Greetings,
lammps-users
I have been trying to shrink the box size of my system, a general fix npt works like a charm for shrinking the box size but the atoms migrated outside the box as seen when visualized with VMD, In order to avoid it, being an amateur at lammps I resorted to the use of ‘dump_modify pbc yes’ to remap the atoms into the box but always ran into the following error -
‘mpirun noticed that process rank 6 with PID 0 on node node22 exited on signal 11 (Segmentation fault).’
The simulation is running one of the nodes of a cluster. I understand I might not be able to achieve the end goal with dump_modify given my minuscule knowledge about lammps, but the query I have is why is it that the usage of this particular command leads to a specific error.
Running the simulation without that particular command in the script works and the simulation is terminated normally.
I am using the lampps29oct20 stable release.
The input script is as follows -
####VARIABLES####
variable datf index relax_HDPE12K.data
variable jid index HDPE12K
####Initialize####
dimension 3
atom_style full
boundary p p p
units real
log log.${jid}
####Potential_Initialize####
pair_style lj/cut 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
####Data_Input####
read_data ${datf}
####Interatomic_Potential####
pair_coeff 1 1 0.023775 3.8983
pair_coeff 2 2 0.0038 3.195
pair_coeff 1 2 0.009505 3.5292
bond_coeff 1 350 1.33
bond_coeff 2 350 0.99
angle_coeff 1 33 109.47
angle_coeff 2 63 112.4
angle_coeff 3 50 109.5
dihedral_coeff 1 -2.5 1 3
dihedral_coeff 2 -2.0 1 3
dihedral_coeff 3 -3.4 1 3
####Shrink####
timestep 0.1
dump 1 all custom 1000 shrink_{jid}.lammpstrj id type x y z ix iy iz
dump_modify 1 pbc yes
fix 1 all npt temp 1 1 (100.0*dt) tchain 1 iso 1 1 500
run 1000000
write_data shrink_${jid}.data pair ij