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Which basis sets and/or pseudopotentials should I use?
When in doubt, always use the DZVP-MOLOPT-GTH basis set and the GTH-PBE pseudopotential.
In some cases (for example for tin) there is only a short-range basis set available, called DZVP-MOLOPT-SR-GTH.
You can find all available MOLOPT basis sets in BASIS_MOLOPT, which is located in the folder $CP2K_DATA_DIR (after loading the CP2K module).
How do I run CP2K in parallel?
The command cp2k.sopt is the single-process variant of CP2K.
To run CP2K in parallel, you have to use a different executable named cp2k.popt and prefix that with mpirun -n 8 to run it on 8 CPUs in parallel. So, a complete command line to run CP2K on 8 CPUs would then be:
mpirun -n 8 cp2k.popt -i yourinput.inp -o youroutput.out
How do I obtain a charge density difference?
In Exercise 2 a series of *.cube files was already produced for MOs.
To obtain the electronic charge density in a *.cube, file the following snippet of input file can be used (see also the reference manual):
&FORCE_EVAL
&DFT
&PRINT
&E_DENSITY_CUBE
&END E_DENSITY_CUBE
...
&END PRINT
... ...
&END DFT
&END FORCE_EVAL
The cubecruncher tool can be used to obtain charge density differences. A precompiled executable is available on the server tcopt3, its path being /users/scaravat/bin/cubecruncher.x.
The basic usage to obtain a charge density difference is:
$PATH/cubecruncher.x -i input.cube -o output.cube -subtract subsystem.cube