Differences

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

--- exercises:2017_uzh_cmest:stm [2017/11/08 10:32] – [Calculating the nanoribbon] tmueller
+++ exercises:2017_uzh_cmest:stm [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ 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>
-  * 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 =====
@@ Line 37: / Line 37: @@
 ===== Generating the STM image =====
 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!
 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>
-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.
-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>
-# zcut is the minim z-height
+# zcut is the minimum z-height
 stm.py --stmcubes stm_*.cube --isovalues 1.0e-7 --zcut 22 --plot
 </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?