# `07_GelSystems/optimize_parameter_gel_other_solvents`

This directory archives fitted gel-parameter sets for PNIPAAm swelling in
solvent combinations beyond the PNIPAAm-water baseline.

## Prerequisites

Use the root repository environment. No setup is required to inspect the JSON,
NPY, or CSV files directly.

## File Groups

- `pnipaam_best_params_W_AA*.json` and matching `...last_y_lst*.npy`: archived
  fits and continuation seeds for water/acetic-acid swelling studies
- `pnipaam_best_params_AA_BA*.json` and matching `...last_y_lst*.npy`: archived
  fits and continuation seeds for acetic-acid/butyl-acetate studies
- `pnipaam_best_params_BA_B*.json` and matching `...last_y_lst*.npy`: archived
  fits and continuation seeds for butyl-acetate/n-butanol studies
- `pnipaam_best_params_just13.json` and `pnipaam_best_params_diffvref.json`:
  exploratory archived parameter snapshots kept alongside the curated fits
- `pnipaam_ter_*_de_gen.csv`: optimizer histories, including script-named runs
  and legacy notebook-generated files such as `ipykernel_launcher`

## Naming

- `W`: water
- `AA`: acetic acid
- `BA`: butyl acetate
- `B`: n-butanol
- `NETWORK_FUNCTIONALITY`: network functionality was included in the fit
- `comp12_kij_intercept`, `comp13_kij_intercept`, `comp23_kij_intercept`:
  selected binary interaction terms were included in the fit
- `last_y_lst`: stored traced state vectors used as continuation seeds for
  later runs

## Consumers

The binary gel comparison scripts in the parent directory consume these files:

- [`../plot_gel_lle_binaries_wa_aa.py`](../plot_gel_lle_binaries_wa_aa.py)
- [`../plot_gel_lle_binaries_aa_ba.py`](../plot_gel_lle_binaries_aa_ba.py)
- [`../plot_gel_lle_binaries_ba_bu.py`](../plot_gel_lle_binaries_ba_bu.py)

## Commands

The current optimizer scripts that can produce new candidate files are:

```bash
cd 07_GelSystems
python optimize_parameters_example_gels_wa_aa.py
python optimize_parameters_example_gels_aa_ba.py
python optimize_parameters_example_gels_ba_bu.py
```

## Notes

As currently written, the cross-solvent optimizer scripts can write candidate
outputs to the current working directory while also reading initial guesses from
this archive. Treat reruns as candidate refreshes and move reviewed files into
this directory intentionally.
