====== 38 atom Lennard-Jones cluster: nudged elastic band ======


{{:exercises:2017_ethz_mmm:pathneb.png?600|}}

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 $HOME folder and unzip it. 
<code>
you@eulerX ~$ 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
</code>

<note tip>
All files of this exercise be downloaded from the wiki: {{exercise_1.2.zip|}}</note> 

The goal is to check the dependence of the result on the initial guess. The relevant section is the following (**neb_linear.inp**):
<code>
&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
</code>
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**.
<note tip>
  - Run the neb using neb.inp <code>cp2k.popt -i neb_linear.inp -o neb_linear.out </code>
  - You will get SEVERAL files. They are the improved paths that tend to optimize the band energy. 
  - Count how many optimization steps you have in each file <code>m_xyzcountframes NEB_LINEAR-pos-Replica_nr_01-1.xyz </code>. You will get the number NFRAMES (mark it).
  - For each of the replica files, extract only the last (final) step, and put everything in a single path file (the optimized path): <code>rm path_linear.xyz ; for a in NEB_LINEAR-pos-Replica_nr_*xyz ; do m_xyzframes NFRAMES NFRAMES $a >> path_l.xyz ; done</code> (put the value of NFRAMES).
  - Examine **path_linear.xyz** with vmd. 
  - Apply the script **myq4** to this path, to extract q4 and energies. <code>./myq4 path_linear.xyz > linear.q4.ene </code>
  - Do the same with **neb_better.inp**
</note>

<note tip>Assignment: 
  - Report the energy of the transition states. Write them in the same units of the paper.  
  - 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.
  - Discuss the "movie" of the transition paths in the two cases.
</note>