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!
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.
The installation of the library for python use can be done simply with:
pip install .
assuming that python 3.5 (or higher) and gcc or clang are available.
Before installing librascal, please make sure you have at least the following packages installed:
|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 compression||skcosmo||0.1.0 or later|
|Rotational algebra (Clebsch-Gordan coeffs.)||sympy||1.4 or later|
|sphinx||2.1.2 or later|
|breathe||4.14.1 or later|
|nbsphinx||0.8.1 or later|
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:
- Boost (only the unit test framework library)
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:
pip install -r requirements.txt
To configure and compile the code with the default options, on *nix systems (Windows is not supported):
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.
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:
cd build cmake -DBUILD_TESTS=ON .. make ctest -V
You can also run the tests with Valgrind (a memory-error checker) by passing
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:
sudo apt-get install clang-format-8 pip3 install black
Several build types are available Release (default), Debug and RelWithDebInfo. To build an alternative mode
cd build cmake -DCMAKE_BUILD_TYPE=Debug .. make
cd build cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo \\ CMAKE_C_FLAGS_RELWITHDEBUBINFO="-03 -g -DNDEBUG" .. make
The documentation relies on the sphinx (with nbsphinx and breathe extensions), doxygen, pandoc, and graphviz packages. To install them on ubuntu:
pip3 install sphinx sphinx_rtd_theme breathe nbsphinx sudo apt-get install pandoc doxygen graphviz
Then to build the documentation run:
cd build cmake -DBUILD_DOC=ON .. make doc
and open :file:`build/docs/html/index.html` in a browser.
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:
cd build cmake -DBUILD_BINDINGS=OFF .. make
To install the python library with c++ bindings:
pip install .
Helpers for Developers
To remove all the cmake files/folders except for the external library (enable glob and remove):
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:
sudo apt-get install clang-format pip install black
The automatic formatting of the c++ and python files can be triggered by:
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:
// clang-format off SOME CODE TO IGNORE // clang-format on
SOME LINE TO IGNORE # noqa
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
init_cell set to
True, so use these fields
judiciously. You can ignore these settings with the following command:
git config filter.nbstripout.extrakeys '\ cell.metadata.keep_output cell.metadata.init_cell'
metadata.kernel_spec.display_name may also be useful to reduce diff
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) for
inclusion in the
- Common cmake flags:
- Special flags:
- ON (default) -> build python binding
- OFF -> does not build python binding
- empty (default) -> does not install in a custom folder
- custom string -> root path for the installation
To build librascal as a docker environment:
sudo docker build -t test -f ./docker/install_env.dockerfile . sudo docker run -it -v /path/to/repo/:/home/user/ test