From b666f7324c25063cb3d189fba0abec742c14e220 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndtrung@uchicago.edu>
Date: Mon, 11 Apr 2022 14:44:02 -0500
Subject: [PATCH] Updated the example input script with the set command for
 per-atom dielectric constant

---
 examples/PACKAGES/dielectric/data.confined |  6 +++---
 examples/PACKAGES/dielectric/in.confined   | 16 ++++++++++------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/examples/PACKAGES/dielectric/data.confined b/examples/PACKAGES/dielectric/data.confined
index 2e166151bb..8145c829d1 100644
--- a/examples/PACKAGES/dielectric/data.confined
+++ b/examples/PACKAGES/dielectric/data.confined
@@ -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
 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
 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
-4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0
-4002 0 3 -1 25 20 25 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 1.0 8 6 10 0
diff --git a/examples/PACKAGES/dielectric/in.confined b/examples/PACKAGES/dielectric/in.confined
index c9ae6d712a..0bff4b2a1d 100644
--- a/examples/PACKAGES/dielectric/in.confined
+++ b/examples/PACKAGES/dielectric/in.confined
@@ -4,6 +4,8 @@
 # top interface:    n = (0, 0, -1)
 # 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 epsilon2 index 8
 
@@ -21,6 +23,8 @@ variable    method index gmres  # gmres = BEM/GMRES
                                 # dof   = Direct optimization of the functional
                                 # none
 
+# compute the relevant values for the interface particles
+
 variable ed      equal "v_epsilon2 - v_epsilon1"
 variable em      equal "(v_epsilon2 + v_epsilon1)/2"
 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 anions  type 3
 
-# 1.0 = q * epsilon2 = qreal for cations
-# -1.0 = q * epsilon2 = qreal for anions
-variable qscale equal "1.0 / v_epsilon2"
-set group cations charge ${qscale}
-variable qscale equal "-1.0 / v_epsilon2"
-set group anions charge ${qscale}
+# set the dielectric constant of the medium where the ions belong
+
+set group cations epsilon ${epsilon2}
+set group anions  epsilon ${epsilon2}
 
 pair_style      lj/cut/coul/long/dielectric 1.122 10.0
 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 modify is used to set the properties of the interface particle group
+
 if "${method} == gmres" then &
   "fix             3 interface polarize/bem/gmres 1 1.0e-4" &
   "fix_modify      3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &