def test_CRC_aqueous_thermodynamics():
assert all([checkCAS(i) for i in CRC_aqueous_thermodynamics.index])
# Check CASs match up
assert all([CAS_from_any(i) == i for i in CRC_aqueous_thermodynamics.index])
# Check search by formula matches up
for formula, CAS in zip(CRC_aqueous_thermodynamics['Formula'], CRC_aqueous_thermodynamics.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
# Check the MWs match up
for CAS, MW_specified in zip(CRC_aqueous_thermodynamics.index, CRC_aqueous_thermodynamics['MW']):
c = pubchem_db.search_CAS(CAS)
assert_allclose(c.MW, MW_specified, atol=0.05)
# Checking names is an option too but of 173, only 162 are unique
# and many of the others have names that seem ambiguous for ions which can
# have more than one charge
assert CRC_aqueous_thermodynamics.index.is_unique
assert CRC_aqueous_thermodynamics.shape == (173, 7)
Hf_tot = CRC_aqueous_thermodynamics['Hf(aq)'].abs().sum()
assert_allclose(Hf_tot, 70592500.0)
Gf_tot = CRC_aqueous_thermodynamics['Gf(aq)'].abs().sum()
assert_allclose(Gf_tot, 80924000.0)
S_tot = CRC_aqueous_thermodynamics['S(aq)'].abs().sum()
assert_allclose(S_tot, 17389.9)
Cp_tot = CRC_aqueous_thermodynamics['Cp(aq)'].abs().sum()
assert_allclose(Cp_tot, 2111.5)
def test_CRC_aqueous_thermodynamics():
assert all([checkCAS(i) for i in CRC_aqueous_thermodynamics.index])
# Check CASs match up
assert all([CAS_from_any(i) == i for i in CRC_aqueous_thermodynamics.index])
# Check search by formula matches up
for formula, CAS in zip(CRC_aqueous_thermodynamics['Formula'], CRC_aqueous_thermodynamics.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
# Check the MWs match up
for CAS, MW_specified in zip(CRC_aqueous_thermodynamics.index, CRC_aqueous_thermodynamics['MW']):
c = pubchem_db.search_CAS(CAS)
assert_allclose(c.MW, MW_specified, atol=0.05)
# Checking names is an option too but of 173, only 162 are unique
# and many of the others have names that seem ambiguous for ions which can
# have more than one charge
assert CRC_aqueous_thermodynamics.index.is_unique
assert CRC_aqueous_thermodynamics.shape == (173, 7)
Hf_tot = CRC_aqueous_thermodynamics['Hf(aq)'].abs().sum()
assert_allclose(Hf_tot, 70592500.0)
Gf_tot = CRC_aqueous_thermodynamics['Gf(aq)'].abs().sum()
assert_allclose(Gf_tot, 80924000.0)
S_tot = CRC_aqueous_thermodynamics['S(aq)'].abs().sum()
assert_allclose(S_tot, 17389.9)
Cp_tot = CRC_aqueous_thermodynamics['Cp(aq)'].abs().sum()
assert_allclose(Cp_tot, 2111.5)
def test_dissociation_reactions():
from thermo.electrochem import electrolyte_dissociation_reactions as df
from collections import Counter
# Check there's only one dissociation reaction for each product
assert len(df['Electrolyte Formula'].values) == len(
set(df['Electrolyte Formula'].values))
# Check the chemicals match up with the database
for name, CAS, formula in zip(df['Electrolyte name'],
df['Electrolyte CAS'],
df['Electrolyte Formula']):
assert CAS_from_any(CAS) == CAS
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the anions match up with the database
for formula, CAS, charge in zip(df['Anion formula'], df['Anion CAS'],
df['Anion charge']):
assert CAS_from_any(CAS) == CAS
assert CAS_from_any(formula) == CAS
assert pubchem_db.search_CAS(CAS).charge == charge
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the cations match up with the database
for formula, CAS, charge in zip(df['Cation formula'], df['Cation CAS'],
df['Cation charge']):
assert CAS_from_any(CAS) == CAS
assert CAS_from_any(formula) == CAS
assert pubchem_db.search_CAS(CAS).charge == charge
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the charges and counts of ions sums to zero
for index, row in df.iterrows():
an_charge = row['Anion charge']
an_count = row['Anion count']
cat_charge = row['Cation charge']
cat_count = row['Cation count']
err = an_charge * an_count + cat_charge * cat_count
assert err == 0
# Check the reactant counts and product counts sum to be equal and conserve
# moles
for index, row in df.iterrows():
elec = nested_formula_parser(row['Electrolyte Formula'])
cat = nested_formula_parser(row['Cation formula'])
cat_count = row['Cation count']
an = nested_formula_parser(row['Anion formula'])
an_count = row['Anion count']
product_counter = Counter()
for _ in range(cat_count):
product_counter.update(cat)
for _ in range(an_count):
product_counter.update(an)
assert dict(product_counter.items()) == elec
def test_Marcus_ion_conductivities():
# Check the CAS numbers are the "canonical" ones
assert all([CAS_from_any(i) == i for i in Marcus_ion_conductivities.index])
# Check the charges match up
for v, CAS in zip(Marcus_ion_conductivities['Charge'], Marcus_ion_conductivities.index):
assert v == charge_from_formula(pubchem_db.search_CAS(CAS).formula)
# Even check the formulas work!
for formula, CAS in zip(Marcus_ion_conductivities['Formula'], Marcus_ion_conductivities.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
def test_Marcus_ion_conductivities():
# Check the CAS numbers are the "canonical" ones
assert all([CAS_from_any(i) == i for i in Marcus_ion_conductivities.index])
# Check the charges match up
for v, CAS in zip(Marcus_ion_conductivities['Charge'], Marcus_ion_conductivities.index):
assert v == charge_from_formula(pubchem_db.search_CAS(CAS).formula)
# Even check the formulas work!
for formula, CAS in zip(Marcus_ion_conductivities['Formula'], Marcus_ion_conductivities.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
def test_dissociation_reactions():
from thermo.electrochem import electrolyte_dissociation_reactions as df
from collections import Counter
# Check there's only one dissociation reaction for each product
assert len(df['Electrolyte Formula'].values) == len(set(df['Electrolyte Formula'].values))
# Check the chemicals match up with the database
for name, CAS, formula in zip(df['Electrolyte name'], df['Electrolyte CAS'], df['Electrolyte Formula']):
assert CAS_from_any(CAS) == CAS
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the anions match up with the database
for formula, CAS, charge in zip(df['Anion formula'], df['Anion CAS'], df['Anion charge']):
assert CAS_from_any(CAS) == CAS
assert CAS_from_any(formula) == CAS
assert pubchem_db.search_CAS(CAS).charge == charge
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the cations match up with the database
for formula, CAS, charge in zip(df['Cation formula'], df['Cation CAS'], df['Cation charge']):
assert CAS_from_any(CAS) == CAS
assert CAS_from_any(formula) == CAS
assert pubchem_db.search_CAS(CAS).charge == charge
assert pubchem_db.search_CAS(CAS).formula == serialize_formula(formula)
# Check the charges and counts of ions sums to zero
for index, row in df.iterrows():
an_charge = row['Anion charge']
an_count = row['Anion count']
cat_charge = row['Cation charge']
cat_count = row['Cation count']
err = an_charge*an_count + cat_charge*cat_count
assert err == 0
# Check the reactant counts and product counts sum to be equal and conserve
# moles
for index, row in df.iterrows():
elec = nested_formula_parser(row['Electrolyte Formula'])
cat = nested_formula_parser(row['Cation formula'])
cat_count = row['Cation count']
an = nested_formula_parser(row['Anion formula'])
an_count = row['Anion count']
product_counter = Counter()
for _ in range(cat_count):
product_counter.update(cat)
for _ in range(an_count):
product_counter.update(an)
assert dict(product_counter.items()) == elec
def test_CRC_ion_conductivities():
# Check CASs match up
assert all([CAS_from_any(i) == i for i in CRC_ion_conductivities.index])
# Check search by formula matches up
for formula, CAS in zip(CRC_ion_conductivities['Formula'], CRC_ion_conductivities.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
def test_CRC_ion_conductivities():
# Check CASs match up
assert all([CAS_from_any(i) == i for i in CRC_ion_conductivities.index])
# Check search by formula matches up
for formula, CAS in zip(CRC_ion_conductivities['Formula'], CRC_ion_conductivities.index):
assert pubchem_db.search_CAS(CAS_from_any(formula)).CASs == CAS
def test_McCleskey_data():
# Check the CAS lookups
for CAS, d in McCleskey_conductivities.items():
assert pubchem_db.search_CAS(CAS).CASs == CAS
# Check the formula lookups
for CAS, d in McCleskey_conductivities.items():
assert CAS_from_any(d.Formula) == CAS
def test_McCleskey_data():
# Check the CAS lookups
for CAS, d in McCleskey_conductivities.items():
assert pubchem_db.search_CAS(CAS).CASs == CAS
# Check the formula lookups
for CAS, d in McCleskey_conductivities.items():
assert CAS_from_any(d.Formula) == CAS