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exercises:2017_ethz_mmm:lennard_jones_cluster

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exercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/24 09:07] – dpasseroneexercises:2017_ethz_mmm:lennard_jones_cluster [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ====== 38 atom Lennard-Jones cluster ====== ====== 38 atom Lennard-Jones cluster ======
 +
 +{{:exercises:2017_ethz_mmm:lj38bs.jpg?400|}} (picture by Luke Abraham)
 <note warning> <note warning>
 TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
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 <note tip> <note tip>
-All files of this exercise (**input and scripts are all commented**) can be downloaded from the wiki: {{exercise_1.1.zip|}} +All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}} 
 </note> </note>
  
 In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster: In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster:
-<note tip>{{ :exercises:2017_ethz_mmm:1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf |}}+<note tip>[[doi>10.1063/1.478595]]
 </note> </note>
 Login to euler using your nethz credentials. Login to euler using your nethz credentials.
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   - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.<code>module load new gcc/4.8.2 python/2.7.12     - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.<code>module load new gcc/4.8.2 python/2.7.12  
 python stein.py file.xyz </code>. You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**.  python stein.py file.xyz </code>. You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. 
-  - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc.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>module load cp2k</code>(this has only to be done once)<code>cp2k.opt -i geo_opt.inp -o geo_opt.out </code> +  - run cp2k <code>module load cp2k</code>(this has only to be done once)<code>cp2k.popt -i geo_opt.inp -o geo_opt.out </code> 
   - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**   - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**
   - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)   - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
exercises/2017_ethz_mmm/lennard_jones_cluster.1487927247.txt.gz · Last modified: (external edit)