User Tools

Site Tools


exercises:2017_uzh_cmest:stm

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
exercises:2017_uzh_cmest:stm [2017/11/08 10:33]
tmueller [Generating the STM image]
exercises:2017_uzh_cmest:stm [2018/01/13 23:14] (current)
jglan [Generating the STM image]
Line 9: Line 9:
  
   * 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 =====
Line 37: Line 37:
  
 ===== 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:
  
Line 43: Line 43:
 # 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>​
  
exercises/2017_uzh_cmest/stm.1510137237.txt.gz ยท Last modified: 2017/11/08 10:33 by tmueller