Through comprehensive density functional calculations, the crystallographic, magnetic and electronic properties of $Na_xCoO_2$ ($x$ = 1, 0.875, 0.75, 0.625 and 0.50) were investigated. We found that all Na ions in $NaCoO_2$ and $Na_{0.875}CoO_2$ share the basal coordinates with O ions. However, as $x$ decreases, some of Na ions move within the basal plane in order to reduce the in-plane Na$-$Na electrostatic repulsion. Magnetically, there was strong tendency for type A antiferromagnetism in the $Na_{0.75}CoO_2$ system, while all other Na deficient systems had a weaker ferromagnetic tendency. The results on magnetism were in excellent agreement with the experiments.
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