Prooblem reading the data file & MPI job aborted

LAMMPS LAMMPS Beginners
1

I would like to have a system combined with water & polymer. I have used topotools of VMD to combine water & the equilibrated polymer data file. Here in the combined data file, the distance between the water & polymer is almost 6 Å so that it doesn’t overlap to each other. However, I am getting the error MPI Job aborted.

To check if my merging method is correct or not, I tried to combine the water with a graphene wall & run a short simulation successfully. To check the polymer,I have also separately simulate only the polymer successfully. Therefore, I am guessing either the problem is combing the water with the polymer & read that data file to lammps or in my input script.

As I am only getting the error MPI job aborted, I don’t understand where eaxctly I should look for to solve this problem. Could anyone please help me with the problem?
For your reference , My Lammps version is 2 Aug 2023.

Data :
combined_data.data (2.1 MB)

Script:
input_script.in (6.2 KB)

Thanks for your help in advance.

Sincerely,
Morshed Mahmud
Phd Student
Rennes Institute of Chemical Science

2

That is not a message from LAMMPS but from the MPI library. Thus there has to be some error message from LAMMPS before that. If necessary, you can run interactively just a single process to see what error this is. However, before doing that, please read on.

Before running a simulation, you should visualize your input geometry.
You can see below what I get to see. It looks like your bonds are wrong because you must have use wrapped coordinates instead of unwrapped for the upper part and also the box dimensions seem to be wrong.

You can also see an indication of the wrong bonds from this warnings:

WARNING: Inconsistent image flags (src/domain.cpp:814)
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:935)

…and the excessive potential energy for bonded interactions in the thermodynamic data:

Per MPI rank memory allocation (min/avg/max) = 70.16 | 70.16 | 70.16 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              32420.12       1.2260094e+08  1.2263336e+08 -15296605

initial_geometry
initial_geometry672×848 274 KB

You have to correct your creation of the data file.

3

Dear Dr. Axel,

Thanks a lot for your wonderful details solution.
Now, I am getting the full understanding why it was giving that error.