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# 13.5.8 Examples

(July 14, 2022)

Example 13.7  Input for the NEO-HF calculation on H${}_{2}$O molecule with the second proton treated quantum-mechanically. The electronic basis set is cc-pVDZ and the protonic is an uncontracted 2s2p2d basis set with exponents 4.0 and 8.0.

$molecule 0 1 H -3.5008791 1.2736107 0.7596000 O -3.9840791 1.3301107 -0.0574000 H -4.9109791 1.2967107 0.1521000$end

$rem METHOD hf BASIS cc-pvdz NEO true$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 S 1 1.000000 8.0 1.0 P 1 1.000000 4.0 1.0 P 1 1.000000 8.0 1.0 D 1 1.000000 4.0 1.0 D 1 1.000000 8.0 1.0 ****$end


Example 13.8  Input for the NEO-DFT-epc172 geometry optimization calculation of all centers on CH${}_{2}$O molecule with both protons treated quantum-mechanically. The electronic exchange-correlation functional is PBE0. The electronic basis set is STO-3G and the protonic is an uncontracted 1s1p basis set with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 302 spherical quadrature points along with the DIIS algorithm.

$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.000000 -0.540000 H -0.935307 0.000000 -0.540000$end

$rem JOBTYPE OPT METHOD pbe0 BASIS sto-3g NEO true NEO_EPC epc172 SYM_IGNORE 1 SCF_CONVERGENCE 11 MAX_SCF_CYCLES 100 SCF_ALGORITHM diis XC_GRID 000099000302$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 4 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end


Example 13.9  Input for the NEO-DFT-epc19 geometry optimization calculation of the NEO center only on open-shell OH radical molecule with a proton treated quantum-mechanically. The electronic exchange-correlation functional is PBE0. The electronic basis set is 6-31G and the protonic is an uncontracted 1s1p basis set with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 230 spherical quadrature points along with the DIIS algorithm.

$molecule 0 2 O -4.511414 1.264878 0.000000 H -2.739325 1.866123 0.000000$end

$rem JOBTYPE OPT METHOD pbe0 BASIS 6-31g UNRESTRICTED true INPUT_BOHR true NEO true SYM_IGNORE 1 SCF_CONVERGENCE 6 MAX_SCF_CYCLES 100 SCF_ALGORITHM diis NEO_EPC epc19 XC_GRID 000099000230$end

$opt FIXED 1 XYZ ENDFIXED$end

$neo_basis H 2 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end


Example 13.10  Input for NEO-HF analytic Hessian calculation on HCN molecule with a proton treated quantum mechanically. The electronic basis set is STO-3G and the protonic basis is 1s1p with exponents 4.0.

$molecule 0 1 C 0.0000000000 0.0000000000 0.9684140792 N 0.0000000000 0.0000000000 -1.2085828830 H 0.0000000000 0.0000000000 2.9046475823$end

$rem jobtyp = freq input_bohr = true sym_ignore = true method = hf basis = sto-3g neo = true SCF_ALGORITHM = gdm$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end



Example 13.11  Input for NEO-HF(V) on HCN molecule with a proton treated quantum mechanically. The electronic basis set is STO-3G and the protonic basis is 1s1p with exponents 4.0.

$molecule 0 1 C 0.0000000000 0.0000000000 0.9684140792 N 0.0000000000 0.0000000000 -1.2085828830 H 0.0000000000 0.0000000000 2.9046475823$end

$rem jobtyp = freq input_bohr = true sym_ignore = true method = hf SCF_ALGORITHM = gdm basis = sto-3g neo = true neo_scfv = 1$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end



Example 13.12  Input for the NEO-TDDFT-epc19 calculation on CH${}_{2}$O molecule (both protons treated quantum-mechanically) of the first five roots obtained with the Davidson algorithm. The electronic exchange-correlation functional is PBE0. The electronic basis set is STO-3G and the protonic is an uncontracted 1s1p basis set with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 302 spherical quadrature points.

$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.000000 -0.540000 H -0.935307 0.000000 -0.540000$end

$rem METHOD pbe0 BASIS sto-3g THRESH 14 XC_GRID 000099000302 S2THRESH 12 NEO true NEO_EPC epc172 SET_ROOTS 5 RPA true SCF_CONVERGENCE 12 NEO_E_CONV 12$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 4 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end



Example 13.13  Input for the NEO-TDHF calculation on the FDF${}^{-}$ molecule treating quantum nuclei as deuterium and employing NO_VPP option. The electronic basis set is cc-pVDZ and the protonic is an uncontracted even-tempered 8s8p basis set.

$molecule -1 1 F 0.000000 0.000000 -1.122987 F 0.000000 0.000000 1.122987 H 0.000000 0.000000 0.000000$end

$rem METHOD hf BASIS cc-pvdz NEO true SCF_ALGORITHM GDM RPA true CIS_N_ROOTS 100 THRESH 14 S2THRESH 12 SCF_CONVERGENCE 11 MAX_SCF_CYCLES 300 NEO_VPP 0 NEO_ISOTOPE 2 NEO_E_CONV 11$end

$neo_basis H 3 S 1 1.000000 2.828400 1.0 S 1 1.000000 4.0 1.0 S 1 1.000000 5.6569 1.0 S 1 1.000000 8.0 1.0 S 1 1.000000 11.3137 1.0 S 1 1.000000 16.0 1.0 S 1 1.000000 22.6274 1.0 S 1 1.000000 32.0 1.0 P 1 1.000000 2.828400 1.0 P 1 1.000000 4.0 1.0 P 1 1.000000 5.6569 1.0 P 1 1.000000 8.0 1.0 P 1 1.000000 11.3137 1.0 P 1 1.000000 16.0 1.0 P 1 1.000000 22.6274 1.0 P 1 1.000000 32.0 1.0 ****$end


Example 13.14  Input for the analytic NEO-TDDFT gradient calculation on the CH${}_{2}$ molecule with both protons treated quantum mechanically. A total of four excited states are requested and the gradient is computed for the 3rd excited state. The electronic exchange-correlation functional is CAM-B3LYP, and electron-proton correlation functional epc17-2 is used. The electronic basis set is STO-3G and the protonic basis is 1s1p with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 302 spherical quadrature points along with the GDM algorithm.

$molecule 0 3 C 0.00000000000000e+00 0.00000000000000e+00 -5.63654429543699e-02 H 1.81800983405161e+00 0.00000000000000e+00 -9.92269386019353e-01 H -1.81800983405161e+00 0.00000000000000e+00 -9.92269386019353e-01$end

$rem sym_ignore = 1 input_bohr = true method = cam-b3lyp basis = sto-3g thresh = 14 s2thresh = 12 neo = true SET_ROOTS = 4 RPA = true xc_grid = 000099000302 unrestricted = 1 neo_epc = epc172 SCF_ALGORITHM = gdm SET_STATE_DERIV = 3$end

$neo_basis H 2 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end



Example 13.15  Input for NEO-TDDFT geometry optimization on the C${}_{2}$H${}_{2}$ molecule with both protons treated quantum mechanically. A total of three excited states are requested and the geometry optimization is computed for the 1st excited state. The electronic exchange-correlation functional is B3LYP, and electron-proton correlation functional epc17-2 is used. The electronic basis set is STO-3G and the protonic basis is 1s1p with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 302 spherical quadrature points along with the GDM algorithm.

$molecule 0 1 C 0.4142076725 1.0563578037 0.0000000223 C -0.4142118956 -1.0563667882 0.0000000223 H 1.1661939287 2.9673893099 0.0000000246 H -1.1661909474 -2.9673788285 0.0000000246$end

$rem sym_ignore = 1 NEO_SET_OPT = 1 neo_epc = epc172 SET_STATE_DERIV = 1 jobtype = opt input_bohr = true method = b3lyp neo = true SCF_ALGORITHM = gdm thresh = 14 s2thresh = 12 basis = sto-3g rpa = true SET_ROOTS = 3 xc_grid = 000099000302$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 4 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end



Example 13.16  Input for NEO-TDDFT on the C${}_{2}$H${}_{2}$ molecule with both protons treated quantum mechanically. A total of 12 excited states are requested. Ground-state protonic and electronic densities are printed in the cube files. Protonic and electronic transition densities of the first and the second vibronic excitations with electronic dominant characters are also printed in the cube files. The electronic exchange-correlation functional is B3LYP, and electron-proton correlation functional epc17-2 is used. The electronic basis set is STO-3G and the protonic basis is 1s1p with exponents 4.0. This calculation utilizes DFT grid with 99 radial and 302 spherical quadrature points along with the GDM algorithm.

$molecule 0 1 C -0.2315710674 1.2702261467 0.0000001295 C 0.2315702809 -1.2702255666 0.0000001295 H 1.2946585350 2.6676952886 -0.0000000923 H -1.2946589903 -2.6676943717 -0.0000000923$end

$rem sym_ignore = 1 input_bohr = true method = b3lyp neo = true NEO_SET_ESTATE = 1 SCF_ALGORITHM = gdm thresh = 14 s2thresh = 12 basis = sto-3g GEOM_OPT_MAX_CYCLES = 500 rpa = true SET_ROOTS = 12 xc_grid = 000099000302 MAKE_CUBE_FILES = true plots = true$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 4 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end

$plots grid information to plot protonic and electronic ground state densities and transition densities for two eletronic dominant transitions 100 -4.0 6.0 100 -5.0 4.0 100 -4.0 4.0 0 1 2 0 0 0 1$end



Example 13.17  Input for the NEO-RICCSD calculation on H${}_{2}$O molecule with the second proton treated quantum-mechanically. The electronic basis set is STO-3G and the protonic is an uncontracted 1s1p basis set with exponents 4.0. The electronic auxiliary basis set is RIMP2-aug-cc-pVDZ and the protonic auxiliary basis set is an uncontracted even-tempered 8s8p basis set.

$molecule 0 1 O 0.00000 -0.07579 0.00000 H 0.86681 0.60144 0.00000 H -0.86681 0.60144 0.00000$end

$rem neo = true basis = sto-3g aux_basis = rimp2-aug-cc-pVDZ NEO_RICCSD 1$end

$neo_basis H 3 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 ****$end

$neo_aux_basis H 3 S 1 1.000000 2.8284 1.0 S 1 1.000000 4.0 1.0 S 1 1.000000 5.6569 1.0 S 1 1.000000 8.0 1.0 S 1 1.000000 11.3137 1.0 S 1 1.000000 16.0 1.0 S 1 1.000000 22.6274 1.0 S 1 1.000000 32.0 1.0 P 1 1.000000 2.8284 1.0 P 1 1.000000 4.0 1.0 P 1 1.000000 5.6569 1.0 P 1 1.000000 8.0 1.0 P 1 1.000000 11.3137 1.0 P 1 1.000000 16.0 1.0 P 1 1.000000 22.6274 1.0 P 1 1.000000 32.0 1.0 ****$end