ADFreport ($ADFBIN/adfreport) gets information (including images from molecules or fields) from an ADF result file. The result file is the TAPE21 produced by ADF and should have a .t21 extension. If you use the ADF-GUI or adfprep to generate your job scripts this is already the case. The selected information is printed as concisely as possible on standard output. Alternatively, you can write the information to a tab separated file or to an HTML file. If the file does not exist, adfreport will also generate one line with headers to identify the information. Images are generated using the ADF-GUI.
Results on a .t21 file may depend on the ordering of atoms. adfreport will report such results in the input order when you use one of the predefined keys, which is the order that you will normally expect. If you ask for a dump of a particular KF variable you will get the data exactly as it is present in the file, and it is up to you to make sense of the data.
A simple example to get the bonding energy from a file:
adfreport job.t21 BondingEnergy
or to generate high-quality pictures of some orbitals:
adfreport job.t21 HOMO LUMO+1 -v "-grid Fine" -v "-antialias" -v "-bgcolor #ffffff"
The most convenient way to see the optoins of adfreport is to run the adfreport command without arguments. You will get output very much alike the following description, but probably more up-to-date.
Usage: adfreport [-i] result.t21 [-o result.html] [[-r] result] [-v adfview]
Successive calls will with the same output file will update the information contained in that file.
The following flags may be used:
-i: result.t21 is the name of the input .t21 file with the ADF results
the -i is optional, if no -i flag found the first argument without flag will be used
-o: result.tsv is the name of the tab separated file in which the results will be saved
: result.html is the name of the html formatted file (a simple html table) to save the results
: absent: the output will be written to standard output, only the requested result (no headers)
-r: result is a particular result to be reported from the .t21 file.
The -r flag is optional: all arguments without flags will be considered to be result arguments,
with exception of the first argument if the -i flag is also absent
Any proper KF variable is allowed (section%variable, see the KF utilities documentation)
After the variable you can specify details, all separated with #
- range: one or two numbers, separated with a :, array counts start at 1
- format: TclTk format string for one number, like 8.3f or 12.6g
- %nperline: (% with number) insert new line after nperline items (not used for .tsv)
For example: -r "Geometry%xyz#12.4f##3" prints a nicely formatted table of the coordinates
-r "Geometry%xyz#1:9#12.4f##3" similar, for the first two atoms only
-r "Geometry%xyz#12.4f#1:9" the coordinates of the first two atoms, all on one line
-r "Geometry%xyz#1" print just the first coordinate
-r "Energys%Bond Energy" print the bond energy (a scalar)
When a result without % is specified, it must be one of the pre-defined keys.
If you use HTML output, the name of the keys are used as table headers.
The keys are not cases-sensitive, and * matches any text.
title : title of the calculation
type : calculation type (single point, geometry optimization, ...)
weight : molecular weight
symmetry : molecular symmetry
natoms : number of atoms
integration : integration accuracy
integration-min : minimum integration accuracy
integration-max : maximum integration accuracy
charges : shorthand for Voronoi, Hirshfeld and Mulliken charges
voronoi : voronoi deformation charges
hirshfeld : hirshfeld fragment charges, will only work with atomic fragments
mdc : all available MDC atom charges
mdc-m : MDC-M charges
mdc-d : MDC-D charges
mdc-q : MDC-Q charges
mulliken : mulliken charges
nmr : nmr chemical shifts
nmr-c* : nmr chemical shifts
nmr-shielding-tensor : nmr shielding tensor
nmr-j-coupling-tensor : nmr j coupling tensor
nmr-k-coupling-tensor : nmr k coupling tensor
nmr-j-coupling-constant : nmr j coupling constant
nmr-k-coupling-constant : nmr k coupling constant
dipolev* : dipole vector
dipole : dipole moment (length of dipole vector)
quadrupole : quadrupole tensor
orbital-info : orbital info (energy, occupation and label), format for energy after #,
range after # with HOMO or LUMO, for examples:
orbital-info#HOMO, orbital-info#HOMO-1, orbital-info#HOMO-2:LUMO+2,
orbital-info#HOMO#12.8f
orbital-e* : orbital energies, format and range after # as in orbital-info
orbital-o* : orbital occupations, format and range after # as in orbital-info
orbital-l* : orbital labels, format and range after # as in orbital-info
atomlabel : name of atoms with sequence number, starting at 0
atomlabel-from0 : name of atoms with sequence number, starting at 0
atomlabel-from1 : name of atoms with sequence number, starting at 1
geometry,
geometry-a*,
geometry-b* : geometry (element type and coordinates), in input order,
in angstrom or bohr (default bohr)
hessian* : hessian (from GeoOpt%Hessian_CART),
in input order, fmt and nperline options after #
gradients* : gradients (from GeoOpt%Gradients),
in input order, fmt and nperline options after #
energies : all avaliable energies (bonding up to xc, with labels)
bonding* : total bonding energy
pauli* : total pauli repulsion
steric* : total steric interaction
orbital* : total orbital interaction
electrostatic* : electrostatic energy
kinetic* : electrostatic energy
coulomb* : coulomb (steric +OrbInt) energy
xc* : XC energy
frequencies* : IR Frequencies, format, nperline and range (n, or n:n, start at 1) after #
freqint* : IR Intensities, format, nperline and range (n, or n:n, start at 1) after #
freqlabel* : IR Frequencies label (symmetry),
format, nperline and range (n, or n:n, start at 1) after #
normalmode* : Normal Modes (mass weighted),
format, nperline and range(n, or n:n, start at 1) after #
zeropoint* : Zero-Point energy
excitation* : Excitation energies,
format, nperline and range (n, or n:n, start at 1) after #
oscillatorstrength*: Oscillator strengths for the excitation energies
format, nperline and range (n, or n:n, start at 1) after #
excitlabel* : Excitation labels (symmetry),
format, nperline and range (n, or n:n, start at 1) after #
The -r flag (or arguments without flag) may be repeated for multiple results
-v: command line to pass to adfview (without filenames) to generate an image
The image will be generated by ADFview, the image will be stored in a
directory with a name based on the result file, and with extension .jpgs.
The result file will contain a path to the image file (directly, or in an IMG tag)
After the -v the arguments must be listed, with proper quoting.
Repeat the -v flag for multiple arguments.
Some shortcuts have been defined (HOMO, HOMO+1, LUMO, Molecule, Density, Potential)
Some useful flags include -scmgeometry (default 200x200), -bgcolor (default #220000),
-zoom (default 1.0), -viewplane (default {1 2 5}),
-antialias (off when not present, especially useful with light bgcolors),
-grid (Coarse when not present,
Medium when specified, or value after flag if present)
Examples: Molecule HOMO LUMO
HOMO-1 LUMO+1 -v "-viewplane {0 0 1}" -v "-grid Fine" -v "-antialias"
