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README.md
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[![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)
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.
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.
## 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.
## Minimal requirements (for users):
@ -15,24 +34,34 @@ TREXIO is an open-source file format and library developed for the storage and m
- HDF5 library (>= 1.8) [optional, recommended for high performance]
## Installation procedure from the tarball (for users):
## Installation procedure from the release tarball (for users):
1. Download the `trexio-<version>.tar.gz` file
1. Download the `trexio-<version>.tar.gz` file from the GitHub release page
2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
3. `cd trexio-<version>`
4. `./configure`
5. ```make -j`getconf _NPROCESSORS_ONLN` ```
6. ```make -j`getconf _NPROCESSORS_ONLN` check```
5. ```make -j 4 ```
6. ```make -j 4 check```
7. `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. Specifically,
one can substitute the standard `./configure` with `./configure
prefix=$HOME/.local`. The directory `$HOME/.local` is frequently utilized for
installing software within user space, serving as an alternative to the
system-wide `/usr/local`.
**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.**
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.
## Additional requirements (for developers):
- python3 (>= 3.6)
- Python3 (>= 3.6)
- Emacs (>= 26.0)
- SWIG (>= 4.0) [required for the Python API]
@ -44,8 +73,8 @@ TREXIO is an open-source file format and library developed for the storage and m
2. `cd trexio`
3. `./autogen.sh`
4. `./configure`
5. ```make -j`getconf _NPROCESSORS_ONLN` ```
6. ```make -j`getconf _NPROCESSORS_ONLN` check```
5. ```make -j 4```
6. ```make -j 4 check```
7. `sudo make install`
## Installation procedure for CMake users (from the tarball or GitHub repo clone):
@ -55,8 +84,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
1. `cmake -S. -Bbuild`
2. `cd build`
3. ```make -j`getconf _NPROCESSORS_ONLN` ```
4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
3. ```make -j 4```
4. ```ctest -j 4```
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.**

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src/templates_front/templator_front.org
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@ -1858,7 +1858,8 @@ def _inquire(file_name: str) -> bool:
** File copy
~trexio_cp~ copies a TREXIO file using =cp=.
~trexio_cp~ copies a TREXIO file using =cp=. The destination file
is not overwritten if it exists, an error is returned.
**Input parameters:**
1) ~source_file_name~ - string containing the name of the source file