What is the problem with my data file? I am getting an error in the Bonds section after changing the coordinates

LAMMPS
1

I am running a polymer in solvent simulation. However, I am getting the following error:

ERROR on proc 0: Invalid atom ID in Bonds section of data file (src/atom.cpp:1296)

I do not quite understand why this is happening? How do I diagnose such an error in how LAMMPS is processing my data file? The only way I have tweaked my datafile that works is by taking a different initial configuration and plugging it in the atoms section.

I have attached my settings, data and input file to this. The one I am having issues with is labelled “sys.0.data” and the one that works is called “sys.pnipam.water.data”.

I would appreciate any advice you have for me.

in.nvt (4.0 KB)
sys.pnipam.water.settings (6.4 KB)
sys.pnipam.water.data (4.4 MB)
sys.0.data (3.7 MB)

2

Your data file contains incorrect information.

For starters you should use a more recent LAMMPS version. Then you would get a more meaningful error message:

Reading data file ...
  orthogonal box = (0 0 0) to (75 75 75)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  42572 atoms
  scanning bonds ...
ERROR: Expected integer parameter instead of '0.4238' in input script or data file (src/atom.cpp:1291)
Last command: read_data       sys.0.data

So, apparently when you edited your data file, you also edited parts that should not be changed and replaced atom IDs in the Bonds section with bogus data.

3

Yep, I realized where the error in the awk script was.

thank you! this was subtle bug…