Hi there,
I have been trying to simulate polycrystalline surfaces of copper. I’m exposing a copper surface to methane molecules and other small hydrocarbons including atomic carbon. To do so, I use the lattice command to create a first lattice orientation, then I create copper atoms in the region I define. This initially create the 211 surface. Then I do the same, but create the 001 surface of Copper. When Creating the region, I let the two overlap, then I use the delete atoms command to create the polycrystalline surface. This simulation takes a long time to run as it is, and sometimes, if I make the runtime too long, it will terminate telling me that some atoms have been lost on a proc. I was wondering if you have any suggestions that could help me improve the speed of the simulations and help me resolve the issue of lost atoms. My Code is pasted below (this one creates a polycrystalline surface with 211 and 001 in the presence of methane:
units metal
atom_style full
dimension 3
boundary p p p
lattice fcc 3.6149 orient x 0 -1 1 orient y 1 -1 -1 orient z 2 1 1
region box block 0 20 0 20 0 16 #Define a box for the super-cell
create_box 3 box bond/types 1 angle/types 1 extra/bond/per/atom 4 extra/angle/per/atom 4
region in block 0 10 0 10 0 9.33 side in
create_atoms 1 region in
molecule CH4 methane3.mol
mass 1 63.54 #Define mass of Cu atom
group one region in
lattice fcc 3.6149 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region in2 block 0 20 9 20 0 9.33 side in
create_atoms 1 region in2
mass 2 12.01 #Define mass of C atom
group two region in2
pair_style comb3 polar_off #Make use of comb3 potential
pair_coeff * * ffield.comb3 Cu C H #Define comb3 for Cu and C and H
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
mass 2 12.01 #Define mass of C and H atoms
mass 3 1.01
delete_atoms overlap 0.3 all all
lattice diamond 3.567 # Lattice constant of C
region out block 0 10 0 10 0 9.33 side out
create_atoms 1 random 10 1 out mol CH4 1
bond_style harmonic
bond_coeff * 5.0 1.0
compute eng all pe/atom
compute eatoms all reduce sum c_eng
timestep 0.00025
min_style cg
minimize 1e-4 1e-6 100 1000
fix 1 all npt temp 1 300 0.025 iso 0 0 0.25
thermo_style custom step temp etotal pe evdwl ecoul c_eatoms press vol lx ly lz xz
thermo_modify norm yes
thermo 1000