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Keywords for wave function analysis and generation of plotting data

Properties of RHF, UHF and (two-component) GHF wave functions as well as those of SCF+MP2 densities or such from excited state DFT-calculations can be directly analyzed within the respective programs (dscf, ridft, mpgrad, rimp2 and egrad). In case of spin-unrestricted calculations results are given for total densities ( Dα + Dβ) and spin densities ( Dα - Dβ). If not explicitly noted otherwise, in the following "D" is the SCF density, D(SCF), in case of dscf and ridft, the MP2-corrected density, D(SCF)+D(MP2), for mpgrad and rimp2 and the entire density of the excited state in case of egrad. For modules dscf and ridft the analysis of properties may be directly started by calling dscf -proper (or ridft -proper). In case of mpgrad and rimp2 this is possible only, if the MP2 density has already been generated, i.e. after a complete run of mpgrad or rimp2.

Functionalities of analyses are driven by the following keywords.

$mvd

leads to calculation of relativistic corrections for the SCF total density in case of dscf and ridft, for the SCF+MP2 density in case of rimp2 and mpgrad and for that of the calculated excited state in case of egrad. Quantities calculated are expectation values < p2 > , < p4 > and the Darwin term ( $ \sum$1/ZA*ρ(RA)).
$moments

yields calculation of electrostatic moments arising from nuclear charges and total electron densities. Also without setting this keyword moments up to quadrupole are calculated, with respect to reference point (0,0,0). Supported extensions:

$moments <i>
x1 y1 z1
x2 y2 z2
.
.
By integer i; the maximum order of moments is specified, maximum and default is i=3 (octopole moments), real numbers x, y, z allow for the specification of one or more reference points.
$pop

drives the options for population analyses. By default a Mulliken PA in the basis of cartesian atomic orbitals (CAOs) is performed for the total density ( Dα + Dβ) leading to Mulliken (brutto) charges and, in case of spin-unrestricted calculations also for the spin density ( Dα - Dβ) leading to Mulliken (brutto) numbers for unpaired electrons. Besides total numbers also contributions from s-, p-, ...functions are listed separately.

Two-component wavefunctions (only module ridft and only if $soghf is set): In two-component calculations instead of Sz |(Sx, Sy, Sz)| is written to the output. Additionally a vector-file named spinvec.txt is written, which includes the resulting spinvector for each atom in the system (also the direction).

The following modifications and extensions are supported, if the respective commands are written in the same line as $pop:

lall
Additional information about px, py, pz (and analogous for d and f functions) is displayed (lengthy output).
atoms list of atoms

Contributions are plotted only if arising from atoms selected by list.
thrpl=real

Contributions smaller than thrpl are not displayed (default: 0.01).
overlap
Mulliken atomic overlap matrix is displayed.
netto
Mulliken netto populations (diagonal elements of Mulliken overlap matrix) are calculated.
mosum list of MOs

Summed Mulliken contributions for a group of molecular orbitals defined by numbers referring to the numbering obtained e.g. from the tool eiger. Note that occupancy of MOs is ignored, i.e. all orbitals are treated as occupied.
mo list of MOs

Mulliken contributions for single MOs defined by numbers (independent of whether they are occupied or not). If this option is valid, one may additionally set
dos width=real points=integer

to calculate a (simulated) density of states by broadening the discrete energy levels with Gaussians and superimposing them. The width of each Gaussian may be set by input (default: 0.01a.u.). The resolution (number of points) may be chosen automatically (default values are usually sufficient to generate a satisfactory plot) or specified by hand. The output files (dos in case of RHF wave functions, and dos_a+b, dos_a-b, dos_alpha, dos_beta; for UHF cases) contain energies (first column), resulting DOS for the respective energy (second column) as well as s-, p-, d-contributions for the respective energy (following columns).
Example:
$pop mo 23-33 dos atoms 2,3,7-8
leads to Mulliken PA (CAO-basis) for each of the eleven MOs 23-33, regarding only contributions from atoms 2-3 and 7-8 (results are written to standard output) and generation of file(s) with the respective simulated density of states.

$pop nbo

to perform a natural population analyses [127]. The possible options (specified in the same line) are

 idbgl=integer Debug level. 

AOmust be provided, the CAO case is notimplemented.
tw=realThreshold tw to circumvent numericaldifficulties incomputing Ow
(default: tw=1.d-6).
idbgl=integer Debug level
(default: idbgl=0).
abFor UHF cases: Print alpha and beta density results.
shortPrint only natural electron configuration and summary.
Example:
$pop nbo AO ab short atoms 1,2,6
leads to a natural population analysis (AO-basis) with printing the results of alpha and beta densities (only the electron configuration and the summary) for the atoms 1,2 and 6.

To change the NMB set for atoms, one has to add a $nbonmb-block in the control file. Example:

$nbonmb
  ni s:4 p:2 d:1
  o  s:2 p:1
leads to a NMB set for Ni of 4 s-, 2 p- and 1d-functions and for O of 2 s- and 1 p-functions.
$pop paboon

to perform a population analyses based on occupation numbers [128] yielding "shared electron numbers (SENs)" and multicenter contributions. For this method always the total density is used, i.e. the sum of alpha and beta densities in case of UHF, the SCF+MP2-density in case of MP2 and the GHF total density for (two-component-)GHF.

The results of such an analysis may depend on the choice of the number of modified atomic orbitals ("MAOs"), which can be specified by an additional line; without further specification their number is calculated by the method "mix", see below. Note: One should carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers.

$mao selection options

to specify how MAOs are selected per atom.

Available options are:

a) for the way of sorting MAOs of each atom:

eig

MAOs are sorted according to their eigenvalue (those with largest EW finally are chosen). This is the default.
occ

MAOs are sorted according to their occupation; note that the number of all occupation is NOT the number of electrons in the system. This option is kept rather for historical reasons.
b) for the determination of the number of MAOs:
fix

A fixed number of MAOs is taken for each atom; usually this is the number of shells up to the complete valence shell, e.g. 5 for B-Ne, 6 for Na-Mg, etc. Exceptions are Elements Sc (Y, La), Ti (Zr, Hf), V (Nb, Ta) for which not all five d-shells are included, but only 2, 3 or 4, respectively. This modification leads to better agreement with partial charges calculated by an ESP-fit.
thr <real>

All MAOs with an eigenvalue larger than <real> are chosen; default is <real>=0.1. This and the following two options are not valid in connection with occ.
max

Maximum of numbers calculated from fix and thr=0.1 is taken.
mix

2:1 mixture of fix and thr=0.1. This choice gives best agreement (statistical) with charges from an ESP-fit. It is the default choice.
c) for additional information about MAOs:
info

Eigenvalues and occupations for each MAO are written to output.
dump

Entire information about each MAO is written to output. Lengthy.
Further for each atom the number of MAOs and the sorting mode can be specified individually in lines below this keyword. Example:

atom 1,3-4 eig 7

leads to choice of the 7 MAOs with largest eigenvalue at atoms 1, 3-4.

$localize

enables the generation of localized molecular orbitals (LMOs) using Boys localization. By default, all occupied orbitals are included, localized orbitals are written (by default in the AO-basis) to file(s) lmo in case of RHF and lalp and lbet in case of UHF orbitals. Note, that LMOs usually break the molecular symmetry; so, even for symmetric cases the AO (not the SAO) basis is used for the output. The localized orbitals are sorted with respect to the corresponding diagonal element of the Fock matrix in the LMO basis. In order to characterize these orbitals, dominant contributions of (canonical) MOs are written to standard output as well as results of a Mulliken PA for each LMO (for plotting of LMOs see option $pointval).

The keyword allows for following options (to be written in the same line):

mo list of MOs

Include only selected MOs (e.g. valence MOs) in localization procedure (numbering as available from Eiger).
sweeps=integer

maximum number of orbital rotations to get LMOs; default value is 10000 (sometimes not enough, in particular for highly delocalised systems).
thrcont=real

lower threshold for displaying MO and Mulliken contributions (default: 0.1).
CAO
LMOs are written to file in the CAO basis (instead of AO)
$esp_fit

fits point charges at the positions of nuclei to electrostatic potential arising from electric charge distribution (also possible for two-component calculations, for UHF cases also for spin density). For this purpose the ("real") electrostatic potential is calculated at spherical shells of grid points around the atoms. By default, Bragg-Slater radii, rBS, are taken as shell radii, for each atom the number of points is given by 1000⋅rBS2, the total number of points is the sum of points for each atom reduced by the number of points of overlapping spheres. Non-default shells (one or more) can be specified as follows:

$esp_fit
shell i1 s1
shell i2 s2
$ \vdots$

Integer numbers i define the number of points for the respective shell, real numbers s constants added to radii (default corresponds to one shell with s=1.0).

A parameterization very close to that by Kollman (U.C. Singh, P.A. Kollman, J. Comput. Chem. 5(2), 129-145 (1984)) may be obtained by

$esp_fit kollman

Here five shells are placed around each atom with r=1.4*rvdW + k, k=0pm, 20pm, 40pm, 60pm, 80pm, and rvdW are the van-der-Waals radii of the atoms.

$pointval

drives the calculation of space-dependent molecular quantities at 3D grids, planes, lines or single points. Without further specifications the values of densities are plotted on a three-dimensional grid adapted to the molecular size. Data are deposed to output files (suffix plt) that can be visualized directly with the gOpenMol program. In case of RHF-dscf/ridft calculations you get the total density on file td.plt, for UHF-dscf/ridft calculations one gets both values for the total density ( Dα + Dβ) on td.plt and the "spin density" ( Dα - Dβ) on sd.plt. For mpgrad/rimp2 calculations one gets in the RHF case the total density (D(SCF+MP2)) on td.plt and the MP2 contribution on mp2d.plt and in the UHF case one obtains the total density ( Dα(SCF + MP2) + Dβ(SCF + MP2)) on td.plt, the "spin density" ( Dα(SCF + MP2) - Dβ(SCF + MP2)) on td.plt, and the respective MP2 contributions on files mp2d.plt and mp2sd.plt. For egrad it is similar, just replace in the filenames mp2 by e.

Integration of density (if absolute value greater than eps) within a sphere (origin x, y, z, radius r) is performed for

$pointval integrate x y z r eps

By default the origin is at (0,0,0), the radius is chosen large enough to include the whole 3D box and all contributions are regarded (eps=0).

Data different from total and spin densities are generated by following (combinable) settings (to be written in the same line as statement $pointval):

pot
leads to calculation of electrostatic potential arising from electron densities, nuclei and--if present--constant electric fields and point charges. The densities used for calculation of potentials are the same as above; the respective filenames are generated from those of densities by replacement of the "d" (for density) by a "p" (for potential). By "pot eonly" only the electronic contribution to the electrostatic potential is calculated.
fld
calculation of electric field. Note, that for 3D default output format (.plt, see below) only norm is displayed. Densities used are the same as above, filenames are generated from those of densities by replacement of "d" (for density) by "f" (for field).
mo list of MO numbers

calculation of amplitudes of MOs specified by numbers referring to the numbering obtained e.g. from the tool eiger in the same format. The respective filenames are self-explanatory and displayed in the output. Note, that also in MP2 and excited state calculations the HF/DFT ground state orbitals are plotted (and not natural MP2/excited orbitals).

Two-component cases: The density of the spinors specified by numbers referring to the numbering obtained e.g. from the file EIGS are visualized. By setting the keyword minco also the amplitudes of the spinor-parts are calculated, whose weights (the probability of finding the electron in this part) lie above the threshold.

lmo list of LMO numbers

calculation of amplitudes of LMOs (previously generated by $localize) ordered by the corresponding diagonal element of the Fock matrix in the LMO basis.
nmo list of NMO numbers

calculation of amplitudes of NMOs (previously generated by
$natural orbitals file=natural and
$natural orbital occupation file=natural
dens
has to be set, if additionally to one of the above quantities also the density is to be computed.
xc
calculation of the Kohn-Sham exchange-correlation potential. It is only valid for DFT calculations and it works for all exchange-correlation functionals, including LHF. Note that for hybrid functionals, only the Kohn-Sham part of the potential will be computed (the HF part is a non-local-operator and can't be plotted). For GGA/MGGA functional only the local part is (currently) computed.

For line plots the output file is tx.vec . For UHF calculations the output files are tx.vec (alpha-spin potential) and sx.vec (beta-spin potential).

For line plot the files has three columns: 1: total potential 2: local part ( or Slater-potential for LHF) 3: non-local part ( or Correction term for LHF)

Output formats may be specified by e.g. fmt=xyz if written to the same line as $pointval. Supported are:

xyz
in case of scalars (density, (L)MO amplitudes, electrostatic potential) this format is: (x, y, z, f (x, y, z)). In case of vectors components of the vector and its norm are displayed. This format is valid for all types of grid (3D, plane, line, points, see below), it is the default format in case of calculation of values at single points. Output file suffix is .xyz.
plt
only for 3D, default in this case. Data are written to binary files that can be directly read by gOpenMol. Note, that this output is restricted to scalar quantities; thus in case of vectors (E-field) only the norm is plotted. Output file suffix is .plt.
map
only for 3D. Data are written to ASCII files that can be imported by e.g. gOpenMol. Note, that this output is restricted to scalar quantities; thus in case of vectors (E-field) only the norm is plotted. Output file suffix is .map.
txt
a format compatible with gOpenMol for visualization of vectors v. The format is x, y, z, vx, vy, vz.
vec
for planes and lines (default in these cases). In case of a line specified by α$ \vec{{v}} $ (see below) output is α, f (x, y, z) for scalars, for vectors components and norm are displayed. vectors. Analogously, in case of planes it is α, β, f (x, y, z). The output (file suffix .vec) may be visualized by plotting programs suited for two-dimensional plots. A command file (termed gnuset) to get a contour plot by gnuplot is automatically generated.
cub
only for 3D, writes out data in Cube format which can be imported by many external visualization programs.

For 3D grids non-default boundarys, basis vector directions, origin and resolutions may be specified as follows:

$pointval 
grid1 vector 0 3 0 range -2,2 points 200
grid2 vector 0 0 -7 range -1,4 points 300
grid3 vector 1 0 0 range -1,1 points 300
origin 1 1 1
Grid vectors (automatically normalized) now are (0, 1, 0),(0, 0, - 1),(1, 0, 0), the grid is centered at (1, 1, 1), and e.g. for the first direction 200 points are distributed between -2 and 2.

Grids of lower dimensionality may be specified (in the same line as $pointval) by typing either geo=plane or geo=line or geo=point The way to use is best explained by some examples:

$pointval geo=plane
grid1 vector 0 1 0 range -2,2 points 200
grid2 vector 0 0 1 range -1,4 points 300
origin 1 1 1
Values are calculated at a plane spanned by vectors (0,1,0) and (0,0,1) centered at (1,1,1).
$pointval geo=line
grid1 vector 0 1 0 range -2,2 points 50
origin 0 0 1
Values are calculated at a line in direction (0,1,0) centered at (0,0,1). Output format as above.
$pointval geo=point
7 5 3
0 0 7
Values are calculated at the two points (7.0, 5.0, 3.0) and (0.0, 0.0, 7.0).


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Next: Keywords for Module Frog Up: Format of Keywords and Previous: Keywords for Module Moloch   Contents   Index
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