Example 13.7 Input for the NEO-HF calculation on HO 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/epc17-2 calculation of CHO molecule treating both protons quantum mechanically and using simultaneous DIIS algorithm to perform NEO-SCF. The electronic basis set is cc-pVDZ and the protonic basis set is an uncontracted 1s1p basis set with exponents 4.0 and 4.0. A maximum of 10 previous Fock matrices is used to form the next guess in interpolation/extrapolation, and the NEO wavefunction is considered converged when all three criteria are met (all in atomic units): (1) the largest element of the electronic error vector is below the cutoff threshold of , (2) the largest element of the protonic error vector is below the cutoff threshold of , and (3) the energy difference between two consecutive steps is below .
$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.0000000 -0.5400000 H -0.935307 0.000000 -0.540000 $end $rem JOBTYPE SP SYM_IGNORE TRUE INPUT_BOHR FALSE BASIS cc-pvdz NEO TRUE METHOD pbe0 xc_grid = 000099000302 NEO_EPC epc172 NEO_N_SCF_CONVERGENCE = 7 SCF_CONVERGENCE = 8 NEO_E_CONV = 8 SCF_ALGORITHM DIIS NEO_SIMULTANEOUS_SCF TRUE NEO_STEPWISE_SCF_STEPS = 2 DIIS_SUBSPACE_SIZE = 10 DIIS_ERR_RMS FALSE $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/epc17-2 geometry optimization calculation of all centers on CHO 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 point_group_symmetry False 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 13.10 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 point_group_symmetry False 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 13.11 Input for a NEO-MSDFT calculation on FHF with a fixed F–F distance of 2.70 Å. The proton in between the two F atoms is quantized and the proton basis function centers are optimized on the NEO-MSDFT ground state. The electronic basis set is STO-3G, and the protonic basis set is an uncontracted 1s1p basis set with exponents 4.0. The electronic exchange-correlation functional is B3LYP, and the electron-proton correlation functional is epc17-2. The second basis function center for the quantum proton is input as a ghost center.
$molecule -1 1 F 0.00000000 0.00000000 -1.35000000 F 0.00000000 0.00000000 1.35000000 H 0.00000000 0.00000000 -0.25220000 @H 0.00000000 0.00000000 0.25220000 $end $rem jobtype = opt input_bohr = false method = b3lyp basis = sto-3g neo = true neo_epc = epc172 neo_msdft = 1 sym_ignore = 1 max_scf_cycles 500 scf_convergence 6 NEO_N_SCF_CONVERGENCE 6 NEO_E_CONV = 6 SCF_ALGORITHM gdm $end $OPT FIXED 1 XYZ 2 XYZ ENDFIXED $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 13.12 Input for a NEO-MSDFT calculation on a fixed average reactant-product structure of the formic acid dimer with a C–C distance of 3.86 Å, where both transferring protons are quantized. The electronic basis set is STO-3G, and the protonic basis set is an uncontracted 1s1p basis set with exponents 4.0. The electronic exchange-correlation functional is B3LYP, and the electron-proton correlation functional is epc17-2. Only the two trans states are included in the adiabatic state expansion (note the spaces between the ones and zeros of the $neo_msdft_diabat_control section). The second center for each quantum proton is input as a ghost center. Proton density plotting for both the ground and first excited state has been enabled.
$molecule 0 1 H -3.0310572606 0.0000000000 0.0000000000 H -0.4438453003 1.0873992328 0.0000000000 @H 0.4438452993 1.0873992291 0.0000000000 O -1.3616953972 -1.1310228162 0.0000000000 O -1.3616953971 1.1310228163 0.0000000000 C -1.9296657251 0.0000000000 0.0000000000 H 3.0310572606 0.0000000000 0.0000000000 H 0.4438452993 -1.0873992291 0.0000000000 @H -0.4438453003 -1.0873992328 0.0000000000 O 1.3616953972 1.1310228162 0.0000000000 O 1.3616953971 -1.1310228163 0.0000000000 C 1.9296657251 0.0000000000 0.0000000000 $end $rem jobtype = sp input_bohr = false method = b3lyp basis = sto-3g neo = true neo_epc = epc172 neo_msdft = 1 sym_ignore = 1 scf_convergence 6 NEO_N_SCF_CONVERGENCE = 6 NEO_E_CONV = 6 max_scf_cycles 500 SCF_ALGORITHM GDM $end $neo_msdft denplt = 1 $end $neo_msdft_diabat_control 1 0 1 0 0 1 0 1 $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 **** H 8 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 9 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** $end
Example 13.13 Input for a NEO-MSDFT calculation on a protonated water dimer with a fixed O–O distance of 2.80 Å, where all protons in the system are quantized, but only the proton between the two oxygen atoms is treated as transferring. The two centers for the transferring proton are written consecutively in the $molecule section, with the first one written as an H atom center and the second one is written as a ghost H atom center. The other centers do not have corresponding ghost centers and are therefore not recognized as being transferring. The electronic basis set is STO-3G, and the protonic basis set is an uncontracted 1s1p basis set with exponents 4.0. The electronic exchange-correlation functional is B3LYP, and the electron-proton correlation functional is epc17-2.
$molecule 1 1 O -1.4000000000 0.0000000000 0.0000000000 O 1.4000000000 0.0000000000 0.0000000000 H -0.3000000000 0.0000000000 0.0000000000 @H 0.3000000000 0.0000000000 0.0000000000 H 1.6600000000 0.7500000000 -0.5500000000 H 1.6600000000 -0.7500000000 -0.5500000000 H -1.6600000000 0.7500000000 0.5500000000 H -1.6600000000 -0.7500000000 0.5500000000 $end $rem jobtype = sp input_bohr = false method = b3lyp basis = sto-3g neo = true neo_epc = epc172 neo_msdft = 1 sym_ignore = 1 scf_convergence 6 NEO_N_SCF_CONVERGENCE = 6 NEO_E_CONV = 6 max_scf_cycles 500 SCF_ALGORITHM GDM $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 **** H 5 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 6 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 7 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 8 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** $end
Example 13.14 Input for the NEO-DFT/epc17-2 geometry optimization calculation of a CHO molecule in C-PCM water. A van der Waals surface is constructed around the fixed, classical nuclear point charge positions and the nuclear basis function center positions of the two quantum hydrogens. Here, the Bondi radii for hydrogen is used in the construction of the spherical cavity surrounding the delocalized proton densities, but the user has the option to specify a custom-defined atomic radii in a $van_der_waals input section. The entire cavity is scaled by a factor of , and is then discretized via the SwiG approach.
$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.0000000 -0.5400000 H -0.935307 0.000000 -0.540000 $end $rem point_group_symmetry False JOBTYPE OPT INPUT_BOHR FALSE BASIS sto-3g NEO TRUE METHOD pbe0 xc_grid = 000099000302 NEO_EPC epc172 SCF_CONVERGENCE = 8 NEO_E_CONV = 8 SCF_ALGORITHM GDM SOLVENT_METHOD PCM $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 $pcm Theory CPCM Method SWIG Solver INVERSION HeavyPoints 194 HPoints 194 Radii Bondi vdwScale 1.2 $end $solvent Dielectric 78.39 $end
Example 13.15 Input for the NEO-DFT/epc17-2 geometry optimization calculation of a AuH, C molecule utilizing the fit-LANL2DZ effective core potential for the gold atoms.
$molecule 1 1 Au 0.000000 0.000000 2.222000 Au 0.000000 0.000000 5.502000 H 0.000000 0.000000 3.842000 $end $rem JOBTYPE OPT SYM_IGNORE TRUE INPUT_BOHR FALSE BASIS mixed NEO TRUE METHOD b3lyp xc_grid = 000099000302 NEO_EPC epc172 NEO_N_SCF_CONVERGENCE = 8 SCF_CONVERGENCE = 8 NEO_E_CONV = 8 SCF_ALGORITHM GDM ECP fit-LANL2DZ $end $basis Au 1 LANL2DZ **** Au 2 LANL2DZ **** H 3 def2-qzvp **** $end $neo_basis H 3 S 1 1.000000 5.973 1.0 S 1 1.000000 10.645 1.0 S 1 1.000000 17.943 1.0 S 1 1.000000 28.950 1.0 P 1 1.000000 7.604 1.0 P 1 1.000000 14.701 1.0 P 1 1.000000 23.308 1.0 D 1 1.000000 9.011 1.0 D 1 1.000000 19.787 1.0 F 1 1.000000 10.914 1.0 F 1 1.000000 20.985 1.0 **** $end
Example 13.16 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 point_group_symmetry = False 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 13.17 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 point_group_symmetry = False 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 13.18 Input for CNEO-DFT analytic Hessian calculation on HCN molecule with a proton treated quantum mechanically. The electronic basis set is STO-3G, and the protonic basis set is an uncontracted 1s1p basis set with exponents 4.0. The electronic exchange-correlation functional is BLYP, and the electron-proton correlation functional is epc17-2.
$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.0000000 -0.5400000 H -0.935307 0.000000 -0.540000 $end $rem JOBTYPE SP SYM_IGNORE TRUE INPUT_BOHR FALSE BASIS cc-pvdz NEO TRUE METHOD pbe0 xc_grid = 000099000302 NEO_EPC epc172 NEO_N_SCF_CONVERGENCE = 7 SCF_CONVERGENCE = 8 NEO_E_CONV = 8 SCF_ALGORITHM DIIS NEO_SIMULTANEOUS_SCF TRUE NEO_STEPWISE_SCF_STEPS = 2 DIIS_SUBSPACE_SIZE = 10 DIIS_ERR_RMS FALSE $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 13.19 Input for the LR-NEO-TDDFT/epc19 calculation on CHO 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 13.20 Input for the LR-NEO-TDHF calculation on the FDF molecule treating quantum nuclei as deuterium and employing the 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 13.21 Input for the analytic LR-NEO-TDDFT gradient calculation on the CH 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 point_group_symmetry = False 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 13.22 Input for LR-NEO-TDDFT geometry optimization on the CH 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
point_group_symmetry = False
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 13.23 Input for LR-NEO-TDDFT on the CH 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
point_group_symmetry = False
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 13.24 Formate ion simulated with RT-NEO-TDHF and excited by a Gaussian impulse response from all three orthogonal directions, , , and .
$molecule -1 1 C 0.000000 0.000000 0.316833 H 0.000000 0.000000 1.430087 O 0.000000 1.135580 -0.208193 O 0.000000 -1.135580 -0.208193 $end $rem NEO = true SYM_IGNORE = true INPUT_BOHR = false BASIS = cc-pvtz METHOD = hf SCF_CONVERGENCE = 9 NEO_N_SCF_CONVERGENCE = 9 NEO_E_CONV = 9 NEO_VPP = 0 NEO_TDKS = true $end $neo_basis H 2 S 1 1.000000 5.973 1.0 S 1 1.000000 10.645 1.0 S 1 1.000000 17.943 1.0 S 1 1.000000 28.950 1.0 P 1 1.000000 7.604 1.0 P 1 1.000000 14.701 1.0 P 1 1.000000 23.308 1.0 D 1 1.000000 9.011 1.0 D 1 1.000000 19.787 1.0 F 1 1.000000 10.914 1.0 F 1 1.000000 20.985 1.0 **** $end $neo_tdks METHOD = realtime DT = 0.04 MAXITER = 20000 FIELD_TYPE = gaussian FIELD_AMP = 0.02 FIELD_PEAK = 0.0 FIELD_TAU = 800.0 FIELD_FREQUENCY = 6.0 FIELD_DIRECTION = xyz FIELD_PARTICLE_TYPE = both $end
Example 13.25 Excited-state intramolecular proton transfer in -hydroxylbenzaldehyde simulated with RT-NEO-TDDFT-Ehrenfest utilzing the B3LYP electronic exchange-correlation functional and epc17-2 electron-proton correlation functional. Two additional basis function centers are added along the proton transfer path, the total simulation time was specified to be 19.35 fs, and an electronic HOMO to LUMO swap was performed to prepare the initial state.
$molecule 0 1 C -1.310008 1.258755 0.000000 C 0.019289 0.780580 0.000000 C 0.322586 -0.621636 0.000000 C -0.761283 -1.465586 0.000000 C -2.125342 -0.985468 0.000000 C -2.398971 0.362640 0.000000 O 1.008708 1.658363 0.000000 C 1.725826 -1.062678 0.000000 O 2.682115 -0.219090 0.000000 H -3.414260 0.733314 0.000000 H -0.596742 -2.537818 0.000000 H -2.926679 -1.713458 0.000000 H -1.459388 2.331114 0.000000 H 1.924136 -2.138192 0.000000 H 1.844187 1.135044 0.000000 @H 2.042593 0.928022 0.000000 @H 2.241000 0.721000 0.000000 $end $rem NEO = true SYM_IGNORE = true INPUT_BOHR = false BASIS = cc-pvtz METHOD = b3lyp SCF_CONVERGENCE = 9 NEO_N_SCF_CONVERGENCE = 9 NEO_E_CONV = 9 NEO_EPC = epc172 NEO_VPP = 0 NEO_TDKS = true $end $neo_basis H 15 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 16 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** H 17 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** $end $neo_tdks METHOD = ehrenfest DT = 0.04 MAXITER = 20000 ELECTRONIC_HOMO_TO_LUMO = true $end
Example 13.26 Ground-state intramolecular proton transfer in malonaldehyde simulated with BO-RT-NEO-TDDFT-Ehrenfest. Minimal basis sets are employed as a proof of principle. Note the large time step of 4.2 atomic units is employed since the electronic dynamics are no longer being propagated.
$molecule 0 1 O 0.000000 -1.300873 2.045662 O 0.000000 1.290832 2.045662 C 0.000000 -1.216031 0.759259 C 0.000000 1.205990 0.759259 C 0.000000 -0.005020 0.053344 H 0.000000 -0.005020 -1.024823 H 0.000000 -2.163146 0.218967 H 0.000000 2.153105 0.218967 H 0.000000 -0.301012 2.355420 $end $rem NEO = true SYM_IGNORE = true INPUT_BOHR = false BASIS = sto-3g METHOD = b3lyp SCF_CONVERGENCE = 9 NEO_N_SCF_CONVERGENCE = 9 NEO_E_CONV = 9 NEO_EPC = epc172 NEO_VPP = 0 NEO_TDKS = true $end $neo_basis H 9 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** $end $neo_tdks METHOD = bo-ehrenfest DT = 4.2 MAXITER = 1335 $end
Example 13.27 Ground-state intramolecular proton transfer in malonaldehyde simulated with BO-RT-NEO-TDDFT-Ehrenfest, and utilizing the B3LYP-D3(0) empirical dispersion correction with custom parameters.
$molecule 0 1 O 0.000000 -1.300873 2.045662 O 0.000000 1.290832 2.045662 C 0.000000 -1.216031 0.759259 C 0.000000 1.205990 0.759259 C 0.000000 -0.005020 0.053344 H 0.000000 -0.005020 -1.024823 H 0.000000 -2.163146 0.218967 H 0.000000 2.153105 0.218967 H 0.000000 -0.301012 2.355420 $end $rem NEO = true SYM_IGNORE = true INPUT_BOHR = false BASIS = sto-3g METHOD = b3lyp SCF_CONVERGENCE = 9 NEO_N_SCF_CONVERGENCE = 9 NEO_E_CONV = 9 NEO_EPC = epc172 NEO_VPP = 0 NEO_TDKS = true DFT_D = D3_ZERO DFT_D3_S6 = 100000 DFT_D3_RS6 = 126100 DFT_D3_S8 = 170300 DFT_D3_3BODY = FALSE $end $neo_basis H 9 S 1 1.000000 4.0 1.0 P 1 1.000000 4.0 1.0 **** $end $neo_tdks METHOD = bo-ehrenfest DT = 4.2 MAXITER = 1335 $end
Example 13.28 Input for the NEO-RICCSD calculation on HO 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
Example 13.29 Input for the NEO-SCS-MP2 calculation on CHO molecule with the both protons 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. SCS scaling corresponds to , and .
$molecule 0 1 C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 H 0.935307 0.0000000 -0.5400000 H -0.935307 0.000000 -0.540000 $end $rem method = hf basis = sto-3g neo = true sym_ignore = 1 aux_basis = rimp2-cc-pVDZ scf_convergence 10 max_scf_cycles 100 SCF_ALGORITHM diis NEO_E_CONV 10 NEO_RIMP2 1 SCS 1 $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 $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 D 1 1.000000 2.8284 1.0 D 1 1.000000 4.0 1.0 D 1 1.000000 5.6569 1.0 D 1 1.000000 8.0 1.0 D 1 1.000000 11.3137 1.0 D 1 1.000000 16.0 1.0 D 1 1.000000 22.6274 1.0 D 1 1.000000 32.0 1.0 **** H 4 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 D 1 1.000000 2.8284 1.0 D 1 1.000000 4.0 1.0 D 1 1.000000 5.6569 1.0 D 1 1.000000 8.0 1.0 D 1 1.000000 11.3137 1.0 D 1 1.000000 16.0 1.0 D 1 1.000000 22.6274 1.0 D 1 1.000000 32.0 1.0 **** $end
Example 13.30 Input for the NEO-OOMP2 calculation on HO 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 input_bohr = false method = hf basis = sto-3g aux_basis = rimp2-aug-cc-pVDZ neo = true sym_ignore = 1 scf_convergence 10 max_scf_cycles 100 SCF_ALGORITHM diis NEO_E_CONV 10 NEO_VPP 0 NEO_RIMP2 2 $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 D 1 1.000000 2.8284 1.0 D 1 1.000000 4.0 1.0 D 1 1.000000 5.6569 1.0 D 1 1.000000 8.0 1.0 D 1 1.000000 11.3137 1.0 D 1 1.000000 16.0 1.0 D 1 1.000000 22.6274 1.0 D 1 1.000000 32.0 1.0 **** $end
Example 13.31 Input for the NEO-SOS-OOMP2 calculation on HO 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. SOS scaling corresponds to and , with a custom value of .
$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 input_bohr = false method = hf basis = sto-3g aux_basis = rimp2-aug-cc-pVDZ neo = true sym_ignore = 1 scf_convergence 10 max_scf_cycles 100 SCF_ALGORITHM diis NEO_E_CONV 10 NEO_VPP 0 NEO_RIMP2 2 SCS 2 EP_FACTOR 1500000 $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 D 1 1.000000 2.8284 1.0 D 1 1.000000 4.0 1.0 D 1 1.000000 5.6569 1.0 D 1 1.000000 8.0 1.0 D 1 1.000000 11.3137 1.0 D 1 1.000000 16.0 1.0 D 1 1.000000 22.6274 1.0 D 1 1.000000 32.0 1.0 **** $end