| import sys, json, numpy as np, pandas as pd |
| from multiprocessing import Pool |
| from pymatgen.core import Structure, Lattice |
| from pymatgen.analysis.structure_matcher import StructureMatcher |
| W=sys.argv[1] |
| L=pd.read_parquet(W+"/lemat_review_rows.parquet",columns=["immutable_id","lattice_vectors","cartesian_site_positions","species_at_sites"]).drop_duplicates("immutable_id").set_index("immutable_id") |
| reps=[json.loads(l) for l in open(W+"/replacements.jsonl")] |
| reps=[p for p in reps if p["action"]=="replace_structure"] |
| sm=StructureMatcher(ltol=0.02,stol=0.05,angle_tol=1,primitive_cell=False,scale=False,attempt_supercell=True) |
| def job(p): |
| l=L.loc[p["immutable_id"]] |
| a=Structure(Lattice(np.stack(l.lattice_vectors)),list(l.species_at_sites),np.stack(l.cartesian_site_positions),coords_are_cartesian=True) |
| b=Structure(Lattice(p["lattice"]),p["species"],p["xyz"],coords_are_cartesian=True) |
| try: m=sm.fit(a,b) |
| except Exception: m=False |
| return p["immutable_id"], "same_crystal_new_cell" if m else "re_relaxed", b.volume/len(b)/(a.volume/len(a))-1 |
| with Pool(16) as pool: res=pool.map(job,reps,chunksize=20) |
| r=pd.DataFrame(res,columns=["immutable_id","geometry_match","dvol"]); r.to_parquet(W+"/rs_geo.parquet") |
| print(r.geometry_match.value_counts().to_dict(), r.dvol.abs().quantile([.5,.9,.99,1]).round(4).to_dict()) |
|
|
