CP2K Open Source Molecular Dynamics

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exercises:2015_pitt:gga [2015/02/27 08:48] – [3. Task: relative stabilities] vondeleexercises:2015_pitt:gga [2015/03/03 08:21] – [1. Task: Familiarize yourself with system and setup] vondele
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   * Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''   * Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''
   * To edit the input files provided below, use an editor such as ''vi'' or ''nano''. While ''nano'' is simple to use, ''vi'' can be [[http://www.cp2k.org/tools| configured to colour-code cp2k inputs]].   * To edit the input files provided below, use an editor such as ''vi'' or ''nano''. While ''nano'' is simple to use, ''vi'' can be [[http://www.cp2k.org/tools| configured to colour-code cp2k inputs]].
-  * You will need files named ''BASIS_MOLOPT'' ''GTH_POTENTIALS'' ''dftd3.dat'' that are provided as part of CP2K in a directory ''cp2k/data'' +  * You will need files named ''BASIS_MOLOPT'' ''GTH_POTENTIALS'' ''dftd3.dat'' that are provided as part of CP2K in a directory ''cp2k/data'', unless the code has been compiled with the proper flag ('' -D__DATA_DIR'') so that these are found automatically. 
-  * Use a job script to submit jobs on the cluster, an example job submission script might look like (TODO: adjust for environment)+  * Use a job script to submit jobs on the cluster, an example job submission script might look like 
  
 <code - job> <code - job>
-#!/bin/bash --login +#PBS -N mode1 
-#SBATCH --job-name=mode1 +#PBS -j oe 
-#SBATCH --nodes=6 +#PBS -q dist_small 
-#SBATCH --time=0:10:00 +#PBS -l nodes=4:ppn=16 
-#SBATCH --account=ch5 +#PBS -l walltime=10:00 
-aprun -n 144 -N 24 -d 1 cp2k.popt -i mode1.inp -o mode1.out+#PBS -A cp2k2015 
 + 
 +cd $PBS_O_WORKDIR 
 + 
 +module purge 
 +module load cp2k/2.6 
 + 
 +prun cp2k.popt -i mode1.inp -o mode1.out
 </code> </code>
  
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 What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ?  What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ? 
 Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced. Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced.
-===== Required Files =====+====== Required Files ======
  
 (right) click on the filename to download to your local machine. (right) click on the filename to download to your local machine.
exercises/2015_pitt/gga.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1