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exercises:2017_uzh_cmest:stm [2017/11/08 10:32]
tmueller [Calculating the nanoribbon]
exercises:2017_uzh_cmest:stm [2018/01/13 23:14] (current)
jglan [Generating the STM image]
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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: <​code>​tar xf /​users/​tiziano/​CHE437_ex7.tar.gz</​code>​   * 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: <​code>​tar xf /​users/​tiziano/​CHE437_ex7.tar.gz</​code>​
-  * The scripts are contained in yet another python package: <​code>​pip install --user https://​github.com/​ltalirz/​asetk/​archive/​master.zip</​code>​... and since you have setup the path variable in [[exercises:​2017_uzh_cmest:​phonon_calculation|a previous exercise]], you should now have the following new commands available: ''​stm.py'',​ ''​cube-plot.py'',​ ''​cp2k-sumbias.py''​.+  * The scripts are contained in yet another python package: <​code>​pip install --user https://​github.com/​ltalirz/​asetk/​archive/​master.zip</​code>​... and since you have setup the path variable in [[exercises:​2017_uzh_cmest:​phonon_calculation|a previous exercise]], you should now have the following new commands available: ''​stm.py'',​ ''​cube-plot.py'',​ ''​cp2k-sumbias.py''​. If the installation fails, make sure that you do **not** have the CP2K module loaded: ''​module list''​ should return an empty list. To explicitly unload the CP2K module, run ''​module unload cp2k''​.
  
 ===== 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 ​by using '​tee'​
 </​code>​ </​code>​
  
-The parameters ''​--vmin'',​ ''​--vmax''​ and ''​--vstep''​ determine which bias voltages for the tip (the potential between the substrate/​molecule and the tip) you want to simulate ​(in our case $-2.0$, $-1.5$, ... $2.0$).+The parameters ''​--vmin'',​ ''​--vmax''​ and ''​--vstep''​ determine which bias voltages for the tip (the potential between the substrate/​molecule and the tip) you want to simulatein our case $-2.0$, $-1.5$, ... $2.0$.
  
-It is important to note that for a given bias voltage, for example $-2.0$ (current from the substrate/​molecule ​towards ​the tip) all orbitals with an energy between $-2.0 eV$ and $0 eV$ have to be taken into account.+It is important to note that for a given bias voltage, for example $-2.0$ (current ​goes from the substrate/​molecule ​to the tip) all orbitals with an energy between $-2.0 eV$ and $0 eV$ have to be taken into account.
  
 At this point you should have a new set of combined CUBE files: ''​stm_-2.00V.cube''​..''​stm_+0.00V.cube''​..''​stm_+2.00V.cube'',​ one for each bias voltage, containing the respective electron density. At this point you should have a new set of combined CUBE files: ''​stm_-2.00V.cube''​..''​stm_+0.00V.cube''​..''​stm_+2.00V.cube'',​ one for each bias voltage, containing the respective electron density.
  
-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 ''​stm_*V.cube.iso1e-07.png''​:
  
 <code bash> <code bash>
-# zcut is the minim z-height+# 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
 </​code>​ </​code>​
- 
-Which should give you a set of files ''​stm_*V.cube.iso1e-07.png''​. 
  
 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 ยท Last modified: 2017/11/08 10:32 by tmueller