The following visualization tools are enabled in EDA2:
Automated generation of complementary occupied-virtual pairs (COVP)
Electron density difference (EDD) maps between intermediate states (FRZ$\to $POL, POL$\to $Full)
Plots for Natural Orbitals for Chemical Valence (NOCV)
Plots of frozen and polarized ALMOs
As introduced in Sec. 12.5.2, the COVPs can help elucidate the details of a charge-transfer process by showing the chemically most relevant donor-acceptor orbitals. In its implementation in EDA2, we enabled an automated selection of the most significant occupied-virtual pairs (based on a threshold on singular values). The MO cube files of these selected COVPs are then generated, and thus there is no need to specify which orbitals to plot. This new feature can be turned on by setting EDA_COVP_PRINT = AUTOMATED. Also, both the old and new formats of the $plots section are supported for automated COVP cube generation in EDA2. The old format requires MAKE_CUBE_FILES = TRUE and the new format requires PLOTS = TRUE. The plotted COVPs are indexed as covp_a.N.cube and covp_b.N.cube and the energetic significance of each of them can be looked up from the output file.
EDA2 also enabled electron density difference (EDD) plots to show the redistribution of electron density upon polarization ($\mathrm{\Delta}{\mathbf{P}}_{\mathrm{pol}}={\mathbf{P}}_{\mathrm{pol}}-{\mathbf{P}}_{\mathrm{frz}}$) and charge transfer ($\mathrm{\Delta}{\mathbf{P}}_{\mathrm{ct}}={\mathbf{P}}_{\mathrm{full}}-{\mathbf{P}}_{\mathrm{pol}}$). For unrestricted ALMO-EDA calculations, the spin density at FRZ, POL, and fully relaxed states are plotted together. Another related quantity that can be visualized is the so-called natural orbitals for chemical valence (NOCV), ^{Mitoraj:2009} which are defined as the eigenvectors of $\mathrm{\Delta}\mathbf{P}={\mathbf{P}}_{\mathrm{full}}-{\mathbf{P}}_{\mathrm{frz}}$. The NOCVs appear in pairs ${\psi}_{k}$ and ${\psi}_{-k}$, whose associated eigenvalues are ${n}_{k}$ and $-{n}_{k}$, respectively. The energy lowering associated with each pair of NOCVs can be calculated using the extended transition state (ETS) approach (see ref. Mitoraj:2009 for details). The NOCVs are useful tools for illustrating the underlying orbital interactions in chemical bonding.
In EDA2, the EDD maps are plotted when EDA_PLOT_DIFF_DEN = TRUE. The calculation of NOCVs can be turned on by EDA_NOCV = TRUE, and the most significant NOCVs are automatically selected based on a threshold on the eigenvalues $\{{n}_{k}\}$ and then plotted. Note that the new format of the $plots section is required for these visualizations (see Sec. 10.5.3.1 for details).
Finally, in the 5.2.2 release we enabled the visualization of frozen and polarized ALMOs, which is controlled by $rem variables PLOT_ALMO_FRZ and PLOT_ALMO_POL. The user needs to specify which orbitals to plot for each fragment through the $almo_print section:
$almo_print frgm_idx1 orb1 orb2 ... (spin) frgm_idx2 orb1 orb2 ... (spin) . . . $end
One can use the format “orb1:orb2” to sepcify a range of orbitals to plot for each fragment. For unrestricted cases, at the end of each line one can write “a” or “b” to specify whether alpha or beta orbitals are plotted (alpha orbitals will be plotted by default if there is no specification). As above, a $plots section with its new format is required for the visualization of ALMOs.
In the following table, we summarize the names of the cube files generated by each type of plots. Note that for the EDD plots, “0” refers to the EDD between POL and FRZ states, while “1” refers to the EDD between full SCF and POL states; for the spin density plots, “0”, ”1”, and ”2” corresond to the FRZ, POL, and fully relaxed states, respectively.
Plot type | Orbital type | Cube file name |
COVP | R | covp_a.N.cube |
U | covp_a.N.cube, covp_b.N.cube | |
EDD | R | dens.0.cube, dens.1.cube |
U | dens_alpha.0.cube, dens_alpha.1.cube | |
dens_beta.0.cube, dens_beta.1.cube | ||
dens_spin.0.cube, dens_spin.1.cube, dens_spin.2.cube | ||
NOCV | R | nocv_a.N.cube |
U | nocv_a.N.cube, nocv_b.N.cube | |
ALMO | R | almo_frz_a.N.cube, almo_pol_a.N.cube |
U | almo_frz_a.N.cube, almo_frz_b.N.cube | |
almo_pol_a.N.cube, almo_pol_b.N.cube |
EDA_PLOT_DIFF_DEN
Plot changes in electron density due to POL and CT
TYPE:
BOOLEAN
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not make EDD plots
TRUE
Make EDD plots
RECOMMENDATION:
None
EDA_NOCV
Perform the NOCV analysis and plot the significant NOCVs
TYPE:
BOOLEAN
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not perform NOCV analysis
TRUE
Perform NOCV analysis
RECOMMENDATION:
None
PLOT_ALMO_FRZ
Plot ALMOs at the frozen stage of EDA2 calculations
TYPE:
BOOLEAN
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not plot frozen ALMOs
TRUE
Plot frozen ALMOs
RECOMMENDATION:
None
PLOT_ALMO_POL
Plot ALMOs after the polarization calculation
TYPE:
BOOLEAN
DEFAULT:
FALSE
OPTIONS:
FALSE
Do not plot polarized ALMOs
TRUE
Plot polarized ALMOs
RECOMMENDATION:
None
$molecule 0 1 -- 0 1 O -1.521720 0.129941 0.000000 H -1.924536 -0.737533 0.000000 H -0.571766 -0.039961 0.000000 -- 0 1 O 1.362840 -0.099704 0.000000 H 1.727645 0.357101 -0.759281 H 1.727645 0.357101 0.759281 $end $rem JOBTYPE EDA METHOD B3LYP BASIS 6-31+G(d) SYMMETRY FALSE SYM_IGNORE FALSE MEM_TOTAL 8000 MEM_STATIC 2000 BASIS_LIN_DEP_THRESH 6 THRESH 14 SCF_CONVERGENCE 8 MAXSCF 200 EDA_COVP TRUE EDA_PRINT_COVP AUTOMATED !auto-generation of covp cube files MAKE_CUBE_FILES TRUE PLOTS TRUE !new format for the plot section $end $plots grid_points 100 100 100 $end
$molecule 0 1 -- 0 1 N 0.0000001517 0.7279666667 0.0000000000 H 0.9488005016 1.0881357449 0.0000000000 H -0.4743994984 1.0881371276 -0.8216800000 H -0.4743994984 1.0881371276 0.8216800000 -- 0 1 B -0.0000014567 -0.9275533333 0.0000000000 H -1.1719117610 -1.2408021948 0.0000000000 H 0.5859582390 -1.2408039026 -1.0149100000 H 0.5859582390 -1.2408039026 1.0149100000 $end $rem JOBTYPE eda EDA2 2 !ALMO-POL METHOD b3lyp BASIS 6-31g(d) SCF_ALGORITHM diis XC_GRID 1 SCF_CONVERGENCE 8 MAX_SCF_CYCLES 200 THRESH 14 SYMMETRY false SYM_IGNORE true EDA_PLOT_DIFF_DEN TRUE !plot EDD maps EDA_NOCV TRUE !plot NOCVs $end $plots grid_points 100 100 100 $end
$molecule 0 1 -- 0 1 H1 O1 H1 0.95641 H2 O1 0.96500 H1 104.77306 -- 0 1 O2 H2 dist O1 171.85474 H1 180.000 H3 O2 0.95822 H2 111.79807 O1 -58.587 H4 O2 0.95822 H2 111.79807 O1 58.587 dist = 2.0 $end $rem jobtype eda eda2 2 !ALMO-POL method b3lyp basis 6-31g unrestricted false scf_algorithm diis scf_convergence 8 max_scf_cycles 200 thresh 14 symmetry false sym_ignore true plot_almo_frz true plot_almo_pol true $end $almo_print 1 5:6 2 5:6 $end $plots grid_points 60 60 60 $end