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I am trying to calculate cohesive energy of a bulk structure by subtracting the total energy of atom from that of bulk.

I find the total energy of some atom with PAW potential
is positive. For example, PBE-PAW potential of Ca gives a positive energy.

In this case, the cohesive energy should be meaningless ?

Which factor in the pseudization is related to this positive total energy of atom ?

you must have done something wrong in your calculation, both PAW-PBE Ca potentials give negative total energies for the free atoms.
please check your
box size
KPOINTS (Gamma only!)
smearing parameter (SIGMA has to be small to give discrete atomic levels)