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--- exercise:dye_tio [2014/04/04 12:50] – oschuett
+++ exercises:2014_ethz_mmm:dye_tio [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Dye anchoring to TiO$_2$ ======
-In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in [[wp>Dye-sensitized_solar_cell|Dye-Sensitized Solar Cells]] as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: http://dx.doi.org/10.1021/jp4117563
+In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in [[wp>Dye-sensitized_solar_cell|Dye-Sensitized Solar Cells]] as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: [[doi>10.1021/jp4117563]]
-{{ :exercise:dye2.png?600 |}}
+{{ dye2.png?600 |}}
 ===== 1. Task: Familiarize yourself  =====
@@ Line 29: / Line 29: @@
 To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on brutus.
-Therefore, a compiled binary of the tool is provided at ''/cluster/home03/matl/schuetto/cubecruncher.x''. To simplify the following steps you should create a symbolic link to it in your working directory:
+Therefore, a compiled binary of the tool is provided at ''/cluster/home03/matl/schuetto/cubecruncher.x''. Before invoking the cubecruncher, you have to load the cp2k module. To simplify the following steps you should create a symbolic link to it in your working directory:
 <code>
 you@brutusX ~$ ln -s /cluster/home03/matl/schuetto/cubecruncher.x .
@@ Line 50: / Line 50: @@
 What you get should look similar to this:
-{{ :exercise:dye_tio_bonding_density.png?300 |}}
+{{ dye_tio_bonding_density.png?300 |}}
 ===== 3. Task: Bonding energies  =====
@@ Line 65: / Line 65: @@
 <note important>
 You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first. This has been covered in a
-[[exercise:geometry_optimization|previous exercise]].
+[[geometry_optimization|previous exercise]].
 </note>
@@ Line 79: / Line 79: @@
 <note warning>
-The provided [[wp>XYZ_file_format|XYZ-files]] can not be included into CP2K's input directly. You have convert them to ''.coord'' files by removing the first line, which states the number of atoms, and the following empty comment line.
+The provided [[wp>XYZ_file_format|XYZ-files]] can not be included into CP2K's input directly. You have to convert them to ''.coord'' files by removing the first line, which states the number of atoms, and the following empty comment line.
 </note>