| """Source of truth for the composite-model ablation-study notebook. Edit the cell sources here, |
| then regenerate: |
| |
| python3 build_nb_composite_models.py --write |
| jupyter nbconvert --to notebook --execute --inplace ../si_figures/si_composite_models_ablations.ipynb |
| |
| Regenerating overwrites the .ipynb, so do not hand-edit the notebook. All real code lives in |
| composite_models.py (numbers and the openpyxl table-writing layer, which itself calls delta22.py's |
| existing fitting harness); the notebook only runs it. The notebook itself lives in |
| analysis/si_figures/ (grouped by role), not here. |
| |
| Run with no arguments to see this usage message; pass --write to regenerate. This generator produces |
| a single notebook and takes no name argument, so a bare run must not silently overwrite it. |
| """ |
| import os |
| import sys |
|
|
| from nb_build import md, code, save_notebook as _save |
|
|
|
|
| _BOOTSTRAP = r""" |
| import os, sys |
| |
| # make the in-repo modules importable (not pip-installed) |
| REPO = os.path.abspath("../..") |
| for _p in ("data/delta22", "analysis/code", "analysis/code/shared"): |
| sys.path.insert(0, os.path.join(REPO, _p)) |
| """ |
|
|
| _IMPORTS = r""" |
| import matplotlib.pyplot as plt |
| |
| import delta22 |
| import composite_models |
| import composite_plots |
| import paths |
| """ |
|
|
| _SETUP = r""" |
| DELTA22_HDF5 = paths.dataset_file("delta22", root=REPO) |
| XLSX = os.path.join(REPO, "data", "delta22", "delta22_experimental.xlsx") |
| |
| def figure_path(name): |
| os.makedirs("figures", exist_ok=True) |
| return os.path.join("figures", name) |
| |
| def document_path(name): |
| os.makedirs("documents", exist_ok=True) |
| return os.path.join("documents", name) |
| |
| # the shipped ablations.xlsx used 250 seeded train/test splits per (formula, solvent) |
| N_SPLITS = 250 |
| """ |
|
|
| si_composite_models_ablations = [ |
| md(r""" |
| # Composite-formula ablation workbook |
| |
| Rebuilds the composite-formula ablation grid: ~25 composite-formula variants (stationary geometry |
| plus some combination of implicit PCM, explicit Desmond, and rovibrational QCD corrections) across |
| all 12 delta-22 solvents, at two reference levels: DSD-PBEP86/pcSseg-3 (geometry PBE0/tz) and the |
| MagNET-Zero training reference (WP04/pcSseg-2 for ¹H, ωB97X-D/pcSseg-2 for ¹³C). Also reports the |
| solvent-averaged correlations between the composite-model features. |
| """), |
| code(_BOOTSTRAP), |
| code(_IMPORTS), |
| code(_SETUP), |
| code(r""" |
| query_df_dft = delta22.add_composite_columns(delta22.load_query_df_dft(DELTA22_HDF5, XLSX, verbose=False)) |
| solutes = delta22.delta22_solutes(DELTA22_HDF5) |
| print(len(query_df_dft), "rows;", len(solutes), "solutes") |
| """), |
| md("## Preview: one formula's mean test RMSE at the DSD-PBEP86 reference level"), |
| code(r""" |
| # preview before the full build (all ~25 formulas x 12 solvents x 250 splits x 2 nuclei x 2 |
| # reference levels) |
| level = composite_models.REFERENCE_LEVELS["dsd"] |
| preview = composite_models.ablation_rmse_table(query_df_dft, "H", level["method_h"], level["basis_h"], |
| level["geometry_h"], solutes, n_splits=20) |
| preview[["chloroform", "benzene", "Mean Test RMSE"]].round(3) |
| """), |
| md("## Build the full ablations workbook (both reference levels, both nuclei)"), |
| code(r""" |
| output_path = document_path("ablations.xlsx") |
| composite_models.build_ablations_workbook(query_df_dft, solutes, output_path, n_splits=N_SPLITS) |
| """), |
| md(r""" |
| ## Correlations Between Features |
| |
| Solvent-averaged Pearson r correlation matrix between the five composite-model features (stationary |
| shielding, PCM, Desmond, its vibrational analogue, QCD), both nuclei, plus a per-solvent |
| PCM-vs-Desmond table. |
| """), |
| code(r""" |
| for nucleus, label in [("H", "Proton"), ("C", "Carbon")]: |
| corr = delta22.ablations_feature_correlations(query_df_dft, nucleus) |
| nuc_label = "1H" if nucleus == "H" else "13C" |
| nuc_title = "$^{1}$H" if nucleus == "H" else "$^{13}$C" |
| composite_plots.plot_feature_correlation_heatmap( |
| corr["r"], vmin=-1, vmax=1, cmap="RdBu", |
| title=f"Solvent-Averaged Pearson $r$ Correlation Matrix for {nuc_title}", |
| save_path=figure_path(f"ablations_feature_corr_r_{nuc_label}.png")) |
| plt.show() |
| """), |
| code(r""" |
| pcm_desmond_corr = delta22.pcm_desmond_correlation_by_solvent(query_df_dft) |
| print("PCM vs. Desmond Pearson R by nucleus and solvent:") |
| display(pcm_desmond_corr.round(3)) |
| composite_plots.plot_pcm_desmond_correlation_table(pcm_desmond_corr, |
| save_path=figure_path("ablations_pcm_desmond_corr_table.png")) |
| plt.show() |
| """), |
| ] |
|
|
|
|
| if __name__ == "__main__": |
| if "--write" not in sys.argv: |
| print("usage: python3 build_nb_composite_models.py --write") |
| print("regenerates analysis/si_figures/si_composite_models_ablations.ipynb -- pass --write to actually do it,") |
| print("since regenerating clears the notebook's execution outputs.") |
| sys.exit(0) |
| here = os.path.dirname(os.path.abspath(__file__)) |
| repo = os.path.abspath(os.path.join(here, "..", "..")) |
| _save(si_composite_models_ablations, os.path.join(repo, "analysis", "si_figures", "si_composite_models_ablations.ipynb")) |
|
|
