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Add F* diagram generator to pymatgen #3277

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19f1b2c
reimplemented fstar diagram
jonathanjdenney Jul 3, 2023
42ec13e
upstream/master
jonathanjdenney Aug 24, 2023
634b871
update fstar
jonathanjdenney Aug 28, 2023
fbc2e32
Merge remote-tracking branch 'upstream/master' into fstar
jonathanjdenney Aug 28, 2023
99c6001
pre-commit auto-fixes
pre-commit-ci[bot] Aug 28, 2023
9cbbdaf
ruff fixes
jonathanjdenney Aug 28, 2023
6314751
Merge branch 'fstar' of https://github.com/jonathanjdenney/pymatgen i…
jonathanjdenney Aug 28, 2023
e9cea13
make edits
jonathanjdenney Sep 1, 2023
8cb1729
Merge remote-tracking branch 'upstream/master' into fstar
jonathanjdenney Sep 1, 2023
3ba6384
pre-commit auto-fixes
pre-commit-ci[bot] Sep 1, 2023
df81873
Update fstar.py
jonathanjdenney Sep 1, 2023
0d91711
Update fstar.py
jonathanjdenney Sep 1, 2023
4e680d1
Update fstar.py
jonathanjdenney Sep 1, 2023
27c680d
Update test_fstar.py
jonathanjdenney Sep 1, 2023
a149fc2
pre-commit auto-fixes
pre-commit-ci[bot] Sep 1, 2023
df3f597
Update test_fstar.py
jonathanjdenney Sep 1, 2023
e244c89
Merge branch 'fstar' of https://github.com/jonathanjdenney/pymatgen i…
jonathanjdenney Sep 1, 2023
3c22459
simplify test files
jonathanjdenney Sep 2, 2023
347fc77
Merge remote-tracking branch 'upstream/master' into fstar
jonathanjdenney Sep 2, 2023
a16a184
pre-commit auto-fixes
pre-commit-ci[bot] Sep 2, 2023
1a9db44
Update test_fstar.py
jonathanjdenney Sep 2, 2023
3837ff5
Merge branch 'fstar' of https://github.com/jonathanjdenney/pymatgen i…
jonathanjdenney Sep 2, 2023
7990af0
git diff --name-only origin/master...HEAD | tail -n +4 | xargs git ch…
janosh Sep 16, 2023
fc95d65
gzip pymatgen/analysis/fstar/neutron_factors.csv
janosh Sep 16, 2023
cd617d7
Merge remote-tracking branch 'upstream/master' into fstar
jonathanjdenney Sep 18, 2023
b83a4b5
Update fstar.py
jonathanjdenney Sep 18, 2023
9ccf8cf
Update fstar.py
jonathanjdenney Sep 18, 2023
f888dba
Update fstar.py
jonathanjdenney Sep 18, 2023
97574ca
pre-commit auto-fixes
pre-commit-ci[bot] Sep 18, 2023
c5715a7
Update fstar.py
jonathanjdenney Sep 18, 2023
46fffbc
Merge branch 'fstar' of https://github.com/jonathanjdenney/pymatgen i…
jonathanjdenney Sep 18, 2023
1a92f85
pre-commit auto-fixes
pre-commit-ci[bot] Sep 18, 2023
21961b9
Merge branch 'master' into fstar
shyuep Nov 13, 2024
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pre-commit-ci[bot] Nov 13, 2024
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ruff fixes
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jonathanjdenney committed Aug 28, 2023

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commit 9cbbdaf5b44752e57b7114abf3d3f9992b12c6da
6 changes: 1 addition & 5 deletions pymatgen/analysis/fstar/fstar.py
Original file line number Diff line number Diff line change
@@ -76,7 +76,7 @@ def edit_fstar_diagram(self, combine_list=False, plot_list=False, **kwargs):

def get_site_labels(self):
"""
Generates unique site labels based on composition, order, and symetry equivalence in the structure object.
Generates unique site labels based on composition, order, and symmetry equivalence in the structure object.
Ex:
Structure Summary
Lattice
@@ -144,14 +144,10 @@ def get_fstar_coords(self):
if n == str(sp.element):
f_occ = float(NEUTRON_SCATTER_DF.loc[i]['Coh b']) * occ
break
else:
continue
else:
if n == str(sp):
f_occ = float(NEUTRON_SCATTER_DF.loc[i]['Coh b']) * occ
break
else:
continue
if self._scatter == 'Custom':
if hasattr(sp, "element"):
f_occ = self._custscat(str(sp.element), occ, ind1, ind2)
4 changes: 2 additions & 2 deletions tests/analysis/fstar/test_fstar.py
Original file line number Diff line number Diff line change
@@ -23,8 +23,8 @@ def test_edit_fstar_diagram(self):
new.edit_fstar_diagram(combine_list=[['[0. 0. 0.5]Co', '[0. 0. 0.]Li']])
self.assertEqual(new.site_labels, ['[0. 0. 0.]Li', '[0. 0. 0.5]Co', '[0. 0. 0.25]O',
"['[0. 0. 0.5]Co', '[0. 0. 0.]Li']"])
self.assertEqual(list(new.coords["['[0. 0. 0.5]Co', '[0. 0. 0.]Li']"].values),
list(self.fstar.coords['[0. 0. 0.]Li'].values+self.fstar.coords['[0. 0. 0.5]Co'].values))
self.assertEqual(list(new.coords["['[0. 0. 0.5]Co', '[0. 0. 0.]Li']"].to_numpy()),
list(self.fstar.coords['[0. 0. 0.]Li'].values+self.fstar.coords['[0. 0. 0.5]Co'].to_numpy()))
self.assertEqual(self.fstar.plot, new.plot)
new.edit_fstar_diagram(plot_list=['[0. 0. 0.5]Co', '[0. 0. 0.25]O', '[0. 0. 0.]Li'])
self.assertTrue(self.fstar.plot != new.plot)