Hi folks,
I am using an atomic configuration as obtained from an NPT run.
The first few lines of the frame (with desired timestep) of the dump file is :
ITEM: TIMESTEP
49000
ITEM: NUMBER OF ATOMS
403200
ITEM: BOX BOUNDS pp pp pp
-0.177268 183.035
-0.0590892 61.0117
-0.350972 362.391
ITEM: ATOMS id type x y z
… … … … … … … … … … …
But I have seen that for a number of atoms, the coordinates lie outside the dimension of the simulation box:
For example,
example 1:
19740 1 183.174 54.8737 12.5966 (x : out of the box)
example 2 :
379078 2 129 39.7042 362.388 (z- coordinate is out pf the box)
example 3:
168564 2 75.6738 61.1543 137.879 (y : out of box)
and there are many … !!!
As a result, when I am using this config file for the next run, it is ending with the following error :
Reading data file …
orthogonal box = (-0.177268 -0.0590892 -0.350972) to (183.035 61.0117 362.392)
2 by 1 by 2 MPI processor grid
403197 atoms
ERROR: Did not assign all atoms correctly (read_data.cpp:575)
Is there any known BUG in LAMMPS which produce such funny dump file ?
If "there are many" as you said, then why is it that only 3 atoms are
disappeared (403200 original, 403197 afterwards)? Therefore, this can
not the cause of the problem.
The fact is that atoms get wrapped around the periodic boundary
conditions, since the bounds are "pp pp pp". You are seeing the error
possibly due to incorrect conversion of the dump file to a data file,
or other errors we do not know.
Ray
Hi shan,
Thanks for the reply.
But, I am not converting the dump file to data file. In fact, I am splitting the dump file into a number of frames and using the final frame as the input to a new run. I am ONLY changing the FORMAT of the header to be consistent with the LAMMPS format.
But, I missed one point in my last mail.
The the dump file was generated with " boundary p p p" .
But in the next run, I am using “boundary p p f” : a FIXED bounday in the z - direction.
is this the origin of the error ?
The the dump file was generated with " boundary p p p" .
But in the next run, I am using "boundary p p f" : a FIXED bounday in the z
- direction.
is this the origin of the error ?
Yes, that could be a source of error. Try first wrap atoms around the
periodic boundary, then change boundary (with change_box command).
Ray
Dump files can list atoms slightly outside the box.
See the dump doc page for an explanation.
If you read them back into a box that is not
periodic, then the atoms have to be inside the
box, else they will be lost.
You can read them back into a periodic
box, and they won't be lost, then you can
use the change_box command to change the
box to non-periodic.
Steve