Manual:Visualization

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Every given number of time iterations, or after ground-state calculations, some of the functions that characterise the system may be written to disk so that they may be analized. Files are written within static/ output directory after the self-consistent field, or within td.x/ directories, during evolution, where “x” stands for the iteration number at which each write is done.

The function that you want to plot is selected by the Output variable and the output format is chosen by the OutputFormat.

dx

This is an OpenDX network, aimed at the visualization of wavefunctions. To be able to use it, you need to have properly installed the OpenDX program, as well as the Chemistry extensions developed at the Cornell Theory Center. Please take a look here to see how to obtain and install this software. Unfortunately, since this software is old and unmaintained, you are likely to have trouble installing.

Once these are working, you may follow the tutorial for the benzene molecule.

XCrySDen

Atomic coordinates (finite or periodic), forces, and functions on a grid can be plotted with the free program XCrySDen. Its XSF format also can be read by V_Sim and Vesta. Beware, these all probably assume that your output is in Angstrom units (according to the specification), so use UnitsOutput = eV_Angstrom, or your data will be misinterpreted by the visualization software.

CUBE

The Gaussian cube format (http://paulbourke.net/dataformats/cube/) can be output, and can be read by VMD, XCrysDen, Avogadro, and other software. Beware: these all seem to assume the output is in atomic units, so use UnitsOutput = atomic and remove the negative sign in the number of voxels, or your data will be misinterpreted by the visualization software. This is despite the fact that the CUBE specification has a way of identifying the units used (https://gaussian.com/cubegen/), as it is implemented in Octopus. VMD ignores it (http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html) and will actually (version 1.9) crash with a memory allocation error if it sees the negative number of voxels that marks the file as using Bohrs.

PDB

Everything is supposed to be in Angstroms: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

XYZ

Generally considered to be in Angstroms: http://openbabel.org/wiki/XYZ_%28format%29, https://en.wikipedia.org/wiki/XYZ_file_format, https://www.molpro.net/info/2012.1/doc/manual/node100.html, http://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node32.html


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