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atomicrex file names #443

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merged 3 commits into from
Dec 19, 2022
Merged

atomicrex file names #443

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07d0e5a
atomicrex file names
Leimeroth Jun 29, 2022
5145086
check when writing
Leimeroth Jun 29, 2022
7cfb578
Merge branch 'main' into atomicrex-file-names
liamhuber Dec 5, 2022
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15 changes: 15 additions & 0 deletions pyiron_contrib/atomistics/atomicrex/structure_list.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,12 @@ def add_structure(
relative_weight=1,
clamp=True,
):
if "/" in identifier:
raise ValueError(
"Structure identifiers must not contain '/'. "
"Use .structure_file_path to use existing POSCAR files"
)

self._structures.add_structure(structure, identifier)
self._structures._per_chunk_arrays["fit"][
self._structures.prev_chunk_index
Expand Down Expand Up @@ -392,6 +398,14 @@ def from_hdf(self, hdf, group_name="structures"):
"relative_weight"
]

def _check_identifiers(self):
identifiers = self._structures.get_array("identifier")
if not np.all(np.char.find(identifiers, "/")==-1):
raise ValueError(
"Structure identifiers must not contain '/'. "
"Use .structure_file_path to use existing POSCAR files"
)

def write_xml_file(self, directory, name="structures.xml"):
"""
Internal helper function that writes an atomicrex style
Expand All @@ -401,6 +415,7 @@ def write_xml_file(self, directory, name="structures.xml"):
directory (string): Working directory.
name (str, optional): . Defaults to "structures.xml".
"""
self._check_identifiers()
self._shrink()
root = ET.Element("group")
if self.structure_file_path is None and "atomic-forces" in self.fit_properties:
Expand Down