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

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)

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.

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

thank you! this was subtle bug…