I tried to build an ordered water molecule structure using the replicate command, but I encountered a “bond atom missing” error right at the beginning. Below is my input script.
units metal
atom_style full
boundary p p f
read_data 1H2O1
replicate 26 26 26
pair_style lj/cut/tip4p/cut 1 2 1 1 0.1546 12
bond_style harmonic
angle_style harmonic
pair_coeff 1 1 0.008039 3.1589 # O-O
pair_coeff 2 2 0.0 0.0 # H-H
pair_coeff 1 2 0.0 0.0 # O-H
pair_modify tail yes
bond_coeff 1 43.36 0.9572 # O-H
angle_coeff 1 4.336 104.52 # H-O-H
group water type 1 2
neighbor 3.0 bin
neigh_modify delay 0 every 1 check yes
velocity all create 300 12345 dist gaussian
#fix 1 water shake 1.0e-4 100 0 b 1 a 1
variable massAll equal mass(all)/6.022e23
variable volCm3 equal vol*1.0e-24
variable density_sys equal v_massAll/v_volCm3
thermo 1000
thermo_style custom step temp vol etotal pe ke epair ecoul lx ly lz v_density_sys cpuremain
thermo_modify flush yes
fix nvt all nvt temp 300 300 200.0
timestep 1.0
run 150000
write_data 26by26by26_H2O1.data
Step Temp Volume TotEng PotEng KinEng E_pair E_coul Lx Ly Lz v_density_sys CPULeft
0 300 1058712.9 128807.35 126762.7 2044.6499 126762.7 127272.04 101.92 101.92 101.92 0.49663825 0
ERROR on proc 0: Bond atoms 16825 16826 missing on proc 0 at step 1 (…/ntopo_bond_all.cpp:63)
Last command: run 150000