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exercises:2018_ethz_mmm:lennard_jones_cluster_2018

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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:34] – dpasseroneexercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:34] – dpasserone
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   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
   - run cp2k  <code>cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </code> (to see the output on the screen as well), or **AS AN ALTERNATIVE** <code>cp2k.ssmp -i geo_opt.inp > geo_opt.out </code> (to retain the output in the geo_opt.out file only)    - run cp2k  <code>cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </code> (to see the output on the screen as well), or **AS AN ALTERNATIVE** <code>cp2k.ssmp -i geo_opt.inp > geo_opt.out </code> (to retain the output in the geo_opt.out file only) 
-  - in the output file, grep the final energy <code>grep "ENERGY|“ geo_opt.out</code> and transform it in the unit of the paper (epsilon units)**+  - in the output file, grep the final energy <code>grep "ENERGY|“ geo_opt.out</code> and transform it in the unit of the paper (epsilon units)
   - Open vmd and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)   - Open vmd and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
   - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <code>./myq4 OPT-pos-1.xyz > fcc.ene.q4</code>    - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <code>./myq4 OPT-pos-1.xyz > fcc.ene.q4</code> 
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1