Hello LAMMPS users,
I am simulating a system consisting of two material in the presence of water.
I have created the LAMMPS data file using msi2lmp tool with CVFF force field parameters.
But after optimization when I try to move water molecules and epoxy to perform SMD by applying velocity to end carbon atom of epoxy molecule it gives me the error of "Bond missing on Proc".
I have tried changing the parameter values of neighbor and timesteps but it just changed the error from " Bond missing on Proc to Angle the missing on Proc".
I have already gone through the SourceForge mailing list and could not find a solution yet. It would be really helpful if anyone could provide me a solution to this problem on how to deal with the errors.
please find attached LAMMPS file.
Thanks and Regards,
Manish
Test.in (2.65 KB)
WetMod.data (329 KB)
It’s usually due to bad dynamics. If you bonded atoms far away from each
other then LAMMPS cannot find the bond pair. So check that your dynamics
is stable (thermo ouptput every step, viz, etc).
Steve
Hi Steve,
The system which I’m simulating consist of organic(Epoxy) and inorganic material(SiO2) and the force field I’m using is CVFF and this force field lacks some data of bond between two atoms.
This missing data I have entered manually which is mention in the research paper I’m referring ( Actually I am trying to produce the same result as in the research paper ).
Also, the thermo output shows that atom is experiencing a huge amount of force ( I think that is the reason of bad dynamic)
If, you could suggest to me some method or solution to deal with this error would be really helpful for me.
Thanks and Regards,
Manish
Hi Steve,
The system which I'm simulating consist of organic(Epoxy) and inorganic
material(SiO2) and the force field I'm using is CVFF and this force field
lacks some data of bond between two atoms.
This missing data I have entered manually which is mention in the research
paper I'm referring ( Actually I am trying to produce the same result as in
the research paper ).
Also, the thermo output shows that atom is experiencing a huge amount of
force ( I think that is the reason of bad dynamic)
actually, your input doesn't even run with the current version of
LAMMPS reporting the following error:
LAMMPS (16 Mar 2018)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (-3.03103 -0.966296 -0.964147) to (25.4947 36.696 18.6069)
1 by 1 by 1 MPI processor grid
reading atoms ...
1625 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
ERROR on proc 0: Invalid atom ID in Dihedrals section of data file
(../atom.cpp:1167)
Last command: read_data WetMod.data
this would mean your data file is not correct.
axel
[...]
actually, your input doesn't even run with the current version of
LAMMPS reporting the following error:
LAMMPS (16 Mar 2018)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (-3.03103 -0.966296 -0.964147) to (25.4947 36.696 18.6069)
1 by 1 by 1 MPI processor grid
reading atoms ...
1625 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
ERROR on proc 0: Invalid atom ID in Dihedrals section of data file
(../atom.cpp:1167)
Last command: read_data WetMod.data
this would mean your data file is not correct.
...and to explain a bit further, this error message means, that your
atom IDs in the Dihedrals section are either out of range or your
dihedral definition is invalid, e.g. by having duplicate atom IDs.
axel.
Dr. Axel,
I have created the new data file for my system using the same msi2lmp tool and when I run my input file in Aug 2017 version of LAMMPS it gives me the same error of "bond atom missing on proc"( please find attached log file and input file ) but when I run my input file in 2018 version of LAMMPS it gives me the error which you mention as show below:
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (…/comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
Reading data file …
orthogonal box = (0.306346 -6.41639 -2.71385) to (33.8937 34.5864 40.9376)
1 by 1 by 1 MPI processor grid
reading atoms …
1942 atoms
scanning bonds …
4 = max bonds/atom
scanning angles …
6 = max angles/atom
scanning dihedrals …
ERROR on proc 0: Invalid atom ID in Dihedrals section of data file (…/atom.cpp:1167)
Last command: read_data WetSystem.data
why the old and current version gives different errors and if the there are duplicate atom IDs then what method should i use to correct them.
Thanks and Regards,
Manish
log.lammps (21.4 KB)
System.in (2.68 KB)
WetSystem.data (424 KB)
Dr. Axel,
I have created the new data file for my system using the same msi2lmp tool
and when I run my input file in Aug 2017 version of LAMMPS it gives me the
same error of "bond atom missing on proc"( please find attached log file and
input file ) but when I run my input file in 2018 version of LAMMPS it
gives me the error which you mention as show below:
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
(../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.306346 -6.41639 -2.71385) to (33.8937 34.5864 40.9376)
1 by 1 by 1 MPI processor grid
reading atoms ...
1942 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
ERROR on proc 0: Invalid atom ID in Dihedrals section of data file
(../atom.cpp:1167)
Last command: read_data WetSystem.data
why the old and current version gives different errors and if the there are
duplicate atom IDs then what method should i use to correct them.
the old version doesn't complain, because it does not have the check
for invalid topology data.
i don't know why msi2lmp produces these files, but i suspect that
already the topology data you have as input may be incorrect.
axel.