Simulation not proceeding beyond step 0 and is hung up indefinitely serially as well as parallely

This is the description of my problem broken down in 3 sections:

Setup :

I am trying to run a very simple simulation of creating a grain boundary in Cu FCC crystal of size 57.76 x 57.76 x 57.76 A in x, y and z directions.

The created system looks alright when visualised, so that is not a problem, however due to the grain separating the two regions, the top region is somewhat above the grain boundary leading to a small gap of 2-3 A between atoms, so could this be a problem causing this issue?

Schedule:

The schedule is quite simple,

  1. read the data through data.Cu file written in atomic style
  2. Do CG run to minimize the system energy and get proper configuration
  3. Run a npt simulation at 10 K for 10000 steps.

Problem:

I dont get any error message as simulation does not proceeds beyond first step and hangs their forever.

And it happens even if I use just 1 processor instead of many.

Attached is the in.CuGrain input file for lammps, combined with the potential file and data file, so that you all can have a look.

log.out is the output file for the simulation which shows the problem, and
Cu_mishin1.eam.alloy is the potential file used for the simulation,

I am unable to provide you all with the input data file due to size restriction for the mailing list.

First few lines of the input file are as shown below:

Cu grain

59904 atoms

1 atom types

0.0 57.7600 xlo xhi

0.0 57.7600 ylo yhi

0.0 57.7600 zlo zhi

Masses

1 63.55 # Mass of Cu atom

Atoms

1 1 0.0603333 0.0603333 0.0603333

2 1 0.0603333 0.0603333 0.0603333

3 1 0.0603333 0.0603333 3.67033

4 1 0.0603333 0.0603333 3.67033

5 1 0.0603333 0.0603333 7.28033

6 1 0.0603333 0.0603333 7.28033

7 1 0.0603333 0.0603333 10.8903

8 1 0.0603333 0.0603333 10.8903

Any suggestions regarding the issue will be really helpful and I will greatly appreciate your time and concern.

Thanks,

log.out (1.22 KB)

in.CuGrain (1.14 KB)

Cu_mishin1.eam.alloy (690 KB)

This is the description of my problem broken down in 3 sections:

*Setup :*

I am trying to run a very simple simulation of creating a grain boundary
in Cu FCC crystal of size 57.76 x 57.76 x 57.76 A in x, y and z directions.

The created system looks alright when visualised, so that is not a
problem, however due to the grain separating the two regions, the top
region is somewhat above the grain boundary leading to a small gap of 2-3 A
between atoms, so could this be a problem causing this issue?

​you have -NaN for your potential energy in step 0, so you *do* have a
problem with your geometry.​

​[...]

I am unable to provide you all with the input data file due to size

restriction for the mailing list.

First few lines of the input file are as shown below:

  # Cu grain

   59904 atoms

   1 atom types

   0.0 57.7600 xlo xhi

   0.0 57.7600 ylo yhi

    0.0 57.7600 zlo zhi

   Masses

   1 63.55 # Mass of Cu atom

  Atoms

    1 1 0.0603333 0.0603333
0.0603333

    2 1 0.0603333 0.0603333
0.0603333

​here you have two atoms on top of each other!​

    3 1 0.0603333 0.0603333
3.67033

    4 1 0.0603333 0.0603333
3.67033

​and two ​more atoms on top of each other!!

    5 1 0.0603333 0.0603333
7.28033

    6 1 0.0603333 0.0603333
7.28033

and ​another pair of atoms with the same coordinates!!!​

    7 1 0.0603333 0.0603333
10.8903

    8 1 0.0603333 0.0603333
10.8903

​and so on. how can you in clean conscience claim, that there is no problem
with your geometry, when there so obviously is one??

​axel.​