Tutorial: Visualizing Volumetric Data from the ADF 2008 Calculations


ADF distribution comes with an auxiliary program, densf, to generate values of molecular orbitals, charge densities and potentials in a user-specified grid. Starting from the ADF version 2008 densf can write volumetric data in gaussian cube format. For example, to generate cubes for electrostatic potential, electron density and molecular orbitals run densf:

densf << eor

INPUTFILE my_molecule.t21

CUBOUTPUT my_molecule

density scf

orbitals scf

All HOMO-1

end

coulpot scf

grid fine

end input

eor

Where INPUTFILE keyword specifies path to the TAPE21 file from which densf reads the input data. Absence of the keyword is treated as if INPUTFILE TAPE21 has been specified.

Presence of the CUBOUTPUT keyword tells densf to save all computed quantities as gaussian cube files using my_molecule as filename prefix. The prefix can also contain a complete path including directories. For example, the above input will result in files my_molecule%SCF%Density.cub, my_molecule%SCF%Coulpot.cub, my_molecule%SCF_A%59.cub and my_molecule%SCF_A%60.cub being created containing volume data for the total SCF density, electrostatic potential and two molecular orbitals. One file per requested quantity is created.

The grid key is available either as simple key, or as block key. In the abobe example the simple key is used. Either coarse, medium or fine may be specified. This instructs the program to generate the grid automatically within a box enclosing all atoms of the molecule. The distance between grid points is 0.5, 0.2 or 0.1 bohr for respectively a coarse, medium or fine grid.

For full description of all available densf options consult ADF manual.

After generating cube files follow Visualizing Volumetric Data from the Gaussian Cube Files tutorial


Send all questions, suggestions and comments to Vlad (vvv900@gmail.com)

Dr. Vladislav Vasilyev

Supercomputer Facility,

The Australian National University,

Canberra, ACT, 0200, Australia