exercises:2015_pitt:gga
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exercises:2015_pitt:gga [2015/02/27 08:31] – [Required Files] vondele | exercises:2015_pitt:gga [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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* Use vmd to vizualize the geometries (provided below) named '' | * Use vmd to vizualize the geometries (provided below) named '' | ||
* To edit the input files provided below, use an editor such as '' | * To edit the input files provided below, use an editor such as '' | ||
- | * You will need files named '' | + | * You will need files named '' |
- | * 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> | ||
- | #!/ | + | #PBS -N mode1 |
- | #SBATCH | + | #PBS -j oe |
- | #SBATCH --nodes=6 | + | #PBS -q dist_small |
- | #SBATCH | + | #PBS -l nodes=4:ppn=16 |
- | #SBATCH | + | #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 | ||
</ | </ | ||
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In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized. | In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized. | ||
- | To do so, turn of the generation of cubes (''& | + | To do so, turn off the generation of cubes (''& |
input topics: | input topics: | ||
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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. | ||
<code - mode1.inp> | <code - mode1.inp> | ||
&GLOBAL | &GLOBAL |
exercises/2015_pitt/gga.1425025882.txt.gz · Last modified: 2020/08/21 10:15 (external edit)