User Tools

Site Tools


exercises:2017_ethz_mmm:mc_and_kmc

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
exercises:2017_ethz_mmm:mc_and_kmc [2017/03/08 15:47]
dpasserone
exercises:2017_ethz_mmm:mc_and_kmc [2020/08/21 10:15] (current)
Line 1: Line 1:
-====== 38 atom Lennard-Jones cluster: molecular dynamics with python ====== +====== Monte Carlo simulations for the estimation of molecule pair interatcion ====== 
 =====  ===== 
 In this exercise you will perform a MC simulation for different coverages of "sumanene" mlecules In this exercise you will perform a MC simulation for different coverages of "sumanene" mlecules
Line 7: Line 7:
  
 <note tip> <note tip>
-All files of this exercise be downloaded from the wiki: {{e3_bis.zip|}} +All files of this exercise can be downloaded from the wiki: {{exercise_3.zip|}} 
 Download the exercise into your $HOME folder and unzip it.  Download the exercise into your $HOME folder and unzip it. 
  
 <code> <code>
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:e3_bis.zip +you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_3.zip 
-you@eulerX ~$ unzip exercises:2017_ethz_mmm:e3_bis.zip+you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_3.zip
 you@eulerX ~$ cd exercise_3 you@eulerX ~$ cd exercise_3
 </code> </code>
Line 20: Line 20:
 In an experiment performed at Empa, sumanene molecules were adsorbed on a Ag(111) surface. In an experiment performed at Empa, sumanene molecules were adsorbed on a Ag(111) surface.
 It was found that at very low coverage (0.02) 30% of the molecules were weakly bound into dimers. It was found that at very low coverage (0.02) 30% of the molecules were weakly bound into dimers.
 +[ [[http://dx.doi.org/10.1021/ja504126z]]  J. Am. Chem. Soc. 2014, 136, 13666−13671]
  
-IMAGE+{{:exercises:2017_ethz_mmm:coverage.jpg?200|}}
  
 <note tip> <note tip>
Line 27: Line 28:
 (blue dots) are allowed to move by random discrete steps (blue dots) are allowed to move by random discrete steps
  
-IMAGE LATTICE+{{:exercises:2017_ethz_mmm:hex_0.jpg?200|}}
  
 While in execution, the code will show you snapshots of the positions of the molecules on the lattice While in execution, the code will show you snapshots of the positions of the molecules on the lattice
 on the left panel. on the left panel.
 +
 +{{:exercises:2017_ethz_mmm:plots_0.0_200.0.png?600|}}
 +
 In the central panel average values for the number of isolated molecules, the number of dimers and the number of clusters In the central panel average values for the number of isolated molecules, the number of dimers and the number of clusters
 is plotted. is plotted.
Line 55: Line 59:
 where k is Boltzmann's constant where k is Boltzmann's constant
 T is the simulation (and experiment) temperature T is the simulation (and experiment) temperature
-n0 is teh concentration of dimers in the case of zero interaction+n0 is the concentration of dimers in the case of zero interaction
 nexp is the concentration of dimers found in the experiment nexp is the concentration of dimers found in the experiment
 +To compute the concentration consider that at coverage 0.02, in the simulation, the total number of molecules is 50
 </note> </note>
  
Line 74: Line 79:
  
 <code> <code>
-#### MAIN MC LOOP+clusters_plot=[] 
 +for i in range(nouter):
  
 and also the section and also the section
Line 102: Line 108:
 The function "allconnected" is quite intuitive and inefficient. Can The function "allconnected" is quite intuitive and inefficient. Can
 you imagine roughly a more efficient function to perform the same task?  you imagine roughly a more efficient function to perform the same task? 
 +</note>
 +<note warning>
 +The code, at each step, moves a particle chosen randomly to a new site chosen randomly.
 +**Would it be correct to move all particles in a step?
 +what would change?**
 </note> </note>
  
exercises/2017_ethz_mmm/mc_and_kmc.1488988078.txt.gz · Last modified: 2020/08/21 10:15 (external edit)