mirror of https://github.com/lammps/lammps.git
85c394453c
This update contains several fixes and small new features or usability improvements. Descriptions and authorship information can be accessed from the pull requests listed below. Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin) https://github.com/Colvars/colvars/pull/357 Do not accumulate data at step 0 (@giacomofiorin) https://github.com/Colvars/colvars/pull/345 Support for symmetry permutations of atoms in RMSD (@jhenin) https://github.com/Colvars/colvars/pull/344 Detect new grid parameters (@jhenin) https://github.com/Colvars/colvars/pull/341 Only access the output streams in non-threaded regions (@giacomofiorin) https://github.com/Colvars/colvars/pull/338 Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin) https://github.com/Colvars/colvars/pull/334 Fix typo (@e-kwsm) https://github.com/Colvars/colvars/pull/333 Convert the input keyword to lowercase in read_state_data_key (@HanatoK) https://github.com/Colvars/colvars/pull/332 Implement reflecting b.c. for ext Lagrangian (@jhenin) https://github.com/Colvars/colvars/pull/329 |
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| Makefile | ||
| README | ||
| documentation_conventions.md | ||
| github-development-workflow.md | ||
| include-file-conventions.md | ||
| lammps.1 | ||
| msi2lmp.1 | ||
README
LAMMPS Documentation Depending on how you obtained LAMMPS and whether you have built the manual yourself, this directory has a varying number of sub-directories and files. Here is a list with descriptions: README this file src content files for LAMMPS documentation html HTML version of the LAMMPS manual (see html/Manual.html) utils utilities and settings for building the documentation Manual.pdf PDF version of entire manual Developer.pdf PDF with info about how LAMMPS is structured LAMMPS.epub Manual in ePUB format LAMMPS.mobi Manual in MOBI (Kindle) format lammps.1 man page for the lammps command msi2lmp.1 man page for the msi2lmp command mathjax code and fonts for rendering math in html doctree temporary data docenv python virtual environment for generating the manual doxygen Doxygen configuration and output .gitignore list of files and folders to be ignored by git doxygen-warn.log logfile with warnings from running doxygen and: github-development-workflow.md notes on the LAMMPS development workflow include-file-conventions.md notes on LAMMPS' include file conventions documentation_conventions.md notes on writing documentation for LAMMPS If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html folder and the PDF manual should be included. If you downloaded LAMMPS from GitHub then you either need to download them or build them. (a) You can "fetch" the current HTML and PDF files from the LAMMPS web site. Just type "make fetch". This should create a html_www dir and Manual_www.pdf/Developer_www.pdf files. These files will always represent the latest published patch/development version of LAMMPS. (b) You can build the HTML and PDF files yourself, by typing "make html" or by "make pdf", respectively. This requires various tools and files. Some of them have to be installed (more on that below). For the rest the build process will attempt to download and install into a python virtual environment and local folders. ---------------- Installing prerequisites for the documentation build To run the HTML documention build toolchain, python 3.x, doxygen, git, and virtualenv have to be installed. Also internet access is initially required to download external files and tools. Building the PDF format manual requires in addition a compatible LaTeX installation with support for PDFLaTeX and several add-on LaTeX packages installed. This includes: - amsmath - anysize - babel - capt-of - cmap - fncychap - framed - geometry - hyperref - hypcap - needspace - times - tabulary - upquote - wrapfig Building the EPUB format requires LaTeX installation with the same packages as for the PDF format plus the 'dvipng' command to convert the embedded math into images. The MOBI format is generated from the EPUB format file by using the tool 'ebook-convert' from the 'calibre' e-book management software (https://calibre-ebook.com). ---------------- More details this can be found in the manual itself. The online version is at: https://lammps.sandia.gov/doc/Manual_build.html