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exercises:2015_ethz_mmm:dye_tio

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exercises:2015_ethz_mmm:dye_tio [2015/02/06 17:49] – external edit 127.0.0.1exercises:2015_ethz_mmm:dye_tio [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ===== 1. Task: Familiarize yourself  ===== ===== 1. Task: Familiarize yourself  =====
-The coordinate of the two binding modes are provided you as ''mode1.xyz'' and ''mode2.xyz''. Visualize the two geometries with VMD and familiarize yourself with the system.+The coordinates of the two binding modes are provided to you as ''mode1.xyz'' and ''mode2.xyz''. Visualize the two geometries with VMD and familiarize yourself with the system.
  
 ===== 2. Task: Bond induced density differences ===== ===== 2. Task: Bond induced density differences =====
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 </note> </note>
  
-To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on brutus. +To process the cube files we are going to use the [[tools:cubecruncher | cubecruncher]] tool. It is part of CP2K, but not installed on euler. 
-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:+Therefore, you'll have to download and compile it yourself:
 <code> <code>
-you@brutusX ~$ ln -s /cluster/home03/matl/schuetto/cubecruncher.x .+you@eulerX ~$ svn checkout http://svn.code.sf.net/p/cp2k/code/trunk/cp2k/tools/cubecruncher 
 +you@eulerX ~$ cd cubecruncher 
 +you@eulerX ~$ make 
 +you@eulerX ~$ ./cubecruncher.x -help
 </code> </code>
- 
  
 Now subtract the densities of the lone systems from the bonded system: Now subtract the densities of the lone systems from the bonded system:
 <code> <code>
-you@brutusX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube +you@eulerX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube 
-you@brutusX ~$ ./cubecruncher.x -i tmp.cube -subtract mode1_slab-ELECTRON_DENSITY-1_0.cube -o mode1_delta.cube+you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract mode1_slab-ELECTRON_DENSITY-1_0.cube -o mode1_delta.cube
 </code> </code>
  
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 The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:
 <code> <code>
-you@brutusX ~$ cubecruncher.x -center geo -i mode1_delta.cube -o mode1_delta-centered.cube+you@eulerX ~$ ./cubecruncher.x -center geo -i mode1_delta.cube -o mode1_delta-centered.cube
 </code> </code>
  
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