Dear,
I have a difficulty in calculating and asking for advice from the experts.
My model is nanofluid, which includes water molecules and nanoparticles. Now, I want to calculate the number density of water molecules on the surface of the nanoparticel, starting from the surface of the nanoparticle, as the distance increases.
I want to output the result is similar to “compute chunk/atom bin/sphere”. How to I implement it??? Please help me, thank you very much.
For now, I look at the manual and use the following command:
echo screen
units real
dimension 3
boundary p p p
region aa block -30 110 -30 110 -30 70
atom_style full
atom_modify id yes map array
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
kspace_style pppm 1.0e-4
pair_style lj/cut/coul/long 10 12
read_data data.681.218_msGnH1 extra/atom/types 2 extra/bond/types 1 extra/angle/types 1
molecule spce spce.mol offset 5 6 12 13 1
lattice sc 4
create_atoms 0 region aa mol spce 12346 units lattice
change_box all x final -30 110 y final -30 110 z final -30 70 units box
mass 1
mass 2
mass 3
mass 4
mass 5
mass 6 15.9994
mass 7 1.008 #h
set type 6 charge -0.8472
set type 7 charge 0.4236
group G1 type 1:5
group G2 type 6:7
delete_atoms overlap 2.5 G2 G1 mol yes compress yes
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
minimize 1.0e-4 1.0e-6 1000 1000
min_modify dmax 0.2
min_style cg #共轭梯度法
dump 1 all custom 10000 water-np-min.lammpstrj id type x y z mass element q
dump_modify 1 sort id element X X X X o h
timestep 1
fix 2 all npt temp 298 298 100 iso 1 1 1000 #drag 1
variable density equal mass(G2)10/(6.0221417930vol)
thermo 1000
thermo_style custom step temp press vol etotal epair emol pxx pyy pzz pe density v_density
restart 1000 restart.water-np-npt1ns1 restart.water-np-npt1ns2
run 2000
unfix 2
reset_timestep 0
timestep 1
compute chunk1 G2 chunk/atom molecule region aa nchunk once ids once compress yes
fix 3 G1 spring/chunk 100 chunk1 com1
fix 4 G2 ave/chunk 100 10 1000 chunk1 density/number file Ndensity.txt
run 20000