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fix pymatgen imports #4794

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Mar 8, 2021
Merged

fix pymatgen imports #4794

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6 changes: 3 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 @@ -1852,7 +1852,7 @@ def _get_object_pymatgen_structure(self, **kwargs):
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors)
"""
from pymatgen import Structure
from pymatgen.core.structure import Structure

if self.pbc != (True, True, True):
raise ValueError('Periodic boundary conditions must apply in all three dimensions of real space')
Expand All @@ -1862,7 +1862,7 @@ def _get_object_pymatgen_structure(self, **kwargs):

if (kwargs.pop('add_spin', False) and any([n.endswith('1') or n.endswith('2') for n in self.get_kind_names()])):
# case when spins are defined -> no partial occupancy allowed
from pymatgen import Specie
from pymatgen.core.periodic_table import Specie
oxidation_state = 0 # now I always set the oxidation_state to zero
for site in self.sites:
kind = self.get_kind(site.kind_name)
Expand Down Expand Up @@ -1907,7 +1907,7 @@ def _get_object_pymatgen_molecule(self, **kwargs):
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors)
"""
from pymatgen import Molecule
from pymatgen.core.structure import Molecule

if kwargs:
raise ValueError(f'Unrecognized parameters passed to pymatgen converter: {kwargs.keys()}')
Expand Down
2 changes: 1 addition & 1 deletion aiida/tools/dbimporters/plugins/materialsproject.py
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Expand Up @@ -12,7 +12,7 @@
import os
import requests

from pymatgen import MPRester
from pymatgen.ext.matproj import MPRester

from aiida.tools.dbimporters.baseclasses import CifEntry, DbImporter, DbSearchResults

Expand Down
44 changes: 24 additions & 20 deletions tests/test_dataclasses.py
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Expand Up @@ -2227,25 +2227,27 @@ def test_partial_occ_and_spin(self):
Tests pymatgen -> StructureData, with partial occupancies and spins.
This should raise a ValueError.
"""
import pymatgen

Fe_spin_up = pymatgen.Specie('Fe', 0, properties={'spin': 1})
Mn_spin_up = pymatgen.Specie('Mn', 0, properties={'spin': 1})
Fe_spin_down = pymatgen.Specie('Fe', 0, properties={'spin': -1})
Mn_spin_down = pymatgen.Specie('Mn', 0, properties={'spin': -1})
FeMn1 = pymatgen.Composition({Fe_spin_up: 0.5, Mn_spin_up: 0.5})
FeMn2 = pymatgen.Composition({Fe_spin_down: 0.5, Mn_spin_down: 0.5})
a = pymatgen.Structure(
from pymatgen.core.periodic_table import Specie
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure

Fe_spin_up = Specie('Fe', 0, properties={'spin': 1})
Mn_spin_up = Specie('Mn', 0, properties={'spin': 1})
Fe_spin_down = Specie('Fe', 0, properties={'spin': -1})
Mn_spin_down = Specie('Mn', 0, properties={'spin': -1})
FeMn1 = Composition({Fe_spin_up: 0.5, Mn_spin_up: 0.5})
FeMn2 = Composition({Fe_spin_down: 0.5, Mn_spin_down: 0.5})
a = Structure(
lattice=[[4, 0, 0], [0, 4, 0], [0, 0, 4]], species=[FeMn1, FeMn2], coords=[[0, 0, 0], [0.5, 0.5, 0.5]]
)

with self.assertRaises(ValueError):
StructureData(pymatgen=a)

# same, with vacancies
Fe1 = pymatgen.Composition({Fe_spin_up: 0.5})
Fe2 = pymatgen.Composition({Fe_spin_down: 0.5})
a = pymatgen.Structure(
Fe1 = Composition({Fe_spin_up: 0.5})
Fe2 = Composition({Fe_spin_down: 0.5})
a = Structure(
lattice=[[4, 0, 0], [0, 4, 0], [0, 0, 4]], species=[Fe1, Fe2], coords=[[0, 0, 0], [0.5, 0.5, 0.5]]
)

Expand All @@ -2257,12 +2259,13 @@ def test_partial_occ_and_spin(self):
def test_multiple_kinds_partial_occupancies():
"""Tests that a structure with multiple sites with the same element but different
partial occupancies, get their own unique kind name."""
import pymatgen
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure

Mg1 = pymatgen.Composition({'Mg': 0.50})
Mg2 = pymatgen.Composition({'Mg': 0.25})
Mg1 = Composition({'Mg': 0.50})
Mg2 = Composition({'Mg': 0.25})

a = pymatgen.Structure(
a = Structure(
lattice=[[4, 0, 0], [0, 4, 0], [0, 0, 4]], species=[Mg1, Mg2], coords=[[0, 0, 0], [0.5, 0.5, 0.5]]
)

Expand All @@ -2275,12 +2278,13 @@ def test_multiple_kinds_alloy():
Tests that a structure with multiple sites with the same alloy symbols but different
weights, get their own unique kind name
"""
import pymatgen
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Structure

alloy_one = pymatgen.Composition({'Mg': 0.25, 'Al': 0.75})
alloy_two = pymatgen.Composition({'Mg': 0.45, 'Al': 0.55})
alloy_one = Composition({'Mg': 0.25, 'Al': 0.75})
alloy_two = Composition({'Mg': 0.45, 'Al': 0.55})

a = pymatgen.Structure(
a = Structure(
lattice=[[4, 0, 0], [0, 4, 0], [0, 0, 4]],
species=[alloy_one, alloy_two],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]]
Expand Down