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ADFPLT

CD Spectra Toolkit (for ADF and Turbomole)

Review Papers published by us

ADFPLT: plotting MOs, densities etc. from ADF calculations

ADFPLT is a graphical tool to visualize the orbitals of an atom or molecule calculated with ADF. It can produce nice 2D isoline and 3D isosurface plots and it is very simple to use. A number of command line options are available, e.g. whether to plot automatically atomic coordinates, bond lines, contour values etc..
One simply needs to generate a TAPE41 file with the ADF tool DENSF. ADFPLT plots any data set stored in TAPE41, provided it contains 2D or 3D data grids. Data on onedimensional grids are written to a table and can be plotted with gnuplot, for example. The 3D iso-surface plots are perhaps not quite as nice as those from other grapical tools, but ADFPLT displays them very fast. It is therefore a useful tool to get an overview of a large set of orbitals or other visualizable molecular data.
ADFPLT uses the GR-GR3 graphics library from http://www.kfa-juelich.de/vislab/software/ (note: the download location has frequently changed in the past, therefore it might be outdated) to create the pictures. This library is freely available for non-profit purposes. Rotation matrices for interactive rotations of 3D plots are produced by the little X11 open source utility ROTATE. It is part of the so-called LASSPTools available at http://www.lassp.cornell.edu/LASSPTools/LASSPTools.html.
You can download binaries from this web page (see the links in the following sentence). I have compiled versions for IBM RS/6000 (AIX 4), Linux, and DEC Alpha (OSF 1) available. They should work with most versions of ADF. There is a shell script in which you need to adjust some environment variables so that it finds the executables. You can also get the source code if you want to compile it yourself . You also need to compile the GR-GR3 library in that case, plus there need a few changes to be applied to the GR3 source code in order to enable interactive rotations. Unfortunately due to copyright restrictions I'm not allowed to re-distribute modified GR3 sources. Please consider to use the precompiled binaries instead. Really! Email me if you still want to compile it yourself, and I'll send you the source code.

Below are some examples of 2D contour line diagrams of orbitals (localized molecular orbitals of benzene). ADFPLT generates these plots automatically from TAPE41 data, including the lines and markers for the atoms:

Contour line diagrams plotted with ADFPLT

Here is a screenshot how 3D isosurface plots look like on screen. In the small window on the left the user can rotate the picture interactively. Postscript files (or other formats) for subsequently rotated plots can automatically be stored. Below is an example for how ADFPLT can store GIF hardcopies of the graphics (pi-MO in ethene).

ADFPLT 3D screen shot

ADFPLT graphics hardcopy example

CD Spectra Toolkit

Here you can download a package containing a few shell scripts and the Fortran source code for two programs. Compiled binaries for a Linux system are included. The Fortran source code should compile with any f90 compiler. Please email me if it doesn't.
Download gzipped tar archive (781 kByte)
Together the scripts and programs process the output of a time-dependent DFT CD spectrum calculation and generate a nice simulated spectrum. The CD spectrum can be calculated either with the ADF or with the Turbomole program. See the included README file for instructions. You need gnuplot to generate the spectra. Here is an example from Reference [17]:

Simulated CD spectrum of [Co(en)3](2+)

Review Papers

  • Autschbach, J., ‘The calculation of NMR parameters in transition metal complexes’, in Kaltsoyannis, N.; McGrady, J. E. (editors), ‘Principles and Applications of Density Functional Theory in Inorganic Chemistry I’, volume 112 of Structure and Bonding, Springer, Heidelberg, 2004, 1-48. Download author's manuscript (PDF ,433 kBytes)

  • Autschbach, J.; Ziegler, T., ‘Double perturbation theory: A powerful tool in computational coordination chemistry’, Coord. Chem. Rev. 2003, 238/239, 83-126.
    A review with 400+ references dealing with second order and related properties such as NMR observables, ESR properties, harmonic frequencies, polarizabilities, excitation energies, CD and optical rotations, vibrational CD, relativity and relativistic forces. Applications discussed in this paper are concerned with properties of transition metal complexes. Download author's manuscript (PDF ,582 kBytes)

  • Autschbach, J.; Ziegler, T., ‘Relativistic Computation of NMR shieldings and Spin-spin Coupling Constants’, in Grant, D. M.; Harris, R. K. (editors), ‘Encyclopedia of Nuclear Magnetic Resonance’, volume 9, John Wiley & Sons, Chichester, 2002, 306-323.
    A review article specifically dealing with heavy atom NMR computations. Download author's manuscript (PDF ,276 kBytes)
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