Differences

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

--- exercises:2017_uzh_cmest:adsorption [2017/11/07 14:14] – [CO adsorption on graphene] tmueller
+++ exercises:2017_uzh_cmest:adsorption [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 121: / Line 121: @@
 ===== CO adsorption on graphene =====
-Adsorb one <chem>CO</chem> molecule on a 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.
+Adsorb one <chem>CO</chem> molecule on a graphene 6X6X1 supercell at the top (//T//), bridge (//B//) and center (//C//) sites with oxygen atop the carbon (and both perpendicular to the graphene, the //u// orientation) and optimize the geometry. See the paper for the definitions as well as initial values for the distances.
 You need change the ''RUN_TYPE'' to ''GEO_OPT'' and also specify the (absolute) coordinates by yourself.
 <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 before the actual calculation starts):
+You can get a 6x6x1 unit cell with absolute coordinates by using ''MULTIPLE_UNIT_CELL'' for the original/geometry-optimized input file like shown in a 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>
@@ Line 146: / Line 146: @@
 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.
+This means that you also have to run an auxiliary geometry optimization calculation for <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?
+Which one is the most stable adsorption site?