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LAMMPS (30 Aug 2013)
units metal
atom_style full
dimension 3
neighbor 2 bin
neigh_modify every 1 check yes
boundary f f f
timestep 0.0005
thermo 100
dielectric 81.
newton off
pair_style lj/cut 13.000000
pair_modify mix arithmetic
read_data waternve.init
Scanning data file ...
Reading data file ...
orthogonal box = (-19.38 -19.38 -21.88) to (19.38 19.38 23.94)
1 by 2 by 2 MPI processor grid
1982 atoms
1982 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
reset_timestep 0
variable nsteps equal 1000
variable dumpfreq equal ${nsteps}/10
variable dumpfreq equal 1000/10
variable nx equal 4
variable ny equal 4
variable nz equal 4
variable x_min equal -19.38
variable x_max equal 19.38
variable x_goldmin equal -11.22
variable x_goldmax equal 11.22
variable x_fluidmin equal ${x_goldmin}
variable x_fluidmin equal -11.220000000000000639
variable x_fluidmax equal ${x_goldmax}
variable x_fluidmax equal 11.220000000000000639
variable x_wallmin equal ${x_goldmin}-1.5
variable x_wallmin equal -11.220000000000000639-1.5
variable x_wallmax equal ${x_goldmax}+1.5
variable x_wallmax equal 11.220000000000000639+1.5
variable y_min equal -19.38
variable y_max equal 19.38
variable y_goldmin equal -11.22
variable y_goldmax equal 11.22
variable surface_charge equal -0.3125/(4.08*4.08)
variable y_fluidmin equal ${y_goldmin}
variable y_fluidmin equal -11.220000000000000639
variable y_fluidmax equal ${y_goldmax}
variable y_fluidmax equal 11.220000000000000639
variable y_wallmin equal ${y_goldmin}-1.5
variable y_wallmin equal -11.220000000000000639-1.5
variable y_wallmax equal ${y_goldmax}+1.5
variable y_wallmax equal 11.220000000000000639+1.5
variable downshift equal 2.5
variable zshiftlatt equal 1-${downshift}/4.08
variable zshiftlatt equal 1-2.5/4.08
variable z_min equal -20.4-${downshift}+0.25*4.08
variable z_min equal -20.4-2.5+0.25*4.08
variable z_max equal 22.44+1.5
variable z_goldmin equal -12.24-${downshift}+0.25*4.08
variable z_goldmin equal -12.24-2.5+0.25*4.08
variable z_goldmax equal -${downshift}+0.25*4.08
variable z_goldmax equal -2.5+0.25*4.08
variable z_goldtopmin equal ${z_goldmax}-0.5*4.08
variable z_goldtopmin equal -1.4799999999999999822-0.5*4.08
variable z_goldtopmax equal ${z_goldmax}
variable z_goldtopmax equal -1.4799999999999999822
variable z_fluidmin equal 0.
variable z_fluidmax equal 22.44
variable z_wallmax equal ${z_max}
variable z_wallmax equal 23.940000000000001279
lattice sc 8.16 origin 0 0 0.75
Lattice spacing in x,y,z = 8.16 8.16 8.16
group pos type 4
27 atoms in group pos
group neg type 5
0 atoms in group neg
group allfluid type 3 4 5
177 atoms in group allfluid
compute fluidT allfluid temp
thermo_style custom step epair emol etotal press c_fluidT
fix zhiwall allfluid wall/lj93 zhi ${z_wallmax} 0.0195 3.45 10.000000 units box
fix zhiwall allfluid wall/lj93 zhi 23.940000000000001279 0.0195 3.45 10.000000 units box
fix xlowall allfluid wall/lj93 xlo ${x_wallmin} 0.0195 3.45 10.000000 units box
fix xlowall allfluid wall/lj93 xlo -12.720000000000000639 0.0195 3.45 10.000000 units box
fix xhiwall allfluid wall/lj93 xhi ${x_wallmax} 0.0195 3.45 10.000000 units box
fix xhiwall allfluid wall/lj93 xhi 12.720000000000000639 0.0195 3.45 10.000000 units box
fix ylowall allfluid wall/lj93 ylo ${y_wallmin} 0.0195 3.45 10.000000 units box
fix ylowall allfluid wall/lj93 ylo -12.720000000000000639 0.0195 3.45 10.000000 units box
fix yhiwall allfluid wall/lj93 yhi ${y_wallmax} 0.0195 3.45 10.000000 units box
fix yhiwall allfluid wall/lj93 yhi 12.720000000000000639 0.0195 3.45 10.000000 units box
group solvent type 3
150 atoms in group solvent
fix fluidnvt solvent nvt temp 300.0 300.0 0.100 drag 0.2
##########################################################################
region ATC_BOX block ${x_wallmin} ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 12.720000000000000639 ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 ${z_goldtopmin} ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 -3.5200000000000000178 ${z_wallmax} units box
region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 -3.5200000000000000178 23.940000000000001279 units box
group ATC_ATOMS type 4 5
27 atoms in group ATC_ATOMS
fix ATC ATC_ATOMS atc species_electrostatic Ar_species_dl.mat
ATC: constructing electrostatic species coupling with parameter file Ar_species_dl.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 5
ATC: 1 materials defined from Ar_species_dl.mat
ATC: creating fem_efield extrinsic model
ATC: 1 materials defined from Ar_species_dl.mat
fix_modify ATC add_species P group pos
fix_modify ATC add_species N group neg
fix_modify ATC mesh create ${nx} ${ny} ${nz} ATC_BOX f f f
fix_modify ATC mesh create 4 ${ny} ${nz} ATC_BOX f f f
fix_modify ATC mesh create 4 4 ${nz} ATC_BOX f f f
fix_modify ATC mesh create 4 4 4 ATC_BOX f f f
ATC: created uniform mesh with 125 nodes, 125 unique nodes, and 64 elements
fix_modify ATC atom_element_map eulerian 1
fix_modify ATC internal_quadrature off
fix_modify ATC initial mass_density all 0.
fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF ${z_goldtopmin} INF
fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF -3.5200000000000000178 INF
ATC: created faceset BOTTOM_FACE with 16 faces
## OLD
fix_modify ATC extrinsic fix_charge BOTTOM_FACE ${surface_charge}
fix_modify ATC extrinsic fix_charge BOTTOM_FACE -0.018772827758554402194
## NEW
# ERROR: Poisson solver needs Dirichlet data
#fix_modify ATC control charge conductor ${surface_charge}
#fix_modify ATC control charge effective_charge ATC_ATOMS BOTTOM_FACE
## END
fix_modify ATC output double_layerFE ${dumpfreq} text binary
fix_modify ATC output double_layerFE 100 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
dump chargenve all atom ${dumpfreq} double_layer.dmp
dump chargenve all atom 100 double_layer.dmp
run ${nsteps}
run 1000
Setting up run ...
ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero
ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
Memory usage per processor = 54.1045 Mbytes
Step E_pair E_mol TotEng Press fluidT
0 -9252.0858 0 -9228.1564 -55763.67 293.65526
100 -9252.3246 0 -9228.0767 -55827.604 307.65619
200 -9251.4773 0 -9227.8252 -55739.237 281.46665
300 -9251.4162 0 -9227.6021 -55712.377 288.58631
400 -9251.4192 0 -9227.3092 -55688.538 301.59217
500 -9251.3116 0 -9226.6162 -55652.69 327.32164
600 -9251.1532 0 -9226.2326 -55637.593 337.22358
700 -9250.5037 0 -9226.425 -55610.998 300.21653
800 -9250.72 0 -9226.768 -55686.507 294.64934
900 -9251.0634 0 -9227.1621 -55774.601 292.41664
1000 -9250.8046 0 -9227.0389 -55778.639 286.45437
Loop time of 29.457 on 4 procs for 1000 steps with 1982 atoms
Pair time (%) = 6.51268 (22.1092)
Bond time (%) = 0.000497997 (0.00169059)
Neigh time (%) = 0.0405927 (0.137803)
Comm time (%) = 0.125795 (0.427047)
Outpt time (%) = 0.0581216 (0.19731)
Other time (%) = 22.7193 (77.127)
Nlocal: 495.5 ave 976 max 63 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 916.5 ave 1083 max 778 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 132292 ave 269908 max 8168 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 219310 ave 455907 max 9552 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 877238
Ave neighs/atom = 442.602
Ave special neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
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