| """Minimal reader for ORCA 6 .gbw files (reverse-engineered, validated against orca.out on OMol25 data). |
| |
| Layout: 64-byte header of little-endian int64 words; word 3 (byte 24) points to the MO block: |
| int32 n_operators (1 = RHF/RKS, 2 = UHF/UKS), int32 dim, then for each operator |
| dim*dim float64 coefficients stored so that reshape(dim, dim) gives C[ao, mo], dim float64 occupations, |
| dim float64 orbital energies (Eh), dim int32 irreps, dim int32 core flags. |
| Returns C[ao, mo] (columns = MOs) in ORCA AO ordering; C^T S C = I verified to 1e-7 against pyscf S. |
| """ |
| import struct, numpy as np, zstandard as zstd |
|
|
| def read_gbw(path): |
| b = open(path, "rb").read() |
| if path.endswith(".zstd0") or b[:4] == b"\x28\xb5\x2f\xfd": |
| b = zstd.ZstdDecompressor().decompressobj().decompress(b) |
| hdr = struct.unpack_from("<8q", b, 0) |
| ptr = hdr[3] |
| nop, dim = struct.unpack_from("<ii", b, ptr); off = ptr + 8 |
| ops = [] |
| for _ in range(nop): |
| C = np.frombuffer(b, dtype="<f8", count=dim*dim, offset=off).reshape(dim, dim).copy(); off += dim*dim*8 |
| occ = np.frombuffer(b, dtype="<f8", count=dim, offset=off).copy(); off += dim*8 |
| en = np.frombuffer(b, dtype="<f8", count=dim, offset=off).copy(); off += dim*8 |
| irrep = np.frombuffer(b, dtype="<i4", count=dim, offset=off).copy(); off += dim*4 |
| core = np.frombuffer(b, dtype="<i4", count=dim, offset=off).copy(); off += dim*4 |
| ops.append(dict(C=C, occ=occ, energies=en, irrep=irrep, core=core)) |
| return dict(nbas=dim, nop=nop, ops=ops, header=hdr) |
|
|
| if __name__ == "__main__": |
| import sys |
| sys.path.insert(0, "/global/u1/e/ericqu/omol_elec_process") |
| from check_overlap import parse, orca_overlap |
| from pyscf import gto |
| G = "/global/cfs/projectdirs/m5293/ericqu/omol_elec_process/gbw_pilot"; S_ = "/global/cfs/projectdirs/m5293/ericqu/omol_elec_process/samples" |
| def inflate(v): |
| n = int((np.sqrt(8*len(v)+1)-1)//2); M = np.zeros((n,n)); M[np.triu_indices(n)] = v; return M + M.T - np.diag(M.diagonal()) |
| for rel in sys.argv[1:]: |
| name = rel.split("/")[0] |
| g = read_gbw(f"{G}/{rel}/orca.gbw.zstd0"); z = np.load(f"{G}/{rel}/density_mat.npz") |
| atoms, charge, mult, hftyp, nbas, eps, F = parse(f"{S_}/{rel}/orca.out") |
| a = g["ops"][0]; C, occ, en = a["C"], a["occ"], a["energies"] |
| nmo = int((eps != 0).sum()) |
| line = f"== {name:22s} {hftyp} nbas={g['nbas']} nop={g['nop']} | eps(gbw)-eps(printed) max {np.abs(en[:nmo]-eps[:nmo]).max():.1e} Eh | occ sum {occ.sum():.2f}" |
| |
| P_npz = inflate(z["orca.scfp"]) |
| if g["nop"] == 2: |
| b_ = g["ops"][1]; Pg = C @ np.diag(occ) @ C.T + b_["C"] @ np.diag(b_["occ"]) @ b_["C"].T |
| else: |
| Pg = C @ np.diag(occ) @ C.T |
| line += f" | P(gbw)-P(npz) max {np.abs(Pg-P_npz).max():.1e}" |
| |
| if nmo == nbas: |
| Ci = np.linalg.inv(C); F_rec = Ci.T @ np.diag(en) @ Ci; S_rec = Ci.T @ Ci |
| line += f" | F(gbw)-F(printed): max {np.abs(F_rec-F).max():.1e}, rms {np.sqrt(((F_rec-F)**2).mean()):.1e}" |
| try: |
| mol = gto.M(atom=atoms, basis="def2-tzvpd", ecp="def2-tzvpd", unit="Angstrom", charge=charge, spin=mult-1, verbose=0) |
| S, _ = orca_overlap(mol); line += f" | S(gbw)-S(pyscf) max {np.abs(S_rec-S).max():.1e}" |
| except Exception as e: |
| line += f" | pyscf basis unavailable ({type(e).__name__})" |
| else: |
| line += f" | {nbas-nmo} lin.dep. removed: C is {nbas}x{nmo}, F/S not invertible from C alone" |
| try: |
| mol = gto.M(atom=atoms, basis="def2-tzvpd", ecp="def2-tzvpd", unit="Angstrom", charge=charge, spin=mult-1, verbose=0) |
| S, _ = orca_overlap(mol); Ck = C[:, :nmo] |
| line += f" | C^T S C - I max {np.abs(Ck.T @ S @ Ck - np.eye(nmo)).max():.1e}" |
| F_rec = S @ Ck @ np.diag(en[:nmo]) @ Ck.T @ S |
| line += f" | F(S C e C^T S)-F(printed) max {np.abs(F_rec-F).max():.1e}" |
| except Exception as e: |
| line += f" | pyscf basis unavailable ({type(e).__name__})" |
| print(line, flush=True) |
|
|
