Set of tools for TREXIO files.
- python3 (>=3.6)
- trexio (>=1.0.0) [Python API]
- numpy (>=1.17.3)
- resultsFile [optional, for GAMESS/GAU$$IAN conversion]
- VeloxChem [optional, for VLX/VeloxChem HDF5 conversion]
- docopt [for CLI] Note: the pyscf<--->trexio converter has been moved to pyscf-forge. Please install the pyscf-forge plugin for the pyscf<--->trexio interface (including multi-reference wave function I/O).
pip install trexio-tools
pip install git+https://github.com/TREX-CoE/trexio_tools
Optional converter back ends rely on additional packages in the active Python
environment. In particular, the VLX converter requires veloxchem, while the
Gaussian/GAMESS converters require resultsFile.
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.
For ORCA,
trexio convert-from -t orca -i data/h2o.json -b 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 the hdf5 back end of TREXIO.
Note that ORCA AOs and MOs are written in spherical coordinates. If you need a cartesian TREXIO file, run the additional conversion step below.
trexio convert-to -t cartesian -o trexio_orca_cart.hdf5 trexio_orca.hdf5
This converts the spherical AOs and MOs from trexio_orca.hdf5 into cartesian
coordinates and writes the result to trexio_orca_cart.hdf5.
For VeloxChem,
trexio convert-from -w -t vlx -i /path/to/biphenyl-scf.h5 -b hdf5 biphenyl-scf-trexio.hdf5
converts data from a VeloxChem HDF5 file into the TREXIO file called
biphenyl-scf-trexio.hdf5 using the hdf5 back end. The -w flag is useful
when rerunning the converter against an existing output file. The active Python
environment must provide the veloxchem package.
The VeloxChem converter writes and validates the following quantities when they are present in the input HDF5 file: molecular geometry, electron counts, Gaussian basis data, AO shell map, MO coefficients, MO energies, MO occupations, AO overlap matrix, and SCF energy.
For local regression checks, use:
python utilities/run_vlx_regression.py --case biphenyl=/path/to/biphenyl-scf.h5 --case tempo_roscf=/path/to/tempo-roscf.h5 --case trityl_uscf=/path/to/trityl-uscf.h5
This script converts each VeloxChem file to TREXIO and then compares the written
TREXIO contents numerically against the source VeloxChem data using
utilities/compare_vlx_trexio.py.