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Replace site.species_and_occu with site.species property for compatible pymatgen versions #3480

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merged 7 commits into from
Nov 9, 2019
Merged

Replace site.species_and_occu with site.species property for compatible pymatgen versions #3480

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5ec4b02
Select correct property based on the used python version
astamminger Oct 29, 2019
aed4b2f
Use packaging.version to compare versions
astamminger Oct 30, 2019
e3aeac2
Switch to pkg_resources for version parsing
astamminger Oct 30, 2019
7f00674
Fix trailing whitespace
astamminger Nov 6, 2019
4a216cd
Merge branch 'develop' into issue_3297_replace_deprecated_species_and…
greschd Nov 6, 2019
b02b31e
relocate pkg_resources import to function
astamminger Nov 9, 2019
1c87c69
Merge branch 'develop' into issue_3297_replace_deprecated_species_and…
sphuber Nov 9, 2019
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16 changes: 13 additions & 3 deletions aiida/orm/nodes/data/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -856,6 +856,8 @@ def set_pymatgen_structure(self, struct):
:raise ValueError: if there are partial occupancies together with spins.
"""

from pkg_resources import parse_version

def build_kind_name(species_and_occu):
"""
Build a kind name from a pymatgen Composition, including an additional ordinal if spin is included,
Expand Down Expand Up @@ -896,16 +898,24 @@ def build_kind_name(species_and_occu):
self.pbc = [True, True, True]
self.clear_kinds()

required_pmg_version = parse_version('2019.3.13')
current_pmg_version = parse_version(get_pymatgen_version())
for site in struct.sites:

# site.species property first introduced in pymatgen version 2019.3.13
if current_pmg_version < required_pmg_version:
species_and_occu = site.species_and_occu
else:
species_and_occu = site.species

if 'kind_name' in site.properties:
kind_name = site.properties['kind_name']
else:
kind_name = build_kind_name(site.species_and_occu)
kind_name = build_kind_name(species_and_occu)

inputs = {
'symbols': [x.symbol for x in site.species_and_occu.keys()],
'weights': [x for x in site.species_and_occu.values()],
'symbols': [x.symbol for x in species_and_occu.keys()],
'weights': [x for x in species_and_occu.values()],
'position': site.coords.tolist()
}

Expand Down