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bulk_stability calculation unit test fixed #100

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Jun 29, 2020
Merged

bulk_stability calculation unit test fixed #100

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bf00a47
PEP update, assertion update for bulk stability calculation function …
May 18, 2020
d987758
change and verified the bulk stability expected numbers with MP website
Jun 27, 2020
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3 changes: 2 additions & 1 deletion gaspy/gasdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from pymongo import MongoClient
from pymongo.collection import Collection
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, ELEMENTS_HO, PourbaixPlotter
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, ELEMENTS_HO
from . import defaults
from .utils import read_rc
from .fireworks_helper_scripts import get_launchpad
Expand Down Expand Up @@ -812,6 +812,7 @@ def purge_adslabs(fwids):
with get_mongo_collection('adsorption') as collection:
collection.delete_many({'fwids.slab+adsorbate': {'$in': fwids}})


def get_electrochemical_stability(mpid, pH, potential):
'''
A wrapper for pymatgen to construct Pourbaix amd calculate electrochemical
Expand Down
9 changes: 6 additions & 3 deletions gaspy/tests/gasdb_test.py
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Expand Up @@ -36,6 +36,7 @@
get_electrochemical_stability)

# Things we need to do the tests
import math
import pytest
import warnings
import copy
Expand Down Expand Up @@ -507,10 +508,12 @@ def test_get_low_coverage_ml_docs(adsorbate, model_tag):
low_cov_energy = low_coverage_docs_by_surface[surface]['energy']
assert low_cov_energy <= energy


def test_get_electrochemical_stability():
# at pH=0, V=0.9
expected_stabilities = {'mp-126':0.884, # Pt
'mp-81': 0.0} # Au
expected_stabilities = {'mp-126': 0.861, # Pt
'mp-81': 0.0, # Au
'mp-2723': 0.0} #IrO2
for mpid, expected_stability in expected_stabilities.items():
stability = get_electrochemical_stability(mpid, 0, 0.9)
assert stability == expected_stability
assert math.isclose(stability, expected_stability, rel_tol=1e-6)