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--- exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 15:48] – dpasserone
+++ exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/04/14 14:50] – replace pdf with doi link oschuett
@@ Line 4: / Line 4: @@
-The command to run cp2k is the following:
-<code>
+<note tip>
-max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out
+All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}}
-</code>
+</note>
-Download the 1.1 exercise into your $HOME folder and unzip it.
+Download the 1.1 exercise into your **EXERCISES** folder and unzip it.
 <code>
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_1.1.zip
+max@qmobile:~$ cd ; cd EXERCISES
-you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_1.1.zip
+max@qmobile:~$ wget http://www.cp2k.org/_media/exercises:2018_ethz_mmm:exercise_1.1.zip
+max@qmobile:~$ unzip exercises:2018_ethz_mmm:exercise_1.1.zip
+max@qmobile:~$ cd exercise_1.1
 </code>
-<note tip>
-All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}}
-</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:
-<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.
-Then go to the directory "exercise_1.1".
-<code>
-you@eulerX ~$ cd exercise_1.1
+The command to run cp2k is the following (with a generic **file.inp** input file):
+<code>
+max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out
+</code>
-</code>
 ===== Geometry optimization  =====
@@ Line 147: / 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>
-  - load the module with the special m_* bash functions and initialize the module: <code>module load courses mmm ; mmm-init </code>
+  - randomize the coordinate files **fcc.xyz** (which represents the "cubic" structure) <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code>Do the same with **ico.xyz** which represents the icosahedral structure. You can look at all files with **vmd**.
-  - randomize the coordinate files **fcc.xyz**  <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code> . Do the same with ico.xyz
+  - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.
-  - 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
+  - <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.
-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_rand.xyz in.xyz</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>
+  - 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.
-  - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**
+  - 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)
-  - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
+  - 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>
   - plot q4 and energies with **gnuplot** (ask the teacher)
   - have a look at the myq4 script <code>nano myq4</code>
   - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <code>mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC</code>
-  - finally, run the bash script <code>./curve</code>. Look inside, and try to understand what you get.
+  - Run the bash script <code>./curve</code>Look inside, and try to understand what you get.
+  - create a FCC_OUT subdirectory (**mkdir FCC_OUT ; cd FCC_OUT**) and copy there the files you want to keep; then go back one dir (**cd ..**), delete all the OPT* files (**rm OPT* **) and repeat the exercise with ico.xyz
 </note>
@@ Line 180: / 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
   - Use "gnuplot" to make the output of "./curve" understandable, discuss the results.
 </note>
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