Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/srd/in.srd.mixture
e915461c5fdaefficient_neuronet

Last Change
Raw File

in.srd.mixture
View Options

# 2d SRD test: big + small particles
units lj
atom_style colloid
atom_modify first big
dimension 2
# create big particles with sigma 1.0
lattice sq 0.4
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
mass 1 1.0
mass 2 0.01
shape 1 1.0 1.0 1.0
shape 2 0.0 0.0 0.0
group big type 1
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
run 1000
unfix 1
unfix 2
# add small particles as hi density lattice
lattice sq 0.4
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
create_atoms 2 region plane
group small type 2
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 &
radius 0.88 search 0.2 collision slip
fix 3 all enforce2d
# diagnostics
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[8] f_2[9] f_2[10]
thermo_modify temp tbig
thermo 100
dump 1 all atom 250 dump.srd.mixture
run 5000
c4science · Help