forked from lijiext/lammps
replace more parsed-literal with code-block sections
This commit is contained in:
Axel Kohlmeyer
parent
f9b451de32
commit
ff316aa4d0
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@ -8,14 +8,14 @@ instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
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environment (named `my-lammps-env` or whatever you prefer) for your lammps
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install:
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.. parsed-literal::
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.. code-block:: bash
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% conda config --add channels conda-forge
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% conda create -n my-lammps-env
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Then, you can install lammps on your system with the following command:
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.. parsed-literal::
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.. code-block:: bash
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% conda activate my-lammps-env
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% conda install lammps
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@ -25,8 +25,7 @@ results in Conda also installing the `kim-api` binaries when LAMMPS is
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installed. In order to use potentials from `openkim.org <openkim_>`_, you can
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install the `openkim-models` package
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.. parsed-literal::
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.. code-block:: bash
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% conda install openkim-models
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@ -36,9 +35,6 @@ Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
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up the Conda capability.
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.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
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.. _openkim: https://openkim.org
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.. _conda: https://docs.conda.io/en/latest/index.html
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.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
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@ -1,4 +1,4 @@
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Download the LAMMPS source with Git
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Download the LAMMPS source with git
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===================================
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All LAMMPS development is coordinated through the "LAMMPS GitHub
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@ -11,32 +11,30 @@ has several advantages:
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* You can submit your new features back to GitHub for inclusion in
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LAMMPS.
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You must have `Git <git_>`_ installed on your system to communicate with
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the public Git server for LAMMPS.
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You must have `git <git_>`_ installed on your system to communicate with
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the public git server for LAMMPS.
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.. warning::
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As of October 2016, the official home of public LAMMPS development is
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on GitHub. The previously advertised LAMMPS git repositories on
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git.lammps.org and bitbucket.org are now deprecated, may not be
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up-to-date, and may go away at any time.
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git.lammps.org and bitbucket.org are now deprecated, and may go away at any time.
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.. _git: https://git-scm.com
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You can follow LAMMPS development on 3 different Git branches:
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You can follow LAMMPS development on 3 different git branches:
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* **stable** : this branch is updated with every stable release
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* **unstable** : this branch is updated with every patch release
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* **master** : this branch continuously follows ongoing development
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To access the Git repositories on your box, use the clone command to
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To access the git repositories on your box, use the clone command to
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create a local copy of the LAMMPS repository with a command like:
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.. parsed-literal::
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.. code-block:: bash
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git clone -b unstable https://github.com/lammps/lammps.git mylammps
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$ git clone -b unstable https://github.com/lammps/lammps.git mylammps
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where "mylammps" is the name of the directory you wish to create on
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your machine and "unstable" is one of the 3 branches listed above.
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@ -52,33 +50,32 @@ typing "make html" from the doc directory.
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After initial cloning, as bug fixes and new features are added to
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LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
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up-to-date by typing the following Git commands from within the
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up-to-date by typing the following git commands from within the
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"mylammps" directory:
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.. parsed-literal::
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.. code-block:: bash
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git checkout unstable # not needed if you always stay in this branch
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git checkout stable # use one of the 3 checkout commands
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git checkout master
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git pull
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$ git checkout unstable # not needed if you always stay in this branch
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$ git checkout stable # use one of the 3 checkout commands
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$ git checkout master
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$ git pull
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Doing a "pull" will not change any files you have added to the LAMMPS
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directory structure. It will also not change any existing LAMMPS
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files you have edited, unless those files have changed in the
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repository. In that case, Git will attempt to merge the new
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repository. In that case, git will attempt to merge the new
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repository file with your version of the file and tell you if there
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are any conflicts. See the Git documentation for details.
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are any conflicts. See the git documentation for details.
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If you want to access a particular previous release version of LAMMPS,
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you can instead "checkout" any version with a published tag. See the
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output of "git tag -l" for the list of tags. The Git command to do
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output of "git tag -l" for the list of tags. The git command to do
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this is as follows.
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.. code-block:: bash
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.. parsed-literal::
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git checkout tagID
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$ git checkout tagID
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Stable versions and what tagID to use for a particular stable version
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are discussed on :doc:`this page <Errors_bugs>`. Note that this command
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@ -92,11 +89,11 @@ checkout"), you still need to re-build LAMMPS if any source files have
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changed. To do this, you should cd to the src directory and type:
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.. parsed-literal::
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.. code-block:: bash
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make purge # remove any deprecated src files
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make package-update # sync package files with src files
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make foo # re-build for your machine (mpi, serial, etc)
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$ make purge # remove any deprecated src files
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$ make package-update # sync package files with src files
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$ make foo # re-build for your machine (mpi, serial, etc)
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just as described on the :doc:`Install patch <Install_patch>` doc page,
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after a patch has been installed.
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@ -11,10 +11,8 @@ Binaries are available for different versions of Linux:
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| :ref:`Arch Linux build-script <arch>`
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----------
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.. _ubuntu:
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Pre-built Ubuntu Linux executables
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@ -29,42 +27,37 @@ operating system.
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To install the appropriate personal-package archive (PPA), do the
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following once:
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.. code-block:: bash
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.. parsed-literal::
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sudo add-apt-repository ppa:gladky-anton/lammps
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sudo apt-get update
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$ sudo add-apt-repository ppa:gladky-anton/lammps
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$ sudo apt-get update
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To install LAMMPS do the following once:
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.. code-block:: bash
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.. parsed-literal::
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sudo apt-get install lammps-daily
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$ sudo apt-get install lammps-daily
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This downloads an executable named "lmp\_daily" to your box, which
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can then be used in the usual way to run input scripts:
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.. code-block:: bash
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.. parsed-literal::
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lmp_daily -in in.lj
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$ lmp_daily -in in.lj
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To update LAMMPS to the most current version, do the following:
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.. code-block:: bash
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.. parsed-literal::
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sudo apt-get update
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$ sudo apt-get update
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which will also update other packages on your system.
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To get a copy of the current documentation and examples:
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.. code-block:: bash
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.. parsed-literal::
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sudo apt-get install lammps-daily-doc
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$ sudo apt-get install lammps-daily-doc
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which will download the doc files in
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/usr/share/doc/lammps-daily-doc/doc and example problems in
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@ -75,26 +68,27 @@ files and auxiliary tools.
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To un-install LAMMPS, do the following:
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.. code-block:: bash
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.. parsed-literal::
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sudo apt-get remove lammps-daily
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$ sudo apt-get remove lammps-daily
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Note that the lammps-daily executable is built with the following
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sequence of make commands, as if you had done the same with the
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unpacked tarball files in the src directory:
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make yes-all; make no-lib; make openmpi
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.. code-block:: bash
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$ make yes-all
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$ make no-lib
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$ make mpi
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Thus it builds with FFTW3 and OpenMPI.
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Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
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Ubuntu package capability.
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----------
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.. _fedora:
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Pre-built Fedora Linux executables
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@ -118,12 +112,11 @@ The same mechanism applies when loading the LAMMPS python module.
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To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
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.. code-block:: bash
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.. parsed-literal::
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dnf install lammps-openmpi
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module load mpi/openmpi-x86_64
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mpirun -np 2 lmp -in in.lj
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$ dnf install lammps-openmpi
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$ module load mpi/openmpi-x86_64
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$ mpirun -np 2 lmp -in in.lj
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The "dnf install" command is needed only once. In case of a new LAMMPS
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stable release, "dnf update" will automatically update to the newer
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@ -137,9 +130,9 @@ results in the above command also installing the `kim-api` binaries when LAMMPS
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is installed. In order to use potentials from `openkim.org <openkim_>`_, you
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can install the `openkim-models` package
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.. parsed-literal::
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.. code-block:: bash
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dnf install openkim-models
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$ dnf install openkim-models
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Please use "lmp -help" to see which compilation options, packages,
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and styles are included in the binary.
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@ -150,7 +143,6 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
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----------
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.. _epel:
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Pre-built EPEL Linux executable
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@ -169,10 +161,8 @@ and styles are included in the binary.
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Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
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----------
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.. _opensuse:
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Pre-built OpenSuse Linux executable
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@ -181,18 +171,16 @@ Pre-built OpenSuse Linux executable
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A pre-built LAMMPS package for stable releases is available
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in OpenSuse as of Leap 15.0. You can install the package with:
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.. code-block:: bash
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.. parsed-literal::
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zypper install lammps
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$ zypper install lammps
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This includes support for OpenMPI. The name of the LAMMPS executable
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is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:
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.. code-block:: bash
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.. parsed-literal::
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mpirun -np 2 lmp -in in.lj
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$ mpirun -np 2 lmp -in in.lj
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Please use "lmp -help" to see which compilation options, packages,
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and styles are included in the binary.
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@ -202,16 +190,14 @@ results in the above command also installing the `kim-api` binaries when LAMMPS
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is installed. In order to use potentials from `openkim.org <openkim_>`_, you
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can install the `openkim-models` package
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.. parsed-literal::
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.. code-block:: bash
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zypper install openkim-models
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$ zypper install openkim-models
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Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
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----------
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.. _gentoo:
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Gentoo Linux executable
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@ -221,7 +207,7 @@ LAMMPS is part of Gentoo's main package tree and can be installed by
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typing:
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.. parsed-literal::
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.. code-block:: bash
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% emerge --ask lammps
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@ -231,7 +217,7 @@ built on the your machine.
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Certain LAMMPS packages can be enable via USE flags, type
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.. parsed-literal::
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.. code-block:: bash
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% equery uses lammps
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@ -240,40 +226,32 @@ for details.
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Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
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this Gentoo capability.
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----------
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.. _arch:
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Archlinux build-script
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---------------------------------
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LAMMPS is available via Arch's unofficial Arch User repository (AUR).
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There are three scripts available, named lammps, lammps-beta and lammps-git.
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They respectively package the stable, patch and git releases.
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To install, you will need to have the git package installed. You may use
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any of the above names in-place of lammps.
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.. parsed-literal::
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.. code-block:: bash
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$ git clone https://aur.archlinux.org/lammps.git
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$ cd lammps
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$ makepkg -s
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# makepkg -i
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$ makepkg -i
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To update, you may repeat the above, or change into the cloned directory,
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and execute the following, after which, if there are any changes, you may
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use makepkg as above.
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.. parsed-literal::
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.. code-block:: bash
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$ git pull
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@ -11,7 +11,7 @@ After installing Homebrew, you can install LAMMPS on your system with
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the following commands:
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.. parsed-literal::
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.. code-block:: bash
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% brew install lammps
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@ -22,7 +22,7 @@ Once LAMMPS is installed, you can test the installation with the
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Lennard-Jones benchmark file:
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.. parsed-literal::
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.. code-block:: bash
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% brew test lammps -v
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@ -32,7 +32,7 @@ installed. In order to use potentials from `openkim.org <openkim_>`_, you can
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install the `openkim-models` package
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.. parsed-literal::
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.. code-block:: bash
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% brew install openkim-models
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@ -2,7 +2,7 @@ Applying patches
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================
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It is easy to stay current with the most recent LAMMPS patch releases
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if you use Git or SVN to track LAMMPS development. Instructions for
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if you use git or SVN to track LAMMPS development. Instructions for
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how to stay current are on the :doc:`Install git <Install_git>` and
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:doc:`Install svn <Install_svn>` doc pages.
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@ -15,8 +15,8 @@ LAMMPS directory.
|
|||
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.. note::
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You should not apply patch files to a local Git or SVN repo of
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LAMMPS, only to an unpacked tarball. Use Git and SVN commands to
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You should not apply patch files to a local git or SVN repo of
|
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LAMMPS, only to an unpacked tarball. Use git and SVN commands to
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update repo versions of LAMMPS.
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Here are the steps to apply a patch file. Note that if your version
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@ -33,9 +33,9 @@ up to date.
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LAMMPS directory, where the redirected file is the name of the patch
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file.
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.. parsed-literal::
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.. code-block:: bash
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patch -bp1 < patch.12Dec16
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$ patch -bp1 < patch.12Dec16
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* A list of updated files print out to the screen. The -b switch
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creates backup files of your originals (e.g. src/force.cpp.orig), so
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@ -47,10 +47,10 @@ up to date.
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command removes deprecated src files if any were removed by the patch
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from package sub-directories.
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.. parsed-literal::
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.. code-block:: bash
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make purge
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make package-update
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$ make purge
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$ make package-update
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* Re-build LAMMPS via the "make" command.
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|
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@ -9,7 +9,6 @@ of the `LAMMPS website <lws_>`_.
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.. _older: http://lammps.sandia.gov/tars
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.. _lws: http://lammps.sandia.gov
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You have two choices of tarballs, either the most recent stable
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release or the most current patch release. Stable releases occur a
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few times per year, and undergo more testing before release. Patch
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@ -25,27 +24,23 @@ Older versions of LAMMPS can also be downloaded from `this page <older_>`_.
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Once you have a tarball, unzip and untar it with the following
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command:
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.. code-block:: bash
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.. parsed-literal::
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tar -xzvf lammps\*.tar.gz
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$ tar -xzvf lammps\*.tar.gz
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This will create a LAMMPS directory with the version date
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in its name, e.g. lammps-23Jun18.
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|
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|
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----------
|
||||
|
||||
|
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You can also download a zip file via the "Clone or download" button on
|
||||
the `LAMMPS GitHub site <git_>`_. The file name will be lammps-master.zip
|
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which can be unzipped with the following command, to create
|
||||
a lammps-master dir:
|
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|
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.. code-block:: bash
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.. parsed-literal::
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unzip lammps\*.zip
|
||||
$ unzip lammps\*.zip
|
||||
|
||||
This version is the most up-to-date LAMMPS development version. It
|
||||
will have the date of the most recent patch release (see the file
|
||||
|
|
@ -55,9 +50,6 @@ the next patch release tarball.
|
|||
|
||||
.. _git: https://github.com/lammps/lammps
|
||||
|
||||
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -14,8 +14,8 @@ Specifically, LAMMPS was not conceived and designed for:
|
|||
* visualize your MD simulation interactively
|
||||
* plot your output data
|
||||
|
||||
Although over the years these limitations have been somewhat
|
||||
reduced through features added to LAMMPS or external tools
|
||||
Over the years some of these limitations have been reduced or
|
||||
removed, through features added to LAMMPS or external tools
|
||||
that either closely interface with LAMMPS or extend LAMMPS.
|
||||
|
||||
Here are suggestions on how to perform these tasks:
|
||||
|
|
|
|||
Loading…
Reference in New Issue