File size: 5,199 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 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | """Verify ORCA's printed AO Fock matrix + pyscf overlap reproduces ORCA orbital energies.
Established convention (ORCA 6.0, def2-TZVPD):
* AO order per atom = def2-TZVP shells grouped by l (s,p,d,f,g; basis order within l),
then the def2-TZVPD augmentation (diffuse) shells appended in l order.
* m order: p = (z, x, y); d = (z2, xz, yz, x2-y2, xy); f = (0,+1,-1,+2,-2,+3,-3); g = (0,+1,-1,...,+4,-4)
* relative to pyscf real solid harmonics, f(+3) and f(-3) have opposite sign (g signs searched if present).
"""
import re, sys, time, itertools
import numpy as np
from scipy.linalg import eigh
from pyscf import gto
def parse(path):
lines = open(path, errors="replace").read().split("\n")
i = lines.index("CARTESIAN COORDINATES (ANGSTROEM)")
atoms = []
for l in lines[i+2:]:
p = l.split()
if len(p) != 4: break
atoms.append((p[0], (float(p[1]), float(p[2]), float(p[3]))))
charge = int([l for l in lines if "Total Charge" in l][0].split("....")[1])
mult = int([l for l in lines if l.strip().startswith("Multiplicity") and "Mult " in l][0].split("....")[1])
hftyp = [l for l in lines if "Hartree-Fock type" in l][0].split("....")[1].strip()
nbas = int([l for l in lines if l.startswith("Number of basis functions")][0].split("...")[1])
k = lines.index("ORBITAL ENERGIES")
start = k + 4
eps = []
for l in lines[start:]:
p = l.split()
if len(p) != 4: break
eps.append(float(p[2]))
fi = lines.index("FOCK"); i = fi + 2
F = np.zeros((nbas, nbas)); done = 0
while done < nbas:
ncol = len(lines[i].split())
F[:, done:done+ncol] = np.fromstring("\n".join(lines[i+1:i+1+nbas]), sep=" ").reshape(nbas, ncol+1)[:, 1:]
done += ncol; i += 1 + nbas
return atoms, charge, mult, hftyp, nbas, np.array(eps), F
ORCA_M = {l: [0] + [m for k in range(1, l+1) for m in (k, -k)] for l in range(6)}
FLIP = {(3, 3), (3, -3)} # sign flips relative to pyscf
def orca_perm_and_sign(mol, extra_flips=()):
tzvp = {}
for ia in range(mol.natm):
el = mol.atom_symbol(ia)
if el not in tzvp:
tzvp[el] = {(sh[0], tuple(round(p[0], 6) for p in sh[1:])) for sh in gto.basis.load("def2-tzvp", el)}
perm = []; sgn = []; labels = []
ao = 0; table = {}
for ish in range(mol.nbas):
ia = mol.bas_atom(ish); l = mol.bas_angular(ish)
for c in range(mol.bas_nctr(ish)):
for m in ([1, -1, 0] if l == 1 else list(range(-l, l+1))):
table[(ish, c, m)] = ao; ao += 1
for ia in range(mol.natm):
el = mol.atom_symbol(ia)
shells = []
for ish in [i for i in range(mol.nbas) if mol.bas_atom(i) == ia]:
l = mol.bas_angular(ish); ex = tuple(round(float(e), 6) for e in mol.bas_exp(ish))
for c in range(mol.bas_nctr(ish)):
shells.append((l, ish, c, (l, ex) not in tzvp[el]))
shells = sorted([s for s in shells if not s[3]], key=lambda s: (s[0], s[1], s[2])) + \
sorted([s for s in shells if s[3]], key=lambda s: (s[0], s[1], s[2]))
for l, ish, c, aug in shells:
for m in ORCA_M[l]:
perm.append(table[(ish, c, m)])
sgn.append(-1.0 if ((l, m) in FLIP) ^ ((l, m) in extra_flips) else 1.0)
labels.append((ia, el, l, m, aug))
return np.array(perm), np.array(sgn), labels
def orca_overlap(mol, extra_flips=()):
perm, sgn, labels = orca_perm_and_sign(mol, extra_flips)
S = mol.intor("int1e_ovlp")[np.ix_(perm, perm)] * np.outer(sgn, sgn)
return S, labels
if __name__ == "__main__":
for path in sys.argv[1:]:
t0 = time.time(); name = path.split("/samples/")[1].split("/")[0]
try:
atoms, charge, mult, hftyp, nbas, eps, F = parse(path)
mol = gto.M(atom=atoms, basis="def2-tzvpd", ecp="def2-tzvpd", unit="Angstrom", charge=charge, spin=mult-1, verbose=0)
except Exception as e:
print(f"{name:24s} SKIP: {type(e).__name__}: {str(e)[:120]}"); continue
if mol.nao != nbas:
print(f"{name:24s} SKIP: pyscf nao {mol.nao} != ORCA nbas {nbas}"); continue
nmo = int((eps != 0).sum()); nocc = (mol.nelectron + (mult-1)) // 2
S, labels = orca_overlap(mol)
w = eigh(F, S, eigvals_only=True); d = np.abs(w[:nmo] - eps[:nmo])
note = ""
has_g = any(l == 4 for _, _, l, _, _ in labels)
if d[:nocc].max() > 1e-4 and has_g:
gl = [(4, m) for m in ORCA_M[4] if m != 0]
for flips in itertools.product([0, 1], repeat=len(gl)):
ef = tuple(x for x, f in zip(gl, flips) if f)
S2, _ = orca_overlap(mol, ef)
w2 = eigh(F, S2, eigvals_only=True); d2 = np.abs(w2[:nmo] - eps[:nmo])
if d2[:nocc].max() < d[:nocc].max():
d = d2; note = f" g-flips={ef}"
if d[:nocc].max() < 1e-4: break
sS = np.linalg.eigvalsh(S)
print(f"{name:24s} {hftyp} nbas={nbas} nmo={nmo} Smin={sS.min():.1e} | occ max|de|={d[:nocc].max():.1e} all max={d.max():.1e} mean={d.mean():.1e}{note} | {time.time()-t0:.0f}s", flush=True)
|