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equilibrate: modify total conc check for missing elements #352

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Merged
rkingsbury merged 2 commits into from
Feb 14, 2026
Merged

equilibrate: modify total conc check for missing elements #352

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equilibrate: modify total conc check
rkingsbury Feb 14, 2026
12fa836
Merge branch 'main' into rk/eqmissing
rkingsbury Feb 14, 2026
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11 changes: 9 additions & 2 deletions src/pyEQL/engines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -761,7 +761,7 @@ def equilibrate(
# tolerance (in moles) for detecting cases where an element amount
# is no longer balanced because of species that are not recognized
# by PHREEQC.
_atol = 1e-16
_rtol = 0.05 # differing by more than 5%

new_el_dict = solution.get_el_amt_dict(nested=True)
for el in orig_el_dict:
Expand All @@ -770,7 +770,8 @@ def equilibrate(

# If this element went "missing", add back all components that
# contain this element (for any valence value)
if orig_el_amount - new_el_amount > _atol:
# if orig_el_amount - new_el_amount > _atol:
if new_el_amount == 0 and orig_el_amount > 0:
logger.info(
f"PHREEQC discarded element {el} during equilibration. Adding all components for this element."
)
Expand All @@ -782,6 +783,12 @@ def equilibrate(
if component not in solution.components
}
)
elif abs(orig_el_amount - new_el_amount) / orig_el_amount > _rtol:
logger.warning(
f"PHREEQC returned a total Element {el} concentration of {new_el_amount} mol, "
f"which differs from the original concentration of {orig_el_amount}. This "
"should never occur and indicates an error in the PHREEQC database or calculation."
)

# re-adjust charge balance for any missing species
# note that if balance_charge is set, it will have been passed to PHREEQC, so the only reason to re-adjust charge balance here is to account for any missing species.
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