diff --git a/.jules/bolt.md b/.jules/bolt.md index b140c4a7c..ccc42dffd 100644 --- a/.jules/bolt.md +++ b/.jules/bolt.md @@ -5,3 +5,7 @@ ## 2024-05-19 - Caching YAML Load for Framework Registry **Learning:** `yaml.safe_load` on `frameworks.yml` within `load_framework_registry()` was taking ~2-3 ms per call and it was repeatedly called for every framework entry via `get_framework_config()`. This was a micro-bottleneck, especially when dealing with lists or multiple frameworks. **Action:** Applied the `@lru_cache` and `deepcopy` pattern successfully again to `load_framework_registry()` and `get_framework_config()` to avoid caching a mutable dictionary directly and avoid repeated YAML I/O parsing. + +## 2024-05-20 - Fast DataFrame Iteration Avoids Overhead +**Learning:** Iterating over Pandas DataFrames using `.iterrows()` introduces significant overhead because it creates a new `pd.Series` object for every single row. In calculation scripts (like elasticity, solvMPCONF196, etc.), this causes notable slowdowns when processing large datasets or many files. +**Action:** Replace `.iterrows()` with `.itertuples(index=False)` (or `name=None` if accessing by index `row[0]`) for purely positional or namedtuple-based attribute access, which is drastically faster. If variable column names require string keys, use `for row in df.to_dict('records'):`. Always check if `.iterrows()` is a bottleneck and optimize it. diff --git a/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py b/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py index 90628dad1..d5256c94b 100644 --- a/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py +++ b/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py @@ -235,7 +235,7 @@ def run_elasticity_benchmark( # Save relaxed structures to extxyz for visualisation atoms_list = [] - for _, row in results.iterrows(): + for row in results.to_dict("records"): struct = row.get("final_structure") if struct is not None: atoms = AseAtomsAdaptor.get_atoms(struct).copy() diff --git a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py index 145bd924a..3574bf30f 100644 --- a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py +++ b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py @@ -85,9 +85,9 @@ def get_ref_energies(data_path: Path) -> dict[str, float]: ) ref_energies = {} - for row in df.iterrows(): - label = row[1][0] - ref_energies[label] = float(row[1][2]) * KCAL_TO_EV + for row in df.itertuples(index=False, name=None): + label = row[0] + ref_energies[label] = float(row[2]) * KCAL_TO_EV return ref_energies diff --git a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py index c6cc078dd..6c105458c 100644 --- a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py +++ b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py @@ -83,9 +83,9 @@ def get_ref_energies(data_path: Path) -> dict[str, float]: ) ref_energies = {} - for row in df.iterrows(): - label = row[1][0] - e_ref = float(row[1][1]) * units.Hartree + for row in df.itertuples(index=False, name=None): + label = row[0] + e_ref = float(row[1]) * units.Hartree ref_energies[label] = e_ref return ref_energies diff --git a/ml_peg/calcs/utils/gscdb138.py b/ml_peg/calcs/utils/gscdb138.py index 4d0a019ca..430ebeed0 100644 --- a/ml_peg/calcs/utils/gscdb138.py +++ b/ml_peg/calcs/utils/gscdb138.py @@ -105,11 +105,13 @@ def run_gscdb138( df_refs["Reference"] *= units.Hartree # Calculate relative energy for each entry. - for _, row in tqdm(df_refs.iterrows(), dataset, total=df_refs.shape[0]): + for row in tqdm( + df_refs.itertuples(index=False), dataset, total=df_refs.shape[0] + ): atoms_list = [] - identifier = row["Reaction"] - reactions = row["Stoichiometry"].split(",") # Parse stoichiometry string. - e_rel_ref = row["Reference"] + identifier = row.Reaction + reactions = row.Stoichiometry.split(",") # Parse stoichiometry string. + e_rel_ref = row.Reference num_species = len(reactions) // 2 # Each species has coefficient and name. e_rel_model = 0