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I have a molecule above a slab. I've broken this into 3 systems: 1) the full system of molecule and slab, 2) the slab and 3) just the molecule. Each one runs successfully. However, the CHGCAR files are different sizes, and I want to use VESTA to produce charge density difference images, by subtracting the 3 systems.

I use the same KPOINTS file, with a 3x3x1 Monkhorst-pack grid. NGX, Y, and Z appear to be the same (112, 112, 140), in the vasprun.xml file. What other setting do I need to ensure that all 3 systems will have the same size CHGCAR?

Thanks,
Mark

At the end of CHGCAR augmentaion occupancies are written, which depend on atom types.
Therefore is the size of CHGCAR of your three systems different.
Because augmentation occupancies are for displaying of the electron density not important
you can delete this additional information and you will get CHGCARs of the same size.