A battery model ran to completion on every revision and lost 2.4% of its lithium

The model conserves lithium: the total in electrolyte and particles stays constant over a discharge and charge cycle, up to solver tolerance.

1. Froze three revisions of the library, the v26.4.1 release, main at 258fdc8 and the head of then-under-review pull request #5524, with 1,228 files hashed before any run.
2. Assembled the lithium inventory independently from the mesh, the parameters and the raw concentrations, never from the library's own totals, with a second explicit-loop implementation checked against the first on every run.
3. Ran 84 jobs across two models, three revisions and seven mesh and tolerance settings, with the constant-transference model and the full modular model as controls.
4. Compared the measured rate of loss, instant by instant, with the rate the equation predicts if one term is missing.

• The BasicDFN model with a concentration-dependent transference number lost 2.44% of its lithium on every revision and at every refinement. Tightening the time tolerance to 1e-10 and refining to 80 cells changed the fourth digit.
• The loss matched the rate predicted from the missing transference-gradient term to 2.9e-18 mol/s. The equation, not the discretisation, is the cause.
• The then-under-review pull request #5524 left both reported cases byte-identical to main: neither model selects the option it adds.
• Separately, the half-cell diagnostic Total lithium in electrolyte multiplies by the full-cell thickness (767 µm) where the electrolyte occupies 67 µm, overweighting that term by 11.45.
• The controls held: the constant-transference model conserved to 7.7e-15 mol and the full model to 3.5e-14 mol.

CONTRADICTED

BasicDFN conserves lithium with a concentration-dependent transference number. Equation-level. A project contributor confirmed the missing term and asked for a separate report: issue #5745.

CONTRADICTED

The half-cell electrolyte lithium diagnostic reports moles of lithium. Wrong length scale by a factor of 11.45; confirmed and split out as issue #5746.

CONTRADICTED

The then-under-review pull request #5524 changes the reported cases. Byte-identical time series on all 24 completed pairs.

One library, two models, one protocol, one parameter set. The full DFN conserved; nothing is said against it. Eleven half-cell jobs failed inside the solver at tight tolerance, so no half-cell convergence order is claimed. The finite-volume treatment of nonlinear source terms, which the contributor raised, was not investigated. The #5745 fix is on the default branch but not in a tagged release; #5746 is not fixed.

• PyBaMM MERGED fixWhether the BasicDFN model conserves lithium when the transference number depends on concentration. Issue #5745, 6 September 2026, split from #5700 at a contributor's request. Warren's pull request #5747, covering the lithium and sodium BasicDFN variants, was approved and merged by the maintainer on 18 September 2026. On the default branch; in no tagged release as of 20 September 2026.
• PyBaMM MERGED fixWhether the half-cell diagnostic Total lithium in electrolyte uses the electrolyte's own thickness. Issue #5746, 6 September 2026, split from #5700 at a contributor's request. Maintainer-authored pull request #5765 corrects the half-cell lithium diagnostic and adds regression tests. Merged 2026-09-22; merge commit 9daad126258db8f6e621e4746cd3bdac062e7f1f.

Released means the fix is in a tagged release. Merged means it is on the default branch but not verified in a tagged release. Open pull request means an Omega-authored change awaits upstream action. Open issue means a report remains open without a merged fix. Maintainer acceptance is review of one change, not endorsement of Omega.

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