Source code for pyiron_atomistics.sphinx.potential

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

import os

import pandas
from pyiron_base import state
from pyiron_snippets.resources import ResourceResolver

from pyiron_atomistics.vasp.potential import VaspPotentialAbstract

__author__ = "Osamu Waseda"
__copyright__ = (
    "Copyright 2019, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Osamu Waseda"
__email__ = "waseda@mpie.de"
__status__ = "development"
__date__ = "Sep 20, 2019"




class SphinxJTHPotentialFile(VaspPotentialAbstract):
    """
    The Potential class is derived from the PotentialAbstract class, but instead of loading the potentials from a list,
    the potentials are loaded from a file.

    Args:
        xc (str): Exchange correlation functional ['PBE', 'LDA']
    """

    resource_plugin_name = "sphinx"

    @classmethod
    def _get_resolver(cls):
        env = os.environ
        return (
            super()
            ._get_resolver()
            .chain(
                ResourceResolver(
                    [env[var] for var in ("CONDA_PREFIX", "CONDA_DIR") if var in env],
                    "share",
                    "sphinxdft",
                )
            )
        )



    def __init__(self, xc=None, selected_atoms=None):
        potential_df = self._get_potential_df(
            file_name_lst={"potentials_sphinx.csv"},
        )
        if xc == "PBE":
            default_df = self._get_potential_default_df(
                file_name_lst={"potentials_sphinx_jth_default.csv"},
            )
            potential_df = potential_df[(potential_df["Model"] == "jth-gga-pbe")]
        else:
            raise ValueError(
                'The exchange correlation functional has to be set to "PBE" currently there are no "LDA" potentials.'
            )
        super(SphinxJTHPotentialFile, self).__init__(
            potential_df=potential_df,
            default_df=default_df,
            selected_atoms=selected_atoms,
        )




    def add_new_element(self, parent_element, new_element):
        """
        Adding a new user defined element with a different POTCAR file. It is assumed that the file exists

        Args:
            parent_element (str): Parent element
            new_element (str): Name of the new element (the name of the folder where the new POTCAR file exists

        """
        ds = self.find_default(element=parent_element)
        ds["Species"].values[0][0] = new_element
        path_list = ds["Filename"].values[0][0].split("/")
        path_list[-2] = new_element
        name_list = ds["Name"].values[0].split("-")
        name_list[0] = new_element
        ds["Name"].values[0] = "-".join(name_list)
        ds["Filename"].values[0][0] = "/".join(path_list)
        self._potential_df = self._potential_df.append(ds)
        ds = pandas.Series()
        ds.name = new_element
        ds["Name"] = "-".join(name_list)
        self._default_df = self._default_df.append(ds)