[lammps-users] Problems with NEB method

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1

Hi,

I am trying to do an analysis on punctual defects migration energy using the nudged elastic band method. I built a simple model bcc with adding an intersitial atom.

I did a previous simulation dumping a data file to use it as initial file.

Then I created a final file in which I insterted just the interstitial atom ID and its final coordinates, supposing it jumps on an adjacent interstitial location.

I use the following two lines for running the neb simulation and 6 replica

fix 1 nebatoms neb 1.0

neb 0.0 0.01 100 100 10 final final.vac

First of all I would ask if there is a quick way for running the analysis for many defects and many migration paths for each defect (instead of generating a defect and writing its .final file by hand each time).

Secondly, my master log.lammps file shows just the data about one of the replica and its timesteps. I guess it is the highest energy replica, the one on the saddle point, but I would like to see data of all the 6 replica. For instance for plotting the pe against the reaction coordinate.

Thank you.

Cheers,

Stefano

2

  1. LAMMPS has no automated mechanism for generating all possible NEB end points
    for multiple defects and paths. That is probably more of a job for a pre-processing script
    which generates a series of LAMMPS NEB scripts. If you write such a tool,
    please contribute it to the LAMMPS distribution!

  2. For any multi-replica simulation, including NEB, LAMMPS should generate a collection
    of log and screen files which correspond to each replica. The neb doc page explains this.

Steve