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lab-cosmo / librascal

A scalable and versatile library to generate representations for atomic-scale learning
https://lab-cosmo.github.io/librascal/
GNU Lesser General Public License v2.1
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librascal

.. start-intro

librascal is a versatile and scalable fingerprint and machine learning code. It focuses on the efficient construction of representations of atomic structures, that can then be fed to any supervised or unsupervised learning algorithm. Simple regression code will be included for testing purposes, but the long-term goal is to develop a separate collection of tools to this end.

librascal is currently considered a standalone code. However, we aim to provide enough flexibility to interface it with other codes such as LAMMPS and PLUMED-2.0. It can be used as a C++ library as well as a python module. To be able to call it from python, we have used the pybind11_ library.

Although at the moment is a serial-only code, we aim to write it in MPI so that it will be possible to take advantage of parallelization to speed up the calculations significantly. Parallelization is possible especially over atoms in a structure (for large structures), over structures in a collection (for large collections of small structures), or over components of a representation (for representations with a large number of independent functions or components).

librascal is distributed under the GNU Lesser General Public License version 2.1 or later, at your convenience. This means that it can be modified and freely distributed, although we take no responsibility for its misuse.

For more information, have a look at the documentation_!

.. _documentation: https://lab-cosmo.github.io/librascal/ .. _pybind11: https://pybind11.readthedocs.io

Development

The code is currently in the alpha development phase; it is not yet suitable for public use. Nevertheless, there is a significant amount of functionality (including two tutorials) currently working and available to test if you’re feeling adventurous. Feedback and bug reports are welcome, as long as you keep the above in mind.

.. end-intro

See Helpers for Developers below for some essential tools if you want to help develop libRascal. Be sure to also read CONTRIBUTING.rst <CONTRIBUTING.rst> if you plan on making a contribution.

Installation

.. start-install

The installation of the library for python use can be done simply with:

.. code:: bash

pip install .

assuming that python 3.5 (or higher) and gcc or clang are available.

Dependencies


Before installing librascal, please make sure you have at least the
following packages installed:

+-------------+--------------------+
| Package     | Required version   |
+=============+====================+
| gcc (g++)   | 4.9 or higher      |
+-------------+--------------------+
| clang       | 4.0 or higher      |
+-------------+--------------------+
| cmake       | 2.8 or higher      |
+-------------+--------------------+
| python      | 3.6 or higher      |
+-------------+--------------------+
| numpy       | 1.13 or higher     |
+-------------+--------------------+
| scipy       | 1.4.0 or higher    |
+-------------+--------------------+
| ASE         | 3.18 or higher     |
+-------------+--------------------+

Other necessary packages (such as Eigen and pybind11) are downloaded
automatically when compiling Rascal.

The following packages are required for some optional features:

+--------------------------+-------------+--------------------+
| Feature                  | Package     | Required version   |
+==========================+=============+====================+
| Feature compression      | skmatter    | 0.1.0 or later     |
+--------------------------+-------------+--------------------+
| Rotational algebra       | sympy       | 1.4 or later       |
| (Clebsch-Gordan coeffs.) |             |                    |
+--------------------------+-------------+--------------------+
| Building documentation   | pandoc      | (latest)           |
+--------------------------+-------------+--------------------+
|                          | sphinx      | 2.1.2 or later     |
+--------------------------+-------------+--------------------+
|                          | breathe     | 4.14.1 or later    |
+--------------------------+-------------+--------------------+
|                          | nbsphinx    | 0.8.1 or later     |
+--------------------------+-------------+--------------------+

Compiling

To compile the code it is necessary to have CMake 3.0 and a C++ compiler supporting C++14. During the configuration, it will automatically try to download the external libraries on which it depends:

And the following libraries to build the documentation:

Beware, Python3 is mandatory. The code won’t work with a Python version older than 3.

You can then use pip to install all python packages required for the usage and development of rascal:

.. code:: bash

pip install -r requirements.txt

To configure and compile the code with the default options, on *nix systems (Windows is not supported):

.. code:: shell

mkdir build cd build cmake .. make

Customizing the build


The library supports several alternative builds that have additional
dependencies. Note that the ``ncurses`` GUI for cmake (ccmake) is quite
helpful to customize the build options.

Tests
^^^^^

Librascal source code is extensively tested (both c++ and python).
The BOOST unit_test_framework is required to build the tests (see
BOOST.md for further details on how to install the boost library). To
build and run the tests:

.. code:: shell

   cd build
   cmake -DBUILD_TESTS=ON ..
   make
   ctest -V

You can also run the tests with Valgrind (a memory-error checker) by passing
``-DRASCAL_TESTS_USE_VALGRIND=ON`` to ``cmake``.

In addition to testing the behaviour of the code, the test suite also check
for formatting compliance with clang-format 8.0 or higher and black packages
(these dependencies are optional). To install these dependencies on Ubuntu:

.. code:: shell

   sudo apt-get install clang-format-8
   pip3 install black

Build Type
^^^^^^^^^^

Several build types are available Release (default), Debug and
RelWithDebInfo. To build an alternative mode

.. code:: shell

   cd build
   cmake -DCMAKE_BUILD_TYPE=Debug
   ..
   make

Or

.. code:: shell

   cd build
   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo  \\
      CMAKE_C_FLAGS_RELWITHDEBUBINFO="-03 -g -DNDEBUG" ..
   make

Documentation
^^^^^^^^^^^^^

The documentation relies on the sphinx (with nbsphinx and breathe
extensions), doxygen, pandoc, and graphviz
packages. To install them on ubuntu:

.. code:: shell

  pip3 install sphinx sphinx_rtd_theme breathe nbsphinx
  sudo apt-get install pandoc doxygen graphviz

Then to build the documentation run:

.. code:: shell

  cd build
  cmake -DBUILD_DOC=ON ..
  make doc

and open :file:`build/docs/html/index.html` in a browser.

Bindings
^^^^^^^^

Librascal relies on the pybind11 library to automate the generation
of the python bindings which are built by default. Nevertheless, to
build only the c++ library:

.. code:: shell

   cd build
   cmake -DBUILD_BINDINGS=OFF ..
   make

Installing rascal
^^^^^^^^^^^^^^^^^
To install the python library with c++ bindings:

.. code:: shell

   pip install .

Helpers for Developers

Deepclean ^^^^^^^^^

To remove all the cmake files/folders except for the external library (enable glob and remove):

.. code:: shell

shopt -s extglob rm -fr -- !(external|third-party)

Automatic code formatting ^^^^^^^^^^^^^^^^^^^^^^^^^

To help developers conform their contribution to the coding convention, the formatting of new functionalities can be automated using clang-format (for the c++ files) and black (for the python files). The .clang-format and .pycodestyle files define common settings to be used.

To enable these functionalities (optional) you can install these tools with:

.. code:: shell

sudo apt-get install clang-format pip install black

The automatic formatting of the c++ and python files can be triggered by:

.. code:: shell

cd build cmake .. make pretty-cpp make pretty-python

Please use these tools with caution as they can potentially introduce unwanted changes to the code. If code needs to be specifically excluded from auto formatting, e.g. a matrix which should be human-readable, code comments tells the formatters to ignore lines:

Jupyter notebooks ^^^^^^^^^^^^^^^^^

If you are contributing any code in IPython/Jupyter notebooks, please install the nbstripout extension (available e.g. on github <https://github.com/kynan/nbstripout#installation> and PyPI <https://pypi.org/project/nbstripout/>). After installing, activate it for this project by running:

.. code:: shell

nbstripout --install --attributes .gitattributes

from the top-level repository directory. Please note that that nbstripout will not strip output from cells with the metadata fields keep_output or init_cell set to True, so use these fields judiciously. You can ignore these settings with the following command:

.. code:: shell

git config filter.nbstripout.extrakeys '\ cell.metadata.keep_output cell.metadata.init_cell'

(The keys metadata.kernel_spec.name and metadata.kernel_spec.display_name may also be useful to reduce diff noise.)

Nonetheless, it is highly discouraged to contribute code in the form of notebooks; even with filters like nbstripout they're a hassle to use in version control. Use them only for tutorials or stable examples that are either meant to be run interactively or are meant to be processed by sphinx (nbsphinx <https://nbsphinx.readthedocs.io/en/latest/>) for inclusion in the tutorials page <https://lab-cosmo.github.io/librascal/tutorials/tutorials.html>.

Miscellaneous Information

To build librascal as a docker environment:

.. code:: shell

sudo docker build -t test -f ./docker/install_env.dockerfile . sudo docker run -it -v /path/to/repo/:/home/user/ test