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TREXIO tools

PyPI version

Set of tools for TREXIO files.

Requirements

  • python3 (>=3.6)
  • trexio (>=1.0.0) [Python API]
  • numpy (>=1.17.3)
  • resultsFile [for GAMESS/GAU$$IAN conversion]
  • docopt [for CLI]
  • pyscf [only if you use the pyscf->trexio converter]

Installation

Installation via PyPI, periodically updated

pip install trexio-tools

Installation from source code

  1. Clone the repository
  • git clone https://github.com/TREX-CoE/trexio_tools.git
  1. Create an isolated virtual environment, for example using
  • python3 -m venv trexio_tools
  1. Activate the previously created environment, for example using
  • source trexio_tools/bin/activate
  1. Install the Python packages that are required for trexio-tools to work
  • pip install -r requirements.txt
  1. Install trexio-tools via pip (also works in --editable mode)
  • pip install .

Instructions for users

After installation, trexio-tools provides an entry point, which can be accessed via CLI:

trexio --help

This will list all currently supported command line arguments. For example,

trexio convert-from -t gamess -i data/GAMESS_CAS.log -b hdf5 trexio_cas.hdf5

converts data from the GAMESS_CAS.log output file of the GAMESS code (note also -t gamess argument) into the TREXIO file called trexio_cas.hdf5 using -b hdf5 back end of TREXIO.

and,

trexio convert-from -t orca -i data/h2o.json -b hdf5 trexio_orca.hdf5

Note that since ORCA AOs and MOs are in spherical coordinates, one needs to convert these to cartesian to be able to use trexio functions.

trexio convert-to -t cartesian -o trexio_orca_cart.hdf5 trexio_orca.hdf5

converts data from the h2o.json output file of the ORCA code into the TREXIO file called trexio_orca.hdf5 using -b hdf5 back end of TREXIO followed by converting the spherical AOs and MOs to cartesian coordinates.