TREX library for efficient I/O.
- 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]
- Download the
trexio-<version>.tar.gzfile gzip -cd trexio-<version>.tar.gz | tar xvf -cd trexio-<version>./configuremake -j`getconf _NPROCESSORS_ONLN`make -j`getconf _NPROCESSORS_ONLN` checksudo 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.
- 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.gitcd trexio./autogen.sh./configuremake -j`getconf _NPROCESSORS_ONLN`make -j`getconf _NPROCESSORS_ONLN` checksudo make install
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. -Bbuildcd buildmake -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.
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.
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
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
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
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-hdf5cmake -S. -Bbuild -DENABLE_HDF5=OFF
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.
The primary TREXIO API is composed of the following functions:
trexio_opentrexio_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.
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 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.
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 generated from TREXIO org-mode files.
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},
}
Journal paper:
ArXiv paper:
The code should be compliant with the C99
CERT C coding standard.
This can be checked with the cppcheck tool.
