comparison larch_feff.py @ 1:8ee2cc3374fe draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 0f66842e802430e887d1c6cb7be1cc5436408fd2

0:edf7f8ccf4af

import shutil
import sys
from pathlib import Path

from larch.xafs.feffrunner import feff6l

from pymatgen.io.cif import CifParser
from pymatgen.io.feff import Atoms, Header, Potential


def get_path_labels(paths_file):
    is_meta = True
    count = 0

def main(structure_file: str, file_format: dict):
    crystal_f = Path(structure_file)
    feff_dir = "feff"
    feff_inp = "feff.inp"
    header_inp = "header"
    atoms_inp = "atoms"
    potential_inp = "potential"
    path = Path(feff_dir, feff_inp)
    path.parent.mkdir(parents=True, exist_ok=True)

    if file_format["format"] == "cif":
        print(f"Parsing {crystal_f.name} and saving to {path}")
        cif_parser = CifParser(crystal_f)
        structures = cif_parser.get_structures()
        length = len(structures)
        if length != 1:
            raise ValueError(
                f"Execpted single structure in cif file but found {length}"
            )
        try:
            aborsbing_atom = int(file_format["absorbing_atom"])
        except ValueError:
            # aborsbing_atom can be int or chemical symbol
            aborsbing_atom = file_format["absorbing_atom"]

        feff_header = Header(structures[0])
        potential = Potential(structures[0], aborsbing_atom)
        atoms = Atoms(structures[0], aborsbing_atom, file_format["radius"])
        # if len(atoms.struct.sites) < len(potential.):

        # print(atoms.as_dict())
        feff_header.write_file(header_inp)
        potential.write_file(potential_inp)
        atoms.write_file(atoms_inp)
        with open(path, "w") as feff_inp_file:
            with open(header_inp) as f:
                header_text = f.read()
                print(header_text)
                feff_inp_file.write(header_text + "\n")
            with open(potential_inp) as f:
                potential_text = f.readlines()
                print(*potential_text)
                feff_inp_file.writelines(potential_text + ["\n"])
            with open(atoms_inp) as f:
                atoms_text = f.readlines()
                print(*atoms_text)
                feff_inp_file.writelines(atoms_text + ["\n"])
        if len(atoms_text) <= len(potential_text):
            print(
                "WARNING: Every potential in the structure must be represented"
                " by at least one atom, consider increasing the radius"
            )
    else:
        print(f"Copying {crystal_f.name} to {path}")
        shutil.copy(crystal_f, path)

    feff6l(folder=feff_dir, feffinp=feff_inp)

1:8ee2cc3374fe

import shutil
import sys
from pathlib import Path

from larch.xafs.feffrunner import feff6l
from larch.xrd import cif2feff

from pymatgen.core import Species
from pymatgen.io.cif import CifParser


def get_path_labels(paths_file):
    is_meta = True
    count = 0

def main(structure_file: str, file_format: dict):
    crystal_f = Path(structure_file)
    feff_dir = "feff"
    feff_inp = "feff.inp"
    path = Path(feff_dir, feff_inp)
    path.parent.mkdir(parents=True, exist_ok=True)

    if file_format["format"] == "cif":
        print(f"Parsing {crystal_f.name} and saving to {path}")

        # Parse the cif file here... but only so that we can extract the
        # chemical symbols present in the crystal
        cif_parser = CifParser(crystal_f)
        structures = cif_parser.get_structures()
        length = len(structures)
        if length != 1:
            raise ValueError(
                f"Expected single structure in cif file but found {length}"
            )

        # cif2feffinp below will take the absorber to be a chemical symbol,
        # while this tool should support integer site index or chemical symbol
        # of site (string). Hence convert any integer input to the relevant
        # chemical symbol string.
        try:
            absorbing_atom_int = int(file_format["absorbing_atom"])
            specie = structures[0][absorbing_atom_int].specie
            if isinstance(specie, Species):
                absorbing_atom = str(specie.element)
            else:
                absorbing_atom = str(specie)
        except ValueError:
            absorbing_atom = file_format["absorbing_atom"]

        # NOTE: Here the first site listed in the cif file with the species
        # 'absorbing_atom' is selected as the absorbing atom.
        # NOTE: This generates output for FEFF6 via the 'version8' flag
        inp_data = cif2feff.cif2feffinp(
            crystal_f,
            absorber=absorbing_atom,
            edge=None,
            cluster_size=file_format["radius"],
            absorber_site=1,
            site_index=None,
            extra_titles=None,
            with_h=False,
            version8=False,
        )
        with open(path, "w") as feff_inp_file:
            feff_inp_file.write(inp_data + "\n")
            print(inp_data + "\n")

    else:
        print(f"Copying {crystal_f.name} to {path}")
        shutil.copy(crystal_f, path)

    feff6l(folder=feff_dir, feffinp=feff_inp)