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exercises:2018_ethz_mmm:kmc2018 [2018/03/08 08:21] – created dpasseroneexercises:2018_ethz_mmm:kmc2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 =====  ===== 
  
 +<note tip>
 +Please download the program **kinetic_monte_carlo.py** from [[https://polybox.ethz.ch/index.php/s/CH5VdcI40YdELez|this link]] 
 +</note>
 The  molecule shown in the image (hexaiodo-substituted The  molecule shown in the image (hexaiodo-substituted
 macrocycle cyclohexa-m-phenylene (CHP) ), when deposited on a noble metal substrate such as macrocycle cyclohexa-m-phenylene (CHP) ), when deposited on a noble metal substrate such as
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 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 ] show 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.
  
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 <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
-once the energy barriers for the diffusion event and for the binding event as well as the simulation temperature will be defined.+once the energy barriers for the diffusion event and for the binding event as well as the simulation temperature are provided.
  
  
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 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.+A few snapshots of the system during time evloution are saved as images. 
 + 
 +Execute the program  
 +<code> 
 +python kinetic_monte_carlo.py 
 +</code> 
 The program asks you for some input: The program asks you for some input:
  
 <code>  <code> 
-coverage 
 update graph each steps update graph each steps
 +coverage
 temperature in K temperature in K
 diffusion barrier diffusion barrier
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 </note> </note>
-<note warning>+<note important>
 **TASK 1** **TASK 1**
 execute the program with the following parameters: execute the program with the following parameters:
 <code> <code>
-coverage 0.1 +update graph each steps 1000 
-update graph each steps 500 +coverage 0.3 
-number of steps 100000+number of steps 130000
 temperature in K 300 temperature in K 300
 diffusion barrier 0.1 diffusion barrier 0.1
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 Observe how events occur. 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 300000 steps? Why?
 Observe the patterns obtained. Observe the patterns obtained.
 </note> </note>
  
-<note warning>+<note important>
 **TASK 2** **TASK 2**
 execute the program with the following parameters: execute the program with the following parameters:
 <code> <code>
-coverage 0.1 +update graph each steps 1000 
-update graph each steps 500 +coverage 0.3 
-number of steps 100000+number of steps 300000
 temperature in K 300 temperature in K 300
 diffusion barrier 0.3 diffusion barrier 0.3
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 Do you notice differences in the way events occur? Do you notice differences in the way events occur?
 How is evolving time compared to the previous case? How is evolving time compared to the previous case?
-How does the final geometry differ form the previous case?+How does the final geometry differ from the previous case?
 </note> </note>
-<note tip>+<note important> 
 +**TASK 3** 
 Now have a look at the python code. Now have a look at the python code.
 The MAIN section The MAIN section
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 </code> </code>
 </note> </note>
-<note warning> +<note important> 
-**TASK 3** +**TASK 4** 
-Have a look on the section of the code that create the list of events,+Have a look at the section of the code that creates the list of events,
 comment on which are the critical points in setting up a KMC simulation comment on which are the critical points in setting up a KMC simulation
 to describe a real process. to describe a real process.
- +</note> 
-**TASK 4** +<note important> 
-At each step of the simulaiton the list of possible events is created (or, betetr, updated) +**TASK 5** 
-an event is chosen randomly and is then actuated.+At each step of the simulaiton the list of possible events is created (or, better, updated). 
 +An event is chosen randomly and is then actuated.
 Would it be possible to execute simultaneously more events at each KMC step? Would it be possible to execute simultaneously more events at each KMC step?
 </note> </note>
exercises/2018_ethz_mmm/kmc2018.1520497284.txt.gz · Last modified: 2020/08/21 10:15 (external edit)