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Restructured README, and added TOC
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README.md
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README.md
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# TREXIO
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<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2022-01/TREXIO%20Code.png" width=200>
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[](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml)
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@ -15,18 +15,88 @@ which enables fast read and write operations. It is compatible with a variety
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of platforms and has interfaces for the Fortran, Python, OCaml and Rust
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programming languages.
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## Distributing TREXIO with your code
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* [TREXIO](#trexio)
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* [Installation](#installation)
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* [Installation from a package](#installation-from-a-package)
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* [Debian/Ubuntu](#debianubuntu)
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* [Conda](#conda)
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* [Spack](#spack)
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* [Guix](#guix)
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* [Installation from source](#installation-from-source)
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* [Minimal requirements (for users):](#minimal-requirements-for-users)
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* [Recommended: Installation from the release tarball](#recommended-installation-from-the-release-tarball)
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* [Compilation without the HDF5 library](#compilation-without-the-hdf5-library)
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* [For TREXIO developers: from the GitHub repo clone](#for-trexio-developers-from-the-github-repo-clone)
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* [Using CMake instead of Autotools](#using-cmake-instead-of-autotools)
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* [Using TREXIO](#using-trexio)
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* [Naming convention](#naming-convention)
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* [Tutorial](#tutorial)
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* [Documentation](#documentation)
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* [Linking to your program](#linking-to-your-program)
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* [Distributing TREXIO with your code](#distributing-trexio-with-your-code)
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* [APIs for other languages](#apis-for-other-languages)
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* [Python](#python)
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* [Rust](#rust)
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* [OCaml](#ocaml)
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* [Citation](#citation)
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* [Miscellaneous](#miscellaneous)
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The TREXIO software is distributed under the 3-clause BSD license, renowned for
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its permissiveness. Consequently, it is entirely acceptable for you to
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provide the TREXIO release tarball in conjunction with your own code.
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Should you opt to include TREXIO with your software, it is recommended to
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distribute the release tarball, instead of the content of the git repository.
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The release tarballs contain pre-generated source files. This not only
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accelerates the compilation process but also significantly reduces dependency
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requirements.
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## Minimal requirements (for users):
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## Installation
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### Installation from a package
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#### Debian/Ubuntu
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The official release of TREXIO `2.2.0` is available as a Debian (`.deb`) package thanks to the [Debichem Team](https://wiki.debian.org/Debichem).
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The source code is hosted [here](https://salsa.debian.org/debichem-team/libtrexio) and
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the pre-built binary files are available via the [Debian package registry](https://packages.debian.org/bookworm/libtrexio-dev).
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TREXIO is also available on [Ubuntu 23.04 (Lunar Lobster)](https://packages.ubuntu.com/lunar/libtrexio-dev) and newer and can be installed as follows:
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```
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sudo apt-get update && sudo apt-get install libtrexio-dev
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```
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#### Conda
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[](https://anaconda.org/conda-forge/trexio)
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[](https://anaconda.org/conda-forge/trexio)
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The official releases of TREXIO `>2.0.0` are also available via the `conda-forge` channel.
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The pre-compiled stable binaries of `trexio` can be installed as follows:
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```
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conda install -c conda-forge trexio
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```
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More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
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Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.
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#### Spack
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The official releases `>=2.0.0` and the development version of TREXIO can be installed using the
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[Spack](https://spack.io/) package manager.
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The [trexio/package.py](https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/trexio/package.py)
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file contains the Spack specifications required to build different variants of `trexio` library.
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It can be installed as follows
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```
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spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
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```
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#### Guix
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The official releases of TREXIO `>=2.0.0` can be installed using the
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[GNU Guix](https://guix.gnu.org) functional package manager.
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The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
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Schema file contains the manifest specification for the `trexio` package.
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It can be installed as follows:
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```
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guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
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```
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### Installation from source
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#### Minimal requirements (for users):
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- Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
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- C compiler (gcc/icc/clang)
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@ -34,7 +104,7 @@ requirements.
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- HDF5 library (>= 1.8) [optional, recommended for high performance]
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## Installation procedure from the release tarball (for users):
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#### Recommended: Installation from the release tarball
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1. Download the `trexio-<version>.tar.gz` file from the GitHub release page
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2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
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@ -62,7 +132,18 @@ command. However, as TREXIO does not utilize MPI features, it is advisable to
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link against a non-MPI (serial) version of the HDF5 library for the sake of
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simplicity.
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## Additional requirements (for developers):
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#### Compilation without the HDF5 library
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By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).
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This search can be disabled if HDF5 is not present/installable on the user machine.
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To build TREXIO without HDF5 back end, append `--without-hdf5` option to `configure` script or `-DENABLE_HDF5=OFF` option to `cmake`. For example,
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- `./configure --without-hdf5`
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- `cmake -S. -Bbuild -DENABLE_HDF5=OFF`
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#### For TREXIO developers: from the GitHub repo clone
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Additional requirements:
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- Python3 (>= 3.6)
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- Emacs (>= 26.0)
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@ -70,8 +151,6 @@ simplicity.
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**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.
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## Installation procedure from the GitHub repo clone (for developers):
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1. `git clone https://github.com/TREX-CoE/trexio.git`
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2. `cd trexio`
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3. `./autogen.sh`
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@ -80,7 +159,7 @@ simplicity.
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6. ```make -j 4 check```
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7. `sudo make install`
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## Installation procedure for CMake users (from the tarball or GitHub repo clone):
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#### Using CMake instead of Autotools
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The aforementioned instructions rely on [Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html) build system.
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[CMake](https://cmake.org) users can achieve the same with the following steps (an example of out-of-source build):
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@ -95,67 +174,42 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
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**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.**
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## Installation procedure for conda users
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## Using TREXIO
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### Naming convention
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[](https://anaconda.org/conda-forge/trexio)
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[](https://anaconda.org/conda-forge/trexio)
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The primary TREXIO API is composed of the following functions:
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The official releases of TREXIO `>2.0.0` are also available via the `conda-forge` channel.
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The pre-compiled stable binaries of `trexio` can be installed as follows:
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- `trexio_open`
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- `trexio_write_[group]_[variable]`
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- `trexio_read_[group]_[variable]`
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- `trexio_has_[group]_[variable]`
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- `trexio_close`
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```
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conda install -c conda-forge trexio
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```
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where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file
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(for more details, see the corresponding [documentation](https://trex-coe.github.io/trexio/trex.html) page).
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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.
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More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
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Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.
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Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`.
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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).
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These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively.
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## Installation procedure for Guix users
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The official releases of TREXIO `>=2.0.0` can be installed using the
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[GNU Guix](https://guix.gnu.org) functional package manager.
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The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
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Schema file contains the manifest specification for the `trexio` package.
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It can be installed as follows:
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### Tutorial
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```
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guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
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```
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TREXIO tutorials in Jupyter notebook format can be found in the
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[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
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or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
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## Installation procedure for Spack users
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For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
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[](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
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The official releases `>=2.0.0` and the development version of TREXIO can be installed using the
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[Spack](https://spack.io/) package manager.
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The [trexio/package.py](https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/trexio/package.py)
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file contains the Spack specifications required to build different variants of `trexio` library.
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It can be installed as follows
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```
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spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
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```
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### Documentation
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## Installation procedure for Debian/Ubuntu users
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[Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)
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The official release of TREXIO `2.2.0` is available as a Debian (`.deb`) package thanks to the [Debichem Team](https://wiki.debian.org/Debichem).
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The source code is hosted [here](https://salsa.debian.org/debichem-team/libtrexio) and
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the pre-built binary files are available via the [Debian package registry](https://packages.debian.org/bookworm/libtrexio-dev).
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TREXIO is also available on [Ubuntu 23.04 (Lunar Lobster)](https://packages.ubuntu.com/lunar/libtrexio-dev) and newer and can be installed as follows:
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```
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sudo apt-get update && sudo apt-get install libtrexio-dev
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```
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## Compilation without the HDF5 library
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By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).
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This search can be disabled if HDF5 is not present/installable on the user machine.
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To build TREXIO without HDF5 back end, append `--without-hdf5` option to `configure` script or `-DENABLE_HDF5=OFF` option to `cmake`. For example,
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- `./configure --without-hdf5`
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- `cmake -S. -Bbuild -DENABLE_HDF5=OFF`
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## Linking to your program
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### Linking to your program
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The `make install` command takes care of installing the TREXIO shared library on the user machine.
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After installation, append `-ltrexio` to the list of compiler (`$LIBS`) options.
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@ -179,26 +233,19 @@ The `trexio_f.f90` module file can be found in the `include/` directory of the T
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Only the installed library and the Fortran module file are required.
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## Naming convention
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### Distributing TREXIO with your code
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The primary TREXIO API is composed of the following functions:
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The TREXIO software is distributed under the 3-clause BSD license, renowned for
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its permissiveness. Consequently, it is entirely acceptable for you to
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provide the TREXIO release tarball in conjunction with your own code.
|
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Should you opt to include TREXIO with your software, it is recommended to
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distribute the release tarball, instead of the content of the git repository.
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The release tarballs contain pre-generated source files. This not only
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accelerates the compilation process but also significantly reduces dependency
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requirements.
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- `trexio_open`
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- `trexio_write_[group]_[variable]`
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- `trexio_read_[group]_[variable]`
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- `trexio_has_[group]_[variable]`
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- `trexio_close`
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where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file
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(for more details, see the corresponding [documentation](https://trex-coe.github.io/trexio/trex.html) page).
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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.
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Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`.
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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).
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These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively.
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## Python API
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## APIs for other languages
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### Python
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[](https://badge.fury.io/py/trexio)
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@ -223,7 +270,7 @@ make python-test
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We highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.
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## Rust API
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### Rust
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The Rust API is available on Crates.io, so you can simply run
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```
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cargo add --path /path/to/trexio/rust/trexio
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```
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## OCaml API
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### OCaml
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The TREXIO OCaml API is available in OPAM:
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```
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opam install .
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```
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## Tutorial
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TREXIO tutorials in Jupyter notebook format can be found in the
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[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
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or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
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For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
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[](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
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## Documentation
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[Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)
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## Citation
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The journal article reference describing TREXIO can be cited as follows:
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||||
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