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Added lots of docs, finished CMake script

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This commit is contained in:
Andreas Singraber
2021-02-24 17:57:24 +01:00
parent c56f665c5b
commit e713a931d3
12 changed files with 238 additions and 54 deletions
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25
doc/src/Build_extras.rst
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@ -1592,17 +1592,38 @@ on your system.
USER-NNP package
---------------------------------
To build with the USER-NNP package it is required to download and build the
external `n2p2 <https://github.com/CompPhysVienna/n2p2>`__ library ``v2.2.0``
(or higher) before starting the LAMMPS build process. More specifically, only
the *n2p2* core library ``libnnp`` and interface library ``libnnpif`` are
actually needed: when using GCC it should suffice to execute ``make libnnpif``
in the *n2p2* ``src`` directory. For more details please see the `n2p2 build
documentation <https://compphysvienna.github.io/n2p2/topics/build.html>`__. If
*n2p2* is downloaded and compiled in the LAMMPS directory ``lib/nnp/n2p2`` no
special flags need to be set besides the usual package activation. If you prefer
to install *n2p2* somewhere else on your system you must specify the path via
the ``N2P2_DIR`` variable.
.. tabs::
.. tab:: CMake build
There is one additional setting besides ``-D PKG_USER-NNP=yes`` in case
*n2p2* is not installed in the ``lib/nnp/n2p2`` directory:
.. code-block:: bash
ADD STUFF HERE
-D N2P2_DIR=path # path ... n2p2 installation path
.. tab:: Traditional make
ADD STUFF HERE
There is one additional variable that needs to be set besides ``make
yes-user-nnp`` in case *n2p2* is not installed in the ``lib/nnp/n2p2``
directory:
.. code-block:: bash
make N2P2_DIR=path ...
----------

2
doc/src/Packages_user.rst
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@ -79,7 +79,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NNP <PKG-USER-NNP>` | High-dimensional neural network potenials | :doc:`pair_style nnp <pair_nnp>` | USER/nnp | ext |
| :ref:`USER-NNP <PKG-USER-NNP>` | High-dimensional neural network potentials | :doc:`pair_style nnp <pair_nnp>` | USER/nnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

12
doc/src/pair_nnp.rst
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@ -112,7 +112,7 @@ function setup, ``scaling.data`` with symmetry function scaling data and
The keyword *showew* can be used to turn on/off the display of extrapolation
warnings (EWs) which are issued whenever a symmetry function value is out of
bounds defined by minimum/maximum values in "scaling.data". An extrapolation
bounds defined by minimum/maximum values in ``scaling.data``. An extrapolation
warning may look like this:
.. code-block:: LAMMPS
@ -221,14 +221,14 @@ present elements (see above).
.. _Behler_Parrinello_2007:
**(Behler and Parrinello 2007)** Behler, J.; Parrinello, M. Generalized
**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized
Neural-Network Representation of High-Dimensional Potential-Energy Surfaces.
Phys. Rev. Lett. 2007, 98 (14), 146401.
https://doi.org/10.1103/PhysRevLett.98.146401
<https://doi.org/10.1103/PhysRevLett.98.146401>`__
.. _Singraber_et_al_2019:
**(Singraber et al 2019)** Singraber, A.; Behler, J.; Dellago, C. Library-Based
**(Singraber et al 2019)** `Singraber, A.; Behler, J.; Dellago, C. Library-Based
LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem.
Theory Comput. 2019, 15 (3), 1827–1840.
https://doi.org/10.1021/acs.jctc.8b00770.
Theory Comput. 2019, 15 (3), 1827-1840
<https://doi.org/10.1021/acs.jctc.8b00770>`__