Dear Users and Developers,
I am simulating water transport through graphene sheet. To this aim I am doing a non-equilibrium simulation applying DPD thermostat. When running the simulation (reservoir combined with graphene sheet) I got the following error
ERROR on proc 0: Bond atoms 5691 5693 missing on proc 0 at step 110 (…/neigh_bond.cpp:65)
I already searched about that in mailing list archive. Some experts commented that this issue might be resolved by modifying the following items
bad dynamics, e.g. blowing atoms out of the box and/or Bad initial state,
bad potential parameters, bad timestep
But, I think I regulated the above items before running. In the meanwhile, when checking out it via viz everything seems fine.
I would be appreciated if anybody who encountered this problem shares his/her experiences.
Here is my input
***************** Initialization *********************
units real
dimension 3
boundary p p p
atom_style full
read_data LAMMPS-DaTa.dat
group carbon type 1
group hydrogen type 2
group oxygen type 3
group water type 2 3
set group oxygen charge -0.8476
set group hydrogen charge 0.4238
set group carbon charge 0.0000
comm_style brick
comm_modify vel yes
pair_style hybrid/overlay lj/cut/coul/long 10.0 10.0 dpd/tstat 300.0 300.0 10.0 34387
pair_coeff 1 1 lj/cut/coul/long 0.000000 0.0000 #lj/cut/coul/long
pair_coeff 1 2 lj/cut/coul/long 0.00000 0.00000
pair_coeff 1 3 lj/cut/coul/long 0.093627 3.1900
pair_coeff 2 2 lj/cut/coul/long 0.000000 0.0000
pair_coeff 2 3 lj/cut/coul/long 0.000000 0.0000
pair_coeff 3 3 lj/cut/coul/long 0.155300 3.16900
#pair_coeff * * tersoff SiC_1994.tersoff NULL NULL C
pair_coeff 1 1 dpd/tstat 0.02 10.0
pair_coeff 1 2 dpd/tstat 0.02 10.0
pair_coeff 1 3 dpd/tstat 0.02 10.0
pair_coeff 2 2 dpd/tstat 0.02 10.0
pair_coeff 2 3 dpd/tstat 0.02 10.0
pair_coeff 3 3 dpd/tstat 0.02 10.0
bond_style harmonic
bond_coeff 1 529.581 1.0
angle_style harmonic
angle_coeff 1 37.95 109.47
fix force_zero carbon setforce 0.0 0.0 0.0
fix vel_zero carbon move linear 0.0 0.0 0.0 units lattice
velocity water create 300.0 34387 rot yes dist gaussian # for water
kspace_style ewald 1.0e-6
*************** Setting ******************************
neighbor 3.0 bin
neigh_modify delay 0 every 10 check yes
reset_timestep 0
delete_atoms overlap 0.3 all all
#minimize 1.0e-4 1.0e-6 100 100000
#min_style cg
compute peatom all pe/atom
compute keatom all ke/atom
thermo 200
thermo_style custom step temp pe etotal press vol
thermo_modify norm no flush yes
fix ensemble_set water nve #temp 300.0 300.0 100.0
fix spce_model water shake 0.0001 20 0 b 1 a 1
fix 3 water addforce 0.0 0.0 0.2
variable end equal 3000
dump pos all custom ${end} pos_filename id element type q x y z
dump_modify pos format “%5d %5s %d %13.10f %17.12f %17.12f %17.12f”
dump_modify pos sort id
dump_modify pos element C HW OW
dump vel all custom ${end} vel_filename id element vx vy vz
dump_modify vel format “%5d %5s %18.15f %18.15f %18.15f”
dump_modify vel sort id
dump_modify vel element C HW OW
dump trj all custom 500 wat.dat id element type x y z vx vy vz fx fy fz
dump_modify trj sort id
dump_modify trj element C HW OW
write_data waterinfo.data
write_restart waterinfo.restart
timestep 2
run 3000