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--- exercises:2017_uzh_cmest:adsorption [2017/11/07 10:06] – tmueller
+++ exercises:2017_uzh_cmest:adsorption [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 15: / Line 15: @@
 \end{align*}
-Use the following input file as a starting point, and an adapted version of the script you documented in a [[exercises:2017_uzh_cmest:calculation_pbc|previous exercise]] to generate a number of input files for different lattice constants and run the respective calculation.
+Use the following input file as a starting point, and an adapted version of the script you documented in a [[exercises:2017_uzh_cmest:calculation_pbc|previous exercise]] to generate a number of input files for different lattice constants and run the respective calculation. A good interval for the fraction of the lattice constant is $0.90-1.10$ with a step size of $0.025$.
 Extract the energies and fit $E_0$, $V_0$, $B_0$, $B_1$ using the Birch–Murnaghan EOS and using the new $V0$ determine the lattice constant.
@@ Line 111: / Line 112: @@
 <code>
 a=3.54
-sed -e "s/2.4612/$a/g" graphene.inp > "graphene_V-${x}.inp"
+sed -e "s|2.4612|$a|g" graphene.inp > "graphene_V-${x}.inp"
 </code>
 </note>
+<note warning>
+Be careful when fitting values for the Birch-Murnaghan EOS: the volume is usually the volume per atom (and the total volume of the cell you can also get from the CP2K output).
+</note>
 ===== 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 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 right at the beginning):
+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>
+[...]
+ MODULE QUICKSTEP:  ATOMIC COORDINATES IN angstrom
+  Atom  Kind  Element       X           Y           Z          Z(eff)       Mass
-<code>
+     1 C    6    1.267080    0.731549    0.000000      4.00      12.0107
+     1 C    6    2.534160    1.463098    0.000000      4.00      12.0107
+     1 C    6    3.801240    0.731549    0.000000      4.00      12.0107
+     1 C    6    5.068320    1.463098    0.000000      4.00      12.0107
+     1 C    6    6.335400    0.731549    0.000000      4.00      12.0107
+[...]
 </code>
 </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 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?