: LAMMPS pair_coeff i j eps sigma @@ -30,7 +28,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style cosine/squared 3.0 @@ -53,7 +50,6 @@ Style *cosine/squared* computes a potential of the form 0& \quad r \geq r_c \end{cases} - 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. @@ -76,7 +72,6 @@ specifically the following: 2\left(\frac{\sigma}{r}\right)^6 + 1\right] , \quad r < \sigma - In this case, and this case only, the :math:`\sigma` parameter can be equal to *cutoff* (:math:`\sigma =` cutoff) which will result in ONLY the WCA potential being used (and print a warning), so the minimum will be attained at @@ -91,10 +86,8 @@ in the graphs below: .. image:: JPG/pair_cosine_squared_graphs.jpg :align: center - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Mixing is not supported for this style. @@ -108,14 +101,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - The *cosine/squared* style is part of the "USER-MISC" package. It is only enabled if LAMMPS is build with that package. See the :doc:`Build package ` doc page for more info. @@ -129,12 +119,8 @@ Related commands .. _CKD: - - **(Cooke)** "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)" .. _WCA: - - **(Weeks)** "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)" diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 59a95db2a6..55a6b9b057 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -81,7 +81,6 @@ pair_style tip4p/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style coul/cut cutoff @@ -101,7 +100,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style coul/cut 2.5 @@ -144,16 +142,13 @@ potential given by E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c - where C is an energy-conversion constant, Qi and Qj are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric constant which can be set by the :doc:`dielectric ` command. The cutoff :math:`r_c` truncates the interaction distance. - ---------- - Style *coul/debye* adds an additional exp() damping factor to the Coulombic term, given by @@ -161,14 +156,11 @@ Coulombic term, given by E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c - where :math:`\kappa` is the Debye length. This potential is another way to mimic the screening effect of a polar solvent. - ---------- - Style *coul/dsf* computes Coulombic interactions via the damped shifted force model described in :ref:`Fennell `, given by: @@ -177,17 +169,14 @@ shifted force model described in :ref:`Fennell `, given by: E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c - where :math:`\alpha` is the damping parameter and erfc() is the complementary error-function. The potential corrects issues in the Wolf model (described below) to provide consistent forces and energies (the Wolf potential is not differentiable at the cutoff) and smooth decay to zero. - ---------- - Style *coul/wolf* computes Coulombic interactions via the Wolf summation method, described in :ref:`Wolf `, given by: @@ -198,7 +187,6 @@ summation method, described in :ref:`Wolf `, given by: \frac{1}{2} \sum_{j \neq i} \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c - where :math:`\alpha` is the damping parameter, and erc() and erfc() are error-function and complementary error-function terms. This potential is essentially a short-range, spherically-truncated, @@ -212,10 +200,8 @@ forces calculated by the Wolf summation method approach those of the Ewald sum. So it is a means of getting effective long-range interactions with a short-range potential. - ---------- - Style *coul/streitz* is the Coulomb pair interaction defined as part of the Streitz-Mintmire potential, as described in :ref:`this paper `, in which charge distribution about an atom is modeled as a Slater 1\ *s* orbital. More details can be found in the referenced @@ -226,7 +212,6 @@ short-range potential that has been parameterized appropriately) via the :doc:`pair_style hybrid/overlay ` command. Likewise, charge equilibration must be performed via the :doc:`fix qeq/slater ` command. For example: - .. code-block:: LAMMPS pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy @@ -240,7 +225,6 @@ parameter is required for the Wolf summation, as described for the coul/wolf potential above. Alternatively, Coulombic interactions can be computed via an Ewald summation. For example: - .. code-block:: LAMMPS pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy @@ -269,10 +253,8 @@ any other pair style such as EAM, MEAM, Tersoff, or LJ in hybrid/overlay mode. To do this, you would need to provide a Streitz-Mintmire parameterization for the material being modeled. - ---------- - Styles *coul/long* and *coul/msm* compute the same Coulombic interactions as style *coul/cut* except that an additional damping factor is applied so it can be used in conjunction with the @@ -310,10 +292,8 @@ 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. - ---------- - Note that these potentials are designed to be combined with other pair potentials via the :doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence if they @@ -338,10 +318,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -360,10 +338,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the cutoff distance for the @@ -388,14 +364,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - The *coul/long*\ , *coul/msm* and *tip4p/long* 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 @@ -408,34 +381,24 @@ Related commands **Default:** none - ---------- - .. _Wolf1: - - **(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem Phys, 110, 8254 (1999). .. _Fennell1: - - **(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). .. _Streitz2: - - **(Streitz)** F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 (1994). .. _Jorgensen3: - - **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 1c2ddd7f91..8011137199 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -9,7 +9,6 @@ pair_style coul/diel/omp command Syntax """""" - .. code-block:: LAMMPS pair_style coul/diel cutoff @@ -19,7 +18,6 @@ cutoff = global cutoff (distance units) Examples """""""" - .. code-block:: LAMMPS pair_style coul/diel 3.5 @@ -43,7 +41,6 @@ in the Coulomb correction term for small ion separations as follows E = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\ \epsilon_D(r) = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right) - 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 @@ -72,10 +69,8 @@ commands: The global cutoff (:math:`r_c`) specified in the pair\_style command is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support parameter mixing. Coefficients must @@ -99,7 +94,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - This style 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. @@ -111,27 +105,19 @@ Related commands **Default:** none - ---------- - .. _Stiles: - - **(Stiles)** Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982). .. _Lenart1: - - **(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007). .. _Jusufi1: - - **(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 97df7d4a13..14de8c773f 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -6,7 +6,6 @@ pair_style coul/shield command Syntax """""" - .. code-block:: LAMMPS pair_style coul/shield cutoff tap_flag @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style coul/shield 16.0 1 @@ -48,7 +46,6 @@ the pair style :doc:`ilp/graphene/hbn ` 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 - Where Tap(:math:`r_{ij}`) is the taper function which provides a continuous cutoff (up to third derivative) for inter-atomic separations larger than :math:`r_c` :ref:`(Leven1) `, :ref:`(Leven2) ` and :ref:`(Maaravi) `. @@ -63,10 +60,8 @@ in the example above, or in the data file or restart files read by the The global cutoff (:math:`r_c`) specified in the pair\_style command is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support parameter mixing. Coefficients must @@ -86,7 +81,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - This style 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. @@ -98,24 +92,16 @@ Related commands **Default:** tap\_flag = 1 - ---------- - .. _Leven3: - - **(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). .. _Leven4: - - **(Leven2)** I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). .. _Maaravi1: - - **(Maaravi)** T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index ebbbdcaeca..c1aeef745e 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -33,7 +33,6 @@ pair_style lj/cut/coul/long/cs command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -41,7 +40,6 @@ Syntax * style = *born/coul/dsf/cs* or *born/coul/long/cs* or *born/coul/wolf/cs* or *buck/coul/long/cs* or *coul/long/cs* or *coul/wolf/cs* or *lj/cut/coul/long/cs* * args = list of arguments for a particular style - .. parsed-literal:: *born/coul/dsf/cs* args = alpha cutoff (cutoff2) @@ -70,7 +68,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style born/coul/dsf/cs 0.1 10.0 12.0 @@ -142,7 +139,6 @@ pair is treated, as follows E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0 - where C is an energy-conversion constant, :math:`q_i` and :math:`q_j` are the charges on the core and shell, epsilon is the dielectric constant and :math:`r_{min}` is the minimal distance. @@ -152,10 +148,8 @@ For styles that are not used with a long-range solver, i.e. those with a minimal distance to avoid the possible r = 0.0 case for a core/shell pair. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -174,24 +168,19 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : See the corresponding doc pages for pair styles without the "cs" suffix to see how mixing, shifting, tabulation, tail correction, restarting, and rRESPA are handled by theses pair styles. - ---------- - Restrictions """""""""""" - These pair styles are part of the CORESHELL package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -203,13 +192,9 @@ Related commands **Default:** none - ---------- - .. _MitchellFinchham2: - - **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 8d42371a7a..8cbc949e13 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -30,7 +30,6 @@ pair_style lj/long/dipole/long command Syntax """""" - .. code-block:: LAMMPS pair_style lj/cut/dipole/cut cutoff (cutoff2) @@ -55,12 +54,9 @@ Syntax *long* = use long-range damping on Coulombic 1/r and point-dipole terms *off* = omit Coulombic and point-dipole terms entirely - - Examples """""""" - .. code-block:: LAMMPS pair_style lj/cut/dipole/cut 10.0 @@ -117,7 +113,6 @@ interactions are computed by these formulas for the energy (E), force \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \times \vec{r}) - where :math:`q_i` and :math:`q_j` are the charges on the two particles, :math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole moment vectors of the two particles, r is their separation distance, and the vector r = @@ -210,7 +205,6 @@ potentials are computed by these formulas for the energy (E), force 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \times \vec{r}) - where :math:`\epsilon` and :math:`\sigma` are the standard LJ parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are the charges on the two particles, :math:`\vec{p_i}` and @@ -292,10 +286,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -314,10 +306,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -351,7 +341,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , and *lj/long/dipole/long* styles are part of the DIPOLE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -370,32 +359,22 @@ Related commands **Default:** none - ---------- - .. _Allen2: - - **(Allen)** Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. .. _Toukmaji2: - - **(Toukmaji)** Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000). .. _Stoddard: - - **(Stoddard)** Stoddard and Ford, Phys Rev A, 8, 1504 (1973). .. _Price2: - - **(Price)** Price, Stone and Alderton, Mol Phys, 52, 987 (1984). diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index a827627870..9fd2f00321 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -24,7 +24,6 @@ pair_style dpd/tstat/omp command Syntax """""" - .. code-block:: LAMMPS pair_style dpd T cutoff seed @@ -38,7 +37,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style dpd 1.0 2.5 34387 @@ -75,7 +73,6 @@ of 3 terms F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\ w(r) = & 1 - r/r_c - where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative force, and :math:`F^R` is a random force. :math:`r_{ij}` is a unit vector in the direction :math:`r_i - r_j`, :math:`V_{ij} is the vector @@ -135,7 +132,6 @@ the work of :ref:`(Afshar) ` and :ref:`(Phillips) `. ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -154,10 +150,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -193,14 +187,11 @@ runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. - ---------- - Restrictions """""""""""" - The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd* simulations since particles move rapidly @@ -225,26 +216,18 @@ Related commands **Default:** none - ---------- - .. _Groot1: - - **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). .. _Afshar: - - **(Afshar)** Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys Comm, 184, 1119-1128 (2013). .. _Phillips: - - **(Phillips)** C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011). diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index c66350b46d..223caf7681 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -12,7 +12,6 @@ pair_style dpd/fdt/energy/kk command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -20,7 +19,6 @@ Syntax * style = *dpd/fdt* or *dpd/fdt/energy* * args = list of arguments for a particular style - .. parsed-literal:: *dpd/fdt* args = T cutoff seed @@ -34,7 +32,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style dpd/fdt 300.0 2.5 34387 @@ -62,7 +59,6 @@ given as a sum of 3 terms F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\ w(r) = & 1 - r/r_c - where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative force, and :math:`F^R` is a random force. :math:`r_{ij}` is a unit vector in the direction :math:`r_i - r_j`, :math:`V_{ij} is the vector @@ -111,7 +107,6 @@ energies are computed within style *dpd/fdt/energy* as: \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} - where .. math:: @@ -120,7 +115,6 @@ where \sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\ \Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}}) - :math:`\zeta_ij^q` is a second Gaussian random number with zero mean and unit variance that is used to compute the internal conductive energy. The fluctuation-dissipation theorem defines :math:`alpha^2` to be set @@ -158,10 +152,8 @@ Shardlow splitting algorithm is advantageous, especially when performing DPD under isoenergetic conditions, as it allows significantly larger timesteps to be taken. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -180,14 +172,11 @@ 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. - ---------- - Restrictions """""""""""" - These commands are part of the USER-DPD package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -206,14 +195,10 @@ Related commands **Default:** none - ---------- - .. _Lisal3: - - **(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index e2dc88648f..5628aa6d66 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -6,7 +6,6 @@ pair_style drip command Syntax """""" - .. code-block:: LAMMPS pair_style hybrid/overlay drip [styles ...] @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay drip @@ -45,7 +43,6 @@ The total potential energy of a system is E = & \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} \phi_{ij} \\ \phi_{ij} = &f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] - where the :math:`r^{-6}` term models the attractive London dispersion, the exponential term is designed to capture the registry effect due to overlapping *pi* bonds, and *fc* is a cutoff function. @@ -72,10 +69,8 @@ If you want, you can enforce this by assigning different atom types to atoms in different layers, and apply an intralayer potential to one atom type. See :doc:`pair_hybrid ` for details. - ---------- - The :doc:`pair_coeff ` command for DRIP takes *4+N* arguments, where *N* is the number of LAMMPS atom types. The fist three arguments must be fixed to be *\* \* drip*, the fourth argument is the path to the DRIP parameter file, @@ -84,7 +79,6 @@ parameter file and atom types. For example, if your LAMMPS simulation has 3 atom types and you want all of them to be C, you would use the following pair\_coeff command: - .. code-block:: LAMMPS pair_coeff * * drip C.drip C C C @@ -95,7 +89,6 @@ element exists. Suppose you have a hydrocarbon system, with C of atom type 1 and H of atom type 2, you can use the following command to inform DRIP not to model H atoms: - .. code-block:: LAMMPS pair_style hybrid/overlay drip rebo @@ -109,10 +102,8 @@ model H atoms: 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, @@ -125,7 +116,6 @@ pair\_coeff commands in an input script that reads a restart file. Restrictions """""""""""" - This pair style is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -147,19 +137,13 @@ Related commands :doc:`pair_style kolmogorov/crespi/full `, :doc:`pair_style ilp/graphene/hbn `. - ---------- - .. _Wen2018: - - **(Wen)** M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018) .. _Kolmogorov2005: - - **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index c42e6e5b82..daf63a3752 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -6,7 +6,6 @@ pair_style dsmc command Syntax """""" - .. code-block:: LAMMPS pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style dsmc 2.5 34387 10 1.0 100 20 @@ -61,10 +59,8 @@ simulation box such that an integer number of cells are created in each direction for each processor's sub-domain. Cell lengths are adjusted up to the user-specified maximum cell size. - ---------- - To perform a DSMC simulation with LAMMPS, several additional options should be set in your input script, though LAMMPS does not check for these settings. @@ -73,7 +69,6 @@ Since this pair style does not compute particle forces, you should use the "fix nve/noforce" time integration fix for the DSMC particles, e.g. - .. code-block:: LAMMPS fix 1 all nve/noforce @@ -84,7 +79,6 @@ possible to perform all collisions between pairs of particles that are on the same processor. To ensure this occurs, you should use these commands: - .. code-block:: LAMMPS neighbor 0.0 bin @@ -104,15 +98,12 @@ uniform, which will not give good DSMC collision rates. Specify "dist gaussian" when using the :doc:`velocity ` command as in the following: - .. code-block:: LAMMPS velocity all create 594.6 87287 loop geom dist gaussian - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -141,14 +132,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style 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. @@ -161,13 +149,9 @@ Related commands **Default:** none - ---------- - .. _Bird: - - **(Bird)** G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994). diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 84c793d192..08fd7bc56f 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -6,7 +6,6 @@ pair_style e3b command Syntax """""" - .. code-block:: LAMMPS pair_style e3b Otype @@ -43,7 +42,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style e3b 1 @@ -70,7 +68,6 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r 0 & r>R_f\\ \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*. The three body interactions are split into three types: A, B, and C. @@ -116,10 +113,8 @@ The 4 values correspond to the terms in the first equation above: the E2 term, t See the examples/USER/misc/e3b directory for a complete example script. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -131,14 +126,11 @@ script that reads a restart file. This pair style is incompatible with :doc:`respa `. - ---------- - Restrictions """""""""""" - This pair style 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. @@ -161,22 +153,16 @@ Default The option default for the *neigh* keyword is 10. - ---------- - .. _Kumar: - - .. _Tainter2011: **(Kumar)** Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008) - .. _Tainter2015: **(Tainter 2011)** Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011) - **(Tainter 2015)** Tainter, Shi, and Skinner, 11, 2268 (2015) diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index c428141b89..8c3db11687 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -69,7 +69,6 @@ pair_style eam/fs/opt command Syntax """""" - .. code-block:: LAMMPS pair_style style @@ -79,7 +78,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style eam @@ -107,7 +105,6 @@ energy Ei of an atom I is given by E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) + \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) - where F is the embedding energy which is a function of the atomic electron density rho, phi is a pair potential interaction, and alpha and beta are the element types of atoms I and J. The multi-body @@ -147,7 +144,6 @@ are parameterized in terms of LAMMPS :doc:`metal units `. There are several WWW sites that distribute and document EAM potentials stored in DYNAMO or other formats: - .. parsed-literal:: http://www.ctcms.nist.gov/potentials @@ -160,10 +156,8 @@ and described on this page. The NIST site is maintained by Chandler Becker (cbecker at nist.gov) who is good resource for info on interatomic potentials and file formats. - ---------- - For style *eam*\ , potential values are read from a file that is in the DYNAMO single-element *funcfl* format. If the DYNAMO file was created by a Fortran program, it cannot have "D" values in it for exponents. @@ -181,7 +175,6 @@ single argument: Thus the following command - .. code-block:: LAMMPS pair_coeff *2 1*2 cuu3.eam @@ -232,17 +225,14 @@ sqrt(Hartree \* Bohr-radii). For two interacting atoms i,j this is used by LAMMPS to compute the pair potential term in the EAM energy expression as r\*phi, in units of eV-Angstroms, via the formula - .. math:: r \cdot \phi = 27.2 \cdot 0.529 \cdot Z_i \cdot Z_j where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. - ---------- - Style *eam/alloy* computes pairwise interactions using the same formula as style *eam*\ . However the associated :doc:`pair_coeff ` command reads a DYNAMO *setfl* file @@ -276,7 +266,6 @@ 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 command: - .. code-block:: LAMMPS pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al @@ -334,10 +323,8 @@ the tabulated values for each phi function are listed in *setfl* files directly as r\*phi (in units of eV-Angstroms), since they are for atom pairs. - ---------- - Style *eam/cd* is similar to the *eam/alloy* style, except that it computes alloy pairwise interactions using the concentration-dependent embedded-atom method (CD-EAM). This model can reproduce the enthalpy @@ -365,10 +352,8 @@ the input EAM file are always taken as the *A* and *B* species. *CD-EAM* files in the *potentials* directory of the LAMMPS distribution have a ".cdeam" suffix. - ---------- - Style *eam/fs* computes pairwise interactions for metals and metal alloys using a generalized form of EAM potentials due to Finnis and Sinclair :ref:`(Finnis) `. The total energy Ei of an atom I is @@ -380,7 +365,6 @@ given by \rho_{\alpha\beta} (r_{ij})\right) + \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) - This has the same form as the EAM formula above, except that rho is now a functional specific to the atomic types of both atoms I and J, so that different elements can contribute differently to the total @@ -401,7 +385,6 @@ FS potential files. 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 pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al @@ -451,10 +434,8 @@ eV-Angstroms) as in EAM *setfl* files. Note that in Finnis/Sinclair, the phi(r) arrays are still symmetric, so only phi arrays for i >= j are listed. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -473,10 +454,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -495,14 +474,11 @@ The eam pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - All of these styles are part of the MANYBODY package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -513,45 +489,31 @@ Related commands **Default:** none - ---------- - .. _Ackland1: - - **(Ackland1)** Ackland, Condensed Matter (2005). .. _Ackland2: - - **(Ackland2)** Ackland, Mendelev, Srolovitz, Han and Barashev, Journal of Physics: Condensed Matter, 16, S2629 (2004). .. _Daw: - - **(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983). Daw, Baskes, Phys Rev B, 29, 6443 (1984). .. _Finnis1: - - **(Finnis)** Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984). .. _Stukowski: - - **(Stukowski)** Stukowski, Sadigh, Erhart, Caro; Modeling Simulation Materials Science & Engineering, 7, 075005 (2009). .. _Caro: - - **(Caro)** A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005) diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 13f0ef7fa9..0e8a4aab59 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -12,7 +12,6 @@ pair_style edip/multi command Syntax """""" - .. code-block:: LAMMPS pair_style style @@ -53,7 +52,6 @@ In EDIP, the energy E of a system of atoms is h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\ Q(Z) = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z}) - 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 = a. Both terms depend on the @@ -125,10 +123,8 @@ multi-element EDIP parameterization. If you know any and you are interest in that, please contact the author of the EDIP package. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -147,10 +143,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -164,14 +158,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -192,12 +183,8 @@ Related commands **Default:** none - ---------- - .. _EDIP: - - **(EDIP)** J F Justo et al, Phys Rev B 58, 2539 (1998). diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index b873e9d6e4..6726dee2f9 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -6,7 +6,6 @@ pair_style eff/cut command Syntax """""" - .. code-block:: LAMMPS pair_style eff/cut cutoff keyword args ... @@ -23,12 +22,9 @@ Syntax type = LAMMPS atom type (1 to Ntypes) element = element symbol (e.g. H, Si) - - Examples """""""" - .. code-block:: LAMMPS pair_style eff/cut 39.7 @@ -154,10 +150,8 @@ individual I,J type pair via the :doc:`pair_coeff ` command. All type pairs use the same global cutoff specified in the pair\_style command. - ---------- - The *limit/eradius* and *pressure/evirials* keywords are optional. Neither or both must be specified. If not specified they are unset. @@ -208,10 +202,8 @@ representations, after the "ecp" keyword. significant over long-term averaged runs (i.e. even though the energy partitioning changes, the total energy remains similar). - ---------- - .. note:: This implementation of eFF gives a reasonably accurate description @@ -266,10 +258,8 @@ metals (e.g. beryllium) and semimetals such as boron; and various compounds containing ionic and/or multicenter bonds, such as boron dihydride. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the cutoff distance for the @@ -294,14 +284,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - These pair styles will only be enabled if LAMMPS is built with the USER-EFF package. It will only be enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for @@ -325,21 +312,15 @@ Default If not specified, limit\_eradius = 0 and pressure\_with\_evirials = 0. - ---------- - .. _Su: - - **(Su)** Su and Goddard, Excited Electron Dynamics Modeling of Warm Dense Matter, Phys Rev Lett, 99:185003 (2007). .. _Jaramillo-Botero: - - **(Jaramillo-Botero)** Jaramillo-Botero, Su, Qi, Goddard, Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, J Comp diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index a3fee3fb96..7eb850c5ac 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -9,7 +9,6 @@ pair_style eim/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style eim @@ -81,10 +79,8 @@ atoms in the atomic pair. EIM potential infers the charge on an atom from the equation above for q\_i; you do not assign charges explicitly. - ---------- - All the EIM parameters are listed in a potential file which is specified by the :doc:`pair_coeff ` command. This is an ASCII text file in a format described below. The "ffield.eim" file @@ -117,7 +113,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * Na Cl ffield.eim Na Na Na Cl @@ -159,10 +154,8 @@ r\_(s,psi), and p. The lines in the file can be in any order; LAMMPS extracts the info it needs. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -181,14 +174,11 @@ 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. - ---------- - Restrictions """""""""""" - This style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. @@ -199,13 +189,9 @@ Related commands **Default:** none - ---------- - .. _Zhou2: - - **(Zhou)** Zhou, submitted for publication (2010). Please contact Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov. diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index 44ba319566..823da19ccc 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -9,7 +9,6 @@ pair_style exp6/rx/kk command Syntax """""" - .. code-block:: LAMMPS pair_style exp6/rx cutoff ... @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style exp6/rx 10.0 @@ -47,7 +45,6 @@ particle through a site-site interaction potential model. The U_{ij}(r) = \frac{\epsilon}{\alpha-6}\{6\exp[\alpha(1-\frac{r_{ij}}{R_{m}})]-\alpha(\frac{R_{m}}{r_{ij}})^6\} - where the :math:`\epsilon` parameter determines the depth of the potential minimum located at :math:`R_m`, and :math:`\alpha` determines the softness of the repulsion. @@ -96,14 +93,11 @@ arguments. This is equivalent to specifying the *exponent* option with The final argument specifies the interaction cutoff (optional). - ---------- - The format of a tabulated file is as follows (without the parenthesized comments): - .. parsed-literal:: # exponential-6 parameters for various species (one or more comment or blank lines) @@ -116,7 +110,6 @@ parenthesized comments): The format of the polynomial scaling file as follows (without the parenthesized comments): - .. parsed-literal:: # POLYNOMIAL FILE (one or more comment or blank lines) @@ -158,14 +151,11 @@ where R_{m,ab} = & \frac{R_{m,a}+R_{m,b}}{2} \\ \alpha_{ab} = & \sqrt{\alpha_{a}\alpha_{b}} - and :math:`x_a` and :math:`x_b` are the mole fractions of a and b, respectively, which comprise the gas mixture. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -178,10 +168,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -200,14 +188,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD 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/pair_extep.rst b/doc/src/pair_extep.rst index 4618c44804..ab15d56d9f 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -6,7 +6,6 @@ pair_style extep command Syntax """""" - .. code-block:: LAMMPS pair_style extep @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style extep @@ -26,10 +24,8 @@ Description Style *extep* computes the Extended Tersoff Potential (ExTeP) interactions as described in :ref:`(Los2017) `. - ---------- - Restrictions """""""""""" none @@ -41,14 +37,10 @@ Related commands **Default:** none - ---------- - .. _Los2017: - - **(Los2017)** J. H. Los et al. "Extended Tersoff potential for boron nitride: Energetics and elastic properties of pristine and defective h-BN", Phys. Rev. B 96 (184108), 2017. diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 2d81628c0d..e8cef41eda 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -63,7 +63,6 @@ pair_style morse/soft command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -71,7 +70,6 @@ Syntax * style = *lj/cut/soft* or *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* or *lj/cut/tip4p/long/soft* or *lj/charmm/coul/long/soft* or *lj/class2/soft* or *lj/class2/coul/cut/soft* or *lj/class2/coul/long/soft* or *coul/cut/soft* or *coul/long/soft* or *tip4p/long/soft* or *morse/soft* * args = list of arguments for a particular style - .. parsed-literal:: *lj/cut/soft* args = n alpha_lj cutoff @@ -127,7 +125,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/cut/soft 2.0 0.5 9.5 @@ -231,7 +228,6 @@ every 0.1. .. image:: JPG/lj_soft.jpg .. image:: JPG/coul_soft.jpg - For the *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* pair styles, as well as for the equivalent *class2* versions, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` @@ -313,10 +309,8 @@ example hydrogen atoms in several water models). the *coul/long/soft* or similar sub-style can be used via the :doc:`pair_style hybrid/overlay ` command. - ---------- - The *morse/soft* variant modifies the :doc:`pair_morse ` style at short range to have a soft core. The functional form differs from that of the *lj/soft* styles, and is instead given by: @@ -345,10 +339,8 @@ The *morse/soft* style requires the following pair coefficients: The last coefficient is optional. If not specified, the global morse cutoff is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -368,10 +360,8 @@ command in your input script. See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - **Mixing, shift, tail correction, restart info**\ : The different versions of the *lj/cut/soft* pair styles support mixing. For @@ -419,14 +409,11 @@ 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 in an input script that reads a restart file. - ---------- - Restrictions """""""""""" - The pair styles with soft core are only enabled if LAMMPS was built with the USER-FEP package. The *long* versions also require the KSPACE package to be installed. The soft *tip4p* versions also require the MOLECULE package to be @@ -442,13 +429,9 @@ Related commands **Default:** none - ---------- - .. _Beutler: - - **(Beutler)** Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994). diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 911b1c1504..b1bab752df 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -18,7 +18,6 @@ pair_style gauss/cut/omp command Syntax """""" - .. code-block:: LAMMPS pair_style gauss cutoff @@ -29,7 +28,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style gauss 12.0 @@ -48,7 +46,6 @@ Style *gauss* computes a tethering potential of the form E = - A \exp(-B r^2) \qquad r < r_c - between an atom and its corresponding tether site which will typically be a frozen atom in the simulation. :math:`r_c` is the cutoff. @@ -72,7 +69,6 @@ between pairs of particles: E = \frac{H}{\sigma_h\sqrt{2\pi}} \exp\left[-\frac{(r-r_{mh})^2}{2\sigma_h^2}\right] - where H determines together with the standard deviation :math:`\sigma_h` the peak height of the Gaussian function, and :math:`r_{mh}` the peak position. Examples of the use of the Gaussian potentials include @@ -117,10 +113,8 @@ 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. - ---------- - **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 @@ -174,21 +168,17 @@ sites have an atom within the distance at which the force is a maximum To print this quantity to the log file (with a descriptive column heading) the following commands could be included in an input script: - .. code-block:: LAMMPS compute gauss all pair gauss variable occ equal c_gauss[1] thermo_style custom step temp epair v_occ - ---------- - Restrictions """""""""""" - The *gauss/cut* style is part of the "user-misc" package. It is only enabled if LAMMPS is build with that package. See the :doc:`Build package ` doc page for more info. @@ -202,14 +192,10 @@ Related commands .. _Lenart2: - - **(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007). .. _Jusufi2: - - **(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index e69d30a834..1d73c6ef8b 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -15,7 +15,6 @@ pair_style gayberne/omp command Syntax """""" - .. code-block:: LAMMPS pair_style gayberne gamma upsilon mu cutoff @@ -28,7 +27,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style gayberne 1.0 1.0 1.0 10.0 @@ -173,10 +171,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -203,14 +199,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - The *gayberne* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -241,31 +234,21 @@ Related commands **Default:** none - ---------- - .. _Everaers2: - - **(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). .. _Berardi: - - **(Berardi)** Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008). .. _Perram: - - **(Perram)** Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996). .. _Allen3: - - **(Allen)** Allen and Germano, Mol Phys 104, 3225-3235 (2006). diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 3548b5528a..6327f09f35 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -24,7 +24,6 @@ pair_style gran/hertz/history/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style Kn Kt gamma_n gamma_t xmu dampflag @@ -37,7 +36,6 @@ Syntax * xmu = static yield criterion (unitless value between 0.0 and 1.0e4) * dampflag = 0 or 1 if tangential damping force is excluded or included - .. note:: Versions of LAMMPS before 9Jan09 had different style names for @@ -52,7 +50,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1 @@ -77,7 +74,6 @@ The two Hookean styles use this formula: (k_t \mathbf{ \Delta s}_t + m_{eff} \gamma_t \mathbf{v}_t) - The Hertzian style uses this formula: .. math:: @@ -89,7 +85,6 @@ The Hertzian style uses this formula: (k_t \mathbf{ \Delta s}_t + m_{eff} \: \gamma_t \mathbf{v}_t) \Big] - In both equations the first parenthesized term is the normal force between the two particles and the second parenthesized term is the tangential force. The normal force has 2 terms, a contact force and a @@ -203,7 +198,6 @@ 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 - .. code-block:: LAMMPS pair_coeff * * @@ -214,10 +208,8 @@ potential is used as a sub-style of :doc:`pair_style hybrid `, then pair\_coeff command to determine which atoms interact via a granular potential. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -236,10 +228,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The :doc:`pair_modify ` mix, shift, table, and tail options @@ -267,14 +257,11 @@ tangential direction. These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., *p10*\ . - ---------- - Restrictions """""""""""" - All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -299,26 +286,18 @@ Related commands **Default:** none - ---------- - .. _Brilliantov: - - **(Brilliantov)** Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, p 5382-5392 (1996). .. _Silbert: - - **(Silbert)** Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001). .. _Zhang3: - - **(Zhang)** Zhang and Makse, Phys Rev E, 72, p 011301 (2005). diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 6d5dfbdba8..d8dc7b3b3e 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -6,7 +6,6 @@ pair_style granular command Syntax """""" - .. code-block:: LAMMPS pair_style granular cutoff @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style granular @@ -70,10 +68,8 @@ coefficients cannot be determined, so 1-2 interactions must be 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 contact model. Currently supported options for normal contact models and their required arguments are: @@ -95,7 +91,6 @@ damping mode, see below); E is Young's modulus in units of For the *hooke* model, the normal, elastic component of force acting on particle *i* due to contact with particle *j* is given by: - .. math:: \mathbf{F}_{ne, Hooke} = k_N \delta_{ij} \mathbf{n} @@ -109,7 +104,6 @@ for *hooke*\ , the units of the spring constant :math:`k_n` are For the *hertz* model, the normal component of force is given by: - .. math:: \mathbf{F}_{ne, Hertz} = k_N R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} @@ -121,7 +115,6 @@ equivalently *pressure*\ . For the *hertz/material* model, the force is given by: - .. math:: \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} @@ -136,7 +129,6 @@ The *dmt* model corresponds to the :ref:`(Derjaguin-Muller-Toporov) ` cohesive model, where the force is simply Hertz with an additional attractive cohesion term: - .. math:: \mathbf{F}_{ne, dmt} = \left(\frac{4}{3} E R^{1/2}\delta_{ij}^{3/2} - 4\pi\gamma R\right)\mathbf{n} @@ -144,7 +136,6 @@ is simply Hertz with an additional attractive cohesion term: The *jkr* model is the :ref:`(Johnson-Kendall-Roberts) ` model, where the force is computed as: - .. math:: \mathbf{F}_{ne, jkr} = \left(\frac{4Ea^3}{3R} - 2\pi a^2\sqrt{\frac{4\gamma E}{\pi a}}\right)\mathbf{n} @@ -152,7 +143,6 @@ where the force is computed as: Here, *a* is the radius of the contact zone, related to the overlap :math:`\delta` according to: - .. math:: \delta = a^2/R - 2\sqrt{\pi \gamma a/E} @@ -168,14 +158,11 @@ initially will not experience force until they come into contact experience a tensile force up to :math:`3\pi\gamma R`, at which point they lose contact. - ---------- - In addition, the normal force is augmented by a damping term of the following general form: - .. math:: \mathbf{F}_{n,damp} = -\eta_n \mathbf{v}_{n,rel} @@ -204,7 +191,6 @@ used by default. For *damping velocity*\ , the normal damping is simply equal to the user-specified damping coefficient in the *normal* model: - .. math:: \eta_n = \eta_{n0} @@ -214,7 +200,6 @@ contact model, in units of *mass*\ /\ *time*\ . For *damping mass\_velocity*, the normal damping is given by: - .. math:: \eta_n = \eta_{n0} m_{eff} @@ -229,7 +214,6 @@ The *damping viscoelastic* model is based on the viscoelastic treatment of :ref:`(Brilliantov et al) `, where the normal damping is given by: - .. math:: \eta_n = \eta_{n0}\ a m_{eff} @@ -243,7 +227,6 @@ The *tsuji* model is based on the work of :ref:`(Tsuji et al) `. Here the normal model is interpreted as a restitution coefficient :math:`e`. The damping constant :math:`\eta_n` is given by: - .. math:: \eta_n = \alpha (m_{eff}k_n)^{1/2} @@ -251,7 +234,6 @@ the normal model is interpreted as a restitution coefficient For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. The parameter :math:`\alpha` is related to the restitution coefficient *e* according to: - .. math:: \alpha = 1.2728-4.2783e+11.087e^2-22.348e^3+27.467e^4-18.022e^5+4.8218e^6 @@ -263,15 +245,12 @@ no error check is performed on this. The total normal force is computed as the sum of the elastic and damping components: - .. math:: \mathbf{F}_n = \mathbf{F}_{ne} + \mathbf{F}_{n,damp} - ---------- - 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 @@ -291,14 +270,12 @@ 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: - .. math:: \mathbf{F}_t = -min(\mu_t F_{n0}, \|\mathbf{F}_\mathrm{t,damp}\|) \mathbf{t} The tangential damping force :math:`\mathbf{F}_\mathrm{t,damp}` is given by: - .. math:: \mathbf{F}_\mathrm{t,damp} = -\eta_t \mathbf{v}_{t,rel} @@ -306,7 +283,6 @@ The tangential damping force :math:`\mathbf{F}_\mathrm{t,damp}` is given by: The tangential damping prefactor :math:`\eta_t` is calculated by scaling the normal damping :math:`\eta_n` (see above): - .. math:: \eta_t = -x_{\gamma,t} \eta_n @@ -327,7 +303,6 @@ depends on the form of the contact model. For non-cohesive models (\ *hertz*\ , *hertz/material*\ , *hooke*\ ), it is given by the magnitude of the normal force: - .. math:: F_{n0} = \|\mathbf{F}_n\| @@ -337,7 +312,6 @@ adjusted so that the critical tangential force approaches :math:`\mu_t F_{pullof :ref:`Thornton `. For both models, :math:`F_{n0}` takes the form: - .. math:: F_{n0} = \|\mathbf{F}_ne + 2 F_{pulloff}\| @@ -352,7 +326,6 @@ accumulated displacement applies to the other options as well. For *tangential linear\_history*, the tangential force is given by: - .. math:: \mathbf{F}_t = -min(\mu_t F_{n0}, \|-k_t\mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t} @@ -360,7 +333,6 @@ For *tangential linear\_history*, the tangential force is given by: Here, :math:`\mathbf{\xi}` is the tangential displacement accumulated during the entire duration of the contact: - .. math:: \mathbf{\xi} = \int_{t0}^t \mathbf{v}_{t,rel}(\tau) \mathrm{d}\tau @@ -382,7 +354,6 @@ preserve the magnitude. This follows the discussion in :ref:`Luding `, see equation 17 and relevant discussion in that work: - .. math:: \mathbf{\xi} = \left(\mathbf{\xi'} - (\mathbf{n} \cdot \mathbf{\xi'})\mathbf{n}\right) \frac{\|\mathbf{\xi'}\|}{\|\mathbf{\xi'}\| - \mathbf{n}\cdot\mathbf{\xi'}} @@ -399,7 +370,6 @@ tangential displacement is re-scaled to match the value for the critical force (see :ref:`Luding `, equation 20 and related discussion): - .. math:: \mathbf{\xi} = -\frac{1}{k_t}\left(\mu_t F_{n0}\mathbf{t} + \mathbf{F}_{t,damp}\right) @@ -409,12 +379,10 @@ damping) to produce the total force on the particle. The tangential force also acts at the contact point (defined as the center of the overlap region) to induce a torque on each particle according to: - .. math:: \mathbf{\tau}_i = -(R_i - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t - .. math:: \mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t @@ -422,7 +390,6 @@ overlap region) to induce a torque on each particle according to: 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:: \mathbf{F}_t = -min(\mu_t F_{n0}, \|-k_t a \mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t} @@ -438,7 +405,6 @@ normal contact model that specifies material parameters :math:`E` and case, mixing of the shear modulus for different particle types *i* and *j* is done according to: - .. math:: 1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j @@ -447,7 +413,6 @@ 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}}`: - .. math:: \mathbf{\xi} = \mathbf{\xi_{t_{n-1}}} \frac{a}{a_{t_{n-1}}} @@ -460,10 +425,8 @@ created without the rescaling above (:ref:`Walton ` ). See also discussion in :ref:`Thornton et al, 2013 ` , particularly equation 18(b) of that work and associated discussion. - ---------- - The optional *rolling* keyword enables rolling friction, which resists pure rolling motion of particles. The options currently supported are: @@ -480,7 +443,6 @@ rolling displacement due to changes in the frame of reference of the contacting pair. The rolling pseudo-force is computed analogously to the tangential force: - .. math:: \mathbf{F}_{roll,0} = k_{roll} \mathbf{\xi}_{roll} - \gamma_{roll} \mathbf{v}_{roll} @@ -489,7 +451,6 @@ Here, :math:`\mathbf{v}_{roll} = -R(\mathbf{\Omega}_i - \mathbf{\Omega}_j) \time velocity, as given in :ref:`Wang et al ` and :ref:`Luding `. This differs from the expressions given by :ref:`Kuhn and Bagi ` and used in :ref:`Marshall `; see :ref:`Wang et al ` for details. The rolling displacement is given by: - .. math:: \mathbf{\xi}_{roll} = \int_{t_0}^t \mathbf{v}_{roll} (\tau) \mathrm{d} \tau @@ -497,7 +458,6 @@ velocity, as given in :ref:`Wang et al ` and A Coulomb friction criterion truncates the rolling pseudo-force if it exceeds a critical value: - .. math:: \mathbf{F}_{roll} = min(\mu_{roll} F_{n,0}, \|\mathbf{F}_{roll,0}\|)\mathbf{k} @@ -514,20 +474,16 @@ The rolling pseudo-force does not contribute to the total force on either particle (hence 'pseudo'), but acts only to induce an equal and opposite torque on each particle, according to: - .. math:: \tau_{roll,i} = R_{eff} \mathbf{n} \times \mathbf{F}_{roll} - .. math:: \tau_{roll,j} = -\tau_{roll,i} - ---------- - The optional *twisting* keyword enables twisting friction, which resists rotation of two contacting particles about the vector :math:`\mathbf{n}` that connects their centers. The options currently @@ -546,7 +502,6 @@ changes in the frame of reference due to rotations of the particle pair. The formulation in :ref:`Marshall ` therefore provides the most straightforward treatment: - .. math:: \tau_{twist,0} = -k_{twist}\xi_{twist} - \gamma_{twist}\Omega_{twist} @@ -555,7 +510,6 @@ Here :math:`\xi_{twist} = \int_{t_0}^t \Omega_{twist} (\tau) \mathrm{d}\tau` is :math:`\Omega_{twist} = (\mathbf{\Omega}_i - \mathbf{\Omega}_j) \cdot \mathbf{n}` is the relative twisting angular velocity. The torque is then truncated according to: - .. math:: \tau_{twist} = min(\mu_{twist} F_{n,0}, \tau_{twist,0}) @@ -564,7 +518,6 @@ Similar to the sliding and rolling displacement, the angular displacement is rescaled so that it corresponds to the critical value if the twisting torque exceeds this critical value: - .. math:: \xi_{twist} = \frac{1}{k_{twist}} (\mu_{twist} F_{n,0}sgn(\Omega_{twist}) - \gamma_{twist}\Omega_{twist}) @@ -577,37 +530,30 @@ 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): - .. math:: k_{twist} = 0.5k_ta^2 - .. math:: \eta_{twist} = 0.5\eta_ta^2 - .. math:: \mu_{twist} = \frac{2}{3}a\mu_t Finally, the twisting torque on each particle is given by: - .. math:: \mathbf{\tau}_{twist,i} = \tau_{twist}\mathbf{n} - .. math:: \mathbf{\tau}_{twist,j} = -\mathbf{\tau}_{twist,i} - ---------- - The *granular* pair style can reproduce the behavior of the *pair gran/\** styles with the appropriate settings (some very minor differences can be expected due to corrections in @@ -620,10 +566,8 @@ The second example is equivalent to The third example is equivalent to *pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ . - ---------- - 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. @@ -644,10 +588,8 @@ then LAMMPS will use that cutoff for the specified atom type combination, and automatically set pairwise cutoffs for the remaining atom types. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -666,10 +608,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The :doc:`pair_modify ` mix, shift, table, and tail options @@ -685,7 +625,6 @@ for type1-type2 interactions is computed as :math:`\sqrt{\mu_1\mu_2}` applicable to *hertz/material*\ , *dmt* and *jkr* normal contact models. In that case, the effective elastic modulus is computed as: - .. math:: E_{eff,ij} = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1} @@ -693,14 +632,12 @@ models. In that case, the effective elastic modulus is computed as: If the *i-j* coefficients :math:`E_{ij}` and :math:`\nu_{ij}` are explicitly specified, the effective modulus is computed as: - .. math:: E_{eff,ij} = \left(\frac{1-\nu_{ij}^2}{E_{ij}} + \frac{1-\nu_{ij}^2}{E_{ij}}\right)^{-1} or - .. math:: E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})} @@ -729,14 +666,11 @@ 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*\ . - ---------- - Restrictions """""""""""" - All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -770,16 +704,12 @@ For the *pair\_coeff* settings: *damping viscoelastic*\ , *rolling none*\ , .. _Brill1996: - - **(Brilliantov et al, 1996)** Brilliantov, N. V., Spahn, F., Hertzsch, J. M., & Poschel, T. (1996). Model for collisions in granular gases. Physical review E, 53(5), 5382. .. _Tsuji1992: - - **(Tsuji et al, 1992)** Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3), @@ -787,39 +717,29 @@ cohesionless particles in a horizontal pipe. Powder technology, 71(3), .. _JKR1971: - - **(Johnson et al, 1971)** Johnson, K. L., Kendall, K., & Roberts, A. D. (1971). Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313. .. _DMT1975: - - **Derjaguin et al, 1975)** Derjaguin, B. V., Muller, V. M., & Toporov, Y. P. (1975). Effect of contact deformations on the adhesion of particles. Journal of Colloid and interface science, 53(2), 314-326. .. _Luding2008: - - **(Luding, 2008)** Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235. .. _Marshall2009: - - **(Marshall, 2009)** Marshall, J. S. (2009). Discrete-element modeling of particulate aerosol flows. Journal of Computational Physics, 228(5), 1541-1561. .. _Silbert2001: - - **(Silbert, 2001)** Silbert, L. E., Ertas, D., Grest, G. S., Halsey, T. C., Levine, D., & Plimpton, S. J. (2001). Granular flow down an inclined plane: Bagnold scaling and rheology. Physical Review E, @@ -827,38 +747,28 @@ inclined plane: Bagnold scaling and rheology. Physical Review E, .. _Kuhn2004: - - **(Kuhn and Bagi, 2005)** Kuhn, M. R., & Bagi, K. (2004). Contact rolling and deformation in granular media. International journal of solids and structures, 41(21), 5793-5820. .. _Wang2015: - - **(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015). Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55. .. _Thornton1991: - - **(Thornton, 1991)** Thornton, C. (1991). Interparticle sliding in the presence of adhesion. J. Phys. D: Appl. Phys. 24 1942 .. _Mindlin1949: - - **(Mindlin, 1949)** Mindlin, R. D. (1949). Compliance of elastic bodies in contact. J. Appl. Mech., ASME 16, 259-268. .. _Thornton2013: - - **(Thornton et al, 2013)** Thornton, C., Cummins, S. J., & Cleary, P. W. (2013). An investigation of the comparative behaviour of alternative contact force models during inelastic collisions. Powder @@ -866,6 +776,4 @@ Technology, 233, 30-46. .. _WaltonPC: - - **(Otis R. Walton)** Walton, O.R., Personal Communication diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 4a4d482282..234e7c6894 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -24,7 +24,6 @@ pair_style lj/gromacs/coul/gromacs/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -32,7 +31,6 @@ Syntax * style = *lj/gromacs* or *lj/gromacs/coul/gromacs* * args = list of arguments for a particular style - .. parsed-literal:: *lj/gromacs* args = inner outer @@ -44,7 +42,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/gromacs 9.0 12.0 @@ -76,7 +73,6 @@ the coarse-grained models of :ref:`(Marrink) `. B = & (2 E'(r_c) - (r_c - r_1) E''(r_c))/(r_c - r_1)^3 \\ C = & -E(r_c) + \frac{1}{2} (r_c - r_1) E'(r_c) - \frac{1}{12} (r_c - r_1)^2 E''(r_c) - :math:`r_1` is the inner cutoff; :math:`r_c` is the outer cutoff. The 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 @@ -117,10 +113,8 @@ The last 2 coefficients cannot be used with style varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in the pair\_style command. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -139,10 +133,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -170,10 +162,8 @@ All of the GROMACS pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" none @@ -185,12 +175,8 @@ Related commands **Default:** none - ---------- - .. _Marrink: - - **(Marrink)** Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004). diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 06dfd240b3..33ddaf2a10 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -9,7 +9,6 @@ pair_style gw/zbl command Syntax """""" - .. code-block:: LAMMPS pair_style style @@ -58,7 +57,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * SiC.gw Si Si Si C @@ -79,10 +77,8 @@ is similar to other many-body potentials supported by LAMMPS. You have to refer to the comments in the files and the literature to learn more details. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -100,14 +96,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -127,13 +120,9 @@ Related commands **Default:** none - ---------- - .. _Gao: - - **(Gao)** Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 1f4f179623..9c02311008 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -15,7 +15,6 @@ pair_style hbond/dreiding/morse/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof @@ -30,7 +29,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 @@ -61,7 +59,6 @@ force field, given by: \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } - where :math:`r_{\rm in}` is the inner spline distance cutoff, :math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is the angle cutoff, and *n* is the cosine periodicity. @@ -118,10 +115,8 @@ on the DREIDING force field. special\_bonds command (e.g. "special\_bonds lj 0.0 0.0 1.0") to turn these interactions on. - ---------- - The following coefficients must be defined for pairs of eligible donor/acceptor types via the :doc:`pair_coeff ` command as in the examples above. @@ -196,10 +191,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -218,10 +211,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. You must explicitly identify @@ -252,7 +243,6 @@ command as a vector of values of length 2. To print these quantities to the log file (with a descriptive column heading) the following commands could be included in an input script: - .. code-block:: LAMMPS compute hb all pair hbond/dreiding/lj @@ -260,10 +250,8 @@ heading) the following commands could be included in an input script: variable E_hbond equal c_hb[2] #hbond energy thermo_style custom step temp epair v_E_hbond - ---------- - Restrictions """""""""""" none @@ -275,20 +263,14 @@ Related commands **Default:** none - ---------- - .. _pair-Mayo: - - **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). .. _Liu: - - **(Liu)** Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) 2798 (2009) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index d8abec1f4a..9a3c1af423 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -15,7 +15,6 @@ pair_style hybrid/overlay/kk command Syntax """""" - .. code-block:: LAMMPS pair_style hybrid style1 args style2 args ... @@ -26,7 +25,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0 @@ -100,7 +98,6 @@ For example, consider a simulation with 3 atom types: types 1 and 2 are Ni atoms, type 3 are LJ atoms with charges. The following commands would set up a hybrid simulation: - .. code-block:: LAMMPS pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0 @@ -113,7 +110,6 @@ simulation with 2 atom types. Type 1 is Si, type 2 is C. The following commands would model the Si atoms with Tersoff, the C atoms with Tersoff, and the cross-interactions with Lennard-Jones: - .. code-block:: LAMMPS pair_style hybrid lj/cut 2.5 tersoff tersoff @@ -126,7 +122,6 @@ If pair coefficients are specified in the data file read via the E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for each line in the "Pair Coeffs" section, e.g. - .. parsed-literal:: Pair Coeffs @@ -158,7 +153,6 @@ 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 commands are the same: - .. code-block:: LAMMPS pair_style lj/cut 2.5 @@ -189,14 +183,12 @@ 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: - .. code-block:: LAMMPS pair_coeff 2 3 none or this form in the "Pair Coeffs" section of the data file: - .. parsed-literal:: 3 none @@ -210,10 +202,8 @@ command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair potentials. - ---------- - Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 @@ -229,7 +219,6 @@ Here is an example for mixing CHARMM and AMBER: The global *amber* setting sets the 1-4 interactions to non-zero scaling factors and then overrides them with 0.0 only for CHARMM: - .. code-block:: LAMMPS special_bonds amber @@ -238,7 +227,6 @@ then overrides them with 0.0 only for CHARMM: The this input achieves the same effect: - .. code-block:: LAMMPS special_bonds 0.0 0.0 0.1 @@ -253,7 +241,6 @@ Tersoff part of the system the force constants for the bonded interactions have been set to 0. Note the global settings are effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: - .. code-block:: LAMMPS special_bonds lj/coul 1e-20 1e-20 0.5 @@ -269,17 +256,13 @@ the compute tally styles, for example, if those pair styles See the :doc:`pair_modify ` doc page for details on the specific syntax, requirements and restrictions. - ---------- - The potential energy contribution to the overall system due to an individual sub-style can be accessed and output via the :doc:`compute pair ` command. - ---------- - .. note:: Several of the potentials defined via the pair\_style command in @@ -322,7 +305,6 @@ to use a Tersoff potential to compute interactions within each surface, but not between surfaces. Then either of these two command sequences would implement that model: - .. code-block:: LAMMPS pair_style hybrid tersoff @@ -343,7 +325,6 @@ potentials together, in an overlapping manner. Imagine you have CNT interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work: - .. code-block:: LAMMPS pair_style hybrid/overlay tersoff airebo 3.0 @@ -355,10 +336,8 @@ interactions, you would need to modify the SiC.tersoff file to turn off C/C interaction, i.e. by setting the appropriate coefficients to 0.0. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -383,10 +362,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Any pair potential settings made via the @@ -423,7 +400,6 @@ their sub-styles do. Restrictions """""""""""" - When using a long-range Coulombic solver (via the :doc:`kspace_style ` command) with a hybrid pair\_style, one or more sub-styles will be of the "long" variety, diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index ef1207fffe..03ac896f1f 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -6,7 +6,6 @@ pair_style ilp/graphene/hbn command Syntax """""" - .. code-block:: LAMMPS pair_style [hybrid/overlay ...] ilp/graphene/hbn cutoff tap_flag @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 @@ -55,7 +53,6 @@ in :ref:`(Kolmogorov) `. 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 - Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than :math:`r_c` :ref:`(Maaravi) `. The definitions of @@ -119,7 +116,6 @@ The 2 values correspond to the following sub-categories: To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: - .. code-block:: LAMMPS compute 0 all pair ilp/graphene/hbn @@ -127,10 +123,8 @@ headings) the following commands could be included in an input script: variable Erep equal c_0[2] thermo_style custom step temp epair v_Erep v_Evdw - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the pair\_modify mix, shift, table, and @@ -144,7 +138,6 @@ that reads a restart file. Restrictions """""""""""" - 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. @@ -171,42 +164,28 @@ Related commands **Default:** tap\_flag = 1 - ---------- - .. _Leven1: - - **(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). .. _Leven2: - - **(Leven2)** I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). .. _Maaravi2: - - **(Maaravi)** T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). .. _Kolmogorov2: - - **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005). .. _Ouyang1: - - **(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). .. _Ouyang2: - - **(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 72f4908b53..4a134f7037 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -6,7 +6,6 @@ pair_style kim command Syntax """""" - .. code-block:: LAMMPS pair_style kim model @@ -16,7 +15,6 @@ model = name of a KIM model (the KIM ID for models archived in OpenKIM) Examples """""""" - .. code-block:: LAMMPS pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 @@ -43,10 +41,8 @@ used by the :doc:`kim_commands interface ` as needed. Since *pair\_style kim* is called by *kim\_interactions* as needed, is not recommended to be directly used in input scripts. - ---------- - The argument *model* is the name of the KIM PM. For potentials archived in OpenKIM this is the extended KIM ID (see :doc:`kim_commands ` @@ -67,7 +63,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * Si Si Si C @@ -76,10 +71,8 @@ The first two arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as defined within KIM PM. The final C argument maps LAMMPS atom type 4 to C. - ---------- - In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this case it is also useful to check the *kim.log* file for additional error @@ -91,10 +84,8 @@ the *lib/kim/README* file. Once you have done this and built LAMMPS with the KIM package installed you can run the example input scripts in *examples/kim*\ . - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -108,14 +99,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the KIM package. See details on restrictions in :doc:`kim_commands `. diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index d8b1f6db12..f1a647f7a0 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -6,7 +6,6 @@ pair_style kolmogorov/crespi/full command Syntax """""" - .. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0 @@ -43,7 +41,6 @@ No simplification is made, \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\ f(\rho) & = e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n} - It is important to have a sufficiently large cutoff to ensure smooth forces and to include all the pairs to build the neighbor list for calculating the normals. Energies are shifted so that they go @@ -99,7 +96,6 @@ The 2 values correspond to the following sub-categories: To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: - .. code-block:: LAMMPS compute 0 all pair kolmogorov/crespi/full @@ -107,10 +103,8 @@ headings) the following commands could be included in an input script: variable Erep equal c_0[2] thermo_style custom step temp epair v_Erep v_Evdw - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the pair\_modify mix, shift, table, @@ -124,7 +118,6 @@ that reads a restart file. Restrictions """""""""""" - 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. @@ -150,24 +143,16 @@ Related commands **Default:** tap\_flag = 0 - ---------- - .. _Kolmogorov1: - - **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) .. _Ouyang3: - - **(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). .. _Ouyang4: - - **(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index c697226504..0ed073d5af 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -6,7 +6,6 @@ pair_style kolmogorov/crespi/z command Syntax """""" - .. code-block:: LAMMPS pair_style [hybrid/overlay ...] kolmogorov/crespi/z cutoff @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/z 20.0 @@ -39,8 +37,6 @@ which is to take all normals along the z-axis. \rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\ f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n} - - It is important to have a sufficiently large cutoff to ensure smooth forces. Energies are shifted so that they go continuously to zero at the cutoff assuming that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast. @@ -62,7 +58,6 @@ Other interactions can be set to zero using pair\_style *none*\ . Restrictions """""""""""" - This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -79,19 +74,13 @@ Related commands **Default:** none - ---------- - .. _KC05: - - **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) .. _vanWijk: - - **(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014) diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index f492b79919..b39b149a73 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -6,7 +6,6 @@ pair_style lcbop command Syntax """""" - .. code-block:: LAMMPS pair_style lcbop @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lcbop @@ -42,7 +40,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * C.lcbop C C C NULL @@ -59,10 +56,8 @@ are listed in the C.lcbop file to agree with the original :ref:`(Los and Fasolin potential and the way it was fit, so modifying the file should be done carefully. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -79,7 +74,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - This pair styles is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -99,13 +93,9 @@ Related commands **Default:** none - ---------- - .. _Los: - - **(Los and Fasolino)** J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107 (2003). diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index b78a29fb54..b8217ccdcc 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -6,7 +6,6 @@ pair_style lebedeva/z command Syntax """""" - .. code-block:: LAMMPS pair_style [hybrid/overlay ...] lebedeva/z cutoff @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay lebedeva/z 20.0 @@ -40,8 +38,6 @@ which is to take all normals along the z-axis. & - A \left(\frac{z_0}{r_ij}\right)^6 + A \left( \frac{z_0}{r_c} \right)^6 \\ \rho^2_{ij} = & x^2_{ij} + y^2_{ij} \qquad (\mathbf{n_i} \equiv \mathbf{\hat{z}}) - - It is important to have a sufficiently large cutoff to ensure smooth forces. Energies are shifted so that they go continuously to zero at the cutoff assuming that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast. @@ -57,7 +53,6 @@ Other interactions can be set to zero using pair\_style *none*\ . Restrictions """""""""""" - This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -74,12 +69,8 @@ Related commands **Default:** none - ---------- - .. _Leb01: - - **(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011) diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index 8320d1701c..908b912aea 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -6,7 +6,6 @@ pair_style line/lj command Syntax """""" - .. code-block:: LAMMPS pair_style line/lj cutoff @@ -16,7 +15,6 @@ cutoff = global cutoff for interactions (distance units) Examples """""""" - .. code-block:: LAMMPS pair_style line/lj 3.0 @@ -113,10 +111,8 @@ and a point particle is calculated. The *cutoff* coefficient is optional. If not specified, the global cutoff is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, coefficients must be specified. @@ -131,14 +127,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style is part of the ASPHERE 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/pair_list.rst b/doc/src/pair_list.rst index f70c2f76b1..e3fc4ac682 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -6,7 +6,6 @@ pair_style list command Syntax """""" - .. code-block:: LAMMPS pair_style list listfile cutoff keyword @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style list restraints.txt 200.0 @@ -59,14 +57,11 @@ The format of the list file is as follows: coeffs = list of coeffs cutoff = cutoff for interaction (optional) - - The cutoff parameter is optional. If not specified, the global cutoff is used. Here is an example file: - .. parsed-literal:: # this is a comment @@ -81,7 +76,6 @@ The style *lj126* computes pairwise interactions with the formula E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - and the coefficients: * :math:`\epsilon` (energy units) @@ -93,7 +87,6 @@ The style *morse* computes pairwise interactions with the formula E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c - and the coefficients: * :math:`D_0` (energy units) @@ -113,10 +106,8 @@ and the coefficients: Note that the usual 1/2 factor is included in :math:`K`. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing since all parameters are @@ -135,14 +126,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style does not use a neighbor list and instead identifies atoms by their IDs. This has two consequences: 1) The cutoff has to be chosen sufficiently large, so that the second atom of a pair has to be diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index e2bffb4531..a0b49ee577 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -108,7 +108,6 @@ pair_style lj/cut/tip4p/long/opt command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -116,7 +115,6 @@ Syntax * style = *lj/cut* or *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/tip4p/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/cut* args = cutoff @@ -158,7 +156,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/cut 2.5 @@ -217,7 +214,6 @@ given by \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - Rc is the cutoff. Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by @@ -226,7 +222,6 @@ Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c - 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. @@ -241,7 +236,6 @@ to the Coulombic term, given by E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c - where :math:`\kappa` is the inverse of the Debye length. This potential is another way to mimic the screening effect of a polar solvent. @@ -254,7 +248,6 @@ shifted force model described in :ref:`Fennell `, given by: q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c - where :math:`\alpha` is the damping parameter and erfc() is the complementary error-function. This potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, pairwise *1/r* @@ -286,7 +279,6 @@ summation method, described in :ref:`Wolf `, given by: \frac{1}{2} \sum_{j \neq i} \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c - where :math:`\alpha` is the damping parameter, and erfc() is the complementary error-function terms. This potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, @@ -358,10 +350,8 @@ 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. - ---------- - A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` @@ -369,10 +359,8 @@ styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -391,10 +379,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -424,14 +410,11 @@ 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 details. - ---------- - Restrictions """""""""""" - The *lj/cut/coul/long* and *lj/cut/tip4p/long* styles are part of the KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE package. These styles are only enabled if LAMMPS was built with those @@ -445,20 +428,14 @@ Related commands **Default:** none - ---------- - .. _Jorgensen2: - - **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). .. _Fennell2: - - **(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 2bb914c0b2..7c81803e34 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -12,7 +12,6 @@ pair_style lj96/cut/omp command Syntax """""" - .. code-block:: LAMMPS pair_style lj96/cut cutoff @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj96/cut 2.5 @@ -41,7 +39,6 @@ of the standard 12/6 potential, given by \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - :math:`r_c` is the cutoff. The following coefficients must be defined for each pair of atoms @@ -57,10 +54,8 @@ commands, or by mixing as described below: The last coefficient is optional. If not specified, the global LJ cutoff specified in the pair\_style command is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,10 +74,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -109,10 +102,8 @@ pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for details. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 5ef497cf6e..52f42e5e13 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -12,7 +12,6 @@ pair_style lj/cubic/omp command Syntax """""" - .. code-block:: LAMMPS pair_style lj/cubic @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/cubic @@ -45,7 +43,6 @@ the energy and force are zero. & = u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\ & = 0 \qquad r > r_c - The location of the inflection point :math:`r_s` is defined by the LJ diameter, :math:`r_s/\sigma = (26/7)^{1/6}`. The cutoff distance is defined by :math:`r_c/r_s = 67/48` or :math:`r_c/\sigma = 1.737...` @@ -71,10 +68,8 @@ zero-crossing distance for the potential, not as the energy minimum, which is located at :math:`r_{min} = 2^{\frac{1}{6}} \sigma`. In the above example, :math:`\sigma = 0.8908987`, so :math:`r_{min} = 1.0`. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -93,10 +88,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -124,10 +117,8 @@ The lj/cubic pair 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. - ---------- - Restrictions """""""""""" none @@ -139,17 +130,12 @@ Related commands **Default:** none - ---------- - .. _Holian: - - .. _Ravelo2: **(Holian)** Holian and Ravelo, Phys Rev B, 51, 11275 (1995). - **(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 113080ea1e..f27eb83631 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -21,7 +21,6 @@ pair_style lj/expand/coul/long/gpu command Syntax """""" - .. code-block:: LAMMPS pair_style lj/expand cutoff @@ -31,7 +30,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/expand 2.5 @@ -57,7 +55,6 @@ formula: \left(\frac{\sigma}{r - \Delta}\right)^6 \right] \qquad r < r_c + \Delta - :math:`r_c` is the cutoff which does not include the :math:`\Delta` distance. I.e. the actual force cutoff is the sum of :math:`r_c + \Delta`. @@ -103,10 +100,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon, sigma, and shift @@ -133,10 +128,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index ac7b6c4c50..7a256256fc 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -21,7 +21,6 @@ pair_style lj/long/tip4p/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -29,7 +28,6 @@ Syntax * style = *lj/long/coul/long* or *lj/long/tip4p/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/long/coul/long* args = flag_lj flag_coul cutoff (cutoff2) @@ -58,7 +56,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/long/coul/long cut off 2.5 @@ -90,7 +87,6 @@ potential parameters, plus the Coulomb potential, given by: E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c - 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 @@ -181,19 +177,15 @@ 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. - ---------- - A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -212,10 +204,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -244,14 +234,11 @@ command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for details. - ---------- - Restrictions """""""""""" - These 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. @@ -262,19 +249,13 @@ Related commands **Default:** none - ---------- - .. _Veld2: - - **(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007). .. _Jorgensen4: - - **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 681425acc0..182de5b40c 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -9,7 +9,6 @@ pair_style lj/smooth/omp command Syntax """""" - .. code-block:: LAMMPS pair_style lj/smooth Rin Rc @@ -20,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/smooth 8.0 10.0 @@ -41,7 +39,6 @@ applied between the inner and outer cutoff. F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 \qquad r_{in} < r < r_c - The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to cause the force to vary smoothly from the inner cutoff :math:`r_{in}` to the outer cutoff :math:`r_c`. @@ -72,10 +69,8 @@ commands, or by mixing as described below: The last 2 coefficients are optional inner and outer cutoffs. If not specified, the global values for :math:`r_{in}` and :math:`r_c` are used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -94,10 +89,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon, sigma, Rin @@ -125,10 +118,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index bf15205fad..41f980d75f 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -9,7 +9,6 @@ pair_style lj/smooth/linear/omp command Syntax """""" - .. code-block:: LAMMPS pair_style lj/smooth/linear cutoff @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/smooth/linear 2.5 @@ -41,7 +39,6 @@ continuously to zero at the cutoff Rc :ref:`(Toxvaerd) `: \left(\frac{\sigma}{r}\right)^6 \right] \\ 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 following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the @@ -55,10 +52,8 @@ commands, or by mixing as described below: The last coefficient is optional. If not specified, the global LJ cutoff specified in the pair\_style command is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -77,10 +72,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -106,10 +99,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none @@ -121,12 +112,8 @@ Related commands **Default:** none - ---------- - .. _Toxvaerd: - - **(Toxvaerd)** Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 5f3a797040..9f7ab4cf22 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -6,7 +6,6 @@ pair_style lj/switch3/coulgauss/long command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -14,7 +13,6 @@ Syntax * style = *lj/switch3/coulgauss/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/switch3/coulgauss/long* args = cutoff (cutoff2) width @@ -25,7 +23,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/switch3/coulgauss/long 12.0 3.0 @@ -55,7 +52,6 @@ by the switching function 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} \end{array} \right. - where w is the width defined in the arguments. This potential is combined with Coulomb interaction between Gaussian charge densities: @@ -86,7 +82,6 @@ commands: ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Shifting the potential energy is not necessary because the switching @@ -95,7 +90,6 @@ function ensures that the potential is zero at the cut-off. Restrictions """""""""""" - These styles are part of the USER-YAFF 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/pair_local_density.rst b/doc/src/pair_local_density.rst index 7aa570925a..4b7564266e 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -6,7 +6,6 @@ pair_style local/density command Syntax """""" - .. code-block:: LAMMPS pair_style style arg @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style local/density benzene_water.localdensity.table @@ -53,10 +51,8 @@ upon initialization. hybrid/overlay option, the corresponding pair\_coeff command must be supplied \* \* as placeholders for the atom types. - ---------- - **System with a single CG atom type:** A system of a single atom type (e.g., LJ argon) with a single local density (LD) @@ -66,7 +62,6 @@ potential would have an energy given by: U_{LD} = \sum_i F(\rho_i) - where :math:`\rho_i` is the LD at atom *i* and :math:`F(\rho)` is similar in spirit to the embedding function used in EAM potentials. The LD at atom *i* is given by the sum @@ -75,7 +70,6 @@ LD at atom *i* is given by the sum \rho_i = \sum_{j \neq i} \varphi(r_{ij}) - where :math:`\varphi` is an indicator function that is one at r=0 and zero beyond a cutoff distance R2. The choice of the functional form of :math:`\varphi` is somewhat arbitrary, but the following piecewise cubic @@ -104,10 +98,8 @@ It can be shown that the total force between two atoms due to the LD potential takes the form of a pair force, which motivates its designation as a LAMMPS pair style. Please see :ref:`(Sanyal1) ` for details of the derivation. - ---------- - **Systems with arbitrary numbers of atom types:** The potential is easily generalized to systems involving multiple atom types: @@ -116,14 +108,12 @@ The potential is easily generalized to systems involving multiple atom types: U_{LD} = \sum_i a_\alpha F(\rho_i) - with the LD expressed as .. math:: \rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij}) - where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the type of atom *j*\ , and the coefficients *a* and *b* filter for atom types as specified by the user. *a* is called the central atom filter as @@ -155,7 +145,6 @@ pair\_style local/density is: 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: @@ -163,7 +152,6 @@ potentials N\_LD. Each LD is calculated as before with: \rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij}) - 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), @@ -178,7 +166,6 @@ one must specify: **Tabulated input file format:** - .. parsed-literal:: Line 1: comment or blank (ignored) @@ -227,14 +214,11 @@ The local/density pair style does not write its information to :doc:`binary rest Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. - ---------- - Restrictions """""""""""" - The local/density pair style is a 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. @@ -245,23 +229,16 @@ Related commands **Default:** none - ---------- - .. _Sanyal1: - - .. _Sanyal2: **(Sanyal1)** Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109. - **(Sanyal2)** Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693. .. _Rosenberger: - - **(Rosenberger)** Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111. diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index d97ba80fe9..602d40de6b 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -15,7 +15,6 @@ pair_style lubricate/poly/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF @@ -31,7 +30,6 @@ Syntax **Examples:** (all assume radius = 1) - .. code-block:: LAMMPS pair_style lubricate 1.5 1 1 2.01 2.5 @@ -61,7 +59,6 @@ Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) ` command as in the examples above, or in the data file or restart files read by the @@ -160,10 +154,8 @@ The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair\_style command are used. Otherwise both must be specified. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -182,10 +174,8 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch See :doc:`this section ` of the manual for more 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 two cutoff distances for this @@ -209,14 +199,11 @@ This pair 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. - ---------- - 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. @@ -242,20 +229,14 @@ Default The default settings for the optional args are flagHI = 1 and flagVF = 1. - ---------- - .. _Ball1: - - **(Ball)** Ball and Melrose, Physica A, 247, 444-472 (1997). .. _Kumar1: - - **(Kumar)** Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also his thesis for more details: A. Kumar, "Microscale Dynamics in Suspensions of Non-spherical Particles", Thesis, University of diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index aacb26bfa3..eaf71ac79e 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -9,7 +9,6 @@ pair_style lubricateU/poly command Syntax """""" - .. code-block:: LAMMPS pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF @@ -25,7 +24,6 @@ Syntax **Examples:** (all assume radius = 1) - .. code-block:: LAMMPS pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 @@ -53,7 +51,6 @@ Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) ` command as in the examples above, or in the data file or restart files read by the @@ -165,10 +159,8 @@ The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair\_style command are used. Otherwise both must be specified. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the two cutoff distances for this @@ -192,14 +184,11 @@ This pair 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. - ---------- - 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. @@ -230,18 +219,12 @@ Default The default settings for the optional args are flagHI = 1 and flagVF = 1. - ---------- - .. _Ball2: - - **(Ball)** Ball and Melrose, Physica A, 247, 444-472 (1997). .. _Kumar2: - - **(Kumar)** Kumar and Higdon, Phys Rev E, 82, 051401 (2010). diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 328fc9d4bf..52120eab61 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -12,7 +12,6 @@ pair_style lennard/mdf command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -32,12 +31,9 @@ Syntax cutoff1 = inner cutoff for the start of the tapering function cutoff1 = out cutoff for the end of the tapering function - - Examples """""""" - .. code-block:: LAMMPS pair_style lj/mdf 2.5 3.0 @@ -64,7 +60,6 @@ inner and outer cutoff. E_{smooth}(r) = E(r)*f(r) - The tapering, *f(r)*\ , is done by using the Mei, Davenport, Fernando function :ref:`(Mei) `. @@ -80,14 +75,11 @@ where x = \frac{(r-r_m)}{(r_{cut}-r_m)} - Here :math:`r_m` is the inner cutoff radius and :math:`r_{cut}` is the outer cutoff radius. - ---------- - For the *lj/mdf* pair\_style, the potential energy, *E(r)*\ , is the standard 12-6 Lennard-Jones written in the epsilon/sigma form: @@ -95,7 +87,6 @@ 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 the examples above, or in the data file read by the :doc:`read_data @@ -119,7 +110,6 @@ global values: E(r) = A e^{(-r/\rho)} -\frac{C}{r^6} - * *A* (energy units) * :math:`\rho` (distance units) * *C* (energy-distance\^6 units) @@ -135,7 +125,6 @@ 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. @@ -184,12 +173,8 @@ Related commands **Default:** none - ---------- - .. _Mei: - - **(Mei)** Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991) diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 7e91d6185a..7bf82da846 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -9,7 +9,6 @@ pair_style meam/spline/omp command Syntax """""" - .. code-block:: LAMMPS pair_style meam/spline @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code:: LAMMPS pair_style meam/spline @@ -91,7 +89,6 @@ your LAMMPS simulation has 3 atoms types and they are all to be treated with this potentials, you would use the following pair\_coeff command: - .. code-block:: LAMMPS pair_coeff * * Ti.meam.spline Ti Ti Ti @@ -108,7 +105,6 @@ on the command line to that single type. An example with a two component spline (new style) is TiO.meam.spline, where the command - .. code-block:: LAMMPS pair_coeff * * TiO.meam.spline Ti O @@ -119,10 +115,8 @@ names of the elements in the TiO.meam.spline file; otherwise an error will be raised. This behavior is different than the old style MEAM files. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -141,10 +135,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -158,14 +150,11 @@ 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 *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. @@ -180,20 +169,14 @@ Related commands **Default:** none - ---------- - .. _Lenosky1: - - **(Lenosky)** Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). .. _Zhang4: - - **(Zhang)** Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016). diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 827497e1a0..c61ae0a54f 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -6,7 +6,6 @@ pair_style meam/sw/spline command Syntax """""" - .. code-block:: LAMMPS pair_style meam/sw/spline @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style meam/sw/spline @@ -96,10 +94,8 @@ potentials. Example input scripts that use this pair style are provided in the examples/USER/misc/meam\_sw\_spline directory. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The pair style does not support multiple element types or mixing. @@ -117,14 +113,11 @@ The *meam/sw/spline* pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. @@ -140,27 +133,19 @@ Related commands **Default:** none - ---------- - .. _Lenosky2: - - **(Lenosky)** Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000). .. _Stillinger1: - - **(Stillinger)** Stillinger, Weber, Phys. Rev. B 31, 5262 (1985). .. _Nicklas: - - **(Nicklas)** The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger, diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 60a6585e5b..78b04f90de 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -13,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style meam/c @@ -48,7 +47,6 @@ given by: E = \sum_i \left\{ F_i(\bar{\rho}_i) + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\} - where *F* is the embedding energy which is a function of the atomic electron density :math:`\rho`, and :math:`\phi` is a pair potential interaction. The pair interaction is summed over all neighbors J of @@ -90,7 +88,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * library.meam Si C sic.meam Si Si Si C @@ -149,7 +146,6 @@ finds and ignores the rest. Other parameters in the MEAM library file correspond to single-element potential parameters: - .. parsed-literal:: lat = lattice structure of reference configuration @@ -170,7 +166,6 @@ is typically 1.0 for single-element systems. The ibar parameter selects the form of the function G(Gamma) used to compute the electron density; options are - .. parsed-literal:: 0 => G = sqrt(1+Gamma) @@ -188,7 +183,6 @@ blank and comment lines (start with #) which can appear anywhere, each line has one of the following forms. Each line can also have a trailing comment (starting with #) which is ignored. - .. parsed-literal:: keyword = value @@ -200,7 +194,6 @@ The indices I, J, K correspond to the elements selected from the MEAM library file numbered in the order of how those elements were selected starting from 1. Thus for the example given below - .. code-block:: LAMMPS pair_coeff * * library.meam Si C sic.meam Si Si Si C @@ -214,7 +207,6 @@ augt1, gsmooth\_factor, re where - .. parsed-literal:: rc = cutoff radius for cutoff function; default = 4.0 @@ -306,7 +298,6 @@ where N is the number of MEAM elements being used. Thus these lines - .. parsed-literal:: rho0(2) = 2.25 @@ -347,7 +338,6 @@ 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: - .. parsed-literal:: astar = alpha \* (r/re - 1.d0) @@ -371,10 +361,8 @@ recent published MEAM parameter sets, such as :ref:`(Valone) ` literature). An alternative form (see e.g. :ref:`(Lee2) `) is available using erose\_form = 2. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -393,14 +381,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - The *meam/c* style is provided in the USER-MEAMC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -420,54 +405,36 @@ Related commands **Default:** none - ---------- - .. _Baskes: - - **(Baskes)** Baskes, Phys Rev B, 46, 2727-2742 (1992). .. _Gullet: - - **(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 - - .. _Lee: - - **(Lee)** Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000). .. _Lee2: - - **(Lee2)** Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001). .. _Valone: - - **(Valone)** Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). .. _Wang2: - - **(Wang)** Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004). .. _ZBL: - - **(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges of Ions in Matter", Vol 1, 1985, Pergamon Press. diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 46ae7f3ccb..c7c9059704 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -6,7 +6,6 @@ pair_style mesocnt command Syntax """""" - .. code-block:: LAMMPS pair_style mesocnt @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style mesocnt @@ -97,10 +95,8 @@ A full summary of the method and LAMMPS implementation details is expected to soon become available in Computer Physics Communications. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. @@ -117,14 +113,11 @@ This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - This style 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. @@ -138,19 +131,13 @@ Related commands **Default:** none - ---------- - .. _Volkov1: - - **(Volkov1)** Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010). .. _Volkov2: - - **(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008). diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index c5cf52330d..72c2a02a72 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -15,7 +15,6 @@ pair_style tdpd command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -38,12 +37,9 @@ Syntax cutoff = global cutoff for tDPD interactions (distance units) seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed) - - Examples """""""" - .. code-block:: LAMMPS pair_style edpd 1.58 9872598 @@ -109,7 +105,6 @@ 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) `. @@ -135,10 +130,8 @@ heat friction :math:`s_T(T) = \kappa (1 + c_1 (T-1) + c_2 (T-1)^2 + c_3 specified, the eDPD system will use constant power\_f and :math:`\kappa`, which is independent to temperature changes. - ---------- - The *mdpd/rhosum* style computes the local particle mass density :math:`\rho` for mDPD particles by kernel function interpolation. @@ -312,34 +305,24 @@ Related commands **Default:** none - ---------- - .. _Li2014\_JCP: - - **(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)** Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI: 10.1039/C5CC01684C. .. _Li2013\_POF: - - **(Li2013\_POF)** Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366. .. _Li2015\_JCP: - - **(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 67078252da..562f1f5802 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -6,7 +6,6 @@ pair_style mgpt command Syntax """""" - .. code-block:: LAMMPS pair_style mgpt @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style mgpt @@ -40,7 +38,6 @@ elemental bulk material in the form + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) - 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 @@ -150,10 +147,8 @@ before proceeding to more complex simulations. as provided, it will build with whatever low-level compiler (g++, icc, etc) is the default for your MPI installation. - ---------- - **Mixing, shift, table tail correction, restart**\ : This pair style does not support the :doc:`pair_modify ` @@ -167,14 +162,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the USER-MGPT package and is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. @@ -214,41 +206,29 @@ Default The options defaults for the :doc:`pair_coeff ` command are volpress yes, nbody 1234, and precision double. - ---------- - .. _Moriarty1: - - **(Moriarty1)** Moriarty, Physical Review B, 38, 3199 (1988). .. _Moriarty2: - - **(Moriarty2)** Moriarty, Physical Review B, 42, 1609 (1990). Moriarty, Physical Review B 49, 12431 (1994). .. _Moriarty3: - - **(Moriarty3)** Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, Journal of Materials Research, 21, 563 (2006). .. _Glosli: - - **(Glosli)** Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006). .. _Oppelstrup: - - **(Oppelstrup)** Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published. diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index 17018ddf97..165ad7a787 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -9,7 +9,6 @@ pair_style mie/cut/gpu command Syntax """""" - .. code-block:: LAMMPS pair_style mie/cut cutoff @@ -19,7 +18,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style mie/cut 10.0 @@ -37,7 +35,6 @@ The *mie/cut* style computes the Mie potential, given by E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right] \qquad r < r_c - Rc is the cutoff and C is a function that depends on the repulsive and attractive exponents, given by: @@ -45,7 +42,6 @@ attractive exponents, given by: C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)} - Note that for 12/6 exponents, C is equal to 4 and the formula is the same as the standard Lennard-Jones potential. @@ -64,10 +60,8 @@ commands, or by mixing as described below: The last coefficient is optional. If not specified, the global cutoff specified in the pair\_style command is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -93,10 +87,8 @@ pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the :doc:`run_style ` command for details. - ---------- - Restrictions """""""""""" none @@ -108,19 +100,13 @@ Related commands **Default:** none - ---------- - .. _Mie: - - **(Mie)** G. Mie, Ann Phys, 316, 657 (1903). .. _Avendano: - - **(Avendano)** C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011). diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index ab683f321c..537cdde457 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -6,7 +6,6 @@ pair_style mm3/switch3/coulgauss/long command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -14,7 +13,6 @@ Syntax * style = *mm3/switch3/coulgauss/long* * args = list of arguments for a particular style - .. parsed-literal:: *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width @@ -25,7 +23,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style mm3/switch3/coulgauss/long 12.0 3.0 @@ -46,7 +43,6 @@ 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 by the switching function @@ -58,7 +54,6 @@ by the switching function 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} \end{array} \right. - where w is the width defined in the arguments. This potential is combined with Coulomb interaction between Gaussian charge densities: @@ -66,7 +61,6 @@ is combined with Coulomb interaction between Gaussian charge densities: E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} - where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, ::math:`\gamma_i` and @@ -100,7 +94,6 @@ function ensures that the potential is zero at the cut-off. Restrictions """""""""""" - These styles are part of the USER-YAFF 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/pair_modify.rst b/doc/src/pair_modify.rst index 63622623cf..c248a3fcd0 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -6,7 +6,6 @@ pair_modify command Syntax """""" - .. code-block:: LAMMPS pair_modify keyword values ... @@ -39,11 +38,9 @@ Syntax w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive *compute/tally* value = *yes* or *no* - Examples """""""" - .. code-block:: LAMMPS pair_modify shift yes mix geometric @@ -92,7 +89,6 @@ performed. - mix *geometric* - .. math:: \epsilon_{ij} = & \sqrt{\epsilon_i \epsilon_j} \\ @@ -100,7 +96,6 @@ performed. - mix *arithmetic* - .. math:: \epsilon_{ij} = & \sqrt{\epsilon_i \epsilon_j} \\ @@ -108,7 +103,6 @@ performed. - mix *sixthpower* - .. math:: \epsilon_{ij} = & \frac{2 \sqrt{\epsilon_i \epsilon_j} \sigma_i^3 \sigma_j^3}{\sigma_i^6 + \sigma_j^6} \\ @@ -207,7 +201,6 @@ including the following: pressure reported by the simulation include an estimated contribution from those interactions. - The *compute* keyword allows pairwise computations to be turned off, even though a :doc:`pair_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging @@ -228,7 +221,6 @@ The *nofdotr* keyword allows to disable an optimization that computes the global stress tensor from the total forces and atom positions rather than from summing forces between individual pairs of atoms. - ---------- The *pair* keyword can only be used with the :doc:`hybrid and @@ -289,10 +281,8 @@ the *pair* keyword. Use *no* to disable, or *yes* to enable. The "pair_modify pair compute/tally" command must be issued **before** the corresponding compute style is defined. - ---------- - Restrictions """""""""""" @@ -317,18 +307,12 @@ tabinner = sqrt(2.0), tail = no, and compute = yes. Note that some pair styles perform mixing, but only a certain style of mixing. See the doc pages for individual pair styles for details. - ---------- - .. _Wolff1: - - **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). .. _Sun: - - **(Sun)** Sun, J Phys Chem B, 102, 7338-7364 (1998). diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index 81a3eb3320..ed9a0b98dd 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -6,7 +6,6 @@ pair_style momb command Syntax """""" - .. code-block:: LAMMPS pair_style momb cutoff s6 d @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style momb 12.0 0.75 20.0 @@ -41,7 +39,6 @@ dispersion in density functional theory calculations. E & = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\ f_{damp}(r,R_r) & = \frac{1}{1 + \exp^{-d(r/R_r - 1)}} - For the *momb* pair style, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files @@ -69,10 +66,8 @@ Related commands **Default:** none - ---------- - .. _Grimme: **(Grimme)** Grimme, J Comput Chem, 27(15), 1787-1799 (2006). diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index a9abebc982..83fb897cdb 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -24,7 +24,6 @@ pair_style morse/kk command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -32,7 +31,6 @@ Syntax * style = *morse* or *morse/smooth/linear* or *morse/soft* * args = list of arguments for a particular style - .. parsed-literal:: *morse* args = cutoff @@ -43,7 +41,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style morse 2.5 @@ -61,7 +58,6 @@ Style *morse* computes pairwise interactions with the formula E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c - Rc is the cutoff. The following coefficients must be defined for each pair of atoms @@ -78,10 +74,8 @@ commands: The last coefficient is optional. If not specified, the global morse cutoff is used. - ---------- - The *morse/smooth/linear* variant is similar to the lj/smooth/linear variant in that it adds to the potential a shift and a linear term so that both, potential energy and force, go to zero at the cut-off: @@ -91,14 +85,11 @@ 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 *morse* and *morse/smooth/linear* styles. - ---------- - A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with the :doc:`pair_style */soft @@ -106,10 +97,8 @@ package and is documented with the :doc:`pair_style */soft LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -128,10 +117,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : None of these pair styles support mixing. Thus, coefficients for all @@ -154,14 +141,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - The *morse/smooth/linear* pair style is only enabled if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 26b681e08b..4a412ca460 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -6,7 +6,6 @@ pair_style multi/lucy command Syntax """""" - .. code-block:: LAMMPS pair_style multi/lucy style N keyword ... @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style multi/lucy linear 1000 @@ -35,7 +33,6 @@ the many-body form described in :ref:`(Moore) ` and F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} - which consists of a density-dependent function, :math:`A(\rho)`, and a radial-dependent weight function, :math:`\omega_{DD}(r_{ij})`. The radial-dependent weight function, :math:`\omega_{DD}(r_{ij})`, is taken @@ -45,14 +42,12 @@ as the Lucy function: \omega_{DD}\left(r_{ij}\right) = \left(1+\frac{3r_{ij}}{r_{cut}}\right)\left(1+\frac{r_{ij}}{r_{cut}}\right)^3 - The density-dependent energy for a given particle is given by: .. math:: u_{i}^{DD}\left(\rho_{i}\right) = \frac{\pi r_{cut}^4}{84} \int_{\rho_0}^{\rho_i} A\left(\rho'\right) d\rho' - See the supporting information of :ref:`(Brennan) ` or the publication by :ref:`(Moore) ` for more details on the functional form. @@ -94,14 +89,11 @@ tabulated distance. If specified, only file values up to the cutoff are used to create the interpolation table. The format of this file is described below. - ---------- - The format of a tabulated file is a series of one or more sections, defined as follows (without the parenthesized comments): - .. parsed-literal:: # Density-dependent function (one or more comment or blank lines) @@ -174,10 +166,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -197,14 +187,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -215,24 +202,16 @@ Related commands **Default:** none - ---------- - .. _Warren1: - - **(Warren)** Warren, Phys Rev E, 68, 066702 (2003). .. _Brennan1: - - **(Brennan)** Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). .. _Moore1: - - **(Moore)** Moore, J Chem Phys, 144, 104501 (2016). diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index a197fc1ec1..6d9b00f1a1 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -9,7 +9,6 @@ pair_style multi/lucy/rx/kk command Syntax """""" - .. code-block:: LAMMPS pair_style multi/lucy/rx style N keyword ... @@ -21,7 +20,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style multi/lucy/rx linear 1000 @@ -48,7 +46,6 @@ following from the many-body form described in :ref:`(Moore) ` and F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} - which consists of a density-dependent function, :math:`A(\rho)`, and a radial-dependent weight function, :math:`\omega_{DD}(r_{ij})`. The radial-dependent weight function, :math:`\omega_{DD}(r_{ij})`, is taken @@ -58,14 +55,12 @@ as the Lucy function: \omega_{DD}\left(r_{ij}\right) = \left(1+\frac{3r_{ij}}{r_{cut}}\right)\left(1+\frac{r_{ij}}{r_{cut}}\right)^3 - The density-dependent energy for a given particle is given by: .. math:: u_{i}^{DD}\left(\rho_{i}\right) = \frac{\pi r_{cut}^4}{84} \int_{\rho_0}^{\rho_i} A\left(\rho'\right) d\rho' - See the supporting information of :ref:`(Brennan) ` or the publication by :ref:`(Moore) ` for more details on the functional form. @@ -122,14 +117,11 @@ associated with the interacting coarse-grained particles (see the stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). - ---------- - The format of a tabulated file is a series of one or more sections, defined as follows (without the parenthesized comments): - .. parsed-literal:: # Density-dependent function (one or more comment or blank lines) @@ -202,10 +194,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -225,10 +215,8 @@ This pair 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -247,14 +235,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -265,24 +250,16 @@ Related commands **Default:** fractional weighting - ---------- - .. _Warren2: - - **(Warren)** Warren, Phys Rev E, 68, 066702 (2003). .. _Brennan2: - - **(Brennan)** Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). .. _Moore2: - - **(Moore)** Moore, J Chem Phys, 144, 104501 (2016). diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index b1c3e5c077..e039accd1a 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -6,7 +6,6 @@ pair_style nb3b/harmonic command Syntax """""" - .. code-block:: LAMMPS pair_style nb3b/harmonic @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style nb3b/harmonic @@ -30,7 +28,6 @@ energy E of a system of atoms as E = K (\theta - \theta_0)^2 - 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*\ , @@ -53,7 +50,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * SiC.nb3b.harmonic Si Si Si C @@ -96,14 +92,11 @@ parameters should be set to zero. The potential file can also contain entries for additional elements which are not used in a particular simulation; LAMMPS ignores those entries. - ---------- - Restrictions """""""""""" - This pair style can only be used if LAMMPS was built with the MANYBODY package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 49761afc6b..c600432a06 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -21,7 +21,6 @@ pair_style nm/cut/coul/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -40,12 +39,9 @@ Syntax cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) - - Examples """""""" - .. code-block:: LAMMPS pair_style nm/cut 12.0 @@ -124,10 +120,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -152,10 +146,8 @@ All of the *nm* pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -177,7 +169,6 @@ instructions on how to use the accelerated styles effectively. Restrictions """""""""""" - These pair styles are part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -188,12 +179,8 @@ Related commands **Default:** none - ---------- - .. _Clarke: - - **(Clarke)** Clarke and Smith, J Chem Phys, 84, 2290 (1986). diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index 11a4a79163..2cb9cb608a 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -13,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style none diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index b34515868c..748a3affe7 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -18,7 +18,6 @@ pair_style oxdna/coaxstk command Syntax """""" - .. code-block:: LAMMPS pair_style style1 @@ -30,7 +29,6 @@ Syntax * style2 = *oxdna/excv* or *oxdna/stk* or *oxdna/hbond* or *oxdna/xstk* or *oxdna/coaxstk* * args = list of arguments for these particular styles - .. parsed-literal:: *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 @@ -45,7 +43,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk @@ -106,11 +103,9 @@ and :ref:`(Sulc) `. ---------- - Restrictions """""""""""" - These pair styles can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -125,7 +120,6 @@ Related commands **Default:** none - ---------- .. _Henrich1: diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 6897eb859f..465f46a913 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -21,7 +21,6 @@ pair_style oxdna2/dh command Syntax """""" - .. code-block:: LAMMPS pair_style style1 @@ -33,7 +32,6 @@ Syntax * style2 = *oxdna2/excv* or *oxdna2/stk* or *oxdna2/hbond* or *oxdna2/xstk* or *oxdna2/coaxstk* or *oxdna2/dh* * args = list of arguments for these particular styles - .. parsed-literal:: *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 @@ -52,7 +50,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh @@ -112,11 +109,9 @@ Please cite also the relevant oxDNA2 publications ---------- - Restrictions """""""""""" - These pair styles can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -131,7 +126,6 @@ Related commands **Default:** none - ---------- .. _Henrich2: diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index ebaf085341..0cca929c49 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -21,7 +21,6 @@ pair_style oxrna2/dh command Syntax """""" - .. code-block:: LAMMPS pair_style style1 @@ -33,7 +32,6 @@ Syntax * style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh* * args = list of arguments for these particular styles - .. parsed-literal:: *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 @@ -52,7 +50,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh @@ -113,11 +110,9 @@ Please cite also the relevant oxRNA2 publications ---------- - Restrictions """""""""""" - These pair styles can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. @@ -134,7 +129,6 @@ Related commands none - ---------- .. _Henrich3: diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index d08da012f2..2d95785fff 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -21,7 +21,6 @@ pair_style peri/eps command Syntax """""" - .. code-block:: LAMMPS pair_style style @@ -31,7 +30,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style peri/pmb @@ -146,10 +144,8 @@ 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 details please see the description in "(Mtchell2011a)". - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -168,10 +164,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : These pair styles do not support mixing. Thus, coefficients for all @@ -190,14 +184,11 @@ These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - All of these styles are part of the PERI package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -208,42 +199,30 @@ Related commands **Default:** none - ---------- - .. _Parks: - - **(Parks)** Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008). .. _Silling2000: - - **(Silling 2000)** Silling, J Mech Phys Solids, 48, 175-209 (2000). .. _Silling2007: - - **(Silling 2007)** Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007). .. _Mitchell2011: - - **(Mitchell2011)** Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011). .. _Mitchell2011a: - - **(Mitchell2011a)** Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011). diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 22d262e288..93de3fe65f 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -6,7 +6,6 @@ pair_style polymorphic command Syntax """""" - .. code-block:: LAMMPS pair_style polymorphic @@ -16,7 +15,6 @@ style = *polymorphic* Examples """""""" - .. code-block:: LAMMPS pair_style polymorphic @@ -71,7 +69,6 @@ Stillinger-Weber potential (:ref:`SW `) if we set G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2 \end{array}\right. - The potential reduces to Tersoff types of potential (:ref:`Tersoff ` or :ref:`Albe `) if we set @@ -87,7 +84,6 @@ The potential reduces to Tersoff types of potential G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right] \end{array}\right. - .. math:: f_{c,IJ}=\left\{\begin{array}{lr} @@ -96,7 +92,6 @@ The potential reduces to Tersoff types of potential 0, & r \geq r_{c,IJ} \\ \end{array}\right. - The potential reduces to Rockett-Tersoff (:ref:`Wang `) type if we set .. math:: @@ -119,7 +114,6 @@ The potential reduces to Rockett-Tersoff (:ref:`Wang `) type if we set G_{JIK}\left(\theta\right)=1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2} \end{array}\right. - .. math:: f_{c,IJ}=\left\{\begin{array}{lr} @@ -128,7 +122,6 @@ The potential reduces to Rockett-Tersoff (:ref:`Wang `) type if we set 0, & r \geq r_{c,IJ} \\ \end{array}\right. - .. math:: f_{c,1,IJ}=\left\{\begin{array}{lr} @@ -137,7 +130,6 @@ The potential reduces to Rockett-Tersoff (:ref:`Wang `) type if we set 0, & r \geq r_{c,1,IJ} \\ \end{array}\right. - The potential becomes embedded atom method (:ref:`Daw `) if we set .. math:: @@ -152,7 +144,6 @@ The potential becomes embedded atom method (:ref:`Daw `) if we set G_{JIK}\left(\theta\right)=1 \end{array}\right. - In the embedded atom method case, :math:`\phi_{IJ}(r_{ij})` is the pair energy, :math:`F_I(X)` is the embedding energy, *X* is the local electron density, and :math:`f_K(r)` is the atomic electron density function. @@ -189,7 +180,6 @@ 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: - .. parsed-literal:: pair_coeff \* \* SiC_tersoff.poly Si Si Si C @@ -208,7 +198,6 @@ have a ".poly" suffix. At the beginning of the files, an unlimited number of lines starting with '#' are used to describe the potential and are ignored by LAMMPS. The next line lists two numbers: - .. parsed-literal:: ntypes :math:`\eta` @@ -222,7 +211,6 @@ set to :math:`\delta_{ij}`. The next ntypes lines each lists two numbers and a character string representing atomic number, atomic mass, and name of the species of the ntypes elements: - .. parsed-literal:: atomic_number atomic-mass element (1) @@ -232,7 +220,6 @@ of the species of the ntypes elements: The next ntypes\*(ntypes+1)/2 lines contain two numbers: - .. parsed-literal:: cut :math:`xi` (1) @@ -280,14 +267,11 @@ This pair style does not write their information to :doc:`binary restart files < need to re-specify the pair\_style and pair\_coeff commands in an input 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 atomic structure data file. @@ -308,44 +292,30 @@ Related commands :doc:`pair_coeff ` - ---------- - .. _Zhou3: - - **(Zhou)** X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). .. _SW: - - **(SW)** F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985). .. _Tersoff: - - **(Tersoff)** J. Tersoff, Phys. Rev. B, 39, 5566 (1989). .. _poly-Albe: - - **(Albe)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002). .. _Wang3: - - **(Wang)** J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). .. _poly-Daw: - - **(Daw)** M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index f848cba6dc..886c9c2b53 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -6,7 +6,6 @@ pair_style python command Syntax """""" - .. code-block:: LAMMPS pair_style python cutoff @@ -16,7 +15,6 @@ cutoff = global cutoff for interactions in python potential classes Examples """""""" - .. code-block:: LAMMPS pair_style python 2.5 @@ -61,7 +59,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 @@ -76,13 +73,10 @@ skipped. This can be used when a *python* potential is used as part of the *hybrid* or *hybrid/overlay* pair style. The NULL values are then placeholders for atom types that will be used with other potentials. - ---------- - The python potential file has to start with the following code: - .. code-block:: python from __future__ import print_function @@ -114,7 +108,6 @@ Here is an example for a single type Lennard-Jones potential class *LJCutMelt* in reduced units, which defines an atom type *lj* for which the parameters epsilon and sigma are both 1.0: - .. code-block:: python class LJCutMelt(LAMMPSPairPotential): @@ -139,7 +132,6 @@ and use the result as return value. The functions need to use the value of the internal potential parameter data structure. Following the *LJCutMelt* example, here are the two functions: - .. code-block:: python def compute_force(self,rsq,itype,jtype): @@ -167,10 +159,8 @@ the *LJCutMelt* example, here are the two functions: multiplied by delta x, delta y, and delta z to conveniently obtain the three components of the force vector between these two atoms. - ---------- - .. note:: The evaluation of scripted python code will slow down the @@ -180,7 +170,6 @@ the *LJCutMelt* example, here are the two functions: fly using the :doc:`pair_write ` command. Please see below for an example LAMMPS input of how to build a table file: - .. code-block:: LAMMPS pair_style python 2.5 @@ -198,7 +187,6 @@ table file is first deleted. After switching the pair style to *table*\ , the potential tables need to be assigned to the LAMMPS atom types like this: - .. code-block:: LAMMPS pair_style table linear 2000 @@ -207,10 +195,8 @@ to be assigned to the LAMMPS atom types like this: This can also be done for more complex systems. Please see the *examples/python* folders for a few more examples. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Mixing of potential parameters has to be handled inside the provided @@ -230,14 +216,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the PYTHON 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/pair_quip.rst b/doc/src/pair_quip.rst index 4c91677f08..032519e4b6 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -6,7 +6,6 @@ pair_style quip command Syntax """""" - .. code-block:: LAMMPS pair_style quip @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style quip @@ -76,7 +74,6 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - This pair style is part of the USER-QUIP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -100,20 +97,14 @@ Related commands :doc:`pair_coeff ` - ---------- - .. _Bartok\_2010: - - **(Bartok\_2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010). .. _Bartok\_PhD: - - **(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 e9196fc4b3..acaac5fce1 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -12,7 +12,6 @@ pair_style reax/c/omp command Syntax """""" - .. code-block:: LAMMPS pair_style reax/c cfile keyword value @@ -29,12 +28,9 @@ Syntax *safezone* = factor used for array allocation *mincap* = minimum size for array allocation - - Examples """""""" - .. code-block:: LAMMPS pair_style reax/c NULL @@ -188,7 +184,6 @@ code): To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: - .. code-block:: LAMMPS compute reax all pair reax/c @@ -226,18 +221,14 @@ 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: - .. code-block:: LAMMPS pair_coeff * * ffield.reax C C N H - ---------- - The format of a line in the control file is as follows: - .. parsed-literal:: variable_name value @@ -303,10 +294,8 @@ bond\_info: 1 prints bonds in the trajectory file (default = 0) angle\_info: 1 prints angles in the trajectory file (default = 0) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -320,10 +309,8 @@ This pair 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -342,14 +329,11 @@ 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. - ---------- - Restrictions """""""""""" - This pair style is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -370,27 +354,19 @@ Default The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2, mincap = 50. - ---------- - .. _Chenoweth\_20082: - - **(Chenoweth\_2008)** Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008). .. _Aktulga: - - (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). .. _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 a28549c344..d133274fa4 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -12,7 +12,6 @@ pair_style resquared/omp command Syntax """""" - .. code-block:: LAMMPS pair_style resquared cutoff @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style resquared 10.0 @@ -84,7 +82,6 @@ units: A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2 - where :math:`\rho` gives the number density of the spherical particles composing the ellipsoids and :math:`\epsilon_{\mathrm{LJ}}` determines the interaction strength of the spherical particles. @@ -159,10 +156,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -181,10 +176,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -217,14 +210,11 @@ This pair 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 of the :doc:`run_style command `. - ---------- - Restrictions """""""""""" - This style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -247,18 +237,12 @@ Related commands **Default:** none - ---------- - .. _Everaers3: - - **(Everaers)** Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). .. _Babadi: - - **(Berardi)** Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 9c17abb862..734759477c 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -30,7 +30,6 @@ pair_style lj/sdk/coul/msm/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -38,7 +37,6 @@ Syntax * style = *lj/sdk* or *lj/sdk/coul/long* * args = list of arguments for a particular style - .. parsed-literal:: *lj/sdk* args = cutoff @@ -50,7 +48,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/sdk 2.5 @@ -82,7 +79,6 @@ given by \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c - as required for the SDK Coarse-grained MD parameterization discussed in :ref:`(Shinoda) ` and :ref:`(DeVane) `. Rc is the cutoff. @@ -121,10 +117,8 @@ 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp* or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -143,10 +137,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, and rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -170,14 +162,11 @@ 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 the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command. - ---------- - Restrictions """""""""""" - All of the lj/sdk pair styles are part of the USER-CGSDK package. The *lj/sdk/coul/long* style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was @@ -191,18 +180,12 @@ Related commands **Default:** none - ---------- - .. _Shinoda3: - - **(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). .. _DeVane: - - **(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index 7a60fdef65..aeca957071 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -30,8 +30,6 @@ particles according to the Smoothed Dissipative Particle Dynamics model described in this paper by :ref:`(Espanol and Revenga) ` under the following assumptions: - - #. The temperature is constant and uniform. #. The shear viscosity is constant and uniform. #. The volume viscosity is negligible before the shear viscosity. @@ -81,7 +79,6 @@ above. ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -99,7 +96,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SDPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -114,12 +110,8 @@ Default The default seed is 0 (before mixing). - ---------- - .. _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 6395c76a1b..53253da3d6 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -6,7 +6,6 @@ pair_style smd/hertz command Syntax """""" - .. code-block:: LAMMPS pair_style smd/hertz scale_factor @@ -37,24 +36,19 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : No mixing is performed automatically. Currently, no part of USER-SMD supports restarting nor minimization. rRESPA does not apply to this pair style. - ---------- - Restrictions """""""""""" - This fix is part of the USER-SMD 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/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index 4b5d7cf1cc..ea819325b4 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -26,7 +26,6 @@ Smooth-Particle Hydrodynamics algorithm. This pair style is invoked with the following command: - .. code-block:: LAMMPS pair_style smd/tlsph @@ -52,24 +51,19 @@ be added. Please see the `SMD user guide `_ for a complete listing of the possible keywords and material models. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : No mixing is performed automatically. Currently, no part of USER-SMD supports restarting nor minimization. rRESPA does not apply to this pair style. - ---------- - Restrictions """""""""""" - This fix is part of the USER-SMD 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/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 14495d6b06..cf271a0393 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -37,24 +37,19 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : No mixing is performed automatically. Currently, no part of USER-SMD supports restarting nor minimization. rRESPA does not apply to this pair style. - ---------- - Restrictions """""""""""" - This fix is part of the USER-SMD 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/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 32a49b14ea..81bcc6364c 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -6,14 +6,12 @@ pair_style smd/ulsph command Syntax """""" - .. code-block:: LAMMPS pair_style smd/ulsph args * these keywords must be given - .. parsed-literal:: keyword = *\*DENSITY_SUMMATION* or *\*DENSITY_CONTINUITY* and *\*VELOCITY_GRADIENT* or *\*NO_VELOCITY_GRADIENT* and *\*GRADIENT_CORRECTION* or *\*NO_GRADIENT_CORRECTION* @@ -21,7 +19,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION @@ -35,7 +32,6 @@ Smooth-Particle Hydrodynamics algorithm. This pair style is invoked similar to the following command: - .. code-block:: LAMMPS pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION @@ -66,24 +62,19 @@ is recommended. Please see the `SMD user guide `_ for a complete listing of the possible keywords and material models. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : No mixing is performed automatically. Currently, no part of USER-SMD supports restarting nor minimization. rRESPA does not apply to this pair style. - ---------- - Restrictions """""""""""" - This fix is part of the USER-SMD 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/pair_smtbq.rst b/doc/src/pair_smtbq.rst index bccf53344a..d0d5c1e031 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -6,7 +6,6 @@ pair_style smtbq command Syntax """""" - .. code-block:: LAMMPS pair_style smtbq @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style smtbq @@ -36,7 +34,6 @@ is given by three contributions: E_{OO} & = \sum_{i,j}^{i,j = O}{\biggl[Cexp( -\frac{r_{ij}}{\rho} ) - Df_{cut}^{r_1^{OO}r_2^{OO}}(r_{ij}) exp(Br_{ij})\biggr]} \\ E_{MO} & = \sum_i{E_{cov}^{i} + \sum_{j\neq i}{ Af_{cut}^{r_{c1}r_{c2}}(r_{ij})exp\bigl[-p(\frac{r_{ij}}{r_0} -1) \bigr] } } - where :math:`E_{tot}` is the total potential energy of the system, :math:`E_{ES}` is the electrostatic part of the total energy, :math:`E_{OO}` is the interaction between oxygen atoms and @@ -57,7 +54,6 @@ correspond to oxygen atoms. As an example, to simulate a :math:`\mathrm{TiO_2}` atom type 1 has to be oxygen and atom type 2 Ti. The following pair\_coeff command should then be used: - .. code-block:: LAMMPS pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti @@ -98,7 +94,6 @@ ffield.SMTBQ.Syst. The energy band term is given by: \delta Q_i \bigl( 2\frac{n_0}{\eta_i} - \delta Q_i \bigr) \biggr\}^{1/2} \\ \delta Q_i & = | Q_i^{F} | - | Q_i | - where :math:`\eta_i` is the stoichiometry of atom *i*\ , :math:`\delta Q_i` is the charge delocalization of atom *i*\ , compared to its formal charge @@ -126,7 +121,6 @@ relationship: \xi^0 & = \frac{\xi_O}{m} = \frac{\xi_C}{n} \\ \frac{\beta_O}{\sqrt{m}} & = \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2} - Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = \frac{1}{2}(\sqrt{n}+\sqrt{m})` The potential offers the possibility to consider the polarizability of diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 815b1614be..246a461070 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -9,7 +9,6 @@ pair_style snap/kk command Syntax """""" - .. code-block:: LAMMPS pair_style snap @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style snap @@ -42,7 +40,6 @@ expressed as a weighted sum over bispectrum components. E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i - where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ , and :math:`\beta_k^{\alpha_i}` is the corresponding linear coefficient that depends on :math:\alpha_i`, the SNAP element of atom *i*\ . The @@ -70,7 +67,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P @@ -105,7 +101,6 @@ tantalum potential provided in the LAMMPS potentials directory combines the *snap* and *zbl* pair styles. It is invoked by the following commands: - .. code-block:: LAMMPS variable zblcutinner equal 4 @@ -173,10 +168,8 @@ for each element, the upper-triangular elements of alpha. The previously used *diagonalstyle* keyword was removed in 2019, since all known SNAP potentials use the default value of 3. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -195,10 +188,8 @@ This pair 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -217,14 +208,11 @@ 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. - ---------- - Restrictions """""""""""" - This style is part of the SNAP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -237,24 +225,16 @@ Related commands **Default:** none - ---------- - .. _Thompson20142: - - **(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015). .. _Bartok20102: - - **(Bartok2010)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). .. _Bartok2013: - - **(Bartok2013)** Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013). diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index f1fa0af802..460f97194e 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -12,7 +12,6 @@ pair_style soft/omp command Syntax """""" - .. code-block:: LAMMPS pair_style soft cutoff @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style soft 1.0 @@ -44,7 +42,6 @@ Style *soft* computes pairwise interactions with the formula E = A \left[ 1 + \cos\left(\frac{\pi r}{r_c}\right) \right] \qquad r < r_c - It is useful for pushing apart overlapping atoms, since it does not blow up as r goes to 0. A is a pre-factor that can be made to vary in time from the start to the end of the run (see discussion below), @@ -82,7 +79,6 @@ 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: - .. code-block:: LAMMPS variable prefactor equal ramp(0,30) @@ -93,10 +89,8 @@ can use the current timestep, elapsed time in the current run, elapsed time since the beginning of a series of runs, as well as access other variables. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -115,10 +109,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the A coefficient and cutoff @@ -140,10 +132,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index efd4b426da..cc265ac8c5 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -6,7 +6,6 @@ pair_style sph/heatconduction command Syntax """""" - .. code-block:: LAMMPS pair_style sph/heatconduction @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/heatconduction @@ -36,10 +34,8 @@ above. * D diffusion coefficient (length\^2/time units) * h kernel function cutoff (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -57,7 +53,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SPH 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/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 2e1a2b9d53..5d99576aad 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -6,7 +6,6 @@ pair_style sph/idealgas command Syntax """""" - .. code-block:: LAMMPS pair_style sph/idealgas @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/idealgas @@ -30,7 +28,6 @@ according to the ideal gas equation of state: p = (\gamma - 1) \rho e - where :math:`\gamma = 1.4` is the heat capacity ratio, :math:`\rho` is the local density, and e is the internal energy per unit mass. This pair style also computes Monaghan's artificial viscosity to prevent @@ -46,10 +43,8 @@ above. * :math:`\nu` artificial viscosity (no units) * h kernel function cutoff (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -67,7 +62,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -78,13 +72,9 @@ Related commands **Default:** none - ---------- - .. _ideal-Monoghan: - - **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index 45b611e441..defb1bb6fe 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -6,7 +6,6 @@ pair_style sph/lj command Syntax """""" - .. code-block:: LAMMPS pair_style sph/lj @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/lj @@ -40,10 +38,8 @@ above. * :math:`\nu` artificial viscosity (no units) * h kernel function cutoff (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -61,7 +57,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - As noted above, the Lennard-Jones parameters epsilon and sigma are set to unity. @@ -75,19 +70,13 @@ Related commands **Default:** none - ---------- - .. _Ree: - - **(Ree)** Ree, Journal of Chemical Physics, 73, 5401 (1980). .. _Monoghan: - - **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 68f55021e3..ff749eac78 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -6,7 +6,6 @@ pair_style sph/rhosum command Syntax """""" - .. code-block:: LAMMPS pair_style sph/rhosum Nstep @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/rhosum 10 @@ -37,10 +35,8 @@ above. * h (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -58,7 +54,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SPH 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/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index ae200ee024..498faccdd1 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -6,7 +6,6 @@ pair_style sph/taitwater command Syntax """""" - .. code-block:: LAMMPS pair_style sph/taitwater @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/taitwater @@ -30,7 +28,6 @@ according to Tait's equation of state: p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr] - where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with :math:`\rho_0` being the reference density and :math:`c_0` the reference speed of sound. @@ -50,10 +47,8 @@ above. * :math:`\nu` artificial viscosity (no units) * h kernel function cutoff (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -71,7 +66,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -82,13 +76,9 @@ Related commands **Default:** none - ---------- - .. _Monaghan: - - **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index c4dcb87758..b56be5fa67 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -6,7 +6,6 @@ pair_style sph/taitwater/morris command Syntax """""" - .. code-block:: LAMMPS pair_style sph/taitwater/morris @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style sph/taitwater/morris @@ -30,7 +28,6 @@ particles according to Tait's equation of state: p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr] - where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with :math:`\rho_0` being the reference density and :math:`c_0` the reference speed of sound. @@ -49,10 +46,8 @@ above. * :math:`\nu` dynamic viscosity (mass\*distance/time units) * h kernel function cutoff (distance units) - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This style does not support mixing. Thus, coefficients for all @@ -70,7 +65,6 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" - This pair style is part of the USER-SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -81,12 +75,8 @@ Related commands **Default:** none - ---------- - .. _Morris: - - **(Morris)** Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index ddd678a860..1b6bade399 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -9,7 +9,6 @@ pair_style spin/dipole/long command Syntax """""" - .. code-block:: LAMMPS pair_style spin/dipole/cut cutoff @@ -18,7 +17,6 @@ Syntax * cutoff = global cutoff for magnetic dipole energy and forces (optional) (distance units) - Examples """""""" @@ -81,10 +79,8 @@ A :doc:`kspace_style ` must be defined to use this pair style. Currently, :doc:`kspace_style ewald/dipole/spin ` and :doc:`kspace_style pppm/dipole/spin ` support long-range magnetic dipole-dipole interactions. - ---------- - The :doc:`pair_modify ` table option is not relevant for this pair style. @@ -98,7 +94,6 @@ to be specified in an input script that reads a restart file. Restrictions """""""""""" - The *spin/dipole/cut* and *spin/dipole/long* styles are part of the SPIN package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 26df9a86ed..023de43475 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -12,7 +12,6 @@ Syntax * cutoff = global cutoff pair (distance in metal units) - Examples """""""" @@ -75,14 +74,11 @@ the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. None of those coefficients is optional. If not specified, the *spin/dmi* pair style cannot be used. - ---------- - 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. @@ -95,7 +91,6 @@ Related commands **Default:** none - ---------- .. _Rohart: @@ -105,6 +100,5 @@ Related commands **(Rohart)** Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013). - **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index bd3a811f7f..cd3d9a202e 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -6,18 +6,15 @@ pair_style spin/exchange command Syntax """""" - .. code-block:: LAMMPS pair_style spin/exchange cutoff * cutoff = global cutoff pair (distance in metal units) - Examples """""""" - .. code-block:: LAMMPS pair_style spin/exchange 4.0 @@ -89,14 +86,11 @@ of the function :math:`J(r_{ij})` defined above. None of those coefficients is optional. If not specified, the *spin/exchange* pair style cannot be used. - ---------- - 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. @@ -111,13 +105,9 @@ Related commands none - ---------- - .. _Tranchida3: - - **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 526806959f..7caa98d96d 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -6,18 +6,15 @@ pair_style spin/magelec command Syntax """""" - .. code-block:: LAMMPS pair_style spin/magelec cutoff * cutoff = global cutoff pair (distance in metal units) - Examples """""""" - .. code-block:: LAMMPS pair_style spin/magelec 4.5 @@ -53,18 +50,14 @@ electric polarization vector. The norm and direction of E are giving the intensity and the direction of a screened dielectric atomic polarization (in eV). - More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. - ---------- - 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. @@ -77,19 +70,13 @@ Related commands **Default:** none - ---------- - .. _Katsura1: - - **(Katsura)** H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) .. _Tranchida4: - - **(Tranchida)** Tranchida, Plimpton, Thibaudeau, and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index 872b40d522..49adce9ed5 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -6,18 +6,15 @@ pair_style spin/neel command Syntax """""" - .. code-block:: LAMMPS pair_style spin/neel cutoff * cutoff = global cutoff pair (distance in metal units) - Examples """""""" - .. code-block:: LAMMPS pair_style spin/neel 4.0 @@ -76,14 +73,11 @@ calculations only). More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. - ---------- - 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. @@ -98,13 +92,9 @@ Related commands none - ---------- - .. _Tranchida6: - - **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 8762f3e4a9..317e417bfc 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -21,12 +21,9 @@ Syntax *bptype* value = atom type for bond particles *exclude* value = *yes* or *no* - - Examples """""""" - .. code-block:: LAMMPS pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes @@ -62,7 +59,6 @@ bond-pairwise potential, such that the force on bond *i* due to bond F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c - where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector between the two bonds. Note that *btype* can be specified as an asterisk "\*", which case the interaction is applied to all bond types. @@ -77,7 +73,6 @@ lever rule, F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\ F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L) - where *L* is the normalized distance from the atom to the point of closest approach of bond *i* and *j*\ . The *mid* option takes *L* as 0.5 for each interaction as described in :ref:`(Sirk) `. @@ -124,10 +119,8 @@ by particle number, as if the command :doc:`thermo_modify norm no ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. - ---------- - Restrictions """""""""""" - This pair style is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. @@ -181,13 +171,9 @@ Default The default keyword value is exclude = yes. - ---------- - .. _Sirk2: - - **(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012. diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index f2c1ed7c97..5533e6440b 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -6,7 +6,6 @@ pair_style command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style lj/cut 2.5 @@ -79,10 +77,8 @@ 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. - ---------- - 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. @@ -327,14 +323,11 @@ accelerated styles exist. * :doc:`yukawa/colloid ` - screened Yukawa potential for finite-size particles * :doc:`zbl ` - Ziegler-Biersack-Littmark potential - ---------- - Restrictions """""""""""" - This command must be used before any coefficients are set by the :doc:`pair_coeff `, :doc:`read_data `, or :doc:`read_restart ` commands. @@ -353,7 +346,6 @@ Related commands Default """"""" - .. code-block:: LAMMPS pair_style none diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 52f68da9f7..3cf425536a 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -18,7 +18,6 @@ pair_style sw/omp command Syntax """""" - .. code-block:: LAMMPS pair_style sw @@ -51,7 +50,6 @@ potential for the energy E of a system of atoms as \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right) - 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`. @@ -165,10 +163,8 @@ used for anything and can be set to 0.0 if desired. This is also true for the parameters in :math:`\phi_3` that are taken from the ij and ik pairs (:math:`\sigma`, *a*\ , :math:`\gamma`) - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -192,10 +188,8 @@ These parameters are common for modeling silicon and water. See the :doc:`Speed packages ` doc page for more 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, where types I and J correspond to @@ -213,14 +207,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -240,12 +231,8 @@ Related commands **Default:** none - ---------- - .. _Stillinger2: - - **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 9bfd22f8dc..6062329fbe 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -15,7 +15,6 @@ pair_style table/omp command Syntax """""" - .. code-block:: LAMMPS pair_style table style N keyword ... @@ -103,10 +102,8 @@ short-range pair styles, such as :doc:`pair_style lj/cut/coul/long `. the tabulated values for each pair of atom types has the correct functional form to be compatible with the matching long-range solver. - ---------- - Here are some guidelines for using the pair\_style table command to best effect: @@ -125,15 +122,11 @@ best effect: * Use as large an inner cutoff as possible. This avoids fitting splines to very steep parts of the potential. - - ---------- - The format of a tabulated file is a series of one or more sections, defined as follows (without the parenthesized comments): - .. parsed-literal:: # Morse potential for Fe (one or more comment or blank lines) @@ -224,10 +217,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -246,10 +237,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -269,10 +258,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none @@ -284,12 +271,8 @@ Related commands **Default:** none - ---------- - .. _Wolff2: - - **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index c98e3372e0..79e8a8475f 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -9,7 +9,6 @@ pair_style table/rx/kk command Syntax """""" - .. code-block:: LAMMPS pair_style table style N ... @@ -98,10 +97,8 @@ associated with the interacting coarse-grained particles (see the stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). - ---------- - Here are some guidelines for using the pair\_style table/rx command to best effect: @@ -119,15 +116,11 @@ best effect: * Use as large an inner cutoff as possible. This avoids fitting splines to very steep parts of the potential. - - ---------- - The format of a tabulated file is a series of one or more sections, defined as follows (without the parenthesized comments): - .. parsed-literal:: # Morse potential for Fe (one or more comment or blank lines) @@ -208,10 +201,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support mixing. Thus, coefficients for all @@ -231,10 +222,8 @@ This pair 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. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -253,14 +242,11 @@ 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. - ---------- - Restrictions """""""""""" - This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -271,12 +257,8 @@ Related commands **Default:** fractional weighting - ---------- - .. _Wolff: - - **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 183c149a11..a289c01ccf 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -33,7 +33,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style tersoff @@ -67,7 +66,6 @@ The *tersoff* style computes a 3-body Tersoff potential g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - \frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right) - where :math:`f_R` is a two-body term and :math:`f_A` 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. @@ -95,7 +93,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * SiC.tersoff Si Si Si C @@ -201,7 +198,6 @@ 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 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 @@ -221,10 +217,8 @@ Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou for helping clarify how Tersoff parameters for alloys have been defined in various papers. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -243,10 +237,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -264,14 +256,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -291,25 +280,17 @@ Related commands **Default:** none - ---------- - .. _Tersoff\_11: - - **(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\_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 bcbeb6f138..e3f26a31b8 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -21,7 +21,6 @@ pair_style tersoff/mod/c/omp command Syntax """""" - .. code-block:: LAMMPS pair_style tersoff/mod @@ -67,7 +66,6 @@ E of a system of atoms as g_o(\theta) & = \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\ g_a(\theta) & = 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\ - where :math:`f_R` is a two-body term and :math:`f_A` 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. @@ -78,7 +76,6 @@ formulation of the V\_ij term, where it contains an additional c0 term. V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right] - The modified cutoff function :math:`f_C` proposed by :ref:`(Murty) ` and having a continuous second-order differential is employed. The angular-dependent term :math:`g(\theta)` was modified to increase the @@ -103,7 +100,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * Si.tersoff_mod Si Si Si @@ -163,10 +159,8 @@ the center atom in a three-body interaction and it is bonded to the 2nd atom and the bond is influenced by the 3rd atom. Thus an entry for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -185,10 +179,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : This pair style does not support the :doc:`pair_modify ` @@ -202,14 +194,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -229,37 +218,25 @@ Related commands **Default:** none - ---------- - .. _Kumagai: - - **(Kumagai)** T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007). .. _Tersoff\_12: - - **(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). .. _Tersoff\_22: - - **(Tersoff\_2)** J. Tersoff, Phys Rev B, 38, 9902 (1988). .. _Murty: - - **(Murty)** M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995). .. _Schelling: - - **(Schelling)** Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008). diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index be7cfcc331..854f2630a4 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -15,7 +15,6 @@ pair_style tersoff/zbl/omp command Syntax """""" - .. code-block:: LAMMPS pair_style tersoff/zbl @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style tersoff/zbl @@ -65,7 +63,6 @@ system of atoms as g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - \frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right) - The :math:`f_F` term is a fermi-like function used to smoothly connect the ZBL repulsive potential with the Tersoff potential. There are 2 parameters used to adjust it: :math:`A_F` and :math:`r_C`. :math:`A_F` @@ -105,7 +102,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * SiC.tersoff Si Si Si C @@ -216,7 +212,6 @@ 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 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 @@ -237,10 +232,8 @@ for helping clarify how Tersoff parameters for alloys have been defined in various papers. Also thanks to Ram Devanathan for providing the base ZBL implementation. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -259,10 +252,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -280,14 +271,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -308,32 +296,22 @@ Related commands **Default:** none - ---------- - .. _zbl-Tersoff\_1: - - **(Tersoff\_1)** J. Tersoff, Phys Rev B, 37, 6991 (1988). .. _zbl-ZBL: - - **(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press. .. _zbl-Albe: - - **(Albe)** J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). .. _zbl-Tersoff\_2: - - **(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 b3d33f6036..4e0ce8844a 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -12,7 +12,6 @@ pair_style lj/cut/thole/long/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -20,7 +19,6 @@ Syntax * style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp* * args = list of arguments for a particular style - .. parsed-literal:: *thole* args = damp cutoff @@ -34,7 +32,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style hybrid/overlay ... thole 2.6 12.0 @@ -70,7 +67,6 @@ Drude particles. The *thole* pair styles compute the Coulomb interaction damped at short distances by a function - .. math:: T_{ij}(r_{ij}) = 1 - \left( 1 + @@ -87,7 +83,6 @@ the atom types. The mixing rule for Thole damping parameters is the arithmetic average, and for polarizabilities the geometric average between the atom-specific values. - .. math:: s_{ij} = \frac{ a_{ij} }{ @@ -135,10 +130,8 @@ command. The last two coefficients are optional and default to the global values from the *pair\_style* command line. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -165,7 +158,6 @@ for all I,J pairs must be specified explicitly. The *lj/cut/thole/long* pair style does support mixing. Mixed coefficients are defined using - .. math:: \alpha_{ij} = & \sqrt{\alpha_i\alpha_j} \\ @@ -175,7 +167,6 @@ are defined using 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. @@ -195,18 +186,12 @@ Related commands **Default:** none - ---------- - .. _Noskov1: - - **(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). .. _Thole1: - - **(Thole)** Chem Phys, 59, 341 (1981). diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 9d021f79a4..1546d954d5 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -79,10 +79,8 @@ commands: The last coefficient is optional. If not specified, the global cutoff is used. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the epsilon and sigma coefficients @@ -99,14 +97,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style is part of the ASPHERE 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/pair_ufm.rst b/doc/src/pair_ufm.rst index bf567bb821..a26dd582be 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -15,7 +15,6 @@ pair_style ufm/opt command Syntax """""" - .. code-block:: LAMMPS pair_style ufm cutoff @@ -46,7 +45,6 @@ Style *ufm* computes pairwise interactions using the Uhlenbeck-Ford model (UFM) E & = -\varepsilon\, \ln{\left[1-\exp{\left(-r^{2}/\sigma^{2}\right)}\right]} \qquad r < r_c \\ \varepsilon & = p\,k_B\,T - where :math:`r_c` is the cutoff, :math:`\sigma` is a distance-scale and :math:`\epsilon` is an energy-scale, i.e., a product of Boltzmann constant :math:`k_B`, temperature *T* and the Uhlenbeck-Ford p-parameter which @@ -73,7 +71,6 @@ 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: - .. code-block:: LAMMPS variable prefactor equal ramp(10,100) @@ -89,10 +86,8 @@ of a run: use this command and perform nonequilibrium thermodynamic integration in LAMMPS is given in the paper by :ref:`(Freitas) `. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -111,10 +106,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the A coefficient and cutoff @@ -137,10 +130,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none @@ -154,20 +145,14 @@ Related commands .. _PL1: - - **(Paula Leite2017)** Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017). .. _PL2: - - **(Paula Leite2016)** Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016). .. _Freitas2: - - **(Freitas)** Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016). diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index f3e9ce1db0..ca4751d07f 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -21,7 +21,6 @@ pair_style vashishta/table/omp command Syntax """""" - .. code-block:: LAMMPS pair_style style args @@ -29,7 +28,6 @@ Syntax * style = *vashishta* or *vashishta/table* or *vashishta/omp* or *vashishta/table/omp* * args = list of arguments for a particular style - .. parsed-literal:: *vashishta* or *vashishta/omp* args = none @@ -40,7 +38,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style vashishta @@ -70,7 +67,6 @@ The potential for the energy U of a system of atoms is U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = B_{ijk} \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\ & \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right) \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik} - where we follow the notation used in :ref:`Branicio2009 `. :math:`U^2` is a two-body term and U3 is a three-body term. The summation over two-body terms is over all neighbors J within @@ -108,7 +104,6 @@ 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: - .. code-block:: LAMMPS pair_coeff * * SiC.vashishta Si Si Si C @@ -196,10 +191,8 @@ an Si atom and a second C atom will take three-body parameters from the CSiC entry, but two-body parameters from the CCC and CSiSi entries. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -218,10 +211,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, where types I and J correspond to @@ -239,14 +230,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - These pair style are part of the MANYBODY package. They is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -266,27 +254,19 @@ Related commands **Default:** none - ---------- - .. _Vashishta1990: - - **(Vashishta1990)** P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990). .. _Vashishta2007: - - **(Vashishta2007)** P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007). .. _Branicio2009: - - **(Branicio2009)** Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 69639e3f99..e11b631853 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -6,7 +6,6 @@ pair_write command Syntax """""" - .. code-block:: LAMMPS pair_write itype jtype N style inner outer file keyword Qi Qj @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_write 1 3 500 r 1.0 10.0 table.txt LJ @@ -67,7 +65,6 @@ and a force (in force units). Restrictions """""""""""" - All force field coefficients for pair and other kinds of interactions must be set before this command can be invoked. diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 15b9f0fc0b..4170b32275 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -15,7 +15,6 @@ pair_style yukawa/kk command Syntax """""" - .. code-block:: LAMMPS pair_style yukawa kappa cutoff @@ -26,7 +25,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style yukawa 2.0 2.5 @@ -42,7 +40,6 @@ Style *yukawa* computes pairwise interactions with the formula E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c - :math:`r_c` is the cutoff. The following coefficients must be defined for each pair of atoms @@ -57,10 +54,8 @@ commands, or by mixing as described below: The last coefficient is optional. If not specified, the global yukawa cutoff is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -79,10 +74,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the A coefficient and cutoff @@ -107,10 +100,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index c8659cb157..83e834d7f4 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -12,7 +12,6 @@ pair_style yukawa/colloid/omp command Syntax """""" - .. code-block:: LAMMPS pair_style yukawa/colloid kappa cutoff @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style yukawa/colloid 2.0 2.5 @@ -39,7 +37,6 @@ Style *yukawa/colloid* computes pairwise interactions with the formula E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c - where :math:`r_i` and :math:`r_j` are the radii of the two particles and :math:`r_c` is the cutoff. @@ -73,7 +70,6 @@ that the A for this potential style has different units than the A used in :doc:`pair_style yukawa `. For low surface potentials, i.e. less than about 25 mV, A can be written as: - .. math:: A = 2 \pi R\varepsilon\varepsilon_0 \kappa \psi^2 @@ -89,10 +85,8 @@ where The last coefficient is optional. If not specified, the global yukawa/colloid cutoff is used. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -111,10 +105,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the A coefficient and cutoff @@ -139,14 +131,11 @@ This pair 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. - ---------- - Restrictions """""""""""" - This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -166,13 +155,9 @@ Related commands **Default:** none - ---------- - .. _Safran: - - **(Safran)** Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003). diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index f2f310dae9..59b9b52702 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -15,7 +15,6 @@ pair_style zbl/omp command Syntax """""" - .. code-block:: LAMMPS pair_style zbl inner outer @@ -26,7 +25,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style zbl 3.0 4.0 @@ -85,10 +83,8 @@ be included in a pair\_coeff command. always be given as multiples of a proton's charge, e.g. 29.0 for copper. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -107,10 +103,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs *i,j* and :math:`i \neq i`, the :math:`Z_i` and @@ -144,10 +138,8 @@ This pair 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. - ---------- - Restrictions """""""""""" none @@ -159,13 +151,9 @@ Related commands **Default:** none - ---------- - .. _Ziegler: - - **(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 0a9db6472a..86b3fa64fb 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -6,7 +6,6 @@ pair_style zero command Syntax """""" - .. code-block:: LAMMPS pair_style zero cutoff [nocoeff] @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS pair_style zero 10.0 @@ -60,10 +58,8 @@ 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. - ---------- - **Mixing, shift, table, tail correction, restart, rRESPA info**\ : The cutoff distance for this pair style can be mixed. The default mix @@ -78,10 +74,8 @@ to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command. - ---------- - Restrictions """""""""""" none diff --git a/doc/src/pairs.rst b/doc/src/pairs.rst index 4fdf2b2c69..b764c74cc7 100644 --- a/doc/src/pairs.rst +++ b/doc/src/pairs.rst @@ -1,7 +1,6 @@ Pair Styles ########### - .. toctree:: :maxdepth: 1 :glob: diff --git a/doc/src/partition.rst b/doc/src/partition.rst index 7ad5a4b3ed..7edddb6f92 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -6,7 +6,6 @@ partition command Syntax """""" - .. parsed-literal:: partition style N command ... @@ -18,7 +17,6 @@ Syntax Examples """""""" - .. parsed-literal:: partition yes 1 processors 4 10 6 diff --git a/doc/src/prd.rst b/doc/src/prd.rst index d6cda1ac28..d3a9dcf339 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -6,7 +6,6 @@ prd command Syntax """""" - .. parsed-literal:: prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ... @@ -37,12 +36,9 @@ Syntax *steps* = simulation runs for N timesteps on each replica (default) *clock* = simulation runs for N timesteps across all replicas - - Examples """""""" - .. parsed-literal:: prd 5000 100 10 10 100 1 54982 @@ -100,7 +96,6 @@ A PRD run has several stages, which are repeated each time an "event" occurs in one of the replicas, as explained below. The logic for a PRD run is as follows: - .. parsed-literal:: while (time remains): @@ -186,10 +181,8 @@ elapsed. This aggregate time is the "clock" time defined below, which typically advances nearly M times faster than the timestepping on a single replica, where M is the number of replicas. - ---------- - Four kinds of output can be generated during a PRD run: event statistics, thermodynamic output by each replica, dump files, and restart files. @@ -246,10 +239,8 @@ 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. - ---------- - When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For the PRD command, these contain the thermodynamic output for each @@ -262,10 +253,8 @@ After the PRD command completes, timing statistics for the PRD run are printed in each replica's log file, giving a breakdown of how much CPU time was spent in each stage (dephasing, dynamics, quenching, etc). - ---------- - Any :doc:`dump files ` defined in the input script, will be written to during a PRD run at timesteps corresponding to both uncorrelated and correlated events. This means the requested dump @@ -280,10 +269,8 @@ snapshot corresponding to the initial minimum state used for event detection is written to the dump file at the beginning of each PRD run. - ---------- - If the :doc:`restart ` command is used, a single restart file for all the partitions is generated, which allows a PRD run to be continued by a new input script in the usual manner. @@ -309,14 +296,11 @@ 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. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. @@ -348,19 +332,13 @@ Default The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = geom gaussian, and time = steps. - ---------- - .. _Voter1998: - - **(Voter1998)** Voter, Phys Rev B, 57, 13985 (1998). .. _Voter2002prd: - - **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). diff --git a/doc/src/print.rst b/doc/src/print.rst index cbb042b7d9..b1a4a681d0 100644 --- a/doc/src/print.rst +++ b/doc/src/print.rst @@ -6,7 +6,6 @@ print command Syntax """""" - .. parsed-literal:: print string keyword value @@ -22,12 +21,9 @@ Syntax *screen* value = *yes* or *no* *universe* value = *yes* or *no* - - Examples """""""" - .. parsed-literal:: print "Done with equilibration" file info.dat diff --git a/doc/src/processors.rst b/doc/src/processors.rst index e9c3175df6..7c5db5563b 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -6,7 +6,6 @@ processors command Syntax """""" - .. parsed-literal:: processors Px Py Pz keyword args ... @@ -39,12 +38,9 @@ Syntax *file* arg = outfile outfile = name of file to write 3d grid of processors to - - Examples """""""" - .. parsed-literal:: processors \* \* 5 @@ -97,7 +93,6 @@ Px,Py,Pz values for different partitions. You can use the :doc:`partition ` command to specify different processor grids for different partitions, e.g. - .. parsed-literal:: partition yes 1 processors 4 4 4 @@ -127,10 +122,8 @@ different sizes and shapes which no longer have a logical 3d connectivity. If that occurs, all the information specified by the processors command is ignored. - ---------- - The *grid* keyword affects the factorization of P into Px,Py,Pz and it can also affect how the P processor IDs are mapped to the 3d grid of processors. @@ -194,7 +187,6 @@ blank or comment lines (starting with a "#" character) can be present. The first non-blank, non-comment line should have 3 values: - .. parsed-literal:: Px Py Py @@ -205,7 +197,6 @@ and the Px, Py, Pz settings of the processors command. This line should be immediately followed by P = Px\*Py\*Pz lines of the form: - .. parsed-literal:: ID I J K @@ -215,10 +206,8 @@ processors location in the 3d grid. I must be a number from 1 to Px (inclusive) and similarly for J and K. The P lines can be listed in any order, but no processor ID should appear more than once. - ---------- - The *map* keyword affects how the P processor IDs (from 0 to P-1) are mapped to the 3d grid of processors. It is only used by the *onelevel* and *twolevel* grid settings. @@ -241,7 +230,6 @@ ID in the K direction varies slowest. For example, if you select style *xyz* and you have a 2x2x2 grid of 8 processors, the assignments of the 8 octants of the simulation domain will be: - .. parsed-literal:: proc 0 = lo x, lo y, lo z octant @@ -267,10 +255,8 @@ used to first map the nodes to the 3d grid, then again to the cores within each node. For the latter step, the *cart* and *cart/reorder* styles are not supported, so an *xyz* style is used in their place. - ---------- - The *part* keyword affects the factorization of P into Px,Py,Pz. It can be useful when running in multi-partition mode, e.g. with the @@ -310,10 +296,8 @@ processors, it could create a 4x2x10 grid, but it will not create a this, but your simulation will likely hang in its setup phase if this error has been made. - ---------- - The *file* keyword writes the mapping of the factorization of P processors and their mapping to the 3d grid to the specified file *outfile*\ . This is useful to check that you assigned physical @@ -349,14 +333,11 @@ 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*\ . - ---------- - Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. It can be used before a restart file is read to change the 3d diff --git a/doc/src/python.rst b/doc/src/python.rst index 64d0c8e459..6c54fb8872 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -6,7 +6,6 @@ python command Syntax """""" - .. parsed-literal:: python func keyword args ... @@ -44,12 +43,9 @@ Syntax inline = one or more lines of Python code which will be executed immediately must be a single argument, typically enclosed between triple quotes - - Examples """""""" - .. code-block:: LAMMPS python pForce input 2 v_x 20.0 return v_f format fff file force.py @@ -110,10 +106,8 @@ A broader overview of how Python can be used with LAMMPS is given on the :doc:`Python ` doc page. There is an examples/python directory which illustrates use of the python command. - ---------- - The *func* setting specifies the name of the Python function. The code for the function is defined using the *file* or *here* keywords as explained below. In case of the *source* keyword, the name of @@ -162,7 +156,6 @@ of a python-style variable associates a Python function name with the variable. This must match the *func* setting for this command. For example these two commands would be self-consistent: - .. code-block:: LAMMPS variable foo python myMultiply @@ -195,10 +188,8 @@ include the string terminator). If the Python function generates a string longer than the default 63 or the specified *Nlen*\ , it will be truncated. - ---------- - Either the *file*\ , *here*\ , or *exists* keyword must be used, but only one of them. These keywords specify what Python code to load into the Python interpreter. The *file* keyword gives the name of a file, @@ -226,10 +217,8 @@ later invoked, the function code must match the *input* and *return* and *format* keywords specified by the python command. Otherwise Python will generate an error. - ---------- - This section describes how Python code can be written to work with LAMMPS. @@ -261,7 +250,6 @@ python-style variable associated with the function. For example, consider this function loaded with two global variables defined outside the function: - .. code-block:: python nsteplast = -1 @@ -318,16 +306,13 @@ 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. - ---------- - Your Python function can "call back" to LAMMPS through its library interface, if you use the SELF input to pass Python a pointer to LAMMPS. The mechanism for doing this in your Python function is as follows: - .. code-block:: python def foo(lmpptr,...): @@ -347,7 +332,6 @@ string argument which is a LAMMPS input script command for LAMMPS to execute, the same as if it appeared in your input script. In this case, LAMMPS should output - .. parsed-literal:: Hello from inside Python @@ -363,7 +347,6 @@ library interface. A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py: - .. code-block:: python def loop(N,cut0,thresh,lmpptr): @@ -387,7 +370,6 @@ which loads and runs the following function from examples/python/funcs.py: with these input script commands: - .. parsed-literal:: python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py @@ -440,10 +422,8 @@ being attempted. The same applies to Python functions called during a simulation run at each time step using :doc:`fix python/invoke `. - ---------- - If you run Python code directly on your workstation, either interactively or by using Python to launch a Python script stored in a file, and your code has an error, you will typically see informative @@ -456,7 +436,6 @@ logic errors, you may get an error from Python pointing to the offending line, or you may get one of these generic errors from LAMMPS: - .. parsed-literal:: Could not process Python file @@ -465,7 +444,6 @@ LAMMPS: When the Python function is invoked, if it does not return properly, you will typically get this generic error from LAMMPS: - .. parsed-literal:: Python function evaluation failed @@ -485,7 +463,6 @@ Third, use Python exception handling. For example, say this statement in your Python function is failing, because you have not initialized the variable foo: - .. code-block:: python foo += 1 @@ -493,7 +470,6 @@ variable foo: If you put one (or more) statements inside a "try" statement, like this: - .. code-block:: python import exceptions @@ -505,7 +481,6 @@ like this: then you will get this message printed to the screen: - .. parsed-literal:: FOO error: local variable 'foo' referenced before assignment @@ -514,14 +489,11 @@ If there is no error in the try statements, then nothing is printed. Either way the function continues on (unless you put a return or sys.exit() in the except clause). - ---------- - Restrictions """""""""""" - This command is part of the PYTHON 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/quit.rst b/doc/src/quit.rst index 9741a7477d..08b96e28ce 100644 --- a/doc/src/quit.rst +++ b/doc/src/quit.rst @@ -6,7 +6,6 @@ quit command Syntax """""" - .. parsed-literal:: quit status @@ -16,7 +15,6 @@ status = numerical exit status (optional) Examples """""""" - .. parsed-literal:: quit diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index abdb838c57..02e47e9c0e 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -6,7 +6,6 @@ read_data command Syntax """""" - .. code-block:: LAMMPS read_data file keyword args ... @@ -48,12 +47,9 @@ Syntax header-string = header lines containing this string will be passed to fix section-string = section names with this string will be passed to fix - - Examples """""""" - .. code-block:: LAMMPS read_data data.lj @@ -95,10 +91,8 @@ styles defined, or to read a data file for a different force field. 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 @@ -219,10 +213,8 @@ 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. - ---------- - **Format of a data file** The structure of the data file is important, though many settings and @@ -266,10 +258,8 @@ be capitalized as shown and can't have extra white-space between their words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or the 2 words in "Bond Coeffs", is not valid. - ---------- - **Format of the header of a data file** These are the recognized header keywords. Header lines can come in @@ -440,10 +430,8 @@ are point particles. See the discussion of ellipsoidflag and the keywords, though it is not necessary. If specified, they must match the maximum values defined in any of the template molecules. - ---------- - **Format of the body of a data file** These are the section keywords for the body of the file. @@ -460,7 +448,6 @@ currently defined style: For example, these lines: - .. parsed-literal:: Atoms # sphere @@ -480,15 +467,12 @@ Any individual line in the various sections can have a trailing comment starting with "#" for annotation purposes. E.g. in the Atoms section: - .. parsed-literal:: 10 1 17 -1.0 10.0 5.0 6.0 # salt ion - ---------- - *Angle Coeffs* section: * one line per angle type @@ -505,18 +489,14 @@ Atoms section: 6 70 108.5 0 0 - - The number and meaning of the coefficients are specific to the defined angle style. See the :doc:`angle_style ` and :doc:`angle_coeff ` commands for details. Coefficients can also be set via the :doc:`angle_coeff ` command in the input script. - ---------- - *AngleAngle Coeffs* section: * one line per improper type @@ -527,12 +507,8 @@ input script. ID = improper type (1-N) coeffs = list of coeffs (see :doc:`improper_coeff `) - - - ---------- - *AngleAngleTorsion Coeffs* section: * one line per dihedral type @@ -543,12 +519,8 @@ input script. ID = dihedral type (1-N) coeffs = list of coeffs (see :doc:`dihedral_coeff `) - - - ---------- - *Angles* section: * one line per angle @@ -566,18 +538,14 @@ example: 2 2 17 29 430 - - The 3 atoms are ordered linearly within the angle. Thus the central atom (around which the angle is computed) is the atom2 in the list. E.g. H,O,H for a water molecule. The *Angles* section must appear after the *Atoms* section. All values in this section must be integers (1, not 1.0). - ---------- - *AngleTorsion Coeffs* section: * one line per dihedral type @@ -588,12 +556,8 @@ integers (1, not 1.0). ID = dihedral type (1-N) coeffs = list of coeffs (see :doc:`dihedral_coeff `) - - - ---------- - *Atoms* section: * one line per atom @@ -763,14 +727,12 @@ example, for the "charge" sub-style, a "q" value would appear. For the "full" sub-style, a "molecule-ID" and "q" would appear. These are listed in the same order they appear as listed above. Thus if - .. parsed-literal:: atom_style hybrid charge sphere were used in the input script, each atom line would have these fields: - .. parsed-literal:: atom-ID atom-type x y z q diameter density @@ -779,7 +741,6 @@ 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: - .. parsed-literal:: atom-ID atom-type x y z q mux muy myz molecule-ID q @@ -827,7 +788,6 @@ that use unwrapped coordinates internally are as follows: continued run (restarted from a data file) begins with image flags that are consistent with the previous run. - .. note:: If your system is an infinite periodic crystal with bonds then @@ -841,10 +801,8 @@ a *Velocities* section in the data file or by a :doc:`velocity ` or :doc:`set ` command in the input script. - ---------- - *Bodies* section: * one or more lines per body @@ -873,8 +831,6 @@ script. 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0 2.0 4.0 4.0 2.0 - - The *Bodies* section must appear if :doc:`atom_style body ` is used and any atoms listed in the *Atoms* section have a bodyflag = 1. The number of bodies should be specified in the header section via @@ -896,10 +852,8 @@ particular type, no lines appear for that type. The *Bodies* section must appear after the *Atoms* section. - ---------- - *Bond Coeffs* section: * one line per bond type @@ -916,18 +870,14 @@ The *Bodies* section must appear after the *Atoms* section. 4 250 1.49 - - The number and meaning of the coefficients are specific to the defined bond style. See the :doc:`bond_style ` and :doc:`bond_coeff ` commands for details. Coefficients can also be set via the :doc:`bond_coeff ` command in the input script. - ---------- - *BondAngle Coeffs* section: * one line per angle type @@ -938,12 +888,8 @@ script. ID = angle type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff `) - - - ---------- - *BondBond Coeffs* section: * one line per angle type @@ -954,12 +900,8 @@ script. ID = angle type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff `) - - - ---------- - *BondBond13 Coeffs* section: * one line per dihedral type @@ -970,12 +912,8 @@ script. ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) - - - ---------- - *Bonds* section: * one line per bond @@ -993,15 +931,11 @@ script. 12 3 17 29 - - The *Bonds* section must appear after the *Atoms* section. All values in this section must be integers (1, not 1.0). - ---------- - *Dihedral Coeffs* section: * one line per dihedral type @@ -1018,18 +952,14 @@ in this section must be integers (1, not 1.0). 3 0.6 1 0 1 - - The number and meaning of the coefficients are specific to the defined dihedral style. See the :doc:`dihedral_style ` and :doc:`dihedral_coeff ` commands for details. Coefficients can also be set via the :doc:`dihedral_coeff ` command in the input script. - ---------- - *Dihedrals* section: * one line per dihedral @@ -1047,16 +977,12 @@ Coefficients can also be set via the 12 4 17 29 30 21 - - The 4 atoms are ordered linearly within the dihedral. The *Dihedrals* section must appear after the *Atoms* section. All values in this section must be integers (1, not 1.0). - ---------- - *Ellipsoids* section: * one line per ellipsoid @@ -1074,8 +1000,6 @@ section must be integers (1, not 1.0). 12 1 2 1 1 0 0 0 - - The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid ` is used and any atoms are listed in the *Atoms* section with an ellipsoidflag = 1. The number of ellipsoids should be specified in the header section via the "ellipsoids" @@ -1099,10 +1023,8 @@ specified as a unit vector. The *Ellipsoids* section must appear after the *Atoms* section. - ---------- - *EndBondTorsion Coeffs* section: * one line per dihedral type @@ -1113,12 +1035,8 @@ The *Ellipsoids* section must appear after the *Atoms* section. ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) - - - ---------- - *Improper Coeffs* section: * one line per improper type @@ -1135,18 +1053,14 @@ The *Ellipsoids* section must appear after the *Atoms* section. 2 20 0.0548311 - - The number and meaning of the coefficients are specific to the defined improper style. See the :doc:`improper_style ` and :doc:`improper_coeff ` commands for details. Coefficients can also be set via the :doc:`improper_coeff ` command in the input script. - ---------- - *Impropers* section: * one line per improper @@ -1164,8 +1078,6 @@ Coefficients can also be set via the 12 3 17 29 13 100 - - The ordering of the 4 atoms determines the definition of the improper angle used in the formula for each :doc:`improper style `. See the doc pages for individual styles for details. @@ -1173,10 +1085,8 @@ for details. The *Impropers* section must appear after the *Atoms* section. All values in this section must be integers (1, not 1.0). - ---------- - *Lines* section: * one line per line segment @@ -1194,8 +1104,6 @@ values in this section must be integers (1, not 1.0). 12 1.0 0.0 2.0 0.0 - - The *Lines* section must appear if :doc:`atom_style line ` is used and any atoms are listed in the *Atoms* section with a lineflag = 1. The number of lines should be specified in the header @@ -1210,10 +1118,8 @@ for defining some interactions. The *Lines* section must appear after the *Atoms* section. - ---------- - *Masses* section: * one line per atom type @@ -1230,17 +1136,13 @@ The *Lines* section must appear after the *Atoms* section. 3 1.01 - - This defines the mass of each atom type. This can also be set via the :doc:`mass ` command in the input script. This section cannot be used for atom styles that define a mass for individual atoms - e.g. :doc:`atom_style sphere `. - ---------- - *MiddleBondTorsion Coeffs* section: * one line per dihedral type @@ -1251,12 +1153,8 @@ e.g. :doc:`atom_style sphere `. ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) - - - ---------- - *Pair Coeffs* section: * one line per atom type @@ -1273,8 +1171,6 @@ e.g. :doc:`atom_style sphere `. 3 0.022 2.35197 0.022 2.35197 - - The number and meaning of the coefficients are specific to the defined pair style. See the :doc:`pair_style ` and :doc:`pair_coeff ` commands for details. Since pair @@ -1284,10 +1180,8 @@ individual pair\_style doc pages and the :doc:`pair_modify mix ` co be set via the :doc:`pair_coeff ` command in the input script. - ---------- - *PairIJ Coeffs* section: * one line per pair of atom types for all I,J with I <= J @@ -1306,8 +1200,6 @@ script. 3 3 0.022 2.35197 0.022 2.35197 3 5 0.022 2.35197 0.022 2.35197 - - This section must have N\*(N+1)/2 lines where N = # of atom types. The number and meaning of the coefficients are specific to the defined pair style. See the :doc:`pair_style ` and @@ -1318,10 +1210,8 @@ individual pair\_style doc pages and the :doc:`pair_modify mix ` co be set via the :doc:`pair_coeff ` command in the input script. - ---------- - *Triangles* section: * one line per triangle @@ -1340,8 +1230,6 @@ script. 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 - - The *Triangles* section must appear if :doc:`atom_style tri ` is used and any atoms are listed in the *Atoms* section with a triangleflag = 1. The number of lines should be specified in the header section via the "triangles" keyword. @@ -1354,10 +1242,8 @@ orientation may be important for defining some interactions. The *Triangles* section must appear after the *Atoms* section. - ---------- - *Velocities* section: * one line per atom @@ -1400,7 +1286,6 @@ example, for the "sphere" sub-style, "wx", "wy", "wz" values would appear. These are listed in the same order they appear as listed above. Thus if - .. code-block:: LAMMPS atom_style hybrid electron sphere @@ -1408,7 +1293,6 @@ above. Thus if were used in the input script, each velocity line would have these fields: - .. parsed-literal:: atom-ID vx vy vz ervel wx wy wz @@ -1416,14 +1300,11 @@ fields: Translational velocities can also be set by the :doc:`velocity ` command in the input script. - ---------- - Restrictions """""""""""" - To read gzipped data files, you must compile LAMMPS with the -DLAMMPS\_GZIP option. See the :doc:`Build settings ` doc page for details. diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 8e35030666..3023f719e3 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -6,7 +6,6 @@ read_dump command Syntax """""" - .. code-block:: LAMMPS read_dump file Nstep field1 field2 ... keyword values ... @@ -50,12 +49,9 @@ Syntax style = *dcd* or *xyz* or others supported by molfile plugins path = optional path for location of molfile plugins - - Examples """""""" - .. code-block:: LAMMPS read_dump dump.file 5000 x y z @@ -99,10 +95,8 @@ 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, after the dump snapshot is read. - ---------- - If the dump filename specified as *file* ends with ".gz", the dump file is read in gzipped format. You cannot (yet) read a dump file that was written in binary format with a ".bin" suffix. @@ -154,10 +148,8 @@ to wait on the reader side for the arrival of the requested step. Support for other dump format readers may be added in the future. - ---------- - Global information is first read from the dump file, namely timestep and box information. @@ -174,7 +166,6 @@ variable *ntimestep*: uint64_t ntimestep 5*scalar (0) 0 50 100 150 200 - Note that the *xyz* and *molfile* formats do not store the timestep. For these formats, timesteps are numbered logically, in a sequential manner, starting @@ -201,10 +192,8 @@ orthogonal/triclinic box shape is available. The USER-MOLFILE package makes a best effort to guess based on heuristics, but this may not 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 @@ -215,7 +204,6 @@ text label listed in the file. A matching label for each field must appear, e.g. the label "vy" for the field *vy*\ . For the *x*\ , *y*\ , *z* fields any of the following labels are considered a match: - .. parsed-literal:: x, xs, xu, xsu for field *x* @@ -271,11 +259,8 @@ The list of fields stored in an adios .bp file is recorded in the attributes string columns attr = {"id", "type", "x", "y", "z", "vx", "vy", "vz"} string columnstr attr = "id type x y z vx vy vz " - - ---------- - Information from the dump file snapshot is used to overwrite or replace properties of the current system. There are various options for how this is done, determined by the specified fields and optional @@ -330,10 +315,8 @@ Any other attributes (e.g. charge or particle diameter for spherical particles) will be set to default values, the same as if the :doc:`create_atoms ` command were used. - ---------- - Atom coordinates read from the dump file are first converted into unscaled coordinates, relative to the box dimensions of the snapshot. These coordinates are then be assigned to an existing or new atom in @@ -382,14 +365,11 @@ coordinates are scaled and the simulation box is triclinic, then all 3 of the *x*\ , *y*\ , *z* fields must be specified, since they are all needed to generate absolute, unscaled coordinates. - ---------- - Restrictions """""""""""" - To read gzipped dump files, you must compile LAMMPS with the -DLAMMPS\_GZIP option. See the :doc:`Build settings ` doc page for details. diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index e4c7a7b7cf..58f6c113fc 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -6,7 +6,6 @@ read_restart command Syntax """""" - .. code-block:: LAMMPS read_restart file flag @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS read_restart save.10000 @@ -124,7 +122,6 @@ MPI-IO is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO package installed, e.g. - .. code-block:: bash make yes-mpiio # installs the MPIIO package @@ -135,10 +132,8 @@ does not have to end in ".mpiio", just contain those characters. Unlike MPI-IO dump files, a particular restart file must be both written and read using MPI-IO. - ---------- - Here is the list of information included in a restart file, which means these quantities do not need to be re-specified in the input script that reads the restart file, though you can redefine many of @@ -263,14 +258,11 @@ Bonds that have been broken by the :doc:`fix bond/break ` comman system. No information about these bonds is written to the restart file. - ---------- - Restrictions """""""""""" - To write and read restart files in parallel with MPI-IO, the MPIIO package must be installed. diff --git a/doc/src/region.rst b/doc/src/region.rst index 2dcbd76628..d791ab8642 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -6,7 +6,6 @@ region command Syntax """""" - .. parsed-literal:: region ID style args keyword arg ... @@ -70,11 +69,9 @@ Syntax * accelerated styles (with same args) = *block/kk* - Examples """""""" - .. parsed-literal:: region 1 block -3.0 5.0 INF 10.0 INF INF @@ -218,10 +215,8 @@ consisting of the volume that is common to all the listed regions. from their list of sub-regions. Thus you cannot delete the sub-regions after defining a *union* or *intersection* region. - ---------- - The *side* keyword determines whether the region is considered to be inside or outside of the specified geometry. Using this keyword in conjunction with *union* and *intersect* regions, complex geometries @@ -266,10 +261,8 @@ define the lattice spacings which are used as follows: applied to the sphere center x,y,z. The spacing in dimension x is applied to the sphere radius. - ---------- - If the *move* or *rotate* keywords are used, the region is "dynamic", meaning its location or orientation changes with time. These keywords cannot be used with a *union* or *intersect* style region. Instead, @@ -296,7 +289,6 @@ For example, these commands would displace a region from its initial position, in the positive x direction, effectively at a constant velocity: - .. parsed-literal:: variable dx equal ramp(0,10) @@ -307,7 +299,6 @@ Note that the initial displacement is 0.0, though that is not required. Either of these variables would "wiggle" the region back and forth in the y direction: - .. parsed-literal:: variable dy equal swiggle(0,5,100) @@ -327,10 +318,8 @@ The *move* and *rotate* keywords can be used together. In this case, the displacement specified by the *move* keyword is applied to the *P* point of the *rotate* keyword. - ---------- - The *open* keyword can be used (multiple times) to indicate that one or more faces of the region are ignored for purposes of particle/wall interactions. This keyword is only relevant for regions used by the @@ -380,10 +369,8 @@ For all other styles, the *open* keyword is ignored. As indicated above, this includes the *intersect* and *union* regions, though their sub-regions can be defined with the *open* keyword. - ---------- - Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -405,14 +392,11 @@ 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. - ---------- - Restrictions """""""""""" - A prism cannot be of 0.0 thickness in any dimension; use a small z thickness for 2d simulations. For 2d simulations, the xz and yz parameters must be 0.0. diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst index 0ae37c1415..8aef4086aa 100644 --- a/doc/src/replicate.rst +++ b/doc/src/replicate.rst @@ -6,7 +6,6 @@ replicate command Syntax """""" - .. parsed-literal:: replicate nx ny nz *keyword* @@ -19,12 +18,9 @@ nx,ny,nz = replication factors in each dimension *bbox* = only check atoms in replicas that overlap with a processor's sub-domain - - Examples """""""" - .. parsed-literal:: replicate 2 3 2 @@ -66,7 +62,6 @@ replicated. Restrictions """""""""""" - A 2d simulation cannot be replicated in the z dimension. If a simulation is non-periodic in a dimension, care should be used diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 9637b30c95..0df10088fc 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -6,7 +6,6 @@ rerun command Syntax """""" - .. parsed-literal:: rerun file1 file2 ... keyword args ... @@ -31,12 +30,9 @@ Syntax Nstop = timestep to which pseudo run will end *dump* args = same as :doc:`read_dump ` command starting with its field arguments - - Examples """""""" - .. parsed-literal:: rerun dump.file dump x y z vx vy vz @@ -69,7 +65,6 @@ initial simulation produced the dump file: Doing this in the original script would result in different (bad) dynamics. - Conceptually, using the rerun command is like running an input script that has a loop in it (see the :doc:`next ` and :doc:`jump ` commands). Each iteration of the loop reads one snapshot from the @@ -101,10 +96,8 @@ same as for output from any LAMMPS simulation. See further info below as to what that means if the timesteps for snapshots read from dump files do not match the specified output frequency. - ---------- - If more than one dump file is specified, the dump files are read one after the other. It is assumed that snapshot timesteps will be in ascending order. If a snapshot is encountered that is not in @@ -162,10 +155,8 @@ options it allows for extracting information from the dump file snapshots, and for using that information to alter the LAMMPS simulation. - ---------- - In general, a LAMMPS input script that uses a rerun command can include and perform all the usual operations of an input script that uses the :doc:`run ` command. There are a few exceptions and @@ -209,14 +200,11 @@ but no output will be produced. If you want output for every dump snapshot, you can simply use N=1 for an output frequency, e.g. for thermodynamic output or new dump file output. - ---------- - Restrictions """""""""""" - To read gzipped dump files, you must compile LAMMPS with the -DLAMMPS\_GZIP option. See the :doc:`Build settings ` doc page for details. diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 29b8c1ca70..42b4047c79 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -6,7 +6,6 @@ reset_ids command Syntax """""" - .. code-block:: LAMMPS reset_ids @@ -14,7 +13,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS reset_ids diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst index 5dcaf9daf4..b985bd4154 100644 --- a/doc/src/reset_timestep.rst +++ b/doc/src/reset_timestep.rst @@ -6,7 +6,6 @@ reset_timestep command Syntax """""" - .. code-block:: LAMMPS reset_timestep N @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS reset_timestep 0 diff --git a/doc/src/restart.rst b/doc/src/restart.rst index 9000b7e9c6..e11fe00971 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -6,7 +6,6 @@ restart command Syntax """""" - .. parsed-literal:: restart 0 @@ -27,12 +26,9 @@ Syntax *nfile* arg = Nf Nf = write this many files, one from each of Nf processors - - Examples """""""" - .. parsed-literal:: restart 0 @@ -89,7 +85,6 @@ file via the MPI-IO library, which is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO package installed, e.g. - .. parsed-literal:: make yes-mpiio # installs the MPIIO package @@ -122,16 +117,13 @@ For example, the following commands will write restart files every step from 1100 to 1200, and could be useful for debugging a simulation where something goes wrong at step 1163: - .. parsed-literal:: variable s equal stride(1100,1200,1) restart v_s tmp.restart - ---------- - See the :doc:`read_restart ` command for information about what is stored in a restart file. @@ -152,10 +144,8 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` command for information about what is stored in a restart file. - ---------- - The optional *nfile* or *fileper* keywords can be used in conjunction with the "%" wildcard character in the specified restart file name(s). As explained above, the "%" character causes the restart file to be @@ -174,14 +164,11 @@ file for every Np processors. For example, if Np = 4, every 4th processor (0,4,8,12,etc) will collect information from itself and the next 3 processors and write it to a restart file. - ---------- - Restrictions """""""""""" - To write and read restart files in parallel with MPI-IO, the MPIIO package must be installed. @@ -193,7 +180,6 @@ Related commands Default """"""" - .. parsed-literal:: restart 0 diff --git a/doc/src/run.rst b/doc/src/run.rst index 46eca78d35..15c2b3c030 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -6,7 +6,6 @@ run command Syntax """""" - .. parsed-literal:: run N keyword values ... @@ -29,12 +28,9 @@ Syntax c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes c1 = NULL means no command will be invoked - - Examples """""""" - .. parsed-literal:: run 10000 @@ -74,7 +70,6 @@ keywords. For example, consider this fix followed by 10 run commands: - .. parsed-literal:: fix 1 all nvt 200.0 300.0 1.0 @@ -149,7 +144,6 @@ of M steps each. After each M-length run, the specified commands are invoked. If only a single command is specified as NULL, then no command is invoked. Thus these lines: - .. parsed-literal:: variable q equal x[100] @@ -157,7 +151,6 @@ command is invoked. Thus these lines: are the equivalent of: - .. parsed-literal:: variable q equal x[100] @@ -176,7 +169,6 @@ Note that by using the line continuation character "&", the run every command can be spread across many lines, though it is still a single command: - .. parsed-literal:: run 100000 every 1000 & @@ -195,7 +187,6 @@ skipped for intermediate runs. You might wish to specify a command that exits the run by jumping out of the loop, e.g. - .. parsed-literal:: variable t equal temp @@ -210,7 +201,6 @@ has additional options for how to exit the run. Restrictions """""""""""" - When not using the *upto* keyword, the number of specified timesteps N must fit in a signed 32-bit integer, so you are limited to slightly more than 2 billion steps (2\^31) in a single run. When using *upto*\ , diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index b0d3aae553..5d72f00eaf 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -6,7 +6,6 @@ run_style command Syntax """""" - .. code-block:: LAMMPS run_style style args @@ -52,8 +51,6 @@ Syntax *kspace* value = M M = which level (1-N) to compute kspace forces in - - Examples """""""" @@ -72,10 +69,8 @@ simulations performed by LAMMPS. The *verlet* style is a standard velocity-Verlet integrator. - ---------- - The *verlet/split* style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of processors. See the :doc:`-partition command-line switch ` @@ -110,7 +105,6 @@ match the integer multiple constraint. See the :doc:`processors ` command with its *part* keyword for a way to control this, e.g. - .. code-block:: LAMMPS processors * * * part 1 2 multiple @@ -119,7 +113,6 @@ You can also use the :doc:`partition ` command to explicitly specify the processor layout on each partition. E.g. for 2 partitions of 60 and 15 processors each: - .. code-block:: LAMMPS partition yes 1 processors 3 4 5 @@ -139,10 +132,8 @@ processors in the 2 partitions to the physical cores of a parallel machine. The :doc:`processors ` command has options to support this, and strategies are discussed in :doc:`Section 5 ` of the manual. - ---------- - The *respa* style implements the rRESPA multi-timescale integrator :ref:`(Tuckerman) ` with N hierarchical levels, where level 1 is the innermost loop (shortest timestep) and level N is the outermost @@ -233,7 +224,6 @@ cutoffs) works reasonably well. We thus recommend the following settings for use of the *respa* style without SHAKE in biomolecular simulations: - .. code-block:: LAMMPS timestep 4.0 @@ -255,7 +245,6 @@ the size of the time steps in the respa hierarchy. The following settings can be used for biomolecular simulations with SHAKE and rRESPA: - .. code-block:: LAMMPS fix 2 all shake 0.000001 500 0 m 1.0 a 1 @@ -271,7 +260,6 @@ advantageous if there is a clear separation of time scales - fast and slow modes in the simulation. For example, a system of slowly-moving charged polymer chains could be setup as follows: - .. code-block:: LAMMPS timestep 4.0 @@ -290,16 +278,13 @@ In real units, for a pure LJ fluid at liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings seem to work well: - .. code-block:: LAMMPS timestep 36.0 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 - ---------- - The *respa/omp* style is a variant of *respa* adapted for use with pair, bond, angle, dihedral, improper, or kspace styles with an *omp* suffix. It is functionally equivalent to *respa* but performs @@ -316,14 +301,11 @@ input script. See the :doc:`Speed packages ` doc page for more instructions on how to use the accelerated styles effectively. - ---------- - Restrictions """""""""""" - The *verlet/split* style can only be used if LAMMPS was built with the REPLICA package. Correspondingly the *respa/omp* style is available only if the USER-OMP package was included. See the :doc:`Build package ` doc page for more info. @@ -340,7 +322,6 @@ Related commands Default """"""" - .. code-block:: LAMMPS run_style verlet @@ -356,13 +337,9 @@ to rRESPA levels is as follows: * kspace forces = same level as pair forces * inner, middle, outer forces = no default - ---------- - .. _Tuckerman3: - - **(Tuckerman)** Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992). diff --git a/doc/src/server.rst b/doc/src/server.rst index c0aeef2565..ce83c4c12a 100644 --- a/doc/src/server.rst +++ b/doc/src/server.rst @@ -6,7 +6,6 @@ server command Syntax """""" - .. parsed-literal:: server protocol @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: server md @@ -53,14 +51,11 @@ For protocol *md*\ , LAMMPS can be either a client (via the :doc:`fix client/md For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. - ---------- - Restrictions """""""""""" - This command is part of the MESSAGE 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/server_mc.rst b/doc/src/server_mc.rst index 1953cac687..7ef92fac02 100644 --- a/doc/src/server_mc.rst +++ b/doc/src/server_mc.rst @@ -6,7 +6,6 @@ server mc command Syntax """""" - .. parsed-literal:: server mc @@ -16,7 +15,6 @@ mc = the protocol argument to the :doc:`server ` command Examples """""""" - .. parsed-literal:: server mc @@ -45,10 +43,8 @@ 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. - ---------- - When using this command, LAMMPS (as the server code) receives instructions from a Monte Carlo (MC) driver to displace random atoms, compute the energy before and after displacement, and run dynamics to @@ -73,7 +69,6 @@ Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. **Client sends one of these kinds of message**\ : - .. parsed-literal:: cs->send(NATOMS,0) # msgID = 1 with no fields @@ -92,7 +87,6 @@ Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. **Server replies**\ : - .. parsed-literal:: cs->send(NATOMS,1) # msgID = 1 with 1 field @@ -109,14 +103,11 @@ Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. cs->send(RUN,0) # msgID = 5 with no fields - ---------- - Restrictions """""""""""" - This command is part of the MESSAGE 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/server_md.rst b/doc/src/server_md.rst index 9a2ae5e880..73d6196dfc 100644 --- a/doc/src/server_md.rst +++ b/doc/src/server_md.rst @@ -6,7 +6,6 @@ server md command Syntax """""" - .. parsed-literal:: server md @@ -16,7 +15,6 @@ md = the protocol argument to the :doc:`server ` command Examples """""""" - .. parsed-literal:: server md @@ -45,10 +43,8 @@ The :doc:`server ` 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. - ---------- - 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, @@ -78,7 +74,6 @@ The following pseudo-code uses these values, defined as enums. Define: - .. parsed-literal:: SETUP=1, STEP=2 @@ -87,7 +82,6 @@ Define: **Client sends 2 kinds of messages**\ : - .. parsed-literal:: # required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS @@ -117,7 +111,6 @@ Define: **Server replies to either kind of message**\ : - .. parsed-literal:: # required fields: FORCES, ENERGY, PRESSURE @@ -129,10 +122,8 @@ Define: cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector) cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) - ---------- - 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 @@ -151,14 +142,11 @@ If you wish to run LAMMPS in another its non-atomic units, e.g. :doc:`lj units < message as indicated above, and both the client and server should agree on the units for the data they exchange. - ---------- - Restrictions """""""""""" - This command is part of the MESSAGE 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/set.rst b/doc/src/set.rst index 0cadf9d8ef..790ed5040c 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -6,7 +6,6 @@ set command Syntax """""" - .. parsed-literal:: set style ID keyword values ... @@ -118,12 +117,9 @@ Syntax *i_name* value = value for custom integer vector with name *d_name* value = value for custom floating-point vector with name - - Examples """""""" - .. parsed-literal:: set group solvent type 2 @@ -158,10 +154,8 @@ their properties reset. The remaining keywords specify which properties to reset and what the new values are. Some strings like *type* or *mol* can be used as a style and/or a keyword. - ---------- - This section describes how to select which atoms to change the properties of, via the *style* and *ID* arguments. @@ -184,10 +178,8 @@ style *region* selects all the atoms in the specified geometric region. See the :doc:`group ` and :doc:`region ` commands for details of how to specify a group or region. - ---------- - This section describes the keyword options for which properties to change, for the selected atoms. @@ -483,7 +475,6 @@ specified as the "name" portion of *i\_name* or *d\_name*. Restrictions """""""""""" - You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if the :doc:`atom_style ` does not have that attribute. diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 94cc52b8bb..9374a32c9a 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -6,7 +6,6 @@ shell command Syntax """""" - .. parsed-literal:: shell cmd args @@ -30,12 +29,9 @@ Syntax var=value = one of more definitions of environment variables anything else is passed as a command to the shell for direct execution - - Examples """""""" - .. parsed-literal:: shell cd sub1 @@ -93,7 +89,6 @@ Any other cmd is passed as-is to the shell along with its arguments as one string, invoked by the C-library system() call. For example, these lines in your input script: - .. parsed-literal:: variable n equal 10 @@ -102,7 +97,6 @@ these lines in your input script: would be the same as invoking - .. parsed-literal:: % my_setup file1 10 file2 @@ -113,7 +107,6 @@ with 3 arguments: file1 10 file2. Restrictions """""""""""" - LAMMPS does not detect errors or print warnings when any of these commands execute. E.g. if the specified directory does not exist, executing the *cd* command will silently do nothing. diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 536da208d3..da5a6279f1 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -6,7 +6,6 @@ special_bonds command Syntax """""" - .. code-block:: LAMMPS special_bonds keyword values ... @@ -29,11 +28,8 @@ Syntax *angle* value = *yes* or *no* *dihedral* value = *yes* or *no* - - Examples: - .. code-block:: LAMMPS special_bonds amber @@ -187,10 +183,8 @@ interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the *dihedral* keyword is specified as *no* which is the default, then the 2,5 interaction will also be weighted by 0.5. - ---------- - .. note:: LAMMPS stores and maintains a data structure with a list of the @@ -205,17 +199,14 @@ default, then the 2,5 interaction will also be weighted by 0.5. neighbors to be added. If you do not do this, you may get an error when bonds (or molecules) are added. - ---------- - .. note:: If you reuse this command in an input script, you should set all the options you need each time. This command cannot be used a 2nd time incrementally. E.g. these two commands: - .. code-block:: LAMMPS special_bonds lj 0.0 1.0 1.0 @@ -223,14 +214,12 @@ default, then the 2,5 interaction will also be weighted by 0.5. are not the same as - .. code-block:: LAMMPS special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 In the first case you end up with (after the 2nd command): - .. parsed-literal:: LJ: 0.0 0.0 0.0 @@ -238,7 +227,6 @@ In the first case you end up with (after the 2nd command): while only in the second case, you get the desired settings of: - .. parsed-literal:: LJ: 0.0 1.0 1.0 @@ -263,33 +251,23 @@ Default All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0, angle = no, dihedral = no. - ---------- - .. _Cornell: - - **(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). .. _Kremer: - - **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). .. _MacKerell: - - **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). .. _Mayo: - - **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index f24bdadfdc..f9dd9a32f7 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -6,7 +6,6 @@ suffix command Syntax """""" - .. parsed-literal:: suffix style args @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: suffix off @@ -59,7 +57,6 @@ These are the variants these packages provide: performance * HYBRID = a combination of two packages can be specified (see below) - 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 diff --git a/doc/src/tad.rst b/doc/src/tad.rst index ee311ef49c..2a036218a5 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -6,7 +6,6 @@ tad command Syntax """""" - .. parsed-literal:: tad N t_event T_lo T_hi delta tmax compute-ID keyword value ... @@ -39,12 +38,9 @@ Syntax dtneb = timestep for NEB damped dynamics minimization *neb_log* value = file where NEB statistics are printed - - Examples """""""" - .. parsed-literal:: tad 2000 50 1800 2300 0.01 0.01 event @@ -103,7 +99,6 @@ page for further discussion of multi-replica simulations. A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows: - .. parsed-literal:: while (time remains): @@ -154,10 +149,8 @@ the :doc:`timestep ` command is used by TAD for performing dynamics, there is a *neb\_step* keyword which can be used to set a larger timestep for each NEB calculation if desired. - ---------- - A key aspect of the TAD method is setting the stopping criterion appropriately. If this criterion is too conservative, then many events must be generated before one is finally executed. Conversely, @@ -177,10 +170,8 @@ 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*. - ---------- - Five kinds of output can be generated during a TAD run: event statistics, NEB statistics, thermodynamic output by each replica, dump files, and restart files. @@ -276,14 +267,11 @@ files do not always increase monotonically. However, the timestep values printed to the master log file, dump files, and restart files are always monotonically increasing. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. @@ -316,19 +304,13 @@ 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". - ---------- - .. _Voter2000: - - **(Voter2000)** Sorensen and Voter, J Chem Phys, 112, 9599 (2000) .. _Voter2002: - - **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). diff --git a/doc/src/temper.rst b/doc/src/temper.rst index 0329c069b1..fe0976d28b 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -6,7 +6,6 @@ temper command Syntax """""" - .. parsed-literal:: temper N M temp fix-ID seed1 seed2 index @@ -22,7 +21,6 @@ Syntax Examples """""""" - .. parsed-literal:: temper 100000 100 $t tempfix 0 58728 @@ -52,7 +50,6 @@ variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: - .. parsed-literal:: variable t world 300.0 310.0 320.0 330.0 @@ -80,7 +77,6 @@ The main screen and log file (log.lammps) will list information about which temperature is assigned to each replica at each thermodynamic output timestep. E.g. for a simulation with 16 replicas: - .. parsed-literal:: Running on 16 partitions of processors @@ -106,7 +102,6 @@ screen.N files as time proceeds. You can have each replica create its own dump file in the following manner: - .. parsed-literal:: variable rep world 0 1 2 3 4 5 6 7 @@ -142,14 +137,12 @@ the variable to the *N* values listed in the log file for the previous run for the replica temperatures at that timestep. For example if the log file listed the following for a simulation with 5 replicas: - .. parsed-literal:: 500000 2 4 0 1 3 then a setting of - .. parsed-literal:: variable w world 2 4 0 1 3 @@ -157,14 +150,11 @@ then a setting of would be used to restart the run with a tempering command like the example above with $w as the last argument. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the REPLICA package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst index 150e2f27db..e5103ed39b 100644 --- a/doc/src/temper_grem.rst +++ b/doc/src/temper_grem.rst @@ -6,7 +6,6 @@ temper/grem command Syntax """""" - .. parsed-literal:: temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. parsed-literal:: temper/grem 100000 1000 $\ *lambda* fxgREM fxnvt 0 58728 @@ -54,7 +52,6 @@ which is typically a variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: - .. parsed-literal:: variable lambda world 400 420 440 460 @@ -84,14 +81,12 @@ replica) which had previously swapped to new lambda. This is done using a variable. For example if the log file listed the following for a simulation with 5 replicas: - .. parsed-literal:: 500000 2 4 0 1 3 then a setting of - .. parsed-literal:: variable walkers world 2 4 0 1 3 @@ -100,14 +95,11 @@ would be used to restart the run with a grem command like the example above with $\ *walkers* as the last argument. This functionality is identical to :doc:`temper `. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -123,6 +115,4 @@ Related commands .. _KimStraub: - - **(Kim)** Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010). diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index e8db3eca86..98ae977696 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -6,7 +6,6 @@ temper/npt command Syntax """""" - .. parsed-literal:: temper/npt N M temp fix-ID seed1 seed2 pressure index @@ -23,7 +22,6 @@ Syntax Examples """""""" - .. parsed-literal:: temper/npt 100000 100 $t nptfix 0 58728 1 @@ -48,14 +46,11 @@ of pressure, this command works much like the :doc:`temper ` command. See the documentation on :doc:`temper ` for information on how the parallel tempering is handled in general. - ---------- - Restrictions """""""""""" - This command can only be used if LAMMPS was built with the USER-MISC package. See the :doc:`Build package ` doc page for more info. @@ -72,12 +67,8 @@ Related commands .. _Okabe2: - - **(Okabe)** T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001). .. _Mori2: - - **(Mori)** Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010). diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index 08e1e4cbbb..5419ca1860 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -6,7 +6,6 @@ thermo command Syntax """""" - .. parsed-literal:: thermo N @@ -17,7 +16,6 @@ Syntax Examples """""""" - .. parsed-literal:: thermo 100 @@ -47,7 +45,6 @@ options for :doc:`equal-style variables `. For example, the following commands will output thermodynamic info at timesteps 0,10,20,30,100,200,300,1000,2000,etc: - .. parsed-literal:: variable s equal logfreq(10,3,10) @@ -65,7 +62,6 @@ Related commands Default """"""" - .. parsed-literal:: thermo 0 diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 163aa2c6f3..b2d4b877fe 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -6,7 +6,6 @@ thermo_modify command Syntax """""" - .. code-block:: LAMMPS thermo_modify keyword value ... @@ -27,12 +26,9 @@ Syntax *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure - - Examples """""""" - .. code-block:: LAMMPS thermo_modify lost ignore flush yes diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index ebbf98a742..a51d9aaf5e 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -83,8 +83,6 @@ Syntax v_name = value calculated by an equal-style variable with name v_name[I] = value calculated by a vector-style variable with name - - Examples """""""" @@ -143,16 +141,13 @@ atoms in the system), and the numeric precision of each printed value. if your input script specifies a thermo\_style command, you should use the thermo\_modify command after it. - ---------- - Several of the thermodynamic quantities require a temperature to be computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By default this is done by using a *temperature* compute which is created when LAMMPS starts up, as if this command had been issued: - .. code-block:: LAMMPS compute thermo_temp all temp @@ -171,7 +166,6 @@ computed: "press", "enthalpy", "pxx", etc. By default this is done by using a *pressure* compute which is created when LAMMPS starts up, as if this command had been issued: - .. code-block:: LAMMPS compute thermo_press all pressure thermo_temp @@ -190,7 +184,6 @@ be computed: "pe", "etotal", "ebond", etc. This is done by using a *pe* compute which is created when LAMMPS starts up, as if this command had been issued: - .. code-block:: LAMMPS compute thermo_pe all pe @@ -200,10 +193,8 @@ 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. - ---------- - The kinetic energy of the system *ke* is inferred from the temperature of the system with :math:`\frac{1}{2} k_B T` of energy for each degree of freedom. Thus, using different :doc:`compute commands ` for @@ -225,10 +216,8 @@ is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the corresponding tail correction to the pressure is included in *press* and *pxx*\ , *pyy*\ , etc. - ---------- - The *step*\ , *elapsed*\ , and *elaplong* keywords refer to timestep count. *Step* is the current timestep, or iteration count when a :doc:`minimization ` is being performed. *Elapsed* is the @@ -283,7 +272,6 @@ If the timeout timer is inactive, the value of this keyword is 0.0 and if the timer is expired, it is negative. This allows for example to exit loops cleanly, if the timeout is expired with: - .. code-block:: LAMMPS if "$(timeremain) < 0.0" then "quit 0" @@ -314,10 +302,8 @@ of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell dimensions *lx*\ , *ly*\ , *lz*\ , *yz*\ , *xz*\ , *xy*\ . - ---------- - 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 using a wildcard asterisk with the index to effectively specify @@ -334,7 +320,6 @@ 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. - .. code-block:: LAMMPS compute myTemp all temp @@ -343,10 +328,8 @@ creates a global vector with 6 values. c_myTemp[1] c_myTemp[2] c_myTemp[3] & c_myTemp[4] c_myTemp[5] c_myTemp[6] - ---------- - 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, @@ -416,14 +399,11 @@ produce "intensive" global quantities, which are thus printed as-is, without normalization by thermo\_style custom. You can include a division by "natoms" in the variable formula if this is not the case. - ---------- - Restrictions """""""""""" - This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. @@ -438,7 +418,6 @@ Related commands Default """"""" - .. code-block:: LAMMPS thermo_style one diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index ad8512d9f7..63b236148e 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -6,7 +6,6 @@ third_order command Syntax """""" - .. code-block:: LAMMPS third_order group-ID style delta args keyword value ... @@ -22,12 +21,9 @@ Syntax *file* name = name of output file for the third order tensor *binary* arg = *yes* or *no* or *gzip* - - Examples """""""" - .. code-block:: LAMMPS third_order 1 regular 0.000001 @@ -56,7 +52,6 @@ will simplify operations using dynamical matrices with third order tensors. Restrictions """""""""""" - The command collects a 9 times the number of atoms in the group on every single MPI rank, so the memory requirements can be very significant for large systems. diff --git a/doc/src/timer.rst b/doc/src/timer.rst index b833542d09..7aa9184622 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -6,7 +6,6 @@ timer command Syntax """""" - .. parsed-literal:: timer args @@ -27,7 +26,6 @@ Syntax Examples """""""" - .. parsed-literal:: timer full sync @@ -127,7 +125,6 @@ Related commands Default """"""" - .. parsed-literal:: timer normal nosync diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index f3faaf25d2..a1f0cea7a9 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -6,7 +6,6 @@ timestep command Syntax """""" - .. parsed-literal:: timestep dt @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: timestep 2.0 diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst index 0950dd6bb2..3721bbf614 100644 --- a/doc/src/uncompute.rst +++ b/doc/src/uncompute.rst @@ -6,7 +6,6 @@ uncompute command Syntax """""" - .. parsed-literal:: uncompute compute-ID @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: uncompute 2 diff --git a/doc/src/undump.rst b/doc/src/undump.rst index 98c18ea8f7..79f0859663 100644 --- a/doc/src/undump.rst +++ b/doc/src/undump.rst @@ -6,7 +6,6 @@ undump command Syntax """""" - .. parsed-literal:: undump dump-ID @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: undump mine diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst index d85436c275..5b74cb7dcb 100644 --- a/doc/src/unfix.rst +++ b/doc/src/unfix.rst @@ -6,7 +6,6 @@ unfix command Syntax """""" - .. parsed-literal:: unfix fix-ID @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. parsed-literal:: unfix 2 diff --git a/doc/src/units.rst b/doc/src/units.rst index 4104b428ce..95792f7edf 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -6,7 +6,6 @@ units command Syntax """""" - .. parsed-literal:: units style @@ -16,7 +15,6 @@ Syntax Examples """""""" - .. code-block:: LAMMPS units metal @@ -51,10 +49,8 @@ new units. And you must correctly convert all output from the new units to the old units when comparing to the original results. That is often not simple to do. - ---------- - For style *lj*\ , all quantities are unitless. Without loss of generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`, :math:`\epsilon`, and the Boltzmann constant :math:`k_B = 1`. The @@ -219,7 +215,6 @@ distance to default values for each style: Restrictions """""""""""" - This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. @@ -228,7 +223,6 @@ This command cannot be used after the simulation box is defined by a Default """"""" - .. code-block:: LAMMPS units lj diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 572ae757db..9c5506319a 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -6,7 +6,6 @@ variable command Syntax """""" - .. parsed-literal:: variable name style args ... @@ -74,12 +73,9 @@ Syntax fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] variable references = v_name, v_name[i] - - Examples """""""" - .. parsed-literal:: variable x index run1 run2 run3 run4 run5 run6 run7 run8 @@ -206,10 +202,8 @@ from the list of active variables, and is thus available to be re-defined in a subsequent variable command. The *delete* style does the same thing. - ---------- - The :doc:`Commands parse ` doc page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if @@ -231,7 +225,6 @@ script or when the input script is looped over. This can be useful when breaking out of a loop via the :doc:`if ` and :doc:`jump ` commands before the variable would become exhausted. For example, - .. parsed-literal:: label loop @@ -243,10 +236,8 @@ commands before the variable would become exhausted. For example, label break variable a delete - ---------- - This section describes how all the various variable styles are defined and what they store. Except for the *equal* and *vector* and *atom* styles, which are explained in the next section. @@ -379,7 +370,6 @@ the count N of per-atom lines to immediately follow. N can be the total number of atoms in the system, or only a subset. The next N lines have the following format - .. parsed-literal:: ID value @@ -398,7 +388,6 @@ to match a function name specified in a :doc:`python ` command which returns a value to this variable as defined by its *return* keyword. For example these two commands would be self-consistent: - .. parsed-literal:: variable foo python myMultiply @@ -430,10 +419,8 @@ internal-style variable can be used in place of an equal-style variable anywhere else in an input script, e.g. as an argument to another command that allows for equal-style variables. - ---------- - For the *equal* and *vector* and *atom* styles, a single string is specified which represents a formula that will be evaluated afresh each time the variable is used. If you want spaces in the string, @@ -468,7 +455,6 @@ simple, but multiple quantities can be nested and combined in various ways to build up formulas of arbitrary complexity. For example, this is a valid (though strange) variable formula: - .. parsed-literal:: variable x equal "pe + c_MyTemp / vol\^(1/3)" @@ -530,10 +516,8 @@ the atom-style variable, only atoms in the group are included in the formula evaluation. The variable evaluates to 0.0 for atoms not in the group. - ---------- - Numbers, constants, and thermo keywords --------------------------------------- @@ -551,7 +535,6 @@ adapt automatically to LAMMPS versions, when non-backwards compatible syntax changes are introduced. Here is an illustrative example (which will not work, since the *version* has been introduced more recently): - .. parsed-literal:: if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" @@ -570,10 +553,8 @@ evaluated directly in an input script (not during a run), then the values accessed by the thermo keyword must be current. See the discussion below about "Variable Accuracy". - ---------- - Math Operators -------------- @@ -622,10 +603,8 @@ whose properties satisfy one or more criteria could be calculated by taking the returned per-atom vector of ones and zeroes and passing it to the :doc:`compute reduce ` command. - ---------- - Math Functions -------------- @@ -673,7 +652,6 @@ The ramp(x,y) function uses the current timestep to generate a value linearly interpolated between the specified x,y values over the course of a run, according to this formula: - .. parsed-literal:: value = x + (y-x) \* (timestep-startstep) / (stopstep-startstep) @@ -691,7 +669,6 @@ timestep in the sequence is returned. Thus if stagger(1000,100) is used in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: - .. parsed-literal:: 100,1000,1100,2000,2100,3000,etc @@ -706,7 +683,6 @@ any current timestep, the next timestep in the sequence is returned. Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump_modify every ` command, it will generate this sequence of output timesteps: - .. parsed-literal:: 100,200,300,400,1000,2000,3000,4000,10000,20000,etc @@ -718,7 +694,6 @@ logfreq2(100,18,10) is used in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: - .. parsed-literal:: 1000,1100,1200, ... ,1900,2000 @@ -766,7 +739,6 @@ if stride2(1000,2000,100,1350,1360,1) is used in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: - .. parsed-literal:: 1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000 @@ -776,7 +748,6 @@ velocity, and uses the elapsed time to change the value by a linear displacement due to the applied velocity over the course of a run, according to this formula: - .. parsed-literal:: value = value0 + velocity\*(timestep-startstep)\*dt @@ -794,7 +765,6 @@ x = value0, y = amplitude, z = period. They use the elapsed time to oscillate the value by a sin() or cos() function over the course of a run, according to one of these formulas, where omega = 2 PI / period: - .. parsed-literal:: value = value0 + Amplitude \* sin(omega\*(timestep-startstep)\*dt) @@ -808,10 +778,8 @@ the *start* keyword of the :doc:`run ` command. See the :doc:`thermo_style ` keyword elaplong = timestep-startstep. - ---------- - Group and Region Functions -------------------------- @@ -845,10 +813,8 @@ The function is computed for all atoms that are in both the group and the region. If the group is "all", then the only criteria for atom inclusion is that it be in the region. - ---------- - Special Functions ----------------- @@ -933,10 +899,8 @@ invoked more times than there are lines or sets of lines in the file, the variable is deleted, similar to how the :doc:`next ` command operates. - ---------- - Feature Functions ----------------- @@ -975,7 +939,6 @@ the checking is also done using suffix flags, if available and enabled. Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP). - .. parsed-literal:: pair_style lj/cut/coul/long 14.0 @@ -984,7 +947,6 @@ Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step - .. parsed-literal:: timestep $(2.0\*(1.0+2.0\*is_active(pair,respa)) @@ -1009,17 +971,14 @@ and C++ exceptions for error handling. Corresponding values for name are This enables writing input scripts which only dump using a given format if the compiled binary supports it. - .. parsed-literal:: if "$(is_available(feature,png))" then "print 'PNG supported'" else "print 'PNG not supported'" if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0" - ---------- - Atom Values and Vectors ----------------------- @@ -1052,10 +1011,8 @@ Note that many other atom attributes can be used as inputs to a variable by using the :doc:`compute property/atom ` command and then specifying a quantity from that compute. - ---------- - Compute References ------------------ @@ -1099,7 +1056,6 @@ global vector. Consider a compute with ID "foo" that does this, referenced as follows by variable "a", where "myVec" is another vector-style variable: - .. parsed-literal:: variable a vector c_foo\*v_myVec @@ -1117,10 +1073,8 @@ an input script (not during a run), then the values accessed by the compute must be current. See the discussion below about "Variable Accuracy". - ---------- - Fix References -------------- @@ -1176,10 +1130,8 @@ error is generated. For example, the :doc:`fix ave/time ` command may only generate averaged quantities every 100 steps. See the doc pages for individual fix commands for details. - ---------- - Variable References ------------------- @@ -1233,10 +1185,8 @@ 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. - ---------- - **Immediate Evaluation of Variables:** If you want an equal-style variable to be evaluated immediately, it @@ -1269,7 +1219,6 @@ evaluated. As an example, suppose you use this command in your input script to define the variable "v" as - .. parsed-literal:: variable v equal vol @@ -1284,7 +1233,6 @@ evaluated continuously during the run. If you want to store the initial volume of the system, you can do it this way: - .. parsed-literal:: variable v equal vol @@ -1294,7 +1242,6 @@ The second command will force "v" to be evaluated (yielding the initial volume) and assign that value to the variable "v0". Thus the command - .. parsed-literal:: thermo_style custom step v_v v_v0 @@ -1305,7 +1252,6 @@ during the run. Note that it is a mistake to enclose a variable formula in double quotes if it contains variables preceded by $ signs. For example, - .. parsed-literal:: variable vratio equal "${vfinal}/${v0}" @@ -1314,10 +1260,8 @@ This is because the quotes prevent variable substitution (explained on the :doc:`Commands parse ` doc page), and thus an error will occur when the formula for "vratio" is evaluated later. - ---------- - **Variable Accuracy:** Obviously, LAMMPS attempts to evaluate variables containing formulas @@ -1365,7 +1309,6 @@ timestep of the preceding run, e.g. by thermodynamic output. One way to get around this problem is to perform a 0-timestep run before using the variable. For example, these commands - .. parsed-literal:: variable t equal temp @@ -1378,7 +1321,6 @@ a compute for calculating the temperature to be invoked. However, this sequence of commands would be fine: - .. parsed-literal:: run 0 @@ -1413,7 +1355,6 @@ a 0-timestep run before printing the variable has the desired effect. way to detect this has occurred. Consider the following sequence of commands: - .. parsed-literal:: pair_coeff 1 1 1.0 1.0 @@ -1440,7 +1381,6 @@ the system is up-to-date. For example, this sequence of commands would print a potential energy that reflected the changed pairwise coefficient: - .. parsed-literal:: pair_coeff 1 1 1.0 1.0 @@ -1450,14 +1390,11 @@ coefficient: variable e equal pe print "Final potential energy = $e" - ---------- - Restrictions """""""""""" - Indexing any formula element by global atom ID, such as an atom value, requires the :doc:`atom style ` to use a global mapping in order to look up the vector indices. By default, only atom styles diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index d111a194f1..90df45bda6 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -6,7 +6,6 @@ velocity command Syntax """""" - .. parsed-literal:: velocity group-ID style args keyword value ... @@ -49,12 +48,9 @@ Syntax fix-ID = ID of rigid body fix *units* value = *box* or *lattice* - - Examples """""""" - .. parsed-literal:: velocity all create 300.0 4928459 rot yes dist gaussian @@ -124,10 +120,8 @@ coordinates depend on whether the *units* keyword is set to *box* or For all styles, no atoms are assigned z-component velocities if the simulation is 2d; see the :doc:`dimension ` command. - ---------- - The keyword/value options are used in the following ways by the various styles. @@ -145,10 +139,8 @@ The *mom* and *rot* keywords are used by *create*\ . If mom = yes, the linear momentum of the newly created ensemble of velocities is zeroed; if rot = yes, the angular momentum is zeroed. - ---------- - If specified, the *temp* keyword is used by *create* and *scale* to specify a :doc:`compute ` that calculates temperature in a desired way, e.g. by first subtracting out a velocity bias, as @@ -156,7 +148,6 @@ discussed on the :doc:`Howto thermostat ` doc page. If this keyword is not specified, *create* and *scale* calculate temperature using a compute that is defined internally as follows: - .. parsed-literal:: compute velocity_temp group-ID temp @@ -190,10 +181,8 @@ specifying the ID of a :doc:`compute temp/ramp ` or :doc:`compute temp/profile ` command, and the *bias* keyword set to a *yes* value. - ---------- - The *loop* keyword is used by *create* in the following ways. If loop = all, then each processor loops over all atoms in the @@ -226,10 +215,8 @@ This is because the computations based on xyz coordinates are sensitive to tiny differences in the double-precision value for a coordinate as stored on a particular machine. - ---------- - The *rigid* keyword only has meaning when used with the *zero* style. It allows specification of a fix-ID for one of the :doc:`rigid-body fix ` variants which defines a set of rigid bodies. The zeroing of linear or angular momentum is then performed for each rigid @@ -243,14 +230,11 @@ are in units of lattice spacings per time (e.g. spacings/fmsec) and coordinates are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacing. - ---------- - Restrictions """""""""""" - Assigning a temperature via the *create* style to a system with :doc:`rigid bodies ` or :doc:`SHAKE constraints ` may not have the desired outcome for two reasons. First, the velocity command can be invoked before all of the relevant fixes are created and @@ -262,7 +246,6 @@ temperature than desired. A workaround for this is to perform a :doc:`run 0 ` commands for any desired I,J pairs. - ---------- - Restrictions """""""""""" - This command requires inter-processor communication to migrate atoms before the data file is written. This means that your system must be ready to perform a simulation before using this command (force fields diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index 54a55db6c6..d0daa73052 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -6,7 +6,6 @@ write_dump command Syntax """""" - .. code-block:: LAMMPS write_dump group-ID style file dump-args modify dump_modify-args @@ -18,11 +17,9 @@ Syntax * modify = all args after this keyword are passed to :doc:`dump_modify ` (optional) * dump-modify-args = args for :doc:`dump_modify ` (optional) - Examples """""""" - .. code-block:: LAMMPS write_dump all atom dump.atom @@ -62,14 +59,11 @@ in the same fashion to create the new filename(s). Normally, :doc:`dump image < for the timestep. That is not the case for the write\_dump command; no wildcard "\*" character is necessary. - ---------- - Restrictions """""""""""" - All restrictions for the :doc:`dump ` and :doc:`dump_modify ` commands apply to this command as well, with the exception of the :doc:`dump image ` filename not diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index 0aa036aaba..41193d05b7 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -6,7 +6,6 @@ write_restart command Syntax """""" - .. code-block:: LAMMPS write_restart file keyword value ... @@ -22,12 +21,9 @@ Syntax *nfile* arg = Nf Nf = write this many files, one from each of Nf processors - - Examples """""""" - .. code-block:: LAMMPS write_restart restart.equil @@ -62,7 +58,6 @@ file via the MPI-IO library, which is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO package installed, e.g. - .. code-block:: bash make yes-mpiio # installs the MPIIO package @@ -92,10 +87,8 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` command for general information about what is stored in a restart file. - ---------- - The optional *nfile* or *fileper* keywords can be used in conjunction with the "%" wildcard character in the specified restart file name. As explained above, the "%" character causes the restart file to be @@ -114,14 +107,11 @@ file for every Np processors. For example, if Np = 4, every 4th processor (0,4,8,12,etc) will collect information from itself and the next 3 processors and write it to a restart file. - ---------- - Restrictions """""""""""" - This command requires inter-processor communication to migrate atoms before the restart file is written. This means that your system must be ready to perform a simulation before using this command (force