| import sys, numpy as np, pandas as pd, pyarrow.parquet as pq, pyarrow.compute as pc, pyarrow as pa, glob, os |
| from pymatgen.core import Structure, Lattice, Composition |
| from pymatgen.analysis.structure_matcher import StructureMatcher |
| W=sys.argv[1] |
| a=pd.read_parquet("/home/kna/.local/share/wyformer/staging/lemat_bulk_fixed/audit/changes.parquet") |
| rem=a[a.reason=="below_all_mlips"].immutable_id.tolist() |
| j=pd.read_parquet(W+"/joined.parquet").drop_duplicates("immutable_id") |
| red=lambda f: Composition(f).reduced_formula |
| j["red"]=j.chemical_formula_reduced.map(red) |
| targets=j[j.immutable_id.isin(rem)] |
| sib=j[j.red.isin(set(targets.red))] |
| S=os.path.expanduser("~/.cache/huggingface/hub/datasets--LeMaterial--LeMat-Bulk/snapshots/0dc17eea904b860ad7288141e9870f67f8e6bb2c/compatible_pbe") |
| ids=pa.array(sib.immutable_id.tolist()); rows=[] |
| for fn in sorted(glob.glob(S+"/*.parquet")): |
| t=pq.read_table(fn,columns=["immutable_id","lattice_vectors","cartesian_site_positions","species_at_sites"]) |
| rows.append(t.filter(pc.is_in(t.column("immutable_id"),value_set=ids)).to_pandas()) |
| rows=pd.concat(rows).drop_duplicates("immutable_id").set_index("immutable_id") |
| st={i:Structure(Lattice(np.stack(r.lattice_vectors)),list(r.species_at_sites),np.stack(r.cartesian_site_positions),coords_are_cartesian=True) for i,r in rows.iterrows()} |
| sm=StructureMatcher(ltol=0.2,stol=0.3,angle_tol=5,scale=True) |
| J=j.set_index("immutable_id"); out=[] |
| for t in targets.itertuples(): |
| for s in sib[(sib.red==t.red)&(sib.immutable_id!=t.immutable_id)].itertuples(): |
| if sm.fit(st[t.immutable_id],st[s.immutable_id]): |
| out.append(dict(removed=t.immutable_id,formula=t.red,sibling=s.immutable_id,dE_dft=t.epa-s.epa,dE_mlip=(t.epa-t.d_med)-(s.epa-s.d_med), |
| vol_ratio=(st[t.immutable_id].volume/len(st[t.immutable_id]))/(st[s.immutable_id].volume/len(st[s.immutable_id])), sib_vs_mlip=s.d_med)) |
| o=pd.DataFrame(out); o.to_parquet(W+"/siblings.parquet") |
| pd.set_option("display.width",250) |
| print(o.round(3).to_string()) |
| print("removed rows with a matching sibling:",o.removed.nunique(),"of",len(targets)) |
|
|
