88 lines
2.8 KiB
Plaintext
88 lines
2.8 KiB
Plaintext
# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1
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# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2
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# bottom interface: n = (0, 0, 1)
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# top interface: n = (0, 0, -1)
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# so that ed's are the same for both interfaces
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# Dielectric constants can be set to be different from the input data file
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variable epsilon1 index 20
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variable epsilon2 index 8
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variable data index data.confined
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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 = Direct optimization of the functional
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# none
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# compute the relevant values for the interface particles
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variable ed equal "v_epsilon2 - v_epsilon1"
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variable em equal "(v_epsilon2 + v_epsilon1)/2"
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variable epsilon equal 1.0 # epsilon at the patch, not used for now
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variable area equal 0.866 # patch area, same as in the data file
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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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group cations type 2
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group anions type 3
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# set the dielectric constant of the medium where the ions reside
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set group cations epsilon ${epsilon2}
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set group anions epsilon ${epsilon2}
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pair_style lj/cut/coul/long/dielectric 1.122 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 0.0 1.0
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kspace_style pppm/dielectric 0.0001
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kspace_modify slab 3.0
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neigh_modify every 1 delay 0 check yes one 5000
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#compute ef all efield/atom
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dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
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dump_modify 1 sort id
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dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3]
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fix 1 ions nve
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# fix modify is used to set the properties of the interface particle group
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if "${method} == gmres" then &
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"fix 3 interface polarize/bem/gmres 1 1.0e-4" &
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"fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &
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elif "${method} == icc"&
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"fix 3 interface polarize/bem/icc 1 1.0e-4 itr_max 50" &
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"fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &
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elif "${method} == dof" &
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"fix 3 interface polarize/functional 1 0.001" &
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"fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &
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else &
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"print 'Unsupported polarization solver' "
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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_modify flush yes
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run 0
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