[lammps-users] restart2data tool

LAMMPS LAMMPS Mailing List Mirror
1

hi

when i use the restart2data tool on a restart file for a system containing water molecules, everything seems to be fine in the data file that is produced, except that in the “Bonds” section, all the lines are like this:

Bonds

1 0 0 0
2 0 0 0
3 0 0 0
4 0 0 0
5 0 0 0
6 0 0 0
7 0 0 0
8 0 0 0
9 0 0 0
…

In the data file that I used to start the calculation in the first place, the corresponding lines were (there’s only 1 bond type in my system, the O-H bond in water):

Bonds

1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14

However, the “Angles” section in the restart file produced by restart2data comes out fine.

I compiled and ran restart2data and LAMMPS on the same machine, so the binary restart file produced by LAMMPS should have been readable by restart2data. I’m using a “fix shake” to keep the bond lengths and angles fixed.

Any ideas why this might be happening?

Thanks
David

2

Can you email me a simple, small example of a binary restart
file that produces this problem? I don't think SHAKE should
matter, but you might try creating the restart file
without the fix shake enabled and see if the result is
different. This is probably a bug with restart2data ...

Also, if you could email your input script that produced the restart file.

Steve