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README.md
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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)
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![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
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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.
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TREXIO is an open-source file format and library developed for the storage and
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manipulation of data produced by quantum chemistry calculations. It is designed
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with the goal of providing a reliable and efficient method of storing and
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exchanging wave function parameters and matrix elements. The library consists
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of a front-end implemented in the C programming language and two different
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back-ends: a text back-end and a binary back-end utilizing the HDF5 library
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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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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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- HDF5 library (>= 1.8) [optional, recommended for high performance]
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## Installation procedure from the tarball (for users):
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## Installation procedure from the release tarball (for users):
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1. Download the `trexio-<version>.tar.gz` file
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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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3. `cd trexio-<version>`
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4. `./configure`
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5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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6. ```make -j`getconf _NPROCESSORS_ONLN` check```
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5. ```make -j 4 ```
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6. ```make -j 4 check```
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7. `sudo make install`
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In environments where `sudo` access is unavailable, a common workaround for
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executing `make install/uninstall` commands without requiring superuser
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privileges involves a modification to the `./configure` command.
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This modification typically includes specifying an installation prefix within
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the user's home directory to circumvent the need for system-wide installation
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permissions. For instance, `./configure prefix=$HOME/.local` can be employed,
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where `$HOME/.local` is often recommended for user-space software installations.
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However, this is merely a suggestion, and users are free to choose any suitable
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directory as their installation prefix, depending on their specific
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requirements and system configurations.
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**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.**
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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., `CC=mpicc` to the `./configure` command.**
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Regarding the integration with an MPI (Message Passing Interface) enabled HDF5
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library, it's typical to specify the MPI compiler wrapper for the C compiler.
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This is done by appending a directive like `CC=mpicc` to the `./configure`
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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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- python3 (>= 3.6)
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- Python3 (>= 3.6)
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- Emacs (>= 26.0)
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- SWIG (>= 4.0) [required for the Python API]
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@ -44,8 +76,8 @@ TREXIO is an open-source file format and library developed for the storage and m
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2. `cd trexio`
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3. `./autogen.sh`
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4. `./configure`
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5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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6. ```make -j`getconf _NPROCESSORS_ONLN` check```
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5. ```make -j 4```
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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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@ -55,8 +87,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
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1. `cmake -S. -Bbuild`
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2. `cd build`
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3. ```make -j`getconf _NPROCESSORS_ONLN` ```
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4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
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3. ```make -j 4```
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4. ```ctest -j 4```
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5. `sudo make install`
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**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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** File copy
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~trexio_cp~ copies a TREXIO file using =cp=.
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~trexio_cp~ copies a TREXIO file using =cp=. The destination file
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is not overwritten if it exists, an error is returned.
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**Input parameters:**
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1) ~source_file_name~ - string containing the name of the source file
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