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--- exercises:2018_ethz_mmm:stm_2018 [2018/05/10 13:04] – dpasserone
+++ exercises:2018_ethz_mmm:stm_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 =====Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination=====
-download from the tar file exercise_10.tar, move the file to your exercise directory, and extract the content
+<note warning>
+In case you do not want to use the quantum-mobile VM, you will need to install the asetk and ProbeParticle packages:
+<code>
+git clone https://github.com/ltalirz/asetk
+pip install -e asetk
+</code>
+and
+<code>
+git clone https://github.com/ProkopHapala/ProbeParticleModel.git
+cd ProbeParticleModel/
+git checkout dev
+</code>
+</note>
+download from [[https://polybox.ethz.ch/index.php/s/CH5VdcI40YdELez|here]] the tar file exercise_10.tar, move the file to your exercise directory, and extract the content
-connect to hypatia:
 <code>
 tar -xvf exercise_10.tar
@@ Line 80: / Line 94: @@
 </code>
 The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals.
-visualize the orbitals with VMD
+Visualize the orbitals with VMD (remember **+** and **-**)
@@ Line 108: / Line 122: @@
 Now we can simulate for the same ribbon a nc-AFM image:
 <note important>
-Go the the AFM directory of TASK_1
+Go the the AFM directory of TASK_1 (and have a look to the parameter file params.ini)
-copy there the p.xyz file that you have  in the STM directory
+copy there the p.xyz file that you havein the STM directory
 and execute:
@@ Line 162: / Line 176: @@
 </note>
+<note important>
+Look at the KS orbitals (especially HOMO and LUMO) for both spin UP and DOWN
+</note>
 <note important>
 Notice the difference between the images in TASK_2 and the images in TASK_1