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exercises:2017_uzh_cmest:adsorption [2017/11/07 13:50]
tmueller [Lattice constant optimization]
exercises:2017_uzh_cmest:adsorption [2017/11/07 14:15]
tmueller [CO adsorption on graphene]
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 ===== CO adsorption on graphene ===== ===== CO adsorption on graphene =====
  
-Adsorb one CO molecule on the graphene 6X6X1 supercell at the top(T), bridge(B) and center(C) sites (see the paper for the definitions) and optimize ​the geometry.+Adsorb one <​chem>​CO</​chem> ​molecule on graphene 6X6X1 supercell at the top(T), bridge(B) and center(C) sites and optimize the geometry. See the paper for the definitions ​as well as the initial distances. 
 You need change the ''​RUN_TYPE''​ to ''​GEO_OPT''​ and also specify the (absolute) coordinates by yourself. You need change the ''​RUN_TYPE''​ to ''​GEO_OPT''​ and also specify the (absolute) coordinates by yourself.
  
 <note tip> <note tip>
-You can get a 6x6x1 unit cell with absolute coordinates by using ''​MULTIPLE_UNIT_CELL''​ for the original input file like shown in previous examples, run it with CP2K and get the calculated absolute coordinates from the CP2K output (you can interrupt the actual calculation since the coordinates are printed ​right at the beginning):+You can get a 6x6x1 unit cell with absolute coordinates by using ''​MULTIPLE_UNIT_CELL''​ for the original input file like shown in previous examples, run it with CP2K and get the calculated absolute coordinates from the CP2K output (you can interrupt the actual calculation since the coordinates are printed ​before ​the actual calculation starts):
  
 +<​code>​
 +[...]
 + ​MODULE QUICKSTEP: ​ ATOMIC COORDINATES IN angstrom
  
 +  Atom  Kind  Element ​      ​X ​          ​Y ​          ​Z ​         Z(eff) ​      Mass
  
-<​code>​ +       ​1 ​    1 C    6    1.267080 ​   0.731549 ​   0.000000 ​     4.00      12.0107 
 +       2     1 C    6    2.534160 ​   1.463098 ​   0.000000 ​     4.00      12.0107 
 +       ​3 ​    1 C    6    3.801240 ​   0.731549 ​   0.000000 ​     4.00      12.0107 
 +       ​4 ​    1 C    6    5.068320 ​   1.463098 ​   0.000000 ​     4.00      12.0107 
 +       ​5 ​    1 C    6    6.335400 ​   0.731549 ​   0.000000 ​     4.00      12.0107 
 +[...]
 </​code>​ </​code>​
 </​note> ​ </​note> ​
  
-<​code>​ 
-&GLOBAL 
-  PROJECT graphene 
-  RUN_TYPE GEO_OPT 
-  PRINT_LEVEL MEDIUM 
-&END GLOBAL 
-</​code>​ 
  
-The adsorption energy is given by:$ E_{ad} = E_{CO-graphene} - E_{CO} - E_{graphene}$+The adsorption energy is given by:$ E_{ad} = E_{CO+graphene} - E_{CO} - E_{graphene}$ 
 + 
 +This means that you also have to make an auxiliary geometry optimization calculation using <​chem>​CO</​chem>​ in vacuum, using the same settings as for the other calculations except for the periodicity. Use a large enough cell (~ 15 Å) and ''​[[https://​manual.cp2k.org/​trunk/​CP2K_INPUT/​FORCE_EVAL/​SUBSYS/​TOPOLOGY/​CENTER_COORDINATES.html|CENTER_COORDINATES]]''​ for this.
  
 Find the most stable adsorption site and study the coverage effect such like 1/2 and 1. What do you observe when increasing the coverage? Find the most stable adsorption site and study the coverage effect such like 1/2 and 1. What do you observe when increasing the coverage?
exercises/2017_uzh_cmest/adsorption.txt · Last modified: 2017/11/07 14:36 by tmueller