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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 03:15]
dpasserone
exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/04/14 14:50] (current)
oschuett replace pdf with doi link
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-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>​ <​code>​
 +max@qmobile:​~$ cd ; cd EXERCISES
 max@qmobile:​~$ wget http://​www.cp2k.org/​_media/​exercises:​2018_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:​~$ unzip exercises:​2018_ethz_mmm:​exercise_1.1.zip
 +max@qmobile:​~$ cd exercise_1.1
 </​code>​ </​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: 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>​ </​note>​
-Login to euler using your nethz credentials. 
-Then go to the directory "​EXERCISES"​. ​ 
-<​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 ​ ===== ===== Geometry optimization ​ =====
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 <note important>​NOTE ON THE UNITS: CP2K USES SO CALLED "​atomic units"​. Meaning that the resulting energies are expressed in Hartree, ​ <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**.  **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>​
 <note tip> <note tip>
-  - randomize the coordinate files **fcc.xyz** ​ <​code>​m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</​code>​Do the same with ico.xyz. You can look at all files with **vmd**.+  - 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**.
   - 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>​ 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**. ​+  - <​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 the simulation, copy the input coordinate file into in.xyz <​code>​cp fcc_rand.xyz in.xyz</​code>​
-  - run cp2k  <​code>​cp2k.ssmp -i geo_opt.inp -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)  
 +  - 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)   - 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> ​   - 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> ​
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   - have a look at the myq4 script <​code>​nano myq4</​code>​   - 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>​   - 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>​ </​note>​
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 <note tip>​Assignment: ​ <note tip>​Assignment: ​
   - Report the energy of the minima, compare it with the ones of the initial configurations. ​   - 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?   - 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   - Report the value of the order parameter of the minumum, and discuss what you see
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.1519355700.txt.gz · Last modified: 2018/02/23 03:15 by dpasserone