5302074b3f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
185 lines
7.5 KiB
Plaintext
185 lines
7.5 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style full
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########### BEGIN PARAMETERS ####################################
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variable a equal 5.719025032
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variable i equal 1
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variable s equal 100
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variable n equal 1000 # 500 2000
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variable dt equal 4.0
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variable W equal 4
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variable L equal 20
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variable Ls equal 4 # surface
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variable h equal 10
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variable phiInf equal -1. # 0. 10 -10.0
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variable perm2 equal 2.
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variable depth equal 17.1571
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# 1 1 0.1 0.1 1 1
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variable w1 equal 4/$L # relative wall width
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variable w1 equal 4/20
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variable w2 equal ${w1}+2/$L # relative wall width
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variable w2 equal 0.2000000000000000111+2/$L
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variable w2 equal 0.2000000000000000111+2/20
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variable w3 equal ${w2}+2/$L
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variable w3 equal 0.30000000000000004441+2/$L
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variable w3 equal 0.30000000000000004441+2/20
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variable w4 equal ${w3}+2/$L
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variable w4 equal 0.4000000000000000222+2/$L
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variable w4 equal 0.4000000000000000222+2/20
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############## END PARAMETERS #################################
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dimension 3
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boundary f p p
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pair_style lj/cut 13.0
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lattice fcc $a
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lattice fcc 5.7190250320000002304
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Lattice spacing in x,y,z = 5.71903 5.71903 5.71903
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read_data interface.init
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Scanning data file ...
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Reading data file ...
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orthogonal box = (0 0 0) to (114.381 22.8761 22.8761)
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4 by 1 by 1 MPI processor grid
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544 atoms
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544 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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atom_modify sort 0 1
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mass * 39.948
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pair_coeff * * 0.2381 3.405
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dielectric 1.0
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region BOX block 0 $L 0 $W 0 $W
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region BOX block 0 20 0 $W 0 $W
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region BOX block 0 20 0 4 0 $W
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region BOX block 0 20 0 4 0 4
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group SOLID type 1
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288 atoms in group SOLID
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group FLUID type 2 3 4
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256 atoms in group FLUID
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group P type 3
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66 atoms in group P
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group N type 4
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76 atoms in group N
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set group SOLID charge 0 # use ATC to provide charge to the surface
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Setting atom values ...
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288 settings made for charge
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timestep ${dt}
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timestep 4
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neigh_modify every $i check no
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neigh_modify every 1 check no
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fix WALLS all wall/reflect xlo EDGE xhi EDGE
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fix PP all atc field
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ATC: constructing shape function field estimate
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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fix_modify PP add_species IONS type 1 2 3 4
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fix_modify PP fields add species_concentration mass_density charge_density
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fix_modify PP atom_element_map eulerian $s
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fix_modify PP atom_element_map eulerian 100
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fix_modify PP mesh create $h 1 1 BOX f p p
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fix_modify PP mesh create 10 1 1 BOX f p p
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ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
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fix_modify PP output volume_integral all mass_density
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fix_modify PP output volume_integral all charge_density
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fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat
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ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: 1 materials defined from Ar_electrostatic.mat
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ATC: creating fem_efield extrinsic model
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ATC: 1 materials defined from Ar_electrostatic.mat
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fix_modify ATC add_species P type 3
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fix_modify ATC add_species N type 4
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fix_modify ATC boundary SOLID
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fix_modify ATC atom_element_map eulerian $i
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fix_modify ATC atom_element_map eulerian 1
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fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error)
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fix_modify ATC mass_matrix fe
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fix_modify ATC include atomic_charge
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# mesh
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fix_modify ATC mesh create $h 2 2 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0
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fix_modify ATC mesh create 10 2 2 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0
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ATC: created structured mesh with 99 nodes, 44 unique nodes, and 40 elements
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fix_modify ATC mesh create_elementset fluidElts ${Ls} INF -INF INF -INF INF
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fix_modify ATC mesh create_elementset fluidElts 4 INF -INF INF -INF INF
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ATC: created elementset fluidElts with 32 elements
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fix_modify ATC internal_element_set fluidElts
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fix_modify ATC output volume_integral fluidElts mass_density
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fix_modify ATC output volume_integral fluidElts charge_density
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fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF
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ATC: created nodeset lbc with 4 nodes
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fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF
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fix_modify ATC mesh create_nodeset rbc 20 $L -INF INF -INF INF
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fix_modify ATC mesh create_nodeset rbc 20 20 -INF INF -INF INF
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ATC: created nodeset rbc with 4 nodes
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fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4
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fix_modify ATC mesh create_nodeset wall 0 4 0 4 0 4
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ATC: created nodeset wall with 12 nodes
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fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4
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fix_modify ATC mesh create_elementset wall 0 4 0 4 0 4
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ATC: created elementset wall with 8 elements
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#fix_modify ATC mesh create_faceset lbc plane x 0
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fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF
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fix_modify ATC mesh create_faceset surface -INF 4 -INF INF -INF INF
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ATC: created faceset surface with 4 faces
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fix_modify ATC mesh output dielectric_interfaceMESH text binary
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# ic/bcs
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#fix_modify ATC initial charge_density all 0.
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fix_modify ATC initial mass_density all 0.
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fix_modify ATC initial electric_potential all 0.
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# output
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thermo $s
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thermo 100
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variable cFLUID equal count(FLUID)
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compute PAVE P reduce ave x
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compute PMIN P reduce min x
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compute PMAX P reduce max x
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compute NAVE N reduce ave x
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compute NMIN N reduce min x
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compute NMAX N reduce max x
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compute q all property/atom q
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compute Q all reduce sum c_q
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compute m all property/atom mass
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compute M all reduce sum c_m
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compute Qf FLUID reduce sum c_q
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compute Mf FLUID reduce sum c_m
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compute F FLUID reduce sum fx fy fz
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thermo_style custom step temp press etotal pe c_Q c_M c_Qf c_Mf c_PMIN c_PAVE c_PMAX c_NMIN c_NAVE c_NMAX c_F[1] c_F[2] c_F[3]
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compute T FLUID temp
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thermo_modify temp T
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
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thermo_modify flush yes
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log dielectric_interface.log
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fix_modify ATC output dielectric_interfaceFE $s full_text binary
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fix_modify ATC output dielectric_interfaceFE 100 full_text binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN
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species_concentration : species_concentrationP
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species_concentration : species_concentrationN
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fix_modify PP output dielectric_interfacePP $s full_text binary
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fix_modify PP output dielectric_interfacePP 100 full_text binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_1
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_2
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_3
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_4
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species_concentration : species_concentrationIONS_1
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species_concentration : species_concentrationIONS_2
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species_concentration : species_concentrationIONS_3
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species_concentration : species_concentrationIONS_4
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dump X all custom $s dielectric_interface.dmp id type x y z q vx vy vz fx fy fz
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dump X all custom 100 dielectric_interface.dmp id type x y z q vx vy vz fx fy fz
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fix_modify ATC fix electric_potential rbc 0.
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# stage 1 : active source controlling far-field shielding
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fix_modify ATC control charge FLUID dielectric ${phiInf} ${perm2} ${depth}
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fix_modify ATC control charge FLUID dielectric -1 ${perm2} ${depth}
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fix_modify ATC control charge FLUID dielectric -1 2 ${depth}
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fix_modify ATC control charge FLUID dielectric -1 2 17.157099999999999795
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ERROR: Illegal fix_modify command (../fix.cpp:104)
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