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--- exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:34] – dpasserone
+++ exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:37] – dpasserone
@@ Line 153: / Line 153: @@
   - <code> 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**. You will also be asked **"value of l"** This means the symmetry of the order parameter, which is **l=4** in this case.
   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
+  - Before running cp2k, check if the file **OPT-pos-1.xyz** is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization.
   - 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)
   - 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>