Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/USER/atc/fluids/in.double_layer
bf8dc7e0698defficient_neuronet

Last Change
Raw File

in.double_layer
View Options

# AtC electric field module and BCs
# This benchmark using fix_charge to set up a charged surface
# and computes the resulting double layer dynamics
log double_layer.log
echo both
units metal
atom_style full
dimension 3
neighbor 2 bin
neigh_modify every 1 check yes
boundary f f f
timestep 0.0005
thermo 100
dielectric 81.
newton off
pair_style lj/cut 13.000000
pair_modify mix arithmetic
read_data waternve.atm
reset_timestep 0
variable nsteps equal 1000
variable dumpfreq equal ${nsteps}/10
variable nx equal 4
variable ny equal 4
variable nz equal 4
variable x_min equal -19.38
variable x_max equal 19.38
variable x_goldmin equal -11.22
variable x_goldmax equal 11.22
variable x_fluidmin equal ${x_goldmin}
variable x_fluidmax equal ${x_goldmax}
variable x_wallmin equal ${x_goldmin}-1.5
variable x_wallmax equal ${x_goldmax}+1.5
variable y_min equal -19.38
variable y_max equal 19.38
variable y_goldmin equal -11.22
variable y_goldmax equal 11.22
variable surface_charge equal -0.3125/(4.08*4.08)
variable y_fluidmin equal ${y_goldmin}
variable y_fluidmax equal ${y_goldmax}
variable y_wallmin equal ${y_goldmin}-1.5
variable y_wallmax equal ${y_goldmax}+1.5
variable downshift equal 2.5
variable zshiftlatt equal 1-${downshift}/4.08
variable z_min equal -20.4-${downshift}+0.25*4.08
variable z_max equal 22.44+1.5
variable z_goldmin equal -12.24-${downshift}+0.25*4.08
variable z_goldmax equal -${downshift}+0.25*4.08
variable z_goldtopmin equal ${z_goldmax}-0.5*4.08
variable z_goldtopmax equal ${z_goldmax}
variable z_fluidmin equal 0.
variable z_fluidmax equal 22.44
variable z_wallmax equal ${z_max}
lattice sc 8.16 origin 0 0 0.75
group pos type 4
group neg type 5
group allfluid type 3 4 5
compute fluidT allfluid temp
thermo_style custom step epair emol etotal press c_fluidT
fix zhiwall allfluid wall/lj93 zhi ${z_wallmax} 0.0195 3.45 10.000000 units box
fix xlowall allfluid wall/lj93 xlo ${x_wallmin} 0.0195 3.45 10.000000 units box
fix xhiwall allfluid wall/lj93 xhi ${x_wallmax} 0.0195 3.45 10.000000 units box
fix ylowall allfluid wall/lj93 ylo ${y_wallmin} 0.0195 3.45 10.000000 units box
fix yhiwall allfluid wall/lj93 yhi ${y_wallmax} 0.0195 3.45 10.000000 units box
group solvent type 3
fix fluidnvt solvent nvt temp 300.0 300.0 0.100 drag 0.2
##########################################################################
region ATC_BOX block ${x_wallmin} ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box
group ATC_ATOMS type 4 5
fix ATC ATC_ATOMS atc species_electrostatic Ar_species_dl.mat
fix_modify ATC add_species P group pos
fix_modify ATC add_species N group neg
fix_modify ATC mesh create ${nx} ${ny} ${nz} ATC_BOX f f f
fix_modify ATC atom_element_map eulerian 1
fix_modify ATC internal_quadrature off
fix_modify ATC initial mass_density all 0.
fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF ${z_goldtopmin} INF
## OLD
fix_modify ATC extrinsic fix_charge BOTTOM_FACE ${surface_charge}
## NEW
# ERROR: Poisson solver needs Dirichlet data
#fix_modify ATC control charge conductor ${surface_charge}
#fix_modify ATC control charge effective_charge ATC_ATOMS BOTTOM_FACE
## END
fix_modify ATC output double_layerFE ${dumpfreq} text binary
dump chargenve all atom ${dumpfreq} double_layer.dmp
run ${nsteps}
c4science · Help