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exercises:2015_pitt:gga [2015/03/02 15:54]
vondele [Required Files]
exercises:2015_pitt:gga [2015/03/03 08:21]
vondele [1. Task: Familiarize yourself with system and setup]
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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 -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>​
  
exercises/2015_pitt/gga.txt · Last modified: 2015/03/03 08:21 by vondele