Updated example input scripts, data files and README
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Trung Nguyen
@ -2,17 +2,11 @@ This folder contains some example data and input scripts for the USER-DIELECTRIC
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Nguyen TD, Li H, Bagchi D, Solis FJ, Olvera de la Cruz, Incorporating surface polarization effects into large-scale coarse-grained molecular dynamics simulation, Computer Physics Communications 2019, 241, 80--91.
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- data.minimal : two point opposite charges facing a flat interface
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- data.plane : two point opposite charges facing a larger flat interface
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- data.confined : two point opposite charges confined between two interfaces (epsilon1=2/epsilon2=10/epsilon2=2)
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- data.sphere : two point opposite charges outside a spherical interface (epsilon_in=1/epsilon2=10)
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- data.cylinder : single point charge facing a cylindrical interface
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- data.confined : two point opposite charges confined between two interfaces (epsilon1=2/epsilon2=10/epsilon2=2)
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- data.sphere : two point opposite charges outside a spherical interface (epsilon_in=1/epsilon2=10)
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- in.minimal : read in data.minimal
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- in.nopbc : read in data.* files, using non-periodic boundary conditions, with a large cutoff
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using "-v data data.foo" from the LAMMPS command line arguments
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- in.pbc : read in data.* files using periodic boundary conditions
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with a slab correction for kspace_style pppm and ewald; not required for msm
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- in.confined : read in data.confined
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- in.nopbc : read in data.* files, using non-periodic boundary conditions, with a large cutoff
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For "atom_style dielectric" the Atoms section in the data file contains 15 following columns:
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@ -20,28 +14,31 @@ id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
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where
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id, mol, type, q, x, y and z are similar to those in atom_style full
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* id, mol, type, q, x, y and z are similar to those in atom_style full
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normx, normy and normz are the three components of the normal unit vector
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of the interface at the patch (vertex). For real charges (ions), these 3 values
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are irrelevant and can be anything (e.g. 0,0,1).
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* normx, normy and normz are the three components of the normal unit vector
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of the interface at the boundary element (also called vertex, or patch).
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For real charges (ions), these 3 values are irrelevant,
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and can be anything (e.g. 0,0,1). normx, normy, and normz can be
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accessed through mux, muy and muz as if they were dipole components.
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ed = dielectric difference at the vertex along the normal vector direction.
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For example, if (normx,normy,normz) points from medium with epsilon_in to medium with epsilon_out,
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then ed = epsilon_out - epsilon_in
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* ed = dielectric difference at the vertex along the normal vector direction.
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For example, if (normx,normy,normz) points from medium with epsilon_in
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to medium with epsilon_out, then ed = epsilon_out - epsilon_in
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em = (epsilon_out + epsilon_in)/2: the mean dielectric value
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epsilon = the local epsilon value at the vertex or at the ion.
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For real charges, epsilon is the medium dielectric constant, q is the actual real charges.
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For interface particles, if q is zero (zero surface charges), epsilon is set to be 1.0;
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if q is nonzero (charged surfaces), epsilon is set to be em (the mean dielectric value above).
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area_per_patch: surface area of the patch. For real charges, this value is irrelevant, can be 1.0.
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curvature: surface curvature at the patch.
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For example, for spherical interfaces, curvature = 1/spherical radius.
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For planar interfaces, curvature = 0.
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* em = (epsilon_out + epsilon_in)/2: the mean dielectric value
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* epsilon = the local epsilon value at the vertex or at the ion.
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For real charges, epsilon is the medium dielectric constant,
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and q is the real (unscaled) charges.
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For interface particles:
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+ if q is zero (zero surface charges), epsilon is set to be 1.0;
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+ if q is nonzero (charged surfaces), epsilon is set to be em
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(the mean dielectric value above).
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* area_per_patch: the surface area of the patch (element).
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For real charges, this value is irrelevant, can be 1.0.
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* curvature: surface mean curvature at the patch.
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For example, for spherical interfaces, curvature = 1/spherical radius.
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For planar interfaces, curvature = 0.
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@ -1,4 +1,4 @@
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LAMMPS data file: using 2001 atoms for single point charge (no pbc), or 2002 atoms for two opposite charges (to have charge neutrality for pbc)
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LAMMPS data file: two oppositely charged ions confined between two walls
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4002 atoms
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3 atom types
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File diff suppressed because it is too large
Load Diff
@ -1,50 +0,0 @@
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LAMMPS data file via write_data, version 22 Nov 2016, timestep = 0
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32 atoms
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3 atom types
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0.0000000000000000e+00 5.0000007843669128e+00 xlo xhi
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0.0000000000000000e+00 5.1961532151380023e+00 ylo yhi
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0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi
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Masses
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1 1
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2 1
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3 1
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Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
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1 1 1 0 0 0 5 0 0 1 1 8 6 1 0
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2 1 1 0 0.5 0.866026 5 0 0 1 1 8 6 1 0
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3 1 1 0 1 0 5 0 0 1 1 8 6 1 0
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4 1 1 0 1.5 0.866026 5 0 0 1 1 8 6 1 0
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5 1 1 0 2 0 5 0 0 1 1 8 6 1 0
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6 1 1 0 2.5 0.866026 5 0 0 1 1 8 6 1 0
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7 1 1 0 3 0 5 0 0 1 1 8 6 1 0
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8 1 1 0 3.5 0.866026 5 0 0 1 1 8 6 1 0
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9 1 1 0 4 0 5 0 0 1 1 8 6 1 0
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10 1 1 0 4.5 0.866026 5 0 0 1 1 8 6 1 0
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11 1 1 0 0 1.73205 5 0 0 1 1 8 6 1 0
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12 1 1 0 0.5 2.59808 5 0 0 1 1 8 6 1 0
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13 1 1 0 1 1.73205 5 0 0 1 1 8 6 1 0
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14 1 1 0 1.5 2.59808 5 0 0 1 1 8 6 1 0
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15 1 1 0 2 1.73205 5 0 0 1 1 8 6 1 0
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16 1 1 0 2.5 2.59808 5 0 0 1 1 8 6 1 0
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17 1 1 0 3 1.73205 5 0 0 1 1 8 6 1 0
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18 1 1 0 3.5 2.59808 5 0 0 1 1 8 6 1 0
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19 1 1 0 4 1.73205 5 0 0 1 1 8 6 1 0
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20 1 1 0 4.5 2.59808 5 0 0 1 1 8 6 1 0
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21 1 1 0 0 3.4641 5 0 0 1 1 8 6 1 0
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22 1 1 0 0.5 4.33013 5 0 0 1 1 8 6 1 0
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23 1 1 0 1 3.4641 5 0 0 1 1 8 6 1 0
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24 1 1 0 1.5 4.33013 5 0 0 1 1 8 6 1 0
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25 1 1 0 2 3.4641 5 0 0 1 1 8 6 1 0
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26 1 1 0 2.5 4.33013 5 0 0 1 1 8 6 1 0
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27 1 1 0 3 3.4641 5 0 0 1 1 8 6 1 0
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28 1 1 0 3.5 4.33013 5 0 0 1 1 8 6 1 0
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29 1 1 0 4 3.4641 5 0 0 1 1 8 6 1 0
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30 1 1 0 4.5 4.33013 5 0 0 1 1 8 6 1 0
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31 2 2 1 1 1 7 0 0 1 1 8 6 10 0
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32 2 3 -1 3 3 7 0 0 1 1 8 6 10 0
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File diff suppressed because it is too large
Load Diff
@ -14,11 +14,11 @@ units lj
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atom_style dielectric
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atom_modify map array
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dimension 3
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boundary f f f
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boundary p p f
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variable method index gmres # gmres = BEM/GMRES
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# icc = BEM/ICC*
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# dof = Variational
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# dof = Direct optimization of the functional
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# none
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variable ed equal "v_epsilon2 - v_epsilon1"
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@ -41,10 +41,13 @@ set group cations charge ${qscale}
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variable qscale equal "-1.0 / v_epsilon2"
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set group anions charge ${qscale}
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pair_style lj/cut/coul/cut/dielectric 1.122 20.0
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pair_style lj/cut/coul/long/dielectric 1.122 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 0.0 1.0
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kspace_style pppm/dielectric 0.0001
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kspace_modify slab 3.0
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neigh_modify every 1 delay 0 check yes one 5000
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#compute ef all efield/atom
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@ -1,39 +0,0 @@
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# Interface
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newton off
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units lj
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atom_style dielectric
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atom_modify map array
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dimension 3
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boundary p p f
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read_data data.minimal
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group interface type 1
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group ions type 2 3
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pair_style coul/long/dielectric 5.0
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#pair_style coul/cut/dielectric 20.0
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pair_coeff * *
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thermo 1000
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thermo_style custom step evdwl ecoul elong epair
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thermo_modify flush yes
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#compute ef all efield/atom
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dump 1 all custom 100 dump.txt id type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump_modify 1 sort id
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fix 1 ions nve
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fix 3 interface polarize/bem/icc 1 1.0e-4
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kspace_style pppm/dielectric 0.0001
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kspace_modify slab 3.0
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velocity all create 1.0 2947942 mom yes dist gaussian
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run 0
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@ -8,25 +8,25 @@ boundary f f f
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variable method index gmres # gmres = BEM/GMRES
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# icc = BEM/ICC*
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# dof = Variational
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# dof = Direct optimization of the functional
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# none
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variable data index data.sphere #data.plane # data.minimal
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variable data index data.sphere
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read_data ${data}
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group interface type 1
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group ions type 2 3
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pair_style lj/cut/coul/cut/dielectric 50.0
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pair_style lj/cut/coul/cut/dielectric 1.122 20.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 0.0 1.0
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neigh_modify one 5000
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#compute ef all efield/atom
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dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
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dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
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dump_modify 1 sort id
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@ -42,7 +42,7 @@ else &
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"print 'Unsupported method for polarization' "
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thermo 1000
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thermo_style custom step evdwl ecoul elong epair #f_3
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thermo_style custom step evdwl ecoul elong epair
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thermo_modify flush yes
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run 0
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@ -1,54 +0,0 @@
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# Interface
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newton off
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units lj
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atom_style dielectric
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atom_modify map array
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dimension 3
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boundary p p f
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variable method index gmres # gmres = BEM/GMRES
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# icc = BEM/ICC*
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# dof = Variational
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# none
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variable data index data.sphere #data.plane # data.minimal
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read_data ${data}
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group interface type 1
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group ions type 2 3
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pair_style lj/cut/coul/long/dielectric 1.122 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 0.0 1.0
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kspace_style pppm/dielectric 0.0001
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kspace_modify slab 3.0
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neigh_modify every 1 delay 0 check yes one 5000
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#compute ef all efield/atom
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dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump_modify 1 sort id
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fix 1 ions nve
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if "${method} == gmres" then &
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"fix 3 interface polarize/bem/gmres 1 1.0e-4" &
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elif "${method} == icc"&
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"fix 3 interface polarize/bem/icc 1 1.0e-4 itr_max 50" &
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elif "${method} == dof" &
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"fix 3 interface polarize/functional 1 0.0001" &
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else &
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"print 'Unsupported method for polarization' "
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thermo 100
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thermo_style custom step evdwl ecoul elong epair cpu
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thermo_modify flush yes
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run 0
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