Hello LAMMPS Experts,
Recently, i installed the openmpi version of LAMMPS in Desktop Computer (i5) which has 4 CPU.
The LAMMPS script running successfully in serial version using this command.
./lmp_openmpi < in.lammps
but when i am running in parallel using this command.
mpirun -np 4 ./lmp_openmpi < in.lammps
then it giving the error “ERROR on proc 0: Bond atom missing in image check (…/domain.cpp:625)”
I have gone through this error thread and people recommend it because of bad dynamics. So, i run the script for 10K steps in serial version and save current simulation using write_restart command.
Then i read again the binary file using read_restart command and run in parallel mode but still i am getting the same error.
I do not know where am i wrong?. So, please suggest me something.
My snippet of lammps script is here.
units lj
atom_style bond
read_restart restart.next.polymer
neighbor 0.5 bin
neigh_modify every 1 delay 1
bond_style harmonic
bond_coeff 1 0.29296875 0.0
pair_style gauss 3.5
pair_coeff * * -1.5 1.0
region mySphere sphere 0.0 0.0 0.0 21.16
velocity all create 1.0 808966
fix 1 all nve
fix 2 all langevin 1.0 1.0 1.0 904297
fix wall all wall/region mySphere lj126 1.0 1.0 1.0
thermo 100
timestep 0.005
run 24000000
Thanks.
Ankit Agrawal
Computational Biology
Institute of Mathematical Science
INDIA
Hello LAMMPS Experts,
Recently, i installed the openmpi version of LAMMPS in Desktop Computer (i5) which has 4 CPU.
The LAMMPS script running successfully in serial version using this command.
./lmp_openmpi < in.lammps
but when i am running in parallel using this command.
mpirun -np 4 ./lmp_openmpi < in.lammps
then it giving the error “ERROR on proc 0: Bond atom missing in image check (…/domain.cpp:625)”
I have gone through this error thread and people recommend it because of bad dynamics. So, i run the script for 10K steps in serial version and save current simulation using write_restart command.
There is not a single possible explanation for this. Other options are: too large a timestep, too short a communication cutoff, too small a neighbor list skin, too infrequent neighbor list updates, bad potential parameters, bad bond topology.
Then i read again the binary file using read_restart command and run in parallel mode but still i am getting the same error.
I do not know where am i wrong?.
You didn’t follow through the many other possible reasons, which means you didn’t do a thorough enough search through the mailing list archives.
So, please suggest me something.
Keep on digging and debugging.
My snippet of lammps script is here.
Providing only script fragments is a very annoying habit. How do you know the problem is not in the part you don’t show us?
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