Merge pull request #10 from JuDFTteam/develop

🚀 Release `0.4.1`

Author: janssenhenning

.pre-commit-config.yaml

@@ -15,13 +15,13 @@ repos:
       - id: flake8
         args: ["--max-line-length=120"]
   - repo: https://github.com/psf/black
-    rev: 22.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
+    rev: 22.10.0 # Replace by any tag/version: https://github.com/psf/black/tags
     hooks:
     - id: black
       language_version: python3 # Should be a command that runs python3.6+
 
   - repo: https://github.com/ikamensh/flynt/
-    rev: '0.76'
+    rev: '0.77'
     hooks:
     -   id: flynt
         args: [
@@ -46,7 +46,7 @@ repos:
         additional_dependencies: ['toml']
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.942'  # Use the sha / tag you want to point at
+    rev: 'v0.991'  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         args: [

pymatgen/io/fleur/__init__.py

@@ -9,5 +9,5 @@
 
 __copyright__ = "Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. All rights reserved."
 __license__ = "MIT license, see LICENSE.txt file."
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 __authors__ = "The JuDFT team"

pymatgen/io/fleur/fleurinput.py

@@ -8,7 +8,7 @@
 from fleur input files (http://flapw.de).
 """
 import warnings
-from typing import Union, Any
+from typing import Optional, Union, Any
 from pathlib import Path
 from monty.io import zopen
 from monty.json import MSONable
@@ -42,8 +42,8 @@ class FleurInput(MSONable):
     def __init__(
         self,
         structure: Structure,
-        title: str = None,
-        lapw_parameters: dict = None,
+        title: Optional[str] = None,
+        lapw_parameters: Optional[dict] = None,
         **kwargs: Any,
     ):
         """
@@ -98,7 +98,7 @@ def from_string(data: Union[str, bytes], inpgen_input: bool = True, **kwargs) ->
             parameters = get_parameter_data(xmltree, schema_dict)
             title_in = parameters.pop("title", "")
 
-        positions, elements, _ = zip(*atoms)
+        positions, elements = zip(*[(site.position, site.symbol) for site in atoms])
         # create lattice and structure object
         lattice_in = Lattice(cell, pbc=pbc)
         structure_in = Structure(lattice_in, elements, positions, coords_are_cartesian=True)
@@ -128,7 +128,7 @@ def from_file(filename: PathLike) -> "FleurInput":
         return FleurInput.from_string(data, inpgen_input=inpgen_input, base_url=filename)
 
     def get_inpgen_file_content(
-        self, parameters: dict = None, ignore_set_parameters: bool = False, **kwargs: Union[int, bool]
+        self, parameters: Optional[dict] = None, ignore_set_parameters: bool = False, **kwargs: Union[int, bool]
     ):
         """
         Produce the inpgen input file corresponding to the given information
@@ -143,6 +143,7 @@ def get_inpgen_file_content(
         returns: str of the inpgen input file
         """
         from masci_tools.io.fleur_inpgen import write_inpgen_file
+        from masci_tools.io.common_functions import AtomSiteProperties
 
         if parameters is None:
             parameters = {}
@@ -153,7 +154,10 @@ def get_inpgen_file_content(
         if "title" not in parameters:
             parameters["title"] = self.title
 
-        atom_sites = [(site.coords, site.specie.symbol, site.specie.symbol) for site in self.structure.sites]
+        atom_sites = [
+            AtomSiteProperties(position=site.coords, symbol=site.specie.symbol, kind=site.specie.symbol)
+            for site in self.structure.sites
+        ]
 
         return write_inpgen_file(
             self.structure.lattice.matrix,