Differences

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

--- exercise:simple_stm [2014/05/09 09:21] – dpasserone
+++ exercise:simple_stm [2014/06/10 00:27] – dpasserone
@@ Line 10: / Line 10: @@
 <note tip>
 You should run these calculations on 16 nodes with ''bsub -n 16''.
-Copy, as usual, the files from the directory **/cluster/home03/matl/danielep/LECTURE10/EXERCISE_10.2** (and later here on the media manager).
+Download, as usual, the files from the media manager: {{:exercise:exercise_10.2.tar.gz|}}. The 1h.1.5.inp file is **commented**).
 </note>
@@ Line 45: / Line 45: @@
-<note tip>Hitting ** ls -ltr ** will allow you to see on the last lines of the screen the most recent files.</note>
+<note tip>
+Hitting ** ls -ltr ** will allow you to see on the last lines of the screen the most recent files.
+</note>
+<note important>
-<note important>  - Draw the energy level diagram for the two molecules. What is the energy gap in the two cases? What are the differences?
+  - Draw the energy level diagram for the two molecules. What is the energy gap in the two cases? What are the differences?
-  - Look with vmd at the cube files corresponding to the most interesting levels (close to Fermi...). Comment on the distribution of the states.</note>
+  - Look with vmd at the cube files corresponding to the most interesting levels (close to Fermi...). Comment on the distribution of the states.
+</note>
 ===== 2. Task: Producing a simple STM image =====
@@ Line 60: / Line 63: @@
 <code>
 Run the program in the following way:
-> stm -c 2h*STM*.cube --isovalues 1E-5 > stm.out
+$ module load boost/1.54.0
+$ module load mkl
+$ stm -c 2h*STM*.cube --isovalues 1E-5 > stm.out
 </code>
 The resulting .igor files contain the z profile (in bohr) and may for example be plotted by gnuplot:
+<code>
+gnuplot
+set pm3d map
+set size square
+set xrange [......
+set yrange [.....
+splot "mystm.igor" matrix using 2:1:3
+</code>
+Where instead of "mystm" you use an appropriate filename.
+<note important>
+  - In the output file of cp2k, the program tells you how many states have contributed to each STM image. Discuss the images that you see in the two cases.
+  - What makes the 1h* case particular with respect to the 2h*?
+  - Change the isosurface and look at the z-range. Discuss the changes in the range.
+  - Would you define the differences between 1h and 2h in the STM images as more of structural origin or electronic origin?
+</note>