Visualizing orbital shape¶
Using the ioncat/ionplot tools to process .ion files¶
You can look at the shape of the orbitals by plotting the contents of the .ion files produced by Siesta. These files are not easily readable, but the ‘ioncat’ program can extract the relevant pieces of information, and the “ionplot” script can drive ‘ioncat’ to plot the desired graphs. For example:
ionplot -o 1 O
will plot the orbital with number “1” in the O.ion file.:
ioncat -i O
will print the numbers of the representative orbitals of each nlz shell (i.e., disregarding the ‘m’ quantum number, which does not affect the radial part).:
ioncat -o 1 O
will output the data for the first orbital in O.ion.
ioncat -h produces a display of the full set of options for
Usage: ioncat [options] Species_Label Options: -s : Show header information -i : Print indexes of unique orbitals -j : Print indexes of unique KB projectors -o ORBINDEX : Generate table for orbital ORBINDEX -k KBINDEX : Generate table for KB proj KBINDEX -v : Generate table for Vna potential -c : Generate table for pseudocore charge -l : Generate table for Vlocal charge -Z : Zoom in near rc for table generation -O rlog : Zoom near zero (up to 10^rlog) -h : Print this help message
ionplot accepts the options (such as -o)
that generate data and drives also gnuplot to plot the information.
By combining the two one could plot all the orbitals:
for i in $(ioncat -i O); do ionplot -o $i; done
Note that each orbital will appear in a different window.
sh ionplot.sh -o 3 H.ion for i in $(ioncat -i H.ion) ; do ionplot.sh -Z -o $i H.ion done
The ionplot script is not installed by default. Simply copy this file (name it ionplot) to your $HOME/.local/bin directory, or anywhere in your PATH:
#!/bin/sh # string="$@" ioncat $@ > .tmp_ioncat cat > .plot.g << EOF set title "$string" plot ".tmp_ioncat" using 1:2 w l title "f" replot ".tmp_ioncat" using 1:3 w l title "grad f" EOF # gnuplot -persist .plot.g
Using sisl to process .ion.nc files¶
When Siesta is compiled with netcdf support, information about basis orbitals, KB projectors, etc, is also written to .ion.nc files. These netcdf files can be read by sisl.
In particular, plots that include orbital information as one of the
panels can be obtained, for example, by executing the
of the sisl distribution:
sdata Al.ion.nc --plot
You might need to install sisl and/or activate a specific
python environment on your machine to access its functionality.
In the School, type
workon to see the environments, and then
workon school or the appropriate environment.