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LAMMPS (30 Aug 2013)
units real
atom_style full
########### BEGIN PARAMETERS ####################################
variable a equal 5.719025032
variable i equal 1
variable s equal 100
variable n equal 1000 # 500 2000
variable dt equal 4.0
variable W equal 4
variable L equal 20
variable Ls equal 4 # surface
variable h equal 10
variable phiInf equal -1. # 0. 10 -10.0
variable R equal 2*$a
variable R equal 2*5.7190250320000002304
############## END PARAMETERS #################################
dimension 3
boundary f p p
pair_style lj/cut 13.0
lattice fcc $a
lattice fcc 5.7190250320000002304
Lattice spacing in x,y,z = 5.71903 5.71903 5.71903
read_data interface.init
Scanning data file ...
Reading data file ...
orthogonal box = (0 0 0) to (114.381 22.8761 22.8761)
4 by 1 by 1 MPI processor grid
544 atoms
544 velocities
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
atom_modify sort 0 1
mass * 39.948
pair_coeff * * 0.2381 3.405
dielectric 1.0
region BOX block 0 $L 0 $W 0 $W
region BOX block 0 20 0 $W 0 $W
region BOX block 0 20 0 4 0 $W
region BOX block 0 20 0 4 0 4
group SOLID type 1
288 atoms in group SOLID
group FLUID type 2 3 4
256 atoms in group FLUID
group P type 3
66 atoms in group P
group N type 4
76 atoms in group N
set group SOLID charge 0 # use ATC to provide charge to the surface
Setting atom values ...
288 settings made for charge
# charged layer -- NOTE on an element boundary
variable b equal ${Ls}-0.1
variable b equal 4-0.1
variable c equal ${Ls}+0.1
variable c equal 4+0.1
region LAYER block $b $c INF INF INF INF
region LAYER block 3.8999999999999999112 $c INF INF INF INF
region LAYER block 3.8999999999999999112 4.0999999999999996447 INF INF INF INF
group LAYER region LAYER
32 atoms in group LAYER
timestep ${dt}
timestep 4
neigh_modify every $i check no
neigh_modify every 1 check no
fix WALLS all wall/reflect xlo EDGE xhi EDGE
fix PP all atc field
ATC: constructing shape function field estimate
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
fix_modify PP add_species IONS type 1 2 3 4
fix_modify PP fields add species_concentration mass_density charge_density # temperature
fix_modify PP output volume_integral all mass_density
fix_modify PP output volume_integral all charge_density
fix_modify PP atom_element_map eulerian $s
fix_modify PP atom_element_map eulerian 100
fix_modify PP mesh create $h 1 1 BOX f p p
fix_modify PP mesh create 10 1 1 BOX f p p
ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat
ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from Ar_electrostatic.mat
ATC: creating fem_efield extrinsic model
ATC: 1 materials defined from Ar_electrostatic.mat
fix_modify ATC add_species P type 3
fix_modify ATC add_species N type 4
fix_modify ATC boundary SOLID
#fix_modify ATC kernel cell $R $R $W
fix_modify ATC atom_element_map eulerian $i
fix_modify ATC atom_element_map eulerian 1
fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error)
fix_modify ATC mass_matrix fe
fix_modify ATC include atomic_charge
# mesh : 2x2 tosses an atom to infinity and beyond
#fix_modify ATC mesh create $h 4 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0
#fix_modify ATC mesh create $h 1 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 # 0.0 1.0 0.2 1.0 0.207812 0.1 1.0 1.0
### >>> node h vs list reepat and scale to box
fix_modify ATC mesh create $h 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5
fix_modify ATC mesh create 10 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5
ATC: created structured mesh with 110 nodes, 44 unique nodes, and 40 elements
fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF
ATC: created nodeset lbc with 4 nodes
fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF
fix_modify ATC mesh create_nodeset rbc 20 $L -INF INF -INF INF
fix_modify ATC mesh create_nodeset rbc 20 20 -INF INF -INF INF
ATC: created nodeset rbc with 4 nodes
fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4
fix_modify ATC mesh create_nodeset wall 0 4 0 4 0 4
ATC: created nodeset wall with 12 nodes
fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4
fix_modify ATC mesh create_elementset wall 0 4 0 4 0 4
ATC: created elementset wall with 8 elements
#fix_modify ATC mesh create_faceset lbc plane x 0
fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF
fix_modify ATC mesh create_faceset surface -INF 4 -INF INF -INF INF
ATC: created faceset surface with 4 faces
fix_modify ATC mesh create_elementset fluidElts ${Ls} INF -INF INF -INF INF
fix_modify ATC mesh create_elementset fluidElts 4 INF -INF INF -INF INF
ATC: created elementset fluidElts with 32 elements
fix_modify ATC internal_element_set fluidElts
fix_modify ATC mesh output conducting_interfaceMESH full_text binary
fix_modify ATC output volume_integral fluidElts mass_density
fix_modify ATC output volume_integral fluidElts charge_density
# ic/bcs
#fix_modify ATC initial charge_density all 0.
fix_modify ATC initial mass_density all 0.
fix_modify ATC initial electric_potential all 0.
# output
thermo $s
thermo 100
variable cFLUID equal count(FLUID)
compute PAVE P reduce ave x
compute PMIN P reduce min x
compute PMAX P reduce max x
compute NAVE N reduce ave x
compute NMIN N reduce min x
compute NMAX N reduce max x
compute q all property/atom q
compute Q all reduce sum c_q
compute Qf FLUID reduce sum c_q
compute m all property/atom mass
compute M all reduce sum c_m
compute Mf FLUID reduce sum c_m
compute F FLUID reduce sum fx fy fz
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]
compute T FLUID temp
thermo_modify temp T
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
thermo_modify flush yes
log conducting_interface.log
fix_modify ATC output conducting_interfaceFE $s full_text binary
fix_modify ATC output conducting_interfaceFE 100 full_text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN
species_concentration : species_concentrationP
species_concentration : species_concentrationN
fix_modify PP output conducting_interfacePP $s full_text binary
fix_modify PP output conducting_interfacePP 100 full_text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_1
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_2
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_3
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationIONS_4
species_concentration : species_concentrationIONS_1
species_concentration : species_concentrationIONS_2
species_concentration : species_concentrationIONS_3
species_concentration : species_concentrationIONS_4
dump X all custom $s conducting_interface.dmp id type x y z q vx vy vz fx fy fz
dump X all custom 100 conducting_interface.dmp id type x y z q vx vy vz fx fy fz
fix_modify ATC fix electric_potential rbc 0.
# stage 1 : active source controlling far-field shielding
fix_modify ATC control charge LAYER conductor ${phiInf}
fix_modify ATC control charge LAYER conductor -1
ERROR: Illegal fix_modify command (../fix.cpp:104)
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