We address here general issues and show how to properly extract the local charge order in two-dimensional systems from scanning tunneling microscopy/spectroscopy (STM/STS) measurements. When the charge order presents spatial variations at the atomic scale inside the unit cell and is energy dependent, particular care should be taken. We show that the widely used lock-in technique performed while acquiring an STM topography in a closed feedback loop cannot be used to extract this local charge order from STS $dI/dV$ differential conductance maps. In such situations, the use of the lock-in technique leads to systematically incorrect $dI/dV$ measurements, giving a false local charge order. We show that a correct method is either to perform a constant height measurement or to perform a full grid of $dI/dV(V)$ spectroscopies, using a set point for the bias voltage outside the bandwidth of the correlated material where the local density of states (LDOS) is expected to be spatially homogeneous. We take as a paradigmatic example of two-dimensional material the 1/3 single-layer Pb/Si(111) phase. As large areas of this phase cannot be grown, charge ordering in this system is not accessible to angular resolved photoemission or grazing x-ray diffraction. Two previous investigations by STM/STS supplemented by ab initio density functional theory (DFT) calculations concluded that this material undergoes a phase transition to a low-temperature $3\ifmmode\times\else\texttimes\fi{}3$ reconstruction where one Pb atom moves up, the two remaining Pb atoms shifting down. A third STM/STS study by Adler et al. [F. Adler, S. Rachel, M. Laubach, J. Maklar, A. Fleszar, J. Sch\"afer, and R. Claessen, Phys. Rev. Lett. 123, 086401 (2019)] came to the opposite conclusion, i.e., that two Pb atoms move up, while one Pb atom shifts down. We show that this latter erroneous conclusion comes from an artifact induced by the lock-in technique. In contrast, using a full grid of $dI/dV$($V$) spectroscopy measurements, our results show that the energy-dependent LDOS maps agree very well with state-of-the-art DFT calculations, confirming the one-up two-down charge ordering. We show that this structural and charge reordering inside the $3\ifmmode\times\else\texttimes\fi{}3$ unit cell is equally driven by electron-electron interactions and the coupling to the substrate.
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