exercises:2017_uzh_cmest:stm
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exercises:2017_uzh_cmest:stm [2017/11/08 10:05] – [Generating the STM image] tmueller | exercises:2017_uzh_cmest:stm [2017/11/10 15:06] – [Preparation] tmueller | ||
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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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===== Calculating the nanoribbon ===== | ===== Calculating the nanoribbon ===== | ||
- | To get the actual electron density, we are now going to run a full DFT calculation using a large basis set ('' | + | 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 ('' | This calculation will take a while to finish: run it in parallel using 4 processes ('' | ||
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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 |
</ | </ | ||
- | At this point you should | + | 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> | <code bash> | ||
+ | # zcut is the minimum z-height | ||
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 images '' | + | Why are there no images for certain bias voltages? Would you expect the same for a metallic substrate? |
exercises/2017_uzh_cmest/stm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1