AiiDA plugin for the OpenMX DFT code.

pip install aiida-openmx

To simplify the use of pseudopotentials and orbital bases in aiida-openmx, aiida-pseudo and aiida-basis have support for OpenMX's VPS pseudopotential and PAO pseudoatomic orbital formats respectively. For high-throughput studies, it is additionally useful to create PseudoPotentialFamily and BasisSet AiiDA Groups, which hold many pseudopotentials and orbital bases as well as various metadata.

As an example, lets create a PseudoPotentialFamily for OpenMX's soft PBE19 pseudopotentials and a BasisSet for OpenMX's soft 'standard' recommendation.

First, we collect the appropriate .vps pseudopotentials in a directory:

export OPENMX_SOURCE=$HOME/openmx3.9/  # Path to the extracted OpenMX source code on your computer
mkdir PBE_19_soft                                              # Directory to hold the .vps files
cp ${OPENMX_SOURCE}/DFT_DATA19/VPS/*PBE19.vps ./PBE_19_soft/   # Copy non-hard/soft .vps files
cp ${OPENMX_SOURCE}/DFT_DATA19/VPS/*PBE19S.vps ./PBE_19_soft/  # Copy soft version of hard/soft .vps files

Next, we'll create a PseudoPotentialFamily which contains all of the pseudopotentials in our directory. First, run python, ipython, or verdi shell. Then, run something like the following code:

from aiida_pseudo.groups.family import PseudoPotentialFamily
from aiida_pseudo.data.pseudo import VpsData

PBE_19_soft_family = PseudoPotentialFamily(
    dirpath='./PBE_19_soft/',          # Directory where we copied our .vps files
    label='OpenMX/19/PBE/S',           # Name of the PseudoPotentialFamily in the AiiDA database
    description='OpenMX PBE19 (soft)'  # Longer description of what the PseudoPotentialFamily contains
    pseudo_type=VpsData                # AiiDA data type for VPS pseudopotentials
)

We can then check that the PseudoPotentialFamily is listed in our AiiDA Groups:

verdi group list -a

  PK  Label              Type string    User
----  -----------------  -------------  ---------------------
   1  OpenMX/19/PBE/S    pseudo.family  [email protected]

Great! Now we can set up our pseudoatomic orbitals in a similar manner. Because it's a bit trickier to collect all the appropriate files in this case, aiida-openmx provides some PAO tables based on OpenMX's recommendations.

export OPENMX_SOURCE=$HOME/openmx3.9/
export AIIDA_OPENMX=$(python -c "import pathlib; import aiida_openmx; print(pathlib.Path(aiida_openmx.__file__).parent)")
mkdir standard_19_soft
for paofile in $(cat $AIIDA_OPENMX/data/pao/standard_s.txt); do cp $OPENMX_SOURCE/DFT_DATA19/PAO/$paofile ./standard_19_soft/; done

Finally, we'll create a BasisSet which contains all of the pseudoatomic orbitals in our directory. First, run python, ipython, or verdi shell. Then, run something like the following code:

from aiida_basis.groups.set import BasisSet
from aiida_basis.data.basis import PaoData

standard_19_soft_set = BasisSet(
    dirpath='./standard_19_soft/',  # Directory where we copied our .pao files
    label='OpenMX/19/standard/S',  # Name of the BasisSet in the AiiDA database
    description='OpenMX standard 19 (soft)'  # Longer description of what the BasisSet contains
    basis_type=PaoData  # AiiDA data type for PAO bases
)

We can then check that the BasisSet is listed in our AiiDA Groups:

verdi group list -a

  PK  Label                 Type string    User
----  --------------------  -------------  ---------------------
   1  OpenMX/19/PBE/S       pseudo.family  [email protected]
   2  OpenMX/19/standard/S  basis.set      [email protected]

If you would like to contribute to the development of aiida-openmx, please clone this Github repository and install aiida-openmx as follows:

git clone https://github.com/zooks97/aiida-openmx .
cd aiida-openmx
pip install -e .[pre-commit,testing,docs]  # Install extra dependencies
pre-commit install  # Install pre-commit hooks
pytest -v  # Discover and run all tests

See the developer guide for more information.

MIT

[email protected]