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exercises:2017_uzh_cmest:stm [2017/11/08 10:05]
tmueller [Generating the STM image]
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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 ===== 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 (''​TZV2P''​) on the nanoribbon geometry. This time, the input ''​nanoribbon.inp''​ is similar to what you are used to, except the fact that to to speed the calculation ​up, we use the wavefunctions from the previous calculation as a starting point (the ''​RESTART_FILE_NAME''​ option).+To get the actual electron density, we are now going to run a full DFT calculation using a large basis set (''​TZV2P''​) on the nanoribbon geometry. This time, the input ''​nanoribbon.inp''​ is similar to what you are used to, except ​for the fact that to speedup ​the calculation,​ we use the wavefunctions from the previous calculation as a starting point (the ''​RESTART_FILE_NAME''​ option).
  
 This calculation will take a while to finish: run it in parallel using 4 processes (''​mpirun -np 4 ...''​) and in the background. This calculation will take a while to finish: run it in parallel using 4 processes (''​mpirun -np 4 ...''​) and in the background.
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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>​
  
-At this point you should ​then have a new set of combined CUBE files: ''​stm_+0.00V.cube'' ​... ''​stm_+2.00V.cube'',​ one for each bias voltage. From this we can finally generate the actual STM images:+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 $-2.0$, $-1.5$, ... $2.0$. 
 + 
 +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. 
 + 
 +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 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 images ''​stm_*V.cube.iso1e-07.png''​.+Why are there no images for certain bias voltages? Would you expect the same for metallic substrate?
exercises/2017_uzh_cmest/stm.1510135501.txt.gz · Last modified: 2017/11/08 10:05 by tmueller