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Updated the example input script with the set command for per-atom dielectric constant

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Trung Nguyen
2022-04-11 14:44:02 -05:00
parent b05aadf877
commit b666f7324c
2 changed files with 13 additions and 9 deletions
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6
examples/PACKAGES/dielectric/data.confined
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@ -1,4 +1,4 @@
LAMMPS data file: two oppositely charged ions confined between two walls LAMMPS data file: two oppositely charged ions confined between two walls epsilon1=2 | epsilon2=10 | epsilon1=2
4002 atoms 4002 atoms
3 atom types 3 atom types
@ -4015,5 +4015,5 @@ Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em e
3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 6 0 3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 6 0
3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 6 0 3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 6 0
4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 6 0 4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 6 0
4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0 4001 0 2 1 15 20 15 0 0 1 1.0 8 6 10 0
4002 0 3 -1 25 20 25 0 0 1 0.866 8 6 10 0 4002 0 3 -1 25 20 25 0 0 1 1.0 8 6 10 0

16
examples/PACKAGES/dielectric/in.confined
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@ -4,6 +4,8 @@
# top interface: n = (0, 0, -1) # top interface: n = (0, 0, -1)
# so that ed's are the same for both interfaces # so that ed's are the same for both interfaces
# Dielectric constants can be set to be different from the input data file
variable epsilon1 index 20 variable epsilon1 index 20
variable epsilon2 index 8 variable epsilon2 index 8
@ -21,6 +23,8 @@ variable method index gmres # gmres = BEM/GMRES
# dof = Direct optimization of the functional # dof = Direct optimization of the functional
# none # none
# compute the relevant values for the interface particles
variable ed equal "v_epsilon2 - v_epsilon1" variable ed equal "v_epsilon2 - v_epsilon1"
variable em equal "(v_epsilon2 + v_epsilon1)/2" variable em equal "(v_epsilon2 + v_epsilon1)/2"
variable epsilon equal 1.0 # epsilon at the patch, not used for now variable epsilon equal 1.0 # epsilon at the patch, not used for now
@ -34,12 +38,10 @@ group ions type 2 3
group cations type 2 group cations type 2
group anions type 3 group anions type 3
# 1.0 = q * epsilon2 = qreal for cations # set the dielectric constant of the medium where the ions belong
# -1.0 = q * epsilon2 = qreal for anions
variable qscale equal "1.0 / v_epsilon2" set group cations epsilon ${epsilon2}
set group cations charge ${qscale} set group anions epsilon ${epsilon2}
variable qscale equal "-1.0 / v_epsilon2"
set group anions charge ${qscale}
pair_style lj/cut/coul/long/dielectric 1.122 10.0 pair_style lj/cut/coul/long/dielectric 1.122 10.0
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
@ -59,6 +61,8 @@ dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1
fix 1 ions nve fix 1 ions nve
# fix modify is used to set the properties of the interface particle group
if "${method} == gmres" then & if "${method} == gmres" then &
"fix 3 interface polarize/bem/gmres 1 1.0e-4" & "fix 3 interface polarize/bem/gmres 1 1.0e-4" &
"fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &