forked from lijiext/lammps
1773 lines
44 KiB
Markdown
1773 lines
44 KiB
Markdown
# Building LAMMPS using CMake
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LAMMPS recently acquired support for building with CMake thanks to the efforts
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of Christoph Junghans (LANL) and Richard Berger (Temple U). One of the key
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strengths of CMake is that it can generate the necessary build system files of
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your own personal preference. It also enables using common development IDEs such
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as Eclipse, Visual Studio, QtCreator, Xcode and many more for LAMMPS
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development.
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CMake can both be used as a command-line (CLI) utility `cmake` or through one of
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its GUIs. `ccmake` is a text-based ui to configure and build CMake projects.
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`cmake-gui` is a graphical frontend for running CMake operations that works on
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Linux desktop environments, Windows and MacOS X.
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The following is a tutorial-style introduction in using the CMake system. It
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should give you the necessary foundation to understand how to do the most common
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tasks, act as a reference and provide examples of typical use cases.
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## Table of Contents
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* [Quick Start for the Impatient](#quick-start-for-the-impatient)
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* [Building LAMMPS using cmake](#building-lammps-using-cmake-1)
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* [Prerequisites](#prerequisites)
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* [Build directory vs. Source Directory](#build-directory-vs-source-directory)
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* [Defining and using presets](#defining-and-using-presets)
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* [Reference](#reference)
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* [Common CMake Configuration Options](#common-cmake-configuration-options)
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* [LAMMPS Configuration Options](#lammps-configuration-options)
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* [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
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* [Default Packages](#default-packages)
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* [Other Packages](#other-packages)
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* [User Packages](#user-packages)
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* [Package-Specific Configuration Options](#package-specific-configuration-options)
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* [KSPACE Package](#kspace-package)
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* [MKL](#mkl)
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* [FFTW2](#fftw2)
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* [FFTW3](#fftw3)
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* [LAPACK](#lapack)
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* [PYTHON Package](#python-package)
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* [GPU Package](#gpu-package)
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* [VORONOI Package](#voronoi-package)
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* [USER-SMD Package](#user-smd-package)
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* [Optional Features](#optional-features)
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* [zlib support](#zlib-support)
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* [JPEG support](#jpeg-support)
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* [PNG support](#png-support)
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* [GZIP support](#gzip-support)
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* [FFMPEG support](#ffmpeg-support)
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* [Compilers](#compilers)
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* [Building with GNU Compilers](#building-with-gnu-compilers)
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* [Building with Intel Compilers](#building-with-intel-compilers)
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* [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
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* [Examples](#examples)
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## Quick Start for the Impatient
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If you want to skip ahead and just run the compilation using `cmake`, please
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find a minimal example below. Together with the options reference below, this
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should get you started.
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```bash
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git clone https://github.com/lammps/lammps.git
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mkdir lammps/build
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cd lammps/build
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cmake [-D OPTION_A=VALUE_A -D OPTION_B=VALUE_B ...] ../cmake
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make
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```
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# Building LAMMPS using `cmake`
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## Prerequisites
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This tutorial assumes you are running in a command-line environment using a
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shell like Bash.
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* Linux: any terminal window will work
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* MacOS X: launch the Terminal app
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* Windows 10: install and run "Bash on Windows" (aka Ubuntu on Windows)
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Before we start, please download the latest and greatest version of LAMMPS from
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GitHub. You can either download it as a tarball or ZIP file, or via git. When
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you start with a fresh lammps directory, the contents should look like this:
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```bash
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$ ls
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bench doc lib potentials README tools
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cmake examples LICENSE python src
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```
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## Build directory vs. Source Directory
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By using CMake we separate building LAMMPS into multiple phases:
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1. **Configuration**: define which features we want to enable/disable and how it should be compiled
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2. **Compilation**: compile each source file and generate binaries and libraries based on the configuration
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3. **Installation** (Optional): finally we can install the generated binaries on our system
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In the GNU Make based build system of LAMMPS, configuration occurs by running
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special make targets like `make yes-MOLECULAR`. These targets modify the
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**source directory** (`src/`) directory by copying package files and patching
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Makefile. In some cases you are force to manually edit Makefiles to add compiler
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options and/or correct include directory and library paths.
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These edits and copy operations are no longer necessary when compiling with
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CMake. The source directory stays untouched, so you compile LAMMPS in many
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different variants using the same source code checkout. It enables true
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**out-of-source** builds.
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When using Cmake, you can compile in **any** folder outside of the source
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directory. Any working directory you choose becomes a so-called **build
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directory**. All configuration files and compilation results are stored in this
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folder. We recommend calling it something like `build/`.
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Let's have a look a quick example, where we get the greatest and latest version
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of LAMMPS from GitHub via git:
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```bash
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git clone https://github.com/lammps/lammps.git
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```
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We then create a new `build` folder and make it our current working directory:
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```
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mkdir lammps/build
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cd lammps/build
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```
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To configure LAMMPS we run `cmake` inside of this folder. However it requires at
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least one argument. `cmake` needs to read the LAMMPS `CMakeLists.txt` file to
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know what to do. This file is located in the `cmake/` subdirectory of the
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lammps checkout. To run `cmake` add the relative or absolute path to the `cmake/`
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directory as first argument.
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E.g., if the current working directory is `lammps/build` you can specify the
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relative path to `lammps/cmake` as follows:
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```
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cmake ../cmake
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```
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You could also specify the absolute path:
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```
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cmake /path/to/my/lammps/folder/cmake
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```
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Please note: **This does NOT compile the code!** Running cmake only configures
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the next build. It generates the necessary files to compile the code. On
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Unix/Linux it defaults to generating Makefiles. You can also choose other output
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formats to generate files for Eclipse, Xcode or Visual Studio which are
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supported on other platorms.
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To compile LAMMPS once the Makefiles are generated, simply type `make` in the
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build directory.
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```
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make
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```
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# Defining and using presets
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The CMake build exposes a lot of different options. In the old build system
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some of the package selections were possible by using special make target like
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`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
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specifying all options manually. This can quickly become a very long command
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line that is hard to handle. While these could be stored in a simple script
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file, there is another way of defining "presets" to compile LAMMPS in a certain
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way.
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A preset is a regular CMake script file that can use constructs such as
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variables, lists and for-loops to manipulate configuration options and create
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an [*initial cache*](https://cmake.org/cmake/help/v3.12/manual/cmake.1.html).
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Options must be set with the `CACHE` and `FORCE` flag to ensure they are
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considered even during a second cmake run.
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Such a file can then be passed to cmake via the `-C` flag. Several examples of
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presets can be found in the `cmake/presets` folder.
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```bash
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# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
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mkdir build
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cd build
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cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
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```
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# Reference
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## Common CMake Configuration Options
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Description</th>
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<th>Values</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>CMAKE_INSTALL_PREFIX</code></td>
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<td>Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do.</td>
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<td>
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Default setting is <code>$HOME/.local</code>.
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</td>
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</tr>
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<tr>
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<td><code>CMAKE_BUILD_TYPE</code></td>
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<td>Controls if debugging symbols are added to the generated binaries</td>
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<td>
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<dl>
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<dt><code>Release</code> (default)</dt>
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<dt><code>Debug</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
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<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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</tbody>
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</table>
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## LAMMPS Configuration Options
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Description</th>
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<th>Values</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>LAMMPS_SIZE_LIMIT</code></td>
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<td>Controls the integer sizes used by LAMMPS internally</td>
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<td>
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<dl>
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<dt><code>LAMMPS_SMALLBIG</code> (default)</dt>
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<dd>32bit , 64bit</dd>
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<dt><code>LAMMPS_SMALLSMALL</code></dt>
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<dd>32bit , 32bit</dd>
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<dt><code>LAMMPS_BIGBIG</code></dt>
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<dd>64bit , 64bit</dd>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>LAMMPS_MEMALIGN</code></td>
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<td>controls the alignment of blocks of memory allocated by LAMMPS</td>
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<td>
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<dl>
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<dt><code>64</code> (default)</dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>LAMMPS_EXCEPTIONS</code></td>
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<td>controls whether LAMMPS dies after an error or throws a C++ exception. This is particularly useful when running through the C library interface, since an error
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in LAMMPS then doesn't kill the parent process</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>LAMMPS_MACHINE</code></td>
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<td>allows appending a machine suffix to the generate LAMMPS binary</td>
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<td>
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<dl>
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<dt>*none* (default)</dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>BUILD_LIB</code></td>
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<td>control whether to build LAMMPS as a library</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>BUILD_EXE</code></td>
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<td>control whether to build LAMMPS executable</td>
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<td>
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<dl>
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<dt><code>on</code> (default)</dt>
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<dt><code>off</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>BUILD_SHARED_LIBS</code></td>
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<td>control whether to build LAMMPS as a shared-library</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>BUILD_DOC</code></td>
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<td>control whether to build LAMMPS documentation</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
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<td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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</tbody>
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</table>
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## Parallelization and Accelerator Packages
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Description</th>
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<th>Values</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>BUILD_MPI</code></td>
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<td>control whether to build LAMMPS with MPI support. This will look for
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`mpicxx` in your path and use this MPI implementation.</td>
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<td>
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<dl>
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<dt><code>on</code> (default, if found)</dt>
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<dt><code>off</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>BUILD_OMP</code></td>
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<td>control whether to build LAMMPS with OpenMP support.</td>
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<td>
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<dl>
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<dt><code>on</code> (default, if found)</dt>
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<dt><code>off</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>PKG_OPT</code></td>
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<td>
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A handful of pair styles which are optimized for improved CPU performance on
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single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials.
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</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>PKG_USER-OMP</code></td>
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<td>
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Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace
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styles which are altered to enable threading on many-core CPUs via OpenMP
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directives.
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</td>
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<td>
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<dl>
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<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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</td>
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</tr>
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<tr>
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<td><code>PKG_USER-INTEL</code></td>
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<td>
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Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which
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are optimized for Intel CPUs and KNLs (Knights Landing).
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</td>
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||
<td>
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||
<dl>
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||
<dt><code>off</code> (default)</dt>
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<dt><code>on</code></dt>
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</dl>
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||
</td>
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||
</tr>
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<tr>
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<td><code>PKG_GPU</code></td>
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<td>
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Dozens of pair styles and a version of the PPPM long-range Coulombic solver
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optimized for GPUs. All such styles have a “gpu” as a suffix in their style
|
||
name. The GPU code can be compiled with either CUDA or OpenCL, however the
|
||
OpenCL variants are no longer actively maintained and only the CUDA versions
|
||
are regularly tested.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
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||
<dt><code>on</code></dt>
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</dl>
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||
</td>
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||
</tr>
|
||
<tr>
|
||
<td><code>PKG_KOKKOS</code></td>
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<td>Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
## Default Packages
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>PKG_ASPHERE</code></td>
|
||
<td>Computes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_BODY</code></td>
|
||
<td>Body-style particles with internal structure. Computes, time-integration fixes, pair styles, as well as the body styles themselves.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_CLASS2</code></td>
|
||
<td>Bond, angle, dihedral, improper, and pair styles for the COMPASS CLASS2 molecular force field.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_COLLOID</code></td>
|
||
<td>Coarse-grained finite-size colloidal particles. Pair styles and fix wall styles for colloidal interactions. Includes the Fast Lubrication Dynamics (FLD) method for hydrodynamic interactions, which is a simplified approximation to Stokesian dynamics.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_COMPRESS</code></td>
|
||
<td>Compressed output of dump files via the zlib compression library, using dump styles with a “gz” in their style name.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_CORESHELL</code></td>
|
||
<td>Compute and pair styles that implement the adiabatic core/shell model for polarizability. The pair styles augment Born, Buckingham, and Lennard-Jones styles with core/shell capabilities. The compute temp/cs command calculates the temperature of a system with core/shell particles.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_DIPOLE</code></td>
|
||
<td>An atom style and several pair styles for point dipole models with short-range or long-range interactions.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_GRANULAR</code></td>
|
||
<td>Pair styles and fixes for finite-size granular particles, which interact with each other and boundaries via frictional and dissipative potentials.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_KSPACE</code></td>
|
||
<td>A variety of long-range Coulombic solvers, as well as pair styles which compute the corresponding short-range pairwise Coulombic interactions. These include Ewald, particle-particle particle-mesh (PPPM), and multilevel summation method (MSM) solvers.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MANYBODY</code></td>
|
||
<td>
|
||
A variety of manybody and bond-order potentials. These include (AI)REBO, BOP,
|
||
EAM, EIM, Stillinger-Weber, and Tersoff potentials.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MC</code></td>
|
||
<td>
|
||
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
|
||
attributes. These include fixes for creating, breaking, and swapping bonds,
|
||
for performing atomic swaps, and performing grand-canonical MC (GCMC) in
|
||
conjuction with dynamics.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MEAM</code></td>
|
||
<td>
|
||
<p>A pair style for the modified embedded atom (MEAM) potential.</p>
|
||
|
||
<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
|
||
which is a direct translation of the MEAM package to C++. USER-MEAMC contains
|
||
additional optimizations making it run faster than MEAM on most machines, while
|
||
providing the identical features and USER interface.</strong></p>
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MISC</code></td>
|
||
<td>
|
||
A variety of compute, fix, pair, dump styles with specialized capabilities that
|
||
don’t align with other packages.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MOLECULE</code></td>
|
||
<td>
|
||
A large number of atom, pair, bond, angle, dihedral, improper styles that are
|
||
used to model molecular systems with fixed covalent bonds. The pair styles
|
||
include the Dreiding (hydrogen-bonding) and CHARMM force fields, and a TIP4P
|
||
water model.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_PERI</code></td>
|
||
<td>
|
||
An atom style, several pair styles which implement different Peridynamics
|
||
materials models, and several computes which calculate diagnostics.
|
||
Peridynamics is a a particle-based meshless continuum model.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_QEQ</code></td>
|
||
<td>
|
||
Several fixes for performing charge equilibration (QEq) via different
|
||
algorithms. These can be used with pair styles that perform QEq as part of
|
||
their formulation.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_REAX</code></td>
|
||
<td>
|
||
A pair style which wraps a Fortran library which implements the ReaxFF
|
||
potential, which is a universal reactive force field. See the USER-REAXC
|
||
package for an alternate implementation in C/C++. Also a fix reax/bonds
|
||
command for monitoring molecules as bonds are created and destroyed.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_REPLICA</code></td>
|
||
<td>
|
||
A collection of multi-replica methods which can be used when running multiple
|
||
LAMMPS simulations (replicas). See Section 6.5 for an overview of how to run
|
||
multi-replica simulations in LAMMPS. Methods in the package include nudged
|
||
elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated
|
||
dynamics (TAD), parallel tempering, and a verlet/split algorithm for
|
||
performing long-range Coulombics on one set of processors, and the remainder
|
||
of the force field calcalation on another set.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_RIGID</code></td>
|
||
<td>
|
||
Fixes which enforce rigid constraints on collections of atoms or particles.
|
||
This includes SHAKE and RATTLE, as well as varous rigid-body integrators for a
|
||
few large bodies or many small bodies. Also several computes which calculate
|
||
properties of rigid bodies.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_SHOCK</code></td>
|
||
<td>
|
||
Fixes for running impact simulations where a shock-wave passes through a
|
||
material.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_SNAP</code></td>
|
||
<td>
|
||
A pair style for the spectral neighbor analysis potential (SNAP). SNAP is
|
||
methodology for deriving a highly accurate classical potential fit to a large
|
||
archive of quantum mechanical (DFT) data. Also several computes which analyze
|
||
attributes of the potential.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_SRD</code></td>
|
||
<td>
|
||
A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) method
|
||
for coarse-graining of a solvent, typically around large colloidal particles.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
## Other Packages
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>PKG_KIM</code></td>
|
||
<td>A <code>pair_style kim</code> command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, enabling any of them to be used in LAMMPS simulations.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_PYTHON</code></td>
|
||
<td>Enable support for Python scripting inside of LAMMPS.</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MSCG</code></td>
|
||
<td>
|
||
A fix mscg command which can parameterize a Multi-Scale Coarse-Graining (MSCG)
|
||
model using the open-source MS-CG library.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_MPIIO</code></td>
|
||
<td>
|
||
Support for parallel output/input of dump and restart files via the MPIIO library.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_POEMS</code></td>
|
||
<td>
|
||
A fix that wraps the Parallelizable Open source Efficient Multibody Software
|
||
(POEMS) library, which is able to simulate the dynamics of articulated body
|
||
systems. These are systems with multiple rigid bodies (collections of
|
||
particles) whose motion is coupled by connections at hinge points.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_LATTE</code></td>
|
||
<td>
|
||
A fix command which wraps the LATTE DFTB code, so that molecular dynamics can
|
||
be run with LAMMPS using density-functional tight-binding quantum forces
|
||
calculated by LATTE.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
## User Packages
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>PKG_USER-ATC</code></td>
|
||
<td>
|
||
ATC stands for atoms-to-continuum. This package implements a fix atc command
|
||
to either couple molecular dynamics with continuum finite element equations or
|
||
perform on-the-fly conversion of atomic information to continuum fields.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-AWPMD</code></td>
|
||
<td>
|
||
AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This package
|
||
implements an atom, pair, and fix style which allows electrons to be treated
|
||
as explicit particles in a classical molecular dynamics model.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-CGDNA</code></td>
|
||
<td>
|
||
Several pair styles, a bond style, and integration fixes for coarse-grained
|
||
models of single- and double-stranded DNA based on the oxDNA model of Doye,
|
||
Louis and Ouldridge at the University of Oxford. This includes Langevin-type
|
||
rigid-body integrators with improved stability.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-CGSDK</code></td>
|
||
<td>
|
||
Several pair styles and an angle style which implement the coarse-grained SDK
|
||
model of Shinoda, DeVane, and Klein which enables simulation of ionic liquids,
|
||
electrolytes, lipids and charged amino acids.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-COLVARS</code></td>
|
||
<td>
|
||
COLVARS stands for collective variables, which can be used to implement
|
||
various enhanced sampling methods, including Adaptive Biasing Force,
|
||
Metadynamics, Steered MD, Umbrella Sampling and Restraints. A fix colvars
|
||
command is implemented which wraps a COLVARS library, which implements these
|
||
methods. simulations.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-DIFFRACTION</code></td>
|
||
<td>
|
||
Two computes and a fix for calculating x-ray and electron diffraction
|
||
intensities based on kinematic diffraction theory.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-DPD</code></td>
|
||
<td>
|
||
DPD stands for dissipative particle dynamics. This package implements
|
||
coarse-grained DPD-based models for energetic, reactive molecular crystalline
|
||
materials. It includes many pair styles specific to these systems, including
|
||
for reactive DPD, where each particle has internal state for multiple species
|
||
and a coupled set of chemical reaction ODEs are integrated each timestep.
|
||
Highly accurate time integrators for isothermal, isoenergetic, isobaric and
|
||
isenthalpic conditions are included. These enable long timesteps via the
|
||
Shardlow splitting algorithm.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-DRUDE</code></td>
|
||
<td>
|
||
Fixes, pair styles, and a compute to simulate thermalized Drude oscillators as
|
||
a model of polarization.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-EFF</code></td>
|
||
<td>
|
||
EFF stands for electron force field which allows a classical MD code to model
|
||
electrons as particles of variable radius. This package contains atom, pair,
|
||
fix and compute styles which implement the eFF as described in A.
|
||
Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, 2010. The eFF
|
||
potential was first introduced by Su and Goddard, in 2007.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-FEP</code></td>
|
||
<td>
|
||
FEP stands for free energy perturbation. This package provides methods for
|
||
performing FEP simulations by using a fix adapt/fep command with soft-core
|
||
pair potentials, which have a “soft” in their style name.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-H5MD</code></td>
|
||
<td>
|
||
H5MD stands for HDF5 for MD. HDF5 is a portable, binary, self-describing file
|
||
format, used by many scientific simulations. H5MD is a format for molecular
|
||
simulations, built on top of HDF5. This package implements a dump h5md command
|
||
to output LAMMPS snapshots in this format.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-LB</code></td>
|
||
<td>
|
||
Fixes which implement a background Lattice-Boltzmann (LB) fluid, which can be
|
||
used to model MD particles influenced by hydrodynamic forces.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MANIFOLD</code></td>
|
||
<td>
|
||
Several fixes and a “manifold” class which enable simulations of particles
|
||
constrained to a manifold (a 2D surface within the 3D simulation box). This is
|
||
done by applying the RATTLE constraint algorithm to formulate single-particle
|
||
constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of
|
||
the manifold) n = grad(g).
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MEAMC</code></td>
|
||
<td>
|
||
A pair style for the modified embedded atom (MEAM) potential translated from
|
||
the Fortran version in the MEAM package to plain C++. In contrast to the MEAM
|
||
package, no library needs to be compiled and the pair style can be
|
||
instantiated multiple times.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MESO</code></td>
|
||
<td>
|
||
Several extensions of the the dissipative particle dynamics (DPD) method.
|
||
Specifically, energy-conserving DPD (eDPD) that can model non-isothermal
|
||
processes, many-body DPD (mDPD) for simulating vapor-liquid coexistence, and
|
||
transport DPD (tDPD) for modeling advection-diffusion-reaction systems. The
|
||
equations of motion of these DPD extensions are integrated through a modified
|
||
velocity-Verlet (MVV) algorithm.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MGPT</code></td>
|
||
<td>
|
||
A pair style which provides a fast implementation of the quantum-based MGPT
|
||
multi-ion potentials. The MGPT or model GPT method derives from
|
||
first-principles DFT-based generalized pseudopotential theory (GPT) through a
|
||
series of systematic approximations valid for mid-period transition metals
|
||
with nearly half-filled d bands. The MGPT method was originally developed by
|
||
John Moriarty at LLNL. The pair style in this package calculates forces and
|
||
energies using an optimized matrix-MGPT algorithm due to Tomas Oppelstrup at
|
||
LLNL.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MISC</code></td>
|
||
<td>
|
||
A potpourri of (mostly) unrelated features contributed to LAMMPS by users.
|
||
Each feature is a single fix, compute, pair, bond, angle, dihedral, improper,
|
||
or command style.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MOFFF</code></td>
|
||
<td>
|
||
Pair, angle and improper styles needed to employ the MOF-FF force field by
|
||
Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force
|
||
field with the primary aim to simulate MOFs and related porous framework
|
||
materials, using spherical Gaussian charges. It is described in S. Bureekaew
|
||
et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. For the usage of MOF-FF see
|
||
the example in the example directory as well as the MOF+ website.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-MOLFILE</code></td>
|
||
<td>
|
||
A dump molfile command which uses molfile plugins that are bundled with the
|
||
VMD molecular visualization and analysis program, to enable LAMMPS to dump
|
||
snapshots in formats compatible with various molecular simulation tools.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-NETCDF</code></td>
|
||
<td>
|
||
Dump styles for writing NetCDF formatted dump files. NetCDF is a portable,
|
||
binary, self-describing file format developed on top of HDF5. The file
|
||
contents follow the AMBER NetCDF trajectory conventions
|
||
(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-PHONON</code></td>
|
||
<td>
|
||
A fix phonon command that calculates dynamical matrices, which can then be
|
||
used to compute phonon dispersion relations, directly from molecular dynamics
|
||
simulations.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-QTB</code></td>
|
||
<td>
|
||
Two fixes which provide a self-consistent quantum treatment of vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero point energy into the system, altering the energy power spectrum and the heat capacity to account for their quantum nature. This is useful when modeling systems at temperatures lower than their classical limits or when temperatures ramp across the classical limits in a simulation.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-QUIP</code></td>
|
||
<td>
|
||
A pair_style quip command which wraps the QUIP libAtoms library, which
|
||
includes a variety of interatomic potentials, including Gaussian Approximation
|
||
Potential (GAP) models developed by the Cambridge University group.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-QMMM</code></td>
|
||
<td>
|
||
A fix qmmm command which allows LAMMPS to be used in a QM/MM simulation,
|
||
currently only in combination with the Quantum ESPRESSO package.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-REAXC</code></td>
|
||
<td>
|
||
A pair style which implements the ReaxFF potential in C/C++ (in contrast to
|
||
the REAX package and its Fortran library). ReaxFF is universal reactive force
|
||
field. See the src/USER-REAXC/README file for more info on differences between
|
||
the two packages. Also two fixes for monitoring molecules as bonds are created
|
||
and destroyed.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-SMD</code></td>
|
||
<td>
|
||
An atom style, fixes, computes, and several pair styles which implements
|
||
smoothed Mach dynamics (SMD) for solids, which is a model related to smoothed
|
||
particle hydrodynamics (SPH) for liquids (see the USER-SPH package).
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-SMTBQ</code></td>
|
||
<td>
|
||
A pair style which implements a Second Moment Tight Binding model with QEq
|
||
charge equilibration (SMTBQ) potential for the description of ionocovalent
|
||
bonds in oxides.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-SPH</code></td>
|
||
<td>
|
||
An atom style, fixes, computes, and several pair styles which implements
|
||
smoothed particle hydrodynamics (SPH) for liquids. See the related USER-SMD
|
||
package package for smooth Mach dynamics (SMD) for solids.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-TALLY</code></td>
|
||
<td>
|
||
Several compute styles that can be called when pairwise interactions are
|
||
calculated to tally information (forces, heat flux, energy, stress, etc) about
|
||
individual interactions.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-UEF</code></td>
|
||
<td>
|
||
A fix style for the integration of the equations of motion under extensional
|
||
flow with proper boundary conditions, as well as several supporting compute
|
||
styles and an output option.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PKG_USER-VTK</code></td>
|
||
<td>
|
||
A dump vtk command which outputs snapshot info in the VTK format, enabling
|
||
visualization by Paraview or other visualization packages.
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>off</code> (default)</dt>
|
||
<dt><code>on</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
## Package-Specific Configuration Options
|
||
|
||
### KSPACE Package
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>FFT</code></td>
|
||
<td>
|
||
<p>FFT library for KSPACE package</p>
|
||
<p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
|
||
</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>KISS</code></dt>
|
||
<dt><code>FFTW3</code></dt>
|
||
<dt><code>FFTW2</code></dt>
|
||
<dt><code>MKL</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>FFT_PACK</code></td>
|
||
<td>Optimization for FFT</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>array (default)</code></dt>
|
||
<dt><code>pointer</code></dt>
|
||
<dt><code>memcpy</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### MKL
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>MKL_INCLUDE_DIRS</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>MKL_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
TODO static vs dynamic linking
|
||
|
||
### FFTW2
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>FFTW2_INCLUDE_DIRS</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>FFTW2_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### FFTW3
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>FFTW3_INCLUDE_DIRS</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>FFTW3_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### LAPACK
|
||
TODO
|
||
|
||
### PYTHON Package
|
||
|
||
### USER-INTEL Package
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>INTEL_ARCH</code></td>
|
||
<td>Target architecture for USER-INTEL package</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>cpu</code> (default)</dt>
|
||
<dt><code>knl</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### GPU Package
|
||
The GPU package builds a support library which can either use OpenCL or CUDA as
|
||
target API.
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>GPU_API</code></td>
|
||
<td>API used by GPU package</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>opencl</code> (default)</dt>
|
||
<dt><code>cuda</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>GPU_PREC</code></td>
|
||
<td>Precision size used by GPU package kernels</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>mixed</code> (default)</dt>
|
||
<dt><code>single</code></dt>
|
||
<dt><code>double</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>OCL_TUNE</code> (OpenCL only)</td>
|
||
<td>Tuning target for OpenCL driver code</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>generic</code> (default)</dt>
|
||
<dt><code>intel</code> (Intel CPU)</dt>
|
||
<dt><code>phi</code> (Intel Xeon Phi)</dt>
|
||
<dt><code>fermi</code> (NVIDIA)</dt>
|
||
<dt><code>kepler</code> (NVIDIA)</dt>
|
||
<dt><code>cypress</code> (AMD)</dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>GPU_ARCH</code> (CUDA only)</td>
|
||
<td>CUDA SM architecture targeted by GPU package</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>sm_20</code> (Fermi)</dt>
|
||
<dt><code>sm_30</code> (Kepler)</dt>
|
||
<dt><code>sm_50</code> (Maxwell)</dt>
|
||
<dt><code>sm_60</code> (Pascal)</dt>
|
||
<dt><code>sm_70</code> (Volta)</dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>CUDPP_OPT</code> (CUDA only)</td>
|
||
<td>Enable CUDA Performance Primitives Optimizations</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>on</code> (default)</dt>
|
||
<dt><code>off</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>BIN2C</code> (CUDA only)</td>
|
||
<td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>
|
||
<td>(automatic)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### VORONOI Package
|
||
|
||
TODO
|
||
|
||
### USER-SMD Package
|
||
|
||
Requires a Eigen3 installation
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>EIGEN3_INCLUDE_DIR</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
## Optional Features
|
||
|
||
### zlib support
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>ZLIB_INCLUDE_DIR</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>ZLIB_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### JPEG support
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>WITH_JPEG</code></td>
|
||
<td>Enables/Disable JPEG support in LAMMPS</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>yes</code> (default, if found)</dt>
|
||
<dt><code>no</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>JPEG_INCLUDE_DIR</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>JPEG_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### PNG support
|
||
(requires zlib support)
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>WITH_PNG</code></td>
|
||
<td>Enables/Disable PNG support in LAMMPS</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>yes</code> (default, if found)</dt>
|
||
<dt><code>no</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PNG_INCLUDE_DIR</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>PNG_LIBRARIES</code></td>
|
||
<td></td>
|
||
<td>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### GZIP support
|
||
|
||
requires `gzip` to be in your `PATH`
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>WITH_GZIP</code></td>
|
||
<td>Enables/Disable GZIP support in LAMMPS</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>yes</code> (default, if found)</dt>
|
||
<dt><code>no</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>GZIP_EXECUTABLE</code></td>
|
||
<td>Path to gzip executable, will automatically pick up the first one in your $PATH.</td>
|
||
<td>(automatic)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### FFMPEG support
|
||
|
||
requires `ffmpeg` to be in your `PATH`
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Values</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>WITH_FFMPEG</code></td>
|
||
<td>Enables/Disable FFMPEG support in LAMMPS</td>
|
||
<td>
|
||
<dl>
|
||
<dt><code>yes</code> (default, if found)</dt>
|
||
<dt><code>no</code></dt>
|
||
</dl>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>FFMPEG_EXECUTABLE</code></td>
|
||
<td>Path to ffmpeg executable, will automatically pick up the first one in your $PATH.</td>
|
||
<td>(automatic)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
|
||
## Compilers
|
||
|
||
By default, `cmake` will use your environment C/C++/Fortran compilers for a
|
||
build. It uses the `CC`, `CXX` and `FC` environment variables to detect which
|
||
compilers should be used. However, these values will be cached after the first
|
||
run of `cmake`. Subsequent runs of `cmake` will ignore changes in these
|
||
environment variables. To ensure the correct values are used you avoid the
|
||
cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
|
||
`CMAKE_Fortran_COMPILER` options directly.
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Option</th>
|
||
<th>Description</th>
|
||
<th>Default</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td><code>CMAKE_C_COMPILER</code></td>
|
||
<td>C Compiler which should be used by CMake</td>
|
||
<td>value of `CC` environment variable at first `cmake` run</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>CMAKE_CXX_COMPILER</code></td>
|
||
<td>C++ compiler which should be used by CMake</td>
|
||
<td>
|
||
value of `CXX` environment variable at first `cmake` run
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>CMAKE_Fortran_COMPILER</code></td>
|
||
<td>C++ compiler which should be used by CMake</td>
|
||
<td>
|
||
value of `FC` environment variable at first `cmake` run
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td><code>CXX_COMPILER_LAUNCHER</code></td>
|
||
<td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
|
||
<td>
|
||
(empty)
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
### Building with GNU Compilers
|
||
|
||
```bash
|
||
cmake -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ -D CMAKE_Fortran_COMPILER=gfortran ../cmake
|
||
```
|
||
|
||
### Building with Intel Compilers
|
||
|
||
```bash
|
||
cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPILER=ifort ../cmake
|
||
```
|
||
|
||
|
||
### Building with LLVM/Clang Compilers
|
||
|
||
```bash
|
||
cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
|
||
```
|
||
|
||
|
||
## Examples
|