.github/workflows | ||
cmake | ||
docker | ||
docs | ||
helpers-debian | ||
include | ||
lib | ||
m4 | ||
ocaml/trexio | ||
pkgconfig | ||
python | ||
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 |
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, making it an important tool for researchers in the field of quantum chemistry. In this work, we present an overview of the TREXIO file format and library. 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, and OCaml programming languages. In addition, a suite of tools has been developed to facilitate the use of the TREXIO format and library, including converters for popular quantum chemistry codes and utilities for validating and manipulating data stored in TREXIO files. The simplicity, versatility, and ease of use of TREXIO make it a valuable resource for researchers working with quantum chemistry data.
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]
Installation procedure from the tarball (for users):
- Download the
trexio-<version>.tar.gz
file gzip -cd trexio-<version>.tar.gz | tar xvf -
cd trexio-<version>
./configure
make -j`getconf _NPROCESSORS_ONLN`
make -j`getconf _NPROCESSORS_ONLN` check
sudo make install
Note: on systems with no sudo
access, one can
replace ./configure
with
./configure prefix=${PWD}/build
in order to execute
make install/uninstall
commands 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., CC=mpicc
to the ./configure
command.
Additional requirements (for developers):
- 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.
Installation procedure from the GitHub repo clone (for developers):
git clone https://github.com/TREX-CoE/trexio.git
cd trexio
./autogen.sh
./configure
make -j`getconf _NPROCESSORS_ONLN`
make -j`getconf _NPROCESSORS_ONLN` check
sudo make install
Installation procedure for CMake users (from the tarball or GitHub repo clone):
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`getconf _NPROCESSORS_ONLN`
ctest -j`getconf _NPROCESSORS_ONLN`
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.
Installation procedure for conda users
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.
Installation procedure for Guix users
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 procedure for Spack users
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
Installation procedure for Debian/Ubuntu users
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
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
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.
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.
Python API
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 both HDF5 and SWIG are installed and available. At the moment, it is not possible to configure the Python API without HDF5 library.
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.
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.
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.