Merge branch 'master' into collected-doc-fixes (52dd9aee) · Commits · 郑智淋 / lammps

doc/.gitignore

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		/html
		/LAMMPS.epub
		/LAMMPS.mobi
		/Manual.pdf
		/Developer.pdf

doc/Makefile

+16 −1

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		@@ -22,7 +22,7 @@ endif
		SOURCES=$(wildcard src/*.txt)
		OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

		.PHONY: help clean-all clean html pdf old venv
		.PHONY: help clean-all clean epub html pdf old venv

		# ------------------------------------------

		@@ -32,6 +32,7 @@ help:
		@echo " pdf create Manual.pdf and Developer.pdf in this dir"
		@echo " old create old-style HTML doc pages in old dir"
		@echo " fetch fetch HTML and PDF files from LAMMPS web site"
		@echo " epub create ePUB format manual for e-book readers"
		@echo " clean remove all intermediate RST files"
		@echo " clean-all reset the entire build environment"
		@echo " txt2html build txt2html tool"
		@@ -63,6 +64,20 @@ html: $(OBJECTS)
		@rm -rf html/USER//.[sg]*
		@echo "Build finished. The HTML pages are in doc/html."

		epub: $(OBJECTS)
		@mkdir -p epub
		@rm -f LAMMPS.epub
		@cp src/JPG/lammps-logo.png epub/
		@(\
		. $(VENV)/bin/activate ;\
		cp -r src/* $(RSTDIR)/ ;\
		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
		deactivate ;\
		)
		@mv epub/LAMMPS.epub .
		@rm -rf epub
		@echo "Build finished. The ePUB manual file is created."

		pdf: utils/txt2html/txt2html.exe
		@(\
		cd src; \

doc/README

+23 −1

Original line number	Diff line number	Diff line
		LAMMPS Documentation

		Depending on how you obtained LAMMPS, this directory has 2 or 3
		sub-directories and optionally 2 PDF files:
		sub-directories and optionally 2 PDF files and an ePUB file:

		src content files for LAMMPS documentation
		html HTML version of the LAMMPS manual (see html/Manual.html)
		tools tools and settings for building the documentation
		Manual.pdf large PDF version of entire manual
		Developer.pdf small PDF with info about how LAMMPS is structured
		LAMMPS.epub Manual in ePUB format

		If you downloaded LAMMPS as a tarball from the web site, all these
		directories and files should be included.
		@@ -49,6 +50,7 @@ make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
		make old # generate old-style HTML pages in old dir via txt2html
		make fetch # fetch HTML doc pages and 2 PDF files from web site
		# as a tarball and unpack into html dir and 2 PDFs
		make epub # generate LAMMPS.epub in ePUB format using Sphinx
		make clean # remove intermediate RST files created by HTML build
		make clean-all # remove entire build folder and any cached data

		@@ -91,3 +93,23 @@ This will install virtualenv from the Python Package Index.
		----------------

		Installing prerequisites for PDF build

		[TBA]

		----------------

		Installing prerequisites for epub build

		## ePUB

		Same as for HTML. This uses the same tools and configuration
		files as the HTML tree.

		For converting the generated ePUB file to a mobi format file
		(for e-book readers like Kindle, that cannot read ePUB), you
		also need to have the 'ebook-convert' tool from the "calibre"
		software installed. http://calibre-ebook.com/
		You first create the ePUB file with 'make epub' and then do:

		ebook-convert LAMMPS.epub LAMMPS.mobi

doc/src/JPG/lammps-logo.png

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doc/src/Section_packages.txt

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		@@ -1153,6 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
		"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
		"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
		"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
		"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
		"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
		"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
		"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
		@@ -1598,6 +1599,29 @@ The person who created this package is Axel Kohlmeyer at Temple U

		:line

		USER-NC-DUMP package :link(USER-NC-DUMP),h5

		Contents: Dump styles for writing NetCDF format files. NetCDF is a binary,
		portable, self-describing file format on top of HDF5. The file format
		contents follow the AMBER NetCDF trajectory conventions
		(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
		convention. This package implements a "dump nc"_dump_nc.html command
		and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
		in this format. See src/USER-NC-DUMP/README for more details.

		NetCDF files can be directly visualized with the following tools:
		Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
		and all of the above extensions. :ulb,l
		VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
		AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
		a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

		The person who created these files is Lars Pastewka at
		Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
		Contact him directly if you have questions.

		:line

		USER-OMP package :link(USER-OMP),h5

		Supporting info:

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