Show Posts
1
General Questions and Answers / PBC in A/B directions still working for molecule between electrodes?
« on: September 14, 2012, 09:50 »
I'm calculating the transmission spectrum of Au/Molecule/Au systems.
Since the molecule is large (hundreds of atoms
), I make a supercell quite “crowded” in A/B directions to save time.
After relaxation in VASP(it's faster in convergence?) , some H atoms in the molecule go across the boundary in A or B direction and VASP make a translation of them to make them within the supercell (still in bond with a C atom and far away from others), just like the molecule cut by the bounday.
ATK gives extremely large transmission in that case.
However, if I translate these separate H atoms back to form a complete molecule in VNL window, the transmission is reasonable(not sure, no similar publications
).
So how does this happen? Does the periodic boundary condition still working? Or I need to increase A/B length to prevent this from happening?
Thank you for any advice.
Since the molecule is large (hundreds of atoms
), I make a supercell quite “crowded” in A/B directions to save time.After relaxation in VASP(it's faster in convergence?) , some H atoms in the molecule go across the boundary in A or B direction and VASP make a translation of them to make them within the supercell (still in bond with a C atom and far away from others), just like the molecule cut by the bounday.
ATK gives extremely large transmission in that case.
However, if I translate these separate H atoms back to form a complete molecule in VNL window, the transmission is reasonable(not sure, no similar publications
). So how does this happen? Does the periodic boundary condition still working? Or I need to increase A/B length to prevent this from happening?
Thank you for any advice.