wrong definition of Fermi energy in MPSH calculation?

[jhwang]

Dear all users:
I encountered with one quesition when I performed MPSH calculations
I projected the Hamiltonian to the scattering region with 80 C and 24 H atoms, which means that there are 344 valence electrons in total.
However, when I check the MPSH energy spectrum I found 176 orbitals with negative energy, which means that there are 352 valence electrons under Fermi level, and it is contradictory to the previous total number of 344 electrons in the scattering region.
Is the equivalent atoms in the electrode was accounted into the MPSH calculation? or other reasons?

[zh]

There are several points should be clarified:
i) Do you know what is the reference of zero-point energy for MPSH? i.e., why are you sure that the negative value of MPSH means the corresponding energy level should be located below the Fermi level of your two-probe system?
ii) What is the reference of Fermi level in your two-probe system you are talking about?
iii) When the atoms in the scattering region are coupled with two electrodes, they are not isolated. This means that charge transfer could happen nears the contacts between scattering region and electrodes.