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--- exercise:dye_tio [2014/04/04 12:50] – oschuett
+++ exercise:dye_tio [2014/04/05 09:44] – oschuett
@@ 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 |}}
@@ 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 .