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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 08:48] – dpasserone
@@ Line 146: / Line 146: @@
 <note important>NOTE ON THE UNITS: CP2K USES SO CALLED "atomic units". Meaning that the resulting energies are expressed in Hartree,
 **1 Hartree=27.2114 eV**.
-In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in "temperature" units (there is a Boltzmann constant to make units work...). **The sigma value is in Angstrom.**
+In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in "temperature" units (there is a Boltzmann constant K_b to make units work...). <code>1 Kelvin*K_b=3.2E-6 Hartree</code>. Using this conversion factor you can transform the epsilon value into Hartree, and the total energy can be expressed in units of epsilon.  **The sigma value is in Angstrom.**
 </note>
 <note tip>
@@ 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)
@@ Line 179: / Line 180: @@
 <note tip>Assignment:
   - Report the energy of the minima, compare it with the ones of the initial configurations.
+  - After converting the energy into "epsilon" units, estimate the number of bonds in the cluster, assuming a pairwise interaction.
   - Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?
   - Report the value of the order parameter of the minumum, and discuss what you see