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exercises:2016_summer_school:gga

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exercises:2016_summer_school:gga [2016/08/23 06:48]
ibethune
exercises:2016_summer_school:gga [2016/08/23 06:51] (current)
ibethune
Line 80: Line 80:
 Create the .xyz files (check with vmd that they contain the right subsystems),​ and create mode1_dye.inp,​ mode1_slab.inp by changing both ''​COORD_FILE_NAME''​ and ''​PROJECT''​ accordingly. Create the .xyz files (check with vmd that they contain the right subsystems),​ and create mode1_dye.inp,​ mode1_slab.inp by changing both ''​COORD_FILE_NAME''​ and ''​PROJECT''​ accordingly.
  
-After computing these input files, we analyze the results using a tool provided with cp2k ''​cubecruncher.x''​ that manipulates cube files (e.g. can compute difference).+After computing these input files, we analyze the results using a tool provided with cp2k ''​cubecruncher.x''​ that manipulates cube files (e.g. can compute difference). ​ To build cubecruncher,​ make a copy of the code in your own directory and compile it: 
 + 
 +<​code>​ 
 +~$ module load cp2k 
 +~$ cp -r $CP2K/​../​../​tools/​cubecruncher . 
 +~$ cd cubecruncher 
 +~$ module swap PrgEnv-cray PrgEnv-gnu 
 +~$ make 
 +</​code>​ 
 + 
 +Then run it as follows: 
 <​code>​ <​code>​
 ~$ cubecruncher.x -i MODE1-ELECTRON_DENSITY-1_0.cube -subtract MODE1_dye-ELECTRON_DENSITY-1_0.cube -o tmp.cube ~$ cubecruncher.x -i MODE1-ELECTRON_DENSITY-1_0.cube -subtract MODE1_dye-ELECTRON_DENSITY-1_0.cube -o tmp.cube
exercises/2016_summer_school/gga.txt · Last modified: 2016/08/23 06:51 by ibethune