# crystod-mol --diagram examples: molecular-orbital diagrams
# Symmetry + overlap only (default; symmetry-adapted extended Hueckel), or
# quantitative with --pyscf (three SCF calculations in one AO space).
# Every level in the HTML carries a drag-rotatable orbital sketch (hover panel).
# Run in this directory.

crystod-mol --diagram --xyz XYZ_NH3.xyz

* Molecule *
XYZ_NH3.xyz (NH3, 4 atoms)

* Point group *
C3v (Hermann-Mauguin: 3m)

* Fragments *
central atom: N; ligands: 3 H

* Valence Atomic Orbital (AO) parameters (single-zeta STO, extended Hueckel) *
N 2s:  zeta = 1.950 / bohr,  H_ii = -26.0 eV
N 2p:  zeta = 1.950 / bohr,  H_ii = -13.4 eV
H 1s:  zeta = 1.300 / bohr,  H_ii = -13.6 eV

* Ligand SALCs (standard point-group axes) *
-- 3H 1s --
A1: [1s(H1) + 1s(H2) + 1s(H3)]
E: [1s(H1) - 1s(H3), 1s(H1) - 2 1s(H2) + 1s(H3)]

* Ligand SALC | central AO overlap integrals *
  A1:  < a1 (E =  -16.44 eV) | N 2s >  S = 0.7205
  A1:  < a1 (E =  -16.44 eV) | N 2p >  S = 0.2387
   E:  < e (E =  -11.16 eV) | N 2p >  S = 0.5687

* Molecular orbitals (Wolfsberg-Helmholz, K = 1.75) *
    MO    E (eV)  occ  composition
   4a1     21.14    0  70% SALC a1, 25% N 2s, 5% N 2p
 2e x2      2.78    0  59% SALC e, 41% N 2p
   3a1    -13.75    2  95% N 2p, 4% SALC a1, 1% N 2s
 1e x2    -16.49    4  59% N 2p, 41% SALC e
   2a1    -28.00    2  73% N 2s, 27% SALC a1

* Electron filling (8 valence electrons) *
(2a1)^2 (1e)^4 (3a1)^2
(MO numbering counts the core shells, not shown: N 1s -> a1)
HOMO = 3a1 (-13.75 eV), LUMO = 2e (2.78 eV), gap = 16.53 eV

Method: symmetry-adapted extended Hueckel over single-zeta STOs
(exact two-center overlaps; energies are semi-quantitative).
M. Wolfsberg and L. Helmholz, J. Chem. Phys. 20, 837 (1952);
R. Hoffmann, J. Chem. Phys. 39, 1397 (1963).

MO diagram written to MolOD_XYZ_NH3.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_H2O.xyz

* Molecule *
XYZ_H2O.xyz (H2O, 3 atoms)

* Point group *
C2v (Hermann-Mauguin: mm2)

* Fragments *
central atom: O; ligands: 2 H

* Valence Atomic Orbital (AO) parameters (single-zeta STO, extended Hueckel) *
O 2s:  zeta = 2.275 / bohr,  H_ii = -32.3 eV
O 2p:  zeta = 2.275 / bohr,  H_ii = -14.8 eV
H 1s:  zeta = 1.300 / bohr,  H_ii = -13.6 eV

* Ligand SALCs (standard point-group axes) *
-- 2H 1s --
A1: [1s(H1) + 1s(H2)]
B1: [1s(H1) - 1s(H2)]

* Ligand SALC | central AO overlap integrals *
  A1:  < a1 (E =  -15.52 eV) | O 2s >  S = 0.5970
  A1:  < a1 (E =  -15.52 eV) | O 2p >  S = 0.3096
  B1:  < b1 (E =  -10.52 eV) | O 2p >  S = 0.5074

* Molecular orbitals (Wolfsberg-Helmholz, K = 1.75) *
    MO    E (eV)  occ  composition
   4a1     10.65    0  77% SALC a1, 13% O 2s, 9% O 2p
   2b1      0.26    0  67% SALC b1, 33% O 2p
   1b2    -14.80    2  100% O 2p
   3a1    -15.46    2  91% O 2p, 8% SALC a1, 1% O 2s
   1b1    -17.13    2  67% O 2p, 33% SALC b1
   2a1    -33.27    2  86% O 2s, 15% SALC a1

* Electron filling (8 valence electrons) *
(2a1)^2 (1b1)^2 (3a1)^2 (1b2)^2
(MO numbering counts the core shells, not shown: O 1s -> a1)
HOMO = 1b2 (-14.80 eV), LUMO = 2b1 (0.26 eV), gap = 15.06 eV

Method: symmetry-adapted extended Hueckel over single-zeta STOs
(exact two-center overlaps; energies are semi-quantitative).
M. Wolfsberg and L. Helmholz, J. Chem. Phys. 20, 837 (1952);
R. Hoffmann, J. Chem. Phys. 39, 1397 (1963).

MO diagram written to MolOD_XYZ_H2O.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_CH4.xyz

* Molecule *
XYZ_CH4.xyz (CH4, 5 atoms)

* Point group *
Td (Hermann-Mauguin: -43m)

* Fragments *
central atom: C; ligands: 4 H

* Valence Atomic Orbital (AO) parameters (single-zeta STO, extended Hueckel) *
C 2s:  zeta = 1.625 / bohr,  H_ii = -21.4 eV
C 2p:  zeta = 1.625 / bohr,  H_ii = -11.4 eV
H 1s:  zeta = 1.300 / bohr,  H_ii = -13.6 eV

* Ligand SALCs (standard point-group axes) *
-- 4H 1s --
A1: [1s(H1) + 1s(H2) + 1s(H3) + 1s(H4)]
T2: [1s(H1) - 1s(H4), 1s(H1) - 2 1s(H2) + 1s(H4), 1s(H1) + 1s(H2) - 3 1s(H3) + 1s(H4)]

* Ligand SALC | central AO overlap integrals *
  A1:  < a1 (E =  -16.73 eV) | C 2s >  S = 0.8188
  T2:  < t2 (E =  -11.83 eV) | C 2p >  S = 0.6144

* Molecular orbitals (Wolfsberg-Helmholz, K = 1.75) *
    MO    E (eV)  occ  composition
   3a1     33.44    0  62% SALC a1, 38% C 2s
2t2 x3      4.74    0  52% C 2p, 48% SALC t2
1t2 x3    -15.52    6  52% SALC t2, 48% C 2p
   2a1    -24.56    2  62% C 2s, 38% SALC a1

* Electron filling (8 valence electrons) *
(2a1)^2 (1t2)^6
(MO numbering counts the core shells, not shown: C 1s -> a1)
HOMO = 1t2 (-15.52 eV), LUMO = 2t2 (4.74 eV), gap = 20.26 eV

Method: symmetry-adapted extended Hueckel over single-zeta STOs
(exact two-center overlaps; energies are semi-quantitative).
M. Wolfsberg and L. Helmholz, J. Chem. Phys. 20, 837 (1952);
R. Hoffmann, J. Chem. Phys. 39, 1397 (1963).

MO diagram written to MolOD_XYZ_CH4.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_SF6.xyz

* Molecule *
XYZ_SF6.xyz (SF6, 7 atoms)

* Point group *
Oh (Hermann-Mauguin: m-3m)

* Fragments *
central atom: S; ligands: 6 F

* Valence Atomic Orbital (AO) parameters (single-zeta STO, extended Hueckel) *
S 3s:  zeta = 2.122 / bohr,  H_ii = -20.0 eV
S 3p:  zeta = 1.827 / bohr,  H_ii = -13.3 eV
F 2s:  zeta = 2.425 / bohr,  H_ii = -40.0 eV
F 2p:  zeta = 2.425 / bohr,  H_ii = -18.1 eV

* Ligand SALCs (standard point-group axes) *
-- 6F 2s --
A1g: [2s(F1) + 2s(F2) + 2s(F3) + 2s(F4) + 2s(F5) + 2s(F6)]
Eg: [2s(F1) + 2s(F2) - 2s(F5) - 2s(F6), 2s(F1) + 2s(F2) - 2 2s(F3) - 2 2s(F4) + 2s(F5) + 2s(F6)]
T1u: [2s(F1) - 2s(F2), 2s(F3) - 2s(F4), 2s(F5) - 2s(F6)]
-- 6F 2p --
A1g: [2px(F1) - 2px(F2) + 2py(F3) - 2py(F4) - 2pz(F5) + 2pz(F6)]
Eg: [2px(F1) - 2px(F2) + 2pz(F5) - 2pz(F6), 2px(F1) - 2px(F2) - 2 2py(F3) + 2 2py(F4) - 2pz(F5) + 2pz(F6)]
T1g: [2py(F1) - 2py(F2) - 2px(F3) + 2px(F4), 2pz(F1) - 2pz(F2) + 2px(F5) - 2px(F6), 2pz(F3) - 2pz(F4) + 2py(F5) - 2py(F6)]
T2g: [2py(F1) - 2py(F2) + 2px(F3) - 2px(F4), 2pz(F1) - 2pz(F2) - 2px(F5) + 2px(F6), 2pz(F3) - 2pz(F4) - 2py(F5) + 2py(F6)]
T1u: [2px(F1) + 2px(F2), 2py(F1) + 2py(F2) + 2py(F5) + 2py(F6), 2pz(F1) + 2pz(F2) + 2pz(F3) + 2pz(F4), 2px(F3) + 2px(F4) + 2px(F5) + 2px(F6), 2py(F3) + 2py(F4), 2pz(F5) + 2pz(F6)]
T2u: [2py(F1) + 2py(F2) - 2py(F5) - 2py(F6), 2pz(F1) + 2pz(F2) - 2pz(F3) - 2pz(F4), 2px(F3) + 2px(F4) - 2px(F5) - 2px(F6)]

* Ligand SALC | central AO overlap integrals *
 A1g:  < 1a1g (E =  -41.16 eV) | S 3s >  S = 0.4057
 A1g:  < 2a1g (E =  -18.64 eV) | S 3s >  S = 0.3760
 T1u:  < 1t1u (E =  -39.99 eV) | S 3p >  S = 0.4343
 T1u:  < 2t1u (E =  -18.44 eV) | S 3p >  S = 0.3508
 T1u:  < 3t1u (E =  -17.76 eV) | S 3p >  S = 0.1358

* Molecular orbitals (Wolfsberg-Helmholz, K = 1.75) *
    MO    E (eV)  occ  composition
6t1u x3      3.67    0  84% S 3p, 9% SALC 2t1u, 5% SALC 1t1u, 2% SALC 3t1u
  6a1g     -1.59    0  67% S 3s, 25% SALC 2a1g, 7% SALC 1a1g
3eg x2    -17.77    4  100% SALC 2eg
1t1g x3    -17.78    6  100% SALC t1g
5t1u x3    -17.85    6  92% SALC 3t1u, 7% SALC 2t1u
1t2u x3    -18.03    6  100% SALC t2u
1t2g x3    -18.41    6  100% SALC t2g
4t1u x3    -19.09    6  84% SALC 2t1u, 11% S 3p, 6% SALC 3t1u
  5a1g    -20.76    2  75% SALC 2a1g, 23% S 3s, 2% SALC 1a1g
2eg x2    -39.41    4  100% SALC 1eg
3t1u x3    -40.28    6  95% SALC 1t1u, 5% S 3p
  4a1g    -41.96    2  91% SALC 1a1g, 10% S 3s

* Electron filling (48 valence electrons) *
(4a1g)^2 (3t1u)^6 (2eg)^4 (5a1g)^2 (4t1u)^6 (1t2g)^6 (1t2u)^6 (5t1u)^6 (1t1g)^6 (3eg)^4
(MO numbering counts the core shells, not shown: 6F 1s -> a1g + eg + t1u; S 1s -> a1g; S 2s -> a1g; S 2p -> t1u)
HOMO = 3eg (-17.77 eV), LUMO = 6a1g (-1.59 eV), gap = 16.18 eV

Method: symmetry-adapted extended Hueckel over single-zeta STOs
(exact two-center overlaps; energies are semi-quantitative).
M. Wolfsberg and L. Helmholz, J. Chem. Phys. 20, 837 (1952);
R. Hoffmann, J. Chem. Phys. 39, 1397 (1963).

MO diagram written to MolOD_XYZ_SF6.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_H2O.xyz --pyscf

* Molecule *
XYZ_H2O.xyz (H2O, 3 atoms)

* Point group *
C2v (Hermann-Mauguin: mm2)

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : H2 (H, H), spin 2S = 0
right: O (O), spin 2S = 0
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
      H2 (RHF): E_tot = -1.002688 Ha (converged)
       O (RHF): E_tot = -74.301396 Ha (converged)
     H2O (RHF): E_tot = -75.961329 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -0.657244 Ha = -17.885 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
   2b1       6.99    0  60% H2 1b1, 33% H2 2b1, 4% H2 5b1, 3% O 1b1
   4a1       4.84    0  51% H2 2a1, 43% H2 1a1, 2% H2 4a1
   1b2     -13.58    2  100% O 1b2
   3a1     -15.51    2  82% O 3a1, 6% H2 1a1, 5% O 2a1, 5% H2 7a1
   1b1     -19.31    2  54% O 1b1, 31% H2 1b1, 9% H2 2b1, 6% H2 5b1
   2a1     -36.04    2  54% O 2a1, 35% H2 1a1, 5% H2 2a1, 3% O 3a1
(+ 1 core level(s) below; visible in the HTML by panning the energy window)
(21 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (10 electrons, molecule spin 2S = 0) *
(1a1)^2 (2a1)^2 (1b1)^2 (3a1)^2 (1b2)^2
HOMO = 1b2 (-13.58 eV), LUMO = 4a1 (4.84 eV), gap = 18.42 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_H2O_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_O2.xyz --pyscf --spin 2 --ao-left O --ao-right O

* Molecule *
XYZ_O2.xyz (O2, 2 atoms)

* Point group *
D*h

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : O (O), spin 2S = 0
right: O (O), spin 2S = 0
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
       O (RHF): E_tot = -74.196504 Ha (converged)
       O (RHF): E_tot = -74.196504 Ha (converged)
      O2 (ROHF): E_tot = -149.464165 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -1.071157 Ha = -29.148 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
   3σu      12.17    0  32% O(R) 3σ, 32% O(L) 3σ, 12% O(L) 6σ, 12% O(R) 6σ, 4% O(L) 9σ, 4% O(R) 9σ, 2% O(R) 2σ, 2% O(L) 2σ
1πg x2      -6.13    2  50% O(R) 1π, 50% O(L) 1π
1πu x2     -19.04    4  50% O(L) 1π, 50% O(R) 1π
   3σg     -19.85    2  40% O(R) 3σ, 40% O(L) 3σ, 5% O(L) 2σ, 5% O(R) 2σ, 5% O(L) 9σ, 5% O(R) 9σ
   2σu     -29.51    2  31% O(L) 2σ, 31% O(R) 2σ, 17% O(L) 3σ, 17% O(R) 3σ
   2σg     -44.03    2  37% O(L) 2σ, 37% O(R) 2σ, 12% O(L) 3σ, 12% O(R) 3σ
(+ 2 core level(s) below; visible in the HTML by panning the energy window)
(20 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (16 electrons, molecule spin 2S = 2) *
(1σg)^2 (1σu)^2 (2σg)^2 (2σu)^2 (3σg)^2 (1πu)^4 (1πg)^2
HOMO = 1πg (-6.13 eV), LUMO = 3σu (12.17 eV), gap = 18.30 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_O2_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_NH3.xyz --pyscf

* Molecule *
XYZ_NH3.xyz (NH3, 4 atoms)

* Point group *
C3v (Hermann-Mauguin: 3m)

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : H3 (H, H, H), spin 2S = 1
right: N (N), spin 2S = 1
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
      H3 (ROHF): E_tot = -1.481205 Ha (converged)
       N (ROHF): E_tot = -54.333783 Ha (converged)
     NH3 (RHF): E_tot = -56.148806 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -0.333817 Ha = -9.084 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
 2e x2       7.40    0  46% H3 1e, 43% H3 2e, 5% N 1e, 4% H3 5e
   4a1       4.88    0  55% H3 2a1, 41% H3 1a1
   3a1     -11.38    2  86% N 3a1, 6% H3 7a1, 4% N 2a1
 1e x2     -17.04    4  51% N 1e, 38% H3 1e, 5% H3 2e, 4% H3 5e
   2a1     -30.57    2  52% N 2a1, 41% H3 1a1, 4% H3 2a1, 2% N 3a1
(+ 1 core level(s) below; visible in the HTML by panning the energy window)
(18 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (10 electrons, molecule spin 2S = 0) *
(1a1)^2 (2a1)^2 (1e)^4 (3a1)^2
HOMO = 3a1 (-11.38 eV), LUMO = 4a1 (4.88 eV), gap = 16.26 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_NH3_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_CH4.xyz --pyscf

* Molecule *
XYZ_CH4.xyz (CH4, 5 atoms)

* Point group *
Td (Hermann-Mauguin: -43m)

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : H4 (H, H, H, H), spin 2S = 0
right: C (C), spin 2S = 0
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
      H4 (RHF): E_tot = -1.633418 Ha (converged)
       C (RHF): E_tot = -37.288483 Ha (converged)
     CH4 (RHF): E_tot = -40.169175 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -1.247273 Ha = -33.940 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
3t2 x3      16.14    0  45% H4 3t2, 41% C 3t2, 7% C 4t2, 4% C 1t2
2t2 x3       7.46    0  76% H4 1t2, 16% H4 4t2, 5% C 1t2, 2% H4 3t2
   3a1       5.08    0  92% H4 2a1, 7% H4 1a1
1t2 x3     -14.83    6  48% C 1t2, 44% H4 1t2, 4% H4 4t2
   2a1     -25.37    2  53% C 2a1, 43% H4 1a1, 3% H4 2a1
(+ 1 core level(s) below; visible in the HTML by panning the energy window)
(14 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (10 electrons, molecule spin 2S = 0) *
(1a1)^2 (2a1)^2 (1t2)^6
HOMO = 1t2 (-14.83 eV), LUMO = 3a1 (5.08 eV), gap = 19.91 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_CH4_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_CH3OH.xyz --pyscf --ao-left H4 --ao-right CO

* Molecule *
XYZ_CH3OH.xyz (CH4O, 6 atoms)

* Point group *
Cs (Hermann-Mauguin: m)

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : H4 (H, H, H, H), spin 2S = 0
right: CO (O, C), spin 2S = 0
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
      H4 (RHF): E_tot = -1.811294 Ha (converged)
      CO (RHF): E_tot = -112.517443 Ha (converged)
    CH4O (RHF): E_tot = -114.954806 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -0.626069 Ha = -17.036 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
  11a'       9.97    0  78% CO 11a', 5% H4 10a', 4% H4 4a', 3% H4 9a'
  10a'       7.30    0  43% H4 6a', 40% H4 3a', 4% H4 8a', 3% H4 16a', 2% H4 2a', 2% H4 15a'
  3a''       7.26    0  79% H4 1a'', 15% H4 7a'', 3% H4 3a''
   9a'       6.06    0  36% H4 2a', 33% H4 4a', 7% H4 3a', 6% H4 6a', 5% CO 11a', 3% H4 1a', 3% H4 8a', 2% H4 13a'
   8a'       4.88    0  62% H4 4a', 15% H4 2a', 10% H4 1a', 4% H4 3a'
  2a''     -12.11    2  44% CO 2a'', 22% CO 1a'', 18% H4 1a'', 11% H4 3a''
   7a'     -13.52    2  41% CO 7a', 23% H4 3a', 10% H4 8a', 6% CO 5a', 4% CO 6a', 4% CO 4a', 2% H4 2a', 2% H4 16a'
   6a'     -16.24    2  34% CO 5a', 13% H4 3a', 12% CO 6a', 10% CO 7a', 8% CO 4a', 5% H4 2a', 5% H4 10a', 3% H4 1a', 2% H4 6a', 2% H4 8a'
  1a''     -16.89    2  47% CO 1a'', 33% H4 1a'', 12% CO 2a'', 3% H4 7a''
   5a'     -18.87    2  44% CO 6a', 17% CO 5a', 12% H4 2a', 8% H4 1a', 3% H4 9a', 2% CO 3a', 2% H4 8a'
   4a'     -24.88    2  47% CO 4a', 28% H4 1a', 9% H4 2a', 7% CO 5a', 2% H4 4a', 2% CO 6a'
   3a'     -36.55    2  62% CO 3a', 12% H4 2a', 8% H4 1a', 7% H4 3a', 2% H4 4a'
(+ 2 core level(s) below; visible in the HTML by panning the energy window)
(35 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (18 electrons, molecule spin 2S = 0) *
(1a')^2 (2a')^2 (3a')^2 (4a')^2 (5a')^2 (1a'')^2 (6a')^2 (7a')^2 (2a'')^2
HOMO = 2a'' (-12.11 eV), LUMO = 8a' (4.88 eV), gap = 16.99 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_CH3OH_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104


crystod-mol --diagram --xyz XYZ_C6H6.xyz --pyscf --ao-left H6 --ao-right C6

* Molecule *
XYZ_C6H6.xyz (C6H6, 12 atoms)

* Point group *
D6h (Hermann-Mauguin: 6/mmm)

* Fragments (pre-bonding states; removed atoms kept as ghost basis) *
left : H6 (H, H, H, H, H, H), spin 2S = 0
right: C6 (C, C, C, C, C, C), spin 2S = 0
(fragments are spin/spherically averaged: fractional occupation of degenerate frontier shells)

* PySCF calculations (Hartree-Fock method / def2-svp basis) *
      H6 (RHF): E_tot = -2.634414 Ha (converged)
      C6 (RHF): E_tot = -226.488924 Ha (converged)
    C6H6 (RHF): E_tot = -230.535765 Ha (converged)
interaction energy E(mol) - E(left) - E(right) = -1.412427 Ha = -38.434 eV
(counterpoise-consistent: all three calculations use the full molecular basis)

* Molecular orbitals *
    MO     E (eV)  occ  composition
  5a1g      14.39    0  92% C6 5a1g
5e1u x2      12.87    0  83% C6 5e1u, 9% C6 6e1u, 3% C6 3e1u, 2% C6 8e1u
5e2g x2      12.38    0  93% C6 5e2g, 3% H6 7e2g, 3% H6 2e2g
  1b1g       9.46    0  99% C6 1b1g
  3b2u       7.64    0  66% H6 2b2u, 33% H6 1b2u
4e2g x2       7.05    0  55% H6 2e2g, 42% H6 1e2g
4e1u x2       6.03    0  52% H6 1e1u, 37% H6 3e1u, 7% H6 7e1u, 2% C6 3e1u
  4a1g       4.95    0  61% H6 3a1g, 31% H6 1a1g, 4% C6 3a1g, 2% H6 6a1g
1e2u x2       3.63    0  100% C6 1e2u
1e1g x2      -9.18    4  100% C6 1e1g
3e2g x2     -13.50    4  53% C6 3e2g, 25% H6 1e2g, 12% C6 2e2g, 7% H6 7e2g
  1a2u     -13.67    2  100% C6 1a2u
3e1u x2     -16.01    4  51% C6 3e1u, 23% H6 1e1u, 14% H6 3e1u, 5% H6 7e1u, 3% C6 2e1u
  1b1u     -16.94    2  88% C6 1b1u, 12% H6 2b1u
  2b2u     -17.32    2  47% C6 2b2u, 44% H6 1b2u, 5% H6 2b2u, 2% C6 4b2u
  3a1g     -19.28    2  54% C6 3a1g, 26% H6 1a1g, 11% H6 3a1g, 4% H6 6a1g
2e2g x2     -22.21    4  57% C6 2e2g, 31% H6 1e2g, 6% C6 3e2g, 4% H6 2e2g
2e1u x2     -27.30    4  63% C6 2e1u, 28% H6 1e1u, 5% H6 3e1u, 2% C6 3e1u
  2a1g     -31.01    2  72% C6 2a1g, 24% H6 1a1g, 3% H6 3a1g
(+ 6 core level(s) below; visible in the HTML by panning the energy window)
(69 fragment level(s) dominated by the ghost basis (BSSE artifacts) are omitted from the diagram and the compositions)

* Electron filling (42 electrons, molecule spin 2S = 0) *
(1a1g)^2 (1e1u)^4 (1e2g)^4 (1b2u)^2 (2a1g)^2 (2e1u)^4 (2e2g)^4 (3a1g)^2 (2b2u)^2 (1b1u)^2 (3e1u)^4 (1a2u)^2 (3e2g)^4 (1e1g)^4
HOMO = 1e1g (-9.18 eV), LUMO = 1e2u (3.63 eV), gap = 12.82 eV

Method: fragment-resolved SCF MO diagram

If you use PySCF in your research, please cite:
Q. Sun et al., J. Chem. Phys. 153, 024109 (2020);
Q. Sun et al., WIREs Comput. Mol. Sci. 8, e1340 (2018);
Q. Sun, J. Comput. Chem. 36, 1664 (2015).

MO diagram written to MolOD_XYZ_C6H6_pyscf.html

If you use CrystOD in your research, please cite:
  H. Koiso and Y. Mochizuki et al., Phys. Rev. B 110, 064104 (2024). https://doi.org/10.1103/PhysRevB.110.064104

