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Oxidation States 24 #329
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Oxidation States 24 #329
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da611fb
Initial cleanup of oxidation state data files
aronwalsh b3c544f
ICSD (2024) oxidation states
aronwalsh fbd1be3
Create oxidation_states_icsd24_common.txt
aronwalsh ba132de
Update oxidation_states_icsd24_counts.json
aronwalsh 0be9b0b
Make the filtered 2024 icsd oxidation states available through data_l…
e062c1c
Make oxidation_states_icsd24 available through the Element class
09ebea0
Merge branch 'docs_updates' of https://github.com/WMD-group/SMACT int…
1e668fc
Add oxidation states utility functions
ec8120e
Add test files
3875854
Update ICSD24OxStatesFilter
bf75145
Add tests for utils/oxidation
ef94fcb
Run pre-commit
AntObi 88e83ac
Update filter
AntObi e580d58
Add method for creating species lists
AntObi c1642ab
Add option to format species as 'X1+' or 'X+'
AntObi 49e7568
Add test for oxidation filter
AntObi 41d7bbb
Fixed ICSD24 List
aronwalsh 13e6eb9
Add function for getting a dataframe of species occurrences
AntObi b8982be
Update tests and add test for getting occurences
AntObi 9125edb
Update test files
AntObi 99acd4e
Merge branch 'develop' into oxidationstates24
AntObi 3c73285
Run pre-commit
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,3 +1,7 @@ | ||
# | ||
# Oxidation state set | ||
# Source: Original SMACT set manually compiled (2014) | ||
# | ||
H -1 +1 | ||
He | ||
Li +1 | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,3 +1,7 @@ | ||
# | ||
# Oxidation state set | ||
# Source: Pymatgen structure predictor (2017) | ||
# | ||
H 1 | ||
He | ||
Li 1 | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,3 +1,7 @@ | ||
# | ||
# Oxidation state set | ||
# Source: ICSD (2016) | ||
# | ||
H -1 1 | ||
He | ||
Li 1 | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,107 @@ | ||
# | ||
# Oxidation state set | ||
# Source: ICSD (2024, V2), most common non-zero values | ||
# | ||
H 1 | ||
He | ||
Li 1 | ||
Be 2 | ||
B 3 | ||
C 4 | ||
N -3 | ||
O -2 | ||
F -1 | ||
Ne | ||
Na 1 | ||
Mg 2 | ||
Al 3 | ||
Si 4 | ||
P 5 | ||
S -2 | ||
Cl -1 | ||
Ar | ||
K 1 | ||
Ca 2 | ||
Sc 3 | ||
Ti 4 | ||
V 5 | ||
Cr 3 | ||
Mn 2 | ||
Fe 3 | ||
Co 2 | ||
Ni 2 | ||
Cu 2 | ||
Zn 2 | ||
Ga 3 | ||
Ge 4 | ||
As 5 | ||
Se -2 | ||
Br -1 | ||
Kr 2 | ||
Rb 1 | ||
Sr 2 | ||
Y 3 | ||
Zr 4 | ||
Nb 5 | ||
Mo 6 | ||
Tc 7 | ||
Ru 4 | ||
Rh 3 | ||
Pd 2 | ||
Ag 1 | ||
Cd 2 | ||
In 3 | ||
Sn 4 | ||
Sb 3 | ||
Te -2 | ||
I -1 | ||
Xe 6 | ||
Cs 1 | ||
Ba 2 | ||
La 3 | ||
Ce 3 | ||
Pr 3 | ||
Nd 3 | ||
Pm 3 | ||
Sm 3 | ||
Eu 3 | ||
Gd 3 | ||
Tb 3 | ||
Dy 3 | ||
Ho 3 | ||
Er 3 | ||
Tm 3 | ||
Yb 3 | ||
Lu 3 | ||
Hf 4 | ||
Ta 5 | ||
W 6 | ||
Re 7 | ||
Os 5 | ||
Ir 4 | ||
Pt 4 | ||
Au 1 | ||
Hg 2 | ||
Tl 1 | ||
Pb 2 | ||
Bi 3 | ||
Po 4 | ||
At | ||
Rn | ||
Fr | ||
Ra 2 | ||
Ac 3 | ||
Th 4 | ||
Pa 5 | ||
U 6 | ||
Np 6 | ||
Pu 3 | ||
Am 3 | ||
Cm 3 | ||
Bk 3 | ||
Cf 3 | ||
Es 3 | ||
Fm | ||
Md | ||
No | ||
Lr |
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💡 Codebase verification
Implementation for ICSD24 oxidation states is missing
The verification reveals critical issues:
lookup_element_oxidation_states_icsd24
function implementation is not found in the codebaseoxidation_states_icsd24.txt
is missingThis change cannot be safely integrated without:
🔗 Analysis chain
Verify data loader implementation and error handling
The initialization of the new oxidation states attribute follows the established pattern. However, as this is a breaking change, please ensure:
lookup_element_oxidation_states_icsd24
function in data_loader handles missing data gracefullyLet me gather more information about the data loader implementation for the new ICSD24 function.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
Length of output: 1925
Script:
Length of output: 243