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exercises:2017_ethz_mmm:lennard_jones_cluster_neb

38 atom Lennard-Jones cluster: nudged elastic band

In this second exercise we will find a transition path between a icosahedral-like minimum and a fcc-like minimum.

Download the 1.1 exercise into your $HOME folder and unzip it.

you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_1.2.zip
you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_1.2.zip
All files of this exercise be downloaded from the wiki: exercise_1.2.zip

The goal is to check the dependence of the result on the initial guess. The relevant section is the following (neb_linear.inp):

&MOTION
  &BAND
   NPROC_REP 1
   BAND_TYPE IT-NEB 
   NUMBER_OF_REPLICA 20
    &OPTIMIZE_BAND
      OPT_TYPE DIIS
      &DIIS
       MAX_STEPS 1000
       N_DIIS 3
      &END
    &END
    &REPLICA
     COORD_FILE_NAME a.xyz
    &END REPLICA
    &REPLICA
     COORD_FILE_NAME b.xyz
    &END REPLICA
  &END BAND
&END MOTION

where the initial and final states are specified. There is a second version called (neb_better.inp). Check the differences… note that we input more configurations. This means that we start from a more advanced start with respect to a linear interpolation between a and b.

  1. Run the neb using neb.inp
    cp2k.popt -i neb_linear.inp -o neb_linear.out 
  2. You will get SEVERAL files. They are the improved paths that tend to optimize the band energy.
  3. Count how many optimization steps you have in each file
    m_xyzcountframes NEB_LINEAR-pos-Replica_nr_01-1.xyz 

    . You will get the number NFRAMES (mark it).

  4. For each of the replica files, extract only the last (final) step, and put everything in a single path file (the optimized path):
    rm path_linear.xyz ; for a in NEB_LINEAR-pos-Replica_nr_*xyz ; do m_xyzframes NFRAMES NFRAMES $a >> path_l.xyz ; done

    (put the value of NFRAMES).

  5. Examine path_linear.xyz with vmd.
  6. Apply the script myq4 to this path, to extract q4 and energies.
    ./myq4 path_linear.xyz > linear.q4.ene 
  7. Do the same with neb_better.inp
Assignment:
  1. Report the energy of the transition states. Write them in the same units of the paper.
  2. Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Compare the transition state energies with the units of the paper.
  3. Discuss the “movie” of the transition paths in the two cases.
exercises/2017_ethz_mmm/lennard_jones_cluster_neb.txt · Last modified: 2017/02/24 10:43 by dpasserone