trexio/README.md

# TREXIO

[![build](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml/badge.svg)](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml)
![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)

TREX library for efficient I/O.


## 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):

1. Download the `trexio-<version>.tar.gz` file
2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
3. `cd trexio-<version>`
4. `./configure`
5. `make`
6. `make check`
7. `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]

## Installation procedure from the GitHub repo clone (for developers):

1. `git clone https://github.com/TREX-CoE/trexio.git`
2. `cd trexio`
3. `./autogen.sh`
4. `./configure`
5. `make`
6. `make check`
7. `sudo make install`

## Installation procedure for CMake users (from the tarball or GitHub repo clone):

The aforementioned instructions rely on [Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html) build system.
[CMake](https://cmake.org) users can achieve the same with the following steps (an example of out-of-source build):

1. `cmake -S. -Bbuild`
2. `cd build`
3. `make`
4. `ctest` (or `make test`)
5. `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

[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/version.svg)](https://anaconda.org/conda-forge/trexio)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/platforms.svg)](https://anaconda.org/conda-forge/trexio)

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 trexio -c conda-forge
```

More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.

## Compilation without the HDF5 library

By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).
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.
Once installed, add `-ltrexio` to the list of compiler options.

In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
In order to link the program against TREXIO, the search paths can be modified as follows:

`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`

(same holds for `$LD_LIBRARY_PATH`). 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](https://github.com/TREX-CoE/trexio/blob/master/cmake/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](https://trex-coe.github.io/trexio/trex.html) 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

[![PyPI version](https://badge.fury.io/py/trexio.svg)](https://badge.fury.io/py/trexio)

For more details regarding the installation and usage of the TREXIO Python API,
see [this page](python/README.md).

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](https://github.com/TREX-CoE/trexio-tutorials)
or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).

For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)


## Documentation

[Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)


### Miscellaneous

Note: The code should be compliant with the C99
[CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf).
This can be checked with the `cppcheck` tool.



-----------------
![European flag](https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg)
[TREX: Targeting Real Chemical Accuracy at the Exascale](https://trex-coe.eu) 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.