LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] problems about neb calculations
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] problems about neb calculations

From: "Alice" <34340657@...1204...>
Date: Tue, 5 Dec 2017 11:35:43 +0800

Hi everyone,

I have a few questions about the neb calculation.

1. About the output files. How can I know the image number of each log.lammps.* files? And, which energy in each log.lammps.* file should I pick as the data point on the MEP curve for the corresponding replica? Specifically, in the lines like this:

"Energy initial, next-to-last, final ="        

As I understand, I should choose the value of the "final" column, is that correct? Meanwhile, should I pick these values to make the plot by hand? Or, is there any more convenient way for this?

2. I generated the dump.combine and files by using the python scripts in the tool folder. But the files do not seem right. The last part of the coordinations contains atoms 4 times more than it should be. I am using OVITO to visualize. I cannot open the files as a continuous serial of snapshots. When I split the file into segments and open them by OVITO, I did not get reasonable snapshots.

I am wondering that what was wrong with my case. Really appreciate the possible help!