hi dear lammps users.
i was trying to run a simulation on windows. it has an error with data file saying unknown identifier for one line of data file while it’s similar in to other lines of file.
this is the line making the problem:
40 1 1 0.00 0.00 -3.5
the atom_style is angle.
can you tell me what’s the problem with this part of data file
this atom is the last atom in my data file.
hi dear lammps users.
i was trying to run a simulation on windows. it has an error with data file
saying unknown identifier for one line of data file while it's similar in
to other lines of file.
this is the line making the problem:
40 1 1 0.00 0.00 -3.5
the atom_style is angle.
can you tell me what's the problem with this part of data file
this atom is the last atom in my data file.
that would hint at a misformatted or inconsistent data file. e.g. you
might have entries that are not consistent with the numbers in the
header of the data file.
did you write your data file manually, with a program of your own or
one of the available tools?
axel.
the data file is written manually. i can’t find the inconsistency unfortunately.
here is the header of the data file:
40 atoms
114 bonds
228 angles
1 atom types
1 bond types
1 angle types
-15.700 15.700 xlo xhi
-15.700 15.700 ylo yhi
-15.700 15.700 zlo zhi
Atoms
the data file is written manually. i can't find the inconsistency
unfortunately.
here is the header of the data file:
40 atoms
114 bonds
228 angles
the first line is skipped.
1 atom types
1 bond types
1 angle types-15.700 15.700 xlo xhi
-15.700 15.700 ylo yhi
-15.700 15.700 zlo zhiAtoms
it is impossible to help debugging something with incomplete data.
due to a few quirks, it is generally recommended to use some kind tool
or script to build data files. there are several converters and build
tools bundled with LAMMPS and there is the topotools plugin for VMD
(which is bundled with VMD since it supports more than just writing
data files for LAMMPS).
axel.
LAMMPS does not give very helpful error messages when there is any
problem in a user's data file.
1) Look at the last line in your log.lammps file, and look at the .cpp
file referenced in the error message. If the error message contains
read_data:575, then open the "read_data.cpp" file and go to line 575.
See if you can figure out what went wrong. (For example, in this
particular case try recompiling LAMMPS and use printf() to print out
the nread and natoms variables before it crashes. If it helps,
there's a makefile for ubuntu with debugger support at
http://lammps.sandia.gov/threads/msg37461.html. Download
"Makefile.ubuntu_dbg")
This may not be very illuminating. If not, try:
2) ...Try loading your data file in another program, such as topotools
or moltemplate.sh, and see what it says.
I have found topotools error messages can be useful to help me
figure out where the problem is.
Since your system is quite small (less than 200000 atoms), you could
try using ltemplify.py and moltemplate.sh to check for errors in your
files. This will give you detailed error messages, but it is more
work. You will also need an input script for your system containing
the atom_style and force-field coeffs (both input scripts and data
files are checked.) The process is described here:
http://lammps.sandia.gov/threads/msg37461.html
(BUGS: Be sure to download a recent version of moltemplate tools (from
moltemplate.org) before you try this. (v1.14 or later). The
ltemplify.py bug with impropers discussed later in that particular
thread has since been fixed, although there may be other problems.
Please report any bugs you run into.)
Cheers
Andrew