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