Merge branch 'master' into library_interface_update

  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)

  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)

  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)

  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})

  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)

  add_custom_command(

    OUTPUT docenv

    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters

  )

  set(RST_FILES "")

  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)

  file(MAKE_DIRECTORY ${RST_DIR})

  foreach(TXT_FILE ${DOC_SOURCES})

    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)

    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)

    list(APPEND RST_FILES ${RST_FILE})

    add_custom_command(

      OUTPUT ${RST_FILE}

      DEPENDS requirements.txt docenv ${TXT_FILE}

      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}

    )

  endforeach()

  add_custom_command(

    OUTPUT html

    DEPENDS ${RST_FILES}

    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}

    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html

    DEPENDS ${DOC_SOURCES} docenv requirements.txt

    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html

  )

  add_custom_target(

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

utils           utilities 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

code will not, unless you update your local repository).

(b) You can build the HTML and PDF files yourself, by typing "make

html" followed by "make pdf".  Note that the PDF make requires the

HTML files already exist.  This requires various tools including

Sphinx, which the build process will attempt to download and install

on your system, if not already available.  See more details below.

(c) You can genererate an older, simpler, less-fancy style of HTML

documentation by typing "make old".  This will create an "old"

directory.  This can be useful if (b) does not work on your box for

some reason, or you want to quickly view the HTML version of a doc

page you have created or edited yourself within the src directory.

E.g. if you are planning to submit a new feature to LAMMPS.

html" or by "make pdf", respectively.  This requires various tools

including the Python documentation processing tool Sphinx, which the

build process will attempt to download and install on your system into

a python virtual environment, if not already available.  The PDF file

will require a working LaTeX installation with several add-on packages

in addition to the Python/Sphinx setup.  See more details below.

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

make html         # generate HTML in html dir using Sphinx

make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)

                  #   in this dir via htmldoc and pdflatex

make old          # generate old-style HTML pages in old dir via txt2html

                  #   in this dir via Sphinx and PDFLaTeX

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

Installing prerequisites for PDF build

[TBA]

Same as for HTML plus a compatible LaTeX installation with

support for PDFLaTeX. Also the following LaTeX packages need

to be installed (e.g. from texlive):

- amsmath

- babel

- cmap

- fncychap

- geometry

- hyperref

- hypcap

- times

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

Installing prerequisites for epub build

## ePUB

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

files as the HTML tree.

files as the HTML tree. The ePUB format conversion currently

does not support processing mathematical expressions via MathJAX,

so there will be limitations on some pages. For the time being

until this is resolved, building and using the PDF format file

is recommended instead.

For converting the generated ePUB file to a mobi format file

(for e-book readers like Kindle, that cannot read ePUB), you

.TH LAMMPS "30 October 2019" "2019-10-30"

.TH LAMMPS "20 November 2019" "2019-11-20"

.SH NAME

.B LAMMPS

\- Molecular Dynamics Simulator.

Eqs

JPG

/Eqs

/JPG

/false_positives.txt

   :maxdepth: 1

   Commands_removed

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html