Hello,
I am using lj/cut/tip4p/long pair style. The data file with initial configuration has TIP4P2005 water (dummy atom not specified). I am getting the following warning, which implies that LAMMPS is not creating the dummy atom with the negative charge for the water model:
WARNING: System is not charge neutral, net charge = 111.28 (src/kspace.cpp:327)
The simulation box has only water. i would appreciate any help with this!
Below is my input script:
units real
dimension 3
boundary p p p
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 12 8.5
read_data waterphasedatafile.txt
pair_coeff 1 1 0.1852 3.1589
pair_coeff 1 2 0 0
pair_coeff 2 2 0 0
bond_style harmonic
bond_coeff 1 540.76499 0.9572
angle_style harmonic
angle_coeff 1 87.90879 107.4
group water type 1:100
kspace_style pppm/tip4p 1.0e-4
fix 1 water shake 0.0001 100 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
neigh_modify delay 0 every 1 check yes
timestep 2.0
thermo_style custom step temp press pe
thermo 100
dump 0 all custom 500 all.*.xyz id mol type x y z ix iy iz vx vy vz
run 2000
write_restart restart1.save
Below is the snapshot of part of the log file:
SLURM_NTASKS: 1
LAMMPS (23 Jun 2022)
using 1 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
using multi-threaded neighbor list subroutines
Reading data file …
orthogonal box = (0 0 0) to (30 30 30)
1 by 1 by 1 MPI processor grid
reading atoms …
300 atoms
scanning bonds …
2 = max bonds/atom
scanning angles …
1 = max angles/atom
reading bonds …
200 bonds
reading angles …
100 angles
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
300 atoms in group water
Finding SHAKE clusters …
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
100 = # of frozen angles
find clusters CPU = 0.000 seconds
PPPM initialization …
extracting TIP4P info from pair style
WARNING: System is not charge neutral, net charge = 111.28 (src/kspace.cpp:327)
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20642969
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.021501536
estimated relative force accuracy = 6.4751236e-05
using double precision FFTW3
3d grid and FFT values/proc = 3375 1000
Below is the snapshot of my initial configuration file:
LAMMPS data file for Water
300 atoms
200 bonds
100 angles
0 dihedrals
2 atom types
1 bond types
1 angle types
0 dihedral types
0 30 xlo xhi
0 30 ylo yhi
0 30 zlo zhi
Masses
1 15.9994
2 1.008
Atoms
1 1 1 0 12.674 17.86 16.857
2 1 2 0.5564 12.372 17 17.146
3 1 2 0.5564 12.78 18.687 17.328
4 2 1 0 23.484 14.139 18.994
5 2 2 0.5564 23.124 14.491 19.807
6 2 2 0.5564 23.062 13.74 18.233
7 3 1 0 19.735 26.785 22.122
8 3 2 0.5564 20.681 26.797 22.261
9 3 2 0.5564 19.198 26.364 21.449
10 4 1 0 5.33 11.827 27.126
11 4 2 0.5564 5.135 10.943 26.819
12 4 2 0.5564 4.835 12.43 27.681
13 5 1 0 8.3 26.308 6.054
14 5 2 0.5564 8.122 27.241 5.94
15 5 2 0.5564 9.11 25.836 6.248