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select md ensemble and thermostat explicitly - #438
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Addresses review feedback: the ensemble was partly inferred (`pressure=None` is NVT, `langevin=True` is Langevin thermostat) and partly specified (`nve=True`). It is now always explicit, and arguments that only apply to one ensemble carry its name as a prefix. The changes: - `md_simulation` / `_run_lammps_md`: required `ensemble` (`"nve"`, `"nvt"`, `"npt"`, `"nvt_langevin"`, `"npt_langevin"`). `pressure` / `pressure_end` to `npt_pressure` / `npt_pressure_end`. The `nve` and `langevin` flags are removed. - `melt_quench_simulation`, `diffusion_simulation`, `viscosity_simulation`, `viscosity_ensemble`: `langevin: bool` is required `thermostat` (`"nose_hoover"` | `"langevin"`). Each protocol still decides NVT/NPT per stage. - `elastic_simulation`: required `ensemble` + `npt_pressure`; `"nve"` is rejected. - `cte_from_fluctuations_simulation`, `temperature_scan_simulation`: `pressure` → `npt_pressure`. - Arguments that don't fit the chosen ensemble raise a `ValueError` before LAMMPS starts. - API: the config schema is unchanged. `pipeline.py` turns the elastic config's `pressure=None` into an explicit `ensemble`. - Docs, docstring examples and tutorials are updated. Some of these changes are breaking - The parameters above are renamed or removed, and `ensemble` / `thermostat` are required. - `md_simulation`'s `temperature_sim` now defaults to `None` (was 5000 K).
Atilaac
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type: refactor
Codecov Report✅ All modified and coverable lines are covered by tests. 📢 Thoughts on this report? Let us know! |
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Great, thanks for following up on this @Atilaac ! |
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Addresses review feedback: the ensemble was partly inferred (
pressure=Noneis NVT,langevin=Trueis Langevin thermostat) and partly specified (nve=True). It is now always explicit, and arguments that only apply to one ensemble carry its name as a prefix.The changes:
md_simulation/_run_lammps_md: requiredensemble("nve","nvt","npt","nvt_langevin","npt_langevin").pressure/pressure_endtonpt_pressure/npt_pressure_end. Thenveandlangevinflags are removed.melt_quench_simulation,diffusion_simulation,viscosity_simulation,viscosity_ensemble:langevin: boolis requiredthermostat("nose_hoover"|"langevin"). Each protocol still decides NVT/NPT per stage.elastic_simulation: requiredensemble+npt_pressure;"nve"is rejected.cte_from_fluctuations_simulation,temperature_scan_simulation:pressure→npt_pressure.ValueErrorbefore LAMMPS starts.pipeline.pyturns the elastic config'spressure=Noneinto an explicitensemble.Some of these changes are breaking
ensemble/thermostatare required.md_simulation'stemperature_simnow defaults toNone(was 5000 K).