.github/workflows | ||
cmake | ||
docker | ||
docs | ||
helpers-debian | ||
include | ||
lib | ||
m4 | ||
ocaml/trexio | ||
pkgconfig | ||
python | ||
rust/trexio | ||
src | ||
tests | ||
tools | ||
.devel | ||
.gitignore | ||
.gitmodules | ||
.pre-commit-config.yaml | ||
AUTHORS | ||
autogen.sh | ||
ChangeLog | ||
CITATION.cff | ||
CMakeLists.txt | ||
configure.ac | ||
COPYING | ||
INSTALL | ||
LICENSE | ||
Makefile.am | ||
NEWS | ||
README | ||
README.md | ||
trex.org | ||
version_memo.txt |
TREXIO
TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations. It is compatible with a variety of platforms and has interfaces for the Fortran, Python, OCaml and Rust programming languages.
Installation
Installation from a package
Debian/Ubuntu
The official release of TREXIO 2.2.0
is available as a
Debian (.deb
) package thanks to the Debichem Team. The source
code is hosted here and the
pre-built binary files are available via the Debian package
registry.
TREXIO is also available on Ubuntu 23.04 (Lunar Lobster) and newer and can be installed as follows:
sudo apt-get update && sudo apt-get install libtrexio-dev
Conda
The official releases of TREXIO >2.0.0
are also
available via the conda-forge
channel. The pre-compiled
stable binaries of trexio
can be installed as follows:
conda install -c conda-forge trexio
More details can be found in the corresponding trexio-feedstock.
Note that both parallel (see mpi_openmpi
prefix) and serial
(nompi
) variants are provided.
Spack
The official releases >=2.0.0
and the development
version of TREXIO can be installed using the Spack package manager. The trexio/package.py
file contains the Spack specifications required to build different
variants of trexio
library. It can be installed as
follows
spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
Guix
The official releases of TREXIO >=2.0.0
can be
installed using the GNU Guix
functional package manager. The trexio.scm
Schema file contains the manifest specification for the
trexio
package. It can be installed as follows:
guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
Installation from source
Minimal requirements (for users):
- Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
- C compiler (gcc/icc/clang)
- Fortran compiler (gfortran/ifort)
- HDF5 library (>= 1.8) [optional, recommended for high performance]
Recommended: Installation from the release tarball
- Download the
trexio-<version>.tar.gz
file from the GitHub release page gzip -cd trexio-<version>.tar.gz | tar xvf -
cd trexio-<version>
./configure
make -j 4
make -j 4 check
sudo make install
In environments where sudo
access is unavailable, a
common workaround for executing make install/uninstall
commands without requiring superuser privileges involves a modification
to the ./configure
command. This modification typically
includes specifying an installation prefix within the user’s home
directory to circumvent the need for system-wide installation
permissions. For instance, ./configure prefix=$HOME/.local
can be employed, where $HOME/.local
is often recommended
for user-space software installations. However, this is merely a
suggestion, and users are free to choose any suitable directory as their
installation prefix, depending on their specific requirements and system
configurations.
Regarding the integration with an MPI (Message Passing Interface)
enabled HDF5 library, it’s typical to specify the MPI compiler wrapper
for the C compiler. This is done by appending a directive like
CC=mpicc
to the ./configure
command. However,
as TREXIO does not utilize MPI features, it is advisable to link against
a non-MPI (serial) version of the HDF5 library for the sake of
simplicity.
Compilation without the HDF5 library
By default, the configuration step proceeds to search for the HDF5 library.
This search can be disabled if HDF5 is not present/installable on the
user machine. To build TREXIO without HDF5 back end, append
--without-hdf5
option to configure
script or
-DENABLE_HDF5=OFF
option to cmake
. For
example,
./configure --without-hdf5
cmake -S. -Bbuild -DENABLE_HDF5=OFF
For TREXIO developers: from the GitHub repo clone
Additional requirements:
- Python3 (>= 3.6)
- Emacs (>= 26.0)
- SWIG (>= 4.0) [required for the Python API]
Note: The source code is auto-generated from the
Emacs org-mode (.org
) files following the literate
programming approach. This is why the src
directory is
initially empty.
git clone https://github.com/TREX-CoE/trexio.git
cd trexio
./autogen.sh
./configure
make -j 4
make -j 4 check
sudo make install
Using CMake instead of Autotools
The aforementioned instructions rely on Autotools build system. CMake users can achieve the same with the following steps (an example of out-of-source build):
cmake -S. -Bbuild
cd build
make -j 4
ctest -j 4
sudo make install
Note: on systems with no sudo
access, one can
add -DCMAKE_INSTALL_PREFIX=build
as an argument to the
cmake
command so that make install/uninstall
can be run without sudo
privileges.
Note: when linking against an MPI-enabled HDF5 library one
usually has to specify the MPI wrapper for the C compiler by adding,
e.g., -DCMAKE_C_COMPILER=mpicc
to the cmake
command.
Using TREXIO
Naming convention
The primary TREXIO API is composed of the following functions:
trexio_open
trexio_write_[group]_[variable]
trexio_read_[group]_[variable]
trexio_has_[group]_[variable]
trexio_close
where [group]
and [variable]
substitutions
correspond to the contents of the trex.json
configuration
file (for more details, see the corresponding documentation
page). For example, consider the coord
variable (array),
which belongs to the nucleus
group. The TREXIO user can
write or read it using trexio_write_nucleus_coord
or
trexio_read_nucleus_coord
functions, respectively.
Note: the [variable]
names have to be unique only within
the corresponding parent [group]
. There is no naming
conflict when, for example, num
variable exists both in the
nucleus
group (i.e. the number of nuclei) and in the
mo
group (i.e. the number of molecular orbitals). These
quantities can be accessed using the corresponding
trexio_[has|read|write]_nucleus_num
and
trexio_[has|read|write]_mo_num
, respectively.
Tutorial
TREXIO tutorials in Jupyter notebook format can be found in the corresponding GitHub repository or on Binder.
For example, the tutorial covering TREXIO basics using benzene
molecule as an example can be viewed and executed online by clicking on
this badge:
Documentation
Documentation generated from TREXIO org-mode files.
Linking to your program
The make install
command takes care of installing the
TREXIO shared library on the user machine. After installation, append
-ltrexio
to the list of compiler ($LIBS
)
options.
In some cases (e.g. when using custom installation prefix during
configuration), the TREXIO library might end up installed in a
directory, which is absent in the default $LD_LIBRARY_PATH
.
In order to link the program against TREXIO, the search path can be
modified as follows:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib
where the <path_to_trexio>
has to be replaced by
the prefix used during the installation.
If your project relies on CMake build system, feel free to use the FindTREXIO.cmake module to find and link TREXIO library automatically.
In Fortran applications, make sure that the trexio_f.f90
module file is included in the source tree. You might have to manually
copy it into your program source directory. The
trexio_f.f90
module file can be found in the
include/
directory of the TREXIO source code
distribution.
Note: there is no need to include
trexio.h
header file during compilation of Fortran
programs. Only the installed library and the Fortran module file are
required.
Distributing TREXIO with your code
The TREXIO software is distributed under the 3-clause BSD license, renowned for its permissiveness. Consequently, it is entirely acceptable for you to provide the TREXIO release tarball in conjunction with your own code. Should you opt to include TREXIO with your software, it is recommended to distribute the release tarball, instead of the content of the git repository. The release tarballs contain pre-generated source files. This not only accelerates the compilation process but also significantly reduces dependency requirements.
APIs for other languages
Python
For more details regarding the installation and usage of the TREXIO Python API, see this page.
The aforementioned instructions are adapted for users installing from the source code distribution (periodically updated). In order to install the Python API with the latest changes, follow the developer installation guide and run the following command in the end
make python-install
Note: this implies that SWIG is installed and available.
We rely on the pytest
package for unit testing. It can
be installed via pip install pytest
. To test the
installation, run
make python-test
We highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.
Rust
The Rust API is available on Crates.io, so you can simply run
cargo add trexio
to your Rust project.
If you prefer to install the Rust API provided with this repository:
cargo add --path /path/to/trexio/rust/trexio
OCaml
The TREXIO OCaml API is available in OPAM:
opam install trexio
If you prefer to install it from this repository,
cd ocaml/trexio
make
opam install .
Citation
The journal article reference describing TREXIO can be cited as follows:
@article{10.1063/5.0148161,
author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Michał and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josué and Filippi, Claudia and Nakano, Kosuke and Kohulák, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and Ríos, Pablo López and Alavi, Ali and Scemama, Anthony},
title = "{TREXIO: A file format and library for quantum chemistry}",
journal = {The Journal of Chemical Physics},
volume = {158},
number = {17},
year = {2023},
month = {05},
issn = {0021-9606},
doi = {10.1063/5.0148161},
url = {https://doi.org/10.1063/5.0148161},
note = {174801},
eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0148161/17355866/174801\_1\_5.0148161.pdf},
}
Miscellaneous
The code should be compliant with the C99 CERT
C coding standard. This can be checked with the
cppcheck
tool.
TREX: Targeting
Real Chemical Accuracy at the Exascale project has received funding
from the European Union’s Horizon 2020 - Research and Innovation program
- under grant agreement no. 952165. The content of this document does
not represent the opinion of the European Union, and the European Union
is not responsible for any use that might be made of such content.