Hi all,
I am trying to carve out a droplet from a hydrocarbon simulation. I am defining a region outside the sphere of desired radius, and then deleting the atoms, with complete molecules. The simulation box is 140 nm x 140 nm x 140 nm big. I am able to carve out a sphere of 15 nm radius, but when I try to carve out a bigger liquid sphere, it throws the error, “Bond atom missing in image check”. I have tried increasing the one and page in neigh_modify. Also, tried to use different restart file. I think this might be due to some atoms with non-zero image, but not sure how to rectify this.
Below is the chunk of code to carve out the sphere (This works fine)
region NPsphere sphere 250.0 250.0 250.0 157.8
region emptySpace sphere 250.0 250.0 250.0 157.8 side out
delete_atoms region emptySpace compress no mol yes
But
region NPsphere sphere 250.0 250.0 250.0 257.8
region emptySpace sphere 250.0 250.0 250.0 257.8 side out
delete_atoms region emptySpace compress no mol yes
does not work.
The complete script is given below for your reference.
units real
dimension 3
boundary p p p
atom_style full
comm_modify vel yes
neighbor 1.5 bin
neigh_modify one 300000 page 3000000
variable Nsteps equal 800000
variable dt equal 1
variable seed equal 12345
variable T equal 300
variable P equal 7
pair_style lj/cut/coul/cut 8.75 25.0
#Bonds
bond_style harmonic
#Angles
angle_style harmonic
#Dihedrals
dihedral_style opls
#Non-bonded
special_bonds lj/coul 0.0 0.0 0.5
read_restart ../../step_2_liquid_simulation/liqP7.restart.3000000
pair_coeff 1 1 0.065999 3.500000 # C00 C00
pair_coeff 2 2 0.065999 3.500000 # C01 C01
pair_coeff 3 3 0.065999 3.500000 # C02 C02
pair_coeff 4 4 0.065999 3.500000 # C03 C03
pair_coeff 5 5 0.065999 3.500000 # C04 C04
pair_coeff 6 6 0.065999 3.500000 # C05 C05
pair_coeff 7 7 0.065999 3.500000 # C06 C06
pair_coeff 8 8 0.065999 3.500000 # C07 C07
pair_coeff 9 9 0.065999 3.500000 # C08 C08
pair_coeff 10 10 0.065999 3.500000 # C09 C09
pair_coeff 11 11 0.065999 3.500000 # C0A C0A
pair_coeff 12 12 0.065999 3.500000 # C0B C0B
pair_coeff 13 13 0.030000 2.500000 # H0C H0C
pair_coeff 14 14 0.030000 2.500000 # H0D H0D
pair_coeff 15 15 0.030000 2.500000 # H0E H0E
pair_coeff 16 16 0.026291 2.500000 # H0F H0F
pair_coeff 17 17 0.026291 2.500000 # H0G H0G
pair_coeff 18 18 0.026291 2.500000 # H0H H0H
pair_coeff 19 19 0.026291 2.500000 # H0I H0I
pair_coeff 20 20 0.026291 2.500000 # H0J H0J
pair_coeff 21 21 0.026291 2.500000 # H0K H0K
pair_coeff 22 22 0.026291 2.500000 # H0M H0M
pair_coeff 23 23 0.026291 2.500000 # H0N H0N
pair_coeff 24 24 0.026291 2.500000 # H0O H0O
pair_coeff 25 25 0.026291 2.500000 # H0P H0P
pair_coeff 26 26 0.026291 2.500000 # H0Q H0Q
pair_coeff 27 27 0.026291 2.500000 # H0R H0R
pair_coeff 28 28 0.026291 2.500000 # H0S H0S
pair_coeff 29 29 0.026291 2.500000 # H0T H0T
pair_coeff 30 30 0.026291 2.500000 # H0U H0U
pair_coeff 31 31 0.026291 2.500000 # H0V H0V
pair_coeff 32 32 0.026291 2.500000 # H0W H0W
pair_coeff 33 33 0.026291 2.500000 # H0X H0X
pair_coeff 34 34 0.026291 2.500000 # H0Y H0Y
pair_coeff 35 35 0.026291 2.500000 # H0Z H0Z
pair_coeff 36 36 0.030000 2.500000 # H10 H10
pair_coeff 37 37 0.030000 2.500000 # H11 H11
pair_coeff 38 38 0.030000 2.500000 # H12 H12
pair_coeff 39 39 0.0739378 3.29155 # N N
group Catoms type 1 2 3 4 5 6 7 8 9 10 11 12
group Hatoms type 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
thermo_style custom step etotal ke pe press vol density temp
thermo 10
timestep ${dt}
fix rigidbonds all shake 0.0001 20 0 b 2 3 4 6 7 9 10 12 13 15 16 18 19 21 22 24 25 27 28 30 31 33 34 35 36 37
fix liq all npt temp ${T} ${T} $(50*dt) iso ${P} ${P} $(2000*dt)
run 1 # Ran for one step to see if the simulation is ready to run; it runs fine for this step
region NPsphere sphere 250.0 250.0 250.0 257.8
region emptySpace sphere 250.0 250.0 250.0 257.8 side out
delete_atoms region emptySpace compress no mol yes
run 0
write_data liqP7.50nm.data
Thanks in advance. I am using LAMMPS (2 Aug 2023 - Update 2) in NERSC.