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--- exercises:2017_ethz_mmm:lennard_jones_cluster [2017/02/24 05:40] – dpasserone
+++ exercises:2017_ethz_mmm:lennard_jones_cluster [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== 38 atom Lennard-Jones cluster ======
+{{:exercises:2017_ethz_mmm:lj38bs.jpg?400|}} (picture by Luke Abraham)
 <note warning>
 TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
@@ Line 31: / Line 33: @@
 <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>
 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 42: / Line 44: @@
 you@eulerX ~$ cd exercise_1.1
-===== Geometry optimization  =====
 </code>
+===== Geometry optimization  =====
+In this first part you will perform a simple energy optimization, to find the two lowest lying minima in the potential energy surface.
 The input file structure of the template is the following:
@@ Line 154: / Line 159: @@
 </code>
+<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.**
+</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**  <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.<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_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>
+  - 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)
+  - 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.
+</note>
-<code bash c2h2.chain>
-</code>
-At this point submit the job grid, first loading the module for cp2k entering
-<code>
-you@eulerX c2h2$ module load cp2k
-you@eulerX c2h2$ bsub cp2k.popt < c2h2.chain
-</code>
-<code>
-</code>
-<code - fit.gnu>
-</code>
-Compare the values that you obtain with the ones listed in the "human readable" potential file c2h2-force_field.pot that was generated by cp2k.
-Now, perform the same exercise in another directory for the molecule C2H4.
-<code>
-you@eulerX c2h2$ cd ../c2h4
-</code>
-<code coo.ch4>
-</code>
-<code bash c2h4.chain>
-</code>
 <note tip>Assignment:
-  - Report the energy of the minimum
+  - Report the energy of the minima, compare it with the ones of the initial configurations.
+  - 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
-  - Plot the energy curve as a function of the homogeneous contraction/expansion of the cluster
+  - Use "gnuplot" to make the output of "./curve" understandable, discuss the results.
 </note>