Dear LAMMPS users,
I prepared very simple systems consisting of 4 TIP4P water molecules.
I tried to run the simulations but I got an error message “ERROR: Out of range atoms - cannot compute PPPM”
But, I checked the data files several times. And there was no problem there.
Could you check my input script?
Thank you very much.
====================================================================
Define variables
====================================================================
input data file
variable lmp_data string data.test
temperature and pressure
variable T equal 270.0
variable p equal 3/0.101325
interactions / rcut
variable rcut equal 12
number of steps / timestep
variable nstep equal “10000000”
variable dt equal 0.001
output
variable freq_thermo equal “1” # thermo output every
variable freq_frame equal “1” # frame output every
variable freq_snap equal “1” # xyz output every for safety (rerun)
====================================================================
Initialization
====================================================================
units real
boundary p p p
comm_modify vel yes cutoff 4
neigh_modify delay 0 every 1 check yes page 500000 one 50000
atom_style full
====================================================================
====================================================================
read_data ${lmp_data}
1 WH
2 WO
mass 1 1.008
mass 2 15.9994
pair_style lj/cut/tip4p/long 2 1 1 1 0.1546 12.0
pair_modify mix arithmetic
pair_coeff 1 1 0 0
pair_coeff 1 2 0 0
pair_coeff 2 2 0.1852 3.1589
bond_style harmonic
bond_coeff 1 0 0
angle_style harmonic
angle_coeff 1 0 0
kspace_style pppm/tip4p 1.0e-4
====================================================================
Constraints
====================================================================
fix shake all shake 0.0001 20 10 b 1 a 1
====================================================================
1. RELAX / NVE limit
====================================================================
fix thermostat all temp/berendsen {T} {T} 100.0
#fix barostat all press/berendsen aniso {p} {p} 1000.0
thermo ${freq_thermo}
thermo_style custom step cpuremain temp press etotal ebond
thermo_modify flush yes
dump dtrj all custom {freq_frame} {lmp_data}.lammpstrj id type x y z mol
dump dsnap all custom {freq_snap} {lmp_data}_*.lammpstrj id type x y z mol
reset_timestep 0
timestep ${dt}
run ${nstep}
unfix nvelim
undump dtrj
undump dsnap
write_restart restart.RELAX01
print “01.RELAX done”
12 atoms
8 bonds
4 angles
2 atom types
1 WH
2 WO
1 bond types
1 WH-WO
1 angle types
1 WH-WO-WH
-5.0000000 100.7137586 xlo xhi
-5.0000000 100.9912000 ylo yhi
-5.0000000 100.6824000 zlo zhi
-0.0000000 0.0000000 0.0000000 xy xz yz
Atoms
1 1 2 -1.1128000 40.3911473 33.0061704 31.9715144
2 1 1 0.5564000 40.1511599 33.9327975 31.9715144
3 1 1 0.5564000 41.3483473 33.0061704 31.9715144
4 2 2 -1.1128000 40.3911473 33.0061704 27.5520856
5 2 1 0.5564000 40.1511599 33.9327975 27.5520856
6 2 1 0.5564000 41.3483473 33.0061704 27.5520856
7 3 2 -1.1128000 40.3911473 33.0061704 37.4726856
8 3 1 0.5564000 40.1511599 33.9327975 37.4726856
9 3 1 0.5564000 41.3483473 33.0061704 37.4726856
10 4 2 -1.1128000 41.2379475 34.4728714 29.7618000
11 4 1 0.5564000 40.9979601 35.3994986 29.7618000
12 4 1 0.5564000 42.1951475 34.4728714 29.7618000
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12