File size: 4,268 Bytes
39ea985 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | """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}"
# density from gbw vs npz
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}"
# S from C when no linear dependence: S = C^-T C^-1 ; F = C^-T diag(eps) C^-1
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)
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