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exercises:2018_ethz_mmm:stm_2018

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exercises:2018_ethz_mmm:stm_2018 [2018/05/10 12:32] – 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> 
-<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> <code>
 tar -xvf exercise_10.tar tar -xvf exercise_10.tar
Line 68: Line 82:
  
  
-Now go to the STM directory andsubmit the run script+Now go to the directorySTM
 <code> <code>
-qsub run+cd STM
 </code> </code>
-The program will compute the 10 highest and 10 lowest KS orbitals. +and have a look to the input file cp2k.inp used to converge the 
-You can produce a contour plot of each orbital on a plane ~2A above the ribbon running a pyhton script: +wavefunction of the system and to plot the cube files for the KS orbitals. 
 +Execute the program
 <code> <code>
-./plotorbitals.sc+cd STM 
 +./run
 </code> </code>
-I will also show you how to visualize the orbitals with VMD.+The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals. 
 +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:
  
 <code> <code>
-qsub run_sumbias+./run_sumbias
 </code> </code>
 you will then obtain a cube file for each desired bias voltage (see the script run_sumbias) you will then obtain a cube file for each desired bias voltage (see the script run_sumbias)
  
-Now you can compuyte a constant current STM image runnong the script+Now you can compute a constant current STM image running the script
  
 <code> <code>
-qsub run_stm+./run_stm
 </code> </code>
  
 Please note that we are simulating a molecule, we do not include the electrons of the substrate Please note that we are simulating a molecule, we do not include the electrons of the substrate
-thus we have a disceret spectrum of energies and it is quite likely that for  values of the bias voltage +thus we have a discrete spectrum of energies 
-that fall in the HOMO-LUMO gap we will obtain an empty image+
  
-Now we can simulate for teh same ribbon a AFM image: +<note warning> 
-Go the the AFM directory of TASK_1 +why some of the STM images look empty? 
-copy there the p.xyz file that you find in the STM directory+</note> 
 +</note> 
 + 
 +Now we can simulate for the same ribbon a nc-AFM image: 
 +<note important> 
 +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: and execute:
  
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 </code> </code>
 It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image. It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image.
 +</note>
 ===TASK_2=== ===TASK_2===
-Repeat all the instructions of TASK_1 for the scripts present in the dir TASK_2+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> <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  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> <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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