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--- exercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/24 09:45] – dpasserone
+++ exercises:2017_ethz_mmm:lennard_jones_cluster [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 37: / Line 37: @@
 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>
 Login to euler using your nethz credentials.
@@ Line 168: / Line 168: @@
   - 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**.
-  - 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)**
   - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)