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--- exercise:simple_stm [2014/05/09 09:21] – dpasserone
+++ exercise:2014_ethz_mmm:simple_stm [2014/10/15 13:34] – oschuett
@@ Line 7: / Line 7: @@
 We will show how a simple change in the termination (1 vs. 2 Hydrogens) changes the state structure completely.
-{{ :exercise:2rib.jpg?direct&300 |}}
+{{ 2rib.jpg?direct&300 |}}
 <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_10.2.tar.gz|}}. The 1h.1.5.inp file is **commented**).
 </note>
@@ Line 20: / Line 20: @@
 <code>
     &PRINT
+! controls the printing of cubes for the generation of STM images.
     &STM
+! set of sample bias
+! negative for occupied states and positive for unoccupied states
       BIAS -2.0 -1.0 1.0 2.0
+! orbital symmetry of the tip
+! The change in the tip symmetry can radically alter the contrast of the topographic
+! image due to changes in tip-surface overlap
       TH_TORB S
     &END STM
+! print molecular orbitals
     &MO_CUBES
+! 10 occupied orbitals
        NHOMO 10
+! 10 unoccupied orbitals
        NLUMO 10
+! limit the size of cube files
        STRIDE 2 2 2
        WRITE_CUBE T
     &END
+! a cube file with eletrostatic potential generated by the total density (electrons+ions).
     &V_HARTREE_CUBE
     &END
       &MO
+! molecular orbitals eigenvalues and molecular ocuupations after each scf
        FILENAME EIG
+! add the last iteration with description
        ADD_LAST NUMERIC
+! printing of eigenvalues of molecular orbitals
        EIGENVALUES
+! also print occupation of the molecular orbitals
        OCCUPATION_NUMBERS
       &END
@@ Line 45: / Line 60: @@
-<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 78: @@
 <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>