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exercises:2017_uzh_cmest:stm [2017/11/08 10:30] – [Generating the STM image] tmuellerexercises: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: <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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 # 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 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 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1