User Tools

Site Tools


exercises:2015_ethz_mmm:dye_tio

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revisionBoth sides next revision
exercises:2015_ethz_mmm:dye_tio [2015/04/23 14:30] oschuettexercises:2015_ethz_mmm:dye_tio [2015/04/23 14:32] oschuett
Line 28: Line 28:
 </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 cubecruncher tool. It is part of CP2K, but not installed on euler.
 Therefore, a compiled binary of the tool is provided at ''/cluster/home/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, a compiled binary of the tool is provided at ''/cluster/home/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> <code>
-you@brutusX ~$ ln -s /cluster/home/schuetto/cubecruncher.x .+you@eulerX ~$ ln -s /cluster/home/schuetto/cubecruncher.x .
 </code> </code>
  
Line 37: Line 37:
 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>
  
Line 44: Line 44:
 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>
  
exercises/2015_ethz_mmm/dye_tio.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1