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exercises:2018_ethz_mmm:stm_2018 [2018/05/09 16:39] – created 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 a graphene nanoribbons adsorbed on a metallic substrate===== +=====Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination===== 
- +<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> <code>
-ssh -X EMPA-USER@jump1.empa.ch +git clone https://github.com/ltalirz/asetk 
-ssh -X hypatia +pip install -e asetk 
-</code> +</code> 
 +and
 <code> <code>
-module load python/2.7.12 +git clone https://github.com/ProkopHapala/ProbeParticleModel.git 
 +cd ProbeParticleModel/ 
 +git checkout dev
 </code> </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
  
  
-**go to your scratch directory:** 
 <code> <code>
-cd /mnt/scratch/your_username+tar -xvf exercise_10.tar 
 +cd exercise_10 
 </code> </code>
-and copy there the tar file of the exercise: + 
-<code> + 
-cp /home/cpi/exercise_12.tar ./ +
-tar -xvf exercise_12.tar +
-cd exercise_12 +
-</code> +
-</note>+
  
 We consider two possible chemical terminations for a finite size 7-AGNR. We consider two possible chemical terminations for a finite size 7-AGNR.
Line 31: Line 32:
  
 ===TASK_1=== ===TASK_1===
 +<code>
 +cd TASK_1
 +</code>
 +
 Have a look to the cp2k input file cp2k.inp Have a look to the cp2k input file cp2k.inp
 used to obtain quickly the optimized geometry of a ribbon adsorbed on a Au substrate. used to obtain quickly the optimized geometry of a ribbon adsorbed on a Au substrate.
 The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled
 via Embedded Atom Model. via Embedded Atom Model.
-An empirical potential in teh form of C6/R^6 plus a pauli repulsion +An empirical potential in the form of C6/R^6 plus a Pauli repulsion term 
-is added to couple the adsorbate/substrate systems.+are added to couple the adsorbate/substrate systems.
  
  
 Two geometry fiels are present: mol.xyz and all.xyz Two geometry fiels are present: mol.xyz and all.xyz
-The input needs both of them.+The cp2k program will need both of them.
  
-Have a look at the geometry of the system using ASE:+Have a look at the geometry of the system using ASE or vmd 
 +for both all.xyz and mol.xyz:
  
 <code> <code>
Line 58: Line 64:
  
 <note important> <note important>
-submit the geometry optimization run+submit the geometry optimisation run
 <code> <code>
-qsub run+./run
 </code> </code>
  
 +
 +Have a look at the final geometry optained (you can extract the last frame from
 +the file PROJ-pos-1.xyz)
 After completion of the optimization you should extract the final coordinates of the molecule After completion of the optimization you should extract the final coordinates of the molecule
-and copy them in the STM directory to compute the KS orbitals and to ocmpute the STM images +(first 80 atoms) and copy them in the STM directory (call them p.xyz) to compute the KS orbitals  
-you can extract the coordinates running the following script:+and to compute the STM images 
 <code> <code>
-./pos.sc+tail -442 PROJ-pos-1.xyz | head -82 > p.xyz 
 +mv p.xyz STM
 </code> </code>
-</note> 
  
-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:
  
Line 110: Line 130:
 </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>
  
exercises/2018_ethz_mmm/stm_2018.1525883960.txt.gz · Last modified: 2020/08/21 10:15 (external edit)