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exercises:2018_ethz_mmm:stm_2018 [2018/05/10 12:44] – dpasseroneexercises:2018_ethz_mmm:stm_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 =====Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination===== =====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> <code>
 tar -xvf exercise_10.tar tar -xvf exercise_10.tar
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 </code> </code>
 The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals. 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: into a single cube file:
  
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 </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:
 <note important> <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: and execute:
  
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 </note> </note>
 ===TASK_2=== ===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 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 repeating all the instructions of TASK_1 for the scripts present in the dir TASK_2
 <note warning> <note warning>
-Be careful: here we do a spin polarised 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  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. For these atoms three of the opposite terminus calling them C1 and C2. For these atoms
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 and note that the calculation is performed for a spin multiplicity of 1) 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> <code>
-222 +     78  
-    + 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> </code>
  
 </note> </note>
  
 +<note important>
 +Look at the KS orbitals (especially HOMO and LUMO) for both spin UP and DOWN
 +</note>
 <note important> <note important>
 Notice the difference between the images in TASK_2 and the images in TASK_1 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. 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 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> </note>
  
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