exercises:2017_uzh_cmest:stm
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exercises:2017_uzh_cmest:stm [2017/11/08 08:02] – tmueller | exercises:2017_uzh_cmest:stm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== Preparation ===== | ===== Preparation ===== | ||
- | * On the server is a package for you to unpack: '' | + | * On the server is a package for you to unpack |
- | * The scripts are contained in yet another python package: | + | * The scripts are contained in yet another python package: |
+ | |||
+ | ===== Geometry optimization ===== | ||
+ | |||
+ | First take a look at the complete geometry in '' | ||
+ | |||
+ | Like with the geometry optimization in the previous examples, you now should have a file '' | ||
+ | From this we have to extract only the molecule into a new '' | ||
+ | |||
+ | <code bash> | ||
+ | echo " | ||
+ | echo " | ||
+ | tail -n 1064 nanoribbon-geo_opt-pos-1.xyz | head -n 224 >> nanoribbon.xyz | ||
+ | </ | ||
+ | |||
+ | ===== Calculating the nanoribbon ===== | ||
+ | |||
+ | To get the actual electron density, we are now going to run a full DFT calculation using a large basis set ('' | ||
+ | |||
+ | This calculation will take a while to finish: run it in parallel using 4 processes ('' | ||
+ | |||
+ | At the end of it, you can visualize the orbitals using either VMD as shown in previous exercises, or using one of the scripts provided in the newly installed Python package, which will generate a series of images ('' | ||
+ | |||
+ | <code bash> | ||
+ | cube-plot.py --cubes *WFN*.cube --plot --position 22 # the position for the contour plot should be 2 angstrom above the surface | ||
+ | </ | ||
+ | |||
+ | ===== Generating the STM image ===== | ||
+ | |||
+ | To get an actual STM image, we now have to combine the wavefunctions into a single one: | ||
+ | |||
+ | <code bash> | ||
+ | # use your output file of the full DFT calculation as your levelsfile! | ||
+ | cp2k-sumbias.py --cubes *WFN*.cube --levelsfile nanoribbon.out --vmin -2.0 --vmax 2.0 --vstep 0.5 | tee sumbias.out | ||
+ | # and pipe the output to the file sumbias.out and the screen simultaneously by using ' | ||
+ | </ | ||
+ | |||
+ | The parameters '' | ||
+ | |||
+ | It is important to note that for a given bias voltage, for example $-2.0$ (current goes from the substrate/ | ||
+ | |||
+ | At this point you should have a new set of combined CUBE files: '' | ||
+ | |||
+ | From these we can finally generate the actual STM images, which should give you a set of files '' | ||
+ | |||
+ | <code bash> | ||
+ | # zcut is the minimum z-height | ||
+ | stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot | ||
+ | </ | ||
+ | |||
+ | Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate? |
exercises/2017_uzh_cmest/stm.1510128121.txt.gz · Last modified: 2020/08/21 10:15 (external edit)