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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 14:33]
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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 +<note tip>
 +All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}} ​
 +</​note>​
 +
 +Download the 1.1 exercise into your **EXERCISES** folder and unzip it. 
 +
 +<​code>​
 +max@qmobile:​~$ cd ; cd EXERCISES
 +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>​
 +
 +
 +
 +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>​[[doi>​10.1063/​1.478595]]
 +</​note>​
 +
 +The command to run cp2k is the following (with a generic **file.inp** input file):
  
 <​code>​ <​code>​
 max@qmobile:​~$ cp2k.ssmp -i file.inp -o file.out max@qmobile:​~$ cp2k.ssmp -i file.inp -o file.out
 </​code> ​ </​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:
 +
 +<code - geo_opt.inp>​
 +&GLOBAL
 + ​FLUSH_SHOULD_FLUSH
 + ​PRINT_LEVEL low
 + ​PROJECT geo_opt_bfgs
 + ​RUN_TYPE geo_opt
 + ​WALLTIME 600
 +&END GLOBAL
 +
 +&MOTION
 + &​GEO_OPT
 +  OPTIMIZER BFGS
 +  MAX_ITER ​ 200
 +  MAX_DR ​   0.001
 +  RMS_DR ​   0.0003
 +  MAX_FORCE 0.0001
 +  RMS_FORCE 0.00003
 +  &BFGS
 +   ​USE_MODEL_HESSIAN yes
 +  &END BFGS
 + &​END GEO_OPT
 + &​PRINT
 +  &​TRAJECTORY on
 +   ​FORMAT xyz
 +   &​EACH
 +    GEO_OPT 1
 +   &​END EACH
 +  &END TRAJECTORY
 + &​END PRINT
 +&END MOTION
 +
 +&​FORCE_EVAL
 + ​METHOD Fist
 + ​STRESS_TENSOR ANALYTICAL
 + &​MM
 +    &​FORCEFIELD
 +      &CHARGE
 +        ATOM Ar
 +        CHARGE 0.0
 +      &END
 +      &​NONBONDED
 +        &​LENNARD-JONES
 +          atoms Ar Ar
 +          EPSILON 119.8
 +          SIGMA 3.405
 +          RCUT 8.4
 +        &END LENNARD-JONES
 +      &END NONBONDED
 +      &CHARGE
 +        ATOM Kr
 +        CHARGE 0.0
 +      &END CHARGE
 +    &END FORCEFIELD
 +  &​POISSON
 +   ​PERIODIC NONE
 +   &​EWALD
 +    EWALD_TYPE none
 +   &​END EWALD
 +  &END POISSON
 +  &PRINT
 +   &​FF_INFO OFF
 +    SPLINE_DATA
 +    SPLINE_INFO
 +   &​END FF_INFO
 +  &END PRINT
 + &​END MM
 + &​PRINT
 +  &FORCES off
 +  &END FORCES
 +  &​GRID_INFORMATION
 +  &END GRID_INFORMATION
 +  &​PROGRAM_RUN_INFO
 +   &​EACH
 +    GEO_OPT 1
 +   &​END EACH
 +  &END PROGRAM_RUN_INFO
 +  &​STRESS_TENSOR
 +   &​EACH
 +    GEO_OPT 1
 +   &​END EACH
 +  &END STRESS_TENSOR
 + &​END PRINT
 + &​SUBSYS
 +  &CELL
 +   ​A ​     100 0 0
 +   ​B ​     0   100 0
 +   ​C ​     0 0 100
 +   ​PERIODIC NONE
 +  &END CELL
 +  &​TOPOLOGY
 +      COORD_FILE_NAME in.xyz
 +      COORDINATE xyz
 +  &END
 +  &PRINT
 +   &​CELL
 +   &​END CELL
 +   &​KINDS
 +   &​END KINDS
 +   &​MOLECULES OFF
 +   &​END MOLECULES
 +   &​SYMMETRY
 +   &​END SYMMETRY
 +  &END PRINT
 + &​END SUBSYS
 +&END FORCE_EVAL
 +                                                                                                                                                                                            ​
 +</​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 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>
 +  - 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.
 +  - <​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)
 +  - 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>​
 +  - 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>​
 +
 +
 +
 +
  
  
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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
   - Use "​gnuplot"​ to make the output of "​./​curve"​ understandable,​ discuss the results.   - Use "​gnuplot"​ to make the output of "​./​curve"​ understandable,​ discuss the results.
 </​note>​ </​note>​
--->+
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.1519310029.txt.gz · Last modified: 2018/02/22 14:33 by dpasserone