exercises:2017_uzh_cmest:stm
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exercises:2017_uzh_cmest:stm [2017/11/08 10:32] – [Calculating the nanoribbon] tmueller | exercises:2017_uzh_cmest:stm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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* On the server is a package for you to unpack (hohoho ;-)), containing a number of input files. Run the following in a new and empty directory: < | * On the server is a package for you to unpack (hohoho ;-)), containing a number of input files. Run the following in a new and empty directory: < | ||
- | * The scripts are contained in yet another python package: < | + | * The scripts are contained in yet another python package: < |
===== Geometry optimization ===== | ===== Geometry optimization ===== | ||
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===== Generating the STM image ===== | ===== Generating the STM image ===== | ||
+ | |||
To get an actual STM image, we now have to combine the wavefunctions into a single one: | To get an actual STM image, we now have to combine the wavefunctions into a single one: | ||
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# use your output file of the full DFT calculation as your levelsfile! | # 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 | 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 | + | # and pipe the output to the file sumbias.out and the screen simultaneously |
</ | </ | ||
- | The parameters '' | + | The parameters '' |
- | It is important to note that for a given bias voltage, for example $-2.0$ (current from the substrate/ | + | It is important to note that for a given bias voltage, for example $-2.0$ (current |
At this point you should have a new set of combined CUBE files: '' | At this point you should have a new set of combined CUBE files: '' | ||
- | From these we can finally generate the actual STM images: | + | From these we can finally generate the actual STM images, which should give you a set of files '' |
<code bash> | <code bash> | ||
- | # zcut is the minim z-height | + | # zcut is the minimum |
stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot | stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot | ||
</ | </ | ||
- | |||
- | Which should give you a set of files '' | ||
Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate? | Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate? |
exercises/2017_uzh_cmest/stm.1510137121.txt.gz · Last modified: 2020/08/21 10:15 (external edit)