update docs
This commit is contained in:
Axel Kohlmeyer
@ -90,7 +90,7 @@ For *Fix* classes there is an optional second argument to the
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fix performs multiple modes of communication, with different numbers
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of values per atom. The fix should set the *comm_forward* and
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*comm_reverse* variables to the maximum value, but can invoke the
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communication for a particulard mode with a smaller value. For this
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communication for a particular mode with a smaller value. For this
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to work, the *pack_forward_comm()*, etc methods typically use a class
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member variable to choose which values to pack/unpack into/from the
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buffer.
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@ -25,11 +25,10 @@ Installing the LAMMPS Python Module and Shared Library
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======================================================
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Making LAMMPS usable within Python and vice versa requires putting the
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LAMMPS Python package (``lammps``) into a location where the
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Python interpreter can find it and installing the LAMMPS shared library
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into a folder that the dynamic loader searches or inside of the installed
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``lammps`` package folder. There are multiple ways to achieve
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this.
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LAMMPS Python package (``lammps``) into a location where the Python
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interpreter can find it and installing the LAMMPS shared library into a
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folder that the dynamic loader searches or inside of the installed
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``lammps`` package folder. There are multiple ways to achieve this.
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#. Do a full LAMMPS installation of libraries, executables, selected
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headers, documentation (if enabled), and supporting files (only
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@ -159,33 +158,30 @@ this.
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make install-python
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This will try to install (only) the shared library and the Python
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package into a system folder and if that fails (due to missing
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write permissions) will instead do the installation to a user
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folder under ``$HOME/.local``. For a system-wide installation you
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This will try to build a so-called (binary) 'wheel', a compressed
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binary python package and then install it with the python package
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manager 'pip'. Installation will be attempted into a system-wide
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``site-packages`` folder and if that fails into the corresponding
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folder in the user's home directory. For a system-wide installation you
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would have to gain superuser privilege, e.g. though ``sudo``
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
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| File | Location | Notes |
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+========================+=================================================================+=============================================================+
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| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+========================+==========================================================+=============================================================+
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| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
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For a system-wide installation those folders would then become.
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+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+-------------------------------------------------+-------------------------------------------------------------+
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| File | Location | Notes |
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+========================+=========================================================+=============================================================+
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| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
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+========================+=================================================+=============================================================+
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| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+-------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+-------------------------------------------------+-------------------------------------------------------------+
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No environment variables need to be set for those, as those
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folders are searched by default by Python or the LAMMPS Python
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@ -201,16 +197,12 @@ this.
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.. code-block:: bash
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$ python install.py -p <python package> -l <shared library> -v <version.h file> [-d <pydir>]
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$ python install.py -p <python package> -l <shared library> [-n]
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* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
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* the ``-l`` flag points to the LAMMPS shared library file to be installed,
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* the ``-v`` flag points to the ``version.h`` file in the LAMMPS source
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* and the optional ``-d`` flag to a custom (legacy) installation folder
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If you use a legacy installation folder, you will need to set your
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``PYTHONPATH`` and ``LD_LIBRARY_PATH`` (and/or ``DYLD_LIBRARY_PATH``) environment
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variables accordingly as explained in the description for "In place use".
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* and the optional ``-n`` instructs the script to only build a wheel file
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but not attempt to install it.
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.. tab:: Virtual environment
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@ -257,32 +249,29 @@ this.
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package and the shared library file are installed into the
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following locations:
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| File | Location | Notes |
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+========================+=================================================================+=============================================================+
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| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+========================+========================================================+=============================================================+
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| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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If you do a full installation (CMake only) with "install", this
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leads to the following installation locations:
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| File | Location | Notes |
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+========================+=================================================================+=============================================================+
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| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
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| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+========================+========================================================+=============================================================+
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| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
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| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
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+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
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+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
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In that case you need to modify the ``$HOME/myenv/bin/activate``
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script in a similar fashion you need to update your
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