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exercises:2017_ethz_mmm:mc_and_kmc_2 [2017/03/09 12:41] – dpasseroneexercises:2017_ethz_mmm:mc_and_kmc_2 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 =====  ===== 
  
-The hexaiodobenzene molecule shown in the image, when deposited on a noble metal substrate such as+The  molecule shown in the image (hexaiodo-substituted 
 +macrocycle cyclohexa-m-phenylene (CHP) ), when deposited on a noble metal substrate such as
 Cu(111) , Ag(111) or Au(111), at room temperature looses the I atoms and starts diffusing. Cu(111) , Ag(111) or Au(111), at room temperature looses the I atoms and starts diffusing.
 +
 +
 +{{:exercises:2017_ethz_mmm:hexaiodobenzene.jpg?400|}}
 +
 The relative probability of diffusion and of binding to a neighboring molecule The relative probability of diffusion and of binding to a neighboring molecule
 determine the shape of the network that will be obtained. determine the shape of the network that will be obtained.
 The experiments performed at Empa [ [[http://dx.doi.org/10.1021/ja107947z]] J. AM. CHEM. SOC. 2010, 132, 16669–16676 ] shows that on a Cu substrate dendrites will form The experiments performed at Empa [ [[http://dx.doi.org/10.1021/ja107947z]] J. AM. CHEM. SOC. 2010, 132, 16669–16676 ] shows that on a Cu substrate dendrites will form
 while on a Au substrate 2D networks will form. while on a Au substrate 2D networks will form.
 +
 +{{:exercises:2017_ethz_mmm:dendrites.jpg?400|}}
 +
 <note tip> <note tip>
 The python program KMC.py will allow you to simulate the diffusion and binding of molecules The python program KMC.py will allow you to simulate the diffusion and binding of molecules
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 During the execution the program shows snapshots of the positions of the molecules. During the execution the program shows snapshots of the positions of the molecules.
 +
 +{{:exercises:2017_ethz_mmm:final_0.1_300_0.1_0.1.png?400|}}
 +
 Molecules free to diffuse will be represented via blue dots. Molecules free to diffuse will be represented via blue dots.
 Molecules that irreversibly formed a bond with a neighboring molecule will be represented by red dots. Molecules that irreversibly formed a bond with a neighboring molecule will be represented by red dots.
 At the end of the execution a snapshot of the final configuration of the system is saved an image file. At the end of the execution a snapshot of the final configuration of the system is saved an image file.
 The program asks you for some input: The program asks you for some input:
 +
 <code>  <code> 
 coverage coverage
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 binding barrier binding barrier
 </code> </code>
 +
 </note> </note>
 <note warning> <note warning>
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 <code> <code>
 coverage 0.1 coverage 0.1
-update graph each steps 10+update graph each steps 500
 number of steps 100000 number of steps 100000
 temperature in K 300 temperature in K 300
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 binding barrier 0.1 binding barrier 0.1
 </code> </code>
-Observe how events occurr.+Observe how events occur.
 Observe how time evolves. Observe how time evolves.
 Did the job perform all the 100000 steps? Why? Did the job perform all the 100000 steps? Why?
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 <code> <code>
 coverage 0.1 coverage 0.1
-update graph each steps 100+update graph each steps 500
 number of steps 100000 number of steps 100000
 temperature in K 300 temperature in K 300
-diffusion barrier 0.4 +diffusion barrier 0.3 
-binding barrier 0.3+binding barrier 0.4
 </code> </code>
 Do you notice differences in the way events occur? Do you notice differences in the way events occur?
exercises/2017_ethz_mmm/mc_and_kmc_2.1489063283.txt.gz · Last modified: 2020/08/21 10:15 (external edit)