Merge branch 'develop' into mdi-tweak
This commit is contained in:
Steve Plimpton
@ -788,8 +788,10 @@ library.
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.. code-block:: bash
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-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
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-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
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-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
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-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
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-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
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# value = no (default) or yes
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If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
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and built inside the CMake build directory. If the LATTE library
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@ -797,6 +799,13 @@ library.
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``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
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file, not the directory the library file is in.
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The LATTE library requires LAPACK (and BLAS) and CMake can identify
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their locations and pass that info to the LATTE build script. But
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on some systems this triggers a (current) limitation of CMake and
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the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
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those cases to use the bundled linear algebra library and work around
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the limitation.
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.. tab:: Traditional make
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You can download and build the LATTE library manually if you
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@ -1913,14 +1922,25 @@ within CMake will download the non-commercial use version.
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.. code-block:: bash
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-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
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-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
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-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
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-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
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-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
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# value = no (default) or yes
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CMake will try to download and build the QUIP library from GitHub, if it is not
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found on the local machine. This requires to have git installed. It will use the same compilers
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and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
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Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
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and installed QUIP library and CMake cannot find it.
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CMake will try to download and build the QUIP library from GitHub,
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if it is not found on the local machine. This requires to have git
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installed. It will use the same compilers and flags as used for
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compiling LAMMPS. Currently this is only supported for the GNU
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and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
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want to use a previously compiled and installed QUIP library and
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CMake cannot find it.
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The QUIP library requires LAPACK (and BLAS) and CMake can identify
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their locations and pass that info to the QUIP build script. But
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on some systems this triggers a (current) limitation of CMake and
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the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
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those cases to use the bundled linear algebra library and work around
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the limitation.
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.. tab:: Traditional make
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@ -48,18 +48,15 @@ Build using GNU make
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The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
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can be translated to different output format using the `Sphinx
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<sphinx_>`_ document generator tool. It also incorporates programmer
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documentation extracted from the LAMMPS C++ sources through the `Doxygen
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<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
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(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
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readers) are supported. For that to work a Python 3 interpreter, the
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``doxygen`` tools and internet access to download additional files and
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tools are required. This download is usually only required once or
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after the documentation folder is returned to a pristine state with
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``make clean-all``.
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.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
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.. _sphinx: https://www.sphinx-doc.org
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<https://sphinx-doc.org>`_ document generator tool. It also
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incorporates programmer documentation extracted from the LAMMPS C++
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sources through the `Doxygen <https://doxygen.nl>`_ program. Currently
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the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
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and MOBI (for Amazon Kindle readers) are supported. For that to work a
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Python 3 interpreter, the ``doxygen`` tools and internet access to
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download additional files and tools are required. This download is
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usually only required once or after the documentation folder is returned
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to a pristine state with ``make clean-all``.
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For the documentation build a python virtual environment is set up in
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the folder ``doc/docenv`` and various python packages are installed into
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@ -252,6 +249,5 @@ manual with ``make spelling``. This requires `a library called enchant
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positives* (e.g. keywords, names, abbreviations) those can be added to
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the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
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.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
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.. _lws: https://www.lammps.org
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.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
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@ -100,13 +100,14 @@ Documentation (strict)
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Contributions that add new styles or commands or augment existing ones
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must include the corresponding new or modified documentation in
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`ReStructuredText format <rst>`_ (.rst files in the ``doc/src/`` folder). The
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documentation shall be written in American English and the .rst file
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must use only ASCII characters so it can be cleanly translated to PDF
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files (via `sphinx <sphinx>`_ and PDFLaTeX). Special characters may be included via
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embedded math expression typeset in a LaTeX subset.
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`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
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folder). The documentation shall be written in American English and the
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.rst file must use only ASCII characters so it can be cleanly translated
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to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
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Special characters may be included via embedded math expression typeset
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in a LaTeX subset.
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.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
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.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
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When adding new commands, they need to be integrated into the sphinx
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documentation system, and the corresponding command tables and lists
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@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and
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also a spell check, a check for correct anchors and labels, and a check
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for completeness of references all styles in their corresponding tables
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and lists is run. In case the spell check reports false positives they
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can be added to the file doc/utils/sphinx-config/false_positives.txt
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can be added to the file ``doc/utils/sphinx-config/false_positives.txt``
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Contributions that add or modify the library interface or "public" APIs
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from the C++ code or the Fortran module must include suitable doxygen
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