Guangcun's Blog分享 http://blog.sciencenet.cn/u/gcshan 哥伦比亚大学访问学者,香港城市大学校董 (2011-2012)

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Simulated STM

已有 2739 次阅读 2014-3-26 02:14 |个人分类:科学札记|系统分类:科研笔记| STM

Simulated STM using VASP

Quick Description of STM: Scanning Tunneling Microscopy (STM) functions via quantum tunneling. When two conductive materials are brought very close to each other (within a few angstroms), applying a bias voltage between the two materials will allow electrons to tunnel through the vacuum space between them. This flow of electrons is referred to as tunneling current and is dependent on three factors: the vacuum distance, the applied voltage, and the local density of states (LDOS). Because tunneling current exhibits an exponential relationship with distance, the tunneling signal is dominated by the current between the two closest atoms between the materials and thus exhibits atomic-scale resolution. For reduced noise, it is thus ideal to have an atomically sharped tip that scans of the sample of interest. Depending on the bias (positive or negative), electrons will either tunnel from sample to tip or from tip to sample. Functionally, a feedback system is used such that tip-sample distance (measured as height along the z-axis)is readjusted during scanning (a raster over x- and y- axes) of the sample to produce a constant current. In this manner, the topography of the sample is measured, thus enabling atomic-scale imaging of the sample.

The Point: Simulated STM creates an atomic scale image based off of computer-based model system. Generally, we can use simulated STM as a test device for evaluating the accuracy of the model. Should the model reproduce characteristic features displayed in experimental images, we are provided with some level of confirmation for the understanding of our sample system.
Prerequisites: An optimized model with a PARCHG file.

Notes: Traditionally, our lab uses much of the Mathematica code developed by Jon. We can also use VESTA to simply open the PARCHG file.

Mathematica:
  1. Use the function chgData = ReadPARGHG[<filepath>] to read out the charge values

  2. Display the simulated STM with iso = DispIsoSurf[chgData, .1, SphereScale -> .2]

    • adjust parameters as necessary

  3. Use additional options to make the image more viewable. e.g...

    • maxCell = cell[[1]] + cell[[2]] + cell[[3]];

    • Show[ iso, PlotRange -> {{0, maxCell[[1]]}, {0, maxCell[[2]]},(*z-range:*){Surf[atoms] + .25, Surf[atoms] + 4}}, ImageSize -> 800 ]

VESTA (notes provided by Mark Micklich):
  1. Open CHGCAR

  2. Utilities > 2D Data Display

  3. Press the "Slice" button and confirm "OK"

HIVE (email Danny Vanpoucke for the program and manual):
"The HIVE-STM program is a small piece of software ...to generate STM images based on ... DFT-calculations. Starting from ab-initio VASP calculations, it uses the resulting output to allow the simulation of an STM experiment on your simulated model."




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