Dear SIESTA users,
I now calculate molecule A and then the other calculation putting
molecule A on a metal surface. I do the PDOS for molecule A in both
calculations. If I want to see how the PDOS evolute after absorbing on a
surface, I need to compare the PDOS of molecule in both cases.
1. As Marcos suggested here
(http://www.mail-archive.com/siesta-l%40uam.es/msg02720.html), I can
compare the PDOS after shifting the Fermi energy to zero for both
calculations separately. But I think this may not correct, because the
zero energy reference in the two calculation may be different, that is,
the energy for the vacuum in the two calculation may be different.
2. To do this, Min Gao has suggested here
(http://www.mail-archive.com/siesta-l%40uam.es/msg02719.html) to put
molecule A, molecule A+surface in one calculation, where molecule A does
not interact with molecule A+surface. Then there is only one zero energy
reference in one calculation. So the PDOS of the molecule A can be
compared directly with the PDOS of absorbed molecule A. However, this
method would give a larger simulation box and consequently a larger
computation.
3. As I know, if we want to get the work function of a metal, we should
do a calculation for a slab. After the simulation we get the Fermi
energy E_f and also we should find the energy of the vacuum E_vac, then
(E_f - E_vac) will be the calculated work function. Inspired by this, I
think I can find the energy of the vacuum E_vac1 for molecule A and and
E_vac2 for molecule A+surface, then the PDOS can be compared by shifting
E_vac1 and E_vac2 respectively. Am I right?
Please correct me if there is something wrong.
/Guangping
