13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing…
Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measured cycling data. Use for SPM or DFN electrochemical battery modeling, C-rate
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill pybamm --agent claude-codeHow it fires
How this skill gets triggered: by you, by Claude, or both.
/pybammContext preview
The summary Claude sees to decide when to auto-load this skill.
Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measured cycling data. Use for SPM or DFN electrochemical battery modeling, C-rate
name: pybamm description: Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measured cycling data. Use for SPM or DFN electrochemical battery modeling, C-rate protocols, voltage cutoffs, parameter studies and numerical validation of battery simulations. license: MIT compatibility: Requires Python 3.12 with PyBaMM 26.9.0.0 and pybammsolvers 0.10.0 (IDAKLU). NumPy and CasADi are supplied by PyBaMM. Network is needed for installation and optional upstream dataset retrieval; bundled simulations and CSV comparisons run locally without credentials. metadata: version: "1.1" skill-author: K-Dense Inc. upstream-version: "26.9.0.0" last-reviewed: "2026-10-01"
Use this skill to model single-cell constant-current charge/discharge and rest, examine voltage and charge trajectories, or compare SPM/DFN predictions to cycling measurements. The helper runs real PyBaMM experiments and three numerical resolutions; it does not control a battery cycler or establish an operating envelope for hardware.
uv venv --python 3.12 battery-env uv pip install --python battery-env/bin/python pybamm==26.9.0.0 pybammsolvers==0.10.0
This release requires `pybammsolvers>=0.10.0`, NumPy 2 or newer, and CasADi 3.8.1. The tested environment used Python 3.12.10, NumPy 2.5.3 and SciPy 1.18.1. IDAKLU is the recommended solver; `CasadiSolver` and `ScipySolver` are deprecated in this release. Refer to the **26.9.0.0** manual below, since `latest` can describe unreleased APIs.
The included [assets/chen2020-protocol.json](assets/chen2020-protocol.json) is a synthetic isothermal 298.15-K SPM case: 80% initial SOC, discharge at 0.5C for 600 s, rest for 120 s, charge at 0.5C for 600 s. Chen2020 supplies an LG M50 parameterization with 5-Ah nominal capacity; here 0.5C means 2.5 A. This is an executable reference example, not a claim that an arbitrary user's cell has those parameters. The helper disables PyBaMM usage telemetry unless the caller has already explicitly configured that variable.
1. Establish the cell chemistry, geometry, nominal capacity, initial state, temperature and current-sign convention. Use an appropriate parameter set and explain its source. Distinguish a paper's fitted parameters from measurements of this particular cell. Do not transplant degradation parameters without checking their meaning and applicable conditions. 2. Convert the requested protocol to the JSON contract in [references/protocol-and-comparison.md](references/protocol-and-comparison.md). Positive simulation current discharges; negative current charges. Every step has a finite duration. A specified voltage cutoff can end it earlier; the report records actual termination times. C-rates use the selected set's nominal capacity. A change in that capacity changes current. 3. Choose SPM when its reduced transport assumptions are adequate; use DFN when resolving electrolyte/electrode transport matters. The helper's tested models are isothermal and exclude aging, mechanics, plating and pack control. Increasing rate can invalidate SPM predictions even if numerical convergence is excellent. 4. Run the helper. It validates protocol fields, rejects unknown or overridden-by-protocol parameter inputs, uses IDAKLU, and snapshots the base parameters **after SOC initialization**. Keep the protocol with that snapshot: experiment steps supply their own currents. Infeasible or skipped steps are errors, rather than silently presenting a partial protocol as complete. 5. Read the two numerical comparisons separately: baseline versus tighter tolerances isolates solver error; tight tolerances on the original versus doubled mesh isolates discretization. Compare voltage differences and event-time differences against the accuracy the question needs. Refine again when these are too large; one doubling does not prove convergence. 6. If measurements are available, check current, time origin, temperature, SOC and capacity before interpreting residuals. Supply matching seconds, volts and amps. The helper reports voltage RMSE/MAE/bias and current RMSE, preserving residuals. A small voltage error under a mismatched input current does not validate the model. This workflow compares curves; it does not claim to identify unique kinetic parameters from voltage alone.
From the skill directory, point `battery-env/bin/python` at the environment created above:
battery-env/bin/python scripts/simulate_battery.py assets/chen2020-protocol.json \ --output battery-reference # measured.csv is user data with time_s,voltage_V,current_A columns. battery-env/bin/python scripts/simulate_battery.py protocol.json \ --measured measured.csv --mesh-points 30 --output battery-comparison
The first command was executed as written with an external output location. The second uses illustrative user filenames; the measurement path was exercised against a frozen synthetic reference curve in the tests. Output directories must be new.
| Artifact | Interpretation | | --- | --- | | `curve.csv` | Baseline time, step, voltage, current and **net** discharge capacity | | `tight-tolerance.csv` | Same mesh, tighter solver | | `refined-mesh.csv` | Doubled mesh with tighter solver | | `parameters.json` | Base parameters after SOC initialization; step currents remain in the protocol | | `report.json` | Protocol/checksum, package versions, parameter source, numerical comparisons and terminations | | `measurement-residuals.csv` | Prediction minus measurement and current mismatch, when measurements were supplied |
The reference case conserved integrated charge: 600 s at 2.5 A yielded 0.4166667 Ah, then equal charge returned net discharge capacity to zero. Voltage stayed
🔔 Claude Scientific Skills is now Scientific Agent Skills. Same skills, broader compatibility — now works with any AI agent that supports the open Agent Skills standard, not just Claude.
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing…
Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization…
This skill should be used for time series machine learning tasks including classification,…
AlphaGenome API key, free for non-commercial use from…
Plans, executes, and documents validation, verification, and transfer of analytical…
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration…