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--- exercises:2018_ethz_mmm:stm_2018 [2018/05/10 12:40] – dpasserone
+++ exercises:2018_ethz_mmm:stm_2018 [2018/05/10 17:22] – dpasserone
@@ 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>
-<note important>
+In case you do not want to use the quantum-mobile VM, you will need to install the asetk and ProbeParticle packages:
-connect to hypatia:
+<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
 <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 **-**)
-To obtain teh stm images you have to combine different KS orbitals (depending on the bias voltage applied)
+To obtain the STM images you have to combine different KS orbitals (depending on the bias voltage applied)
 into a single cube file:
@@ Line 102: / Line 116: @@
 <note warning>
-why some of the STM images look empty?</note>
+why some of the STM images look empty?
+</note>
+</note>
-Now we can simulate for teh same ribbon a nc-AFM image:
+Now we can simulate for the same ribbon a nc-AFM image:
-Go the the AFM directory of TASK_1
+<note important>
-copy there the p.xyz file that you have  in the STM directory
+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 havein the STM directory
 and execute:
@@ Line 113: / Line 130: @@
 </code>
 It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image.
+</note>
 ===TASK_2===
-Modify the geometry of TASK_1 removing one H atom from each C-H2 at the termini of the ribbon.
+Modify the geometry of TASK_1 removing one H atom from each C-H2 at the termini of the ribbon (remove two H atoms in total).
 Create the corresponding mol.xyz and all.xyz files, optimize the geometry, compute STM and nc-AFM images
 repeating all the instructions of TASK_1 for the scripts present in the dir TASK_2
 <note warning>
-Be carefulhere we do a spin polarized simulation,
+Be careful: here we do a spin polarised simulation. **When doing the STM simulation (ONLY for the STM)**
 we have to distinguish the three C atoms of one terminus of the ribbon from the
-three of the opposite terminus calling them C1 and C2.
+three of the opposite terminus calling them C1 and C2. For these atoms
+we will define a guess electronic configuration with spin up on one side and spin down on the opposite side.
+This is achieved defining a occupation unbalance in the alpha and beta orbitals (try to identify this section of the input
+and note that the calculation is performed for a spin multiplicity of 1)
-When the file p.xyz is created in the STM dir (after running ./pos.sc)
+The file p.xyz in teh STM directory should look similar to:
-copy it immediateli to the AFM dir.
-Now, before executing the instructions for the STM dir
-edit the file p.xyz and modify it in such a way that
-the first three C atoms will be labelled as C1
-and the C atoms from 4 to 6 will be labelled as C2
 <code>
+ i =       49, E =      -140.2738100175
-  C1        6.0848407282        7.8280098155       21.6125989354
+  H         4.2914607718       10.2130614763       21.2815435017
-  C1        6.0865671686       12.7633436664       21.6071222309
+  H         4.2778729017        7.7509218987       21.2954986738
-  C1        6.1020007836       10.2957686990       21.6036624306
+  H         4.2782723704       12.6751364096       21.2955091278
-  C2       56.3447906713       10.2958157091       21.6033852713
+  C         7.4704758534        6.5236639413       21.2352922076
-  C2       56.3619529363        7.8280149623       21.6128774460
+  .
-  C2       56.3601930737       12.7634261117       21.6063533886
+  .
-  H         4.9837063610        7.8327959357       21.5912164696
+  .
-  H         4.9855872642       12.7623732365       21.5844580428
+  C1        5.3788157746        7.7465647443       21.2687198580
+  .
+  .
+  C1        5.3936844253       10.2129317839       21.2797918647
+  .
+  .
+  C1        5.3792136407       12.6792819903       21.2687263656
+  .
+  .
+  .
+  C2       21.1530397078        7.7456205579       21.2687376504
+  .
+  C2       21.1385072480       10.2118877383       21.2797955201
+  .
+  C2       21.1533012965       12.6781430186       21.2687326678
+  .
+  .
 </code>
 </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
 In TASK_2 we have KS states localised at the termini of the ribbon.
 These states are suppressed by the addiitonal H atoms in TASK_1
+</note>
+<note important>
+why some STM images are remarkably asymmetric? Is this correct?
 </note>