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
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.
- Run the neb using neb.inp
cp2k.popt -i neb_linear.inp -o neb_linear.out
- 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
. 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):
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).
- Examine path_linear.xyz with vmd.
- Apply the script myq4 to this path, to extract q4 and energies.
./myq4 path_linear.xyz > linear.q4.ene
- Do the same with neb_better.inp
- 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.