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TREXIO

build GitHub release (latest by date)

TREX library for efficient I/O.

Minimal requirements (for users):

  • Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2)
  • C compiler (gcc/icc/clang)
  • Fortran compiler (gfortran/ifort)
  • HDF5 library (>= 1.8)

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 --enable-silent-rules
  5. make
  6. make check
  7. sudo make install

Note: on systems with no sudo access, one can replace ./configure with ./configure prefix=${PWD}/_install in order to execute make install/uninstall commands without sudo privileges.

Additional requirements (for developers):

  • python3 (>= 3.6)
  • Emacs (>= 26.0)
  • SWIG (>= 4.0)

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. TREXIO_DEVEL=1 ./configure --enable-maintainer-mode
  5. make
  6. make check
  7. sudo make install

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 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

For more details regarding the installation and usage of the TREXIO Python API, see this page.

Tutorial

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: Binder

Technical documentation

Documentation generated from TREXIO org-mode files.

Miscellaneous

Note: The code should be compliant with the C99 CERT C coding standard. This can be checked with the cppcheck tool.

European flag TREX: Targeting Real Chemical Accuracy at the Exascale 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.